WO2021195723A1 - Méthodes de traitement d'infections à coronavirus - Google Patents

Méthodes de traitement d'infections à coronavirus Download PDF

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WO2021195723A1
WO2021195723A1 PCT/AU2021/050317 AU2021050317W WO2021195723A1 WO 2021195723 A1 WO2021195723 A1 WO 2021195723A1 AU 2021050317 W AU2021050317 W AU 2021050317W WO 2021195723 A1 WO2021195723 A1 WO 2021195723A1
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lsd1
polypeptide
cell
trans
agent
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PCT/AU2021/050317
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English (en)
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Sudha RAO
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The Council Of The Queensland Institute Of Medical Research
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Publication of WO2021195723A1 publication Critical patent/WO2021195723A1/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/13—Amines
    • A61K31/15—Oximes (>C=N—O—); Hydrazines (>N—N<); Hydrazones (>N—N=) ; Imines (C—N=C)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/16—Amides, e.g. hydroxamic acids
    • A61K31/165—Amides, e.g. hydroxamic acids having aromatic rings, e.g. colchicine, atenolol, progabide
    • A61K31/167—Amides, e.g. hydroxamic acids having aromatic rings, e.g. colchicine, atenolol, progabide having the nitrogen of a carboxamide group directly attached to the aromatic ring, e.g. lidocaine, paracetamol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/4409—Non condensed pyridines; Hydrogenated derivatives thereof only substituted in position 4, e.g. isoniazid, iproniazid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/713—Double-stranded nucleic acids or oligonucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/19—Cytokines; Lymphokines; Interferons
    • A61K38/21—Interferons [IFN]
    • A61K38/215—IFN-beta
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/44—Oxidoreductases (1)
    • A61K38/443—Oxidoreductases (1) acting on CH-OH groups as donors, e.g. glucose oxidase, lactate dehydrogenase (1.1)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.

Definitions

  • This invention relates generally to methods for treating coronavirus infections. More specifically, the invention relates to the use of LSD antagonists to treat coronavirus infections, including betacoronavirus infections.
  • Coronaviruses are enveloped RNA viruses that infect mammals and birds.
  • the severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) are both members of the genus Betacoronavirus, and responsible for hundreds of deaths in Asia and the Middle East, respectively.
  • SARS-CoV-2 SARS-coronavirus 2
  • the coronaviruses are a virus family grouped into four genera, being the alphacoronavirus, betacoronavirus (b-CoVs), gammacoronavirus, and deltacoronavirus.
  • the alphacoronaviruses and betacoronaviruses infect a wide range of species, including humans.
  • the b-CoVs that are of particular clinical importance in humans include OC43 and HKU1 of the A lineage, Severe Acute Respiratory Syndrome coronavirus (8ARS ⁇ CoV) and SARS-CoV-2 (which causes the disease COVID-19) of the B lineage, and Middle Eastern Respiratory Syndrome-related coronavirus (MERS-CoV) of the C lineage.
  • the present invention is predicated, at least in part, on the discovery that LSD1 plays a part in regulating key demethylation/methylation sites of the ACE2 polypeptide, which is an important part of the molecular machinery used by SARS- CoV-2 to gain entry into the host cell. Additionally, LSD1 also plays a role in demethylation/methylation of key lysine residues present on the C-terminal cytoplasmic tail of the ACE2 polypeptide, which is known to regulate the translocation of the ACE2 polypeptide from the cell membrane to the cell nucleus. Accordingly, these findings lead the present inventors to contemplate the use of LSD1 inhibitors for the treatment and/or prevention of virus infections, namely coronavirus infections.
  • a coronavirus infection in a subject having a coronavirus infection comprising administering to the subject an agent that inhibits or reduces an activity of a lysine-specific demethylase 1 (LSD1) polypeptide, to thereby treat the coronavirus infection in the subject.
  • LSD1 lysine-specific demethylase 1
  • the invention provides methods of preventing a coronavirus from entering a cell, the method comprising, exposing the cell to an agent that inhibits or reduces an activity of a LSD1 polypeptide , to thereby reduce or prevent the coronavirus from entering the cell.
  • the agent that inhibits or reduces an activity of a LSD1 polypeptide is exposed to the cell for a time and under conditions sufficient to antagonise a TMPRSS2 polypeptide.
  • the agent that inhibits or reduces an activity of a LSD1 polypeptide is exposed to the cell for a time and under conditions sufficient to antagonise a virus cell entry receptor polypeptide.
  • the virus cell entry receptor polypeptide is selected from the group comprising an ACE2 polypeptide, a DPP4 polypeptide, and a CD13 polypeptide.
  • the invention provides a method of reducing or preventing entry of a coronavirus into a cell, the method comprising exposing the cell to an agent that inhibits an activity of a lysine-specific demethylase 1 (LSD1) polypeptide, to thereby antagonise, or otherwise reduce the level or amount of TMPRSS2 polypeptide present on the surface of the cell.
  • LSD1 lysine-specific demethylase 1
  • the invention provides a method of reducing or preventing entry of a coronavirus into a cell, the method comprising exposing the cell to an agent that inhibits an activity of a lysine-specific demethylase 1 (LSD1) polypeptide, to thereby antagonise, or otherwise reduce the level or amount of a virus cell entry receptor polypeptide present on the surface of the cell.
  • LSD1 lysine-specific demethylase 1
  • the agent is a selective LSD1 inhibitor.
  • the agent that inhibits or reduces an activity of a LSD1 polypeptide is selected from the group comprising: a small molecule; a polypeptide; and an antigen-binding molecule.
  • the agent is a monoamine oxidase (MAO) inhibitor.
  • MAO monoamine oxidase
  • a large number of MAO inhibitor are known to be suitable for the purposes of the present invention.
  • the MAO inhibitor comprises, consists, or consists essentially of, phenelzine.
  • the agent is a selective LSD1 inhibitor.
  • the selective LSD1 inhibitor can be selected from the group comprising or consisting of GSK-LSD1 , SP-2509, and SP-2577.
  • the agent is GSK-LSD1 , which has the following molecular structure:
  • the agent is SP-2509, which has the following molecular structure:
  • the agent is SP-2577, which has the following molecular structure:
  • the agent is bizine, which has the following molecular structure:
  • the agent is an isolated or purified proteinaceous molecule comprising, consisting or consisting essentially of sequence corresponding to residues 108 to 118 of LSD1.
  • the isolated or purified proteinaceous molecule is an isolated or purified proteinaceous molecule represented by Formula (I):
  • Zi and Z2 are independently absent or are independently selected from at least one of a proteinaceous moiety comprising from about 1 to about 50 amino acid residues (and all integers in between), and a protecting moiety; and
  • Xi is selected from small amino acid residues, including S, T, A, G, and modified forms thereof.
  • Xi is selected from S and A.
  • Zi is a proteinaceous molecule represented by Formula (II):
  • X2 is absent or is a protecting moiety
  • X3 is absent or is selected from any amino acid residue
  • X4 is selected from any amino acid residue.
  • X3 is selected from basis amino acid residues including R, K, and modified forms thereof.
  • X4 is selected from aromatic amino acid residues, including F, Y, W, and modified forms thereof.
  • Z2 is absent.
  • the isolated or purified proteinaceous molecule of Formula (I) comprises, consists or consists essentially of an amino acid sequence represented by SEQ ID NO: 1 , 2, or 3 (RRTSRRKRAKV [SEQ ID NO: 1]; RRTARRKRAKV [SEQ ID NO: 2]; or RWRRTARRKRAKV [SEQ ID NO: 3]).
  • the proteinaceous molecule of Formula (I) further comprises at least one membrane permeating moiety.
  • the membrane permeating moiety is a lipid moiety.
  • the membrane permeating moiety is a myristoyl group.
  • the coronavirus is selected from the group comprising SARS-CoV, SARS-CoV-2, and MERS-CoV.
  • the coronavirus is SARS-CoV-2.
  • the subject is a human.
  • the agent that inhibits or reduces an activity of a LSD1 polypeptide is an indirect inhibitor of the LSD1 polypeptide.
  • the agent that inhibits or reduces an activity of a LSD polypeptide may prevent the interaction between an LSD polypeptide and a RKOQ polypeptide.
  • the agent prevents the phosphorylation of a phosphorylation site of the LSD polypeptide.
  • the present invention provides a method of treating a coronavirus infection in a subject having a coronavirus infection, the method comprising administering to the subject an agent that reduces the level of a lysine-specific demethylase (LSD) polypeptide, to thereby treat the coronavirus infection in the subject.
  • the agent may be an interfering nucleic acid.
  • the LSD polypeptide is selected from an LSD1 polypeptide or an LSD2 polypeptide. In some preferred embodiments, the LSD polypeptide is an LSD1 polypeptide.
  • the present invention provides a method of treating a coronavirus infection in a subject having a coronavirus infection, the method comprising administering to the subject an agent that reduces the level or activity of a CoREST polypeptide, to thereby treat the coronavirus infection in the subject.
  • an agent that reduces the level or activity of a CoREST polypeptide to thereby treat the coronavirus infection in the subject.
  • the present invention provides a LSD1 inhibitor for use in the treatment of a coronavirus infection.
  • the present invention provides a PKC9 inhibitor for use in the treatment of a coronavirus infection.
  • the coronavirus is a betacoronavirus.
  • the betacoronavirus is SARS- CoV-2.
  • the LSD1 inhibitor is selected from GSK-LSD1 , SP-2509, SP-2577, bizine, and phenelzine.
  • the present invention provides the use of a LSD1 inhibitor in the manufacture of a medicament for the prevention and/or treatment of a coronavirus infection (e.g., a betacoronavirus infection).
  • a coronavirus infection e.g., a betacoronavirus infection
  • compositions for treating coronavirus comprising (i) an agent that inhibits or reduces an activity of a lysine-specific demethylase-1 (LSD1) polypeptide; and (ii) an antiviral agent.
  • LSD1 lysine-specific demethylase-1
  • the antiviral agent is selected from the group comprising hydroxychloroquine, chloroquine, lopinavir, ritonavir, favipiravir, and remdesivir.
  • the antiviral agent comprises an IFN-b polypeptide.
  • the present invention provides methods of inhibiting the phosphorylating activity of a protein kinase C (PKC), comprising contacting a cell infected with a coronavirus with an isolated or purified proteinaceous molecule comprising, consisting or consisting essentially of a sequence corresponding to residues 108 to 118 of LSD1.
  • PLC protein kinase C
  • the present invention provides methods of preventing S protein priming by a coronavirus, the method comprising administering a TMPRSS2 antagonist to a cell infected by the coronavirus, wherein the TMPRSS2 antagonist is an inhibitor of at least one interaction between an LSD1 polypeptide and another polypeptide (e.g., a PKC0 polypeptide).
  • a TMPRSS2 antagonist is an inhibitor of at least one interaction between an LSD1 polypeptide and another polypeptide (e.g., a PKC0 polypeptide).
  • the present invention provides a method of preventing or reducing coronavirus entry into a cell, the method comprising exposing the cell to an LSD1 inhibitor, wherein the LSD1 inhibitor reduces the expression of ACE2 by the cell, to thereby inhibit coronavirus entry into the cell.
  • Figure 1 provides a graphical representations showing the role of LSD1 on virus entry.
  • A Nanostring analysis of TMPRSS2 expression in MDA- MB-231 (TNBC breast cancer cell line) or MCF7 (epithelial breast cancer cell line) treated with siRNA targeting LSD1 or control siRNA.
  • B Nanostring analysis of TMPRSS2 expression in MDA-MB-231 (TNBC breast cancer cell line) MCF7 (epithelial breast cancer cell line), CT26 (Colorectal cancer cell line) or Huh7 (liver cancer cell line).
  • GSK-LSD1 catalytic LSD1 inhibitor
  • Phenelzine Dual catalytic/nuclear axis LSD1p inhibitor.
  • FIG. 2 shows that LSD1 and ACE2 associate as a complex on cell surface in SARS-CoV-2 susceptible cells.
  • A Representative images of CaCo2 cells imaged with the ASI digital pathology system. Cells are either permeabilized (intracellular) or not permeabilized (surface) and stained for expression of ACE2, LSD1 and TRMPSS2. Scale bar represents 10 pm.
  • B Dot graphs display the nuclear fluorescence intensity in Caco-2 cells for ACE2, LSD1 and TRMPSS2 from (A). > 50 cells counted per group. Data represent mean ⁇ SE. Mann-Whitney-test. **p ⁇ 0.01 , ***p ⁇ 0.001 , ****p ⁇ 0.0001 denote significant differences n.s. denotes non-significant.
  • +1 perfect colocalization.
  • C Representative FACS plot showing the cell surface and intracellular expression of ACE2 and LSD1 in Caco-2 cells. The numbers in each quadrant indicate the percentage of the total cell population, which also shown in dot plot (D). Data in dot plot represent two independent biological replicates.
  • E Representative image of MRC5 cells imaged with the ASI digital pathology system, that are either permeabilized (intracellular) or not permeabilized (surface) and stained for expression of ACE2, LSD1 and TRMPSS2. Scale bar represents 10 pm.
  • F Dot graphs displays the nuclear fluorescence intensity in MRC5 cells for ACE2, LSD1 and TRMPSS2 from (E). > 50 cells counted per group. Data represent mean ⁇ SE. Mann-Whitney-test. **p ⁇ 0.01 , ***p ⁇ 0.001 , ****p ⁇ 0.0001 denote significant differences n.s. denotes non-significant.
  • Figure 3 provides graphical representation showing LSD1 and ACE2 have increased association on the cell surface in SARS-CoV-2 infected cells.
  • A, B Representative image of Caco-2-SARS-CoV-2 infected cells imaged with the ASI digital pathology system (MRC5/Caco-2 uninfected not show) are shown, cells were either (A) permeabilized (intracellular) with 0.5% Triton X-100 for 15 minutes or (B) not permeabilized (surface) and stained for with primary antibodies against ACE2, LSD1 and SARS-CoV-2 nucleocapsid protein. Scale bar represents 12 mm.
  • Dot graphs displays the nuclear fluorescence intensity in Caco-2 cells for ACE2, LSD1 and SARS-CoV-2 from (A). >50 cells counted per group. Data represent mean ⁇ SE. Mann-Whitney-test. **p ⁇ 0.01 , ***p ⁇ 0.001 , ****p ⁇ 0.0001 denote significant differences n.s. denotes non-significant.
  • C Representative image of Caco-2 or Caco-2-SARS-CoV-2 infected cells imaged with the ASI digital pathology system are shown, cells were either permeabilized (intracellular) with 0.5% Triton X-100 for 15 minutes or not permeabilized (surface) and stained for with primary antibodies against ACE2, LSD1 and SARS-CoV-2 SPIKE protein. Scale bar represents 12 mm. Dot graphs displays the nuclear fluorescence intensity in Caco-2 cells for ACE2, LSD1 and SARS-CoV-2 from (C). > 50 cells counted per group. Data represent mean ⁇ SE. Mann-Whitney-test.
  • (E) FACS analysis of the expression of SARS-CoV-2 nucleocapsid protein, cell surface ACE2 and intracellular LSD1 in Caco-2 cells after 48 hours post infection. The unit of / axis indicates the percentage of the total cell population. Data represent mean ⁇ SD, n 2.
  • FIG. 4 provides graphical representations showing LSD1 directly interacting with the ACE2 cytoplasmic tail that harbours high affinity LSD1 demethylation domain.
  • A, B Representative image of Caco-2 cells imaged with the ASI digital pathology system are shown. Caco-2 cells were treated with vehicle control or 200 mM of phenelzine and imaged with the ASI digital pathology system are shown, cells were either (A) permeabilized (intracellular) with 0.5% Triton X-100 for 15 minutes or (B) non-permeabilized (surface) and stained for with primary antibodies against ACE2, LSD1 and SARS-CoV-2 nucleocapsid protein. Scale bar represents 12 mm.
  • Figure 5 provides a graphical representation of LSD1 inhibitors abrogating ACE2 expression and inhibiting SARS-CoV-2 expression.
  • n.s. denotes non-significant.
  • C Representative image of CaCo2-SARS-CoV-2 infected cells treated with phenelzine (P400 mM), GSK (G400 mM) or EPI-111 (50 mM) imaged with the ASI digital pathology system are shown, cells were permeabilized with 0.5% Triton X-100 for 15 minutes and stained for with primary antibodies against ACE2, LSD1 and SARS-CoV-2. Scale bar represents 15 mm.
  • Representative images are show for the following pairs: LSD1 & ACE2.
  • PLA signal intensity of the Duolink® assay is shown for average dot intensity (single Duolink® dot) or overall cell intensity for each cell (G)
  • Duolink® proximity ligation assay measurements of protein interactions were performed on Caco-2 cells infected with SARS-CoV-2 and treated with Control, Nardil® 400 mM, or GSK-LSD1 400 mM, permeabilized with 0.5% Triton X-100 and subject to Duolink® assay which produces a single bright dot per interaction within the cell.
  • Representative images are show for the following pairs: LSD1 & ACE2.
  • PLA signal intensity of the Duolink® assay is shown for average dot intensity (single Duolink® dot) or overall cell intensity for each cell.
  • FIG. 6 provides a graphical representation of a global transcript analysis.
  • A Caco-2 cells were treated with phenelzine, GSK-LSD1 or L1 and global RNA transcriptome analysis shows that key anti-viral and transcription processes are impacted.
  • the heat map above focuses on a DEGs list related to ISG, IFN-I, cytokine/chemokine activity, and viral entry, nuclear import/RNA synthesis, translation and replication.
  • the heatmap graph depicts the log2 (fold change) of DEGs of inhibition treated compared with control cells. Those selected DEGs have a log2(fold change) of more than 1 and FDR value of less than 0.01.
  • the heatmap values depict the log2-fold change (logFC) of DEGs from treated cells compared with control cells (GSK-LSD1 vs.
  • E Dot plot visualization of the top enriched Reactome pathways in treated cells compared to control cells. The dot colour represents the false discovery rate (FDR) value for each enriched Reactome pathway and size represents the gene ratio.
  • F Dot plot visualization of enriched Reactome pathways for GSK-LSD1 vs. control (left) and phenelzine vs. control (right). The dot colour represents the false discovery rate (FDR) value for each enriched Reactome pathway and size represents the gene ratio.
  • Figure 7 shows a graphical representation of the interplay of intracellular ACE2 in infected cells.
  • A Representative image of Caco-2 or MRC5 SARS-CoV-2 infected cells are depicted. Scale bar represents 15 mm.
  • B Cells were permeabilized and imaged with the ASI digital pathology system are shown, cells were stained for with primary antibodies against SARS-CoV-2 (nucleocapsid), ACE2 and LSD1. Dot graphs displays the nuclear fluorescence intensity in Caco-2 cells for ACE2, LSD1. 20 or more cells counted per group. Data represent mean ⁇ SEM. Mann-Whitney-test.
  • Dot graphs displays the nuclear fluorescence intensity in Caco-2 cells for ACE2, LSD1. 20 or more cells counted per group. Data represent mean ⁇ SEM. Mann-Whitney-test. * p ⁇ 0.0181 , **p ⁇ 0.01 , ***p ⁇ 0.001 , ****p ⁇ 0.0001 denote significant differences n.s. denotes non-significant.
  • the nuclear/cytoplasmic fluorescence ratio (Fn/c) using the equation: Fn/c (Fn- Fb)/(Fc - Fb), where Fn is nuclear fluorescence, Fc is cytoplasmic fluorescence, and the dotted line indicates background fluorescence.
  • the Mann- Whitney nonparametric test (GraphPad Prism, GraphPad Software, San Diego, CA) was used to determine significant differences between datasets.
  • Figure 8 shows graphical representations of ACE2 peptide inhibitor effect on nucleocapsid and Spike protein of SARS-Cov-2.
  • Figure 9 shows a graphical representation showing HBEC ALI cell culture with SARS-CoV-2 infection.
  • HBECs were pre-treated with and without Phenelzine (400 mM) for 24hr, followed by SARS-CoV-2 infection (10 4 PFU) for 2 hr.
  • Virus was removed by HBSS wash.
  • Infected HEBCs were cultured with and without Phenelzine (400 mM) for 24 hr and 48 hr post-infection.
  • qRT-PCR analysis was performed to detect the replicates of SARS-CoV-2 in infected cells at indicated time points of post-infection. The limit of detection is 100 copies/ml.
  • FIG. 10 provides graphical representations of LSD1-ACE2 interactions and the effect of LSD1 on the spike protein.
  • A Dot plot quantification of the fluorescence intensity (cell surface) of SARS-CoV-2 spike protein in SARS-CoV-2- infected Caco-2 cells with phenelzine or GSK treatment. >50 cells were analyzed for each group and were quantified using the digital pathology assay (ASI system).
  • the graph illustrates the number of gene transcripts from three replicates normalized to the geometric mean of HPRT1, GAPDH, and ACTB. Statistical significance was calculated using one-way ANOVA. NS, not significant.
  • D Schematic of SARS-CoV-2 infection assays. Caco-2 cells were seeded 24 h before the experiment. Then, cells were treated with each drug component for 48 h followed by SARS-CoV-2 infection
  • Representative images are shown for ACE2 and pan-methylation lysine antibody.
  • Duolink ® proximity ligation assay measurements of protein interactions were performed on unpermeabilized Caco-2 cells infected with SARS-CoV-2 and treated with control, or GSK inhibitors. The Duolink assay produces a single bright dot per interaction within the cell.
  • Representative images are shown for ACE2 and SARS-CoV-2 Spike Duolink ® .
  • a cell means one cell or more than one cell.
  • administering concurrently or “co-administering” and the like refer to the administration of a single composition containing two or more actives, or the administration of each active as separate compositions and/or delivered by separate routes either contemporaneously or simultaneously or sequentially within a short enough period of time that the effective result is equivalent to that obtained when all such actives are administered as a single composition.
  • simultaneous is meant that the active agents are administered at substantially the same time, and desirably together in the same formulation.
  • temporary it is meant that the active agents are administered closely in time, e.g., one agent is administered within from about one minute to within about one day before or after another.
  • any contemporaneous time is useful. However, it will often be the case that when not administered simultaneously, the agents will be administered within about one minute to within about eight hours and suitably within less than about one to about four hours. When administered contemporaneously, the agents are suitably administered at the same site on the subject.
  • the term “same site” includes the exact location, but can be within about 0.5 to about 15 cm, preferably from within about 0.5 to about 5 cm.
  • the term “separately” as used herein means that the agents are administered at an interval, for example at an interval of about a day to several weeks or months.
  • the active agents may be administered in either order.
  • agent includes a compound that induces a desired pharmacological and/or physiological effect.
  • agent also encompasses pharmaceutically acceptable and pharmacologically active ingredients of those compounds specifically mentioned herein including but not limited to salts, esters, amides, prodrugs, active metabolites, analogues and the like.
  • agent perse as well as pharmaceutically acceptable, pharmacologically active salts, esters, amides, prodrugs, metabolites, analogues, etc.
  • agent is not to be construed narrowly but extends to small molecules, proteinaceous molecules such as peptides, polypeptides and proteins as well as compositions comprising them and genetic molecules such as RNA, DNA and mimetics and chemical analogues thereof as well as cellular agents.
  • agent includes a cell that is capable of producing and secreting a polypeptide referred to herein as well as a polynucleotide comprising a nucleotide sequence that encodes that polypeptide.
  • agent extends to nucleic acid constructs including vectors such as viral or non-viral vectors, expression vectors and plasmids for expression in and secretion in a range of cells.
  • the “amount” or “level” of a biomarker is a detectable level in a sample. These can be measured by methods known to one skilled in the art and also disclosed herein. The expression level or amount of biomarker assessed can be used to determine the response to treatment.
  • antagonist refers to a substance that prevents, blocks, inhibits, neutralizes, or reduces a biological activity or effect of another molecule, such as a receptor.
  • binding refers to measurable and reproducible interactions such as binding between a target and a binding molecule, which is determinative of the presence of the target in the presence of a heterogeneous population of molecules including biological molecules.
  • binding molecule that binds to or specifically binds to a target is a molecule that binds this target with greater affinity, avidity, more readily, and/or with greater duration than it binds to other targets.
  • the extent of binding of a binding molecule to an unrelated target is less than about 10% of the binding of the molecule to the target as measured, e.g., by a radioimmunoassay (RIA).
  • a binding molecule that specifically binds to a target has a dissociation constant (Kd) of ⁇ 1 mM, ⁇ 100 nM, ⁇ 10 nM, ⁇ 1 nM, or ⁇ 0.1 nM.
  • Kd dissociation constant
  • a binding molecule specifically binds to a region on a protein that is conserved among the protein from different species.
  • specific binding can include, but does not require exclusive binding.
  • binding agent refers to an agent that binds to a target antigen and does not significantly bind to unrelated compounds.
  • binding agents that can be effectively employed in the disclosed methods include, but are not limited to, lectins, proteins, and antibodies, such as monoclonal antibodies, chimeric antibodies, or polyclonal antibodies, or antigen binding fragments thereof, as well as aptamers, Fc domain fusion proteins, and aptamers having or fused to hydrophobic protein domain, e.g., Fc domain, etc.
  • the binding agent is an exogenous antibody.
  • An exogenous antibody is an antibody not naturally produced in a mammal, e.g. in a human, by the mammalian immune system.
  • the term “complex” refers to an assemblage or aggregate of molecules ⁇ e.g., peptides, polypeptides, etc.) in direct or indirect contact with one another.
  • “contact”, or more particularly, “direct contact” means two or more molecules are close enough so that attractive noncovalent interactions, such as Van der Waal forces, hydrogen bonding, ionic and hydrophobic interactions, and the like, dominate the interaction of the molecules.
  • a complex of molecules ⁇ e.g., a peptide and polypeptide) is formed under conditions such that the complex is thermodynamically favoured ⁇ e.g., compared to a non-aggregated, or non-complexed, state of its component molecules).
  • polypeptide complex or “protein complex,” as used herein, refers to a trimer, tetramer, pentamer, hexamer, heptamer, octamer, nonamer, decamer, undecamer, dodecamer, or higher order oligomer.
  • amino acid sequence that displays substantial sequence similarity or identity to a reference amino acid sequence.
  • amino acid sequence will display at least about 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 97, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99% or even up to 100% sequence similarity or identity to at least a portion of the reference amino acid sequence.
  • an “effective amount” is at least the minimum amount required to effect a measurable improvement or prevention of a particular disorder.
  • An effective amount herein may vary according to factors such as the disease state, age, sex, and weight of the patient, and the ability of the antibody to elicit a desired response in the individual.
  • An effective amount is also one in which any toxic or detrimental effects of the treatment are outweighed by the therapeutically beneficial effects.
  • beneficial or desired results include results such as eliminating or reducing the risk, lessening the severity, or delaying the onset of the disease, including biochemical, histological and/or behavioural symptoms of the disease, its complications and intermediate pathological phenotypes presenting during development of the disease.
  • beneficial or desired results include clinical results such as decreasing one or more symptoms resulting from the disease, increasing the quality of life of those suffering from the disease, decreasing the dose of other medications required to treat the disease, enhancing effect of another medication such as via targeting, delaying the progression of the disease, and/or prolonging survival.
  • an effective amount of the drug may have the effect in reducing pathogen (bacterium, virus, etc.) titres in the circulation or tissue; reducing the number of pathogen infected cells; inhibiting (/.
  • an effective amount can be administered in one or more administrations.
  • an effective amount of drug, compound, or pharmaceutical composition is an amount sufficient to accomplish prophylactic or therapeutic treatment either directly or indirectly.
  • an effective amount of a drug, compound, or pharmaceutical composition may or may not be achieved in conjunction with another drug, compound, or pharmaceutical composition.
  • an “effective amount” may be considered in the context of administering one or more therapeutic agents, and a single agent may be considered to be given in an effective amount if, in conjunction with one or more other agents, a desirable result may be or is achieved.
  • an “effective response” of a patient or a patient’s “responsiveness” to treatment with a medicament and similar wording refers to the clinical or therapeutic benefit imparted to a patient at risk for, or suffering from, a disease or disorder, such as a pathogenic infection.
  • a disease or disorder such as a pathogenic infection.
  • such benefit includes any one or more of: extending survival (including overall survival and progression free survival); resulting in an objective response (including a complete response or a partial response); or improving signs or symptoms of the pathogenic infection.
  • a patient who “does not have an effective response” to treatment refers to a patient who does not have any one of extending survival (including overall survival and progression free survival); resulting in an objective response (including a complete response or a partial response); or improving signs or symptoms of the pathogenic infection.
  • RNA transcript e.g ., mRNA, antisense RNA, siRNA, shRNA, miRNA, etc.
  • expression of a coding sequence results from transcription and translation of the coding sequence.
  • expression of a non-coding sequence results from the transcription of the non-coding sequence.
  • level of expression or “expression level” in general are used interchangeably and generally refer to the amount of a biomarker in a sample. “Expression” generally refers to the process by which information (e.g ., gene- encoded and/or epigenetic) is converted into the structures present and operating in the cell. Therefore, as used herein, “expression” may refer to transcription into a polynucleotide, translation into a polypeptide, or even polynucleotide and/or polypeptide modifications ⁇ e.g., posttranslational modification of a polypeptide).
  • Fragments of the transcribed polynucleotide, the translated polypeptide, or polynucleotide and/or polypeptide modifications ⁇ e.g., post-translational modification of a polypeptide) shall also be regarded as expressed whether they originate from a transcript generated by alternative splicing or a degraded transcript, or from a post translational processing of the polypeptide, e.g., by proteolysis.
  • “Expressed genes” include those that are transcribed into a polynucleotide as mRNA and then translated into a polypeptide, and also those that are transcribed into RNA but not translated into a polypeptide ⁇ e.g., transfer and ribosomal RNAs).
  • “Elevated expression”, “elevated expression levels”, or “elevated levels” refers to an increased expression or increased levels of a biomarker in an individual or part of an individual ⁇ e.g., a cell, tissue or organ) relative to a control, such as an individual or individuals who are not suffering from the disease or disorder ⁇ e.g., T cell dysfunctional disorder) or parts thereof ⁇ e.g., a cell, tissue or organ) or an internal control ⁇ e.g., housekeeping biomarker).
  • Reduced expression refers to a decreased expression or decreased levels of a biomarker in an individual or part of an individual ⁇ e.g., a cell, tissue or organ) relative to a control, such as an individual or individuals who are not suffering from the disease or disorder ⁇ e.g., T-cell dysfunctional disorder) or parts thereof ⁇ e.g., a cell, tissue or organ) or an internal control ⁇ e.g., housekeeping biomarker).
  • reduced expression is little or no expression.
  • infection refers to invasion of body tissues by disease- causing microorganisms, their multiplication and the reaction of body tissues to these microorganisms and the toxins they produce. “Infection” includes but are not limited to infections by viruses, prions, bacteria, viroids, parasites, protozoans and fungi. In the context of the present invention, however, “infection” generally refers to virus infection of the family Coronnavitidae ( e.g ., coronaviruses);
  • “instructional material” includes a publication, a recording, a diagram, or any other medium of expression which can be used to communicate the usefulness of the compositions and methods of the invention.
  • the instructional material of the kit of the invention may, for example, be affixed to a container which contains the therapeutic or diagnostic agents of the invention or be shipped together with a container which contains the therapeutic or diagnostic agents of the invention.
  • LSD1 refers to any form of LSD1 and variants thereof that retain at least part of the activity of LSD1. Unless indicated differently, such as by specific reference to human LSD1 , LSD1 includes all mammalian species of native sequence LSD1, e.g., human, canine, feline, equine, and bovine. One exemplary human LSD1 is found as UniProt Accession Number 060341.
  • LSD2 refers to any form of LSD2 and variants thereof that retain at least part of the activity of LSD2. Unless indicated differently, such as by specific reference to human LSD2, LSD2 includes all mammalian species of native sequence LSD2, e.g., human, canine, feline, equine, and bovine. One exemplary human wild-type LSD2 peptide sequence is deposited as UniProt Accession Number Q8NB78.
  • LSD inhibitor refers to a molecule that decreases, blocks, inhibits, abrogates or interferes with the epigenetic function of an LSD (e.g., LSD1 or LSD2).
  • the LSD inhibitor is a direct inhibitor of LSD.
  • the LSD inhibitor is a molecule that inhibits the binding of LSD to one or more of its binding partners.
  • the LSD inhibitor inhibits the binding of the LSD binding partner PKC0 to LSD.
  • the LSD inhibitor is an indirect inhibitor of LSD.
  • the LSD inhibitors contemplated include molecules that bind specifically to PKC0, and thus decrease, block, inhibit, abrogate or interfere with the phosphorylation (and therefore subsequent activation) of LSD.
  • patient refers to any subject, particularly a vertebrate subject, and even more particularly a mammalian subject, for whom therapy or prophylaxis is desired.
  • Suitable vertebrate animals that fall within the scope of the invention include, but are not restricted to, any member of the subphylum Chordata including primates (e.g ., humans, monkeys and apes, and includes species of monkeys such from the genus Macaca ⁇ e.g., cynomologus monkeys such as Macaca fascicularis, and/or rhesus monkeys (Macaca mulatta)) and baboon (Papio ursinus), as well as marmosets (species from the genus Callithrix), squirrel monkeys (species from the genus Saimiri) and tamarins (species from the genus Saguinus), as well as species of apes such as chimpanzees (Pan troglodytes)), rodents ⁇ e.g., mice rats, guinea pigs), lagomorphs ⁇ e.g., rabbits, hares), bovines ⁇ e.
  • composition or “pharmaceutical formulation” refers to a preparation which is in such form as to permit the biological activity of the active ingredient(s) to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the composition or formulation would be administered. Such formulations are sterile. “Pharmaceutically acceptable” excipients (vehicles, additives) are those which can reasonably be administered to a subject mammal to provide an effective dose of the active ingredient employed.
  • the terms “prevent”, “prevented”, or “preventing”, refer to a prophylactic treatment which increases the resistance of a subject to developing the disease or condition or, in other words, decreases the likelihood that the subject will develop the disease or condition as well as a treatment after the disease or condition has begun in order to reduce or eliminate it altogether or prevent it from becoming worse. These terms also include within their scope preventing the disease or condition from occurring in a subject which may be predisposed to the disease or condition but has not yet been diagnosed as having it.
  • selective refers to compounds that inhibit or display antagonism towards a LSD without displaying substantial inhibition or antagonism towards another LSD or another enzyme such as a monoamine oxidase (MAO) (e.g ., MAO A or MAO B). Accordingly, a compound that is selective for LSD1 exhibits a LSD1 selectivity of greater than about 2-fold, 5-fold, 10-fold, 20-fold, 50-fold or greater than about 100-fold with respect to inhibition or antagonism of another LSD (i.e., a LSD other than LSD1 such as LSD2) or of another enzyme ⁇ e.g., a MAO).
  • a LSD other than LSD1 such as LSD2
  • another enzyme ⁇ e.g., a MAO
  • selective compounds display at least 50-fold greater inhibition or antagonism towards a specified LSD than towards another LSD or another enzyme ⁇ e.g., a MAO). In still other embodiments, selective compounds inhibit or display at least 100-fold greater inhibition or antagonism towards a specified LSD than towards another LSD or another enzyme ⁇ e.g., a MAO). In still other embodiments, selective compounds display at least 500-fold greater inhibition or antagonism towards a specified LSD than towards another LSD or another enzyme ⁇ e.g., a MAO). In still other embodiments, selective compounds display at least 1000- fold greater inhibition or antagonism towards a specified LSD than towards another LSD or another enzyme ⁇ e.g., a MAO).
  • sequence identity refers to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by- amino acid basis over a window of comparison.
  • a “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base ⁇ e.g., A, T, C, G, I) or the identical amino acid residue ⁇ e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, lie, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys, and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison ⁇ i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
  • sequence identity will be understood to mean the “match percentage” calculated by an appropriate method.
  • sequence identity analysis may be carried out using the DNASIS computer program (Version 2.5 for windows; available from Hitachi Software engineering Co., Ltd., South San Francisco, California, USA) using standard defaults as used in the reference manual accompanying the software.
  • small molecule refers to a compound that has a molecular weight of less than 3 kilodalton (kDa), and typically less than 1.5 kDa, and more preferably less than about 1 kDa.
  • Small molecules may be nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic (carbon-containing) or inorganic molecules.
  • kDa kilodalton
  • small molecules may be nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic (carbon-containing) or inorganic molecules.
  • extensive libraries of chemical and/or biological mixtures often fungal, bacterial, or algal extracts, may be screened with any of the assays of the invention to identify compounds that modulate a bioactivity.
  • a “small organic molecule” is an organic compound (or organic compound complexed with an inorganic compound (e.g ., metal)) that has a molecular weight of less than 3 kDa, less than 1.5 kDa, or even less than about 1 kDa.
  • “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridisable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel etal., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).
  • “Stringent conditions” or “high stringency conditions”, as defined herein, can be identified by those that: (1) employ low ionic strength and high temperature for washing, for example 15 mM sodium chloride/1.5 mM sodium citrate/0.1 % sodium dodecyl sulphate at 50 Q C; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42 Q C; or (3) overnight hybridization in a solution that employs 50% formamide, 5 x SSC (0.75 M NaCI, 75 mM sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 x Denhardt's solution, sonicated salmon sperm DNA (50 pg/mL),
  • the term “synergistic” means that the therapeutic effect of a LSD inhibitor (e.g ., a LSD1 inhibitor or a LSD2 inhibitor) when administered in combination with an antiviral agent (or vice-versa) is greater than the predicted additive therapeutic effects of the LSD inhibitor and the antiviral agent when administered alone.
  • a LSD inhibitor e.g ., a LSD1 inhibitor or a LSD2 inhibitor
  • compositions generally a pharmaceutical formulation
  • an antiviral agent refers to the amount of each component in a composition (generally a pharmaceutical formulation), which is effective for enhancing immune effector function including any one or more of increased recognition of an antigen or an antigen peptide derived from an antigen in the context of MHC class II molecules by T cell receptors, increased release of cytokines and/or the activation of CD8 + lymphocytes (CTLs) and/or B cells, increased recognition of an antigen or an antigen peptide derived from an antigen in the context of MHC class I molecules by T cell receptors, increased elimination of cells presented in the context of MHC class I molecules, i.e., cells characterized by presentation of an antigen with class I MHC, for example, via apoptosis or perforin- mediated cell lysis, increased production of cytokines such as IL-2, IFN-y and TNF-a, and increased specific cytolytic killing of antigen expressing target cells
  • CTLs CD8 + lymphocytes
  • the dose response curve used to determine synergy in the art is described for example by Sande etal., (see, p. 1080-1105 in A. Goodman, The Pharmacological Basis of Therapeutics, MacMillan Publishing Co., Inc., New York (1980)).
  • the optimum synergistic amounts can be determined, using a 95% confidence limit, by varying factors such as dose level, schedule and response, and using a computer-generated model that generates isobolograms from the dose response curves for various combinations of the LSD inhibitor and the antiviral agent.
  • the highest enhancement of immune effector function on the dose response curve correlates with the optimum dosage levels.
  • treatment refers to clinical intervention designed to alter the natural course of the individual or cell being treated during the course of clinical pathology. Desirable effects of treatment include decreasing the rate of disease progression, ameliorating or palliating the disease state, and remission or improved prognosis.
  • an individual is successfully “treated” if one or more symptoms associated with a T cell dysfunctional disorder are mitigated or eliminated, including, but are not limited to, reducing the proliferation of (or destroying) cancerous cells, reducing pathogen infection, decreasing symptoms resulting from the disease, increasing the quality of life of those suffering from the disease, decreasing the dose of other medications required to treat the disease, and/or prolonging survival of individuals.
  • underscoring or italicizing the name of a gene shall indicate the gene, in contrast to its protein product, which is indicated by the name of the gene in the absence of any underscoring or italicizing.
  • LSD1 shall mean the LSD1 gene
  • LSD1 shall indicate the protein product or products generated from transcription and translation and/or alternative splicing of the LSD1 gene.
  • coronaviruses display spike (S) protein trimers on their cell surface, and these glycosylated proteins accommodate binding to a host cell surface receptor. Upon receptor binding, the viral membrane fuses with that of the host cell, allowing the viral RNA entry into the host cell.
  • S spike
  • the coronavirus S protein mediates the first essential step in coronavirus infection, i.e., viral entry into host cells.
  • the S protein contains an N-terminal signal peptide which primes the nascent polypeptide for import into the endoplasmic reticulum (ER).
  • ER endoplasmic reticulum
  • the S protein is extensively modified with N-linked glycans, which are thought to provide protection against the neutralising antibodies of the host.
  • the S proteins which are present as trimers on the virus surface, combine two biological functions. First, its surface unit, Si, binds to a specific receptor located at the surface of host cells (e.g., the ACE protein receptor) and thereby determines cellular tropism and, as a consequence, viral pathogenesis. Second, the transmembrane unit, S2, mediates fusion between the viral envelope and a target cell membrane. Priming (the proteolytic separation of the Si and S2 subunits) provides the coronavirus S protein with the structural flexibility required for the subsequent membrane fusion reaction.
  • Si its surface unit
  • S2 mediates fusion between the viral envelope and a target cell membrane. Priming (the proteolytic separation of the Si and S2 subunits) provides the coronavirus S protein with the structural flexibility required for the subsequent membrane fusion reaction.
  • TMPRSS2 polypeptide has been demonstrated to cleave and activate S protein (Glowacha etal., 2011). Activation by the TMPRSS2 polypeptide is therefore believed to occur at the plasma membrane, likely after S protein binding to a virus cell entry receptor polypeptide (e.g., an ACE2 polypeptide). Notably, TMPRSS2 is reported to bind the virus cell entry polypeptide (e.g., ACE2, as described in Shulla etal., (2011)), and it is likely that the conformational changes in the S protein that are induced upon virus cell entry receptor polypeptide-binding expose the TMPRSS2 polypeptide cleavage site in the S protein.
  • virus cell entry polypeptide e.g., ACE2
  • the present inventors have determined that post-translational modifications play a significant role in the regulation of functional activity of the TMPRSS2 polypeptide. For example, a plurality of methylation sites have been identified in both (i) nuclear localisation signal domain of the TMPRSS2 polypeptide; and (ii) the catalytic domain of the TMPRSS2 polypeptide. Accordingly, administering an LSD1 inhibitor reduces the demethylation activity asserted on the TMPRSS2, causing a decrease in its functional activity.
  • an LSD inhibitor ⁇ e.g., a LSD1 inhibitor or a LSD2 inhibitor
  • a subject is administered to a subject to prevent or reduce the ability of the TMPRSS2 polypeptide from transporting the coronavirus into the host cell.
  • the TMPRSS2 polypeptide is a human TMPRSS2 polypeptide, with the amino acid sequence identified as UniProt Accession No. 015393, and set forth below: MALNSGSPPAIGPYYENHGYQPENPYPAQPTVVPTVYEVHPAQYYPSPVP
  • Lysine residues K340 and K362 of the TMPRSS2 amino acid sequence set forth above are identified as being key LSD1 -mediated methylation/demethylation residues. Accordingly, in some embodiments the present invention provides methods of antagonising TMPRSS2 polypeptide, the method comprising administering an inhibitor of LSD1 -mediated demethylation of one or both residues K340 and K362.
  • the present inventors have also determined that post-translational modifications play a significant role in the regulation of functional activity of the viral cell entry receptor polypeptides (e.g ., an ACE2 polypeptide). For example, a plurality of methylation sites are identified in both (i) nuclear localisation signal domain of the viral cell entry receptor polypeptide; and (ii) the catalytic domain of the viral cell entry receptor polypeptide. Accordingly, administering an LSD1 inhibitor reduces the demethylation activity asserted on the viral cell entry receptor polypeptide, causing a decrease in its functional activity. Accordingly, in some embodiments, an LSD inhibitor ⁇ e.g., a LSD1 inhibitor) is administered to a subject to prevent or reduce the ability of the virus cell entry receptor polypeptide to transporting a coronavirus into the host cell.
  • an LSD inhibitor ⁇ e.g., a LSD1 inhibitor
  • the virus cell entry polypeptide is a human ACE2 polypeptide, with the amino acid sequence identified as UniProt Accession No. Q9BYF1 , and set forth below:
  • Lysine residues K26 and K353 of the ACE2 polypeptide amino acid sequence set forth above are identified as key LSD1 -mediated methylation/ demethylation residues. Accordingly, in some embodiments the present invention provides methods of antagonising an ACE2 polypeptide, the method comprising administering an inhibitor of LSD1 -mediated demethylation. In some embodiments, the LSD1 -mediated demethylation includes demethylation of residues K26 and/or K353 of the ACE2 polypeptide.
  • the present invention provides methods of antagonising an ACE2 polypeptide, the method comprising administering an inhibitor of LSD1 -mediated demethylation of one or both residues K340 and K362.
  • lysine residue K31 of the ACE2 polypeptide amino acid sequence set forth above is identified as key LSD1 -mediated methylation/demethylation residue for virus entry into the host cell. Accordingly, in some embodiments, the present invention provides methods of preventing entry of a coronavirus into a host cell, the method comprising administering an inhibitor of LSD1 -mediated demethylation of an ACE polypeptide (e.g., a human ACE polypeptide as set forth in UniProt Accession No. Q9BYF1).
  • an ACE polypeptide e.g., a human ACE polypeptide as set forth in UniProt Accession No. Q9BYF1
  • the LSD1 -mediated demethylation of the ACE polypeptide includes demethylation of residue K31 of the ACE2 polypeptide [0104]
  • the viral cell entry receptor polypeptide is selected from the group comprising an ACE2 polypeptide, a dipeptidyl peptidase 4 (DPP4) polypeptide, and a CD13 polypeptide.
  • the present invention extends to a method of inhibiting the entry of a coronavirus into a cell of the host, the method comprising administering to the subject an LSD1 inhibitor (e.g ., a selective LSD1 inhibitor).
  • an LSD1 inhibitor e.g ., a selective LSD1 inhibitor.
  • the coronavirus cell entry machinery is prevented from transporting the coronavirus into the cell.
  • post-translational modifications by way of phosphorylation plays a significant role in the regulation of functional activity of the TMPRSS2 polypeptide.
  • at least one PKC0 serine phosphorylation site has been identified in the catalytic domain of the TMPRSS2 polypeptide. Accordingly, administering a PKC0 inhibitor reduces the phosphorylation activity asserted on the TMPRSS2, causing a decrease in its functional activity. Accordingly, in some embodiments, a PKC0 inhibitor is administered to a subject to prevent or reduce the ability of the TMPRSS2 polypeptide from transporting the coronavirus into the host cell.
  • Serine residue S441 of the TMPRSS2 amino acid sequence set forth above is a key PKC0-mediated phosphorylated residue. Accordingly, in some embodiments the present invention provides methods of antagonising TMPRSS2 polypeptide, the method comprising administering an inhibitor of the PKC0-mediated phosphorylation of one or both residues S441.
  • phosphorylation post-translational modifications play a significant role in the regulation of functional activity of the viral cell entry receptor polypeptides ⁇ e.g., an ACE2 polypeptide).
  • a plurality of PKC0-mediated phosphorylation sites are present in both (i) the nuclear localisation signal domain of the viral cell entry receptor polypeptide; and (ii) the catalytic domain of the viral cell entry receptor polypeptide.
  • administering a PKC0 inhibitor reduces the phosphorylation activity asserted on the viral cell entry receptor polypeptide, causing a decrease in its functional activity.
  • a PKC0 inhibitor is administered to a subject to prevent or reduce the ability of the virus cell entry receptor polypeptide to transporting a coronavirus into the host cell.
  • Residues S47, S109, S254 and T763 of the ACE2 polypeptide amino acid sequence set forth above are identified as key PKC0-mediated phosphorylation sites. Accordingly, in some embodiments the present invention provides methods of antagonising an ACE2 polypeptide, the method comprising administering an inhibitor of PKC0-mediated phosphorylation of one or more residues S47, S109, S254 and T763 of the ACE2 polypeptide.
  • post-translational modifications by way of phosphorylation plays a significant role in the regulation of functional activity of the viral cell entry receptor polypeptides (e.g ., an ACE2 polypeptide).
  • a plurality of methylation sites are identified in both (i) nuclear localisation signal domain of the viral cell entry receptor polypeptide; and (ii) the catalytic domain of the viral cell entry receptor polypeptide. Accordingly, administering an LSD1 inhibitor reduces the demethylation activity asserted on the viral cell entry receptor polypeptide, causing a decrease in its functional activity.
  • an LSD inhibitor ⁇ e.g., a LSD1 inhibitor or a LSD2 inhibitor
  • a subject is administered to a subject to prevent or reduce the ability of the virus cell entry receptor polypeptide to transporting a coronavirus into the host cell.
  • the coronavirus is a SARS-CoV-2.
  • the present invention is based in part on the determination that coronavirus infections take advantage of host machinery to enter the host cell, and that these essential host machinery are regulated at the post-translational level and the transcriptional level by methylation, by LSD1.
  • LSDs including LSD1 , play a critical role in two levels: (1) the post-transcriptional methylation of the chromatin domains across the regulatory regions of the cell entry machinery and that prevention of the demethylation by LSD1 prevents the ability of the cell to express the polypeptide expression products of the TMPRSS2 gene and/or the virus cell entry receptor gene; and (2) the post-translational methylation of the active (e.g., catalytic) domains of the TMPRSS2 polypeptide and/or the viral host cell entry polypeptide (e.g., an ACE2 polypeptide).
  • active e.g., catalytic
  • LSD1 inhibitor e.g., a selective LSD1 inhibitor
  • the LSD1 inhibitor is used in combination with an additional antiviral agent.
  • the methods and compositions of the present invention are thus particularly useful in the treatment or prophylaxis of a coronavirus infection ⁇ e.g., a coronavirus infection), as described hereafter.
  • the LSD inhibitor includes and encompasses any active agent that reduces the accumulation, function or stability of a LSD; or decrease expression of a LSD gene, and such inhibitors include without limitation, small molecules and macromolecules such as nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, polysaccharides, lipopolysaccharides, lipids or other organic (carbon containing) or inorganic molecules.
  • the LSD inhibitor is an antagonistic nucleic acid molecule that functions to inhibit the transcription or translation of LSD (e.g., LSD1 or LSD2) transcripts.
  • LSD LSD1 or LSD2
  • Representative transcripts of this type include nucleotide sequences corresponding to any one the following sequences: (1) human LSD1 nucleotide sequences as set forth for example in GenBank Accession Nos.
  • NP_694587.3 nucleotide sequences that encode an amino acid sequence that shares at least 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83,
  • nucleotide sequences that encode an amino acid sequence that shares at least 70, 71 , 72, 73, 74, 75, 76, 77,
  • Illustrative antagonist nucleic acid molecules include antisense molecules, aptamers, ribozymes and triplex forming molecules, RNAi and external guide sequences.
  • the nucleic acid molecules can act as effectors, inhibitors, modulators, and stimulators of a specific activity possessed by a target molecule, or the functional nucleic acid molecules can possess a de novo activity independent of any other molecules.
  • Antagonist nucleic acid molecules can interact with any macromolecule, such as DNA, RNA, polypeptides, or carbohydrate chains.
  • antagonist nucleic acid molecules can interact with LSD (e.g., LSD1) mRNA or the genomic DNA of LSD (e.g., LSD1) or they can interact with a LSD polypeptide (e.g., LSD1).
  • LSD LSD1
  • LSD polypeptide e.g., LSD1
  • antagonist nucleic acid molecules are designed to interact with other nucleic acids based on sequence homology between the target molecule and the antagonist nucleic acid molecule.
  • the specific recognition between the antagonist nucleic acid molecule and the target molecule is not based on sequence homology between the antagonist nucleic acid molecule and the target molecule, but rather is based on the formation of tertiary structure that allows specific recognition to take place.
  • anti-sense RNA or DNA molecules are used to directly block the translation of LSD (e.g., LSD1) by binding to targeted mRNA and preventing protein translation.
  • Antisense molecules are designed to interact with a target nucleic acid molecule through either canonical or non-canonical base pairing. The interaction of the antisense molecule and the target molecule may be designed to promote the destruction of the target molecule through, for example, RNAseH mediated RNA-DNA hybrid degradation. Alternatively, the antisense molecule may be designed to interrupt a processing function that normally would take place on the target molecule, such as transcription or replication. Antisense molecules can be designed based on the sequence of the target molecule.
  • Non-limiting methods include in vitro selection experiments and DNA modification studies using DMS and DEPC.
  • the antisense molecules bind the target molecule with a dissociation constant (Kd) less than or equal to 10 6 , 10 8 , 10 10 , or 10 12 .
  • Kd dissociation constant
  • antisense oligodeoxyribonucleotides derived from the translation initiation site e.g., between - 10 and +10 regions are employed.
  • Aptamers are molecules that interact with a target molecule, suitably in a specific way.
  • Aptamers are generally small nucleic acids ranging from 15-50 bases in length that fold into defined secondary and tertiary structures, such as stem-loops or G-quartets.
  • Aptamers can bind small molecules, such as ATP and theophiline, as well as large molecules, such as reverse transcriptase and thrombin.
  • Aptamers can bind very tightly with KdS from the target molecule of less than 10 12 M.
  • the aptamers bind the target molecule with a Kd less than 10 6 , 10 8 , 10 10 , or 10 12
  • Aptamers can bind the target molecule with a very high degree of specificity.
  • aptamers have been isolated that have greater than a 10,000-fold difference in binding affinities between the target molecule and another molecule that differ at only a single position on the molecule. It is desirable that an aptamer have a Kd with the target molecule at least 10-, 100-, 1000-, 10,000-, or 100,000-fold lower than the Kd with a background-binding molecule.
  • a suitable method for generating an aptamer to a target of interest is the “Systematic Evolution of Ligands by Exponential Enrichment” (SELEXTM).
  • SELEXTM Systematic Evolution of Ligands by Exponential Enrichment
  • the SELEXTM method is described in U.S. Pat. Nos. 5,475,096 and 5,270,163 (see also WO 91/19813). Briefly, a mixture of nucleic acids is contacted with the target molecule under conditions favourable for binding. The unbound nucleic acids are partitioned from the bound nucleic acids, and the nucleic acid -target complexes are dissociated.
  • the dissociated nucleic acids are amplified to yield a ligand-enriched mixture of nucleic acids, which is subjected to repeated cycles of binding, partitioning, dissociating and amplifying as desired to yield highly specific high affinity nucleic acid ligands to the target molecule.
  • anti-LSD1 ribozymes are used for catalysing the specific cleavage of LSD1 RNA.
  • the mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by an endonucleolytic cleavage.
  • ribozymes that catalyse nuclease or nucleic acid polymerase type reactions, which are based on ribozymes found in natural systems, such as hammerhead ribozymes, hairpin ribozymes, and tetrahymena ribozymes.
  • ribozymes that are not found in natural systems, but which have been engineered to catalyse specific reactions de novo.
  • Representative ribozymes cleave RNA or DNA substrates.
  • ribozymes that cleave RNA substrates are employed.
  • Specific ribozyme cleavage sites within potential RNA targets are initially identified by scanning the target molecule for ribozyme cleavage sites, which include the following sequences, GUA, GUU and GUC.
  • RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target gene containing the cleavage site may be evaluated for predicted structural features such as secondary structure that may render the oligonucleotide sequence unsuitable.
  • the suitability of candidate targets may also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.
  • Triplex forming functional nucleic acid molecules are molecules that can interact with either double-stranded or single-stranded nucleic acid.
  • triplex molecules When triplex molecules interact with a target region, a structure called a triplex is formed, in which there are three strands of DNA forming a complex dependent on both Watson-Crick and Hoogsteen base pairing. Triplex molecules are preferred because they can bind target regions with high affinity and specificity. It is generally desirable that the triplex forming molecules bind the target molecule with a Kd less than 10 6 , 10 8 , 10 10 , or 10- 12 .
  • EGSs External guide sequences
  • RNAse P RNAse P
  • RNAse P RNAse P
  • tRNA transfer RNA
  • RNAse P Bacterial RNAse P can be recruited to cleave virtually any RNA sequence by using an EGS that causes the target RNA: EGS complex to mimic the natural tRNA substrate. Similarly, eukaryotic EGS/RNAse P-directed cleavage of RNA can be utilized to cleave desired targets within eukaryotic cells.
  • RNA molecules that mediate RNA interference (RNAi) of a LSD1 gene or LSD1 transcript can be used to reduce or abrogate gene expression.
  • RNAi refers to interference with or destruction of the product of a target gene by introducing a single-stranded or usually a double- stranded RNA (dsRNA) that is homologous to the transcript of a target gene.
  • dsRNAi methods including double-stranded RNA interference (dsRNAi) or small interfering RNA (siRNA), have been extensively documented in a number of organisms, including mammalian cells and the nematode C. elegans (Fire etal., 1998. Nature 391 , 806-811 ).
  • RNAi can be triggered by 21 - to 23-nucleotide (nt) duplexes of small interfering RNA (siRNA) (Chiu etal., 2002 Mol. Cell. 10: 549- 561 ; Elbashir et al., 2001. Nature 411 : 494-498), or by micro-RNAs (miRNA), functional small-hairpin RNA (shRNA), or other dsRNAs which are expressed in vivo using DNA templates with RNA polymerase III promoters (Zeng et al., 2002. Mol.
  • siRNA small interfering RNA
  • dsRNA per se and especially dsRNA- producing constructs corresponding to at least a portion of a LSD1 gene are used to reduce or abrogate its expression.
  • RNAi-mediated inhibition of gene expression may be accomplished using any of the techniques reported in the art, for instance by transfecting a nucleic acid construct encoding a stem-loop or hairpin RNA structure into the genome of the target cell, or by expressing a transfected nucleic acid construct having homology for a LSD1 gene from between convergent promoters, or as a head to head or tail to tail duplication from behind a single promoter.
  • Any similar construct may be used so long as it produces a single RNA having the ability to fold back on itself and produce a dsRNA, or so long as it produces two separate RNA transcripts, which then anneal to form a dsRNA having homology to a target gene.
  • RNAi-encoding nucleic acids can vary in the level of homology they contain toward the target gene transcript, i.e., with dsRNAs of 100 to 200 base pairs having at least about 85% homology with the target gene, and longer dsRNAs, i.e., 300 to 100 base pairs, having at least about 75% homology to the target gene.
  • RNA-encoding constructs that express a single RNA transcript designed to anneal to a separately expressed RNA, or single constructs expressing separate transcripts from convergent promoters are suitably at least about 100 nucleotides in length.
  • RNA-encoding constructs that express a single RNA designed to form a dsRNA via internal folding are usually at least about 200 nucleotides in length.
  • the promoter used to express the dsRNA-forming construct may be any type of promoter if the resulting dsRNA is specific for a gene product in the cell lineage targeted for destruction.
  • the promoter may be lineage specific in that it is only expressed in cells of a particular development lineage. This might be advantageous where some overlap in homology is observed with a gene that is expressed in a non-targeted cell lineage.
  • the promoter may also be inducible by externally controlled factors, or by intracellular environmental factors.
  • RNA molecules of about 21 to about 23 nucleotides which direct cleavage of specific mRNA to which they correspond, as for example described by in U.S. Pat. Pub. No. 2002/0086356, can be utilized for mediating RNAi.
  • Such 21- to 23-nt RNA molecules can comprise a 3' hydroxyl group, can be single-stranded or double stranded (as two 21 - to 23-nt RNAs) wherein the dsRNA molecules can be blunt ended or comprise overhanging ends ( e.g ., 5', 3').
  • the antagonist nucleic acid molecule is a siRNA.
  • siRNAs can be prepared by any suitable method. For example, reference may be made to International PCT Pat. Pub. No. WO 02/44321 , which discloses siRNAs capable of sequence-specific degradation of target mRNAs when base- paired with 3' overhanging ends, which is incorporated by reference herein. Sequence specific gene silencing can be achieved in mammalian cells using synthetic, short double-stranded RNAs that mimic the siRNAs produced by the enzyme dicer.
  • siRNA can be chemically or in v/ ro-synthesized or can be the result of short double-stranded hairpin-like RNAs (shRNAs) that are processed into siRNAs inside the cell.
  • Synthetic siRNAs are generally designed using algorithms and a conventional DNA/RNA synthesizer. Suppliers include Ambion (Austin, Tex.), ChemGenes (Ashland, Mass.), Dharmacon (Lafayette, Colo.), Glen Research (Sterl ing, Va.), MWB Biotech (Esbersberg, Germany), Proligo (Boulder, Colo.), and Qiagen (Vento, The Netherlands).
  • siRNA can also be synthesized in vitro using kits such as Ambion's SILENCERTM siRNA Construction Kit.
  • siRNAs short hairpin RNAs
  • Kits for the production of vectors comprising shRNA are available, such as, for example, Imgenex's GENESUPPRESSORTM Construction Kits and Invitrogen's BLOCK-ITTM inducible RNAi plasmid and lentivirus vectors.
  • methods for formulation and delivery of siRNAs to a subject are also well known in the art. See, e.g.,
  • RNAi molecules ⁇ e.g., LSD ⁇ e.g., LSD1 or LSD2) siRNA and shRNA
  • LSD Long RNA
  • shRNA siRNA
  • siRNA and shRNA are described in the art ⁇ e.g., Yang, etat, 2010. Proc. Natl. Acad. Sci. USA 107: 21499-21504 and He et al., 2012. Transcription 3: 1-16) or available commercially from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA) and OriGene Technologies, Inc. (Rockville, MD, USA) .
  • the present invention further contemplates peptide or polypeptide- based inhibitor compounds.
  • BHC80 also known as PHD finger protein 21 A
  • the present invention further contemplates the use of BHC80 or biologically active fragments thereof for inhibiting LSD1 enzymatic activity.
  • Amino acid sequences of BHC80 polypeptides, and nucleotide sequences encoding BHC80 polypeptides, are publicly available. In this regard, reference may be made for example to (1) GenBank Accession No.
  • NP057705 for a Homo sapiens BHC80 amino acid sequence
  • GenBank NM016621 for a nucleotide sequence encoding the amino acid sequence set forth in GenBank Accession No. NP057705
  • GenBank Accession No. NP620094 for a Mus musculus BHC80 amino acid sequence
  • GenBank NM138755 for a nucleotide sequence encoding the amino acid sequence set forth in GenBank Accession No. NP620094
  • GenBank Accession No. NP00118576.1 for a Gallus gallus BHC80 amino acid sequence
  • GenBankNMOO1 199647 for a nucleotide sequence encoding the amino acid sequence set forth in GenBank Accession No. NP00118576.1
  • GenBank Accession No. DAA21793 for a Bos taurus BHC80 amino acid sequence.
  • Illustrative BHC80 polypeptides are selected from the group consisting of: (1) a polypeptide comprising an amino acid sequence that shares at least 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99% sequence similarity with the amino acid sequence listed in any one of the GenBank BHC80 polypeptide entries noted above; (2) a polypeptide comprising an amino acid sequence that shares at least 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99% sequence identity with
  • a BHC80 polypeptide can be introduced into a cell by delivering a polypeptide perse, or by introducing into the cell a BHC80 nucleic acid comprising a nucleotide sequence encoding a BHC80 polypeptide.
  • a BHC80 nucleic acid comprises a nucleotide sequence selected from: (1) a BHC80 nucleotide sequence listed in any one of the GenBank BHC80 polynucleotide entries noted above; (2) a nucleotide sequence that shares at least 70, 71 , 72, 73, 74, 75,
  • the BHC80 nucleic acid can be in the form of a recombinant expression vector.
  • the BHC80 nucleotide sequence can be operably linked to a transcriptional control element(s), e.g., a promoter, in the expression vector.
  • Suitable vectors include, e.g., recombinant retroviruses, lentiviruses, and adenoviruses; retroviral expression vectors, lentiviral expression vectors, nucleic acid expression vectors, and plasmid expression vectors.
  • the expression vector is integrated into the genome of a cell. In other cases, the expression vector persists in an episomal state in a cell.
  • Suitable expression vectors include, but are not limited to, viral vectors ⁇ e.g., viral vectors based on vaccinia virus; poliovirus; adenovirus (see, e.g.,
  • WO 93/03769 WO 93/19191 ; WO 94/28938; WO 95/11984 and WO 95/00655); adeno-associated virus (see, e.g., AN etal., Hum Gene Ther 9 :8186, 1998,
  • SV40 herpes simplex virus
  • human immunodeficiency virus see, e.g., Miyoshi etal., PNAS 94: 1031923, 1997; Takahashi etal., J Virol 73: 78127816, 1999
  • a retroviral vector ⁇ e.g., Murine Leukemia Virus, spleen necrosis virus, and vectors derived from retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, a lentivirus, human immunodeficiency virus, myeloproliferative sarcoma virus, and mammary tumour virus
  • retroviral vector ⁇ e.g., Murine Leukemia Virus, spleen necrosis virus, and vectors derived from retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, a lentivirus, human immunodeficiency virus, mye
  • Small molecule agents that reduce enzymatic activity of LSD1 that are suitable for use in the present invention include monoamine oxidase (MAO) inhibitors that also inhibit LSD1 enzymatic activity; polyamine compounds that inhibit LSD1 enzymatic activity; phenylcyclopropylamine derivatives that inhibit LSD1 enzymatic activity; and the like.
  • MAO monoamine oxidase
  • MAO inhibitors include MAO-A-selective inhibitors, MAO-B-selective inhibitors, and MAO non-selective inhibitors.
  • Illustrative examples of MAO inhibitors include reported inhibitors of the MAO-A isoform, which preferentially deaminates 5-hydroxytryptamine (serotonin) (5-HT) and norepinephrine (NE), and/or the MAO-B isoform, which preferentially deaminates phenylethylamine (PEA) and benzylamine (both MAO-A and MAO-B metabolize Dopamine (DA)).
  • MAO inhibitors may be irreversible or reversible ⁇ e.g., reversible inhibitors of MAO-A (RIMA)), and may have varying potencies against MAO-A and/or MAO-B ⁇ e.g., non-selective dual inhibitors or isoform-selective inhibitors).
  • RIMA reversible inhibitors of MAO-A
  • the MAO inhibitors are selected from : clorgyline; L-deprenyl; isocarboxazid (MARPLANTM); ayahuasca; nialamide; iproniazide; iproclozide; moclobemide (AURORIXTM; 4-chloro-N-(2-morpholin-4- ylethyl)benzamide); phenelzine (NARDILTM; ( ⁇ )-2-phenylethylhydrazine); tranylcypromine (PARNATETM; ( ⁇ )-trans-2-phenylcyclopropan-l-amine) (the congeneric of phenelzine); bizine (described in Prusevich et al., ACS Chem.
  • selegiline hydrochloride L-deprenyl, ELDEPRYLTM, ZELAPARTM
  • dimethylselegilene dimethylselegilene
  • safinamide rasagiline
  • AZILECTTM bifemelane
  • desoxypeganine harmine (also known as telepathine or banasterine); linezolid (ZYVOXTM, ZYVOXIDTM); pargyiine (EUDATINTM, SUPIRDYLTM); dienolide kavapyrone desmethoxyyangonin; 5-(4- Arylmethoxyphenyl)-2-(2-cyanoethyl)tetrazoles; and the like.
  • Small molecule LSD1 inhibitors may also be selected from polyamine compounds as described for example in United States Publication No.
  • Illustrative polyamine inhibitors of LSD1 include compounds according to formula (I):
  • n is an integer from 1 to 12; m and p are independently an integer from 1 to 5; q is 0 or 1 ; each Ri is independently selected from the group consisting of C-i-Cs alkyl, C4-C15 cycloalkyl, C3-C15 branched alkyl, C6-C20 aryl, C6-C20 heteroaryl, C7-C24 aralkyl, C7-C24 heteroaralkyl, and
  • R3 is selected from the group consisting of C-i-Cs alkyl, C4-C15 cycloalkyl, C3-C15 branched alkyl, C6-C20 aryl, C6-C20 heteroaryl, C7-C24 aralkyl and C7-C24 heteroaralkyl;
  • each R2 is independently selected from hydrogen or a C-i-Cs alkyl.
  • a suitable polyamine compound is a compound of Formula (I), wherein one or both Ri is a C6-C20 aryl, such as a single ring aryl, including without limitation, a phenyl.
  • the compound is of the formula (I) and each Ri is phenyl.
  • q is 1 , m and p are 3, and n is 4. In another embodiment, q is 1 , m and p are 3, and n is 7.
  • a suitable polyamine compound is a compound of Formula (I), where at least one or both Ri is a C8-C12 or a C-i-Cs alkyl, such as a linear alkyl.
  • One or both Ri may be a C-i-Cs linear alkyl, such as methyl or ethyl.
  • each Ri is methyl.
  • One or both Ri may comprise or be a C4-C15 cycloalkyl group, such as a cycloalkyl group containing a linear alkyl group, where the cycloalkyl group is connected to the molecule either via its alkyl or cycloalkyl moiety.
  • one or both Ri may be cyclopropylmethyl or cyclohexylmethyl.
  • one Ri is cyclopropylmethyl or cyclohexyl methyl and the other Ri is a linear alkyl group, such as a linear C-i-Cs unsubstituted alkyl group, including without limitation an ethyl group.
  • Ri is a C3-C15 branched alkyl group such as isopropyl.
  • the substituted alkyl may be substituted with any substituent, including a primary, secondary, tertiary or quaternary amine.
  • Ri is a C-i-Cs alkyl group substituted with an amine such that Ri may be e.g., alkyl-NH2 or an alkyl-amine-alkyl moiety such as -(CFl2)yNFI(CFl2)zCFl3 where y and z are independently an integer from 1 to 8. In one embodiment, Ri is -(CFl2)3NFl2.
  • the compound is of the formula (I) where one or both Ri is a C7-C24 substituted or unsubstituted aralkyl, which in one embodiment is an aralkyl connected to the molecule via its alkyl moiety ⁇ e.g., benzyl).
  • both Ri are aralkyl moieties wherein the alkyl portion of the moiety is substituted with two aryl groups and the moiety is connected to the molecule via its alkyl group.
  • one or both Ri is a C7-C24 aralkyl wherein the alkyl portion is substituted with two phenyl groups, such as when Ri is
  • both Ri of Formula (I) is
  • each Ri of Formula (I) is
  • n 1 , 2 or 5 and m and p are each 1.
  • At least one Ri is hydrogen.
  • the other Ri may be any moiety listed above for Ri, including an aryl group such as benzyl.
  • Any of the compounds of Formula (I) listed above include compounds where at least one or both of R2 is hydrogen or a C-i-Cs substituted or unsubstituted alkyl.
  • each R2 is an unsubstituted alkyl such as methyl.
  • each R2 is hydrogen.
  • Any of the compounds of Formula (I) listed above may be compounds where q is 1 and m and p are the same.
  • the polyaminoguanidines of Formula (I) may be symmetric with reference to the polyaminoguanidine core ⁇ e.g., excluding Ri).
  • the compounds of Formula (I) may be asymmetric, e.g., when q is 0.
  • m and p are 1 .
  • q is 0.
  • n is an integer from 1 to 5.
  • the compound is a polyaminobiguanide or N- alkylated polyaminobiguanide.
  • An N-alkylated polyaminobiguanide intends a polyaminobiguanide where at least one imine nitrogen of at least one biguanide is alkylated.
  • the compound is a polyaminobiguanide of the Formula (I), or a salt, solvate, or hydrate thereof, where q is 1 , and at least one or each R, is of the structure:
  • each R3 is independently selected from the group consisting of C1-C8 alkyl, C6-C20 aryl, C6-C20 heteroaryl, C7-C24 aralkyl, and C7-C24 heteroaralkyl; and each R2 is independently hydrogen or a C-i-Cs alkyl.
  • each R3 is a C-i-Cs alkyl.
  • the alkyl may be substituted with any substituent, including a primary, secondary, tertiary or quaternary amine.
  • R3 is a C-i-Cs alkyl group substituted with an amine such that R3 may be e.g., alkyl-NFte or an alkyl-amine-alkyl moiety such as -(CH2) y NH(CH2)zCH3 where y and z are independently an integer from 1 to 8.
  • R3 is -(CH2)3NH2.
  • R3 may also be a C4-C15 cycloalkyl or a C3-C15 branched alkyl.
  • at least one or each R3 is a C6-C20 aryl.
  • q is 1 , m and p are 3, and n is 4.
  • q is 1 , m and p are 3, and n is 7.
  • the compound is a polyaminobiguanide of Formula (I) where at least one R3 is a C7-C24 aralkyl, which in one embodiment is an aralkyl connected to the molecule via its alkyl moiety.
  • each R3 is an aralkyl moiety where the alkyl portion of the moiety is substituted with one or two aryl groups and the moiety is connected to the molecule via its alkyl moiety.
  • at least one or each R3 is an aralkyl where the alkyl portion is substituted with two phenyl or benzyl groups, such as when R3 is 2,2- diphenylethyl or 2,2-dibenzylethyl.
  • each R3 is 2,2- diphenylethyl and n is 1 , 2 or 5.
  • each R3 is 2,2-diphenylethyl and n is 1 , 2 or 5 and m and p are each 1.
  • any of the polyaminobiguanide compounds of Formula (I) listed above include compounds where at least one or both of R2 is hydrogen or a C-i-Cs alkyl.
  • each R2 is an unsubstituted alkyl, such as methyl.
  • each R2 is a hydrogen.
  • any of the polyaminobiguanide compounds of formula (I) listed above include compounds where q is 1 and m and p are the same. Accordingly, the polyaminobiguanides of Formula (I) may be symmetric with reference to the polyaminobiguanide core. Alternatively, the compounds of Formula (I) may be asymmetric. In one embodiment, m and p are 1. In some embodiments, q is 0. In some embodiments, n is an integer from 1 to 5. In some embodiments, q, m and p are each 1 and n is 1 , 2 or 5.
  • each Ri, R2, R3, m, n, p and q disclosed in reference to Formula (I) intends and includes all combinations thereof the same as if each and every combination of R-i, R2, R3, m, n, p and q were specifically and individually listed.
  • Representative compounds of the Formula (I) include:
  • polyamine compound is represented by the structure according to Formula (II):
  • n 1 , 2 or 3;
  • each L is independently a linker of from about 2 to 14 carbons in length, for example of about 2, 3, 4, 5, 6, 8, 10, 12 or 14 carbon atoms in length, where the linker backbone atoms may be saturated or unsaturated, usually not more than one, two, three, or four unsaturated atoms will be present in a tether backbone, where each of the backbone atoms may be substituted or unsubstituted (for example with a C1-C8 alkyl), where the linker backbone may include a cyclic group (for example, a cyclohex-1 ,3-diyl group where 3 atoms of the cycle are included in the backbone);
  • each R12 is independently selected from hydrogen and a C-i-Cs alkyl
  • each Rn is independently selected from hydrogen, C2-C8alkenyl, Ci- C8 alkyl or C3-C8 branched alkyl ( e.g ., methyl, ethyl, tert-butyl, isopropyl, pentyl, cyclobutyl, cyclopropylmethyl, 3-methylbutyl, 2-ethylbutyl, 5-NH2-pent-1-yl, propyl-1 - ylmethyl(phenyl)phosphinate, dimethylbicyclo[3.1.1 ]heptyl)ethyl, 2- (decahydronaphthyl)ethyl and the like), C6-C20 aryl or heteroaryl, C1-C23 aralkyl or heteroaralkyl (2-phenylbenzyl, 4-phenylbenzyl, 2-benzylbenzyl, 3-benzylbenzyl, 3,3- diphenylpropyl, 3-(benzo
  • each L is independently selected from: -CHRi3-(CH )m-, -CHRi3-(CH )n-CHRi3-, -(CH )mCHRi3-, -CH2-A-CH2- and -(CH 2 )p- where :
  • m is an integer from 1 to 5;
  • A is (CH2)m, ethane-1, 1-diyl or cyclohex-1 ,3-diyl;
  • p is an integer from 2 to 14, such as 1 , 2, 3, 4 or 5;
  • n is an integer from 1 to 12;
  • Ri3 is a C-i-Cs alkyl.
  • the alkyl portion of the aralkyl or heteroaralkyl moiety is connected to the molecule via its alkyl moiety.
  • Rn may be an aralkyl moiety such as 2-phenylbenzyl, 4-phenylbenzyl, 3,3,-diphenylpropyl, 2-(2- phenylethyl)benzyl, 2-methyl-3-phenylbenzyl, 2-napthylethyl, 4-(pyrenyl)butyl, 2-(3- methylnapthyl)ethyl, 2-(1 ,2-dihydroacenaphth-4-yl)ethyl and the like.
  • aralkyl moiety such as 2-phenylbenzyl, 4-phenylbenzyl, 3,3,-diphenylpropyl, 2-(2- phenylethyl)benzyl, 2-methyl-3-phenylbenzyl, 2-napthylethyl, 4-(pyrenyl)butyl, 2-(3- methylnapthyl)ethyl, 2-(1 ,2-dihydroacenaphth-4-
  • Rn may be a heteroaralkyl moiety such as 3-(benzoimidazolyl)propanoyl, 1 -(benzoimidazolyl)methanoyl, 2-(benzoimidazolyl)ethanoyl, 2-(benzoimidazolyl)ethyl and the like.
  • the compound of Formula (II) comprises at least one moiety selected from the group consisting of t-butyl, isopropyl, 2-ethylbutyl, 1-methylpropyl, 1-methylbutyl, 3-butenyl, isopent-2-enyl, 2-methylpropan-3-olyl, ethylthiyl, phenylthiyl, propynoyl, 1 -methyl-1 H-pyrrole-2-yl; trifluoromethyl, cyclopropanecarbaldehyde, halo-substituted phenyl, nitro-substituted phenyl, alkyl- substituted phenyl, 2,4,6-trimethylbenzyl, halo-5-substituted phenyl (such as para- (F3S)-phenyl, azido and 2-methylbutyl.
  • t-butyl isopropyl, 2-ethylbutyl, 1-methylpropyl,
  • each Rn is independently selected from hydrogen, n-butyl, ethyl, cyclohexylmethyl, cyclopentylmethyl, cyclopropylmethyl, cycloheptylmethyl, cyclohexyleth-2-yl, and benzyl.
  • the polyamine compound is of the structure of Formula (II), where n is 3, such that the compound has a structure according to Formula (III):
  • Li, L2 and L3 are independently selected from -CHRi3-(CH )m-, -CHRi3-(CH 2 )n-CHRi3-, -(CH 2 )m-CHRi 3 -, -CH 2 -A-CH 2 - and -(CH 2 )p-;
  • the polyamine compound is of the structure of Formula (III) where: Li is -CHRi3-(CH 2 )m-; l_ 2 is -CHRi3-(CH 2 ) n -CHRi3-; and L3 is - (CH 2 )m-CHRi3-; where Rn, R12, R13, m and n are as defined above.
  • the polyamine compound is of the structure of Formula (III) where: Li, l_2, and L3 are independently -CH 2 -A-CH 2 -; and R12 is hydrogen; where R11 and A are as defined above.
  • at least one of an A and an Rn comprises an alkenyl moiety.
  • the polyamine compound is of the structure of Formula (III) where: Li, L2 and l_3are independently -(CFl2)p- where p is as defined above; and R121S hydrogen.
  • Li and L3 are independently -(CFl2)p- where p is as defined above; and R121S hydrogen.
  • p is an integer from 3 to 7
  • L3 p is an integer from 3 to 14.
  • the polyamine compound is of the structure of Formula (III) where: Li, and L3 are independently -(CH2) P -; L2 is -CFI2-A-CFI2-; and R12 is hydrogen; where R12, p and A are as defined above.
  • p is an integer from 2 to 6
  • L3 A is (CFl2) x where x is an integer from 1 to 5, or cyclohex-1 ,3-diyl.
  • the polyamine compound is of the structure of Formula (II), where n is 2, such that the compound has a structure according to Formula (IV):
  • Li and L2 are independently selected from -CHRi3-(CH2)m- CHRi3-(CH 2 )n-CHRi3-, -(CH 2 )n, CHR13-, -CH2-A-CH2- and -(CH2 ) P -;
  • the polyamine compound is of the structure of Formula (IV) where: Li is -(CH2) P -; and L2 is -(CH2)m-CHRi3-; where R13, m and p are as defined above.
  • Li p is an integer from 3 to 10
  • L2 n is an integer from 2 to 9.
  • the polyamine compound is of the structure of Formula (IV) where: Li and L2 are -(CH2) P -; where p is as defined above. In particular embodiments, p is an integer from 3 to 7. [0184] In certain embodiments, the polyamine compound is of the structure of Formula (II), where n is 1 , such that the compound has a structure according to Formula (V);
  • Li is -(CFl2)p- where p is as defined above.
  • p is an integer from 2 to 6.
  • one Rn is an amino- substituted cycloalkyl (e.g ., a cycloalkyl group substituted with a primary, secondary, tertiary or quaternary amine) or a C2-C8 alkanoyl (which alkanoyl may be substituted with one or more substituents such as a methyl or an alkylazide group); and the other R11 is a C-i-Cs alkyl or a C7-C24 aralkyl.
  • a cycloalkyl group substituted with a primary, secondary, tertiary or quaternary amine e.g a cycloalkyl group substituted with a primary, secondary, tertiary or quaternary amine
  • a C2-C8 alkanoyl which alkanoyl may be substituted with one or more substituents such as a methyl or an alkylazide group
  • the other R11 is a C-i-Cs
  • Representative compounds of the Formula (II) include, e.g. ⁇
  • Phenylcyclopropylamine derivatives that are inhibitors of include compounds represented by Formula (VI):
  • each of R1-R5 is independently selected from H, halo, alkyl, alkoxy, cycloalkoxy, haloalkyl, haloalkoxy, -L-aryl, -L-heterocyclyl, -L-carbocyclyl, acylamino, acyloxy, alkylthio, cycloalkylthio, alkynyl, amino, alkylamino, aryl, arylalkyl, arylalkenyl, arylalkynyl, arylalkoxy, aryloxy, arylthio, heteroarylthio, cyano, cyanato, haloaryl, hydroxyl, heteroaryloxy, heteroarylalkoxy, isocyanato, isothiocyanate, nitro, sulfinyl, sulfonyl, sulfonamide, thiocarbonyl, thiocyanato,
  • R6 is H or alkyl
  • R7 is H, alkyl, or cycloalkyl
  • R8 is a -L-heterocyclyl wherein the ring or ring system of the -L-heterocyclyl has from 0 to 3 substituents selected from halo, alkyl, alkoxy, cycloalkoxy, haloalkyl, haloalkoxy, -L-aryl, -L-heterocyclyl, -L-carbocyclyl, acylamino, acyloxy, alkylthio, cycloalkylthio, alkynyl, amino, alkylamino, aryl, arylalkyl, arylalkenyl, arylalkynyl, arylalkoxy, aryloxy, arylthio, heteroarylthio, cyano, cyanato, haloaryl, hydroxyl, heteroaryloxy, heteroarylalkoxy, isocyanato, isothiocyanate, nitro, sulfin,
  • R8 is -L-aryl wherein the ring or ring system of the -L-aryl has from 1 to 3 substituents selected from halo, alkyl, alkoxy, cycloalkoxy, haloalkyl, haloalkoxy, -L-aryl, -L-heterocyclyl, -L-carbocyclyl, acylamino, acyloxy, alkylthio, cycloalkylthio, alkynyl, amino, alkylamino, aryl, arylalkyl, arylalkenyl, arylalkynyl, arylalkoxy, aryloxy, arylthio, heteroarylthio, cyano, cyanato, haloaryl, hydroxyl, heteroaryloxy, heteroarylalkoxy, isocyanato, isothiocyanate, nitro, sulfinyl, sulfony
  • each L is independently selected from -(CH 2 )n- (CH 2 )n-, -(CH2)nNH(CH 2 )n-, -(CH 2 ) n O(CH 2 ) n -, and -(CH 2 )nS(CH 2 ) n -, and where each n is independently chosen from 0, 1 , 2, and 3;
  • L is a covalent bond.
  • R6 and R7 are hydro.
  • one of R1 -R5 is selected from -L-aryl, -L-heterocyclyl, and -L-carbocyclyl.
  • a compound of the invention is of Formula (VI) where: [0200] each R1 -R5 is optionally substituted and independently chosen from -H, halo, alkyl, alkoxy, cycloalkoxy, haloalkyl, haloalkoxy, -L-aryl, -L-heteroaryl, -L- heterocyclyl, -L-carbocyclyl, acylamino, acyloxy, alkylthio, cycloalkylthio, alkynyl, amino, aryl, arylalkyl, arylalkenyl, arylalkynyl, arylalkoxy, aryloxy, arylthio, heteroarylthio, cyano, cyanato, haloaryl, hydroxyl, heteroaryloxy, heteroarylalkoxy, isocyanato, isothiocyanato, nitro, sulf
  • R6 is chosen from -H and alkyl
  • R7 is chosen from -H, alkyl, and cycloalkyl
  • Rx when present is chosen from -H, alkyl, alkynyl, alkenyl, -L- carbocyclyl, -L-aryl, and -L-heterocyclyl, all of which are optionally substituted (except -H);
  • Ry when present is chosen from -H, alkyl, alkynyl, alkenyl, -L- carbocyclyl, -L-aryl, and -L-heterocyclyl, all of which are optionally substituted (except -H), where Rx and Ry may be cyclically linked;
  • Rz when present is chosen from -H, alkoxy, -L-carbocyclyl, -L- heterocyclyl, -L-aryl, wherein the aryl, heterocyclyl, or carbocyclyl are optionally substituted; each L is a linker that links the main scaffold of Formula I to a carbocyclyl, heterocyclyl, or aryl group, wherein the hydrocarbon portion of the linker -L- is saturated, partially saturated, or unsaturated, and is independently chosen from a saturated parent group having a formula of -(CH2)n-(CH2)2-,
  • optionally substituted refers to zero or 1 to 4 optional substituents independently chosen from acylamino, acyloxy, alkenyl, alkoxy, cycloalkoxy, alkyl, alkylthio, cycloalkylthio, alkynyl, amino, aryl, arylalkyl, arylalkenyl, arylalkynyl, arylalkoxy, aryloxy, arylthio, heteroarylthio, carbocyclyl, cyano, cyanato, halo, haloalkyl, haloaryl, hydroxyl, heteroaryl, heteroaryloxy, heterocyclyl, heteroarylalkoxy, isocyanato, isothiocyanato, nitro, sulfinyl, sulfonyl, sulfonamide, thiocarbonyl, thiocyanato, trihalomethanesulphonamido, O-
  • R8 is -CORz, such that the compound is of the following structure:
  • R1-R7 are described above; and Rz is -L-heterocyclyl which is optionally substituted with from 1-4 optional substituents independently chosen from acylamino, acyloxy, alkenyl, alkoxy, cycloalkoxy, alkyl, alkylthio, cycloalkylthio, alkynyl, amino, aryl, arylalkyl, arylalkenyl, arylalkynyl, arylalkoxy, aryloxy, arylthio, heteroarylthio, carbocyclyl, cyano, cyanato, halo, haloalkyl, haloaryl, hydroxyl, heteroaryl, heteroaryloxy, heterocyclyl, heteroarylalkoxy, isocyanato, isothiocyanato, nitro, sulfinyl, sulfonyl, sulfonamide, thiocarbonyl
  • each L is independently chosen from -(CH 2 )n-(CH 2 )n- and -(CH 2 )n-0-(CH 2 )n where each n is independently chosen from 0, 1 , 2, and 3.
  • each L is chosen from a bond, -CH 2 -, -CH2CH2-, -OCH2-, -OCH2CH2-, -CH2OCH2-, -CH2CH2CH2-, -OCH2CH2CH2-, and -CH2OCH2CH2-.
  • each L is chosen from a bond, -CH2-, -CH2CH2-, OCH2-, and -CH2CH2CH2-.
  • L is chosen from a bond and -CH2-.
  • Exemplary compounds of Formula (VI) include:
  • Exemplary compounds of Formula VI include: N-cyclopropyl-2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ acetamide; 2- ⁇ [(trans)-2- phenylcyclopropyl]amino acetamide; N-cyclopropyl-2- ⁇ [(trans)-2- phenylcyclopropyl]amino ⁇ propanamide; 2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ -N- prop-2-ynylacetamide; N-isopropyl-2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ acetamide; N-(tert-butyl)-2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ acetamide; N-(2-morpholin-4-yl- 2-oxoethyl)-N-[(trans)-2-phenylcyclopropyl]amine; 2- ⁇ [(trans)
  • Alternative small molecule LSD inhibitor compounds may be selected from selective LSD1 and LSD1/MAOB dual inhibitors disclosed for example in International PCT Patent Pub. No. WO 2010/043,721 , WO 2010/084,160,
  • Representative compounds of this type include phenylcyclopropylamine derivatives or homologs, illustrative examples of which include phenylcyclopropylamine with one or two substitutions on the amine group; phenylcyclopropylamine with zero, one or two substitutions on the amine group and one, two, three, four, or five substitution on the phenyl group; phenylcyclopropylamine with one, two, three, four, or five substitution on the phenyl group; phenylcyclopropylamine with zero, one or two substitutions on the amine group wherein the phenyl group of PCPA is substituted with (exchanged for) another ring system chosen from aryl or heterocyclyl to give an aryl- or heteroaryl- cycl
  • Non-limiting embodiments of phenylcyclopropylamine derivatives or analogues include “cyclopropylamine amide” derivatives and “cyclopropylamine” derivatives.
  • Specific examples of “cyclopropylamine acetamide” derivatives include, but are not limited to: N-cyclopropyl-2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ acetamide; 2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ acetamide; N-cyclopropyl-2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ propanamide; 2- ⁇ [(trans)-2-phenylcyclopropyl] amino ⁇ -N-prop-2-ynylacetamide; N-isopropyl-2- ⁇ [(trans)-2-phenylcyclopropyl]amino ⁇ acetamide; N-(tert-butyl)-2- ⁇ [(trans)-2-
  • cyclopropylamine derivatives, include, but are not limited to: N-4-fluorobenzyl-N- ⁇ (trans)-2-[4-(benzyloxy)phenyl]cyclopropyl ⁇ amine, N-4-methoxybenzyl-N- ⁇ (trans)-2-[4-(benzyloxy)phenyl]cyclopropyl ⁇ amine, N-benzyl- N- ⁇ (trans)-2-[4-(benzyloxy)phenyl]cyclopropyl ⁇ amine, N-[(trans)-2- phenylcyclopropyl]amino-methyl)pyridin-3-ol, N-[(trans)-2-phenylcyclopropyl]-N-(3- methylpyridin-2-ylmethyl)amine, N-[(trans)-2-phenylcyclopropyl]-N-(4-chloropyridin-3- ylmethyl)amine, N-[(trans)-2-phenylcyclopropyl]
  • LSD1 inhibitors are, e.g., phenelzine or pargyline (propargylamine) or a derivative or analogue thereof.
  • Derivatives and analogues of phenelzine and pargyline (propargylamine) include, but are not limited to, compounds where the phenyl group of the parent compound is replaced with a heteroaryl or optionally substituted cyclic group or the phenyl group of the parent compound is optionally substituted with a cyclic group.
  • the phenelzine or pargyline derivative or analogue thereof has selective LSD1 or dual LSD1/MAOB inhibitory activity as described herein.
  • the phenelzine derivative or analogue has one, two, three, four or five substituents on the phenyl group.
  • the phenelzine derivative or analogue has the phenyl group substituted with (exchanged for) an aryl or heterocyclyl group wherein said aryl or heterocyclyl group has zero, one, two, three, four or five substituents.
  • the pargyline derivative or analogue has one, two, three, four or five substituents on the phenyl group.
  • the pargyline derivative or analogue has the phenyl group substituted with (exchanged for) an aryl or heterocyclyl group wherein said aryl or heterocyclyl group has zero, one, two, three, four or five substituents.
  • the present invention also contemplates tranylcypromine derivatives as described for example by Binda etal., (2010. J . Am. Chem. Soc. 132: 6827- 6833, which is hereby incorporated by reference herein in its entirety) as inhibitors of LSD (e.g ., LSD1 and/or LSD2) enzymatic function.
  • LSD e.g ., LSD1 and/or LSD2
  • LSD1 inhibitor compounds may be selected from tranylcypromine analogues described by Benelkebir etal. (2011. Bioorg. Med. Chem. doi: 10.1016/j.bmc.2011.02.017, which is hereby incorporated by reference herein in its entirety),
  • Representative analogues of this type, including o-, m-, and p- bromo analogues include: (1 R, 2S)-2-(4-bromophenyl)cyclopropanamine hydrochloride (Compound 4c), (1 R, 2S)-2-(3-bromophenyl)cyclopropanamine hydrochloride (Compound 4d), : (1 R, 2S)-2-(2-bromophenyl)cyclopropanamine hydrochloride (Compound 4e), : (1 R, 2S)-2-(biphenyl-4-yl)cyclopropanamine hydrochloride (Compound 4f).
  • Non-limiting compounds disclosed by Culhane etal. include propargyl-Lys-4, N-methylpropargyl-Lys-4 H3- 21 , c/s-3-chloroallyl-Lys-4 H3-21 , trans- 3-chloroallyl-Lys-4 H3-21 , exo-cyclopropyl- Lys-4 H3-21 , endo- cyclopropyl-Lys-4 H3-21 , enc/o-dimethylcyclopropyl-Lys-4, hydrazino-Lys-4 H3-21 and hydrazino-Lys-4 H3-21.
  • cyclopropylamine compounds that are useful for inhibiting LSD1 include those disclosed by Fyfe etal., in U.S. Pat. Pub. No. 2013/0197013, which is incorporated herein by reference in its entirety.
  • Illustrative cyclopropylamine inhibitors of LSD1 which are disclosed as being selective for inhibiting LSD1 , include compounds according to Formula VII:
  • X 1 and X 2 are independently C(R2) or N;
  • X 3 and X 4 when present, are independently C(R2) or N;
  • (G) is a cyclyl group (as shown in Formula VII, the cyclyl group (G) has n substituents (R1));
  • each (R1) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulfinyl, sulfonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl;
  • each (R2) is independently chosen from -H, alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulfinyl, sulfonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl, wherein each (R2) group has 1 , 2, or 3 independently chosen optional substituents or two (R2) groups can be taken together to form a heterocyclyl or aryl group having 1 , 2, or 3 independently chosen optional substituents, wherein said optional substituents are independently chosen from alkyl, alkanoyl, heteroalkyl, heterocyclyl, haloalkyl, cycloalkyl, carbocyclyl, arylalk
  • R3 is -H or a (Ci-C6)alkyl group
  • each L1 is independently alkylene or heteroalkylene
  • n 0, 1 , 2, 3, 4 or 5
  • compounds of Formula (VII) are represented by Formula (VIII):
  • X 1 is CH or N;
  • G is a cyclyl group;
  • each (R1) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulfinyl, sulfonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl;
  • each (R2) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulfinyl, sulfonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl, wherein each (R2) group has 1 , 2, or 3 optional substituents, wherein said optional substituents are independently chosen from alkyl, alkanoyl, heteroalkyl, heterocyclyl, haloalkyl, cycloalkyl, carbocyclyl, arylalkoxy, heterocyclylalkoxy, aryl, aryloxy, heterocyclyloxy, alkoxy, haloalkoxy, oxo,
  • each L1 is independently alkylene or heteroalkylene
  • (G) is a cyclyl group
  • each (R1) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulfinyl, sulfonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl;
  • each (R2) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulfinyl, sulfonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl, wherein each (R2) group has 0, 1 , 2, or 3 optional substituents, wherein said optional substituents are independently chosen from alkyl, alkanoyl, heteroalkyl, heterocyclyl, haloalkyl, cycloalkyl, carbocyclyl, arylalkoxy, heterocyclylalkoxy, aryl, aryloxy, heterocyclyloxy, alkoxy, haloalkoxy, oxo,
  • each L1 is independently alkylene or heteroalkylene; m is 0, 1 , 2 or 3; and
  • n 0, 1 , 2, 3, 4 or 5
  • (G) is a cyclyl group; each (R1 ) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyi, haloalkoxy, cyano, sulphinyl, sulphonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl;
  • each (R2) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, - L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyi, haloalkoxy, cyano, sulphinyl, sulphonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl, wherein each (R2) group has 1 , 2, or 3 optional substituents, wherein said optional substituents are independently chosen from alkyl, alkanoyl, heteroalkyl, heterocyclyl, haloalkyi, cycloalkyi, carbocyclyl, arylalkoxy, heterocyclylalkoxy, aryl, aryloxy, heterocyclyloxy, alkoxy, haloalkoxy, oxo, acyl
  • R3 is -H or a (Ci-C6)alkyl group; each L1 is alkylene or heteroalkylene; and n is 0, 1 , 2, 3, 4 or 5,
  • X 1 , X 2 , X 3 and X 4 are independently CH or N, provided that at least one of X 1 , X 2 , X 3 and X 4 is N;
  • (G) is a cyclyl group; each (R1 ) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulfinyl, sulphonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl;
  • each (R2) is independently chosen from alkyl, alkenyl, alkynyl, cyclyl, -L1 -cyclyl, -L1 -amino, -L1 -hydroxyl, amino, amido, nitro, halo, haloalkyl, haloalkoxy, cyano, sulphinyl, sulphonyl, sulphonamide, hydroxyl, alkoxy, urea, carbamate, acyl, or carboxyl, wherein each (R2) group has 1 , 2, or 3 optional substituents, wherein said optional substituents are independently chosen from alkyl, alkanoyl, heteroalkyl, heterocyclyl, haloalkyl, cycloalkyl, carbocyclyl, arylalkoxy, heterocyclylalkoxy, aryl, aryloxy, heterocyclyloxy, alkoxy, haloalkoxy, oxo, acyl
  • Representative compounds according to Formula VII are suitably selected from: (trans)-2-(3'-(trifluoromethyl)biphenyl-4-yl)cyclopropanamine; (trans)- 2-(terphenyl-4-yl)cyclopropanamine; 4'-((trans)-2-aminocyclopropyl)biphenyl-4-ol; 4'- ((trans)-2-aminocyclopropyl)biphenyl-3-ol; (trans)-2-(6-(3- (trifluoromethyl)phenyl)pyridin-3-yl)cyclopropanamine; (Trans)-2-(6-(3,5- dichlorophenyl)pyridin-3-yl)cyclopropanamine; (trans)-2-(6-(4-chlorophenyl)pyridin-3- yl)cyclopropanamine; (trans)-2-(6-(3-chlorophenyl)pyridin-3-yl)cyclopropanamine
  • LSD1 inhibitor compounds are selected from phenylcyclopropylamine derivatives, as described for example by Ogasawara etal. (2013, Angew. Chem. Int. Ed. 52: 8620-8624, which is hereby incorporated by reference herein in its entirety).
  • Representative compounds of this type are represented by Formula (XII):
  • An is a 5 to 7 membered aryl or heteroaryl ring
  • Ar2 and Ar3 are each independently selected from a 5 to 7 membered aryl or heteroaryl ring, optionally substituted with 1 to 3 substituents;
  • R3 is selected from hydrogen, -Ci ealkyl or -OH; [0268] m is an integer from 1 to 5; and
  • n is an integer from 1 to 3;
  • An is a six membered aryl or heteroaryl ring, especially phenyl, pyridine, pyrimidine, pyrazine 1 ,3,5-triazine, 1 ,2,4-trazine and 1 ,2,3-triazine, more especially phenyl;
  • Ar2 is a six membered aryl or heteroaryl ring, especially phenyl, pyridine, pyrimidine, pyrazine 1 ,3,5-triazine, 1 ,2,4-trazine and 1 ,2,3-triazine, especially phenyl; especially where the six membered aryl or heteroaryl ring is optionally substituted with one optional substituent, especially in the 3 or 4 position;
  • Ar3 is a six membered aryl or heteroaryl ring, especially phenyl, pyridine, pyrimidine, pyrazine 1 ,3,5-triazine, 1 ,2,4-trazine and 1 ,2,3-triazine, especially phenyl; especially where the six membered aryl or heteroaryl ring is optionally substituted with one optional substituent, especially in the 3 or 4 position.
  • Particular optional substituents for An and Ar2 include -Ci ealkyl, -C2- 6alkenyl, -CH2F, -CFIF2, -CF3, halo, aryl, heteroaryl, -C(0)NFICi-6alkyl, -C(0)NFICI-6 alkylNH2, -C(0)-heterocyclyl, especially methyl, ethyl, propyl, butyl, t-butyl, -CFI2F, - CHF2, -CH3, Cl, F, phenyl, -C(0)NH(CH2)I- NH and -C(0)-heterocyclyl ;
  • R3 is FI, -Ci salkyl or -OFI, especially FI, -CFI3 or -OFI.
  • m is 2 to 5, especially 3 to 5, more especially 4,
  • n is 1 or 2, especially 1.
  • the compounds of Formula (XII) are compounds of Formula (Xlla): (XI la)
  • Non-limiting compounds represented by Formula (XII) include the following:
  • LSD1 inhibitors include, but are not limited to those, e.g., disclosed in Ueda et al. (2009. J. Am. Chem. Soc. 131 (48): 17536-17537) and Mimasu et al., (2010, Biochemistry, 49(30): 6494-503).
  • Other phenylcyclopropylamine derivatives and analogues are found, e.g., in Kaiser etal. (1962, J. Med. Chem. 5: 1243-1265); Zirkle etal. (1962. J. Med. Chem. 1265-1284; U.S. Pat. Nos.
  • the inhibitory agent is GSK- LSD1 , which has the following molecular structure:
  • the agent is SP- 2509, which has the following molecular structure:
  • the agent is SP- 2577, which has the following molecular structure:
  • the invention not only encompasses known LSD (e.g ., LSD1 or LSD2) inhibitors but LSD inhibitors identified by any suitable screening assay. Accordingly, the present invention extends to methods of screening for modulatory agents that are useful for inhibiting a LSD1 and, in turn, for preventing demethylation of an ACE2 polypeptide.
  • LSD e.g ., LSD1 or LSD2
  • the screening methods comprise (1) contacting a preparation with a test agent, wherein the preparation comprises (i) a polypeptide comprising an amino acid sequence corresponding to at least a biologically active fragment of LSD1 or to a variant or derivative thereof; or (ii) a polynucleotide comprising a nucleotide sequence from which a transcript of a LSD1 gene or portion thereof is producible, or (iii) a polynucleotide comprising at least a portion of a genetic sequence (e.g.
  • a transcriptional element that regulates the expression of a LSD1 gene, which is operably linked to a reporter gene; and (2) detecting a change in the level or functional activity of the polypeptide, the polynucleotide or an expression product of the reporter gene, relative to a reference level or functional activity in the absence of the test agent.
  • a detected reduction in the level and/or functional activity of the polypeptide, transcript or transcript portion or an expression product of the reporter gene, relative to a normal or reference level and/or functional activity in the absence of the test agent indicates that the agent is useful for preventing demethylation of an ACE2 polypeptide.
  • this is confirmed by analysing or determining whether the test agent prevents the demethylation of an ACE2 polypeptide, and would therefore be useful as an agent for preventing or treatment a coronavirus infection.
  • Modulators falling within the scope of the present invention include inhibitors of the level or functional activity of a LSD (e.g., LSD1 or LSD2), including antagonistic antigen-binding molecules, and inhibitor peptide fragments, antisense molecules, ribozymes, RNAi molecules and co-suppression molecules as well as polysaccharide and lipopolysaccharide inhibitors of a LSD (e.g., LSD1 or LSD2) .
  • Candidate agents encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 50 and less than about 2,500 Dalton.
  • Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, desirably at least two of the functional chemical groups.
  • the candidate agent often comprises cyclical carbon or heterocyclic structures or aromatic or polyaromatic structures substituted with one or more of the above functional groups.
  • Candidate agents are also found among biomolecules including, but not limited to: peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogues or combinations thereof.
  • Small (non-peptide) molecule modulators of a LSD ⁇ e.g., LSD1 or LSD2) are particularly advantageous.
  • small molecules are desirable because such molecules are more readily absorbed after oral administration, have fewer potential antigenic determinants, or are more likely to cross the cell membrane than larger, protein-based pharmaceuticals.
  • Small organic molecules may also have the ability to gain entry into an appropriate cell and affect the expression of a gene ( e.g ., by interacting with the regulatory region or transcription factors involved in gene expression); or affect the activity of a gene by inhibiting or enhancing the binding of accessory molecules.
  • libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced.
  • natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries.
  • Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogues.
  • Screening may also be directed to known pharmacologically active compounds and chemical analogues thereof.
  • Screening for modulatory agents according to the invention can be achieved by any suitable method.
  • the method may include contacting a cell expressing a polynucleotide corresponding to a gene that encodes a LSDIwith an agent suspected of having the modulatory activity and screening for the modulation of the level or functional activity of the LSD1 , or the modulation of the level of a transcript encoded by the polynucleotide, or the modulation of the activity or expression of a downstream cellular target of the polypeptide or of the transcript (hereafter referred to as target molecules).
  • target molecules a downstream cellular target of the polypeptide or of the transcript
  • Detecting such modulation can be achieved utilizing techniques including, but not restricted to, ELISA, cell-based ELISA, inhibition ELISA, Western blots, immunoprecipitation, slot or dot blot assays, immunostaining, RIA, scintillation proximity assays, fluorescent immunoassays using antigen-binding molecule conjugates or antigen conjugates of fluorescent substances such as fluorescein or rhodamine, Ouchterlony double diffusion analysis, immunoassays employing an avidin-biotin or a streptavidin-biotin detection system, and nucleic acid detection assays including reverse transcriptase polymerase chain reaction (RT-PCR).
  • a polynucleotide from which LSD1 is regulated or expressed may be naturally occurring in the cell which is the subject of testing or it may have been introduced into the host cell for the purpose of testing.
  • the naturally-occurring or introduced polynucleotide may be constitutively expressed - thereby providing a model useful in screening for agents which down- regulate expression of an encoded product of the sequence wherein the down regulation can be at the nucleic acid or expression product level.
  • a polynucleotide may comprise the entire coding sequence that codes for LSD1 or it may comprise a portion of that coding sequence (e.g., the active site of LSD1) or a portion that regulates expression of the corresponding gene that encodes LSD1 (e.g., a LSD1 promoter).
  • the promoter that is naturally associated with the polynucleotide may be introduced into the cell that is the subject of testing.
  • detecting modulation of the promoter activity can be achieved, for example, by operably linking the promoter to a suitable reporter polynucleotide including, but not restricted to, green fluorescent protein (GFP), luciferase, b-galactosidase and catecholamine acetyl transferase (CAT). Modulation of expression may be determined by measuring the activity associated with the reporter polynucleotide.
  • GFP green fluorescent protein
  • CAT catecholamine acetyl transferase
  • These methods provide a mechanism for performing high throughput screening of putative modulatory agents such as proteinaceous or non- proteinaceous agents comprising synthetic, combinatorial, chemical and natural libraries. These methods will also facilitate the detection of agents which bind either the polynucleotide encoding the target molecule or which modulate the expression of an upstream molecule, which subsequently modulates the expression of the polynucleotide encoding the target molecule. Accordingly, these methods provide a mechanism of detecting agents that either directly or indirectly modulate the expression or activity of a target molecule according to the invention.
  • test agents are screened using commercially available assays, illustrative examples of which include EpiQuik Flistone Demethylase LSD1 Inhibitor Screening Assay Kit (Epigentek Group, Brooklyn, NY) or the LSD1 Inhibitor Screening Assay Kit (Cayman Chemical Company, Ann Arbor, Ml).
  • Compounds may be further tested in the animal models to identify those compounds having the most potent in vivo effects. These molecules may serve as “lead compounds” for the further development of pharmaceuticals by, for example, subjecting the compounds to sequential modifications, molecular modelling, and other routine procedures employed in rational drug design.
  • the LSD1 inhibitor inhibits the binding between an LSD1 polypeptide and a CoRest polypeptide.
  • the inhibitor specifically binds a polypeptide that is known to play an important role in activating LSD1.
  • a polypeptide that is known to play an important role in activating LSD1.
  • PKC0 activates the transcription of LDS1
  • any inhibitor sufficient to reduce or prevent the phosphorylation of LSD by PKC0 is equally as applicable for use with the present invention.
  • an isolated or purified proteinaceous molecule represented by any one of SEQ ID NOs:1 or 2:
  • RKEIDPPFRPKVK [SEQ ID NO: 1 ]
  • the proteinaceous molecule of SEQ ID NO: 1 is also referred to herein as “importinib4759” and the proteinaceous molecule of SEQ ID NO: 2 is also referred to herein as "importinib4759_01”.
  • the present invention also contemplates proteinaceous molecules that are variants of SEQ ID NO: 1 and/or 2.
  • variant proteinaceous molecules include proteins derived from the native protein by deletion (so-called truncation) or addition of one or more amino acids to the N-terminal and/or C-terminal end of the native protein; deletion or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein.
  • variant proteins encompassed by the present invention are biologically active, that is, they continue to possess the desired biological activity of the native protein. Such variants may result from, for example, genetic polymorphism or from human manipulation.
  • the proteinaceous molecules of SEQ ID NO: 1 and/or 2 may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art.
  • amino acid sequence variants of SEQ ID NO: 1 and/or 2 can be prepared by mutagenesis of nucleic acids encoding the amino acid sequence of SEQ ID NO: 1 and/or 2. Methods for mutagenesis and nucleotide sequence alterations are well known in the art.
  • Variant peptides or polypeptides of the invention may contain conservative amino acid substitutions at various locations along their sequence, as compared to a parent (e.g ., naturally- occurring or reference) amino acid sequence, such as SEQ ID NO: 1 and/or 2.
  • a “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art as discussed in detail below.
  • the amino acid sequence of the proteinaceous molecules of the invention is defined in terms of amino acids of certain characteristics or sub-classes. Amino acid residues are generally sub-classified into major sub-classes as follows:
  • Acidic The residue has a negative charge due to loss of a proton at physiological pH and the residue is attracted by aqueous solution so as to seek the surface positions in the conformation of a peptide in which it is contained when the peptide is in aqueous medium at physiological pH.
  • Amino acids having an acidic side chain include glutamic acid and aspartic acid.
  • Basic The residue has a positive charge due to association with protons at physiological pH or within one or two pH units thereof (e.g. histidine) and the residue is attracted by aqueous solution so as to seek the surface positions in the conformation of a peptide in which it is contained when the peptide is in aqueous medium at physiological pH.
  • Amino acids having a basic side chain include arginine, lysine and histidine.
  • the residue is charged at physiological pH and, therefore, includes amino acids having acidic or basic side chains, such as glutamic acid, aspartic acid, arginine, lysine and histidine.
  • Hydrophobic The residue is not charged at physiological pH and the residue is repelled by aqueous solution so as to seek the inner positions in the conformation of a peptide in which it is contained when the peptide is in aqueous medium at physiological pH.
  • Amino acids having a hydrophobic side chain include tyrosine, valine, isoleucine, leucine, methionine, phenylalanine and tryptophan.
  • Amino acids having a neutral/polar side chain include asparagine, glutamine, cysteine, histidine, serine and threonine.
  • proline differs from all the other naturally-occurring amino acids in that its side chain is bonded to the nitrogen of the a-amino group, as well as the a-carbon.
  • amino acid similarity matrices e.g ., PAM120 matrix and PAM250 matrix as disclosed for example by Dayhoff etal., (1978), A model of evolutionary change in proteins. Matrices for determining distance relationships In M. O. Dayhoff, (ed.), Atlas of protein sequence and structure, Vol. 5, pp.
  • proline in the same group as glycine, serine, alanine and threonine. Accordingly, for the purposes of the present invention, proline is classified as a “small” amino acid.
  • Amino acid residues can be further sub-classified as cyclic or non- cyclic, and aromatic or non-aromatic, self-explanatory classifications with respect to the side-chain substituent groups of the residues, and as small or large.
  • the residue is considered small if it contains a total of four carbon atoms or less, inclusive of the carboxyl carbon, provided an additional polar substituent is present; three or less if not.
  • Small amino acid residues are, of course, always non-aromatic.
  • amino acid residues may fall in two or more classes.
  • sub classification according to this scheme is presented in Table 1.
  • Conservative amino acid substitution also includes groupings based on side chains.
  • a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulphur-containing side chains is cysteine and methionine.
  • Amino acid substitutions falling within the scope of the invention are, in general, accomplished by selecting substitutions that do not differ significantly in their effect on maintaining (a) the structure of the peptide backbone in the area of the substitution, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. After the substitutions are introduced, the variants are screened for biological activity.
  • amino acids for making conservative substitutions can be grouped into three categories based on the identity of the side chains.
  • the first group includes glutamic acid, aspartic acid, arginine, lysine, histidine, which all have charged side chains;
  • the second group includes glycine, serine, threonine, cysteine, tyrosine, glutamine, asparagine;
  • the third group includes leucine, isoleucine, valine, alanine, proline, phenylalanine, tryptophan, methionine, as described in Zubay, Biochemistry, third edition, Wm.C. Brown Publishers (1993).
  • a predicted non-essential amino acid residue in a peptide of the invention is typically replaced with another amino acid residue from the same side chain family.
  • mutations can be introduced randomly along all or part of the coding sequence of a peptide of the invention, such as by saturation mutagenesis, and the resultant mutants can be screened for an activity of the parent polypeptide, as described for example herein, to identify mutants which retain that activity.
  • the encoded peptide can be expressed recombinantly and its activity determined.
  • a “non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of an embodiment peptide of the invention without abolishing or substantially altering one or more of its activities.
  • the alteration does not substantially alter one of these activities, for example, the activity is at least 20%, 40%, 60%, 70% or 80% of that of the wild-type.
  • an “essential” amino acid residue is a residue that, when altered from the wild-type sequence of an embodiment peptide of the invention, results in abolition of an activity of the parent molecule such that less than 20% of the wild-type activity is present.
  • variants of the proteinaceous molecules of SEQ ID NO 1 and/or 2 of the invention wherein the variants are distinguished from the parent sequence by the addition, deletion, or substitution of one or more amino acid residues.
  • variants will display at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence similarity to a parent or reference proteinaceous molecule sequence as, for example, set forth in SEQ ID NO: 1 or 2, as determined by sequence alignment programs described elsewhere herein using default parameters.
  • variants will have at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to a parent or reference peptide sequence as, for example, set forth in SEQ ID NO: 1 or 2, as determined by sequence alignment programs described herein using default parameters.
  • Variants of importinib4759 and importinib4759_01 which fall within the scope of a variant peptide of the invention, may differ from the parent molecule generally by at least 1 , but by less than 5, 4, 3, 2 or 1 amino acid residue(s).
  • a variant peptide of the invention differs from the corresponding sequence in SEQ ID NO: 1 or 2 by at least 1 , but by less than 5, 4, 3, 2 or 1 amino acid residue(s).
  • the amino acid sequence of the variant peptide of the invention comprises lie (or modified form thereof) at position 5, Asp (or modified form thereof) at position 6, Pro (or modified form thereof) at position 8 and/or Pro (or modified form thereof) at position 9, relative to the numbering of SEQ ID NO: 2.
  • the variant peptide of the invention inhibits PKC- Q nuclear translocation.
  • agents that inhibit LSD1 e.g ., a selective LSD1 inhibitor
  • actives and/or pharmaceutical compositions for treating or preventing a virus infection ⁇ e.g., a coronavirus infection.
  • treatment or prevention includes the prevention of incurring a symptom, holding in check such symptoms, or treating existing symptoms associated with the pathogenic infection, when administered to an individual in need thereof.
  • the S protein of many betacoronaviruses including but not limited to SARS-CoV and SARS-CoV-2, have been demonstrated to employ an ACE2 polypeptide for entry into the host cell.
  • the virus host cell entry receptor polypeptide used by MERS-CoV is a DPP4 polypeptide, and for hCoV-229, a CD13polypeptide.
  • Any LSD1 inhibitor can be used in the compositions and methods of the present invention, provided that the inhibitor is pharmaceutically active.
  • a “pharmaceutically active” LSD1 inhibitor is in a form that results in the treatment and/or prevention of a pathogenic infection, particularly a coronavirus infection, including the prevention of incurring a symptom, holding in check such symptoms or treating existing symptoms associated with the metastatic cancer, when administered to an individual in need thereof.
  • Modes of administration, amounts of LSD1 inhibitor administered, and LSD1 inhibitor formulations, for use in the methods of the present invention, are routine and within the skill of practitioners in the art. Whether a pathogenic infection, particularly a coronavirus infection, has been treated is determined by measuring one or more diagnostic parameters indicative of the course of the disease, compared to a suitable control. In the case of an animal experiment, a “suitable control” is an animal not treated with the LSD1 inhibitor, or treated with the pharmaceutical composition without the LSD1 inhibitor. In the case of a human subject, a “suitable control” may be the individual before treatment, or may be a human ( e.g ., an age- matched or similar control) treated with a placebo.
  • the treatment of a pathogenic infection includes and encompasses without limitation: (1) preventing the uptake of a pathogenic infection ⁇ e.g., a coronavirus infection) into a cell of the host; (2) treating a pathogenic infection ⁇ e.g., a coronavirus infection) in a subject; (3) preventing a pathogenic infection ⁇ e.g., a coronavirus infection) in a subject that has a predisposition to the pathogenic infection but has not yet been diagnosed with the pathogenic infection and, accordingly, the treatment constitutes prophylactic treatment of the pathogenic infection; or (iii) causing regression of a pathogenic infection ⁇ e.g., a coronavirus infection).
  • compositions and methods of the present invention are thus suitable for treating an individual who has been diagnosed with a coronavirus infection, who is suspected of having a coronavirus infection, who is known to be susceptible and who is considered likely to develop a coronavirus infection, or who is considered likely to develop a recurrence of a previously treated coronavirus infection.
  • the coronavirus infection may be a SARS-CoV-2 infection.
  • the coronavirus infection is a SARS-CoV-1 or a SARS-CoV-2 infection.
  • the LSD1 inhibitor-containing compositions will generally contain about 0.000001% to 90%, about 0.0001% to 50%, or about 0.01% to about 25%, by weight of LSD inhibitor, the remainder being suitable pharmaceutical carriers or diluents etc.
  • the dosage of the LSD1 inhibitor can depend on a variety of factors, such as mode of administration, the species of the affected subject, age, sex, weight and general health condition, and can be easily determined by a person of skill in the art using standard protocols. The dosages will also take into consideration the binding affinity of the LSD1 inhibitor to its target molecule, its bioavailability and its in vivo and pharmacokinetic properties.
  • precise amounts of the agents for administration can also depend on the judgment of the practitioner.
  • the physician or veterinarian may evaluate the progression of the disease or condition over time.
  • suitable dosages of the LSD1 inhibitor without undue experimentation.
  • the dosage of the actives administered to a patient should be sufficient to effect a beneficial response in the patient over time such as impairment, abrogation or prevention in the uptake of the virus into a cell of the host, and/or in the treatment and/or prevention of a pathogenic infection (e.g ., a coronavirus infection).
  • the dosages may be administered at suitable intervals to ameliorating the symptoms of the hematologic malignancy.
  • Such intervals can be ascertained using routine procedures known to persons of skill in the art and can vary depending on the type of active agent employed and its formulation. For example, the interval may be daily, every other day, weekly, fortnightly, monthly, bimonthly, quarterly, half-yearly or yearly.
  • Dosage amount and interval may be adjusted individually to provide plasma levels of the active agent, which are sufficient to maintain LSD-inhibitory effects.
  • Usual patient dosages for systemic administration range from 1 -2000 mg/day, commonly from 1-250 mg/day, and typically from 10-150 mg/day. Stated in terms of patient body weight, usual dosages range from 0.02-25 mg/kg/day, commonly from 0.02-3 mg/kg/day, typically from 0.2-1.5 mg/kg/day. Stated in terms of patient body surface areas, usual dosages range from 0.5-1200 mg/m 2 /day, commonly from 0.5-150 mg/m 2 /day, typically from 5-100 mg/m 2 /day.
  • the present invention further contemplates administering the LSD1 inhibitor concurrently with at least one antiviral agent.
  • the LSD1 inhibitor may be used therapeutically after the antiviral agent or may be used before the antiviral agent is administered or together with the antiviral agent.
  • combination therapies which employ a LSD1 inhibitor and concurrent administration of an antiviral agent, non-limiting examples of which include: broad-spectrum antiviral agents and coronavirus-specific antivirus agents.
  • the LSD inhibitors described above or elsewhere herein are particularly effective antiviral agents for monotherapeutic or combined-therapeutic use in treating coronavirus infection.
  • One of the benefits of such combination therapies is that lower doses of the other antiviral agents can be administered while still achieving a similar level of antiviral efficacy.
  • Such lower dosages can be particularly advantageous for drugs known to have genotoxicity and mitochondrial toxicity (for example, some nucleoside analogues).
  • greater efficacy might be achieved using therapeutic doses of two drugs than could be achieved using only a single drug.
  • Examples of other cancer therapies include phototherapy, cryotherapy, toxin therapy or pro-apoptosis therapy.
  • phototherapy is not exhaustive of the types of treatment modalities available for cancer and other hyperplastic lesions.
  • the antiviral drug is suitably selected from antimicrobials, which include without limitation compounds that kill or inhibit the growth of microorganisms (including viruses), and antivirals.
  • Illustrative antivirals include abacavir sulphate, acyclovir sodium, amantadine hydrochloride, amprenavir, chloroquine, cidofovir, delavirdine mesylate, didanosine, efavirenz, favipiravir, famciclovir, fomivirsen sodium, foscarnet sodium, ganciclovir, hydroxychloroquine, hydroquinone.
  • indinavir sulphate lamivudine, lamivudine/zidovudine, lopinavir, nelfinavir mesylate, nevirapine, oseltamivir phosphate, ribavirin, remdesivir, rimantadine hydrochloride, ritonavir, saquinavir, saquinavir mesylate, stavudine, valacyclovir hydrochloride, zalcitabine, zanamivir, and zidovudine.
  • the LSD1 inhibitor may be co administered with an antimicrobial agent including chloroquine, hydroxychloroquine and/or hydroquinone.
  • the antiviral agent comprises a recombinant IFN-b polypeptide (UniProt Accession No. P01574). In some embodiments of this type, the antiviral agent comprises at least a portion of an IFN-b polypeptide, or a variant of an IFN-b polypeptide.
  • the present invention encompasses co administration of an LSD1 inhibitor in concert with an additional agent.
  • the dosages of the actives in the combination may on their own comprise an effective amount and the additional agent(s) may further augment the therapeutic or prophylactic benefit to the patient.
  • the LSD1 inhibitor and the additional agent(s) may together comprise an effective amount for preventing or treating the pathogenic infection.
  • effective amounts may be defined in the context of particular treatment regimens, including, e.g., timing and number of administrations, modes of administrations, formulations, etc.
  • the LSD1 inhibitor and optionally the antiviral agent are administered on a routine schedule.
  • routine schedule refers to a predetermined designated period of time.
  • the routine schedule may encompass periods of time which are identical or which differ in length, as long as the schedule is predetermined.
  • routine schedule may involve administration of the LSD inhibitor on a daily basis, every two days, every three days, every four days, every five days, every six days, a weekly basis, a monthly basis or any set number of days or weeks there-between, every two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, eleven months, twelve months, etc.
  • the predetermined routine schedule may involve concurrent administration of the LSD1 inhibitor and the antiviral agent on a daily basis for the first week, followed by a monthly basis for several months, and then every three months after that. Any particular combination would be covered by the routine schedule as long as it is determined ahead of time that the appropriate schedule involves administration on a certain day.
  • the present invention provides pharmaceutical compositions for reducing or abrogating the uptake a viruses ⁇ e.g., a coronavirus) to a cell of the host, the pharmaceutical compositions comprising a LSD inhibitor and optionally an antiviral agent useful for treating malignancies.
  • the formulations of the invention are administered in pharmaceutically acceptable solutions, which may routinely contain pharmaceutically acceptable concentrations of salt, buffering agents, preservatives, compatible carriers, adjuvants, and optionally other therapeutic ingredients. Depending on the specific conditions being treated, the formulations may be administered systemically or locally. Techniques for formulation and administration may be found in “Remington’s Pharmaceutical Sciences”, Mack Publishing Co., Easton, Pa., latest edition.
  • Suitable routes may, for example, include oral, rectal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.
  • the active agents or drugs of the invention may be formulated in aqueous solutions, suitably in physiologically compatible buffers such as Hanks’ solution, Ringer’s solution, or physiological saline buffer.
  • penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
  • the drugs can be formulated readily using pharmaceutically acceptable carriers well known in the art into dosages suitable for oral administration.
  • Such carriers enable the compounds of the invention to be formulated in dosage forms such as tablets, pills, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated.
  • These carriers may be selected from sugars, starches, cellulose and its derivatives, malt, gelatin, talc, calcium sulphate, vegetable oils, synthetic oils, polyols, alginic acid, phosphate buffered solutions, emulsifiers, isotonic saline, and pyrogen-free water.
  • compositions for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents, which increase the solubility of the compounds to allow for the preparation of highly, concentrated solutions.
  • compositions for oral use can be obtained by combining the active compounds with solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores.
  • suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, or polyvinylpyrrolidone (PVP).
  • disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
  • Such compositions may be prepared by any of the methods of pharmacy but all methods include the step of bringing into association one or more drugs as described above with the carrier, which constitutes one or more necessary ingredients.
  • the pharmaceutical compositions of the present invention may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.
  • Dragee cores are provided with suitable coatings.
  • suitable coatings may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
  • compositions which can be used orally include push- fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol.
  • the push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, or lubricants such as talc or magnesium stearate and, optionally, stabilizers.
  • the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols.
  • stabilizers may be added.
  • Dosage forms of the drugs of the invention may also include injecting or implanting controlled releasing devices designed specifically for this purpose or other forms of implants modified to act additionally in this fashion.
  • Controlled release of an agent of the invention may be achieved by coating the same, for example, with hydrophobic polymers including acrylic resins, waxes, higher aliphatic alcohols, polylactic and polyglycolic acids and certain cellulose derivatives such as hydroxypropyl methyl cellulose.
  • controlled release may be achieved by using other polymer matrices, liposomes or microspheres.
  • the drugs of the invention may be provided as salts with pharmaceutically compatible counterions.
  • Pharmaceutically compatible salts may be formed with many acids, including but not limited to hydrochloric, sulphuric, acetic, lactic, tartaric, malic, succinic, etc. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose can be formulated in animal models to achieve a circulating concentration range that includes the IC50 as determined in cell culture (e.g ., the concentration of an active agent, which achieves a half-maximal inhibition in activity of a LSD1 polypeptide). Such information can be used to more accurately determine useful doses in humans.
  • Toxicity and therapeutic efficacy of such drugs can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50:ED50.
  • Compounds that exhibit large therapeutic indices are preferred.
  • the data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human.
  • the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilised.
  • the exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient’s condition (see, for example, Fingl etal., 1975, in “The Pharmacological Basis of Therapeutics”, Ch. 1 ).
  • the liposomes will be targeted to and taken up selectively by the tissue.
  • the effective local concentration of the agent may not be related to plasma concentration.
  • MAO inhibitors such as phenelzine, tranylcypromine, and isocarboxazid are currently used clinically to treat depression and cancer, and Phase 1 b clinical trials are currently in progress for metastatic breast cancer which show that LSD1 inhibitors, including phenelzine (NARDIL), are safe and re-invigorate T cell-mediated immunity in humans.
  • LSD1 inhibitors including phenelzine (NARDIL)
  • LSD1 inhibitors can be re-purposed for SARS-CoV-2 therapy by targeting viral entry into host cells and enhancing T cell-mediated immunity. Proving the efficacy of pre-existing drugs would rapidly transform clinical practice and outcomes in the current pandemic.
  • Our efficacy, safety, and toxicity data on LSD1 inhibitors and optimised biomarkers in the oncology setting are readily transferrable to SARS-CoV-2 patients and provide not only a drug but also the biomarkers to monitor the exhaustion phenotype and disease progression.
  • a series of protein domains within both the ACE2 protein and the TMPRSS2 protein were identified as being critical for the entry of the SARS-CoV-2 into the cell. These protein domains are subject to epigenetic post-translational modification (lysine methylation, de-methylation, sumoylation and phosphorylation).
  • the present inventors identified within the TMPRSS2 and ACE2 proteins a series of key serine residues that are phosphorylated by PKCq and key lysine residue methylation sites, these methylated lysine residues also represent sites of LSD1 -mediated de-methylation.
  • Other proteins have been demonstrated to be dynamically regulated by lysine methylation and demethylation or phosphorylation include p53.
  • LSD1 is a key epigenetic regulator
  • the importance of LSD1 on the direct regulation of TMPRSS2 was investigated. Specifically, an examination was performed on the effect of LSD1p inhibition or LSDIp’s upstream regulator PKC0 on the expression dynamics of TMPRSS2.
  • LSD1 siRNA knockouts resulted in significant loss of TMPRSS2 mRNA in both MDA- MB-231 and MCF7 breast cancer cell lines ( Figure 1 A).
  • Samples were either control or phenelzine (FAD and nuclear LSD1p:CoREST inhibitor) or C27 (PKCq catalytic inhibitor) and CHiP enrichment assay carried out by pulling down chromatin fragments with either LSD1p or PKC0 antibodies.
  • PKCq catalytic inhibitor CHiP enrichment assay carried out by pulling down chromatin fragments with either LSD1p or PKC0 antibodies.
  • RNA from each treatment group/sample was hybridized using the human Nanostring custom Panel.
  • the absolute RNA counts were quantified by the nCounter NanoString system (NanoString Technologies, Seattle, WA, USA) and mRNA expression was analysed using the nSolver software and R v.3.3.2 for the Advanced analysis (NanoString Technologies), following the manufacturer’s recommendations) and plotted as fold change versus control.
  • ChIP assays were performed in accordance with the protocol supplied by Upstate Biotechnology. Fixation steps were performed as detailed, and fixed chromatin was sonicated with an Ultrasonic processor (Cole/Parmer) under optimized conditions that gave average DNA fragments of approximately 500 bp, as determined by 2% agarose gel electrophoresis. Prior to antibody addition, samples were precleared with salmon sperm DNA-protein A-agarose and the soluble chromatin fraction was incubated overnight at 4°C with 5 to 10 pg of LSD1p (Merck Millipore) or PKC-0 (Abeam) antibody or without antibody as a control.
  • LSD1p Merck Millipore
  • PKC-0 Abeam
  • Immune complexes were bound to salmon sperm DNA-protein A-agarose and then washed and eluted as described. Protein-DNA cross-links were reversed by incubation at 65°C overnight, and the DNA in each sample was recovered by phenol-chloroform extraction and ethanol precipitation. DNA pellets were washed in 70% ethanol, resuspended in Tris (pH 8.0), and subsequently used for SYBR green real-time PCR amplification (Applied Biosystems). Standard curves were generated for each primer set to correct for differences in primer efficiency. ChIP enrichment ratios were calculated for TMPRSS2 as per standard methods.
  • MDA-MB-231 mesenchymal cells or MCF7 epithelial cells were treated with either control, phenelzine or GSK-LSD1. Cells were then fixed for IFA Microscopy Analysis. Cells were permeabilised by incubating with 1% Triton X-100 for 20 min and were probed with rabbit TRMPSS2 mouse and visualized with a donkey anti-rabbit AF 488. Cover slips were mounted on glass microscope slides with ProLong Glass Antifade reagent (Life Technologies). Protein targets were localised by confocal laser scanning microscopy. Single 0.5 pm sections were obtained using the Metagene-ASI Digital Pathology platform. The final image was obtained by averaging four sequential images of the same section. Digital images were analysed using ASI proprietary analysis software to determine the mean Fluorescent Intensity (mean FI). Graph represents the mean FI values for TMPRS2 using ImageJ to select the nucleus minus background (n > 50 individual cells).
  • LSD1 inhibition significantly inhibits both message and protein expression of TMPRSS2 in a variety of cell lines including in a siLSDI knockdown model. This clearly demonstrates the specificity of LSD1p in regulating TMPRSS2 expression. Flowever, there was a slight decrease on ACE2 transcription in metastatic lung tissue. Despite this it is still likely that LSD1 plays a role in post-translationally modifying ACE2.
  • LSD1 is a key eraser enzyme, that demethylates key histone proteins and key proteins such as transcription factors whereby this demethylation/ methylation post-translational modification has resulted in induction, inhibition or stabilization of the expression of the targeted proteins such as p53. Based on these data, the role of LSD1 as a key regulator of the receptor ACE2 and TMPRSS2 responsible for shuttling SARS-CoV-2 into the cell was investigated.
  • LSD1 significantly co-localized higher with ACE2 in cells infected with SARS-CoV-2, as compared to ACE2/LSD1 expression in uninfected CaCo2 and MRC5 cells (which are not susceptible to SARS-CoV-2 infection) as demonstrated by the PCC(r) co efficient which adjudicates the degree of co-localisation between two protein targets, as well as significantly upregulated expression of both LSD1 and ACE2 was demonstrated in infected cells.
  • MRC5 had no expression of ACE2 and no staining of virus proteins (Figure 3D).
  • LSD1 co-localized with both SARS-CoV-2 spike protein and the nucleocapsid proteins.
  • ACE2 exhibits three high probability lysine residues for post-translation modification by LSD1 and that these lysine residues are part of the C-terminal domain and a novel, putative nuclear localization sequence (NLS).
  • NLS nuclear localization sequence
  • Ddigital images were also analysed using ImageJ software (ImageJ, NIH, Bethesda, MD, USA) to determine the total cell fluorescence or cell surface only fluorescence for non-permeabilised cells.
  • Digital images were analysed using ImageJ software (ImageJ, NIH, Bethesda, MD, USA) to determine the either the Total Nuclear Fluorescent Intensity (TNFI), the Total Cytoplasmic Fluorescent Intensity (TCFI).
  • ImageJ software with automatic thresholding and manual selection of regions of interest (ROIs) specific for cell nuclei was used to calculate the Pearson’s co-efficient correlation (PCC) for each pair of antibodies.
  • the Mann-Whitney nonparametric test (GraphPad Prism, GraphPad Software, San Diego, CA) was used to determine significant differences between datasets.
  • Binding affinity measurements were performed on a Monolith NT.115 (NanoTemper Technologies).
  • the fluorescein-Ahx tagged Ace2 peptide sequence RDRKKKNKARSGEN was manufactured by Genescript. Purified Each reaction consisted of 10 pL of the labelled peptide at 444 nM, mixed with unlabelled LSD1 at the indicated concentrations. All experiments were measured at 25°C with laser off/on/off times of 5/30/5 s. Experiments were conducted at 20% light-emitting diode power and 20-40% MST infra-red laser power. Data from three independently performed experiments were fitted to the single binding model via the NT. Analysis software version 1.5.41 (NanoTemper Technologies) using the signal from Thermophoresis + T-Jump.
  • LSD1 regulates ACE2
  • SARS-CoV-2 expression will be inhibited by LSD1 inhibition via blocking viral entry by down-regulation of ACE2.
  • LSD1 expression at the cell surface is inhibited more significantly by phenelzine but not GSK-LSD1 or L1 (EPI-111) ( Figure 5). This is explained by GSK- LSD1 being only a FAD domain demethylase inhibitor whereas phenelzine is known to be a FAD domain inhibitor that also causes structural alterations in LSD1.
  • L1 (EPI- 111) is a nuclear translocation inhibitor, with its effect attributed to blocking the shuttling of LSD1 into the nucleus.
  • phenelzine is superior at inhibiting expression of ACE2, LSD1 and consequently expression of SARS-CoV-2 is also inhibited.
  • Duolink analysis which detects interacting proteins only demonstrated that LSD1 and ACE2 strongly interact and this interaction is significantly inhibited by phenelzine and to a lesser extent, GSK-LSD1.
  • RT-PCR analysis to measure the impact on SARS-CoV-2 RNA transcription showed that the nuclear targeting inhibitor L1 (EPI-111) was the most superior at inhibiting transcription, with both GSK-LSD1 and phenelzine having an effect (Figure 5I).
  • Phenelzine also induced higher levels of SARS-CoV-2 RNA in the supernatant as a consequence of disrupting virus nucleocapsid formation which encapsulates the virus RNA. Furthermore, while LSD1, ACE2, and TMPRSS2 transcript remained unaltered in SARS-CoV-2-infected Caco-2 cells following phenelzine or GSK-LSD1 treatment, a limited type I interferon response was induced in Caco-2 cells following SARS-CoV-2 infection (Figure 5J).
  • phenelzine treatment showed a 1.72-fold increase of cellular viral RNA replication compared to control, much less viral replication increase was detected in cell supernatant in phenelzine treatment between 24 hpi and 48 hpi (data not shown). This indicated that the virus can replicate within phenelzine-treated cells but much less virus were released into cell culture supernatant compared to control cells. This potentially suggests that replicated viral RNA was accumulated in phenelzine-treated cells due to a block in viral protein translation and viral assembly processes, such that less intact viral pathogens were released to infect other cells.
  • TaqMan quantitative real-time PCR was performed using the Applied Biosystems ViiATM7 Real-Time PCR System (Applied Biosystems, Waltham, MA) with the following human TaqMan probes: ACTB (Hs01060665_g1), GAPDH (Hs02786624_g1), HPRT1 (Hs02800695_m1), ACE2 (Hs01085333_m1), TMPRSS2 (Hs01122322_m1), IFNa (Hs03044218_g1 ), /F/V3 (Hs01077958_s1 ), IFNA (Hs00820125_g1), DDX58 (Hs01061436_m1), IFIH1 (Hs00223420_m1), ISG15 (Hs01921425_s1), OASL (Hs00984387_m1 ), IL-6 (Hs00174131_m1), IL-10 (Hs00961622_m1
  • RNA sequencing was performed to identify global gene expression programs impacted by LSD1 inhibition in SARS-CoV-2-infected Caco-2 cells. LSD1 inhibition albeit at different degrees, impacts on key anti-viral processes, key proteins responsible for viral entry and the transcription and replication of the SARS-CoV-2 virus in the host cell (Figure 6A). Principal component analysis (PCA) demonstrated good separation of samples according to their treatment type and high similarity between biological replicates ( Figure 6B). Principal component (PC)1 separated phenelzine-treated samples from all other samples and accounted for 66% of the variance, whilst PC2 further separated GSK-treated samples from the control samples and accounted for 12% of the variance ( Figure 6B).
  • PCA Principal component analysis
  • the Fn/c ratio (a score > than 1 indicates nuclear bias) of ACE2 also increased significantly upon infection. A similar pattern was demonstrated for LSD1.
  • RNA-seq data were obtained from Caco-2 cell line infected with SARS-CoV-2. Three different treatments were tested (named Phe, GSK, and L1), with each of the treatments targeting the same gene but in different ways. A total of 8 samples from four experimental groups were collected:
  • RNA-seq data were generated, fastq data were downloaded to the QIMR Berghofer server, and then archived to the HSM by Scott Wood. Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.9; Martin (2011 )) and aligned using STAR (version 2.5.2a; Dobin et al. (2013)) to the GRCh37 assembly with the gene, transcript, and exon features of Ensembl (release 89) gene model, and the SARS-CoV-2 RefSeq accession NC_045512. Quality control metrics were computed using RNA-SeQC (version 1.1.8; DeLuca et al. (2012)) and expression was estimated using RSEM (version 1.2.30; Li and Dewey (2011)).
  • RNA-Seq samples The quality control of RNA-seq samples is an important step to guarantee quality and reproducible analytical results.
  • RNA-SeQC was run for this purpose, the results of which can be found on the HPC cluster.
  • Another common quality metric is whether the RNA sample is contaminated with mitochondrial DNA (mtDNA) or whether there is a high amount of ribosomal RNA (rRNA) in the sample.
  • mtDNA mitochondrial DNA
  • rRNA ribosomal RNA
  • the aim of normalisation is to remove differences between samples based on systematic technical effects to warrant that these technical biases have a minimal effect on the results.
  • the library size is important to correct for as differences in the initial RNA quantity sequenced will have an impact on the number of reads sequenced. Differences in RNA sequence composition occurs when RNAs are over-represented in one sample compared to others. In these samples, other RNAs will be under-sampled which will lead to higher false-positive rates when predicting differentially expressed genes.
  • HBECs were obtained from two healthy donor (#501936 and #549138) and cultured in PneumaCultTM-ALI Medium on collagen-coated transwell inserts with a 0.4-micron pore size (Costar, Corning, Tewksbury, MA, USA) and inserted into 24 well culture plates according to manufacturer instructions (StemCell Technologies, Cambridge, MA, USA). HBECs were maintained at air-liquid interface allowing them to differentiate. Medium in the basal chamber was changed every 2-3 days (500 mI).
  • HBECs 24 h prior to infection, HBECs were treated with Phenelzine (400 mM; Sigma) in the basal chamber. All infection experiments were performed in a PC3 facility. At the time of infection, the inhibitor-containing media was removed and replaced with fresh media in the basal chamber. 10 4 plaque forming units (PFU) of SARS-CoV-2 virus inoculum in 100 mI was added to the apical compartment. After 2hr of virus adsorption at 37 °C, 5% C02, the unbound virus inoculum was removed, and cells were cultured with an air-liquid interface with inhibitor-containing media in the basal chamber for 24 hr and 48 hr post infection (24 hpi and 48 hpi).
  • PFU plaque forming units
  • ASI digital pathology cells were fixed with 4% formaldehyde for 30 min at room temperature
  • Viral titers (TCID50 equivalents per ml) in the extracted RNA was determined by qRT-PCR, using Real-time fluorescent RT-PCR kit for detecting 2019- nCoV (BGI, China) following the manufacturer’s instructions. Positive control (mix of pseudo-virus with target virus genes and internal reference) and blank control (DNase/RNase free water) were used as quality control. Limit of detection is 100 copies/ml. The quantity of viral genomes was calculated by normalizing to a viral stock with a known viral titer.
  • BALCs Bronchoalveolar lavage cells
  • PBMCs peripheral blood mononuclear cells
  • a proximity ligation assay was used to assess the co-localization of ACE2 and spike protein at the surface of SARS-CoV-2 infected Caco-2 cells.
  • GSK- LSD1 treatment significantly decreased interaction between ACE2 spike protein Figure 9F. This suggests that methylation of ACE2 via inhibition of LSD1 activity contributes to blocking access to ACE2 by the SARS-CoV-2 spike protein.
  • Caco-2 cells were tested negative for Mycoplasma contamination prior to experiments. Caco-2 cells were seeded at 2 x 10 5 cells per well in six-well plates in DEME (10% FBS) and incubated overnight at 37°C, 5% CO2. 48 h prior to infection, cells were treated with either 400 mM phenelzine or 400 mM GSK-LSD1. At the time of infection, plates were transferred to the BSL3 facility and inhibitor- containing medium was removed and replaced with SARS-CoV-2 virus inoculum (MOI 1) containing DEME (5% FBS).
  • MOI 1 SARS-CoV-2 virus inoculum
  • the virus inoculum was removed and cells were washed three times with PBS to remove unbound virus prior to adding inhibitor-containing medium.
  • 48 h post infection 48 hpi
  • the cell culture supernatant and cells were collected separately in TRIzol reagent and RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA) following the manufacturer’s instructions.
  • RNA miniprep kit Zymo Research, Irvine, CA
  • Viral titers (TCID50 equivalents per ml) in the extracted RNA were determined by qRT-PCR using a real-time fluorescent RT-PCR kit for detecting 2019-nCoV (BGI Genomics, China) following the manufacturer’s instructions.
  • Positive control mixture of pseudo-virus with target virus genes and internal reference
  • blank control DNase/RNase free water
  • the limit of detection was 100 copies/ml.
  • the quantity of viral genomes was calculated by normalizing to a viral stock with a known viral titre.
  • PBMCs are pre-treated with inhibitors and killing assays performed using the xCELLigence® Real Time Cell Analyzer.
  • the Duolink proximity ligation assay was employed using PLA probe anti-mouse PLUS (DU092001), PLA probe anti-rabbit MINUS (DU092005), and Duolink In Situ Detection Reagent Red Kit (DU092008) (Sigma Aldrich). Cells were fixed, permeabilized, and incubated with primary antibodies targeting LSD1 and ACE2. Cells were processed according to the manufacturer’s recommendations. Finally, coverslips were mounted onto slides and examined as above
  • RNA will be extracted from cell supernatants and quantified by qRT- PCR (Thevarajan etai, 2020) and inhibition of viral replication assayed using a modified plaque reduction assay and EC50s.
  • the SARS-CoV-2 highly susceptible cell lines (Floffman etal., 2020) Calu-3, H1299, FlepG2, and Caco- 2 will be virus infected (MRC-5 cells as negative control).
  • SARS-CoV-2-infected cells with/without inhibitor treatments will be assayed by qRT-PCR for ACE2 and TMPRSS2 and flow cytometry and digital pathology using antibodies targeting ACE2 and TMPRSS2.
  • PBMCs will be pre-treated with inhibitors and killing assays performed using the xCELLigence® Real Time Cell Analyzer.
  • Enriched BALCs and PBMCs will be treated in vitro with 3 MOAi and FACS and ASI’s mIF digital analysis used to: (i) phenotype immune cells; (ii) quantify T cell exhaustion, proliferation, and effector markers. High-resolution single-cell RNA, ATAC-seq, and LSD1p CFIIP-seq will be performed with our bioinformatics pipeline we will identify predictive biomarkers of SARS-CoV-2 progression related to immune exhaustion.
  • Enriched BALCs and PBMCs will be profiled with our established liquid biopsy digital pathology platform for our novel EOMES exhaustion biomarker in samples taken within 48 hours of presentation and matched samples taken 7-9 and 20 days later and related to clinical progression.
  • MOA inhibitors are assessed in vivo at two doses with four animals per dose. Parameters include: Haematological, Clinical follow up (body weight, temperature), Xray scanner, blood chemistry, local and systemic reaction. Inflammation parameters, Full pathology after necropsy in case of dose lethality. This will track both the safety profile of our MOAi inhibitors as well as their effect on effect on the NHP immunological model and if MOAi inhibition is able to improve recovery from SARS-CoV-2 challenge.
  • MOA inhibitors were assessed at two doses for each. Four animals per dose are tested (8 animals per group), challenged with SARS-CoV-2. A control group with no drugs will be included. In total the study will include 4 groups with 8 animals for 3 of them and 4 animals for the control group (28 animals). We will test multiple parameters will be followed and studied at the IDMIT, to check safety and efficacy.
  • the facility is equipped with state-of-the-art instruments for in vivo imaging technologies with the following objectives: (1) track antigens and therapeutics in infected hosts; (2) visualize host responses to vaccination and/or treatment, with a specific focus on dynamics of immune effectors: (3) track microbes dissemination in the host; (4) refine and reduce using high numbers of animal models for preclinical research; (5) translate part of the technology to the clinical practice in humans.

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Abstract

L'invention concerne des méthodes de traitement d'infections à coronavirus. Plus particulièrement, l'invention concerne l'utilisation d'inhibiteurs de LSD pour traiter des infections à coronavirus, y compris des infections par le bêtacoronavirus.
PCT/AU2021/050317 2020-04-03 2021-04-06 Méthodes de traitement d'infections à coronavirus WO2021195723A1 (fr)

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WO2022221920A1 (fr) * 2021-04-20 2022-10-27 The Council Of The Queensland Institute Of Medical Research Nouvelles compositions et nouvelles méthodes de traitement d'infections à coronavirus
WO2024020646A1 (fr) * 2022-07-27 2024-02-01 The Council Of The Queensland Institute Of Medical Research Biomarqueur de méthylation pour la résistance à une infection

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WO2011106105A2 (fr) * 2010-02-24 2011-09-01 Oryzon Genomics, S.A. Inhibiteurs destinés à une utilisation antivirale
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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2022221920A1 (fr) * 2021-04-20 2022-10-27 The Council Of The Queensland Institute Of Medical Research Nouvelles compositions et nouvelles méthodes de traitement d'infections à coronavirus
WO2024020646A1 (fr) * 2022-07-27 2024-02-01 The Council Of The Queensland Institute Of Medical Research Biomarqueur de méthylation pour la résistance à une infection

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