Patent Application
20210188930
Various biochemical complexes, drug candidates and methods of making and using the complexes and drug candidates, with a wide range of medical and therapeutic applications, including cancer therapy, cosmetic, research, and industrial applications are disclosed herein.
Various drug candidates and methods of for treating p53 related disorders, such as cancer have been proposed. Because these drug candidates and methods are not optimal, there is a need in the field for improved drug candidate and methods.
Applicant has described herein a novel p53 AND Agent complex (“PANDA”); a collection of compounds with useful characteristics and can tightly associate with the PANDA Pocket (each compound a “PANDA Agent”); a pocket on p53 that interacts with PANDA Agent to form a PANDA (as used herein “PANDA Pocket” when PANDA Agent is not bound or “PANDA Core” when PANDA Agent is bound); three cysteine residues on p53 that are important in the formation of various PANDA and PANDA Cores, namely the cysteines are the amino acid corresponding to wtp53 positions cysteine 124 (“C124”), cysteine 135 (“C135”), and cysteine 141 (“C141”) (each a “PANDA Cysteine” and together a “PANDA Triad”); methods of making and using PANDA and/or PANDA Core, including in the diagnosis, prognosis, and treatment of p53 related disorders such as cancer and aging; and methods of using PANDA Agents, including in the diagnosis, prognosis, and treatment of p53 related disorders such as cancer and aging.
In certain embodiments, the PANDA Core is a tertiary structure formed on a p53 comprising of a PANDA Pocket, a PANDA Agent, and at least one tight association between the PANDA Pocket and the PANDA Agent. In a preferred embodiment, the PANDA Pocket is a region consisting essentially of an area of about 7 Å from a properly folded PANDA Cysteine, and includes, all amino acids adjacent to one or more properly folded PANDA Cysteine, all amino acids that contact with one or more properly folded PANDA Cysteine, and all PANDA Cysteines. In a preferred embodiment, the PANDA Agent is a composition of matter that has one or more useful characteristics. Examples of such useful characteristics of PANDA Agent include (a) can cause a substantial increase in the population of properly folded p53, preferably the increase is at least about 3 times more than the increase caused by PRIMA-1, more preferably the increase is at least about 5 times more than the increase caused by PRIMA-1, further preferably the increase is at least about 10 times more than the increase caused by PRIMA-1, further preferably the increase is at least about 100 times more than the increase caused by PRIMA-1; (b) can cause a substantial improvement in the transcription function of p53, preferably the improvement is at least about 3 times more than the improvement caused by PRIMA-1; more preferably the improvement is at least about 5 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 10 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 100 times than the improvement caused by PRIMA-1; and (c) can cause a substantial enhancement of stabilization of p53 as measured by, for example, an increase p53 Tm, preferably the enhancement is at least about 3 times more than the enhancement caused by PRIMA-1, more preferably the improvement is at least about 5 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 10 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 100 times than the improvement caused by PRIMA-1. In a preferred embodiment, a PANDA Agent has two or more useful characteristics. In a more preferred embodiment, a PANDA Agent has three or more useful characteristics.
In certain embodiments, the PANDA Pocket consists essentially of the PANDA Triad and the amino acids corresponding to wtp53 positions S116, C275, R273, Y234, V122, T123, T125, Y126, M133, F134, Q136, L137, K139, T140, P142, V143, L114, H115, G117, T118, A119, K120, S121, A138, I232, H233, N235, Y236, M237, C238, N239, F270, E271, V272, V274, A276, C277, P278, G279, R280, D281, and R282. In certain preferred embodiments, the PANDA Pocket is arranged essentially as in
A preferred p53 is any wildtype p53 (“wtp53”), any mutated p53 (“mp53”), all natural and artificial forms of wtp53 and mp53, and any combinations thereof. Preferred examples of wtp53 include p53α, p53β, p53γ, A40p53α, A40p53β, A40p53γ, and any acceptable variants, such as those with one or more single nucleotide polymorphism (“SNP”). Exemplar sequences of wtp53 human wtp53 isoforms as show in Section 7.25.
A preferred mp53 has at least one mutation on p53, including any single amino acid mutation. Preferably, the mutation alters and/or partially alters the structure and/or function of p53 Preferred examples of mp53 include one or more mutations at R175, G245, R248, R249, R273, R282, C176, H179, Y220, P278, V143, I232, and F270. Exemplar mp53 mutations include R175H, G245D/S, R248Q/W, R249S, R273C/H, R282W, C176F, H179R, Y220C, P278S, V143A, I232T, and F270C.
A preferred artificial p53 includes any artificially engineered p53. Preferred examples of an artificially engineered p53 include a p53 fusion protein, a p53 fragment, a p53 peptide, a p53-derived fusion macromolecule, a p53 recombinant protein, a p53 with second-site suppressor mutation (“SSSM”), and a super p53.
In certain embodiments, the tight association formed by PANDA Agent and PANDA Pocket can be a bond, covalent bond, a non-covalent bond (such as a hydrogen bond), and a combination thereof. In certain embodiments, the tight association is formed between PANDA Agent and one or more PANDA Cysteines, preferably two or more PANDA Cysteines, and more preferably all three PANDA Cysteines.
In certain embodiments, the PANDA Agent can regulate the level of one or more p53 target gene. Exemplar target genes include Apaf1, Bax, Fas, Dr5, mir-34, Noxa, TP53AIP1, Perp, Pidd, Pig3, Puma, Siva, YWHAZ, Btg2, Cdknla, Gadd45a, mir-34a, mir-34b/34c, Pri3, Ptprv, Reprimo, Pai1, Pml, Ddb2, Ercc5, Fancc, Gadd45a, Ku86, Mgmt, Mlh1, Msh2, P53r2, Polk, Xpc, Adora2b, Aldh4, Gamt, GIs2, Gpx1, Lpin1, Parkin, Prkab1, Prkab2, Pten, Sco1, Sesn1, Sesn2, Tigar, Tp53inp1, Tsc2, Atg10, Atg2b, Atg4a, Atg4c, Atg7, Ctsd, Ddit4, Dram1, Foxo3, Laptm4a, Lkb1, Pik3r3, Prkag2, Puma, Tpp1, Tsc2, Ulk1, Ulk2, Uvrag, Vamp4, Vmp1, Bai1, Cx3d1, Icam1, Irf5, Irf9, Isg15, Maspin, Mcp1, Ncf2, Pai1, Tir1-Tlr10, Tsp1, Ulbp1, Ulbp2, mir-34a, mir-200c, mir-145, mir-34a, mir-34b/34c, and Notch1.
In certain embodiments, the tight association formed by PANDA Agent and PANDA Core substantially stabilizes p53. Preferably, the tight association increases the Tm of p53 by at least about 0.5° C., more preferably by at least about 1° C., further preferably by at least about 2° C., further preferably by at least about 5° C., further preferably by at least about 8° C.
In certain embodiments, the tight association formed by PANDA Agent and PANDA Core increases the population of properly folded p53 by at least about 3 times, preferably by about 5 times, more preferably by about 10 times, and further preferably by about 100 times. In preferred embodiments, the increase is measured by a PAb1620 immunoprecipitation assay.
In certain embodiments, the PANDA Agent includes one or more PANDA Pocket-binding group (“R”) capable of binding one or more amino acids on PANDA Pocket, preferably one or more cysteine, more preferably two or more cysteines, further preferably more than three cysteines, further preferably from about three cysteines to about 12 cysteines. R is preferred to include metallic group(s), metalloid group(s), and other group(s) capable of binding to PANDA Pocket such as Michael acceptor(s) and thiol group(s). R is further preferred to include one or more arsenic, antimony, and bismuth, including any analogue(s) thereof, and any combinations thereof. Exemplar R(s) include compounds containing a 3-valence and/or 5-valence arsenic atom, a 3-valence and/or 5-valence antimony atom, a 3-valence and/or 5-valence bismuth atom, and/or a combination thereof. Exemplar PANDA Agents include Table 1-Table 6, which Applicant has predicted to efficiently bind to PANDA Cysteines and efficiently rescue p53 in vitro, in vivo and/or in situ. More exemplar PANDA Agents include of As2O3, As2O5, KAsO2, NaAs2, HAsNa2O4, HAsK2O4, AsF3, AsCl3, AsBr3, AsI3, AsAc3, As(OC2H5)3, As(OCH3)3, As2(SO4)3, (CH3CO2)3As, C6H4K2O12As2.xH2O, HOC6H4COOAsO, [O2CCH2C(OH)(CO2)CH2CO2]As, Sb2O3, Sb2O5, KSbO2, NaSbO2, HSbNa2O4, HSbK2O4, SbF3, SbCl3, SbBr3, SbI3, SbAc3, Sb(OC2H5)3, Sb(OCH3)3, Sb2(SO4)3, (CH3CO2)3Sb, C8H4K2O12Sb2.xH2O, HOC6H4COOSbO, [O2CCH2C(OH)(CO2)CH2CO2]Sb, Bi2O3, Bi2O5, KBiO2, NaBiO2, HBiNa2O4, HBiK2O4, BiF3, BiCl3, BiBr3, BiI3, BiAc3, Bi(OC2H5)3, Bi(OCH3)3, Bi2(SO4)3, (CH3CO2)3Bi, C6H4K2O12Bi2.xH2O, HOC8H4COOBiO, C16H18As2N4O2 (NSC92909), C13H14As2O (NSC48300), C10H13NO8Sb (NSC31660), C6H12NaO8Sb+ (NSC15609), C13H21NaO9Sb+ (NSC15623), and a combination thereof. Further exemplar PANDA Agents include Table 7, which Applicant has confirmed by experiment to show strong degree of structural rescue and transcriptional activity rescue.
In certain embodiments, the PANDA Core is produced by a reaction between the PANDA Pocket and the PANDA Agent. Preferably, the reaction is preferably mediated by an As, Sb, and/or Bi group oxidizing one or more thiol groups of PANDA Cysteines (PANDA Cysteines lose between one to three hydrogens) and the As, Sb, and/or Bi group of PANDA Agent is reduced (PANDA Agent loses oxygen). In certain embodiments, the PANDA Agents are the reduzate formed from having tightly associated with p53. In certain embodiments, the PANDA Agent is an arsenic atom, an antimony atom, a bismuth atom, any analogue thereof, or a combination thereof.
An exemplar PANDA Core is substantially similar to the corresponding amino acids on the three-dimensional structure of
In certain embodiments, the structure of PANDA is substantially similar to the three-dimensional structure of
In certain embodiments, formed PANDA can be purified and isolated using any conventional methods, including any methods disclosed in this Application, such as by immunoprecipitation using PAb1620.
In certain preferred embodiments, as compared to when the PANDA Agent is not bound, formed PANDA has gained one or more wtp53 structure, preferably a DNA binding structure; has gained one or more wtp53 function, preferably a transcription function; and/or has lost and/or diminishes one or more mp53 function, preferably an oncogenic function. The wildtype function can be gained in vitro and/or in vivo. Exemplar wildtype function gained can be at the molecule-level, such as association to nucleic adds, transcriptional activation or repression of target genes, association to wtp53 or mp53 partners, dissociation to wtp53 or mp53 partners, and reception to post-translational modification; at the cell-level, such as, responsiveness to stresses such as nutrient deprivation, hypoxia, oxidative stress, hyperproliferative signals, oncogenic stress, DNA damage, ribonucleotide depletion, replicative stress, and telomere attrition, promotion of cell cycle arrest, promotion of DNA-repair, promotion of apoptosis, promotion of genomic stability, promotion of senescence, and promotion of autophagy, regulation of cell metabolic reprogramming, regulation of tumor microenvironment signaling, inhibition of cell stemness, survival, invasion and metastasis; and at the organism-level, such as delay or prevention of cancer relapse, increase of cancer treatment efficacy, increase of response ratio to cancer treatment, regulation of development, senescence, longevity, immunological processes, and aging. The mp53 functions can be lost, impaired and/or abrogated in vitro and/or in vivo. Exemplar mp53 function lost can include any functions, such as oncogenic functions that promotes cancer cell metastasis, genomic instability, invasion, migration, scattering, angiogenesis, stem cell expansion, survival, proliferation, tissue remodelling, resistance to therapy, and mitogenic defects.
In certain preferred embodiments, the formed PANDA can gain and/or lose the ability to upregulate or downregulate one or more p53 downstream targets, at an RNA level and/or protein level, in a biological system, preferably by 3 times, more preferably by 5 times, further preferably by 10-100 times.
In certain preferred embodiments, the PANDA Agent any of the preceding claims having the ability to treat a p53-relevant disease in a subject with mp53 and/or without functional p53, wherein the disease is a cancer, a tumor, a consequence of aging, a developmental disease, accelerated aging, an immunological disease, or a combination thereof.
In certain preferred embodiments, the formed PANDA has the ability to suppress tumors, preferably least to a level that is statistically significant; more preferably having the ability to strongly suppress tumors at a level that is statistically significant. In certain preferred embodiments, the formed PANDA has the ability to regulate cell growth or tumor growth preferably to at least about 10% of the wtp53 level, further preferably at least about 100% of the wtp53 level, further preferably exceeding about 100% of the wtp53 level.
In certain preferred embodiments, PANDA or PANDA Core can be made by combining one or more PANDA Agent to a p53, preferably a mp53 with at least one mutation on p53, including a single amino acid mutation. Preferably, the mutation alters and/or partially alters the structure and/or function of p53. Preferred examples of mp53 include one or more mutations at R175, G245, R248, R249, R273, R282, C176, H179, Y220, P278, V143, I232, and F270. Exemplar mp53 mutations include R175H, G245D/S, R248Q/W, R249S, R273C/H, R282W, C176F, H179R, Y220C, P278S, V143A, I232T, and F270C.
In certain preferred embodiments, the PANDA Agent can rescue one or more wtp53 structure, preferably a DNA binding structure; rescue one or more wtp53 function, preferably a transcription function, eliminating and/or diminishes one or more mp53 function, preferably an oncogenic function.
In certain preferred embodiments, one or more wtp53 structure, preferably a DNA binding structure can be rescued by combining one or more PANDA Agent to a p53 to form PANDA, preferably a mp53 with at least one mutation on p53, including a single amino acid mutation. Preferably, the mutation alters and/or partially alters the structure and/or function of p53. Preferred examples of mp53 include one or more mutations at R175, G245, R248, R249, R273, R282, C176, H179, Y220, P278, V143, I232, and F270. Exemplar mp53 mutations include R175H, G245D/S, R248Q/W, R249S, R273C/H, R282W, C176F, H179R, Y220C, P278S, V143A, I232T, and F270C.
In certain preferred embodiments, one or more wtp53 function, preferably a preferably a transcription function can be rescued by combining one or more PANDA Agent to a p53 to form PANDA, preferably a mp53 with at least one mutation on p53, including a single amino acid mutation. Preferably, the mutation alters and/or partially alters the structure and/or function of p53. Preferred examples of mp53 include one or more mutations at R175, G245, R248, R249, R273, R282, C176, H179, Y220, P278, V143, I232, and F270. Exemplar mp53 mutations include R175H, G245D/S, R248Q/W, R249S, R273C/H, R282W, C176F, H179R, Y220C, P278S, V143A, I232T, and F270C.
In certain preferred embodiments, one or more mp53 function, preferably an oncogenic function, can be eliminated and/or diminished by combining one or more PANDA Agent to a p53 to form PANDA, preferably a mp53 with at least one mutation on p53, including a single amino acid mutation. Preferably, the mutation alters and/or partially alters the structure and/or function of p53. Preferred examples of mp53 include one or more mutations at R175, G245, R248, R249, R273, R282, C176, H179, Y220, P278, V143, I232, and F270. Exemplar mp53 mutations include R175H, G245D/S, R248Q/W, R249S, R273C/H, R282W, C176F, H179R, Y220C, P278S, V143A, I232T, and F270C.
In certain preferred embodiments, one or more wtp53 structure, preferably a DNA binding structure can be rescued by adding a PANDA and/or a PANDA Agent to a cell, preferably a human cell, and/or a subject, preferably a human subject.
In certain preferred embodiments, one or more wtp53 function, preferably a preferably a transcription function can be rescued by adding a PANDA and/or a PANDA Agent to a cell, preferably a human cell, and/or a subject, preferably a human subject.
In certain preferred embodiments, one or more mp53 function, preferably an oncogenic function, can be eliminated and/or diminished by adding a PANDA and/or a PANDA Agent to a cell, preferably a human cell, and/or a subject, preferably a human subject.
Applicant discloses herein a method of turning on and off a wtp53 function of a mp53, the method comprising the steps:
(a) combining a first PANDA Agent with the mp53 to turn on the wtp53 function of a mp53; and
(b) adding a second compound that (i) removes the PANDA Agent from the mp53, such as, British Anti-Lewisite (BAL), succimer (DMSA), Unithiol (DMPS), and/or a combination thereof; (ii) inhibits expression of p53, such as doxycycline in engineered cells or subjects, and/or (iii) turning off p53 expression, such as tamoxifen, in engineered cells or subjects.
Applicant discloses herein a method of using the PANDA or PANDA Core in vitro and/or in vivo to rescue one or more wtp53 structure, preferably a DNA binding structure; rescue one or more wtp53 function, preferably a transcription function; eliminate and/or diminishes one or more mp53 function, preferably an oncogenic function, the method comprising the step of adding a PANDA or PANDA Agent to a cell, preferably a human cell, and/or subject, preferably a human subject.
Applicant discloses herein group of PANDA Agents having the ability to treat a disease in a subject with mp53, the disease is preferably cancer.
Applicant discloses herein a method of treating a p53 related disorder in a subject in need thereof such as cancer, tumour, aging, developmental diseases, accelerated aging, immunological diseases, and/or a combination thereof. The method comprises the step of administering to a subject an effective amount of a therapeutic, wherein the therapeutic is (a) one or more PANDA Agents or (b) one or more PANDA or PANDA Core. In a preferred embodiment, the therapeutic is administered in combination with one or more additional therapeutic, preferably any known therapeutic effective at treating cancer and/or DNA damaging agent.
Applicant further discloses a highly efficient personalized method of treatment for a p53 related disorder in a subject in need thereof. The method comprises the steps of: (a) obtaining a p53 DNA sample from the subject; (b) sequencing the p53 DNA sample; (c) determining whether the p53 of the subject is rescuable and identifying one or more PANDA Agent and/or a combination of PANDA Agent that is most appropriate to rescue the p53 in the subject; and (d) administering an effective amount of the PANDA Agent and/or the combination of PANDA Agent to the subject; wherein step (c) includes the step(s) (i) determining in silico whether the sequence of the p53 DNA sample is comparable to a to a database of rescuable p53s and identifying the corresponding PANDA Agent(s) and/or combination of PANDA Agents most appropriate to rescue the p53 using the database; and/or (ii) determining in vitro and/or in vivo whether the p53 of the subject can be rescued by screening it against a panel of PANDA Agents.
Applicant further discloses a method of identifying PANDA or PANDA Core. The method comprising the step of: using an antibody specific for properly folded PANDA, such as PAb1620, PAb246, and/or PAb240, to perform immunoprecipitation; measuring increase of molecular weight by mass spectroscopy; measuring whether transcriptional activity is restored in a luciferase assay; measuring the mRNA and protein levels of p53 targets; co-crystalizing to construct 3-D structure; and/or measuring increase of Tm.
Applicant discloses herein a collection of PANDA Agents having the ability to regulate the levels of p53 targets in a biological system expressing a mp53 or lacking any functional p53. Applicant further discloses a method of controlling one or more protein and/or RNA regulated by p53 and/or PANDA, the method comprising the step of administering a regulator to a biological system, wherein the regulator is selected from a group consisting of:
(i) one or more PANDA Agent(s);
(ii) one or more PANDA or PANDA Core;
(iii) one or more compound that removes the PANDA Agent from the p53;
(iv) one or more mp53;
(v) one or more compound that removes PANDA, including an anti-p53 antibody, a doxycycline, and anti-PANDA antibody; and
(vi) a combination thereof.
Applicant discloses herein a collection of PANDA Agents having the ability to suppress tumors in a biological system, preferably a system that expresses a mp53. Applicant further discloses a method of suppressing tumors, the method comprising the step(s) of administering to a subject in need thereof an effective amount of a therapeutic, wherein the suppressor is selected from a group consisting of:
(i) one or more PANDA Agent(s); and
(ii) one or more PANDA and/or PANDA Core.
In a preferred embodiment, the suppressor is administered in combination with one or more additional suppressor, preferably any known suppressor effective at suppressing tumor growth and/or DNA damaging agent.
Applicant discloses herein a collection of PANDA Agents having the ability to regulate cell growth or tumor growth in a biological system, preferably a system that expresses a mp53. Applicant further discloses a method of regulating cell growth or tumor growth, the method comprising the step of administering to a subject in need thereof an effective amount of a regulator, wherein the regulator is selected from a group consisting of:
(i) one or more PANDA Agent(s); and (ii) one or more PANDA and/or PANDA Core. In a preferred embodiment, the regulator is administered in combination with one or more additional regulator, preferably any known regulator effective at slowing cell growth and/or DNA damaging agent.
Applicant discloses herein a method of diagnosing a p53 related disorder, such as cancer, tumor, aging, developmental diseases, accelerated aging, immunological diseases, or a combination thereof, in a subject in need thereof. The diagnosis method comprising the steps of administering to the subject an effective amount of a therapeutic, and detecting whether PANDA or PANDA Core is formed wherein the therapeutic is selected from a group consisting of:
(i) one or more PANDA Agent(s); and
(ii) one or more PANDA and/or PANDA Core.
In a preferred embodiment, the diagnosing method includes a treatment step wherein the therapeutic is administered in combination with one or more additional therapeutic, such as one or more additional PANDA Agent(s) and/or any other known therapeutic effective at treating cancer and/or DNA damaging agent, to effectively treat the p53 related disorder in the subject.
In certain embodiments, the PANDA Agent is not CP-31398; PRIMA-1; PRIMA-1-MET, SCH529074, Zinc; stictic acid, p53R3; methylene quinuclidinone; STIMA-1; 3-methylene-2-norbornanone; MIRA-1; MIRA-2; MIRA-3; NSC319725; NSC319726; SCH529074; PARP-PI3K; 5,50-(2,5-furandiyl)bis-2-thiophenemethanol; MPK-09; Zn-curc or curcumin-based Zn(III)-complex; P53R3; a (2-benzofuranyl)-quinazoline derivative; a nucleolipid derivative of 5-fluorouridine; a derivative of 2-aminoacetophenone hydrochloride; PK083; PK5174; or PK7088; and other previously identified mp53 rescue compound.
In certain embodiments, the PANDA Agent can be formulated in a pharmaceutical composition suitable for treating a subject with a p53 related disorder. A pharmaceutical composition will typically contain a pharmaceutically acceptable carrier. Although oral administration of a compound is the preferred route of administration, other means of administration such as nasal, topical or rectal administration, or by injection or inhalation, are also contemplated. Depending on the intended mode of administration, the pharmaceutical compositions may be in the form of solid, semi-solid, or liquid dosage forms, such as, for example, tablets, suppositories, pills, capsules, powders, liquids, suspensions, ointments, or lotions, preferably in unit dosage form suitable for single administration of a precise dosage. One skilled in this art may further formulate the compound in an appropriate manner, and in accordance with accepted practices, such as those disclosed in Remington's Pharmaceutical Sciences, Gennaro, Ed., Mack Publishing Co., Easton, Pa. 1990.
In certain embodiments, a carrier can be any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. A pharmaceutical carrier can include, liposomes, albumin microspheres, soluble synthetic polymers, DNA complexes, protein-drug conjugates, carrier erythrocytes, and any other substance that is incorporated to improve the delivery and the effectiveness of drugs. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
In certain embodiments, therapies used for the treatment of p53 related disorder, such as cancer, include, surgery, chemotherapy, and radiation therapy. Experimental therapies include, but are not limited to, expression of wildtype p53 in tumors based on viral or viral like particle based delivery vectors.
In certain embodiments, a p53 cancer therapeutic include, general chemotherapeutics. Examples of general chemotherapeutics include, but are not limited to, Avastin, Rituxan, Herceptin, Taxol, and Gleevec.
In certain embodiments, “a person in need of” can refer to an individual who has a p53 related disorder, such as a cancer, wherein the cancer expresses a mutated version of p53. In some embodiments, the p53 mutant is susceptible to PANDA Agent.
In certain embodiments, PANDA Agents can be formulated in a pharmaceutically acceptable salt. The pharmaceutically acceptable salt can be an ionizable drug that has been combined with a counter-ion to form a neutral complex. Converting a drug into a salt through this process can increase its chemical stability, render the complex easier to administer, and allow manipulation of the agent's pharmacokinetic profile (Patel, et al., 2009).
In certain embodiments, the PANDA Agent and PANDA have the following features:
(1) PANDA Agent ATO binds directly to p53 to form PANDA, in a process that changes p53 structure, including folds the mp53;
(2) PANDA Agent mediated PANDA formation can take place both in vitro and in vivo, including in humans;
(3) PANDA is remarkably similar to wtp53 in both structure and function;
(4) PANDA Agent ATO folds the structure of Structural mp53s with a striking high efficiency so that the structure of PANDA is remarkably similar to that of wtp53;
(5) PANDA Agent ATO rescues the transcriptional activity of Structural mp53 through PANDA with a strikingly high efficiency;
(6) PANDA Agent ATO inhibits growth of mp53 expressing cells in vitro and in vivo through PANDA;
(7) mp53 expressing cells treated with PANDA Agent ATO or cells containing PANDA actively responds to DNA-damaging treatment;
(8) PANDA Agent ATO is highly effective and specific to mp53 and an effective mp53 rescue agent;
(9) PANDA Agent ATO and PANDA can directly combat a wide range of cancers, including acute myeloid leukemia (“AML”) and myelodysplastic syndromes (“MDS”); and
(10) cancer patients, including patients with AML and MDS begin to show remarkable response to anti-cancer treatments when first treated with ATO or PANDA.
In certain embodiments, the PANDA Agents, such as those containing elemental arsenic, through the formation of PANDA, can wide-broad and efficiently rescue mp53s. For example, As2O3 and its analogues can rescue the most frequent mp53s in varying degrees. These mp53s include but are not limited to: six hotspot mp53s (mp53s with mutations on either R175, G245, R249, or R282 (commonly considered as structural hotspot mp53s), mp53s with mutations on either R248 or R273 (commonly considered as contacting hotspot mp53s), and mp53s with mutations on C176, H179, Y220, or P278, V143, F270, or 1232.
In certain embodiments, PANDA Agents has the potential to bind multiple cysteines and can selectively inhibit Structural mp53 expressing cells via promoting mp53 folding.
In certain embodiments, PANDA Agents transforms cancer-promoting mp53 to tumor suppressive PANDA and have significant advantages over existing therapeutic strategies such as by reintroducing wtp53 or promoting degradation/inactivation of endogenous mp53 in the patient. The PANDA Agent mediated mp53 rescue through PANDA, high rescue efficiency and mp53 selectivity are the two superior characteristics over previously-reported compounds. In certain embodiments, the PANDA Agent ATO can provide a near complete rescue of p53-R175H, from a level equivalent to about 1% of that of wtp53 to about 97% of that of wtp53 using the robust PAb1620 (also for PAb246) IP assay. In certain embodiments, the PANDA Agent ATO also provides a near complete rescue of the transcriptional activity of p53-G245S and p53-R282W on some pro-apoptotic targets, from a level equivalent to about 4% of that of wtp53 to about 80% of that of wtp53, using a standard luciferase reporter assay. Applicant has robustly reproduced these superior results, as compared to existing compounds, in numerous contexts and know no existing compound that can rescue the structure or transcriptional activity of a hotspot mp53 by a level equivalent to about 5% of that of wtp53 in our assays.
In certain embodiments, the PANDA Agent ATO and PANDA can selectively target Structural mp53 with strikingly high efficiency. In addition, Contracting mp53s can also be rescued with moderate efficiency. For example, Applicant found a wide range of Structural mp53s, including a large percentage of hotspot mp53s, can be efficiently rescued by the PANDA Agent ATO through the formation of PANDA. In addition, Applicant also found that the Contacting mp53s can be rescued by ATO through PANDA with a limited efficiency. This remarkable property is not only superior but is conceptually different from most of the reported compounds, including CP-31398 (Foster et al., 1999), PRIMA-1 (Bykov et al., 2002), SCH529074 (Demma et al., 2010), Zinc (Puca et al., 2011), stictic acid (Wassman et al., 2013), p53R3 (Weinmann et al., 2008), and others that are reported to be able to rescue both types of mp53.
Our discovery further shows that PANDA Agent ATO can be used for a wide range of ATO-responsive cancers in clinical trials. It is preferred that patient recruitment follow a specific, highly precise, recruitment prerequisite, in order to achieve maximum efficacy. While ATO was approved by FDA to treat acute promyelocytic leukemia (APL), a subtype of leukemia. Although ATO has been intensively trialed, aiming to broaden its application to non-APL cancer types over the past two decades, it has not yet been approved for this purpose. This is largely attributed to a failure to reveal an ATO-affecting cancer spectrum. Indeed, no mp53 dependency can be observed in the sensitivity profile of ATO on the NCI60 cell panel simply by differentiating lines into a mp53 group and a wtp53 group. By further separating ATO-rescuable mp53s out of the mp53s, we have successfully revealed the key elements for ATO and PANDA dependent response. The ATO-affecting cancer spectrum we discovered is considerably wide, covering an estimated amount of 15%-30% cancer cases. For example, we have identified at least 4 of the 6 hotspot mp53s and a large number of non-hotspot mp53s to be efficiently rescuable by ATO and PANDA. Indeed, in the earliest ATO clinical trial in China in 1971 (n>1000 patients), ATO showed an efficacy in treating many cancer types including colorectal, esophageal, liver, and particularly APL cancers (Zhang et al., 2001; Zhu et al., 2002).
While ATO and PANDA can be used to treat a wide range of cancers, it is preferable that ATO be precisely administrated to patients harboring ATO rescuable mp53, as demonstrated by some of the tests described in this application. It is known that different missense mutations will confer different activities to mp53 (Freed-Pastor and Prives, 2012), which can lead to different treatment outcomes in patients harboring different mp53s. Accordingly, others like us advocate tailoring treatments to the types of mp53 mutations present rather than whether mp53 or wtp53 is present (Muller and Vousden, 2013, 2014). Remarkably, our discoveries on the MDS patient-derived p53-S241F, p53-S241C as well as the other artificially generated p53 mutants on S241 support that ATO rescuing efficiency is determined not only by the p53 mutation site but also by the new residue generated. Based on the current promising outcomes observed in our small-scale AML/MDS trial, we have launched two large-scale multi-center prospective trials on AML/MDS patients (NCT03381781 and NCT03377725). In one trial, 300 MDS patients are being blindly recruited and trialed, aiming to confirm the dependency of ATO on p53 mutation status. In the other trial, approximately 1500-2000 AML patients are being recruited, the mp53-positive patients confirmed by sanger sequencing are being trialed to determine the efficacy of ATO in treating mp53-expressing non-APL leukemia.
Despite many rescue principles that have been proposed, the void of an atom-level rationale on how to pharmacologically rescue mp53 has blocked the advances of cancer research for too long (Bullock and Fersht, 2001; Joerger and Fersht, 2007; Joerger and Fersht, 2016). This void has significantly hindered scientists from identifying an efficient and selective mp53 rescue compound (Bullock and Fersht, 2001; Joerger and Fersht, 2007; Joerger and Fersht, 2016). To rationally design and screen mp53 stabilizer is particularly challenging because of the pockets on the p53 for a mp53 stabilizer to bind have not been known (Joerger and Fersht, 2016).
Applicant has further describe a rational 4C Screening method. Using this method, Applicant has identified compounds that covalently crosslinked to cysteine-pairs on mp53. Applicant predicts that covalently crosslinking cysteines may be robust enough to immobilize the local region, neutralize the flexibility caused by the nearby mutations and stabilize p53 globally.
Using our 4C screening, we successfully identified at least two arsenic-containing compounds that can act as rescuers for a wide spectrum of mp53s. When we explored the properties of these arsenic compounds, we identified an unexpected and deeply buried PANDA Pocket that the stabilizer binds to. In doing so, we provided an atom-level MOA of how a wide-spectrum of mp53s can be stabilized by a compound.
In certain embodiments, the PANDA Pocket plays a key role in stabilizing mp53 globally. We discovered that a large number of reported SSSMs is located on the PANDA Pocket. In addition, our rationally designed SSSMs, also located on the PANDA Pocket function to stabilize it. Our rescue mechanism and highly druggable PANDA Pocket can now explain why the previously reported Michael acceptor-containing compounds have barely detectable mp53 rescue efficiency (Joerger and Fersht, 2016; Muller and Vousden, 2014). Computer modelling suggested that many of these compounds bind to C124 (Wassman et al., 2013), one of the cysteines of the key PANDA Triad, however remaining to be determined experimentally (Joerger and Fersht, 2016) Because these Michael acceptor containing compounds contact the rims of the PANDA Triad, they can only very weakly stabilize PANDA Pocket, thus rescue mp53 with limited efficiency.
Arsenic's selectivity for cysteines of PANDA Triad in Structural mp53s are particularly attracting. So far, many compounds including PRIMA-1, STIMA-1, MIRA-1, “compound 1”, PK11007, and ellipticine have a Michael acceptor group and are predicted to bind a single cysteine to function (Bauer et al., 2016; Joerger and Fersht, 2016; Wassman et al., 2013). Since p53 possesses of more than one exposed cysteines, these compounds may bind to many other undesired cysteine(s). Indeed, PRIMA-1 and “compound 1” have been reported to bind mp53 with a ratio high than 1:1 in vitro (Bauer et al., 2016; Lambert et al., 2009). These compounds can also have off-target tendencies to wtp53 or other cellular proteins with exposed cysteines.
Our current arsenic-containing compounds are conceptually different from any previously reported compounds due to its multiple cysteine binding potential, which may explain the selectivity for the PANDA Triad. Arsenic selectively binds to the inert cysteines on the PANDA Triad rather than cysteines that are more accessible (e.g.: C277 and C182) or other tri-cysteine dusters (e.g.: C176/C238/C242 in zinc region). This suggests that the PANDA Triad is unique and are arranged in a special pattern particularly receptive to arsenic.
We also discovered that although ATO binds to wtp53 and Contacting mp53 to significantly stabilize them and enhance their function, by far, Structural mp53s benefited the most from ATO binding. One reason is Structural mp53s are highly unstable.
As discussed in other Sections of this application, the Structural mp53 selectivity we discovered is also conceptually different from most of the reported compounds such as CP-31398 (Foster et al., 1999), PRIMA-1 (Bykov et al., 2002), SCH529074 (Demma et al., 2010), Zinc (Puca et al., 2011), stictic acid (Wassman et al., 2013), and p53R3 (Weinmann et al., 2008). Our observed Structural mp53s selectivity is also of particularly high clinical value because cysteine-binding compounds have been intensively debated (and often disputed) for their druggability, due their high potential for off-targeting (and thus toxicity) in cells. Indeed, others have identified that one of the major milestones to turn research on current mp53-rescuing compounds from its current proof-of-concept studies into clinical trials is to improve mp53 selectivity (Joerger and Fersht, 2016; Kaar et al., 2010). Compared to PRIMA-1 and its analogue, which is under phase II clinical trial (Bauer et al., 2016; Joerger and Fersht, 2016), and which increasingly have been suggested to target oxidative stress signaling components in cells, rather than mp53, our PANDA Agents are highly effective and specific towards p53.
The clear rescue MOA we revealed here and the druggable PANDA Pocket we identified here will enable us and others to perform ultra-large-scale Screening to greatly expand our arsenal against cancer and greatly accelerate our effort to beat cancer. As disclosed here, we identified a large number of arsenic, antimony, and/or bismuth containing compounds that can efficiently rescue mp53. We are excited that some of the identified arsenic analogues may be superior to the approved clinically approved ATO. For example, while Fowler's solution (KAsO2) has significant side-effects and are not used in clinical settings any more in past decades, As4S4 has been shown to be as effective as conventional intravenous ATO in treating APL patients while it can be conveniently orally administrated (Zhu et al., 2013). The additional class of Sb and Bi compounds we identified, including many organic compounds, are also of significant clinical value, because they are known to be less toxic in the body.
Finally, the organic As, Sb, and/or Bi compounds are particularly interesting. On one hand, the diversity of organic groups supplies millions of modification choices to generate an enhanced version of mp53 rescuer. For example, introducing a large organic group may have more profound influence on mp53's structure, facilitating identification of an efficient mp53 inhibitor. A direct mp53 inhibitor with a clear atom-level MOA is very attracting because existing mp53 inhibitors (HSP90 inhibitor, HDAC inhibitors, RETRA, ATRA etc.) do not target mp53 directly and yet some of them have diverse effects on many ubiquitous cellular pathways (Sabapathy and Lane, 2018).
Here, we describe that both inorganic and organic As, Sb, and/or Bi compounds are mp53 rescuers. In addition, we describe that As, Sb, and/or Bi compounds with potential to bind a cysteine or bi-cysteine pairs can also rescue mp53. Furthermore, we describe that As, Sb, and/or Bi compounds with three or more cysteine binding potential have even higher rescue efficiency, some at levels comparable to wtp53.
Since we have identified that PANDA Pocket is a switch that controls p53 stability, we predict that other compounds, in addition to compounds containing As, Sb, and/or Bi, that can bind to PANDA Pocket will have profound influence on p53 structure. These compounds may either rescue mp53 by restoring the wildtype (or functional) structure to rescue mp53, or inhibit mp53 by distorting mp53's oncogenic structures. While the former compounds can be developed into mp53 rescue agents, the latter compounds are also of huge value as mp53 inhibitors.
Using the 4C screen method, we discovered, for the first time, a number of PANDA Agents with the remarkable capability that can almost completely rescue the structure of a wide range of mp53s, including mp53-R175H, to that of the wildtype. We further identified at least 31 leading PANDA Agents (Table 7), including the clinical pharmaceutical compound arsenic trioxide (“ATO”). ATO is thus used as an example in the followed context. Previously, our colleagues have combined ATO with all-trans retinoic acid (“ATRA”) to efficiently target the cysteine-enriched promyelocytic leukaemia (“PML”) moiety of PML-RARα fusion protein (Zhang et al., 2010), making acute promyelocytic leukemia (“APL”) the only malignancy that can be definitively cured by a targeted therapy (Hu et al., 2009; Lo-Coco et al., 2013).
Unless otherwise indicated, this description employs conventional chemical, biochemical, molecular biology, genetics and pharmacology methods and terms that have their ordinary meaning to persons of skill in this field. All publications, references, patents and patent applications cited herein are hereby incorporated herein by reference in their entireties.
As used herein, the biological sample corresponds to any sample taken from a subject, and can include tissue samples and fluid samples such as blood, lymph or interstitial fluid and combinations thereof and the like.
As used in this specification and the appended claims, the following general rules apply. Singular forms “a,” “an” and “the” include plural references unless the content dearly indicates otherwise. General nomenclature rules for genes and proteins also apply. That is, genes are italicized or underlined (e.g.: TP53 or TP53), but gene products, such as proteins and peptides, are in standard font, not italicized or underlined (e.g.: p53). General rules for nomenclature of amino acid location also applies; that is, the amino acid abbreviation followed by number (e.g.: R175, R 175, R-175), where the amino acid name is represented by the abbreviation (e.g.: arginine by “R,” “arg,” “Arg” any other abbreviations familiar to those skilled in the art) and the location of the amino acid on the protein or peptide is represented by the number (e.g.: 175 for position 175). General rules for nomenclature of mutations also apply; for example, R175H, means arginine at location 175 is substituted by histidine. As another example mutation on p53 at location 175 from R to H can be represented by for example “p53-R175H” or “mp53-R175H.” Unless specified otherwise, any amino acid position corresponds to the amino acid location on a wildtype p53, preferably the human wtp53 isoform “a” listed in Section 7.24. General nomenclature rules for organism classification also apply. That is order, family, genus and species names are italicized.
As used herein, the following terms shall have the specified meaning. The term “about” takes on its plain and ordinary meaning of “approximately” as a person of skill in the art would understand, and generally plus or minus 20%, unless specified otherwise. The term “comprise,” “comprising,” “contain,” “containing,” “include,” “including,” “include but not limited to,” or “characterized by” is inclusive or open-ended and does not exclude additional, unrecited elements.
As used herein, the following terms shall have the specified meaning:
“diagnosis” means any method to identify a particular disease, and includes, among others, detecting the symptoms of a disease, assessing the severity of the disease, determining the stages of the disease, and monitoring the progression of the disease.
“expression” or “level of expression” means the level of mRNAs or proteins encoded by the gene marker.
“prognosis” means any method to determine the likely course of a disease, and includes, among others, determining the predisposition of a disease, determining the likelihood a disease will onset, assessing the likely severity of the disease, determining the likely stages of the disease, and predicting the likely progression of the disease.
“screening of effective treatments” means screening of effective therapeutic product or method for the treatment of a certain disease. It can involve in vitro and/or ex vivo screening methods, and includes, among others, both the product or composition to treat a disease and the method to prepare the composition for treatment.
“subject” means any organism. It includes animal, including vertebrate, further including a mammal such as a human. It also includes any unborn child and any un-conceived, hypothetical child of two parents.
“treatment” means the administration and/or application of therapeutic product or method to a subject with a certain disease, and includes, among others, monitoring the efficacy of a type of treatment for the disease.
“PANDA” means a complex comprised of one or more p53 and one or more PANDA Agent.
“PANDA Agent” means a composition of matter capable of binding to the PANDA Pocket that has one or more useful characteristics, examples of such useful characteristics include: (a) can cause a substantial increase in the population of properly folded p53, preferably the increase is at least about 3 times more than the increase caused by PRIMA-1, more preferably the increase is at least about 5 times more than the increase caused by PRIMA-1, further preferably the increase is at least about 10 times more than the increase caused by PRIMA-1, further preferably the increase is at least about 100 times more than the increase caused by PRIMA-1; (b) can cause a substantial improvement in the transcriptional function of p53, preferably the improvement is at least about 3 times more than the improvement caused by PRIMA-1; more preferably the improvement is at least about 5 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 10 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 100 times than the improvement caused by PRIMA-1; and (c) can cause a substantial enhancement of stabilization of p53 as measured by, for example, an increase p53 Tm, preferably the enhancement is at least about 3 times more than the enhancement caused by PRIMA-1, more preferably the improvement is at least about 5 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 10 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 100 times than the improvement caused by PRIMA-1. A PANDA Agent is preferably to have two or more useful characteristics and more preferably has three or more useful characteristics. Exemplar PANDA Agents is ATO and its analogs. More exemplar PANDA Agents can be found in Table 1-Table 7.
“PANDA Pocket” means a region consisting essentially of an area of about 7 Å from a properly folded PANDA Cysteine, including, all amino acids adjacent to one or more properly folded PANDA Cysteine, all amino acids that contact with one or more properly folded PANDA Cysteine, and all PANDA Cysteines. Exemplar 3D structures of a PANDA Pockets can be found
“PANDA Core” means the tertiary structure formed on the PANDA Pocket of a p53 when a PANDA Agent forms at least one tight association between the PANDA Pocket and the PANDA Agent.
“PANDA Cysteine” means a cysteine corresponding to the wtp53 positions cysteine 124 (“C124” or “cys124”), cysteine 135 (“C135” or “cys135”), and cysteine 141 (“C141” or “cys141”) (together the “PANDA Triad”).
“p53” means any wildtype p53 (“wtp53”), including all natural and artificial p53; any mutated p53 (“mp53”), including all natural and artificial p53; or a combination thereof.
“wtp53” means all wildtype p53 that is commonly considered as wildtype, or has a wildtype sequence, and includes any commonly acceptable variations, such as variations caused by single nucleotide polymorphism (“SNP”). Exemplar wtp53 can be found in
“SNP” means single-nucleotide polymorphism, which is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is presented to some appreciable degree within a population. An exemplary list of known SNP on p53 is Table 8.
“mp53” means mutated p53, which includes all p53 and p53 like macromolecules that is not a wtp53. mp53 includes, artificial mp53, such as recombinant p53, chimeric p53, p53 derivative, fusion p53, p53 fragment, and p53 peptide. Exemplar mp53 include one or more mutations corresponding to the wtp53 positions R175, G245, R248, R249, R273, R282, C176, H179, Y220, P278, V143, I232, and F270. Exemplar mp53 mutations include R175H, G245D/S, R248QW, R249S, R273C/H, R282W, C176F, H179R, Y220C, P278S, V143A, I232T, and F270C mutations.
“mp53 hotspot” means a mutation on mp53 located at R175, G245, R248, R249, R273, or R282.
“hotspot mp53” means an mp53 with at least one mutation in mp53 hotspots, namely, R175, G245, R248, R249, R273, R282, and combinations thereof.
“biological system” means a cell, bacteria, artificial system containing p53 pathway and relevant proteins.
“p53 inhibiting protein” means a protein that inhibits a function of activity of p53, and includes, for example, murine double minute 2 (“MDM2”), inhibitor of apoptosis-stimulating protein of p53 (“iASPP”) and sirtuin-1 (“SIRT1”).
“Contacting mp53” means a mp53 that loses its DNA binding ability without drastically affecting the p53 structure. Contacting mp53s are represented by, for example, p53-R273H, p53-R273C, p53-R248Q and p53-R248W.
“Structural mp53” means a mp53 that has significantly disrupted three-dimensional structure as compared to wtp53. Structural mp53s are represented by, for example, p53-R175H, p53-G245D, p53-G245S, p53-R249S, and p53-R282W.
“useful characteristics” a means capable of efficiently and effectively rescuing at least one of mp53 structure, transcriptional activity, cell growth inhibition, tumor-suppressive function to that of wtp53. Exemplar useful characteristics include: (a) can cause a substantial increase in the population of properly folded p53, preferably the increase is at least about 3 times more than the increase caused by PRIMA-1, more preferably the increase is at least about 5 times more than the increase caused by PRIMA-1, further preferably the increase is at least about 10 times more than the increase caused by PRIMA-1, further preferably the increase is at least about 100 times more than the increase caused by PRIMA-1; (b) can cause a substantial improvement in the transcription function of p53, preferably the improvement is at least about 3 times more than the improvement caused by PRIMA-1; more preferably the improvement is at least about 5 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 10 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 100 times than the improvement caused by PRIMA-1; and (c) can cause a substantial enhancement of stabilization of p53 as measured by, for example, an increase p53 Tm, preferably the enhancement is at least about 3 times more than the enhancement caused by PRIMA-1, more preferably the improvement is at least about 5 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 10 times more than the improvement caused by PRIMA-1, further preferably the improvement is at least about 100 times than the improvement caused by PRIMA-1. A PANDA Agent is preferably to have two or more useful characteristics and more preferably has three or more useful characteristics. Exemplar PANDA Agents is ATO and its analogs. More exemplar PANDA Agents can be found in Table 1-Table 7
“DTP” means Developmental Therapeutics Program as understood by a person of ordinary skill in the art.
“ATO” or “As2A” means arsenic trioxide and compounds generally understood as arsenic trioxide.
“analog” or “analogue” means a compound obtained by varying the chemical structure of an original compound, for example, via a simple reaction or the substitution of an atom, moiety, or functional group of the original compound. Such analog may involve the insertion, deletion, or substitution of one or more atoms, moieties, or functional groups without fundamentally altering the essential scaffold of the original compound. Examples of such atoms, moieties, or functional groups include, but are not limited to, methyl, ethyl, propyl, butyl, hydroxyl, ester, ether, acyl, alkyl, carboxyl, halide, ketyl, carbonyl, aldehyde, alkenyl, azide, benzyl, fluoro, formyl, amide, imide, phenyl, nitrile, methoxy, phosphate, phosphodiester, vinyl, thiol, sulfide, or sulfoxide atoms, moieties, or functional groups. Many methods for creating a chemical analog from an original compound are known in the art.
“a therapeutically effective amount” is an amount of a compound effective to prevent, alleviate, or ameliorate symptoms of a disorder or prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. The effective dosage, level, or amount of a compound to be used in vivo can be determined by those skilled in the art, taking into account the disorder to be treated, the condition of the individual patient, the site of delivery, the method of administration, the potency, bioavailability, and metabolic characteristics of the compound, and other factors.
“efficiently” as used to describe enhancement for a useful characteristics, such as rescuing one or more wtp53 structure or function, rescuing one or more wtp53 transcriptional activity, cell growth inhibition activity, tumor-suppressive function to that of wtp53, generally means enhancing the useful characteristics by more than 3 times, as compared to the enhancement by PRIMA-1, preferably 5 times, more preferably 10 times, more preferably 100 times. For example, an efficient enhancement would be enhancing the Tm of mp53 by 3-100 times of those of PRIMA-1, and/or folds mp53 by 3-100 times of those of PRIMA-1, and/or stimulates mp53's transcriptional activity by 3-100 times of those of PRIMA-1.
Examples of a p53 related disorder include cancer, such as lung, breast, colorectal, ovarian, and pancreatic cancers; a tumor, a consequence of aging, a developmental disease, accelerated aging, an immunological disease.
p53 is one of the most important proteins in cell biology. The apparently 53-kilodalton protein p53 is a transcription factor. Wildtype p53 (wtp53) has a sequence that has been identified. (See public gene banks, such as gene bank, protein bank, Uniport; see also Section 7.25). Exemplar wtp53 sequences are listed under Section 7.25). Unless specified otherwise, this application uses the wtp53 sequences of human p53 isoform “a” listed under Section 7.25 to reference locations.
The human wtp53 is active as a homotetramer of 4×393 amino acids with multiple domains including an intrinsically disordered N-terminal transactivation domain (“TAD”), a proline-rich domain (“PRD”), a structured DNA-binding domain (“DBD”) and tetramerization domain (“TET”) connected via a flexible linker, and an intrinsically disordered C-terminal regulatory domain (“CTD”). Many p53 family genes expressing multiple isoforms exist, and often exhibit antagonistic functions.
Wtp53 plays a central part in the cells and is frequently considered as the most important tumor suppressor. Upon cellular stresses, such as DNA damage or oncogenic stress, p53 is activated and transcriptionally regulates a batch of genes (for example, Apaf1, Bax, Fas, Dr5, mir-34, Noxa, TP53AIP1, Perp, Pidd, Pig3, Puma, Siva, YWHAZ, Btg2, Cdkn1a, Gadd45a, mir-34a, mir-34b/34c, Prl3, Ptprv, Reprimo, Pai1, Pml, Ddb2, Ercc5, Fancc, Gadd45a, Ku86, Mgmt, Mih1, Msh2, P53r2, Polk, Xpc, Adora2b, Aldh4, Gamt, Gls2, Gpx1, Lpin1, Parkin, Prkab1, Prkab2, Pten, Sco1, Sesn1, Sesn2, Tigar, Tp53inp1, Tsc2, Atg10, Atg2b, Atg4a, Atg4c, Atg7, Ctsd, Ddit4, Dram1, Foxo3, Laptm4a, Lkb1, Pik3r3, Prkag2, Puma, Tpp1, Tsc2, Ulk1, Ulk2, Uvrag, Vamp4, Vmp1, Bai1, Cx3cl1, Icam1, Irf5, rf9, Isg15, Maspin, Mcp1, Ncf2, Pai1, Tlr1-Tlr10, Tsp1, Ulbp1, Ulbp2, mir-34a, mir-200c, mir-145, mir-34a, mir-34b/34c, and Notch1) to trigger cell-cycle arrest, DNA repair, apoptosis, cell repair, cell death and others. Apart from anti-cancer role, p53 target genes also have important roles in senescence, angiogenesis, and autophagy, connecting, regulating oxidative stress, regulating metabolic homeostasis, stem cell maintenance, and others.
A mutation to wtp53 can have a wide range of implications. The p53 protein is such a powerful tumor suppressor that it is inactivated by mutation in nearly half of all human cancers. A mutation to wtp53 can have a wide range of implications. First, the resultant p53 protein, mutant p53 (“mp53”), will substantially lose its tumor-suppressive function. mp53 expressing mice and humans develop a large number of cancer types at early onset. Second, some of the mp53s will, in addition gain oncogenic properties, such as, for example, promoting cancer metastasis, conferring resistance to treatment, and causing cancer patients to relapse.
Accordingly, understanding p53, and more importantly, achieving structural and functional restoration of mp53, is the holy grail of modern cell biology, medicine, and cancer research. p53 is the most actively researched protein in cancer, medicine, and biology. Moreover, research in p53 far exceeds that being done with respect to even the second most actively researched protein, namely, TNF, by 60%, and exceeds the third most actively researched protein, namely, EGFR, by 80% (Dolgin, 2017). Since 2001, p53 has been on the top of the most actively researched proteins, far exceeding others. One of the reason for this is that p53 is the most commonly mutated protein in cancer, far exceeding other cancer mutations (Kandoth et al., 2013).
Around half of all human tumors harbor partially functional, but silent wtp53s, while the other half carry mutant p53s (Vogelstein et al., 2000). Mouse studies suggest that restoration of wtp53 function can completely or partially regress tumor growth (Feldser et al., 2010; Martins et al., 2006; Ventura et al., 2007; Xue et al., 2007).
Most existing efforts toward restoring wtp53 function have focused on p53 inhibiting proteins (“PIP”), including murine double minute 2 (“MDM2”), inhibitor of apoptosis-stimulating protein of p53 (“iASPP”), and sirtuin-1 (“SIRT1”). For example, since amplification of MDM2 or loss of p14ARF, its inhibiting protein, closely correlates with sarcomas and glioblastomas, respectively (see TCGA database) (Gao et al.), the MDM2-inhibiting compound, Nutin, was identified to counteract MDM2's activities (Vassilev et al., 2004). As another example, we have reported that iASPP exposes the RaDAR nudear localization code (Lu et al., 2014), enters the nudeus (Lu et al., 2016a), and inhibits wtp53 in metastatic melanoma (Lu et al., 2013), and accordingly, we are exploring ASPP inhibiting compounds. Many of these anti-PIP compounds are highly efficient, have a clear mechanism of action (“MOA”), and are progressing to clinical investigations (Khoo et al., 2014).
Others are attempting to target mp53, a protein that not only loses its tumor suppressive function but also frequently gains oncogenic properties. This approach, while attractive, is not easy, however.
Simply introducing wtp53 to mp53-expressing cells is problematic because mp53 is dominant-negative, and as seen in a mouse model-based study, can dampen the effect of the exogenous wtp53 introduced (Wang et al., 2011).
Selectively inhibiting mp53-expressing cells by blocking mp53 upstream pathways, downstream pathways, or relevant pathways are also problematic. While the mp53 upstream inhibitor, suberanilohydroxamic acid (“SAHA”), can inhibit the mp53-upstream histone deacetylases (“HDAC”), thereby promoting mp53 degradation (Li et al., 2011); the mp53 downstream inhibitor, statins (a cholesterol inhibitor), can block the mp53-downstream mevalonate pathway, thereby decreasing the survival rate of mp53-expressing cells (Parrales et al., 2016); and certain kinase inhibitors can selectively inhibit mp53-expressing cells by interfering with mp53-associated activation of receptor tyrosine kinase signaling, thereby inhibiting cell invasion by blocking integrin recycling (Muller et al., 2009) all show promises, none of these strategies can restore mp53's tumor-suppressive functions. Accordingly, it is not known whether these strategies are sufficient to treat cancer clinically in the long-term (Muller and Vousden, 2014). Indeed, mouse studies show that eliminating mp53 only extends the survival of mp53-expressing animals to p53−/− (null) levels (Alexandrova et al., 2015).
The tumor-suppressive functions of mp53 were reported to be rescuable in 1993 (Halazonetis and Kandil, 1993; Hupp et al., 1993). Since then, identifying an efficient, effective, mp53 specific rescue agent has been the holy grail of cancer biology and medicine. Indeed the direct medical expenses for mp53 patients in 2017 alone amounts to approximately 65 billion USD. By successfully identifying a highly efficient and effective mp53 rescue agent, Applicants seek to address the tremendous financial, physical and emotional hardships faced by these mp53 patients and their families.
Despite countless screening efforts of varying scale, there is still no efficient and effective mp53 rescue agent. This is partly because rescuing mp53's tumor suppressive function (Joerger and Fersht, 2016; Muller and Vousden, 2013, 2014) is extremely challenging (Joerger and Fersht, 2016; Muller and Vousden, 2013, 2014) (Bykov et al., 2017) (Sabapathy and Lane, 2018). In fact, it may be one of the most difficult scientific problems of our generation. To successfully rescue mp53, the rescue agent must do more than simply inhibit or destroy specific mp53 functions. The rescue agent must repair or rescue the wildtype functions of mp53.
Without a doubt, rescue is much more challenging than destruction. Understandably, of the over 80 clinically approved targeted drugs, the vast majority of them are inhibitors of oncoproteins. None of them can rescue a tumor suppressor's function.
To add to the challenge, like RAS, the mp53 surface provides no obvious druggable pocket (Joerger and Fersht, 2016). Accordingly, despite having more than 15 mp53 rescue candidates reported in the past two decades and having attracted tens, and even hundreds, of millions of dollars in investments, to date, only one candidate (PRIMA-1/APR-246) has entered a clinical trial. Even among the 15 reported mp53 rescue candidates, all of them have barely detectable efficacy, with an increase of less than 2 times for structural rescue, and with an increase of less than 2 times for transcriptional rescue. By comparison, a fully rescued p53-R175H is about 100 times for structural rescue. As another example, a fully rescued p53-282 20× for functional fully rescue. Moreover, the MOA for these rescue agents are largely unknown (Bykov et al., 2017) (Sabapathy and Lane, 2018). With these unfavorable numbers and without any clear MOA, the utility of these rescue candidates for cancer therapy is very limited.
Accordingly, Applicants have made it their priority to identify a highly efficient and effective rescue agent that directly rescue mp53 with a clear MOA.
5.4.1 mp53 Rescue Agents Identified by In Vitro Screenings are not Ideal
Initial screenings for mp53 rescue agents were primarily based on mp53 recombinant proteins in vitro. These include CP-31398, which was identified because it promoted recombinant mp53 stability (Foster et al., 1999) and SCH529074 and p53R3, which were identified because they improved recombinant mp53 to DNA binding (Demma et al., 2010; Weinmann et al., 2008). However, these rescue agents are inefficient, nonspecific, and face serious challenges in cells.
For example, CP-31398 was shown to have limited efficiency in cells. Not only do they have limited specificity to mp53 and can cause substantial toxicity to the cells, they may also have trouble entering the cells. Moreover, it is reported that the toxic effect is nonspecific to and independent of mp53 expression (Rippin et al., 2002), suggesting that CP-31398 does not function by directly targeting mp53. Furthermore, unlike earlier in vitro studies, which show CP-31398 binds to the mp53 protein, later in vivo studies show that CP-31398 binds to DNA in cells instead (Rippin et al., 2002).
5.4.2 mp53 Rescue Agents Identified by Cell-Based Screenings are not Ideal
In 2002, a cell-based screening found PRIMA-1 and MIRA to selectively inhibit mp53 expressing cells (Bykov et al., 2002). In silico screenings found NSC319726 to selectively inhibit a panel of mp53 expressing cell lines (Yu et al., 2012). Another cell-based screening found Chetomin to enhance mp53-dependent luciferase reporter activity in cells (Hiraki et al., 2015). However, like the in vitro screenings, the rescue agents identified by cell-based screenings are also problematic.
Using PRIMA-1 as an example, studies have shown that, like the other rescue agents, it has limited rescue efficiency. Moreover, an increasing number of studies have reported that PRIMA-1 and its structural analog PRIMA-1Met (“APR-246”) inhibited cell growth irrespective of whether mp53 is present or not (Aryee et al., 2013; Grellety et al., 2015; Lu et al., 2016b; Patyka et al., 2016; Tessoulin et al., 2014). In addition, studies have increasingly reported that PRIMA-1 targets oxidative stress signaling components (Bauer et al., 2016; Joerger and Fersht, 2016; Lambert et al., 2009) and that the observed sensitivity caused by PRIMA-1 and other alkylating agents, such as PK11007, to mp53 expressing cells is contributed by a loss of antioxidant functions in mp53s (Bauer et al., 2016; Joerger and Fersht, 2016; Lambert et al., 2009)
Furthermore, studies have increasingly reported confusing results and questioned their MOA and pointed to their limited efficiency. In addition, while Lambert and Bykov reported that PRIMA-1 binds to mp53 covalently and promotes mp53-DNA binding activity in vitro (Bykov et al., 2002; Lambert et al., 2009), at least one other study reported that it is CP-31398, but not PRIMA-1, that restores DNA-binding activity to mp53 in vitro (Demma et al., 2004). These findings appear to be at odds with the initial reports that PRIMA-1 selectively inhibit p53-R273H-expressing Saos-2 cells (Bykov et al., 2002). In fact, these later studies suggest that PRIMA-1 does not directly target and rescue mp53 and may instead be killing mp53 cells by synthetic lethality, that is, inhibiting other cellular the proteins such as above mentioned oxidative stress signaling components, rather than mp53, that are essential for the survival of mp53 cells. (Weidle et al., 2011). Supporting this theory, studies have shown that many proteins, including CHK1, WEE-1, PLK-1, and ATM, are synthetic lethal targets of mp53 cells (Weidle et al., 2011). In one clinical trial, WEE-1 inhibitor had efficacy in treating patients expressing mp53 (Leijen et al., 2016a; Leijen et al., 2016b).
5.4.3 Having an Established MOA is Crucial for Identifying an Effective and Efficient Rescue Agent for Mp53
Presently, the vast majority of known mp53-rescue agents, including CP-31398 (Foster et al., 1999) and PRIMA-1 (Bykov et al., 2002), are thought to stabilize the p53's wild-type structure (Muller and Vousden, 2014). However as discussed above, they are not ideal. One of the major problems with these rescue agents is that their MOA unclear.
The vast majority of reported rescue agents were identified via random screenings. Only very few, such as PhiKan083 and PK7088 (Basse et al., 2010; Boeckler et al., 2008; Liu et al., 2013), were identified via rational screenings. However, these compounds can only rescue p53 with mutation on Y220. Accordingly, the MOA for the vast majority of rescue agents remains largely unknown.
This is particularly problematic. As seen for example in PRIMA-1, not knowing the MOA of an rescue agent or which proteins it targets in cells (Joerger and Fersht, 2016) can lead to puzzling results and conflicting theories. To further illustrate, without a concrete MOA, it is puzzling why many of the identified rescue agents can rescue different categories of mp53s.
In general, the vast majority of wtp53 populations are properly folded and thus, functional. When p53 mutates, it falls roughly into two categories: (1) contacting mp53 that loses its DNA binding ability without drastically affecting the p53 structure (“Contacting mp53”); and (2) structural mp53 that has disrupted three-dimensional structures as compared to the wildtype (“Structural mp53”). A representative Contacting mp53 is p53-R273H, with other common examples, including p53-R273C, p53-R248Q and p53-R248W. A representative Structural mp53 is p53-R175H, with other common examples, including mp53s include p53-G245D, p53-G245S, p53-R249S, and p53-R282W. Accordingly, for Structural mp53s, the population of unfolded p53s dramatically increase. To rescue Structural mp53s, one would need to increase the population of unfolded p53s to folded p53s.
Because these mp53s lose their wildtype p53 function indifferent ways, it would be reasonable that a rescue agent for one category of mp53 would not rescue the other category. In fact, there is a proposition to classify mp53s into five different categories, where each category has its own specific set of rescue requirements (Bullock and Fersht, 2001; Bullock et al., 2000; Joerger and Fersht, 2007).
In general, it is substantially more challenging to rescue Contacting mp53 than Structural mp53. For example, to compensate for Contacting mp53's loss of DNA-contact residue(s), such as R248 and R273, the rescue agent must create a new contact for DNA binding (Joerger and Fersht, 2007). Accordingly, without a defined MOA, it is puzzling how a single rescue agent, such as CP-31398 (Foster et al., 1999), PRIMA-1 (Bykov et al., 2002), SCH529074 (Demma et al., 2010), Zinc (Puca et al., 2011), stictic acid (Wassman et al., 2013), and p53R3 (Weinmann et al., 2008), can rescue both Structural mp53s (such as p53-R175H) and Contacting mp53s (such as p53-R273H) (Joerger and Fersht, 2016; Khoo et al., 2014).
We believe one of the most important deficiencies of existing screening methods, both protein-based and cell-based, is that their selection criteria are more or less random. Accordingly, they fail to elucidate the MOA of the rescue agents they identify. Here, Applicants have set out to develop a novel method for a rational, effective screening of mp53 rescue candidates with and a concrete MOA.
The first rationally designed screening was carried out in 2008, in which mp53s were differentially treated and structurally analyzed (Basse et al., 2010; Boeckler et al., 2008). Since mp53s are highly diverse, a rational basis was developed to analyze individual mp53s (Joerger and Fersht, 2007; Joerger and Fersht, 2016; Muller and Vousden, 2013; Muller and Vousden, 2014). PhiKan083 and PK7088 were identified through this screening and were found to selectively bind and rescue p53-Y220C with an intelligible MOA. However, p53-Y220C is not among the six most frequently occurring mp53s, there is a need to identify a rescue agent capable of rescuing a broader range of mp53s.
As explained above, there is a need for an efficient, rational based screen to identify rescue agents for hotspot mp53s with desirable characteristics and a concrete MOA. Others have attempted, but this need has not been filled. Here, we disclose such a screening method, an efficient, rational based screening method that integrates in silico rational Classification of mp53s, in silico rational analysis of Compound structure, Cell growth assay, and experimental mp53 Conformation determination (“4C Screening”). Using our 4C Screening method, we screened compound repositories, such as the compound repository of DTP (
Through our 4C Screening, we can identify rescue candidates that, upon hydroxylation, can simultaneously bind to three cysteines of mp53s; can refold p53-R175H with a strikingly high efficiency, to a level comparable to that of wtp53 as measured by assays, such as by PAb1620 and PAb246 immunoprecipitation; can rescue transcriptional activity of p53-R282W and p53-G245S to a level comparable to that of wtp53 as measured by luciferase report assay; can selectively inhibit mp53 expressing cell lines, such as the NCI60 cell lines that expresses the Structural hotspot mp53; can inhibit mouse xenografts dependent on structural mp53s; and can be used to treat mp53 harboring cancer patients in combination with DNA-damaging agents.
As an example, we predicted ATO (As2O3) and NSC3060 (KAsO2) to be able to simultaneously bind 3 cysteines upon hydroxylation (
5.5.1 in-Silico Rational Classification of mp53s
One of the challenges in designing a rational screening method for mp53 rescue agents is that mp53 dysfunctions are diverse. Accordingly, a rational screening strategy designed specifically for different types of mp53 mutation is necessary. In addition, a strategy designed to screen rescue agents that can simultaneously correct the structural defects of Structural mp53s and re-introduce the DNA contacting region of Contacting mp53s may be unrealistic, because such rescue agent may not exist.
There is, however, a class of mp53s that are mainly unfolded at body temperature but refolded (and regains transcriptional activity) at lower temperatures (Bullock et al., 1997; Bullock et al., 2000). For example, the four hotspot Structural mp53s (p53-R175H, p53-G245S/D, p53-R249S, and p53-R282W) (
We thus predicted that a broad spectrum rescue agent, capable of rescuing this class of mp53s, may exist.
5.5.2 Cell Growth Assay
The independently performed NCI60 screening project supplied cell line sensitivity profiles for a large number of the DTP compounds (Shoemaker, 2006). We hypothesized that the compounds that selectively inhibit Structural mp53-expressing NCI60 cell lines would have higher chance to act as stabilizer of this class of mp53s (
Of the overall approximately 292.000 structures deposited in DTP, approximately 21 000 compounds have sensitivity profiles that passed the quality control according to CellMiner (Reinhold et al., 2012) (
5.5.3 in-Silico Rational Analysis of Compound Structure
Based on our mp53 classification analysis described in Section 6.5.1 above, we predicted that there may be a broad spectrum rescue agent capable of rescuing the class of Structural hotspot mp53s (p53-R175H, p53-G245S/D, p53-R249S, and p53-R282W). In addition, we hypothesize that immobilizing mutation regions may stabilize this class of mp53 globally. Importantly, we found that 8 of the 10 mp53 cysteines are in close proximity to the Structural mp53 hotspots (
We further narrowed down compounds from the DTP library in-silico, selecting compounds with multiple cysteine-binding potential, such as compounds with heavy metals such as Zn, Hg, As, and Au; thiol containing compounds; and Michael acceptors (
After the two-step rational selection process described above, we narrowed an initial pool of 1,975 compounds to a pool of about 100 mp53 rescue candidates.
5.5.4 Experimental Mp53 Conformation Determination
We next experimentally tested whether p53-R175H was properly folded in the presence of the rescue candidates using a wtp53 specific antibody, PAb1620 antibody (Wang et al., 2001), by immunoprecipitation (
To expand our pool of rescue candidates, we conducted an ultra-large 4C+ Screening. We in silico analyzed approximately 94.2 million compounds derived from PubChem (https://oubchem.ncbi.nlm.nih.ov/). Since we identified two arsenic containing compounds in our 4C Screening, in our 4C+ Screening, we selected compounds containing the metal arsenic or its analogues, such as antimony, and bismuth, with at least one cysteine-binding potential. About 32957 compounds were discovered to contain As, and/or Sb, and/or Bi. Under these criteria, we included any organic five-valence arsenic, five-valence antimony, and five-valence bismuth, as long as they have the potential to bind one or more cysteine. After this in-silico pre-screening step, we in silico narrowed an initial pool of approximately 94.2 million compounds to a pool of thousands of rescue candidates. We then selected and experimentally tested some structural mp53s for their abilities to refold protein, increase Tm, and stimulate transcriptional activity.
Nearly half of human cancers harbor a mp53 that loses its tumor-suppressive function and/or frequently gain some oncogenic functions. While dysfunctional p53 mutations are created via a diversity of mechanisms on a variety of sites, approximately one-third of the p53 mutations are located on one of six mp53 hotspots: R175, G245, R248, R249, R273, and R282, (each a “mp53 hotspot”) (Freed-Pastor and Prives, 2012). The resulting mp53s are commonly classified as Contacting mp53 which loses DNA-contacting residue without drastically altering the mp53 structure and Structural mp53 which loses the wtp53 structure. DNA-binding ability and transcriptional activity are greatly impaired in both Contacting mp53s and Structural mp53s. Moreover, most of cancer-derived mp53s lose wtp53's tumor-suppressive functions and many also gain oncogenic properties.
Using our efficient and highly rational 4C Screening, we can experimentally identify at least two wide-spectrum mp53 recusing agents with remarkably high rescue efficiency. They are arsenic trioxide (ATO: NSC92859 & NSC759274) and potassium arsenite (KAsO2: NSC3060). Our results show that these mp53 rescue agents can rescue mp53's structure; increase thermodynamic stability; rescue mp53's transcriptional activity; rescue mp53's tumor suppressive function in vitro, in vivo, and in patients; rescue different mp53s; remarkable rescue capacity for Structural mp53. We also identified an atom-level rescue mechanism based on these rescue agents.
Using our efficient and highly rational ultra-large-scale 4C+ Screening, we further discovered thousands of clinically relevant and efficient mp53 stabilizers, many of which contain arsenic (Table 1-Table 6). We experimentally confirmed 31 mp53 recusing agents with key supporting data (rescue efficiency on mp53's structure and transcriptional activity) (Table 7). We further disclose here the atom-level mechanism by which Structural hotspot mp53s can be pharmacologically stabilized.
Using our 4C Screen, we discovered that elemental arsenic and its analogues, whether alone or in a compound, rapidly, effectively and selectively stabilizes p53. In particular, we found that elemental arsenic and its analogues are particularly useful for the class of Structural mp53s because they are heavily destabilized. We further discovered that arsenic and its analogues directly and covalently binds mp53s and raises the melting temperature of numerous p53s, particularly the Structural mp53s, including four hotspot Structural mp53s (p53 with mutations on R175, G245, R249, R282), by approximately 1-8° C., supporting that arsenic is covalently bound to the Structural mp53. We further discovered that arsenic and its analogues efficiently rescue the structure and transcriptional activity of mp53 through the formation of a highly stable complex—PANDA.
Here, we disclose, for the first time, a batch of highly resolved crystal structures of PANDA, at approximately 1-3 Å. By analyzing the PANDA crystal structure, we were able to analyze in detail, at the atomic level, how mp53s, such as Structural mp53s are pharmacologically stabilized. In doing so, we discovered a druggable pocket on p53 that can be bound and immobilized by a arsenic, which consequently leads to the global stability of p53 core domain. Based on these findings and through our ultra-large 4C+ screening study, we discovered a vast treasure trove of thousands of clinically relevant mp53 stabilizers (Table 1-Table 6).
5.8.1 A Class of Rescue Agent Contains Arsenic and can Dramatically Elevate the Tm of mp53
We based our screening method on a hypothesis that there are compounds that can rescue wide spectrum of Structural mp53s by increasing Tm, thereby stabilizing mp53. We tested this hypothesis on the four purified recombinant Structural hotspot mp53s and discovered ATO is capable of raising the Tm of all four mp53s by approximately 1-8° C., to a level comparable to wtp53. For example, ATO raises the Tm of p53-R249S by up to 4.9° C. (
5.8.2 the Arsenic Rescue Agent is Highly Effective in Rescuing the Structure and Function of mp53s
We systematically and quantitatively determined the structural and transcriptional rescue profile of the rescue agent ATO Before ATO treatment, we confirmed that the folding status of the 6 hotspot mp53s determined by PAb1620 IP efficiency is largely consistent with the thermodynamic stability previously determined by Bullock and colleagues (Bullock et al., 2000) (
Functionally, As2O3 also significantly enhanced the transcriptional activity of the 4 Structural hotspot mp53s on PUMA (
We further saw that As2O3 structurally and transcriptionally rescued Contacting hotspot mp53s, such as mp53-R248Q and mp53-R273H, but at a lower rescue efficiency. It is notable that mp53 structural rescuing efficiency is not necessarily proportionate to the functional rescuing efficiency. While structure of p53-R282W is far from fully rescued, its transcription function is greatly rescued (equivalent to 80% of wtp53 levels). This may be because PAb1620 epitope fails to reflect p53's local structure, for example, the key LSH motif and L3 loop that respond to DNA binding.
In addition to the six hotspot mp53s, As2O3 also rescued the other most commonly-occurring mp53s, such as p53-C176F, p53-H179R, p53-Y220C (low efficiency), and p53-P278S (low efficiency) (http://p53.iarc.fr/, IACR) and the representative mp53s with mutations outside of DNA-binding region (p53-V143A, p53-F270C, and p53-I232T) (
The Structural and transcriptional rescue profile for some of the mp53s are shown in (
5.8.3 p53 is Rescued by Binding to a Single Arsenic Atom or Analogue
We further hypothesized a single arsenic atom can bind the key cysteines on mp53 to alter it structures and/or functions. To test this, we created a recombinant mp53(94-293) core with an R249S mutation (“mp53(94-293)-R249S”). We then purified the mp53(94-293)-R249S, incubated the purified mp53(94-293)-R249S with As2O3, and measured the molecular weight of the resulting mp53s by mass spectroscopy under denaturing condition.
We discovered that the recombinant mp53's molecular weight increased by approximately 72 Daltons (Da) upon incubation, roughly corresponding to the gain of an arsenic atom (74.9) and the loss of 3 protons (
5.8.4 the Class of Arsenic Rescue Agents Binds to Cysteines on p53 Via its Multiple-Cysteine-Binding Potential
To further understand the interaction between this class of arsenic rescue agents, we turned to the DTP library. We noticed that the DTP library contains many arsenic-containing compounds (n=47). However most of them did not survive in the ‘4C’ Screening. This suggest that the arsenic has to be presented in a correct scaffold to be able to bind p53.
To understand the prerequisite conditions to be an arsenic rescue agent, we compared the 47 arsenic rescue agents, we compared these compounds and their NCI60 cell line inhibition profile. We found that arsenic compounds with three or more cysteine binding potential, such as NSC3060 (KAsO2, Pearson's correlation 0.837, p<0.01), NSC157382 (Pearson's correlation 0.812, p<0.01), and NSC48300 (Pearson's correlation 0.627, p<0.01), have the most similar NCI60 inhibition profiles as the ATO. Moreover, we found that compounds with bi-cysteine-binding potential also have largely similar NCI60 inhibition profiles as the ATO, though with less extensive (NSC92909, Pearson's correlation 0.797, p<0.01; NSC92915, Pearson's correlation 0.670, p<0.01; NSC33423, Pearson's correlation 0.717, p<0.01).
Moreover, we found that mono-cysteine-binding potential compounds also have significantly similar NCI60 inhibition profiles as the ATO, although the extent was even lower (NSC727224, Pearson's correlation 0.598, p<0.01; NSC724597, Pearson's correlation 0.38, p<0.01; NSC724599, Pearson's correlation 0.553). Summarily, our results showed that compounds with three or more cysteine binding potential, bi-cysteine-binding potential and mono-cysteine-binding potential can selectively inhibit the growth of mp53-expressing cells. Moreover, we showed that the efficiencies among these three classes of arsenic rescue agents decrease with the number of cysteine binding potential it has.
Accordingly, we discovered, for the first time, three separate classes of mp53 rescue compounds, with different rescuing potential. At the very top, those with three or more cysteine binding potential can restore mp53s to near wildtype-like conditions.
Notably, the above mentioned NSC48300 not only has the potential to simultaneously bind 3 cysteines, it also has the potential to simultaneously bind 4 cysteines. This suggests arsenic compound is an efficient mp53 rescuer when it has potential to bind at least three cysteines. It is possible that arsenic compounds with more than three cysteines binding potential can have the same level of rescue efficiency as those compounds with only three cysteines binding potential, because three cysteines were found to be clustered together on p53 (
Since we named the p53 and arsenic analogue complex, PANDA, we decided to follow the nomenclature theme. Based on the crystal structure of PANDA we obtained (described herein), we created the following names. PANDA Cysteine as one of C124, C135, or C141. PANDA Triad as C124, C135, C141 together. PANDA Pocket as the three-dimensional structure centered around PANDA Triad. The PANDA Pocket includes PANDA Triad and directly contacting residues (S116 contacts C124, C275 and R273 contact C135, Y234 contacts C141), residues adjacent to PANDA Triad (V122, T123, T125, and Y126; M133, F134, Q136, and L137; K139, T140, P142, and V143), and residues in 7-A distance to PANDA Triad (L114, H115, G117, T118, A119, K120, S121, A138, I232, H233, N235, Y236, M237, C238, N239, F270, E271, V272, V274, A276, C277, P278, G279, R280, D281, and R282) (
PANDA Core as the PANDA Pocket with a PANDA Agent bounded to it. PANDA as the complex of p53 and PANDA Agent. PANDA is characterized by containing a PANDA Core.
With the identification of a three or more cysteine potential as an important criterion for an efficient PANDA Agent, we started to work on understanding the 3D structure of the PANDA Pocket. In particular, we worked to manipulate the PANDA Pocket to stabilize the mp53.
5.9.1 Remarkable Stability of PANDAs Facilitate Crystallization of PANDA and Identification of the PANDA Pocket
While the core of the wtp53 has been previously crystalized, it is notoriously difficult to crystalize the core of a Structural hotspot mp53. This is because Structural hotspot mp53s have very low stability.
However mp53s can be artificially stabilized by introducing four SSSMs (M133L, V203A, N239Y, and N268D), resulting in a quadruple mutant p53-QMs. The four SSSM elevates Tm of the p53 by 5.2° C. This enhanced stability facilitate crystallizations, and many Structural mp53s, including hotspot mp53-G245S and mp53-R282W and non-hotspot mp53-V143A and mp53-F270L, were resolved.
Our PANDA is remarkably stable.
In fact, PANDA Agent can elevate the Tm of a mp53 to a level comparable to the QMs (
The remarkable stability of our PANDAs can enable us to crystalize Structural hotspot mp53s, including p53-R249S and As in a batch of conditions and p53-G245S and p53-R282Q without SSSM.
Based on our PANDA crystals, we confirmed our mass spectroscopy results that a single arsenic (or analogue) atom covalently binds to three cysteines. These three cysteines are: C124, C135, and C141 (each a “PANDA Cysteine” and together a “PANDA Triad”) within the PANDA Pocket.
5.9.2 the Most Effective PANDA Agent Binds to the Highly Inert PANDA Triad Despite Other More Accessible Cysteines are Available and Despite Alternative Tri-Cysteine Metal Binding Site is Available.
To understand the MOA of the PANDA Triad, we knew we need to find out what are the PANDA Triad and where are they located. In addition, one of the major challenges for a cysteine binding compound in clinical studies is off-targeting of undesired cysteines (Joerger and Fersht, 2016; Kaar et al., 2010). Accordingly, it is crucial to map out the cysteines of p53 responsible for PANDA Agent binding.
We listed all of the 10 cysteines on p53 (
In our crystal, in the presence of arsenic, we found that the arsenic selectively bound the highly inert PANDA Cysteines (C135 and C141) in vivo to form the PANDA Core on PANDA (
Our results also show this is the case in vitro. When we soaked a mp53 crystal with arsenic, we produced a PANDA crystal, that once again demonstrated that arsenic selected for and bound to the highly inert PANDA (
Based on our crystal structures, we reasoned that arsenic is attracted by the inert PANDA Cysteines on PANDA Pocket over reactive cysteines that are more readily available, such as C277 and C182, may be due to arsenic's prefers to bind tri-cysteines clusters over bi-cysteine dusters and mono-cysteines. Consistent with this theory, it has been reported that arsenic prefers to bind Zinc finger domains containing 3 and 4 cysteines (CCCC-Zinc finger and CCHC-Zinc finger) rather than CCHH-Zinc finger domain, which contains 2 cysteines (Zhou et al., 2011). Accordingly, we evaluated arsenic's binding potential to other tri-cysteine clusters, such as the zinc region composed of C176/C238/C242 (“Zinc Region”).
There are many reasons that this Zinc Region is an ideal site for arsenic. First, the Zinc Region harbors three of the mp53 mutation hotspots, namely, R175, G245, and R249. These mutation hotspots are more efficiently structurally rescued by As2O3 as compared to other mp53s, such as mp53-R282W (
Surprisingly, despite these promising characteristics, our studies show that the arsenic atom did not bind to the Zinc Region on our PANDA crystal structure. This is the case even when we depleted zinc atoms using EDTA to promote arsenic binding (data not shown). Instead, our studies show that arsenic binds to the deeply buried Site on the PANDA Pocket. Our results show that arsenic's cysteine selectivity is nontrivial. Selectivity of arsenic to p53's cysteines is not simply based on accessibility of an individual cysteine, and it is not simply based on the presence of tri-cysteine clusters. This is true even when a ti-cysteine site can attract and form bonds with other metallic elements, such as zinc.
Our results emphasize that the PANDA Triad (C124/C135/C141) and PANDA Pocket we discovered are special and unique for arsenic and its analogues.
The 3D structure of p53 has been solved for over 24 years and hundreds of different-size pockets can be visually identified on its surface. However, none of them are experimentally tested to be functional. Here, we identified the PANDA Triad to locate below a pocket spanning L1 loop, S2 sheet, and S3 loop of p53, which we designated as L1-S2-S3 pocket. This L1-S2-S3 pocket is previously named as L1-S3 pocket or L1/S3 pocket (Joerger and Fersht, 2016; Wassman et al., 2013).
Many of the previously reported compounds were predicted to bind to C124 of L1-S2-S3 pocket in a computer modelling (Joerger and Fersht, 2016; Wassman et al., 2013). Most of the agents used clinically contain about 10-100 atoms, as are the previously reported mp53 rescue compounds. The L1-S2-S3 pocket is relatively small so that the previously reported mp53 rescue compounds can only enter into it occasionally, only when it is open (
Our single atom PANDA Agent, such as the single arsenic atom, is fundamentally different from any of clinically using agents and the previously reported mp53 rescue compounds by the fact that it is just a single atom. Arsenic atom is smaller than any of the reported mp53 rescue compounds by one or two orders of magnitude (about 1/10- 1/100 size of reported compounds). It is so small that it can freely enter into L1-S2-S3 pocket at any time, even when it is closed (
We further discovered that arsenic stabilizes mp53 by immobilizing PANDA Pocket. Taking advantage of the atom-level rationale of how mp53 is stabilized by arsenic, we further discovered that PANDA Pocket is in fact a key switch that controls mp53 stability. More importantly, it can be utilized to identify p53 rescue agents (or PANDA Agents).
By analyzing the intramolecular interaction between the residues of PANDA Pocket (
Many SSSMs were previously identified by sequence evolutional analysis or function-guided screening in the past two decades (Baroni et al., 2004; Nikolova et al., 1998). Interestingly the majority of reported SSSMs locate near PANDA Pocket. Moreover, our rationally designed and discovered batch of SSSMs efficiently rescued Structural mp53, stabilizing the PANDA Pockets and demonstrating the discovery of a novel method of using arsenic compounds to rescue Structural mp53s by immobilizing PANDA Pocket.
The L1 loop (F113-T123) on the top of PANDA Pocket is particularly interesting because it is a coldspot for cancer mutation (IACR, http://p53.iarc.fr/TP53SomaticMutations.aspx) and it is the most dynamic DNA-binding element (Lukman et al., 2013). Notably, mutations on these residues frequently boost p53's function, again supporting our findings that manipulating PANDA Pocket is able to rescue mp53.
In brief, we discovered a PANDA Pocket that is a key switch in controlling mp53 stability. PANDA Pocket locates at the “dorsal end of PANDA” (
With insights of the PANDA Pocket, extremely high efficiency of tri-cysteine binding arsenic in rescuing mp53s, and the MOA of arsenic, we conducted an ultra-large C4+ Screening. We predicted thousands of compounds have the potential to efficiently bind 3 or more cysteines and thus act as efficient mp53 rescuers (Table 1-Table 6). We randomly selected some compounds from Table 1-Table 6, together with some compounds with only one or two cysteine-binding potential and experimentally confirmed 31 mp53 recusing agents with key supporting data (rescue mp53's structure; rescue mp53's transcriptional activity). They are listed in Table 7.
We discovered that Sb and Bi compounds, like arsenic compounds, can also rescue mp53s (Table 7). We confirmed in mass spectroscopy that As, Sb and Bi can directly and covalently bind mp53 (
We further discovered that organic As, Sb, and/or Bi containing compounds can also efficiently rescue mp53s (Table 7).
We further discovered that both 3-valence and 5-valence As, Sb, and/or Bi containing compounds can efficiently rescue mp53s.
We further discovered one of the prerequisite of being an efficient mp53 rescuer is tri-cysteine binding capacity. For example, NSC43800 (which can simultaneously binds 3-4 cysteines) rescues the transcriptional activity of mp53 with higher efficiency than NSC721951 (which can only bind 1 cysteine).
Worth noting here is that the ability of organic As, Sb, and/or Bi to efficiently rescue mp53 through the PANDA Pocket, despite the limited space in the PANDA Triad is unlikely to accommodate an organic compound, particularly those with a benzene, suggest that the cysteine binding potential of arsenic is so strong that it can robustly insert into the small space in PANDA Triad, probably leaving bulky organic groups, such as benzenes, in the L1-S2-S3 pocket and outside of the PANDA Triad. Moreover, it is possible that more profound influence on the mp53's structure may be going on when organic arsenic is bounded.
We further found that As, Sb, and/or Bi compounds with mono-cysteine binding potential (e.g.: NSC721951) or bi-cysteine binding potential (e.g.: NSC92909) can also rescue mp53's structure and transcriptional activity. When compared to compounds with cysteine binding potential, we found that compounds with three or more cysteine binding potential have the highest rescue efficiency, followed by compounds with bi-cysteine binding potential, and followed by compounds with mono-cysteine binding potential (
The discovery of compounds containing Bi and/or Sb, and organic As, Sb, and/or Bi compounds with mp53 rescue capacity has tremendous clinical value because these compounds generally have lower toxicities than inorganic As compounds in the body.
We conducted a small scale trial treating patients harboring ATO-rescuable mp53s. We conclude that ATO is a PANDA Agent with definite effectiveness and mp53 selectivity Based on current finding, two large-scale multi-center prospective trials on AML/MDS patients have been carried out (NCT03381781 and NCT03377725).
Since our 4C Screening identified ATO as a PANDA Agent, we studied whether ATO directs proper folding of the unfolded population of p53. Using an antibody specific to the properly folded wtp53, PAb1620, we immunoprecipitate (“IP”) properly folded p53s. Consistent with our predictions, we found wtp53 and Contacting mp53s, such as p53-R273H/C, to be largely folded (See
The ability of ATO to fold mp53 was further supported using two other p53 conformation-specific antibodies, the PAb246 antibody specific to properly folded p53 (for mouse p53) and the PAb240 antibody specific to unfolded p53 (
We also carefully characterized the ATO mediated mp53 folding under a variety of conditions. We found that 0.1 μg/ml of ATO was sufficient to properly fold some mp53s (
One of our focuses is p53-R175H, the most frequent individual mp53 found in cancers and the most representative Structural mp53 (Freed-Pastor and Prives, 2012). We carefully compared the ATO mediated mp53 folding efficiency to previously reported rescue compounds such as PRIMA-1, NSC319726, Ellipticine, STIMA, PhKan083, and others (
We observed an 1.9 times increase in the properly folded population of p53-R175H as measured by PAb1620 upon PRIMA-1 treatment (see
Very strikingly, we observed ATO increased the properly folded population of human p53-R175H by about 74 times, as measured by PAb1620. (See
Because of the low kinetic stability of mp53, others have proposed that a compound rescuing the structure of mp53 must act immediately upon mp53 translation (Joerger and Fersht, 2007). We tested this hypothesis by pre-treating cells with the translation-inhibitor cycloheximide (“CHX”), so that p53-R175H stays at its unfolded or denaturing status. We also confirmed that the CHX pre-treatment efficiently blocked p53 translation in our system (See
Others have reported that stabilizing p53 in its native state can inhibit p53 aggregation (Bullock et al., 1997). Here, we discovered that ATO mediated stabilization reduces the number of p53-R175H aggregates (See
Arsenic was reported to bind multiple closely spaced cysteines rather than single cysteine on peptides (Donoghue et al., 2000). Accordingly, we explored As-mediated mp53 folding. We studied all of the three pairs of cysteines, including C135/C141, C238C242, and C275/C277, and the cysteine neighboring R175, namely C176 (see
The characteristics of ATO mediated folding include:
(a) able to properly fold all tested Structural hotspot mp53s with a range of efficiency, including high to extremely high efficiency;
(b) instant folding (<15 min);
(c) folding is independent of cell types and treatment contexts, including resistant to EDTA in IP buffer;
(d) folding is much more efficient than any of the reported compounds;
(e) p53-R175H is almost fully restored as measured by the PAb1620 epitope;
(f) efficient for both human mp53 and mouse mp53;
(g) works in both mammalian cells and bacterial cells;
(h) can fold mp53 that has been previously unfolded;
(i) inhibits mp53 aggregation; and
(j) Cys135 and Cys141 are involved in As-mediated mp53 folding.
Since As is able to properly fold Structural mp53s rapidly and effectively, we studied whether As directly interacted with p53-R175H. We treated p53s with biotin-labeled As (“Bio-As”) (Zhang et al., 2010), pulled down Bio-As to determine any As associated complexes. (See
We further tested the selectivity of arsenic among cellular p53s. We labelled arsenic atom with biotin to form biotin-As and incubated the biotin-As with cells expressing a variety of p53s. We then lysed the cells and pulled down biotin-As for by immunoblotting. Our results show that biotin-As prefers to bind Structural mp53s rather than Contacting mp53s (
When the binding efficiency between biotin-As and p53-R175H or wtp53 is carefully titrated, it was found that biotin-As bound p53-R175H with at least 10 times higher efficiency than wtp53 (
The biotin-As relevant data needs to be carefully evaluated because a bond for cysteine binding on biotin-As is occupied by biotin, and thus the results may not precisely reflect the selectivity of ATO on wtp53 and mp53s. These data implies a potential arsenic selectively binding unfolded mp53s rather than folded mp53s and wtp53s.
We further discovered that cysteine is involved in As mediated PANDA formation. For example, we found that treatments with Bio-Dithi-As, a compound where As is protected by dithiols and cannot bind to cysteines (Heredia-Moya and Kirk, 2008), cannot pull down p53-R175H. (See
To further characterize PANDA, a fusion protein combining a recombinant GST and the full-length p53-R175H (“GST-p53-R175H”) was expressed in bacteria, purified, and then incubated with Bio-As in vitro. Remarkably, using this method, we discovered an As-Biotin-GST-p53-R175H complex that survived protein denaturation and protein electrophoresis, such as SDS-PAGE. (See
We further determined the direct and covalent interaction between the core domain of p53 and compounds containing As, Sb, or Bi. We expressed a recombinant wtp53 core (“wtp53(62-292)”) and a recombinant mp53 core (“mp53(91-292)-R175H”) in the presence of ZnSO4 and ATO, respectively. We then purified these core fragments and determined their molecular weight by mass spectroscopy (“MS”). In their native conditions, the molecular weight of wtp53(62-292) and mp53(91-292)-R175H are higher than expected, at approximately 64 Da and approximately 69 Da higher, respectively. This supports the formation of wtp53(62-292)/Zn complexes and mp53(91-292)-R175H/As complexes at 1:1 p53:metal ratio. (See
We further confirmed that As binds to p53 in an 1:1 ratio by inductively coupled plasma mass spectroscopy (“ICP-MS”). For example, our results not only show that As binds covalently to p53s, but that each p53 binds to approximately one As atom (0.93±0.19 As per p53). (See
The characteristics of PANDA-forming reactions include the following:
(a) prefers to bind Structural mp53;
(b) works for both human mp53 and mouse mp53;
(c) works in both mammalian cells and bacterial cells;
(d) works in vivo (in cells) and in vitro (in reaction buffer)
(e) mp53 cysteine(s) are involved;
(f) reaction is in a 1:1 molar ratio between mp53 and As atom
(g) direct reaction; and
(h) covalent reaction.
Since As mediates PANDA formation and efficiently rescues the structure of p53s, we further examined the DNA binding and transcriptional activity of PANDA.
5.22.1 PANDA Regains Wildtype DNA-Binding Ability
We biotin labelled a wide range of p53 targets and p53-binding consensus sequence and found that a wide range of PANDAs, including PANDA formed from p53-R175H (“PANDA-R175H”), can bind a wide range of p53 targets. For example, we showed that PANDA, including PANDA formed from p53-R175H can bind to MDM2, which is involved in p53 self-regulation; CDKN1A, which encoding p21 protein and is involved in senescence, invasion, metastasis, cell stemness and cell cycle arrest; PIG3, which is involved in apoptosis; PUMA, which is involved in apoptosis; BAX, which is involved in apoptosis; and the p53-binding consensus sequence. (See
When we measured the ability of As2O3 to rescue p53 transcriptional activities in luciferase assays, we discovered PANDAs significant enhanced the transcription activities p53 targets, such as PUMA, CDKN1A and MDM2 in the luciferase assay. (See
Comparing to other rescue agents, we found that ATO mediated PANDA formation is a far more superior rescue agent for p53 transcriptional activity. In particular, we found the other rescue agents measured at negligible for SCH529074, negligible PhiKan083, negligible for MIRA-1, negligible for PRIMA-1, 1.5 times for NSC319726, 1.5 times for CP31398, negligible for RITA, negligible for STIMA-1 and 3.3 times for Ellipticine and 21 times for ATO. (See
5.22.2 PANDA Dramatically Increases Wildtype Transcriptional Activities
In particular, we found the other rescue agents measured at negligible for SCH529074, negligible PhiKan083, negligible for MIRA-1, negligible for PRIMA-1, 1.5 times for NSC319726, 1.5 times for CP31398, negligible for RITA, negligible for STIMA-1 and 3.3 times for Ellipticine and 21 times for ATO. (See
PANDA dramatically increases p53 downstream mRNA production levels in cells expressing exogenous mp53s or endogenous mp53s. Adding ATO to H1299 cells expressing exogenous p53-R175H can dramatically stimulate the levels of p53 downstream mRNAs, including MDM2, PIG3, PUMA, CDKN1A, and BAX in 24 hr. Expectedly, the wtp53-stimulating Nutlin significantly enhanced PUMA, PIG3, CDKN1A and MDM2 mRNA levels in HCT116 cells expressing wtp53.
Adding ATO to BT549 cells expressing endogenous p53-R249S can dramatically stimulate the levels of p53 downstream mRNAs, including PUMA and CDKN1A. (
At the protein level, PANDA can dramatically increase p53 downstream protein production levels in cells expressing mp53. For example, by adding ATO to cells that express mp53s, such as H1299 cells, which expresses p53-R175H, we detected an increase in p53 targets (i.e. downstream proteins), such as PUMA, BAX, PIG3, p21, and MDM2 (See
We further discovered, for the first time, that PANDAs, such as PANDA-R175H, not only regain wtp53 transcriptional activity, but that they regain wtp53 tumor suppressive abilities in vitro and in vivo, including in xenograft models. We found that combining ATO with p53-R175H expressing cells dramatically increased the sensitivity of mp53 expressing cells, such as H1299 cells, to cell death, suggesting that the formed PANDA-R175H plays a tumor-suppressive role in the cells by suppressing cell growth (See
To test whether ATO targets Structural mp53 to inhibit malignancies, we applied ATO to 10 cell lines with differing p53 status, including wtp53, p534 (null), truncated p53, p53-R249S, p53-R175L, and p53-R175H. Expectedly, the lines expressing Structural mp53 (R175 and R249) had lower IC50 of ATO treatment (ranging between 0.1-1 μg/ml) than those expressing wtp53 or null/truncated p53 (ranging between 0.5-10 μg/ml) (
We further analyzed 60 cell lines of the NCI60 drug screen project (Shoemaker, 2006). This independently performed NCI60 screen project supplies an unbiased cell line sensitivity profile, reflecting the association between compounds and genetic features of cell lines. We separated cell lines expressing ATO-rescuable mp53 (R175, G245, R249, and R282) and designated them as “Struc”. We also separated cell lines expressing wtp53 or null/splicing p53 that was not able to be rescued by ATO (designating these as “WT” and “Null”, respectively). We then pooled the remaining cell lines were pooled together due to uncertainty regarding their rescue potential and designated them as “Others”. We found that NSC92859 (ATO) selectively inhibited the cell lines harbouring structural mp53 by exhibiting a lower G150 (concentration causing 50% growth inhibition) (Shoemaker, 2006) (
We further found that the effects of PANDA to be synergetic to the effects of wtp53-reactivating agents, such as an MDM2 inhibitor or an MDM4 inhibitor, towards killing mp53-expressing cells. The ability of a p53 rescuer and a wtp53-reactivator to work synisgetically (or at least not antagonistically) is particularly important. One reason is because one of the first targets of a rescued mp53 include its negative regulators MDM2 and MDM4. MDM2, for example is a powerful inhibitor of p53 and functions to efficiently degrade p53. In other words, when mp53 is rescued, its level also decreases. Indeed, we found p53-R175H in Detroit 562 and CEM-C1 is downregulated by ATO treatment (
We found that the effect of the MDM2 inhibitor, Nutlin3, synergizes with the effects of ATO. (
Our finding is of significant clinical value because we showed that ATO can function in synergetic fashion with other cancer inhibition therapies, that combination anticancer therapy containing ATO has significant promises, and that ATO may increase the efficacy of the wtp53-reactivating agents, such as MDM2 inhibitors, many of which are currently under clinical trials.
We further discovered, for the first time, that PANDAs, such as PANDA-R175H, also regains wtp53 tumor suppressive abilities in vivo, including in xenograft models. For example, we discovered that ATO and PANDA suppresses tumors in vivo, in at least two xenograft models: the H1299 cells expressing tet-off-regulated p53-R175H (solid tumor) (
Using the H1299 system, we injected H1299 cells subcutaneously to mouse treated with and without 5 mg/kg of ATO. We discovered that at day 28, the tumors were suppressed by over 90% according to both tumor size and tumor weight. (See
Using the hematological CEM-C1 system, we xenografted CEM-C1 cells to mouse on day 1 by intravenously injecting the cells. We were able to detect the xenographed CEM-C1 cancer cells in the mouse peripheral blood (“PB”) on day 22 (See
Taken together, we demonstrated here that ATO and PANDA significantly suppresses solid tumor and hematocancer in vivo and extends the life of subjects.
To study the combination therapeutic effect of ATO, we studied the effect of widely used DNA-damaging agents in the presence or absence of ATO.
mp53 is associated with considerably poor overall survival and prognosis of a wide range of cancers, including myeloid leukemia (AML/MDS) patients (Cancer Genome Atlas Research et al., 2013; Lindsley et al., 2017). Under NCCN guidelines, the majority of recommended AMLMDS treatments, aside from APL, are DNA-damaging agents. These DNA-damaging agents are known to activate wtp53 function to kill cancer cells through p53 post-translational modifications (“PTM”s) (Murray-Zmijewski et al., 2008). These PTMs include, for example, phosphorylation, acetylation, sumoylation, neddylation, methylation, and ubiquitylation.
Notably, we discovered that mp53 (for example, p53-R175H) and PANDA (for example, PANDA-R175H) responded differently to the DNA-damaging agents, such as Cisplatin, Etoposide, Adriamycin/Doxorubicin, 5-Fluorouracil, Cytarabine, Azacitidine, Decitabine, and Paclitaxel, suggesting they may trigger distinctly treatment outcomes. We discovered Ser15, Ser37, and Lys382 were inertly modified on p53-R175H upon DNA-damaging treatment; however, they are actively modified on PANDA-R175H upon DNA-damaging treatment (we designated such PTM as type #1 PTM) (
The identification of type #1 PTM and type #2 PTM suggests p53-R175H and PANDA-R175H distinctly respond to therapies and thus may trigger distinctly treatment outcomes (
In addition to showing that combination therapy of ATO and DNA-damaging agents can stimulate mp53 PTM and thus reactivate mp53, we showed that the PTM differences between p53-R175H and structurally rescued PANDA-R175H supports the previously notion that Contacting mp53 (also for wtp53) differed from Structural mp53 in phosphorylation potential under DNA-damaging stress (Gillotin et al., 2010).
We further discovered that ATO and PANDA are effective in treating AMLMDS patients.
For example, we tested the therapeutic effect of treating AML/MDS patients with a combination of ATO and DNA-damaging agents. In one of our clinical trials, 50 AML/MDS patients were recruited for TP53 exome sequencing (
We also discovered a third patient, R273L, which expressed p53-R273L and found that this mp53 behaves like a wtp53 and its PAb1620 epitope cannot be further enhanced by ATO at both 4° C. and physiological temperature (37° C.) (
Focusing on S241, we substituted all possible amino acids into this position and discovered that p53-S241R/N/C/Q/LF were ATO rescuable as demonstrated from their properly folded PAb1620 epitope as well as PUMA and p21 inducing ability (
The resultant p53-S241A is not an obvious structural mp53 and thus it fails to be rescued by ATO (
To further extend the finding, we tested at least 35 AML/MDS-derived mp53s in vitro and discovered that ATO can rescue the structure of these mp53 with a diversity of efficiency.
We thus selected the two ATO-rescuable MDS patients expressing p53-S241F and p53-S241C (but not the patient expressing p53-R274L) in the trial to test the combination therapeutic effects of ATO and a cytidine analog used as a first-line drug in MDS patients, such as Decitabine (“DAC”, a compound that binds to DNA and damages and also demethylates DNA), and discovered a remarkable, complete remission in both patients. Compared with standard first-line DAC regimen, we discovered mp53 expressing patients to benefit more from a combination regimen of ATO and clinically using drugs, such as DAC, as judged from their extended relapse-free survival time to about 11 months. Taken together, we have confirmed that ATO and PANDA are effective in treating cancer patients, such as AML/MDS patients, particularly those harboring PANDA-rescuable mp53s. We further discovered that treatment can be enhanced by first sequencing p53 status and then selecting patients with mp53 mutations on residues most responsive to ATO, such as mutations on S241C and S241F.
pcDNA3.1 expressing human full length p53 was gift from Prof. Xin Lu (the University of Oxford), pGEX-2TK expressing fusion protein of GST and human full length p53 was purchased from Addgene (#24860), pET28a expressing p53 core was cloned for crystallization experiment without introducing any tag.
Primary antibodies were purchased from the following companies: D01 (ab1101, Abcam), PAb1620 (MABE339, EMD Millipore), PAb240 (OP29, EMD Millipore), PAb246 (sc-100, Santa Cruz), PUMA (4976, Cell signaling), PIG3 (ab96819, Abcam), BAX (sc-493, Santa Cruz), p21 (sc-817, Santa Cruz), MDM2 (OP46-100UG, EMD Millipore), Biotin (ab19221, Abcam), Tubulin (ab11308, Abcam), β-actin (A00702, Genscript), p53-S15 (9284, Cell signaling), p53-S20 (9287, Cell signaling), p53-S37 (9289, Cell signaling), p53-S392 (9281, Cell signaling), p53-K382 (ab75754, Abcam), KU80 (2753, Cell signaling). CM5 antibody was gift from Prof. Xin Lu. HRP conjugated secondary antibody specifically reacts with light chain was from Abcam (ab99632).
H1299 and Saos-2 cell lines expressing null p53 was gift from Prof. Xin Lu. H1299 cell lines expressing tet-off regulated p53-R175H or tet-on regulated wtp53 were prepared as reported previously (Fogal et al., 2005). MEFs were prepared from E13.5 TP53−/− and TP53-R172H/R172H embryos. The other cell lines were obtained from ATCC.
Compounds were purchased from the following companies: DMSO (D2650, sigma), CP31398 (PZ0115, sigma), Arsenic trioxide (202673, sigma), STIMA-1 (506168, Merck Biosciences), SCH 529074 (4240, Tocris Bioscience), PhiKan 083 (4326, Tocris Bioscience), MiRA-1 (3362, Tocris Bioscience), Ellipticine (3357, Tocris Bioscience), NSC 319726 (S7149, selleck), PRIMA-1 (S7723, selleck), RITA (NSC 652287, S2781, selleck), Cydoheximide (C7698, sigma), Biotin (A600078, Sangon Biotech), Doxycycline hydate (D9891, sigma), Cisplatin (CIS, P4394, sigma), Etoposide (ETO, E1383, sigma), Adriamycin (ADM, S1208, selleck), 5-Fluorouracil (5-FU, F6627, sigma), Cytarabine (ARA, S1648, selleck), Azacitidine (AZA, A2385, sigma), Decitabine (DAC, A3656, sigma), Paclitaxel (TAX, S1150, selleck). Bio-As and Bio-Dithi-As were gift from Kenneth L. Kirk (NIH; PMID: 18396406).
The TP53 wild-type mice, female nude mice and NOD/SCID mice were obtained from the Shanghai Laboratory Animal Center, Chinese Academy of Sciences. TP53-R172H/R172H mice were generated from the parent mice (026283) purchased from Jackson Lab. TP53−/− mice (002101) were purchased from National Resource Center of Model Mice of China.
DNA samples were sequenced in rainbow-genome technique Ltd (Shanghai) and Shanghai Biotechnology corporation (Shanghai).
Constructions expressing recombinant p53 core were transformed into E. coli strain BL21-Gold. Cells were cultured in either LB or M9 medium at 37° C. to mid-log phase. 0.5 mM isopropyl-β-D-thiogalactopyranoside (IPTG) was added in presence/absence of 50 μM As/Sb/Bi and 1 mM ZnCl2 at 25° C. for overnight. Cells were harvested by centrifugation at 4 000 RPM for 20 minutes (˜10 g cell paste yielded from 1 liter of medium) and then sonicated in lysate buffer (50 mM Tris, pH 7.0, 50 mM NaCl, 10 mM DTT and 1 mM phenylmethylsulfonyl fluoride) in presence/absence of 50 μM As/SbBi. Soluble lysate was loaded onto a SP-Sepharose cation exchange column (Pharmacia) and eluted with a NaCl gradient (0-1 M) then, if necessary, additionally purified by affinity chromatography with a heparin-Sepharose column (Pharmacia) in Tris.HCl, pH 7.0, 10 mM DTT with a NaCl gradient (0-1 M) for elution. Future purification was performed by gel-filtration using Superdex 75 column using standard procedure.
Processes after cell lysing are done at 4° C. Protein concentration was measured spectrophotometrically by using an extinction coefficient of 16 530 cm−1M−1 at 280 nm. All protein purification steps were monitored by 4-20% gradient SDS-PAGE to ensure they were virtually homogeneous.
Constructions expressing GST-p53 (or GST-mp53) were transformed into E. coli strain BL21-Gold. Cells were grown in 800 ml LB medium at 37° C. to mid-log phase. 0.3 mM IPTG with/without 50 μM As/Sb/Bi was added at 16° C. for 24 h. Cells were harvested by centrifugation at 4 000 RPM for 20 minutes and then sonicated in 30 ml lysate buffer (58 mM Na2HPO4.12H2O, 17 mM NaH2 PO4.12H2O, 68 mM NaCl, 1% Triton X-100) in presence/absence of 50 μM As/Sb/Bi. Cell supernatant after 9000 RMP for 1 hour was added with 400 μl glutathione beads (Pharmacia) and incubated overnight. Beads were washed with lysate buffer for 3 times. Recombinant protein was then eluted by 300 μl elution buffer (10 mM GSH, 100 mM NaCl, 5 mM DTT and 50 mM Tris-HCl, pH 8.0). Processes after cell lysing are done at 4° C. All protein purification steps were monitored by 4-20% gradient SDS-PAGE to ensure they were virtually homogeneous.
Baculovirus infected Sf9 cells expressing recombinant human full-length p53 or p53 core in presence/absence of 50 μM As/Sb/Bi were harvested. They lysed in lysate buffer (50 mM Tris-HCl, pH 7.5, 5 mM EDTA, 1% NP-40, 5 mM DTT, 1 mM PMSF, and 0.15 M NaCl) in presence/absence of 50 μM As/SbBi. The lysates were then incubated on ice for 30 min, followed by centrifuging at 13000 rpm for 30 min. The supernatant was diluted 4-fold using 15% glycerol, 25 mM HEPES, pH 7.6, 0.1% Triton X-100, 5 mM DTT and 1 mM Benzamidine. They were further filtered using a 0.45 mm filter, and purified by Heparin-Sepharose column (Pharmacia). Purified protein was then concentrated using YM30 Centricon (EMD, Millipore). All protein purification steps were monitored by 4-20% gradient SDS-PAGE to ensure they were virtually homogeneous.
PANDA can be efficiently formed by mixing p53, either purified p53 or p53 in cell lysate, with PANDA Agents. For example, in reaction buffer (20 mM HEPES, 150 mM NaCl, pH 7.5), we mixed purified recombinant p53 core and As/Sb/Bi compounds in a ratio ranging from 10:1-1:100 at 4° C. for overnight. The formed PANDA was then purified using dialysis to eliminate compounds.
50 μM purified recombinant protein GST-p53-R175H in reaction buffer (10 mM GSH, 100 mM NaCl, 5 mM DTT and 50 mM Tris-HCl, pH 8.0) was added with Biotin-As to obtain arsenic to p53 molar ratio of either 10:1 or 1:1. The mixture solution was incubated at 4° C. for overnight and then divided into three parts. Each part was subjected to SDS-PAGE, followed by Coomassie blue staining (5 μg GST-p53-R175H applied), p53 immunoblotting (0.9 μg GST-p53-R175H applied) or Biotin immunoblotting (5 μg GST-p53-R175H applied), respectively.
For immunoprecipitation, mammalian cells or bacteria cells were harvested and lysed in NP40 buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% NP40) with cocktail of protease inhibitors (Roche Diagnostics). Cell lysates were then sonicated for 3 times, followed by spinning at 13,000 RPM for 20 min. Supernatant was adjusted to a final concentration of 1 mg/ml total protein using 450 μl NP40 buffer and incubated with 20 μl protein G beads and 1-3 μg corresponding primary antibody for 2 hr at 4° C. The beads were washed for three times with 20-25° C. NP40 buffer at room temperature. After spinning down, the beads were boiled for 5 min in 2×SDS loading buffer, followed by Western blotting.
Cells were treated with 4 μg/ml Bio-As or Bio-dithi-As for 2 hours. Cells were lysed in NP40 buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% NP40) with cocktail of protease inhibitors (Roche Diagnostics). Cell lysates were then sonicated for 3 times, followed by spinning at 13,000 RPM for 1 hr. Supernatant was adjusted to a final concentration of 1 mg/ml total protein using 450 μl NP40 buffer and incubated with 20 μl streptavidin beads for 2 hr at 4° C., followed by bead washing and Western blotting.
To prepare double-stranded oligonucleotides, equal amount of complementary single stranded oligonucleotides were heated at 80° C. for 5 min in 0.25 M NaCl, followed by slow cooling to room temperature. Sequences of single stranded oligonucleotides were followed:
Cells were harvested and lysed in NP40 buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% NP40) with cocktail of protease inhibitors (Roche Diagnostics). Cell lysates were then sonicated for 3 times, followed by spinning at 13,000 RPM for 1 hr. Supernatant was adjusted to a final concentration of 1 mg/ml total protein using 450 μl NP40 buffer and incubated with 20 μl streptavidin beads (s-951, Invitrogen), 20 μmoles of biotinylated double-stranded oligonucleotides, and 2 μg of poly(dI-dC) (sc-286691, Santaz cruz). Lysates were incubated for 2 hr at 4° C., followed by bead washing and immunoblotting.
Immunoblotting was performed as reported previously (Lu et al., 2013).
Cells were plated at a concentration of 2×104 cells/well in 24-well plates, followed by transfection of luciferase reporter plasmids for 24 hr. All transfection contained 300 ng p53 expressing plasmid, 100 ng of luciferase reporter plasmid and 5 ng of Renilla plasmid per well. After agent treatment, cells were lysed in luciferase reporter assay buffer and determined using a luciferase assay kit (Promega). Activities of luciferase were divided by that of Renilla to normalize the transfection efficiency. For more details, see (Lu et al., 2013).
Treated cells were digested with trypsin. 100, 1000 or 10,000 cells/well were seeded in 12-well plates and kept in culture for 2-3 weeks. Fresh medium was replaced every three days.
Cells were lysed in either CHAPS buffer (18 mM 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonic acid in TBS) or M-PER buffer (78501, Invitrogen) containing DNase and protease inhibitors for 15 min at 4° C. or 37° C. Cell lysate was added with 20% glycerol and 5 mM Coomassie G-250 before loading into 3-12% Novex Bis-Tris gradient gels. The electrophoresis was performed at 4° C. according to the manufacturer's instructions. Proteins were transferred onto the polyvinylidene fluoride membranes and fixed with 8% acetic acid for 20 min. The fixed membranes were then air dried and destained with 100% methanol. Membranes were blocked for overnight with 4% BSA in TBS at 4° C. before immunoblotting.
Total RNA was isolated from cells using Total RNA Purification Kit (B518651, Sangon Biotech). 1 μg total RNA was reverse-transcribed using the GoScript®™ Reverse Transciptase System (A5001, Promega) following manufacturer's protocol. PCR was performed in triplicate using SYBR green mix (Applied Biosystems), and a ViiA™ 7 Real-Time PCR System (Applied Biosystems) under the following conditions: 10 min at 95° C. followed by 40 cycles of 95° C. for 15 s and 60° C. for 1 min. Specificity of the PCR product was checked for each primer set and samples from the melting curve analysis. Expression levels of targeted genes were normalized relative to levels of β-actin adopting comparative Ct method. The primer sequences are as follows: MDM2 forward 5′-CCAGGGCAGCTACGGTTTC-3′, reverse 5′-CTCCGTCATGTGCTGTGACTG-3′; PIG3 forward 5′-CGCTGAAATTCACCAAAGGTG-3′, reverse 5′-AACCCATCGACCATCAAGAG-3′; PUMA forward 5′-ACGACCTCAACGCACAGTACG-3′, reverse 5′-TCCCATGATGAGATTGTACAGGAC-3′; p21 forward 5′-GTCTTGTACCCTTGTGCCTC-3′, reverse 5′-GGTAGAAATCTGTCATGCTGG-3′; Bax forward 5′-GATGCGTCCACCAAGAAGCT-3′, reverse 5′-CGGCCCCAGTTGAAGTTG-3′; β-actin forward 5′-ACTTAGTTGCGTTACACCCTTTCT-3′, reverse 5′-GACTGCTGTCACCTTCACCGT-3′.
H1299 xenograft. H1299 cells expressing tet-off regulated p53-R175H (1*106 cells) suspended in 100 μl saline solution were subcutaneously injected into the flanks of 8-9 weeks old female nude mice. When the tumor area reached 0.1 cm (day 1), 5 mg/kg ATO were intraperitoneally injected 6 consecutive days per week. In DOX groups, 0.2 mg/ml doxycycline was added to drinking water. Tumor size was measured every 3 days with vernier callipers. Tumor volumes were calculated using the following formula: (L*W*W)/2, in which L represents the large diameter of the tumor, and W represents the small diameter. When tumor area reached ˜1 cm diameter in any group, mice were sacrificed and isolated tumors were weighed. The analysis of the differences between the groups was performed by Two-way RM ANOVA with Bonferroni correction.
CEM-C1 xenograft. 8-9 week old NOD/SCID mice were intravenously injected through the tail vein with 1*107 cells of CEM-C1 T-ALL cells (day 1). After engraftment, peripheral blood samples were obtained from the mice retro-orbital sinus every 3 or 4 days from day 16 to day 26. Residual red blood cells were removed using erythrocyte lysis buffer (NH4Cl 1.5 mM, NaHCO3 10 Mm, EDTA-2Na 1 mM). The isolated cells were double stained with PerCP-Cy5.5-conjugated anti-mouse CD45 (mCD45) (BD Pharmigenm, San Diego, Calif.) and FITC-conjugated anti-human CD45 (hCD45) (BD Pharmigen™, San Diego, Calif.) antibodies before flow cytometric analysis conducted. When the percent of hCD45+ cells in peripheral blood reached 0.1% one mice (day 22), ATO was prepared for injection. On day 23, 5 mg/kg ATO were intravenously injected via tail-vein in 0.1 ml saline solution 6 consecutive days per week. The comparison of the hCD45+ cells percent between the groups was performed by unpaired t test. The life-span of mice was analyzed by Log-rank (Mantel-Cox) test.
All statistical analysis was performed using GraphPad Prism 6.00 for Windows (La Jolla Calif., USA). The animals were housed in specific pathogen-free conditions. Experiments were carried out according to the National Institutes of Health Guide for Care and Use of Laboratory Animals.
We measured the melting curve of the purified p53 core domain R175H(94-293) recorded via differential scanning fluorimetry (DSF) at the indicated ratio of ATO in pH 7.5 HEPES buffer. (See
We further mixed ATO and the purified recombinant p53C (p53C-WT, p53C-R175H, p53C-G245S, p53C-R249S and p53C-R282W, 5 μM for each reaction) at the ratios indicated in
We further measured the melting curve of the purified p53 core domain R175H(94-293) recorded via differential scanning fluorimetry at the indicated ratio of ATO in pH 7.5 HEPES, 150 mM NaCl buffer. (See
We further mixed ATO and the purified recombinant p53C (p53C-WT, p53C-R175H, p53C-G245. p53C-R249S and p53C-R282W, 5 μM for each reaction) at the ratios in FIG. 70D in pH 7.5 HEPES, 150 mM NaCl buffer for overnight. Melting curves of the p53C were measured by DSF in pH 7.5 HEPES, 150 mM NaCl buffer. The apparent Tm of the p53C-R175H, p53C-G245S, p53C-R249S, and p53C-R282W can be raised by 1.0-5.1° C. by maximum in pH 7.5 HEPES, 150 mM NaCl buffer. The melting temperatures of p53 core were shown (mean±SD, n=3). (See
We further measured the melting curve of the purified p53 core domain (p53C-WT, p53C-G245S, p53C-R249S and p53C-R282W) via differential scanning fluorimetry at the indicated ratio of ATO in pH 7.5 HEPES buffer. (See
We further measured the melting curve of the purified p53 core domain (p53C-WT, p53C-G245S, p53C-R249S and p53C-R282W) via differential scanning fluorimetry at the indicated ratio of ATO in pH 7.5 HEPES, 150 mM NaCl buffer. (See
Together, our results showed that the melting temperature of the p53 incubated with ATO was recorded via differential scanning fluorimetry. The Tm of p53 incubated was raised in pH 7.5 HEPES buffer in the presence or absence of 150 mM NaCl. In HEPES buffer, Tm of the p53C-R175H, p53C-G245S, p53C-R249S, and p53C-R282W can be raised by for example, 6.5° C., 1.1° C., 3.7° C., and 4.7° C. respectively (
We transfected SaOS-2 cells with wtp53, p53-R273H or p53-R282W and were treated with 1 μg/ml ATO for 24 hr. Expression levels of the p53 targets were determined by RNA-sequencing. The heatmap of the fold change values (the indicated sample groups versus vector) of the reported 116 p53-activated targets were measured. (See
We further determined the function of formed PANDA among p53 targets using RNA sequencing (RNA-seq). It was found that, among the reported 116 genes p53-activated targets, the majority of the genes were up-regulated by PANDA-R282W, including the well-known p53 targets BBC3, BAX, TP5313, CDKN1A, and MDM2 (
Statistical analysis was carried out using Fisher's exact test (two-tailed) unless otherwise indicated. p values less than 0.05 were considered statistically significant unless otherwise indicated.
Wildtype human p53 isoform a (NCBI Reference Sequence: NP_000537.3 cellular tumor antigen p53 isoform a [Homo sapiens]; NCBI Reference Sequence: NP_001119584.1, NP_001119584.1 cellular tumor antigen p53 isoform a [Homo sapiens]), also known as p53 isoform 1 (UniProt database identifier: P04637-1, sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS≡Homo sapiens GN=TP53 PE=1 SV=4), also known as p53, full-length p53, and p53α. PANDA Cysteines are underlined.
Wildtype human p53 isoform b (NCBI Reference Sequence: NP_001119586.1, NP_001119586.1 cellular tumor antigen p53 isoform b [Homo sapiens]), also known as p53 isoform 2 (UniProt database identifier: P04637-2, sp|P04637-2|P53_HUMAN Isoform 2 of Cellular tumor antigen p53 OS=Homo sapiens GN=TP53), also known as p53β. PANDA Cysteines are underlined.
Wildtype human p53 isoform c (NCBI Reference Sequence: NP_001119585.1, NP_001119585.1 cellular tumor antigen p53 isoform c [Homo sapiens]) also known as p53 isoform 3 (UniProt database identifier P04637-3, sp|P04637-3|P53_HUMAN Isoform 3 of Cellular tumor antigen p53 OS=Homo sapiens GN=TP53), also known as p53γ. PANDA Cysteines are underlined.
Wildtype human p53 isoform g (NCBI Reference Sequence: NP_001119590.1, NP_001119590.1 cellular tumor antigen p53 isoform g [Homo sapiens]; NCBI Reference Sequence: NP_001263689.1, NP_001263689.1 cellular tumor antigen p53 isoform g [Homo sapiens]; NCBI Reference Sequence: NP_001263690.1, NP_001263690.1 cellular tumor antigen p53 isoform g [Homo sapiens]) also known as p53 isoform 4 (UniProt database identifier: P04637-4, sp|P04637-4|P53_HUMAN Isoform 4 of Cellular tumor antigen p53 OS=Homo sapiens GN=TP53), also known as A40p53α. PANDA Cysteines are underlined.
Wildtype human p53 isoform i (NCBI Reference Sequence: NP_001263625.1, NP_001263625.1 cellular tumor antigen p53 isoform i [Homo sapiens]), also known as p53 isoform 5 (UniProt database identifier P04637-5, sp|P04637-5|P53_HUMAN Isoform 5 of Cellular tumor antigen p53 OS=Homo sapiens GN=TP53), also known as A40p53β. PANDA Cysteines are underlined.
Wildtype human p53 isoform h (NCBI Reference Sequence: NP_001263624.1, NP_001263624.1 cellular tumor antigen p53 isoform h [Homo sapiens]), also known as p53 isoform 6 (UniProt database identifier: P04637-6, sp|P04637-6|P53_HUMAN Isoform 6 of Cellular tumor antigen p53 OS=Homo sapiens GN=TP53), also known as A40p53γ. PANDA Cysteines are underlined.
The following publications, references, patents and patent applications are hereby incorporated by reference in their entireties.
C
N
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2018/085190 | 4/28/2018 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/CN2018/070051 | Jan 2018 | US |
| Child | 16959906 | US |
