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Zheng W, Dai X, Xu B, Tian W, Shi J. Discovery and development of Factor Xa inhibitors (2015-2022). Front Pharmacol 2023; 14:1105880. [PMID: 36909153 PMCID: PMC9993480 DOI: 10.3389/fphar.2023.1105880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
As a pathological coagulation process, thrombus can lead to many serious diseases, including ischemic stroke, acute myocardial infarction (AMI), acute coronary syndrome (ACS), and deep venous thrombosis (DVT). And anticoagulant drugs are one of the most effective ways to prevent and treat these diseases. Although macromolecular anticoagulant drugs such as low molecular weight heparins (LMWHs) are widely used in the clinic, their characteristics of requiring injectable use hinder their further promotion in the clinic, and the disadvantages of oral anticoagulant drugs, such as warfarin and dabigatran etexilate, which can easily cause bleeding adverse effects, are also not addressed. Factor Xa (FXa) has gained attention because it lies at the intersection of the coagulation cascade pathways, whereas subsequently introduced Factor Xa inhibitors such as rivaroxaban and apixaban, among others, have gained market popularity because of their high potency for anticoagulation and high specificity for Factor Xa when administered orally. But some of the drawbacks that these Factor Xa inhibitors have simultaneously such as fewer indications and the lack of an effective reversal drug when bleeding occurs are urgently addressed. The development of new Factor Xa inhibitors therefore becomes one means of addressing these questions. This article summarizes the small molecule Factor Xainhibitors developed from 2015 to 2022, classifies them according to their scaffolds, focuses on the analysis of their structure-activity relationships, and provides a brief assessment of them.
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Affiliation(s)
- Wei Zheng
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.,Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqin Dai
- Department of Traditional Chinese Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Binyao Xu
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Tian
- Operations Management Department, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu Sichuan China School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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2
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Davie RL, Edwards HJ, Evans DM, Hodgson ST, Stocks MJ, Smith AJ, Rushbrooke LJ, Pethen SJ, Roe MB, Clark DE, McEwan PA, Hampton SL. Sebetralstat (KVD900): A Potent and Selective Small Molecule Plasma Kallikrein Inhibitor Featuring a Novel P1 Group as a Potential Oral On-Demand Treatment for Hereditary Angioedema. J Med Chem 2022; 65:13629-13644. [PMID: 36251573 PMCID: PMC9620001 DOI: 10.1021/acs.jmedchem.2c00921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 11/29/2022]
Abstract
Hereditary angioedema (HAE) is a rare genetic disorder in which patients experience sudden onset of swelling in various locations of the body. HAE is associated with uncontrolled plasma kallikrein (PKa) enzyme activity and generation of the potent inflammatory mediator, bradykinin, resulting in episodic attacks of angioedema. Herein, we disclose the discovery and optimization of novel small molecule PKa inhibitors. Starting from molecules containing highly basic P1 groups, which typically bind to an aspartic acid residue (Asp189) in the serine protease S1 pocket, we identified novel P1 binding groups likely to have greater potential for oral-drug-like properties. The optimization of P4 and the central core together with the particularly favorable properties of 3-fluoro-4-methoxypyridine P1 led to the development of sebetralstat, a potent, selective, orally bioavailable PKa inhibitor in phase 3 for on-demand treatment of HAE attacks.
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Affiliation(s)
- Rebecca L. Davie
- KalVista
Pharmaceuticals Limited, Porton Science Park, Salisbury, SP4 0BF, U.K.
| | - Hannah J. Edwards
- KalVista
Pharmaceuticals Limited, Porton Science Park, Salisbury, SP4 0BF, U.K.
| | - D. Michael Evans
- KalVista
Pharmaceuticals Limited, Porton Science Park, Salisbury, SP4 0BF, U.K.
| | - Simon T. Hodgson
- KalVista
Pharmaceuticals Limited, Porton Science Park, Salisbury, SP4 0BF, U.K.
| | - Michael J. Stocks
- School
of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, U.K.
| | - Alun J. Smith
- Sygnature
Discovery, Biocity, Pennyfoot Street, Nottingham, NG1 1GR, U.K.
| | | | - Stephen J. Pethen
- KalVista
Pharmaceuticals Limited, Porton Science Park, Salisbury, SP4 0BF, U.K.
| | - Michael B. Roe
- KalVista
Pharmaceuticals Limited, Porton Science Park, Salisbury, SP4 0BF, U.K.
| | - David E. Clark
- Charles
River Early Discovery, 6-9 Spire Green Centre, Harlow, Essex CM19 5TR, U.K.
| | - Paul A. McEwan
- Evotec, 114 Innovation Drive Milton Science
Park, Abingdon, OX14 4RZ, U.K.
| | - Sally L. Hampton
- KalVista
Pharmaceuticals Limited, Porton Science Park, Salisbury, SP4 0BF, U.K.
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3
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Lin S, Liu C, Zhao X, Han X, Li X, Ye Y, Li Z. Recent Advances of Pyridinone in Medicinal Chemistry. Front Chem 2022; 10:869860. [PMID: 35402370 PMCID: PMC8984125 DOI: 10.3389/fchem.2022.869860] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
Pyridinones have been adopted as an important block in medicinal chemistry that could serve as hydrogen bond donors and acceptors. With the help of feasible synthesis routes via established condensation reactions, the physicochemical properties of such a scaffold could be manipulated by adjustment of polarity, lipophilicity, and hydrogen bonding, and eventually lead to its wide application in fragment-based drug design, biomolecular mimetics, and kinase hinge-binding motifs. In addition, most pyridinone derivatives exhibit various biological activities ranging from antitumor, antimicrobial, anti-inflammatory, and anticoagulant to cardiotonic effects. This review focuses on recent contributions of pyridinone cores to medicinal chemistry, and addresses the structural features and structure–activity relationships (SARs) of each drug-like molecule. These advancements contribute to an in-depth understanding of the potential of this biologically enriched scaffold and expedite the development of its new applications in drug discovery.
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Affiliation(s)
- Shibo Lin
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
- *Correspondence: Shibo Lin,
| | - Chun Liu
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Xiaotian Zhao
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Xiao Han
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Xuanhao Li
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Yongqin Ye
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Zheyu Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, China
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4
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Factor Xa inhibitors: critical considerations for clinical development and testing. J Thromb Thrombolysis 2021; 52:397-402. [PMID: 33991266 PMCID: PMC8122197 DOI: 10.1007/s11239-021-02455-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 12/25/2022]
Abstract
The selection of factor (F) X and its activated protease FXa for targeted inhibition to prevent and treat thrombotic conditions is based on an understanding of coagulation biochemistry, sequential steps that occur on tissue factor bearing cells and the interface of coagulation proteins, platelets, mononuclear cells and the nuclear constituents of inflammatory cells. The goal for developing direct oral FXa inhibitors was to achieve rapid, selective, predictable, safe and effective anticoagulation across a broad group of patients expected to derive benefit. The history and development in patient care are exemplars of knowledge, translation and collaboration between the public and private sectors.
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5
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Algar S, Martín-Martínez M, González-Muñiz R. Evolution in non-peptide α-helix mimetics on the road to effective protein-protein interaction modulators. Eur J Med Chem 2020; 211:113015. [PMID: 33423841 DOI: 10.1016/j.ejmech.2020.113015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023]
Abstract
Modulation of interactome networks, essentially protein-protein interactions (PPIs), might represent valuable therapeutic approaches to different pathological conditions. Since a high percentage of PPIs are mediated by α-helical structures at the interacting surface, the development of compounds able to reproduce the amino acid side-chain organization of α-helices (e.g. stabilized α-helix peptides and β-derivatives, proteomimetics, and α-helix small-molecule mimetics) focuses the attention of different research groups. This appraisal describes the recent progress in the non-peptide α-helix mimetics field, which has evolved from single-face to multi-face reproducing compounds and from oligomeric to monomeric scaffolds able to bear different substituents in similar spatial dispositions as the side-chains in canonical helices. Grouped by chemical structures, the review contemplates terphenyl-like molecules, oligobenzamides and heterocyclic analogues, benzamide-amino acid conjugates and non-oligomeric small-molecules mimetics, among others, and their effectiveness to stabilize/disrupt therapeutically relevant PPIs. The X-ray structures of a couple of oligomeric peptidomimetics and of some small-molecules complexed with the MDM2 protein, as well as the state of the art on their development in clinical trials, are also remarked. The discovery of a continuously increasing number of new disease-relevant PPIs could offer future opportunities for these and other forthcoming α-helix mimetics.
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Affiliation(s)
- Sergio Algar
- Instituto de Química Médica, IQM-CSIC, Juan de La Cierva 3, 28006, Madrid, Spain
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6
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Highly efficient synthesis of pyrazolylphosphonate derivatives in biocompatible deep eutectic solvent. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.110396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Hao X, Zuo X, Kang D, Zhang J, Song Y, Liu X, Zhan P. Contemporary medicinal-chemistry strategies for discovery of blood coagulation factor Xa inhibitors. Expert Opin Drug Discov 2019; 14:915-931. [DOI: 10.1080/17460441.2019.1626821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Xiaofang Zuo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Jinan, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
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8
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Ilin I, Lipets E, Sulimov A, Kutov D, Shikhaliev K, Potapov A, Krysin M, Zubkov F, Sapronova L, Ataullakhanov F, Sulimov V. New factor Xa inhibitors based on 1,2,3,4-tetrahydroquinoline developed by molecular modelling. J Mol Graph Model 2019; 89:215-224. [PMID: 30913501 DOI: 10.1016/j.jmgm.2019.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 10/27/2022]
Abstract
Factor Xa is a serine protease representing a crucial element in the coagulation process and an attractive target for anticoagulant therapy. At the present time there are several chemical classes of factor Xa inhibitors with proven activity. Furthermore, three factor Xa inhibitors have been approved for the medical use to date. However, therapy with these medications is accompanied by substantial adverse effects. In this background, the structure-based computational approach combining molecular docking and semiempirical quantum chemical calculations was applied for a search for new effective factor Xa inhibitors. We have undertaken a few virtual screening procedures to select potential candidates for synthesis and subsequent testing. The first screen of the focused library resulted in identifying 20 compounds among which 7 compounds showed the noticeable inhibition of factor Xa at maximal concentrations, allowed by solubility. The subsequent additional screens identified 20 additional candidates. Of these, 5 substances were shown to be capable of inhibiting factor Xa at 5 μM. The best two found 1,2,3,4-tetrahydroquinoline derivatives identified by means of modelling have demonstrated IC50 values in the micromolar range. One of them turned out to be selective factor Xa inhibitor over trypsin, factors IIa, IXa and XIa.
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Affiliation(s)
- Ivan Ilin
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia.
| | - Elena Lipets
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, 1 Samory Mashela Str., Moscow, 117997, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences Kosygina Str. 4, Moscow, 119334, Russia
| | - Alexey Sulimov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
| | - Danil Kutov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
| | - Khidmet Shikhaliev
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Andrey Potapov
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Michael Krysin
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Fedor Zubkov
- Department of Organic Chemistry, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow, Russia
| | - Lyudmila Sapronova
- Department of Organic Chemistry, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow, Russia
| | - Fazoyl Ataullakhanov
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, 1 Samory Mashela Str., Moscow, 117997, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences Kosygina Str. 4, Moscow, 119334, Russia
| | - Vladimir Sulimov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
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9
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Liao G, Yang D, Ma L, Li W, Hu L, Zeng L, Wu P, Duan L, Liu Z. The development of piperidinones as potent MDM2-P53 protein-protein interaction inhibitors for cancer therapy. Eur J Med Chem 2018; 159:1-9. [DOI: 10.1016/j.ejmech.2018.09.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 11/29/2022]
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10
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Patel NR, Patel DV, Murumkar PR, Yadav MR. Contemporary developments in the discovery of selective factor Xa inhibitors: A review. Eur J Med Chem 2016; 121:671-698. [PMID: 27322757 DOI: 10.1016/j.ejmech.2016.05.039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/25/2016] [Accepted: 05/19/2016] [Indexed: 11/25/2022]
Abstract
Thrombosis is a leading cause of death in cardiovascular diseases such as myocardial infarction (MI), unstable angina and acute coronary syndrome (ACS) in the industrialized world. Venous thromboembolism is observed in about 1 million people every year in United States causing significant morbidity and mortality. Conventional antithrombotic therapy has been reported to have several disadvantages and limitations like inconvenience in oral administration, bleeding risks (heparin analogs), narrow therapeutic window and undesirable interactions with food and drugs (vitamin K antagonist-warfarin). The unmet medical demand for orally active safe anticoagulants has generated widespread interest among the medicinal chemists engaged in this field. To modulate blood coagulation, various enzymes involved in the coagulation process have received great attention as potential targets by various research groups for the development of oral anticoagulants. Among these enzymes, factor Xa (FXa) has remained the centre of attention in the last decade. Intensive research efforts have been made by various research groups for the development of small, safe and orally bioavailable FXa inhibitors. This review is an attempt to compile the research work of various researchers in the direction of development of FXa inhibitors reported since 2010 onward.
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Affiliation(s)
- Nirav R Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Dushyant V Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India.
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11
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Wang W, Yuan J, Fu X, Meng F, Zhang S, Xu W, Xu Y, Huang C. Novel Anthranilamide-Based FXa Inhibitors: Drug Design, Synthesis and Biological Evaluation. Molecules 2016; 21:491. [PMID: 27089317 PMCID: PMC6274369 DOI: 10.3390/molecules21040491] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/31/2016] [Accepted: 04/07/2016] [Indexed: 01/26/2023] Open
Abstract
Factor Xa (FXa) plays a significant role in the blood coagulation cascade and it has become a promising target for anticoagulation drugs. Three oral direct FXa inhibitors have been approved by the FDA for treating thrombotic diseases. By structure-activity relationship (SAR) analysis upon these FXa inhibitors, a series of novel anthranilamide-based FXa inhibitors were designed and synthesized. According to our study, compounds 1a, 1g and 1s displayed evident FXa inhibitory activity and excellent selectivity over thrombin in in vitro inhibition activities studies. Compounds 1g and 1s also exhibited pronounced anticoagulant activities in in vitro anticoagulant activity studies.
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Affiliation(s)
- Wenzhi Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China.
| | - Jing Yuan
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China.
| | - Xiaoli Fu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China.
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China.
| | - Shijun Zhang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China.
| | - Weiren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China.
| | - Yongnan Xu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Changjiang Huang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China.
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12
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Kumar KA, Kannaboina P, Jaladanki CK, Bharatam PV, Das P. Copper-CatalyzedN-Arylation of Tautomerizable Heterocycles with Boronic Acids and Its Application to Synthesis of Oxygenated Carbazoles. ChemistrySelect 2016. [DOI: 10.1002/slct.201600147] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Karampoori Anil Kumar
- Academy of Scientific and Innovative Research (AcSIR); Jammu-Campus; Canal Road Jammu- 180001 India
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine (CSIR); Canal Road Jammu- 180001 India
| | - Prakash Kannaboina
- Academy of Scientific and Innovative Research (AcSIR); Jammu-Campus; Canal Road Jammu- 180001 India
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine (CSIR); Canal Road Jammu- 180001 India
| | - Chaitanya K. Jaladanki
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER), Sector 67; S.A.S. Nagar - 160 062 Punjab India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER), Sector 67; S.A.S. Nagar - 160 062 Punjab India
| | - Parthasarathi Das
- Academy of Scientific and Innovative Research (AcSIR); Jammu-Campus; Canal Road Jammu- 180001 India
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine (CSIR); Canal Road Jammu- 180001 India
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13
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Kumar SP, Rawal RM, Pandya HA, Jasrai YT. Qualitative and quantitative pharmacophore-similarity assessment of anthranilamide-based factor Xa inhibitors: applications on similar molecules with identical biological endpoints. J Recept Signal Transduct Res 2015; 36:189-206. [PMID: 26416308 DOI: 10.3109/10799893.2015.1075040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It is a conventional practice to exclude molecules with identical biological endpoints to avoid bias in the resulting hypothesis model. Despite the diverse chemical functionalities, the receptor interactions of such molecules are often unexplored. The present study motivates the selection of these molecules diversified by single atom or functional group compared to internal molecules as external set and helps in the understanding of corresponding effects toward receptor interactions and biological endpoints. Applied on anthranilamide-series of factor Xa analogs, the inhibitory activities were correlated (r(2) = 0.99) and validated (q(2) = 0.68) with distance-based pharmacophore descriptors using support vector machine. The selected external set molecules exhibited better prediction accuracy by securing activities less than one residual threshold. The effect on inhibitory activity was assessed by the examination of pharmacophore-similarity and its interactions with key residues of Human factor Xa enzyme using molecular docking approach. Furthermore, qualitative pharmacophore models were developed on the subset of molecular dataset divided as most actives, moderately actives and least actives, to recognize crucial activity governing pharmacophore features. The outcome of this study will bring new insights about the requirements of pharmacophore features and prioritizes its selection in the design and optimization of potent Xa inhibitors.
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Affiliation(s)
- Sivakumar Prasanth Kumar
- a Department of Bioinformatics , Applied Botany Centre (ABC), Gujarat University , Ahmedabad , Gujarat , India and
| | - Rakesh M Rawal
- b Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology , The Gujarat Cancer and Research Institute , Ahmedabad , Gujarat , India
| | - Himanshu A Pandya
- a Department of Bioinformatics , Applied Botany Centre (ABC), Gujarat University , Ahmedabad , Gujarat , India and
| | - Yogesh T Jasrai
- a Department of Bioinformatics , Applied Botany Centre (ABC), Gujarat University , Ahmedabad , Gujarat , India and
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14
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Xing J, Yang L, Li H, Li Q, Zhao L, Wang X, Zhang Y, Zhou M, Zhou J, Zhang H. Identification of anthranilamide derivatives as potential factor Xa inhibitors: drug design, synthesis and biological evaluation. Eur J Med Chem 2015; 95:388-99. [PMID: 25839438 DOI: 10.1016/j.ejmech.2015.03.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/21/2015] [Accepted: 03/23/2015] [Indexed: 11/30/2022]
Abstract
The coagulation enzyme factor Xa (fXa) plays a crucial role in the blood coagulation cascade. In this study, three-dimensional fragment based drug design (FBDD) combined with structure-based pharmacophore (SBP) model and structural consensus docking were employed to identify novel fXa inhibitors. After a multi-stage virtual screening (VS) workflow, two hit compounds 3780 and 319 having persistent high performance were identified. Then, these two hit compounds and several analogs were synthesized and screened for in-vitro inhibition of fXa. The experimental data showed that most of the designed compounds displayed significant in vitro potency against fXa. Among them, compound 9b displayed the greatest in vitro potency against fXa with the IC50 value of 23 nM and excellent selectivity versus thrombin (IC50 = 40 μM). Moreover, the prolongation of the prothrombin time (PT) was measured for compound 9b to evaluate its in vitro anticoagulant activity. As a result, compound 9b exhibited pronounced anticoagulant activity with the 2 × PT value of 8.7 μM.
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Affiliation(s)
- Junhao Xing
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Lingyun Yang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Hui Li
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Qing Li
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Leilei Zhao
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Xinning Wang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Yuan Zhang
- Department of Medicinal Chemistry, China Pharmaceutical University, TongjiaXiang 24, 210009 Nanjing, PR China
| | - Muxing Zhou
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, TongjiaXiang 24, 210009 Nanjing, PR China
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, PR China.
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15
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Cheney DL, Bozarth JM, Metzler WJ, Morin PE, Mueller L, Newitt JA, Nirschl AH, Rendina AR, Tamura JK, Wei A, Wen X, Wurtz NR, Seiffert DA, Wexler RR, Priestley ES. Discovery of novel P1 groups for coagulation factor VIIa inhibition using fragment-based screening. J Med Chem 2015; 58:2799-808. [PMID: 25764119 DOI: 10.1021/jm501982k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A multidisciplinary, fragment-based screening approach involving protein ensemble docking and biochemical and NMR assays is described. This approach led to the discovery of several structurally diverse, neutral surrogates for cationic factor VIIa P1 groups, which are generally associated with poor pharmacokinetic (PK) properties. Among the novel factor VIIa inhibitory fragments identified were aryl halides, lactams, and heterocycles. Crystallographic structures for several bound fragments were obtained, leading to the successful design of a potent factor VIIa inhibitor with a neutral lactam P1 and improved permeability.
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Affiliation(s)
- Daniel L Cheney
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Jeffrey M Bozarth
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | | | | | | | | | - Alexandra H Nirschl
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Alan R Rendina
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | | | - Anzhi Wei
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Xiao Wen
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Nicholas R Wurtz
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Dietmar A Seiffert
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Ruth R Wexler
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - E Scott Priestley
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
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16
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Kang SR, Lee YR. Efficient one-pot protocol for diverse pyrazolylphosphonates by multi-component reactions: their antioxidant and antibacterial activities. Mol Divers 2015; 19:293-304. [PMID: 25652237 DOI: 10.1007/s11030-015-9568-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/11/2015] [Indexed: 11/29/2022]
Abstract
Efficient one-pot three-component reactions of pyrazolones with arylaldehydes and triethyl phosphite were carried out in the presence of ethylenediammonium diacetate as catalyst to synthesize biologically interesting pyrazolylphosphonate derivatives. This methodology offers several significant advantages such as environmentally benign character, the use of a mild catalyst, high yields, and ease of handling. The synthesized compounds were screened for their antioxidant and antibacterial activities. The result showed that compound 4d [Formula: see text] exhibited a strong free radical scavenger toward DPPH free radicals compared with standard BHT [Formula: see text]. In addition, compounds 4e and 4p showed potent antibacterial activities against Gram-negative bacteria of E. coli and compound 4o exhibited a potent activity against Gram-positive bacteria of S. aureus compared with standard Ampicillin.
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Affiliation(s)
- So Rang Kang
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 712-749, Republic of Korea
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17
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Structure-function relationships of factor Xa inhibitors: implications for the practicing clinician. J Thromb Thrombolysis 2014; 37:234-41. [PMID: 23996500 DOI: 10.1007/s11239-013-0991-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The recent development and approval of novel oral anticoagulants represents a significant success in the intelligent design of target-specific therapeutics. However, while these agents obviate many of the shortcomings of their predecessor (warfarin), they present novel challenges in pharmacologic management as well. Each was designed to have high oral bioavailability and high affinity for its target molecule, conveying significant anticoagulant effects. Yet, such unique drug-ligand binding, coupled with unfamiliar drug interactions and renal-based clearance, represent challenges to clinical management. The current review describes the development and pharmacokinetic properties of these agents, in the context of their clinical utility and pitfalls.
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18
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Synthesis and structure–activity relationship of potent, selective and orally active anthranilamide-based factor Xa inhibitors: Application of weakly basic sulfoximine group as novel S4 binding element. Eur J Med Chem 2012; 58:136-52. [DOI: 10.1016/j.ejmech.2012.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/04/2012] [Accepted: 10/04/2012] [Indexed: 12/29/2022]
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19
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Wang JF, Hao P, Li YX, Dai JL, Li X. Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model 2011; 18:2717-25. [PMID: 22116613 DOI: 10.1007/s00894-011-1295-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 10/24/2011] [Indexed: 11/25/2022]
Abstract
Human coagulation Factor X (FX), a member of the vitamin K-dependent serine protease family, is a crucial component of the human coagulation cascade. Activated FX (FXa) participates in forming the prothrombinase complex on activated platelets to convert prothrombin to thrombin in coagulation reactions. In the current study, 30-ns MD simulations were performed on both the open and closed states of human FXa. Root mean squares (RMS) fluctuations showed that structural fluctuations concentrated on the loop regions of FXa, and the presence of a ligand in the closed system resulted in larger fluctuations of the gating residues. The open system had a gating distance from 9.23 to 11.33 Å, i.e., significantly larger than that of the closed system (4.69-6.35 Å), which allows diversified substrates of variable size to enter. Although the solvent accessible surface areas (SASA) of FXa remained the same in both systems, the open system generally had a larger total SASA or hydrophobic SASA (or both) for residues surrounding the S4 pocket. Additionally, more hydrogen bonds were formed in the closed state than in the open state of FXa, which is believed to play a significant role in maintaining the closed confirmation of the aryl-binding site. Based on the results of MD simulations, we propose that an induced-fit mechanism governs the functioning of human coagulation FX, which helps provide a better understanding of the interactions between FXa and its substrate, and the mechanism of the conformational changes involved in human coagulation.
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Affiliation(s)
- Jing-Fang Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China.
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20
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Lee YK, Player MR. Developments in factor Xa inhibitors for the treatment of thromboembolic disorders. Med Res Rev 2011; 31:202-83. [DOI: 10.1002/med.20183] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Pinto DJP, Smallheer JM, Cheney DL, Knabb RM, Wexler RR. Factor Xa Inhibitors: Next-Generation Antithrombotic Agents. J Med Chem 2010; 53:6243-74. [PMID: 20503967 DOI: 10.1021/jm100146h] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Donald J. P. Pinto
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Joanne M. Smallheer
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Daniel L. Cheney
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Robert M. Knabb
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
| | - Ruth R. Wexler
- Research and Development, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey, 08543
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22
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de Candia M, Lopopolo G, Altomare C. Novel factor Xa inhibitors: a patent review. Expert Opin Ther Pat 2010; 19:1535-80. [PMID: 19743898 DOI: 10.1517/13543770903270532] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD New oral anticoagulants with favorable safety profiles and fixed doses are required for the management of thromboembolism and stroke prevention in patients with atrial fibrillation. Among them, fXa inhibitors (the so-called xabans) are attractive options that can overcome limitations (e.g., bleeding) of the current oral antithrombotic therapy. The rational design of small-molecule direct fXa inhibitors, whose importance is testified by the growing number of publications and patents recently registered, has been fully supported by the X-ray crystallography of enzyme-ligand complexes. AREAS COVERED IN THIS REVIEW Pubmed, SciFinder Scholar, ISI web of knowledge(SM), http://ep.espacenet.com/ and Google websites were used as the main sources for literature retrieving, and > 100 patents filed between 2006 and April 2009, reviewed and discussed herein, highlight the variety among the P1 and P4 moieties on suitable scaffolds. WHAT THE READER WILL GAIN The replacement of the benzamidine P1 moiety, which characterizes the first generation, with less basic bioisosteric or nonpolar neutral P1 groups led to the disclosure of numerous fXa inhibitors with high potency, selectivity and oral bioavailability. Novel selective fXa inhibitors with stable pharmacokinetics, better therapeutic windows and ease-of-use than the existing anticoagulants are currently under advanced stage clinical trials. TAKE-HOME MESSAGE Available data from Phase II and Phase III studies reflect the drive towards fXa inhibitors as potentially more effective and safer antithrombotic drugs. Their development is expected to address two major needs for anticoagulation, namely safety and ease-of-use, and to significantly affect the anticoagulant market.
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Affiliation(s)
- Modesto de Candia
- University of Bari, Dipartimento Farmaco-Chimico, Via E. Orabona 4, I-70125 Bari, Italy
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23
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Zhang P, Huang W, Wang L, Bao L, Jia ZJ, Bauer SM, Goldman EA, Probst GD, Song Y, Su T, Fan J, Wu Y, Li W, Woolfrey J, Sinha U, Wong PW, Edwards ST, Arfsten AE, Clizbe LA, Kanter J, Pandey A, Park G, Hutchaleelaha A, Lambing JL, Hollenbach SJ, Scarborough RM, Zhu BY. Discovery of betrixaban (PRT054021), N-(5-chloropyridin-2-yl)-2-(4-(N,N-dimethylcarbamimidoyl)benzamido)-5-methoxybenzamide, a highly potent, selective, and orally efficacious factor Xa inhibitor. Bioorg Med Chem Lett 2009; 19:2179-85. [DOI: 10.1016/j.bmcl.2009.02.111] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 02/25/2009] [Accepted: 02/26/2009] [Indexed: 10/21/2022]
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24
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Zhang P, Bao L, Fan J, Jia ZJ, Sinha U, Wong PW, Park G, Hutchaleelaha A, Scarborough RM, Zhu BY. Anthranilamide-based N,N-dialkylbenzamidines as potent and orally bioavailable factor Xa inhibitors: P4 SAR. Bioorg Med Chem Lett 2009; 19:2186-9. [DOI: 10.1016/j.bmcl.2009.02.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 02/25/2009] [Accepted: 02/26/2009] [Indexed: 11/29/2022]
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