Main Article Content
Abstract
The effect of inhibition of temozolomide, an alkylating agent widely used in cancer treatments, with carbonic anhydrase XIII protein was investigated using docking studies. The stability of temozolomide in the protein environment was assessed and analyzed by molecular dynamics simulation. The topological and charge density variations of temozolomide were studied in detail to perceive the primary insight of the pharmaceutical actions.
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Article Details
References
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References
A.F. Tamimi and M. Juweid, ed.: S. De Vleeschouwer, Epidemiology and Outcome of Glioblastoma, in: Glioblastoma, Codon Publications, Brisbane, Australia, Chap. 8, pp. 143-153 (2017).
E.M. Sizoo, H.R.W. Pasman, L. Dirven, C. Marosi, W. Grisold, R. Grant, G. Stockhammer, J. Egeter, S. Chang, J.J. Heimans, L. Deliens, J.C. Reijneveld and M.J.B. Taphoorn, The End-of-life Phase of High-Grade Glioma Patients: A Systematic Review, Support. Care Cancer, 22, 847 (2014); https://doi.org/10.1007/s00520-013-2088-9
D. Wang, C. Wang, L. Wang and Y. Chen, A Comprehensive Review in Improving Delivery of Small-Molecule Chemotherapeutic Agents Overcoming the Blood-Brain/Brain Tumor Barriers for Glioblastoma Treatment, Drug Deliv., 26, 551 (2019); https://doi.org/10.1080/10717544.2019.1616235
H.S. Friedman, T. Kerby and H. Calvert, Temozolomide and Treatment of Malignant Glioma, Clin. Cancer Res., 6, 2585 (2000).
P. Mujumdar, J. Kopecka, S. Bua, C.T. Supuran, C. Riganti and S.A. Poulsen, Carbonic Anhydrase XII Inhibitors Overcome Temozolomide Resistance in Glioblastoma, J. Med. Chem., 62, 4174 (2019); https://doi.org/10.1021/acs.jmedchem.9b00282
M.Y. Mboge, B.P. Mahon, R. McKenna and S.C. Frost, Carbonic Anhydrases: Role in pH Control and Cancer, Metabolites, 8, 19 (2018); https://doi.org/10.3390/metabo8010019
A. Zakšauskas, E. Èapkauskaitë, L. Jezepèikas, V. Linkuvienë, M. Kisonaitë, A. Smirnov, E. Manakova, S. Gražulis and D. Matulis, Design of Two-Tail Compounds with Rotationally Fixed Benzenesulfonamide Ring as Inhibitors of Carbonic Anhydrases, Eur. J. Med. Chem., 156, 61 (2018); https://doi.org/10.1016/j.ejmech.2018.06.059
Schrödinger, Maestro | Schrödinger, Schrödinger Release 2018-1. (2018).
W.L. DeLano, The PyMOL Molecular Graphics System, Version 1.1, Schr{ö}dinger LLC (2002).
J.A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K.E. Hauser and C. Simmerling, ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB, J. Chem. Theory Comput., 11, 3696 (2015); https://doi.org/10.1021/acs.jctc.5b00255
D.A. Case, T.E. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, A. Onufriev, C. Simmerling, B. Wang and R.J. Woods, The Amber Biomolecular Simulation Programs, J. Comput. Chem., 26, 1668 (2005); https://doi.org/10.1002/jcc.20290
M.F. Harrach and B. Drossel, Structure and Dynamics of TIP3P, TIP4P, and TIP5P Water near Smooth and Atomistic Walls of Different Hydroaffinity, J. Chem. Phys., 140, 174501 (2014); https://doi.org/10.1063/1.4872239
M.P. Jacobson, D.L. Pincus, C.S. Rapp, T.J.F. Day, B. Honig, D.E. Shaw and R.A. Friesner, A Hierarchical Approach to All-Atom Protein Loop Prediction, Proteins, 55, 351 (2004); https://doi.org/10.1002/prot.10613
G.J. Martyna, A. Hughes and M.E. Tuckerman, Molecular Dynamics Algorithms for Path Integrals at Constant Pressure, J. Chem. Phys., 110, 3275 (1999); https://doi.org/10.1063/1.478193
D.R. Roe and T.E. Cheatham III, PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data, J. Chem. Theory Comput., 9, 3084 (2013); https://doi.org/10.1021/ct400341p
W. Humphrey, A. Dalke and K. Schulten, VMD: Visual Molecular Dynamics, J. Mol. Graph., 14, 33 (1996); https://doi.org/10.1016/0263-7855(96)00018-5
P. Turner, XMGRACE, Version 5.1.19., Cent. Coast. Land-Margin Res. Oregon Grad. Inst. Sci. Technol. Beavert, USA (2005).
S. Genheden and U. Ryde, The MM/PBSA and MM/GBSA Methods to Estimate Ligand-Binding Affinities, Expert Opin. Drug Discov., 10, 449 (2015); https://doi.org/10.1517/17460441.2015.1032936
B.R. Miller III, T.D. McGee Jr., J.M. Swails, N. Homeyer, H. Gohlke and A.E. Roitberg, MMPBSA.py: An Efficient Program for End-State Free Energy Calculations, J. Chem. Theory Comput., 8, 3314 (2012); https://doi.org/10.1021/ct300418h
P. Geerlings, F. De Proft and W. Langenaeker, Conceptual Density Functional Theory, Chem. Rev., 103, 1793 (2003); https://doi.org/10.1021/cr990029p
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, N.J. 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.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski and D.J. Fox Gaussian 09, Gaussian, Inc., Wallingford CT (2009).
AIM2000, J. Comput. Chem., 22, 545 (2001); https://doi.org/10.1002/1096-987X(20010415)22:5<545::AID-JCC1027>3.0.CO;2-Y
C. Köhler, J. Lübben, L. Krause, C. Hoffmann, R. Herbst-Irmer and D. Stalke, Comparison of Different Strategies for Modelling Hydrogen Atoms in Charge Density Analyses, Acta Crystallogr. B Struct. Sci. Cryst. Eng. Mater., 75, 434 (2019); https://doi.org/10.1107/S2052520619004517
A. Stash and V. Tsirelson, WinXPRO: A Program for Calculating Crystal and Molecular Properties Using Multipole Parameters of the Electron Density, J. Appl. Cryst., 35, 371 (2002); https://doi.org/10.1107/S0021889802003230
H. Birkedal, D. Madsen, R.H. Mathiesen, K. Knudsen, H.P. Weber, P. Pattison and D. Schwarzenbach, The Charge Density of Urea from Synchrotron Diffraction Data, Acta Crystallogr. A, 60, 371 (2004); https://doi.org/10.1107/S0108767304015120
D.S. Arputharaj, V.R. Hathwar, T.N. Guru Row and P. Kumaradhas, Topological Electron Density Analysis and Electrostatic Properties of Aspirin: An Experimental and Theoretical Study, Cryst. Growth Des., 12, 4357 (2012); https://doi.org/10.1021/cg300269n
A. Volkov, Y. Abramov, P. Coppens and C. Gatti, On the Origin of Topological Differences between Experimental and Theoretical Crystal Charge Densities, Acta Crystallogr. A, 56, 332 (2000); https://doi.org/10.1107/S0108767300003202