Multilayer precision-based screening of potential inhibitors targeting Mycobacterium tuberculosis acetate kinase using in silico approaches.

[1]  Cathy H. Wu,et al.  UniProt: the Universal Protein Knowledgebase in 2023 , 2022, Nucleic Acids Res..

[2]  E. Azhar,et al.  Repositioning of anti-dengue compounds against SARS-CoV-2 as viral polyprotein processing inhibitor , 2022, PloS one.

[3]  Jose M. Duarte,et al.  RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D , 2022, Protein science : a publication of the Protein Society.

[4]  Rania Bouzeyen,et al.  Therapeutic Vaccines for Tuberculosis: An Overview , 2022, Frontiers in Immunology.

[5]  Jonathan E. Allen,et al.  Accelerators for Classical Molecular Dynamics Simulations of Biomolecules , 2022, Journal of chemical theory and computation.

[6]  V. Umashankar,et al.  Deciphering the conformational transitions of LIMK2 active and inactive states to ponder specific druggable states through microsecond scale molecular dynamics simulation , 2022, Journal of Computer-Aided Molecular Design.

[7]  Pooja,et al.  Mycobacterium tuberculosis carbon and nitrogen metabolic fluxes , 2022, Bioscience Reports.

[8]  Suhkmann Kim,et al.  Regulation of the icl1 Gene Encoding the Major Isocitrate Lyase in Mycobacterium smegmatis , 2021, Journal of bacteriology.

[9]  N. Mutharasappan,et al.  Characterization of putative transcriptional regulator (PH0140) and its distal homologue. , 2021, Cellular signalling.

[10]  X. Guan,et al.  Metabolic Versatility of Mycobacterium tuberculosis during Infection and Dormancy , 2021, Metabolites.

[11]  K. Bettenbrock,et al.  The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12 , 2020, Frontiers in Microbiology.

[12]  Manikandan Jayaraman,et al.  Structural insight into conformational dynamics of non-active site mutations in KasA: A Mycobacterium tuberculosis target protein. , 2019, Gene.

[13]  W. Jiao,et al.  Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2 , 2019, Nature Communications.

[14]  J. Locasale,et al.  Acetate Metabolism in Physiology, Cancer, and Beyond. , 2019, Trends in cell biology.

[15]  J. Tyagi,et al.  Cognate sensor kinase‐independent activation of Mycobacterium tuberculosis response regulator DevR (DosR) by acetyl phosphate: implications in anti‐mycobacterial drug design , 2019, Molecular microbiology.

[16]  Jingpu Zhang,et al.  In silico ADME and Toxicity Prediction of Ceftazidime and Its Impurities , 2019, Front. Pharmacol..

[17]  Sangyoub Lee,et al.  New Method for Constant- NPT Molecular Dynamics. , 2019, The journal of physical chemistry. A.

[18]  Sanna P. Niinivehmas,et al.  Suitability of MMGBSA for the selection of correct ligand binding modes from docking results , 2018, Chemical biology & drug design.

[19]  H. Derendorf,et al.  Mycobacterium tuberculosis Strains H37ra and H37rv have equivalent minimum inhibitory concentrations to most antituberculosis drugs , 2018, International journal of mycobacteriology.

[20]  Sebastian M. Gygli,et al.  Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives , 2017, FEMS microbiology reviews.

[21]  P. Lu,et al.  Targeting Energy Metabolism in Mycobacterium tuberculosis, a New Paradigm in Antimycobacterial Drug Discovery , 2017, mBio.

[22]  Xiaoyan Qian,et al.  Modulation of Central Carbon Metabolism by Acetylation of Isocitrate Lyase in Mycobacterium tuberculosis , 2017, Scientific Reports.

[23]  N. Bragazzi,et al.  The history of tuberculosis: from the first historical records to the isolation of Koch's bacillus , 2017, Journal of preventive medicine and hygiene.

[24]  Aman Kumar Sharma,et al.  In silico characterization of hypothetical proteins obtained from Mycobacterium tuberculosis H37Rv , 2017, Network Modeling Analysis in Health Informatics and Bioinformatics.

[25]  S. Choubey,et al.  Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches , 2016 .

[26]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[27]  C. Wittmann,et al.  Acetate Dissimilation and Assimilation in Mycobacterium tuberculosis Depend on Carbon Availability , 2015, Journal of bacteriology.

[28]  J. Ferry Acetate Metabolism in Anaerobes from the Domain Archaea , 2015, Life.

[29]  D. Warner Mycobacterium tuberculosis metabolism. , 2015, Cold Spring Harbor perspectives in medicine.

[30]  David Fox,et al.  Increasing the structural coverage of tuberculosis drug targets. , 2015, Tuberculosis.

[31]  G. Stock,et al.  Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates. , 2014, The Journal of chemical physics.

[32]  Rajendra Kumar,et al.  g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations , 2014, J. Chem. Inf. Model..

[33]  C. Ingram-Smith,et al.  Direct detection of the acetate-forming activity of the enzyme acetate kinase. , 2011, Journal of visualized experiments : JoVE.

[34]  Elena Papaleo,et al.  Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case. , 2009, Journal of molecular graphics & modelling.

[35]  J. Ferry,et al.  Structural and Kinetic Analyses of Arginine Residues in the Active Site of the Acetate Kinase from Methanosarcina thermophila* , 2005, Journal of Biological Chemistry.

[36]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[37]  Mitsunori Ikeguchi,et al.  Partial rigid‐body dynamics in NPT, NPAT and NPγT ensembles for proteins and membranes , 2004, J. Comput. Chem..

[38]  Julie D Thompson,et al.  Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.

[39]  L. Riley,et al.  Mycobacterium tuberculosis CDC1551 Is Resistant to Reactive Nitrogen and Oxygen Intermediates In Vitro , 2002, Infection and Immunity.

[40]  A. Pym,et al.  Molecular epidemiology of tuberculosis , 2002, European Respiratory Journal.

[41]  James G. Ferry,et al.  Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases , 2001, Journal of bacteriology.

[42]  A. Danchin,et al.  Catabolite Regulation of the pta Gene as Part of Carbon Flow Pathways in Bacillus subtilis , 1999, Journal of bacteriology.

[43]  B. Prüß,et al.  Acetyl phosphate and the phosphorylation of OmpR are involved in the regulation of the cell division rate in Escherichia coli , 1998, Archives of Microbiology.

[44]  Christophe Geourjon,et al.  SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments , 1995, Comput. Appl. Biosci..

[45]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[46]  A. Sali,et al.  Modeller: generation and refinement of homology-based protein structure models. , 2003, Methods in enzymology.

[47]  Josep Ramón Goñi,et al.  Molecular dynamics simulations: advances and applications , 2015, Advances and applications in bioinformatics and chemistry : AABC.