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Ma H, Murray JB, Luo H, Cheng X, Chen Q, Song C, Duan C, Tan P, Zhang L, Liu J, Morgan BA, Li J, Wan J, Baker LM, Finnie W, Guetzoyan L, Harris R, Hendrickson N, Matassova N, Simmonite H, Smith J, Hubbard RE, Liu G. PAC-FragmentDEL - photoactivated covalent capture of DNA-encoded fragments for hit discovery. RSC Med Chem 2022; 13:1341-1349. [PMID: 36426238 PMCID: PMC9667776 DOI: 10.1039/d2md00197g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/03/2022] [Indexed: 09/27/2023] Open
Abstract
We describe a novel approach for screening fragments against a protein that combines the sensitivity of DNA-encoded library technology with the ability of fragments to explore what will bind. Each of the members of the library consists of a fragment which is linked to a photoactivatable diazirine moiety. Split and pool synthesis combines each fragment with a set of linkers with the version of the library reported here containing some 70k different compounds, each with an individual DNA code. Incubation of the library with a protein sample is followed by photoactivation, washing and subsequent PCR and sequencing which allows the individual fragment hits to be identified. We illustrate how the approach allows successful hit fragment identification using only microgram quantities of material for two targets. PAK4 is a kinase for which conventional fragment screening has generated many advance leads. The as yet undrugged target, 2-epimerase, presents a more challenging active site for identification of hit compounds. In both cases, PAC-FragmentDEL identified fragments validated as hits by ligand-observed NMR measurements and crystal structure determination of off-DNA sample binding to the proteins.
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2
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Ding Y, Belyanskaya S, DeLorey JL, Messer JA, Joseph Franklin G, Centrella PA, Morgan BA, Clark MA, Skinner SR, Dodson JW, Li P, Marino JP, Israel DI. Discovery of soluble epoxide hydrolase inhibitors through DNA-encoded library technology (ELT). Bioorg Med Chem 2021; 41:116216. [PMID: 34023664 DOI: 10.1016/j.bmc.2021.116216] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 10/21/2022]
Abstract
Inhibition of soluble epoxide hydrolase (sEH) has recently emerged as a new approach to treat cardiovascular disease and respiratory disease. Inhibitors based on 1,3,5-triazine chemotype were discovered through affinity selection against two triazine-based DNA-encoded libraries. The structure and activity relationship study led to the expansion of the original 1,4-cycloalkyl series to related aniline, piperidine, quinoline, aryl-ether and benzylic series. The 1,3-cycloalkyl chemotype led to the discovery of a clinical candidate (GSK2256294) for COPD.
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3
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Kölmel DK, Zhu H, Flanagan ME, Sakata SK, Harris AR, Wan J, Morgan BA. Cover Picture: Employing Photocatalysis for the Design and Preparation of DNA‐Encoded Libraries: A Case Study (Chem. Rec. 4/2021). CHEM REC 2021. [DOI: 10.1002/tcr.202180401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Kölmel DK, Zhu H, Flanagan ME, Sakata SK, Harris AR, Wan J, Morgan BA. Employing Photocatalysis for the Design and Preparation of DNA‐Encoded Libraries: A Case Study. CHEM REC 2021; 21:616-630. [DOI: 10.1002/tcr.202000148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
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5
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Kung PP, Bingham P, Burke BJ, Chen Q, Cheng X, Deng YL, Dou D, Feng J, Gallego GM, Gehring MR, Grant SK, Greasley S, Harris AR, Maegley KA, Meier J, Meng X, Montano JL, Morgan BA, Naughton BS, Palde PB, Paul TA, Richardson P, Sakata S, Shaginian A, Sonnenburg WK, Subramanyam C, Timofeevski S, Wan J, Yan W, Stewart AE. Characterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library. ACS Med Chem Lett 2020; 11:1175-1184. [PMID: 32550998 DOI: 10.1021/acsmedchemlett.0c00029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/10/2020] [Indexed: 11/29/2022] Open
Abstract
Two novel compounds were identified as Naa50 binders/inhibitors using DNA-encoded technology screening. Biophysical and biochemical data as well as cocrystal structures were obtained for both compounds (3a and 4a) to understand their mechanism of action. These data were also used to rationalize the binding affinity differences observed between the two compounds and a MLGP peptide-containing substrate. Cellular target engagement experiments further confirm the Naa50 binding of 4a and demonstrate its selectivity toward related enzymes (Naa10 and Naa60). Additional analogs of inhibitor 4a were also evaluated to study the binding mode observed in the cocrystal structures.
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Ding Y, O’Keefe H, DeLorey JL, Israel DI, Messer JA, Chiu CH, Skinner SR, Matico RE, Murray-Thompson MF, Li F, Clark MA, Cuozzo JW, Arico-Muendel C, Morgan BA. Discovery of Potent and Selective Inhibitors for ADAMTS-4 through DNA-Encoded Library Technology (ELT). ACS Med Chem Lett 2015; 6:888-93. [PMID: 26288689 DOI: 10.1021/acsmedchemlett.5b00138] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022] Open
Abstract
The aggrecan degrading metalloprotease ADAMTS-4 has been identified as a novel therapeutic target for osteoarthritis. Here, we use DNA-encoded Library Technology (ELT) to identify novel ADAMTS-4 inhibitors from a DNA-encoded triazine library by affinity selection. Structure-activity relationship studies based on the selection information led to the identification of potent and highly selective inhibitors. For example, 4-(((4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-6-(((4-methylpiperazin-1-yl)methyl)amino)-1,3,5-triazin-2-yl)amino)methyl)-N-ethyl-N-(m-tolyl)benzamide has IC50 of 10 nM against ADAMTS-4, with >1000-fold selectivity over ADAMT-5, MMP-13, TACE, and ADAMTS-13. These inhibitors have no obvious zinc ligand functionality.
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Deng H, Zhou J, Sundersingh FS, Summerfield J, Somers D, Messer JA, Satz AL, Ancellin N, Arico-Muendel CC, (Sargent) Bedard KL, Beljean A, Belyanskaya SL, Bingham R, Smith SE, Boursier E, Carter P, Centrella PA, Clark MA, Chung CW, Davie CP, Delorey JL, Ding Y, Franklin GJ, Grady LC, Herry K, Hobbs C, Kollmann CS, Morgan BA, (Pothier) Kaushansky LJ, Zhou Q. Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library. ACS Med Chem Lett 2015; 6:919-24. [PMID: 26288694 DOI: 10.1021/acsmedchemlett.5b00179] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/21/2015] [Indexed: 12/27/2022] Open
Abstract
As a potential target for obesity, human BCATm was screened against more than 14 billion DNA encoded compounds of distinct scaffolds followed by off-DNA synthesis and activity confirmation. As a consequence, several series of BCATm inhibitors were discovered. One representative compound (R)-3-((1-(5-bromothiophene-2-carbonyl)pyrrolidin-3-yl)oxy)-N-methyl-2'-(methylsulfonamido)-[1,1'-biphenyl]-4-carboxamide (15e) from a novel compound library synthesized via on-DNA Suzuki-Miyaura cross-coupling showed BCATm inhibitory activity with IC50 = 2.0 μM. A protein crystal structure of 15e revealed that it binds to BCATm within the catalytic site adjacent to the PLP cofactor. The identification of this novel inhibitor series plus the establishment of a BCATm protein structure provided a good starting point for future structure-based discovery of BCATm inhibitors.
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Kollmann CS, Bai X, Tsai CH, Yang H, Lind KE, Skinner SR, Zhu Z, Israel DI, Cuozzo JW, Morgan BA, Yuki K, Xie C, Springer TA, Shimaoka M, Evindar G. Application of encoded library technology (ELT) to a protein–protein interaction target: Discovery of a potent class of integrin lymphocyte function-associated antigen 1 (LFA-1) antagonists. Bioorg Med Chem 2014; 22:2353-65. [DOI: 10.1016/j.bmc.2014.01.050] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/15/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022]
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9
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Deng H, Bernier SG, Doyle E, Lorusso J, Morgan BA, Westlin WF, Evindar G. Discovery of Clinical Candidate GSK1842799 As a Selective S1P1 Receptor Agonist (Prodrug) for Multiple Sclerosis. ACS Med Chem Lett 2013; 4:942-7. [PMID: 24900589 DOI: 10.1021/ml400194r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 08/27/2013] [Indexed: 02/06/2023] Open
Abstract
To develop effective oral treatment for multiple sclerosis (MS), we discovered a series of alkyl-substituted biaryl amino alcohols as selective S1P1 modulators. One exemplar is (S)-2-amino-2-(5-(4-(octyloxy)-3-(trifluoromethyl)phenyl)-1,3,4-thiadiazol-2-yl)propan-1-ol (10, GSK1842799). Upon phosphorylation, the compound (10-P) showed subnanomole S1P1 agonist activity with >1000× selectivity over S1P3. The alcohol 10 demonstrated good oral bioavailability and rapid in vivo conversion to 10-P. Dosed orally at 0.1 mg/kg, 10 significantly reduced blood lymphocyte counts 6 h postdose, and at 3 mg/kg, 10 achieved efficacy equivalent to FTY720 in the mouse EAE model of MS. Further pharmacokinetic/pharmacodynamic (PK/PD) study with cynomolgus monkeys indicated that, after oral dosing of 10 at 3.8 mg/kg, the active phosphate reached plasma levels that are comparable to FTY-720 phosphate (FTY-P) revealed in human clinical pharmacokinetics studies. On the basis of the favorable in vitro ADME and in vivo PK/PD properties as well as broad toxicology evaluations, compound 10 (GSK1842799) was selected as a candidate for further clinical development.
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10
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Arico-Muendel CC, Blanchette H, Benjamin DR, Caiazzo TM, Centrella PA, DeLorey J, Doyle EG, Johnson SR, Labenski MT, Morgan BA, O’Donovan G, Sarjeant AA, Skinner S, Thompson CD, Griffin ST, Westlin W, White KF. Orally active fumagillin analogues: transformations of a reactive warhead in the gastric environment. ACS Med Chem Lett 2013; 4:381-6. [PMID: 24900682 DOI: 10.1021/ml3003633] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/22/2013] [Indexed: 11/29/2022] Open
Abstract
Semisynthetic analogues of fumagillin, 1, inhibit methionine aminopeptidase-2 (MetAP2) and have entered the clinic for the treatment of cancer. An optimized fumagillin analogue, 3 (PPI-2458), was found to be orally active, despite containing a spiroepoxide function that formed a covalent linkage to the target protein. In aqueous acid, 3 underwent ring-opening addition of water and HCl, leading to four products, 4-7, which were characterized in detail. The chlorohydrin, but not the diol, products inhibited MetAP2 under weakly basic conditions, suggesting reversion to epoxide as a step in the mechanism. In agreement, chlorohydrin 6 was shown to revert rapidly to 3 in rat plasma. In an ex vivo assay, rats treated with purified acid degradants demonstrated inhibition of MetAP2 that correlated with the biochemical activity of the compounds. Taken together, the results indicate that degradation of the parent compound was compensated by the formation of active equivalents leading to a pharmacologically useful level of MetAP2 inhibition.
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Podolin PL, Bolognese BJ, Foley JF, Long E, Peck B, Umbrecht S, Zhang X, Zhu P, Schwartz B, Xie W, Quinn C, Qi H, Sweitzer S, Chen S, Galop M, Ding Y, Belyanskaya SL, Israel DI, Morgan BA, Behm DJ, Marino JP, Kurali E, Barnette MS, Mayer RJ, Booth-Genthe CL, Callahan JF. In vitro and in vivo characterization of a novel soluble epoxide hydrolase inhibitor. Prostaglandins Other Lipid Mediat 2013; 104-105:25-31. [PMID: 23434473 DOI: 10.1016/j.prostaglandins.2013.02.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 01/29/2013] [Accepted: 02/08/2013] [Indexed: 11/17/2022]
Abstract
Soluble epoxide hydrolase (sEH, EPHX2) metabolizes eicosanoid epoxides, including epoxyeicosatrienoic acids (EETs) to the corresponding dihydroxyeicosatrienoic acids (DHETs), and leukotoxin (LTX) to leukotoxin diol (LTX diol). EETs, endothelium-derived hyperpolarizing factors, exhibit potentially beneficial properties, including anti-inflammatory effects and vasodilation. A novel, potent, selective inhibitor of recombinant human, rat and mouse sEH, GSK2256294A, exhibited potent cell-based activity, a concentration-dependent inhibition of the conversion of 14,15-EET to 14,15-DHET in human, rat and mouse whole blood in vitro, and a dose-dependent increase in the LTX/LTX diol ratio in rat plasma following oral administration. Mice receiving 10 days of cigarette smoke exposure concomitant with oral administration of GSK2256294A exhibited significant, dose-dependent reductions in pulmonary leukocytes and keratinocyte chemoattractant (KC, CXCL1) levels. Mice receiving oral administration of GSK2256294A following 10 days of cigarette smoke exposure exhibited significant reductions in pulmonary leukocytes compared to vehicle-treated mice. These data indicate that GSK2256294A attenuates cigarette smoke-induced inflammation by both inhibiting its initiation and/or maintenance and promoting its resolution. Collectively, these data indicate that GSK2256294A would be an appropriate agent to evaluate the role of sEH in clinical studies, for example in diseases where cigarette smoke is a risk factor, such as chronic obstructive pulmonary disease (COPD) and cardiovascular disease.
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Arico-Muendel CC, Belanger B, Benjamin D, Blanchette HS, Caiazzo TM, Centrella PA, DeLorey J, Doyle EG, Gradhand U, Griffin ST, Hill S, Labenski MT, Morgan BA, O’Donovan G, Prasad K, Skinner S, Taghizadeh N, Thompson CD, Wakefield J, Westlin W, White KF. Metabolites of PPI-2458, a Selective, Irreversible Inhibitor of Methionine Aminopeptidase-2: Structure Determination and In Vivo Activity. Drug Metab Dispos 2013; 41:814-26. [DOI: 10.1124/dmd.112.048355] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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13
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Evindar G, Deng H, Bernier SG, Doyle E, Lorusso J, Morgan BA, Westlin WF. Exploring amino acids derivatives as potent, selective, and direct agonists of sphingosine-1-phosphate receptor subtype-1. Bioorg Med Chem Lett 2012; 23:472-5. [PMID: 23245510 DOI: 10.1016/j.bmcl.2012.11.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 11/11/2012] [Accepted: 11/14/2012] [Indexed: 11/19/2022]
Abstract
In the quest to discover a potent and selective class of direct agonists to the sphingosine-1-phosphate receptor, we explored the carboxylate functional group as a replacement to previously reported lead phosphates. This has led to the discovery of potent and selective direct agonists with moderate to substantial in vivo lymphopenia. The previously reported selectivity enhancing moiety (SEM) and selectivity enhancing orientation (SEO) in the phenylamide and phenylimidazole scaffolds were crucial to obtaining selectivity for S1P receptor subtype 1 over 3.
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14
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Deng H, O'Keefe H, Davie CP, Lind KE, Acharya RA, Franklin GJ, Larkin J, Matico R, Neeb M, Thompson MM, Lohr T, Gross JW, Centrella PA, O'Donovan GK, Bedard KLS, van Vloten K, Mataruse S, Skinner SR, Belyanskaya SL, Carpenter TY, Shearer TW, Clark MA, Cuozzo JW, Arico-Muendel CC, Morgan BA. Discovery of highly potent and selective small molecule ADAMTS-5 inhibitors that inhibit human cartilage degradation via encoded library technology (ELT). J Med Chem 2012; 55:7061-79. [PMID: 22891645 DOI: 10.1021/jm300449x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The metalloprotease ADAMTS-5 is considered a potential target for the treatment of osteoarthritis. To identify selective inhibitors of ADAMTS-5, we employed encoded library technology (ELT), which enables affinity selection of small molecule binders from complex mixtures by DNA tagging. Selection of ADAMTS-5 against a four-billion member ELT library led to a novel inhibitor scaffold not containing a classical zinc-binding functionality. One exemplar, (R)-N-((1-(4-(but-3-en-1-ylamino)-6-(((2-(thiophen-2-yl)thiazol-4-yl)methyl)amino)-1,3,5-triazin-2-yl)pyrrolidin-2-yl)methyl)-4-propylbenzenesulfonamide (8), inhibited ADAMTS-5 with IC(50) = 30 nM, showing >50-fold selectivity against ADAMTS-4 and >1000-fold selectivity against ADAMTS-1, ADAMTS-13, MMP-13, and TACE. Extensive SAR studies showed that potency and physicochemical properties of the scaffold could be further improved. Furthermore, in a human osteoarthritis cartilage explant study, compounds 8 and 15f inhibited aggrecanase-mediated (374)ARGS neoepitope release from aggrecan and glycosaminoglycan in response to IL-1β/OSM stimulation. This study provides the first small molecule evidence for the critical role of ADAMTS-5 in human cartilage degradation.
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Evindar G, Bernier SG, Doyle E, Kavarana MJ, Satz AL, Lorusso J, Blanchette HS, Saha AK, Hannig G, Morgan BA, Westlin WF. Exploration of amino alcohol derivatives as novel, potent, and highly selective sphingosine-1-phosphate receptor subtype-1 agonists. Bioorg Med Chem Lett 2010; 20:2520-4. [PMID: 20304639 DOI: 10.1016/j.bmcl.2010.02.098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 02/24/2010] [Accepted: 02/26/2010] [Indexed: 10/19/2022]
Abstract
In pursuit of a potent and highly selective sphingosine-1-phosphate receptor agonists with an improved in vivo conversion of the precursor to the active phospho-drug, we have utilized previously reported phenylamide and phenylimidazole scaffolds to identify a selectivity enhancing moiety (SEM) and selectivity enhancing orientation (SEO) within both pharmacophores. SEM and SEO have allowed for over 100 to 500-fold improvement in selectivity for S1P receptor subtype 1 over subtype 3. Utility of SEM and SEO and further SAR study allowed for discovery of a potent and selective preclinical candidate PPI-4955 (21b) with an excellent in vivo potency and dose responsiveness and markedly improved overall in vivo pharmacodynamic properties upon oral administration.
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Arico-Muendel CC, Benjamin DR, Caiazzo TM, Centrella PA, Contonio BD, Cook CM, Doyle EG, Hannig G, Labenski MT, Searle LL, Lind K, Morgan BA, Olson G, Paradise CL, Self C, Skinner SR, Sluboski B, Svendsen JL, Thompson CD, Westlin W, White KF. Carbamate analogues of fumagillin as potent, targeted inhibitors of methionine aminopeptidase-2. J Med Chem 2010; 52:8047-56. [PMID: 19929003 DOI: 10.1021/jm901260k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inhibition of methionine aminopeptidase-2 (MetAP2) represents a novel approach to antiangiogenic therapy. We describe the synthesis and activity of fumagillin analogues that address the pharmacokinetic and safety liabilities of earlier candidates in this compound class. Two-step elaboration of fumagillol with amines yielded a diverse series of carbamates at C6 of the cyclohexane spiroepoxide. The most potent of these compounds exhibited subnanomolar inhibition of cell proliferation in HUVEC and BAEC assays. Although a range of functionalities were tolerated at this position, alpha-trisubstituted amines possessed markedly decreased inhibitory activity, and this could be rationalized by modeling based on the known fumagillin-MetAP2 crystal structure. The lead compound resulting from these studies, (3R,4S,5S,6R)-5-methoxy-4-((2R,3R)-2-methyl-3-(3-methylbut-2-enyl)oxiran-2-yl)-1-oxaspiro[2.5]octan-6-yl (R)-1-amino-3-methyl-1-oxobutan-2-ylcarbamate, (PPI-2458), demonstrated an improved pharmacokinetic profile relative to the earlier clinical candidate TNP-470, and has advanced into phase I clinical studies in non-Hodgkin's lymphoma and solid cancers.
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Clark MA, Acharya RA, Arico-Muendel CC, Belyanskaya SL, Benjamin DR, Carlson NR, Centrella PA, Chiu CH, Creaser SP, Cuozzo JW, Davie CP, Ding Y, Franklin GJ, Franzen KD, Gefter ML, Hale SP, Hansen NJV, Israel DI, Jiang J, Kavarana MJ, Kelley MS, Kollmann CS, Li F, Lind K, Mataruse S, Medeiros PF, Messer JA, Myers P, O'Keefe H, Oliff MC, Rise CE, Satz AL, Skinner SR, Svendsen JL, Tang L, van Vloten K, Wagner RW, Yao G, Zhao B, Morgan BA. Erratum: Design, synthesis and selection of DNA-encoded small-molecule libraries. Nat Chem Biol 2009. [DOI: 10.1038/nchembio1009-772] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Arico-Muendel C, Centrella PA, Contonio BD, Morgan BA, O'Donovan G, Paradise CL, Skinner SR, Sluboski B, Svendsen JL, White KF, Debnath A, Gut J, Wilson N, McKerrow JH, DeRisi JL, Rosenthal PJ, Chiang PK. Antiparasitic activities of novel, orally available fumagillin analogs. Bioorg Med Chem Lett 2009; 19:5128-31. [PMID: 19648008 DOI: 10.1016/j.bmcl.2009.07.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 06/20/2009] [Accepted: 07/02/2009] [Indexed: 11/26/2022]
Abstract
Fumagillin, an irreversible inhibitor of MetAP2, has been shown to potently inhibit growth of malaria parasites in vitro. Here, we demonstrate activity of fumagillin analogs with an improved pharmacokinetic profile against malaria parasites, trypanosomes, and amoebas. A subset of the compounds showed efficacy in a murine malaria model. The observed SAR forms a basis for further optimization of fumagillin based inhibitors against parasitic targets by inhibition of MetAP2.
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19
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Evindar G, Satz AL, Bernier SG, Kavarana MJ, Doyle E, Lorusso J, Taghizadeh N, Halley K, Hutchings A, Kelley MS, Wright AD, Saha AK, Hannig G, Morgan BA, Westlin WF. Synthesis and evaluation of arylalkoxy- and biarylalkoxy-phenylamide and phenylimidazoles as potent and selective sphingosine-1-phosphate receptor subtype-1 agonists. Bioorg Med Chem Lett 2009; 19:2315-9. [DOI: 10.1016/j.bmcl.2009.02.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/17/2009] [Accepted: 02/19/2009] [Indexed: 11/26/2022]
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20
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Sedgwick SG, Morgan BA, Nguyen TM, Morris GE. An improved method for mapping epitopes of recombinant antigens by transposon mutagenesis. Methods Mol Biol 2003; 66:343-53. [PMID: 8959726 DOI: 10.1385/0-89603-375-9:343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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21
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Hu Y, Webb E, Singh J, Morgan BA, Gainor JA, Gordon TD, Siahaan TJ. Rapid determination of substrate specificity of Clostridium histolyticum beta-collagenase using an immobilized peptide library. J Biol Chem 2002; 277:8366-71. [PMID: 11724807 DOI: 10.1074/jbc.m111042200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular basis of the substrate specificity of Clostridium histolyticum beta-collagenase was investigated using a combinatorial method. An immobilized positional peptide library, which contains 24,000 sequences, was constructed with a 7-hydroxycoumarin-4-propanoyl (Cop) fluorescent group attached at the N terminus of each sequence. This immobilized peptide library was incubated with C. histolyticum beta-collagenase, releasing fluorogenic fragments in the solution phase. The relative substrate specificity (k(cat)/K(m)) for each member of the library was determined by measuring fluorescence intensity in the solution phase. Edman sequencing was used to assign structure to subsites of active substrate mixtures. Collectively, the substrate preference for subsites (P(3)-P(4)') of C. histolyticum beta-collagenase was determined. The last position on the C-terminal side in which the identity of the amino acids affects the activity of the enzyme is P(4)', and an aromatic side chain is preferred in this position. The optimal P(1)'-P(3)' extended substrate sequence is P(1)'-Gly/Ala, P(2)'-Pro/Xaa, and P(3)'-Lys/Arg/Pro/Thr/Ser. The Cop group in either the P(2) or P(3) position is required for a high substrate activity with C. histolyticum beta-collagenase. S(2) and S(3) sites of the protease play a dominant role in fixing the substrate specificity. The immobilized peptide library proved to be a powerful approach for assessing the substrate specificity of C. histolyticum beta-collagenase, so it may be applied to the study of other proteases of interest.
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22
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Stupian GW, Ives NA, Marquez N, Morgan BA. The application of lead isotope analysis to bullet individualization in two homicides. J Forensic Sci 2001; 46:1342-51. [PMID: 11714144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Bullets were characterized by lead isotope ratio analysis and trace element analysis in two homicides. In one case, we concluded that a fatal bullet did not share a common origin with bullets in a box of ammunition containing 24 cartridges taken from suspects. Evidence in the second case included two bullets from the crime scene and 163 bullets taken from various suspects. We were able to infer that the two bullets from the crime scene did not share a common origin and that they differed from all of the bullets taken from suspects. All of the suspects' ammunition had been reloaded as was evident both from trace and isotopic analysis and, indeed, from visual inspection.
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Abstract
Cells have evolved complex and efficient strategies for dealing with variable and often-harsh environments. A key aspect of these stress responses is the transcriptional activation of genes encoding defense and repair proteins. In yeast members of the AP-1 family of proteins are required for the transcriptional response to oxidative stress. This sub-family of AP-1 (called yAP-1) proteins are sensors of the redox-state of the cell and are activated directly by oxidative stress conditions. yAP-1 proteins are bZIP-containing factors that share homology to the mammalian AP-1 factor complex and bind to very similar DNA sequence sites. The generation of reactive oxygen species and the resulting potential for oxidative stress is common to all aerobically growing organisms. Furthermore, many of the features of this response appear to be evolutionarily conserved and consequently the study of model organisms, such as yeast, will have widespread utility. The important structural features of these factors, signaling pathways controlling their activity and the nature of the target genes they control will be discussed.
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Buck V, Quinn J, Soto Pino T, Martin H, Saldanha J, Makino K, Morgan BA, Millar JB. Peroxide sensors for the fission yeast stress-activated mitogen-activated protein kinase pathway. Mol Biol Cell 2001; 12:407-19. [PMID: 11179424 PMCID: PMC30952 DOI: 10.1091/mbc.12.2.407] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Schizosaccharomyces pombe stress-activated Sty1p/Spc1p mitogen-activated protein (MAP) kinase regulates gene expression through the Atf1p and Pap1p transcription factors, homologs of human ATF2 and c-Jun, respectively. Mcs4p, a response regulator protein, acts upstream of Sty1p by binding the Wak1p/Wis4p MAP kinase kinase kinase. We show that phosphorylation of Mcs4p on a conserved aspartic acid residue is required for activation of Sty1p only in response to peroxide stress. Mcs4p acts in a conserved phospho-relay system initiated by two PAS/PAC domain-containing histidine kinases, Mak2p and Mak3p. In the absence of Mak2p or Mak3p, Sty1p fails to phosphorylate the Atf1p transcription factor or induce Atf1p-dependent gene expression. As a consequence, cells lacking Mak2p and Mak3p are sensitive to peroxide attack in the absence of Prr1p, a distinct response regulator protein that functions in association with Pap1p. The Mak1p histidine kinase, which also contains PAS/PAC repeats, does not regulate Sty1p or Atf1p but is partially required for Pap1p- and Prr1p-dependent transcription. We conclude that the transcriptional response to free radical attack is initiated by at least two distinct phospho-relay pathways in fission yeast.
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Ross SJ, Findlay VJ, Malakasi P, Morgan BA. Thioredoxin peroxidase is required for the transcriptional response to oxidative stress in budding yeast. Mol Biol Cell 2000; 11:2631-42. [PMID: 10930459 PMCID: PMC14945 DOI: 10.1091/mbc.11.8.2631] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A genetic screen was performed in Saccharomyces cerevisiae to identify mechanisms important for the transcriptional activation of genes encoding antioxidant proteins. Thioredoxin peroxidase, Tsa1p, of the thioredoxin system, was found to be essential for the transcriptional induction of other components of the thioredoxin system, TRX2 (thioredoxin) and TRR1 (thioredoxin reductase), in response to H(2)O(2). The expression of TRX2 and TRR1 is known to be regulated by the transcription factors Yap1p and Skn7p in response to H(2)O(2), and the Tsa1p-dependent regulation of TRX2 requires the Yap1p/Skn7p pathway. The data suggest that expression of components of the thioredoxin system is dependent on the activity of Tsa1p in response to H(2)O(2) in a Yap1p/Skn7p-dependent pathway.
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