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Liu SJ, Zhao Q, Liu XC, Gamble AB, Huang W, Yang QQ, Han B. Bioactive atropisomers: Unraveling design strategies and synthetic routes for drug discovery. Med Res Rev 2024; 44:1971-2014. [PMID: 38515232 DOI: 10.1002/med.22037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
Atropisomerism, an expression of axial chirality caused by limited bond rotation, is a prominent aspect within the field of medicinal chemistry. It has been shown that atropisomers of a wide range of compounds, including established FDA-approved drugs and experimental molecules, display markedly different biological activities. The time-dependent reversal of chirality in atropisomers poses complexity and obstacles in the process of drug discovery and development. Nonetheless, recent progress in understanding atropisomerism and enhanced characterization methods have greatly assisted medicinal chemists in the effective development of atropisomeric drug molecules. This article provides a comprehensive review of their special design thoughts, synthetic routes, and biological activities, serving as a reference for the synthesis and biological evaluation of bioactive atropisomers in the future.
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Affiliation(s)
- Shuai-Jiang Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Qian Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiao-Chen Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qian-Qian Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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2
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Hu S, Wu J, Lu Z, Wang J, Tao Y, Jiang M, Chen F. TfOH-Catalyzed N-H Insertion of α-Substituted-α-Diazoesters with Anilines Provides Access to Unnatural α-Amino Esters. J Org Chem 2021; 86:3223-3231. [PMID: 33378204 DOI: 10.1021/acs.joc.0c02588] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A time-economical TfOH-catalyzed N-H insertion between anilines and α-alkyl and α-aryl-α-diazoacetates provides a straightforward approach to access unnatural α-amino esters, which readily undergo various transformations and can thus be used for the synthesis of pharmaceutically relevant molecules. The α-amino esters were obtained in moderate to excellent yields.
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Affiliation(s)
- Sha Hu
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Jiale Wu
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Zuolin Lu
- Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, 18 Chao Wang Road, Hangzhou 310014, China
| | - Jiaqi Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Yuan Tao
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Meifen Jiang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.,Shanghai Engineering Center of Industrial Catalysis for Chiral Drugs, Shanghai 200433, China.,Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, 18 Chao Wang Road, Hangzhou 310014, China
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3
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Shao B, Bagdasarian AL, Popov S, Nelson HM. Arylation of hydrocarbons enabled by organosilicon reagents and weakly coordinating anions. Science 2017; 355:1403-1407. [DOI: 10.1126/science.aam7975] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/09/2017] [Indexed: 11/02/2022]
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4
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Richter JM, Cheney DL, Bates JA, Wei A, Luettgen JM, Rendina AR, Harper TM, Narayanan R, Wong PC, Seiffert D, Wexler RR, Priestley ES. Design and Synthesis of Novel Meta-Linked Phenylglycine Macrocyclic FVIIa Inhibitors. ACS Med Chem Lett 2017; 8:67-72. [PMID: 28105277 DOI: 10.1021/acsmedchemlett.6b00375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/01/2016] [Indexed: 12/28/2022] Open
Abstract
Two novel series of meta-linked phenylglycine-based macrocyclic FVIIa inhibitors have been designed to improve the rodent metabolic stability and PK observed with the precursor para-linked phenylglycine macrocycles. Through iterative structure-based design and optimization, the TF/FVIIa Ki was improved to subnanomolar levels with good clotting activity, metabolic stability, and permeability.
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Affiliation(s)
- Jeremy M. Richter
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Daniel L. Cheney
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - J. Alex Bates
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Anzhi Wei
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Joseph M. Luettgen
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Alan R. Rendina
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Timothy M. Harper
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Rangaraj Narayanan
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Pancras C. Wong
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Dietmar Seiffert
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - Ruth R. Wexler
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
| | - E. Scott Priestley
- Research & Development, Bristol-Myers Squibb, Hopewell, New Jersey 08534, United States
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5
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Ladziata V(U, Glunz PW, Zou Y, Zhang X, Jiang W, Jacutin-Porte S, Cheney DL, Wei A, Luettgen JM, Harper TM, Wong PC, Seiffert D, Wexler RR, Priestley ES. Synthesis and P1′ SAR exploration of potent macrocyclic tissue factor-factor VIIa inhibitors. Bioorg Med Chem Lett 2016; 26:5051-5057. [DOI: 10.1016/j.bmcl.2016.08.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
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6
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Zhang X, Glunz PW, Johnson JA, Jiang W, Jacutin-Porte S, Ladziata V, Zou Y, Phillips MS, Wurtz NR, Parkhurst B, Rendina AR, Harper TM, Cheney DL, Luettgen JM, Wong PC, Seiffert D, Wexler RR, Priestley ES. Discovery of a Highly Potent, Selective, and Orally Bioavailable Macrocyclic Inhibitor of Blood Coagulation Factor VIIa-Tissue Factor Complex. J Med Chem 2016; 59:7125-37. [PMID: 27455395 DOI: 10.1021/acs.jmedchem.6b00469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Inhibitors of the tissue factor (TF)/factor VIIa complex (TF-FVIIa) are promising novel anticoagulants which show excellent efficacy and minimal bleeding in preclinical models. Starting with an aminoisoquinoline P1-based macrocyclic inhibitor, optimization of the P' groups led to a series of highly potent and selective TF-FVIIa inhibitors which displayed poor permeability. Fluorination of the aminoisoquinoline reduced the basicity of the P1 group and significantly improved permeability. The resulting lead compound was highly potent, selective, and achieved good pharmacokinetics in dogs with oral dosing. Moreover, it demonstrated robust antithrombotic activity in a rabbit model of arterial thrombosis.
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Affiliation(s)
- Xiaojun Zhang
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Peter W Glunz
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - James A Johnson
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Wen Jiang
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Swanee Jacutin-Porte
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Vladimir Ladziata
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Yan Zou
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Monique S Phillips
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Nicholas R Wurtz
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Brandon Parkhurst
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Alan R Rendina
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Timothy M Harper
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Daniel L Cheney
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - Joseph M Luettgen
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Pancras C Wong
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Dietmar Seiffert
- Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States
| | - Ruth R Wexler
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
| | - E Scott Priestley
- Bristol-Myers Squibb R&D , 350 Carter Road, Hopewell, New Jersey 08540, United States
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Priestley ES, Cheney DL, DeLucca I, Wei A, Luettgen JM, Rendina AR, Wong PC, Wexler RR. Structure-Based Design of Macrocyclic Coagulation Factor VIIa Inhibitors. J Med Chem 2015; 58:6225-36. [PMID: 26151189 DOI: 10.1021/acs.jmedchem.5b00788] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an acyclic analog. Further potency optimization by incorporation of P1' alkyl sulfone and P2 methyl groups provided a macrocycle with TF/FVIIa Ki = 1.6 nM, excellent selectivity against a panel of seven serine proteases, and FVII-deficient prothrombin time EC2x = 1.2 μM. Discovery of this potent, selective macrocyclic scaffold opens new possibilities for the development of orally bioavailable FVIIa inhibitors.
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8
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Design and synthesis of potent, selective phenylimidazole-based FVIIa inhibitors. Bioorg Med Chem Lett 2015; 25:2169-73. [DOI: 10.1016/j.bmcl.2015.03.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/17/2022]
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9
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Henry BL, Desai UR. Discovery methodology for the development of direct factor VIIa inhibitors. Expert Opin Drug Discov 2014; 9:859-72. [PMID: 24882057 DOI: 10.1517/17460441.2014.923398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Heparin and warfarin have historically been the only antithrombotics available. Recently, however, newer anticoagulants have been developed. Factor VIIa (fVIIa) inhibitors represent one of the new and potentially exciting classes of anticoagulants currently under development. Indeed, several methodologies have been used to develop fVIIa inhibitors. AREAS COVERED The authors highlight some of the methologies applied for the discovery of fVIIa inhibitors including phage display, isolation of endogenous peptides from hematophagous animals and the use of the 1,5-benzothiazepine molecular scaffolds and screens of large chemical libraries previously used to identify other serine protease inhibitors. Although these screens were intended to identify thrombin and factor Xa inhibitors, the compounds often had concomitant fVIIa activity. The authors also discuss the utilization of medical chemistry techniques for the discovery of these compounds. EXPERT OPINION FVIIa inhibitors represent a viable option for the development of new anticoagulants. There are theoretical advantages that fVIIa inhibitors may possess over existing anticoagulants and highly specific inhibitors that possess oral bioavailability and low bleeding risk may succeed.
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Affiliation(s)
- Brian L Henry
- University of Pittsburgh Medical Center, Heart and Vascular Institute Pittsburgh, Department of Cardiology , Scaife Hall, Suite B-571.3, 200 Lothrop Street, Pittsburgh, PA 15213 , USA +1 412 647 3429 ; +1 412 647 0481 ;
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10
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Priestley ES. Tissue factor-fVIIa inhibition: update on an unfinished quest for a novel oral antithrombotic. Drug Discov Today 2014; 19:1440-4. [PMID: 24881783 DOI: 10.1016/j.drudis.2014.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 05/22/2014] [Indexed: 12/11/2022]
Abstract
The tissue factor-coagulation factor VIIa complex (TF-fVIIa) is a well-validated biological target and has been the focus of extensive research directed toward the discovery of novel oral antithrombotics. This review briefly summarizes the key antithrombotic target validation data and provides an update on recent advances in small molecule TF-fVIIa inhibitors.
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Affiliation(s)
- E Scott Priestley
- Bristol-Myers Squibb Research, 311 Pennington-Rocky-Hill Road, Pennington, NJ 08534, USA.
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11
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Priestley ES, De Lucca I, Zhou J, Zhou J, Saiah E, Stanton R, Robinson L, Luettgen JM, Wei A, Wen X, Knabb RM, Wong PC, Wexler RR. Discovery and gram-scale synthesis of BMS-593214, a potent, selective FVIIa inhibitor. Bioorg Med Chem Lett 2013; 23:2432-5. [DOI: 10.1016/j.bmcl.2013.02.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 11/15/2022]
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12
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Affiliation(s)
- Alexander Dömling
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
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13
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Havemeyer A, Lang J, Clement B. The fourth mammalian molybdenum enzyme mARC: current state of research. Drug Metab Rev 2011; 43:524-39. [DOI: 10.3109/03602532.2011.608682] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. J Med Chem 2010; 53:3862-86. [PMID: 20158188 PMCID: PMC2874267 DOI: 10.1021/jm900818s] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The eight contributions here provide ample evidence that shape as a volume or as a surface is a vibrant and useful concept when applied to drug discovery. It provides a reliable scaffold for "decoration" with chemical intuition (or bias) for virtual screening and lead optimization but also has its unadorned uses, as in library design, ligand fitting, pose prediction, or active site description. Computing power has facilitated this evolution by allowing shape to be handled precisely without the need to reduce down to point descriptors or approximate metrics, and the diversity of resultant applications argues for this being an important step forward. Certainly, it is encouraging that as computation has enabled our intuition, molecular shape has consistently surprised us in its usefulness and adaptability. The first Aurelius question, "What is the essence of a thing?", seems well answered, however, the third, "What do molecules do?", only partly so. Are the topics covered here exhaustive, or is there more to come? To date, there has been little published on the use of the volumetric definition of shape described here as a QSAR variable, for instance, in the prediction or classification of activity, although other shape definitions have been successful applied, for instance, as embodied in the Compass program described above in "Shape from Surfaces". Crystal packing is a phenomenon much desired to be understood. Although powerful models have been applied to the problem, to what degree is this dominated purely by the shape of a molecule? The shape comparison described here is typically of a global nature, and yet some importance must surely be placed on partial shape matching, just as the substructure matching of chemical graphs has proved useful. The approach of using surfaces, as described here, offers some flavor of this, as does the use of metrics that penalize volume mismatch less than the Tanimoto, e.g., Tversky measures. As yet, there is little to go on as to how useful a paradigm this will be because there is less software and fewer concrete results.Finally, the distance between molecular shapes, or between any shapes defined as volumes or surfaces, is a metric property in the mathematical sense of the word. As yet, there has been little, if any, application of this observation. We cannot know what new application to the design and discovery of pharmaceuticals may yet arise from the simple concept of molecular shape, but it is fair to say that the progress so far is impressive.
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Affiliation(s)
- Anthony Nicholls
- OpenEye Scientific Software, Inc., Santa Fe, New Mexico 87508, USA.
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Shiraishi T, Kadono S, Haramura M, Kodama H, Ono Y, Iikura H, Esaki T, Koga T, Hattori K, Watanabe Y, Sakamoto A, Yoshihashi K, Kitazawa T, Esaki K, Ohta M, Sato H, Kozono T. Design and synthesis of peptidomimetic factor VIIa inhibitors. Chem Pharm Bull (Tokyo) 2010; 58:38-44. [PMID: 20045964 DOI: 10.1248/cpb.58.38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is regarded as a promising target for developing new anticoagulant drugs. In previous reports, we described a S3 subsite found in the X-ray crystal structure of compound 2 that bound to FVIIa/soluble tissue factor (sTF). Based on the X-ray crystal structure information and with the aim of improving the inhibition activity for FVIIa/TF and selectivity against other serine proteases, we synthesized derivatives by introducing substituents at position 5 of the indole ring of compound 2. Among them, compound 16 showed high selectivity against other serine proteases. Contrary to our expectations, compound 16 did not occupy the S3-subsite; X-ray structure analysis revealed that compound 16 improved selectivity by forming hydrogen bonds with Gln217, Thr99 and Asn100.
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Affiliation(s)
- Takuya Shiraishi
- Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co., Ltd., Japan.
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16
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Kotian PL, Krishnan R, Rowland S, El-Kattan Y, Saini SK, Upshaw R, Bantia S, Arnold S, Sudhakar Babu Y, Chand P. Design, parallel synthesis, and crystal structures of biphenyl antithrombotics as selective inhibitors of tissue factor FVIIa complex. Part 1: Exploration of S2 pocket pharmacophores. Bioorg Med Chem 2009; 17:3934-58. [DOI: 10.1016/j.bmc.2009.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 04/06/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
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17
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Shiraishi T, Kadono S, Haramura M, Kodama H, Ono Y, Iikura H, Esaki T, Koga T, Hattori K, Watanabe Y, Sakamoto A, Yoshihashi K, Kitazawa T, Esaki K, Ohta M, Sato H, Kozono T. Factor VIIa inhibitors: Target hopping in the serine protease family using X-ray structure determination. Bioorg Med Chem Lett 2008; 18:4533-7. [DOI: 10.1016/j.bmcl.2008.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 07/09/2008] [Accepted: 07/11/2008] [Indexed: 10/21/2022]
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Chandrasekaran V, Lee CJ, Duke RE, Perera L, Pedersen LG. Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling. Protein Sci 2008; 17:1354-61. [PMID: 18493021 DOI: 10.1110/ps.034801.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Although protein Z (PZ) has a domain arrangement similar to the essential coagulation proteins FVII, FIX, FX, and protein C, its serine protease (SP)-like domain is incomplete and does not exhibit proteolytic activity. We have generated a trial sequence of putative activated protein Z (PZa) by identifying amino acid mutations in the SP-like domain that might reasonably resurrect the serine protease catalytic activity of PZ. The structure of the activated form was then modeled based on the proposed sequence using homology modeling and solvent-equilibrated molecular dynamics simulations. In silico docking of inhibitors of FVIIa and FXa to the putative active site of equilibrated PZa, along with structural comparison with its homologous proteins, suggest that the designed PZa can possibly act as a serine protease.
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Affiliation(s)
- Vasu Chandrasekaran
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Abstract
The formation of the proteolytic complex composed of the serine protease Factor VIIa and the cell-associated glycoprotein tissue factor (FVIIa/TF) initiates a cascade of amplified zymogen activation reactions leading to thrombus formation. The critical role of the coagulation cascade in pathological thrombosis has been the basis for significant efforts to design selective inhibitors of the protease components as new anticoagulant alternatives for the treatment of thrombotic diseases. However, for the new generation of anticoagulant drugs in development that primarily target protease complexes distal from FVIIa/TF, the differential between efficacy and safety as defined by bleeding is unresolved. Targeting the FVIIa/TF complex has several theoretical advantages that exploit the amplified nature of the coagulation cascade. However, progress on the development of clinical-stage FVIIa/TF-based anticoagulants has not been as successful to date. This review summarizes recent efforts in the discovery of synthetic inhibitors of FVIIa/TF.
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Affiliation(s)
- Rebecca A Shirk
- Department of Cardiovascular and Metabolic Diseases Research, Wyeth Research, P.O. Box 42528, Philadelphia, PA 19101-2528, USA.
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