Patent Application
20220177531
Activating mutants of RAS are found in more than 25% of all human cancers, and to date direct targeting of RAS in the clinic has been limited to KRAS(G12C) through allele-specific covalent inhibitors. The majority of the oncogenic RAS mutants do not possess a unique reactive group suitable for targeting with covalent inhibitors, and hence how to develop selective, non-covalent warheads that are broadly applicable to RAS mutants, and how to turn such warheads into effective therapeutic strategies remain major unanswered questions in RAS drug discovery.
Recent clinical trials of G12C allele-specific inhibitors revealed high dose tolerance and effective tumor reduction in certain patients, supporting selective targeting of RAS mutants as a viable therapeutic strategy against RAS-driven cancer. By contrast, despite extensive effort, potent and selective inhibitors against other RAS mutants are still lacking, suggesting that developing such inhibitors requires a different approach. Covalent inhibitors bind to an area under the switch II region, called S-II pocket, that is present in the GDP-bound state and form covalent linkage to Cys12. These G12C-selective inhibitors are effective, because KRAS(G12C) cycles intrinsically between the active, GTP-bound form and the inactive GDP-bound form and the compounds lock KRAS(G12C) in the inactive state. Most mutants, such as KRAS(G12V), have slow intrinsic nucleotide exchange rates and thus remain in the active state for an extended period, which predicts challenges in achieving efficacy by trapping them in the GDP-bound form. Thus, targeting the GTP-bound state should be the preferred approach for many RAS mutants. However, there have been no reports of small molecules that selectively bind to a RAS mutant in the GTP-bound state. For proof-of-concept purposes, many binding proteins targeting to the GTP-bound state of RAS mutants have been developed, but they are either not selective for mutants (over wild-type (WT) KRAS) or not effective in inhibiting RAS-mediated signaling in cells. Their lack of efficacy might reflect their inability to effectively compete against multiple RAS-binding effectors. Alternatively, these molecules may have insufficient selectivity to effectively engage in RAS mutants in cells where potentially excess concentrations of wild-type RAS isoforms serve as a sink for low-specificity inhibitors.
There is currently a need for an inhibitor with high selectivity and affinity.
The present disclosure provides proteins or peptides, which may be referred to as monobodies. Fusion proteins and proteolysis targeting chimeras (PROTACs) comprising the proteins or peptides are also provided. Also provided are compositions comprising proteins or peptides of the present disclosure, as well as fusion proteins and PROTACs.
Methods of treating an individual in need of treatment are also provided. The methods may be to treat an individual suffering from or suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers. A method may be for inhibiting ERK activation and/or proliferation of KRAS(G12V), KRAS(G125), KRAS(G12A) and/or KRAS(G12C)-associated cancers. A method may be for reducing levels of endogenous RAS mutants. A method may also be for crystallizing a protein. A method may be for determining one or more potential drug(s) for treatment of KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers. A method may be for pulling down active RAS mutants.
For a fuller understanding of the nature and objects of the disclosure, reference should be made to the following detailed description taken in conjunction with the accompanying figures.
Although claimed subject matter will be described in terms of certain embodiments, other embodiments, including embodiments that do not provide all of the benefits and features set forth herein, are also within the scope of this disclosure. Various structural, logical, and process step changes may be made without departing from the scope of the disclosure.
Ranges of values are disclosed herein. The ranges set out a lower limit value and an upper limit value. Unless otherwise stated, the ranges include all values to the magnitude of the smallest value (either lower limit value or upper limit value) and ranges between the values of the stated range.
As used herein, the terms “including,” “containing,” and “comprising” are used in their open, non-limiting sense.
As used in this disclosure, the singular forms include the plural forms and vice versa unless the context clearly indicates otherwise.
The articles “a” and “an” are used in this disclosure to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
As used herein, unless otherwise stated or indicated, “s” refers to second(s), “min” refers to minute(s), and “h” refers to hour(s).
To provide a more concise description, some of the quantitative expressions given herein are not qualified with the term “about.” It is understood that, whether the term “about” is used explicitly or not, every quantity given herein is meant to refer to the actual given value, and it is also meant to refer to the approximation to such given value that would reasonably be inferred based on the ordinary skill in the art, including equivalents and approximations due to the experimental and/or measurement conditions for such given value. In an example, about refers to ±1%, ±2%, ±3%, ±4%, ±5%. ±6%, ±7%, ±8%, ±9%, ±10%, ±15%, or ±20%
The term “treatment” as used herein refers to reduction or delay in one or more symptoms or features associated with the presence of the particular condition being treated Treatment does not necessarily mean complete cure and does not preclude relapse, but may be used in connection with any such relapse.
The term “therapeutically effective amount” as used herein is the amount sufficient to achieve, in a single or multiple doses, the intended purpose of treatment. The exact amount desired or required will vary depending on the mode of administration, patient specifics and the like. Appropriate effective amounts can be determined by one of ordinary skill in the art (such as a clinician) with the benefit of the present disclosure.
The present disclosure also provides sequences that have homology with the protein or peptides sequences (including antibody sequences) described herein. In various examples, the homologous sequences have at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity with a protein or peptide sequence of the present disclosure.
The present disclosure provides proteins or peptides, which may be referred to as monobodies. Fusion proteins and proteolysis targeting chimeras (PROTACs) comprising the proteins or peptides are also provided. Also provided are compositions comprising proteins or peptides of the present disclosure, as well as fusion proteins and PROTACs. Methods of treating an individual in need of treatment are also provided. The methods may be to treat an individual suffering from or suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers. A method may be for inhibiting ERK activation and/or proliferation of KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers. A method may be for reducing levels of endogenous RAS mutants. A method may also be for crystallizing a protein. A method may be for determining one or more potential drug(s) for treatment of KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers. A method may be for pulling down active RAS mutants.
In an aspect, the present disclosure provides proteins or peptides, which may be referred to monobodies. The proteins or peptides may have the following sequence or comprise the following sequence or a comprise a truncated variant of the following sequence: XXXVPTXLEVVAATXXSLLISWDAPAVTVXFYVIXYGETGHGVGAFXAFXVXXXXS TATISGLXPGVDYTITVYARXXSKQGXYXPSPISINYRT (SEQ ID NO:26), where each X is an amino acid residue. X may be a canonical or non-canonical amino acid, such as, for example, a hydrophilic amino acid (e.g., a hydrophilic canonical amino acid or a hydrophilic non-canonical amino acid). In various examples, up to the first four residues at the N-terminus or C-terminus may be removed.
In various examples, the residues in bold are present in a protein or peptide of the present disclosure:
In various examples, a peptide or protein may have the following sequence or comprise the following sequence or comprise a truncated variant of the following sequence: VSSVPTKLEVVAATPTSLLISWDAPAVTVXFYVIXYGETGHGVGAFXAFXVXXSKST ATISGLKPGVDYTITVYARXXSKQGXYXPSPISINYRT (SEQ ID NO:27), where each X is an amino acid residue, such as, for example, a hydrophilic amino acid (e.g., a hydrophilic canonical amino acid or a hydrophilic non-canonical amino acid). Each X may be the same or different. In various examples, up to the first four residues at the N-terminus or C-terminus may be removed.
In various other examples, a peptide or protein may have the following sequence or comprise the following sequence or comprise a truncated variant of the following sequence: XXXVPTXLEVVAATXXSLLISWDAPAVTVFFYVITYGETGHGVGAFQAFKVPGXXS TATISGLXPGVDYTITVYARGYSKQGPYKPSPISINYRT (SEQ ID NO:28), where X is an amino acid residue, such as, for example, a hydrophilic amino acid (e.g., a hydrophilic canonical amino acid or a hydrophilic non-canonical amino acid). In various examples, up to the first four residues at the N-terminus or C-terminus may be removed. Each X may be the same or different.
In an aspect, a peptide or protein may have the following sequence or a truncated variant thereof or comprise the following sequence or comprise a truncated variant of the following sequence: VSSVPTKLEVVAATPTSLLISWDAPAVTVFFYVITYGETGHGVGAFQAFKVPGSKST ATISGLKPGVDYTITVYARGYSKQGPYKPSPISINYRT (12VC1) (SEQ ID NO:1); or a sequence with at least 75% homology, at least 80% homology, at least 85% homology, at least 90% homology, or at least 95% homology to 12VC1. SEQ ID NOs:26-28 represent variants of SEQ ID NO:1, where “X” represents amino acids of SEQ ID NO:1 that can be substituted (e.g., substituted by a hydrophilic amino acid). In various examples, variants of SEQ ID NO:1 have substitutions at the positions labeled X in SEQ ID NOs:26-28. In various examples, one or more (e.g., 1, 2, 3, 4, 5, or more) of the X residues in SEQ ID NOs: 26-28 differ from the corresponding amino acid residues in SEQ ID NO:1 (e.g., with alanine, or serine or another hydrophilic amino acid residue)). In various examples, all of the X residues in SEQ ID NOs: 26-28 differ from the corresponding amino acid residues in SEQ ID NO:1 (i.e., they have been substituted (e.g., with alanine, or serine or another hydrophilic amino acid residue)). Each X may be the same or different. For example, the hydrophilic amino acid residue is a canonical amino acid residue or a non-canonical amino acid residue. Examples of hydrophilic amino acids include, but are not limited to, arginine, glutamine, asparagine, threonine, tyrosine, and serine. In various examples, when a protein or peptide of the present disclosure has or comprises the following sequence or comprises a truncated variant of the following sequence: VSSVPTKLEVVAATPTSLLISWDAPAVTVFFYVITYGETGHGVGAFQAFKVPGSKST ATISGLKPGVDYTITVYARGYSKQGPYKPSPISINYRT (12VC1) (SEQ ID NO:1), the bold residues are present (e.g., the same) in any variant sequence.
The proteins or peptides may be provided as a multivalent display or disposed (e.g., displayed) on a scaffold forming a multivalent display. Various examples of scaffolds include, but are not limited to, beads, resins, or membranes (e.g., cell membranes). In various examples, a protein or peptide may be provided on a yeast display. The one or more proteins or peptides may be the same or different.
In various examples, proteins or peptides of the present disclosure are non-covalently bound or covalently conjugated to one or more other proteins or peptides of the present disclosure. The one or more proteins or peptides may be the same or different. The resulting conjugate or oligomer may be a dimer, trimer, or the like.
In various examples, proteins or peptides of the present disclosure may be fused to a larger protein or peptide. Examples of larger proteins or peptides include, but are not limited to GFP, GFP variants, yeast Aga2, epitope tags, and the like.
In various examples, a peptide of the present disclosure has the following sequence or comprises any one of the following sequences or is a truncated variant of any one of the following sequences or is a variant (e.g., homolog) of any one of the following:
Examples of variants of SEQ ID NO:1 include, but are not limited to, SEQ ID NOs:2-20. SEQ ID NO:1 or variant may be a portion of a larger protein or attached to another compound or may be a truncated variant thereof. In various examples, the bolded residues do not change in any variants of the following sequences or a peptide or protein comprising any one of the following sequences or a truncated variant of any one of the following sequences:
A protein or peptide of the present disclosure may be modified at various locations on the protein or peptide. For example, a protein or peptide may be modified at a sidechain of one or more amino acid residue(s), the C-terminus, the N-terminus, or a combination thereof. For example, Cys residues may be modified site specifically using a reagent that is reactive with a Cys residue (e.g., maleimide). Examples of modification include, but are not limited to, PEGylation, biotinylation, conjugation of dyes, conjugation of E3 ligase ligands, small molecules (e.g., small molecule drugs), and the like, and combinations thereof. In various examples, lysines, series, glutamic acids, and the N-terminus of a protein or peptide may be modified such that the binding interface is not disrupted.
The peptides or proteins can be synthesized via methods known in the art (e.g., recombinant expression or solid phase peptide synthesis (SPPS)). Depending on the vector utilized, any of a number of suitable transcription and translation elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etcetera, may be used in the expression vector. Such construction of expression vectors and the expression of genes in transfected cells can involve the use of molecular cloning techniques (for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo recombination/genetic recombination), bacterial systems for the expression of vectors, yeast systems with constitutive or inducible promoters, insect systems, prokaryotic and eukaryotic systems using transfection or co-transfections of DNA vectors, transgenic animals using for example viral infection, and embryonic stem cells. Methods and procedures for using and applying such vectors are widespread in publications and are known or easily obtainable by persons of ordinary skill in the art. Both Boc and Fmoc SPPS chemistries may be used.
In an aspect, the present disclosure provides a fusion protein or PROTAC comprising a protein or peptide of the present disclosure.
A fusion protein or PROTAC may comprise an E3 ligase subunit or fragment of an E3 subunit. Examples of an E3 ligase are Von Hippel-Lindau tumor suppressor (VHL), cereblon (CRBN), mouse double minute 2 (MDM2), cellular inhibitor of apoptosis (cIAP), and speckle-type POZ protein (SPOP). Various other E3 ligases are known in the art. Examples of fusion partners include the UBOX domain of the CHIP E3 ligase. Small molecules include VHL ligand, pomalidomide (CRBN ligand), Bestatin (cIAP ligand), Nutlin-3a (MDM2 ligand), and the like. Examples of peptides that target E3 ligase include, but are not limited to, HIF-1alpha (VHL directing peptide).
In an aspect, the present disclosure provides compositions comprising proteins, peptides, fusion proteins, and/or PROTACs of the present disclosure. The compositions further comprise one or more pharmaceutically acceptable carriers.
A composition may comprise additional components. For example, the composition comprises a buffer solution suitable for administration to an individual (e.g., a mammal such as, for example, a human or a non-human). An individual may be a subject. The buffer solution may be a pharmaceutically acceptable carrier.
A composition may include one or more standard pharmaceutically acceptable carrier(s). Non-limiting examples of compositions include solutions, suspensions, emulsions, solid injectable compositions that are dissolved or suspended in a solvent before use, and the like. Injections may be prepared by dissolving, suspending, or emulsifying one or more of the active ingredient(s) in a diluent. Non-limiting examples of diluents include distilled water for injection, physiological saline, vegetable oil, alcohol, and the like, and combinations thereof. Further, injections may contain stabilizers, solubilizers, suspending agents, emulsifiers, soothing agents, buffers, preservatives, and the like. Injections may be sterilized in the final formulation step or prepared by sterile procedure. The composition may also be formulated into a sterile solid preparation, for example, by freeze-drying, and can be used after sterilized or dissolved in sterile injectable water or other sterile diluent(s) immediately before use. Non-limiting examples of pharmaceutically acceptable carriers can be found in: Remington: The Science and Practice of Pharmacy (2012) 22nd Edition, Philadelphia, Pa. Lippincott Williams & Wilkins.
Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include, but are not limited to, buffers such as, for example, phosphate, citrate, histidine and other organic acids; antioxidants including, but not limited to, ascorbic acid and methionine; preservatives (such as, for example, octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as, for example, methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids, such as, for example, glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™, polyethylene glycol (PEG) and the like. In an embodiment, the pharmaceutical composition may comprise buffer components and stabilizers, including, but not limited to, sucrose, polysorbate 20, NaCl, KCl, sodium acetate, sodium phosphate, arginine, lysine, trehalose, glycerol, and maltose.
In an aspect, the present disclosure provides a method for treating an individual having or suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers. Also provided are methods of reducing levels of endogenous RAS mutants and/or inhibiting ERK activation and/or proliferation of KRAS(G12V), KRAS(G12S), KRAS(G12A), and/or KRAS(G12C)-associated cancers.
Examples of KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers include, but are not limited to, non-small cell lung cancer (NSCLC), colorectal cancer (CRC), pancreatic cancer (PDAC), uterine cancer, and gastric cancer.
A method for treating an individual having or suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers and/or reducing levels of endogenous RAS mutants may comprise: administering to a subject who has been diagnosed with or is suspected of having KRAS(G12V)- and/or KRAS(G12C)-associated cancers a therapeutically effective amount of: i) a protein or peptide of the present disclosure, and optionally a carrier protein; ii) an mRNA capable of encoding a protein or peptide of the present disclosure; iii) a DNA capable of encoding a protein or peptide of the present disclosure; iv) a microorganism (e.g., virus or bacteria) that carries the gene for a protein or peptide of the present disclosure; v) a fusion protein or PROTAC of the present disclosure; vi) a composition of the present disclosure vii) an mRNA capable of encoding a fusion protein or PROTAC comprising a protein or peptide of the present disclosure; viii) a DNA capable of encoding a fusion protein or PROTAC comprising a protein or peptide of the present disclosure; or ix) a microorganism that carries the gene for a fusion protein or PROTAC comprising a protein or peptide of the present disclosure.
A protein or peptide of the present disclosure may be administered to an individual by various means. For example, the peptides can be administered directly or within a pharmaceutical agent or in combination with other delivery agents. Alternatively, in another embodiment, an expression vector can be used. Including, but not limited to, to a variety of viral-based vector systems, non-limiting examples of which include, adenoviral vectors and adenoviral-associated vectors and oncolytic vectors. In another embodiment, mRNA encoding a protein or peptide of the present disclosure or DNA encoding a protein or peptide of the present disclosure may be administered to an individual in need of treatment. A protein or peptide may be delivered on its own or with a carrier protein.
A method for treating an individual having or suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers may be carried out in combination with one or more known therapy(ies), including, but not limited to, surgery, radiation therapy, chemotherapy, photodynamic therapy, and/or immunotherapy.
The proteins or peptides may be administered by various means. Administration of the proteins or peptides (including as compositions) as described herein can be carried out using any suitable route of administration known in the art. For example, the compositions may be administered via intravenous, intramuscular, intraperitoneal, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, oral, or topical. The compositions may be administered parenterally or enterically. The compositions may be introduced as a single administration or as multiple administrations or may be introduced in a continuous manner over a period of time. For example, the administration(s) can be a pre-specified number of administrations or daily, weekly or monthly administrations, which may be continuous or intermittent, as may be clinically needed and/or therapeutically indicated.
In various examples, a subject in need of treatment is administered a therapeutically effective amount of a composition of the present disclosure. A dose of a therapeutically effective amount of a protein, peptide, fusion protein, or PROTAC of the present disclosure may have a concentration of 1 nM to 10 mM, including all 0.1 nM values and ranges therebetween.
The compositions may be administered to an individual or subject in need of treatment such as a human or a non-human animal. An individual in need of treatment may be a human. In other examples, the individual is a non-human mammal or other animal. Non-limiting examples of non-human mammals include cows, horses, pigs, mice, rats, rabbits, cats, dogs, or other agricultural mammals, pets, or service animals, and the like.
In an aspect, the present disclosure provides a method of crystallizing a protein. A method for crystallizing a protein comprises contacting the protein with a protein or peptide of the present disclosure, where the binding results in crystallization of the protein.
In an aspect, the present disclosure provides a method for determining one or more potential drug(s) for treatment of KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers.
A method may comprise structure guided design based on crystal structures of the protein or peptide-RAS mutant complexes; screening the compounds that displace the protein or peptide from RAS; and quantifying the amount of active RAS using the protein or peptide of the present disclosure after treatment with the compounds.
The steps of the method described in the various embodiments and examples disclosed herein are sufficient to carry out the methods of the present disclosure. Thus, in an embodiment, the method consists essentially of a combination of the steps of the methods disclosed herein. In another embodiment, the method consists of such steps.
The following Statements provide examples of the present disclosure:
Statement 1. A protein or peptide (which may be referred to a monobody) comprising: i) the following sequence: VSSVPTKLEVVAATPTSLLISWDAPAVTVFFYVITYGETGHGV GAFQAFKVPGSKSTATISGLKPGVDYTITVYARGYSKQGPYKPSPISINYRT (12VC1) (SEQ ID NO:1); or ii) a sequence with at least 75% homology, at least 80% homology, at least 85% homology, at least 90% homology, or at least 95% homology to 12VC1.
Statement 2. A protein or peptide according to Statement 1, wherein one or more of the proteins or peptides are disposed (e.g., displayed) on a bead or resin or membrane (e.g., cell membrane).
Statement 3. A protein or peptide according to Statement 1, wherein a yeast display is used to display one or more proteins or peptides of Statement 1.
Statement 4. A protein or peptide according to Statement 1, wherein the protein or peptide is non-covalently bound and/or covalently conjugated to one or more other proteins and peptides such that a dimer, trimer, or the like is formed. In various examples, combination of proteins or peptides are an oligomer.
Statement 5. A protein or peptide according to Statement 1, wherein the protein or peptide is fused to a larger protein or peptide.
Statement 6. A protein or peptide according to Statement 1, wherein the larger protein or peptide is GFP, a GFP variant, yeast Aga2, an epitope tag, and the like.
Statement 7. A protein or peptide (which may be referred to a monobody) according to any of the preceding claims, wherein the homological sequence is:
Statement 8. A protein or peptide (which may be referred to a monobody) according to any one of the preceding claims, wherein the protein or peptide has the following sequence or comprises the following sequence:
Statement 9. A protein or peptide (which may be referred to a monobody) according to any one of the preceding Statements, wherein the protein or peptide is modified at a sidechain of one or more amino acid residue(s), the C-terminus, the N-terminus, or a combination thereof.
Statement 10. A fusion protein or proteolysis targeting chimera (PROTAC) comprising a protein or peptide according to any one of the preceding Statements.
Statement 11. A fusion protein or PROTAC according to Statement 10, further comprising an E3 ligase subunit or fragment of an E3 subunit.
Statement 12. A fusion protein or PROTAC according to Statement 11, wherein the E3 ligase is Von Hippel-Lindau tumor suppressor (VHL). Fusion partners for a fusion protein include UBOX domain of the CHIP E3 ligase. Possible small molecules that may be utilized include: VHL ligands, pomalidomide (CRBN ligand), Bestatin (cIAP ligand), Nutlin-3a (MDM2 ligand). Possible peptides that may be utilized include peptides that targets subunits of E3 ligase, e.g., HIF-1alpha (VHL directing peptide).
Statement 13. A composition comprising a protein or peptide according to any one of Statements 1-9 and a pharmaceutically acceptable carrier.
Statement 14. A composition comprising a fusion protein or PROTAC according to any one of Statements 10-12 and a pharmaceutically acceptable carrier.
Statement 15. A method for treating KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers comprising: administering to a subject who has been diagnosed with or is suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers a therapeutically effective amount of:
i) a protein or peptide according to any one of Statements 1-9, and optionally a carrier protein; ii) an mRNA capable of encoding a protein or peptide according to any one of Statements 1-9; iii) a DNA capable of encoding a protein or peptide according to any one of Statements 1-9; iv) a microorganism (e.g., virus or bacteria) that carries the gene for a protein or peptide according to any one of Statements 1-9; v) a fusion protein or PROTAC according to any one of Statements 10-12; or vi) a composition according to Statement 13 or Statement 14, wherein the subject's cancer is treated.
Statement 16. A method for inhibiting ERK activation and/or proliferation of KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers comprising:
contacting one or more KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancer cells with a therapeutically effective amount of
i) a protein or peptide according to any one of Statements 1-9, and optionally a carrier protein; ii) an mRNA capable of encoding a protein or peptide according to any one of Statements 1-9; iii) a DNA capable of encoding a protein or peptide according to any one of Statements 1-9; iv) a microorganism (e.g., virus or bacteria) that carries the gene for a protein or peptide according to any one of Statements 1-9; v) a fusion protein or PROTAC according to any one of Statements 10-12; or vi) a composition according to Statement 13 or Statement 14, wherein ERK activation is and/or proliferation of KRAS(G12V), KRAS(G12S), KRAS(G12A), and/or KRAS(G12C)-associated cancers is inhibited.
Statement 17. A method for reducing levels of endogenous RAS mutants comprising: administering to a subject who has been diagnosed with or is suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A), and/or KRAS(G12C)-associated cancers a therapeutically effective amount of
i) a protein or peptide according to any one of Statements 1-9, and optionally a carrier protein; ii) an mRNA capable of encoding a protein or peptide according to any one of Statements 1-9; iii) a DNA capable of encoding a protein or peptide according to any one of Statements 1-9; iv) a microorganism (e.g., virus or bacteria) that carries the gene for a protein or peptide according to any one of Statements 1-9; v) a fusion protein or PROTAC according to any one of Statements 10-12; or vi) a composition according to Statement 13 or Statement 14, wherein the levels of endogenous RAS mutant are reduced.
Statement 18. A method for crystallizing a protein comprising: contacting the protein with a protein or peptide according to any one of Statements 1-9, wherein binding of the protein to the protein or peptide according to any one of Statements 1-9 results in crystallization of the protein.
Statement 19. A method for determining one or more potential drug(s) for treatment of KRAS(G12V)- and/or KRAS(G12C)-associated cancers, comprising:
(1) designed compounds through structure-guided design based on the crystal structures of protein or peptide-RAS mutant (e.g., 12VC1-RAS mutant) complexes;
(2) screening for molecules that displace the monobody from RAS; and
(3) quantifying the amount of active RAS using the monobody after treatment with compounds.
Statement 20. A protein or peptide comprising or having: i) the following sequence: VSSVPTKLEVVAATPTSLLISWDAPAVTVFFYVITYGETGHGVGAFQAFKVPGSKST ATISGLKPGVDYTITVYARGYSKQGPYKPSPISINYRT (12VC1) (SEQ ID NO:1) or a truncated variant thereof; or ii) a variant with at least 80% homology to SEQ ID NO:1.
Statement 21. A protein or peptide according to claim Statement 21, where one or more of the proteins or peptides are disposed on a bead or resin or membrane or where a yeast display is used to display the one or more proteins or peptides or where the protein or peptide is non-covalently bound and/or covalently conjugated to one or more other proteins and peptides such that a dimer, trimer, or oligomer is formed.
Statement 22. A protein or peptide according to Statement 20 or 21, wherein the protein or peptide is fused to a larger protein or peptide.
Statement 23. A protein or peptide according to Statement 22, wherein the larger protein or peptide is GFP, a GFP variant, yeast Aga2, or an epitope tag.
Statement 24. The protein or peptide according to any one of Statements 20-23 1, wherein the variant is:
Statement 25. A protein or peptide according to any one of Statements 20-24, wherein the protein or peptide is modified at a sidechain of one or more amino acid residue(s), the C-terminus, the N-terminus, or a combination thereof.
Statement 26. A fusion protein or proteolysis targeting chimera (PROTAC) comprising the protein or peptide according to any one of Statements 20-25.
Statement 27. A fusion protein or PROTAC according to Statement 26, further comprising an E3 ligase subunit or fragment of an E3 subunit.
Statement 28. A fusion protein or PROTAC according to Statement 27, wherein the E3 ligase is Von Hippel-Lindau tumor suppressor (VHL), cereblon (CRBN), mouse double minute 2 (MDM2), cellular inhibitor of apoptosis (cIAP), and speckle-type POZ protein (SPOP).
Statement 29. A composition comprising a protein or peptide according to any one of Statements 20-25 and a pharmaceutically acceptable carrier.
Statement 30. A composition comprising a fusion protein or PROTAC according to any one of Statements 26-28 and a pharmaceutically acceptable carrier.
Statement 31. A method for treating an individual having or suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers and/or inhibiting ERK activation and/or proliferation of KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers comprising: administering to a subject who has been diagnosed with or is suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers a therapeutically effective amount of:
i) a protein or peptide according to any one of Statements 20-25, and optionally a carrier protein; ii) an mRNA capable of encoding a protein or peptide according to any one of Statements 20-25; iii) a DNA capable of encoding a protein or peptide according to any one of Statements 20-25; iv) a microorganism that carries the gene for a protein or peptide according to any one of Statements 20-25; v) a fusion protein or PROTAC comprising a protein or peptide according to any one of Statements 20-25 (e.g., according to any one of Statements 26-28); vi) an mRNA capable of encoding a fusion protein or PROTAC comprising a protein or peptide according to claim 1; vii) a DNA capable of encoding a fusion protein or PROTAC comprising a protein or peptide according to any one of Statements 20-25 (e.g., according to any one of Statements 26-28); or viii) a microorganism that carries the gene for a fusion protein or PROTAC comprising a protein or peptide according to any one of Statements 20-25 (e.g., according to any one of Statements 26-28), wherein the subject's cancer is treated and/or the activation and/or proliferation is inhibited.
Statement 32. A method according to Statement 31, wherein the cancer is non-small cell lung cancer (NSCLC), colorectal cancer (CRC), pancreatic cancer (PDAC), uterine cancer, or gastric cancer.
Statement 33. A method according to Statement 31 or Statement 32, wherein levels of endogenous RAS mutants are reduced.
Statement 34. A protein or peptide comprising the following sequence or a truncated variant thereof, or having the following sequence or truncated variant thereof:
XXXVPTXLEVVAATXXSLLISWDAPAVTVXFYVIXYGETGHGVGAFXAFXVXXXXS TATISGLXPGVDYTITVYARXXSKQGXYXPSPISINYRT (SEQ ID NO:26), wherein each X is a canonical or non-canonical amino acid.
Statement 35. The protein or peptide according to Statement 34, wherein the sequence is:
Statement 36. The protein or peptide according to Statement 34 or Statement 35, wherein each X is individually chosen from alanine, serine, arginine, glutamine, asparagine, threonine, and tyrosine.
Statement 37. A method for treating an individual having or suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers and/or inhibiting ERK activation and/or proliferation of KRAS(G12V), KRAS(G125), KRAS(G12A) and/or KRAS(G12C)-associated cancers comprising: administering to a subject who has been diagnosed with or is suspected of having KRAS(G12V), KRAS(G12S), KRAS(G12A) and/or KRAS(G12C)-associated cancers a therapeutically effective amount of:
i) a protein or peptide according to any one of Statements 34-36, and optionally a carrier protein; ii) an mRNA capable of encoding a protein or peptide according to any one of Statements 34-36; iii) a DNA capable of encoding a protein or peptide according to any one of Statements 34-36; iv) a microorganism that carries the gene for a protein or peptide according to any one of Statements 34-36; v) a fusion protein or PROTAC comprising a protein or peptide according to any one of Statements 34-36; vi) an mRNA capable of encoding a fusion protein or PROTAC comprising a protein or peptide according to any one of Statements 34-36; vii) a DNA capable of encoding a fusion protein or PROTAC comprising a protein or peptide according to any one of Statements 34-36; or viii) a microorganism that carries the gene for a fusion protein or PROTAC comprising a protein or peptide according to any one of Statements 34-36, wherein the subject's cancer is treated and/or the activation and/or proliferation is inhibited.
The following example is presented to illustrate the present disclosure. It is not intended to be limiting in any matter.
This example provides a description of a peptide of the present disclosure.
Presented herein is a monobody, termed 12VC1, that selectively recognizes the active state of KRAS(G12V) and KRAS(G12C). This monobody bound noncovalently to these KRAS mutants by up to 400-fold more tightly than to wild type KRAS, exhibiting a high level of selectivity. The crystal structure of an HRAS-12VC1 complex revealed that 12VC1 presents a shallow pocket that selectively recognized the mutations and it targets the Switch I and II regions of RAS, thereby directly inhibiting RAS-effector interactions. When expressed intracellularly, 12VC1 potently inhibited ERK activation and the proliferation of KRAS(G12V)- and KRAS(G12C)-driven cancer cell lines in vitro and in a mouse xenograft model. The selectivity of 12VC1 was used for selective degradation of endogenous RAS mutants, resulting in more sustained signaling inhibition than direct inhibition. This shows selective and non-covalent inhibition and degradation of the active state of oncogenic KRAS mutants is achievable and potentially therapeutically effective.
Monobody technology, a synthetic binding protein platform that has produced potent and selective binders to diverse protein targets, was employed. The developed monobody, termed 12VC1, demonstrated exceptionally high selectivity for KRAS(G12V) and KRAS(G12C) (
12VC1 selectively engaged KRAS mutants and potently inhibited RAS-mediated signaling, when expressed intracellularly as a genetically encoded reagent (
The crystal structure of 12VC1 bound to HRAS(G12C) with GTPγS (Table 2) was determined. We used HRAS because it crystallizes more readily than KRAS. The binding interface of this structure should be relevant to how 12VC1 recognizes KRAS mutants, because HRAS and KRAS have the identical amino acid sequence in the effector lobe to which 12VC1 binds, and the binding data confirmed that 12VC1 maintained selectivity toward the G12C mutation in HRAS (
The structure and the interface energetics suggested two possible mechanisms for the high selectivity of 12VC1: first, the monobody directly discriminates the mutated residue at position 12, and second it recognizes a conformation of the epitope that is unique to RAS mutants. To examine the first possibility, computational structural analysis was utilized, which revealed a shallow pocket, comprising residues V33, A48 and K50, that accommodates the Cys12 side chain (
The selectivity and potency of 12VC1 allowed proof-of-concept evaluation on whether a mutant-selective, non-covalent reagent can effectively inhibit the growth of cancer cells driven by endogenous KRAS mutants by using monobodies as genetically encoded, intracellular reagents. Several stable cancer cell lines that express 12VC1 or MB(Neg), a non-binding monobody, were generated under the control of a Dox-inducible promotor (
Next, the anti-tumor activity of 12VC1 was evaluated using a mouse xenograft model. Two separate derivatives of PATU8902, a cancer cell line of pancreatic origin, that express 12VC1 or MB(Neg) under control of a dox-inducible promoter were prepared and injected them subcutaneously into nude mice. Expression of each monobody was induced after the average tumor size exceeded 100 mm3. 12VC1 expression significantly reduced tumor growth, whereas expression of MB(Neg) had no impact (
To answer another major question in RAS drug discovery as to whether one can selectively degrade an endogenous RAS mutant, which should offer advantage over inhibition by occupancy, we engineered a proteolysis targeting chimera (PROTAC)-like fusion protein based on 12VC1. Although RAS has been shown to undergo ubiquitination via E3 ligases and degradation, targeted degradation of endogenous KRAS(G12C) was deemed not feasible using PROTAC derivatives of a covalent inhibitor. Furthermore, the covalent inhibitors are not ideal warheads for designing degraders, as their irreversible nature excludes the possibility of multiple cycles of target degradation, an important factor potentiating degraders. Due to a lack of suitable noncovalent ligands, no PROTAC molecules have been developed that are selective to other RAS mutants. We developed variants of 12VC1 termed 12VC1.1 and 12VC1.2 that contained fewer Lys resides and fused them to VHL (
The development of a selective degrader for a KRAS mutant made it possible to compare effects of selective inhibition and degradation of a KRAS mutant in a signaling assay. Treatment with the covalent inhibitor, ARS1620, or non-covalent 12VC1 inhibitor was initially effective but the pERK level quickly rebounded within 24 hours after the withdrawal of ARS1620 and dox, respectively (
Finally, the effectiveness of mutant-selective degradation was examined in a mouse xenograft model using the H23 cell line (
Using monobodies as “tool biologics,” the present disclosure describes that oncogenic RAS mutants can be selectively recognized and inhibited using non-covalent approaches. Furthermore, it was demonstrated that a single inhibitor that possesses an appropriate pocket in the binding interface is capable of selectively recognizing multiple oncogenic RAS mutants. This broad spectrum may be therapeutically important in light of reports describing the presence of multiple RAS mutations in a single patient. The structure of the monobody-RAS interface will guide the design of non-covalent inhibitors. Furthermore, these results conclusively establish that endogenous RAS mutants can be selectively degraded, which strongly support the potential of mutant RAS degraders as an effective therapeutic strategy. 12VC1 itself has substantial potential to aid the future drug development effort against RAS mutants, either through protein or gene delivery technologies.
Methods.
Protein expression and purification. All proteins used for monobody development and binding assays, including RAS constructs (KRAS4B residues 1-174 containing G12C, G12V, G12D, G13D, Q61L, WT, NRAS(WT), and HRAS(WT)), Monobodies, and RAF-1 RBD (residues 51-131) were produced with an N-terminal tag containing His6, Avi-tag for biotinylation and a TEV protease recognition site using the pHBT vector. The proteins were produced in E. coli BL21(DE3). To produce biotinylated proteins, E. coli BL21(DE3) with the pBirA plasmid was used as the host and grown in the presence of 50 μM of biotin. Expressed proteins were purified using Ni-Sepharose columns (GE Healthcare) via gravitational flow, followed by dialysis in Tris buffered saline (TBS, 50 mM Tris-Cl pH7.5 containing 150 mM NaCl) for non-RAS proteins. TBS containing 20 mM MgCl2 and 0.5 mM DTT was used for RAS proteins. Samples were further purified using a Superdex 75 size exclusion column on AKTA Pure systems (GE Healthcare). HRAS(WT) and HRAS(G12C) (residues 1-166) used for crystallization was produced as a fusion protein with His6 and yeast SUMO at the N terminus using an in-house vector described previously. The tag was removed with SUMO hydrolase, followed by overnight dialysis in RAS buffer (50 mM Tris-Cl pH 7.5, 150 mM NaCl, 20 mM MgCl2, 5 mM BME). For monobodies (12VC1 and 12VC3) used in crystallization and RAS used in BLI experiments, proteins were cleaved with TEV-protease in the presence of 0.5 mM EDTA and 1 mM DTT after the Nickel column purification step. Cleaved tags and His-tagged ySUMO hydrolase or TEV-proteases were removed by passing samples through a Ni-Sepharose column, followed by size-exclusion chromatography as described above.
Nucleotide exchange of RAS. Purified RAS proteins used in binding experiment and crystallization were prepared by diluting stock protein (typically containing 20-250 μM RAS) 25 times with 20 mM Tris-Cl buffer pH 7.5 containing 5 mM EDTA, 0.1 mM DTT and 1 mM final concentration of a nucleotide (GDP or GTPγS). Samples were incubated at 30° C. for 30 minutes. MgCl2 was then added to the sample at a final concentration of 20 mM and the solution was further incubated on ice for at least 5 minutes prior to use.
Monobody development. General procedures for the development of monobodies against purified protein targets have been described previously. After four rounds of phage display library selection using biotinylated KRAS(G12C) at concentrations of 100 nM, 100 nM, 50 nM and 50 nM, the genes encoding monobodies from the enriched phage pool were transferred to a yeast display vector, which was used to construct yeast-display libraries. The yeast display libraries were sorted using a Bio-Rad S3e fluorescence-activated cell sorter or a FACSARIA II cell sorter (BD Biosciences). The first round of sorting recovered clones that bound to KRAS(G12C); the second round recovered clones that did not bind to KRAS(WT); and the third round recovered clones that bound to KRAS(G12C). Single clones were then screened for selective binding to RAS mutants. The expression of monobodies on the surface of yeast cells were detected using mouse anti-VS and anti-mouse IgG-FITC conjugate. Target binding was detected with neutravidin Dylight650. Yeast cells were analyzed using an iQue flow cytometer (Sartorius). The median of the signal intensity in the Dylight650 channel for the 75-95th percentile population was taken as representative signal. This sampling method of flow cytometry events minimizes erroneous contributions from events with anomalously high signals while retaining events with high signals. For degradation experiment, monobody degraders were developed by fusing Monobodies 12VC1.1 and 12VC1.2 C-terminal to the VHL domain (1-213) with a SSSSG (SEQ ID NO:24) linker and N-terminal HA tag (YPYDVPDYA (SEQ ID NO:25)) following a published design.
Biolayer interferometry (BLI) analysis. BLI experiments were performed on an Octet Red96 instrument (Molecular Devices). Biotinylated monobodies were immobilized on streptavidin biosensor tips. Samples were diluted in 20 mM HEPES-NaOH buffer (pH 7.4) containing 150 mM NaCl, 5 mM MgCl2, 0.2 mM TCEP and 0.005% Tween-20. BLI signals were analyzed using Octet Data Analysis software (Molecular Devices).
Cell culture. All cell line used in the study were either directly purchased from ATCC (HEK293T, A375, HPAF-II) or validated externally via IDEXX (PATU8902, H23, H358). HEK293T, Flp293, PATU8902, A375, and HPAF-II cells were maintained in DMEM high glucose with L-glutamine (Hyclone) supplemented with 10% FBS (Gemini Bio-products) and antibiotics-antimycotics (Gibco). H358, H23, and H441 cells were maintained in RPMI-1640 high glucose with sodium pyruvate, L-glutamine (Thermo), supplemented with 10% FBS and antibiotic-antimycotic. The absence of mycoplasma contamination was periodically confirmed using a PCR-based mycoplasma testing kit (LiLIF).
Transient expression of KRAS and monobody for confocal imaging and signaling experiments. HEK293T cells were cultured in glass-bottom 8-well chambers (ibidi GmbH) for colocalization assays or in a 12-well plate for signaling assays for one day prior to transfection. On the day of transfection at 70-90% confluency, media were replaced with antibiotics-free complete media (DMEM supplemented with 10% FBS). Transfection of pEGFP vectors encoding the appropriate mCherry fused monobodies and EGFP fused KRAS4B constructs was performed with lipofectamine 3000 (Thermo Fisher Scientific) and according to the manufacturer's recommended protocol. On the following day, transfected cells were imaged with a LSM710 confocal microscope (Zeiss) for colocalization experiment or harvested for Western blot analysis.
Pull-down assays. H358, PATU8902, and HEK293T cells were cultured in 10 cm plates (Corning, #430167). H358 and PATU8902 cells were treated with and without ARS1620 (SelleckChem, 58707) at a final concentration of 10 μM for 1.5 hours, and HEK293T cells were treated with EGF (PeproTech; AF-100-15) at a final concentration of 50 ng/mL for 4 minutes. Cells were lysed by incubating them on ice for 15 minutes in GTPase lysis buffer (25 mM Tris-Cl pH 7.2, 150 mM NaCl, 5 mM MgCl2, 1% NP-40 and 5% glycerol supplemented with protease tablet (Roche, 5892991001) and phosphatase inhibitors (1 mM sodium orthovanadate, 10 mM NAF, 54 mM β-glycerol phosphate)) immediately before analysis. After centrifugation for 15 minutes at 15,000 g, the supernatants were collected and incubated with SA agarose resins (Thermo Fisher Scientific) for 1 hour at 4° C. to remove non-specific binders to the resins. After the removal of resins via centrifugation, the pre-cleared lysates were then incubated with biotinylated monobodies bound to SA agarose resins for 3 hours at 4° C. while rotating. The agarose resins were then washed twice with the GTPase lysis buffer and boiled in 1×SDS buffer with 37.5 mM β-mercaptoethanol and processed for Western blotting using a pan-RAS antibody (Santa Cruz Biotechnology, C-4).
Cell signaling assay and quantification of immunoblots. Cells were lysed in RIPA buffer (50 mM Tris-Cl pH 8, 150 mM NaCl, 5 mM EDTA pH8, 0.1% SDS, 1% NP40) supplemented with protease inhibitors (Roche; 5892991001) and phosphatase inhibitors (54 mM β-glycerophosphate, 10 mM NaF, 1 mM sodium vanadate) for 15 minutes on ice, and centrifuged at 15,000 g for 15 minutes. The supernatant was collected and measured for total protein amount using BCA assay (Thermo Scientific; 23227). Lysate (7-20 μg per well) was loaded onto a pre-cast SDS gel (BioRad; 456-1096) followed by electrophoresis. The proteins were then transferred from the gel to a low fluorescence background PVDF membrane (Millipore; IPFL00010) or regular PVDF membrane (Millipore; ISEQ00010) depending on whether fluorescence or chemiluminescence detection was performed. Phospho-ERK was detected using a rabbit anti-pERK antibody (Cell Signaling; 9101S) and total ERK was detected using a rabbit anti-ERK antibody (Cell Signaling; 9102S). Monobody expression was detected using mouse anti-Flag antibody (Sigma; F3165) or anti-HA tag antibody (BioLegend; 901516). Loading control was detected with primary antibody against tubulin-alpha (Thermo Scientific, 62204) or against cytochrome oxidase (COX IV) (Li-Cor, 926-42214). The total RAS level was detected using a pan-RAS antibody (SCBT, sc-166691). The KRAS level was determined using a KRAS-specific antibody (Sigma, WH0003845M1). For fluorescence detection of immunoblots, the membranes were imaged with a Licor Odyssey Clx imager (Li-Cor Bioscience) using IRDye anti-Rabbit 800CW and anti-Mouse 680LT (Li-Cor Bioscience, 926-32211 and 926-68020, respectively) as secondary antibodies. For chemiluminescence detection, the membrane was imaged with a ChemiDoc imager (BioRad) using anti-Mouse or anti-Rabbit secondary antibody conjugated to HRP (Pierce; 31432 and 31462, respectively). Band intensities of western blot were analyzed with Image Studio Lite version 5.2 (Li-Cor Bioscience). To quantify protein abundance in the degradation experiment, the intensities of pERK, RAS, KRAS, and Flag/HA tag bands were first normalized against the loading control of the perspective blot, which were either tubulin-α, COX IV or total ERK, followed by subsequent normalization to the zero time point. The relative concentrations of intracellular FLAG-tagged monobody inhibitor or HA-tagged monobodies were determined by comparing the intensity of protein bands with the intensity of the bands from equal amounts of loading control proteins (GenScript, M0101) containing both FLAG and HA tag.
Proteomics analysis. Protein samples captured by monobody pull-down, as described above, were digested on beads using trypsin. An aliquot was loaded onto an Acclaim PepMap trap column (2 cm) in line with an EASY-Spray analytical column (50 cm) using the auto sampler with either a data dependent mode on an Easy-nLC 1000 interfaced to a Thermo Fisher Scientific Q Exactive mass spectrometer or a targeted analysis on an Easy-nLC 1200 interfaced to a Thermo Fisher Scientific Q Exactive HF-X mass spectrometer for peptides specific to either the KRAS G12V mutant or KRAS/KRAS 2B. All Acquired MS2 spectra were searched against the Uniprot Homo sapiens reference database containing common contaminant proteins and the mutant KRAS4B G12V using Sequest within Proteome Discoverer 1.4 for the data dependent analysis and using Byonic for the targeted analysis search.
Crystallization and x-ray structure determination. Purified and tag-cleaved H-RAS(G12C) or H-RAS(WT) bound to GTPγS were incubated with purified monobody 12VC1 or 12VC3 at a 1:1.1 molar ratio. The complexes were purified with a Superdex 75 10/300 SEC column (GE Healthcare) in 20 mM Tris-Cl buffer pH 8 containing 100 mM NaCl, 20 mM MgCl2 and 0.2 mM TCEP and concentrated to approximately 10 mg/mL. Both complexes (12CS1:H-RAS(G12C) and 12VC3:H-RAS(WT)) were crystallized in 0.225 M sodium tartrate and 20% PEG3350 when mixed 1:1 in a total volume of 200 nl dispensed by a Mosquito crystallization robot (TTP Labtech) using the hanging drop vapor diffusion method. Crystals were preserved in the mother liquid plus additional 10% (v/v) of PEG3350 for the H-RAS(G12C):12VC1 complex and mother liquid plus 20% glucose for the H-RAS(WT):12VC3 complex. X-ray diffraction data were collected at the Advance Photon Source at the Argonne National Laboratory using beam line 19ID. Diffraction data were processed using HKL3000 and the starting model was built by molecular replacement using PDB entry 4g0n as search models using Phaser. Refinement was performed by phenix refinement, Coot, and PDBredo.
Computational Analysis of Crystal Structures. Fragment-centric topographical mapping (FCTM) as well as molecular dynamics (MD) simulations were performed to investigate the underlying reasons for selective binding of monobody 12VC1 against different RAS mutants. FCTM was performed using AlphaSpace, which utilizes a geometric model based on Voronoi tessellation. Briefly, AlphaSpace identify and represent all concave interaction space across the protein-protein interface as a set of alpha-atom/alpha-space pairs, which are then clustered into discrete fragment-centric pockets. MD simulations were performed with Amber14 molecular dynamics package, employing the Amber14SB force field for the protein. The initial structures for each simulation system were constructed based on our crystal structure of the HRAS-12VC1 complex. The protonation states of charged residues were determined at constant pH 7 based on pKa calculations via the PDB2PQR server. Each system was neutralized with Na+ counterions and solvated with explicit TIP3P water in a rectangular periodic box with 12.0 Å buffer. The Particle-Mesh Ewald (PME) method with 12.0 Å cutoff for the non-bonded interactions was used in the energy minimizations and MD simulations. After a series of minimizations and equilibrations, standard molecular dynamics simulations were performed on GPUs using PMEMD. For each system, MD simulation was carried out for 250-ns with periodic boundary condition and snapshots are saved every 10 ps. The SHAKE algorithm was applied to constrain all bonds involving hydrogen atoms and the Berendsen thermostat method has been used to control the system temperature at 300 K. All other parameters were default values. Saved snapshots were analyzed using cpptraj module in AmberTools 15. Based on the crystal structure of the HRAS(G12C)-12VC1 complex, we have carried out a series of molecular dynamics (MD) simulations to investigate how the monobody 12VC1 interacts with different single mutants of HRAS (G12C, G12V, G12D, G13D and Q61L) as well as its wild type. In addition, in order to investigate the stability of HRAS conformations captured by 12VC1 and 12VC3 monobodies, MD simulations of HRAS structures in absence of monobody binding have also been carried out, the resulted MD snapshots are clustered and representative snapshots were compared with the two HRAS conformations in the monobody complex crystal structures and other 36 GTP analogue-bound HRAS crystal structures obtained from PDB database. All MD simulations were carried out with Amber 16 package using Amber FF14SB force field. Each system was neutralized by adding counter-ions, and was solvated in explicit TIP3P water box. The GSP molecule was parametrized with general amber force field second version (GAFF2). AmberTools were used to prepare structures and analyze MD trajectories. DBSCAN method is used for MD snapshots clustering. AlphaSpace is employed for analysis of binding pockets on monobody 12VC1.
Stable cell line generation. Genes encoding fluorescent protein, EGFP or mVenus, and genes encoding Monobodies were cloned into pRetro-TetOne vector (CloneTech) with a flag tag spacer using In-Fusion cloning (Takara Bioscience). The mVenus gene was a gift from Steve Vogel (Addgene Plasmid #27793). For degradation studies, genes encoding N-terminally HA-tagged VHL-monobody fusion proteins were cloned into pRetro-TetOne vector using In-Fusion cloning. The VHL gene was a gift from William Kaelin (Addgene Plasmid #19999). Retroviruses were generated by co-transfecting the packaging cell line GP2-293 using Lipofectamine 3000 with the pRetro vector derivatives and the virus envelope vector pVSV-G. After six hours, the transfection mixture was replaced with fresh complete media. Retroviral supernatant was collected 48 hours post transfection and filtered using a 0.45 μm filter. Prior to retroviral transduction, cells of interest were plated in a 6-well cell culture plate (Thermo Scientific; 130184). Polybrene (final concentration of 4 μg/mL) was added to each well containing cells follow by viral transduction using 500 μL of filtered viral supernatant. After the addition of retroviruses, the 6-well plate was centrifuged at 1200 g for 1.5 hours to increase the transduction efficiency. After eight hours, viral supernatants were replaced with new complete media with Tet-Approved FBS (Takara Biosciences; 631367 or Gemini Biosciences, 100-800). Cells were sub-cultured in complete media containing 1 μg/mL puromycin for selection 48 hours post transduction. After puromycin resistance was established, cell lines expressing VHL monobody fusions were aliquoted and used for experiment at the lowest passage number possible. Cells expressing a fluorescent protein-fused monobody were sorted using FACS. Prior to sorting, expression of the monobody was induced by adding 0.1 μg/mL of doxycycline (Clonetech; 631311) for 6 hours. The short induction period and low doxycycline concentration were designed to alleviate potential stress caused by inhibition of RAS function by monobodies. Sorted cells were expanded and monobody expression upon induction was confirmed before they were used for experiments. Cells that express VHL-fused monobody were not sorted due to a lack of selection marker. Cells were maintained in media supplemented with Tet-Approved FBS.
For generating stable cell line that expresses EGFP fused KRAS, Flp293 cell line (Thermo Scientific) was cultured in complete DMEM supplemented with Zeocin (100 μg/mL) for at least 1 passage prior to co-transfection with pOG44 and pFRT vector derivatives (Thermo Scientific) contained cDNA encoding an EGFP fused KRAS construct of interest and hygromycin B resistance gene. 48 hours after transfection, cells were expanded into media containing Hygromycin B (200 μg/mL) for selection. Individual colonies were then screened or pooled and sorted. The resulting cells were verified via flow cytometry for tightly distributed levels of EGFP expression.
Cell proliferation assay. Dox-inducible stable cell lines expressing 12VC1 or MB(Neg) were mixed with the parental cell line at an approximately 1:1 ratio and seeded in a 12 well or 24 well plate. Cells were then cultured in the presence of 1 μg/mL doxycycline for the entire duration of experiment (7-8 days) and subcultured into a new 12 well or 24 well plate every 2 days. For a control experiment to eliminate the possibility that the growth bias is caused by retroviral transduction but not by monobody expression, cells transduced with the 12VC1 vector were grown in the absence of Dox and then induced 24 hours prior to the last measurement. The mixed culture was sampled periodically and the ratio between monobody expressing cells (mVenus and GFP positive) and non-expressing cells was determined using flow cytometry analysis (
Cell viability assay. A total of 3000 cells were seeded in the well of a 96-well flat-bottom plate with clear window. Cells were either treated with 15 μM of ARS1620 or 1 μg/mL doxycycline. Fresh reagents were added every three days. To measure cell viability the presto blue reagent (Thermo Fisher) was added at 10% of the culture volume. After two hours of incubation at 37° C., the fluorescence intensity of the wells was measured (ex:560 nm/em:590 nm) with a FlexStation 3 multi-mode plate reader (Molecular Devices).
Mouse xenograft experiments. Animal experiments were approved by NYU Langone Institutional Animal Care and Use Committee (IACUC, protocol 170602). PATU8902 or H23 cells expressing monobody under a dox-inducible promotor (5×106) were subcutaneously injected into athymic nude mice (Charles River). Once the average tumor size exceeded 100 mm3, the mice were given food containing doxycycline (Envigo; TD.01306). Tumor sizes were measured using a digital caliper thrice a week along with body weight to ensure that mice were healthy through the duration of doxycycline treatment.
Data Availability: Atomic coordinates for HRAS(G12C)-12VC1 and HRAS(WT)-12VC3 structures will be available in the Protein Data Bank. The data sets generated during and/or analyzed during the current study are available on reasonable request.
Although the present disclosure has been described with respect to one or more particular embodiments and/or examples, it will be understood that other embodiments and/or examples of the present disclosure may be made without departing from the scope of the present disclosure.
This application claims priority to U.S. Provisional Application No. 63/121,903, filed on Dec. 5, 2020, the disclosure of which is incorporated herein by reference.
This invention was made with government support under grant nos. CA212608, CA194864, and CA201717 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63121903 | Dec 2020 | US |
