Identification of potential inhibitors for AIRS from de novo purine biosynthesis pathway through molecular modeling studies – a computational approach

References

• Adam, T. (2005). Purine de novo synthesis – Mechanisms and clinical implications. Klinicka Biochemie a Metabolismus, 13, 177–181.
   Google Scholar
• Arfeen, M., Patel, R., Khan, T., & Bharatam, V. P. (2015). Molecular dynamics simulation studies of GSK-3β ATP competitive inhibitors: Understanding the factors contributing to selectivity. Journal of Biomolecular Structure and Dynamics, 33, 2578–2593. doi:10.1080/07391102.2015.1063457
   PubMed Web of Science ®Google Scholar
• Balasco, N., Barone, D., & Vitagliano, L. (2015). Structural conversion of the transformer protein RfaH: New insights derived from protein structure prediction and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 33, 2173–2179. doi:10.1080/07391102.2014.994188
   PubMed Web of Science ®Google Scholar
• Binkley, J. S., Pople, J. A., & Hehre, W. J. (1980). Self-consistent molecular orbital methods. 21. Small split-valence basis sets for first row elements. Journal of the American Chemical Society, 102, 939–947. doi:10.1021/ja00523a008
   Web of Science ®Google Scholar
• Buchanan, J. M., & Wilson, D. W. (1953). Biosynthesis of purines and pyrimidines. Federation Proceedings, 12, 646–650.
   PubMedGoogle Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2, 1511–1519. doi:10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092. doi:10.1063/1.464397
   Web of Science ®Google Scholar
• Engh, R. A., & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallographica Section A Foundations of Crystallography, 47, 392–400. doi:10.1107/S0108767391001071
   Web of Science ®Google Scholar
• Eswar, N., Eramian, D., Webb, B., Shen, M. Y., & Sali, A. (2008). Protein structure modeling with MODELLER. Methods Molecular Biology, 426, 145–159. doi:10.1007/978-1-60327-058-8_8
   PubMedGoogle Scholar
• Fan, J.-R. Zheng, Q.-C., Cui, Y.-L., Li, W.-K., & Zhang, H.-X. (2015). Investigation of ligand selectivity in CYP3A7 by molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 33, 2360–2367. doi:10.1080/07391102.2015.1054884
   PubMed Web of Science ®Google Scholar
• Firestine, S. M., Paritala, H., McDonnell, J. E., Thoden, J. B., & Holden, H. M. (2009). Identification of inhibitors of N5-carboxyaminoimidazole ribonucleotide synthetase by high-throughput screening. Bioorganic & Medicinal Chemistry, 17, 3317–3323. doi:10.1016/j.bmc.2009.03.043
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., … Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein−ligand complexes. Journal of Medicinal Chemistry, 49, 6177–6196. doi:10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47, 1750–1759. doi:10.1021/jm030644s.
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463:AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Kirubakaran, P., Muthusamy, K., Singh, K. D., & Nagamani, S. (2012). Homology modeling, molecular dynamics, and molecular docking studies of Trichomonas vaginalis carbamate kinase. Medicinal Chemistry Research, 21, 2105–2116. doi:10.1007/s0044-011-9719-9
   Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied. Crystallography, 26, 283–291. doi:10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lee, C., Yang, W., & Parr, R. G. (1988). Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785–789. doi:10.1103/PhysRevB.37.785
   PubMed Web of Science ®Google Scholar
• Li, C., Kappock, T. J., Stubbe, J., Weaver, T. M., & Ealick, S. E. (1999). X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 Å resolution. Structure, 7, 1155–1166. doi:10.1016/S0969-2126(99)80182-8
   PubMed Web of Science ®Google Scholar
• Maestro, Version 9.9, Schrödinger. (2014). New York, NY: LLC.
   Google Scholar
• Marolewski, A., Smith, J. A., & Benkovic, S. J. (1994). Cloning and characterization of a new purine biosynthetic enzyme: A non-folate glycinamide ribonucleotide transformylase from E. coli. Biochemistry, 33, 2531–2537. doi:10.1021/bi00175a023
   PubMed Web of Science ®Google Scholar
• Mathews, I. I., Kappock, T. J., Stubbe, J. A., & Ealick, S. E. (1999). Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Structure, 7, 1395–1406. doi:10.1016/S0969-2126(00)80029-5
   PubMed Web of Science ®Google Scholar
• McFarland, W. C., & Stocker, B. A. D. (1987). Effect of different purine auxotrophic mutations on mouse-virulence of a Vi-positive strain of Salmonella dublin and of two strains of Salmonella typhimurium. Microbial Pathogenesis, 3, 129–141. doi:10.1016/0882-4010(87)90071-4
   PubMed Web of Science ®Google Scholar
• Protein Preparation Wizard, Epik Version 2.8, Schrödinger. (2014). New York, NY: LLC.
   Google Scholar
• QikProp, Version 4.5, Schrödinger. (2015). New York, NY: LLC.
   Google Scholar
• Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42, W320–W324. doi:10.1093/nar/gku316
   PubMed Web of Science ®Google Scholar
• Samant, S., Lee, H., Ghassemi, M., Chen, J., Cook, J. L., Mankin, A. S., & Neyfakh, A. A. (2008). Nucleotide biosynthesis is critical for growth of bacteria in human blood. PLoS Pathogens, 4, 1–10. doi:10.1371/journal.ppat.0040037
   Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60, 1355–1363. doi:10.1107/S0907444904011679
   PubMed Web of Science ®Google Scholar
• Shen, M. Y., & Sali, A. (2006). Statistical potential for assessment and prediction of protein structures. Protein Science, 15, 2507–2524. doi:10.1110/ps.062416606
   PubMed Web of Science ®Google Scholar
• Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., & Faid, R. (2006). Novel procedure for modeling ligand/receptor induced fit effects. Journal of Medicinal Chemistry, 49, 534–553. doi:10.1021/jm050540c
   PubMed Web of Science ®Google Scholar
• Singh, K. D., Kirubakaran, P., Nagarajan, S., Sakkiah, S., Muthusamy, K., Velmurugan, D., & Jeyakanthan, J. (2012). Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of chikungunya virus nsP2 protease. Journal of Molecular Modeling, 18, 39–51. doi:10.1007/s00894-011-1018-3
   PubMed Web of Science ®Google Scholar
• Thoden, J. B., Kappock, T. J., Stubbe, L., & Holden, H. M. (1999). Three dimensional structure of N5-carboxyaminoimidazole ribonucleotide(N5-CAIR) synthetase: A member of the ATP-Grasp protein superfamily. Biochemistry, 38, 15480–15492. doi:10.1021/bi991618s
   PubMed Web of Science ®Google Scholar
• Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673–4680. doi:10.1093/nar/22.22.4673
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718. doi:10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Virtual Screening Workflow. (2014-2) New York, NY: LLC.
   Google Scholar
• Waldrop, G. L., Rayment, I., & Holden, H. M. (1994). Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase. Biochemistry, 33, 10249–10256. doi:10.1021/bi00200a004
   PubMed Web of Science ®Google Scholar
• Welin, M., Grossmann, J. G., Flodin, S., Nyman, T., Stenmark, P., Tresaugues, L., … Lehtio, L. (2010). Structural studies of tri-functional human GART. Nucleic Acids Research, 38, 7308–7319. doi:10.1093/nar/gkq595
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, W407–W410. doi:10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Yamashita, F., & Hashida, M. (2004). In silico approaches for predicting ADME properties of drugs. Drug Metabolism and Pharmacokinetics, 19, 327–338. doi:10.2133/dmpk.19.327
   PubMedGoogle Scholar
• Zalkin, H., & Dixon, J. E. (1992). De novo purine nucleotide biosynthesis. Progress in Nucleic Acid Research and Molecular Biology, 42, 259–287. doi:10.1002/9780470015902.a0001396.pub3
   PubMed Web of Science ®Google Scholar