1
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Roemer M, Proschogo N, Luck I. Copper(I) Chloride Mediated Amination of Halobenzenes via Azides: Scope, Mechanistic Aspects, and C-C Cleavage Reactions. J Org Chem 2023; 88:1522-1532. [PMID: 36668998 DOI: 10.1021/acs.joc.2c02549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Selective azidation-amination of long-chain alkanoyl halobenzenes with sodium azide, promoted by copper(I) chloride, is reported. The protocol is, apart from CuCl and NaN3, additive free and allows the isolation of versatile amine-azides. Alkyl cleavage occurs as a side reaction through an unusual Schmidt-type azide insertion adjacent to the carbonyl group, forming alkyl nitriles possibly via radical pathways. Mechanistic studies involving 15N labeling experiments and test substrates indicate that the reaction occurs via 1-azido-4-alkanoyl benzenes. The amination is applicable for substrates with electron-withdrawing groups and proceeds under mild conditions. The mechanism of the amine formation involves nitrenes. Intermediates were trapped by carrying out the reaction in the presence of the 2,2,6,6-(tetramethylpiperidin-1-yl)oxyl stable radical and characterized by high-resolution mass spectrometry. The intermediates are consistent with earlier mechanistic proposals.
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Affiliation(s)
- Max Roemer
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nicholas Proschogo
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ian Luck
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales 2006, Australia
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2
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Li X, Guo T, Feng Q, Bai T, Wu L, Liu Y, Zheng X, Jia J, Pei J, Wu S, Song Y, Zhang Y. Progress of thrombus formation and research on the structure-activity relationship for antithrombotic drugs. Eur J Med Chem 2022; 228:114035. [PMID: 34902735 DOI: 10.1016/j.ejmech.2021.114035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/11/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
Many populations suffer from thrombotic disorders such as stroke, myocardial infarction, unstable angina and thromboembolic disease. Thrombus is one of the major threatening factors to human health and the prevalence of cardio-cerebrovascular diseases induced by thrombus is growing worldwide, even some persons got rare and severe blood clots after receiving the AstraZeneca COVID vaccine unexpectedly. In terms of mechanism of thrombosis, antithrombotic drugs have been divided into three categories including anticoagulants, platelet inhibitors and fibrinolytics. Nowadays, a large number of new compounds possessing antithrombotic activities are emerging in an effort to remove the inevitable drawbacks of previously approved drugs such as the high risk of bleeding, a slow onset of action and a narrow therapeutic window. In this review, we describe the causes and mechanisms of thrombus formation firstly, and then summarize these reported active compounds as potential antithrombotic candidates based on their respective mechanism, hoping to promote the development of more effective bioactive molecules for treating thrombotic disorders.
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Affiliation(s)
- Xiaoan Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China; Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tiantian Guo
- College of Food Science and Technology, Northwest University, Xi'an, 710069, China
| | - Qian Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Tiantian Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Lei Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Yubo Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Xu Zheng
- Shaanxi Institute for Food and Drug, Xi'an, 710000, China
| | - Jianzhong Jia
- Shaanxi Institute for Food and Drug, Xi'an, 710000, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shaoping Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China.
| | - Yiming Song
- School of Chemical Engineering, Northwest University, 229 Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Yongmin Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China; Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 Place Jussieu, 75005, Paris, France
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3
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Duchamp E, Hanessian S. Cyanide-Free Synthesis of Air Stable N-Substituted Li and K Cyanamide Salts from Tetrazoles. Applications toward the Synthesis of Primary and Secondary Cyanamides as Precursors to Amidines. Org Lett 2020; 22:8487-8491. [PMID: 33090802 DOI: 10.1021/acs.orglett.0c03085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A practical two-step synthesis of N,N'-disubstituted cyanamides consists in the low-temperature metalation of N-substituted 5H-tetrazoles that undergo spontaneous cycloreversion at 0 °C releasing dinitrogen, and forming N-metalated cyanamides that can be reacted in situ with a variety of electrophiles. Remarkably, the N-substituted Li and K cyanamides are air stable white solids at room temperature. Addition of lithium organometallics to the N,N'-disubstituted cyanamides provides a new method for accessing N,N'-disubstituted amidines.
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Affiliation(s)
- Edouard Duchamp
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ., Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ., Centre-ville, Montréal, Québec, Canada H3C 3J7
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4
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Crystal Structure and Computational Study on Methyl-3-Aminothiophene-2-Carboxylate. CRYSTALS 2020. [DOI: 10.3390/cryst10010019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Methyl-3-aminothiophene-2-carboxylate (matc) is a key intermediate in organic synthesis, medicine, dyes, and pesticides. Single crystal X-ray diffraction analysis reveals that matc crystallizes in the monoclinic crystal system P21/c space group. Three matc molecules in the symmetric unit are crystallographically different and further linked through the N–H⋯O and N–H⋯N hydrogen bond interactions along with weak C–H⋯S and C–H⋯Cg interactions, which is verified by the three-dimensional Hirshfeld surface, two-dimensional fingerprint plot, and reduced density gradient (RDG) analysis. The interaction energies within crystal packing are visualized through dispersion, electrostatic, and total energies using three-dimensional energy-framework analyses. The dispersion energy dominates in crystal packing. To better understand the properties of matc, electrostatic potential (ESP) and frontier molecular orbitals (FMO) were also calculated and discussed. Experimental and calculation results suggested that amino and carboxyl groups can participate in various inter- and intra-interactions.
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5
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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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6
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Recent progress on inhibitors of the type II transmembrane serine proteases, hepsin, matriptase and matriptase-2. Future Med Chem 2019; 11:743-769. [DOI: 10.4155/fmc-2018-0446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Members of the type II transmembrane serine proteases (TTSP) family play a vital role in cell growth and development but many are also implicated in disease. Two of the well-studied TTSPs, matriptase and hepsin proteolytically process multiple protein substrates such as the inactive single-chain zymogens pro-HGF and pro-macrophage stimulating protein into the active heterodimeric forms, HGF and macrophage stimulating protein. These two proteases also have many other substrates which are associated with cancer and tumor progression. Another related TTSP, matriptase-2 is expressed in the liver and functions by regulating iron homoeostasis through the cleavage of hemojuvelin and thus is implicated in iron overload diseases. In the present review, we will discuss inhibitor design strategy and Structure activity relationships of TTSP inhibitors, which have been reported in the literature.
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7
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Balachandra B, Shanmugam S. A Simple and Direct Synthesis of Pentasubstituted Pyrroles via [3+4] Annulation and Their In Vitro Evaluation as Thrombolytic Agents and Cytotoxicity Studies on L929 Cells. ChemistrySelect 2018. [DOI: 10.1002/slct.201702476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Biguvu Balachandra
- Department of Organic Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai - 625021
| | - Sivakumar Shanmugam
- Department of Organic Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai - 625021
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8
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Newton MA, Brazier JB, Barreiro EM, Emerich H, Adrio LA, Mulligan CJ, Hellgardt K, Hii KK(M. Restructuring of supported Pd by green solvents: an operando quick EXAFS (QEXAFS) study and implications for the derivation of structure–function relationships in Pd catalysis. Catal Sci Technol 2016. [DOI: 10.1039/c6cy02073a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aqueous ethanolic solvents rearrange Pd catalysts facilely toward a common state irrespective of starting Pd dispersion or support material.
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Affiliation(s)
| | - John B. Brazier
- Department of Chemistry
- Imperial College London
- London SW7 2AZ
- UK
| | | | - Hermann Emerich
- Swiss-Norwegian Beamline (SNBL)
- European Synchrotron Radiation Facility (ESRF)
- Grenoble
- France
| | - Luis A. Adrio
- Department of Chemistry
- Imperial College London
- London SW7 2AZ
- UK
| | | | - Klaus Hellgardt
- Department of Chemical Engineering
- Imperial College London
- London SW7 2AZ
- UK
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9
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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11
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Schneider N, Hindle S, Lange G, Klein R, Albrecht J, Briem H, Beyer K, Claußen H, Gastreich M, Lemmen C, Rarey M. Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. J Comput Aided Mol Des 2011; 26:701-23. [PMID: 22203423 DOI: 10.1007/s10822-011-9531-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/12/2011] [Indexed: 12/16/2022]
Abstract
The HYDE scoring function consistently describes hydrogen bonding, the hydrophobic effect and desolvation. It relies on HYdration and DEsolvation terms which are calibrated using octanol/water partition coefficients of small molecules. We do not use affinity data for calibration, therefore HYDE is generally applicable to all protein targets. HYDE reflects the Gibbs free energy of binding while only considering the essential interactions of protein-ligand complexes. The greatest benefit of HYDE is that it yields a very intuitive atom-based score, which can be mapped onto the ligand and protein atoms. This allows the direct visualization of the score and consequently facilitates analysis of protein-ligand complexes during the lead optimization process. In this study, we validated our new scoring function by applying it in large-scale docking experiments. We could successfully predict the correct binding mode in 93% of complexes in redocking calculations on the Astex diverse set, while our performance in virtual screening experiments using the DUD dataset showed significant enrichment values with a mean AUC of 0.77 across all protein targets with little or no structural defects. As part of these studies, we also carried out a very detailed analysis of the data that revealed interesting pitfalls, which we highlight here and which should be addressed in future benchmark datasets.
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Affiliation(s)
- Nadine Schneider
- Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany
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12
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Hirayama F, Koshio H, Ishihara T, Hachiya S, Sugasawa K, Koga Y, Seki N, Shiraki R, Shigenaga T, Iwatsuki Y, Moritani Y, Mori K, Kadokura T, Kawasaki T, Matsumoto Y, Sakamoto S, Tsukamoto SI. Discovery of N-[2-Hydroxy-6-(4-methoxybenzamido)phenyl]-4- (4-methyl-1,4-diazepan-1-yl)benzamide (Darexaban, YM150) as a Potent and Orally Available Factor Xa Inhibitor. J Med Chem 2011; 54:8051-65. [DOI: 10.1021/jm200868m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Fukushi Hirayama
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Hiroyuki Koshio
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Tsukasa Ishihara
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Shunichiro Hachiya
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Keizo Sugasawa
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Yuji Koga
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Norio Seki
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Ryouta Shiraki
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Takeshi Shigenaga
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Yoshiyuki Iwatsuki
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Yumiko Moritani
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Kenichi Mori
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
| | - Takeshi Kadokura
- Development, Astellas Pharma Inc., 17-1, Hasune 3-chome, Itabashi-ku, Tokyo
174-8612, Japan
| | - Tomihisa Kawasaki
- Development, Astellas Pharma Inc., 17-1, Hasune 3-chome, Itabashi-ku, Tokyo
174-8612, Japan
| | - Yuzo Matsumoto
- Drug Discovery
Research, Astellas Pharma Inc., 2-3-11,
Nihonbashi-Honcho, Chuo-ku,
Tokyo 103-8411, Japan
| | - Shuichi Sakamoto
- Technology Supply Chain & Manufacturing, Astellas Pharma Europe B.V., Elisabethhof 19, 2350 AC Leiderdorp, The Netherlands
| | - Shin-ichi Tsukamoto
- Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi,
Ibaraki 305-8585, Japan
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13
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Yoshikawa K, Yoshino T, Yokomizo Y, Uoto K, Naito H, Kawakami K, Mochizuki A, Nagata T, Suzuki M, Kanno H, Takemura M, Ohta T. Design, synthesis and SAR of novel ethylenediamine and phenylenediamine derivatives as factor Xa inhibitors. Bioorg Med Chem Lett 2011; 21:2133-40. [DOI: 10.1016/j.bmcl.2011.01.132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/27/2011] [Accepted: 01/28/2011] [Indexed: 12/16/2022]
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14
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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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15
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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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16
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Tabuchi Y, Ando Y, Kanemura H, Kawasaki I, Ohishi T, Koida M, Fukuyama R, Nakamuta H, Ohta S, Nishide K, Ohishi Y. Preparation of novel (Z)-4-ylidenebenzo[b]furo[3,2-d][1,3]oxazines and their biological activity. Bioorg Med Chem 2009; 17:3959-67. [PMID: 19406645 PMCID: PMC7127799 DOI: 10.1016/j.bmc.2009.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 04/06/2009] [Accepted: 04/07/2009] [Indexed: 11/30/2022]
Abstract
A reaction of 2-acetyl-3-acylaminobenzo[b]furans (9d–o) with Vilsmeier (VM) reagent afforded a mixture of (E)- and (Z)-{(E)-2-aralkenylbenzo[b]furo[3,2-d][1,3]oxazin-4-ylidene}acetaldehydes (5) with a characteristic exo-formylmethylene group on the oxazine ring. The Z-isomer was more stable than the E-isomer. The Z-isomers ((Z)-5) were reacted with phosphonate reagents under two different conditions to obtain various butadiene derivatives (12) containing benzo[b]furo[3,2-d][1,3]oxazine skeleton. Typical compounds (5 and 12) were evaluated for their anti-osteoclastic bone resorption activity, antagonistic activity for the cysLT1 receptor and growth inhibitory activity for MIA PaCa-2 and MCF-7. Compounds 12f and 12j showed potent anti-osteoclastic bone resorption activity comparable to E2 (17β-estradiol).
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Affiliation(s)
- Yukako Tabuchi
- School of Pharmaceutical Sciences, Mukogawa Women's University, 11-68 Koshien Kyubancho, Nishinomiya, Hyogo 663-8179, Japan
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17
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Lin HH, Han LY, Yap CW, Xue Y, Liu XH, Zhu F, Chen YZ. Prediction of factor Xa inhibitors by machine learning methods. J Mol Graph Model 2007; 26:505-18. [PMID: 17418603 DOI: 10.1016/j.jmgm.2007.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 02/04/2007] [Accepted: 03/07/2007] [Indexed: 01/04/2023]
Abstract
Factor Xa (FXa) inhibitors have been explored as anticoagulants for treatment and prevention of thrombotic diseases. Molecular docking, pharmacophore, quantitative structure-activity relationships, and support vector machines (SVM) have been used for computer prediction of FXa inhibitors. These methods achieve promising prediction accuracies of 69-80% for FXa inhibitors and 85-99% for non-inhibitors. Prediction performance, particularly for inhibitors, may be further improved by exploring methods applicable to more diverse range of compounds and by using more appropriate set of molecular descriptors. We tested the capability of several machine learning methods (C4.5 decision tree, k-nearest neighbor, probabilistic neural network, and support vector machine) by using a much more diverse set of 1098 compounds (360 inhibitors and 738 non-inhibitors) than those in other studies. A feature selection method was used for selecting molecular descriptors appropriate for distinguishing FXa inhibitors and non-inhibitors. The prediction accuracies of these methods are 89.1-97.5% for FXa inhibitors and 92.3-98.1% for non-inhibitors. In particular, compared to other studies, support vector machine gives a substantially improved accuracy of 94.6% for FXa non-inhibitors and maintains a comparable accuracy of 98.1% for inhibitors, based-on a more rigorous test with more diverse range of compounds. Our study suggests that machine learning methods such as SVM are useful for facilitating the prediction of FXa inhibitors.
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Affiliation(s)
- H H Lin
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore
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18
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Mendel D, Marquart AL, Joseph S, Waid P, Yee YK, Tebbe AL, Ratz AM, Herron DK, Goodson T, Masters JJ, Franciskovich JB, Tinsley JM, Wiley MR, Weir LC, Kyle JA, Klimkowski VJ, Smith GF, Towner RD, Froelich LL, Buben J, Craft TJ. Anthranilamide inhibitors of factor Xa. Bioorg Med Chem Lett 2007; 17:4832-6. [PMID: 17624775 DOI: 10.1016/j.bmcl.2007.06.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 06/13/2007] [Accepted: 06/14/2007] [Indexed: 11/21/2022]
Abstract
SAR about the B-ring of a series of N(2)-aroyl anthranilamide factor Xa (fXa) inhibitors is described. B-ring o-aminoalkylether and B-ring p-amine probes of the S1' and S4 sites, respectively, afforded picomolar fXa inhibitors that performed well in in vitro anticoagulation assays.
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Affiliation(s)
- David Mendel
- Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.
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Franciskovich JB, Masters JJ, Tinsley JM, Craft TJ, Froelich LL, Gifford-Moore DS, Klimkowski VJ, Smallwood JK, Smith GF, Smith T, Towner RR, Weir LC, Wiley MR. Investigation of factor Xa inhibitors containing non-amidine S1 elements. Bioorg Med Chem Lett 2005; 15:4838-41. [PMID: 16140530 DOI: 10.1016/j.bmcl.2005.07.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 07/08/2005] [Accepted: 07/12/2005] [Indexed: 11/23/2022]
Abstract
Several non-amidino S1 derivatives of the 1,2-diaminobenzene-based scaffold (4) were synthesized and evaluated for their ability to bind to the active site and inhibit the human protease factor Xa. A subset of these compounds were also evaluated for their anticoagulant effects in human plasma as measured by prothrombin time (PT).
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Affiliation(s)
- Jeffry B Franciskovich
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.
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20
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Tang J, Yu CL, Williams SR, Springman E, Jeffery D, Sprengeler PA, Estevez A, Sampang J, Shrader W, Spencer J, Young W, McGrath M, Katz BA. Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein. J Biol Chem 2005; 280:41077-89. [PMID: 16199530 DOI: 10.1074/jbc.m506766200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasma kallikrein is a serine protease that has many important functions, including modulation of blood pressure, complement activation, and mediation and maintenance of inflammatory responses. Although plasma kallikrein has been purified for 40 years, its structure has not been elucidated. In this report, we described two systems (Pichia pastoris and baculovirus/Sf9 cells) for expression of the protease domain of plasma kallikrein, along with the purification and high resolution crystal structures of the two recombinant forms. In the Pichia pastoris system, the protease domain was expressed as a heterogeneously glycosylated zymogen that was activated by limited trypsin digestion and treated with endoglycosidase H deglycosidase to reduce heterogeneity from the glycosylation. The resulting protein was chromatographically resolved into four components, one of which was crystallized. In the baculovirus/Sf9 system, homogeneous, crystallizable, and nonglycosylated protein was expressed after mutagenizing three asparagines (the glycosylation sites) to glutamates. When assayed against the peptide substrates, pefachrome-PK and oxidized insulin B chain, both forms of the protease domain were found to have catalytic activity similar to that of the full-length protein. Crystallization and x-ray crystal structure determination of both forms have yielded the first three-dimensional views of the catalytic domain of plasma kallikrein. The structures, determined at 1.85 A for the endoglycosidase H-deglycosylated protease domain produced from P. pastoris and at 1.40 A for the mutagenically deglycosylated form produced from Sf9 cells, show that the protease domain adopts a typical chymotrypsin-like serine protease conformation. The structural information provides insights into the biochemical and enzymatic properties of plasma kallikrein and paves the way for structure-based design of protease inhibitors that are selective either for or against plasma kallikrein.
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Affiliation(s)
- Jie Tang
- Department of Structural Chemistry, Celera Genomics, South San Francisco, California 94080, USA
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21
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Taha MO, Qandil AM, Zaki DD, AlDamen MA. Ligand-based assessment of factor Xa binding site flexibility via elaborate pharmacophore exploration and genetic algorithm-based QSAR modeling. Eur J Med Chem 2005; 40:701-27. [PMID: 15935905 DOI: 10.1016/j.ejmech.2004.10.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 10/11/2004] [Indexed: 11/23/2022]
Abstract
The flexibility of activated factor X (fXa) binding site was assessed employing ligand-based pharmacophor modeling combined with genetic algorithm (GA)-based QSAR modeling. Four training subsets of wide structural diversity were selected from a total of 199 direct fXa inhibitors and were employed to generate different fXa pharmacophoric hypotheses using CATALYST software over two subsequent stages. In the first stage, high quality binding models (hypotheses) were identified. However, in the second stage, these models were refined by applying variable feature weight analysis to assess the relative significance of their features in the ligand-target affinity. The binding models were validated according to their coverage (capacity as a three-dimensional (3D) database search queries) and predictive potential as three-dimensional quantitative structure-activity relationship (3D-QSAR) models. Subsequently, GA and multiple linear regression (MLR) analysis were employed to construct different QSAR models from high quality pharmacophores and explore the statistical significance of combination models in explaining bioactivity variations across 199 fXa inhibitors. Three orthogonal pharmacophoric models emerged in the optimal QSAR equation suggesting they represent three binding modes accessible to ligands in the binding pocket within fXa.
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Affiliation(s)
- Mutasem O Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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22
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Matter H, Will DW, Nazaré M, Schreuder H, Laux V, Wehner V. Structural requirements for factor Xa inhibition by 3-oxybenzamides with neutral P1 substituents: combining X-ray crystallography, 3D-QSAR, and tailored scoring functions. J Med Chem 2005; 48:3290-312. [PMID: 15857135 DOI: 10.1021/jm049187l] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design, synthesis, and structure-activity relationship of 3-oxybenzamides as potent inhibitors of the coagulation protease factor Xa are described on the basis of X-ray structures, privileged structure motifs, and SAR information. A total of six X-ray structures of fXa/inhibitor complexes led us to identify the major protein-ligand interactions. The binding mode is characterized by a lipophilic dichlorophenyl substituent interacting with Tyr228 in the protease S1 pocket, while polar parts are accommodated in S4. This alignment in combination with docking allowed derivation of 3D-QSAR models and tailored scoring functions to rationalize biological affinity and provide guidelines for optimization. The resulting models showed good correlation coefficients and predictions of external test sets. Furthermore, they correspond to binding site topologies in terms of steric, electrostatic, and hydrophobic complementarity. Two approaches to derive tailored scoring functions combining binding site and ligand information led to predictive models with acceptable predictions of the external set. Good correlations to experimental affinities were obtained for both AFMoC (adaptation of fields for molecular comparison) and the novel TScore function. The SAR information from 3D-QSAR and tailored scoring functions agrees with all experimental data and provides guidelines and reasonable activity estimations for novel fXa inhibitors.
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Affiliation(s)
- Hans Matter
- DI and A Chemistry, Aventis Pharma Deutschland GmbH, A Company of the Sanofi-Aventis Group, Building G 878, D-65926 Frankfurt am Main, Germany.
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23
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Koshio H, Hirayama F, Ishihara T, Shiraki R, Shigenaga T, Taniuchi Y, Sato K, Moritani Y, Iwatsuki Y, Kaku S, Katayama N, Kawasaki T, Matsumoto Y, Sakamoto S, Tsukamoto SI. Synthesis and biological activity of novel 1,2-disubstituted benzene derivatives as factor Xa inhibitors. Bioorg Med Chem 2005; 13:1305-23. [PMID: 15670939 DOI: 10.1016/j.bmc.2004.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Revised: 11/05/2004] [Accepted: 11/05/2004] [Indexed: 10/26/2022]
Abstract
Factor Xa (fXa) is a serine protease that plays a pivotal role in the coagulation cascade. High-throughput screening of the Yamanouchi compound library yielded lead compound 1 with the ability to inhibit fXa at micromolar concentrations. To improve its fXa inhibitory activity and its oral anticoagulant activity, the linker between benzamidine and the central benzene ring was modified and a carboxyl group was introduced at the central benzene ring. The resulting compounds 40b (YM-203552), 41a (YM-202054), and 41c (YM-203558) exhibited potent fXa inhibitory activity and oral anticoagulant activity. In particular, YM-203558 exhibited the most potent oral anticoagulant activity, prolonging PT more than 3-fold at 0.5 and 2.0 h. Additionally, these compounds showed a high degree of selectivity for other serine proteases.
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Affiliation(s)
- Hiroyuki Koshio
- Institute for Drug Discovery Research, Yamanouchi Pharmaceutical Co. Ltd, 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan.
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24
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Murcia M, Ortiz AR. Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors. J Med Chem 2004; 47:805-20. [PMID: 14761183 DOI: 10.1021/jm030137a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A two-step, fully automatic virtual screening procedure consisting of flexible docking followed by activity prediction by COMparative BINding Energy (COMBINE) analysis is presented. This novel approach has been successfully applied, as an example with medicinal chemistry interest, to a recently reported series of 133 factor Xa (fXa)(1) inhibitors whose activities encompass 4 orders of magnitude. The docking algorithm is linked to the COMBINE analysis program and used to derive independent regression models of the 133 inhibitors docked within three different fXa structures (PDB entries 1fjs, 1f0r, and 1xka), so as to explore the effect of receptor conformation on the overall results. Reliable docking conformations and predictive regression models requiring eight latent variables could be derived for two of the fXa structures, with the best model achieving a Q(2) of 0.63 and a standard deviation of errors of prediction (SDEP) of 0.51 (leave-one-out). The two-step procedure was then employed to screen a designed virtual library of 112 ligands, containing both active and inactive compounds. While docking energies alone could show a good performance for selecting hits, including structurally diverse ones, inclusion of COMBINE analysis regression models provided improved rankings for the identification of structurally related molecules in external sets. In our best case, a recognition rate of approximately 80% of known binders at approximately 15% false positives rate was achieved, corresponding to an enrichment factor of approximately 450% over random.
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Affiliation(s)
- Marta Murcia
- Department of Physiology & Biophysics, Mount Sinai School of Medicine, New York University, One Gustave Levy Place, Box 1218, New York, New York 10029, USA
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25
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Kontogiorgis CA, Hadjipavlou-Litina D. Current trends in quantitative structure activity relationships on FXa inhibitors: Evaluation and comparative analysis. Med Res Rev 2004; 24:687-747. [PMID: 15250038 DOI: 10.1002/med.20006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article evaluates the quantitative structure activity relationships of FXa inhibitors, using the C-QSAR program of Biobyte. Diaryloxypyridines, aminophenols, biaryl isoxazoline derivatives, 1,2-dibenzamidobenzenes, 3-amidinophenylalanine derivatives, benzoxazinones, naphthoanilides, tetrazoles, glucolic and mandelic acid derivatives were included in this survey. Clog P plays a significant role in the QSAR, especially as hydrophilicity. In the most of the cases, CMR/MR molar refractivity as well as sterimol parameters (B5 and L) are important. Electronic effects with the exception of the Hammett's constant sigmam, are not found to govern the biological activity. Es was found to be important indicator variables were used after the best model was found to account for the usual structural features.
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Affiliation(s)
- Christos A Kontogiorgis
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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26
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Sheehan SM, Masters JJ, Wiley MR, Young SC, Liebeschuetz JW, Jones SD, Murray CW, Franciskovich JB, Engel DB, Weber WW, Marimuthu J, Kyle JA, Smallwood JK, Farmen MW, Smith GF. A four component coupling strategy for the synthesis of D-phenylglycinamide-derived non-covalent factor Xa inhibitors. Bioorg Med Chem Lett 2003; 13:2255-9. [PMID: 12824013 DOI: 10.1016/s0960-894x(03)00462-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel isonitrile derivative was synthesized and used in an Ugi four component coupling reaction to explore aryl group substitution effects on inhibition of the coagulation cascade serine protease factor Xa.
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Affiliation(s)
- Scott M Sheehan
- Lilly Research Laboratories, A Division of Eli Lilly and Company, IN 46285, Indianapolis, USA.
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27
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Liang AM, Light DR, Kochanny M, Rumennik G, Trinh L, Lentz D, Post J, Morser J, Snider M. Discovery and characterization of a potent and selective non-amidine inhibitor of human factor Xa. Biochem Pharmacol 2003; 65:1407-18. [PMID: 12732352 DOI: 10.1016/s0006-2952(03)00084-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Benzothiophene-anthranilamide 1 (3-chloro-N-[2-[[(4-fluorophenyl)amino]carbonyl]-4-methylphenyl]benzo[b]thiophene-2-carboxamide) was discovered by high throughput screening to be a highly potent and selective non-amidine inhibitor of human factor Xa with a K(i) of 15+/-4nM. Compound 1 is a selective inhibitor of human factor Xa as suggested by the K(i)((app)) determined for nine other human serine proteases and bovine trypsin. The activity of reconstituted human prothrombinase complex was inhibited by compound 1 when assayed in physiological concentrations of the substrate prothrombin. However, 27-fold higher inhibitor concentrations were needed to achieve the same level of inhibition than were required for the inhibition of free factor Xa, due in part to non-specific binding of the inhibitor to phospholipid under the assay conditions. Failure to demonstrate enzymatic cleavage of compound 1 suggests that compound 1 is solely an inhibitor rather than a substrate for factor Xa. The inhibition of factor Xa by compound 1 was reversible upon dilution of the enzyme/inhibitor mixture. Analyses of the inhibition mechanism with Dixon, Cornish-Bowden, and Lineweaver-Burk plots showed that compound 1 is a linear mixed-type inhibitor with 5-fold higher affinity for free factor Xa than the factor Xa/substrate complex. The linear mixed-type inhibition suggests that compound 1 binds to the active site region of factor Xa, but its binding cannot be fully displaced by the substrate S2222 (1:1 mixture of N-benzoyl-Ile-Glu-Gly-Arg-p-nitroanilide and N-benzoyl-Ile-Glu(gamma-OMe)-Gly-Arg-p-nitroanilide hydrochloride). Thus, the inhibition mechanism for compound 1 is novel compared to most serine protease inhibitors including amidine-containing factor Xa inhibitors, which rely on binding to the S1 pocket of the enzyme active site. Compound 1 represents an attractive, novel structural template for further development of efficacious, safe, and potentially orally active human factor Xa inhibitors.
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Affiliation(s)
- Amy M Liang
- Berlex Biosciences, 2600 Hilltop Drive, P.O. Box 4099, Richmond, CA 94806-0099, USA.
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28
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29
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Matter H, Defossa E, Heinelt U, Blohm PM, Schneider D, Müller A, Herok S, Schreuder H, Liesum A, Brachvogel V, Lönze P, Walser A, Al-Obeidi F, Wildgoose P. Design and quantitative structure-activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa. J Med Chem 2002; 45:2749-69. [PMID: 12061878 DOI: 10.1021/jm0111346] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 138 nonchiral 3-amidinobenzyl-1H-indole-2-carboxamides and analogues as inhibitors of the blood coagulation enzyme factor Xa (fXa) were designed, synthesized, and investigated by X-ray structure analysis and 3D quantitative structure-activity relationship (QSAR) studies (CoMFA, CoMSIA) in order to identify important protein-ligand interactions responsible for biological affinity and selectivity. Several compounds from this series are highly potent and selective inhibitors of this important enzyme linking extrinsic and intrinsic coagulation pathways. To rationalize biological affinity and to provide guidelines for further design, all compounds were docked into the factor Xa binding site. Those docking studies were based on X-ray structures of factor Xa in complex with literature-known inhibitors. It was possible to validate those binding modes by four X-ray crystal structures of representative ligands in factor Xa, while one ligand was additionally crystallized in trypsin to rationalize requirements for selective factor Xa inhibition. The 3D-QSAR models based on a superposition rule derived from these docking studies were validated using conventional and cross-validated r(2) values using the leave-one-out method and repeated analyses using two randomly chosen cross-validation groups plus randomization of biological activities. This led to consistent and highly predictive 3D-QSAR models with good correlation coefficients for both CoMFA and CoMSIA, which were found to correspond to experimentally determined factor Xa binding site topology in terms of steric, electrostatic, and hydrophobic complementarity. Subsets selected as smaller training sets using 2D fingerprints and maximum dissimilarity methods resulted in 3D-QSAR models with remarkable correlation coefficients and a high predictive power. The final quantitative SAR information agrees with all experimental data for the binding topology and thus provides reasonable activity predictions for novel factor Xa inhibitors.
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Affiliation(s)
- Hans Matter
- Aventis Pharma Deutschland GmbH, DI&A, Molecular Modeling, Building G 878, D-65926 Frankfurt am Main, Germany.
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30
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Jones SD, Liebeschuetz JW, Morgan PJ, Murray CW, Rimmer AD, Roscoe JM, Waszkowycz B, Welsh PM, Wylie WA, Young SC, Martin H, Mahler J, Brady L, Wilkinson K. The design of phenylglycine containing benzamidine carboxamides as potent and selective inhibitors of factor Xa. Bioorg Med Chem Lett 2001; 11:733-6. [PMID: 11266180 DOI: 10.1016/s0960-894x(01)00042-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Factor Xa, a critical serine protease in the blood coagulation cascade, has become a target for inhibition as a strategy for the invention of novel anti-thrombotic agents. Here we describe the development of phenylglycine containing benzamidine carboxamides as novel, potent and selective inhibitors of factor Xa.
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Affiliation(s)
- S D Jones
- Prosthetics Molecular Design, Beechfield House, Macclesfield, UK.
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31
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Chapter 8. Anticoagulants: Inhibitors of thrombin and factor Xa. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2001. [DOI: 10.1016/s0065-7743(01)36048-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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32
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Kastenholz MA, Pastor M, Cruciani G, Haaksma EE, Fox T. GRID/CPCA: a new computational tool to design selective ligands. J Med Chem 2000; 43:3033-44. [PMID: 10956211 DOI: 10.1021/jm000934y] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a computational procedure aimed at understanding enzyme selectivity and guiding the design of drugs with respect to selectivity. It starts from a set of 3D structures of the target proteins characterized by the program GRID. In the multivariate description proposed, the variables are organized and scaled in a different way than previously published methodologies. Then, consensus principal component analysis (CPCA) is used to analyze the GRID descriptors, allowing the straightforward identification of possible modifications in the ligand to improve its selectivity toward a chosen target. As an important new feature the computational method is able to work with more than two target proteins and with several 3D structures for each protein. Additionally, the use of a 'cutout tool' allows to focus on the important regions around the active site. The method is validated for a total number of nine structures of the three homologous serine proteases thrombin, trypsin, and factor Xa. The regions identified by the method as being important for selectivity are in excellent agreement with available experimental data and inhibitor structure-activity relationships.
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Affiliation(s)
- M A Kastenholz
- Department of Chemical Research/Structural Research, Boehringer Ingelheim Pharma KG, 88397 Biberach/Riss, Germany
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33
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Abstract
The search for the ideal anticoagulant has spanned decades and has resulted in several strategies including the clinical use of heparin, low molecular weight heparins, and the vitamin K antagonist warfarin. Over the past five years, many groups have reported preclinical results with direct-acting thrombin inhibitors and several of these are now moving into clinical trials. In addition, many groups have disclosed the discovery of potent, orally bioavailable factor Xa inhibitors. Several of these compounds are now in early clinical trials and the results are forthcoming.
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Affiliation(s)
- J P Vacca
- Merck Research Laboratories, West Point, PA 18969, USA.
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34
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Masters JJ, Franciskovich JB, Tinsley JM, Campbell C, Campbell JB, Craft TJ, Froelich LL, Gifford-Moore DS, Hay LA, Herron DK, Klimkowski VJ, Kurz KD, Metz JT, Ratz AM, Shuman RT, Smith GF, Smith T, Towner RD, Wiley MR, Wilson A, Yee YK. Non-amidine-containing 1,2-dibenzamidobenzene inhibitors of human factor Xa with potent anticoagulant and antithrombotic activity. J Med Chem 2000; 43:2087-92. [PMID: 10841787 DOI: 10.1021/jm990625b] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J J Masters
- Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA.
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35
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Herron DK, Goodson T, Wiley MR, Weir LC, Kyle JA, Yee YK, Tebbe AL, Tinsley JM, Mendel D, Masters JJ, Franciskovich JB, Sawyer JS, Beight DW, Ratz AM, Milot G, Hall SE, Klimkowski VJ, Wikel JH, Eastwood BJ, Towner RD, Gifford-Moore DS, Craft TJ, Smith GF. 1,2-Dibenzamidobenzene inhibitors of human factor Xa. J Med Chem 2000; 43:859-72. [PMID: 10715153 DOI: 10.1021/jm990326m] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-throughput screening of a combinatorial library of diamidophenols yielded lead compounds with the ability to inhibit human factor Xa (fXa) at micromolar concentrations (e.g. compound 4, fXa apparent K(ass) = 0.64 x 10(6) L/mol). SAR studies in this novel structural series of fXa inhibitors showed that the phenolic hydroxyl group was not essential for activity. The best activity was found in substituted 1,2-dibenzamidobenzenes in which the phenyl group of one benzoyl group (A-ring) was substituted in the 4-position with relatively small lipophilic or polarizable groups such as methoxy, vinyl, or chloro and the phenyl group of the other benzoyl group (B-ring) was substituted in the 4-position with larger lipophilic groups such as tert-butyl or dimethylamino. The central phenyl ring (C-ring) tolerated a wide variety of substituents, but methoxy, methanesulfonamido, hydroxyl, and carboxyl substitution produced slightly higher levels of activity than other substituents when present in combination with favorable B-ring substitution. Methylation of the amide nitrogen atoms was found to greatly decrease activity. Compound 12 is the highest affinity fXa inhibitor in this group of compounds, having fXa apparent K(ass) = 25.5 x 10(6) L/mol, about 40x more active than the original lead. This lead series does not show potent inhibition of human thrombin. A model for the binding of these ligands to the fXa active site is proposed. The model is consistent with the observed SAR and can serve to guide future SAR studies.
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Affiliation(s)
- D K Herron
- Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, USA.
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36
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Yee YK, Tebbe AL, Linebarger JH, Beight DW, Craft TJ, Gifford-Moore D, Goodson T, Herron DK, Klimkowski VJ, Kyle JA, Sawyer JS, Smith GF, Tinsley JM, Towner RD, Weir L, Wiley MR. N(2)-Aroylanthranilamide inhibitors of human factor Xa. J Med Chem 2000; 43:873-82. [PMID: 10715154 DOI: 10.1021/jm990327e] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reversal of the A-ring amide link in 1,2-dibenzamidobenzene 1 (fXa K(ass) = 0.81 x 10(6) L/mol) led to a series of human factor Xa (hfXa) inhibitors based on N(2)-aroylanthranilamide 4. Expansion of the SAR around 4 showed that only small planar substituents could be accommodated in the A-ring for binding to the S1 site of hfXa. Bulky groups such as 4-isopropyl, 4-tert-butyl, and 4-dimethylamino were favored in the B-ring to interact with the S4 site of hfXa. The central (C) ring containing a 5-methanesulfonamido group yielded greater activity than carbamoyl groups. Combining the beneficial features from the B- and C-ring SAR, compound 55 represents the most potent hfXa inhibitor in the N(2)-aroylanthranilamide 4 series with hfXa K(ass) = 58 x 10(6) L/mol (K(i) = 11.5 nM).
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Affiliation(s)
- Y K Yee
- Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, USA
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37
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Leadley RJ, Chi L, Rebello SS, Gagnon A. Contribution of in vivo models of thrombosis to the discovery and development of novel antithrombotic agents. J Pharmacol Toxicol Methods 2000; 43:101-16. [PMID: 11150738 DOI: 10.1016/s1056-8719(00)00095-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cardiovascular and cerebrovascular diseases continue to be the leading cause of death throughout the world. Over the past two decades, great advances have been made in the pharmacological treatment and prevention of thrombotic disorders (e.g., tissue plasminogen activators, platelet GPIIb/IIIa antagonists, ADP receptor antagonists such as clopidogrel, low-molecular weight heparins, and direct thrombin inhibitors). New research is leading to the next generation of antithrombotic compounds such as direct coagulation FVIIa inhibitors, tissue factor pathway inhibitors, gene therapy, and orally active direct thrombin inhibitors and coagulation Factor Xa (FXa) inhibitors. Animal models of thrombosis have played a crucial role in discovering and validiting novel drug targets, selecting new agents for clinical evaluation, and providing dosing and safety information for clinical trials. In addition, these models have provided valuable information regarding the mechanisms of these new agents and the interactions between antithrombotic agents that work by different mechanisms. This review briefly presents the pivitol preclinical studies that led to the development of drugs that have proven to be effective clinicallly. The role that animal models of thrombosis are playing in the discovery and development of novel antithrombotic agents is also described, with specific emphasis on FXa inhibitors. The major issues regarding the use of animal models of thrombosis, such as the use of positive controls, appropriate pharmacodynamic markers of activity, safety evaluation, species-specificity, and pharmacokinetics, are highlighted. Finally, the use of genetic models in thrombosis/hemostasis research and pharmacology is presented using gene-therapy for hemophilia as an example of how animal models have aided in the development of these therapies that are now being evaluated clinically. In summary, animal models have contributed greatly to the discovery of currently available antithrombotic agents and will play a primary role in the discovery and characterization of the novel antithrombotic agents that will provide safe and effective pharmacological treatment for life-threatening thrombotic diseases.
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Affiliation(s)
- R J Leadley
- Cardiovascular Therapeutics Pfizer Global Research and Development, Ann Laboratories, 2800 Plymouth Road, Ann Arbor MI 48105, USA.
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Zhu BY, Scarborough RM. Chapter 9. Factor Xa inhibitors: Recent advances in anticoagulant agents. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2000. [DOI: 10.1016/s0065-7743(00)35010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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