Design of galardine analogs as putative psudolysin inhibitors based on ab initio fragment molecular orbital calculations

References

• Adekoya, O. A., Sjøli, S., Wuxiuer, Y., Bilto, I., Marques, S. M., Santos, M. A., … Sylte, I. (2015). Inhibition of pseudolysin and thermolysin by hydroxamate-based MMP inhibitors. European Journal of Medicinal Chemistry, 89, 340–348. doi:10.1016/j.ejmech.2014.10.009
   PubMed Web of Science ®Google Scholar
• Ara, A., Kadoya, R., Ishimura, H., Shimamura, K., Sylte, I., & Kurita, N. (2017). Specific interactions between zinc metalloproteinase and its inhibitors: Ab initio fragment molecular orbital calculations. Journal of Molecular Graphics and Modelling, 75, 277–286. doi:10.1016/j.jmgm.2017.05.013
   PubMed Web of Science ®Google Scholar
• Burns, F. R., Paterson, C. A., Gray, R. D., & Wells, I. T. (1990). Inhibition of Pseudomonas Aeruginosa elastase and Pseudomonas keratitis using a thiol-based peptide. Antimicrobial Agents and Chemotherapy, 34(11), 2065–2069. doi:10.1128/AAC.34.11.2065
   PubMed Web of Science ®Google Scholar
• Camodeca, C., Nuti, E., Tepshi, L., Boero, S., Tuccinardi, T., Stura, E. A., … Rossello, A. (2016). Discovery of a new selective inhibitor of a disintegrin and metalloprotease 10 (ADAM-10) able to reduce the shedding of NKG2D ligands in Hodgkin’s lymphoma cell models. European Journal of Medicinal Chemistry, 111, 193–201. doi:10.1016/j.ejmech.2016.01.053
   PubMed Web of Science ®Google Scholar
• Case, D. A., Darden, T. E., Cheatham III, C. L., Simmerling, J., Wang, R. E., Duke, R., … Kollman, P. A. (2012). Amber 12. San Francisco, CA: University of California.
   Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. doi:10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Fedorov, D. G., Nagata, T., & Kitaura, K. (2012). Exploring chemistry with the fragment molecular orbital method. Physical Chemistry Chemical Physics, 14(21), 7562–7577. doi:10.1039/c2cp23784a
   PubMed Web of Science ®Google Scholar
• “For the WHO Organization, WHO Association of Japan.” (n.d). Retrieved from https://www.japan-who.or.jp/commodity/themes.html
   Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2009). Gaussian 09 Revision A.02. Wallingford, CT: Gaussian, Inc..
   Google Scholar
• Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., & Tanaka, S. (2006). Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study. Journal of Computational Chemistry, 27(8), 948–960. doi:10.1002/jcc.20399
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. doi:10.1063/1.445869
   Web of Science ®Google Scholar
• Khan, M. T. H., Wuxiuer, Y., & Sylte, I. (2012). Binding modes and pharmacophore modelling of thermolysin inhibitors. Mini-Reviews in Medicinal Chemistry, 12, 515–533. doi:10.2174/138955712800493799
   PubMed Web of Science ®Google Scholar
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber Ff99SB protein force field. Proteins: Structure, Function, and Bioinformatics, 78, 1950–1958.doi:10.1002/prot.22711
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1–3), 3–25. 10.1016/S0169-409X(96)00423-1 doi:10.1016/S0169-409X(00)00129-0
   Web of Science ®Google Scholar
• Mochizuki, Y., Koikegami, S., Nakano, T., Amari, S., & Kitaura, K. (2004). Large scale MP2 calculations with fragment molecular orbital scheme. Chemical Physics Letters, 396(4–6), 473–479. doi:10.1016/j.cplett.2004.08.082
   Web of Science ®Google Scholar
• Mochizuki, Y., Nakano, T., Koikegami, S., Tanimori, S., Abe, Y., Nagashima, U., & Kitaura, K. (2004). A parallelized integral-direct second-order Møller-Plesset perturbation theory method with a fragment molecular orbital scheme. Theoretical Chemistry Accounts, 112(5–6), 442–452. doi:10.1007/s00214-004-0602-3
   Web of Science ®Google Scholar
• Oh, J., Takahashi, R., Adachi, E., Kondo, S., Kuratomi, S., Noma, A., … Noda, M. (2004). Mutations in two matrix metalloproteinase genes, MMP-2 and MT1-MMP, are synthetic lethal in mice. Oncogene, 23(29), 5041–5048. doi:10.1038/sj.onc.1207688
   PubMed Web of Science ®Google Scholar
• Shah, S., Patel, B., & Savjani, J. K. (2018). Pharmacophore mapping based virtual screening, molecular docking and ADMET studies of ROCK II inhibitors. Multiple Sclerosis and Related Disorders, 21, 35–41. doi:10.1016/j.msard.2018.02.011
   PubMed Web of Science ®Google Scholar
• Sjøli, S., Nuti, E., Camodeca, C., Bilto, I., Rossello, A., Winberg, J. O., … Adekoya, O. A. (2016). Synthesis, experimental evaluation and molecular modelling of hydroxamate derivatives as zinc metalloproteinase inhibitors. European Journal of Medicinal Chemistry, 108, 141–153. doi:10.1016/j.ejmech.2015.11.019
   PubMed Web of Science ®Google Scholar
• Spoel, D. V. D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 16, 1701–1718. doi:10.1002/jcc.20291
   Web of Science ®Google Scholar
• Sylte, I., Dawadi, R., Malla, N., Hofsten, S. V., Nguyen, T. M., Solli, A. I., … Winberg, J. O. (2018). The selectivity of galardin and an azasugar-based hydroxamate compound for human matrix metalloproteases and bacterial metalloproteases. PLoS One, 13(8), e0200237. doi:10.1371/journal.pone.0200237
   PubMed Web of Science ®Google Scholar
• Takaishi, H., Kimura, T., Dalal, S., Okada, Y., & Armiento, J. D. (2008). Joint diseases and matrix metalloproteinases: A role for MMP-13. Current Pharmaceutical Biotechnology, 9(1), 47–54. doi:10.2174/138920108783497659
   PubMed Web of Science ®Google Scholar
• Tanaka, S., Mochizuki, Y., Komeiji, Y., Okiyama, Y., & Fukuzawa, K. (2014). Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Physical Chemistry Chemical Physics, 16(22), 10310–10344. doi:10.1039/C4CP00316K
   PubMed Web of Science ®Google Scholar
• Tandon, A., & Sinha, S. (2011). Structural insights into the binding of MMP9 inhibitors. Bioinformation, 5(8), 310–314. doi:10.6026/97320630005310
   PubMedGoogle Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and Testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• WHO. (2013). World Health Day – 7 April 2011. WHO. Retrieved from https://www.who.int/world-health-day/2011/en/
   Google Scholar
• Wirth, M., Zoete, V., Michielin, O., & Sauer, W. H. B. (2013). SwissBioisostere: A database of molecular replacements for ligand design. Nucleic Acids Research, 41(D1), D1137–D1143. doi:10.1093/nar/gks1059
   PubMed Web of Science ®Google Scholar