1
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Liu Y, Ma J, DesJarlais RL, Hagan R, Rech J, Liu C, Miller R, Schoellerman J, Luo J, Letavic M, Grasberger B, Maher MP. Molecular determinants of ASIC1 modulation by divalent cations. Sci Rep 2024; 14:2320. [PMID: 38282035 PMCID: PMC10822848 DOI: 10.1038/s41598-024-52845-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/07/2023] [Accepted: 01/24/2024] [Indexed: 01/30/2024] Open
Abstract
Acid-sensing ion channels (ASICs) are proton-gated cation channels widely expressed in the nervous system. ASIC gating is modulated by divalent cations as well as small molecules; however, the molecular determinants of gating modulation by divalent cations are not well understood. Previously, we identified two small molecules that bind to ASIC1a at a novel site in the acidic pocket and modulate ASIC1 gating in a manner broadly resembling divalent cations, raising the possibility that these small molecules may help to illuminate the molecular determinants of gating modulation by divalent cations. Here, we examined how these two groups of modulators might interact as well as mutational effects on ASIC1a gating and its modulation by divalent cations. Our results indicate that binding of divalent cations to an acidic pocket site plays a key role in gating modulation of the channel.
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Affiliation(s)
- Yi Liu
- Neuroscience Discovery, Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Jichun Ma
- Therapeutics Discovery, Janssen Research & Development, L.L.C., Welsh & McKean Roads, P.O. Box 776, Spring House, PA, 19477, USA
| | - Renee L DesJarlais
- Therapeutics Discovery, Janssen Research & Development, L.L.C., Welsh & McKean Roads, P.O. Box 776, Spring House, PA, 19477, USA
| | - Rebecca Hagan
- Neuroscience Discovery, Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Jason Rech
- Therapeutics Discovery, Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Changlu Liu
- Neuroscience Discovery, Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Robyn Miller
- Therapeutics Discovery, Janssen Research & Development, L.L.C., Welsh & McKean Roads, P.O. Box 776, Spring House, PA, 19477, USA
| | - Jeffrey Schoellerman
- Neuroscience Discovery, Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Jinquan Luo
- Therapeutics Discovery, Janssen Research & Development, L.L.C., Welsh & McKean Roads, P.O. Box 776, Spring House, PA, 19477, USA
| | - Michael Letavic
- Therapeutics Discovery, Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Bruce Grasberger
- Therapeutics Discovery, Janssen Research & Development, L.L.C., Welsh & McKean Roads, P.O. Box 776, Spring House, PA, 19477, USA
| | - Michael P Maher
- Neuroscience Discovery, Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, USA.
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2
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Xu G, Liu Z, Wang X, Lu T, DesJarlais RL, Thieu T, Zhang J, Devine ZH, Du F, Li Q, Milligan CM, Shaffer P, Cedervall PE, Spurlino JC, Stratton CF, Pietrak B, Szewczuk LM, Wong V, Steele RA, Bruinzeel W, Chintala M, Silva J, Gaul MD, Macielag MJ, Nargund R. Discovery of Potent and Orally Bioavailable Pyridine N-Oxide-Based Factor XIa Inhibitors through Exploiting Nonclassical Interactions. J Med Chem 2022; 65:10419-10440. [PMID: 35862732 DOI: 10.1021/acs.jmedchem.2c00442] [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: 11/30/2022]
Abstract
Activated factor XI (FXIa) inhibitors are promising novel anticoagulants with low bleeding risk compared with current anticoagulants. The discovery of potent FXIa inhibitors with good oral bioavailability has been challenging. Herein, we describe our discovery effort, utilizing nonclassical interactions to improve potency, cellular permeability, and oral bioavailability by enhancing the binding while reducing polar atoms. Beginning with literature-inspired pyridine N-oxide-based FXIa inhibitor 1, the imidazole linker was first replaced with a pyrazole moiety to establish a polar C-H···water hydrogen-bonding interaction. Then, structure-based drug design was employed to modify lead molecule 2d in the P1' and P2' regions, with substituents interacting with key residues through various nonclassical interactions. As a result, a potent FXIa inhibitor 3f (Ki = 0.17 nM) was discovered. This compound demonstrated oral bioavailability in preclinical species (rat 36.4%, dog 80.5%, and monkey 43.0%) and displayed a dose-dependent antithrombotic effect in a rabbit arteriovenous shunt model of thrombosis.
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Affiliation(s)
- Guozhang Xu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Zhijie Liu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Xinkang Wang
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Tianbao Lu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Renee L DesJarlais
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Tho Thieu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Jing Zhang
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Zheng Huang Devine
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Fuyong Du
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Qiu Li
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Cynthia M Milligan
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Paul Shaffer
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Peder E Cedervall
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - John C Spurlino
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Christopher F Stratton
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Beth Pietrak
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Lawrence M Szewczuk
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Victoria Wong
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Ruth A Steele
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Wouter Bruinzeel
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Madhu Chintala
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Jose Silva
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Michael D Gaul
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Mark J Macielag
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Ravi Nargund
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
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3
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Seierstad M, Tichenor MS, DesJarlais RL, Na J, Bacani GM, Chung DM, Mercado-Marin EV, Steffens HC, Mirzadegan T. Novel Reagent Space: Identifying Unorderable but Readily Synthesizable Building Blocks. ACS Med Chem Lett 2021; 12:1853-1860. [PMID: 34795876 DOI: 10.1021/acsmedchemlett.1c00340] [Citation(s) in RCA: 3] [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] [Received: 06/14/2021] [Accepted: 10/01/2021] [Indexed: 01/14/2023] Open
Abstract
Drug discovery building blocks available commercially or within an internal inventory cover a diverse range of chemical space and yet describe only a tiny fraction of all chemically feasible reagents. Vendors will eagerly provide tools to search the former; there is no straightforward method of mining the latter. We describe a procedure and use case in assembling chemical structures not available for purchase but that could likely be synthesized in one robust chemical transformation starting from readily available building blocks. Accessing this vast virtual chemical space dramatically increases our curated collection of reagents available for medicinal chemistry exploration and novel hit generation, almost tripling the number of those with 10 or fewer atoms.
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Affiliation(s)
- Mark Seierstad
- Janssen Research and Development, San Diego, California 92121, United States
| | - Mark S. Tichenor
- Janssen Research and Development, San Diego, California 92121, United States
| | - Renee L. DesJarlais
- Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Jim Na
- Janssen Research and Development, San Diego, California 92121, United States
| | - Genesis M. Bacani
- Janssen Research and Development, San Diego, California 92121, United States
| | - De Michael Chung
- Janssen Research and Development, San Diego, California 92121, United States
| | | | - Helena C. Steffens
- Janssen Research and Development, San Diego, California 92121, United States
| | - Taraneh Mirzadegan
- Janssen Research and Development, San Diego, California 92121, United States
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4
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Xu G, Gaul MD, Liu Z, DesJarlais RL, Qi J, Wang W, Krosky D, Petrounia I, Milligan CM, Hermans A, Lu HR, Huang DZ, Xu JZ, Spurlino JC. Hit-to-lead optimization and discovery of a potent, and orally bioavailable G protein coupled receptor kinase 2 (GRK2) inhibitor. Bioorg Med Chem Lett 2020; 30:127602. [PMID: 33038544 DOI: 10.1016/j.bmcl.2020.127602] [Citation(s) in RCA: 2] [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: 08/08/2020] [Revised: 09/26/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022]
Abstract
G-protein coupled receptor kinase 2 (GRK2), which is upregulated in the failing heart, appears to play a critical role in heart failure (HF) progression in part because enhanced GRK2 activity promotes dysfunction of β-adrenergic signaling and myocyte death. An orally bioavailable GRK2 inhibitor could offer unique therapeutic outcomes that cannot be attained by current heart failure treatments that directly target GPCRs or angiotensin-converting enzyme. Herein, we describe the discovery of a potent, selective, and orally bioavailable GRK2 inhibitor, 8h, through high-throughput screening, hit-to-lead optimization, structure-based design, molecular modelling, synthesis, and biological evaluation. In the cellular target engagement assays, 8h enhances isoproterenol-mediated cyclic adenosine 3',5'-monophosphate (cAMP) production in HEK293 cells overexpressing GRK2. Compound 8h was further evaluated in a human stem cell-derived cardiomyocyte (HSC-CM) contractility assay and potentiated isoproterenol-induced beating rate in HSC-CMs.
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Affiliation(s)
- Guozhang Xu
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States.
| | - Michael D Gaul
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - Zhijie Liu
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - Renee L DesJarlais
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - Jenson Qi
- Cardiovascular & Metabolic Research, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - Weixue Wang
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - Daniel Krosky
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - Ioanna Petrounia
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - Cynthia M Milligan
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - An Hermans
- Discovery Sciences, Janssen Research & Development, LLC, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Hua-Rong Lu
- Discovery Sciences, Janssen Research & Development, LLC, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Devine Zheng Huang
- Cardiovascular & Metabolic Research, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - June Zhi Xu
- Cardiovascular & Metabolic Research, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
| | - John C Spurlino
- Discovery Sciences, Janssen Research & Development, L.L.C., Welsh & McKean Roads, Spring House, PA 19477, United States
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5
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DeRatt LG, Lawson EC, Kumar K, Hwang SS, DesJarlais RL, Kuduk SD. Tandem Suzuki Coupling/Intramolecular Oxetane Ring Opening to Form Polycyclic Ring Systems. Org Lett 2020; 22:5828-5832. [PMID: 32702238 DOI: 10.1021/acs.orglett.0c01899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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
A tandem one-pot reaction featuring a cross-coupling followed by an intramolecular oxetane ring opening by mild nucleophiles is reported. The overall transformation comprises a carbon-carbon bond formation along with a carbon-heteroatom bond construction providing diverse multicyclic ring systems with a pendant hydroxymethyl handle for further elaboration. This approach constitutes a convergent method for rapid access to various scaffolds. Furthermore, a comparison of computed low-energy conformers is presented to rationalize instances in which cyclization was not observed.
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Affiliation(s)
- Lindsey G DeRatt
- Discovery Chemistry, Janssen Pharmaceutical Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Edward C Lawson
- Discovery Chemistry, Janssen Pharmaceutical Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Kiran Kumar
- Discovery Chemistry, Janssen Pharmaceutical Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Soyon S Hwang
- Discovery Chemistry, Janssen Pharmaceutical Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Renee L DesJarlais
- Discovery Chemistry, Janssen Pharmaceutical Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Scott D Kuduk
- Discovery Chemistry, Janssen Pharmaceutical Research and Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
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6
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Struble TJ, Alvarez JC, Brown SP, Chytil M, Cisar J, DesJarlais RL, Engkvist O, Frank SA, Greve DR, Griffin DJ, Hou X, Johannes JW, Kreatsoulas C, Lahue B, Mathea M, Mogk G, Nicolaou CA, Palmer AD, Price DJ, Robinson RI, Salentin S, Xing L, Jaakkola T, Green WH, Barzilay R, Coley CW, Jensen KF. Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis. J Med Chem 2020; 63:8667-8682. [PMID: 32243158 PMCID: PMC7457232 DOI: 10.1021/acs.jmedchem.9b02120] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [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: 12/20/2022]
Abstract
![]()
Artificial
intelligence and machine learning have demonstrated
their potential role in predictive chemistry and synthetic planning
of small molecules; there are at least a few reports of companies
employing in silico synthetic planning into their
overall approach to accessing target molecules. A data-driven synthesis
planning program is one component being developed and evaluated by
the Machine Learning for Pharmaceutical Discovery and Synthesis (MLPDS)
consortium, comprising MIT and 13 chemical and pharmaceutical company
members. Together, we wrote this perspective to share how we think
predictive models can be integrated into medicinal chemistry synthesis
workflows, how they are currently used within MLPDS member companies,
and the outlook for this field.
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Affiliation(s)
- Thomas J Struble
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck & Co. Inc., Kenilworth, New Jersey 07033, United States
| | - Scott P Brown
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Milan Chytil
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Justin Cisar
- Janssen Research & Development LLC, Spring House, Pennsylvania 19477, United States
| | - Renee L DesJarlais
- Janssen Research & Development LLC, Spring House, Pennsylvania 19477, United States
| | - Ola Engkvist
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Scott A Frank
- Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Daniel R Greve
- LEO Pharma A/S, Industriparken 55, DK-2750 Ballerup, Denmark
| | | | - Xinjun Hou
- Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Jeffrey W Johannes
- Medicinal Chemistry, Early Oncology, Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Brian Lahue
- Computational and Structural Chemistry, Merck & Co. Inc., Kenilworth, New Jersey 07033, United States
| | - Miriam Mathea
- BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | | | | | - Andrew D Palmer
- BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Daniel J Price
- GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Richard I Robinson
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Li Xing
- WuXi AppTec, Cambridge, Massachusetts 02142, United States
| | - Tommi Jaakkola
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, United States
| | - William H Green
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Regina Barzilay
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, United States
| | - Connor W Coley
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Klavs F Jensen
- Department of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
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7
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Damm-Ganamet KL, DesJarlais RL, Marrone T, Shih AY, Schiffer JM, Perez-Benito L, Mirzadegan T. Breaking the Glass Ceiling in Simulation and Modeling: Women in Pharmaceutical Discovery. J Med Chem 2020; 63:1929-1936. [PMID: 31913036 DOI: 10.1021/acs.jmedchem.9b01512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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
The topic of gender equality within the United States workforce is receiving a great deal of attention. The field of chemistry is no exception and is increasingly focused on taking steps to achieve gender diversity within the chemistry workforce. Over the past several years, many computational chemistry groups within large pharmaceutical companies have realized growth in the number of women, and here we discuss the key factors that we believe have played a role in attracting and retaining the authors of this review as computational chemists in pharma. Furthermore, we combine our professional experiences in the context of how computational methodology and technology have evolved over the past decades and how that evolution has facilitated the inclusion of more women into the field. Our hope is to be a part of a solution and provide insight that will allow the chemistry workforce to continue to make steps forward in attaining gender diversity in the workplace.
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Affiliation(s)
- Kelly L Damm-Ganamet
- Discovery Sciences, Janssen Research and Development, San Diego, California 92121, United States
| | - Renee L DesJarlais
- Discovery Sciences, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Tami Marrone
- Discovery Sciences, Janssen Research and Development, San Diego, California 92121, United States
| | - Amy Y Shih
- Discovery Sciences, Janssen Research and Development, San Diego, California 92121, United States
| | - Jamie M Schiffer
- Discovery Sciences, Janssen Research and Development, San Diego, California 92121, United States
| | - Laura Perez-Benito
- Discovery Sciences, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Taraneh Mirzadegan
- Discovery Sciences, Janssen Research and Development, San Diego, California 92121, United States
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8
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Xu G, Gaul MD, Song F, Du F, Liang Y, DesJarlais RL, DiLoreto K, Shook B, Rentzeperis D, Santulli R, Eckardt A, Demarest K. Discovery of potent and orally bioavailable indazole-based glucagon receptor antagonists for the treatment of type 2 diabetes. Bioorg Med Chem Lett 2019; 29:126668. [DOI: 10.1016/j.bmcl.2019.126668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/27/2022]
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9
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Song F, Xu G, Gaul MD, Zhao B, Lu T, Zhang R, DesJarlais RL, DiLoreto K, Huebert N, Shook B, Rentzeperis D, Santulli R, Eckardt A, Demarest K. Design, synthesis and structure activity relationships of indazole and indole derivatives as potent glucagon receptor antagonists. Bioorg Med Chem Lett 2019; 29:1974-1980. [DOI: 10.1016/j.bmcl.2019.05.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/02/2023]
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10
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Zhang YM, Greco MN, Macielag MJ, Teleha CA, DesJarlais RL, Tang Y, Ho G, Hou C, Chen C, Zhao S, Kauffman J, Camacho R, Qi J, Murray W, Demarest K, Leonard J. 6-Benzhydryl-4-amino-quinolin-2-ones as Potent Cannabinoid Type 1 (CB 1) Receptor Inverse Agonists and Chemical Modifications for Peripheral Selectivity. J Med Chem 2018; 61:10276-10298. [PMID: 30339387 DOI: 10.1021/acs.jmedchem.8b01467] [Citation(s) in RCA: 10] [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] [Indexed: 12/14/2022]
Abstract
A novel series of 6-benzhydryl-4-amino-quinolin-2-ones was discovered as cannabinoid type 1 receptor (CB1R) inverse agonists based on the high-throughput screening hit, compound 1a. Structure-activity relationships were studied to improve in vitro/in vivo pharmacology and restrict distribution to the peripheral circulation. We adopted several strategies such as increasing topological polar surface area, incorporating discrete polyethylene glycol side chains, and targeting P-glycoprotein (P-gp) to minimize access to the brain. Compound 6a is a P-gp substrate and a potent and highly selective CB1R inverse agonist, demonstrating excellent in vivo metabolic stability and a low brain to plasma ratio. However, brain receptor occupancy studies showed that compound 6a may accumulate in brain with repeat dosing. This was evidenced by compound 6a inhibiting food intake and inducing weight loss in diet-induced obese mice. Thus, a strategy based on P-gp efflux may not be adequate for peripheral restriction of the disclosed quinolinone series.
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Affiliation(s)
- Yue-Mei Zhang
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Michael N Greco
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Mark J Macielag
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Christopher A Teleha
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Renee L DesJarlais
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Yuting Tang
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - George Ho
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Cuifen Hou
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Cailin Chen
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Shuyuan Zhao
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Jack Kauffman
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Raul Camacho
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Jenson Qi
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - William Murray
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - Keith Demarest
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
| | - James Leonard
- Janssen Research & Development , 1400 McKean Road , Spring House , Pennsylvania 19477-0776 , United States
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11
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Illig CR, Manthey CL, Meegalla SK, Wall MJ, Chen J, Wilson KJ, DesJarlais RL, Ballentine SK, Schubert C, Crysler CS, Chen Y, Molloy CJ, Chaikin MA, Donatelli RR, Yurkow E, Zhou Z, Player MR, Tomczuk BE. Enhancement of kinase selectivity in a potent class of arylamide FMS inhibitors. Bioorg Med Chem Lett 2013; 23:6363-9. [PMID: 24138939 DOI: 10.1016/j.bmcl.2013.09.061] [Citation(s) in RCA: 3] [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: 05/29/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 11/18/2022]
Abstract
Structure-activity relationship (SAR) studies on a highly potent series of arylamide FMS inhibitors were carried out with the aim of improving FMS kinase selectivity, particularly over KIT. Potent compound 17r (FMS IC50 0.7 nM, FMS cell IC50 6.1 nM) was discovered that had good PK properties and a greater than fivefold improvement in selectivity for FMS over KIT kinase in a cellular assay relative to the previously reported clinical candidate 4. This improved selectivity was manifested in vivo by no observed decrease in circulating reticulocytes, a measure of bone safety, at the highest studied dose. Compound 17r was highly active in a mouse pharmacodynamic model and demonstrated disease-modifying effects in a dose-dependent manner in a strep cell wall-induced arthritis model of rheumatoid arthritis in rats.
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Affiliation(s)
- Carl R Illig
- Janssen Pharmaceutical Research & Development LLC, Welsh & McKean Roads, Spring House, PA 19477, USA
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12
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DesJarlais RL. Insights from structural analysis of cFMS/inhibitor complexes: common interactions via three structurally dissimilar scaffolds. Curr Top Med Chem 2012; 12:1271-81. [PMID: 22571789 DOI: 10.2174/156802612800672835] [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] [Received: 02/09/2012] [Revised: 02/14/2012] [Accepted: 02/16/2012] [Indexed: 11/22/2022]
Abstract
A small-molecule drug discovery effort can benefit from having several chemical series. Where multiple series are not available, it is often the goal of a project to find novel scaffolds. Structural studies of ligand/protein complexes provide important information on the interactions driving binding. By generalizing these, it is possible to find molecules lacking in similarity in their connectivity yet retaining the ability to interact with the same target protein. Our studies on inhibitors of the cFMS tyrosine kinase provide a dramatic example of three different chemical series that make the same key interactions with the target protein. Collectively, these structural data provide a striking example of the pharmacophore hypothesis at work. In addition, they should prompt one to employ a broad approach when attempting scaffold hopping or any search for a novel series. It is clear that molecules that bind with similar interactions to a target need not possess 2-dimensional molecular similarity.
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Affiliation(s)
- Renee L DesJarlais
- Community of Research Excellence & Advanced Technology (CREATe), Department of Structural Biology, Janssen Pharmaceutical Companies of Johnson and Johnson, Welsh and McKean Roads, Spring House, PA 19477-0776, USA.
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13
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Illig CR, Manthey CL, Wall MJ, Meegalla SK, Chen J, Wilson KJ, Ballentine SK, DesJarlais RL, Schubert C, Crysler CS, Chen Y, Molloy CJ, Chaikin MA, Donatelli RR, Yurkow E, Zhou Z, Player MR, Tomczuk BE. Optimization of a Potent Class of Arylamide Colony-Stimulating Factor-1 Receptor Inhibitors Leading to Anti-inflammatory Clinical Candidate 4-Cyano-N-[2-(1-cyclohexen-1-yl)-4-[1-[(dimethylamino)acetyl]-4-piperidinyl]phenyl]-1H-imidazole-2-carboxamide (JNJ-28312141). J Med Chem 2011; 54:7860-83. [DOI: 10.1021/jm200900q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Carl R. Illig
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Carl L. Manthey
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Mark J. Wall
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Sanath K. Meegalla
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jinsheng Chen
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Kenneth J. Wilson
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Shelley K. Ballentine
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Renee L. DesJarlais
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Carsten Schubert
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Carl S. Crysler
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Yanmin Chen
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Christopher J. Molloy
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Margery A. Chaikin
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Robert R. Donatelli
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Edward Yurkow
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Zhao Zhou
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Mark R. Player
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Bruce E. Tomczuk
- Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
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14
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Schalk-Hihi C, Schubert C, Alexander R, Bayoumy S, Clemente JC, Deckman I, DesJarlais RL, Dzordzorme KC, Flores CM, Grasberger B, Kranz JK, Lewandowski F, Liu L, Ma H, Maguire D, Macielag MJ, McDonnell ME, Mezzasalma Haarlander T, Miller R, Milligan C, Reynolds C, Kuo LC. Crystal structure of a soluble form of human monoglyceride lipase in complex with an inhibitor at 1.35 Å resolution. Protein Sci 2011; 20:670-83. [PMID: 21308848 PMCID: PMC3081545 DOI: 10.1002/pro.596] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [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: 12/02/2010] [Accepted: 01/14/2011] [Indexed: 01/07/2023]
Abstract
A high-resolution structure of a ligand-bound, soluble form of human monoglyceride lipase (MGL) is presented. The structure highlights a novel conformation of the regulatory lid-domain present in the lipase family as well as the binding mode of a pharmaceutically relevant reversible inhibitor. Analysis of the structure lacking the inhibitor indicates that the closed conformation can accommodate the native substrate 2-arachidonoyl glycerol. A model is proposed in which MGL undergoes conformational and electrostatic changes during the catalytic cycle ultimately resulting in its dissociation from the membrane upon completion of the cycle. In addition, the study outlines a successful approach to transform membrane associated proteins, which tend to aggregate upon purification, into a monomeric and soluble form.
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Affiliation(s)
- Céline Schalk-Hihi
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477,*Correspondence to: Céline Schalk-Hihi (E-mail: ) or Carsten Schubert (E-mail: )
| | - Carsten Schubert
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477,*Correspondence to: Céline Schalk-Hihi (E-mail: ) or Carsten Schubert (E-mail: )
| | - Richard Alexander
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Shariff Bayoumy
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Jose C Clemente
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Ingrid Deckman
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Renee L DesJarlais
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Keli C Dzordzorme
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Christopher M Flores
- Department of Neuroscience, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Bruce Grasberger
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - James K Kranz
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Frank Lewandowski
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Li Liu
- Department of Medicinal Chemistry, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Hongchang Ma
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Diane Maguire
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Mark J Macielag
- Department of Medicinal Chemistry, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Mark E McDonnell
- Department of Medicinal Chemistry, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Tara Mezzasalma Haarlander
- Department of Lead Generation Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Robyn Miller
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Cindy Milligan
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Charles Reynolds
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
| | - Lawrence C Kuo
- Department of Structural Biology, Johnson & Johnson Pharmaceutical Research and DevelopmentL.L.C., Welsh and McKean Roads, Spring House, Pennsylvania 19477
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15
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16
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Van den Bulck K, Bailey GP, De Garavilla L, Smith R, D’Andrea M, Tegegne G, Duong T, DesJarlais RL. Variations on a theme of paracelsus: Bizarre developmental toxicity findings. Reprod Toxicol 2009. [DOI: 10.1016/j.reprotox.2009.05.031] [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: 11/26/2022]
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17
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Huang H, Hutta DA, Rinker JM, Hu H, Parsons WH, Schubert C, DesJarlais RL, Crysler CS, Chaikin MA, Donatelli RR, Chen Y, Cheng D, Zhou Z, Yurkow E, Manthey CL, Player MR. Pyrido[2,3-d]pyrimidin-5-ones: A Novel Class of Antiinflammatory Macrophage Colony-Stimulating Factor-1 Receptor Inhibitors. J Med Chem 2009; 52:1081-99. [DOI: 10.1021/jm801406h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hui Huang
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Daniel A. Hutta
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - James M. Rinker
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Huaping Hu
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - William H. Parsons
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Carsten Schubert
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Renee L. DesJarlais
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Carl S. Crysler
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Margery A. Chaikin
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Robert R. Donatelli
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Yanmin Chen
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Deping Cheng
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Zhao Zhou
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Edward Yurkow
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Carl L. Manthey
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Mark R. Player
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
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18
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Meegalla SK, Wall MJ, Chen J, Wilson KJ, Ballentine SK, DesJarlais RL, Schubert C, Crysler CS, Chen Y, Molloy CJ, Chaikin MA, Manthey CL, Player MR, Tomczuk BE, Illig CR. Structure-based optimization of a potent class of arylamide FMS inhibitors. Bioorg Med Chem Lett 2008; 18:3632-7. [DOI: 10.1016/j.bmcl.2008.04.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 04/23/2008] [Indexed: 11/27/2022]
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19
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Huang H, Hutta DA, Hu H, DesJarlais RL, Schubert C, Petrounia IP, Chaikin MA, Manthey CL, Player MR. Design and synthesis of a pyrido[2,3-d]pyrimidin-5-one class of anti-inflammatory FMS inhibitors. Bioorg Med Chem Lett 2008; 18:2355-61. [DOI: 10.1016/j.bmcl.2008.02.070] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 02/26/2008] [Accepted: 02/27/2008] [Indexed: 11/24/2022]
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20
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Travins JM, Ali F, Huang H, Ballentine SK, Khalil E, Hufnagel HR, Pan W, Gushue J, Leonard K, Bone RF, Soll RM, DesJarlais RL, Crysler CS, Ninan N, Kirkpatrick J, Cummings MD, Huebert N, Molloy CJ, Gaul M, Tomczuk BE, Subasinghe NL. Biphenylsulfonyl-thiophene-carboxamidine inhibitors of the complement component C1s. Bioorg Med Chem Lett 2008; 18:1603-6. [PMID: 18242991 DOI: 10.1016/j.bmcl.2008.01.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Revised: 01/14/2008] [Accepted: 01/16/2008] [Indexed: 11/28/2022]
Abstract
Complement activation has been implicated in disease states such as hereditary angioedema, ischemia-reperfusion injury, acute respiratory distress syndrome, and acute transplant rejection. Even though the complement cascade provides several protein targets for potential therapeutic intervention only two complement inhibitors have been approved so far for clinical use including anti-C5 antibodies for the treatment of paroxysmal nocturnal hemoglobinuria and purified C1-esterase inhibitor replacement therapy for the control of hereditary angioedema flares. In the present study, optimization of potency and physicochemical properties of a series of thiophene amidine-based C1s inhibitors with potential utility as intravenous agents for the inhibition of the classical pathway of complement is described.
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Affiliation(s)
- Jeremy M Travins
- Johnson & Johnson Pharmaceutical Research and Development, L.L.C., 665 Stockton Drive, Exton, PA 19341, USA
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21
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Abstract
Virtual screening involves the mining of small molecule databases from various sources. The small molecule databases used in virtual screening are typically processed, from simple 2D representations, to maximize their information content and to optimize them for input to the particular virtual screening technology being used. Processing interprets or adds molecular information related to connectivity, stereochemistry, protonation, tautomers and conformation. For virtual screening with an automated docking protocol, a technique that relies on specific intermolecular atom-atom contacts for ranking molecules, it is expected that the pre-processing protocol can affect the results of the docking experiment. The possible effects of processing on docking results have not been extensively studied, and this topic has only recently emerged as a significant aspect of the docking-based virtual screening process. One recent report highlights significant effects of different processing procedures on docking enrichment, while another outlines a general ligand preparation strategy. Here we survey and comment on recent practice in the field.
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Affiliation(s)
- Maxwell D Cummings
- Johnson & Johnson Pharmaceutical Research & Development, 665 Stockton Drive, Exton, PA 19341, USA.
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22
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Subasinghe NL, Travins JM, Ali F, Huang H, Ballentine SK, Marugán JJ, Khalil E, Hufnagel HR, Bone RF, DesJarlais RL, Crysler CS, Ninan N, Cummings MD, Molloy CJ, Tomczuk BE. A novel series of arylsulfonylthiophene-2-carboxamidine inhibitors of the complement component C1s. Bioorg Med Chem Lett 2006; 16:2200-4. [PMID: 16460935 DOI: 10.1016/j.bmcl.2006.01.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 01/10/2006] [Accepted: 01/11/2006] [Indexed: 11/23/2022]
Abstract
Inhibiting the classical pathway of complement activation by attenuating the proteolytic activity of the serine protease C1s is a potential strategy for the therapeutic intervention in disease states such as hereditary angioedema, ischemia-reperfusion injury, and acute transplant rejection. A series of arylsulfonylthiophene-2-carboxamidine inhibitors of C1s were synthesized and evaluated for C1s inhibitory activity. The most potent compound had a Ki of 10nM and >1000-fold selectivity over uPA, tPA, FX(a), thrombin, and plasmin.
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Affiliation(s)
- Nalin L Subasinghe
- Johnson & Johnson Pharmaceutical Research and Development, L.L.C., 665 Stockton Drive, Exton, PA 19341, USA.
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23
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Abstract
The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Recent progress made in the development and application of methods to include target flexibility are summarized. The fundamental issues and challenges involved in comparing various docking methods are discussed. Limitations of current technologies as well as future prospects are presented.
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Affiliation(s)
- Venkatraman Mohan
- 3-Dimensional Pharmaceuticals, Cedarbrook Corporate Center, 8 Clarke Drive, Cranbury, NJ 08512, USA.
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24
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Leonard K, Pan W, Anaclerio B, Gushue JM, Guo Z, DesJarlais RL, Chaikin MA, Lattanze J, Crysler C, Manthey CL, Tomczuk BE, Marugan JJ. Non-peptidic αvβ3 antagonists containing indol-1-yl propionic acids. Bioorg Med Chem Lett 2005; 15:2679-84. [PMID: 15863341 DOI: 10.1016/j.bmcl.2005.01.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 01/11/2005] [Accepted: 01/13/2005] [Indexed: 10/25/2022]
Abstract
We describe the synthesis and structure/activity relationship of RGD mimetics that are potent inhibitors of the integrin alpha(v)beta3. Indol-1-yl propionic acids containing a variety of basic moieties at the 5-position, as well as substitutions alpha and beta to the carboxy terminus were synthesized and evaluated. Novel compounds with improved potency have been identified.
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Affiliation(s)
- Kristi Leonard
- Johnson & Johnson, Pharmaceutical Research and Development, L.L.C., 665, Stockton Drive, Exton, PA 19341, USA
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25
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Abstract
The performance of several commercially available docking programs is compared in the context of virtual screening. Five different protein targets are used, each with several known ligands. The simulated screening deck comprised 1000 molecules from a cleansed version of the MDL drug data report and 49 known ligands. For many of the known ligands, crystal structures of the relevant protein-ligand complexes were available. We attempted to run experiments with each docking method that were as similar as possible. For a given docking method, hit rates were improved versus what would be expected for random selection for most protein targets. However, the ability to prioritize known ligands on the basis of docking poses that resemble known crystal structures is both method- and target-dependent.
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Affiliation(s)
- Maxwell D Cummings
- Johnson & Johnson Pharmaceutical Research & Development, Eagleview Corporate Center, 665 Stockton Drive, Exton, Pennsylvania 19341, USA.
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26
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Carver TE, Bordeau B, Cummings MD, Petrella EC, Pucci MJ, Zawadzke LE, Dougherty BA, Tredup JA, Bryson JW, Yanchunas J, Doyle ML, Witmer MR, Nelen MI, DesJarlais RL, Jaeger EP, Devine H, Asel ED, Springer BA, Bone R, Salemme FR, Todd MJ. Decrypting the biochemical function of an essential gene from Streptococcus pneumoniae using ThermoFluor technology. J Biol Chem 2005; 280:11704-12. [PMID: 15634672 DOI: 10.1074/jbc.m413278200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protein product of an essential gene of unknown function from Streptococcus pneumoniae was expressed and purified for screening in the ThermoFluor affinity screening assay. This assay can detect ligand binding to proteins of unknown function. The recombinant protein was found to be in a dimeric, native-like folded state and to unfold cooperatively. ThermoFluor was used to screen the protein against a library of 3000 compounds that were specifically selected to provide information about possible biological functions. The results of this screen identified pyridoxal phosphate and pyridoxamine phosphate as equilibrium binding ligands (K(d) approximately 50 pM, K(d) approximately 2.5 microM, respectively), consistent with an enzymatic cofactor function. Several nucleotides and nucleotide sugars were also identified as ligands of this protein. Sequence comparison with two enzymes of known structure but relatively low overall sequence homology established that several key residues directly involved in pyridoxal phosphate binding were strictly conserved. Screening a collection of generic drugs and natural products identified the antifungal compound canescin A as an irreversible covalent modifier of the enzyme. Our investigation of this protein indicates that its probable biological role is that of a nucleoside diphospho-keto-sugar aminotransferase, although the preferred keto-sugar substrate remains unknown. These experiments demonstrate the utility of a generic affinity-based ligand binding technology in decrypting possible biological functions of a protein, an approach that is both independent of and complementary to existing genomic and proteomic technologies.
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Affiliation(s)
- Theodore E Carver
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Exton, Pennsylvania 19341, USA
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27
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Subasinghe NL, Ali F, Illig CR, Jonathan Rudolph M, Klein S, Khalil E, Soll RM, Bone RF, Spurlino JC, DesJarlais RL, Crysler CS, Cummings MD, Morris PE, Kilpatrick JM, Sudhakara Babu Y. A novel series of potent and selective small molecule inhibitors of the complement component C1s. Bioorg Med Chem Lett 2004; 14:3043-7. [PMID: 15149641 DOI: 10.1016/j.bmcl.2004.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Revised: 04/13/2004] [Accepted: 04/13/2004] [Indexed: 11/27/2022]
Abstract
Activation of the classical pathway of complement has been implicated in disease states such as hereditary angioedema, ischemia-reperfusion injury and acute transplant rejection. The trypsin-like serine protease C1s represents a pivotal upstream point of control in the classical pathway of complement activation and is therefore likely to be a useful target in the therapeutic intervention of these disease states. A series of thiopheneamidine-based inhibitors of C1s has been optimized to give a 70 nM inhibitor that inhibits the classical pathway of complement activation in vitro.
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Affiliation(s)
- Nalin L Subasinghe
- 3-Dimensional Pharmaceuticals Inc, 665 Stockton Drive, Exton, PA 19341, USA.
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28
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Cywin CL, Zhao BP, McNeil DW, Hrapchak M, Prokopowicz AS, Goldberg DR, Morwick TM, Gao A, Jakes S, Kashem M, Magolda RL, Soll RM, Player MR, Bobko MA, Rinker J, DesJarlais RL, Winters MP. Discovery and SAR of novel Naphthyridines as potent inhibitors of spleen tyrosine kinase (SYK). Bioorg Med Chem Lett 2003; 13:1415-8. [PMID: 12668002 DOI: 10.1016/s0960-894x(03)00163-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The discovery of novel 5,7-disubstituted[1,6]naphthyridines as potent inhibitors of Spleen Tyrosine Kinase (SYK) is discussed. The SAR reveals the necessity for a 7-aryl group with preference towards para substitution and that this in combination with 5-aminoalkylamino substituents further improved the potency of the compounds. The initial SAR as well as a survey of the other positions is discussed in detail.
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Affiliation(s)
- Charles L Cywin
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06801-0368, USA.
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29
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Wilson KJ, Illig CR, Subasinghe N, Hoffman JB, Rudolph MJ, Soll R, Molloy CJ, Bone R, Green D, Randall T, Zhang M, Lewandowski FA, Zhou Z, Sharp C, Maguire D, Grasberger B, DesJarlais RL, Spurlino J. Synthesis of thiophene-2-carboxamidines containing 2-aminothiazoles and their biological evaluation as urokinase inhibitors. Bioorg Med Chem Lett 2001; 11:915-8. [PMID: 11294390 DOI: 10.1016/s0960-894x(01)00102-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The serine protease urokinase (uPa) has been implicated in the progression of both breast and prostate cancer. Utilizing structure based design, the synthesis of a series of substituted 4-[2-amino-1,3-thiazolyl]-thiophene-2-carboxamidines is described. Further optimization of this series by substitution of the terminal amine yielded urokinase inhibitors with excellent activities.
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Affiliation(s)
- K J Wilson
- 3-Dimensional Pharmaceuticals, Inc., Exton, PA 19341, USA.
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30
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Li JG, Chen C, Yin J, Rice K, Zhang Y, Matecka D, de Riel JK, DesJarlais RL, Liu-Chen LY. ASP147 in the third transmembrane helix of the rat mu opioid receptor forms ion-pairing with morphine and naltrexone. Life Sci 1999; 65:175-85. [PMID: 10416823 DOI: 10.1016/s0024-3205(99)00234-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [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: 11/26/2022]
Abstract
We tested the hypotheses that the carboxylate side chain of Asp147 of the mu opioid receptor interacts with the protonated nitrogen of naltrexone and morphine and that this interaction is important for pharmacological properties of the two compounds. Mutation of Asp147 to Ala or Asn substantially reduced the affinity of naltrexone and the affinity, potency and efficacy of morphine, while the Glu mutant had similar properties as the wildtype, indicating the significant role of the carboxylate group of Asp147 in receptor binding and activation. This role could be due to its direct interaction with ligands or involvement in interhelical interactions. The unprotonated analogs of naltrexone and morphine, cyclopropylcarbonyl noroxymorphone (CPCNOM) and N-formylnormorphine (NFNM), respectively, were used to discriminate between these mechanisms. CPCNOM was much less potent as an antagonist and had substantially lower affinity for the mu receptor than naltrexone. Similarly, NFNM was unable to activate the mu receptor and had much lower affinity than morphine. These results indicate the importance of the protonated nitrogen. Notably, the D147A and D147N mutations did not appreciably affect the binding affinities of CPCNOM and NFNM. In addition, the D147E mutant had similar affinities for CPCNOM and NFNM as the D147A and D147N mu receptors. Thus, the carboxylate group of Asp147 is not important for binding of the two unprotonated compounds. These results indicate that the carboxylate group of Asp147 of the mu receptor interacts directly with the protonated nitrogen of naltrexone and morphine and this interaction is important for binding and receptor activation.
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Affiliation(s)
- J G Li
- Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA 19140, USA
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31
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Duffy KJ, Ridgers LH, DesJarlais RL, Tomaszek TA, Bossard MJ, Thompson SK, Keenan RM, Veber DF. Design and synthesis of diaminopyrrolidinone inhibitors of human osteoclast cathepsin K. Bioorg Med Chem Lett 1999; 9:1907-10. [PMID: 10450951 DOI: 10.1016/s0960-894x(99)00322-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The structure-based design and synthesis of lactam-constrained azapeptide inhibitors of human cathepsin K are described. Enhanced stability to proteolytic cleavage over acyclic analogues is discussed.
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Affiliation(s)
- K J Duffy
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, Collegeville, PA 19246, USA
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32
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Thompson SK, Halbert SM, DesJarlais RL, Tomaszek TA, Levy MA, Tew DG, Ijames CF, Veber DF. Structure-based design of non-peptide, carbohydrazide-based cathepsin K inhibitors. Bioorg Med Chem 1999; 7:599-605. [PMID: 10353639 DOI: 10.1016/s0968-0896(99)00010-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Using binding models which were based on the X-ray crystal structure of an amino acid-based active site-spanning inhibitor complexed with cathepsin K, Cbz-leucine mimics have been developed, leading ultimately to the design of a potent cathepsin K inhibitor free of amino acid components. These mimics, which consist of alpha-substituted biphenylacetyl groups in place of Cbz-leucine moieties, effectively mimic all aspects of the Cbz-leucine moieties which are important for inhibitor binding. The predicted directions of binding for the inhibitors were confirmed by mass spectral analysis of their complexes with cathepsin K, which gave results consistent with acylation of the enzyme and loss of the acylhydrazine portion of the inhibitor which binds on the S' side of the active site. The binding models were found to be very predictive of relative inhibitor potency as well as direction of inhibitor binding. These results strengthen the validity of a strategy involving iterative cycles of structure-based design and inhibitor synthesis and evaluation for the discovery of non-peptide inhibitors.
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Affiliation(s)
- S K Thompson
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.
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33
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LaLonde JM, Zhao B, Smith WW, Janson CA, DesJarlais RL, Tomaszek TA, Carr TJ, Thompson SK, Oh HJ, Yamashita DS, Veber DF, Abdel-Meguid SS. Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites. J Med Chem 1998; 41:4567-76. [PMID: 9804696 DOI: 10.1021/jm980249f] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Papain has been used as a surrogate enzyme in a drug design effort to obtain potent and selective inhibitors of cathepsin K, a new member of the papain superfamily of cysteine proteases that is selectively and highly expressed in osteoclasts and is implicated in bone resorption. Here we report the crystal structures of two papain-inhibitor complexes and the rational design of novel cathepsin K inhibitors. Unlike previously known crystal structures of papain-inhibitor complexes, our papain structures show ligand binding extending deep within the S'-subsites. The two inhibitor complexes, carbobenzyloxyleucinyl-leucinyl-leucinal and carbobenzyloxy-L-leucinyl-L-leucinyl methoxymethyl ketone, were refined to 2.2- and 2.5-A resolution with R-factors of 0.190 and 0. 217, respectively. The S'-subsite interactions with the inhibitors are dominated by an aromatic-aromatic stacking and an oxygen-aromatic ring edge interaction. The knowledge of S'-subsite interactions led to a design strategy for an inhibitor spanning both subsites and yielded a novel, symmetric inhibitor selective for cathepsin K. Simultaneous exploitation of both S- and S'-sites provides a general strategy for the design of cysteine protease inhibitors having high specificity to their target enzymes.
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Affiliation(s)
- J M LaLonde
- Departments of Structural Biology, Protein Biochemistry, Physical and Structural Chemistry, Molecular Recognition, and Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, Prussia, Pennsylvania 19406, USA
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34
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Thompson SK, Smith WW, Zhao B, Halbert SM, Tomaszek TA, Tew DG, Levy MA, Janson CA, DAlessio KJ, McQueney MS, Kurdyla J, Jones CS, DesJarlais RL, Abdel-Meguid SS, Veber DF. Structure-based design of cathepsin K inhibitors containing a benzyloxy-substituted benzoyl peptidomimetic. J Med Chem 1998; 41:3923-7. [PMID: 9767629 DOI: 10.1021/jm980474x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidomimetic cathepsin K inhibitors have been designed using binding models which were based on the X-ray crystal structure of an amino acid-based, active site-spanning inhibitor complexed with cathepsin K. These inhibitors, which contain a benzyloxybenzoyl group in place of a Cbz-leucine moiety, maintained good inhibitory potency relative to the amino acid-based inhibitor, and the binding models were found to be very predictive of relative inhibitor potency. The binding mode of one of the inhibitors was confirmed by X-ray crystallography, and the crystallographically determined structure is in close qualitative agreement with the initial binding model. These results strengthen the validity of a strategy involving iterative cycles of structure-based design, inhibitor synthesis and evaluation, and crystallographic structure determination for the discovery of peptidomimetic inhibitors.
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Affiliation(s)
- S K Thompson
- Departments of Medicinal Chemistry, Structural Biology, Molecular Recognition, Protein Biochemistry, and Physical and Structural Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA
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35
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Marquis RW, Yamashita DS, Ru Y, LoCastro SM, Oh HJ, Erhard KF, DesJarlais RL, Head MS, Smith WW, Zhao B, Janson CA, Abdel-Meguid SS, Tomaszek TA, Levy MA, Veber DF. Conformationally constrained 1,3-diamino ketones: a series of potent inhibitors of the cysteine protease cathepsin K. J Med Chem 1998; 41:3563-7. [PMID: 9733481 DOI: 10.1021/jm980295f] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- R W Marquis
- Departments of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA
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36
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DesJarlais RL, Yamashita DS, Oh HJ, Uzinskas IN, Erhard KF, Allen AC, Haltiwanger RC, Zhao B, Smith WW, Abdel-Meguid SS, D'Alessio K, Janson CA, McQueney MS, Tomaszek TA, Levy MA, Veber DF. Use of X-ray Co-crystal Structures and Molecular Modeling To Design Potent and Selective Non-peptide Inhibitors of Cathepsin K. J Am Chem Soc 1998. [DOI: 10.1021/ja981171v] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Renee L. DesJarlais
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Dennis S. Yamashita
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Hye-Ja Oh
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Irene N. Uzinskas
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Karl F. Erhard
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Andrew C. Allen
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - R. Curtis Haltiwanger
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Baoguang Zhao
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Ward W. Smith
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Sherin S. Abdel-Meguid
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Karla D'Alessio
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Cheryl A. Janson
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Michael S. McQueney
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Thaddeus A. Tomaszek
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Mark A. Levy
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
| | - Daniel F. Veber
- Departments of Physical and Structural Chemistry Medicinal Chemistry, Analytical Chemistry Structural Biology, Protein Biochemistry and Molecular Recognition SmithKline Beecham Pharmaceuticals King of Prussia, Pennsylvania 19406
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37
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Thompson SK, Halbert SM, Bossard MJ, Tomaszek TA, Levy MA, Zhao B, Smith WW, Abdel-Meguid SS, Janson CA, D'Alessio KJ, McQueney MS, Amegadzie BY, Hanning CR, DesJarlais RL, Briand J, Sarkar SK, Huddleston MJ, Ijames CF, Carr SA, Garnes KT, Shu A, Heys JR, Bradbeer J, Zembryki D, Lee-Rykaczewski L, James IE, Lark MW, Drake FH, Gowen M, Gleason JG, Veber DF. Design of potent and selective human cathepsin K inhibitors that span the active site. Proc Natl Acad Sci U S A 1997; 94:14249-54. [PMID: 9405598 PMCID: PMC24926 DOI: 10.1073/pnas.94.26.14249] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Potent and selective active-site-spanning inhibitors have been designed for cathepsin K, a cysteine protease unique to osteoclasts. They act by mechanisms that involve tight binding intermediates, potentially on a hydrolytic pathway. X-ray crystallographic, MS, NMR spectroscopic, and kinetic studies of the mechanisms of inhibition indicate that different intermediates or transition states are being represented that are dependent on the conditions of measurement and the specific groups flanking the carbonyl in the inhibitor. The species observed crystallographically are most consistent with tetrahedral intermediates that may be close approximations of those that occur during substrate hydrolysis. Initial kinetic studies suggest the possibility of irreversible and reversible active-site modification. Representative inhibitors have demonstrated antiresorptive activity both in vitro and in vivo and therefore are promising leads for therapeutic agents for the treatment of osteoporosis. Expansion of these inhibitor concepts can be envisioned for the many other cysteine proteases implicated for therapeutic intervention.
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Affiliation(s)
- S K Thompson
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA
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38
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Yamashita DS, Smith WW, Zhao B, Janson CA, Tomaszek TA, Bossard MJ, Levy MA, Oh HJ, Carr TJ, Thompson SK, Ijames CF, Carr SA, McQueney M, D'Alessio KJ, Amegadzie BY, Hanning CR, Abdel-Meguid S, DesJarlais RL, Gleason JG, Veber DF. Structure and Design of Potent and Selective Cathepsin K Inhibitors. J Am Chem Soc 1997. [DOI: 10.1021/ja972204u] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dennis S. Yamashita
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Ward W. Smith
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Baoguang Zhao
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Cheryl A. Janson
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Thaddeus A. Tomaszek
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Mary J. Bossard
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Mark A. Levy
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Hye-Ja Oh
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Thomas J. Carr
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Scott K. Thompson
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Carl F. Ijames
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Steven A. Carr
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Michael McQueney
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Karla J. D'Alessio
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Bernard Y. Amegadzie
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Charles R. Hanning
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Sherin Abdel-Meguid
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Renee L. DesJarlais
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - John G. Gleason
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
| | - Daniel F. Veber
- Departments of Medicinal Chemistry, Macromolecular Sciences, Molecular Recognition, Structural and Physical Chemistry, Protein Biochemistry, and Gene Expression Sciences SmithKline Beecham Pharmaceuticals, 709 Swedeland Rd. King of Prussia, Pennsylvania 19406
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39
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Chen C, Yin J, Riel JK, DesJarlais RL, Raveglia LF, Zhu J, Liu-Chen LY. Determination of the amino acid residue involved in [3H]beta-funaltrexamine covalent binding in the cloned rat mu-opioid receptor. J Biol Chem 1996; 271:21422-9. [PMID: 8702924 DOI: 10.1074/jbc.271.35.21422] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [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] Open
Abstract
We previously demonstrated that [3H]beta-funaltrexamine ([3H]beta-FNA) labeled the rat mu opioid receptor expressed in Chinese hamster ovary cells with high specificity, and [3H]beta-FNA-labeled receptors migrated as one broad band with a mass of 80 kDa. In this study, we determined the region and then the amino acid residue of the mu receptor involved in the covalent binding of [3H]beta-FNA. [3H]beta-FNA-labeled receptors were solubilized and purified to approximately 10% purity by immunoaffinity chromatography with antibodies against a C-terminal domain peptide. The site of covalent bond formation was determined to be within Ala206-Met243 by CNBr cleavage of partially purified labeled mu receptors and determinations of sizes of labeled receptor fragments. The amino acid residue of beta-FNA covalent incorporation was then determined by site-directed mutagenesis studies within this region. Mutation of Lys233 to Ala, Arg, His, and Leu completely eliminated covalent binding of [3H]beta-FNA, although these mutants bound beta-FNA with high affinity. Mutations of other amino acid residues did not affect covalent binding of [3H]beta-FNA. These results indicate that [3H]beta-FNA binds covalently to Lys233. Since [3H]beta-FNA is a rigid molecule, the information will be very useful for molecular modeling of interaction between morphinans and the mu receptor.
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Affiliation(s)
- C Chen
- Department of Pharmacology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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40
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Zhao B, Helms LR, DesJarlais RL, Abdel-Meguid SS, Wetzel R. A paradigm for drug discovery using a conformation from the crystal structure of a presentation scaffold. Nat Struct Biol 1995; 2:1131-7. [PMID: 8846226 DOI: 10.1038/nsb1295-1131] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We describe a structural validation of the use of presentation scaffolds for control and elucidation of bioactive conformations of peptides. The protein REI-RGD34--produced by inserting the sequence RIPRGDMP into the CDR1 loop region of the immunoglobulin VL domain REI--strongly inhibits fibrinogen binding to the integrins alpha IIb beta 3 and alpha V beta 3. In the X-ray crystal structure of their protein at 2.4 A resolution, the RGD-containing loop exhibits defined electron density that is consistent with models for the bioactive conformations of ligands of these receptors based on previous small-molecule studies. Furthermore, a search of a small-molecule database with conformational information derived from the structure of REI-RGD34 identified constrained peptides and peptidomimetics known to be antagonists of the platelet receptor alpha IIb beta 3.
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Affiliation(s)
- B Zhao
- Department of Macromolecular Sciences, SmithKline Beecham Pharmaceuticals, Inc., King of Prussia, Pennsylvania 19406, USA
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41
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Hoog SS, Zhao B, Winborne E, Fisher S, Green DW, DesJarlais RL, Newlander KA, Callahan JF, Moore ML, Huffman WF. A check on rational drug design: crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel gamma-turn mimetic inhibitor. J Med Chem 1995; 38:3246-52. [PMID: 7650677 DOI: 10.1021/jm00017a008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [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: 01/26/2023]
Abstract
We have previously reported (Newlander et al., J. Med. Chem. 1993, 36, 2321-2331) the design of human immunodeficiency virus type 1 (HIV-1) protease inhibitors incorporating C7 mimetics that lock three amino acid residues of a peptide sequence into a gamma-turn. The design of one such compound, SB203238, was based on X-ray structures of reduced amide aspartyl protease inhibitors. It incorporates a gamma-turn mimetic in the P2-P1' position, where the carbonyl of the C7 ring is replaced with an sp3 methylene group yielding a constrained reduced amide. It shows competitive inhibition with Ki = 430 nM at pH 6.0. The three-dimensional structure of SB203238 bound to the active site of HIV-1 protease has been determined at 2.3 A resolution by X-ray diffraction and refined to a crystallographic R-factor (R = sigma magnitude of Fo magnitude of - magnitude of Fc magnitude of /sigma magnitude of Fo magnitude of, where Fo and Fc are the observed and calculated structure factor amplitudes, respectively) of 0.177. The inhibitor lies in an extended conformation in the active site; however, because of the constrained geometry of the C7 ring, it maintains fewer hydrogen bonds with the protein than in most other HIV-1 protease-inhibitor complexes. More importantly, the inhibitor binds to the enzyme differently than predicted in its design, by binding with the P2-P1' alpha-carbon atoms shifted by approximately one-half a residue toward the N-terminus from their presumed positions. This study illustrates the importance of structural information in an approach to rational drug design.
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Affiliation(s)
- S S Hoog
- Department of Macromolecular Sciences, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA
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42
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Abdel-Meguid SS, Metcalf BW, Carr TJ, Demarsh P, DesJarlais RL, Fisher S, Green DW, Ivanoff L, Lambert DM, Murthy KH. An orally bioavailable HIV-1 protease inhibitor containing an imidazole-derived peptide bond replacement: crystallographic and pharmacokinetic analysis. Biochemistry 1994; 33:11671-7. [PMID: 7918383 DOI: 10.1021/bi00205a001] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
(2R,4S,5S,1'S)-2-Phenylmethyl-4-hydroxy-5-(tert-butoxycarbonyl) amino-6-phenylhexanoyl-N-(1'-imidazo-2-yl)-2'-methylpropanamide (compound 2) is a tripeptide analogue inhibitor of HIV-1 protease in which a C-terminal imidazole substituent constitutes an isoelectronic, structural mimic of a carboxamide group. Compound 2 is a potent inhibitor of the protease (K(i) = 18 nM) and inhibits HIV-1 acute infectivity of CD4+ T-lymphocytes (IC50 = 570 nM). Crystallographic analysis of an HIV-1 protease-compound 2 complex demonstrates that the nitrogen atoms of the imidazole ring assume the same hydrogen-bonding interactions with the protease as amide linkages in other peptide analogue inhibitors. The sole substitution of the C-terminal carboxamide of a hydroxyethylene-containing tripeptide analogue with an imidazole group imparts greatly improved pharmacokinetic and oral bioavailability properties on the compound compared to its carboxamide-containing homologue (compound 1). While the oral bioavailability of compound 1 in rats was negligible, compound 2 displayed oral bioavailabilities of 30% and 14%, respectively, in rats and monkeys.
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Affiliation(s)
- S S Abdel-Meguid
- Department of Macromolecular Sciences, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406
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43
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Thompson SK, Murthy KH, Zhao B, Winborne E, Green DW, Fisher SM, DesJarlais RL, Tomaszek TA, Meek TD, Gleason JG. Rational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'--P2' amide bond isostere. J Med Chem 1994; 37:3100-7. [PMID: 7932533 DOI: 10.1021/jm00045a015] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The rational design and synthesis of a highly potent inhibitor of HIV-1 protease have been accomplished. The inhibitor, SB 206343, is based on a model derived from the structure of the MVT-101/HIV-1 protease complex and contains a 4(5)-acylimidazole ring as an isosteric replacement for the P1'--P2' amide bond. It is a competitive inhibitor with an apparent inhibition constant of 0.6 nM at pH 6.0. The three-dimensional structure of SB 206343 bound in the active site of HIV-1 protease has been determined at 2.3 A resolution by X-ray diffraction techniques and refined to a crystallographic discrepancy factor, R (= sigma parallel Fo magnitude of/Fc parallel/sigma magnitude of), of 0.194. The inhibitor is held in the enzyme by a set of hydrophobic and polar interactions. N-3 of the imidazole ring participates in a novel hydrogen-bonding interaction with the bound water molecule, demonstrating the effectiveness of the imidazole ring as an isosteric replacement for the P1'--P2' amide bond in hydroxyethylene-based HIV-1 protease inhibitors. Also present are hydrogen-bonding interactions between N-1 of the imidazole ring and the carbonyl of Gly-127 as well as between the imidazole acyl carbonyl oxygen and the amide nitrogen of Asp-129, exemplifying the peptidomimetic nature of the 4(5)-acylimidazole isostere. All of these interactions are in qualitative agreement with those predicted by the model.
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Affiliation(s)
- S K Thompson
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406
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44
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Abstract
The program DOCK [1,2] has been used successfully to identify molecules which will bind to a specified receptor [3]. The original method ranks molecules based on their shape complementarity to the receptor site and relies on the chemist to bring the appropriate electrostatic or hydrogen bond properties into the molecular skeletons obtained in the search. This is useful when screening a small database of compounds, where it is not likely that molecules with both the correct shape and electrostatic properties will be found. As large databases are more likely to have redundant molecular shapes with a variety of functionality (e.g., members of a congeneric series), it would be useful to have a method which identifies molecules with both the correct shape and functionality. To this end we have modified the DOCK 1.0 method to target user-specified atom types to selected positions in the receptor site. The target sites can be chosen based on structural evidence, calculation or inspection. Targeted-DOCK improves the ability of the DOCK method to find the crystallographically determined binding mode of a ligand. Additionally, targeted-DOCK searches a database of small molecules at 100-1000 times the rate of DOCK 1.0, allowing more molecules to be screened and more sophisticated scoring schemes to be employed. Targeted-DOCK has been used successfully in the design of a novel non-peptide inhibitor of HIV-1 protease.
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Affiliation(s)
- R L DesJarlais
- Department of Physical and Structural Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406-0939
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Chenera B, DesJarlais RL, Finkelstein JA, Eggleston DS, Meek TD, Tomaszek TA, Dreyer GB. Nonpeptide HIV protease inhibitors designed to replace a bound water. Bioorg Med Chem Lett 1993. [DOI: 10.1016/s0960-894x(01)80749-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Lee G, Chan W, Hurle MR, DesJarlais RL, Watson F, Sathe GM, Wetzel R. Strong inhibition of fibrinogen binding to platelet receptor alpha IIb beta 3 by RGD sequences installed into a presentation scaffold. Protein Eng 1993; 6:745-54. [PMID: 8248098 DOI: 10.1093/protein/6.7.745] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In order to probe the structural constraints on binding of RGD sequences to the platelet receptor alpha IIb beta 3 we have used recombinant DNA techniques to install the RGD sequence into 'presentation scaffolds', small proteins of known 3-D structure chosen to present guest sequences in constrained orientations. Using Escherichia coli expression systems we made sequence variants in which loop residues of the immunoglobulin VL domain REI and of human interleukin-1 beta were replaced (without changing polypeptide length) by the RGD sequence at positions predicted, based on small molecule studies, to orient the RGD moiety into an active conformation. These variants do not compete for fibrinogen binding to alpha IIb beta 3 up to almost 1 mM concentration. Unfolded or proteolytically fragmented forms of these same proteins do compete, however, showing that the RGD sequences in the mutants must be prohibited from binding by constraints imposed by scaffold structure. To suppress the effects of such structural constraints we constructed two sequence variants in which RGD-containing sequences 42-57 or 44-55 from the snake venom platelet antagonist kistrin were inserted (this increasing the length of the loop) into the third complementarity determining loop of REI. Both of these variants compete strongly for fibrinogen binding with IC50s in the nM range. These results, plus data on kistrin-related peptides also presented here, suggest that the molecular scaffold REI is capable of providing to an installed sequence a structural context and conformation beneficial to binding. The results also suggest that in order to bind well to alpha IIb beta 3, RGD sequences in protein ligands must either project significantly from the surface of the scaffold and/or retain a degree of conformational flexibility within the scaffold. Molecular scaffolds like REI should prove useful in the elucidation of structure-function relationships and the discovery of new active sequences, and may also serve as the basis for novel therapeutic agents.
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Affiliation(s)
- G Lee
- Macromolecular Sciences, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406
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47
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Abdel-Meguid SS, Zhao B, Murthy KH, Winborne E, Choi JK, DesJarlais RL, Minnich MD, Culp JS, Debouck C, Tomaszek TA. Inhibition of human immunodeficiency virus-1 protease by a C2-symmetric phosphinate. Synthesis and crystallographic analysis. Biochemistry 1993; 32:7972-80. [PMID: 8347601 DOI: 10.1021/bi00082a019] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) protease is a potential target of acquired immune deficiency syndrome (AIDS) therapy. A highly potent, perfectly symmetrical phosphinate inhibitor of this enzyme, SB204144, has been synthesized. It is a competitive inhibitor of HIV-1 protease, with an apparent inhibition constant of 2.8 nM at pH 6.0. The three-dimensional structure of SB204144 bound to the enzyme has been determined at 2.3-A resolution by X-ray diffraction techniques and refined to a crystallographic discrepancy factor, R (= sigma parallel F(o) magnitude to - Fc parallel/sigma magnitude of F(o)), of 0.178. The inhibitor is held in the enzyme active site by a set of hydrophobic and hydrophilic interactions, including an interaction between Arg8 and the center of the terminal benzene rings of the inhibitor. The phosphinate establishes a novel interaction with the two catalytic aspartates; each oxygen of the central phosphinic acid moiety interacts with a single oxygen of one aspartic acid, establishing a very short (2.2-2.4 A) oxygen-oxygen contact. As with the structures of penicillopepsin bound to phosphinate and phosphonate inhibitors [Fraser, M. E., Strynadka, N. C., Bartlett, P. A., Hanson, J. E., & James, M. N. (1992) Biochemistry 31, 5201-14], we interpret this short distance and the stereochemical environment of each pair of oxygens in terms of a hydrogen bond that has a symmetric single-well potential energy curve with the proton located midway between the two atoms.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S S Abdel-Meguid
- Department of Macromolecular Sciences, SmithKline Beecham, King of Prussia, Pennsylvania 19406
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48
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Dreyer GB, Boehm JC, Chenera B, DesJarlais RL, Hassell AM, Meek TD, Tomaszek TA, Lewis M. A symmetric inhibitor binds HIV-1 protease asymmetrically. Biochemistry 1993; 32:937-47. [PMID: 8422397 DOI: 10.1021/bi00054a027] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [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: 01/30/2023]
Abstract
Potential advantages of C2-symmetric inhibitors designed for the symmetric HIV-1 protease include high selectivity, potency, stability, and bioavailability. Pseudo-C2-symmetric monools and C2-symmetric diols, containing central hydroxymethylene and (R,R)-dihydroxyethylene moieties flanked by a variety of hydrophobic P1/P1' side chains, were studied as HIV-1 protease inhibitors. The monools and diols were synthesized in 8-10 steps from D-(+)-arabitol and D-(+)-mannitol, respectively. Monools with ethyl or isobutyl P1/P1' side chains were weak inhibitors of recombinant HIV-1 protease (Ki > 10 microM), while benzyl P1/P1' side chains afforded a moderately potent inhibitor (apparent Ki = 230 nM). Diols were 100-10,000x more potent than analogous monools, and a wider range of P1/P1' side chains led to potent inhibition. Both classes of compounds exhibited lower apparent Ki values under high-salt conditions. Surprisingly, monool and diol HIV-1 protease inhibitors were potent inhibitors of porcine pepsin, a prototypical asymmetric monomeric aspartic protease. These results were evaluated in the context of the pseudosymmetric structure of monomeric aspartic proteases and their evolutionary kinship with the retroviral proteases. The X-ray crystal structure of HIV-1 protease complexed with a symmetric diol was determined at 2.6 A. Contrary to expectations, the diol binds the protease asymmetrically and exhibits 2-fold disorder in the electron density map. Molecular dynamics simulations were conducted beginning with asymmetric and symmetric HIV-1 protease/inhibitor model complexes. A more stable trajectory resulted from the asymmetric complex, in agreement with the observed asymmetric binding mode. A simple four-point model was used to argue more generally that van der Waals and electrostatic force fields can commonly lead to an asymmetric association between symmetric molecules.
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Affiliation(s)
- G B Dreyer
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406
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49
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DesJarlais RL, Seibel GL, Kuntz ID, Furth PS, Alvarez JC, Ortiz de Montellano PR, DeCamp DL, Babé LM, Craik CS. Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc Natl Acad Sci U S A 1990; 87:6644-8. [PMID: 2204060 PMCID: PMC54593 DOI: 10.1073/pnas.87.17.6644] [Citation(s) in RCA: 210] [Impact Index Per Article: 6.2] [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: 12/30/2022] Open
Abstract
By using a structure-based computer-assisted search, we have found a butyrophenone derivative that is a selective inhibitor of the human immunodeficiency virus 1 (HIV-1) protease. The computer program creates a negative image of the active site cavity using the crystal structure of the HIV-1 protease. This image was compared for steric complementarity with 10,000 molecules of the Cambridge Crystallographic Database. One of the most interesting candidates identified was bromperidol. Haloperidol, a closely related compound and known antipsychotic agent, was chosen for testing. Haloperidol inhibits the HIV-1 and HIV-2 proteases in a concentration-dependent fashion with a Ki of approximately 100 microM. It is highly selective, having little inhibitory effect on pepsin activity and no effect on renin at concentrations as high as 5 mM. The hydroxy derivative of haloperidol has a similar effect on HIV-1 protease but a lower potency against the HIV-2 enzyme. Both haloperidol and its hydroxy derivative showed activity against maturation of viral polypeptides in a cell assay system. Although this discovery holds promise for the generation of nonpeptide protease inhibitors, we caution that the serum concentrations of haloperidol in normal use as an antipsychotic agent are less than 10 ng/ml (0.03 microM). Thus, concentrations required to inhibit the HIV-1 protease are greater than 1000 times higher than the concentrations normally used. Haloperidol is highly toxic at elevated doses and can be life-threatening. Haloperidol is not useful as a treatment for AIDS but may be a useful lead compound for the development of an antiviral pharmaceutical.
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Affiliation(s)
- R L DesJarlais
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143-0446
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50
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Grootenhuis PD, Kollman PA, Seibel GL, DesJarlais RL, Kuntz ID. Computerized selection of potential DNA binding compounds. Anticancer Drug Des 1990; 5:237-42. [PMID: 2169249] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using a general shape-search docking algorithm, potential DNA minor groove binding compounds were selected from a subset from the Cambridge Crystallographic Database consisting of almost 10,000 molecules. The crystal structure of the DNA dodecamer as observed in the d(CGCGAATTCGCG)2.netropsin complex served as the target receptor. Surprisingly, the highest scoring compound turned out to be CC-1065, a potent anti-tumour agent. Netropsin itself was number 6 on the list of highest scoring compounds. A number of the top-10 scoring compounds may serve as a source of inspiration for further drug design.
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Affiliation(s)
- P D Grootenhuis
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143
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