Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery.

[1]  C. G. Mohan,et al.  Identification of hotspot regions of MurB oxidoreductase enzyme using homology modeling, molecular dynamics and molecular docking techniques , 2011, Journal of molecular modeling.

[2]  A. Tyagi,et al.  Molecular modeling studies of Fatty acyl-CoA synthetase (FadD13) from Mycobacterium tuberculosis—a potential target for the development of antitubercular drugs , 2011, Journal of molecular modeling.

[3]  Sean Ekins,et al.  Using Open Source Computational Tools for Predicting Human Metabolic Stability and Additional Absorption, Distribution, Metabolism, Excretion, and Toxicity Properties , 2010, Drug Metabolism and Disposition.

[4]  Sean Ekins,et al.  Analysis and hit filtering of a very large library of compounds screened against Mycobacterium tuberculosis. , 2010, Molecular bioSystems.

[5]  S. Cole,et al.  Biological and structural characterization of the Mycobacterium smegmatis nitroreductase NfnB, and its role in benzothiazinone resistance , 2010, Molecular microbiology.

[6]  Manoj Kumar,et al.  In silico structure-based design of a novel class of potent and selective small peptide inhibitor of Mycobacterium tuberculosis Dihydrofolate reductase, a potential target for anti-TB drug discovery , 2010, Molecular Diversity.

[7]  Sean Ekins,et al.  A collaborative database and computational models for tuberculosis drug discovery. , 2010, Molecular bioSystems.

[8]  Ashutosh Kumar,et al.  Receptor based 3D-QSAR to identify putative binders of Mycobacterium tuberculosis Enoyl acyl carrier protein reductase , 2010, Journal of molecular modeling.

[9]  E. Coutinho,et al.  Synthesis, in vitro antitubercular activity and 3D-QSAR study of 1,4-dihydropyridines , 2010, Molecular Diversity.

[10]  Ashutosh Kumar,et al.  New molecular scaffolds for the design of Mycobacterium tuberculosis type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening , 2010, Journal of molecular modeling.

[11]  Gisbert Schneider,et al.  Virtual screening: an endless staircase? , 2010, Nature Reviews Drug Discovery.

[12]  T. Nikolskaya,et al.  Systems Biology: Applications in Drug Discovery , 2010 .

[13]  Anton J. Hopfinger,et al.  3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents , 2010, J. Comput. Aided Mol. Des..

[14]  Sean Ekins,et al.  Troubleshooting computational methods in drug discovery. , 2010, Journal of pharmacological and toxicological methods.

[15]  N. Chandra,et al.  A systems perspective of host-pathogen interactions: predicting disease outcome in tuberculosis. , 2010, Molecular bioSystems.

[16]  Kerly F. M. Pasqualoto,et al.  QSAR Modeling of a Set of Pyrazinoate Esters as Antituberculosis Prodrugs , 2010, Archiv der Pharmazie.

[17]  Nagasuma Chandra,et al.  Computational systems approach for drug target discovery , 2009, Expert opinion on drug discovery.

[18]  R. Vashisht,et al.  Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis. , 2009, Molecular bioSystems.

[19]  Tejender S. Thakur,et al.  Structure-based design of DevR inhibitor active against nonreplicating Mycobacterium tuberculosis. , 2009, Journal of medicinal chemistry.

[20]  Yong-Jun Jiang,et al.  Discovery of potential new InhA direct inhibitors based on pharmacophore and 3D-QSAR analysis followed by in silico screening. , 2009, European journal of medicinal chemistry.

[21]  Nitin Kumar,et al.  TBrowse: an integrative genomics map of Mycobacterium tuberculosis. , 2009, Tuberculosis.

[22]  Lynn Rasmussen,et al.  Antituberculosis activity of the molecular libraries screening center network library. , 2009, Tuberculosis.

[23]  Lynn Rasmussen,et al.  High-throughput screening for inhibitors of Mycobacterium tuberculosis H37Rv. , 2009, Tuberculosis.

[24]  J. Irwin,et al.  Docking and chemoinformatic screens for new ligands and targets. , 2009, Current opinion in biotechnology.

[25]  Melanie I. Stefan,et al.  BMC Systems Biology , 2022 .

[26]  Philip E. Bourne,et al.  Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis , 2009, PLoS Comput. Biol..

[27]  S. Cole,et al.  Benzothiazinones Kill Mycobacterium tuberculosis by Blocking Arabinan Synthesis , 2009, Science.

[28]  Amit Singhal,et al.  Synthetic EthR inhibitors boost antituberculous activity of ethionamide , 2009, Nature Medicine.

[29]  Ashutosh Kumar,et al.  Knowledge Based Identification of Potent Antitubercular Compounds Using Structure Based Virtual Screening and Structure Interaction Fingerprints , 2009, J. Chem. Inf. Model..

[30]  Andreas Bender,et al.  Fishing the target of antitubercular compounds: in silico target deconvolution model development and validation. , 2009, Journal of proteome research.

[31]  Enrique Molina Pérez,et al.  Design of novel antituberculosis compounds using graph-theoretical and substructural approaches , 2009, Molecular Diversity.

[32]  M. Chhabria,et al.  New frontiers in the therapy of tuberculosis: fighting with the global menace. , 2009, Mini reviews in medicinal chemistry.

[33]  Anton J. Hopfinger,et al.  Rational Design and 3D-Pharmacophore Mapping of 5′-Thiourea-Substituted α-Thymidine Analogues as Mycobacterial TMPK Inhibitors , 2009, J. Chem. Inf. Model..

[34]  P. Niyomrattanakit,et al.  Structure-activity relationships of antitubercular nitroimidazoles. 2. Determinants of aerobic activity and quantitative structure-activity relationships. , 2009, Journal of medicinal chemistry.

[35]  Simon J. F. Macdonald,et al.  Analysis of the Calculated Physicochemical Properties of Respiratory Drugs: Can We Design for Inhaled Drugs Yet? , 2009, J. Chem. Inf. Model..

[36]  Sean Ekins,et al.  Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery. , 2009, Drug discovery today.

[37]  George M Church,et al.  Tuberculosis Drug Resistance Mutation Database , 2009, PLoS medicine.

[38]  R. Doležal,et al.  N‐Benzylsalicylthioamides: Highly Active Potential Antituberculotics , 2009, Archiv der Pharmazie.

[39]  D. Ferguson,et al.  Quantitative three dimensional structure linear interaction energy model of 5'-O-[N-(salicyl)sulfamoyl]adenosine and the aryl acid adenylating enzyme MbtA. , 2008, Journal of medicinal chemistry.

[40]  Philip Prathipati,et al.  Global Bayesian Models for the Prioritization of Antitubercular Agents , 2008, J. Chem. Inf. Model..

[41]  Pedro M Alzari,et al.  Rising standards for tuberculosis drug development. , 2008, Trends in pharmacological sciences.

[42]  John P. Overington,et al.  Genomic-scale prioritization of drug targets: the TDR Targets database , 2008, Nature Reviews Drug Discovery.

[43]  R. Kiss,et al.  Signalling inhibitors against Mycobacterium tuberculosis--early days of a new therapeutic concept in tuberculosis. , 2008, Current medicinal chemistry.

[44]  Thomas R Ioerger,et al.  Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. , 2008, Journal of medicinal chemistry.

[45]  Christian Stolte,et al.  TB database: an integrated platform for tuberculosis research , 2008, Nucleic Acids Res..

[46]  J. Buolamwini,et al.  Quantitative structure-activity relationship studies on nitrofuranyl anti-tubercular agents. , 2008, Bioorganic & medicinal chemistry.

[47]  Ashutosh Kumar,et al.  CoMFA based de novo design of Pyrrolidine Carboxamides as Inhibitors of Enoyl Acyl Carrier Protein Reductase from Mycobacterium tuberculosis , 2008, Journal of molecular modeling.

[48]  Anders Karlén,et al.  Evaluation of the amino acid binding site of Mycobacterium tuberculosis glutamine synthetase for drug discovery. , 2008, Bioorganic & medicinal chemistry.

[49]  Sean Ekins,et al.  Computer Applications in Pharmaceutical Research and Development , 2008 .

[50]  Kerly F. M. Pasqualoto,et al.  Fragment-based and classical quantitative structure–activity relationships for a series of hydrazides as antituberculosis agents , 2008, Molecular Diversity.

[51]  H. Moser,et al.  Physicochemical properties of antibacterial compounds: implications for drug discovery. , 2008, Journal of medicinal chemistry.

[52]  Cristina R Ventura,et al.  Application of quantitative structure-activity relationships to the modeling of antitubercular compounds. 1. The hydrazide family. , 2008, Journal of medicinal chemistry.

[53]  C. Bewley,et al.  Synthesis of natural product-inspired inhibitors of Mycobacterium tuberculosis mycothiol-associated enzymes: the first inhibitors of GlcNAc-Ins deacetylase. , 2007, Journal of medicinal chemistry.

[54]  Peter D. Karp,et al.  The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases , 2007, Nucleic Acids Res..

[55]  Christopher N. Larsen,et al.  BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence , 2007, Nucleic Acids Res..

[56]  Sean Ekins,et al.  Computational Approaches That Predict Metabolic Intermediate Complex Formation with CYP3A4 (+b5) , 2007, Drug Metabolism and Disposition.

[57]  P. Tucker,et al.  Structure-based approaches to drug discovery against tuberculosis. , 2007, Current protein & peptide science.

[58]  Ram Sagar,et al.  C-3 alkyl/arylalkyl-2,3-dideoxy hex-2-enopyranosides as antitubercular agents: synthesis, biological evaluation, and QSAR study. , 2007, Journal of medicinal chemistry.

[59]  A. Kierzek,et al.  GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism , 2007, Genome Biology.

[60]  Rahul Jain,et al.  Synthesis, anti-tuberculosis activity, and 3D-QSAR study of 4-(adamantan-1-yl)-2-substituted quinolines. , 2007, Bioorganic & medicinal chemistry.

[61]  David W. Russell,et al.  LMSD: LIPID MAPS structure database , 2006, Nucleic Acids Res..

[62]  A. Malde,et al.  Synthesis, anti-tuberculosis activity, and 3D-QSAR study of ring-substituted-2/4-quinolinecarbaldehyde derivatives. , 2006, Bioorganic & medicinal chemistry.

[63]  Pradeep Reddy Marri,et al.  Comparative genomics of metabolic pathways in Mycobacterium species: gene duplication, gene decay and lateral gene transfer. , 2006, FEMS microbiology reviews.

[64]  H. Tomioka.  Current status of some antituberculosis drugs and the development of new antituberculous agents with special reference to their in vitro and in vivo antimicrobial activities. , 2006, Current pharmaceutical design.

[65]  Suzanne M. Paley,et al.  The Pathway Tools cellular overview diagram and Omics Viewer , 2006, Nucleic acids research.

[66]  T. Scior,et al.  Isoniazid is not a lead compound for its pyridyl ring derivatives, isonicotinoyl amides, hydrazides, and hydrazones: a critical review. , 2006, Current medicinal chemistry.

[67]  Fabrizio Manetti,et al.  Antimycobacterial agents. Novel diarylpyrrole derivatives of BM212 endowed with high activity toward Mycobacterium tuberculosis and low cytotoxicity. , 2006, Journal of medicinal chemistry.

[68]  M. Ferrone,et al.  Antifungal and antimycobacterial activity of new imidazole and triazole derivatives. A combined experimental and computational approach. , 2006, The Journal of antimicrobial chemotherapy.

[69]  Hugo Kubinyi,et al.  Success Stories of Computer‐Aided Design , 2006 .

[70]  Samiul Hasan,et al.  Prioritizing Genomic Drug Targets in Pathogens: Application to Mycobacterium tuberculosis , 2006, PLoS Comput. Biol..

[71]  Marcos Catanho,et al.  GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes. , 2006, Genetics and molecular research : GMR.

[72]  Pierre Baldi,et al.  Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[73]  G. Desiraju,et al.  3D-QSAR studies on antitubercular thymidine monophosphate kinase inhibitors based on different alignment methods. , 2006, Bioorganic & medicinal chemistry letters.

[74]  Rahul Jain,et al.  3D-QSAR study of ring-substituted quinoline class of anti-tuberculosis agents. , 2006, Bioorganic & medicinal chemistry.

[75]  R. Tripathi,et al.  NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis , 2005, Journal of Biological Chemistry.

[76]  A. Dimoglo,et al.  Synthesis of novel 5-aryl-2-thio-1,3,4-oxadiazoles and the study of their structure-anti-mycobacterial activities. , 2005, Bioorganic & medicinal chemistry.

[77]  Robert A. Field,et al.  New Small-Molecule Synthetic Antimycobacterials , 2005, Antimicrobial Agents and Chemotherapy.

[78]  Gopalakrishnan Bulusu,et al.  A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models , 2005, J. Chem. Inf. Model..

[79]  Ramón García-Domenech,et al.  Search of Chemical Scaffolds for Novel Antituberculosis Agents , 2005, Journal of biomolecular screening.

[80]  B. Rupp,et al.  Structural bioinformatic approaches to the discovery of new antimycobacterial drugs. , 2004, Current pharmaceutical design.

[81]  J Andrew McCammon,et al.  Discovery of a novel binding trench in HIV integrase. , 2004, Journal of medicinal chemistry.

[82]  Carolyn L. Talcott,et al.  Pathway logic modeling of protein functional domains in signal transduction , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[83]  A W Munro,et al.  The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology. , 2003, Tuberculosis.

[84]  Gyorgy Snell,et al.  The TB structural genomics consortium crystallization facility: towards automation from protein to electron density. , 2002, Acta crystallographica. Section D, Biological crystallography.

[85]  Shekhar C Mande,et al.  The TB structural genomics consortium: providing a structural foundation for drug discovery. , 2002, Current drug targets. Infectious disorders.

[86]  R. Slayden,et al.  Use of genomics and combinatorial chemistry in the development of new antimycobacterial drugs. , 2000, Biochemical pharmacology.

[87]  S T Cole,et al.  Learning from the genome sequence of Mycobacterium tuberculosis H37Rv , 1999, FEBS letters.

[88]  Alimuddin Zumla,et al.  Science, medicine, and the future: Tuberculosis , 1998 .

[89]  A. Ghose,et al.  Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragmental Methods: An Analysis of ALOGP and CLOGP Methods , 1998 .

[90]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .

[91]  A. Friedman,et al.  Tuberculosis research: going forward with a powerful "translational systems biology" approach. , 2010, Tuberculosis.

[92]  Thomas Scior,et al.  Elucidating Isoniazid Resistance Using Molecular Modeling , 2009, J. Chem. Inf. Model..

[93]  P. Sivakumar,et al.  QSAR studies on chalcones and flavonoids as anti-tuberculosis agents using genetic function approximation (GFA) method. , 2007, Chemical & pharmaceutical bulletin.

[94]  D. Pompliano,et al.  Drugs for bad bugs: confronting the challenges of antibacterial discovery , 2007, Nature Reviews Drug Discovery.

[95]  Shagufta,et al.  CoMFA and CoMSIA 3D-QSAR analysis of diaryloxy-methano-phenanthrene derivatives as anti-tubercular agents , 2007, Journal of molecular modeling.

[96]  Indira Ghosh,et al.  Developing an Antituberculosis Compounds Database and Data Mining in the Search of a Motif Responsible for the Activity of a Diverse Class of Antituberculosis Agents , 2006, J. Chem. Inf. Model..

[97]  Sharmila Anishetty,et al.  Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis , 2005, Comput. Biol. Chem..

[98]  Ying Zhang,et al.  The magic bullets and tuberculosis drug targets. , 2005, Annual review of pharmacology and toxicology.

[99]  Suzanne M. Paley,et al.  MetaCyc: a multiorganism database of metabolic pathways and enzymes , 2004, Nucleic Acids Res..

[100]  Shayne C. Gad,et al.  Drug Discovery Handbook , 1994 .

[101]  BIOINFORMATICS ORIGINAL PAPER Systems biology Differential network expression during drug and stress response , 2022 .