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Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds

Journal of Chemical Biology 2016年第1期9卷 31-40页

作者： Ramachandran, Vanitha Arumugasamy, Karthiga Singh, Sanjeev Kumar Edayadulla, Naushad Ramesh, Penugonda Kamaraj, Sathish-Kumar Department of Natural Products Chemistry School of Chemistry Madurai Kamaraj University Madurai 625021 Tamil Nadu India Department of Zoology Thiagarajar College Madurai 625009 Tamil Nadu India Computer Aided Drug Designing and Molecular Modeling Laboratory Department of Bioinformatics Alagappa University Karaikudi 630 003 Tamil Nadu India School of Chemical Engineering Yeungnam University Gyeongsan 712-749 South Korea Ingeniería en Energía Universidad Politécnica de Aguascalientes Calle Paseo San Gerardo No. 207. Fracc. San Gerardo Aguascalientes 20342 AGS Mexico

The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. Molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors for docking. Finally, the docking score, binding site interaction analysis revealed that DHPMs exhibit more specificity towards 16S rRNA than known antibiotic amikacin. Accordingly, targeting the bacterial ribosomal A site RNA with potential drug leads promises to overcome the bacterial drug resistance. Even though, anti-neoplastic activities of DHPMs were also predicted through prediction of activity spectra for substances (PASS) tool. Further, the results establish that the DHPMs can serve as perfect leads against bacterial drug resistance. © 2015, Springer-Verlag Berlin Heidelberg.

关键词： Bioactivity Grindstone chemistry Molecular modeling Ribosomal RNA

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Targeting the cyclin-binding groove site to inhibit the catalytic activity of CDK2/cyclin A complex using p27^KIP1-derived peptidomimetic inhibitors

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Journal of Chemical Biology 2015年第1期8卷 11-24页

作者： Karthiga, Arumugasamy Tripathi, Sunil Kumar Shanmugam, Ramasamy Suryanarayanan, Venkatesan Singh, Sanjeev Kumar Computer Aided Drug Designing and Molecular Modeling Lab Department of Bioinformatics Alagappa University Karaikudi 630 003 Tamil Nadu India Department of Chemistry Thiagarajar College Madurai 625009 Tamil Nadu India

Functionally activated cyclin-dependent kinase 2 (CDK2)/cyclin A complex has been validated as an interesting therapeutic target to develop the efficient antineoplastic drug based on the cell cycle arrest. Cyclin A binds to CDK2 and activates the kinases as well as recruits the substrate and inhibitors using a hydrophobic cyclin-binding groove (CBG). Blocking the cyclin substrate recruitment on CBG is an alternative approach to override the specificity hurdle of the currently available ATP site targeting CDK2 inhibitors. Greater understanding of the interaction of CDK2/cyclin A complex with p27 (negative regulator) reveals that the Leu-Phe-Gly (LFG) motif region of p27 binds with the CBG site of cyclin A to arrest the malignant cell proliferation that induces apoptosis. In the present study, Replacement with Partial Ligand Alternatives through Computational Enrichment (REPLACE) drug design strategies have been applied to acquire LFG peptide-derived peptidomimetics library. The peptidomimetics function is equivalent with respect to substrate p27 protein fashion but does not act as an ATP antagonist. The combined approach of molecular docking, molecular dynamics (MD), and molecular electrostatic potential and ADME/T prediction were carried out to evaluate the peptidomimetics. Resultant interaction and electrostatic potential maps suggested that smaller substituent is desirable at the position of phenyl ring to interact with Trp217, Arg250, and Gln254 residues in the active site. The best docked poses were refined by the MD simulations which resulted in conformational changes. After equilibration, the structure of the peptidomimetic and receptor complex was stable. The results revealed that the various substrate protein-derived peptidomimetics could serve as perfect leads against CDK2 protein. © 2014, Springer-Verlag Berlin Heidelberg.

关键词： Cyclin-binding groove MD simulation Molecular docking Peptidomimetic inhibitor Protein–protein interaction

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Cover Picture: A BOILED-Egg To Predict Gastrointestinal Absorption and Brain Penetration of Small Molecules (ChemMedChem 11/2016)

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ChemMedChem 2016年第11期11卷 1109-1109页

作者： Antoine Daina Vincent Zoete SIB Swiss Institute of Bioinformatics Molecular Modeling Group Quartier Sorge Bâtiment Génopode 1015 Lausanne Switzerland

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Correction to: Meeting report from the fourth meeting of the Computational modeling in Biology Network (COMBINE)

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Standards in genomic sciences 2018年第1期13卷 17页

作者： Dagmar Waltemath Frank T Bergmann Claudine Chaouiya Tobias Czauderna Padraig Gleeson Carole Goble Martin Golebiewski Michael Hucka Nick Juty Olga Krebs Nicolas Le Novère Huaiyu Mi Ion I Moraru Chris J Myers David Nickerson Brett G Olivier Nicolas Rodriguez Falk Schreiber Lucian Smith Fengkai Zhang Eric Bonnet 1Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany. 2Department of Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA. 4Instituto Gulbenkian de Ciência - IGC Rua da Quinta Grande Oeiras Portugal. 3IPK Gatersleben Gatersleben Germany. 5Department of Neuroscience Physiology and Pharmacology University College London London UK. 6School of Computer Science The University of Manchester Manchester UK. 7Heidelberg Institute for Theoretical Studies Heidelberg Germany. 8EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge UK. 14The Babraham Institute Babraham Research Campus Cambridge UK. 9Department of preventive medicine Keck School of Medicine University of Southern California Los Angeles CA USA. 10Center for Cell Analysis and Modeling University of Connecticut Health Center Farmington CT USA. 11Department of Electrical and Computer Engineering University of Utah Salt Lake City USA. 12Auckland Bioengineering Institute University of Auckland Auckland New Zealand. 13Systems Bioinformatics VU University Amsterdam Amsterdam The Netherlands. 15Martin Luther University Halle-Wittenberg Halle Germany. 16Monash University Melbourne Australia. Computational Biology Unit Laboratory of Systems Biology National Institute of Allergy and Infectious Diseases NIH Bethesda MD USA. 18Institut Curie Paris France. INSERM U900 75248 Paris France. 20Mines ParisTech 77300 Fontainebleau Paris France.

[This corrects the article DOI: 10.4056/sigs.5279417.].

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Erratum to: Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

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BMC bioinformatics 2016年第1期17卷 439页

作者： Luciano A Abriata Christophe Bovigny Matteo Dal Peraro Laboratory for Biomolecular Modeling Institute of Bioengineering School of Life Sciences École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics AAB014 Station 19 Lausanne 1015 Switzerland. luciano.abriata@epfl.ch. Laboratory for Biomolecular Modeling Institute of Bioengineering School of Life Sciences École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics AAB014 Station 19 Lausanne 1015 Switzerland. Present address: Molecular Modeling Group Swiss Institute of Bioinformatics UNIL Bâtiment Génopode Lausanne 1015 Switzerland.

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Author Correction: Multidisciplinary study of the secondary immune response in grandparents re-exposed to chickenpox

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Scientific reports 2018年第1期8卷 10824页

作者： B Ogunjimi J Van den Bergh P Meysman S Heynderickx K Bergs H Jansens E Leuridan A Vorsters H Goossens K Laukens N Cools Viggo Van Tendeloo N Hens P Van Damme Evelien Smits Ph Beutels Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID) Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium. benson.ogunjimi@uantwerp.be. Interuniversity Institute for Biostatistics and Statistical Bioinformatics Hasselt University Hasselt Belgium. benson.ogunjimi@uantwerp.be. Department of Pediatrics Antwerp University Hospital Edegem Belgium. benson.ogunjimi@uantwerp.be. Laboratory of Experimental Hematology (LEH) Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium. benson.ogunjimi@uantwerp.be. Department of Pediatrics Ghent University Hospital Ghent Belgium. benson.ogunjimi@uantwerp.be. Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Antwerp Belgium. benson.ogunjimi@uantwerp.be. Laboratory of Experimental Hematology (LEH) Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium. Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS) Antwerp Belgium. Advanced Database Research and Modelling (ADReM) Department of Mathematics and Computer Science University of Antwerp Antwerp Belgium. Biomedical Informatics Research Network Antwerp (BIOMINA) University of Antwerp/Antwerp University Hospital Edegem Belgium. Center for Cell Therapy and Regenerative Medicine Antwerp University Hospital Edegem Belgium. Department of Laboratory Medicine Antwerp University Hospital Edegem Belgium. Centre for the Evaluation of Vaccination (CEV) Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium. Laboratory of Medical Microbiology Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium. Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID) Vaccine & Infectious Disease Institute (VAXINFECTIO) University of Antwerp Antwerp Belgium. Interuniversity Institute for Biostatistics and Statistical Bio

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

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Author Correction: Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19 from an international collaborative meta-analysis of randomized trials

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Nature communications 2024年第1期15卷 1075页

作者： Cathrine Axfors Andreas M Schmitt Perrine Janiaud Janneke Van't Hooft Sherief Abd-Elsalam Ehab F Abdo Benjamin S Abella Javed Akram Ravi K Amaravadi Derek C Angus Yaseen M Arabi Shehnoor Azhar Lindsey R Baden Arthur W Baker Leila Belkhir Thomas Benfield Marvin A H Berrevoets Cheng-Pin Chen Tsung-Chia Chen Shu-Hsing Cheng Chien-Yu Cheng Wei-Sheng Chung Yehuda Z Cohen Lisa N Cowan Olav Dalgard Fernando F de Almeida E Val Marcus V G de Lacerda Gisely C de Melo Lennie Derde Vincent Dubee Anissa Elfakir Anthony C Gordon Carmen M Hernandez-Cardenas Thomas Hills Andy I M Hoepelman Yi-Wen Huang Bruno Igau Ronghua Jin Felipe Jurado-Camacho Khalid S Khan Peter G Kremsner Benno Kreuels Cheng-Yu Kuo Thuy Le Yi-Chun Lin Wu-Pu Lin Tse-Hung Lin Magnus Nakrem Lyngbakken Colin McArthur Bryan J McVerry Patricia Meza-Meneses Wuelton M Monteiro Susan C Morpeth Ahmad Mourad Mark J Mulligan Srinivas Murthy Susanna Naggie Shanti Narayanasamy Alistair Nichol Lewis A Novack Sean M O'Brien Nwora Lance Okeke Léna Perez Rogelio Perez-Padilla Laurent Perrin Arantxa Remigio-Luna Norma E Rivera-Martinez Frank W Rockhold Sebastian Rodriguez-Llamazares Robert Rolfe Rossana Rosa Helge Røsjø Vanderson S Sampaio Todd B Seto Muhammad Shahzad Shaimaa Soliman Jason E Stout Ireri Thirion-Romero Andrea B Troxel Ting-Yu Tseng Nicholas A Turner Robert J Ulrich Stephen R Walsh Steve A Webb Jesper M Weehuizen Maria Velinova Hon-Lai Wong Rebekah Wrenn Fernando G Zampieri Wu Zhong David Moher Steven N Goodman John P A Ioannidis Lars G Hemkens Meta-Research Innovation Center at Stanford (METRICS) Stanford University Stanford CA USA. Department for Women's and Children's Health Uppsala University Uppsala Sweden. Department of Clinical Research University Hospital Basel University of Basel Basel Switzerland. Department of Medical Oncology University of Basel Basel Switzerland. Amsterdam University Medical Center Amsterdam University Amsterdam the Netherlands. Tropical Medicine and Infectious Diseases Department Faculty of Medicine Tanta University Tanta Egypt. Tropical Medicine and Gastroenterology Department Faculty of Medicine Assiut University Assiut Egypt. Department of Emergency Medicine University of Pennsylvania Philadelphia PA USA. Department of Internal Medicine Vice Chancellor University of Health Sciences Lahore Punjab Pakistan. Abramson Cancer Center and Department of Medicine University of Pennsylvania Philadelphia PA USA. Department of Critical Care Medicine The Clinical Research Investigation and Systems Modeling of Acute Illness (CRISMA) Center University of Pittsburgh Pittsburgh PA USA. the UPMC Health System Office of Healthcare Innovation University of Pittsburgh Medical Centre Pittsburgh PA USA. Intensive Care Department King Saud Bin Abdulaziz University for Health Sciences and King Abdullah International Medical Research Center Riyadh Saudi Arabia. Department of Public Health University of Health Sciences Lahore Punjab Pakistan. Division of Infectious Diseases Brigham and Women's Hospital Boston MA USA. Department of Medicine Division of Infectious Diseases and International Health Duke University Medical Center Durham NC USA. Infectious Diseases Department Cliniques universitaires Saint-Luc Université Catholique de Louvain Brussels Belgium. Center of Research & Disruption of Infectious Diseases Department of Infectious Diseases Copenhagen University Hospital Amager and Hvidovre Hvidovre Denmark. Department of Internal Medicine Elisabeth-Tweesteden hospital Ti

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Creation and analysis of biochemical constraint-based models: The COBRA Toolbox v3.0

arXiv

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arXiv 2017年

作者： Heirendt, Laurent Arreckx, Sylvain Pfau, Thomas Mendoza, Sebastián N. Richelle, Anne Heinken, Almut Haraldsdóttir, Hulda S. Wachowiak, Jacek Keating, Sarah M. Vlasov, Vanja Magnusdóttir, Stefania Ng, Chiam Yu Preciat, German Žagare, Alise Chan, Siu H.J. Aurich, Maike K. Clancy, Catherine M. Modamio, Jennifer Sauls, John T. Noronha, Alberto Bordbar, Aarash Cousins, Benjamin El Assal, Diana C. Valcarcel, Luis V. Apaolaza, Iñigo Ghaderi, Susan Ahookhosh, Masoud Guebila, Marouen Ben Kostromins, Andrejs Sompairac, Nicolas Le, Hoai M. Ma, Ding Sun, Yuekai Wang, Lin Yurkovich, James T. Oliveira, Miguel A.P. Vuong, Phan T. El Assal, Lemmer P. Kuperstein, Inna Zinovyev, Andrei Scott Hinton, H. Bryant, William A. Aragón Artacho, Francisco J. Planes, Francisco J. Stalidzans, Egils Maass, Alejandro Vempala, Santosh Hucka, Michael Saunders, Michael A. Maranas, Costas D. Lewis, Nathan E. Sauter, Thomas Palsson, Bernhard Ø. Thiele, Ines Fleming, Ronan M.T. Luxembourg Centre for Systems Biomedicine University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg Life Sciences Research Unit University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg University of Chile Blanco Encalada 2085 Santiago Chile Department of Pediatrics University of California San Diego School of Medicine San DiegoCA92093 United States Hinxton CambridgeCB10 1SD United Kingdom Department of Chemical Engineering Pennsylvania State University University University ParkPA16802 United States Department of Physics University of California San Diego 9500 Gilman Dr. San DiegoCA92093 United States Bioinformatics and Systems Biology Program University of California San Diego San DiegoCA United States Sinopia Biosciences San DiegoCA United States School of Computer Science Algorithms and Randomness Center Georgia Institute of Technology AtlantaGA United States Biomedical Engineering and Sciences Department TECNUN University of Navarra Paseo de Manuel Lardizabal 13 San Sebastian20018 Spain Institute of Microbiology and Biotechnology University of Latvia Jelgavas iela 1 RigaLV-1004 Latvia Department of Management Science and Engineering Stanford University StanfordCA94305-4026 United States Bioengineering Department University of California San Diego San DiegoCA United States Utah State University Research Foundation 1695 North Research Park Way North LoganUT84341 United States Centre for Integrative Systems Biology and Bioinformatics Department of Life Sciences Imperial College London London United Kingdom Department of Mathematics University of Alicante Spain California Institute of Technology Computing and Mathematical Sciences MC 305-16 1200 E. California Blvd. PasadenaCA91125 United States Mathomics Center for Mathematical Modeling University of Chile Beauchef 851 Santiago Chile Novo Nordisk Foundation Center for Biosustainability University of California San Diego San DiegoCA92093 Uni

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread applications in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. Version 3.0 includes new methods for quality controlled reconstruction, modelling, topological analysis, strain and experimental design, network visualisation as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimisation solvers for multi-scale, multi-cellular and reaction kinetic modelling, respectively. This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios. This protocol is an update to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Data integration

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Pressing topics in the Belgian water sector anno 2015

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Sustainability of Water Quality and Ecology 2016年 7卷 32-36页

作者： De Mulder, C. Van Hoey, S. Van Hulle, S. Agathos, S.N. Cauwenberg, P. Mergen, P. Seuntjens, P. Smets, I. De Gueldre, G. Mouton, A. Schowanek, D. Meesschaert, B. Verstraete, W. Nopens, I. BIOMATH Department of Mathematical Modelling Statistics and Bioinformatics Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium LIWET Department of Industrial Biological Sciences Ghent University Graaf Karel de Goedelaan 5 Kortrijk 8500 Belgium Laboratory of Bioengineering Earth and Life Institute Université Catholique de Louvain Louvain-la-Neuve 1348 Belgium Unit Environmental Modeling Flemish Institute for Technological Research (VITO) Boeretang 200 Mol 2400 Belgium Royal Museum for Central Africa Leuvensesteenweg 13 Tervuren 3080 Belgium Botanic Garden Meise Bouchout Domain Nieuwelaan 38 Meise 1860 Belgium Department of Soil Management Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 Antwerpen 2000 Belgium CREaS Department of Chemical Engineering KU Leuven Celestijnenlaan 200F Leuven 3001 Belgium Aquafin NV Dijkstraat 8 Aartselaar 2630 Belgium Technology Campus Gent Odisee Hogeschool Gebroeders De Smetstraat 1 Gent 9000 Belgium Environmental Stewardship and Sustainability - Brussels Innovation Center Procter and Gamble Temselaan 100 Strombeek-Bever 1853 Belgium Cluster for Bioengineering Technology Department of Microbial and Molecular Systems KU Leuven Technology Campus Ostend Zeedijk 101 Oostende B-8400 Belgium LabMET Department of Biochemical and Microbial Technology Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium

Today's water sector is governed by some hot topics, and this is no different in Belgium. As for the International Water Association (IWA), the goal of its Belgian division (B-IWA) is to gather different stakeholders, i.e. academics, policy makers and people from industry active in the (Belgian) water sector and trigger the debate. In May 2015, a first Nocturnal was organised to accomplish just this. Seven hot water topics, proposed by participants at the time of their online registration, were addressed in rotating round table discussions. These topics included resource recovery, micropollutants, water scarcity, hydroinformatics, integrated water management and modeling, technology vs. legislation and Computational Fluid Dynamics in water applications. The lively discussions led to the idea of this short contribution describing the outcomes of these round table discussions, along with some additional research on the topics. Main conclusions include the need for education (both of scholars and young professionals), inter-domain communication and the growing importance of IT in the water sector. © 2016 Elsevier B.V.

关键词： Education Industry Informatics Legislation Water sector

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182 Molecular recognition between active site contour maps and ligand pharmacophoric sites predicts the future leads of HTLV-PR inhibitors

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Journal of Biomolecular Structure and Dynamics 2015年第SUPP 1期33卷 120页

作者： Sanjeev Kumar Singh[a][*] Chandrabose Selvaraj[a] [a] Computer Aided Drug Design and Molecular Modeling Lab Department of Bioinformatics Science Block Alagappa University Karaikudi 630004 Tamilnadu India

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