Monte Carlo and QSAR Study on Biological Activity of Several Platinum (IV) Anti Cancer Drugs
Subject Areas :
Journal of Physical & Theoretical Chemistry
robabeh sayyadikordabadi
1
,
Abdollah Fallah Shojaei
2
,
Asghar Alizadehdakhel
3
,
leila mohammadinargesi
4
,
Ghasem Ghasemi
5
1 - Depatment of Chemistry and Chemical Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran
2 - Depatment of Chemistry and Chemical Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran
3 - Depatment of Chemistry and Chemical Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran
4 - Department of Chemistry, Faculty of Sciences, University of Guilan, P.O.BOX 1914, Rasht, Iran
5 - Depatment of Chemistry and Chemical Engineering, Rasht Branch, Islamic Azad University, Rasht, Iran
Received: 2021-02-09
Accepted : 2021-09-26
Published : 2021-03-01
Keywords:
QSAR,
Genetic algorithm,
Monte Carlo method,
Platinum (IV) Antitumor Drugs,
Abstract :
QSAR investigations of some platinum (IV) derivatives were conducted using multiple linear regression (MLR) and artificial neural network (ANN) as modelling tools, along with simulated annealing (SA) and genetic algorithm (GA) optimization algorithms. In addition, CORAL software was used to correlate the biological activity to the structural parameters of the drugs. The obtained results from different approaches were compared and GA-ANN combination showed the best performance according to its correlation coefficient (R2) and mean sum square errors (RMSE). From the GA-ANN method, it was revealed that MTAS8e, ESpm05d, BElv3, MWC09, ESpm14u, BEHe2, RDF125e, and S3K are the most important descriptors. From Monte Carlo simulations, it was found that the presence of double bond, present of Platinum, number of chlorine connected to Pt, branching in molecular skeleton and presence of N and O atoms are the most important molecular features affecting the biological activity of the drug. It was concluded that simultaneous utilization of QSAR and Monte Carlo method can lead to a more comprehensive understanding of the relation between physico-chemical, structural or theoretical molecular descriptors of drugs to their biological activities.
References:
L.R. Kelland, Nature Rev., 7 (2007); 573-584.
R. Dolman, T.W. Hambley, G.B. Deacon., J. Inorg. Biochem. 88 (2002); 260-267.
H. R. Mellor, S. Snelling, M. D. Hall, S. Modok, M. JaVar, T.W.Hambley, R. Callaghan, Biochem. Pharmacol. 70 (2005); 1137-1146.
R. Sayyadi kord Abadi, A. Alizadehdakhel and S. Tajadodi Paskiabei, J. Korean Chem. Soc. 60 (2016); 225.
R. Sayyadi kord Abadi, A. Alizadehdakhel, S. Dorani Shiraz, Russ. J. Physic. Chem. B, 11 (2017; 307.
V.O.Černý., J. Optimiz. Theory. App. 45(1985); 41-51.
L.M. Schmitt., Theor. Comput. Sci., 259(2001); 1-61.
D. Bertsimas, J. Tsitsiklis, Statistical Science, 8(1983); 10-15.
N.A. Meanwell , O.B. Wallace, H. Fang., H. Wang, M.Deshpande, T. Wang,Z. Yin., L. Zadjura, D.L.Tweedie, S.Yeola, F. Zhao, S.Ranadive, B.A. Robinson , Y.F.Gong, H.G. Wang , T.P. Spicer, W.S. Blair, P.Y. Shi., R.J. Colonno.P.F. Lin., Bioorg. Med. Chem. Lett. 19 (2009); 1977-1981.
Toropova, A.P.; Toropov, A. A; Benfenati, E.; Gini, G.; Leszczynska, D.; Leszczynski, J. J. Comput. Chem, 32 (2011); 2727.
E. B. DeMelo, M .M. Ferreira., Eur, J.Med.Chem. 44 (2009); 3577-3583.
M. J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr.J.E. Peralta, F. Ogliaro, M. Bearpark, J. J Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas,.; J. B. ForesmanJ.V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09 (Gaussian, Inc., Wallingford CT, 2009).
https://gaussian.com/glossary/g09/
Dragon 3.0 Evaluation Version. Available online: http://www.disat.unimib.it/chm
R. Todeschini, Milano chemometrics, QSAR Group, http://www.disat.unimib.it/chem.
R. Todeschini, V. Consonni, Handbook of Molecular Descriptors (Wiley-VCH), 2000.
A. M. Veselinović, A. A. Toropov, A. P. Toropova, I. Damnjanović, G. M. Nikolić, Scientific Journal of the Faculty of Medicine in Niš, 31(2014);95-103.
V.Consonni, R.Todeschini, M. Pavan. P, Gramatica., J. Chem. Inf. Comput .Sci. 2002, 42, 693-705.
P.Gramatica, V. Consonni. R. Todeschini, Chemosphere, 41(2000); 63-777.
SPSS, Version 19, available at http://www.spssscience.com, (2010).
M.H. Fatemi, S. Gharaghani, Bioorg. Med. Chem. 15(2007); 7746-7754.
N. Kenneth, J.Am. Stat. Assoc, 72 (1997); 865-866.
M. Jalali-Heravi, M.F. Parastar, J. Chem. Inf. Comput. Sci. 40 (2000); 147.
Y-L. Xie, J.-H. Kaliva, Analytica Chemica Acta, 348 (1997); 19-27
L.M. Schmitt, Theor. Comput. Sci., 259 (2001);1-61.
(http://www.insilico.eu/coral)
S. H. Sadat Hayatshahi, P. Abdolmaleki, M. Ghiasi, S. Safarian, FEBS Lett 581 (2007); 506-514.
H. Varbanov; etal, Eur. J. Med. Chem. 46 (2011); 5456-5464.
T. Asadollahi, S. Dadfarnia, A.M. Haji Shabani, J.B. Ghasemi. MATCH Commun. Math. Comput. Chem. 71(2014); 287-304.
A.M.Veselinović, JB. Milosavljević, AA. Toropov, G. M. Nikolić, Eur. J. Pharm. Sci. 48 (2013), 532-41.
A. Bakalova, H. Varbanov, R. Buyukliev, G. Momekov, D. Ivanov, I. Doytchinov., Arch. Pharm. Chem. Life Sci. 11 (2011); 209–216.
P. Sarmah, R.C. Deka, J Comput. Aided. Mol. Des. 23 (2009); 343–354.
H. P. Varbanov, M. A. Jakupec, A. Roller, F. Jensen, M. Galanski, B. K. Keppler, J. Med. Chem. 56 (2013); 330−344.
P. Gramatica, E. Papa, M. Luini., E. Monti, M. B. Gariboldi, M. Ravera, E. Gabano, L. Gaviglio, D. Osella, J. Biol. Inorg. Chem. 15 (2010); 1157–1169.
D. Dimitrijevic, et al., Inorganica Chimica Acta, 402 (2013); 83-89.
S. L. Yoong, Biomaterials, 35 (2014); 748-759.
L. E. Mihajlovic, Int. J. Electrochem. Sci, 8 (2013); 8433-8441.
V. Novohradsky, et al., J. Inorg. Biochem., 140 (2014); 72-79.
Y-R. Zheng, et al, J. Am. Chem. Soc, 136 (2014); 8790-8798.
J. J. Wilson, etal., Inorg. Chem., 50 (2011), 3103-3115.
M. R. Reithofer, et al., J. Inorg. Biochem. 105 (2011); 46-51.
A. Golbraikh, A.Tropsha, A.; J. Mol. Graph. Model. 20 (2002), 269-276.
K. Levenberg, Quarterly of Applied Mathematics, 2 (1944), 164-168.
İ. Yılmaz, N. Acar-Selçuk, S. J. Coles, F. Pekdemir, A. Şengül. J. Mol. Struct. 1223 (2021); 129271.
A. M. .Fathi, H. S.Mandour, El. Hassane Anouar. J. Mol. Struct. 1224 (2021); 129263.
S. Baskaran, M.M Krishnan, R. Kumar, J. Molecul. Struct, 1224 (2021); 129236.
A. Abkari, I. Chaabane, K. Guidara, Physica E: Low-dimensional Systems and Nanostructures, 81 (2016); 136-144.
I. Yılmaz, N. Acar-Selçuki, A. Şengül, J. Molecul. Struct., 1223 (2021), 129271.
R. E. Hag, M. M Abdusalam, C, Aclian, H. Kayi, S. Özalp-Yaman., Polyhedron., 170 (2019), 25-33.
G. P. Rosa., A. Palmeira., D. I. S. P. Resende, I. F. Almeida, A. Kane-Pagès, M. C. Barreto., E. Sousa, M. M. M. Pinto., Bioorganic & Medicinal Chemistry. 29 (2021); 115873.
