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Research Article

Effective interaction studies for inhibition of DNA ligase protein from Staphylococcus aureus

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Pages 15-25 | Received 20 Dec 2013, Accepted 19 May 2014, Published online: 23 Jul 2014

References

  • Kuehnert MJ, Hill HA, Kupronis BA, et al. Methicillin-resistant Staphylococcus aureus hospitalizations United States. Emerg Infect Dis 2005;11:868–72
  • Monecke S, Coombs G, Shore AC, et al. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One 2004:e17936
  • Pfaller MA, Jones RN, Doern GV, Kugler K; The Sentry Participants Group. Bacterial pathogens isolated from patients with bloodstream infection: frequencies of occurrence and antimicrobial susceptibility patterns from the SENTRY surveillance program (United States and Canada, 1997). Antimicroz Agents Chemother 1998:42:1762–70
  • Sader HS, Jones RN, Gales AC, et al. Antimicrobial susceptibility patterns from pathogens isolated from patients in Latin American medical centers with a diagnosis of pneumonia: analysis of results from the SENTRY antimicrobial surveillance program (1997) SENTRY Latin America Study Group. Diagn Microbiol Infect Dis 1998;32:289–301
  • Ishino Y, Shinagawa H, Makino K, et al. Nucleotide sequence of the lig gene and primary structure of DNA ligase of Escherichia coli. Mol Genet Genomics 1986;204:1–7
  • Martin P, Li T, Sun D, et al. Role in cell permeability of an essential two-component system in Staphylococcus aureus. J Bacteriol 1999;181:3666–73
  • Liebert JC, Paolozzi L, Camera MG, et al. The expression of the DNA ligase gene of Escherichia coli is stimulated by relaxation of chromosomal supercoiling. J Mol Microbiol 1989;3:269–73
  • Modrich P, Anraku Y, Lehman IR. Deoxyribonucleic acid ligase: isolation and physical characterization of the homogeneous enzyme from Escherichia coli. J Biol Chem 1973;248:7495–501
  • Montecucco A, Pedrali-Noy G, Spadari S, Ciarrocchi G. Multiple roles of DNA ligase at the replication fork. Biochim Biophys Acta 1988;951:330–4
  • Panasenko S, Modrich MP, Lehman IR. Modification of Escherichia coli DNA ligase by cleavage with trypsin. J Biol Chem 1976;251:3432–5
  • Thorbjarnardottir SH, Jonsson ZO, Andresson OS, et al. Cloning and sequence analysis of the DNA ligase-encoding gene of Rhodothermus marinus, and overproduction, purification and characterization of two thermophilic DNA ligases. Gene 1995;161:1–6
  • Shark KB, Conway T. Cloning and molecular characterization of the DNA ligase gene (lig) from Zymomonas mobilis. Search Results. FEMS Microbiol Lett 1992;75:19–26
  • Timson DJ, Wigley DB. Functional domains of an NAD1- dependent DNA ligase. J Mol Biol 1999;285:73–83
  • Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T. DNA ligases: structure, reaction mechanism, and function. Chem Rev 2006;106:687–99
  • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Delivery Rev 1997;46:3–25
  • Ohtsuki S, Uchida Y, Kubo Y, Terasaki T. Quantitative Targeted Absolute Proteomics-Based ADME Research as a New Path to Drug Discovery and development: methodology, advantages, strategy and prospects. J Pharm Sci 2011;100:3547–59
  • Xu Z, Luo HH, Tieleman DP. Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues. J Comput Chem 2007;28:689–97
  • Chen IJ, Foloppe N. Drug-like bioactive structures and conformational coverage with the LigPrep/ConfGen suite: comparison to programs MOE and catalyst. J Chem Inf Model 2010;50:822–39
  • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005;58:134–43
  • Halgren TA. New method for fast and accurate binding-site identification and analysis. Chem Biol Drug Des 2007;69:146–8
  • Halgren TA. Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model 2009;49:377–89
  • Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem 2005;26:915–31
  • QPLD. Schrödinger Suite, QM-Polarized Ligand Docking protocol; Glide (2010) version 5.6, Jaguar (2010) version 7.7, QSite (2010) version 5.6. Schrödinger Inc, LLC, New York, NY, USA, 2010
  • Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: “what you see e” is not always “what you get”. Structure 2009;17:489–98
  • Lyne PD, Lamb ML, Saeh JC. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. J Med Chem 2006;49:4805–8
  • Das D, Koh Y, Tojo Y, et al. Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model. J Chem Inf Model 2009;49:2851–62
  • QikProp Version 3.3. New York: Schrödinger, LLC; 2011
  • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Delivery Rev 2001;46:3–26
  • Bowie JU, Luthy R, Eisenberg DA. Method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164–70
  • Vivek V, Anurekha J, Avijeet J, Arun G. Virtual screening: a fast tool for drug design. Sci Pharm 2008;76:333–60
  • Chaudhari UP, Trivedi ND, Pat RR, Banerjee S. Molecular docking studies of l-name With the neuronal nitric oxide synthase. Int J ChemTech Res 2010;2:122–8
  • Daisy P, Vijayalakshmi P, Selvaraj C, et al. Targeting multidrug resistant Mycobacterium tuberculosis HtrA2 with identical chemical entities of fluoroquinolones. Indian J Pharm Sci 2012;74:189–280
  • Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein–ligand interactions. Protein Eng 1995;8:127–34
  • Wang R, Liu L, Lai L, Tang Y. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. J Mol Model 1998;4:379–94
  • Qian SB, Waldron L, Choudhary N, et al. Engineering a ubiquitin ligase reveals conformational flexibility required for ubiquitin transfer. J Biol Chem 2009;284:26797–802
  • Patil R, Das S, Stanley A, et al. Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing. PLoS One 2010;5:e12029
  • Rastelli G, Del Rio A, Degliesposti G, Sgobba M. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J Comput Chem 2010;31:797–810
  • Rastelli G, Degliesposti G, Del Rio A, Sgobba A. Binding estimation after refinement, a new automated procedure for the refinement and scoring of docked ligands in virtual screening. Chem Biol Drug Des 2009;73:283–6
  • Hodgson J. ADMET-turning chemicals into drugs. Nat Biotechnol 2001;19:722–6
  • Merlot C. Computational toxicology – a tool for early safety evaluation. Drug Discov Today 2010;15:16–22

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