Cellular data library and methods of using the same

Abstract

The disclosure relates, inter alia, to a library of transcriptional data, and methods for assembling and using same.

Description

[0001] CELLULAR DATA LIBRARY AND METHODS OF USING THE SAME

[0002] TECHNICAL FIELD

[0003] The present disclosure relates generally to a library of cellular transcriptional data, and methods for assembling and using the same.

[0004] CROSS-REFERENCE TO RELATED APPLICATIONS

[0005] This application claims priority to and the benefit of U.S. Provisional Patent Application Nos. 63 / 580,613, filed on September 5, 2023, the entire contents of which are hereby incorporated by reference.

[0006] BACKGROUND

[0007] Existing approaches to drug discovery are notoriously inefficient and generally confined to “reductive” efforts to develop therapies that selectively and potently modulate specific molecular targets of interest, each of which is hypothesized to potentially cause an arrest or reversal in the progression of a disease or disorder. Such approaches may include high-throughput screens of small compound libraries against specific molecular targets of interest to identify initial “hit compounds” for commencement of drug discovery programs. Initial hit compounds are progressed to safer and more efficacious “lead compound” analogs having optimized binding affinity of such analogs against their intended molecular target. Iterative cycles of synthetic chemistry analog generation and “wet biology” assay validations are conducted in pursuit of analogs with improved affinity, selectivity and reduced off-target effects in relation to the intended molecular target. Such conventional “reductive” approaches to drug discovery carry substantial failure rates in view of how few small molecule hit compounds and their analogs under investigation progress to lead compounds, and how few lead compounds, once identified, enter clinical development and exhibit meaningful efficacy and tolerable safety in patients sufficient to gain regulatory approval (e.g. from United States Food & Drug Administration, US FDA, or European Medicines Agency, EMA) for the treatment of disease.

[0008] Relatively non-reductive approaches to drug discovery have been attempted. One example includes the use of phenotypic screening methodologies that ascertain a test compound's impact on a disease phenotype regardless of any underlying mechanism of action or related molecular targets. Unlike molecular target-based approaches, phenotypic screening methods identify bioactive test compounds based on their holistic effect on a desired cellular response or therapeutic impact on an organism. A disadvantage to phenotypic screening methods is that they generally require additional studies to elucidate how the test compound achieves its cellular response to attain bioactivity (i.e. , via some demonstrable mechanism of action), which can impede efforts to thoughtfully and rationally optimize a test compound for progression from hit-to-lead during the drug discovery process.

[0009] More recently, methods and datasets were developed to obtain relatively holistic network-based insights into cell biology as it relates to drug discovery. According to one such approach, a dataset of small molecule interventions in certain cell lines was generated to measure changes in gene expression, on a compound- by-compound basis and the dataset was released for public use for drug discovery efforts. This dataset is called the Library of Integrated Network-based Cellular Signatures (LINCS), and was compiled by the National Institute of Health (NIH). LINCS was generated from hybridization microarray data of approximately 978 preselected genes upon exposure of “bulk” populations cell lines, primarily cancer cell lines, to numerous individual small molecules, largely cancer therapeutics. (On the World Wide Web at lincsproject.org / ). According to its webpage, LINCS “aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents.” The LINCS dataset, although providing a substantial amount of information, is of limited use in drug discovery efforts due to certain significant shortcomings, including:

[0010] • LINCS’ gene expression data type derives from hybridization microarray data against only a limited number of preselected genes that lack transcription data for non-selected genes;

[0011] • LINCS’ cell types derive largely from bulk samples of cancerous cell lines of potentially diminished applicability; and

[0012] • LINCS’ small molecule intervention types include a preponderance of cancer therapeutics that may also be of potentially diminished applicability outside of oncology applications, and a significant proportion of non-drug-like compounds that fall well outside “Lipinski rule of five” metrics and may be of limited applicability to drug discovery applications.

[0013] There thus remains a need in the art for improved and higher quality datasets of transcriptional expression from human cells upon exposure to compound interventions, where the datasets are more readily amenable to contemporary drug discovery efforts and more broadly applicable to a greater variety of diseases and disorders beyond oncology.

[0014] SUMMARY

[0015] In aspects, the present disclosure relates to an assembled library of transcriptional data, comprising: (a) a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; (b) a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; and (c) a compound-specific differential transcriptional signature data set of the cell type generated from differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; wherein the transcriptional signature data sets of (a), (b) and (c) are assembled into the library.

[0016] In aspects, the disclosure provides a method of preparing synthetic analogs of one or more compounds for drug development, the method comprising: (a) analyzing a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; (b) analyzing a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least 10 compounds; (c) generating a compound-specific differential transcriptional signature data set of the cell type upon comparison of the compound-treated transcriptional signature data against the baseline transcriptional signature data from the cell type; (d) assembling the transcriptional signature data sets of (a), (b) and (c) into a library; (e) selecting one or more compounds from the at least about 10 compounds based on the comparison of (b)-(c) in the library; and (f) preparing synthetic analogs of the one or more selected compounds for drug development.

[0017] In aspects, the disclosure provides a method of modifying a candidate compound to yield a lead compound, the method comprising: (a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; (b) obtaining a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; (c) generating a compound-specific differential transcriptional signature data set of the cell type obtained upon differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; (d) comparing the compound-specific differential transcriptional signature data set from the at least about 10 compounds to compound-specific differential transcription signature data from the candidate compound; (e) selecting one or more compounds from the at least about 10 compounds selected based on the comparison of (d); and (f) modifying the candidate compound based on structural features of the one or more compounds selected in (e) to yield a lead compound.

[0018] In aspects, the disclosure provides a method for preparing a library of transcriptional signatures, the method comprising: (a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; (b) obtaining a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compound; (c) generating a compound-specific differential transcriptional signature for each of the at least about 10 compounds upon differential comparison of the compound-treated transcriptional signature data of (b) against the baseline transcriptional signature data of (a); and (d) assembling the compound-specific differential transcriptional signatures generated in (c) into a library.

[0019] In aspects, the disclosure provides a method of identifying one or more compounds associated with or indicative of a desired transcriptional signature, the method comprising: (a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; (b) obtaining a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; (c) generating a compound-specific differential transcriptional signature data set of the cell type upon comparison of the compound-treated transcriptional signature data against the baseline transcriptional signature data from the cell type; (d) assembling the transcriptional signature data sets of (a), (b) and (c) into a library; and (e) selecting one or more compounds from the at least about 10 compounds based on the comparison of the transcriptional signature of interest with the compound-specific differential transcriptional signature data of (c); wherein the one or more compounds are associated with or indicative of the desired transcriptional signature.

[0020] In aspects, the disclosure provides a method of identifying one or more functional groups associated with or indicative of a desired transcriptional signature, the method comprising: (a) selecting from a library of transcriptional data one or more compounds having a compound-specific differential transcriptional signature at least substantially similar to the desired transcriptional signature, wherein: the library comprises: i. a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; ii. a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; and ill. a compound-specific differential transcriptional signature data set of the cell type generated from differential comparison of the compound- treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; wherein each of the at least about 10 compounds comprises at least one functional group, which may be the same or different from the at least one functional group of the remaining at least about 10 compounds; (b) comparing the at least one or more functional groups of the one or more compounds selected in (a); and (c) selecting one or more functional groups based on the comparison of (b), wherein the one or more functional groups are associated with or indicative of the desired transcriptional signature.

[0021] In embodiments, the transcriptional signature data sets are whole transcriptome transcriptional signature data sets. In embodiments, the library comprises compound-treated transcriptional signature data and / or compound-specific differential transcriptional signature data form at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds. In embodiments, the at least about 10 compounds are selected from Table 1. In embodiments, at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 1. In embodiments, at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1. In embodiments, the compounds are selected from Table 2. In embodiments, at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 2. In embodiments, at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 2. In embodiments, the compounds are selected from the Enamine Library Catalog. In embodiments, at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from the Enamine Library Catalog. In embodiments, at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from the Enamine Library Catalog. In embodiments, the at least about 10 compounds are associated with at least about 5, at least about 10, at least about 50, at least about 100, at least about 200, at least about 500, or at least about 1,000 or more known mechanisms of action (MoAs) for the treatment of one or more diseases or disorders. In embodiments, the at least about 10 compounds are associated with a plurality of known mechanisms of action (MoA) for the treatment of one or more diseases. In embodiments, the one or more functional groups are associated with a plurality of known mechanisms of action (MoA) for the treatment of one or more diseases. In embodiments, the one or more cells are treated with the compounds at the same or substantially the same concentration. In embodiments, the one or more cells are treated with the compounds for the same or substantially the same duration of time. In embodiments, the desired transcriptional transition in a cell state is associated with or indicative of a cellular transition from a diseased or disordered state to an undiseased or pre-diseased state. In embodiments, the diseased or disordered state is selected from an acute stage, a chronic stage, a clinical stage, a flare-up, a remission, a progressive stage, a refractory, a subclinical stage, and a terminal phase. In embodiments, the control sample and each of the test samples comprise a solvent, wherein the solvent is the same solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO). In embodiments, the control sample and each of the test samples comprise a polar aprotic solvent, wherein the polar aprotic solvent is the same polar aprotic solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO). In embodiments, the control sample and each of the test samples comprise dimethylsulfoxide (DMSO). In embodiments, the cellular transition is identified and / or generated by subtracting transcriptional data from one or more cells having an undiseased or prediseased state from transcriptional data from one or more cells having a diseased or disordered state. In embodiments, the transcriptional data comprises single nuclei assay and / or single-cell assay data, optionally wherein the single nuclei assay and / or single-cell assay data is selected from single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data, single-nuclei RNA sequencing (snRNA-seq) data, scTag-seq data, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, CyTOF / SCoP data, E-MS / Abseq data, miRNA-seq data, CITE-seq data, or any combinations thereof. In embodiments, the transcriptional data comprises or consists of single-cell RNA sequencing (scRNA-seq) data. In embodiments, the transcriptional data comprises or consists of single-nuclei RNA sequencing (snRNA-seq) data. In embodiments, the one or more cells comprise or consist of hematopoietic stem cells and / or progenitor cells. In embodiments, the one or more cells comprise or consist of untreated hematopoietic stem cells and / or untreated progenitor cells. In embodiments, the one or more cells comprise or consist of CD34+cells. In embodiments, the one or more cells comprise or consist of untreated CD34+cells. In embodiments, the sample comprises or consists of one or more cells from an organ, cells from a tissue, stem cells, human cells, cells from umbilical cord blood, cells from peripheral blood, bone marrow cells, cells from a solid tissue, and / or differentiated cells. In embodiments, the organ is selected from lung, heart, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colon, breast, prostate, brain, esophagus, liver, tissue (e.g. adipose tissue), thymus muscle, and placenta. In embodiments, the sample is a frozen sample.. In embodiments, the one or more compounds and / or the at least about 10 compounds each independently have a molecular weight of less than 2000 Daltons. In embodiments, the one or more compounds each independently satisfy each of the Lipinski rule of five criteria. In embodiments, the at least about 10 compounds each independently satisfy at least three criteria of the Lipinski rule of five criteria. In embodiments, the at least about 10 compounds for drug development each independently exhibit a mechanism of action useful in a therapy. In embodiments, the at least about 10 compounds each independently satisfy at least three criteria of the Lipinski rule of five criteria.

[0022] In embodiments, the one or more functional groups comprise one or more atoms selected from hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorous, or halogen. In embodiments, each functional group independently comprises or consists of one or more of (a)-(g): (a) a hydrogen atom; (b) a carbon atom or a group comprising a carbon atom, optionally selected from an alkane, an alkene, an alpha, beta-unsaturated ketone, an alpha, beta-unsaturated aldehyde, an alpha, beta-unsaturated carboxylic acid ester, an alpha, betaunsaturated carboxylic acid amide, an alpha, beta-unsaturated sulfoxide, an alpha, beta-unsaturated sulfone, an alpha, beta-unsaturated sulfonamide, an alpha, beta-unsaturated sulfonylchloride, a nitro alkene including but not limited to a vinylogous nitro group (e.g. alpha, beta-unsaturated nitroalkene), an alkyne, an arene, a hetarene, a nitrile, an amide, a lactam, an imine, a nitroalkyl group, a nitroaryl group, an amidine group, a carbamate, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, a carbosulfone, a carbosultam, a carbosultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, an alkylchloride, an alkylbromide, an alkyliodide, an alkenylchloride, an alkenylbromide, an alkenyliodide, an alkynylchloride, an alkynylbromide, an alkynyliodide, an arylfluoride, an arylchloride, an arylbromide, a aryliodide, a hetarylfluoride, a hetarylchloride, a hetarylbromide, a hetaryliodide, a carbonylfluoride, a carbonylchloride, a carbonylbromide, a carbonyliodide, an isocyanate, an isothiocyanate, an isocyanide, an alkylphosphonium group including but not limited to alkyltriphenylphosphonium chloride, alkyltriphenylphosphonium bromide, and alkyltriphenylphosphonium iodide, any of which may optionally be substituted by one or more substituents; (c) a nitrogen atom or a group comprising a nitrogen atom, optionally selected from an amine, an isocyanate, an isocyanide, a hydroxylamine, a hydrazine, a nitrile, an amide, a lactam, an imine, an azo group, a nitro group, a nitroso group, an amidine group, a guanidine group, a carbamate, and an azide, any of which may optionally be substituted by one or more substituents; (d) an oxygen atom or a group comprising an oxygen atom, optionally selected from of a hydroxyl group, an ether, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, and a hydroxyl amine, any of which may optionally be substituted by one or more substituents; (e) a sulfur atom or a group comprising a sulfur atom, optionally selected from a thiol, a disulfide, a sulfide, a sulfoxide, a sulfin amide, a sulfonamide, a sulfone, a sultam, a sultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, and a isothiocyanate, any of which may optionally be substituted by one or more substituents; (f) a phosphorous atom or a group comprising a phosphorous atom, optionally selected from a phosphine, a phosphine oxide, a phosphinite, a phosphonite, a phosphite, a phosphinate, a phosphonate, a phosphate, and a phosphonium salt, any of which may optionally be substituted by one or more substituents; and (g) a halogen atom or a group comprising a halogen atom, optionally selected from fluorine, chlorine, bromine, iodine, for example alkylchloride, alkylbromide, alkyliodide, alkenylchloride, alkenylbromide, alkenyliodide, alkynylchloride, alkynylbromide, alkynyliodide, arylfluoride, arylchloride, arylbromide, aryliodide, hetarylfluoride, hetarylchloride, hetarylbromide, hetaryliodide, carbonylfluoride, carbonylchloride, carbonylbromide, carbonyliodide, sulfonylfluoride, sulfonylchloride, sulfonyl bromide, and sulfonyliodide, any of which may optionally be substituted by one or more substituents. In embodiments, each functional group is independently selected from OH, halo, cyano, fluoroalkyl, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, -ORa, -SRa, - OC(O)Ra, -N(Ra)Rb, -C(O)Ra, -C(O)ORa, -OC(O)N(Ra)Rb, -C(O)N(Ra)Rb, -N(Ra)C(O)ORa, - N(Ra)C(O)Ra, -N(Ra)C(O)N(Ra)Rb, -N(Ra)C(NRa)N(Ra)Rb, -N(Ra)S(O)tRa, -C(O)N(Ra)S(O)tRa, - S(O)tORa, -S(O)tN(Ra)Rb, -S(O)tN(Ra)C(O)Rb, or -P(O)(ORa)(ORb), optionally substituted alkyl, optionally substituted alkylaryl, optionally substituted alkylheteroaryl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted aralkyl, optionally substituted haloalkyl, optionally substituted alkoxy, optionally substituted heterocyclyl, and optionally substituted heteroaryl; Raand Rbare each independently selected from the group consisting of hydrogen, alkyl, fluoroalkyl, cycloalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl, heterocycloalkylalkyl, heteroaryl, heteroarylalkyl, halogen, -O-alkyl, -O-aryl, cyano, nitro, -OH, -NH2, -NH- alkyl, and -NH-aryl; and t is 1 or 2. In embodiments, the one or more functional groups provide one or more of (a)-(f) compared to different functional groups and / or the absence of the one or more functional groups: (a) increased activity strength and / or selectivity; (b) increased solubility and / or partition property; (c) increased metabolic and / or chemical stability; (d) modulation of pharmacokinetic parameters (including, without limitation, absorption, distribution, metabolism, and excretion (ADME)), optionally wherein the modulation provides increased or enhanced pharmacokinetic properties compared to the compound prior to the modulation; (d) modulation of pharmacodynamic parameters (including, without limitation, dose-response relationship (e.g. EC50)); optionally wherein the modulation provides increased or enhanced pharmacodynamic properties compared to the compound prior to the modulation; and (f) reduction or ablation of toxicity and / or adverse reactions.

[0023] In embodiments, the compounds are selected from Table 1 (non-LINCS dataset) and / or Table 2 (LINCS dataset).

[0024] DETAILED DESCRIPTION

[0025] The present disclosure is based, in part, on the discovery that a library of transcriptional data, including transcriptional signatures of curated, small molecule compounds with drug-like properties and a variety of mechanisms of action, provides a useful drug discovery tool for identifying compounds with desired transcriptional signatures and / or mechanisms of action that can serve as scaffolds for developing new drug candidates useful for treating diseases or disorders.

[0026] In one aspect, the present disclosure relates to improved methods, systems and datasets for ascertaining how compounds, including new or known compounds, such as known drugs, impact transcriptional expression, including whole transcriptome expression, of any given cell type. In embodiments, methods and systems described herein are used to generate datasets for use in drug discovery, namely for ascertaining how new or known compounds, such as known drugs, impact transcriptional expression, including whole transcriptome expression, of any given cell type for the treatment of a disease or disorder related to the cell type. In embodiments, methods and systems described herein are used to generate datasets for ascertaining how new or known compounds, such as known drugs, can be redirected solely for new uses reasonably related to the development and submission of information under a Federal law which regulates the manufacture, use, or sale of drugs or veterinary biological products.

[0027] In aspects, methods and systems described herein are utilized to generate a dataset of transcriptional expression data for any given cell type, where (a) untreated samples of the cell type are sequenced to provide baseline untreated whole transcriptome expression data, and (b) treated samples of the cell type are each contacted with individual compound “interventions” and each sample of the treated cells is sequenced to provide treated whole transcriptome expression data, and (c) expression data of (a) are subtracted from each sample of expression data of (b) to provide whole transcriptome differential expression data associated with the cell type for each of the interventions.

[0028] In embodiments of each of the aspects herein, the transcriptional expression data comprise whole transcriptome expression data. In embodiments, whole transcriptome expression data of the disclosure, which can be obtained via methods described herein, including but not limited to RNA sequencing (RNA- seq), provides a fuller picture of gene expression relative to LINCS data generated from hybridization microarray data of approximately 978 preselected genes.

[0029] In embodiments of each of the aspects herein, the untreated samples of the cell type of step (a) and treated samples of the cell type of step (b) are both contacted with a solvent, such as an aqueous solvent or dimethylsulfoxide (DMSO) for example, which is used to dissolve the compound “interventions.” In embodiments, use of solvent in “untreated” control cellular samples (i.e., untreated with respect to interventions) as well as the treated cellular samples (i.e., treated with respect to interventions) controls for any impact that the solvent may have on cellular gene expression.

[0030] In embodiments, the present disclosure relates to the systems and methods described herein to generate a vast library of whole transcriptome differential expression data associated with numerous cell types for each of numerous interventions. In embodiments, integration and comparison of these whole transcriptome differential expression data for each cell type, upon individual treatment with numerous interventions, provides uniquely holistic vantage for the development of new medicines, relative to traditional single molecular target-based approaches to drug discovery.

[0031] In embodiments, the at least about 10 compounds or interventions (e.g. the at least about 10 compounds or interventions used in the methods and libraries of the present disclosure) includes more than 10 compounds or interventions, for example at least about 25, at least about 50, at least about 100, at least about 500, at least about 1,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds or interventions, the combined data from which provide unique and meaningful insight into relationships between compound intervention structures and transcriptional signatures and cellular activity that are not evident from analysis of transcriptional or select hybridization data of the individual interventions themselves.

[0032] In embodiments, the compounds or interventions comprise any of the compounds selected from the group of compounds from Table 1 (Non-LINCS compounds), Table 2 (LINCS compounds), and any of the commercially available compound libraries including but not limited to the Enamine Library Catalog. In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from Table 1 (Non-LINCS compounds), Table 2 (LINCS compounds), and any of the commercially available compound libraries such as the Enamine Library Catalog.

[0033] In embodiments, as described in greater detail herein, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 (Non-LINCS compounds), Table 2 (LINCS compounds), and any of the commercially available compound libraries such as the Enamine Library Catalog.

[0034] In embodiments, the compounds or interventions comprise any of the compounds selected from the group of compounds from Table 1 (Non-LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from Table 1 (Non- LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 (Non-LINCS compounds).

[0035] In embodiments, the compounds or interventions comprise any of the compounds selected from the group of compounds from Table 2 (LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from Table 2 (LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 2 (LINCS compounds).

[0036] In embodiments, the compounds or interventions comprise any of the compounds selected from the group of compounds from any of the commercially available compound libraries including but not limited to the Enamine Library Catalog. In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from the Enamine Library Catalog. In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from the Enamine Library Catalog.

[0037] In embodiments, the present disclosure relates to methods and systems described herein related to development of a highly insightful dataset for implementation of drug discovery efforts. In embodiments, the dataset described herein includes: gene expression data type that derives from whole transcriptome single cell or single nuclei RNA sequencing data (i.e., ssRNAseq or snRNAseq); cell types that derive largely from single cells or bulk samples of cell lines relevant to a target indication; and intervention types that derive from small molecules, peptides, proteins, antibodies, polynucleotides, and the like. In embodiments, intervention types that derive from small molecules are carefully selected among drug-like compounds to encompass a diversity of chemical structural features and a diversity of known effects upon cells or a diversity of known mechanisms of action upon cells.

[0038] Moreover, in aspects, the present disclosure implemented rigorous and standardized conditions by which the dataset described herein is obtained under relatively homogenous conditions to minimize experimental variability, including batch effects, so that differences in whole transcriptome expression data can properly be attributed to structural differences among compound interventions rather than experimental artifacts from differences in design or implementation. For example, for any given cell type, methods for obtaining datasets described herein, are conducted under substantially uniform and comparable conditions, including but not limited to:

[0039] • Substantially uniform and comparable conditions and time frames for growth of the cell type;

[0040] • Substantially uniform and comparable conditions and time frames for contacting samples of the cell type with individual interventions, at uniform and comparable doses, and for whole transcriptome sequencing samples of the cell type; and

[0041] • Substantially uniform and comparable conditions and methods for processing resulting whole transcriptome sequence data, including methods to minimize ambient RNA and improve signal to noise ratio in the whole transcriptome sequencing data

[0042] In embodiments, the present disclosure relates to the discovery that the resulting library of whole transcriptome composite data, obtained under substantially uniform and comparable experimental conditions, upon combination of data from 10 or more such interventions, provide unique and meaningful insight into relationships between intervention structures and transcriptional signatures and cellular activity that are not evident from analysis of transcriptional data of the individual interventions themselves or from transcriptional data of interventions obtained from less rigorous (i.e., non-uniform or heterogeneous) experimental methods of growing cells or conducting the intervention procedures upon cells, and / or from transcriptional data of interventions obtained from less rigorous (i.e., non-uniform or heterogeneous) experimental methods processing and curating the resulting transcriptional data. As used herein, the following definitions shall apply unless otherwise indicated. For purposes of this disclosure, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75thEd. Additionally, general principles of organic chemistry are described in “Organic Chemistry”, Thomas Sorrell, University Science Books, Sausalito: 1999, and “March’s Advanced Organic Chemistry”, 5thEd., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001 , the entire contents of which are hereby incorporated by reference.

[0043] Compound Interventions

[0044] The terms “compound,” “intervention,” and “compound intervention” are used interchangeably herein. In aspects, compounds and / or interventions of the present disclosure include those described generally herein, and are further illustrated by the ring systems, classes, subclasses, and species disclosed herein. In embodiments, compounds and / or interventions of the disclosure comprise, where applicable, any pharmaceutically acceptable salts of the compound.

[0045] The term “ring system” as used herein refers to an optionally substituted ring system selected from the group consisting of (i) optionally substituted “aryl” aromatic monocyclic or bicyclic ring system having a total of five to fourteen ring members, (ii) optionally substituted “heteroaryl” aromatic monocyclic or bicyclic ring system having 5 to 10 ring atoms, preferably 5, 6, or 9 ring atoms; having 6, 10, or 14 electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms, (iii) optionally substituted “heterocycle” 5- to 7-membered monocyclic or 7-10-membered bicyclic heterocyclic ring system that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, preferably one to four, heteroatoms, and (iv) optionally substituted “carbocycle” C3-C6 hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic.

[0046] Compounds and Interventions of Table 1 and Compounds and Interventions Comprising Ring Systems from Table 1

[0047] In embodiments, compounds of the comprise any of the compounds of Table 1 (Non-LINCS compounds), as exemplified herein. In embodiments, compounds comprise any of the optionally substituted ring systems of any of the compounds of Table 1 (Non-LINCS compounds), as exemplified herein.

[0048] For example, in embodiments, compounds comprise (8R)-3-[(2R,4S,5R)-4-hydroxy-5- (hydroxymethyl)oxolan-2-yl]-3H,4H,7H,8H-imidazo[4,5-d][1,3]diazepin-8-ol of Table 1 (Non-LINCS compounds).

[0049] In embodiments, compounds comprise any of the optionally substituted ring systems of (8R)-3-[(2R,4S,5R)- 4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H,4H,7H,8H-imidazo[4,5-d][1,3]diazepin-8-ol.

[0050] In embodiments, compounds comprise an optionally substituted ring system of (8R)-3-[(2R,4S,5R)-4- hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H,4H,7H,8H-imidazo[4,5-d][1 ,3]diazepin-8-ol selected from substituted or unsubstituted imidazo[4,5-d][1,3]diazepin-8-ol, substituted or unsubstituted imidazo[4,5- d][1,3]diazepine, substituted or unsubstituted or fused [1 ,3]diazepin-8-ol, substituted or unsubstituted or fused [1 ,3]diazepine, substituted or unsubstituted or fused imidazo[4,5-d], substituted or unsubstituted or fused imidazole, substituted or unsubstituted 4-hydroxy-5-(hydroxymethyl)oxolan-2-yl, substituted or unsubstituted oxolan-2-yl, and substituted or unsubstituted oxolane.

[0051] In embodiments, compounds comprise a ring system selected from unsubstituted imidazo[4,5- d][1,3]diazepin-8-ol, unsubstituted imidazo[4,5-d][1 ,3]diazepine, unsubstituted [1 ,3]diazepin-8-ol, unsubstituted [1 ,3]diazepine, unsubstituted imidazole, unsubstituted 4-hydroxy-5-(hydroxymethyl)oxolan-2- yl, unsubstituted oxolan-2-yl, and unsubstituted oxolane.

[0052] In embodiments, compounds comprise a ring system selected from substituted imidazo[4,5-d][1 ,3]diazepin- 8-ol, substituted imidazo[4,5-d][1 ,3]diazepine, substituted [1,3]diazepin-8-ol, substituted [1 ,3]diazepine, substituted imidazole, substituted 4-hydroxy-5-(hydroxymethyl)oxolan-2-yl, substituted oxolan-2-yl, and substituted oxolane.

[0053] In embodiments, compounds comprise a ring system selected from fused [1 ,3]diazepin-8-ol, fused [1 ,3]diazepine, fused imidazo[4,5-d], and fused imidazole.

[0054] In embodiments, compounds comprise any of the compounds of Table 1 (Non-LINCS compounds), as exemplified herein for (8R)-3-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H,4H,7H,8H- imidazo[4,5-d] [1 ,3]diazepin-8-ol. In embodiments, compounds comprise any of the optionally substituted ring systems of the compounds of Table 1 (Non-LINCS compounds), as exemplified herein, for the optionally substituted ring systems of (8R)-3-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H,4H,7H,8H- imidazo[4,5-d][1 ,3]diazepin-8-ol.

[0055] Compounds and Interventions of Table 2 and Compounds and Interventions Comprising Ring Systems from Table 2

[0056] In embodiments, compounds comprise any of the compounds of Table 2 (LINCS compounds), as exemplified herein. In embodiments, compounds comprise any of the optionally substituted ring systems of any of the compounds of Table 2 (LINCS compounds), as exemplified herein.

[0057] For example, in embodiments, compounds comprise 4-{[3-(4-cyclopropanecarbonylpiperazine-1 -carbonyl)- 4-fluorophenyl]methyl}-1 ,2-dihydrophthalazin-1-one of Table 2 (LINCS compounds).

[0058] In embodiments, compounds comprise any of the optionally substituted ring systems of 4-{[3-(4- cyclopropanecarbonylpiperazine-1-carbonyl)-4-fluorophenyl]methyl}-1 ,2-dihydrophthalazin-1-one.

[0059] In embodiments, compounds comprise an optionally substituted ring system of 4-{[3-(4- cyclopropanecarbonylpiperazine-1-carbonyl)-4-fluorophenyl]methyl}-1 ,2-dihydrophthalazin-1 -one selected from substituted or unsubstituted piperazine, substituted or unsubstituted cyclopropanecarbonyl, substituted or unsubstituted 4-cyclopropanecarbonylpiperazine-1 -carbonyl, substituted or unsubstituted fluorophenyl, and substituted or unsubstituted 1 ,2-dihydrophthalazin-1 -one.

[0060] In embodiments, compounds comprise a ring system of 4-{[3-(4-cyclopropanecarbonylpiperazine-1 - carbonyl)-4-fluorophenyl]methyl}-1,2-dihydrophthalazin-1-one selected from unsubstituted piperazine, unsubstituted cyclopropanecarbonyl, unsubstituted 4-cyclopropanecarbonylpiperazine-1 -carbonyl, unsubstituted fluorophenyl, and unsubstituted 1,2-dihydrophthalazin-1-one.

[0061] In embodiments, compounds comprise a ring system of 4-{[3-(4-cyclopropanecarbonylpiperazine-1 - carbonyl)-4-fluorophenyl]methyl}-1,2-dihydrophthalazin-1-one selected from substituted piperazine, substituted cyclopropanecarbonyl, substituted 4-cyclopropanecarbonylpiperazine-1 -carbonyl, substituted fluorophenyl, and substituted 1,2-dihydrophthalazin-1-one.

[0062] In further embodiments, compounds comprise any of the compounds of Table 2 (LINCS compounds), as exemplified above for 4-{[3-(4-cycloprop anecarbo nylp i perazi ne- 1 -carbonyl)-4-fl uorop henyl] methyl}- 1 ,2- dihydrophthalazin-1-one. In embodiments, compounds comprise any of the optionally substituted ring systems of the compounds of Table 2 (LINCS compounds), as exemplified above for 4-{[3-(4- cyclopropanecarbonylpiperazine-1 -carbonyl)-4-fluorophenyl]methyl}-1 ,2-dihydrophthalazin-1-one.

[0063] Compounds and Interventions from Commercially Available Libraries and Compounds and Interventions Comprising Ring Systems from Commercially Available Libraries

[0064] In embodiments, compounds comprise a compound and / or ring system of a compound selected from any of those available from any of the commercially available compound libraries. In embodiments, compounds comprise a compound and / or ring system of any of those available from the commercially available Enamine Library Catalog (available on the world wide web at: enamine.net / compound-libraries / libraries-catalog). In embodiments, compounds comprise a compound and / or ring system of any of those available from any of the individual libraries within the Enamine Library Catalog, wherein the individual libraries are selected from the group consisting of the Hit Locator Library HLL-460; Discovery Diversity Sets DDS-50 & DDS-10; Covalent Screening Library CSL-1176; Phenotypic Screening Library PSL-5760; PAINS Library PAINS-320; Covalent Screening Library CSL-11760; Covalent Serine Hydrolase Library CSHL-12160; Coronavirus Mpro covalent Library MPC-2640; Covalent Fragment Library CFL-7360; Cysteine focused covalent fragments CYS-3200; Serine focused covalent fragments SER-1600; Lysine focused covalent fragments LYS-1600; Electrophilic Covalent Probe Library ECPL-960; Acrylamide Library sACR-4080; Acrylamide Fragments fACR-2240; Chloroacetamides sCLA-1200; Chloroacetamide Fragment Library fCLA-1360; Sulfonyl Fluorides SFF-640; Agro-like Library AGR-10; Allosteric GPCR Library AGR-14; Allosteric Kinase Library ALK-4; Antiviral Library AVR-3200; Calcium Ion Channel Library CICL-10560; CNS Library CNS-47; Coronavirus Library COV-16800; Glycomimetic Library GML-2470; GPCR Library GPR-54; Hinge Binders Library HBL-24; IDO Targeted Library IDO-1003; Ion Channel Library ICL-36; Kinase Library; KNS-64960; Lipid GPCR Library LGR-5; Molecular Chaperones Library MCL-2; Nucleoside Mimetics NML-320; PDZ Domain Library; PDZ-1920; Protein Mimetics Library; PML-8960; Protein-Protein Interaction Library PPI-40; RNA Library RNA-15520; Serine Hydrolase Library CSHL-12160; Sodium Ion Channel Library SICL-5440; CLOUD; CLOUD-293; FDA approved drugs FAD-1040; Bioactive Library BRL-2320; Phenotypic Screening Library PSL-5760; PAINS Library PAINS-320; Essential Fragment Library ESS-320; High Fidelity Fragment Library HFF-1920; DSI-poised Library DSI-860; MiniFrag Library MiniFrag-80; Covalent Fragment Library CFL-7360; Fluorinated Fragment Library FDS-1000; Fully Functionalized Probe Library FFP-640; Natural Product-like Fragments NPL-4160; 3D Shape Diverse Fragment Library 3DF-1200; PPI Fragment Library PPIF-3600; Single Pharmacophore Fragments SPF-1500; Carboxylic Acid Fragment Library CAF-4000; and Electrophilic Covalent Probe Library ECPL-960.

[0065] The term “aliphatic” or “aliphatic group”, as used herein, means a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation, or a monocyclic hydrocarbon or bicyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as "carbocycle," “cycloaliphatic” or “cycloalkyl”), that has a single point of attachment to the rest of the molecule. Unless otherwise specified, aliphatic groups contain 1-6 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-5 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-4 aliphatic carbon atoms. In still other embodiments, aliphatic groups contain 1-3 aliphatic carbon atoms, and in yet other embodiments, aliphatic groups contain 1-2 aliphatic carbon atoms. In some embodiments, “cycloaliphatic” (or “carbocycle” or “cycloalkyl”) refers to a monocyclic C3-C6 hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point of attachment to the rest of the molecule. Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cycloalkyl)alkyl, (cycloalkenyl)alkyl or (cycloalkyl)alkenyl.

[0066] The term “heteroatom” means one or more of oxygen, sulfur, nitrogen, phosphorus, or silicon (including, any oxidized form of nitrogen, sulfur, phosphorus, or silicon; the quaternized form of any basic nitrogen or; a substitutable nitrogen of a heterocyclic ring, for example N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl) or NR+(as in N-substituted pyrrolidinyl)).

[0067] The term "unsaturated," as used herein, means that a moiety has one or more units of unsaturation.

[0068] As used herein, the term “bivalent C1-8 (or C1-6) saturated or unsaturated, straight or branched, hydrocarbon chain”, refers to bivalent alkylene, alkenylene, and alkynylene chains that are straight or branched as defined herein.

[0069] The term “alkylene” refers to a bivalent alkyl group. An “alkylene chain” is a polymethylene group, i.e., - (CH2)n— , wherein n is a positive integer, preferably from 1 to 6, from 1 to 4, from 1 to 3, from 1 to 2, or from 2 to 3. A substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.

[0070] The term “alkenylene” refers to a bivalent alkenyl group. A substituted alkenylene chain is a polymethylene group containing at least one double bond in which one or more hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.

[0071] The term “halogen” means F, Cl, Br, or I.

[0072] The term “aryl” used alone or as part of a larger moiety as in “aralkyl,” “aralkoxy,” or “aryloxy alky I,” refers to monocyclic or bicyclic ring systems having a total of five to fourteen ring members, wherein at least one ring in the system is aromatic and wherein each ring in the system contains 3 to 7 ring members. The term “aryl” may be used interchangeably with the term “aryl ring.” In certain embodiments of the present disclosure, “aryl” refers to an aromatic ring system which includes, but not limited to, phenyl, biphenyl, naphthyl, anthracyl and the like, which may bear one or more substituents. Also included within the scope of the term “aryl,” as it is used herein, is a group in which an aromatic ring is fused to one or more non-aromatic rings, such as indanyl, phthalimidyl, naphthimidyl, phenanthridinyl, or tetrahydronaphthyl, and the like. The term “fused” means that two ring systems share a common edge comprising the same two adjacent atoms.

[0073] The terms “heteroaryl” and “heteroar-,” used alone or as part of a larger moiety, e.g., “heteroaralkyl,” or “heteroaralkoxy,” refer to groups having 5 to 10 ring atoms, preferably 5, 6, or 9 ring atoms; having 6, 10, or 14 electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms. The term “heteroatom” refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of a basic nitrogen. Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl. The terms “heteroaryl” and “heteroar-”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring. Nonlimiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, 4H— quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and pyrido[2,3-b]—1,4-oxazin— 3(4H)-one. A heteroaryl group may be mono- or bicyclic. The term “heteroaryl” may be used interchangeably with the terms “heteroaryl ring,” “heteroaryl group,” or “heteroaromatic,” any of which terms include rings that are optionally substituted. The term “heteroaralkyl” refers to an alkyl group substituted by a heteroaryl, wherein the alkyl and heteroaryl portions independently are optionally substituted.

[0074] As used herein, the terms “heterocycle,” “heterocyclyl,” “heterocyclic radical,” and “heterocyclic ring” are used interchangeably and refer to a stable 5- to 7-membered monocyclic or 7-10-membered bicyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, preferably one to four, heteroatoms, as defined above. When used in reference to a ring atom of a heterocycle, the term "nitrogen" includes a substituted nitrogen. As an example, in a saturated or partially unsaturated ring having 0-3 heteroatoms selected from oxygen, sulfur or nitrogen, the nitrogen may be N (as in 3,4- dihydro— 2H— pyrrolyl), NH (as in pyrrolidinyl), or+NR (as in N-substituted pyrrolidinyl).

[0075] A heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted. Examples of such saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydrofuranyl, tetrahydrothiophenyl pyrrolidinyl, piperidinyl, pyrrolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and quinuclidinyl. The terms “heterocycle,” “heterocyclyl,” “heterocyclyl ring,” “heterocyclic group,” “heterocyclic moiety,” and “heterocyclic radical,” are used interchangeably herein, and also include groups in which a heterocyclyl ring is fused to one or more aryl, heteroaryl, or cycloaliphatic rings, such as indolinyl, 3H— indolyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl. A heterocyclyl group may be mono- or bicyclic. The term “heterocyclylalkyl” refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted.

[0076] As used herein, the term “partially unsaturated” refers to a ring moiety that includes at least one double or triple bond. The term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aryl or heteroaryl moieties, as herein defined.

[0077] As described herein, compounds of the disclosure may contain “optionally substituted” moieties, i.e., “substituted” or “unsubstituted”. In general, the term “substituted,” whether preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent. Accordingly, the term “unsubstituted” means that the hydrogens of the designated moiety are not replaced with a suitable substituent. Unless otherwise indicated, an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this disclosure are preferably those that result in the formation of stable or chemically feasible compounds. The term “stable,” as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein.

[0078] Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; -(CH2)o-4R°; -(CH2)o-40R°; -0(CH2)o-4R°, -O-(CH2)c-4C(O)OR°; — (CH2)o- 4CH(OR°)2; -(CH2)O-4SR°; — (CH2)o-4Ph, which may be substituted with R°; - (CH2)O-40(CH2)O-I Ph which may be substituted with R°; -CH=CHPh, which may be substituted with R°; — (CH2)o-40(CH2)o-i-pyridyl which may be substituted with R°; -NO2; -CN; -N3; -(CH2)o-4N(R0)2; -(CH2)o-4N(R°)C(0)R0; -N(R°)C(S)R°; -(CH2)o- 4N(R°)C(O)NR°2; -N(RO)C(S)NR°2; -(CH2)O-4N(R°)C(0)OR°; -N(R°)N(R°)C(O)R°; -N(R°)N(R°)C(O)NR°2; -N(R°)N(Ro)C(0)0Ro; -(CH2)o-4C(0)R°; -C(S)R°; -(CH2)o-4C(0)OR°; -(CH2)o -4C(O)SR°; -(CH2)o- 4C(O)OSiR°3; -(CH2)O-40C(0)R°; -OC(0)(CH2)O-4SR- SC(S)SR°; -(CH2)O-4SC(0)R°; -(CH2)O-4C(0)NR02; -C(S)NRO2; -C(S)SR°; -SC(S)SR°, -(CH2)O-40C(0)NR°2; -C(O)N(OR°)R°; -C(O)C(O)R°; - C(O)CH2C(O)R°; -C(NOR°)R°; -(CH2)O-4SSR°; -(CH2)O-4S(0)2R°; -(CH2)O-4S(0)20R°; -(CH2)O-40S(0)2R°; -S(0)2NRO2; -(CH2)O-4S(0)R°; -N(RO)S(0)2NR°2; -N(R°)S(O)2R°; -N(OR°)R°; -C(NH)NRO2; -P(O)2R°; -P(O)R°2; -OP(O)R°2; -OP(O)(OR°)2; SiR°3; — (C1-4 straight or branched alkylene)O-N(R°)2; or — (C1-4 straight or branched alkylene)C(O)O— N(R°)2, wherein each R° may be substituted as defined below and is independently hydrogen, C1-6 aliphatic, -CH2Ph, -0(CH2)o-iPh, -CH2-(5-6 membered heteroaryl ring), or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R°, taken together with their intervening atom(s), form a 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below.

[0079] Suitable monovalent substituents on R° (or the ring formed by taking two independent occurrences of R° together with their intervening atoms), are independently halogen, — (CH2)o-2R , — (haloR ), -(CH2)o-2OH, - (CH2)O-2OR , -(CH2)O-2CH(OR )2; -O(haloR), -CN, -N3, -(CH2)o-2C(0)R , -(CH2)o-2C(0)OH, -(CH2)o-2C(O)OR , — (CH2)O-2SR , -(CH2)O-2SH, -(CH2)O-2NH2, -(CH2)O-2NHR , -(CH2)O-2NR2, -NO2, — SiR3, -OSiR3, -C(O)SR , — (C1-4 straight or branched alkylene)C(O)OR , or-SSR wherein each R is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently selected from C1-4 aliphatic, -CH2PI1, -0(CH2)o-iPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0- 4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents on a saturated carbon atom of R° include =0 and =S.

[0080] Suitable divalent substituents on a saturated carbon atom of an “optionally substituted” group include the following: =0, =S, =NNR*2, =NNHC(O)R*, =NNHC(O)OR*, =NNHS(O)2R*, =NR*, =NOR*, -O(C(R*2))2-3O-, or -S(C(R*2))2-3S-, wherein each independent occurrence of R* is selected from hydrogen, C1-6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: - O(CR*2)2-3O- , wherein each independent occurrence of R* is selected from hydrogen, C1-6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0081] Suitable substituents on the aliphatic group of R* include halogen, -R , -(haloR ), -OH, -OR , -O(haloR ), - CN, -C(O)OH, -C(O)OR , -NH2, -NHR , -NR 2, or-NO2, wherein each R is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C1-4 aliphatic, -CH2Ph, - 0(CH2)o-iPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0082] Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include -Rt, -NRt2, - C(O)Rt, -C(O)ORt, -C(O)C(O)RT, -C(O)CH2C(O)Rt, -S(O)2Rt, -S(O)2NRt2, -C(S)NRt2, -C(NH)NRt2, or - N(Rt)S(O)2Rt; wherein each Rt is independently hydrogen, C1-6 aliphatic which may be substituted as defined below, unsubstituted -OPh, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of Rt, taken together with their intervening atom(s) form an unsubstituted 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0083] Suitable substituents on the aliphatic group of Rt are independently halogen, -R , -(haloR ), -OH, -OR , - O(haloR ), -CN, -C(O)OH, -C(O)OR , -NH2, -NHR , -NR 2, or -NO2, wherein each R is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C1-4 aliphatic, — Cl-bPh, -0(CH2)o-iPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0084] As used herein, the term "pharmaceutically acceptable salt" refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge et al., describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of this disclosure include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphor sulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2- hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3— phenylpropionate, phosphate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like.

[0085] Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(Ci-4alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate and aryl sulfonate.

[0086] Unless otherwise stated, structures depicted herein are also meant to include all isomeric (e.g, enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, Z and E double bond isomers, and Z and E conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the disclosure. Unless otherwise stated, all tautomeric forms of the compounds of the disclosure are within the scope of the disclosure.

[0087] In embodiments, the at least about 10 compounds or interventions (e.g. the at least about 10 compounds or interventions used in the methods and libraries of the present disclosure) includes more than 10 compounds or interventions, for example at least about 25, at least about 50, at least about 100, at least about 500, at least about 1,000, at least about 1,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds or interventions, the combined data from which provide unique and meaningful insight into relationships between compound intervention structures and transcriptional signatures and cellular activity that are not evident from analysis of transcriptional or select hybridization data of the individual interventions themselves.

[0088] In embodiments, the compounds or interventions comprise any of the compounds selected from the group of compounds from Table 1 (Non-LINCS compounds), Table 2 (LINCS compounds), and any of the commercially available compound libraries such as the Enamine Library Catalog. In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from Table 1 (Non-LINCS compounds), Table 2 (LINCS compounds), and any of the commercially available compound libraries such as the Enamine Library Catalog.

[0089] In embodiments, as described in greater detail herein, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 (Non-LINCS compounds), Table 2 (LINCS compounds), and any of the commercially available compound libraries such as the Enamine Library Catalog.

[0090] In embodiments, the compounds or interventions comprise any of the compounds selected from the group of compounds from Table 1 (Non-LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from Table 1 (Non- LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 (Non-LINCS compounds).

[0091] In embodiments, a library of the disclosure comprises transcriptional data (e.g. compound-specific differential transcriptional signature) of at least about 10 compounds. In embodiments, one or more of the at least about 10 compounds are selected from the compounds of Table 1. In embodiments, the compounds of Table 1 provide a set of compounds having diverse structures and representing a variety of different MoAs, which is useful to provide a library of transcriptional data capable of addressing a broad scope of diseases or disorders. In a non-limiting example, a compound-specific differential transcriptional signature is obtained for each of the one or more of the compounds of Table 1 upon differential comparison of the compound-treated transcriptional signature data of a compound-treated transcriptional signature for each of the one or more compounds of Table 1 with a baseline transcriptional signature from a control sample.

[0092] In embodiments, the compounds or interventions comprise any of the compounds selected from the group of compounds from Table 2 (LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from Table 2 (LINCS compounds). In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 2 (LINCS compounds).

[0093] In embodiments, one or more of the at least about 10 compounds are selected from the compounds of Table 2. In embodiments, the compounds of Table 2 provide a set of compounds having diverse structures and representing a variety of different MoAs, which is useful to provide a library of transcriptional data capable of addressing a broad scope of diseases or disorders. In a non-limiting example, a compound-specific differential transcriptional signature is obtained for each of the one or more of the compounds of Table 2 upon differential comparison of the compound-treated transcriptional signature data of a compound-treated transcriptional signature for each of the one or more compounds of Table 2 with a baseline transcriptional signature from a control sample.

[0094] In embodiments, the compounds or interventions comprise any of the compounds selected from a group of compounds from any of the commercially available compound libraries such as the Enamine Library Catalog. In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from the Enamine Library Catalog. In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from the Enamine Library Catalog.

[0095] In embodiments, one or more of the at least about 10 compounds are selected from the compounds of the Enamine Library Catalog. In embodiments, the compounds of the Enamine Library Catalog provide a set of compounds having diverse structures and representing a variety of different MoAs, which is useful to provide a library of transcriptional data capable of addressing a broad scope of diseases or disorders. In a non-limiting example, a compound-specific differential transcriptional signature is obtained for each of the one or more of the compounds of the Enamine Library Catalog upon differential comparison of the compound-treated transcriptional signature data of a compound-treated transcriptional signature for each of the one or more compounds of the Enamine Library Catalog with a baseline transcriptional signature from a control sample.

[0096] Library

[0097] In aspects, the disclosure provides an assembled library of transcriptional data. In embodiments, the library comprises:

[0098] (a) a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;

[0099] (b) a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; and

[0100] (c) a compound-specific differential transcriptional signature data set of the cell type generated from differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; wherein the transcriptional signature data sets of (a), (b) and (c) are assembled into a library.

[0101] In embodiments, during step (a), the control sample of one or more cells of a cell type is treated with solvent, and during step (b), each test sample of one or more cells is separately treated with one of the at least about 10 compounds dissolved in the same solvent. In embodiments, the solvent is dimethylsulfoxide (DMSO).

[0102] In aspects, libraries of the disclosure comprise transcriptional signatures and / or transcriptional data. In embodiments, the transcriptional data comprises or consists of one or more transcriptional signatures. In a non-limiting example, transcriptional signatures are generated and / or prepared by administering and / or contacting a perturbagen (e.g. a small molecule) to one or more cells of a cell type (e.g. CD34+cells), and profiling the resulting gene expression of the cells in response to the perturbagen (e.g. by obtaining whole transcriptome ssRNAseq). In embodiments, transcriptional signatures are useful to diagnose and / or identify diseases or disorders (including but not limited to the prognosis and / or status of a disease or disorder) and / or provide insight into mechanisms of action (MoAs) associated with a disease or disorder. In embodiments, a plurality of transcriptional signatures and / or transcriptional signature data thereof forms a set (e.g. a transcriptional signature data set).

[0103] In embodiments, the transcriptional signature and / or transcriptional data and / or transcriptional signature data set is from a control sample of one or more cells of a cell type (i.e. a baseline transcriptional signature). In a non-limiting example, a baseline transcriptional signature provides a transcriptional signature of one or more cells (e.g. CD34+cells) in the absence of treatment with a perturbagen (e.g. a small molecule), which is useful as a control sample to compare with a cell of the same cell type treated with a perturbagen.

[0104] In embodiments, the transcriptional signature and / or transcriptional data and / or transcriptional signature data set is from a test sample of one or more cells of a cell type treated with a compound (i.e. a compound-treated transcriptional signature). In embodiments, the compound-treated transcriptional signature is from a plurality of at least about 10 test samples of one or more cells of a cell type treated with at least about 10 compounds. In embodiments, each test sample of one or more cells is separately treated with one of the at least about 10 compounds. In a non-limiting example, a compound-treated transcriptional signature sample provides a transcriptional signature of one or more cells (e.g. CD34+cells) treated with a perturbagen (e.g. a small molecule). In embodiments, the plurality of test samples comprises at least at least about 10, at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 test samples treated with one of the at least at least about 10, at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds.

[0105] In embodiments, the transcriptional signature and / or transcriptional data and / or transcriptional signature data set is from a compound-specific differential transcriptional signature. In embodiments, compound-specific differential transcriptional signature (including compound-specific differential transcriptional signature data and / or data sets) is generated from differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with a compound (e.g. at least about 10 compounds) against the baseline transcriptional signature data of the control sample from the same or substantially the same cell type. In a non-limiting method, the differential comparison comprises subtracting (e.g. netting out) the baseline transcription signature (and / or baseline transcriptional signature data and / or data sets) from the compound-treated transcriptional signature (and / or compound-treated transcriptional signature data and / or data sets). In embodiments, the at least about 10 compounds and / or comprises compound-specific differential transcriptional signature data set of a cell type is generated from differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of at least about 10, at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds against baseline transcriptional signature data of a control sample from the cell type. In embodiments, the at least about 10 compounds (e.g. the at least about 10 compounds used in the methods and libraries of the present disclosure) includes more than 10 compounds, for example at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds. In embodiments, the library comprises compound-treated transcriptional signature data and / or compound-specific differential transcriptional signature data form at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds.

[0106] Any cell in which transcriptional signatures and / or associated data (e.g. baseline transcriptional signature, compound-treated transcriptional signature, compound-specific differential transcriptional signature) can be detected and / or measured are contemplated by the present disclosure, as would be understood by one of ordinary skill in the art. Non-limiting examples of cells include hematopoietic stem and progenitor cells including but not limited to hematopoietic stem cells (HSCs) (including CD34+cells (e.g. CD34+hematopoietic stem and progenitor cells) and induced pluripotent stem cells (human stem cells; IPSCs) (e.g. IPSC- astrocytes, IPSC-neural stem cells, IPSC-DopaNeurons, IPSC-cardiomyocytes, IPSC-endothelial cells, IPSC-microglia)), progenitor cells, hepatocytes, choiangiocytes, stellate cells (including but not limited to hepatic stellate cells, human stellate cells, human pancreatic stellate cells), fibroblasts (e.g. lung fibroblasts, cardiac fibroblasts, dermal fibroblasts (e.g. adult human dermal fibroblasts)), endothelial cells (e.g. liver sinusoidal endothelial cells (LSECs), human umbilical cord endothelial cells (HUVEC), brain microvascular endothelial cells (BMECs), human hepatic sinusoidal endothelial cells, human pancreatic microvascular endothelial cells, human small intestine epithelial cells (HSIEpC), human renal cortical epithelial cells), peritoneal exudate cells (PEC), Kupffer cells, monocytes, optionally non-classical monocytes or CD14 monocytes, macrophages (e.g. MO macrophages, M1 macrophages, M2a macrophages scar-associated macrophages (SAMs)), dendritic cells, optionally conventional type 1 dendritic cells (cDC1s), conventional type 2 dendritic cells (cDC2s), or plasmacytoid dendritic cells; T-cells (e.g. CD8+T-cells, a T-cell receptor op + T cell), optionally proliferated T-cells, natural killer (NK) cells, optionally proliferated conventional NK cells or cytotoxic NK cells, B-cells, plasma cells, erythrocytes, mast cells, hematopoietic stem and progenitor cells (HSPC), human bronchial epithelial cells (HBEC), human renal proximal tubular epithelial cells, LX-2 cells, Schwann cells, mesenchymal stem cells (e.g. human pulmonary mesenchymal stem cells, human bone marrow mesenchymal stem cells), smooth muscle cells (e.g. human intestinal smooth muscle cells (HISMC), human bronchial smooth muscle cells), osteoblasts (e.g. human osteoblasts, such as human femoral osteoblasts), chondrocytes (e.g. human chondrocytes), keratinocytes, astrocytes (e.g. human astrocytes), pericytes (e.g. human brain vascular pericytes), microglia (e.g. human microglia), mesangial cells (e.g. human renal mesangial cells), and satellite cells.

[0107] In embodiments, the cells are selected from myoblasts, human umbilical cord endothelial cells (HUVEC), human bronchial epithelial cells (HBEC), human renal proximal tubular epithelial cells, LX-2 cells, lung fibroblasts, IPSC-astrocytes, Schwann cells, CD14 monocytes, CD34+cells, CD8+T-cells, B cells, natural killer (NK) cells, human pulmonary mesenchymal stem cell, dendritic cells, MO macrophages, M1 macrophages, M2a macrophages, IPSC -neural stem cells, IPSC -DopaNeurons, human intestinal smooth muscle cells (HISMC), human stem cells (IPSC), femoral human osteoblasts, human chondrocytes, IPSC- cardiomyocytes, brain microvascular endothelial cells (BMECs), IPSC-endothelial cells, human hepatic sinusoidal endothelial cells, human pancreatic microvascular endothelial cells, human small intestine epithelial cells (HSIEpC), human renal cortical epithelial cells, keratinocyte, cardiac fibroblasts, human stellate cells, human pancreatic stellate cells, adult human dermal fibroblasts, human astrocytes, human bone marrow MSCs, human brain vascular pericytes, human microglia, IPSC-microglia, human renal mesangial cells, human bronchial smooth muscle cells, and satellite cells.

[0108] In embodiments, the cells are selected from CD34+cells, CD8+T-cells, IPSC-neural stem cells, M2a macrophages, human bronchial smooth muscle cells, NK cells, B cells, human stem cells (IPSCs), human brain vascular pericytes, human astrocytes, MO macrophages, dendridic cells, IPSC-microglia, lung fibroblasts, brain microvascular endothelial cells (BMECs), and human stellate cells.

[0109] In embodiments, the cells are selected from CD34+cells, CD8+T-cells, IPSC-neural stem cells, M2a macrophages, and human bronchial smooth muscle cells.

[0110] In embodiments, the cells comprise or consist of CD34+cells. In a non-limiting example, methods for preparing CD34+cells useful within the libraries and methods of the disclosure include culturing the cells in CC100 (StemSpan), and thrombopoietin (TPO).

[0111] In embodiments, the cells comprise or consist of CD8+T-cells. In a non-limiting example, methods for preparing CD8+T-cells useful within the libraries and methods of the disclosure include culturing the cells in XF T cell expansion medium (ImmunoCult), CD3 / CD28 T-cell activator (ImmunoCult), and IL-2.

[0112] In embodiments, the cells comprise or consist of IPSC-neural stem cells. In a non-limiting example, methods for preparing IPSC-neural stem cells useful within the libraries and methods of the disclosure include culturing the cells in SF macrophage medium (ImmunoCult), IL-4, and macrophage colony-stimulating factor (M-CSF).

[0113] In embodiments, the cells comprise or consist of human bronchial smooth muscle cells. In a non-limiting example, methods for preparing CD34+cells useful within the libraries and methods of the disclosure include culturing the cells in fibroblast growth factor (FGF2), epidermal growth factor (EGF), insulin, ascorbic acid, glutamine, and fetal bovine serum (FBS).

[0114] In embodiments, the cells comprise or consist of one type of cell (e.g. only hematopoietic stem cells (HSCs)). In embodiments, the cells comprise or consist of two or more types of cells (e.g. hematopoietic stem cells (HSCs) and hepatocytes). In embodiments, the cells are isolated from and / or harvested from an organ, a tissue, stem cells, human cells, cells from umbilical cord blood, cells from peripheral blood, bone marrow cells, cells from a solid tissue, and / or differentiated cells. In embodiments, the cells comprise or consist of hematopoietic stem cells and / or progenitor cells. In embodiments, the cells comprise or consist of CD34+cells. In embodiments, the cells are untreated (e.g. a control sample not treated with any compounds). In embodiments, the cells comprise or consist of untreated hematopoietic stem cells and / or untreated progenitor cells (e.g. hematopoietic stem cells and / or untreated progenitor cells not treated with any compounds). In embodiments, the cells comprise or consist of untreated CD34+cells.

[0115] In embodiments, the cells are isolated from and / or harvested from blood. Non limiting examples of hematopoietic cells include B cells, human peripheral blood naive pan T cells, monocytes (CD14), NK cells, macrophages (MO), macrophages (M1), macrophages (M2), human peripheral blood-derived dendritic cells, CD34+ HSPCs, MSCs, IPSC - MSCs, IPSC - Endothelial cells, IPSC - Oligodendrocyte progenitors, and IPSC - Hepatocytes.

[0116] In embodiments, the cells are cardiac cells, optionally isolated from and / or harvested from the heart. Non limiting examples of cardiac cells include cardiomyocytes, cardiac fibroblasts, and IPSC - cardiomyocytes.

[0117] In embodiments, the cells are intestinal cells, optionally isolated from and / or harvested from the intestines. Non limiting examples of intestinal cells include Human Intestinal Microvascular Endothelial Cells (HIMEC), Human Intestinal Smooth Muscle Cells (HISMC), and Human Small Intestine Epithelial Cells (HSIEpC).

[0118] In embodiments, the cells are liver cells, optionally isolated from and / or harvested from the liver. Non limiting examples of liver cells include cholangiocyte, hepatocytes, stellate cells, Kupffer cells, and LX-2.

[0119] In embodiments, the cells are pancreatic cells, optionally isolated from and / or harvested from the pancreas. Non limiting examples of pancreatic cells include human pancreatic microvascular endothelial cells, and human pancreatic stellate cells.

[0120] In embodiments, the cells are from the brain and / or nervous system, optionally isolated from and / or harvested from the brain and / or nervous system. Non limiting examples of cells from the brain and / or nervous system include neurons, brain microvascular endothelial cells (BMECs), astrocytes, IPSC - astrocytes, human microglia, GlutaNeurons, neural progenitors / neural precursor cells, DopaNeurons, stem cell-derived oligodendrocyte progenitors, microglia, human brain vascular pericytes, and Schwann cells.

[0121] In embodiments, the cells are kidney cells, optionally isolated from and / or harvested from the kidney. Non limiting examples of kidney cells include human renal mesangial cells, human renal cortical epithelial cells, and human renal proximal tubular epithelial cells.

[0122] In embodiments, the cells are skin cells, optionally isolated from and / or harvested from skin. Non limiting examples of skin cells include pre-adipocytes, human dermal fibroblasts, and keratinocyte.

[0123] In embodiments, the cells are lung cells, optionally isolated from and / or harvested from the lung. Non limiting examples of lung cells include human bronchial smooth muscle cell, human pulmonary mesenchymal stem cell, and lung fibroblasts.

[0124] In embodiments, the cells are bone cells, optionally isolated from and / or harvested from bone. Non limiting examples of bone cells include human osteoblasts (femoral), and IPSC - Hepatoblasts. In embodiments, the cells are muscle cells, optionally isolated from and / or harvested from muscle. Non limiting examples of muscle cells include myoblasts and satellite cells.

[0125] In embodiments, one or more cells are treated with one or more compounds (e.g. at least about 10 compounds) at the same or substantially the same concentration. In a non-limiting example, treatment refers to the administration and / or contacting of the one or more cells with the one or more compounds in an in vitro assay (e.g. an in vitro plate assay). In a non-limiting example, and the concentration refers to the concentration of the one or more compounds in a solution (e.g. a DMSO solution) administered and / or contacted with the cell. In embodiments, the concentration ranges from about 0.01 M to about 10 pM, about 0.1 pM to about 5 M, or about 0.5 pM to about 2 pM. In embodiments, the concentration is about 0.01 pM, about 0.1 pM, about 0.5 pM, about 1.0 pM, about 5 pM, or about 10 pM. In embodiments, the concentration is about 1 pM.

[0126] In embodiments, the one or more cells are treated with one or more compounds (e.g. at least about 10 compounds) for the same or substantially the same duration of time. In a non-limiting example, treatment refers to the administration and / or contacting of the one or more cells with the one or more compounds in an in vitro assay (e.g. an in vitro plate assay). In embodiments, the duration of time ranges from about 1 hour to about 48 hours, about 5 hours to about 36 hours, about 10 hours to about 30 hours, or about 12 hours to about 24 hours. In embodiments, the duration of time is about 1 hour, about 2 hours, about 5 hours, about 10 hours, about 12 hours, about 18 hours, about 24 hours, about 30 hours, about 36 hours, or about 48 hours. In embodiments, the duration of time is about 24 hours.

[0127] In embodiments, the transcriptional signatures and associated data (e.g. baseline transcriptional signature, compound-treated transcriptional signature, compound-specific differential transcriptional signature) are obtained and / or quantified using RNA sequencing. RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample that is useful for studying the cellular responses. Non-limiting examples of methods of conducting RNA-seq include single cell RNA-seq (ss-RNA-seq) and single nuclei RNA-seq (sn-RNA-seq), which are useful for conducting RNA- seq in a specific cell type, and bulk RNA-seq, which is for conducting RNA-seq from a sample of multiple cell types. In embodiments, the transcriptional signatures and associated data (e.g. baseline transcriptional signature, compound-treated transcriptional signature, compound-specific differential transcriptional signature) are obtained and / or quantified using single nuclei and / or single-cell assay experiments, including but not limited to single-cell ribonucleic acid (RNA) sequencing (scRNA-seq), single nuclei ribonucleic acid (RNA) sequencing (scRNA-seq), scTag-seq, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq), CyTOF / SCoP, E-MS / Abseq, miRNA-seq, CITE-seq, or any combinations thereof, or summaries of the same, including combinations, such as linear combinations, representing activated pathways in the single nuclei and / or single-cell cellular-component expression datasets. In embodiments, single nuclei and / or single-cell assay experiments are carried out with and / or performed on samples, including but not limited to fresh samples (e.g. an organ, a tissue, stem cells, human cells, cells from umbilical cord blood, cells from peripheral blood, bone marrow cells, cells from a solid tissue, and / or differentiated cells). In a non-limiting example, and without wishing to be bound by theory, fresh samples are more amenable to sorting cells by cell type as compared to frozen samples, and single-cell types are isolated and analyzed (e.g. sequenced) in single-cell assay experiments (e.g. scRNA-seq). In embodiments, the singlecell transcription data is single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data. In embodiments, the single nuclei transcription data is single nuclei ribonucleic acid (RNA) sequencing (snRNA-seq) data. In embodiments, the single-cell transcription data is transposase-accessible chromatin using sequencing (scATAC-seq) data.

[0128] In embodiments, measurements of transcriptional signatures and / or associated data (e.g. baseline transcriptional signature, compound-treated transcriptional signature, compound-specific differential transcriptional signature) include gene expression measurements, such as RNA levels. In embodiments, the single nuclei data comprises or consists of single-nuclei ribonucleic acid (RNA) sequencing (snRNA-seq) data. In embodiments, the single-cell data comprises or consists of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data.

[0129] In embodiments, the one or more cells of test samples are treated with one or more compounds, each of which is dissolved in solvent. Accordingly, in embodiments, the one or more cells of control samples are likewise treated with the same solvent in which the one or more compounds is dissolved upon treatment with the one or more cells of test samples. I n embodiments, the control samples and / or the test samples comprise a solvent useful for dissolving compounds and obtaining transcriptional signatures. Non-limiting examples of one or more solvents include water or aqueous-based solvents, alcohol-based solvents (e.g., ethanol or isopropyl alcohol), an ether such as bis(2-methoxyethyl) ether, -cyclodextrin, or a polar aprotic solvent such as dimethylsulfoxide (DMSO), dimethylformamide (DMF), N,N-dimethylacetamide (DMAc), tetrahydrofuran (THF) or acetonitrile (CH3CN), . In embodiments, the solvent is a polar aprotic solvent. In embodiments, the solvent is diimethylsulfoxide (DMSO). In embodiments, the control sample comprises dimethylsulfoxide (DMSO). In embodiments, each of the test samples comprise dimethylsulfoxide (DMSO). In embodiments, the control sample and each of the test samples comprise dimethylsulfoxide (DMSO).

[0130] In embodiments, a library of the disclosure comprises at least about 10 compounds, wherein each of the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, has and / or exhibits drug-like properties (e.g. Lipinski’s rule of Five; desirable ADME properties), and / or is structurally distinct (e.g. as assessed by Tanimoto coefficients and / or Dice coefficient (Hodgkin index)) and / or is associated with a different mechanisms of action (MoA) (e.g. MoAs known to address various diseases or disorders) compared to the remaining at least about 10 compounds. In a non-limiting example, the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, provide a set of compounds having diverse structures and representing a variety of different MoAs, which is useful to provide a library of transcriptional data capable of addressing a broad scope of diseases or disorders. In embodiments, the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, are associated with at least about 5, at least about 10, at least about 50, at least about 100, at least about 200, at least about 500, or at least about 1 ,000 or more known mechanisms of action (MoAs) for the treatment of one or more diseases or disorders. In embodiments, the at least about 10 compounds (e.g. compounds for drug development) each independently exhibit a mechanism of action useful in a therapy. Non-limiting examples of mechanisms of action include adenosine receptor agonism, aldosterone-receptor antagonism (e.g. mineralocorticoid receptor antagonists), alpha-adrenoceptor agonism (e.g. alpha-agonists), blocking of alpha-adrenoceptor (e.g. alpha-blockers), inhibition of angiotensin-converting enzyme (ace) (e.g. ace inhibitors), blocking of angiotensin receptor (arbs), beta-adrenoceptor agonism (e.g. beta-agonists), blocking of beta-adrenoceptor (e.g. beta-blockers), blocking of calcium-channel (ccbs), inhibition of adrenergic receptor signaling, promotion of diuresis, endothelin receptor antagonism, nicotinic receptor antagonism, mineralocorticoid receptor antagonism, muscarinic receptor antagonism, Na-t-K-i- atpase pump inhibition (e.g. cardiac glycosides), inhibition of neprilysin, inhibition of phosphodiesterase inhibitors, blocking of potassium-channel, opening of potassium-channel, renin inhibition, blocking of sodium-channel, inhibition of sodium-glucose cotransporter 2, and activation of adrenergic receptors

[0131] In embodiments, the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, each independently have a molecular weight of less than about 1000 Daltons, less than about 1500 Daltons, less than about 2000 Daltons, or less than about 2500 Daltons, optionally about 2000 Daltons. In embodiments, the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, each independently satisfies at least one rule of the four rules of Lipinski’s rule of Five, which include (i) not more than five hydrogen bond donors, (ii) not more than ten hydrogen bond donors, (iii) a molecular weight under about 500 Daltons, and (iv) a LogP under 5. In embodiments, the agent satisfies any two or more rules, any three or more rules, or all four rules of Lipinski’s rule of Five. In embodiments, each of the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, has enhanced oral bioavailability compared to a compound that does not satisfy one or more, two or more, three or more, or all four rules of Lipinski’s rule of Five. In embodiments, the agent causes an improvement and / or resolution of the disease when administered to a patient in need thereof. In embodiments, the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, each independently satisfy each of the Lipinski rule of five criteria. In embodiments, the at least about 10 compounds, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds, each independently satisfy at least three criteria of the Lipinski rule of five criteria.

[0132] In embodiments, the library comprises transcriptional data (e.g. compound-treated transcriptional signature data, compound-specific differential transcriptional signature data) from at least about 25, at least about 50, at least about 100, at least about 500, at least about 1,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds or interventions. In embodiments, the at least about 10 compounds or interventions, or at least 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the at least about 10 compounds or interventions, are selected from Table 1 . In embodiments, the compounds or interventions, or at least 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10% of the compounds or interventions, are selected from Table 1 (non-LINCS dataset) and / or Table 2 (LINCS dataset) and / or any of the commercially available compound libraries such as the Enamine Library Catalog.

[0133] In embodiments, each, or at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds or interventions is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 (Non-LINCS compounds), Table 2 (LINCS compounds), and any of the commercially available compound libraries such as the Enamine Library Catalog. In aspects, the disclosure provides a method of assembling transcriptional data into a library. In embodiments, the method comprises:

[0134] (a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;

[0135] (b) obtaining a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; and

[0136] (c) generating a compound-specific differential transcriptional signature data set of the cell type obtained upon differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; and

[0137] (d) assembling of the transcriptional signature data sets of (a), (b) and (c) into a library.

[0138] In embodiments, during step (a), the control sample of one or more cells of a cell type is treated with solvent, and during step (b), each test sample of one or more cells is separately treated with one of the at least about 10 compounds dissolved in the same solvent. In embodiments, the solvent is dimethylsulfoxide (DMSO).

[0139] In aspects, the disclosure provides a method for preparing a library of transcriptional signatures, the method comprising:

[0140] (a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;

[0141] (b) obtaining a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compound;

[0142] (c) generating a compound-specific differential transcriptional signature for each of the at least about 10 compounds upon differential comparison of the compound-treated transcriptional signature data of (b) against the baseline transcriptional signature data of (a); and (d) assembling the compound-specific differential transcriptional signatures generated in (c) into a library.

[0143] In embodiments, during step (a), the control sample of one or more cells of a cell type is treated with solvent, and during step (b), each test sample of one or more cells is separately treated with one of the at least about 10 compounds dissolved in the same solvent. In embodiments, the solvent is dimethylsulfoxide (DMSO).

[0144] In embodiments, assembling the transcriptional signatures and / or associated data into a library further comprises curating the library. Any known methods useful for curating the library are contemplated by the present disclosure. Non-limiting examples of curating the library include one or more of creating a count data; filtering (e.g. by number of cells, number of reads per cell, number of captured genes, percent of MT genes, and / or detection of singlets, doublets, etc.); or demultiplexing. In embodiments, demultiplexing includes separating pooled libraries of sequencing data into individual and / or separate libraries comprising sequencing data of pooled samples (e.g. according to library-specific molecular hashtags (barcodes)), and / or separating sequencing data of pooled samples into sequencing data of individual samples (e.g. according to samplespecific molecular hashtags (barcodes)). In embodiments, the sequencing data of individual samples is further processed, including but not limited to one or more of normalizing data, removing hashing-related artifacts (e.g. hashtag “negative” cells, doublets, etc.), and annotating each individual sample with relevant metadata (e.g., compound name, dose, etc.).

[0145] In embodiments, assembling the transcriptional signatures into a library further comprises analyzing pseudobulk data and / or cell-type pseudobulk data. As used herein, “pseudobulk” refers to a method of data analysis that averages the expression of an individual gene measured in singular cells across desired input cells. In embodiments, analysis of pseudobulk data includes determination of v-scores. In embodiments, pseudobulk refers to an experimental proxy for bulk sequencing. In embodiments, qualitative differences are present between running true bulk RNA sequencing and bulking single cell RNA sequencing data informatically.

[0146] In embodiments, assembling the transcriptional signatures into a library further comprises additional analysis (e.g. analysis of curated and demultiplexed data), including but not limited to cluster annotation, correlation activity analysis, leave-one-out classifier analysis, nearest-neighbor analysis, and differential expression analysis.

[0147] In embodiments, cluster annotation includes annotating curated data sets using defined markers to score cells and assign cells to a specific cell cluster present in the sequenced cell population. Non-limiting methods for performing cluster annotation include principal component analysis (PCT), and non-limiting examples of methods useful for visualizing the clusters include uniform manifold approximation and projection (UMAP). In embodiments, after cluster annotation is performed, the resulting data is aggregated (e.g. pseudobulk data) and / or v-scores are computed.

[0148] In embodiments, correlation activity analysis includes determining whether a compound induces a transcriptional signature (e.g. compound-specific differential transcriptional signature) different from a control sample (e.g. DMSO) in a statistically significant manner. In a non-limiting embodiment, a correlation between the compound-specific differential transcriptional signature and the transcriptional signature of the control sample is computed and / or a pairwise correlation between the transcriptional signature of each control sample is computed, optionally wherein a t-test is performed on the data resulting from each correlation. In embodiments, v-scores are generated, optionally wherein the v-scores can be utilized in predictive model to determine whether the model correctly classifies and identifies the model. Non-limiting examples of predictive models can be found in U.S. Patent Publication No. US 2020 / 0020419, which is incorporated by reference herein in its entirety.

[0149] In embodiments, a leave-one-out classifier analysis includes distinguishing a compound-specific differential transcriptional signature from the compound-specific differential transcriptional signatures of one or more compounds that were experimentally determined at the same time (e.g. each of the compounds were included in the same plate). In a non-limiting example, compound-specific differential transcriptional signatures for each compound are determined in replicate (e.g. two, three, four, or four or more replicates per compound) with a discrete label assigned to the compound-specific differential transcriptional signatures obtained from each replicate, and the consistency and / or reproducibility of the obtained transcriptional signatures is assessed. Methods for assessing the consistency and / or reproducibility of the obtained compound-specific differential transcriptional signature include, but are not limited to, training a logistic regression classifier on the compound-specific differential transcriptional signature obtained in one of the replicates and using the classifier to classify the compound-specific differential transcriptional signature of the remaining replicates.

[0150] In embodiments, a nearest-neighbor analysis includes assessing the consistency and / or reproducibility of compound-specific differential transcriptional signatures by processing v-scores of the compound-specific differential transcriptional signature for non-control samples of one or more compounds, wherein the transcriptional signatures were that were experimentally determined at the same time (e.g. each of the compounds were included in the same plate). Non-limiting examples of methods to assess the consistency and / or reproducibility of compound-specific differential transcriptional signatures include generating a confusion plot.

[0151] In embodiments, differential expression analysis includes determining which genes are differentially regulated between one or more compounds and control samples. Non-limiting examples of methods for performing differential expression analysis include Deseq2.

[0152] Cellular Transitions

[0153] Tissues are complex ecosystems of individual cells, where dysregulation of cell state is the basis of disease. Existing drug discovery efforts seek to characterize the molecular mechanisms that cause cells to transition from healthy to disease states, and to identify pharmacological approaches to reverse or inhibit these transitions. Past efforts have also sought to identify molecular signatures characterizing these transitions, and to identify pharmacological approaches that reverse these signatures.

[0154] T ranscriptional transitions refer to a transition in a cell’s state from a first transcriptome of the cell to an altered transcriptome (e.g. healthy to diseased). In embodiments, a transcriptional signature (e.g., a compoundspecific differential transcriptional signature) is associated with or indicative of a desired transcriptional transition in a cell state. In embodiments, a transcriptional transition is marked by a change in RNAs transcribed in the cell (e.g. a change in identity and / or amount of RNA).

[0155] In embodiments, the desired transcriptional transition in a cell state is associated with or indicative of a cellular transition, including but not limited to a diseased or disordered state to an undiseased or pre-diseased state. In embodiments, the diseased or disordered state is selected from an acute stage, a chronic stage, a clinical stage, a flare-up, a remission, a progressive stage, a refractory, a subclinical stage, and a terminal phase.

[0156] Cellular transitions refer to a transition in a cell’s state from a first cell state to an altered cell state (e.g., healthy to diseased). In embodiments, a cellular transition is marked by a change in cellular-component expression in the cell, and thus by the identity and quantity of cellular components (e.g., mRNA, transcription factors) produced by the cell.

[0157] In embodiments, the cellular transition is characterized by an upregulation or a down-regulation of one or more cellular components.

[0158] For example, in embodiments, cellular transitions ( .e., a transition in a cell’s state from a first cell state to an altered cell state) are marked by a change in expression of cellular components in the cell. In a non-limiting example, a cellular transition is marked by a change in cellular-component expression in the cell, and thus by the identity and quantity cellular components (e.g., mRNA, transcription factors) produced by the cell. In embodiments, the cellular transition is identified and / or generated by subtracting transcriptional data from one or more cells having an undiseased or pre-diseased state from transcriptional data from one or more cells having a diseased or disordered state.

[0159] As another example, in embodiments, the one or more cellular components comprises a plurality of genes, optionally measured at the RNA level. In embodiments, the plurality of genes comprises at least 2, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, or at least 100 genes. In embodiments, the plurality of genes comprises at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, or at least 1000 genes. In embodiments, the plurality of genes comprises at least 1000, at least 2000, at least 3000, at least 4000, at least 5000, at least 10,000, at least 30,000, at least 50,000, or more than 50,000 genes. In embodiments, the plurality of genes comprises between 2 and 20, between 20 and 50, between 50 and 100, between 100 and 200, between 200 and 500, between 500 and 1000, between 1000 and 5000, between 5000 and 10,000 genes, or between 10,000 and 50,000 genes. In embodiments, the one or more cellular components comprises a plurality of proteins. In embodiments, the plurality of proteins comprises at least 2, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, or at least 100 proteins. In embodiments, the plurality of proteins comprises at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, or at least 1000 proteins. In embodiments, the plurality of proteins comprises at least 1000, at least 2000, at least 3000, at least 4000, at least 5000, at least 10,000, at least 30,000, at least 50,000, or more than 50,000 proteins. In embodiments, the plurality of proteins comprises between 2 and 20, between 20 and 50, between 50 and 100, between 100 and 200, between 200 and 500, between 500 and 1000, between 1000 and 5000, between 5000 and 10,000 proteins, or between 10,000 and 50,000 proteins. In embodiments, cellular components of interest include nucleic acids, including DNA, modified (e.g., methylated) DNA, RNA, including coding (e.g., mRNAs) or non-coding RNA (e.g., sncRNAs), proteins, including post-transcriptionally modified protein (e.g., phosphorylated, glycosylated, myristilated, etc. proteins), lipids, carbohydrates, nucleotides (e.g., adenosine triphosphate (ATP), adenosine diphosphate (ADP) and adenosine monophosphate (AMP)) including cyclic nucleotides such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), other small molecule cellular components such as oxidized and reduced forms of nicotinamide adenine dinucleotide (NADP / NADPH), and any combinations thereof. In embodiments, a cellular transition is determined based upon a change in cytotoxicity, cell viability, genotoxicity, developmental toxicity, and / or mitochondrial toxicity in response to an agonism and / or antagonism of one or more cellular components of interest. Further examples of cellular components, cell states, and / or methods for measuring the same are described in Huang R, 2016, “A Quantitative High- Throughput Screening Data Analysis Pipeline for Activity Profiling,” High-Throughput Screening Assays in Toxicology, Methods in Molecular Biology; 1473(1); Huang et al., 2016, “Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization,” Nat Commun. 7, p. 10425; and Huang et al., 2018, “Expanding biological space coverage enhances the prediction of drug adverse effects in human using in vitro activity profiles,” Sci Rep. 8(1 ):3783, each of which is hereby incorporated herein by reference in its entirety.

[0160] In embodiments, the transcriptional signatures and associated transcriptional data (e.g. baseline transcriptional signature, compound-treated transcriptional signature, compound-specific differential transcriptional signature) are obtained and / or quantified using single nuclei and / or single-cell assay experiments, including but not limited to single-cell RNA sequencing (scRNA-seq) and / or single-nuclei RNA sequencing (snRNA-seq). In embodiments, single nuclei and / or single-cell assay experiments are carried out with and / or performed on samples, including but not limited to frozen samples (e.g. an organ, a tissue, stem cells, human cells, cells from umbilical cord blood, cells from peripheral blood, bone marrow cells, cells from a solid tissue, and / or differentiated cells). In embodiments, frozen samples are samples that were harvested and / or obtained from a donor and stored under freezing conditions (e.g. in a freezer and / or after treatment with liquid nitrogen) about one day, about two days, about 3 days, about 1 week, about 2 weeks, about 3 weeks, about 4 weeks, about 2 months, about 3 months, about 6 months, about 1 year, about 2 years, or about 3 years before analysis. In a non-limiting example, the frozen sample is harvested and / or obtained from a deceased organ donor and then frozen (e.g. treated with and / or frozen in liquid nitrogen), and nuclei of cells from the samples are isolated and analyzed (e.g. sequenced) in single nuclei assay experiments (e.g. snRNA-seq). In embodiments, and without wishing to be bound by theory, single nuclei assay experiments provide improvements over single-cell assay experiments because single nuclei assay experiments are more amendable to scaling and / or performing within short timeframes, and obtaining frozen samples can be more facile than obtaining fresh samples. In embodiments, fresh samples are samples that were harvested and / or obtained from a donor less than about 1 week, less than about 3 days, less than about 2 days, less than about 1 day, or less than about 12 hours before analysis, and not subjected to any freezing procedures prior to analysis) samples. In embodiments, the single nuclei data is single-nucleus ribonucleic acid (RNA) sequencing (snRNA-seq) data.

[0161] In embodiments, the cellular transition is identified by the presence of a diseased cell phenotype in the cell. In embodiments, the diseased cell phenotype is identified by a discrepancy between the diseased cell and a normal cell. For instance, in embodiments, the diseased cell phenotype can be identified by loss of a function of the cell, gain of a function of the cell, progression of the cell (e.g., transition of the cell into a differentiated state), stasis of the cell (e.g., inability of the cell to transition into a differentiated state), intrusion of the cell (e.g., emergence of the cell in an abnormal location), disappearance of the cell (e.g., absence of the cell in a location where the cell is normally present), disorder of the cell (e.g., a structural, morphological, and / or spatial change within and / or around the cell), loss of network of the cell (e.g., a change in the cell that eliminates normal effects in progeny cells or cells downstream of the cell), a gain of network of the cell (e.g., a change in the cell that triggers new downstream effects in progeny cells of cells downstream of the cell), a surplus of the cell (e.g., an overabundance of the cell), a deficit of the cell (e.g., a density of the cell being below a critical threshold, a difference in cellular-component ratio and / or quantity in the cell, a difference in the rate of transitions in the cell, or any combination thereof.

[0162] In embodiments, the diseased cells include cell lines, biopsy sample cells, and cultured primary cells. In embodiments, the normal cells include cultured primary cells and biopsy sample cells. In embodiments, the cells are human cells.

[0163] Any method for detecting and / or monitoring and / or determining and / or measuring cellular transitions are contemplated by the present disclosure, as would be understood by one of ordinary skill in the art. Nonlimiting examples of methods include colorimetric measurement, a fluorescence measurement, a luminescence measurement, a resonance energy transfer (FRET) measurement, a measurement of a protein-protein interaction, a measurement of a protein-polynucleotide interaction, a measurement of a protein-small molecule interaction, mass spectrometry (e.g, liquid chromatography mass spectrometry (LCMR) or Matrix-assisted laser desorption / ionization-time of flight (MALDI-TOF) mass spectrometry (MS)), nuclear magnetic resonance (NMR) (e.g. proton NMR, carbon NMR, COSY, HSQC, HMBC and HSQC- TOCSY), or a microarray measurement.

[0164] Methods of Use

[0165] In aspects, the disclosure provides a method of identifying one or more compounds associated with or indicative of a desired transcriptional signature. In embodiments, the method comprises: (a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;

[0166] (b) obtaining a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds;

[0167] (c) generating a compound-specific differential transcriptional signature data set of the cell type upon comparison of the compound-treated transcriptional signature data against the baseline transcriptional signature data from the cell type;

[0168] (d) assembling the transcriptional signature data sets of (a), (b) and (c) into a library; and

[0169] (e) selecting one or more compounds from the at least about 10 based on the comparison of the transcriptional signature of interest with the compound-specific differential transcriptional signature data of (c); wherein the one or more compounds are associated with or indicative of the desired transcriptional signature.

[0170] In a non-limiting example, a desired transcriptional signature associated with a disease or disorder is selected, and a library of the disclosure is used to identify one or more compounds with a transcriptional signature (e.g. a compound-specific differential transcriptional signature) similar or substantially similar to the desired transcriptional signature. In embodiments, the selected compounds of (e) can be further evaluated using additional assays related to, for example, the mechanism of action of the disease or disorder. In embodiments, preparing synthetic analogues of the one or more selected compounds of (e) includes modifying one or more functional groups of the one or more selected compounds.

[0171] In aspects, libraries of the disclosure are useful in methods of drug development, including but not limited to the preparation of synthetic analogues of compounds with associated transcription data included in a library, and methods of modifying selected (e.g. candidate) compounds to yield a lead compound.

[0172] In aspects, the disclosure provides a method of preparing synthetic analogs of one or more compounds for drug development. In embodiments, the method comprises:

[0173] (a) analyzing a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; (b) analyzing a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least 10 compounds;

[0174] (c) generating a compound-specific differential transcriptional signature data set of the cell type upon comparison of the compound-treated transcriptional signature data against the baseline transcriptional signature data from the cell type;

[0175] (d) assembling the transcriptional signature data sets of (a), (b) and (c) into a library;

[0176] (e) selecting one or more compounds from the at least about 10 compounds based on the comparison of (b)-(c) in the library; and

[0177] (f) preparing synthetic analogues of the one or more selected compounds for drug development.

[0178] In a non-limiting example, the selection of (e) provides one or more compounds with a transcriptional signature (e.g. a compound-specific transcriptional signature and / or a compound-specific differential transcriptional signature) similar or substantially similar to a gene signature of target diseased cells (which would be desirable to reverse in order to treat the disease or disorder of the cell). In embodiments, the selected compounds of (e) can be further evaluated using additional assays related to, for example, the mechanism of action of the disease or disorder. In embodiments, preparing synthetic analogues of the one or more selected compounds of (e) includes modifying one or more functional groups of the one or more selected compounds. Non-limiting methods of selecting compounds include the use of contrastive learning methods, predictive models, and algorithms. Non-limiting examples of predictive models can be found in U.S. Patent Publication No. US 2020 / 0020419, which is incorporated by reference herein in its entirety. Nonlimiting examples of algorithms include K-NN, Logistic Regression, and XGBoost.

[0179] In aspects, the disclosure provides a method of modifying a candidate compound to yield a lead compound, the method comprising:

[0180] (a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;

[0181] (b) obtaining a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; (c) generating a compound-specific differential transcriptional signature data set of the cell type obtained upon differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type

[0182] (d) comparing the compound-specific differential transcriptional signature data set from the at least about 10 compounds to compound-specific differential transcription signature data from the candidate compound;

[0183] (e) selecting one or more compounds from the at least about 10 compounds selected based on the comparison of (d); and

[0184] (f) modifying the candidate compound based on structural features of the one or more compounds selected in (e) to yield a lead compound.

[0185] In a non-limiting example, the selection of (e) provides one or more compounds with a transcriptional signature (e.g. a compound-specific transcriptional signature and / or a compound-specific differential transcriptional signature) similar or substantially similar to a transcription signature (e.g. compound-specific differential transcription signature data) of a candidate compound. In embodiments, a candidate compound is a compound that has been selected and / or identified as a potential lead compound, for example based on desirable drug-like or ADME properties of the compound and / or mechanisms of action (MoAs) of the compound. In embodiments, the candidate compound is further modified in view of structural features of the one or more compounds selected in (e). In embodiments, structural features include functional groups of the one or more compounds selected in (e). In embodiments, modifying the candidate compound comprises modifying one or more functional groups of the candidate compound. Non-limiting methods of selecting compounds include the use of contrastive learning methods, predictive models, and algorithms. Non-limiting examples of predictive models can be found in U.S. Patent Publication No. US 2020 / 0020419, which is incorporated by reference herein in its entirety. Non-limiting examples of algorithms include K-NN, Logistic Regression, and XGBoost.

[0186] In embodiments, modifying a functional group comprises one or more modifications selected from alkylation (e.g. alkylation of ketones, nitriles, and carboxylic esters, N-alkylation of amides or imides), arylation (e.g. N- arylation), substitution (e.g. replacement of a hydroxy by an amino group), amidation, amination, arylation, acylation (e.g acylation of amines by acyl halides, anhydrides, carboxylic acids, carboxylic esters, amides, acylation of amines or other acid derivatives, or N-acylation of amides or imides), cyanation, halide exchange, halogenation, dehalogenation, oxidation (e.g. oxidation of aldehydes to carboxylic acids, aromatization, oxidative cleavage, oxidative decarboxylation), reduction (e.g. reduction of carboxylic acids, esters, anhydrides, amides, alkyl halides, acyl halides, tosylates, other sulfonates, a C— N bond, an alkene, and alkyne, or similar functional groups), reductive amination, reductive alkylation, epoxidation, hydrolysis (e.g. hydrolysis of carbon-nitrogen double bond or nitriles), alcoholysis (e.g. alcoholysis of nitriles), hydrogenolysis (e.g. hydrogenolysis of alcohols, esters, or nitriles), hydrogenation, dehydrogenation, formylation, hydroxylation (e.g. dihydroxylation), acyloxylation, oxygenation, deoxygenation, diazotization, chlorosulfonation, nitration, nitrosation, sulfurization, desulfurization, sulfonation, desulfonation, sulfenylation, halosulfonation, sulfonylation, carboxylation, decarboxylation (e.g. ketonic decarboxylation), selenylation, phosphorylation, salt formation (e.g. conversion of a carboxylic acid to a carboxylate salt), and addition of a suitable protecting group (e.g. 9-fluorenylmethyl carbamate (Fmoc), t-butyl carbamate (Boc), and carboxybenzyl carbamate (cbz), methyl carbamate, ethyl carbamate, benzyloxymethyl (BOM), methylthiomethyl (MTM), phenylthiomethyl (PTM), cyanoethyl, 2,2-dichloro-1 , 1 difluoroethyl, 2-chloroethyl, 2-bromoethyl, tetrahydropyranyl (THP), phenacyl, 4 bromophenacyl, allyl, propargyl, trimethylsilyl (TMS), triethylsilyl (TES), or t-butyldiphenyl silyl (TBDPS)).

[0187] Functional Groups

[0188] In aspects, a compound of the disclosure, including but not limited to a compound included in or selected from a library of the disclosure, a candidate compound, or a lead compound, comprises at least one functional group. In embodiments, the functional group may be the same or different from a functional group of other compounds (e.g. compounds remaining in a set of compounds). In embodiments, each of the at least about 10 compounds comprises at least one functional group, which may be the same or different from the at least one functional group of the remaining at least about 10 compounds.

[0189] Any chemical functional group is contemplated by the present disclosure, as would be understood by one of ordinary skill in the art. In embodiments, the functional group comprises one or more atoms selected from hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorous, or halogen.

[0190] In embodiments, the at least one functional group comprises or consists of one or more of (a)-(g):

[0191] (a) a hydrogen atom;

[0192] (b) a carbon atom or a group comprising a carbon atom, optionally selected from an alkane, an alkene, an alpha, beta-unsaturated ketone, an alpha, beta-unsaturated aldehyde, an alpha, beta-unsaturated carboxylic acid ester, an alpha, beta-unsaturated carboxylic acid amide, an alpha, beta-unsaturated sulfoxide, an alpha, beta-unsaturated sulfone, an alpha, beta-unsaturated sulfonamide, an alpha, beta-unsaturated sulfonylchloride, a nitro alkene including but not limited to a vinylogous nitro group (e.g. alpha, beta-unsaturated nitroalkene), an alkyne, an arene, a hetarene, a nitrile, an amide, a lactam, an imine, a nitroalkyl group, a nitroaryl group, an amidine group, a carbamate, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, a carbosulfone, a carbosultam, a carbosultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, an alkylchloride, an alkylbromide, an alkyliodide, an alkenylchloride, an alkenylbromide, an alkenyliodide, an alkynylchloride, an alkynylbromide, an alkynyliodide, an arylfluoride, an arylchloride, an arylbromide, a aryliodide, a hetarylfluoride, a hetarylchloride, a hetarylbromide, a hetaryliodide, a carbonylfluoride, a carbonylchloride, a carbonylbromide, a carbonyliodide, an isocyanate, an isothiocyanate, an isocyanide, an alkylphosphonium group including but not limited to alkyltriphenylphosphonium chloride, alkyltriphenylphosphonium bromide, and alkyltriphenylphosphonium iodide, any of which may optionally be substituted by one or more substituents;

[0193] (c) a nitrogen atom or a group comprising a nitrogen atom, optionally selected from an amine, an isocyanate, an isocyanide, a hydroxylamine, a hydrazine, a nitrile, an amide, a lactam, an imine, an azo group, a nitro group, a nitroso group, an amidine group, a guanidine group, a carbamate, and an azide, any of which may optionally be substituted by one or more substituents;

[0194] (d) an oxygen atom or a group comprising an oxygen atom, optionally selected from of a hydroxyl group, an ether, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, and a hydroxyl amine, any of which may optionally be substituted by one or more substituents;

[0195] (e) a sulfur atom or a group comprising a sulfur atom, optionally selected from a thiol, a disulfide, a sulfide, a sulfoxide, a sulfin amide, a sulfonamide, a sulfone, a sultam, a sultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, and a isothiocyanate, any of which may optionally be substituted by one or more substituents;

[0196] (f) a phosphorous atom or a group comprising a phosphorous atom, optionally selected from a phosphine, a phosphine oxide, a phosphinite, a phosphonite, a phosphite, a phosphinate, a phosphonate, a phosphate, and a phosphonium salt, any of which may optionally be substituted by one or more substituents; and

[0197] (g) a halogen atom or a group comprising a halogen atom, optionally selected from fluorine, chlorine, bromine, iodine, for example alkylchloride, alkylbromide, alkyliodide, alkenylchloride, alkenylbromide, alkenyliodide, alkynylchloride, alkynylbromide, alkynyliodide, arylfluoride, arylchloride, arylbromide, aryliodide, hetarylfluoride, hetarylchloride, hetaryl bromide, hetaryliodide, carbonylfluoride, carbonylchloride, carbonylbromide, carbonyliodide, sulfonylfluoride, sulfonylchloride, sulfonylbromide, and sulfonyliodide, any of which may optionally be substituted by one or more substituents;

[0198] In embodiments, the functional group is selected from OH, halo, cyano, fluoroalkyl, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, -ORa, -SRa, -OC(O)Ra, -N(Ra)Rb, -C(O)Ra, -C(O)ORa, - OC(O)N(Ra)Rb, -C(O)N(Ra)Rb, -N(Ra)C(O)ORa, -N(Ra)C(O)Ra, -N(Ra)C(O)N(Ra)Rb, N(Ra)C(NRa)N(Ra)Rb, -N(Ra)S(O)tRa, -C(O)N(Ra)S(O)tRa, -S(O)tORa, -S(O)tN(Ra)Rb, -S(O)tN(Ra)C(O)Rb, or - P(O)(ORa)(ORb), optionally substituted alkyl, optionally substituted alkylaryl, optionally substituted alkylheteroaryl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted aralkyl, optionally substituted haloalkyl, optionally substituted alkoxy, optionally substituted heterocyclyl, and optionally substituted heteroaryl; Raand Rbare each independently selected from the group consisting of hydrogen, alkyl, fluoroalkyl, cycloalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl, heterocycloalkylalkyl, heteroaryl, heteroarylalkyl, halogen, - O-alkyl, -O-aryl, cyano, nitro, -OH, -NH2, -NH-alkyl, and -NH-aryl; and t is 1 or 2.

[0199] In embodiments, the functional group provides compounds of the disclosure with enhanced and / or improved and / or modulated properties, including but not limited to properties related to drugability of a compound. In embodiments, the one or more functional groups provide one or more of (a)-(f) compared to different functional groups and / or the absence of the one or more functional groups. In embodiments, the modification of a compound results in the one or more compounds having one or more of (a)-(f) compared to the compound prior to modification. Non-limiting examples of properties include:

[0200] (a) increased activity strength (e.g. dose-response curve); and / or selectivity (e.g. Kd ratio);

[0201] (b) increased solubility (e.g. as determined by ultraviolet absorption, nephlometry, nuclear magnetic resonance and / or potentiometry) and / or partition property (e.g. logP); (c) increased metabolic and / or chemical stability (e.g. as determined by a microsomal stability assay, hepatocyte stability assay, recombinant CYP enzyme assay, plasma assay, and / or enzymatic assay);

[0202] (d) modulation of pharmacokinetic parameters (including, without limitation, absorption, distribution, metabolism, and excretion (ADME)), (e.g. as determined by physicochemical screening, CYP45 inhibition, metabolic stability, hERG inhibition, and / or animal models), optionally wherein the modulation provides increased or enhanced pharmacokinetic properties compared to the compound prior to the modulation;

[0203] (e) modulation of pharmacodynamic parameters (including, without limitation, dose-response relationship (e.g. ECso)) (e.g. as determined by flow cytometry, magnetic resonance imaging (MRI), target binding / engagement assays, biomarker assays), optionally wherein the modulation provides increased or enhanced pharmacodynamic properties compared to the compound prior to the modulation;

[0204] (f) reduction or ablation of toxicity and / or adverse reactions (e.g. LD50 and / or LC50).

[0205] In aspects, the disclosure provides a method of identifying one or more functional groups associated with or indicative of a desired transcriptional signature. In embodiments, the method comprises:

[0206] (a) selecting from a library of transcriptional data one or more compounds having a compound-specific differential transcriptional signature at least substantially similar to the desired transcriptional signature, wherein: the library comprises: i. a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; ii. a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; and ill. a compound-specific differential transcriptional signature data set of the cell type generated from differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; wherein each of the at least about 10 compounds comprises at least one functional group, which may be the same or different from the at least one functional group of the remaining at least about 10 compounds;

[0207] (b) comparing the at least one or more functional groups of the one or more compounds selected in (a); and

[0208] (c) selecting one or more functional groups based on the comparison of (b), wherein the one or more functional groups are associated with or indicative of the desired transcriptional signature.

[0209] In embodiments, the libraries and / or methods disclosed herein are contemplated for uses reasonably related to the development and submission of information under a United States Federal law which regulates the manufacture, use, or sale of drugs or veterinary biological products. See 35 U.S.C. § 271 (e)(1). In embodiments, the Safe Harbor provision (35 U.S.C. § 271 (e)(1)) provides an exception to patent infringement liability when otherwise-infringing activities are solely for uses reasonably related to obtaining FDA approval.

[0210] Compounds

[0211] In aspects, a library of the disclosure comprises transcriptional data (e.g. compound-specific differential transcriptional signature) of at least about 10 compounds. In embodiments, one or more of the at least about 10 compounds are selected from the compounds of Table 1. In embodiments, the compounds of Table 1 provide a set of compounds having diverse structures and representing a variety of different MoAs, which is useful to provide a library of transcriptional data capable of addressing a broad scope of diseases or disorders. In a non-limiting example, a compound-specific differential transcriptional signature is obtained for each of the one or more of the compounds of Table 1 upon differential comparison of the compound-treated transcriptional signature data of a compound-treated transcriptional signature for each of the one or more compounds of Table 1 with a baseline transcriptional signature from a control sample.

[0212] In embodiments, one or more of the at least about 10 compounds are selected from the compounds of Table 2. In embodiments, the compounds of Table 2 provide a set of compounds having diverse structures and representing a variety of different MoAs, which is useful to provide a library of transcriptional data capable of addressing a broad scope of diseases or disorders. In a non-limiting example, a compound-specific differential transcriptional signature is obtained for each of the one or more of the compounds of Table 2 upon differential comparison of the compound-treated transcriptional signature data of a compound-treated transcriptional signature for each of the one or more compounds of Table 2 with a baseline transcriptional signature from a control sample.

[0213] In embodiments, the methods and libraries of the disclosure include transcriptional data (e.g. compound- treated transcriptional signature, compound-specific differential transcriptional signature) from compounds listed in Table 1.

[0214] In embodiments, the methods and libraries of the disclosure include transcriptional data (e.g. compound- treated transcriptional signature, compound-specific differential transcriptional signature) from compounds listed in Table 2.

[0215] In embodiments, the compounds are selected from Table 1 (non-LINCS dataset) and / or Table 2 (LINCS dataset) displayed.

[0216] Additional Definitions

[0217] In general, terms used in the claims and the specification are intended to be construed as having the plain meaning understood by a person of ordinary skill in the art. Certain terms are defined below to provide additional clarity. In case of conflict between the plain meaning and the provided definitions, the provided definitions are to be used.

[0218] Any terms not directly defined herein shall be understood to have the meanings commonly associated with them as understood within the art of the disclosure. Certain terms are discussed herein to provide additional guidance to the practitioner in describing the compositions, the devices, the methods and the like of aspects of the disclosure and how to make or use them. It will be appreciated that the same thing may be said in more than one way. Consequently, alternative language and synonyms may be used for any one or more of the terms discussed herein. No significance is to be placed upon whether or not a term is elaborated or discussed herein. Some synonyms or substitutable methods, materials and the like are provided. Recital of one or a few synonyms or equivalents does not exclude use of other synonyms or equivalents, unless it is explicitly stated. Use of examples, including examples of terms, is for illustrative purposes only and does not limit the scope and meaning of the aspects of the disclosure herein.

[0219] As used herein, the terms “cell fate” and “cell state” are interchangeable and synonymous.

[0220] The term “subject," refers to an individual organism such as a human or an animal. In embodiments, the subject is a mammal (e.g., a human, a non-human primate, or a non-human mammal), a vertebrate, a laboratory animal, a domesticated animal, an agricultural animal, or a companion animal. In embodiments, the subject is a human (e.g., a human patient). In embodiments, the subject is a rodent, a mouse, a rat, a hamster, a rabbit, a dog, a cat, a cow, a goat, a sheep, or a pig.

[0221] As used in this Specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.

[0222] Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive and covers both “or” and “and”. Likewise, the term “and / or” covers both “or” and “and”.

[0223] Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About is understood to be within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1 %, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from the context, all numerical values provided herein are modified by the term “about.”

[0224] The disclosure will be further described in the following examples, which do not limit the scope of the disclosure described in the claims.

[0225] EXAMPLES

[0226] Example 1 : Preparation of Cells

[0227] Peripheral blood mobilized human hematopoietic stem cells and progenitors cells (mPBCD34+ cells) are thawed and cultured for 48hrs before treatment using a cytokine cocktail supporting stem cell expansion (SCF, Flt3L, IL3, IL6, and TPO) in serum and free media. 48hrs post thaw cells are plated in 96 well plates at a density of 300,000 cells / mL (60,000 cells / well) prior to treatment.

[0228] Stock compound plates containing vehicle control (DMSO), positive controls, and compound interventions are diluted in IMDM (1 Ox) using Integra Viaflow 96well liquid handler prior to treatment (see below for methods of preparing compound plates).

[0229] Control cells are treated with DMSO. Treated cells are contacted with compound interventions at a final concentration of 1 uM and incubated for 24hrs.

[0230] 24hrs post-treatment, Control Cells and Treated Cells are processed for downstream scRNA sequencing. Viability and cell counts are measured using flow-cytometry, to ensure that samples exhibiting cell viability of 70% or greater are processed. As part of increasing throughput, individual samples are indexed using CMO labeling kit with minor modifications (3’Cel I P lex Kit Set A, 10X genomicis) for multiplexing (12 samples / library) prior to scRNAseq.

[0231] Pool samples are counted using an automated cells counter to 1.2 x106 cells / ml prior to downstream encapsulation using Chromium 10x system.

[0232] Individual samples are indexed using CMO labeling (3' Cell Plex Kit Set A kit, 10X Genomics) for multiplexing prior to single cell RNA sequencing (ssRNAseq).

[0233] Example 2: Treatment of Cells with Compound Interventions and Sequencing of Treated Cells

[0234] Positive control compounds, stored in 2D barcoded tubes in DMSO at -80 °C, are thawed to room temperature and diluted to target concentrations of 1 uM.

[0235] Diluted positive control compounds (1 mM in DMSO) along with the negative (DMSO) control are added to empty, barcoded 96 well plates which are then stored at -80 °C until needed. These “control plates” are prepared in batches (multiple plates per batch).

[0236] “Test Compound Plates” are prepared at a concentration of 1 mM in DMSO are prepared in 96 well plates and stored at -80 °C prior to use. The concentration is diluted to 1 pM prior to administration of compounds to cells.

[0237] 1-2 days prior to scheduled use, control plates and test compound plates are removed from -80 °C and allowed to thaw to room temperature. Test compounds are then diluted 1 :10 to a concentration of 1 mM and added to available (unused) wells in the control plates (Intermediate Dilution Plates (IDPs) using a Hamilton STAR liquid handler. IDPs are kept at room temperature until added to cells ~1-2 days later.

[0238] Following 24 hours incubation of control cells and treated cells (see above), cell counts and concentrations are established for each sample using automated cell counters. If necessary, the cell concentration is adjusted to meet requirements for downstream processing.

[0239] Samples are then processed using Chromium Next GEM Single Cell 3' Kit v3.1 reagents (10X Genomics) in conjunction with Chromium Single Cell 3' Feature Barcode Library Kit reagents (10X Genomics) according to the manufacturer’s instructions.

[0240] 3' gene expression libraries are barcoded using Dual Index Kit TT reagents (10X Genomics) while Feature Barcode Libraries are barcoded using Dual Index Kit NN reagents (10X Genomics), all according to the manufacturer’s recommended protocols. 3’ gene expression libraries are then normalized and equimolar pooled to a final concentration of 2 nm. separately, feature barcode libraries are normalized and equimolar pooled to a final concentration of 2 nM.

[0241] All libraries are then sequenced on either an Illumina Novaseq6000 or Illumina NextSeq2000 using paired reads to target 50,000 reads per cell (3’ Gene Expression Libraries) or 10,000 reads per cell (Feature Barcode libraries).

[0242] Sequencing data is then processed through our standard pipeline using bcl2fastq (v1 .8.4) to demultiplex libraries, CellRanger (v5) to align to the human hg38 reference and generate count matrices and a custom quality analysis workflow leveraging the functionality of Seurat (v3).

[0243] Example 3: Analyses of Sequencing Data

[0244] Step 1. Curation & Demultiplexing of Data

[0245] Sequencing data that has been run through a standard bioinformatic pipeline for cell hashing is further processed as follows. A standard sequencing flowcell which contains 8 pooled libraries is first demultiplexed into 8 separate libraries according to library-specific molecular barcodes. Each library contains 12 pooled samples which are then demultiplexed into individual samples according to sample-specific molecular hashtags (barcodes). Sample-level processing is then performed to normalize data, remove hashing-related artifacts (hashtag “negative” cells, doublets, etc.) and annotate each sample with all the relevant metadata (e.g., compound name, dose, etc.). Gene count matrices are prepared for each sample and all sample data is collected in a single h5ad file. A non-limiting example of a protocol for curation and demultiplexing of data is shown below:

[0246] “Count Data” are created which correlate each cell to a well, hashtag ID, treatment metadata, bio metadata via the following steps.

[0247] 1 . A path to bxfile on s3 was received.

[0248] 2. An in-house curation was processed which splits reads by library and creates a count data ( cell by genes) for each cell, split by library.

[0249] 3. Basic QC analysis of libraries were processed which includes identifying the number of cells, number of reads per cell, number of captured genes, % of MT genes, and resulting filter cells.

[0250] 4. Demuliplexing was performed within each library, cells were split by their hashtag using an algorithm. 5. QC analysis was performed on each library to determine how many singlets (cells attributed to a single hashtag) were detected, doublets were detected, and so on and filtering was performed.

[0251] The output of these steps is a count data (scanpy ,h5ad file) where each cell has a library, hashtag ID, treatment metadata, and bio metadata.

[0252] In total, from these steps a data package was created and 3 files were uploaded, raw.h5ad (split by library), filtered_normalized.h5ad (where cells were removed based on step 3) and demuxed.h5ad (after splitting filtered cells by their hashtag).

[0253] Step 2. Analysis of Curated & Demultiplexed Data

[0254] Cluster Annotation: Curated datasets are annotated using defined markers to score cells and assign each and every cell to one of 6 clusters (Ery, Mk, ...., ) present in the sequenced CD34+ population. Standard PCA analysis is performed and UMAPs are generated to visualize the clusters. Once cluster annotation has been performed, cluster-level data is aggregated (i.e., “pseudobulk” analysis of each cluster) and v-scores (e.g. a representation of the difference between treatment and DMSO expression values) are computed.

[0255] Correlation Activity Analysis: A correlation activity analysis is performed to determine whether a compound induces a gene expression profile that is different from solvent (e.g. DMSO) in a statistically significant way. Accordingly, the correlation in expression between each treatment well and the DMSO wells on the plate are computed and additionally, pairwise correlations in gene expression between all the DMSO wells on the plate are performed. A t-test is then run on these two distributions. If the FDR-adjusted p-value is less than 0.05, the compound is labeled ‘active’.

[0256] Leave-one-out Classifier: As part of routine library analysis, a “leave-one-out-classifier” is a run that has been trained on plate-specific data (for each plate). This allows for distinguishing a given compound’s transcriptional effects from the rest of the compounds within that plate. All compounds are run in replicate, e.g. at least 2 replicates per compound; for every compound, discrete labels are assigned to each replicate and the consistency of the perturbational signatures is assessed by training a logistic regression classifier on one of the replicates and having it classify the compounds in the unseen replicate.

[0257] Nearest-Neighbor Analysis: The consistency of perturbational signatures is assessed by processing v-scores to compute the nearest neighbors for the non-control compounds. If the perturbational signatures are consistent, the nearest neighbors are from wells dosed with the same compound. This allows for generating a confusion plot to check if replicates of a compound are consistent. Differential Expression Analysis: Using DESeq2, it is determined which genes are differentially regulated between treatment and control wells. Here it is also established if a compound has more differentially expressed genes (DEGs) than expected by random background noise. The results of this analysis are also added to the data package.

[0258] Compound Selection: Once all the above processing / QC steps have been performed, compounds are selected that can be uniquely identified using transcriptional signatures and employ state-of-the-art contrastive learning methods, combined with novel models, to generate a robust embedding space that measures the similarity between transcriptional activities of compounds. This method has high sensitivity and recognizes compounds with variably sized effects in large-dimensional transcriptomic space. Using detection methods, compounds are recommended from this embedding space that best match a transcriptional signature of interest (i.e., cell behaviors). Best-practice algorithms including, but not limited to, K-NN, Logistic Regression, XGBoost are also used to recommend compounds once a transcriptional signature has been reduced to a subset of genes determined to be biologically relevant. Table 1 , Table 2, and the Enamine Library Catalog provide listings of selected compounds.

[0259] A non-limiting example of a protocol for the analysis of the curated and demultiplexed data is shown below:

[0260] Analysis step.

[0261] 1 . Demultiplexed data was gathered from curation step.

[0262] 2. Defined markers were used to score cells and assign to one of 6 clusters (e.g., Ery, and Mk).

[0263] 3. Basic visualization and QC was performed. All cells from the same well were grouped into a “pseudobulk” visualization and plot PCA and UMAP plots to see if particular compounds\libraries are visible outliers.

[0264] 3.1 This step is the same as step 2, but time plots were split by cell type (e.g, only Ery cells were grouped).

[0265] 4. Pseudobulk and cell-type pseudobulk data were pushed to a data package associated with the plate.

[0266] 5. V-scores were computed (data representation of the difference between treatment and DMSO expression values). Both pseudobulk and cell-type pseudobulk and plot PCA and UMAP plots were analyzed to check for visible outliers.

[0267] 6. Correlation Activity Analysis was performed. Compounds that induced a gene expression profile that is different from DMSO in a statistically significant way was analyzed. The correlation in bulk gene expression between each treatment well and the DMSO wells on the plate, and the pairwise correlations in bulk gene expression between all the DMSO wells on the plate was computed. A t-test is then run on these two distributions. If the FDR-adjusted p-value is less than 0.05, the compound was labeled ‘active’.

[0268] 7. Each compound’s correlation with DMSO was plotted which allows for visualization of compounds that are inducing effects that globally different from DMSO.

[0269] 8. Leave-one-out Classifier. A mini-predictive model was trained within the plate. This step is to determine if a compound induced a transcriptional effect that allows the classifier to distinguish it from the rest of the compounds within that plate. Every compound was assigned a distinct replicate labels (1 , 2, and 3) to the three wells dosed with that compound. The consistency of the perturbational signatures was assessed by training a logistic regression classifier on two of the replicates and having it classify the compounds in the unseen replicate.

[0270] 9. Nearest-Neighbor Analysis. The consistency of perturbational signature was assessed by computing the nearest neighbor for all vectors in the set of v-score vectors for the non-control compounds. If the perturbational signatures were consistent, the nearest neighbors of the perturbational signatures are from wells dosed with the same compound. This data is plotted in a confusion plot to check if replicates of a compound are consistent.

[0271] 10. Running DE analysis. Deseq2 is used to run the analysis. Genes that are differentially regulated between treatment and control wells (again, pseudobulk and pseudobulk on a level of a separate cell type) were determined. The analysis also determines if the compound has “more DEGs than expected by a pure noise level”. The results of this analysis were also added to the data package.

[0272] 11. The results of the analysis was compiled. Each treatment was annotated by its correlation with DMSO (from (7)), metric from (9, 10), and number of DEGs. This summary table was also added to the data package. These metrics allow for selection of only reproducible compounds.

[0273] After all the above QC / analysis steps, select compounds that can be uniquely identified using transcriptional signatures are determined. Given this training data, the similarity between transcriptional activities of compounds are measured. This method has high sensitivity and recognizes compounds with low activities in large-dimensional transcriptomic space. Finally, various detection methods are built from this embedding to recommend compounds that best match a transcriptional signature of interest.

[0274] The following tables are included herein.

[0275] • Table 1 : listing of compounds (IUPAC names) not included in LINCS database. Table 2: listing of compounds (IUPAC names) included in LINCS database.

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[0413] INCORPORATION BY REFERENCE

[0414] All patents and publications referenced herein are hereby incorporated by reference in their entireties.

[0415] The publications discussed herein are provided solely fortheir disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present disclosure is not entitled to antedate such publication by virtue of prior disclosure.

[0416] As used herein, all headings are simply for organization and are not intended to limit the disclosure in any manner. The content of any individual section may be equally applicable to all sections.

[0417] EQUIVALENTS

[0418] While the disclosure has been disclosed in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the disclosure following, in general, the principles of the disclosure and including such departures from the present disclosure as come within known or customary practice within the art to which the disclosure pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims. Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific embodiments disclosed specifically herein. Such equivalents are intended to be encompassed in the scope of the following claims.

Claims

CLAIMSWhat is claimed is:1 . An assembled library of transcriptional data, comprising:(a) a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;(b) a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; and(c) a compound-specific differential transcriptional signature data set of the cell type generated from differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; wherein the transcriptional signature data sets of (a), (b) and (c) are assembled into the library.

2. The library of claim 1 , wherein the transcriptional signature data sets are whole transcriptome transcriptional signature data sets.

3. The library of claim 1 or 2, wherein the library comprises compound-treated transcriptional signature data and / or compound-specific differential transcriptional signature data form at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds.

4. The library of any one of claims 1 to 3, wherein the at least about 10 compounds are selected from Table 1.

5. The library of any one of claims 1 to 3, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 1.

6. The library of any one of claims 1 to 3, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 .

7. The library of any one of claims 1 to 3, wherein the compounds are selected from Table 2.

8. The library of any one of claims 1 to 3, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 2.

9. The library of any one of claims 1 to 3, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 2.

10. The library of any one of claims 1 to 3, wherein the compounds are selected from the Enamine Library Catalog.

11. The library of any one of claims 1 to 3, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from the Enamine Library Catalog.

12. The library of any one of claims 1 to 3, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from the Enamine Library Catalog.

13. The library of any one of claims 1 to 12, wherein the at least about 10 compounds are associated with at least about 5, at least about 10, at least about 50, at least about 100, at least about 200, at least about 500, or at least about 1 ,000 or more known mechanisms of action (MoAs) for the treatment of one or more diseases or disorders.

14. The library of any one of claims 1 to 13, wherein the one or more cells are treated with the at least about 10 compounds at the same or substantially the same concentration.

15. The library of any one of claims 1 to 14, wherein the one or more cells are treated with the at least about 10 compounds for the same or substantially the same duration of time.

16. The library of any one of claims 1 to 15, wherein the compound-specific differential transcriptional signature is associated with or indicative of a desired transcriptional transition in a cell state.

17. The library of claim 16, wherein the desired transcriptional transition in a cell state is associated with or indicative of a cellular transition from a diseased or disordered state to an undiseased or pre-diseased state.

18. The library of claim 17, wherein the diseased or disordered state is selected from an acute stage, a chronic stage, a clinical stage, a flare-up, a remission, a progressive stage, a refractory, a subclinical stage, and a terminal phase.

19. The library of any one of claims 1 to 18, wherein the control sample and each of the test samples comprise a solvent, wherein the solvent is the same solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO).

20. The library of any one of claims 1 to 19, wherein the control sample and each of the test samples comprise a polar aprotic solvent, wherein the polar aprotic solvent is the same polar aprotic solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO).

21. The library of any one of claims 1 to 20, wherein the control sample and each of the test samples comprise dimethylsulfoxide (DMSO).

22. The library of any one of claims 18 to 21 , wherein the cellular transition is identified and / or generated by subtracting transcriptional data from one or more cells having an undiseased or pre-diseased state from transcriptional data from one or more cells having a diseased or disordered state.

23. The library of any one of claims 1 to 22, wherein the transcriptional data comprises single nuclei assay and / or single-cell assay data, optionally wherein the single nuclei assay and / or single-cell assay data is selected from single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data, single-nuclei RNA sequencing (snRNA-seq) data, scTag-seq data, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, CyTOF / SCoP data, E-MS / Abseq data, miRNA-seq data, CITE-seq data, or any combinations thereof.

24. The library of claim 23, wherein the transcriptional data comprises or consists of single-cell RNA sequencing (scRNA-seq) data.

25. The library of claim 23, wherein the transcriptional data comprises or consists of single-nuclei RNA sequencing (snRNA-seq) data.

26. The library of any one of claims 1 to 25, wherein the one or more cells comprise or consist of hematopoietic stem cells and / or progenitor cells.

27. The library of any one of claims 1 to 26, wherein the one or more cells comprise or consist of untreated hematopoietic stem cells and / or untreated progenitor cells.

28. The library of any one of claims 1 to 27, wherein the one or more cells comprise or consist of myoblasts, human umbilical cord endothelial cells (HUVEC), human bronchial epithelial cells (HBEC), human renal proximal tubular epithelial cells, LX-2 cells, lung fibroblasts, IPSC-astrocytes, Schwann cells, CD14 monocytes, CD34+cells, CD8+T-cells, B cells, natural killer (NK) cells, human pulmonary mesenchymal stem cell, dendritic cells, MO macrophages, M1 macrophages, M2a macrophages, IPSC -neural stem cells, IPSC -dopaneurons, human intestinal smooth muscle cells (HISMC), human stem cells (IPSC), femoral human osteoblasts, human chondrocytes, IPSC-cardiomyocytes, brain microvascular endothelial cells (BMECs), IPSC-endothelial cells, human hepatic sinusoidal endothelial cells, human pancreatic microvascular endothelial cells, human small intestine epithelial cells (HSIEpC), human renal cortical epithelial cells, keratinocyte, cardiac fibroblasts, human stellate cells, human pancreatic stellate cells, adult human dermal fibroblasts, human astrocytes, human bone marrow MSCs, human brain vascular pericytes, human microglia, IPSC-microglia, human renal mesangial cells, human bronchial smooth muscle cells, and satellite cells, optionally wherein the cells are untreated.

29. The library of any one of claims 1 to 28, wherein the one or more cells comprise or consist of CD34+cells, CD8+T-cells, IPSC-neural stem cells, M2a macrophages, and human bronchial smooth muscle cells, optionally wherein the cells are untreated.

30. The library of any one of claims 1 to 29, wherein the one or more cells comprise or consist of CD34+cells.

31. The library of any one of claims 1 to 30, wherein the one or more cells comprise or consist of untreated CD34+cells.

32. The library of any one of claims 1 to 31, wherein the sample comprises or consists of one or more cells from an organ, cells from a tissue, stem cells, human cells, cells from umbilical cord blood, cells from peripheral blood, bone marrow cells, cells from a solid tissue, and / or differentiated cells.

33. The library of claim 32, wherein the organ is selected from lung, heart, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colon, breast, prostate, brain, esophagus, liver, tissue (e.g. adipose tissue), thymus muscle, and placenta.

34. The library of any one of claims 1 to 33, wherein the sample is a frozen sample.

35. The library of any one of claims 1 to 34, wherein the at least about 10 compounds each independently have a molecular weight of less than 2000 Daltons.

36. The library of any one of claims 1 to 35, wherein the at least about 10 compounds each independently satisfy each of the Lipinski rule of five criteria.

37. The library of any one of claims 1 to 35, wherein the at least about 10 compounds each independently satisfy at least three criteria of the Lipinski rule of five criteria.

38. The library of any one of claims 1 to 37, wherein the at least about 10 compounds each independently exhibit a mechanism of action useful in a therapy.

39. The library of any one of claims 1 to 38, wherein each of the at least about 10 compounds comprises at least one functional group, which is optionally the same or different from the at least one functional group of the remaining at least about 10 compounds.

40. The library of claim 39, wherein the at least one functional group comprises one or more atoms selected from hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorous, or halogen.41 . The library of claim 39 or 40, wherein the at least one functional group comprises or consists of one or more of (a)-(g):(a) a hydrogen atom;(b) a carbon atom or a group comprising a carbon atom, optionally selected from an alkane, an alkene, an alpha, beta-unsaturated ketone, an alpha, beta-unsaturated aldehyde, an alpha, beta-unsaturated carboxylic acid ester, an alpha, beta-unsaturated carboxylic acid amide, an alpha, beta-unsaturated sulfoxide, an alpha, beta-unsaturated sulfone, an alpha, beta-unsaturated sulfonamide, an alpha, beta-unsaturated sulfonylchloride, a nitro alkene including but not limited to a vinylogous nitro group (e.g. alpha, beta-unsaturated nitroalkene), an alkyne, an arene, a hetarene, a nitrile, an amide, a lactam, an imine, a nitroalkyl group, a nitroaryl group, an amidine group, a carbamate, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, a carbosulfone, a carbosultam, a carbosultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, an alkylchloride, an alkylbromide, an alkyliodide, an alkenylchloride, an alkenylbromide, an alkenyliodide, an alkynylchloride, an alkynylbromide, an alkynyliodide, an arylfluoride, an arylchloride, an arylbromide, a aryliodide, a hetarylfluoride, a hetarylchloride, a hetarylbromide, a hetaryliodide, a carbonylfluoride, a carbonylchloride, a carbonylbromide, a carbonyliodide, an isocyanate, an isothiocyanate, an isocyanide, an alkylphosphonium groupincluding but not limited to alkyltriphenylphosphonium chloride, alkyltriphenylphosphonium bromide, and alkyltriphenylphosphonium iodide, any of which may optionally be substituted by one or more substituents;(c) a nitrogen atom or a group comprising a nitrogen atom, optionally selected from an amine, an isocyanate, an isocyanide, a hydroxylamine, a hydrazine, a nitrile, an amide, a lactam, an imine, an azo group, a nitro group, a nitroso group, an amidine group, a guanidine group, a carbamate, and an azide, any of which may optionally be substituted by one or more substituents;(d) an oxygen atom or a group comprising an oxygen atom, optionally selected from of a hydroxyl group, an ether, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, and a hydroxyl amine, any of which may optionally be substituted by one or more substituents;(e) a sulfur atom or a group comprising a sulfur atom, optionally selected from a thiol, a disulfide, a sulfide, a sulfoxide, a sulfin amide, a sulfonamide, a sulfone, a sultam, a sultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, and a isothiocyanate, any of which may optionally be substituted by one or more substituents;(f) a phosphorous atom or a group comprising a phosphorous atom, optionally selected from a phosphine, a phosphine oxide, a phosphinite, a phosphonite, a phosphite, a phosphinate, a phosphonate, a phosphate, and a phosphonium salt, any of which may optionally be substituted by one or more substituents; and(g) a halogen atom or a group comprising a halogen atom, optionally selected from fluorine, chlorine, bromine, iodine, for example alkylchloride, alkylbromide, alkyliodide, alkenylchloride, alkenylbromide, alkenyliodide, alkynylchloride, alkynylbromide, alkynyliodide, arylfluoride, arylchloride, arylbromide, aryliodide, hetarylfluoride, hetarylchloride, hetaryl bromide, hetaryliodide, carbonylfluoride, carbonylchloride, carbonylbromide, carbonyliodide, sulfonylfluoride, sulfonylchloride, sulfonylbromide, and sulfonyliodide, any of which may optionally be substituted by one or more substituents.

42. The library of any one of claims 39 to 41 , wherein the at least one functional group is selected from OH, halo, cyano, fluoroalkyl, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, -ORa, -SRa, -OC(O)Ra, - N(Ra)Rb, -C(0)Ra, -C(0)0Ra, -OC(O)N(Ra)Rb, -C(0)N(Ra)Rb, -N(Ra)C(O)ORa,N(Ra)C(O)Ra, -N(Ra)C(O)N(Ra)Rb, -N(Ra)C(NRa)N(Ra)Rb, -N(Ra)S(O)tRa, -C(O)N(Ra)S(O)tRa, - S(O)tORa, -S(O)tN(Ra)Rb, -S(O)tN(Ra)C(O)Rb, or -P(O)(ORa)(ORb), optionally substituted alkyl, optionally substituted alkylaryl, optionally substituted alkylheteroaryl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted aralkyl, optionally substituted haloalkyl, optionally substituted alkoxy, optionally substituted heterocyclyl, and optionally substituted heteroaryl; Raand Rbare each independently selected from the group consisting of hydrogen, alkyl, fluoroalkyl, cycloalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl, heterocycloalkylalkyl, heteroaryl, heteroarylalkyl, halogen, -O-alkyl, -O-aryl, cyano, nitro, -OH, -NH2, -NH- alkyl, and -NH-aryl; and t is 1 or 2.

43. The library of any one of claims 39 to 42, wherein the wherein the one or more functional groups provide one or more of (a)-(f) compared to different functional groups and / or the absence of the one or more functional groups:(a) increased activity strength and / or selectivity;(b) increased solubility and / or partition property;(c) increased metabolic and / or chemical stability;(d) modulation of pharmacokinetic parameters (including, without limitation, absorption, distribution, metabolism, and excretion (ADME)), optionally wherein the modulation provides increased or enhanced pharmacokinetic properties compared to the compound prior to the modulation;(e) modulation of pharmacodynamic parameters (including, without limitation, dose-response relationship (e.g. EC50)); optionally wherein the modulation provides increased or enhanced pharmacodynamic properties compared to the compound prior to the modulation; and(f) reduction or ablation of toxicity and / or adverse reactions.

44. A method of assembling transcriptional data into a library, the method comprising:(a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;(b) obtaining a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, whereineach test sample of one or more cells is separately treated with one of the at least about 10 compounds;(c) generating a compound-specific differential transcriptional signature data set of the cell type obtained upon differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; and(d) assembling of the transcriptional signature data sets of (a), (b) and (c) into a library.

45. A method of preparing synthetic analogs of one or more compounds for drug development, the method comprising:(a) analyzing a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;(b) analyzing a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least 10 compounds;(c) generating a compound-specific differential transcriptional signature data set of the cell type upon comparison of the compound-treated transcriptional signature data against the baseline transcriptional signature data from the cell type;(d) assembling the transcriptional signature data sets of (a), (b) and (c) into a library;(e) selecting one or more compounds from the at least about 10 compounds based on the comparison of (b)-(c) in the library; and(f) preparing synthetic analogs of the one or more selected compounds for drug development.

46. A method of modifying a candidate compound to yield a lead compound, the method comprising:(a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;(b) obtaining a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, whereineach test sample of one or more cells is separately treated with one of the at least about 10 compounds;(c) generating a compound-specific differential transcriptional signature data set of the cell type obtained upon differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type;(d) comparing the compound-specific differential transcriptional signature data set from the at least about 10 compounds to compound-specific differential transcription signature data from the candidate compound;(e) selecting one or more compounds from the at least about 10 compounds selected based on the comparison of (d); and(f) modifying the candidate compound based on structural features of the one or more compounds selected in (e) to yield a lead compound.

47. A method for preparing a library of transcriptional signatures, the method comprising:(a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;(b) obtaining a compound-treated transcriptional signature data set from a plurality of at least about 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compound;(c) generating a compound-specific differential transcriptional signature for each of the at least about 10 compounds upon differential comparison of the compound-treated transcriptional signature data of (b) against the baseline transcriptional signature data of (a); and(d) assembling the compound-specific differential transcriptional signatures generated in (c) into a library.

48. A method of identifying one or more compounds associated with or indicative of a desired transcriptional signature, the method comprising:(a) obtaining a baseline transcriptional signature data set from a control sample of one or more cells of a cell type;(b) obtaining a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds;(c) generating a compound-specific differential transcriptional signature data set of the cell type upon comparison of the compound-treated transcriptional signature data against the baseline transcriptional signature data from the cell type;(d) assembling the transcriptional signature data sets of (a), (b) and (c) into a library; and(e) selecting one or more compounds from the at least about 10 compounds based on the comparison of the transcriptional signature of interest with the compound-specific differential transcriptional signature data of (c); wherein the one or more compounds are associated with or indicative of the desired transcriptional signature.

49. The method of any one of claims 44 to 48, wherein the transcriptional signature data sets are whole transcriptome transcriptional signature data sets.

50. The method of any one of claims 44 to 49, wherein the library comprises compound-treated transcriptional signature data and / or compound-specific differential transcriptional signature data form at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds.51 . The method of any one of claims 44 to 50, wherein the at least about 10 compounds are selected from Table 1.

52. The method of any one of claims 44 to 50, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 1.

53. The method of any one of claims 44 to 50, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 .

54. The method of any one of claims 44 to 50, wherein the compounds are selected from Table 2.

55. The method of any one of claims 44 to 50, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 2.

56. The method of any one of claims 44 to 50, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 2.

57. The method of any one of claims 44 to 50, wherein the compounds are selected from the Enamine Library Catalog.

58. The method of any one of claims 44 to 50, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from the Enamine Library Catalog.

59. The method of any one of claims 44 to 50, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from the Enamine Library Catalog.

60. The method of any one of claims 44 to 59, wherein the at least about 10 compounds and / or the one or more compounds are associated with at least about 5, at least about 10, at least about 50, at least about 100, at least about 200, at least about 500, or at least about 1 ,000 or more known mechanisms of action (MoAs) for the treatment of one or more diseases.

61. The method of any one of claims 44 to 60, wherein the one or more cells are treated with the compounds at the same or substantially the same concentration.

62. The method of any one of claims 44 to 61, wherein the one or more cells are treated with the compounds for the same or substantially the same duration of time.

63. The method of any one of claims 44 to 62, wherein the compound-specific differential transcriptional signature is associated with or indicative of a desired transcriptional transition in a cell state.

64. The method of claim 63, wherein the desired transcriptional transition in a cell state is associated with or indicative of a cellular transition from a diseased or disordered state to an undiseased or pre-diseased state.

65. The method of claim 64, wherein the diseased or disordered state is selected from an acute stage, a chronic stage, a clinical stage, a flare-up, a remission, a progressive stage, a refractory, a subclinical stage, and a terminal phase.

66. The method of any one of claims 44 to 65, wherein the control sample and each of the test samples comprise a solvent, wherein the solvent is the same solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO).

67. The method of any one of claims 44 to 66, wherein the control sample and each of the test samples comprise a polar aprotic solvent, wherein the polar aprotic solvent is the same polar aprotic solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO).

68. The method of any one of claims 44 to 67, wherein the control sample and each of the test samples comprise dimethylsulfoxide (DMSO).

69. The method of any one of claims 65 to 68, wherein the cellular transition is identified and / or generated by subtracting transcriptional data from one or more cells having an undiseased or pre-diseased state from transcriptional data from one or more cells having a diseased or disordered state.

70. The method of any one of claims 44 to 69, wherein the transcriptional data comprises single nuclei assay and / or single-cell assay data, optionally wherein the single nuclei assay and / or single-cell assay data is selected from single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data, single-nuclei RNA sequencing (snRNA-seq) data, scTag-seq data, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, CyTOF / SCoP data, E-MS / Abseq data, miRNA-seq data, CITE-seq data, or any combinations thereof.

71. The method of claim 68, wherein the transcriptional data comprises or consists of single-cell RNA sequencing (scRNA-seq) data.

72. The method of claim 69, wherein the transcriptional data comprises or consists of single-nuclei RNA sequencing (snRNA-seq) data.

73. The method of any one of claims 44 to 72, wherein the one or more cells comprise or consist of myoblasts, human umbilical cord endothelial cells (HUVEC), human bronchial epithelial cells (HBEC), human renal proximal tubular epithelial cells, LX-2 cells, lung fibroblasts, IPSC-astrocytes, Schwann cells, CD14 monocytes, CD34+cells, CD8+T-cells, B cells, natural killer (NK) cells, human pulmonary mesenchymal stem cell, dendritic cells, MO macrophages, M1 macrophages, M2a macrophages, IPSC -neural stem cells, IPSC-dopaneurons, human intestinal smooth muscle cells (HISMC), human stem cells (IPSC), femoral human osteoblasts, human chondrocytes, IPSC-cardiomyocytes, brain microvascular endothelial cells (BMECs), IPSC-endothelial cells, human hepatic sinusoidal endothelial cells, human pancreatic microvascular endothelial cells, human small intestine epithelial cells (HSIEpC), human renal cortical epithelial cells, keratinocyte, cardiac fibroblasts, human stellate cells, human pancreatic stellate cells, adult human dermal fibroblasts, human astrocytes, human bone marrow MSCs, human brain vascular pericytes, human microglia, IPSC-microglia, human renal mesangial cells, human bronchial smooth muscle cells, and satellite cells, optionally wherein the cells are untreated.

74. The method of any one of claims 44 to 73, wherein the one or more cells comprise or consist of CD34+cells, CD8+T-cells, IPSC-neural stem cells, M2a macrophages, and human bronchial smooth muscle cells, optionally wherein the cells are untreated.

75. The method of any one of claims 44 to 74, wherein the one or more cells comprise or consist of hematopoietic stem cells and / or progenitor cells.

76. The method of any one of claims 44 to 75, wherein the one or more cells comprise or consist of untreated hematopoietic stem cells and / or untreated progenitor cells.

77. The method of any one of claims 44 to 76, wherein the one or more cells comprise or consist of CD34+cells.

78. The method of any one of claims 44 to 77, wherein the one or more cells comprise or consist of untreated CD34+cells.

79. The method of any one of claims 44 to 78, wherein the sample comprises or consists of one or more cells from an organ, cells from a tissue, stem cells, human cells, cells from umbilical cord blood, cells from peripheral blood, bone marrow cells, cells from a solid tissue, and / or differentiated cells.

80. The method of claim 79, wherein the organ is selected from lung, heart, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colon, breast, prostate, brain, esophagus, liver, tissue (e.g. adipose tissue), thymus muscle, and placenta.81 . The method of any one of claims 44 to 80, wherein the sample is a frozen sample.

82. The method of any one of claims 44 to 81 , wherein the one or more compounds and / or the at least about 10 compounds each independently have a molecular weight of less than 2000 Daltons.

83. The method of any one of claims 45, 46, or 48 to 82, wherein the one or more compounds each independently satisfy each of the Lipinski rule of five criteria.

84. The method of any one of claims 45, 46, or 48 to 83, wherein the one or more compounds each independently satisfy at least three criteria of the Lipinski rule of five criteria.

85. The method of any one of claims 44 to 84, wherein the at least about 10 compounds each independently exhibit a mechanism of action useful in a therapy.

86. The method of any one of claims 44 to 85, wherein the at least about 10 compounds each independently satisfy at least three criteria of the Lipinski rule of five criteria.

87. The method of any one of claims 45 or 49 to 86, wherein the one or more compounds for drug development each independently exhibit a mechanism of action useful in a therapy.

88. The method of any one of claims 45, 46, or 48 to 87, wherein each of the one or more compounds comprises at least one functional group, which may be the same or different from the at least one functional group of the remaining one or more compounds.

89. The method of any one of claims 44 to 88, wherein each of the at least about 10 compounds comprises at least one functional group, which may be the same or different from the at least one functional group of the remaining at least about 10 compounds.

90. The method of any one of claims 42 or 49 to 89, wherein preparing synthetic analogs of one or more compounds comprises modifying at least one functional group of at least one of the one or more compounds.91 . The method of claim 90, wherein modifying the at least one functional group comprises one or more of replacing the at least one functional group with one or more functional groups, removing the at least one functional group, and / or adding and / or conjugating one or more functional groups to the at least one functional group, wherein each of the one or more functional groups is independently the same or different from the at least one functional group.

92. The method of any one of claims 88 to 91 , wherein the at least one functional group comprises one or more atoms selected from hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorous, or halogen.

93. The method of any one of claims 88 to 92, wherein the at least one functional group comprises or consists of one or more of (a)-(g):(a) a hydrogen atom;(b) a carbon atom or a group comprising a carbon atom, optionally selected from an alkane, an alkene, an alpha, beta-unsaturated ketone, an alpha, beta-unsaturated aldehyde, an alpha, beta-unsaturated carboxylic acid ester, an alpha, beta-unsaturated carboxylic acid amide, an alpha, beta-unsaturated sulfoxide, an alpha, beta-unsaturated sulfone, an alpha, beta-unsaturated sulfonamide, an alpha, beta-unsaturated sulfonylchloride, a nitro alkene including but not limited to a vinylogous nitro group (e.g. alpha, beta-unsaturated nitroalkene), an alkyne, an arene, a hetarene, a nitrile, an amide, a lactam, an imine, a nitroalkyl group, a nitroaryl group, an amidine group, a carbamate, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, a carbosulfone, a carbosultam, a carbosultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, an alkylchloride, an alkylbromide, an alkyliodide, an alkenylchloride, an alkenylbromide, an alkenyliodide, an alkynylchloride, an alkynylbromide, an alkynyliodide, an arylfluoride, an arylchloride, an arylbromide, a aryliodide, a hetarylfluoride, a hetarylchloride, a hetarylbromide, a hetaryliodide, a carbonylfluoride, a carbonylchloride, a carbonylbromide, a carbonyliodide, an isocyanate, an isothiocyanate, an isocyanide, an alkylphosphonium group including but not limited to alkyltriphenylphosphonium chloride, alkyltriphenylphosphonium bromide, and alkyltriphenylphosphonium iodide, any of which may optionally be substituted by one or more substituents;(c) a nitrogen atom or a group comprising a nitrogen atom, optionally selected from an amine, an isocyanate, an isocyanide, a hydroxylamine, a hydrazine, a nitrile, an amide, a lactam, an imine, an azo group, a nitro group, a nitroso group, an amidine group, a guanidine group, a carbamate, and an azide, any of which may optionally be substituted by one or more substituents;(d) an oxygen atom or a group comprising an oxygen atom, optionally selected from of a hydroxyl group, an ether, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, and a hydroxyl amine, any of which may optionally be substituted by one or more substituents;(e) a sulfur atom or a group comprising a sulfur atom, optionally selected from a thiol, a disulfide, a sulfide, a sulfoxide, a sulfin amide, a sulfonamide, a sulfone, a sultam, a sultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, and a isothiocyanate, any of which may optionally be substituted by one or more substituents;(f) a phosphorous atom or a group comprising a phosphorous atom, optionally selected from a phosphine, a phosphine oxide, a phosphinite, a phosphonite, a phosphite, a phosphinate, a phosphonate, a phosphate, and a phosphonium salt, any of which may optionally be substituted by one or more substituents; and(g) a halogen atom or a group comprising a halogen atom, optionally selected from fluorine, chlorine, bromine, iodine, for example alkylchloride, alkylbromide, alkyliodide, alkenylchloride, alkenylbromide, alkenyliodide, alkynylchloride, alkynylbromide, alkynyliodide, arylfluoride, arylchloride, arylbromide, aryliodide, hetarylfluoride, hetarylchloride, hetaryl bromide, hetaryliodide, carbonylfluoride, carbonylchloride, carbonylbromide, carbonyliodide, sulfonylfluoride, sulfonylchloride, sulfonylbromide, and sulfonyliodide, any of which may optionally be substituted by one or more substituents.

94. The method of any one of claims 88 to 93, wherein the at least one functional group is selected from OH, halo, cyano, fluoroalkyl, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, -ORa, -SRa, -OC(O)Ra, - N(Ra)Rb, -C(O)Ra, -C(O)ORa, -OC(O)N(Ra)Rb, -C(O)N(Ra)Rb, -N(Ra)C(O)ORa, N(Ra)C(O)Ra, -N(Ra)C(O)N(Ra)Rb, -N(Ra)C(NRa)N(Ra)Rb, -N(Ra)S(O)tRa, -C(O)N(Ra)S(O)tRa, - S(O)tORa, -S(O)tN(Ra)Rb, -S(O)tN(Ra)C(O)Rb, or -P(O)(ORa)(ORb), optionally substituted alkyl, optionally substituted alkylaryl, optionally substituted alkylheteroaryl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted aralkyl, optionally substituted haloalkyl, optionally substituted alkoxy, optionally substituted heterocyclyl, and optionally substituted heteroaryl; Raand Rbare each independently selected from the group consisting of hydrogen, alkyl, fluoroalkyl, cycloalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl, heterocycloalkylalkyl, heteroaryl, heteroarylalkyl, halogen, -O-alkyl, -O-aryl, cyano, nitro, -OH, -NH2, -NH- alkyl, and -NH-aryl; and t is 1 or 2.

95. The method of any one of claims 90 to 94, wherein modifying the at least one functional group comprises one or more modifications selected from alkylation (e.g. alkylation of ketones, nitriles, and carboxylic esters, N-alkylation of amides or imides), arylation (e.g. N-arylation), substitution (e.g. replacement of a hydroxy by an amino group), amidation, amination, arylation, acylation (e.g acylation of amines by acyl halides, anhydrides, carboxylic acids, carboxylic esters, amides, acylation of amines or other acid derivatives, or N-acylation of amides or imides), cyanation, halide exchange, halogenation, dehalogenation, oxidation (e.g. oxidation of aldehydes to carboxylic acids, aromatization, oxidative cleavage, oxidativedecarboxylation), reduction (e.g. reduction of carboxylic acids, esters, anhydrides, amides, alkyl halides, acyl halides, tosylates, other sulfonates, a C— N bond, an alkene, and alkyne, or similar functional groups), reductive amination, reductive alkylation, epoxidation, hydrolysis (e.g. hydrolysis of carbon-nitrogen double bond or nitriles), alcoholysis (e.g. alcoholysis of nitriles), hydrogenolysis (e.g. hydrogenolysis of alcohols, esters, or nitriles), hydrogenation, dehydrogenation, formylation, hydroxylation (e.g. dihydroxylation), acyloxylation, oxygenation, deoxygenation, diazotization, chlorosulfonation, nitration, nitrosation, sulfurization, desulfurization, sulfonation, desulfonation, sulfenylation, halosulfonation, sulfonylation, carboxylation, decarboxylation (e.g. ketonic decarboxylation), selenylation, phosphorylation, salt formation (e.g. conversion of a carboxylic acid to a carboxylate salt), and addition of a suitable protecting group (e.g. 9-fluorenylmethyl carbamate (Fmoc), t-butyl carbamate (Boc), and carboxybenzyl carbamate (cbz), methyl carbamate, ethyl carbamate, benzyloxymethyl (BOM), methylthiomethyl (MTM), phenylthiomethyl (PTM), cyanoethyl, 2,2-dichloro-1 ,1 difluoroethyl, 2-chloroethyl, 2-bromoethyl, tetrahydropyranyl (THP), phenacyl, 4 bromophenacyl, allyl, propargyl, trimethylsilyl (TMS), triethylsilyl (TES), or t-butyldiphenyl silyl (TBDPS)).

96. The method of any one of claims 90 to 95, wherein the modification results in the one or more compounds having one or more of (a)-(f) compared to the one or more compounds prior to modification:(a) increased activity strength and / or selectivity;(b) increased solubility and / or partition property;(c) increased metabolic and / or chemical stability;(d) modulation of pharmacokinetic parameters (including, without limitation, absorption, distribution, metabolism, and excretion (ADME)), optionally wherein the modulation provides increased or enhanced pharmacokinetic properties compared to the compound prior to the modulation;(e) modulation of pharmacodynamic parameters (including, without limitation, dose-response relationship (e.g. ECso)); optionally wherein the modulation provides increased or enhanced pharmacodynamic properties compared to the compound prior to the modulation; and(f) reduction or ablation of toxicity and / or adverse reactions.

97. A method of identifying one or more functional groups associated with or indicative of a desired transcriptional signature, the method comprising:(a) selecting from a library of transcriptional data one or more compounds having a compound-specific differential transcriptional signature at least substantially similar to the desired transcriptional signature, wherein: the library comprises: i. a baseline transcriptional signature data set from a control sample of one or more cells of a cell type; ii. a compound-treated transcriptional signature data set from a plurality of at least 10 test samples of one or more cells of the cell type treated with at least about 10 compounds, wherein each test sample of one or more cells is separately treated with one of the at least about 10 compounds; and ill. a compound-specific differential transcriptional signature data set of the cell type generated from differential comparison of the compound-treated transcriptional signature data for each test sample of one or more cells treated with each of the at least about 10 compounds of (b) against the baseline transcriptional signature data of the control sample of (a) from the cell type; wherein each of the at least about 10 compounds comprises at least one functional group, which may be the same or different from the at least one functional group of the remaining at least about 10 compounds;(b) comparing the at least one or more functional groups of the one or more compounds selected in (a); and(c) selecting one or more functional groups based on the comparison of (b), wherein the one or more functional groups are associated with or indicative of the desired transcriptional signature.

98. The method of claim 97, wherein the transcriptional signature data sets are whole transcriptome transcriptional signature data sets.

99. The method of claim 97 and 98, wherein the library comprises compound-treated transcriptional signature data and / or compound-specific differential transcriptional signature data form at least about 25, at least about 50, at least about 100, at least about 500, at least about 1 ,000, at least about 1 ,500, at least about 2,000, at least about 3,000, at least about 4,000, at least about 5,000, at least about 6,000, at least about 7,000, at least about 8,000, at least about 9,000, at least about 10,000, or more than at least about 10,000 compounds.

100. The method of any one of claims 97 to 99, wherein the at least about 10 compounds are selected from Table 1.101 . The method of any one of claims 97 to 99, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 1.

102. The method of any one of claims 97 to 99, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 1 .

103. The method of any one of claims 97 to 99, wherein the compounds are selected from Table 2.

104. The method of any one of claims 97 to 99, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from Table 2.

105. The method of any one of claims 97 to 99, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from Table 2.

106. The method of any one of claims 97 to 99, wherein the compounds are selected from the Enamine Library Catalog.

107. The method of any one of claims 97 to 99, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from the Enamine Library Catalog.

108. The method of any one of claims 97 to 99, wherein at least about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, of the compounds is selected from compounds comprising any of the optionally substituted ring systems of any of the compounds from the Enamine Library Catalog.

109. The method of any one of claims 97 to 108, wherein the at least about 10 compounds are associated with a plurality of known mechanisms of action (MoA) for the treatment of one or more diseases.

110. The method of any one of claims 97 to 109, wherein the one or more functional groups are associated with a plurality of known mechanisms of action (MoA) for the treatment of one or more diseases.

111. The method of any one of claims 97 to 110, wherein the one or more cells are treated with the compounds at the same or substantially the same concentration.

112. The method of any one of claims 97 to 111, wherein the one or more cells are treated with the compounds for the same or substantially the same duration of time.

113. The method of any one of claim 97 to 112, wherein the desired transcriptional transition in a cell state is associated with or indicative of a cellular transition from a diseased or disordered state to an undiseased or pre-diseased state.

114. The method of claim 113, wherein the diseased or disordered state is selected from an acute stage, a chronic stage, a clinical stage, a flare-up, a remission, a progressive stage, a refractory, a subclinical stage, and a terminal phase.

115. The method of any one of claims 97 to 114, wherein the control sample and each of the test samples comprise a solvent, wherein the solvent is the same solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO).

116. The method of any one of claims 97 to 115, wherein the control sample and each of the test samples comprise a polar aprotic solvent, wherein the polar aprotic solvent is the same polar aprotic solvent for the control sample and each of the test samples, optionally wherein the solvent is dimethylsulfoxide (DMSO).

117. The method of any one of claims 97 to 116, wherein the control sample and each of the test samples comprise dimethylsulfoxide (DMSO).

118. The method of any one of claims 113 to 117, wherein the cellular transition is identified and / or generated by subtracting transcriptional data from one or more cells having an undiseased or pre-diseased state from transcriptional data from one or more cells having a diseased or disordered state.

119. The method of any one of claims 97 to 118, wherein the transcriptional data comprises single nuclei assay and / or single-cell assay data, optionally wherein the single nuclei assay and / or single-cell assay data is selected from single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) data, single-nuclei RNA sequencing (snRNA-seq) data, scTag-seq data, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, CyTOF / SCoP data, E-MS / Abseq data, miRNA-seq data, CITE-seq data, or any combinations thereof.

120. The method of claim 119, wherein the transcriptional data comprises or consists of single-cell RNA sequencing (scRNA-seq) data.121 . The method of claim 119, wherein the transcriptional data comprises or consists of single-nuclei RNA sequencing (snRNA-seq) data.

122. The method of any one of claims 97 to 121 , wherein the one or more cells comprise or consist of myoblasts, human umbilical cord endothelial cells (HUVEC), human bronchial epithelial cells (HBEC), humanrenal proximal tubular epithelial cells, LX-2 cells, lung fibroblasts, IPSC-astrocytes, Schwann cells, CD14 monocytes, CD34+cells, CD8+T-cells, B cells, natural killer (NK) cells, human pulmonary mesenchymal stem cell, dendritic cells, MO macrophages, M1 macrophages, M2a macrophages, IPSC -neural stem cells, IPSC -dopaneurons, human intestinal smooth muscle cells (HISMC), human stem cells (IPSC), femoral human osteoblasts, human chondrocytes, IPSC-cardiomyocytes, brain microvascular endothelial cells (BMECs), IPSC-endothelial cells, human hepatic sinusoidal endothelial cells, human pancreatic microvascular endothelial cells, human small intestine epithelial cells (HSIEpC), human renal cortical epithelial cells, keratinocyte, cardiac fibroblasts, human stellate cells, human pancreatic stellate cells, adult human dermal fibroblasts, human astrocytes, human bone marrow MSCs, human brain vascular pericytes, human microglia, IPSC-microglia, human renal mesangial cells, human bronchial smooth muscle cells, and satellite cells, optionally wherein the cells are untreated.

123. The method of any one of claims 97 to 122, wherein the one or more cells comprise or consist of CD34+cells, CD8+T-cells, IPSC-neural stem cells, M2a macrophages, and human bronchial smooth muscle cells, optionally wherein the cells are untreated.

124. The method of any one of claims 117 to 123, wherein the one or more cells comprise or consist of hematopoietic stem cells and / or progenitor cells.

125. The method of any one of claims 97 to 124, wherein the one or more cells comprise or consist of untreated hematopoietic stem cells and / or untreated progenitor cells.

126. The method of any one of claims 97 to 125, wherein the one or more cells comprise or consist of CD34+cells.

127. The method of any one of claims 97 to 126, wherein the one or more cells comprise or consist of untreated CD34+ cells.

128. The method of any one of claims 97 to 127, wherein the sample comprises or consists of one or more cells from an organ, cells from a tissue, stem cells, human cells, cells from umbilical cord blood, cells from peripheral blood, bone marrow cells, cells from a solid tissue, and / or differentiated cells.

129. The method of claim 128, wherein the organ is selected from lung, heart, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colon, breast, prostate, brain, esophagus, liver, tissue (e.g. adipose tissue), thymus muscle, and placenta.

130. The method of any one of claims 97 to 129, wherein the sample is a frozen sample.131 . The method of any one of claims 97 to 130, wherein the one or more compounds and / or the at least about 10 compounds each independently have a molecular weight of less than 2000 Daltons.

132. The method of any one of claims 97 to 131 , wherein the one or more compounds each independently satisfy each of the Lipinski rule of five criteria.

133. The method of any one of claims 97 to 132, wherein the at least about 10 compounds each independently satisfy at least three criteria of the Lipinski rule of five criteria.

134. The method of any one of claims 97 to 133, wherein the at least about 10 compounds for drug development each independently exhibit a mechanism of action useful in a therapy.

135. The method of any one of claims 97 to 131 , wherein the at least about 10 compounds each independently satisfy at least three criteria of the Lipinski rule of five criteria.

136. The method of any one of claims 97 to 135, wherein the one or more functional groups comprise one or more atoms selected from hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorous, or halogen.

137. The method of any one of claims 97 to 136, wherein each functional group independently comprises or consists of one or more of (a)-(g):(a) a hydrogen atom;(b) a carbon atom or a group comprising a carbon atom, optionally selected from an alkane, an alkene, an alpha, beta-unsaturated ketone, an alpha, beta-unsaturated aldehyde, an alpha, beta-unsaturated carboxylic acid ester, an alpha, beta-unsaturated carboxylic acid amide, an alpha, beta-unsaturated sulfoxide, an alpha, beta-unsaturated sulfone, an alpha, beta-unsaturated sulfonamide, an alpha, beta-unsaturated sulfonylchloride, a nitro alkene including but not limited to a vinylogous nitro group (e.g. alpha, beta-unsaturated nitroalkene), an alkyne, an arene, a hetarene, a nitrile, an amide, a lactam, an imine, a nitroalkyl group, a nitroaryl group, an amidine group, a carbamate, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, a carbosulfone, a carbosultam, a carbosultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, an alkylchloride, an alkylbromide, an alkyliodide, an alkenylchloride, an alkenylbromide, an alkenyliodide, an alkynylchloride, an alkynylbromide, an alkynyliodide, an arylfluoride, an arylchloride, an arylbromide, a aryliodide, a hetarylfluoride, a hetarylchloride, a hetarylbromide, a hetaryliodide, a carbonylfluoride, a carbonylchloride, a carbonylbromide, acarbonyliodide, an isocyanate, an isothiocyanate, an isocyanide, an alkylphosphonium group including but not limited to alkyltriphenylphosphonium chloride, alkyltriphenylphosphonium bromide, and alkyltriphenylphosphonium iodide, any of which may optionally be substituted by one or more substituents;(c) a nitrogen atom or a group comprising a nitrogen atom, optionally selected from an amine, an isocyanate, an isocyanide, a hydroxylamine, a hydrazine, a nitrile, an amide, a lactam, an imine, an azo group, a nitro group, a nitroso group, an amidine group, a guanidine group, a carbamate, and an azide, any of which may optionally be substituted by one or more substituents;(d) an oxygen atom or a group comprising an oxygen atom, optionally selected from of a hydroxyl group, an ether, a ketone, an aldehyde, a hemiacetal, a hemiketal, an acetal, a ketal, a carboxylic acid, a carboxylic acid ester, an ortho ester, a carbonate, a carbamate, a lactam, a lactone, and a hydroxyl amine, any of which may optionally be substituted by one or more substituents;(e) a sulfur atom or a group comprising a sulfur atom, optionally selected from a thiol, a disulfide, a sulfide, a sulfoxide, a sulfin amide, a sulfonamide, a sulfone, a sultam, a sultone, a thioketone, a thioaldehyde, a dithioacetal, a carboxylic acid thioester, a thiocarbonate, a thiocarbamate, and a isothiocyanate, any of which may optionally be substituted by one or more substituents;(f) a phosphorous atom or a group comprising a phosphorous atom, optionally selected from a phosphine, a phosphine oxide, a phosphinite, a phosphonite, a phosphite, a phosphinate, a phosphonate, a phosphate, and a phosphonium salt, any of which may optionally be substituted by one or more substituents; and(g) a halogen atom or a group comprising a halogen atom, optionally selected from fluorine, chlorine, bromine, iodine, for example alkylchloride, alkylbromide, alkyliodide, alkenylchloride, alkenylbromide, alkenyliodide, alkynylchloride, alkynylbromide, alkynyliodide, arylfluoride, arylchloride, arylbromide, aryliodide, hetarylfluoride, hetarylchloride, hetaryl bromide, hetaryliodide, carbonylfluoride, carbonylchloride, carbonylbromide, carbonyliodide, sulfonylfluoride, sulfonylchloride, sulfonylbromide, and sulfonyliodide, any of which may optionally be substituted by one or more substituents.

138. The method of any one of claims 97 to 137, wherein each functional group is independently selected from OH, halo, cyano, fluoroalkyl, trifluoromethyl, trifluoromethoxy, nitro, trimethylsilanyl, -ORa, -SRa, -OC(O)Ra, -N(Ra)Rb, -C(O)Ra, -C(O)ORa, -OC(O)N(Ra)Rb, -C(O)N(Ra)Rb, -N(Ra)C(O)ORa, - N(Ra)C(O)Ra, -N(Ra)C(O)N(Ra)Rb, -N(Ra)C(NRa)N(Ra)Rb, -N(Ra)S(O)tRa, -C(O)N(Ra)S(O)tRa, - S(O)tORa, -S(O)tN(Ra)Rb, -S(O)tN(Ra)C(O)Rb, or -P(O)(ORa)(ORb), optionally substituted alkyl, optionally substituted alkylaryl, optionally substituted alkylheteroaryl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted cycloalkyl, optionally substituted aryl, optionally substituted aralkyl, optionally substituted haloalkyl, optionally substituted alkoxy, optionally substituted heterocyclyl, and optionally substituted heteroaryl; Raand Rbare each independently selected from the group consisting of hydrogen, alkyl, fluoroalkyl, cycloalkyl, carbocyclyl, carbocyclylalkyl, aryl, aralkyl, heterocycloalkyl, heterocycloalkylalkyl, heteroaryl, heteroarylalkyl, halogen, -O-alkyl, -O-aryl, cyano, nitro, -OH, -NH2, -NH- alkyl, and -NH-aryl; and t is 1 or 2.

139. The method of any one of claims 97 to 138, wherein the one or more functional groups provide one or more of (a)-(f) compared to different functional groups and / or the absence of the one or more functional groups:(a) increased activity strength and / or selectivity;(b) increased solubility and / or partition property;(c) increased metabolic and / or chemical stability;(d) modulation of pharmacokinetic parameters (including, without limitation, absorption, distribution, metabolism, and excretion (ADME)), optionally wherein the modulation provides increased or enhanced pharmacokinetic properties compared to the compound prior to the modulation;(e) modulation of pharmacodynamic parameters (including, without limitation, dose-response relationship (e.g. EC50)); optionally wherein the modulation provides increased or enhanced pharmacodynamic properties compared to the compound prior to the modulation; and(f) reduction or ablation of toxicity and / or adverse reactions.

140. The library of any one of claims 1 to 43, or the method of any one of claims 44 to 139, wherein assembling the transcriptional signatures into a library further comprises curating the library.141 . The library of any one of claims 1 to 43 or 140, or the method of any one of claims 44 to 140, wherein curating the library comprises one or more of (a) to (c):(a) creating a count data;(b) filtering (e.g. by number of cells, number of reads per cell, number of captured genes, percent of MT genes, and / or detection of singlets, doublets, etc.); and(c) demultiplexing.

142. The library of any one of claims 1 to 43, 140 or 141, or the method of any one of claims 44 to 141 , wherein assembling the transcriptional signatures into a library further comprises analyzing pseudobulk data and / or cell-type pseudobulk data.

143. The library of any one of claims 1 to 43, or 140 to 142, or the method of any one of claims 44 to 142, for uses reasonably related to the development and submission of information under a United States Federal law which regulates the manufacture, use, or sale of drugs or veterinary biological products.

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