1
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Chai J, Arico-Muendel CC, Ding Y, Pollastri MP, Scott S, Mantell MA, Yao G. Synthesis of a DNA-Encoded Macrocyclic Library Utilizing Intramolecular Benzimidazole Formation. Bioconjug Chem 2023. [PMID: 37216465 DOI: 10.1021/acs.bioconjchem.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Macrocycles occupy chemical space "beyond the rule of five". They bridge traditional bioactive small molecule drugs and macromolecules and have the potential to modulate challenging targets such as PPI or proteases. Here we report an on-DNA macrocyclization reaction utilizing intramolecular benzimidazole formation. A 129-million-member macrocyclic library composed of a privileged benzimidazole core, a dipeptide sequence (natural or non-natural), and linkers of varying length and flexibility was designed and synthesized.
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Affiliation(s)
- Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Christopher C Arico-Muendel
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Michael P Pollastri
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sarah Scott
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Mark A Mantell
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Gang Yao
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
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2
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Abstract
Enzymatic catalysis is a highly attractive approach to the DNA encoded library technology (DEL) that has not been widely explored. In this paper, we report an l-threonine aldolase (l-TA)-catalyzed on-DNA aldol reaction to form β-hydroxy-α-amino acids, and its diastereoselectivity determination. l-TAs from three species show good on-DNA aldehyde scope and complementary stereoselectivity. The formed aldol product can be further diversified via various reactions, which demonstrates the utility of this reaction in DEL.
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Affiliation(s)
- Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Xiaojie Lu
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Christopher C Arico-Muendel
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Michael P Pollastri
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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3
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Machutta CA, Kollmann CS, Lind KE, Bai X, Chan PF, Huang J, Ballell L, Belyanskaya S, Besra GS, Barros-Aguirre D, Bates RH, Centrella PA, Chang SS, Chai J, Choudhry AE, Coffin A, Davie CP, Deng H, Deng J, Ding Y, Dodson JW, Fosbenner DT, Gao EN, Graham TL, Graybill TL, Ingraham K, Johnson WP, King BW, Kwiatkowski CR, Lelièvre J, Li Y, Liu X, Lu Q, Lehr R, Mendoza-Losana A, Martin J, McCloskey L, McCormick P, O'Keefe HP, O'Keeffe T, Pao C, Phelps CB, Qi H, Rafferty K, Scavello GS, Steiginga MS, Sundersingh FS, Sweitzer SM, Szewczuk LM, Taylor A, Fern Toh M, Wang J, Wang M, Wilkins DJ, Xia B, Yao G, Zhang J, Zhou J, Donahue CP, Messer JA, Holmes D, Arico-Muendel CC, Pope AJ, Gross JW, Evindar G. Author Correction: Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening. Nat Commun 2018; 9:16227. [PMID: 30004092 PMCID: PMC6054520 DOI: 10.1038/ncomms16227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This corrects the article DOI: 10.1038/ncomms16081.
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4
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Bao J, Krylova SM, Cherney LT, Hale RL, Belyanskaya SL, Chiu CH, Shaginian A, Arico-Muendel CC, Krylov SN. Predicting Electrophoretic Mobility of Protein–Ligand Complexes for Ligands from DNA-Encoded Libraries of Small Molecules. Anal Chem 2016; 88:5498-506. [DOI: 10.1021/acs.analchem.6b00980] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jiayin Bao
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M. Krylova
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Leonid T. Cherney
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Robert L. Hale
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451-8714, United States
| | | | - Cynthia H. Chiu
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451-8714, United States
| | - Alex Shaginian
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451-8714, United States
| | | | - Sergey N. Krylov
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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5
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Deng H, Zhou J, Sundersingh F, Messer JA, Somers DO, Ajakane M, Arico-Muendel CC, Beljean A, Belyanskaya SL, Bingham R, Blazensky E, Boullay AB, Boursier E, Chai J, Carter P, Chung CW, Daugan A, Ding Y, Herry K, Hobbs C, Humphries E, Kollmann C, Nguyen VL, Nicodeme E, Smith SE, Dodic N, Ancellin N. Discovery and Optimization of Potent, Selective, and in Vivo Efficacious 2-Aryl Benzimidazole BCATm Inhibitors. ACS Med Chem Lett 2016; 7:379-84. [PMID: 27096045 DOI: 10.1021/acsmedchemlett.5b00389] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/08/2016] [Indexed: 01/14/2023] Open
Abstract
To identify BCATm inhibitors suitable for in vivo study, Encoded Library Technology (ELT) was used to affinity screen a 117 million member benzimidazole based DNA encoded library, which identified an inhibitor series with both biochemical and cellular activities. Subsequent SAR studies led to the discovery of a highly potent and selective compound, 1-(3-(5-bromothiophene-2-carboxamido)cyclohexyl)-N-methyl-2-(pyridin-2-yl)-1H-benzo[d]imidazole-5-carboxamide (8b) with much improved PK properties. X-ray structure revealed that 8b binds to the active site of BACTm in a unique mode via multiple H-bond and van der Waals interactions. After oral administration, 8b raised mouse blood levels of all three branched chain amino acids as a consequence of BCATm inhibition.
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Affiliation(s)
- Hongfeng Deng
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jingye Zhou
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Flora Sundersingh
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jeffrey A. Messer
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Donald O. Somers
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, U.K
| | - Myriam Ajakane
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Christopher C. Arico-Muendel
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Arthur Beljean
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, U.K
| | - Svetlana L. Belyanskaya
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Ryan Bingham
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, U.K
| | - Emily Blazensky
- Chemistry
Department, Northeastern University, Boston, Massachusetts 02115, United States
| | - Anne-Benedicte Boullay
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Eric Boursier
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Jing Chai
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Paul Carter
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, U.K
| | - Chun-Wa Chung
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, U.K
| | - Alain Daugan
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Yun Ding
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Kenny Herry
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Clare Hobbs
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, U.K
| | - Eric Humphries
- Chemistry
Department, Northeastern University, Boston, Massachusetts 02115, United States
| | - Christopher Kollmann
- Platform
of Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Van Loc Nguyen
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Edwige Nicodeme
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Sarah E. Smith
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, U.K
| | - Nerina Dodic
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Nicolas Ancellin
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
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6
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Abstract
Innovation incubation: DNA encoded library technology (ELT) was invented in academia and biotech, but came of age in a big pharma environment.
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Hongfeng Deng
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jingye Zhou
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Flora S. Sundersingh
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer Summerfield
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Don Somers
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Jeffrey A. Messer
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Alexander L. Satz
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Nicolas Ancellin
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Christopher C. Arico-Muendel
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Katie L. (Sargent) Bedard
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Arthur Beljean
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Svetlana L. Belyanskaya
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Ryan Bingham
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Sarah E. Smith
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Eric Boursier
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Paul Carter
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Paolo A. Centrella
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Matthew A. Clark
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Chun-wa Chung
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Christopher P. Davie
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer L. Delorey
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Yun Ding
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - G. Joseph Franklin
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - LaShadric C. Grady
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Kenny Herry
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Clare Hobbs
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Christopher S. Kollmann
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Barry A. Morgan
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | | | - Quan Zhou
- Chemistry
Department, Brandeis University, Waltham, Massachusetts 02453, United States
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8
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Bao J, Krylova SM, Cherney LT, Hale RL, Belyanskaya SL, Chiu CH, Arico-Muendel CC, Krylov SN. Prediction of Protein–DNA Complex Mobility in Gel-Free Capillary Electrophoresis. Anal Chem 2015; 87:2474-9. [DOI: 10.1021/ac504504c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jiayin Bao
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M. Krylova
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Leonid T. Cherney
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Robert L. Hale
- GlaxoSmithKline, 343 Winter Street, Waltham, Mississippi 02451-8714, United States
| | | | - Cynthia H. Chiu
- GlaxoSmithKline, 343 Winter Street, Waltham, Mississippi 02451-8714, United States
| | | | - Sergey N. Krylov
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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9
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Encinas L, O'Keefe H, Neu M, Remuiñán MJ, Patel AM, Guardia A, Davie CP, Pérez-Macías N, Yang H, Convery MA, Messer JA, Pérez-Herrán E, Centrella PA, Alvarez-Gómez D, Clark MA, Huss S, O'Donovan GK, Ortega-Muro F, McDowell W, Castañeda P, Arico-Muendel CC, Pajk S, Rullás J, Angulo-Barturen I, Alvarez-Ruíz E, Mendoza-Losana A, Ballell Pages L, Castro-Pichel J, Evindar G. Encoded library technology as a source of hits for the discovery and lead optimization of a potent and selective class of bactericidal direct inhibitors of Mycobacterium tuberculosis InhA. J Med Chem 2014; 57:1276-88. [PMID: 24450589 DOI: 10.1021/jm401326j] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Tuberculosis (TB) is one of the world's oldest and deadliest diseases, killing a person every 20 s. InhA, the enoyl-ACP reductase from Mycobacterium tuberculosis, is the target of the frontline antitubercular drug isoniazid (INH). Compounds that directly target InhA and do not require activation by mycobacterial catalase peroxidase KatG are promising candidates for treating infections caused by INH resistant strains. The application of the encoded library technology (ELT) to the discovery of direct InhA inhibitors yielded compound 7 endowed with good enzymatic potency but with low antitubercular potency. This work reports the hit identification, the selected strategy for potency optimization, the structure-activity relationships of a hundred analogues synthesized, and the results of the in vivo efficacy studies performed with the lead compound 65.
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Affiliation(s)
- Lourdes Encinas
- ELT Boston, Platform Technology & Science, GlaxoSmithKline , Waltham, Massachusetts 02451, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Christopher C. Arico-Muendel
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Heather Blanchette
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Dennis R. Benjamin
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Teresa M. Caiazzo
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Paolo A. Centrella
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jennifer DeLorey
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Elisabeth G. Doyle
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Steven R. Johnson
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Matthew T. Labenski
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Barry A. Morgan
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Gary O’Donovan
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Amy A. Sarjeant
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Steven Skinner
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Charles D. Thompson
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Sarah T. Griffin
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - William Westlin
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Kerry F. White
- Praecis Pharmaceuticals, Inc., 830 Winter Street, Waltham, Massachusetts 02451-1420, United States,
and Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Hongfeng Deng
- ELT Boston, Platform Technology and Science, GlaxoSmithKline, Waltham, Massachusetts, United States.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Findeis MA, Musso GM, Arico-Muendel CC, Benjamin HW, Hundal AM, Lee JJ, Chin J, Kelley M, Wakefield J, Hayward NJ, Molineaux SM. Modified-peptide inhibitors of amyloid beta-peptide polymerization. Biochemistry 1999; 38:6791-800. [PMID: 10346900 DOI: 10.1021/bi982824n] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellular toxicity resulting from nucleation-dependent polymerization of amyloid beta-peptide (Abeta) is considered to be a major and possibly the primary component of Alzheimer's disease (AD). Inhibition of Abeta polymerization has thus been identified as a target for the development of therapeutic agents for the treatment of AD. The intrinsic affinity of Abeta for itself suggested that Abeta-specific interactions could be adapted to the development of compounds that would bind to Abeta and prevent it from polymerizing. Abeta-derived peptides of fifteen residues were found to be inhibitory of Abeta polymerization. The activity of these peptides was subsequently enhanced through modification of their amino termini with specific organic reagents. Additional series of compounds prepared to probe structural requirements for activity allowed reduction of the size of the inhibitors and optimization of the Abeta-derived peptide portion to afford a lead compound, cholyl-Leu-Val-Phe-Phe-Ala-OH (PPI-368), with potent polymerization inhibitory activity but limited biochemical stability. The corresponding all-D-amino acyl analogue peptide acid (PPI-433) and amide (PPI-457) retained inhibitory activity and were both stable in monkey cerebrospinal fluid for 24 h.
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Affiliation(s)
- M A Findeis
- PRAECIS Pharmaceuticals Incorporated, Cambridge, Massachusetts, 02139-1572, USA.
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Arico-Muendel CC, Patera A, Pochapsky TC, Kuti M, Wolfson AJ. Solution structure and dynamics of a serpin reactive site loop using interleukin 1beta as a presentation scaffold. Protein Eng 1999; 12:189-202. [PMID: 10235620 DOI: 10.1093/protein/12.3.189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Human interleukin-1beta (IL1beta) was used as a presentation scaffold for the characterization of the reactive site loop (RSL) of the serpin alpha1-antitrypsin (A1AT), the physiological inhibitor of leukocyte elastase. A chimeric protein was generated by replacement of residues 50-53 of IL1beta, corresponding to an exposed reverse turn in IL1beta, with the 10-residue P5-P5' sequence EAIPMSIPPE from A1AT. The chimera (antitrypsin-interleukin, AT-IL) inhibits elastase specifically and also binds the IL1beta receptor. Multinuclear NMR characterization of AT-IL established that, with the exception of the inserted sequence, the structure of the IL1beta scaffold is preserved in the chimera. The structure of the inserted RSL was analyzed relative to that of the isolated 10-residue RSL peptide, which was shown to be essentially disordered in solution. The chimeric RSL was also found to be solvent exposed and conformationally mobile in comparison with the IL1beta scaffold, and there was no evidence of persisting interactions with the scaffold outside of the N- and C-terminal linkages. However, AT-IL exhibits sigificant differences in chemical shift and NOE patterns relative to the isolated RSL that are consistent with local features of non-random structure. The proximity of these features to the P1-P1' residues suggests that they may be responsible for the inhibitory activity of the chimera.
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Affiliation(s)
- C C Arico-Muendel
- Department of Chemistry, Brandeis University, Waltham, MA 02454-9110, USA
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Morozova-Roche LA, Arico-Muendel CC, Haynie DT, Emelyanenko VI, Van Dael H, Dobson CM. Structural characterisation and comparison of the native and A-states of equine lysozyme. J Mol Biol 1997; 268:903-21. [PMID: 9180380 DOI: 10.1006/jmbi.1997.0996] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Native state 1H NMR resonance assignments for 125 of the 129 residues of equine lysozyme have enabled measurement of the hydrogen exchange kinetics for over 60 backbone amide and three tryptophan indole hydrogen atoms in the native state. Native holo equine lysozyme hydrogen exchange protection factors are as large as 10(6), the most protected residues being located in elements of secondary structure. High exchange protection in the domain interface correlates with the binding of Ca2+ in this region. Equine lysozyme differs from most non-Ca2+ binding lysozymes in forming a highly populated partially folded state at low pH. The protein in this A-state at pH 2.0 has been found to bind 1-anilino-naphthalene-8-sulphonate with the enhancement of fluorescent intensity and blue shift in the spectral maximum characteristic of molten globules. NMR spectra indicate that the A-state is globally much less ordered than native equine lysozyme but does not contain significant regions of random coil structure. The amides most protected against hydrogen exchange in the A-state (protection factors up to 10(2) at 5 degrees C) correspond to residues of three of the four alpha-helices of the native state; the side-chains of these residues form a hydrophobic cluster that includes five aromatic residues. Circular dichroism and tryptophan fluorescence indicate that these residues are substantially more constrained than similar residues in "classical" molten globules. Taken together, the data suggest a model for the A-state of equine lysozyme in which a more ordered core is surrounded by a less ordered but still compact polypeptide chain.
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Affiliation(s)
- L A Morozova-Roche
- Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, England
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