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Bridoux A, Mousa SA. Screening of a Library for Factor VIIa Inhibitors. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666211207125903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
As an alternative to the anticoagulant’s strategy using direct or indirect anti-Xa
drugs, considering other targets upstream in the coagulation cascade such as anti-Factor VIIa could represent
an effective and safer strategy in coagulation and pathological angiogenesis.
Objective:
The objective of the study was to assess a high technology methodology composed of virtual
screening, anticoagulant, and anti-angiogenesis assays to identify potent small-molecule FVIIa inhibitors.
Methods:
Chemical databanks were screened to select molecules bearing functional groups that could fit
into the active site of FVIIa, which were then tested. Ligands assigned with the lowest scores were retained
and then biologically assessed.
Results:
From the 500 molecules considered, 8 chemical structures revealed to be effective compounds in
vitro and to inhibit angiogenesis in the chick chorioallantoic membrane (CAM) model.
Conclusion:
New potent small-molecule FVIIa inhibitors have been identified; further biochemical and
chemical developments would be investigated directly from the selected scaffolds.
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Affiliation(s)
- Alexandre Bridoux
- Vascular Vision Pharmaceuticals, 5 University Place, Rensselaer, NY 12144, USA
- Pharmaceutical Research Institute,
One Discovery Drive, Rensselaer, NY 12144, USA
| | - Shaker A. Mousa
- Vascular Vision Pharmaceuticals, 5 University Place, Rensselaer, NY 12144, USA
- Pharmaceutical Research Institute,
One Discovery Drive, Rensselaer, NY 12144, USA
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Langenfeld F, Aderinwale T, Christoffer C, Shin WH, Terashi G, Wang X, Kihara D, Benhabiles H, Hammoudi K, Cabani A, Windal F, Melkemi M, Otu E, Zwiggelaar R, Hunter D, Liu Y, Sirugue L, Nguyen HNH, Nguyen TDH, Nguyen-Truong VT, Le D, Nguyen HD, Tran MT, Montès M. Surface-based protein domains retrieval methods from a SHREC2021 challenge. J Mol Graph Model 2022; 111:108103. [PMID: 34959149 PMCID: PMC9746607 DOI: 10.1016/j.jmgm.2021.108103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/29/2021] [Accepted: 12/04/2021] [Indexed: 12/15/2022]
Abstract
Proteins are essential to nearly all cellular mechanism and the effectors of the cells activities. As such, they often interact through their surface with other proteins or other cellular ligands such as ions or organic molecules. The evolution generates plenty of different proteins, with unique abilities, but also proteins with related functions hence similar 3D surface properties (shape, physico-chemical properties, …). The protein surfaces are therefore of primary importance for their activity. In the present work, we assess the ability of different methods to detect such similarities based on the geometry of the protein surfaces (described as 3D meshes), using either their shape only, or their shape and the electrostatic potential (a biologically relevant property of proteins surface). Five different groups participated in this contest using the shape-only dataset, and one group extended its pre-existing method to handle the electrostatic potential. Our comparative study reveals both the ability of the methods to detect related proteins and their difficulties to distinguish between highly related proteins. Our study allows also to analyze the putative influence of electrostatic information in addition to the one of protein shapes alone. Finally, the discussion permits to expose the results with respect to ones obtained in the previous contests for the extended method. The source codes of each presented method have been made available online.
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Affiliation(s)
- Florent Langenfeld
- Laboratoire de Génomique, Bio-informatique et Chimie Moléculaire (GBCM), EA 7528, Conservatoire National des Arts-et-Métiers, HESAM Université, 2, rue Conté, Paris, 75003, France,Corresponding author: (F. Langenfeld)
| | - Tunde Aderinwale
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Woong-Hee Shin
- Department of Chemical Science Education, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA,Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Halim Benhabiles
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, Junia, UMR 8520, IEMN - Institut d’Electronique de Microélectronique et de Nanotechnologie, F-59 000, Lille, France
| | - Karim Hammoudi
- Université de Haute-Alsace, Department of Computer Science, IRIMAS, F-68 100, Mulhouse, France,Université de Strasbourg, France
| | - Adnane Cabani
- Normandie University, UNIROUEN, ESIGELEC, IRSEEM, 76000, Rouen, France
| | - Feryal Windal
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, Junia, UMR 8520, IEMN - Institut d’Electronique de Microélectronique et de Nanotechnologie, F-59 000, Lille, France
| | - Mahmoud Melkemi
- Université de Haute-Alsace, Department of Computer Science, IRIMAS, F-68 100, Mulhouse, France,Université de Strasbourg, France
| | - Ekpo Otu
- Department of Computer Science, Aberystwyth University, Aberystwyth, SY23 3FL, UK
| | - Reyer Zwiggelaar
- Department of Computer Science, Aberystwyth University, Aberystwyth, SY23 3FL, UK
| | - David Hunter
- Department of Computer Science, Aberystwyth University, Aberystwyth, SY23 3FL, UK
| | - Yonghuai Liu
- Department of Computer Science, Edge Hill University, Ormskirk, L39 4QP, UK
| | - Léa Sirugue
- Laboratoire de Génomique, Bio-informatique et Chimie Moléculaire (GBCM), EA 7528, Conservatoire National des Arts-et-Métiers, HESAM Université, 2, rue Conté, Paris, 75003, France
| | - Huu-Nghia H. Nguyen
- University of Science, VNU-HCM, Viet Nam,Vietnam National University, Ho Chi Minh City, Viet Nam
| | - Tuan-Duy H. Nguyen
- University of Science, VNU-HCM, Viet Nam,Vietnam National University, Ho Chi Minh City, Viet Nam
| | | | - Danh Le
- University of Science, VNU-HCM, Viet Nam,Vietnam National University, Ho Chi Minh City, Viet Nam
| | - Hai-Dang Nguyen
- University of Science, VNU-HCM, Viet Nam,Vietnam National University, Ho Chi Minh City, Viet Nam
| | - Minh-Triet Tran
- University of Science, VNU-HCM, Viet Nam,Vietnam National University, Ho Chi Minh City, Viet Nam,John von Neumann Institute, VNU-HCM, Viet Nam
| | - Matthieu Montès
- Laboratoire de Génomique, Bio-informatique et Chimie Moléculaire (GBCM), EA 7528, Conservatoire National des Arts-et-Métiers, HESAM Université, 2, rue Conté, Paris, 75003, France,Corresponding author: (M. Montès)
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Gupta PK, Hussain MK, Asad M, Kant R, Mahar R, Shukla SK, Hajela K. A metal-free tandem approach to prepare structurally diverse N-heterocycles: synthesis of 1,2,4-oxadiazoles and pyrimidinones. NEW J CHEM 2014. [DOI: 10.1039/c4nj00361f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-heterocycles, namely 1,2,4-oxadiazoles and 2,6 disubstituted pyrimidin-4-ones, have been synthesised in one pot via carboxamidation of amidines with aryl carboxylic acids and aryl propargylic acids under metal-free conditions.
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Affiliation(s)
- Puneet K. Gupta
- Division of Medicinal and Process Chemistry
- CSIR-Central Drug Research Institute
- Lucknow 226031, India
| | - Mohd. Kamil Hussain
- Division of Medicinal and Process Chemistry
- CSIR-Central Drug Research Institute
- Lucknow 226031, India
| | - Mohd. Asad
- Division of Medicinal and Process Chemistry
- CSIR-Central Drug Research Institute
- Lucknow 226031, India
| | - Ruchir Kant
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow 226031, India
| | - Rohit Mahar
- Sophisticated Analytical Instrument Facility
- CSIR-Central Drug Research Institute
- Lucknow 226031, India
| | - Sanjeev K. Shukla
- Sophisticated Analytical Instrument Facility
- CSIR-Central Drug Research Institute
- Lucknow 226031, India
| | - Kanchan Hajela
- Division of Medicinal and Process Chemistry
- CSIR-Central Drug Research Institute
- Lucknow 226031, India
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