Paper Titles in Periodical
International Letters of Chemistry, Physics and Astronomy
Volume 60

Subscribe

Subscribe to our Newsletter and get informed about new publication regulary and special discounts for subscribers!

ILCPA > Volume 60 > Comparison of Molecular Docking and Molecular...
Comparison of Molecular Docking and Molecular Dynamics Simulations of 1,3-Thiazin-4-One with MDM2 Protein
< Back to Volume

Comparison of Molecular Docking and Molecular Dynamics Simulations of 1,3-Thiazin-4-One with MDM2 Protein

Full Text PDF

Abstract:

The molecular docking and molecular dynamics simulations studies of 1,3–thiazin–4–one derivative with a bonafide oncogene protein MDM2 (PDB ID: 4HBM) was investigated. Both the docking and dynamics simulations were performed in Schrödinger software suite 2014 using Glide and Desmond modules. The results of docking and dynamics were compared to investigate the possible binding modes of the thiazinone derivative with 4HBM. The tested molecule shows critical interactions with the important amino acid His 96 which is necessary for the inhibition of MDM2 in both docking and dynamic studies.

Info:

Periodical:
International Letters of Chemistry, Physics and Astronomy (Volume 60)
Pages:
161-167
DOI:
https://doi.org/10.18052/www.scipress.com/ILCPA.60.161
Citation:
S. A. A. Anand et al., "Comparison of Molecular Docking and Molecular Dynamics Simulations of 1,3-Thiazin-4-One with MDM2 Protein", International Letters of Chemistry, Physics and Astronomy, Vol. 60, pp. 161-167, 2015
Online since:
September 2015
Authors:
S. Athavan Alias Anand, C. Loganathan, K. Saravanan, S. Kabilan
Keywords:
Docking, Dynamic Simulations, MDM2, Thiazinone
Export:
RIS, BibTeX, Text
Distribution:
Open Access

Creative Commons License
This work is licensed under a
Creative Commons Attribution 4.0 International License

References:

L.A. Donehower, M. Harvey, B.L. Slagle, M.J. McArthur, C.A. Montgomery, J.S. Butel, A. Bradley, L.A. Donehower, M. Harvey, B.L. Slagle, M.J. McArthur, C.A. Montgomery, J.S. Butel, A. Bradley, Mice deficient for p.53 are developmentally normal but susceptible to spontaneous tumours, Nature, 356 (1992).

D. Bernard, Y. Zhao, S. Wang, AM-8553: a novel MDM2 inhibitor with a promising outlook for potential clinical development, J. Med. Chem. 55 (2012) 4934-4935.

S.A.A. Anand, C. Loganathan, N.S. Thomas, K. Saravanan, A.T. Alphonsa, S. Kabilan, Synthesis, structure prediction, pharmacokinetic properties, molecular docking and antitumor activities of some novel thiazinone derivatives, New J. Chem. 39 (2015).

H. Yamashita, K. Ohno, H. Inami, J. Shishikura, S. Sakamoto, M. Okada, T. Yamaguchi, Suppression of fully kindled seizure and retardation of kindling acquisition by YM928 in the rat kindling model of epilepsy, Eur. J. Pharmacol. 494 (2004).

L.D.S. Yadav, A.R. Misra, H. Singh, Ring transformation of Michael adducts of Benzylidene-5-oxazolones and 3-mercapto-s-triazoles to 2, 3-dihydro-4H-s-triazolo[3, 4b][1, 3] thiazin-4-ones with some antifungal activity, J. Agric. Food Chem. 36 (1988).

V.V. Kouznetsov, A.G. Barrio, Recent developments in the design and synthesis of hybrid molecules based on aminoquinoline ring and their antiplasmodial evaluation, Eur. J. Med. Chem. 44 (2009) 3091-3113.

J. Matysiak, M. Juszczak, M.M. Karpińska, E. Langner, K. Walczak, M.K. Lemieszek, A. Skrzypek, A. Niewiadomy, W. Rzeski, Synthesis of 2-(2, 4-dihydroxyphenyl)thieno-1, 3-thiazin4-ones, their lipophilicity and anticancer activity in vitro, Mol. divers. (2015).

K. Ohno, R. Tsutsumi, N. Matsumoto, H. Yamashita, Y. Amada, J. Shishikura, H.I.S. Yatsugi, M. Okada, S. Sakamoto and T. Yamaguchi, Functional characterization of YM928, a novel moncompetitive alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor antagonist, J. Pharmacol. Exp. Ther. 306 (2003).

K. Michelsen, J.B. Jordan, J. Lewis , A.M. Long, E. Yang , Y. Rew, J. Zhou , P. Yakowec, P.D. Schnier , X. Huang , L. Poppe, Ordering of the N-terminus of human MDM2 by small molecule inhibitors, J. Am. Chem. Soc. 134 (2012) 17059-17067.

Protein Preparation Wizard; Epik version 2. 3, 2014; Impact version 5. 7, 2014, Schrödinger, LLC, New York.

Maestro, 2014 release, Schrödinger suite, LLC, New York, (2014).

W.L. Jorgensen, D.S. Maxwell, J. Tirado-Rives, Development and testing of the OPLS allatom force field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc. 118 (1996) 11225-11236.

LigPrep, version 2. 5, 2014, Schrödinger, LLC, New York.

Glide, version 5. 8, 2014, Schrödinger, LLC, New York.

Desmond Molecular Dynamics System, version 3. 1, 2012, D. E. Shaw Research, New York, Maestro-Desmond Interoperability Tools, version 3. 1, 2012, Schrödinger, New York.

W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983) 926-935.

W.G. Hoover, Canonical dynamics: Equilibrium phase-space distributions, Phys. Rev. A. 31 (1985) 1695-1697.

G.J. Martyna, D.J. Tobias, M.L. Klein, Constant pressure molecular dynamics algorithms, J. Chem. Phys. 101 (1994) 4177-4189.

U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, L.G. Pedersen, A smooth particle mesh Ewald method, J. Chem. Phys. 103 (1995) 8577-8859.

F. Gonzalez-Lopez de Turiso, D. Sun, Y. Rew, M.D. Bartberger, H.P. Beck, J. Canon, A. Chen, D. Chow, T.L. Correll, X. Huang, L.D. Julian, F. Kayser, M.C. Lo, A.M. Long, D. McMinn, J.D. Oliner, T. Osgood, J.P. Powers, A.Y. Saiki, S. Schneider, P. Shaffer, S.H. Xiao, P. Yakowek, X. Yan, Q. Ye, D. Yu, X. Zhao, J. Zhou, J.C. Medina, S.H. Olson, Rational design and binding mode duality of MDM2-p.53 inhibitors, J. Med. Chem. 56 (2013).

Show More Hide