In silico methods for the development of cell-targeted drugs

Abstract

A device may receive, by the computer system, a digital chemical structure for each of a plurality of ligand-drug conjugate compounds. A device may calculate by said one or more processors, an aggregation number for each of said plurality of ligand-drug conjugate compounds. A device may rank, by the computer system, at least a portion of said plurality of ligand-drug conjugate compounds based on said aggregation number. A device may identify, by the computer system, a plurality of low aggregation ligand-drug conjugate compounds based on said ranking, wherein said plurality of low aggregation ligand-drug conjugate compounds is a portion of said plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of a remaining ligand-drug conjugate compounds within said plurality of ligand-drug conjugate compounds.

Description

Mintz Ref.: 048536-783001WOPCT APPLICATIONIN SILICO METHODS FOR THE DEVELOPMENT OF CELL-TARGETED DRUGS CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U. S. Provisional Application No. 63 / 739,380 filed December 27, 2024 of which is incorporated herein by reference in its entirety and for all purposes.TECHNICAL FIELD

[0002] The present disclosure relates to in silico methods for developing cell-targeted drugs.BACKGROUND

[0003] Cell-targeted drugs are pharmaceutical agents that target proteins that control how cancer cells may grow, divide, and spread. One class of cell-targeted drugs involves ligand-drug conjugates that include a ligand that is attached to a linking group which is then attached to a drug. Intermolecular and intramolecular interactions between the ligand linking groups can lead to aggregation between the ligand drug conjugates which can in turn diminish the efficacy of these ligand-drug conjugates as cell-targeted drugs. Understanding the aggregation of liganddrug conjugates using synthesis of these drugs can be a resource intensive process.SUMMARY

[0004] Disclosed are in silico methods for the development of cell-targeted drugs. For example, the aggregation properties of ligand-drug conjugates can be determined using in silico methods in order to synthesize low aggregation ligand-drug conjugate compounds.

[0005] In some aspects, the techniques described herein relate to a method, implemented using a computer system including one or more processors and a system memory, of identifying a plurality of low aggregation ligand-drug conjugate compounds: (a) receiving, by the computer system, a digital chemical structure for each of a plurality of ligand-drug conjugate compounds; (b) calculating, by said one or more processors, an aggregation number for each of said plurality of ligand-drug conjugate compounds; (c) ranking, by the computer system, at least a portion of said plurality of ligand-drug conjugate compounds based on said aggregation number; and (d) identifying, by the computer system, a plurality of low aggregation ligand-drug conjugate compounds based on said ranking, wherein said plurality of low aggregation ligand-drugMintz Ref.: 048536-783001WOPCT APPLICATIONconjugate compounds is a portion of said plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of a remaining ligand-drug conjugate compounds within said plurality of ligand-drug conjugate compounds.

[0006] In some aspects, the techniques described herein relate to a method of synthesizing a low aggregation ligand-drug conjugate compound: (a) receiving, by a computer system, a digital chemical structure for each of a plurality of ligand-drug conjugate compounds, wherein said computer system includes one or more processors and a system memory; (b) calculating, by said one or more processors, an aggregation number for each of said plurality of ligand-drug conjugate compounds; (c) identifying, by the computer system, a plurality of low aggregation ligand-drug conjugate compounds based on said aggregation number, wherein said plurality of low aggregation ligand-drug conjugate compounds is a portion of said plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of a remaining ligand-drug conjugate compounds within said plurality of ligand-drug conjugate compounds; and (d) chemically synthesizing said plurality of low aggregation ligand-drug conjugate compound.

[0007] In some aspects, the techniques described herein relate to a method, wherein each of said plurality of ligand-drug conjugate compounds are different and have the structure: wherein: n is 0, 1, 2, 3 or 4; L is a ligand; R1 is selected from a 6 to 14 membered aryl or a 5 to 13 membered heteroaryl containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur; R1 is unsubstituted or substituted with one or more R5; R5, at each occurrence, is independently selected from halogen, -C(O)NH2, -C(O)OR6, -Cl -3 alkyl, — OR7, and a 6 to 10 membered aryl; wherein, R6 is hydrogen or Cl-3 alkyl; R7 is hydrogen or Cl -3 alkyl; R2 is absent or is selected from a 6 to 10 membered cycloalkyl or a 6 to 10 membered aryl; R3 is hydrogen or — C1-C5COOH; R4 is selected from a group consisting of — Cl-10 alkyl-, -C2-6 alkenyl-, -Cl-3 alkyl-O-Cl-3 alkyl-, -C2-6 alkyl-N(R8)-, -C2-6 alkyl(N(R8)(R8'))—, — N(R8)-C2-6 alkyl—, a 3 to 6 membered cycloalkyl and — Cl-2 alkyl-(-OC2H4)l-8-OCl-2 alkyl—; wherein, R8 and R8' are independently selected from hydrogen, Cl-6 alkyl, -C(O)-Cl-4alkyl-aryl or -C(O)-(-C2H4O)l-8-Cl-2 alkyl-N(R)(R'), wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Cl-3alkyl or -OCl-3alkyl; wherein R and R' are independently selected from hydrogen, -Cl -6 alkyl or -C(O)-Cl-4alkyl-Mintz Ref.: 048536-783001WOPCT APPLICATIONaryl, wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Cl-3alkyl or -OCl-3alkyl; A is an amino acid or a peptide including 2-5 amino acids; A is attached to Q through its C terminal; Q is a self-immolative group; and D is a cytotoxic agent or a therapeutic agent.

[0008] In some aspects, the techniques described herein relate to a method 1 to 3, wherein plurality of ligand-drug conjugate compounds is at least 50 different ligand-drug conjugate compounds.

[0009] In some aspects, the techniques described herein relate to a method 1 to 3, wherein plurality of ligand-drug conjugate compounds is at least 500 different ligand-drug conjugate compounds.

[0010] In some aspects, the techniques described herein relate to a method 1 to 3, wherein plurality of ligand-drug conjugate compounds is at least 5,000 different ligand-drug conjugate compounds.

[0011] In some aspects, the techniques described herein relate to a method 1 to 6, wherein said calculating includes calculating a conformer energy minimization.

[0012] In some aspects, the techniques described herein relate to a method 1 to 6, wherein said aggregation number includes at least one of a propensity to aggregate and / or a predicted aggregation residence time.

[0013] In some aspects, the techniques described herein relate to a method 1 to 8, wherein each of said plurality of low aggregation ligand-drug conjugate compounds includes a ligand covalently bound to a cytotoxic agent or covalently bound to a therapeutic agent, wherein said ligand is capable of binding to a ligand binder under physiological conditions, wherein said ligand binder is PSMA, folate receptor, carbonic anhydrase IX, somatostatin receptor, fibroblast receptor, DLL3, STEAP-1, or PSCA.

[0014] In some aspects, the techniques described herein relate to a method, further including contacting one of said plurality of low aggregation ligand-drug conjugate compounds with a cell including said ligand binder, wherein said low aggregation ligand-drug conjugate compound effectively binds to said ligand binder intracellularly.

[0015] In some aspects, the techniques described herein relate to a method, wherein said cell forms part of an organism and wherein said contacting includes administering said low aggregation ligand-drug conjugate compound to said organism.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0016] In some aspects, the techniques described herein relate to a method wherein said low aggregation ligand-drug conjugate compound includes a detectable moiety.

[0017] In some aspects, the techniques described herein relate to a method wherein said detectable moiety is a fluorescent detectable moiety.

[0018] In some aspects, the techniques described herein relate to a method wherein said fluorescent detectable moiety is fluorescein.

[0019] In some aspects, the techniques described herein relate to a method 12 to 14, further including detecting said detectable moiety.

[0020] In some aspects, the techniques described herein relate to a method, wherein said detecting includes quantitating cell surface binding of said low aggregation ligand-drug conjugate compound.

[0021] In some aspects, the techniques described herein relate to a method 3 to 16, wherein said plurality of ligand-drug conjugate compounds are different and have the structure: Rll is selected from -Cl-3 alkyl-OC(O)-**, -Cl-3 alkyl-O-C(O)-N(R19)-Cl-5 alkyl -N(R19)-C(O)- **, -Cl-3 alkyl-O-C(O)-N[Cl-5 alkyl-N(R20R21)]-Cl-3 alkyl-**, -Cl-3 alkyl-O-C(O)-Het2-Cl-3 alkyl-N(R19)-C(O)— **, or -Cl-3 alkyl-O-C(O)-N(R19)-Cl-5 alkyl-N(R19)-C(O)-**; wherein ** indicates point of attachment to D and R19 is selected from H, —Cl-3 alkyl or —Cl-3 alkyl-O-Cl-3 alkyl-OH; R20 is H or —Cl-3 alkyl; R21 is H or — C1-C3 alkyl; and Het2 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur; R12 is selected from hydrogen, — C(O)N(R13)R14 or — (-OC2H4)1-10-CH3 R13 is hydrogen; R14 is selected from — Cl-5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, -Cl-5 alkyl-N(R15)R16, -Cl-5 alkyl-O-Cl-3 alkyl, -(-C2H4O)l-10C2H5, -(-C2H4O)l-10-C2H4-R17 or -Cl-3 alkyl-Het3-(-C2H4O)l-10-C2H4-R18; wherein R15 is hydrogen or Cl-3 alkyl; R16 is hydrogen or Cl-3 alkyl; or R15 and R16 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl-3 alkyl, halogen or -OH; R17 is selected from hydrogen or --C(O)NH-C2-5 alkyl-N(CH3)2; R18 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; Het3 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur; OR R13 and R14 along with theMintz Ref.: 048536-783001WOPCT APPLICATIONnitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl -3 alkyl, — N(CH3)2 or — CH2N(CH3)2; R22 is selected from hydrogen, — C(O)N(R23)R24 or — (-OC2H4)1-10-CH3 R23 is hydrogen; R24 is selected from --C1-5 alkyl, --C2-5 alkenyl, --C2-5 alkynyl, — Cl -5 alkyl-N(R25)R26, — Cl-5 alkyl-O-Cl-3 alkyl, -(-C2H4O)l-10C2H5, -(-C2H4O)l-10-C2H4-R27 or -Cl-3 alkyl-Het3-(-C2H4O)l-10-C2H4-R28; wherein R25 is hydrogen or Cl to C3 alkyl; R26 is hydrogen or Cl to C3 alkyl; or R25 and R26 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl-3 alkyl, halogen or -OH; R27 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; R28 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; Het3 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur; OR R23 and R24 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl-3 alkyl, -N(CH3)2 or -CH2N(CH3)2.

[0022] In some aspects, the techniques described herein relate to a method 2-16 wherein the ligand is 2-(3-((S)-5-amino-l-carboxypentyl)ureido) pentanedioic acid, 2-[3-(l,3-Dicarboxypropyl)ureido]pentanedioic acid or 2-[3-(l-carboxy-2-mercapto-ethyl)ureido]pentanedioic acid.

[0023] In some aspects, the techniques described herein relate to a method 3 to 18, wherein said ligand is covalently bound to said cytotoxic agent or said covalently bound to a therapeutic agent through a cleavable linker.

[0024] In some aspects, the techniques described herein relate to a method, wherein said cleavable linker is an enzymatically cleavable linker.

[0025] In some aspects, the techniques described herein relate to a method, wherein said cleavable linker includes a val-cit linker moiety.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0026] In some aspects, the techniques described herein relate to a method including: obtaining, by at least one processor communicatively coupled to a database, data including a molecular structure for a plurality of ligand-drug conjugate compounds; simulating, by the at least one processor, based on the obtained data, one or more intra-molecular interactions for each of the ligand-drug conjugate compounds; determining, by the at least one processor, an aggregation score for each of the plurality of ligand-drug conjugate compounds based on their respective simulation; and identifying, by the at least one processor, a subset of the plurality of ligand-drug conjugate compounds having low aggregation by comparing the determined aggregation score to a predetermined threshold.

[0027] In some aspects, the techniques described herein relate to a method, wherein the data including the molecular structure includes: an atom type, an atom charge, an atom angle, an atom mass, and a number of bonds.

[0028] In some aspects, the techniques described herein relate to a method, wherein simulating the one or more intra-molecular interactions includes modeling behavior of one or more components of the ligand-drug conjugate compounds for a run-time.

[0029] In some aspects, the techniques described herein relate to a method, wherein the intramolecular interactions includes one or more of van der Waals contacts, hydrogen bonding, pi-cation interactions, and pi-pi interactions.

[0030] In some aspects, the techniques described herein relate to a method, wherein the aggregation score includes a numerical value indicative of a propensity of a unit of the liganddrug conjugate to have a center of mass within a cutoff distance of the center of mass of another unit of the ligand-drug conjugate.

[0031] In some aspects, the techniques described herein relate to a method, wherein the cutoff distance is within 3.5 angstroms.

[0032] In some aspects, the techniques described herein relate to a method, wherein identifying the subset of the plurality of ligand-drug conjugate compounds having low aggregation further includes ranking the ligand-drug conjugate compounds based on their respective determined aggregation score.

[0033] In some aspects, the techniques described herein relate to a method, wherein the aggregation score includes percentage value indicative of a probability of the ligand-drug conjugate to form a higher order cluster.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0034] In some aspects, the techniques described herein relate to a method, wherein the predetermined threshold includes a predetermined aggregation score determined based on historical data for a plurality of ligand-drug conjugate compounds.

[0035] In some aspects, the techniques described herein relate to a method, wherein each of the plurality of ligand-drug conjugate compounds are different and have the structure: wherein: n is 0, 1, 2, 3 or 4; L is a ligand; R1 is selected from a 6 to 14 membered aryl or a 5 to 13 membered heteroaryl containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur; R1 is unsubstituted or substituted with one or more R5; R5, at each occurrence, is independently selected from halogen, -C(O)NH2, -C(O)OR6, -Cl -3 alkyl, — OR7, and a 6 to 10 membered aryl; wherein, R6 is hydrogen or Cl -3 alkyl; R7 is hydrogen or Cl -3 alkyl; R2 is absent or is selected from a 6 to 10 membered cycloalkyl or a 6 to 10 membered aryl; R3 is hydrogen or — C1-C5COOH; R4 is selected from a group consisting of — Cl-10 alkyl-, — C2-6 alkenyl-, — Cl -3 alkyl-O-Cl-3 alkyl—, — C2-6 alkyl-N(R8)—, — C2-6 alkyl(N(R8)(R8'))—, — N(R8)-C2-6 alkyl—, a 3 to 6 membered cycloalkyl and — Cl-2 alkyl-(-OC2H4)l-8-OCl-2 alkyl—; wherein, R8 and R8' are independently selected from hydrogen, Cl-6 alkyl, -C(O)-Cl-4alkyl-aryl or -C(O)-(-C2H4O)l-8-Cl-2 alkyl-N(R)(R'), wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Cl-3alkyl or -OCl-3alkyl; wherein R and R' are independently selected from hydrogen, -Cl -6 alkyl or -C(O)-Cl-4alkyl-aryl, wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Cl-3alkyl or -OCl-3alkyl; A is an amino acid or a peptide including 2-5 amino acids; A is attached to Q through its C terminal; Q is a self-immolative group; and D is a cytotoxic agent or a therapeutic agent.

[0036] In some aspects, the techniques described herein relate to a method, wherein the plurality of ligand-drug conjugate compounds is at least 50 different ligand-drug conjugate compounds.

[0037] In some aspects, the techniques described herein relate to a method, wherein plurality of ligand-drug conjugate compounds is at least 500 different ligand-drug conjugate compounds.

[0038] In some aspects, the techniques described herein relate to a method, wherein plurality of ligand-drug conjugate compounds is at least 5,000 different ligand-drug conjugatecompounds.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0039] In some aspects, the techniques described herein relate to a method, wherein said simulating, the one or more intra-molecular interactions for each of the ligand-drug conjugate compounds includes calculating a conformer energy minimization.

[0040] In some aspects, the techniques described herein relate to a method, wherein the aggregation score is a predicted aggregation residence time.

[0041] In some aspects, the techniques described herein relate to a method, wherein each of said plurality of low aggregation ligand-drug conjugate compounds includes a ligand covalently bound to a cytotoxic agent or covalently bound to a therapeutic agent, wherein said ligand is capable of binding to a ligand binder under physiological conditions, wherein said ligand binder is PSMA, folate receptor, carbonic anhydrase IX, somatostatin receptor, fibroblast receptor, DLL3, STEAP-1, or PSCA.

[0042] In some aspects, the techniques described herein relate to a method, further including contacting one of said plurality of low aggregation ligand-drug conjugate compounds with a cell including said ligand binder, wherein said low aggregation ligand-drug conjugate compound effectively binds to said ligand binder intracellularly.

[0043] In some aspects, the techniques described herein relate to a method, wherein said cell forms part of an organism and wherein said contacting includes administering said low aggregation ligand-drug conjugate compound to said organism.

[0044] In some aspects, the techniques described herein relate to a method wherein the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation includes a detectable moiety.

[0045] In some aspects, the techniques described herein relate to a method wherein said detectable moiety is a fluorescent detectable moiety.

[0046] In some aspects, the techniques described herein relate to a method wherein said fluorescent detectable moiety is fluorescein.

[0047] In some aspects, the techniques described herein relate to a method, further including detecting said detectable moiety.

[0048] In some aspects, the techniques described herein relate to a method, wherein said detecting includes quantitating cell surface binding of said low aggregation ligand-drug conjugate compound.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0049] In some aspects, the techniques described herein relate to a method, wherein said plurality of ligand-drug conjugate compounds are different and have the structure: Rll is selected from -Cl-3 alkyl-OC(O)-**, -Cl-3 alkyl-O-C(O)-N(R19)-Cl-5 alkyl-N(R19)-C(O)- **, -Cl-3 alkyl-O-C(O)-N[Cl-5 alkyl-N(R20R21)]-Cl-3 alkyl-**, -Cl-3 alkyl-O-C(O)-Het2-Cl-3 alkyl-N(R19)-C(O)— **, or -Cl-3 alkyl-O-C(O)-N(R19)-Cl-5 alkyl-N(R19)-C(O)-**; wherein ** indicates point of attachment to D and R19 is selected from H, —Cl-3 alkyl or —Cl-3 alkyl-O-Cl-3 alkyl-OH; R20 is H or —Cl-3 alkyl; R21 is H or — C1-C3 alkyl; and Het2 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur; R12 is selected from hydrogen, — C(O)N(R13)R14 or — (-OC2H4)1-10-CH3 R13 is hydrogen; R14 is selected from — Cl-5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, -Cl-5 alkyl-N(R15)R16, -Cl-5 alkyl-O-Cl-3 alkyl, -(-C2H4O)l-10C2H5, -(-C2H4O)l-10-C2H4-R17 or -Cl-3 alkyl-Het3-(-C2H4O)l-10-C2H4-R18; wherein R15 is hydrogen or Cl-3 alkyl; R16 is hydrogen or Cl-3 alkyl; or R15 and R16 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl-3 alkyl, halogen or -OH; R17 is selected from hydrogen or --C(O)NH-C2-5 alkyl-N(CH3)2; R18 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; Het3 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur; OR R13 and R14 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl-3 alkyl, — N(CH3)2 or — CH2N(CH3)2; R22 is selected from hydrogen, — C(O)N(R23)R24 or — (-OC2H4)1-10-CH3 R23 is hydrogen; R24 is selected from —Cl-5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, —Cl-5 alkyl-N(R25)R26, — Cl-5 alkyl-O-Cl-3 alkyl, -(-C2H4O)l-10C2H5, -(-C2H4O)l-10-C2H4-R27 or -Cl-3 alkyl-Het3-(-C2H4O)l-10-C2H4-R28; wherein R25 is hydrogen or Cl to C3 alkyl; R26 is hydrogen or Cl to C3 alkyl; or R25 and R26 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygenMintz Ref.: 048536-783001WOPCT APPLICATIONand sulfur and wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl -3 alkyl, halogen or -OH; R27 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; R28 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; Het3 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur; OR R23 and R24 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with Cl -3 alkyl, -N(CH3)2 or -CH2N(CH3)2.

[0050] In some aspects, the techniques described herein relate to a method 22 wherein the ligand-drug conjugate includes a ligand, wherein the ligand is 2-(3-((S)-5-amino-l-carboxypentyljureido) pentanedioic acid, 2-[3-(l,3-Dicarboxypropyl)ureido]pentanedioic acid or 2-[3-(l -carboxy -2-mercapto-ethyl)ureido]pentanedioic acid.

[0051] In some aspects, the techniques described herein relate to a method 22, wherein a ligand in the ligand-drug conjugate is covalently bound to said cytotoxic agent or said covalently bound to a therapeutic agent through a cleavable linker.

[0052] In some aspects, the techniques described herein relate to a method, wherein said cleavable linker is an enzymatically cleavable linker.

[0053] In some aspects, the techniques described herein relate to a method, wherein said cleavable linker includes a val-cit linker moiety.

[0054] In some aspects, the techniques described herein relate to a method, further including: displaying, in at least one graphical user interface communicatively coupled to the at least one processor, the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation.

[0055] In some aspects, the techniques described herein relate to a method, wherein displaying the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation further includes displaying clustered ligand-drug conjugate compounds.

[0056] In some aspects, the techniques described herein relate to a method, further including: generating, a template for a drug treatment based on the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0057] In some aspects, the techniques described herein relate to a system including: at least one data processor; and memory coupled to the at least one data processor and storing instructions which, when executed by the at least one data processor, causes the at least one data processor to perform operations including a method 22-52.

[0058] In some aspects, the techniques described herein relate to a non-transitory computer readable storage medium storing computer readable instructions, which, when executed by at least one data processor, causes the at least one data processor to perform operations including a method 22-52.

[0059] Non-transitory computer program products (i.e., physically embodied computer program products) are also described that store instructions, which when executed by one or more data processors of one or more computing systems, causes at least one data processor to perform operations herein. Similarly, computer systems are also described that may include one or more data processors and memory coupled to the one or more data processors. The memory may temporarily or permanently store instructions that cause at least one processor to perform one or more of the operations described herein. In addition, methods can be implemented by one or more data processors either within a single computing system or distributed among two or more computing systems. Such computing systems can be connected and can exchange data and / or commands or other instructions or the like via one or more connections, including a connection over a network (e.g. the Internet, a wireless wide area network, a local area network, a wide area network, a wired network, or the like), via a direct connection between one or more of the multiple computing systems, etc.

[0060] The details of one or more variations of the subject matter described herein are set forth in the accompanying drawings and the description below. Other features and advantages of the subject matter described herein will be apparent from the description and drawings, and from the claims.BRIEF DESCRIPTION OF THE DRAWINGS

[0061] FIG. 1 provides a block diagram of a system for in silico methods for the development of cell-targeted drugs, in accordance with aspects of the present disclosure.

[0062] FIG. 2 provides a flowchart of a method of identifying low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0063] FIG. 3 provides a flowchart of a method of synthesizing low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure.

[0064] FIG. 4 provides a flowchart of a method of identifying low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure.

[0065] FIG. 5 illustrates a functional block diagram of a machine in the example form of computer system 500, within which a set of instructions for causing the machine to perform any one or more of the methodologies, processes or functions discussed herein may be executed, in accordance with aspects of the present disclosure.

[0066] FIG. 6 illustrates a visualization in connection with a method of identifying low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure.

[0067] FIG. 7 illustrates a visualization in connection with a method of identifying low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure.

[0068] FIG. 8 illustrates a visualization in connection with a method of identifying low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure.

[0069] FIG. 9 illustrates a method of inhibiting growth of tumor cells using low aggregation ligand-drug conjugate compounds identified in accordance with aspects of the present disclosure.

[0070] FIG. 10 illustrates a method of inhibiting growth of tumor cells using low aggregation ligand-drug conjugate compounds identified in accordance with aspects of the present disclosure.DETAILED DESCRIPTION

[0071] As used herein, “pharmaceutically acceptable salts” refer to derivatives of the disclosed compounds wherein the parent compound is modified by making non-toxic acid or base salts thereof. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral acid or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. The pharmaceutically acceptable salts include the conventional non-toxic salts or the quaternary ammonium salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. For example,Mintz Ref.: 048536-783001WOPCT APPLICATIONconventional non-toxic acid salts include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like; and the salts prepared from organic acids such as acetic, propionic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, malefic, hydroxymaleic, phenylacetic, glutamic, aspartic, benzoic, salicylic, mesylic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, malonic, succinic, glutaric, adipic, isethionic and the like. The pharmaceutically acceptable acid addition salts also include salts formed with the addition of one or more equivalents of acids, for example, monohydrochloride, and dihydrochloride salts.

[0072] The term “isotope” as used herein refers to the analog of a compound wherein at least one atom in the compound is replaced by its isotope. For example, when at least one hydrogen atom is replaced by a deuterium atom, the compound formed is called an isotope of the original compound. In particular, when a hydrogen atom in original compound is replaced by a deuterium atom, the resulting compound is called as “deuterated analog”. The isotope may be a fully or partially isotope substituted derivative.

[0073] The term “stereoisomers” as used herein refers to compounds that have identical chemical constitution, but differ with regard to the arrangement of their atoms or groups in space. The compounds of the present invention may contain asymmetric or chiral centers and, therefore, exist in different stereoisomeric forms. It is intended, unless specified otherwise, that all stereoisomeric forms of the compounds of Formula I to Formula VIII as well as mixtures thereof, including racemic mixtures, form part of the present invention. In addition, all geometric and positional isomers (including E and Z-forms) as well as mixtures thereof, are also embraced within the scope of the invention. In general, a reference to a compound is intended to cover its stereoisomers and mixture of various stereoisomers.

[0074] The term “alkyl” as used herein refers to a saturated hydrocarbon chain radical that includes solely carbon and hydrogen atoms in the backbone, either linear or branched, having from 1 to 10 carbon atoms, both inclusive unless defined otherwise. Suitable non-limiting examples of alkyl groups include, for example, methyl, ethyl, n-propyl, 1 -methylethyl (isopropyl), n-pentyl, n-hexyl.

[0075] The numerical in phrases like “C1-4” or “Cl to C4”, refers to the number of carbon atoms in the chain. For example, the phrase “C1-4 alkyl” or “Cl to C4 alkyl” refers to an alkyl chain having 1 to 4 carbon atoms.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0076] The term “alkenyl” as used herein refers to a hydrocarbon chain containing at least one carbon-carbon double bond, and may have (£) or (Z) configuration. An alkenyl group may contain 2 to 8 carbon atoms unless specified otherwise. Unless set forth or recited to the contrary, all alkenyl groups described herein may form part of a straight or branched chain. Suitable nonlimiting examples of alkenyl groups include, e.g., ethylene, 2-propenyl (allyl), 2-methyl-2-propenyl and 2-butenyl. Unless set forth or recited to the contrary, all alkenyl groups described herein may be unsubstituted or substituted.

[0077] The term “alkynyl: as used herein refers to a hydrocarbon chain containing at least one carbon-carbon triple bond. Such group may contain 2 to 5 carbon atoms unless specified otherwise. Unless set forth or recited to the contrary, all alkenyl groups described herein may form part of a straight or branched chain. Non-limiting examples of alkynyl groups are: ethynyl, 2-propynyl, 1-propynyl, 2-butynyl. The alkynyl group of the present invention may be further substituted with the akenyl or alkyl groups as defined above.

[0078] The term “aryl” as used herein refers to an aromatic radical having 6 to 14 carbon atoms, including monocyclic, bicyclic or tricyclic aromatic systems. A bicyclic aryl group includes an aromatic ring fused to a saturated, partially unsaturated ring, or aromatic ring. The bicyclic aryl group may be attached to the rest of the molecule at any suitable position including the position on the aromatic ring or saturated or partially unsaturated ring. Typical aryl groups include, but are not limited to, phenyl, naphthyl, indanyl (for e.g. 1 -indanyl, 5-indanyl), indenyl, anthracenyl and phenanthrenyl. Unless set forth or recited to the contrary, all aryl groups described herein may be unsubstituted or substituted. For example, an aryl group can be substituted with one or more groups independently selected from:

[0079] C₁₋₄ alkyl (for example, methyl, ethyl, propyl and butyl) optionally substituted with one more halogen (for example, chloro, fluoro, iodo or bromo);

[0080] phenyl; 5 to 10 membered heteroaryl ring optionally substituted with one or more groups selected from C1-4 alkyl; amino group, optionally further substituted with a substituted heteroaryl group; and COOH.

[0081] The term “heteroaryl ring” refers to a 5 to 14 membered aromatic heterocyclic ring containing one or more (such as 1, 2 or 3) heteroatoms, each independently selected from nitrogen, oxygen and sulfur. The heteroaryl ring may be a mono-, bi- or tri-cyclic ring system and includes fused ring systems (at least one of which is aromatic). The heteroaryl ring radicalMintz Ref.: 048536-783001WOPCT APPLICATIONmay be attached to the main structure at any heteroatom or carbon atom that results in the creation of a stable structure. Suitable examples of heteroaryl rings include, but are not limited to, oxazolyl, isoxazolyl, imidazolyl, furyl, indolyl, isoindolyl, pyrrolyl, triazolyl, triazinyl, tetrazoyl, thienyl, thiazolyl, isothiazolyl, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, benzofuranyl, benzothiazolyl, benzoxazolyl, benzimidazolyl, benzothienyl, benzopyranyl, carbazolyl, quinolinyl, isoquinolinyl, quinazolinyl, purinyl, quinoxalinyl, quinolinyl, isoquinolinyl, thiadiazolyl, indolizinyl, imidazo[1,2-a]pyridyl and phthalazinyl. Unless set forth or recited to the contrary, all heteroaryl groups described or claimed herein may be unsubstituted or substituted.

[0082] The terms “heterocycloalkyl” or “heterocyclic ring” are used interchangeably and refer to an aromatic or non-aromatic cyclic ring containing one, two or three heteroatoms, each independently selected from nitrogen, sulphur or oxygen. Suitable non-limiting examples of heterocycloalkyl groups include those listed under “heteroaryl ring”. Heterocycloalkyl group may further include but are not limited to, pyrrolidinyl, piperidine, piperazinyl, morpholinyl, thiomorpholine and 1,3-oxazine. Unless set forth or recited to the contrary, a heterocycloalkyl ring described herein may be unsubstituted or substituted.

[0083] As used herein the term “self-immolative group” is a group that has a tendency undergo a cascade of disassembly reactions ultimately leading to release of the active molecule. Such cascade of disassembly reactions are usually triggered due to enzymatic activation of the amino acid or the peptide (A) next to a self-immolative group (Q). Enzymes such as cathepsins and plasmin are non-limiting examples of enzymes that trigger self-immolation of Q of the present invention.

[0084] The term “cytotoxic agent” as used herein refers to any agent that exerts a cytotoxic effect on a cell upon contact. Such cytotoxic agents are well known to a person skilled in the art. Examples of cytotoxic agents that may be used in the of the invention include, but are not limited to, alkylating drugs, anthracyclines, pyrimidine derivatives, vinca alkaloids, photodynamic drugs, platinum- containing compounds, taxanes, topoisomerase inhibitors, ribosome inactivating agents (e.g., gelonin), agents that induce DNA damage (e.g., calicheamicin), tubulin inhibitors (e.g., emtansine), anti-mitotic agents (e.g., monomethyl auristatin), or bacterial toxins. The cytotoxic agents may also be radioisotopes or cytotoxic antibodies.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0085] The terms “therapeutic agent”, “active ingredient”, “active agent” as used herein refer to an agent that is administered to treat a condition, disease or illness or the symptoms thereof. For the purpose of present invention, a therapeutic agent is an agent known for the treatment of a disease or illness involving cells with cancer.

[0086] The terms "subject" or "patient" are used interchangeably and refer to a subject that may benefit from the present invention such as a mammal (e.g., canine, feline, ovine, porcine, equine, bovine, or human). In one specific embodiment, the patient is human. In some aspects, the diagnosis of a disease or disorder associated with expression of cancer may be performed by a skilled physician by methods known in the art.

[0087] The term “subject in need thereof’ in the context of the present invention inter alia refers to mammals, particularly human subjects, suffering from a disease or disorder associated with cancer.

[0088] The terms “disease” and “disorder” are used interchangeably.

[0089] The term “cancer” as used herein refers to the diseases caused by uncontrolled cell division and the ability of cells to metastasize, or to establish new growth in additional sites. The terms “malignant”, “malignancy”, “neoplasm”, “tumor”, “cancer” and variations thereof refer to cancerous cells or groups of cancerous cells.

[0090] It is to be understood that the terms ‘treat’, ‘treating’, ‘treatment’ or forms thereof, as used herein, mean reducing, preventing, curing, reversing, ameliorating, attenuating, alleviating, minimizing, suppressing, or halting the deleterious effects of a disease or a condition or delaying the onset of one or more clinical indications of a disease or disorder.

[0091] A “therapeutically effective amount” of a compound is an amount which is sufficient to reduce or ameliorate the progression, severity and / or duration of a disease or disorder or ameliorate one or more symptoms of a disease or disorder, prevent the recurrence of a disease or disorder, prevent the development or onset of a disease or disorder, or one or more symptoms thereof. For the purpose of the present invention, a therapeutically effective amount is an amount of the compound of the present invention administered to the subject to reduce or ameliorate the progression, severity, duration or symptoms of the diseases associated with the drug target.

[0092] The terms “pharmaceutical composition”, “medicament” and “dosage form” are used interchangeably and mean a pharmaceutical preparation consisting of drug substance(s) and / or excipient(s) to facilitate dosing or administration and delivery of the content of the drug productMintz Ref.: 048536-783001WOPCT APPLICATIONto the subject. The drug substance is an active ingredient or a compound containing active ingredient / s.

[0093] Cell-targeted drugs such as ligand-drug conjugates can include a ligand that is attached to a linking group that is attached to a drug. The efficacy of the resulting ligand-drug conjugate in treating disease can be adversely impacted by the aggregation of the ligand-drug conjugates due to intermolecular and / or intramolecular interactions between ligand linking groups. Disclosed are systems and methods that can model the aggregation characteristics of the ligand-drug conjugates, such that ligand-drug conjugates having low aggregation can be identified and synthesized without requiring synthesis of all potential ligand-drug conjugate candidates.

[0094] For reference, the synthesis of potential ligand-drug conjugate candidates can involve a multi-step resource intensive process that includes coupling reactions, protections and deprotections, oxidations, reductions, additions, eliminations and other reactions. The synthesis of potential ligand-drug conjugate candidates can also include having to separate and ligand-drug conjugate candidates from a reaction mixture using filtration, distillation of solvents, liquidliquid extraction, phase separation, centrifugation, and / or decantation, and the like. Additionally, the synthesis of potential ligand-drug conjugate candidates may involve acid-base or base-acid treatments, distillation, filtration and solvent treatment, chromatographic purification methods such as column chromatography, preparative chromatography etc.

[0095] The disclosed systems and methods can model the aggregation characteristics of the ligand-drug conjugates to identify ligand-drug conjugate candidates having lower aggregation scores and provide improved drug efficacy and allow for the targeted synthesis of ligand-drug conjugates expected to have low aggregation scores, without requiring extensive synthesis of all potential ligand-drug candidates.

[0096] For example, ligand-drug conjugate candidates may form small-order or large-order aggregation complexes due to the intra-molecular and / or inter-molecular forces. The order of the aggregation complex formed by the ligand-drug conjugate can be assessed by the number of monomers in the aggregate. For example, large-order aggregation complexes may be composed of more than four monomers in the aggregate. In another example, small-order aggregation complexes may be composed of two, three or four monomers in the aggregate. In addition to the order of the aggregation complexes formed by the ligand-drug conjugate candidates. Ligand-Mintz Ref.: 048536-783001WOPCT APPLICATIONdrug conjugate candidates can be assessed by their reversibility or ability to revert back to their monomer constituents after forming an aggregation complex. Large-order aggregation complexes and irreversible aggregation complexes can indicate that ligand-drug conjugate is unable to effectively kill cancer cells because the monomer components are no longer able to effectively engage a cell surface marker to induce endocytosis and determine the selective targeting of a cell (i.e., cancer cell). The disclosed methods and systems can be used for more efficient identification of ligand-drug compounds that can provide effective targeting endocytosis.

[0097] FIG. 1 provides a block diagram for a system for identifying low aggregation liganddrug compounds and for synthesizing low aggregation ligand-drug conjugate compounds.

[0098] As shown in FIG. 1, a system 100 includes a computing device 102 with a graphical user interface 108 and a database 110 communicatively coupled using a network 130.

[0099] Database 110 can be coupled to computing system 102 either directly (e.g., through one or more communication cables) or through network 130, which may be the Internet or any other combination of wide-area, local- area, wired, and / or wireless networks. In some embodiments, computing system 102 may be included in or integrated with the database 110. In some embodiments, database 110 may store ligand-drug component data corresponding to the molecular structure of one or more of ligands, linkers, and drug components for a ligand-drug conjugate compound. The ligand-drug component data for the molecular structure of one or more of ligands, linkers, and drug components can include the digital chemical structure for a plurality of ligand-drug conjugate compounds. The ligand-drug component data can be sent to computing system 102 (e.g., through network 130) or stored on a storage device and at a later stage transferred to computing system 102 (e.g., through network 130). In some embodiments, computing system 102 may or may not include a display 108 and one or more input devices (not illustrated) for receiving commands from a user or operator (e.g. a technician or a scientist). In some embodiments, computing system 102 and / or database 110 can be accessed by users or other devices remotely through network 130. Thus, in some embodiments various methods discussed herein may be run remotely on computing system 102.

[0100] Database 110 can include ligand-drug component data including, for example, angles, atoms, lengths, rotations of atoms of the ligand-drug conjugate. In some embodiments databaseMintz Ref.: 048536-783001WOPCT APPLICATION110 can also store trajectories or data from simulations of ligand-drug conjugates. Trajectories can include the disposition of each atom in each conjugate in the simulation.

[0101] Computing system 102 can be configured to include software programs for performing molecular dynamics simulations. Examples of software programs include, but are not limited to, GROMACS, CHARMM, AMBER, NAMD, and LAMMPS. For example, in some aspects computing system 102 can be specialized with graphical processing units configured for efficient simulations using techniques such as Particle Mesh Ewald Molecular Dynamics (PMEMD) and the like.

[0102] As will be described herein, computing system 102 can be configured to include software programs for identifying a plurality of low-aggregation ligand-drug conjugate compounds and synthesizing a low aggregation ligand-drug conjugate compound_based on data obtained from the database 110.

[0103] Computing system 102 may include one computing device or a combination of a number of computing devices of any type, such as personal computers, laptops, network servers (e.g., local servers or servers included on a public / private / hybrid cloud), mobile devices, etc., where some or all of the devices can be interconnected. Computing system 102 may include one or more processors (not illustrated), each of which can have one or more cores. In some embodiments, computing system 102 can include one or more general -purpose processors (e.g., CPUs), special-purpose processors such as graphics processors (GPUs), digital signal processors, or any combination of these and other types of processors. In some embodiments, some or all processors in computing system can be implemented using customized or customizable circuitry, such as application specific integrated circuits (ASICs) or field programmable gate arrays (FPGAs). Computing system 102 can also in some embodiments retrieve and execute non-transitory computer-readable instructions stored in one or more memories or storage devices (not illustrated) integrated into or otherwise communicatively coupled to computing system 102. The memory / storage devices can include any combination of non-transitory computer readable storage media including semiconductor memory chips of various types (DRAM, SRAM, SDRAM, flash memory, programmable read-only memory) and so on. Magnetic and / or optical disks can also be used. The memories / storage devices can also include removable storage media that can be readable and / or writeable; examples of such media include compact disc (CD), readonly digital versatile disc (e.g., DVD-ROM, dual-layer DVD-ROM), read-only and recordableMintz Ref.: 048536-783001WOPCT APPLICATIONBlu-ray® disks, ultra-density optical disks, flash memory cards (e.g., SD cards, mini-SD cards, micro-SD cards, etc.), and so on. In some embodiments, data and other information (e.g. sequencing data) can be stored in one or more remote locations, e.g., cloud storage, and synchronized with other the components of system 100.

[0104] Display 108 may be communicatively coupled with computer system 102 and include a graphical user interface, software application and the like configured to display visualizations for ligand-drug conjugate compounds, data obtained from the database 110 and / or output from one or more software applications run on computer system 102.

[0105] FIG. 2 provides a flow chart for a computer-implemented method for identifying a plurality of low-aggregation ligand-drug conjugate compounds. As illustrated in FIG. 2, the process 200 can include the steps of receiving a digital chemical structure for each of a plurality of ligand-drug conjugate compounds 201, calculating an aggregation number for each of said plurality of ligand-drug conjugate compounds 203, ranking at least a portion of said plurality of ligand-drug conjugate compounds based on said aggregation number 205, and identifying a plurality of low aggregation ligand-drug conjugate compounds based on said ranking 207. In some aspects, the plurality of low aggregation ligand-drug conjugate compounds is a portion of the plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of the remaining ligand-drug conjugate compounds within the plurality of ligand-drug conjugate compounds.

[0106] FIG. 3 provides a flow-chart for a computer-implemented method of synthesizing a low aggregation ligand-drug conjugate compound. As illustrated in FIG. 3, the process 300 can include the steps of receiving a digital chemical structure for each of a plurality of ligand-drug conjugate compounds 301, calculating an aggregation number for each of said plurality of ligand-drug conjugate compounds 303, identifying a plurality of low aggregation ligand-drug conjugate compounds based on said aggregation number 305, and chemically synthesizing the plurality of low aggregation ligand-drug conjugate compound 307. In some aspects, the identified plurality of low aggregation ligand-drug conjugate compounds is a portion of the plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of the remaining ligand-drug conjugate compounds within the plurality of ligand-drug conjugate compounds.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0107] FIG. 4 provides a flow chart for a method and process 400 for identifying low aggregation ligand-drug conjugate compounds. In a first step 401, at least one processor can obtain data including a molecular structure for a plurality of ligand-drug conjugate compounds. In a second step, one or more intra-molecular interactions for each of the ligand-drug conjugate compounds can be simulated 403. In a third step, an aggregation score for each of the plurality of ligand-drug conjugate compounds based on their respective simulation can be determined 405. In a fourth step, a subset of the plurality of ligand-drug conjugate compounds having low aggregation by comparing the determined aggregation score to a predetermined threshold can be identified 407.

[0108] In some embodiments, a processor can obtain or receive data including a molecular structure of one or more ligand-drug conjugate compounds. In some embodiments, this can include a digital chemical structure for each ligand-drug conjugate compound in a plurality of ligand-drug compounds. The obtained data can be retrieved from a database such as database 110 that is communicatively coupled to at least one processor in a computing system such as computing system 102. In some embodiments, the at least one processor receives the digital chemical structure after the data from the database is queried. The digital chemical structure can the molecular structure can undergo a energy minimization process such as a conformer energy minimization prior to a simulation being run on the molecular structure or digital chemical structure.

[0109] In some aspects, the data for the molecular structure can include data and information for the molecular and structural properties of the ligand-drug conjugate compounds. This may include information such as atoms, angles, rotations, lengths, and the like. In some embodiments, the data can be represented in a GROMACS file format and the like. For example, the data file can include atom information such as an atom’s elemental symbol, atom type, charge, mass, number of bonds, and the like.

[0110] In some aspects, the ligand-drug conjugate can be specialized for the treatment of prostate cancer. For example, the ligand-drug conjugate can be for the recognition of prostatespecific membrane antigen (PSMA) as discussed in WO 2024 / 150132 (PCT / IB2024 / 050208) entitled LIGAND-DRUG CONJUGATES, the contents of which are hereby incorporated by reference in their entirety. PSMA binding ligands can be conjugated to a cytotoxic, therapeutic,Mintz Ref.: 048536-783001WOPCT APPLICATIONimaging, diagnostic agents and the like through a linker. In some aspects, each of said plurality of ligand-drug conjugate compounds are different and have the structure:where:n is 0, 1, 2, 3 or 4, L is a ligand, Ri is selected from a 6 to 14 membered aryl or a 5 to 13 membered heteroaryl containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur, Ri is unsubstituted or substituted with one or more Rs, Rs, at each occurrence, is independently selected from halogen, — C(O)NH2, — C(O)ORe, — Ci-3 alkyl, — OR?, and a 6 to 10 membered aryl; Re is hydrogen or C1.3 alkyl, R7 is hydrogen or Ci-3 alkyl, R2 is absent or is selected from a 6 to 10 membered cycloalkyl or a 6 to 10 membered aryl, R3 is hydrogen or — C1-C5COOH, R4 is selected from a group consisting of — Ci-10 alkyl-, — C2-6 alkenyl-, — C1-3 alkyl-O-Ci-3 alkyl —, — C2-6 alkyl-N(Rs) —, — C2- 6 alkyl(N(Rg)(R8')) —, — N(Rs)-C2-6 alkyl —, a 3 to 6 membered cycloalkyl and — C1-2 alkyl-(-OC2H4)i-8-OCi-2 alkyl —; Rs and Rs’ are independently selected from hydrogen, Ci- 6 alkyl, -C(O)-Ci-4alkyl-aryl or -C(O)-(-C2H4O)i-8-Ci-2 alkyl-N(R)(R’), wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Ci-salkyl or -OCi- salkyl, R and R’ are independently selected from hydrogen, -C1-6 alkyl or -C(O)-Ci-4alkyl- aryl, wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Ci-3alkyl or -OCi-3alkyl, A is an amino acid or a peptide comprising 2-5 amino acids, A is attached to Q through its C terminal, Q is a self-immolative group; and D is a cytotoxic agent or a therapeutic agent.

[0111] In some aspects, the described systems and methods can be used to screen a large number of ligand-drug conjugate compounds and provide high-throughput screening. For example, any suitable number of ligand drug conjugate compounds, each of which is different can be screened including 50 different ligand-drug conjugate compounds, 500 different liganddrug conjugate compounds, and / or 5,000 different ligand-drug conjugate compounds.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0112] In some aspects, each of said plurality of low aggregation ligand-drug conjugate compounds can include a ligand covalently bound to a cytotoxic agent or covalently bound to a therapeutic agent, where the ligand is capable of binding to a ligand binder under physiological conditions, and the ligand binder is PSMA, folate receptor, carbonic anhydrase IX, somatostatin receptor, fibroblast receptor, DLL3, STEAP-1, or PSCA.

[0113] In some aspects, one of the plurality of low aggregation ligand-drug conjugate compounds can be contacted with a cell comprising said ligand binder, wherein said low aggregation ligand-drug conjugate compound effectively binds to said ligand binder intracellularly. The cell can form part of an organism and contacting can include administering the low aggregation ligand-drug conjugate compound to said organism. Low aggregation liganddrug conjugate compounds can be associated with efficient targeting of cells such as cancer cells. In some embodiments, aggregation information can be used to adjust dosage for a therapeutic agent that forms a component of the ligand-drug conjugate.

[0114] In some aspects, the low aggregation ligand-drug conjugate compound comprises a detectable moiety. For example, the detectable moiety can be a fluorescent detectable moiety, such as fluorescein. In some aspects, the low aggregation ligand-drug conjugate compound comprises a radio nucleotide. In some applications, the detectable moiety can be detected by quantitating cell surface binding of the low aggregation ligand-drug conjugate compound.

[0115] In some aspects, the plurality of ligand-drug conjugate compounds are different and have the structure:Rn is selected from — C1.3 alkyl-OC(O) — **, — C1-3 alkyl-O-C(O)-N(Ri9)-Ci-5 alkyl-N(Ri9)-C(O)— **, — C1-3 alkyl-O-C(O)-N[C1-5alkyl-N(R20R21)]-C1-3alkyl— **,— C1-3alkyl-O-C(O)-Het2-C1-3alkyl-N(R19)-C(O)— **, or— C1-3alkyl-O-C(O)-N(R19)-C1-5alkyl-N(R19)-C(O)— **; where ** indicates point of attachment to D and R19 is selected from H, — C1.3 alkyl or — C1-3 alkyl-O-Ci-3 alkyl-OH; R20 is H or — C1-3 alkyl; R21is H or — C1-C3 alkyl; and Het2is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected fromMintz Ref.: 048536-783001WOPCT APPLICATIONnitrogen, oxygen or sulfur; R12is selected from hydrogen, — C(O)N(R13)R14or — (-OC2H4)1-10-CH3, R13 is hydrogen; R14 is selected from — C1-5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, — C1-5 alkyl-N(Ri5)Ri6, — C1-5 alkyl-O-Ci-3 alkyl, — (-C2H4O)1-10C2H5, — (-C2H4O)1-10-C2H4-R17or — C1-3 alkyl-Het3-(-C2H4O)1-10-C2H4-R18; where R15 is hydrogen or C1-3 alkyl; Ri6 is hydrogen or Ci-3 alkyl; or R15 and Ri6 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, where 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and where the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with C1-3 alkyl, halogen or -OH; R17 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; Ris is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; Het3 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur; OR R13 and R14 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, where 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and where the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with C1-3 alkyl, — N(CH3)2 or — CH2N(CH3)2; R22 is selected from hydrogen, — C(O)N(R23)R24 or — (-OC2H4)I-IO-CH3 R23 is hydrogen; R24 is selected from — C1-5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, — C1-5 alkyl-N(R2S)R26, — C1-5 alkyl-O-Ci-3 alkyl, — (-C2H4O)1-10C2H5, — (-C2H4O)1-10-C2H4-R27 or — C1-3 alkyl-Het3-(-C2H4O)1-10-C2H4-R28; where R25 is hydrogen or Cl to C3 alkyl; R26 is hydrogen or Cl to C3 alkyl; or R25 and R26 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, where 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and where the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with C1-3 alkyl, halogen or -OH; R27 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; R28 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2; Hets is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur; OR R23 and R24 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, where 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and where the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with C1-3 alkyl, — N(CH3)2or — CH2N(CH3)2.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0116] In some aspects, the ligand is 2-(3-((S)-5-amino-l-carboxypentyl)ureido) pentanedioic acid, 2-[3-(l,3-Dicarboxypropyl)ureido]pentanedioic acid or 2-[3-(l -carboxy -2-mercapto-ethy 1 )urei do]p entanedi oi c aci d.

[0117] In some aspects the plurality of ligand-drug conjugates include a folate recognition element. In some aspects, the folate recognition element and the associated ligand-drug conjugate compounds have the structure:The folate recognition element can be appended with linkers, spacers and payload, and included in a molecular dynamics simulation as described herein.

[0118] In some aspects the ligand-drug conjugate comprises a compound referred to as PS70, and having the structure:and formula CC[C@@H]([C@H](N(C(=O)[C@@H](NC(=O)[C@@H](N(C(=O)OCclccc(ccl)NC(=O)[C @@H](NC(=O)[C@@H](NC(=O)CCCC(=O)NC[C@H]2CC[C@@H](CC2)C(=O)N[C@H](C (=O)NCCCC[C@H](NC(=O)N[C@H](C(=O)O)CCC(=O)O)C(=O)O)Cc3cc4c(cc3)cccc4)C(C) C)CCCNC(=O)N)C)C(C)C)C(C)C)C)[C@H](OC)CC(=O)N5[C@@H](CCC5)[C@H](OC)[C@ H](C(=O)N[C@@H]([C@@H](O)c6ccccc6)C)C)C.

[0119] In some aspects the ligand-drug conjugate comprises a compound referred to as PS97, and having the structure:Mintz Ref.: 048536-783001WOPCT APPLICATIONand formula CC[C@@H]([C@H](N(C(=O)[C@@H](NC(=O)[C@@H](N(C(=O)OCclc(cc(ccl)NC(=O)[C @@H](NC(=O)[C@@H](NC(=O)CCCC(=O)NC[C@H]2CC[C@@H](CC2)C(=O)N[C@H](C (=O)NCCCC[C@H](NC(=O)N[C@H](C(=O)O)CCC(=O)O)C(=O)O)Cc3cc4c(cc3)cccc4)C(C) C)CCCNC(=O)N)C(=O)NCCN(C)C)C)C(C)C)C(C)C)C)[C@H](OC)CC(=O)N5[C@@H](CCC 5)[C@H](OC)[C@H](C(=O)N[C@@H]([C@@H](O)c6ccccc6)C)C)C.

[0120] In some aspects the ligand-drug conjugate comprises a compound referred to as PS50, and having the structure:and formula CCclc2c(nc3clcc(cc3)O)- c4n(c(=O)c5c(c4)[C@@](C(=O)OC5)(OC(=O)N(CCN(C(=O)OCc6ccc(cc6)NC(=O)[C@@H]( NC(-O)[C@@H](NC(-O)CCCC(-O)NC[C@H]7CC[C@@H](CC7)C(-O)N[C@H](C(-O)NC CCC[C@H](NC(=O)N[C@H](C(=O)O)CCC(=O)O)C(=O)O)Cc8cc9c(cc8)cccc9)C(C)C)CCCN C(=O)N)C)C)CC)C2.

[0121] In some aspects the ligand-drug conjugate comprises a compound referred to as PS58, and having the structure:Mintz Ref.: 048536-783001WOPCT APPLICATIONand formula CC[C@H](C)[C@@H]([C@@H](CC(=O)N1CCC[C@H]1[C@@H]([C@@H](C)C(=O)N[C@ H](C)[C@H](c2ccccc2)O)OC)OC)N(C)C(=O)[C@H](C(C)C)NC(=O)[C@H](C(C)C)N(C)C(= O)OCc3ccc(cc3)NC(=O)[C@H](CCCNC(=O)N)NC(=O)[C@H](C(C)C)NC(=O)CCCCCCC(= O)NCCCC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O.

[0122] In some aspects the ligand-drug conjugate comprises a compound referred to as PS48 (fluorescent probe), and having the structure:and formula clcc2c(cclNC(=O)CCCC(=O)NCCCC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(= O)O)C(=O)OC23c4ccc(cc4Oc5c3ccc(c5)O)O.

[0123] The ligand may be covalently bound to the cytotoxic agent or the covalently bound to a therapeutic agent through a cleavable linker. Examples of cleavable linkers include an enzymatically cleavable linker, such as one that includes a val-cit linker moiety.

[0124] In some embodiments, a processor can simulate one or more intra-molecular interactions for each of the ligand-drug conjugate compounds. A simulation can involve modeling behavior of the one or more components of the ligand-drug conjugate compounds for a run-time. Intra-molecular interactions can include van der Waals contacts, hydrogen bonding, pi-cation interactions and pi-pi interactions. For example, counts for each of the intra-molecular interactions can be generated. Hydrogen bonding can be counted if the distance between hydrogen bond donors (HBD) and hydrogen bond acceptors (HBA) is not more than 2.5 A where the donor angle is not less than 120.0°, and the acceptor angle is not less than 90.0°. A pi-pi interaction can be defined as an interaction between two aromatic rings in which either (a) the angle between the ring planes is less than 30° and the distance between the ring centroids is lessMintz Ref.: 048536-783001WOPCT APPLICATIONthan 4.4 A (face-to-face), or (b) the angle between the ring planes is between 60° and 120° and the distance between the ring centroids is less than 5.5 A (edge-to-face). Pi-cation interaction can be defined as an interaction between the cation center and the ring center when the distance between them is not more than 6.6 A and the angle between the ring plane and the line between the cation center and the ring center does not deviate from the perpendicular by more than 30°. In some embodiments, intra-molecular and inter-molecular interactions can be observed in a visualization.

[0125] In some aspects, at least one processor can be used to run one or more simulations using molecular dynamics software. Examples of software programs include, but are not limited to, GROMACS, CHARMM, AMBER, NAMD, and LAMMPS.

[0126] In some embodiments, at least one processor can be used to determine an aggregation score for each of the plurality of ligand-drug conjugate compounds based on their respective simulated intra-molecular interactions.

[0127] In some aspects, the aggregation score can be expressed as a numerical value indicative of a propensity of a unit of the ligand-drug conjugate to have a center of mass within a cutoff distance of the center of mass of another unit of the ligand-drug conjugate. For example, the cutoff distance is within 3.5 angstroms. The aggregation score can be indicative of the propensity of a ligand-drug conjugate to form non-reversible aggregation complexes.

[0128] In some aspects, identifying the subset of the plurality of ligand-drug conjugate compounds having low aggregation includes ranking the ligand-drug conjugate compounds based on their respective determined aggregation score.

[0129] In some aspects, a plurality of ligand-drug conjugate compounds can be sorted based on their aggregations score and a dynamic threshold can be applied. The dynamic threshold can correspond to clusters based on aggregation score. For example, if three ligand-drug conjugates are simulated to have a similar aggregation score they may form a first cluster.

[0130] In some aspects, the aggregation score comprises percentage value indicative of a probability of the ligand-drug conjugate to form a higher order cluster. In some aspects, a higher order cluster can include two or more ligand-drug conjugates forming an irreversible aggregation complex.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0131] In some aspects, probability distributions of the potential for clusters with respect to the total number of molecules in a ligand-drug conjugate compound can be determined and used to determine an aggregation score.

[0132] In some aspects, an aggregation score can also be referred to as an aggregation number. The aggregation number can be calculated for each of the plurality of ligand-drug conjugate compounds. In some aspects, the aggregation score or the aggregation number can be a predicted aggregation residence time, or an indication of the duration of time for which the ligand-drug conjugate compounds form aggregated complexes.

[0133] In some aspects, the computer system can rank at least a portion of said plurality of ligand-drug conjugate compounds based on the aggregation number. Further, a plurality of low aggregation ligand-drug conjugate compounds can be identified based on the ranking. For example, the plurality of low aggregation ligand-drug conjugate compounds can be a portion of the plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of a remaining ligand-drug conjugate compounds within said plurality of ligand-drug conjugate compounds. In some aspects, the ligand-drug conjugate having the lowest aggregation score, or a subset of those under a threshold value can be identified and used for drug development.

[0134] In some embodiments, at least one processor can be used to identify a subset of the plurality of ligand-drug conjugate compounds having low aggregation by comparing the determined aggregation score to a predetermined threshold. For example, the predetermined threshold can be based on a predetermined aggregation score determined based on historical data for a plurality of ligand-drug conjugate compounds.

[0135] In some aspects, the identified low aggregation ligand-drug conjugate compounds can be used in a chemical synthesis process, for example the data generated by identifying the low aggregation ligand-drug conjugate compounds can be used to generate a template for a drug treatment. Additionally, chemically synthesizing the plurality of low aggregation ligand-drug conjugate compound can include sending a control signal to a device configured to generate drug compounds.

[0136] In some aspects, a simulation can be configured to output trajectory information and molecular dynamics information for the ligand-drug conjugate compounds. For example, in some aspects, the simulation can output a matrix of kinetically derived aggregation measures.Mintz Ref.: 048536-783001WOPCT APPLICATIONFor example, the output can be represented in.xtc files or gromol trajectory files which include atoms, atom numbers, simulation time, simulation steps, coordinates for atoms and the like.

[0137] In some aspects, at least one graphical user interface can be communicatively coupled to the at least one processor. The graphical user interface can be configured to display the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation. For example, the graphical user interface may display visualizations of the solvated ligand-drug conjugate molecules over the simulation at various timepoints. In some embodiments, the graphical user interface may provide visualizations for the structural data corresponding to the molecular dynamics at various times during the simulation. For example, in some embodiments, the simulation may illustrate the intra-molecular and / or inter-molecular interactions that correspond to the determined aggregation score. In some embodiments, the graphical user interface may be interactive in that a user can select and view the areas of inter / intra-molecular interactions, view the formed aggregated complexes, and the like. Example visualizations are provided in FIGS. 6-8.

[0138] The subject matter described herein provides many technical advantages. For example, the disclosed systems can be used to identify ligand-drug conjugates having low aggregation with efficiency.

[0139] FIG. 5 illustrates a functional block diagram of a machine in the example form of computer system 500, within which a set of instructions for causing the machine to perform any one or more of the methodologies, processes or functions discussed herein may be executed. In some examples, the machine may be connected (e.g., networked) to other machines as described above. The machine may operate in the capacity of a server or a client machine in a client-server network environment, or as a peer machine in a peer-to-peer (or distributed) network environment. The machine may be any special-purpose machine capable of executing a set of instructions (sequential or otherwise) that specify actions to be taken by that machine for performing the functions describe herein. Further, while only a single machine is illustrated, the term “machine” shall also be taken to include any collection of machines that individually or jointly execute a set (or multiple sets) of instructions to perform any one or more of the methodologies discussed herein. In some examples, the computing system 102 of FIG. 1 may be implemented by the example machine shown in FIG. 5 (or a combination of two or more of such machines).Mintz Ref.: 048536-783001WOPCT APPLICATION

[0140] Example computer system 500 may include processing device 503, memory 507, data storage device 509 and communication interface 515, which may communicate with each other via data and control bus 501. In some examples, computer system 500 may also include display device 513 and / or user interface 511. In some embodiments, the user interface 511 may include a graphical user interface.

[0141] Processing device 503 may include, without being limited to, a microprocessor, a central processing unit, an application specific integrated circuit (ASIC), a field programmable gate array (FPGA), a digital signal processor (DSP) and / or a network processor. Processing device 102 may be configured to execute processing logic 505 for performing the operations described herein. In general, processing device 503 may include any suitable special-purpose processing device specially programmed with processing logic 505 to perform the operations described herein.

[0142] Memory 507 may include, for example, without being limited to, at least one of a read-only memory (ROM), a random access memory (RAM), a flash memory, a dynamic RAM (DRAM) and a static RAM (SRAM), storing computer-readable instructions 517 executable by processing device 303. In general, memory 507 may include any suitable non-transitory computer readable storage medium storing computer-readable instructions 517 executable by processing device 503 for performing the operations described herein. Although one memory device 507 is illustrated in FIG. 5, in some examples, computer system 500 may include two or more memory devices (e.g., dynamic memory and static memory).

[0143] Computer system 500 may include communication interface device 515, for direct communication with other computers (including wired and / or wireless communication), and / or for communication with a network. In some examples, computer system 500 may include display device 513 (e.g., a liquid crystal display (LCD), a touch sensitive display, etc.). In some examples, computer system 500 may include user interface 511 (e.g., an alphanumeric input device, a cursor control device, etc.).

[0144] In some examples, computer system 500 may include data storage device 509 storing instructions (e.g., software) for performing any one or more of the functions described herein. Data storage device 509 may include any suitable non-transitory computer- readable storage medium, including, without being limited to, solid-state memories, optical media and magnetic media.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0145] One or more aspects or features of the subject matter described herein can be realized in digital electronic circuitry, integrated circuitry, specially designed application specific integrated circuits (ASICs), field programmable gate arrays (FPGAs) computer hardware, firmware, software, and / or combinations thereof. These various aspects or features can include implementation in one or more computer programs that are executable and / or interpretable on a programmable system including at least one programmable processor, which can be special or general purpose, coupled to receive data and instructions from, and to transmit data and instructions to, a storage system, at least one input device, and at least one output device. The programmable system or computing system may include clients and servers. A client and server are generally remote from each other and typically interact through a communication network. The relationship of client and server arises by virtue of computer programs running on the respective computers and having a client-server relationship to each other.

[0146] These computer programs, which can also be referred to as programs, software, software applications, applications, components, or code, include machine instructions for a programmable processor, and can be implemented in a high-level procedural language, an object-oriented programming language, a functional programming language, a logical programming language, and / or in assembly / machine language. As used herein, the term “machine-readable medium” refers to any computer program product, apparatus and / or device, such as for example magnetic discs, optical disks, memory, and Programmable Logic Devices (PLDs), used to provide machine instructions and / or data to a programmable processor, including a machine-readable medium that receives machine instructions as a machine-readable signal. The term “machine-readable signal” refers to any signal used to provide machine instructions and / or data to a programmable processor. The machine-readable medium can store such machine instructions non-transitorily, such as for example as would a non-transient solid-state memory or a magnetic hard drive or any equivalent storage medium. The machine-readable medium can alternatively or additionally store such machine instructions in a transient manner, such as for example as would a processor cache or other random access memory associated with one or more physical processor cores.

[0147] To provide for interaction with a user, one or more aspects or features of the subject matter described herein can be implemented on a computer having a display device, such as for example a cathode ray tube (CRT) or a liquid crystal display (LCD) or a light emitting diodeMintz Ref.: 048536-783001WOPCT APPLICATION(LED) monitor for displaying information to the user and a keyboard and a pointing device, such as for example a mouse or a trackball, by which the user may provide input to the computer. Other kinds of devices can be used to provide for interaction with a user as well. For example, feedback provided to the user can be any form of sensory feedback, such as for example visual feedback, auditory feedback, or tactile feedback; and input from the user may be received in any form, including acoustic, speech, or tactile input. Other possible input devices include touch screens or other touch-sensitive devices such as single or multi-point resistive or capacitive trackpads, voice recognition hardware and software, optical scanners, optical pointers, digital image capture devices and associated interpretation software, and the like.

[0148] FIG. 6 illustrates a visualization of a method of identifying low aggregation liganddrug conjugate compounds, in accordance with aspects of the present disclosure. In some aspects, the visualization can be provided on a user interface or a graphical user interface. In some aspects, the graphical user interface can be interactive. FIG. 6 provides an illustration of two ligand-drug conjugates, SN38 conjugate 601 and MMAE conjugate 603 undergoing a seventy (70) nanosecond molecular dynamics simulation. As illustrated, as 70 nanoseconds elapses in a solvated environment, the SN38 conjugate shows an accumulation of higher order aggregates 605. By contrast, as 70 nanoseconds elapses in a solvated environment, the MMAE conjugate shows reversible dimer formation 607. Accordingly, the SN38 conjugate demonstrates a higher propensity to form stable, aggregated complexes and has a higher aggregation score than the MMAE conjugate which forms smaller two-unit dimers in an aggregated state which are seen to be reversed into their respective components. SN38 can be defined as CCC1=C2CN3C(=CC4=C(C3=O)COC(=O)[C@@]4(CC)O)C2=NC5=C1C=C(C=C5)O or 7-Ethyl-10-hydroxycamptothecin. MMAE can be defined as [CC[C@H](C)[C@@H]([C@@H](CC(=O)N1CCC[C@H]1[C@@H]([C@@H](C)C(=O)N[C @H](C)[C@H](C2=CC=CC=C2)O)OC)OC)N(C)C(=O)[C@H](C(C)C)NC(=O)[C@H](C(C)C) NC or (2S)-N-[(2S)-1-[[(3R,4S,5S)-1-[(2S)-2-[(1R,2R)-3-[[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino]-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl]-3-methoxy-5-methyl-1-oxoheptan-4-yl]-methylamino]-3-methyl-1-oxobutan-2-yl]-3-methyl-2-(methylamino)butanamide].

[0149] FIG. 7 illustrates a second visualization of a method of identifying low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure. AsMintz Ref.: 048536-783001WOPCT APPLICATIONshown in FIG. 7, a plurality of ligand-drug conjugates can be modeled and their chemical and molecular structures can be displayed visually in a graphical user interface 701. A simulation can model one or more intra-molecular and / or inter-molecular interactions for each of the liganddrug conjugate compounds for a period of time. In some embodiments, the simulations can be run in a solvated environment. During the simulations, images of the molecules throughout the time-lapse can be generated. For example, 703 illustrates images of molecules during a step of the time-lapse. As shown, one or more of the molecules may appear to be aggregated during the step of the time-lapse. The quantity, strength and reversibility of the aggregated complexes can be used to determine an aggregation score. As shown in FIG. 7 at 705, the aggregated chemical structures of the aggregated complexes can also be illustrated in a visualization. In this manner the reactions that are driving the aggregation can be identified. For example, the visualization 705 shows that C-H pi interactions are driving aggregation.

[0150] FIG. 8 illustrates a third visualization of a method of identifying low aggregation ligand-drug conjugate compounds, in accordance with aspects of the present disclosure. As shown in FIG. 8, distances between atoms in two molecules in a simulation can be displayed over time. For example, the distance can be measured as the distance between the center of mass of one unit of the ligand-drug conjugate and the center of mass of another unit of the ligand-drug conjugate. The distance over time can the propensity of the ligand-drug conjugate molecules to aggregate (i.e., low distance) or stay apart (i.e., high distance). In the illustrated visualization, the compound illustrates a propensity to form an aggregated complex in the initial times of the simulation (e.g., between about 2 and 7 nanoseconds) and then separates. This may be indicative of a ligand-drug conjugate that is forming reversible aggregate complexes.

[0151] The visualizations provided in FIGS. 6-8 advantageously provide a mechanism for viewing and interacting with the molecular structures of ligand-drug conjugates throughout a simulation. In addition to providing a visualization that was not previously available, they may allow for the study of inter-molecular and intra-molecular interactions that are difficult to model and / or visualize.Example #1Abbreviations:

[0152] DMSO - DimethylsulfoxideMintz Ref.: 048536-783001WOPCT APPLICATION

[0153] PS70- molecule of interest for prostate antigen binding

[0154] TIP3P - transferable intermolecular potential with 3 point (water molecules in the molecular dynamics environment)

[0155] NVT - constant temperature molecular dynamics

[0156] HBD- hydrogen bond donors

[0157] HBA- hydrogen bond acceptors

[0158] The experimental conditions were developed in a molecular dynamics simulator which computationally added 11 molecules of solute molecules (~ 14 mM) and then solvated it by DMSO (to roughly reach 5% v / v) and then again solvating it by TIP3P water in an octahedron box.

[0159] PS70, a molecule of interest for prostate antigen binding, and other molecules of interest were prepared using the same protocol above but with a half size system, to speed up the MD simulations, whilst keeping the number of solute molecules the same as the literature standard, miconazole (so that aggregation can be detected clearly). All energy minimizations and MD simulations were performed using the pmemd program from the Amber12 molecular dynamics package.

[0160] The solvated system was minimized in two stages: 1000 steps of minimization whilst applying a 500 kcal / mol restraint force on the solute molecules. A similar minimization procedure was then followed but without applying any restrains on solute atoms.

[0161] The energy -minimized system was heated from 0 to 300 K over 20 ps under NVT conditions using Langevin thermostat; with 10 kcal / mol restraint forces on the ligands atoms. Subsequently, the DMSO molecules were allowed to mix with water for 1.5 ns where the ligand atoms were kept restrained with a 10 kcal / mol force. After the mixing stage, production MD simulations were carried out for 100 ns with coordinates stored every 2 ps.

[0162] The production simulations were conducted under NPT conditions at an average pressure of 1 atm, with a relaxation time of 2 ps and at 300 K temperature, which was controlled by Langevin thermostat using a collision frequency of 1.0 ps-1. All explicit solvent calculations used the particle mesh Ewald (PME) method with a cutoff of 10 A for the long-range electrostatics.

[0163] All MD simulations employed SHAKE to constraint covalent bonds involving hydrogen atoms and a time step of 2 fs.Mintz Ref.: 048536-783001WOPCT APPLICATION

[0164] Three independent replicates for the test systems were done to ensure that the behavior of the system is averaged over three simulations. The “replicates” here refers to simulations of identical structures with identical parameters where only the initial velocities are created randomly according to a Maxwell distribution. The aggregation of two molecules was measured by center of mass of one PS molecule is within a cutoff distance of 3.50 A of center of mass of other PS molecule.

[0165] The types of interaction considered were vdW contacts, hydrogen bonding and p-p stacking. Hydrogen bonding is counted if the distance between HBD and HBA is not more than 2.5 A where the donor angle is not less than 120.0°, and the acceptor angle is not less than 90.0°. A pi-pi interaction is defined as an interaction between two aromatic rings in which either (a) the angle between the ring planes is less than 30° and the distance between the ring centroids is less than 4.4 A (face-to-face), or (b) the angle between the ring planes is between 60° and 120° and the distance between the ring centroids is less than 5.5 A (edge-toface). Pi-cation interaction is defined as an interaction between the cation center and the ring center when the distance between them is not more than 6.6 A and the angle between the ring plane and the line between the cation center and the ring center does not deviate from the perpendicular by more than 30°. Probability distributions of various PS70 clusters (in percentage) with respect to the total number of PS70 molecules present in a given system were measured to understand the probability of forming higher order clusters.

[0166] Subsequent PS compounds were selected with log P ranging from 3.0 to 4.0 so that we make it difficult for aggregation predication. These PS70-like compounds were prepared to be proportional for the previously made system using the same aforementioned procedure. Same MD simulation protocol used in PS70 was carried out to test these ten compounds for their aggregating behavior. The production MD simulation was run for 100 ns since such a timescale appeared sufficient for suggesting aggregation.Example #2

[0167] FIGS. 9-10 illustrates a method of inhibiting growth of tumor cells using low aggregation ligand-drug conjugate compounds identified in accordance with aspects of the present disclosure. As illustrated in FIGS. 9-10, ligand-drug conjugate compounds such as PS-97 were identified as having lower aggregation than MMAE in accordance with the systems andMintz Ref.: 048536-783001WOPCT APPLICATIONmethods described herein. Additionally, the lower aggregation ligand-drug conjugate compounds were associated with lower tumor volumes and the like, indicating more effective targeting endocytosis.

[0168] FIG. 9 illustrates experimental results demonstrating tumor regression, as measured by tumor volume, for various ligand-drug conjugate compounds. The activity of the active conjugate is dose dependent in this xenograft model of tumor inhibition. Notably only tumor tissue expressing PSMA (PIP) is effected by the treatment, indicating a strong targeting effect for the PSMA(+) PIP tumors, while sparing the PSMA(-) FLU tumors

[0169] FIG. 10 illustrates experimental results of on-target accumulation of intact MMAE-conjugate and released MMAE payload, with no MMAE release in circulating plasma during the 5-day time course of the pharmacokinetic experiment.

[0170] In the descriptions above and in the claims, phrases such as “at least one of’ or “one or more of’ may occur followed by a conjunctive list of elements or features. The term “and / or” may also occur in a list of two or more elements or features. Unless otherwise implicitly or explicitly contradicted by the context in which it is used, such a phrase is intended to mean any of the listed elements or features individually or any of the recited elements or features in combination with any of the other recited elements or features. For example, the phrases “at least one of A and B;” “one or more of A and B;” and “A and / or B” are each intended to mean “A alone, B alone, or A and B together.” A similar interpretation is also intended for lists including three or more items. For example, the phrases “at least one of A, B, and C;” “one or more of A, B, and C;” and “A, B, and / or C” are each intended to mean “A alone, B alone, C alone, A and B together, A and C together, B and C together, or A and B and C together.” In addition, use of the term “based on,” above and in the claims is intended to mean, “based at least in part on,” such that an unrecited feature or element is also permissible.

[0171] The subject matter described herein can be embodied in systems, apparatus, methods, and / or articles depending on the desired configuration. The implementations set forth in the foregoing description do not represent all implementations consistent with the subject matter described herein. Instead, they are merely some examples consistent with aspects related to the described subject matter. Although a few variations have been described in detail above, other modifications or additions are possible. In particular, further features and / or variations can beMintz Ref.: 048536-783001WOPCT APPLICATIONprovided in addition to those set forth herein. For example, the implementations described above can be directed to various combinations and subcombinations of the disclosed features and / or combinations and subcombinations of several further features disclosed above. In addition, the logic flows depicted in the accompanying figures and / or described herein do not necessarily require the particular order shown, or sequential order, to achieve desirable results. Other implementations may be within the scope of the following claims.

Claims

Mintz Ref.: 048536-783001WOPCT APPLICATION CLAIMSWhat is claimed is:

1. A method, implemented using a computer system comprising one or more processors and a system memory, of identifying a plurality of low aggregation ligand-drug conjugate compounds:a. receiving, by the computer system, a digital chemical structure for each of a plurality of ligand-drug conjugate compounds;b. calculating, by said one or more processors, an aggregation number for each of said plurality of ligand-drug conjugate compounds;c. ranking, by the computer system, at least a portion of said plurality of ligand-drug conjugate compounds based on said aggregation number; andd. identifying, by the computer system, a plurality of low aggregation liganddrug conjugate compounds based on said ranking, wherein said plurality of low aggregation ligand-drug conjugate compounds is a portion of said plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of a remaining ligand-drug conjugate compounds within said plurality of ligand-drug conjugate compounds.

2. A method of synthesizing a low aggregation ligand-drug conjugate compound: a. receiving, by a computer system, a digital chemical structure for each of a plurality of ligand-drug conjugate compounds, wherein said computer system comprises one or more processors and a system memory;b. calculating, by said one or more processors, an aggregation number for each of said plurality of ligand-drug conjugate compounds;c. identifying, by the computer system, a plurality of low aggregation liganddrug conjugate compounds based on said aggregation number, wherein said plurality of low aggregation ligand-drug conjugate compounds is a portion of said plurality of ligand-drug conjugate compounds having an aggregation number indicative of a predicted molecular aggregation lower than the predicted molecular aggregation of a remaining ligand-drug conjugate compounds within said plurality of ligand-drug conjugate compounds; andMintz Ref.: 048536-783001WOPCT APPLICATIONd. chemically synthesizing said plurality of low aggregation ligand-drug conjugate compound.

3. The method of claim 1 or 2, wherein each of said plurality of ligand-drug conjugate compounds are different and have the structure:wherein:n is 0, 1, 2, 3 or 4;Lis a ligand;Ri is selected from a 6 to 14 membered aryl or a 5 to 13 membered heteroaryl containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur;Ri is unsubstituted or substituted with one or more Rs;Rs, at each occurrence, is independently selected from halogen, — C(O)NH2, — C(O)ORe, — Ci-3 alkyl, — OR?, and a 6 to 10 membered aryl; wherein,Re is hydrogen or C1-3 alkyl;R7 is hydrogen or C1-3 alkyl;R2 is absent or is selected from a 6 to 10 membered cycloalkyl or a 6 to 10 membered aryl;R3 is hydrogen or — C1-C5COOH;R4 is selected from a group consisting of — C1-10 alkyl-, — C2-6 alkenyl-, — C1-3 alkyl-O-Ci.3 alkyl —, — C2-6 alkyl-N(Rs) —, — C2-6 alkyl(N(Rs)(Rs )) —, — N(R8)-C2-6 alkyl —, a 3 to 6 membered cycloalkyl and — Ci-2alkyl-(-OC2H4)i-s-OCi.2 alkyl —; wherein,Rs and Rs- are independently selected from hydrogen, C1-6 alkyl, -C(O)-Ci-4alkyl- aryl or -C(O)-(-C2H4O)I-S-CI-2 alkyl-N(R)(R’), wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Ci-3alkyl or -OCi-salkyl; whereinR and R’ are independently selected from hydrogen, -Ci-6 alkyl or -C(O)-Ci- 4alkyl-aryl, wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Ci-3alkyl or -OCi-salkyl;Mintz Ref.: 048536-783001WOPCT APPLICATIONA is an amino acid or a peptide comprising 2-5 amino acids;A is attached to Q through its C terminal;Q is a self-immolative group; andD is a cytotoxic agent or a therapeutic agent.

4. The method of one of claims 1 to 3, wherein plurality of ligand-drug conjugate compounds is at least 50 different ligand-drug conjugate compounds.

5. The method of one of claims 1 to 3, wherein plurality of ligand-drug conjugate compounds is at least 500 different ligand-drug conjugate compounds.

6. The method of one of claims 1 to 3, wherein plurality of ligand-drug conjugate compounds is at least 5,000 different ligand-drug conjugate compounds.

7. The method of one of claims 1 to 6, wherein said calculating comprises calculating a conformer energy minimization.

8. The method of one of claims 1 to 6, wherein said aggregation number comprises at least one of a propensity to aggregate and / or a predicted aggregation residence time.

9. The method of one of claims 1 to 8, wherein each of said plurality of low aggregation ligand-drug conjugate compounds comprises a ligand covalently bound to a cytotoxic agent or covalently bound to a therapeutic agent, wherein said ligand is capable of binding to a ligand binder under physiological conditions, wherein said ligand binder is PSMA, folate receptor, carbonic anhydrase IX, somatostatin receptor, fibroblast receptor, DLL3, STEAP-1, or PSCA.

10. The method of claim 9, further comprising contacting one of said plurality of low aggregation ligand-drug conjugate compounds with a cell comprising said ligand binder, wherein said low aggregation ligand-drug conjugate compound effectively binds to said ligand binder intracellularly.

11. The method of claim 10, wherein said cell forms part of an organism and wherein said contacting comprises administering said low aggregation ligand-drug conjugate compound to said organism.

12. The method of claim 10 or 11 wherein said low aggregation ligand-drug conjugate compound comprises a detectable moiety.Mintz Ref.: 048536-783001WOPCT APPLICATION13. The method of claim 12 wherein said detectable moiety is a fluorescent detectable moiety.

14. The method of claim 13 wherein said fluorescent detectable moiety is fluorescein.

15. The method of one of claims 12 to 14, further comprising detecting said detectable moiety.

16. The method of claim 15, wherein said detecting comprises quantitating cell surface binding of said low aggregation ligand-drug conjugate compound.

17. The method of one of claims 3 to 16, wherein said plurality of ligand-drug conjugate compounds are different and have the structure:Rn is selected from — C1.3 alkyl-OC(O) — **,— C1-3 alkyl-O-C(O)-N(Ri9)-Ci-5alkyl-N(Ri9)-C(O)— **,— C1-3 alkyl-O-C(O)-N[Ci-5alkyl-N(R20R2i)]-Ci-3alkyl—**,— C1-3alkyl-O-C(O)-Het2-C1-3alkyl-N(R19)-C(O)— **, or— C1-3 alkyl-O-C(O)-N(Ri9)-Ci-5alkyl-N(Ri9)-C(O)— **;wherein ** indicates point of attachment to D andRi$> is selected from H, — C1-3 alkyl or — C1.3 alkyl-O-Ci.3 alkyl-OH;R20 is H or — C1-3 alkyl;R21is H or — C1-C3 alkyl; andHet2is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur;R12 is selected from hydrogen, — C(O)N(R13)R14 or — (-OC2H4)1-10-CH3 R13 is hydrogen;Mintz Ref.: 048536-783001WOPCT APPLICATIONR14 is selected from — C1.5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, — C1-5 alkyl-N(RIS)R16, — C1-5 alkyl-O-Ci-3 alkyl, — (-C2H4O)1-10C2H5, — (-C2H4O)1-10-C2H4-R17or — C1-3 alkyl-Het3-(-C2H4O)1-10-C2H4-R18; whereinR15 is hydrogen or C1-3 alkyl;R16 is hydrogen or C1.3 alkyl; orR15 and Ri6 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with C1-3 alkyl, halogen or OH;R17 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2;Ris is selected from hydrogen or — C(O)NH-C2-salkyl-N(CH3)2;Het3 is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur;ORR13 and R14 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with C1.3 alkyl, — N(CH3)2or — CH2N(CH3)2;R22 is selected from hydrogen, — C(O)N(R23)R24 or — (-OC2H4)i-io-CH3 R23 is hydrogen;R24 is selected from — C1.5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, — C1-5 alkyl-N(R25)R26, — C1-5 alkyl-O-Ci-3 alkyl, — (-C2H4O)1-10C2H5, — (-C2H40)i-io-C2H4-R27 or — C1-3 alkyl-Het3-(-C2H4O)i -10-C2H4-R28; whereinR25 is hydrogen or Cl to C3 alkyl;R26 is hydrogen or Cl to C3 alkyl; orR25 and R26 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfurMintz Ref.: 048536-783001WOPCT APPLICATIONand wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with C1.3 alkyl, halogen or -OH;R27 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2;R28 is selected from hydrogen or — C(O)NH-C2-salkyl-N(CH3)2;Hets is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur;ORR23 and R24 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with C1.3 alkyl, — N(CH3)2or — CH2N(CH3)2.

18. The method of one of claims 2-16 wherein the ligand is 2-(3-((S)-5-amino-1-carboxypentyl)ureido) pentanedioic acid, 2-[3-(l,3-Dicarboxypropyl)ureido]pentanedioic acid or 2-[3-(1-carboxy-2-mercapto-ethyl)ureido]pentanedioic acid.

19. The method of one of claims 3 to 18, wherein said ligand is covalently bound to said cytotoxic agent or said covalently bound to a therapeutic agent through a cleavable linker.

20. The method of claim 19, wherein said cleavable linker is an enzymatically cleavable linker.

21. The method of claim 20, wherein said cleavable linker comprises a val-cit linker moiety.

22. A method comprising:obtaining, by at least one processor communicatively coupled to a database, data comprising a molecular structure for a plurality of ligand-drug conjugate compounds;simulating, by the at least one processor, based on the obtained data, one or more intra-molecular interactions for each of the ligand-drug conjugate compounds; determining, by the at least one processor, an aggregation score for each of the plurality of ligand-drug conjugate compounds based on their respective simulation; andMintz Ref.: 048536-783001WOPCT APPLICATIONidentifying, by the at least one processor, a subset of the plurality of ligand-drug conjugate compounds having low aggregation by comparing the determined aggregation score to a predetermined threshold.

23. The method of claim 22, wherein the data comprising the molecular structure comprises: an atom type, an atom charge, an atom angle, an atom mass, and a number of bonds.

24. The method of claim 22, wherein simulating the one or more intra-molecular interactions comprises modeling behavior of one or more components of the ligand-drug conjugate compounds for a run-time.

25. The method of claim 22, wherein the intra-molecular interactions comprises one or more of van der Waals contacts, hydrogen bonding, pi-cation interactions, and pi-pi interactions.

26. The method of claim 22, wherein the aggregation score comprises a numerical value indicative of a propensity of a unit of the ligand-drug conjugate to have a center of mass within a cutoff distance of the center of mass of another unit of the ligand-drug conjugate.

27. The method of claim 26, wherein the cutoff distance is within 3.5 angstroms.

28. The method of claim 22, wherein identifying the subset of the plurality of liganddrug conjugate compounds having low aggregation further comprises ranking the ligand-drug conjugate compounds based on their respective determined aggregation score.

29. The method of claim 22, wherein the aggregation score comprises percentage value indicative of a probability of the ligand-drug conjugate to form a higher order cluster.

30. The method of claim 22, wherein the predetermined threshold comprises a predetermined aggregation score determined based on historical data for a plurality of liganddrug conjugate compounds.

31. The method of claim 22, wherein each of the plurality of ligand-drug conjugate compounds are different and have the structure:wherein:Mintz Ref.: 048536-783001WOPCT APPLICATIONn is 0, 1, 2, 3 or 4;Lis a ligand;Ri is selected from a 6 to 14 membered aryl or a 5 to 13 membered heteroaryl containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur;Ri is unsubstituted or substituted with one or more Rs;Rs, at each occurrence, is independently selected from halogen, — C(O)NH2, — C(O)ORe, — Ci-3 alkyl, — OR?, and a 6 to 10 membered aryl; wherein,Re is hydrogen or C1-3 alkyl;R7 is hydrogen or C1-3 alkyl;R2 is absent or is selected from a 6 to 10 membered cycloalkyl or a 6 to 10 membered aryl;R3 is hydrogen or — C1-C5COOH;R4 is selected from a group consisting of — C1-10 alkyl-, — C2-6 alkenyl-, — C1-3 alkyl-O-Ci-3 alkyl —, — C2-6 alkyl-N(Rs) —, — C2-6 alkyl(N(Rs)(Rs’)) —, — N(Rs)-C2-6 alkyl —, a 3 to 6 membered cycloalkyl and — Ci-2alkyl-(-OC2H4)i-8-OCi-2 alkyl —; wherein,Rs and Rs’ are independently selected from hydrogen, C1-6 alkyl, -C(O)-Ci-4alkyl-aryl or -C(O)-(-C2H4O)i-s-Ci-2 alkyl-N(R)(R’), wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Ci-3alkyl or -OCi-salkyl; whereinR and R’ are independently selected from hydrogen, -Ci-6 alkyl or -C(O)-Ci-4alkyl-aryl, wherein said aryl is selected from 6 to 14 membered aryl and is optionally substituted by -Ci-3alkyl or -OCi-3alkyl;A is an amino acid or a peptide comprising 2-5 amino acids;A is attached to Q through its C terminal;Q is a self-immolative group; andD is a cytotoxic agent or a therapeutic agent.

32. The method of claim 22, wherein the plurality of ligand-drug conjugate compounds is at least 50 different ligand-drug conjugate compounds.

33. The method of claim 22, wherein plurality of ligand-drug conjugate compounds is at least 500 different ligand-drug conjugate compounds.

34. The method of claim 22, wherein plurality of ligand-drug conjugate compounds is at least 5,000 different ligand-drug conjugate compounds.Mintz Ref.: 048536-783001WOPCT APPLICATION35. The method of claim 22, wherein said simulating, the one or more intra-molecular interactions for each of the ligand-drug conjugate compounds comprises calculating a conformer energy minimization.

36. The method of claim 22, wherein the aggregation score is a predicted aggregation residence time.

37. The method of claim 22, wherein each of said plurality of low aggregation liganddrug conjugate compounds comprises a ligand covalently bound to a cytotoxic agent or covalently bound to a therapeutic agent, wherein said ligand is capable of binding to a ligand binder under physiological conditions, wherein said ligand binder is PSMA, folate receptor, carbonic anhydrase IX, somatostatin receptor, fibroblast receptor, DLL3, STEAP-1, or PSCA.

38. The method of claim 37, further comprising contacting one of said plurality of low aggregation ligand-drug conjugate compounds with a cell comprising said ligand binder, wherein said low aggregation ligand-drug conjugate compound effectively binds to said ligand binder intracellularly.

39. The method of claim 38, wherein said cell forms part of an organism and wherein said contacting comprises administering said low aggregation ligand-drug conjugate compound to said organism.

40. The method of claim 22 wherein the identified subset of the plurality of liganddrug conjugate compounds having low aggregation comprises a detectable moiety.

41. The method of claim 40 wherein said detectable moiety is a fluorescent detectable moiety.

42. The method of claim 41 wherein said fluorescent detectable moiety is fluorescein.

43. The method of claim 42, further comprising detecting said detectable moiety.

44. The method of claim 43, wherein said detecting comprises quantitating cell surface binding of said low aggregation ligand-drug conjugate compound.

45. The method of claim 22, wherein said plurality of ligand-drug conjugate compounds are different and have the structure:Mintz Ref.: 048536-783001WOPCT APPLICATIONRn is selected from — C1.3 alkyl-OC(O) — **,— C1-3 alkyl-O-C(O)-N(Ri9)-Ci-5 alkyl-N(Ri9)-C(O)— **,— C1-3 alkyl-O-C(O)-N[C1-5 alkyl-N(R20R21)]-C1-3 alkyl—**,— C1-3 alkyl-O-C(O)-Het2-Ci-3alkyl-N(Ri9)-C(O)— **, or— C1-3 alkyl-O-C(O)-N(Ri9)-Ci-5alkyl-N(Ri9)-C(O)— **;wherein ** indicates point of attachment to D andRi$> is selected from H, — C1-3 alkyl or — C1.3 alkyl-O-Ci.3 alkyl-OH;R20 is H or — C1-3 alkyl;R21 is H or — C1-C3 alkyl; andHet2is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen or sulfur;R12 is selected from hydrogen, — C(O)N(R13)R14 or — (-OC2H4)1-10-CH3 R13 is hydrogen;R14 is selected from — C1.5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, — C1-5 alkyl-N(R15)R16, — C1-5 alkyl-O-Ci-3 alkyl, — (-C2H4O)1-10C2H5, — (-C2H4O)1-10-C2H4-R17or — C1-3 alkyl-Het3-(-C2H4O)1-10-C2H4-R18; whereinR15 is hydrogen or C1.3 alkyl;R16 is hydrogen or C1-3 alkyl; orR15 and R16 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with C1-3 alkyl, halogen or -OH;R17 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2;Ris is selected from hydrogen or — C(O)NH-C2-salkyl-N(CH3)2;Mintz Ref.: 048536-783001WOPCT APPLICATIONHets is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur;ORR13 and R14 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with C1.3 alkyl, — N(CH3)2or — CH2N(CH3)2;R22 is selected from hydrogen, — C(O)N(R23)R24 or — (-OC2H4)1-10-CH3 R23 is hydrogen;R24 is selected from — C1-5 alkyl, — C2-5 alkenyl, — C2-5 alkynyl, — C1-5 alkyl-N(R25)R26, — C1-5 alkyl-O-C1-3 alkyl, — (-C2H4O)1-10C2H5, — (-C2H4O)1-10-C2H4-R27 or — C1-3 alkyl-Het3-(-C2H4O)1-10-C2H4-R28; whereinR25 is hydrogen or Cl to C3 alkyl;R26 is hydrogen or Cl to C3 alkyl; orR25 and R26 along with the nitrogen atom to which they are attached form a 5 to 6 membered heterocyclic ring, wherein 1 or 2 carbon atoms in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur and wherein the 5 to 6 membered heterocyclic ring is unsubstituted or substituted with C1.3 alkyl, halogen or -OH;R27 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2;R28 is selected from hydrogen or — C(O)NH-C2-5 alkyl-N(CH3)2;Hets is a 5 to 10 membered heterocyclic ring containing one, two or three heteroatoms independently selected from nitrogen, oxygen and sulfur;ORR23 and R24 along with the nitrogen atom to which they are attached form a 4 to 6 membered heterocyclic ring, wherein 1 or 2 carbons in the heterocyclic ring are optionally replaced with additional heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the 4 to 6 membered heterocyclic ring is unsubstituted or substituted with C1.3 alkyl, — N(CH3)2or — CH2N(CH3)2.Mintz Ref.: 048536-783001WOPCT APPLICATION46. The method of one of claim 22 wherein the ligand-drug conjugate includes a ligand, wherein the ligand is 2-(3-((S)-5-amino-1-carboxypentyl)ureido) pentanedioic acid, 2-[3-(1,3-Dicarboxypropyl)ureido]pentanedioic acid or 2-[3-(1-carboxy-2-mercapto-ethyl)ureido]pentanedioic acid.

47. The method of one of claim 22, wherein a ligand in the ligand-drug conjugate is covalently bound to said cytotoxic agent or said covalently bound to a therapeutic agent through a cleavable linker.

48. The method of claim 47, wherein said cleavable linker is an enzymatically cleavable linker.

49. The method of claim 47, wherein said cleavable linker comprises a val-cit linker moiety.

50. The method of claim 22, further comprising:displaying, in at least one graphical user interface communicatively coupled to the at least one processor, the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation.

51. The method of claim 50, wherein displaying the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation further comprises displaying clustered ligand-drug conjugate compounds.

52. The method of claim 22, further comprising:generating, a template for a drug treatment based on the identified subset of the plurality of ligand-drug conjugate compounds having low aggregation.

53. A system comprising:at least one data processor; andmemory coupled to the at least one data processor and storing instructions which, when executed by the at least one data processor, causes the at least one data processor to perform operations comprising a method according to any one of claims 22-52.

54. A non-transitory computer readable storage medium storing computer readable instructions, which, when executed by at least one data processor, causes the at least one data processor to perform operations comprising a method according to any one of claims 22-52.

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