Novel viral production enhancers, methods and uses thereof

Abstract

The present application relates to viral sensitizers. More specifically, the present application relates to compounds, as well as methods of using such compounds as viral sensitizers, specifically for increasing permissiveness of a cell to the production of virus from reverse genetics systems, replicating viruses, and increasing transduction.

Description

NOVEL VIRAL PRODUCTION ENHANCERS, METHODS AND USES THEREOFCROSS REFERENCE TO RELATED APPLICATIONS

[0001] The present application claims the benefit of priority of co-pending U.S. Provisional Patent Application No. 63 / 714,513 which was filed October 31 , 2024, the contents of which are incorporated herein by reference in their entirety.TECHNICAL FIELD

[0002] The present application relates to the field of molecular biology, virology, and genetic engineering and viral sensitizers. Specifically, it focuses on methods and compositions for enhancing or increasing viral production in or from cells, for example through transfection, for the production of various viral vectors, including, but not limited to, lentivirus and adeno- associated virus (AAV). The application contemplates compounds and methods of using such compounds to enhance the yield of replicating viruses or reverse genetics systems geared toward the production of non-replicating or replicating viruses, or their encoded genetic material.BACKGROUND

[0003] Current technologies for viral production in cellular systems face several significant limitations, such as low yield, poor product quality, and inefficiency in the transfection process. Traditional methods often result in insufficient viral titers, which pose challenges for both research and therapeutic applications. Efforts to improve viral production have primarily focused on optimizing culture conditions and transfection protocols, refining plasmid design and enhancing transfection reagents, or cell line and viral vector engineering. Despite these efforts, achieving consistently high levels of viral output remains difficult and context dependent and these efforts have not fully addressed the need for improved viral production efficiency, as high doses are needed for many cell and gene therapy applications, as well as for vaccine production.

[0004] Viral sensitizing compounds are compounds that, for example, increase the production of viruses and viral vectors by increasing the infectivity of cells, for instance by suppressing their innate antiviral programmes. Several compounds with viral sensitizing properties have been previously identified, most of which centrally operate by repressing the type 1 interferon response to increase viral infectivity of treated cells, see for example PCT / CA2010 / 001057, PCT / CA2014 / 050564, PCT / CA2016 / 050061 , PCT / CA2016 / 050062, PCT / CA2017 / 051176, PCT / CA2018 / 051492, and PCT / CA2022 / 050713.

[0005] These compounds have also been successfully applied commercially to improve the production of viral-based products. Small molecules present a number of advantages over other methods to improve virus yields because they are simple additives that can be110518511introduced during the transfection or infection stages of viral production. They integrate seamlessly into existing workflows without requiring significant changes to established protocols, making them user-friendly for current manufacturing processes. Further, small molecule compounds are easily eliminated using typical viral vector purification procedures and do not generally leave residual traces after purification, ensuring that the viral vectors remain pure and suitable for therapeutic use. This characteristic simplifies the downstream purification processes, reducing the need for additional steps to remove contaminants and ensuring regulatory compliance. From this perspective, there is a need to use compounds that have low mutagenic, carcinogenic, and teratogenic potential.

[0006] While different viral sensitizing compounds can be effective in a broad range of applications; their efficacy can fluctuate depending on the context owing to differences in their physicochemical properties as well as their compound-specific off-target effects.

[0007] As such, there is need to provide improved viral sensitizing compounds, for example, for viral-based gene therapies and viral vector production.SUMMARY

[0008] Several compounds that significantly enhance lentivirus production were identified. Compounds also demonstrated activity in enhancing AAV production from HEK293 cells, showing broader applicability across plasmid-based reverse genetics production systems. Given plasmid-based reverse genetics systems have been developed and previously described for many viruses including, but not limited to, influenza A virus (IAV), Ebola virus (EBOV), respiratory syncytial virus (RSV), vesicular stomatitis virus (VSV) and Newcastle disease virus (NDV), the present application also applies to improving the production of both replicating and non-replicating viruses, as well as increasing the spread of replicating viruses, viral transduction, as well as the production of transgenes encoded by such reverse genetics systems.

[0009] It has been shown that the compounds of the present application are effective to increase permissiveness of a cell to the production of virus from a reverse genetics system and thus exhibit viral sensitizing activity, with high potency and versatility.

[0010] Accordingly, the present application includes a method of increasing permissiveness of a cell to a reverse genetics system, comprising administering an effective amount of a compound of the application, or a salt, solvate and / or prodrug thereof, to the cell.

[0011] Accordingly, the present application includes a compound ofthe application, or a salt, solvate and / or prodrug thereof.

[0012] Further included is a method of increasing permissiveness of a cell to a virus, comprising administering an effective amount of a compound of the application, or a salt, solvate and / or prodrug thereof, to the cell.210518511

[0013] The present application also includes a method of increasing permissiveness of a cell to genetic material encoding components of a virus, comprising administering an effective amount of a compound of the application, or a salt, solvate and / or prodrug thereof, to the cell in combination with provision of the genetic material encoding components of a virus to the cell.

[0014] Also included is a method of increasing production of a virus by a cell comprising administering a compound of the application to the cell.

[0015] The present application further includes a method of increasing virus propagation in a cell comprising administering a compound of the application and the virus to the cell.

[0016] Also included is a method of increasing expression of a transgene, including but in no way limited to viral genes, comprising administering a compound of the application and reverse genetics system to a cell.

[0017] Also included is a method of increasing virally-encoded transgene expression comprising administering a compound of the application and the virus to a cell.

[0018] Further included is a method of increasing virus growth in cells comprising administering a compound of the application to the cells in combination with provision of the virus to the cells.

[0019] The present application also includes a method of increasing transduction of a virus into a cell comprising contacting the cell with an effective amount of a compound of the application, or a salt, where applicable, solvate or prodrug thereof, in combination with the virus.

[0020] Other features and advantages of the present application will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating embodiments of the application, are given by way of illustration only and the scope of the claims should not be limited by these embodiments, but should be given the broadest interpretation consistent with the description as a whole.BRIEF DESCRIPTION OF THE DRAWINGS

[0021] The embodiments of the application will now be described in greater detail with reference to the attached drawings in which:

[0022]

[0198] FIG.1A, FIG.1B, FIG.1C, FIG.1D, FIG.1E and FIG.1F show a comparative analysis for enhancement of lentivirus production and producer cell viability for the one hundred thirty-seven compounds of interest. For all panels, the values represent the average of three technical replicates (n=3). An asterisk (*) indicates statistical significance with p-values <0.05 using unpaired, two-tailed t-test. FIG.1A (from left to right, compounds 1-1 , I-2, 1-12, I- 16, 1-41 , I-42, I-44, I-46, I-47, I-49 to I-52, I-68, I-55, I-64 to I-67, I-69, 1-71 to I-75, I-79, I-80, I- 31051851186, 1-81 to I-85, I-87 to I-89, I-93, I-90 to I-92, I-95 to I-97, I-99, 1-104, 1-110, 1-114, 1-116, 1-139, 1-188, 1-159, 1-162, 1-186, 1-187, 1-189 to 1-193, 1-197, 1-194 to 1-196, and 1-198 to I-203) and FIG.1 B (from left to right compounds I-204 to 1-215, I-220, 1-216 to 1-219, 1-221 , I-227, I-222 to I-226, I-228 to I-233, I-238, I-234 to I-237, I-239 to 1-241 , I-245, I-242 to I-244, I-246 to I-249, I-252, I-250, 1-251 , I-253 to I-257, I-260, I-258, I-259, 1-261 to I-265, I-267, I-273, I-268, 1-271 and I-274) are bar graphs illustrating the observed fold enhancement above library vehicle control (1.05% DMSO) in relative light units (RLU), generated through virus-mediated luciferase activity. FIG.1C (from left to right, compounds 1-1 , I-2, 1-12, 1-16, 1-41 , I-42, I-44, I- 46, I-47, I-49 to 1-51 , I-65, I-52, I-55, I-64, I-66 to I-68, I-74, I-69, 1-71 to I-73, I-75, I-79 to I-83, I-87, I-84 to I-86, I-88, I-93, I-89 to I-92, I-95 to I-97, I-99, 1-104, 1-110, 1-114, 1-116, 1-159, I- 162, 1-186, 1-190, 1-187 to 1-189, 1-191 to I-203) and FIG.1 D (from left to right compounds I- 204 to 1-217, I-223, 1-218 to I-222, I-224 to I-227, I-232, I-228 to 1-231 , I-233, I-234, I-239, I- 235 to I-238, I-240 to I-243, I-246, I-244, I-245, I-247 to I-253, I-257, I-254 to I-256, I-258 to I- 265, 1-267, 1-268, 1-271 , 1-273 and I-274) shows fold enhancement above library vehicle control in viral expression units. FIG.1 E (from left to right, compounds 1-1 , I-2, 1-12, 1-16, 1-41 , I-42, I- 44, |-46, I-47, I-49 to I-52, I-55, I-64, I-69, I-65 to I-68, 1-71 to I-75, I-79 to I-93, I-95 to I-97, I- 99, 1-104, 1-110, 1-114, 1-116, 1-139, 1-159, 1-162, 1-186, 1-187 to I-203) and FIG.1 F (from left to right compounds I-204 to I-265, I-267, I-268, 1-271 , I-273 and I-274) shows the relative cell viability in producer HEK293T cells for each of the compounds included in FIG.1 A to FIG.1 D Average cell viability was measured using a resazurin-based cell metabolic activity assay in HEK293T producer cells, 48 hours post-treatment and post-transfection.

[0023] FIG.2 shows lentivirus fold enhancement data, in two HEK293T subclones, for a subset of the exemplary compounds of the application highlighted in FIG.1 , and Table 1. A subset of these compounds were selected for additional testing. This further testing was conducted using the same transient batch transfection methods used for all other HTS studies, at three concentrations (5 .M, 10 .M and 15 .M). FIG.2 is a bar graph showing the fold enhancement of lentivirus production based on virus-mediated luminescent signal over library vehicle control in both HEK293T (solid bars) and HEK293T / 17 (dotted bars) producer cells. The values represent the average of three technical replicates (n=3), with asterisks (*) denoting statistically significant enhancements with p-values <0.05 calculated through unpaired, two-tailed t-test.

[0024] FIG.3A and FIG.3B present bar graphs illustrating greater than 1.1 -fold enhancement of AAV2 production in HEK293T cells as determined by virus-drive luminescent signal for a selected subset of the exemplary compounds of the application (from left to right, FIG.3A compounds 1-1 to I-39, 1-41 , I-52, I-70, 1-71 , I-79, 1-81 , I-89, I-96, 1-100 to 1-103, 1-105 to I-222 and FIG.3B compounds 1-123 to 1-126, 1-128, 1-127, 1-129 to 1-185, I-266, I-270 to I-272).410518511These compounds were tested at a concentration of 10pM, and the values represent the average fold change in viral production compared to the library vehicle control (1 .05% DMSO). This data is averaged from three technical replicates (n=3), and statistical significance is indicated by asterisk (*), with p-values <0.05 (calculated by unpaired, two-tailed t-test). This figure indicates that the identified class of molecules are also effective in enhancing the production of AAV2, suggesting their applicability to a range of plasmid-based reverse genetic systems.

[0025] FIG. 4 shows greater than 1.1 -fold enhancement of AAV2 production in suspension VPC2.0 HEK293 cells with two transfection reagents, FectoVir-AAV and AAV-MAX transfection kit, in 96 well format for a subset of exemplary compounds of the application (I-7 and I-86) at differing peak concentrations. Bars represent fold change of RLU equivalent to functional titer and values represent the average of three technical replicates (n=3). N.T. indicates concentrations not tested for functional titer.

[0026] FIG. 5 shows greater than 1.1 -fold enhancement in replication-competent VSVA51 virus functional titer of (from left to right) I-23, I-29, I-30, I-32, I-34, I-70, 1-81 , I-86, 1-111 , 1-115, 1-117, 1-124, 1-125, 1-127 , 1-129, 1-130 and I-272 (exemplary compounds of the application) treated 786-0 cells at 15 pM relative to control, as measured by the luciferase reporter assay. The values represent the average of three technical replicates (n=3).

[0027] FIG. 6 shows greater than 1.1-fold enhancement of lentivirus-encoded GFP expression in human primary pan T-cells (CD3+) treated with 15 pM of (from left to right) I-9, I-20, 1-26, I- 27, I-28, I-30, I-34, I-39, I-44, I-70, 1-81 , I-82, I-96, 1-107, 1-110, 1-111 , 1-112, 1-114, 1-115, 1-116, 1-117, 1-118, 1-119, 1-120, 1-121 , 1-122, 1-124, 1-125, 1-126, 1-127, 1-128, 1-129 and 1-130 (exemplary compounds of the application) relative to control. GFP expression was determined by quantification of mean fluorescence intensity of GFP following transduction of lentivirus - encoding GFP in T-cells. The values represent the average based on two technical replicates (n=2).

[0028] FIG. 7 shows greater than 2-fold increase in % GFP-positive cells equivalent to lentiviral transduction of human primary pan T-cells (CD3+) treated with I-82, 1-108, 1-110, I- 117, 1-121 , 1-126 and 1-130 (exemplary compounds of the application) at 15 pM as measured by flow cytometry. The values represent the average fold change enhancement of % transduction by GFP expression based on two technical replicates (n=2).DETAILED DESCRIPTIONI. Definitions

[0029] Unless otherwise indicated, the definitions and embodiments described in this and other sections are intended to be applicable to all embodiments and aspects of the present 510518511application herein described for which they are suitable as would be understood by a person skilled in the art.

[0030] As used in this application and claim(s), the words "comprising" (and any form of comprising, such as "comprise" and "comprises"), "having" (and any form of having, such as "have" and "has"), "including" (and any form of including, such as "include" and "includes") or "containing" (and any form of containing, such as "contain" and "contains"), are inclusive or open-ended and do not exclude additional, unrecited elements or process steps.

[0031] The term “consisting” and its derivatives as used herein are intended to be closed terms that specify the presence of the stated features, elements, components, groups, integers, and / or steps, and also exclude the presence of other unstated features, elements, components, groups, integers and / or steps.

[0032] The term “consisting essentially of’, as used herein, is intended to specify the presence of the stated features, elements, components, groups, integers, and / or steps as well as those that do not materially affect the basic and novel characteristic(s) of these features, elements, components, groups, integers, and / or steps.

[0033] The terms "about", “substantially” and “approximately” as used herein mean a reasonable amount of deviation of the modified term such that the end result is not significantly changed. These terms of degree should be construed as including a deviation of at least ±5% of the modified term if this deviation would not negate the meaning of the word it modifies or unless the context suggests otherwise to a person skilled in the art.

[0034] As used in the present application, the singular forms “a”, “an” and “the” include plural references unless the content clearly dictates otherwise. For example, an embodiment including “a compound” should be understood to present certain aspects with one compound, or two or more additional compounds.

[0035] In embodiments comprising an “additional” or “second” component, such as an additional or second compound, the second component as used herein is chemically different from the other components or first component. A “third” component is different from the other, first, and second components, and further enumerated or “additional” components are similarly different.

[0036] The term “and / or” as used herein means that the listed items are present, or used, individually or in combination. In effect, this term means that “at least one of’ or “one or more” of the listed items is used or present. The term “and / or” with respect to salts, solvates and / or prodrugs thereof means that the compounds of the application exist as individual salts, solvates and prodrugs, as well as a combination of, for example, a salt of a solvate of a compound of the application.610518511

[0037] The term “compound of the application” or “compound of the present application” and the like, including plurals thereof, as used herein refers to the compounds listed in Table 1 , as well as salts, solvates and / or prodrugs thereof.

[0038] The term “composition of the application” or “composition of the present application” and the like as used herein refers to a composition comprising one or more compounds of the application and optionally one or more viruses.

[0039] The term “suitable” as used herein means that the selection of the particular composition or conditions would depend on the specific steps to be performed, the identity of the components to be transformed and / or the specific use for the compositions, but the selection would be well within the skill of a person trained in the art.

[0040] The present description refers to a number of chemical terms and abbreviations used by those skilled in the art. Nevertheless, definitions of selected terms are provided for clarity and consistency.

[0041] The term “cell” as used herein refers to a single cell or a plurality of cells and includes a cell in a cell culture or a cell in a subject.

[0042] The term “subject” as used herein includes all members of the animal kingdom including mammals, and suitably refers to humans. Thus the methods and uses of the present application are applicable to both human therapy and veterinary applications.

[0043] The term “pharmaceutically acceptable” means compatible with the treatment of subjects, for example humans.

[0044] The term “pharmaceutically acceptable carrier” means a non-toxic solvent, dispersant, excipient, adjuvant or other material which is mixed with the active ingredient in order to permit the formation of a pharmaceutical composition, i.e., a dosage form capable of administration to a subject.

[0045] The term “pharmaceutically acceptable salt” means either an acid addition salt or a base addition salt which is suitable for, or compatible with the treatment of subjects.

[0046] The term “solvate” as used herein means a compound, or a salt and / or prodrug of a compound, wherein molecules of a suitable solvent are incorporated in the crystal lattice. A suitable solvent is physiologically tolerable at the dosage administered.

[0047] The term “prodrug” as used herein means a compound, or salt and / or solvate of a compound, that, after administration, is converted into an active drug.

[0048] The term “treating” or “treatment” as used herein and as is well understood in the art, means an approach for obtaining beneficial or desired results, including clinical results.

[0049] The term “administered” as used herein means administration of a therapeutically effective amount of a compound, or one or more compounds, or a composition of the application to a cell either in cell culture or in a subject. As used herein, “administration” is an710518511example of “contacting” a cell either in cell culture or in a subject compound with one or more compounds, or a composition of the application.

[0050] As used herein, the term “effective amount” or “therapeutically effective amount” means an amount of a compound, or one or more compounds, of the application that is effective, at dosages and for periods of time necessary to achieve a desired result.

[0051] The term “cancer” as used herein refers to cellular-proliferative disease states.

[0052] The terms “sensitization” or “sensitizing” as used herein, in the context of a cell, refers to a decreased or altered cellular response to an outside agent such that the outside agent has an increased or altered effect on the cell. Where the outside agent is a virus, the terms “sensitization” or “sensitizing” (also referred to as “viral sensitization” or “viral sensitizing”) refers to a decreased or altered cellular response to the virus, thereby increasing the ability of the virus to infect and / or replicate in the cell. Where the outside agent is genetic material encoding a virus, the terms “sensitization” or “sensitizing” (also referred to as “viral sensitization” or “viral sensitizing”) refers to a decreased or altered cellular response to the genetic material, thereby increasing ability of the genetic material to transfect and / or expressed in the cell.

[0053] The term “permissiveness” as used herein, in the context of a cell, refers to an increase in the uptake of an outside agent by the cell and / or an increase in the activity of the outside agent in the cell and / or a reduction in cellular defenses that would otherwise inhibit the expression, replication or stability of the outside agent in the cell. When the outside agent is a virus, “permissiveness” refers to the ability of a virus to infect and / or transduce a cell. When the outside agent is genetic material, “permissiveness” refers to the ability of genetic material; to transfect a cell and / or get processed by a cell into viral particle(s).

[0054] The terms “reverse genetics” and “reverse genetic systems”, as used herein, refer to a method or platform for studying gene function and producing viruses and proteins by first identifying or manipulating a known nucleotide sequence and subsequently observing the phenotypic effects of these manipulations. As used herein, “reverse genetic systems” include any method of providing a nucleic acid to a cell, including transfection, lipofection, electroporation, viral transduction and microinjection. “Reverse genetics” systems are contrasted with “forward genetics” approaches where a mutant cell or organism is identified, and the genetic changes associated with the phenotype are determined. Reverse genetics can include directed gene deletions and point mutations, for example.

[0055] In the context of virus and protein production, reverse genetics systems enable the construction and recovery of virus particles from cloned DNA or RNA. This allows for the generation of recombinant viruses with specific mutations or engineered traits, facilitating the study of viral pathogenesis, vaccine development, cell and gene therapy development and antiviral drug testing. Additionally, reverse genetics systems are used to produce proteins by 810518511manipulating gene sequences to express desired proteins in various host cells, aiding in the development of therapeutic proteins, enzymes, and biopharmaceuticals.

[0056] The term “plasmid-based reverse genetics systems”, as used herein, refers to a method or platform as described above for “reverse genetics systems” but involves the generation of a gene product, including but not limited to recombinant virus particles, using one or more plasmids comprising at least one nucleic acid of interest.

[0057] The terms “transduction” or “transducing” as used herein, refer to the introduction of a virus containing an exogenous nucleic acid into a cell leading to expression of the nucleic acid. The nucleic acid is optionally a gene (also referred to as a transgene). The gene is optionally a therapeutic gene.

[0058] The term “genetic material encoding components of a virus” or “one or more nucleic acids” encoding components of a virus refers to a nucleic acid, and chemically modified variants thereof, that carry viral-like sequences of nucleotides. The sequences encode viral- like proteins and / or functional sequences for targeting, integration, promotion, etc.

[0059] The term “increase” or “increasing” as used herein refers to any detectable increase or enhancement in a function or characteristic in the presence of one or more test variables, compared to otherwise the same conditions except in the absence of the one or more test variables.

[0060] The term “decrease” or “decreasing” as used herein refers to any detectable decrease or reduction in a function or characteristic in the presence of one or more test variables, compared to otherwise the same conditions except in the absence of the one or more test variables.II. Compounds and Compositions of the Application

[0061] It has been shown herein that the compounds listed in Table 1 of the present application (compounds of the application) are effective to increase permissiveness of a cell to nucleic acids suitable for production of a virus, and thus exhibit viral sensitizing activity, with high potency and versatility.

[0062] Accordingly, the present application includes a composition comprising a compound of the application (i.e. a compound as listed in Table 1), or a pharmaceutically acceptable salt (where applicable), solvate and / or prodrug thereof and a virus or genetic material encoding components of the virus, optionally with a pharmaceutically acceptable carrier or excipient.910518511Table 1 : Compounds of the Application.105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511105185111051851110518511or a pharmaceutically acceptable salt, solvate and / or prodrug thereof.10518511

[0063] In some embodiments, the salt is an acid addition salt or a base addition salt. In some embodiments, for pharmaceutical methods and uses on human or animal subjects, the salt is a pharmaceutically acceptable salt (where applicable). The selection of a suitable salt may be made by a person skilled in the art. Suitable salts include acid addition salts that may, for example, be formed by mixing a solution of a compound with a solution of a pharmaceutically acceptable acid such as hydrochloric acid, sulfuric acid, acetic acid, trifluoroacetic acid, or benzoic acid. Additionally, acids that are generally considered suitable for the formation of pharmaceutically useful salts from basic pharmaceutical compounds are discussed, for example, by P. Stahl et al, Camille G. (eds.) and Handbook of Pharmaceutical Salts. Properties, Selection and Use. (2002) Zurich: Wiley VCH; S. Berge et al, Journal of Pharmaceutical Sciences 197766(1) 1-19; P. Gould, International J. of Pharmaceutics (1986) 33 201-217; Anderson et al, The Practice of Medicinal Chemistry (1996), Academic Press, New York; and in The Orange Book (Food & Drug Administration, Washington, D.C. on their website).

[0064] An acid addition salt suitable for, or compatible with, the treatment of subjects is any non-toxic organic or inorganic acid addition salt of any basic compound. Basic compounds that form an acid addition salt include, for example, compounds comprising an amine group. Illustrative inorganic acids which form suitable salts include hydrochloric, hydrobromic, sulfuric, nitric and phosphoric acids, as well as acidic metal salts such as sodium monohydrogen orthophosphate and potassium hydrogen sulfate. Illustrative organic acids which form suitable salts include mono-, di- and tricarboxylic acids. Illustrative of such organic acids are, for example, acetic, trifluoroacetic, propionic, glycolic, lactic, pyruvic, malonic, succinic, glutaric, fumaric, malic, tartaric, citric, ascorbic, maleic, hydroxymaleic, benzoic, hydroxybenzoic, phenylacetic, cinnamic, mandelic, salicylic, 2-phenoxybenzoic, p- toluenesulfonic acid and other sulfonic acids such as methanesulfonic acid, ethanesulfonic acid and 2-hydroxyethanesulfonic acid. In some embodiments, exemplary acid addition salts also include acetates, ascorbates, benzoates, benzenesulfonates, bisulfates, borates, butyrates, citrates, camphorates, camphorsulfonates, fumarates, hydrochlorides, hydrobromides, hydroiodides, lactates, maleates, methanesulfonates (“mesylates”), naphthalenesulfonates, nitrates, oxalates, phosphates, propionates, salicylates, succinates, sulfates, tartarates, thiocyanates, toluenesulfonates (also known as tosylates) and the like. In some embodiments, the mono- or di-acid salts are formed and such salts exist in either a hydrated, solvated or substantially anhydrous form. In general, acid addition salts are more soluble in water and various hydrophilic organic solvents and generally demonstrate higher melting points in comparison to their free base forms. The selection criteria for the appropriate salt will be known to one skilled in the art. Other non-pharmaceutically acceptable salts such as4410518511but not limited to oxalates may be used, for example in the isolation of compounds of the application for laboratory use, or for subsequent conversion to a pharmaceutically acceptable acid addition salt.

[0065] A base addition salt suitable for, or compatible with, the treatment of subjects is any non-toxic organic or inorganic base addition salt of any acidic compound. Acidic compounds that form a basic addition salt include, for example, compounds comprising a carboxylic acid group. Illustrative inorganic bases which form suitable salts include lithium, sodium, potassium, calcium, magnesium or barium hydroxide as well as ammonia. Illustrative organic bases which form suitable salts include aliphatic, alicyclic or aromatic organic amines such as isopropylamine, methylamine, trimethylamine, picoline, diethylamine, triethylamine, tripropylamine, ethanolamine, 2-dimethylaminoethanol, 2-diethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, ethylenediamine, glucosamine, methylglucamine, theobromine, purines, piperazine, piperidine, N-ethylpiperidine, polyamine resins and the like. Exemplary organic bases are isopropylamine, diethylamine, ethanolamine, trimethylamine, dicyclohexylamine, choline and caffeine. The selection of the appropriate salt may be useful, for example, so that an ester functionality, if any, elsewhere in a compound is not hydrolyzed. The selection criteria for the appropriate salt will be known to one skilled in the art. In some embodiments, exemplary basic salts also include ammonium salts, alkali metal salts such as sodium, lithium and potassium salts, alkaline earth metal salts such as calcium and magnesium salts, salts with organic bases (for example, organic amines) such as dicyclohexylamine, Abutyl amine, choline and salts with amino acids such as arginine, lysine and the like. Basic nitrogen containing groups may be quarternized with agents such as lower alkyl halides (e.g., methyl, ethyl and butyl chlorides, bromides and iodides), dialkyl sulfates (e.g., dimethyl, diethyl and dibutyl sulfates), long chain halides (e.g., decyl, lauryl and stearyl chlorides, bromides and iodides), aralkyl halides (e.g., benzyl and phenethyl bromides) and others. Compounds carrying an acidic moiety can be mixed with suitable pharmaceutically acceptable salts to provide, for example, alkali metal salts (e.g., sodium or potassium salts), alkaline earth metal salts (e.g., calcium or magnesium salts) and salts formed with suitable organic ligands such as quaternary ammonium salts. Also, in the case of an acid (-COOH) or alcohol group being present, pharmaceutically acceptable esters can be employed to modify the solubility or hydrolysis characteristics of the compound.

[0066] All such acid salts and base salts are intended to be pharmaceutically acceptable salts within the scope of the application and all acid and base salts are considered equivalent to the free forms of the corresponding compounds for purposes of the application. In addition, when a compound of the application contains both a basic moiety, such as, but not limited to an4510518511aliphatic primary, secondary, tertiary or cyclic amine, an aromatic or heteroaryl amine, pyridine or imidazole and an acidic moiety, such as, but not limited to tetrazole or carboxylic acid, zwitterions (“inner salts”) may be formed and are included within the terms “salt(s)” as used herein. It is understood that certain compounds of the application may exist in zwitterionic form, having both anionic and cationic centers within the same compound and a net neutral charge. Such zwitterions are included within the application. It is also understood by a person skilled in the art that not all compounds of the application contain a basic and / or acidic moiety to allow the formation of pharmaceutically acceptable salts, therefore no salt forms of such compounds are intended to be included within the present application.

[0067] Solvates of compounds of the application include, for example, those made with solvents that are pharmaceutically acceptable. Examples of such solvents include water (resulting solvate is called a hydrate) and ethanol and the like. Suitable solvents are physiologically tolerable at the dosage administered.

[0068] It is understood and appreciated that in some embodiments, compounds of the present application may have at least one chiral center and therefore can exist as enantiomers and / or diastereomers. It is to be understood that all such isomers and mixtures thereof in any proportion are encompassed within the scope of the present application. It is to be further understood that while the stereochemistry of the compounds may be as shown in any given compound listed herein, such compounds may also contain certain amounts (for example, less than 20%, suitably less than 10%, more suitably less than 5%) of compounds of the present application having an alternate stereochemistry. It is intended that any optical isomers, as separated, pure or partially purified optical isomers or racemic mixtures thereof are included within the scope of the present application.

[0069] In some embodiments, the compounds of the present application can also include tautomeric forms, such as keto-enol tautomers and the like. Tautomeric forms can be in equilibrium or sterically locked into one form by appropriate substitution. It is intended that any tautomeric forms which the compounds form, as well as mixtures thereof, are included within the scope of the present application.

[0070] The compounds of the present application may further exist in varying amorphous and polymorphic forms and it is contemplated that any amorphous forms, polymorphs, or mixtures thereof, which form are included within the scope of the present application.

[0071] The compounds of the present application may further be radiolabeled and accordingly all radiolabeled versions of the compounds of the application are included within the scope of the present application. The compounds of the application also include those in which one or more radioactive atoms are incorporated within their structure.4610518511

[0072] In some embodiments, the compounds of the present application are suitably formulated in a conventional manner into compositions using one or more carriers, optionally in combination with one or more reverse genetics systems encoding viral and non-viral components. Accordingly, the present application also includes a composition comprising one or more compounds of the application and a carrier. The present application also includes a composition comprising one or more compounds of the application, one or more reverse genetics systems and a carrier.

[0073] In some embodiments a compound of the application is coupled with soluble polymers as targetable drug carriers. Such polymers include, for example, polyvinylpyrrolidone, pyran copolymer, polyhydroxypropylmethacrylamide-phenol, polyhydroxy-ethylaspartamide-phenol, or polyethyleneoxide-polylysine substituted with palmitoyl residues. Furthermore, in some embodiments, a compound of the application is coupled to a class of biodegradable polymers useful in achieving controlled release of a drug, for example, polylactic acid, polyglycolic acid, copolymers of polylactic and polyglycolic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacrylates and crosslinked or amphipathic block copolymers of hydrogels.

[0074] The compositions of the application are particularly amenable to administration with the aid of nano-carrier systems, such as liposomes, micelles, nanoparticles, nano-emulsions, lipidic nano-systems and the like (see for example, Bhat, M. et al. Chem. and Phys, of Lipids, 2021 , 236, 105053). Accordingly, the present application includes a composition comprising one or more compounds of the application, optionally one or more reverse genetics systems suitable to the production of viruses and one or more components of a nano-carrier system.

[0075] Also included is a kit comprising the compound of the application and a) a reverse genetics system suitable for the production of a virus, suitably an attenuated or genetically modified virus, a gene therapy vector, b) one or more production cells; c) a pharmaceutically acceptable carrier, diluent or excipient; d) cell culture media; f) a transfection reagent g) an enhancer and / or booster, h) a cell culture plate, multi-well dish or large-scale cell culture system i) an apparatus to deliver the viral sensitizing compound to a cell, medium or to a subject; j) instructions for using the viral sensitizing agent; or k) a carrier diluent or excipient, or any combination of a)-k).

[0076] In some embodiments, which are not meant to be limiting in any manner, included is a kit comprising a compound of the application and a medium for growing, culturing or transfecting cells with reverse genetics system suitable for producing a virus and optionally, one or more cells which are capable of producing virus from reverse genetics systems.4710518511

[0077] In some embodiments, the kit comprises instructions for using any component or combination of components and / or practicing any method as described herein.

[0078] In the above, the term "a compound" also includes embodiments wherein one or more compounds are referenced.III. Methods and Uses of the Application

[0079] The application also provides uses and methods relating to the compounds and compositions of the application described herein.

[0080] The compounds and compositions of the application have been shown to increase production of a virus by a cell. Thus, the compounds and compositions exhibit viral sensitizing activity, with high potency and versatility. Accordingly, the compounds and compositions of the application are useful for increasing permissiveness of a cell to one or more nucleic acids suitable for producing a virus and encoded transgene(s) useful for treating diseases, disorders or conditions. The compounds and compositions of the application are also useful for increasing permissiveness of a cell to genetic material encoding components of a virus, increasing virus production, increasing transduction, increasing reverse genetics system- encoded transgene expression, increasing virally-encoded transgene expression and increasing virus growth and / or spread.

[0081] To be clear, in the below methods and uses, the term “a compound of the application, or a salt, solvate and / or prodrug thereof” also includes embodiments wherein one or more compounds of the application, or a salt, solvate and / or prodrug thereof, are referenced or formulated in a composition as described herein.Methods and uses of increasing permissiveness of a cell to one or more nucleic acids

[0082] Accordingly, the present application includes a method, optionally an in vitro method, of increasing permissiveness of a cell to one or more nucleic acids, comprising administering an effective amount of a compound of the application, or a salt, solvate and / or prodrug thereof, to the cell.

[0083] Also provided is use of a compound of the application, or a salt, solvate and / or prodrug thereof, to increase permissiveness of a cell to one or more nucleic acids. In another embodiment, a compound of the application, or a salt, solvate and / or prodrug thereof, is used in the manufacture of a therapeutic to increase permissiveness of a cell to one or more nucleic acids. In yet another embodiment, a compound of the application, or a salt, solvate and / or prodrug thereof, is for use in increasing permissiveness of a cell to one or more nucleic acids.4810518511

[0084] The cell is optionally in vivo, ex vivo or in vitro. In some embodiments, the cell is a cell in vitro, for example a cell line or a cell culture. In some embodiments, the cell is an in vivo cell in a subject.

[0085] As used herein, the expression “contacting” refers to any means for exposing a cell or a subject to a compound or administering a compound to a cell or a subject. For example, a cell in cell culture may be contacted with a compound by adding the compound to the culture medium.

[0086] In some embodiments, the compound of the application, or a salt, solvate and / or prodrug thereof, is contacted with the cell or subject prior, concurrent with, or after provision of the one or more nucleic acids to the cell. Methods of providing nucleic acids for uptake by a cell can include viral infection and / or a non viral process, is generally known as transfection and include any a carrier or method commonly known to a person skilled in the art. In no way limiting, this includes transfection using PEI or lipid-based reagents, electroporation, and nanoparticles, as is generally known in the art.

[0087] In some embodiments, the one of more nucleic acids encode components of a virus. The term “components of a virus” refers to nucleic acids, and chemically modified variants thereof, that comprise or consist of viral and / or viral-like sequences. The sequences can encode viral proteins, viral-like proteins and / or functional sequences for targeting, integration, promotion, etc.

[0088] In some embodiments, the nucleic acids are comprised in one or more plasmids, for example DNA plasmids. In some embodiments, the one or more nucleic acids encoding components of a virus are present on a plasmid.

[0089] Delivery of nucleic acids to a cell is generally described as transfection. Transfection efficiency refers to the degree to which a supplied source of genetic material is taken up and functional for its intended purpose in a cell.

[0090] Such nucleic acids may be delivered to the cell directly, or they may be provided in a carrier to enhance delivery and uptake by the cell. Examples of carriers include diverse polymers known in the art, which may be designed in a variety of nanoparticle formats, either loosely organized or more precision designed. Common carriers of genetic material are described, for example, in Cullis and Hope (2017) and in Mitchell et al. (2021).

[0091] In one example, lentivirus, gamma-Retrovirus, or AAV are produced following transfection of plasmids encoding lentivirus, gamma-Retrovirus, or AAV viral or viral-like sequences into a cell.4910518511

[0092] In some embodiments, the one or more nucleic acids are DNA. In some embodiments, the one or more nucleic acids comprise one or more DNA plasmids. In some embodiments, one or more nucleic acids comprise alternatives to DNA plasmids for example but not limited to Doggy bone DNA, Bacterial artificial chromosomes (BACs), Yeast artificial chromosomes (YACs), P1-derived artificial chromosomes (PACs), Phagemids, or Synthetic chromosomes.

[0093] In some embodiments, the method is used for production of a virus that encodes a non-viral gene product.

[0094] In some embodiments, the method is used for the production of a therapeutic.

[0095] In some embodiments, the virus is an interferon (IFN)-sensitive virus.

[0096] In some embodiments, the virus is a retrovirus (for example a lentivirus (LV)), an attenuated virus, a genetically modified virus, a non-replicating virus, a replicating virus or an oncolytic virus.

[0097] In some embodiments, virus is a non-replicating viral vector, optionally an adenovirus (Ad), an adeno-associated virus (AAV) or lentivirus (LV).

[0098] In some embodiments, the LV is pseudo-typed with alternative glycoproteins including but not limited to VSV glycoprotein, Baboon Endogenous virus glycoprotein, Murine Lukemia Virus glycoprotein, Sindbis virus glycoprotein, Ebola virus glycoproetien, Rabies virus glycoprotein, Measles virus glycoproteins, LCMV virus glycoprotein, Junin virus glycoprotein.

[0099] In some, embodiments, the virus is a double-stranded DNA virus, including but not limited to herpes simplex virus (HSV), vaccinia virus, or viral vectors derived therefrom.

[0100] In some embodiments, the virus is a gene therapy vector. As used herein, the term “gene therapy vector” refers to a viral vector designed to deliver therapeutic genetic material to a cell or subject. Examples of gene therapy vectors include, but are not limited to human Ad5, Ad3, Ad11 , Ad35, canine Ad2, chimp Ad26, chimp AdOx1 , or recombinant serotypes thereof, AAV serotypes 1-9 or recombinant serotypes thereof, Lentivirus, gammaretrovirus, Annellovirus, or Baculovirus.

[0101] In some embodiments, the virus is a component of a vaccine such as, but not limited to, a live attenuated vaccine such as, measles, mumps, rubella, rotavirus, chickenpox, yellow fever or a viral vector vaccine encoding a vaccine antigen transgene such as rVSVAG- ZEBOV-GP (Ervebo) or ChadOx1-S (Vaxzevria).

[0102] In some embodiments, the virus is a rhabdovirus, a togavirus, or an orthomyxovirus.5010518511

[0103] In some embodiments, rhabdovirus is vesicular stomatitis virus (VSV), engineered mutants of VSV (VSVA51), an oncolytic non-VSV rhabdovirus, or a recombinant oncolytic non-VSV rhabdovirus encoding one or more of rhabdoviral N, P, M, G and / or L protein, or variant thereof including chimeras and fusion proteins thereof, having an amino acid identity of at least or at most 20, 30, 40, 50, 60, 65, 70, 75, 80, 85, 90, 92, 94, 96, 98, 99, 100%, including all ranges and percentages there between, to the N, P, M, G and / or L protein of Arajas virus, Chandipura virus, Cocal virus, Isfahan virus, Maraba virus, Piry virus, Vesicular stomatitis Alagoas virus, BeAn 157575 virus, Boteke virus, Calchaqui virus, Eel virus American, Gray Lodge virus, Jurona virus, Klamath virus, Kwatta virus, La Joya virus, Malpais Spring virus, Mount Elgon bat virus, Perinet virus, Tupaia virus, Farmington, Bahia Grande virus, Muir Springs virus, Reed Ranch virus, Hart Park virus, Flanders virus, Kamese virus, Mosqueiro virus, Mossuril virus, Barur virus, Fukuoka virus, Kern Canyon virus, Nkolbisson virus, Le Dantec virus, Keuraliba virus, Connecticut virus, New Minto virus, Sawgrass virus, Chaco virus, Sena Madureira virus, Timbo virus, Almpiwar virus, Aruac virus, Bangoran virus, Bimbo virus, Bivens Arm virus, Blue crab virus, Charleville virus, Coastal Plains virus, DakArK 7292 virus, Entamoeba virus, Garba virus, Gossas virus, Humpty Doo virus, Joinjakaka virus, Kannamangalam virus, Kolongo virus, Koolpinyah virus, Kotonkon virus, Landjia virus, Manitoba virus, Marco virus, Nasoule virus, Navarro virus, Ngaingan virus, Oak-Vale virus, Obodhiang virus, Oita virus, Quango virus, Parry Creek virus, Rio Grande cichlid virus, Sandjimba virus, Sigma virus, Sripur virus, Sweetwater Branch virus, Tibrogargan virus, Xiburema virus, Yata virus, Rhode Island, Adelaide River virus, Berrimah virus, Kimberley virus, or Bovine ephemeral fever virus.

[0104] In some embodiments, the togavirus is sindbis, semliki forest virus or M1 virus.

[0105] In some embodiments, the orthomyxovirus is influenza A, influenza B, influenzaC, influenza D, isavirus, thogotovirus or quanranjavirus.

[0106] In some embodiments, the cell is a eukaryotic cell, for example a human or other mammalian cell. In some embodiments, the cell is a prokaryotic cell.

[0107] In some embodiments, the cell is one or more types of immortalized cells in vitro or in vivo from any cell, cell line, tissue or organism, not limited to, human, rat, mouse, cat, dog, pig, primate, horse and the like, for example, without limitation: Vero, HEK-293 cells or derivatives, HEK293T cells, VPC 1.0, VPC 2.0, Expi293F cells, EB-66 cells, EbX cells, PER. C6 cells, AGE1.CR, Agel.O S, Agel.HN, Agel.RO, Q0R2 / 2E11 , UMNSAH-DF1 , CHO, hybridoma cells, sf9 cells, HT1080 cells or R4 cells.

[0108] In some embodiments, permissiveness of the cell to the one or more nucleic acids is increased 1.1 fold or more, 1.2 fold or more, 1.5 fold or more, 2 fold or more, 2.5 fold5110518511or more, 3 fold or more, 5 fold or more, or 10 fold or more, e.g., compared to permissiveness of the cell, or a comparable cell (also referred to herein as a control cell) prior to, or in absence of, the cell being contacted with a compound or composition of the application. In some cases, the method includes measuring the permissiveness to the cell to the one or more nucleic acids or measuring the production of viruses by the cell.Methods and uses of increasing production of viruses

[0109] The present application also includes a method, optionally an in vitro method, of increasing production of a virus by a cell comprising administering a compound of the application, or a salt, solvate and / or prodrug thereof, to the cell. Also included is a use of a compound of the application, or a salt, solvate and / or prodrug thereof, for increasing production of a virus by a cell, as well as a compound of the application, or a salt, solvate and / or prodrug thereof, for use in increasing production of a virus by a cell.

[0110] In some embodiments, the method or use comprises growing the virus in an appropriate medium in the presence of a compound of the application.

[0111] In some embodiments, the cell is a viral production cell, namely a cell that is used to produce a virus. Examples of viral production cells include, but are not limited to, Vero, HEK-293 or derivatives, HEK293T, VPC 1.0, VPC 2.0, EB-66, EbX, PER. C6, AGE1.CR, Agel.O S, Agel.HN, Agel.RO, Q0R2 / 2E11 , UMNSAH-DF1 , CHO, CEF, MRC-5, WI-38, BHK21 , Hela, A549, R4 cells and sf9 cells.

[0112] In some embodiments, the virus produced by the cell is an oncolytic virus, gene therapy vector or a vaccine.

[0113] In some embodiments, the virus is among those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0114] In some embodiments, the cells are those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0115] In some embodiments, production of the virus increased 1.1 fold or more, 1.2 fold or more, 1.5 fold or more, 2 fold or more, 2.5 fold or more, 3 fold or more, 5 fold or more, or 10 fold or more, e.g., compared to production of the virus by the cell, or a comparable cell, prior to the method or in the absence of the method. In some cases, the method includes measuring the increase in production of the virus, for example by determining the level of the virus in the cell and / or in the cell culture medium. Methods for determining virus production are known in the art and include, but are not limited to plaque assays, TCID50, PCR, ddPCR, ELISA, SRID and HPLC.5210518511

[0116] In some embodiments, the quality of the produced virus is improved by 1 .1 fold or more, e.g., compared to the quality of the virus produced by the cell, or a comparable cell, prior to the method or in the absence of the method. In some cases, the method includes measuring the quality of virus, for example by determining the purity, potency, integrity or infectivity of the virus. Methods for determining virus quality are known in the art and include, but are not limited to, measurements of viral titer, genome integrity, infectivity assays, potency assays, electron microscopy, capillary electrophoresis and high-performance liquid chromatography (HPLC).Methods and uses of increasing transduction

[0117] The present application also includes a method, optionally an in vitro method, of increasing transduction of a virus into a cell comprising administering a compound of the application, or a salt, solvate and / or prodrug thereof, and the virus to the cell. Also included is a use of a compound of the application, or a salt, solvate and / or prodrug thereof, for increasing transduction of a virus into a cell, as well as a compound of the application, or a salt, solvate and / or prodrug thereof, for use in increasing transduction of a virus into a cell.

[0118] “Transduction” or “transducing” as used herein, refers to the introduction of a virus containing an exogenous gene into a cell leading to expression of the gene, e.g., the transgene in the cell. The gene is optionally a therapeutic gene.

[0119] As used herein, the expression “increasing transduction” includes increasing transduction efficiency.

[0120] In some embodiments, the compound of the application, or a salt, solvate and / or prodrug thereof, is administered to the cell before, after and / or concurrently with a virus containing an exogenous gene.

[0121] In some embodiments, the method is used for the production of a therapeutic.

[0122] In some embodiments, the virus is an interferon (IFN)-sensitive virus.

[0123] In some embodiments, the virus is among those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0124] In some embodiments, the cells are those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0125] In some embodiments, the cell is a primary cell, namely a cell that is used for cell therapy. Examples of cell therapy cells include, but are not limited to, T-cells, NK-cells, TILs, Macrophages, mesenchymal stem cells, hematopoietic stem cells, induced-pluripotent stem cells, embryonic stem cells and adult stem cells.5310518511

[0126] In some embodiments, transduction of the virus is increased 1.1 fold or more, 1.2 fold or more, 1.5 fold or more, 2 fold or more, 2.5 fold or more, 3 fold or more, 5 fold or more, or 10 fold or more, e.g., compared to transduction of the virus by the cell, or a comparable cell, prior to the method or in the absence of the method. In some cases, the method includes measuring the increase transduction of the virus, for example by determining the level of the virus in the cell. Methods of measuring transduction efficiency are known in the art and include, but are not limited to Fluorescence imaging, in vitro and in vivo luminometry, immunohistochemistry, PCR, ddPCR and flow cytometry.Methods and uses of increasing transgene expression

[0127] The present application also includes a method, optionally an in vitro method, of increasing transgene expression comprising contacting the cell with an effective amount of a compound of the application, or a salt, solvate and / or prodrug thereof, in combination with one or more nucleic acids, wherein at least one of the nucleic acids encodes the transgene.

[0128] Also included is a use of a compound of the application, or a salt, solvate and / or prodrug thereof, for increasing transgene expression, as well as a compound of the application, or a salt, solvate and / or prodrug thereof, for use in increasing transgene expression. Optionally, the transgene is a therapeutic gene.

[0129] In some embodiments, the compound of the application is contacted with the cell or subject prior, concurrent with, or after provision of the one or more nucleic acids or virus a containing an exogenous gene to the cell. Methods of providing nucleic acids for transgene expression by a cell can include viral infection and / or via a non-viral process, generally known as transfection, and include any a carrier or method commonly known to a person skilled in the art. In no way limiting, this includes transfection using PEI or lipid-based reagents, electroporation, and nanoparticles, as is generally known in the art.

[0130] In some embodiments, the one or more nucleic acids encode components of a virus. The term “components of a virus” refers to nucleic acids, and chemically modified variants thereof, that comprise or consist of viral and / or viral-like sequences. The sequences can encode viral proteins, viral-like proteins and / or functional sequences for targeting, integration, promotion, etc.

[0131] In some embodiments, the nucleic acids are comprised in one or more plasmids, for example DNA plasmids. In some embodiments, the one or more nucleic acids encoding components of a virus are present on a plasmid.5410518511

[0132] Delivery of nucleic acids to a cell is generally described as transfection. Transfection efficiency refers to the degree to which a supplied source of genetic material is taken up and functional for its intended purpose in a cell.

[0133] Such nucleic acids may be delivered to the cell directly, or they may be provided in a carrier to enhance delivery and uptake by the cell. Examples of carriers include diverse polymers known in the art, which may be designed in a variety of nanoparticle formats, either loosely organized or more precision designed.

[0134] In one example, lentivirus, gamma-Retrovirus, or AAV are produced following transfection of plasmids encoding lentivirus, gamma-Retrovirus, or AAV viral or viral-like sequences into a cell.

[0135] In some embodiments, the one or more nucleic acids are DNA. In some embodiments, the one or more nucleic acids comprise one or more DNA plasmids. In some embodiments, one or more nucleic acids comprise alternatives to DNA plasmids for example but not limited to Doggy bone DNA, Bacterial artificial chromosomes (BACs), Yeast artificial chromosomes (YACs), P1 -derived artificial chromosomes (PACs), Phagemids, or Synthetic chromosomes.

[0136] In some embodiments, the method is used for production of a virus that encodes a non-viral gene product.

[0137] In some embodiments, the method is used for the production of a therapeutic.

[0138] In some embodiments, the virus is an interferon (IFN)-sensitive virus.

[0139] In some embodiments, the virus is among those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0140] In some embodiments, the cells are those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0141] In some embodiments, the cell is a primary cell, namely a cell that is used for cell therapy. ExIn some embodiments, the cell is a primary cell, namely a cell that is used for cell therapy. Examples of cell therapy cells include, but are not limited to, T-cells, NK-cells, TILs, Macrophages, mesenchymal stem cells, hematopoietic stem cells, induced-pluripotent stem cells, embryonic stem cells, adult stem cells.

[0142] In some embodiments, the transgene is a virally-encoded transgene and at least one of the nucleic acids encodes one or more components of the virus.5510518511

[0143] In some of the embodiments, the transgene is a non-viral gene, and may include a chimeric antigen receptor, therapeutic protein, antibody, enzyme, or versions thereof.

[0144] In some embodiments, the compound of the application, or a salt, solvate and / or prodrug thereof, is administered to the cell before, after and / or concurrently with the nucleic acid encoding the transgene.

[0145] In some embodiments, expression of the transgene is increased 1.1 fold or more, 1.2 fold or more, 1.5 fold or more, 2 fold or more, 2.5 fold or more, 3 fold or more, 5 fold or more, or 10 fold or more, e.g., compared to expression of the transgene, prior to the method or in the absence of the method. In some cases, the method includes measuring the expression of the transgene. Measuring expression levels of a transgene can be done by any method known in the art, including but not limited to measuring levels of nucleic acid expression or expression levels of protein encoded by the transgene.Methods and uses of increasing virus growth and / or virus spread

[0146] The present application also includes a method, optionally an in vitro method, of increasing virus growth and / or virus spread in cells comprising administering a compound of the application, or a salt, solvate and / or prodrug thereof, to the cells prior to, after or concurrently with the virus. Also included is a use of a compound of the application, or a salt, solvate and / or prodrug thereof, for increasing virus growth and / or virus spread, as well as a compound of the application, or a salt, solvate and / or prodrug thereof, for use in increasing virally-encoded transgene expression for increasing virus growth and / or virus spread.

[0147] In some embodiments, the compound of the application is contacted with the cell or subject prior, concurrent with, or after provision of the one or more nucleic acids or virus to the cell. Methods of providing nucleic acids for uptake by a cell can include viral infection and / or via a non-viral process, generally known as transfection, and include any a carrier or method commonly known to a person skilled in the art. In no way limiting, this includes transfection using PEI or lipid-based reagents, electroporation, and nanoparticles, as is generally known in the art.

[0148] In some embodiments, the one or more nucleic acids encode components of a virus. The term “components of a virus” refers to nucleic acids, and chemically modified variants thereof, that comprise or consist of viral and / or viral-like sequences. The sequences can encode viral proteins, viral-like proteins and / or functional sequences for targeting, integration, promotion, etc.5610518511

[0149] In some embodiments, the nucleic acids are comprised in one or more plasmids, for example DNA plasmids. In some embodiments, the one or more nucleic acids encoding components of a virus are present on a plasmid.

[0150] Delivery of nucleic acids to a cell is generally described as transfection. Transfection efficiency refers to the degree to which a supplied source of genetic material is taken up and functional for its intended purpose in a cell.

[0151] Such nucleic acids may be delivered to the cell directly, or they may be provided in a carrier to enhance delivery and uptake by the cell. Examples of carriers include diverse polymers known in the art, which may be designed in a variety of nanoparticle formats, either loosely organized or more precision designed.

[0152] In one example, lentivirus, gamma-Retrovirus, or AAV are produced following transfection of plasmids encoding lentivirus, gamma-Retrovirus, or AAV viral or viral-like sequences into a cell.

[0153] In some embodiments, the one or more nucleic acids are DNA.

[0154] In some embodiments, the one or more nucleic acids comprise one or more DNA plasmids.

[0155] In some embodiments, one or more nucleic acids comprise alternatives to DNA plasmids for example but not limited to Doggy bone DNA, Bacterial artificial chromosomes (BACs), Yeast artificial chromosomes (YACs), P1-derived artificial chromosomes (PACs), Phagemids, or Synthetic chromosomes.

[0156] In some embodiments, the method is used for production of a virus that encodes a non-viral gene product.

[0157] In some embodiments, the method is used for the production of a therapeutic.

[0158] In some embodiments, the virus is an interferon (IFN)-sensitive virus.

[0159] In some embodiments, the virus is among those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0160] In some embodiments, the cells are those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0161] In some embodiments, virus growth and / or virus spread is increased 1.1 fold or more, 1 .2 fold or more, 1 .5 fold or more, 2 fold or more, 2.5 fold or more, 3 fold or more, 5 fold or more, or 10 fold or more, e.g., compared to virus growth and / or virus spread, prior to the method or in the absence of the method. In some cases, the method includes measuring virus growth and / or virus spread.5710518511Methods and uses for improving manufacturing of therapeutic viral-based products

[0162] Compounds and compositions of the application are useful for improving the manufacturing processes of viral vectors or gene therapies by enhancing the viral production or transduction of cells used in manufacturing. Therefore, the compounds and compositions of the present application are useful in bioprocessing and the application also includes a compound or composition for use in combination with viral vectors or gene therapies.

[0163] Accordingly, the present application includes a method for improving the manufacturing of viral vectors or gene therapies by increasing the viral production or transduction of cells. This method comprises administering a therapeutically effective amount of a compound, or a salt, solvate and / or prodrug thereof, of the application to cells used in the upstream manufacturing process, thereby enhancing the yield and quality of the viral vectors or gene therapies produced.

[0164] In some embodiments, the compound of the application is contacted with the cell or subject prior, concurrent with, or after provision of the one or more nucleic acids, or virus containing an exogenous gene to the cell. Methods of providing nucleic acids for uptake by a cell can include viral infection and / or via a non-viral process, generally known as transfection, and include any a carrier or method commonly known to a person skilled in the art. In no way limiting, this includes transfection using PE, I or lipid-based reagents, electroporation, and nanoparticles, as is generally known in the art.

[0165] In some embodiments, the one or more nucleic acids encode components of a virus. The term “components of a virus” refers to nucleic acids, and chemically modified variants thereof, that comprise or consist of viral and / or viral-like sequences. The sequences can encode viral proteins, viral-like proteins and / or functional sequences for targeting, integration, promotion, etc.

[0166] In some embodiments, the nucleic acids are comprised in one or more plasmids, for example DNA plasmids. In some embodiments, the one or more nucleic acids encoding components of a virus are present on a plasmid.

[0167] Delivery of nucleic acids to a cell is generally described as transfection. Transfection efficiency refers to the degree to which a supplied source of genetic material is taken up and functional for its intended purpose in a cell.

[0168] Such nucleic acids may be delivered to the cell directly, or they may be provided in a carrier to enhance delivery and uptake by the cell. Examples of carriers include diverse polymers known in the art, which may be designed in a variety of nanoparticle formats, either loosely organized or more precision designed.5810518511

[0169] In one example, lentivirus, gamma-Retrovirus, or AAV are produced following transfection of plasmids encoding lentivirus, gamma-Retrovirus, or AAV viral or viral-like sequences into a cell.

[0170] In some embodiments, the one or more nucleic acids are DNA.

[0171] In some embodiments, the one or more nucleic acids comprise one or more DNA plasmids.

[0172] In some embodiments, one or more nucleic acids comprise alternatives to DNA plasmids for example but not limited to Doggy bone DNA, Bacterial artificial chromosomes (BACs), Yeast artificial chromosomes (YACs), P1-derived artificial chromosomes (PACs), Phagemids, or Synthetic chromosomes.

[0173] In some embodiments, the method is used for production of a virus that encodes a non-viral gene product.

[0174] In some embodiments, the method is used for the production of a therapeutic.

[0175] In some embodiments, the virus is an interferon (IFN)-sensitive virus.

[0176] In some embodiments, the virus is among those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0177] In some embodiments, the cells are those disclosed in Methods and uses of increasing permissiveness of a cell to one or more nucleic acids.

[0178] In some embodiments, the cell is a primary cell, namely a cell that is used for cell therapy. Examples of cell therapy cells include, but are not limited to, T-cells, NK-cells, TILs, Macrophages, mesenchymal stem cells, hematopoietic stem cells, induced-pluripotent stem cells, embryonic stem cells and adult stem cells.

[0179] In some embodiments, the compound of the application, or a salt, solvate and / or prodrug thereof, is administered to the cells before, during, and / or after the introduction of genetic material encoding viral components. In further embodiments, the compound of the application, or a salt, solvate and / or prodrug thereof, is used to pre-treat the cells, enhancing their capacity to support viral production, virus transduction and transgene expression, thus improving the overall efficiency of the manufacturing process.

[0180] In some embodiments, the compound of the application, or a salt, solvate and / or prodrug thereof, is administered to the cell during manufacturing as a batch feed, pulse feed, continuous feed, gradient feed, or controlled release.

[0181] In some embodiments, the compound of application, or a salt, solvate and / or prodrug thereof, is administered to the cell through closed or open systems.5910518511

[0182] In some embodiments, the compound of the application, or a salt, solvate and / or prodrug thereof, allows for a reduction in the amount of upstream manufacturing components like genetic material or cells, thereby lowering production costs and increasing the scalability of the manufacturing process.

[0183] In some embodiments, the compound of application, or a salt, solvate and / or prodrug thereof, is integrated within existing production processes in a simple way.

[0184] In some embodiments, the compound of application, or a salt, solvate and / or prodrug thereof, is removed or significantly reduced from the final product using typical viral vector purification procedures resulting in residual traces.

[0185] In some embodiments, the compound, or a salt, solvate and / or prodrug thereof, enhances the replication and packaging efficiency of the viral vectors within the manufacturing cells.

[0186] In some embodiments, the compound of the application, , or a salt, solvate and / or prodrug thereof, is used to improve the production of viral vectors or gene therapies for a variety of conditions, including genetic disorders, and infectious diseases. For example, the compound, or a salt, solvate and / or prodrug thereof, enhances the production of viral vectors designed for use in gene therapy for inherited diseases.

[0187] In some embodiments, the compound, or a salt, solvate and / or prodrug thereof, is applied to enhancing viral production or transduction of cells within large-scale culture systems. In some embodiments, large-scale culture systems include and are not limited to stirred-take bioreactors, wave bioreactors, airlift bioreactors, hollow fiber bioreactors, fixed bed bioreactors and single-use bioreactors.

[0188] In some embodiments, the compound, or a salt, solvate and / or prodrug thereof, is applied to enhancing viral production or transduction of cells within small-scale culture systems. In some embodiments, small-scale culture systems include and are not limited to spinner flasks, T-flasks, roller bottles, cell stacks, hyper stacks, shake flasks, perfusion systems and wave-mixed bag systems.IV. Methods of Preparing the Compounds and Compositions of the Application

[0189] Compounds of the present application can be prepared by various synthetic processes. The choice of particular structural features and / or substituents may influence the selection of one process over another. The selection of a particular process to prepare a given compound of the application is within the purview of the person of skill in the art. Some starting materials for preparing compounds of the present application are available from commercial chemical sources or may be extracted from cells, plants, animals or fungi. Other starting6010518511materials, for example as described below, are readily prepared from available precursors using straightforward transformations that are well known in the art.

[0190] Salts of the compounds of the application are generally formed by dissolving the neutral compound in an inert organic solvent and adding either the desired acid or base and isolating the resulting salt by either filtration or other known means.

[0191] The formation of solvates of the compounds of the application will vary depending on the compound and the solvate. In general, solvates are formed by dissolving the compound in the appropriate solvent and isolating the solvate by cooling or using an antisolvent. The solvate is typically dried or azeotroped under ambient conditions. The selection of suitable conditions to form a particular solvate can be made by a person skilled in the art. Examples of suitable solvents are ethanol, water and the like. When water is the solvent, the molecule is referred to as a “hydrate”.

[0192] Prodrugs of the compounds of the present application may be, for example, conventional esters formed with available hydroxy, thiol, amino or carboxyl groups. For example, available hydroxy or amino groups may be acylated using an activated acid in the presence of a base, and optionally, in inert solvent (e.g. an acid chloride in pyridine). Some common esters which have been utilized as prodrugs are phenyl esters, aliphatic (C1-C24) esters, acyloxymethyl esters, carbamates and amino acid esters.

[0193] Throughout the processes, it is to be understood that, where appropriate, suitable protecting groups will be added to, and subsequently removed from, the various reactants and intermediates in a manner that will be readily understood by one skilled in the art. Conventional procedures for using such protecting groups as well as examples of suitable protecting groups are described, for example, in “Protective Groups in Organic Synthesis", T.W. Green, P.G.M. Wuts, Wiley-lnterscience, New York, (1999). It is also to be understood that a transformation of a group or substituent into another group or substituent by chemical manipulation can be conducted on any intermediate or final product on the synthetic path toward the final product, in which the possible type of transformation is limited only by inherent incompatibility of other functionalities carried by the molecule at that stage to the conditions or reagents employed in the transformation. Such inherent incompatibilities, and ways to circumvent them by carrying out appropriate transformations and synthetic steps in a suitable order, will be readily understood to one skilled in the art. Examples of transformations are given herein, and it is to be understood that the described transformations are not limited only to the generic groups or substituents for which the transformations are exemplified. References and descriptions of other suitable transformations are given in “Comprehensive Organic Transformations - A Guide to Functional Group Preparations” R.C. Larock, VHC6110518511Publishers, Inc. (1989). References and descriptions of other suitable reactions are described in textbooks of organic chemistry, for example, “Advanced Organic Chemistry", March, 4th ed. McGraw Hill (1992) or, “Organic Synthesis", Smith, McGraw Hill, (1994). Techniques for purification of intermediates and final products include, for example, straight and reversed phase chromatography on column or rotating plate, recrystallisation, distillation and liquidliquid or solid-liquid extraction, which will be readily understood by one skilled in the art.EXAMPLESThe following non-limiting examples are illustrative of the present application.Example 1 Materials and MethodsCell lines

[0194] Cell lines: HEK293T (human embryonic kidney epithelium), HEK293, and HT1080 (human connective fibrosarcoma), 786-0 (human renal carcinoma), and Vero (monkey kidney) cells were obtained from the American Type Culture Collection and maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum and buffered with 30mM Hepes. HEK 293T / 17 (human embryonic kidney epithelium) was clonally derived from HEK293T. VPC 2.0 HEK 293 (human embryonic kidney epithelium) were obtained from ThermoFisher and maintained in Viral Production Medi. HEK293T, HEK293, HT1080, 786-0 and Vero cell lines were incubated at 37°C with 5% CO2. VPC2.0 HEK293 cells were incubated at 37°C with 8% CO2.

[0195] Primary human pan (CD3+) T-cells were obtained from STEMCELL Technologies, maintained in 4-Cell Nutri-T Media and IL-2. T-cells were activated using T-Cell TransACT obtained from Miltenyi.Lentiviral vector

[0196] The lentivirus construct for this study is a third-generation self-inactivating vector based on the HIV-1 backbone pseudotyped with the VSV-G glycoprotein, engineered to express a firefly luciferase (fLuc) transgene and manufactured using transient transfection of culture-adapted adherent HEK293T, suspension VPC2.0 HEK293 cells with a four-plasmid system.Compound Testing of HEK293T cells for enhanced LV production

[0197] Compounds of high chemical diversity and low predicted mutagenic, carcinogenic and teratogenic properties were tested in HEK293T in 96 well format following a batch (reverse) transfection method. HEK293T cells were suspended at 4.5e5 cells / mL in complete DMEM prior to transfection. A transfection mixture was prepared containing the 46210518511lentiviral plasmids and a corresponding amount of PEIpro transfection reagent in OptiMEM reduced serum media. The plasmid and PEIpro mixtures were allowed to complex for 30 minutes at room temperature prior to addition to the HEK293T cell mixture. Batch transfected HEK293T cells were immediately plated in 96well format at 4.5e4 cells / well, in triplicate, using a high-through liquid dispenser. Immediately following plating, HEK 293T cells were treated with either small molecule library compounds at a concentration of 10 .M, or a corresponding amount of library vehicle control (1 .05% dimethyl sulfoxide (DMSO)) using a high-throughput liquid handler. Treated cells were incubated at 37°C with 5% CO2for 48 hours.

[0198] The next day following transfection, HT 1080 reporter cells were plated in 96well format at 3e3 cells / well, in order to reach 50% confluence the following day. These cells act as reporter cells that are easily transduced by lentivirus-containing supernatant from producer cells and allow for high throughput virus quantification. 48 hours following transient transfection, a sample of lentivirus containing supernatant from HEK 293T production cultures was transferred on to the HT 1080 reporter cell line for transduction analysis and quantification of lentivirus driven fLuc expression. A standard curve was also added to the HT 1080 reporter plates at the time of supernatant transfer from the HEK 293T producer cells. The standard curve was prepared by adding known amounts of fLuc-encoding lentivirus (in transducing units / mL) to the HT1080 cells at the same time as the transfer of supernatant. Using this standard curve, it is possible to convert the observed luminescence from transduced HT1080 cells into viral expression units (VEU) by for example, plotting input virus level versus observed luminescence (relative light units) and performing a four-parameter non-linear regression analysis. During our studies we observed that increase in raw luminescence corresponded linearly with increases in calculated VEUs. After the supernatant transfer sample had been removed from the HEK 293T producer plates, cell viability was assessed using resazurin assay to determine relative metabolic activity relative to transfected cells treated only with library vehicle control (1.05% DMSO). This allows for interrogation of the relative drop in cell viability caused only by the compounds and not remnant cytotoxicity from the DMSO vehicle. Transduced HT1080 cells were incubated at 37°C with 5% CO2.

[0199] 72 hours following the transduction of with lentivirus-virus containing supernatant from the HEK 293T producer cells, HT1080 reporter cells were read for luminescent activity. Since each well of the reporter cells were transduced with the same volume of supernatant containing luciferase-encoding lentivirus, increases in luminescent output would correspond to increased levels of virus produced following compound treatment and transfection of the producer cell line. The HT1080 reporter cells were treated with a 2mg / ml_ solution of luciferin salt in phosphate buffered saline, were shaken for 5 seconds and allowed to incubate at room temperature in the dark for 30 seconds to allow the luminescent6310518511reaction to occur. Luminescent signal, measured as relative light units per second (RLU / second), was recorded using a high-throughput plate reader.

[0200] Luminescent data obtained from the HT1080 reporter cells was analyzed by calculating the average luminescent value for each compound (in RLU / second) for each of the triplicate wells, and then determining the relative fold change in signal above the average of library vehicle controls (1.05% DMSO) from wells on the same plates. This is reporter as the Average Fold Change Above Vehicle. Significance was assessed using an unpaired, two- tailed t-test to produce a p- value. A z-score was also calculated for each compound compared to all other compounds in the same experiment.

[0201] The criteria used to classify a compound as active was based on average fold change above vehicle greater than or equal to 1 .1 fold, p-value of less than 0.05 and z-score greater than 1.0.Compound testing in HEK293T clones for enhanced LV production

[0202] Experiments were carried out using the same methods described in above, with the exception being that two different HEK 293T clones (HEK 293T and HEK 293T / 17) were used as production cells and three concentrations (5 .M, 10pM, and 15 .M) of drug were used to assess their impact on lentivirus production. Each condition was run in triplicate and supernatant from both producer HEK 293 clones were individually transferred onto HT1080 reporter cells as previously described. Analysis of luminescent signal and calculation of fold changes above vehicle and p-values for significance was performed as previously described in the above sections.

[0203] The average fold change above vehicle and p-values for each concentration of compound was calculated for both cell lines. The criteria used to classify a compound as validated for this experiment was an average fold change above vehicle greater than 1.1 -fold and a p-value less than 0.05.AAV vectors

[0204] A three-plasmid system was used for the production of AAV2 consisting of pAAV-RC2, pHelper and pAAV-transgene, engineered to express a firefly luciferase (fLuc) transgene and manufactured using transient transfection of adherent HEK293 cells and suspension VPC2.0 HEK293 cells.Compound testing for enhanced AAV2 production in HEK293 cells

[0205] Compounds were tested in HEK293 cells in 96 well format following a batch (reverse) transfection method. HEK293 cells were suspended at 5.3e5 cells / mL in complete DMEM prior to transfection. A transfection mixture was prepared containing the three AAV2 6410518511plasmids, and a corresponding amount of PEIpro transfection reagent in serum-free DMEM. The plasmid and PEIpro mixtures were allowed to complex for 15 minutes at room temperature prior to addition to the HEK293 cell mixture. Batch transfected HEK293 cells were then plated in 96 well format at 5.3e4 cells / well, in triplicate, using a high-throughput liquid dispenser. Immediately following plating, HEK293 cells were treated with exemplary compounds of the application at a concentration of 5 .M, 10pM and 15 .M, or a corresponding amount of library vehicle control (Dimethyl sulfoxide (DMSO) using a high-throughput liquid handler. Treated cells were incubated at 37°C with 5% C02for 72 hours.

[0206] Two days following transfection, HEK293T reporter cells were plated in 96well format at 6.26e4 cells / well, in order to reach 65% confluency the following day. These cells act as reporter cells that are easily transduced by AAV-containing lysate (after 3 freeze-thaw cycles) from producer cells and allow for high throughput virus quantification. At 72 hours following transient transfection of HEK 293 production cultures, AAV2 from harvested cell lysate was transferred on to the HEK293T reporter cell line for transduction analysis and quantification of AAV2-driven fLuc expression. A standard curve was also added to the HEK293T reporter plates in a similar manner as described herein. Transduced HEK293T cells were incubated at 37°C with 5% CO2.

[0207] At 72 hours following the transduction, HEK293T reporter cells were read for luminescent activity in a similar manner as described herein. Luminescent data was obtained and analyzed as described in herein.Compound testing for enhanced AAV2 production in VPC2.0 HEK293 cells

[0208] Compounds were tested in VPC2.0 HEK293 cells with FectoVir-AAV transfection reagent or AAV-MAX transfection kit in 96 well format.

[0209] To prepare the FectoVir-AAV transfection mixture, three AAV2 plasmids were added to a corresponding amount of Fectovir-AAV transfection reagent. The plasmids and transfection reagent mixtures were allowed to complex for 30 minutes at room temperature prior to addition to the VPC 2.0 HEK293 cell mixture. Following complexation, the mixture was added to the VPC 2.0 HEK293 cells to transfect cells.

[0210] For the AAV-MAX transfection system, the AAV-MAX enhancer was added to the VPC 2.0 HEK293 cells and incubated at 37°C with 8% CO2for 30 minutes. While the enhancer and cell mixture incubated, the transfection mixture was prepared. The three AAV2 plasmids were added to the corresponding AAV-MAX transfection reagent and booster and allowed to complex for 10 minutes at room temperature. Following complexation, the mixture was added to 3e6 cells / mL of VPC 2.0 HEK293 cells in Viral Production Media.6510518511

[0211] 100 pL of batch-transfected VPC2.0 HEK293 cells were aliquoted in each well of 96-well plates, in triplicate. T ransfected cells were immediately treated with 25 pL exemplary compounds of the application at a range of concentrations or a corresponding amount of library vehicle control (Dimethyl sulfoxide (DMSO)). Treated cells were incubated at 37°C with 8% C02for 72 hours. Three days following transfection, AAV2 from harvested cell lysate was freeze-thawed three times and transferred on to the HEK293T reporter cell line and incubated at 37°C with 5% CO2for 72 hours prior to transduction analysis and quantification of AAV2- driven fLuc expression in a similar manner as described herein.Viruses

[0212] VSVA51 is a recombinant variant of the Indiana serotype of VSV harbouring a deletion of the 51stmethionine in the M protein. VSVA51 expressing firefly luciferase (FLuc) and VSVA51 expressing green fluorescent protein (GFP) were recombinant derivatives of VSVA51. All virus stocks were propagated in Vero cells, purified on Optiprep™ gradient and tittered on Vero cells as described in (Diallo et al. Methods Mol Bio. 2012;797:127:40).

[0213] Lentiviral vector encoding EmGFP (>1e8 TU / mL) was obtained from Genscript.Compound testing in 786-0 cells for enhanced output of VSVA51

[0214] 786-0 cells were seeded at 1.05e4 cells / well in 96well format (100pL / well) in order to reach 100% confluency, the following day. Cells were then treated with exemplary compounds at a concentration of 15pM for 4 hours. After compound treatment, cells were infected with VS A51 at MOI of 0.05. Infected cells were incubated at 37°C with 5% C02for 48 hours.

[0215] One day following infection, Vero cells were plated in 96well format at 1.2e4 cells / well to reach 100% confluency the following day. These cells are susceptible to VSVA51 infection and allow for high throughput virus quantification. At 48 hours following infection of 786-0 cells, VSVA51 in the supernatant was transferred on to Vero cells for quantification of VSVA51-fLuc expression. A standard curve was also added to Vero cells in a similar manner as described herein. Infected Vero cells were incubated at 37°C with 5% CO2for two hours.

[0216] After five hours, Vero cells were read for luminescent activity in a similar manner as described herein. Luminescent data was obtained and analyzed as described herein.6610518511Compound testing for enhanced lentiviral transduction and virally-encoded transqene expression of T-cells

[0217] Primary human Pan T-cells (CD3+) were thawed and re-suspended in media. Following centrifugation at 800xg for 5 minutes, the cell pellet was resuspended in 4Cell Nutri- T Advanced Media supplemented with IL-2. Thawed cells were then activated using T-cell TransAct and incubated with agitation at 37°C and 5% CO2for 24 hours.

[0218] Activated T-cells were seeded in 384-well plates (at 25pL / well) and treated with exemplary compounds of the application at a concentration of 15 pM for 30 minutes. GFP- encoding lentivirus vector was added to the T-cells to achieve a final MOI of 4. Spinoculation was performed by centrifugation at 800xg for 1 hour at 32°C. Plates were then incubated at 37°C and 5% CO2for 72 hours.

[0219] To quantify transduction efficiency, the percentage of GFP-expressing cells from the live cell population was quantified by flow cytometry using the MACSQuant™ Analyzer 16.

[0220] Lentivirus-encoded GFP transgene expression was measured by quantifying the mean fluorescent intensity of GFP in transduced cells. This was done flow cytometry using the MACSQuant™ Analyzer 16.EXPERIMENTAL RESULTSExample 2

[0221] The ability of compounds from the present application to enhance plasmidbased viral vector production in the HEK293T cell line was tested, since this cell line and its related parent line (HEK293) and subclonal derivatives are commonly used to produce viral vectors including but not limited to lentivirus and adeno-associated virus. The reverse genetic system employed consisted of transient transfection of four circular plasmids appropriate to produce lentivirus encoding a luciferase transgene in a small-scale format. The compounds of low predicted mutagenic, carcinogenic and teratogenic properties were tested at a 10 .M concentration using the firefly luciferase (fLuc)-encoding lentivirus production system using a high-throughput batch transfection assay described herein, measuring lentivirus output from HEK293T cells from a secondary transduction assay carried out in an HT1080 reporter cell line.

[0222] Impact on lentivirus production was inferred by measuring the luciferase expression resulting from transfer of lentivirus-containing supernatants from compound- treated / LV plasmid-transfected HEK293T cells. In this assay, the luciferase signal (Relative6710518511Light Units or RLU) ensues from the transduction of HT1080 reporter cells, which correlates with quantity of functional virus as determined from a standard curve tested of LV in parallel. Many actives increasing lentivirus production by at least a 1.1-fold as measured by luciferase transgene over the vehicle control (1.05% DMSO) were identified.

[0223] Compounds of the application can be seen in Table 1 and a detailed overview of their activity in terms of enhancing luminescent signal, correlated viral expression units (VEU), and cytotoxicity profile can be seen in FIG.IA to FIG.1F. The active molecules were found to decrease producer cell viability by no more than 41 % as seen in FIG.1 E and FIG.1 F. Results for one hundred thirty-seven molecules can be seen in Table 2.Table 2. Lentivirus primary data of Compounds of the Application681051851169105185117010518511Example 3

[0224] To confirm the results, a subset of compounds with high and low activity were selected for subsequent validation in HEK293T and an alternative HEK293T subclone, 7110518511HEK293T / 17. In particular, 1-1 , 1-86, 1-87 and 1-91 were tested at 3 concentrations (5 .M, 10 .M, 15 .M). These experiments were carried out using the same method used in the primary testing for assessing relative changes in LV-luciferase production. Data for this subset can be found in FIG.2, demonstrating similar activity across the two HEK293T subclones.Example 4

[0225] To further confirm the applicability of these compounds for additional plasmidbased reverse genetic systems, a subset of actives were investigated for their ability to enhance the production of adeno-associated virus-2 (AAV2) in HEK293 production cells. 1-1 to I-39, 1-41 , I-52, I-70, 1-71 , I-79, 1-81 , I-89, I-96, 1-100 to 1-103, 1-105 to 1-185, I-266, I-207 to I-273 were tested at 10 .M in HEK293 cells. These experiments were carried out using plasmids for the production of AAV2 and the methods as described herein. Data for this experiment can be found in FIG.3A and FIG.3B and Table 3. All compounds tested showed statistically significant enhancement of AAV2 production and indicates that the compounds of the application listed in Table 1 are also effective in enhancing the production of AAV2, suggesting their applicability to a range of plasmid-based reverse genetics systems, for example but not limited to the production of LV or AAV.Table 3. AAV production data of Viral Sensitizing Compounds of the Application7210518511731051851174105185117510518511Example 5

[0226] To further confirm the applicability of these compounds with enhancing AAV2 production in suspension cell lines and multiple transfection reagents, exemplary compounds of the application were evaluated forfold change in RLU, indicative of functional titer. As shown in FIG. 4, 1-7 and 1-86 (exemplary compounds of the application) enhanced AAV2 production in VPC2.0 HEK 293 cells transfected with either AAV-MAX transfection kit (including AAV-MAX enhancer and booster) or FectoVir-AAV™ transfection reagent by greater than 1.1-fold at varying peak concentrations. N.T. indicates concentrations not tested for functional titer. This data confirms that exemplary compounds of the application are broadly-acting AAV2 production enhancers based on increased activity in adherent and suspension cell lines transfected with various transfection reagents. This data also confirms that exemplary compounds of the application increase AAV2 production when used in combination with other enhancers.Example 6

[0227] To test the applicability of these compounds with enhancing replicating viruses including but not limited to rhabdoviruses, compounds were investigated for its ability to enhance replication of a recombinant variant of vesicular stomatitis virus (VSV). Compounds were tested at a concentration of 15 pM in 786-0 cells using the methods described herein.

[0228] As shown in FIG. 5, fold enhancement in functional VSVA51 titers over untreated control was assessed by measuring VSV-mediated reporter signal in target Vero cells following exposure to cell-free viral supernatant from treated and infected 786-0 cells. The assay quantifies functional viral output of VSVA51 in response to compounds.

[0229] Enhancement of VSV replication was observed with I-23, I-29, I-30, I-32, I-34, I-70, 1-81 , I-86, 1-1 1 1 , 1-115, 1-1 17, 1-124, 1-125, 1-127 , 1-129, 1-130 and I-272 at 15 pM. These findings demonstrate that compounds of this application not only enhance plasmid-based reverse genetic systems like AAV and LV production, but also augment the output of actively replicating rhabdovirus, supporting broader applicability of these compounds in viral production systems.7610518511Example 7

[0230] The ability of exermplary compounds of this application to enhance virally- encoded transgenes was evaluated by testing the effect of exemplary compounds on lentivirus-encoded GFP expression in human primary (CD34+) T-cells. As shown in FIG. 6, I- 9, 1-20, 1-26, 1-27, 1-28, 1-30, 1-34, 1-39, 1-44, 1-70, 1-81 , I-82, I-96, 1-107, 1-1 10, 1-1 1 1 , 1-1 12, I- 1 14, 1-1 15, 1-1 16, 1-1 17, 1-1 18, 1-1 19, 1-120, 1-121 , 1-122, 1-124, 1-125, 1-126, 1-127, 1-128, 1-129 and 1-130 (exemplary compounds of the application) enhanced lentivirus-encoded GFP expression by at least 1.1-fold in primary T-cells. This demonstrates that exemplary compounds of the application enhance virally-encoded transgenes.Example 8

[0231] To investigate the ability of compounds in this application to enhance virus transduction, various compounds were evaluated for its impact on primary T-cell transduction using a GFP-encoding lentiviral vector. Human CD3+T cells were activated and subsequently transduced with lentivirus in the presence of 15 pM of each compound. T ransduction efficiency was measured by flow cytometry as the percentage of GFP-positive cells 72 hours posttransduction, and fold enhancement was calculated relative to untreated control.

[0232] As shown in FIG. 7, 15 pM of I-82, 1-108, 1-1 10, 1-1 17, 1-121 , 1-126 and 1-130 (exemplary compounds of the application) enhanced lentiviral transduction in primary T cells by at least 2-fold. Elevated transduction levels indicate that compounds of this application are also effective at increasing virus transduction and consequent expression of virally encoded transgenes.

[0233] While the applicant's teachings described herein are in conjunction with various embodiments for illustrative purposes, it is not intended that the applicant's teachings be limited to such embodiments as the embodiments described herein are intended to be examples. On the contrary, the applicant's teachings described and illustrated herein encompass various alternatives, modifications, and equivalents, without departing from the embodiments described herein, the general scope of which is defined in the appended claims.7710518511

Claims

CLAIMS1. A method of increasing permissiveness of a cell to one or more nucleic acids, comprising contacting the cell with an effective amount of a compound listed in Table 1 , or a pharmaceutically acceptable salt, where applicable, solvate or prodrug thereof.

2. The method of claim 1 , wherein the one or more nucleic acids encode components of a virus.

3. The method of claim 2, wherein the method comprises contacting the cell with an effective amount of the compound of formula (I), or a pharmaceutically acceptable salt, solvate, or prodrug thereof, in combination with the one or more nucleic acids, and the method is for increasing production of the virus by the cell.

4. The method of claim 1 to 3, wherein the one or more nucleic acids comprise one or more plasmids.

5. The method of claim 2 or 3, wherein the virus is an adeno-associated virus (AAV), optionally wherein the AAV is selected from the group consisting of AAV serotypes 1-9 and recombinant serotypes thereof.

6. The method of claim 2 or 3, wherein the virus is a retrovirus.

7. The method of claim 6, wherein the retrovirus is a lentivirus, optionally where the lentivirus is selected from the group consisting of HIV-1 , HIV-2, SIV, and recombinant lentiviruses.

8. The method of any one of claims 1 to 7, wherein the cell is a mammalian cell.

9. The method of claim 2 or 3, wherein production of the virus by the cell is increased by at least 1.1 fold compared to a control cell.

10. The method of claim 3, wherein the one or more nucleic acids are introduced by viral infection of the cell by a virus.11 . The method of claim 10, wherein the virus is an RNA virus.

12. The method of claim 10, wherein the virus is a DNA virus.

13. The method of claim 10, wherein the virus is a Rhabdovirus.

14. The method of claim 1 , wherein at least one of the one or more nucleic acids encodes a transgene, the method comprises contacting the cell with an effective amount of the compound of formula (I), or a salt, solvate or prodrug thereof, in7810518511combination with the one or more nucleic acids, and the method is for increasing expression of the transgene in the cell.

15. The method of claim 15, wherein the transgene is a virally-encoded transgene and wherein at least one of the nucleic acids encodes one or more components of the virus.

16. The method of claim 15 or 16, wherein the transgene is a therapeutic gene.

17. The method of any one of claims 15 to 17, wherein the virus is an adeno-associated virus (AAV), optionally wherein the AAV is selected from AAV serotypes 1-9 and recombinant serotypes thereof.

18. The method of any one of claims 15 to 17, wherein the virus is a retrovirus.

19. The method of claim 18, wherein the retrovirus is a lentivirus, optionally where the lentivirus is selected from HIV-1 , HIV-2, SIV, and recombinant lentiviruses.

20. The method of any one of claims 14 to 16, wherein the virus is a Rhabdovirus.21 . The method of claim 1 , wherein the one or more nucleic acids are encapsulated in a virus, the method comprises contacting the cell with an effective amount of the compound of formula (I), or a pharmaceutically acceptable salt, solvate, or prodrug thereof, in combination with the virus, and the method is for increasing transduction of the virus into the cell.

22. The method of claim 21 , wherein the virus is an adeno-associated virus (AAV), optionally wherein the AAV is selected from AAV serotypes 1-9 and recombinant serotypes thereof.

23. The method of claim 21 , wherein the virus is a retrovirus.

24. The method of claim 23, wherein the retrovirus is a lentivirus, optionally where the lentivirus is selected from HIV-1 , HIV-2, SIV, and recombinant lentiviruses.

25. The method of claim 21 , wherein the virus is a Rhabdovirus.

26. The method of any one of claims 21 to 25, wherein the cell is an immune cell or a T-cell.

27. The method of claim 1 , wherein the one or more nucleic acids encode components of a lentivirus, the method comprises contacting the cell with an effective amount of the compound of formula (I), or a pharmaceutically acceptable salt, solvate, or prodrug thereof, in combination with the one or more nucleic acids, and the method is for increasing production of the lentivirus in the cell.791051851128. The method of any one of claims 1 to 27, wherein the cell is contacted with the compound before, after, or concurrently with the one or more nucleic acids.

29. The method of claim 27 or 28, wherein the compound is used in combination with a booster or an enhancer.

30. The method of claim 29, wherein the booster or enhancer is an histone deacetylase (HDAC) inhibitor.

31. The method of any one of claims 27 to 30, wherein production of the lentivirus is increased by at least 1.1 fold compared to a control cell.

32. The method of any one of claims 27 to 31 , wherein the lentivirus is selected from HIV-1 , HIV-2, SIV, and recombinant lentiviruses.

33. The method of claim 1 , wherein the one or more nucleic acids encode components of an adeno-associated virus (AAV), the method comprises contacting the cell with an effective amount of the compound of the formula (I), or a pharmaceutically acceptable salt, solvate, or prodrug thereof, in combination with the one or more nucleic acids, and the method is for increasing production of the AAV in the cell.

34. The method of claim 33, wherein the cell is contacted with the compound before, after, or concurrently with the one or more nucleic acids.

35. The method of claim 33 or 34, wherein the compound is used in combination with a booster or an enhancer.

36. The method of claim 35, wherein the booster or enhancer is the AAV-MAX booster or the AAV-MAX enhancer.

37. The method of any one of claims 33 to 36, wherein the production of AAV is increased by at least 1.1 fold compared to a control cell.

38. The method of any one of claims 33 to 36, wherein the AAV is selected from AAV serotypes 1-9 and recombinant serotypes thereof.

39. A composition comprising a compound listed in Table 1 , or a pharmaceutically acceptable salt, where applicable, solvate, or prodrug thereof, and a one or more nucleic acids encoding one or more components of a virus or encapsulated in a virus.

40. Use of the composition of claim 39 for increasing production of a virus by a cell.41 . Use of the composition of claim 39 for increasing transduction of a virus in a cell.

42. Use of the composition of claim 39 for increasing transgene expression in a cell.8010518511

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