1
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Candito DA, Simov V, Gulati A, Kattar S, Chau RW, Lapointe BT, Methot JL, DeMong DE, Graham TH, Kurukulasuriya R, Keylor MH, Tong L, Morriello GJ, Acton JJ, Pio B, Liu W, Scott JD, Ardolino MJ, Martinot TA, Maddess ML, Yan X, Gunaydin H, Palte RL, McMinn SE, Nogle L, Yu H, Minnihan EC, Lesburg CA, Liu P, Su J, Hegde LG, Moy LY, Woodhouse JD, Faltus R, Xiong T, Ciaccio P, Piesvaux JA, Otte KM, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Neelamkavil S, Wood HB, Fuller PH, Ellis JM. Discovery and Optimization of Potent, Selective, and Brain-Penetrant 1-Heteroaryl-1 H-Indazole LRRK2 Kinase Inhibitors for the Treatment of Parkinson's Disease. J Med Chem 2022; 65:16801-16817. [PMID: 36475697 DOI: 10.1021/acs.jmedchem.2c01605] [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: 12/13/2022]
Abstract
Inhibition of leucine-rich repeat kinase 2 (LRRK2) kinase activity represents a genetically supported, chemically tractable, and potentially disease-modifying mechanism to treat Parkinson's disease. Herein, we describe the optimization of a novel series of potent, selective, central nervous system (CNS)-penetrant 1-heteroaryl-1H-indazole type I (ATP competitive) LRRK2 inhibitors. Type I ATP-competitive kinase physicochemical properties were integrated with CNS drug-like properties through a combination of structure-based drug design and parallel medicinal chemistry enabled by sp3-sp2 cross-coupling technologies. This resulted in the discovery of a unique sp3-rich spirocarbonitrile motif that imparted extraordinary potency, pharmacokinetics, and favorable CNS drug-like properties. The lead compound, 25, demonstrated exceptional on-target potency in human peripheral blood mononuclear cells, excellent off-target kinase selectivity, and good brain exposure in rat, culminating in a low projected human dose and a pre-clinical safety profile that warranted advancement toward pre-clinical candidate enabling studies.
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Affiliation(s)
- David A Candito
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Solomon Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ryan W Chau
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Blair T Lapointe
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Joey L Methot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Duane E DeMong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Thomas H Graham
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ravi Kurukulasuriya
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ling Tong
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - John J Acton
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Barbara Pio
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Weiguo Liu
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Jack D Scott
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Michael J Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Theodore A Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew L Maddess
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hakan Gunaydin
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hongshi Yu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ellen C Minnihan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Charles A Lesburg
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jing Su
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Paul Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jennifer A Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Santhosh Neelamkavil
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Harold B Wood
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - J Michael Ellis
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
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2
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Chang W, Altman MD, Lesburg CA, Perera SA, Piesvaux JA, Schroeder GK, Wyss DF, Cemerski S, Chen Y, DiNunzio E, Haidle AM, Ho T, Kariv I, Knemeyer I, Kopinja JE, Lacey BM, Laskey J, Lim J, Long BJ, Ma Y, Maddess ML, Pan BS, Presland JP, Spooner E, Steinhuebel D, Truong Q, Zhang Z, Fu J, Addona GH, Northrup AB, Parmee E, Tata JR, Bennett DJ, Cumming JN, Siu T, Trotter BW. Discovery of MK-1454: A Potent Cyclic Dinucleotide Stimulator of Interferon Genes Agonist for the Treatment of Cancer. J Med Chem 2022; 65:5675-5689. [PMID: 35332774 DOI: 10.1021/acs.jmedchem.1c02197] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Stereochemically and structurally complex cyclic dinucleotide-based stimulator of interferon genes (STING) agonists were designed and synthesized to access a previously unexplored chemical space. The assessment of biochemical affinity and cellular potency, along with computational, structural, and biophysical characterization, was applied to influence the design and optimization of novel STING agonists, resulting in the discovery of MK-1454 as a molecule with appropriate properties for clinical development. When administered intratumorally to immune-competent mice-bearing syngeneic tumors, MK-1454 exhibited robust tumor cytokine upregulation and effective antitumor activity. Tumor shrinkage in mouse models that are intrinsically resistant to single-agent therapy was further enhanced when treating the animals with MK-1454 in combination with a fully murinized antimouse PD-1 antibody, mDX400. These data support the development of STING agonists in combination with pembrolizumab (humanized anti-PD-1 antibody) for patients with tumors that are partially responsive or nonresponsive to single-agent anti-PD-1 therapy.
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Affiliation(s)
- Wonsuk Chang
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | | | | | | | | | - Daniel F Wyss
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Saso Cemerski
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Yiping Chen
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Edward DiNunzio
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Andrew M Haidle
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Thu Ho
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Ilona Kariv
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Ian Knemeyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Brian M Lacey
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Jason Laskey
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Jongwon Lim
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Brian J Long
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Yanhong Ma
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Bo-Sheng Pan
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Edward Spooner
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Quang Truong
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Zhibo Zhang
- Pharmaron Beijing Co. Ltd., Beijing 100176, P. R. China
| | - Jianmin Fu
- Pharmaron Beijing Co. Ltd., Beijing 100176, P. R. China
| | - George H Addona
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Alan B Northrup
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Emma Parmee
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - James R Tata
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Jared N Cumming
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Tony Siu
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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3
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Li D, Sloman DL, Achab A, Zhou H, McGowan MA, White C, Gibeau C, Zhang H, Pu Q, Bharathan I, Hopkins B, Liu K, Ferguson H, Fradera X, Lesburg CA, Martinot TA, Qi J, Song ZJ, Yin J, Zhang H, Song L, Wan B, DAddio S, Solban N, Miller JR, Zamlynny B, Bass A, Freeland E, Ykoruk B, Hilliard C, Ferraro J, Zhai J, Knemeyer I, Otte KM, Vincent S, Sciammetta N, Pasternak A, Bennett DJ, Han Y. Oxetane Promise Delivered: Discovery of Long-Acting IDO1 Inhibitors Suitable for Q3W Oral or Parenteral Dosing. J Med Chem 2022; 65:6001-6016. [PMID: 35239336 DOI: 10.1021/acs.jmedchem.1c01670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3,3-Disubstituted oxetanes have been utilized as bioisosteres for gem-dimethyl and cyclobutane functionalities. We report the discovery of a novel class of oxetane indole-amine 2,3-dioxygenase (IDO1) inhibitors suitable for Q3W (once every 3 weeks) oral and parenteral dosing. A diamide class of IDO inhibitors was discovered through an automated ligand identification system (ALIS). Installation of an oxetane and fluorophenyl dramatically improved the potency. Identification of a biaryl moiety as an unconventional amide isostere addressed the metabolic liability of amide hydrolysis. Metabolism identification (Met-ID)-guided target design and the introduction of polarity resulted in the discovery of potent IDO inhibitors with excellent pharmacokinetic (PK) profiles in multiple species. To enable rapid synthesis of the key oxetane intermediate, a novel oxetane ring cyclization was also developed, as well as optimization of a literature route on kg scale. These IDO inhibitors may enable unambiguous proof-of-concept testing for the IDO1 inhibition mechanism for oncology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Huangguang Zhang
- Pharmaron Beijing Co., Ltd., No.6 Taihe Road, Beijing 100176, China
| | - Licheng Song
- Pharmaron Beijing Co., Ltd., No.6 Taihe Road, Beijing 100176, China
| | - Baoqiang Wan
- WuXi AppTec Co., Ltd., No. 1 Building, #288 FuTe ZhongLu, WaiGaoQiao Free Trade Zone, Shanghai 100176, China
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4
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Keylor MH, Gulati A, Kattar SD, Johnson RE, Chau RW, Margrey KA, Ardolino MJ, Zarate C, Poremba KE, Simov V, Morriello GJ, Acton JJ, Pio B, Yan X, Palte RL, McMinn SE, Nogle L, Lesburg CA, Adpressa D, Lin S, Neelamkavil S, Liu P, Su J, Hegde LG, Woodhouse JD, Faltus R, Xiong T, Ciaccio PJ, Piesvaux J, Otte KM, Wood HB, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Structure-Guided Discovery of Aminoquinazolines as Brain-Penetrant and Selective LRRK2 Inhibitors. J Med Chem 2021; 65:838-856. [PMID: 34967623 DOI: 10.1021/acs.jmedchem.1c01968] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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
The leucine-rich repeat kinase 2 (LRRK2) protein has been genetically and functionally linked to Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder whose current therapies are limited in scope and efficacy. In this report, we describe a rigorous hit-to-lead optimization campaign supported by structural enablement, which culminated in the discovery of brain-penetrant, candidate-quality molecules as represented by compounds 22 and 24. These compounds exhibit remarkable selectivity against the kinome and offer good oral bioavailability and low projected human doses. Furthermore, they showcase the implementation of stereochemical design elements that serve to enable a potency- and selectivity-enhancing increase in polarity and hydrogen bond donor (HBD) count while maintaining a central nervous system-friendly profile typified by low levels of transporter-mediated efflux and encouraging brain penetration in preclinical models.
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Affiliation(s)
- Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca E Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan W Chau
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kaila A Margrey
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael J Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cayetana Zarate
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kelsey E Poremba
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - John J Acton
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Barbara Pio
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Charles A Lesburg
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Donovon Adpressa
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Shishi Lin
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Santhosh Neelamkavil
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Harold B Wood
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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5
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Li D, Zhang H, Lyons TW, Lu M, Achab A, Pu Q, Childers M, Mitcheltree MJ, Wang J, Martinot TA, McMinn SE, Sloman DL, Palani A, Beard A, Nogle L, Gathiaka S, Saurí J, Kim HY, Adpressa D, Spacciapoli P, Miller JR, Palte RL, Lesburg CA, Cumming J, Fischer C. Comprehensive Strategies to Bicyclic Prolines: Applications in the Synthesis of Potent Arginase Inhibitors. ACS Med Chem Lett 2021; 12:1678-1688. [PMID: 34795856 PMCID: PMC8591728 DOI: 10.1021/acsmedchemlett.1c00258] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/06/2021] [Indexed: 12/22/2022] Open
Abstract
Comprehensive synthetic strategies afforded a diverse set of structurally unique bicyclic proline-containing arginase inhibitors with a high degree of three-dimensionality. The analogs that favored the Cγ-exo conformation of the proline improved the arginase potency over the initial lead. The novel synthetic strategies reported here not only enable access to previously unknown stereochemically complex proline derivatives but also provide a foundation for the future synthesis of bicyclic proline analogs, which incorporate inherent three-dimensional character into building blocks, medicine, and catalysts and could have a profound impact on the conformation of proline-containing peptides and macrocycles.
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Affiliation(s)
- Derun Li
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Hongjun Zhang
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Thomas W Lyons
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Min Lu
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Abdelghani Achab
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Qinglin Pu
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew Childers
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Mitcheltree
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Theodore A Martinot
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - David L Sloman
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anandan Palani
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Adam Beard
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Symon Gathiaka
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Josep Saurí
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Hai-Young Kim
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Donovon Adpressa
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter Spacciapoli
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - J Richard Miller
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Charles A Lesburg
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jared Cumming
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Christian Fischer
- Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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6
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Yu W, Deng Y, Sloman D, Li D, Liu K, Fradera X, Lesburg CA, Martinot T, Doty A, Ferguson H, Richard Miller J, Knemeyer I, Otte K, Vincent S, Sciammetta N, Jonathan Bennett D, Han Y. Discovery of IDO1 inhibitors containing a decahydroquinoline, decahydro-1,6-naphthyridine, or octahydro-1H-pyrrolo[3,2-c]pyridine scaffold. Bioorg Med Chem Lett 2021; 49:128314. [PMID: 34391891 DOI: 10.1016/j.bmcl.2021.128314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/21/2021] [Accepted: 08/08/2021] [Indexed: 01/25/2023]
Abstract
A series of IDO1 inhibitors containing a decahydroquinoline, decahydro-1,6-naphthyridine, or octahydro-1H-pyrrolo[3,2-c]pyridine scaffold were identified with good cellular and human whole blood activity against IDO1. These inhibitors contain multiple chiral centers and all diastereomers were separated. The absolute stereochemistry of each isomers were not determined. Compounds 15 and 27 stood out as leads due to their good cellular as well as human whole blood IDO1 inhibition activity, low unbound clearance, and reasonable mean residence time in rat cassette PK studies.
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Affiliation(s)
- Wensheng Yu
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - Yongqi Deng
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - David Sloman
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Derun Li
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kun Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xavier Fradera
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Theo Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Amy Doty
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Heidi Ferguson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - J Richard Miller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ian Knemeyer
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Karin Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stella Vincent
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | | | - Yongxin Han
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
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7
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Hopkins B, Zhang H, Bharathan I, Li D, Pu Q, Zhou H, Martinot TA, Fradera X, Lammens A, Lesburg CA, Cohen RD, Ballard J, Knemeyer I, Otte K, Vincent S, Miller JR, Solban N, Cheng M, Geda P, Smotrov N, Song X, Bennett DJ, Han Y. Utilization of Metabolite Identification and Structural Data to Guide Design of Low-Dose IDO1 Inhibitors. ACS Med Chem Lett 2021; 12:1435-1440. [PMID: 34531952 DOI: 10.1021/acsmedchemlett.1c00265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022] Open
Abstract
Herein the discovery of potent IDO1 inhibitors with low predicted human dose is discussed. Metabolite identification (MetID) and structural data were used to strategically incorporate cyclopropane rings into this tetrahydronaphthyridine series of IDO1 inhibitors to improve their metabolic stability and potency. Enabling synthetic chemistry was developed to construct these unique fused cyclopropyl compounds, leading to inhibitors with improved pharmacokinetics and human whole blood potency and a predicted human oral dose as low as 9 mg once daily (QD).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alfred Lammens
- Proteros Biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | | | - Ryan D. Cohen
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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8
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Yu W, Deng Y, Hopkins B, Huang X, Sloman D, Zhang H, Li D, McGowan MA, White C, Pu Q, Liu K, Fradera X, Lesburg CA, Martinot T, Doty A, Ferguson H, Nickbarg EB, Cheng M, Geda P, Song X, Smotrov N, Abeywickrema P, Andrews C, Chamberlin C, Mabrouk O, Curran P, Richards M, Saradjian P, Miller JR, Knemeyer I, Otte K, Vincent S, Sciammetta N, Bennett DJ, Han Y. SAR towards indoline and 3-azaindoline classes of IDO1 inhibitors. Bioorg Med Chem Lett 2021; 47:128214. [PMID: 34166782 DOI: 10.1016/j.bmcl.2021.128214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/22/2021] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022]
Abstract
A novel series of IDO1 inhibitors have been identified with good IDO1 Hela cell and human whole blood activity. These inhibitors contain an indoline or a 3-azaindoline scaffold. Their structure-activity-relationship studies have been explored. Compounds 37 and 41 stood out as leads due to their good potency in IDO1 Hela assay, good IDO1 unbound hWB IC50s, reasonable unbound clearance, and good MRT in rat and dog PK studies.
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Affiliation(s)
- Wensheng Yu
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - Yongqi Deng
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Brett Hopkins
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xianhai Huang
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - David Sloman
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hongjun Zhang
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Derun Li
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Catherine White
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Qinglin Pu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kun Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xavier Fradera
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Theo Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Amy Doty
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Heidi Ferguson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Mangeng Cheng
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Prasanthi Geda
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xuelei Song
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Nadya Smotrov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | | | - Chad Chamberlin
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Omar Mabrouk
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Patrick Curran
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Matthew Richards
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Peter Saradjian
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - J Richard Miller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ian Knemeyer
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Karin Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stella Vincent
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | | | - Yongxin Han
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
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9
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Fradera X, Deng Q, Achab A, Garcia Y, Kattar SD, McGowan MA, Methot JL, Wilson K, Zhou H, Shaffer L, Goldenblatt P, Tong V, Augustin MA, Altman MD, Lesburg CA, Shah S, Katz JD. Discovery of a new series of PI3K-δ inhibitors from Virtual Screening. Bioorg Med Chem Lett 2021; 42:128046. [PMID: 33865969 DOI: 10.1016/j.bmcl.2021.128046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 11/18/2022]
Abstract
PI3K-δ mediates key immune cell signaling pathways and is a target of interest for treatment of oncological and immunological disorders. Here we describe the discovery and optimization of a novel series of PI3K-δ selective inhibitors. We first identified hits containing an isoindolinone scaffold using a combined ligand- and receptor-based virtual screening workflow, and then improved potency and selectivity guided by structural data and modeling. Careful optimization of molecular properties led to compounds with improved permeability and pharmacokinetic profile, and high potency in a whole blood assay.
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Affiliation(s)
- Xavier Fradera
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA, USA.
| | - Qiaolin Deng
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Yudith Garcia
- Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
| | | | | | - Joey L Methot
- Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - Kevin Wilson
- Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - Hua Zhou
- Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - Lynsey Shaffer
- Quantitative Biosciences, Merck & Co., Inc., Boston, MA, USA
| | | | | | | | - Michael D Altman
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - Charles A Lesburg
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - Sanjiv Shah
- Quantitative Biosciences, Merck & Co., Inc., Boston, MA, USA
| | - Jason D Katz
- Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
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10
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Vara BA, Levi SM, Achab A, Candito DA, Fradera X, Lesburg CA, Kawamura S, Lacey BM, Lim J, Methot JL, Xu Z, Xu H, Smith DM, Piesvaux JA, Miller JR, Bittinger M, Ranganath SH, Bennett DJ, DiMauro EF, Pasternak A. Discovery of Diaminopyrimidine Carboxamide HPK1 Inhibitors as Preclinical Immunotherapy Tool Compounds. ACS Med Chem Lett 2021; 12:653-661. [PMID: 33859804 PMCID: PMC8040257 DOI: 10.1021/acsmedchemlett.1c00096] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/12/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic progenitor kinase 1 (HPK1), a serine/threonine kinase, is a negative immune regulator of T cell receptor (TCR) and B cell signaling that is primarily expressed in hematopoietic cells. Accordingly, it has been reported that HPK1 loss-of-function in HPK1 kinase-dead syngeneic mouse models shows enhanced T cell signaling and cytokine production as well as tumor growth inhibition in vivo, supporting its value as an immunotherapeutic target. Herein, we present the structurally enabled discovery of novel, potent, and selective diaminopyrimidine carboxamide HPK1 inhibitors. The key discovery of a carboxamide moiety was essential for enhanced enzyme inhibitory potency and kinome selectivity as well as sustained elevation of cellular IL-2 production across a titration range in human peripheral blood mononuclear cells. The elucidation of structure-activity relationships using various pendant amino ring systems allowed for the identification of several small molecule type-I inhibitors with promising in vitro profiles.
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Affiliation(s)
- Brandon A. Vara
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Samuel M. Levi
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Abdelghani Achab
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - David A. Candito
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Xavier Fradera
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Charles A. Lesburg
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Shuhei Kawamura
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Brian M. Lacey
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Jongwon Lim
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Joey L. Methot
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Zangwei Xu
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Haiyan Xu
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Dustin M. Smith
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Jennifer A. Piesvaux
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - J. Richard Miller
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Mark Bittinger
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Sheila H. Ranganath
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - David J. Bennett
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Erin F. DiMauro
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
| | - Alexander Pasternak
- Discovery Chemistry, Computational and Structural Chemistry, Quantitative Biosciences, Pharmacokinetics
and Drug Metabolism, Oncology Early Discovery, Merck & Co.,
Inc., Boston, Massachusetts 02115, United States
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11
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Methot JL, Zhou H, McGowan MA, Anthony NJ, Christopher M, Garcia Y, Achab A, Lipford K, Trotter BW, Altman MD, Fradera X, Lesburg CA, Li C, Alves S, Chappell CP, Jain R, Mangado R, Pinheiro E, Williams SMG, Goldenblatt P, Hill A, Shaffer L, Chen D, Tong V, McLeod RL, Lee HH, Yu H, Shah S, Katz JD. Projected Dose Optimization of Amino- and Hydroxypyrrolidine Purine PI3Kδ Immunomodulators. J Med Chem 2021; 64:5137-5156. [PMID: 33797901 DOI: 10.1021/acs.jmedchem.1c00237] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The approvals of idelalisib and duvelisib have validated PI3Kδ inhibitors for the treatment for hematological malignancies driven by the PI3K/AKT pathway. Our program led to the identification of structurally distinct heterocycloalkyl purine inhibitors with excellent isoform and kinome selectivity; however, they had high projected human doses. Improved ligand contacts gave potency enhancements, while replacement of metabolic liabilities led to extended half-lives in preclinical species, affording PI3Kδ inhibitors with low once-daily predicted human doses. Treatment of C57BL/6-Foxp3-GDL reporter mice with 30 and 100 mg/kg/day of 3c (MSD-496486311) led to a 70% reduction in Foxp3-expressing regulatory T cells as observed through bioluminescence imaging with luciferin, consistent with the role of PI3K/AKT signaling in Treg cell proliferation. As a model for allergic rhinitis and asthma, treatment of ovalbumin-challenged Brown Norway rats with 0.3 to 30 mg/kg/day of 3c gave a dose-dependent reduction in pulmonary bronchoalveolar lavage inflammation eosinophil cell count.
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Affiliation(s)
- Joey L Methot
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Hua Zhou
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Meredeth A McGowan
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Neville John Anthony
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Matthew Christopher
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Yudith Garcia
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Abdelghani Achab
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Kathryn Lipford
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Benjamin Wesley Trotter
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Michael D Altman
- Computational and Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Xavier Fradera
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Charles A Lesburg
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Chaomin Li
- Process Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Stephen Alves
- Discovery Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Craig P Chappell
- Discovery Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Renu Jain
- Discovery Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Ruban Mangado
- Discovery Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Elaine Pinheiro
- Discovery Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Sybill M G Williams
- Discovery Biology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Peter Goldenblatt
- In Vitro Pharmacology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Armetta Hill
- In Vitro Pharmacology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Lynsey Shaffer
- In Vitro Pharmacology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Dapeng Chen
- Preclinical Pharmacokinetics and Drug Metabolism, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Vincent Tong
- Preclinical Pharmacokinetics and Drug Metabolism, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Robbie L McLeod
- In Vivo Pharmacology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Hyun-Hee Lee
- In Vivo Pharmacology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Hongshi Yu
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Sanjiv Shah
- In Vitro Pharmacology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
| | - Jason D Katz
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115 United States
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12
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Brueckner AC, Deng Q, Cleves AE, Lesburg CA, Alvarez JC, Reibarkh MY, Sherer EC, Jain AN. Conformational Strain of Macrocyclic Peptides in Ligand-Receptor Complexes Based on Advanced Refinement of Bound-State Conformers. J Med Chem 2021; 64:3282-3298. [PMID: 33724820 DOI: 10.1021/acs.jmedchem.0c02159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macrocyclic peptides are an important modality in drug discovery, but molecular design is limited due to the complexity of their conformational landscape. To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures. Unexpectedly large strain energies were observed when the bound-state conformations were modeled with positional restraints. Instead, low-energy conformer ensembles were generated using xGen that fit experimental X-ray electron density maps and gave reasonable strain energy estimates. The ensembles featured significant conformational adjustments while still fitting the electron density as well or better than the original coordinates. Strain estimates suggest the interaction energy in protein-ligand complexes can offset a greater amount of strain for macrocyclic peptides than for small molecules and non-peptidic macrocycles. Across all molecular classes, the approximate upper bound on global strain energies had the same relationship with molecular size, and bound-state ensembles from xGen yielded favorable binding energy estimates.
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Affiliation(s)
- Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ann E Cleves
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
| | - Charles A Lesburg
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mikhail Y Reibarkh
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ajay N Jain
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
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13
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Yu EC, Methot JL, Fradera X, Lesburg CA, Lacey BM, Siliphaivanh P, Liu P, Smith DM, Xu Z, Piesvaux JA, Kawamura S, Xu H, Miller JR, Bittinger M, Pasternak A. Identification of Potent Reverse Indazole Inhibitors for HPK1. ACS Med Chem Lett 2021; 12:459-466. [PMID: 33738073 DOI: 10.1021/acsmedchemlett.0c00672] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
Hematopoietic progenitor kinase (HPK1), a negative regulator of TCR-mediated T-cell activation, has been recognized as a novel antitumor immunotherapy target. Structural optimization of kinase inhibitor 4 through a systematic two-dimensional diversity screen of pyrazolopyridines led to the identification of potent and selective compounds. Crystallographic studies with HPK1 revealed a favorable water-mediated interaction with Asp155 and a salt bridge to Asp101 with optimized heterocyclic solvent fronts that were critical for enhanced potency and selectivity. Computational studies of model systems revealed differences in torsional profiles that allowed for these beneficial protein-ligand interactions. Further optimization of molecular properties led to identification of potent and selective reverse indazole inhibitor 36 that inhibited phosphorylation of adaptor protein SLP76 in human PBMC and exhibited low clearance with notable bioavailability in in vivo rat studies.
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Affiliation(s)
- Elsie C. Yu
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Joey L. Methot
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Xavier Fradera
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Charles A. Lesburg
- Computational and Structural Chemistry, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Brian M. Lacey
- Quantitative Biosciences, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Phieng Siliphaivanh
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Ping Liu
- External Discovery Chemistry, Merck & Co Inc., Rahway, New Jersey, 07065, United States
| | - Dustin M. Smith
- Pharmacokinetics and Drug Metabolism, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Zangwei Xu
- Quantitative Biosciences, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Jennifer A. Piesvaux
- Quantitative Biosciences, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Shuhei Kawamura
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Haiyan Xu
- Quantitative Biosciences, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - J. Richard Miller
- Quantitative Biosciences, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Mark Bittinger
- Oncology Early Discovery, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
| | - Alexander Pasternak
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts, 02115, United States
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14
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Li D, Deng Y, Achab A, Bharathan I, Hopkins BA, Yu W, Zhang H, Sanyal S, Pu Q, Zhou H, Liu K, Lim J, Fradera X, Lesburg CA, Lammens A, Martinot TA, Cohen RD, Doty AC, Ferguson H, Nickbarg EB, Cheng M, Spacciapoli P, Geda P, Song X, Smotrov N, Abeywickrema P, Andrews C, Chamberlin C, Mabrouk O, Curran P, Richards M, Saradjian P, Miller JR, Knemeyer I, Otte KM, Vincent S, Sciammetta N, Pasternak A, Bennett DJ, Han Y. Carbamate and N-Pyrimidine Mitigate Amide Hydrolysis: Structure-Based Drug Design of Tetrahydroquinoline IDO1 Inhibitors. ACS Med Chem Lett 2021; 12:389-396. [PMID: 33738066 PMCID: PMC7957919 DOI: 10.1021/acsmedchemlett.0c00525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 10/14/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as an attractive target for cancer immunotherapy. An automated ligand identification system screen afforded the tetrahydroquinoline class of novel IDO1 inhibitors. Potency and pharmacokinetic (PK) were key issues with this class of compounds. Structure-based drug design and strategic incorporation of polarity enabled the rapid improvement on potency, solubility, and oxidative metabolic stability. Metabolite identification studies revealed that amide hydrolysis in the D-pocket was the key clearance mechanism for this class. Strategic survey of amide isosteres revealed that carbamates and N-pyrimidines, which maintained exquisite potencies, mitigated the amide hydrolysis issue and led to an improved rat PK profile. The lead compound 28 is a potent IDO1 inhibitor, with clean off-target profiles and the potential for quaque die dosing in humans.
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Affiliation(s)
- Derun Li
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Yongqi Deng
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Abdelghani Achab
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Indu Bharathan
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Brett Andrew Hopkins
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Wensheng Yu
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Hongjun Zhang
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Sulagna Sanyal
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Qinglin Pu
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Hua Zhou
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Kun Liu
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Jongwon Lim
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Xavier Fradera
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Charles A. Lesburg
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Alfred Lammens
- Proteros
Biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | - Theodore A. Martinot
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan D. Cohen
- Analytical
Research & Development, Merck &
Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065 United States
| | - Amy C. Doty
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Heidi Ferguson
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Elliott B. Nickbarg
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Mangeng Cheng
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Peter Spacciapoli
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Prasanthi Geda
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Xuelei Song
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Nadya Smotrov
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Pravien Abeywickrema
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Christine Andrews
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Chad Chamberlin
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Omar Mabrouk
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Patrick Curran
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew Richards
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Peter Saradjian
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - J. Richard Miller
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Ian Knemeyer
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M. Otte
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Stella Vincent
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Nunzio Sciammetta
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Alexander Pasternak
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - David Jonathan Bennett
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Yongxin Han
- Departments of Discovery Chemistry, Pharmacokinetics, Pharmacodynamics,
and Drug Metabolism, Computational and Structural Chemistry, Discovery Process Chemistry, Discovery Pharmaceutical
Science, and Quantitative Biosciences, Merck & Co.,
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| |
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15
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Methot JL, Achab A, Christopher M, Zhou H, McGowan MA, Trotter BW, Fradera X, Lesburg CA, Goldenblatt P, Hill A, Chen D, Otte KM, Augustin M, Shah S, Katz JD. Optimization of Versatile Oxindoles as Selective PI3Kδ Inhibitors. ACS Med Chem Lett 2020; 11:2461-2469. [PMID: 33335668 DOI: 10.1021/acsmedchemlett.0c00441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
The 3,3-disubstituted oxindole moiety is a versatile and rigid three-dimensionally shaped scaffold. When engineered with a purine hinge-binding core, exceptionally selective PI3Kδ kinase inhibitors were discovered by exploiting small differences in isoform selectivity pockets. Crystal structures of early lead 2f bound to PI3Kδ and PI3Kα helped rationalize the high selectivity observed with 2f. By attenuating the lypophilicity and metabolic liabilities of an oxindole moiety, we improved the preclinical species PK and solubility and reduced adenosine uptake activity. The excellent potency and kinome selectivity of 7-azaoxindole 4d and spirooxindole 5d, together with a low plasma clearance and good half-life in rat and dog, supported a low once-daily predicted human dose.
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16
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Jain AN, Cleves AE, Brueckner AC, Lesburg CA, Deng Q, Sherer EC, Reibarkh MY. XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps. J Med Chem 2020; 63:10509-10528. [DOI: 10.1021/acs.jmedchem.0c01373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ajay N. Jain
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143 United States
| | - Ann E. Cleves
- BioPharmics LLC, Santa Rosa, California 95404 United States
| | | | | | - Qiaolin Deng
- Merck and Co., Inc., Kenilworth, New Jersey 07033 United States
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17
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Pan BS, Perera SA, Piesvaux JA, Presland JP, Schroeder GK, Cumming JN, Trotter BW, Altman MD, Buevich AV, Cash B, Cemerski S, Chang W, Chen Y, Dandliker PJ, Feng G, Haidle A, Henderson T, Jewell J, Kariv I, Knemeyer I, Kopinja J, Lacey BM, Laskey J, Lesburg CA, Liang R, Long BJ, Lu M, Ma Y, Minnihan EC, O’Donnell G, Otte R, Price L, Rakhilina L, Sauvagnat B, Sharma S, Tyagarajan S, Woo H, Wyss DF, Xu S, Bennett DJ, Addona GH. An orally available non-nucleotide STING agonist with antitumor
activity. Science 2020; 369:369/6506/eaba6098. [DOI: 10.1126/science.aba6098] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
Abstract
Pharmacological activation of the STING (stimulator of interferon
genes)–controlled innate immune pathway is a promising therapeutic strategy for
cancer. Here we report the identification of MSA-2, an orally available
non-nucleotide human STING agonist. In syngeneic mouse tumor models, subcutaneous
and oral MSA-2 regimens were well tolerated and stimulated interferon-β secretion
in tumors, induced tumor regression with durable antitumor immunity, and
synergized with anti–PD-1 therapy. Experimental and theoretical analyses showed
that MSA-2 exists as interconverting monomers and dimers in solution, but only
dimers bind and activate STING. This model was validated by using synthetic
covalent MSA-2 dimers, which were potent agonists. Cellular potency of MSA-2
increased upon extracellular acidification, which mimics the tumor
microenvironment. These properties appear to underpin the favorable activity and
tolerability profiles of effective systemic administration of MSA-2.
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Affiliation(s)
- Bo-Sheng Pan
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Samanthi A. Perera
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Jeremy P. Presland
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Jared N. Cumming
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - B. Wesley Trotter
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Michael D. Altman
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Alexei V. Buevich
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Brandon Cash
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Saso Cemerski
- Department of Discovery Oncology, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Wonsuk Chang
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yiping Chen
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Peter J. Dandliker
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Guo Feng
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Andrew Haidle
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Timothy Henderson
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - James Jewell
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ilona Kariv
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ian Knemeyer
- Department of Pharmacokinetics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Johnny Kopinja
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Brian M. Lacey
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Jason Laskey
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Charles A. Lesburg
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Rui Liang
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Brian J. Long
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Min Lu
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yanhong Ma
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ellen C. Minnihan
- Department of Discovery Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Greg O’Donnell
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Ryan Otte
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Laura Price
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Larissa Rakhilina
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Berengere Sauvagnat
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Sharad Sharma
- Department of Discovery Oncology, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Sriram Tyagarajan
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Hyun Woo
- Department of Pharmacokinetics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Daniel F. Wyss
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Serena Xu
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - George H. Addona
- Department of Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
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18
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Pu Q, Zhang H, Guo L, Cheng M, Doty AC, Ferguson H, Fradera X, Lesburg CA, McGowan MA, Miller JR, Geda P, Song X, Otte K, Sciammetta N, Solban N, Yu W, Sloman DL, Zhou H, Lammens A, Neumann L, Bennett DJ, Pasternak A, Han Y. Discovery of Potent and Orally Available Bicyclo[1.1.1]pentane-Derived Indoleamine-2,3-dioxygenase 1 (IDO1) Inhibitors. ACS Med Chem Lett 2020; 11:1548-1554. [PMID: 32832022 DOI: 10.1021/acsmedchemlett.0c00195] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
Indoleamine-2,3-dioxygenase 1 (IDO1) inhibition and its combination with immune checkpoint inhibitors like pembrolizumab have drawn considerable attention from both academia and the pharmaceutical industry. Here, we describe the discovery of a novel class of highly potent IDO1 heme-displacing inhibitors featuring a unique bicyclo[1.1.1]pentane motif. Compound 1, evolving from an ALIS (automated ligand identification system) hit, exhibited excellent potency but lacked the desired pharmacokinetic profile due to extensive amide hydrolysis of the benzamide moiety. Replacing the central phenyl ring in 1 with a bicyclo[1.1.1]pentane bioisostere effectively circumvented the amide hydrolysis issue, resulting in the discovery of compound 2 with a favorable overall profile such as excellent potency, selectivity, pharmacokinetics, and a low predicted human dose.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wensheng Yu
- External Discovery Chemistry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | | | | | - Alfred Lammens
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Planegg, Martinsried, Germany
| | - Lars Neumann
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Planegg, Martinsried, Germany
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19
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Fradera X, Methot JL, Achab A, Christopher M, Altman MD, Zhou H, McGowan MA, Kattar SD, Wilson K, Garcia Y, Augustin MA, Lesburg CA, Shah S, Goldenblatt P, Katz JD. Corrigendum to “Design of selective PI3Kδ inhibitors using an iterative scaffold-hopping workflow” [Bioorg. Med. Chem. Lett. 29 (2019) 2575–2580]. Bioorg Med Chem Lett 2020; 30:127363. [DOI: 10.1016/j.bmcl.2020.127363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Yan XC, Sanders JM, Gao YD, Tudor M, Haidle AM, Klein DJ, Converso A, Lesburg CA, Zang Y, Wood HB. Augmenting Hit Identification by Virtual Screening Techniques in Small Molecule Drug Discovery. J Chem Inf Model 2020; 60:4144-4152. [PMID: 32309939 DOI: 10.1021/acs.jcim.0c00113] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Two orthogonal approaches for hit identification in drug discovery are large-scale in vitro and in silico screening. In recent years, due to the emergence of new targets and a rapid increase in the size of the readily synthesizable chemical space, there is a growing emphasis on the integration of the two techniques to improve the hit finding efficiency. Here, we highlight three examples of drug discovery projects at Merck & Co., Inc., Kenilworth, NJ, USA in which different virtual screening (VS) techniques, each specifically tailored to leverage knowledge available for the target, were utilized to augment the selection of high-quality chemical matter for in vitro assays and to enhance the diversity and tractability of hits. Central to success is a fully integrated workflow combining in silico and experimental expertise at every stage of the hit identification process. We advocate that workflows encompassing VS as part of an integrated hit finding plan should be widely adopted to accelerate hit identification and foster cross-functional collaborations in modern drug discovery.
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21
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Mitcheltree MJ, Li D, Achab A, Beard A, Chakravarthy K, Cheng M, Cho H, Eangoor P, Fan P, Gathiaka S, Kim HY, Lesburg CA, Lyons TW, Martinot TA, Miller JR, McMinn S, O’Neil J, Palani A, Palte RL, Saurí J, Sloman DL, Zhang H, Cumming JN, Fischer C. Discovery and Optimization of Rationally Designed Bicyclic Inhibitors of Human Arginase to Enhance Cancer Immunotherapy. ACS Med Chem Lett 2020; 11:582-588. [PMID: 32292567 DOI: 10.1021/acsmedchemlett.0c00058] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022] Open
Abstract
The action of arginase, a metalloenzyme responsible for the hydrolysis of arginine to urea and ornithine, is hypothesized to suppress immune-cell activity within the tumor microenvironment, and thus its inhibition may constitute a means by which to potentiate the efficacy of immunotherapeutics such as anti-PD-1 checkpoint inhibitors. Taking inspiration from reported enzyme-inhibitor cocrystal structures, we designed and synthesized novel inhibitors of human arginase possessing a fused 5,5-bicyclic ring system. The prototypical member of this class, 3, when dosed orally, successfully demonstrated serum arginase inhibition and concomitant arginine elevation in a syngeneic mouse carcinoma model, despite modest oral bioavailability. Structure-based design strategies to improve the bioavailability of this class, including scaffold modification, fluorination, and installation of active-transport recognition motifs were explored.
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22
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White C, McGowan MA, Zhou H, Sciammetta N, Fradera X, Lim J, Joshi EM, Andrews C, Nickbarg EB, Cowley P, Trewick S, Augustin M, von Köenig K, Lesburg CA, Otte K, Knemeyer I, Woo H, Yu W, Cheng M, Spacciapoli P, Geda P, Song X, Smotrov N, Curran P, Heo MR, Abeywickrema P, Miller JR, Bennett DJ, Han Y. Strategic Incorporation of Polarity in Heme-Displacing Inhibitors of Indoleamine-2,3-dioxygenase-1 (IDO1). ACS Med Chem Lett 2020; 11:550-557. [PMID: 32292563 DOI: 10.1021/acsmedchemlett.0c00010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as a target of significant interest to the field of cancer immunotherapy, as the upregulation of IDO1 in certain cancers has been linked to host immune evasion and poor prognosis for patients. In particular, IDO1 inhibition is of interest as a combination therapy with immune checkpoint inhibition. Through an Automated Ligand Identification System (ALIS) screen, a diamide class of compounds was identified as a promising lead for the inhibition of IDO1. While hit 1 possessed attractive cell-based potency, it suffered from a significant right-shift in a whole blood assay, poor solubility, and poor pharmacokinetic properties. Through a physicochemical property-based approach, including a focus on lowering AlogP98 via the strategic introduction of polar substitution, compound 13 was identified bearing a pyridyl oxetane core. Compound 13 demonstrated improved whole blood potency and solubility, and an improved pharmacokinetic profile resulting in a low predicted human dose.
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23
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Zhang H, Liu K, Pu Q, Achab A, Ardolino MJ, Cheng M, Deng Y, Doty AC, Ferguson H, Fradera X, Knemeyer I, Kurukulasuriya R, Lam YH, Lesburg CA, Martinot TA, McGowan MA, Miller JR, Otte K, Biju PJ, Sciammetta N, Solban N, Yu W, Zhou H, Wang X, Bennett DJ, Han Y. Discovery of Amino-cyclobutarene-derived Indoleamine-2,3-dioxygenase 1 (IDO1) Inhibitors for Cancer Immunotherapy. ACS Med Chem Lett 2019; 10:1530-1536. [PMID: 31749906 DOI: 10.1021/acsmedchemlett.9b00344] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/18/2019] [Indexed: 12/18/2022] Open
Abstract
Checkpoint inhibitors have demonstrated unprecedented efficacy and are evolving to become standard of care for certain types of cancers. However, low overall response rates often hamper the broad utility and potential of these breakthrough therapies. Combination therapy strategies are currently under intensive investigation in the clinic, including the combination of PD-1/PD-L1 agents with IDO1 inhibitors. Here, we report the discovery of a class of IDO1 heme-binding inhibitors featuring a unique amino-cyclobutarene motif, which was discovered through SBDD from a known and weakly active inhibitor. Subsequent optimization efforts focused on improving metabolic stability and were greatly accelerated by utilizing a robust SNAr reaction of a facile nitro-furazan intermediate to quickly explore different polar side chains. As a culmination of these efforts, compound 16 was identified and demonstrated a favorable overall profile with superior potency and selectivity. Extensive studies confirmed the chemical stability and drug-like properties of compound 16, rendering it a potential drug candidate.
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24
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Siu T, Altman MD, Baltus GA, Childers M, Ellis JM, Gunaydin H, Hatch H, Ho T, Jewell J, Lacey BM, Lesburg CA, Pan BS, Sauvagnat B, Schroeder GK, Xu S. Discovery of a Novel cGAMP Competitive Ligand of the Inactive Form of STING. ACS Med Chem Lett 2019; 10:92-97. [PMID: 30655953 DOI: 10.1021/acsmedchemlett.8b00466] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/06/2018] [Indexed: 11/30/2022] Open
Abstract
Drugging large protein pockets is a challenge due to the need for higher molecular weight ligands, which generally possess undesirable physicochemical properties. In this communication, we highlight a strategy leveraging small molecule active site dimers to inhibit the large symmetric binding pocket in the STING protein. By taking advantage of the 2:1 binding stoichiometry, maximal buried interaction with STING protein can be achieved while maintaining the ligand physicochemical properties necessary for oral exposure. This mode of binding requires unique considerations for potency optimization including simultaneous optimization of protein-ligand as well as ligand-ligand interactions. Successful implementation of this strategy led to the identification of 18, which exhibits good oral exposure, slow binding kinetics, and functional inhibition of STING-mediated cytokine release.
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25
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26
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Siu T, Brubaker J, Fuller P, Torres L, Zeng H, Close J, Mampreian DM, Shi F, Liu D, Fradera X, Johnson K, Bays N, Kadic E, He F, Goldenblatt P, Shaffer L, Patel SB, Lesburg CA, Alpert C, Dorosh L, Deshmukh SV, Yu H, Klappenbach J, Elwood F, Dinsmore CJ, Fernandez R, Moy L, Young JR. The Discovery of 3-((4-Chloro-3-methoxyphenyl)amino)-1-((3R,4S)-4-cyanotetrahydro-2H-pyran-3-yl)-1H-pyrazole-4-carboxamide, a Highly Ligand Efficient and Efficacious Janus Kinase 1 Selective Inhibitor with Favorable Pharmacokinetic Properties. J Med Chem 2017; 60:9676-9690. [DOI: 10.1021/acs.jmedchem.7b01135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tony Siu
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Jason Brubaker
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Peter Fuller
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Luis Torres
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Hongbo Zeng
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Joshua Close
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Dawn M. Mampreian
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Feng Shi
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Duan Liu
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Xavier Fradera
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Kevin Johnson
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Nathan Bays
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Elma Kadic
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Fang He
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Peter Goldenblatt
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Lynsey Shaffer
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Sangita B. Patel
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Charles A. Lesburg
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Carla Alpert
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Lauren Dorosh
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Sujal V. Deshmukh
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Hongshi Yu
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Joel Klappenbach
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Fiona Elwood
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Christopher J. Dinsmore
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Rafael Fernandez
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Lily Moy
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Jonathan R. Young
- Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United
- Department of Chemistry and ◇Department of Biology, Pharmaron Beijing Co. Ltd, 6 Taihe Road BDA, Beijing 100176, P.R. China
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McComas CC, Palani A, Chang W, Holloway MK, Lesburg CA, Li P, Liverton N, Meinke PT, Olsen DB, Peng X, Soll RM, Ummat A, Wu J, Wu J, Zorn N, Ludmerer SW. Front Cover: Development of a New Structural Class of Broadly Acting HCV Non‐Nucleoside Inhibitors Leading to the Discovery of MK‐8876 (ChemMedChem 17/2017). ChemMedChem 2017. [DOI: 10.1002/cmdc.201700490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Casey C. McComas
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | - Anandan Palani
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | | | - M. Katharine Holloway
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | - Charles A. Lesburg
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | | | - Nigel Liverton
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | - Peter T. Meinke
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | - David B. Olsen
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | | | | | - Ajay Ummat
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | - Jie Wu
- WuXi AppTec Shanghai China
| | - Jin Wu
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | - Nicolas Zorn
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
| | - Steven W. Ludmerer
- Merck & Co. Inc. Kenilworth NJ USA
- Present address: International Discovery Service UnitWuXi AppTec, Inc. 1690 Sumneytown Pike, Suite 150 Lansdale PA 19446 USA
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28
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McComas CC, Palani A, Chang W, Holloway MK, Lesburg CA, Li P, Liverton N, Meinke PT, Olsen DB, Peng X, Soll RM, Ummat A, Wu J, Wu J, Zorn N, Ludmerer SW. Development of a New Structural Class of Broadly Acting HCV Non-Nucleoside Inhibitors Leading to the Discovery of MK-8876. ChemMedChem 2017; 12:1436-1448. [PMID: 28741898 DOI: 10.1002/cmdc.201700228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 04/10/2017] [Revised: 06/26/2017] [Indexed: 01/14/2023]
Abstract
Studies directed at developing a broadly acting non-nucleoside inhibitor of HCV NS5B led to the discovery of a novel structural class of 5-aryl benzofurans that simultaneously interact with both the palm I and palm II binding regions. An initial candidate was potent in vitro against HCV GT1a and GT1b replicons, and induced multi-log reductions in HCV viral load when orally dosed to chronic GT1 infected chimpanzees. However, in vitro potency losses against clinically relevant GT1a variants prompted a further effort to develop compounds with sustained potency across a broader array of HCV genotypes and mutants. Ultimately, a biology and medicinal chemistry collaboration led to the discovery of the development candidate MK-8876. MK-8876 demonstrated a pan-genotypic potency profile and maintained potency against clinically relevant mutants. It demonstrated moderate bioavailability in rats and dogs, but showed low plasma clearance characteristics consistent with once-daily dosing. Herein we describe the efforts which led to the discovery of MK-8876, which advanced into Phase 1 monotherapy studies for evaluation and characterization as a component of an all-oral direct-acting drug regimen for the treatment of chronic HCV infection.
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Affiliation(s)
- Casey C McComas
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - Anandan Palani
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | | | - M Katharine Holloway
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - Charles A Lesburg
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - Peng Li
- WuXi AppTec, Shanghai, China
| | - Nigel Liverton
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - Peter T Meinke
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - David B Olsen
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | | | | | - Ajay Ummat
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - Jie Wu
- WuXi AppTec, Shanghai, China
| | - Jin Wu
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - Nicolas Zorn
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
| | - Steven W Ludmerer
- Merck & Co. Inc., Kenilworth, NJ, USA.,Present address: International Discovery Service Unit, WuXi AppTec, Inc., 1690 Sumneytown Pike, Suite 150, Lansdale, PA, 19446, USA
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29
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Chen KX, Venkatraman S, Anilkumar GN, Zeng Q, Lesburg CA, Vibulbhan B, Velazquez F, Chan TY, Bennet F, Jiang Y, Pinto P, Huang Y, Selyutin O, Agrawal S, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG. Discovery of SCH 900188: A Potent Hepatitis C Virus NS5B Polymerase Inhibitor Prodrug As a Development Candidate. ACS Med Chem Lett 2014; 5:244-8. [PMID: 24900812 DOI: 10.1021/ml400192w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 05/17/2013] [Accepted: 08/12/2013] [Indexed: 01/28/2023] Open
Abstract
Starting from indole-based hepatitis C virus (HCV) NS5B polymerase inhibitor lead compound 1, structure modifications were performed at multiple indole substituents to improve potency and pharmacokinetic (PK) properties. Bicyclic quinazolinone was found to be the best substituent at indole nitrogen, while 4,5-furanylindole was identified as the best core. Compound 11 demonstrated excellent potency. Its C2 N,N-dimethylaminoethyl ester prodrug 12 (SCH 900188) demonstrated significant improvement in PK and was selected as the development candidate.
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Affiliation(s)
- Kevin X. Chen
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Srikanth Venkatraman
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Gopinadhan N. Anilkumar
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Qingbei Zeng
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Charles A. Lesburg
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Bancha Vibulbhan
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Francisco Velazquez
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Tin-Yau Chan
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Frank Bennet
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Yueheng Jiang
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Patrick Pinto
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Yuhua Huang
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Oleg Selyutin
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Sony Agrawal
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Hsueh-Cheng Huang
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Cheng Li
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Kuo-Chi Cheng
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Neng-Yang Shih
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Joseph A. Kozlowski
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - Stuart B. Rosenblum
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
| | - F. George Njoroge
- Merck Research Laboratories, 2015 Galloping Hill Road,
Kenilworth, New Jersey 07033, United
States
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30
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Zeng Q, Nair AG, Rosenblum SB, Huang HC, Lesburg CA, Jiang Y, Selyutin O, Chan TY, Bennett F, Chen KX, Venkatraman S, Sannigrahi M, Velazquez F, Duca JS, Gavalas S, Huang Y, Pu H, Wang L, Pinto P, Vibulbhan B, Agrawal S, Ferrari E, Jiang CK, Li C, Hesk D, Gesell J, Sorota S, Shih NY, Njoroge FG, Kozlowski JA. Discovery of an irreversible HCV NS5B polymerase inhibitor. Bioorg Med Chem Lett 2013; 23:6585-7. [DOI: 10.1016/j.bmcl.2013.10.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 12/22/2022]
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31
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Chen KX, Lesburg CA, Vibulbhan B, Yang W, Chan TY, Venkatraman S, Velazquez F, Zeng Q, Bennett F, Anilkumar GN, Duca J, Jiang Y, Pinto P, Wang L, Huang Y, Selyutin O, Gavalas S, Pu H, Agrawal S, Feld B, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG. A novel class of highly potent irreversible hepatitis C virus NS5B polymerase inhibitors. J Med Chem 2012; 55:2089-101. [PMID: 22247956 DOI: 10.1021/jm201322r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Starting from indole-based C-3 pyridone HCV NS5B polymerase inhibitor 2, structure-activity relationship (SAR) investigations of the indole N-1 benzyl moiety were performed. This study led to the discovery of irreversible inhibitors with p-fluoro-sulfone- or p-fluoro-nitro-substituted N-1 benzyl groups which achieved breakthrough replicon assay potency (EC(50) = 1 nM). The formation of a covalent bond with adjacent cysteine-366 thiol was was proved by mass spectroscopy and X-ray crystal structure studies. The C-5 ethyl C-2 carboxylic acid derivative 47 had an excellent oral area-under-the-curve (AUC) of 18 μM·h (10 mg/kg). Its oral exposure in monkeys and dogs was also very good. The NMR ALARM assay, mass spectroscopy experiments, in vitro counter screening, and toxicology assays demonstrated that the covalent bond formation between compound 47 and the protein was highly selective and specific. The overall excellent profile of 47 made it an interesting candidate for further investigation.
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Affiliation(s)
- Kevin X Chen
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA.
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32
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Chen KX, Vibulbhan B, Yang W, Sannigrahi M, Velazquez F, Chan TY, Venkatraman S, Anilkumar GN, Zeng Q, Bennet F, Jiang Y, Lesburg CA, Duca J, Pinto P, Gavalas S, Huang Y, Wu W, Selyutin O, Agrawal S, Feld B, Huang HC, Li C, Cheng KC, Shih NY, Kozlowski JA, Rosenblum SB, Njoroge FG. Structure-activity relationship (SAR) development and discovery of potent indole-based inhibitors of the hepatitis C virus (HCV) NS5B polymerase. J Med Chem 2012; 55:754-65. [PMID: 22148957 DOI: 10.1021/jm201258k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Starting with the indole-based C-3 pyridone lead HCV polymerase inhibitor 2, extensive SAR studies were performed at different positions of the indole core. The best C-5 groups were found to be compact and nonpolar moieties and that the C-6 attachments were not affecting potency. Limited N-1 benzyl-type substituent studies indicated that the best substitutions were fluoro or methyl groups at 2' or 5' positions of the benzyl group. To improve pharmacokinetic (PK) properties, acylsulfonamides were incorporated as acid isosteres at the C-2 position. Further optimization of the combination at N-1, C-2, C-5, and C-6 resulted in the identification of compound 56, which had an excellent potency in both NS5B enzyme (IC(50) = 0.008 μM) and cell-based replicon (EC(50) = 0.02 μM) assays and a good oral PK profile with area-under-the curve (AUC) of 14 and 8 μM·h in rats and dogs, respectively. X-ray structure of inhibitor 56 bound to the enzyme was also reported.
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Affiliation(s)
- Kevin X Chen
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.
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33
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Velázquez F, Venkatraman S, Lesburg CA, Duca J, Rosenblum SB, Kozlowski JA, Njoroge FG. Synthesis of New 4,5-Dihydrofuranoindoles and Their Evaluation as HCV NS5B Polymerase Inhibitors. Org Lett 2012; 14:556-9. [DOI: 10.1021/ol203177g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Francisco Velázquez
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Srikanth Venkatraman
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Charles A. Lesburg
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - José Duca
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Stuart B. Rosenblum
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - Joseph A. Kozlowski
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
| | - F. George Njoroge
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-1300, United States
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34
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Anilkumar GN, Lesburg CA, Selyutin O, Rosenblum SB, Zeng Q, Jiang Y, Chan TY, Pu H, Vaccaro H, Wang L, Bennett F, Chen KX, Duca J, Gavalas S, Huang Y, Pinto P, Sannigrahi M, Velazquez F, Venkatraman S, Vibulbhan B, Agrawal S, Butkiewicz N, Feld B, Ferrari E, He Z, Jiang CK, Palermo RE, Mcmonagle P, Huang HC, Shih NY, Njoroge G, Kozlowski JA. I. Novel HCV NS5B polymerase inhibitors: Discovery of indole 2-carboxylic acids with C3-heterocycles. Bioorg Med Chem Lett 2011; 21:5336-41. [DOI: 10.1016/j.bmcl.2011.07.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 11/25/2022]
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35
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Xiao L, Nickbarg E, Wang W, Thomas A, Ziebell M, Prosise WW, Lesburg CA, Taremi SS, Gerlach VL, Le HV, Cheng KC. Evaluation of in vitro PXR-based assays and in silico modeling approaches for understanding the binding of a structurally diverse set of drugs to PXR. Biochem Pharmacol 2011; 81:669-79. [DOI: 10.1016/j.bcp.2010.12.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 11/30/2010] [Accepted: 12/02/2010] [Indexed: 02/04/2023]
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36
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Newman J, Pearce L, Lesburg CA, Strickland C, Peat TS. Crystallization of an apo form of human arginase: using all the tools in the toolbox simultaneously. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:90-3. [PMID: 21206033 PMCID: PMC3079981 DOI: 10.1107/s1744309110046208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 11/09/2010] [Indexed: 11/10/2022]
Abstract
Arginase (EC 3.5.3.1) is an aminohydrolase that acts on L-arginine to produce urea and ornithine. Two isotypes of the enzyme are found in humans. Type I is predominantly produced in the liver and is a homotrimer of 35 kDa subunits. Human arginase (hArginase) I is seen to be up-regulated in many diseases and is a potential therapeutic target for many diverse indications. Previous reports of crystallization and structure determination of hArginase have always included inhibitors of the enzyme: here, the first case of a true apo crystal form of the enzyme which is suitable for small-molecule soaking is reported. The crystals belonged to space group P2(1)2(1)2(1) and have approximate unit-cell parameters a=53, b=67.5, c=250 Å. The crystals showed slightly anisotropic diffraction to beyond 2.0 Å resolution.
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Affiliation(s)
- Janet Newman
- Materials Science and Engineering, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.
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37
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Cheng CC, Shipps GW, Yang Z, Kawahata N, Lesburg CA, Duca JS, Bandouveres J, Bracken JD, Jiang CK, Agrawal S, Ferrari E, Huang HC. Inhibitors of hepatitis C virus polymerase: Synthesis and characterization of novel 2-oxy-6-fluoro-N-((S)-1-hydroxy-3-phenylpropan-2-yl)-benzamides. Bioorg Med Chem Lett 2010; 20:2119-24. [DOI: 10.1016/j.bmcl.2010.02.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 02/11/2010] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
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38
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Sheth PR, Basso A, Duca JS, Lesburg CA, Ogas P, Gray K, Nale L, Mannarino AF, Prongay AJ, Le HV. Thermodynamics of nucleotide and inhibitor binding to wild-type and ispinesib-resistant forms of human kinesin spindle protein. Biochemistry 2009; 48:11045-55. [PMID: 19824700 DOI: 10.1021/bi900946r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Current antimitotic cancer chemotherapy based on vinca alkaloids and taxanes target tubulin, a protein required not only for mitotic spindle formation but also for the overall structural integrity of terminally differentiated cells. Among many innovations targeting specific mitotic events, inhibition of motor enzymes including KSP (or Eg5) has been validated as a highly productive approach. Many reported KSP inhibitors bind to an induced allosteric site near the site of ATP hydrolysis, and some have been tested in clinical trials with varying degrees of success. This allosteric site was defined in detail by X-ray crystallography of inhibitor complexes, yet complementary information on binding thermodynamics is still lacking. Using two model ATP-uncompetitive inhibitors, monastrol and ispinesib, we report here the results of thermal denaturation and isothermal titration calorimetric studies. These binding studies were conducted with the wild-type KSP motor domain as well as two ispinesib mutants (D130V and A133D) identified to confer resistance to ispinesib treatment. The thermodynamic parameters obtained were placed in the context of the available structural information and corresponding models of the two ispinesib-resistant mutants. The resulting overall information formed a strong basis for future structure-based design of inhibitors of KSP and related motor enzymes.
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Affiliation(s)
- Payal R Sheth
- Protein Science Department, Schering-Plough Research Institute, 320 Bent Street, Cambridge, Massachusetts 02141, USA.
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39
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Lesburg CA, Duca JS. soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts. Nucleic Acids Res 2008; 36:W252-4. [PMID: 18487276 PMCID: PMC2447792 DOI: 10.1093/nar/gkn270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
soaPDB is a web application that allows generation and organization of saved PDB searches, and offers automatic email alerts. This tool is used from a web interface to store PDB searches and results in a backend relational database. Written using the Ruby on Rails open-source web framework, soaPDB is easy to deploy, maintain and customize. soaPDB is freely available upon request for local installation and is also available at http://soapdb.dyndns.org:3000.
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Affiliation(s)
- Charles A Lesburg
- Department of Drug Design, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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40
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Lesburg CA, Christianson DW. X-ray crystallographic studies of engineered hydrogen bond networks in a protein-zinc binding site. J Am Chem Soc 2002. [DOI: 10.1021/ja00131a005] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Affiliation(s)
- J A Hunt
- Novartis Agribusiness, Inc., 3054 Cornwallis Rd., Research Triangle Park, NC 27709, USA
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42
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Lesburg CA, Radfar R, Weber PC. Recent advances in the analysis of HCV NS5B RNA-dependent RNA polymerase. Curr Opin Investig Drugs 2000; 1:289-96. [PMID: 11249710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
An RNA-dependent RNA polymerase denoted nonstructural protein 5B (NS5B) is the central enzyme in replication of the hepatitis C virus genome. Recent advances in the biochemical and structural understanding of NS5B include solubilization and purification of the full-length enzyme and various truncated forms. In vitro conditions for NS5B-catalyzed primer elongation using both homo- and heteropolymeric RNA templates were discovered. The crystal structure of the NS5B apoenzyme revealed a globular shape unique among polymerases, and implicated new structural features important for binding the RNA template and cognate ribonucleotide substrates. The crystallographic results also provided a structure-based framework for biochemical analyses and drug-design efforts. Finally, inhibitors of HCV RNA-dependent RNA polymerase have been reported.
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Affiliation(s)
- C A Lesburg
- Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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43
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Zhong W, Ferrari E, Lesburg CA, Maag D, Ghosh SK, Cameron CE, Lau JY, Hong Z. Template/primer requirements and single nucleotide incorporation by hepatitis C virus nonstructural protein 5B polymerase. J Virol 2000; 74:9134-43. [PMID: 10982360 PMCID: PMC102112 DOI: 10.1128/jvi.74.19.9134-9143.2000] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [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: 11/20/2022] Open
Abstract
Nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) possesses an RNA-dependent RNA polymerase activity responsible for viral genome RNA replication. Despite several reports on the characterization of this essential viral enzyme, little is known about the reaction pathway of NS5B-catalyzed nucleotide incorporation due to the lack of a kinetic system offering efficient assembly of a catalytically competent polymerase/template/primer/nucleotide quaternary complex. In this report, specific template/primer requirements for efficient RNA synthesis by HCV NS5B were investigated. For intramolecular copy-back RNA synthesis, NS5B utilizes templates with an unstable stem-loop at the 3' terminus which exists as a single-stranded molecule in solution. A template with a stable tetraloop at the 3' terminus failed to support RNA synthesis by HCV NS5B. Based on these observations, a number of single-stranded RNA templates were synthesized and tested along with short RNA primers ranging from two to five nucleotides. It was found that HCV NS5B utilized di- or trinucleotides efficiently to initiate RNA replication. Furthermore, the polymerase, template, and primer assembled initiation-competent complexes at the 3' terminus of the template RNA where the template and primer base paired within the active site cavity of the polymerase. The minimum length of the template is five nucleotides, consistent with a structural model of the NS5B/RNA complex in which a pentanucleotide single-stranded RNA template occupies a groove located along the fingers subdomain of the polymerase. This observation suggests that the initial docking of RNA on NS5B polymerase requires a single-stranded RNA molecule. A unique beta-hairpin loop in the thumb subdomain may play an important role in properly positioning the single-stranded template for initiation of RNA synthesis. Identification of the template/primer requirements will facilitate the mechanistic characterization of HCV NS5B and its inhibitors.
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Affiliation(s)
- W Zhong
- Department of Antiviral Therapy, Schering-Plough Research Institute, Kenilworth, New Jersey 07033-0539, USA
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44
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Lesburg CA, Cable MB, Ferrari E, Hong Z, Mannarino AF, Weber PC. Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nat Struct Biol 1999; 6:937-43. [PMID: 10504728 DOI: 10.1038/13305] [Citation(s) in RCA: 621] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Various classes of nucleotidyl polymerases with different transcriptional roles contain a conserved core structure. Less is known, however, about the distinguishing features of these enzymes, particularly those of the RNA-dependent RNA polymerase class. The 1. 9 A resolution crystal structure of hepatitis C virus (HCV) nonstructural protein 5B (NS5B) presented here provides the first complete and detailed view of an RNA-dependent RNA polymerase. While canonical polymerase features exist in the structure, NS5B adopts a unique shape due to extensive interactions between the fingers and thumb polymerase subdomains that serve to encircle the enzyme active site. Several insertions in the fingers subdomain account for intersubdomain linkages that include two extended loops and a pair of antiparallel alpha-helices. The HCV NS5B apoenzyme structure reported here can accommodate a template:primer duplex without global conformational changes, supporting the hypothesis that this structure is essentially preserved during the reaction pathway. This NS5B template:primer model also allows identification of a new structural motif involved in stabilizing the nascent base pair.
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Affiliation(s)
- C A Lesburg
- Department of Structural Chemistry, Schering-Plough Research Institute, Kenilworth, New Jersey 07033, USA
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45
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Lesburg CA, Caruthers JM, Paschall CM, Christianson DW. Managing and manipulating carbocations in biology: terpenoid cyclase structure and mechanism. Curr Opin Struct Biol 1998; 8:695-703. [PMID: 9914250 DOI: 10.1016/s0959-440x(98)80088-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.8] [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: 10/18/2022]
Abstract
Terpenoid cyclases catalyze remarkably complex cyclization cascades that are initiated by the formation of a highly reactive carbocation in a polyisoprene substrate. Recent crystal structures of terpenoid cyclases show how these enzymes provide a template for binding and stabilizing the flexible substrate in the precise orientation required for catalysis, trigger carbocation formation, chaperone the conformations of the reactive carbocation intermediates through a unique cyclization sequence, and sequester and stabilize carbocations from premature quenching. Notably, terpenoid cyclases and catalytic antibodies have converged to similar chemical and structural strategies for managing highly reactive carbocations in polyisoprene cyclization cascades.
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Affiliation(s)
- C A Lesburg
- Department of Structural Chemistry Schering-Plough Research Institute 2015 Galloping Hill Road Kenilworth NJ 07033-0539 USA
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46
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Lesburg CA, Huang C, Christianson DW, Fierke CA. Histidine --> carboxamide ligand substitutions in the zinc binding site of carbonic anhydrase II alter metal coordination geometry but retain catalytic activity. Biochemistry 1997; 36:15780-91. [PMID: 9398308 DOI: 10.1021/bi971296x] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [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: 02/05/2023]
Abstract
The catalytic zinc ion of human carbonic anhydrase II (CAII) is coordinated by three histidine ligands (H94, H96, and H119) and a hydroxide ion with tetrahedral geometry. Structural and functional analysis of variants in which the zinc ligands H94 and H119 are substituted with asparagine and glutamine, and comparison with results obtained with aspartate and glutamate substitutions indicate that the neutral ligand field provided by the protein optimizes the electrostatic environment for the catalytic function of the metal ion, including stabilization of bound anions. This is demonstrated by catalytic activity measurements for ester hydrolysis and CO2 hydration, as well as sulfonamide inhibitor affinity assays. High-resolution X-ray crystal structure determinations of H94N, H119N, and H119Q CAIIs reveal that the engineered carboxamide side chains coordinate to zinc with optimal stereochemistry. However, zinc coordination geometry remains tetrahedral only in H119Q CAII. Metal geometry changes to trigonal bipyramidal in H119N CAII due to the addition of a second water molecule to the zinc coordination polyhedron and also in H94N CAII due to the displacement of zinc-bound hydroxide by the bidentate coordination of a Tris molecule. Possibly, the bulky histidine imidazole ligands of the native enzyme play a role in disfavoring trigonal bipyramidal coordination geometry for zinc. Protein-metal affinity is significantly compromised by all histidine --> carboxamide ligand substitutions. Diminished affinity may result from significant movements (up to 1 A) of the metal ion from its position in the wild-type enzyme, as well as the associated, minor conformational changes of metal ligands and their neighboring residues.
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Affiliation(s)
- C A Lesburg
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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47
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Abstract
The crystal structure of pentalenene synthase at 2.6 angstrom resolution reveals critical active site features responsible for the cyclization of farnesyl diphosphate into the tricyclic hydrocarbon pentalenene. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. The core active site structure of the enzyme may be preserved among the greater family of terpenoid synthases, possibly implying divergence from a common ancestral synthase to satisfy biological requirements for increasingly diverse natural products.
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Affiliation(s)
- C A Lesburg
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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48
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Huang CC, Lesburg CA, Kiefer LL, Fierke CA, Christianson DW. Reversal of the hydrogen bond to zinc ligand histidine-119 dramatically diminishes catalysis and enhances metal equilibration kinetics in carbonic anhydrase II. Biochemistry 1996; 35:3439-46. [PMID: 8639494 DOI: 10.1021/bi9526692] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.0] [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: 02/01/2023]
Abstract
Direct metal ligands to transition metals in metalloproteins exert a profound effect on protein-metal affinity and function. Indirect ligands, i.e., second-shell residues that hydrogen bond to direct metal ligands, typically exert more subtle effects on the chemical properties of the protein-metal complex. However, E117 of human carbonic anhydrase II (CAII), which is part of the E117-119-Zn(2+) triad, is a notable exception: E117-substituted CAIIs exhibit dramatically increased kinetics of zinc complexation, and the E117Q variant exhibits enormously diminished catalytic activity and sulfonamide affinity. The three-dimensional structures of zinc-bound and zinc-free E117Q CAII reveal no discrete structural changes in the active site that are responsible for enhanced zinc equilibration kinetics and decreased activity. Additionally, the structure of the acetazolamide complex is essentially identical to that of the wild-type enzyme despite the 10(4)-fold loss of enzyme-inhibitor affinity. We conclude, therefore, that the functional differences between E117Q and wild-type CAIIs arise from electrostatic and not structural differences in the active site. We propose that the E117Q substitution reverses the polarity of the residue 117-H119 hydrogen bond, thereby stabilizing H119 as a histidinate anion in the E117Q CAII holoenzyme. The additional negative charge in the first coordination sphere of the metal ion increases the pK(a) of the zinc-water ligand, destabilizes the transition state for CO(2) hydration, and facilitates the exchange of a zinc-histidine ligand with an additional water molecule by decreasing the stability of the tetrahedral zinc complex. These novel properties engineered into E117Q CAII facilitate the exploitation of CAII as a rapid and sensitive Zn(2+) biosensor.
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Affiliation(s)
- C C Huang
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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49
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Abstract
Recombinant pentalenene synthase, a 42.5-kDa sesquiterpene cyclase originally isolated from Streptomyces UC5319 and cloned in Escherichia coli, has been crystallized in space group P6(3) with unit cell dimensions a = b = 183.5 A and c = 56.5 A. Hexagonal prismatic crystals, approximately 0.2 x 0.2 x 0.3 mm, diffract to approximately 2.9 A resolution using monochromatic synchrotron radiation. From the universal (and achiral) building block, farnesyl pyrophosphate, pentalenene synthase catalyzes the formation of four stereocenters in the construction of the three fused five-membered rings of pentalenene; this novel sesquiterpene is a precursor to the pentalenolactone family of antibiotics.
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Affiliation(s)
- C A Lesburg
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA
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