In Silico Investigation of Electronic Structure, Binding Patterns and Molecular Docking of Nevirapine: An anti-HIV Type-1 Drug

References

• P. W. Mui, S. P. Jacober, K. D. Hargrave, and J. Adams, “Crystal Structure of Nevirapine, a Non-Nucleoside Inhibitor of HIV-1 Reverse Transcriptase, and Computational Alignment with a Structurally Diverse Inhibitor,” Journal of Medicinal Chemistry 35, no. 1 (1992): 201–2.
   PubMed Web of Science ®Google Scholar
• Ferdinand W. N. M. Wit, Anouk M. Kesselring, Luuk Gras, Clemens Richter, Marchina E. van der Ende, Kees Brinkman, Joep M. A. Lange, Frank de Wolf, and Peter Reiss, “Discontinuation of Nevirapine Because of Hypersensitivity Reactions in Patients with Prior Treatment Experience, Compared with Treatment-Naive Patients: The ATHENA Cohort Study,” Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America 46, no. 6 (2008): 933–40.
   PubMed Web of Science ®Google Scholar
• Jeffrey A. Johnson, Jin-Fen Li, Lynn Morris, Neil Martinson, Glenda Gray, James McIntyre, and Walid Heneine, “Emergence of Drug-Resistant HIV-1 After Intrapartum Administration of Single-Dose Nevirapine is Substantially Underestimated,” The Journal of Infectious Diseases 192, no. 1 (2005): 16–23.
   PubMed Web of Science ®Google Scholar
• B. Conway, M. A. Wainberg, D. Hall, M. Harris, P. Reiss, D. Cooper, S. Vella, R. Curry, P. Robinson, J. M. Lange, et al. “Development of Drug Resistance in Patients Receiving Combinations of Zidovudine, Didanosine and Nevirapine ,”AIDS (London, England) 15, no. 10 (2001): 1269–74.,
   PubMed Web of Science ®Google Scholar
• J. Ren, L. E. Bird, P. P. Chamberlain, G. B. Stewart-Jones, D. I. Stuart, and D. K. Stammer, “Structure of HIV-2 Reverse Transcriptase at 2.35-A Resolution and the Mechanism of Resistance to Non-nucleoside Inhibitors,” Proceedings of the National Academy of Sciences of the United States of America 99, no. 22 (2002): 14410–5.
   PubMed Web of Science ®Google Scholar
• W. Saenger, Principle of Nucleic acid Structure (New York: Springer-Verlag, 1984).
   Google Scholar
• B. C. Bagnley, “DNA Intercalating anti-Tumour Agents,” Anticancer Drug Design 6 (1991): 1–35.
   PubMedGoogle Scholar
• T. Hermann, “Strategies for the Design of Drugs Targeting RNA and RNA-Protein Complexes,” Angewandte Chemie International Edition 39, no. 11 (2000): 1890–904. International Ed. in English)
   PubMed Web of Science ®Google Scholar
• H. Kruse, M. Havrila, and J. Sponer, “QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches,” Journal of Chemical Theory and Computation 10, no. 6 (2014): 2615–29.
   PubMed Web of Science ®Google Scholar
• P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, “Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields,” The Journal of Physical Chemistry 98, no. 45 (1994): 11623–7.
   Web of Science ®Google Scholar
• 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. Nakatsuj, M. Caricato, X. Li, H.P. Hratchian, A.F. Iamaylov, 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. Lyengar, 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.J. Dannenberg, S. Dapprich, A.D. Daniels, O. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian 03, Revision A.1 (Wallingford, CT: Gaussian Inc., 2004).
   Google Scholar
• I.N. Levine, Quantum Chemistry, 5th ed. (Singapore: Pearson Education, 2003).
   Google Scholar
• F. Jensen, Introduction to Computational Chemistry (New York: John Wiley & Sons, 2006).
   Google Scholar
• P. Hohenberg and W. Kohn, “Inhomogeneous Electron Gas,” Physical Review 136, no. 3B (1964): B864–B871.
   Web of Science ®Google Scholar
• A. D. Becke, “ Density-functional Exchange-energy Approximation with Correct Asymptotic Behavior,” Physical Review. A, General Physics 38no. 6 (1988): 3098–100.
   PubMedGoogle Scholar
• C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density,” Physical Review. B, Condensed Matter 37, no. 2 (1988): 785–9.
   PubMed Web of Science ®Google Scholar
• A. D. Becke, “Density Functional Thermochemistry. 111. The Role of Exact Exchange,” The Journal of Chemical Physics 98, no. 7 (1993): 5648–52.
   Web of Science ®Google Scholar
• A. Kumar, A. K. Srivastava, S. Gangwar, N. Misra, A. Mondal, and G. Brahmachari, “Combined Experimental (FT-IR, UV–Visible Spectra, NMR) and Theoretical Studies on the Molecular Structure, Vibrational Spectra, HOMO, LUMO, MESP Surfaces, Reactivity Descriptor and Molecular Docking of Phomarin,” Journal of Molecular Structure 1096 (2015): 94–101.
   Web of Science ®Google Scholar
• A. Dwivedi, A. K. Srivastava, and A. K. Bajpai, “Vibrational Spectra, HOMO, LUMO, MESP Surfaces and Reactivity Descriptors of Amylamine and Its Isomers: A DFT Study,” Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy 149 (2015): 343–51.
   PubMed Web of Science ®Google Scholar
• A. K. Srivastava, A. K. Pandey, S. Jain, and N. Misra, “FT-IR Spectroscopy, Intra-Molecular C-H⋯O Interactions, HOMO, LUMO, MESP Analysis and Biological Activity of Two Natural Products, Triclisine and Rufescine: DFT and QTAIM Approaches,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 136 (2015): 682–9.
   PubMed Web of Science ®Google Scholar
• D. Sharma, and S. N. Tiwari, “Comparative Computational Analysis of Electronic Structure, MEP Surface and Vibrational Assignments of a Nematic Liquid Crystal: 4-n-Methyl-4´-Cyanobiphenyl,” Journal of Molecular Liquids 214 (2016): 128–35.
   Web of Science ®Google Scholar
• S. N. Tiwari and D. Sharma, “Electronic Structure, FT-IR Analysis and Nematic Behaviour Studies of Para-Methoxybenzylidine p-Ethylaniline: Ab-Initio and DFT Approach,” Journal of Molecular Liquids 244 (2017): 241–51.
   Web of Science ®Google Scholar
• E. Scrocco and J. Tomasi, “Electronic Molecular Structure, reactivity and intermolecular Forces: An Euristic Interpretation by Means of Electrostatic Molecular Potentials,” Advances in Quantum Chemistry 2 (1978) : 115–93.
   Google Scholar
• N. H. March, “Electrostatic Potential, Bond Density and Bond Order in Molecules and Clusters,” Theoretical and Computational Chemistry 3 (1996): 619–47.
   Google Scholar
• P. Geerlings, F. De Proft, and W. Langenaeker, “Conceptual Density Functional Theory,” Chemical Reviews 103, no. 5 (2003): 1793–874.
   PubMed Web of Science ®Google Scholar
• R. G. Parr, R. A. Donnelly, M. Levy, and W. E. Palke, “Electronegativity: The Density Functional Viewpoint,” The Journal of Chemical Physics 68, no. 8 (1978): 3801–7.
   Web of Science ®Google Scholar
• J.B. Foresman, A. Frisch, Exploring Chemistry with Electronic Structure Methods, 2nd ed. (Pittsburg: Gaussian, Inc.), 1996.
   Google Scholar
• L. Pauling, The Nature of the Chemical Bond (Ithaca, NY: Cornell University Press, 1960).
   Google Scholar
• P. Senet, “Chemical Hardnesses of Atoms and Molecules from Frontier Orbitals,” Chemical Physics Letters 275, no. 5/6 (1997): 527–32.
   Web of Science ®Google Scholar
• R. G. Parr, L. Szentpaly, and S. Liu, “Electrophilicity Index,” Journal of the American Chemical Society 121, no. 9 (1999): 1922–4.
   Web of Science ®Google Scholar
• R. Rein, "Studies of Biomolecular Interactions: Principles of Nucleic Acid Structure and function from the point of view of Constituent Interactions", in Intermolecular Interactions: From Diatomics to Biolymers, edited by B. Pullman. (New York: John Wiley, 1978), 307–362.
   Google Scholar
• P. Claverie, "Elaboration of Approximate Formulas for the Interactions between Large Molecules: Applications in Organic Chemistry", in Intermolecular Interactions: From Diatomics to Biopolymers, edited by B. Pullman. (New York: John Wiley, 1978), 69–305.
   Google Scholar
• J. Langlet, P. Claverie, F. Caron, and J. C. Boeuve, “Interactions between Nucleic Acid Bases in Hydrogen Bonded and Stacked Configurations: The Role of the Molecular Charge Distribution,” International Journal of Quantum Chemistry 20, no. 2 (1981): 299–338.
   Web of Science ®Google Scholar
• Govindaswamy Ramkumaar, Shanmugam Srinivasan, Thirumazhisai Bhoopathy, Sethu Gunasekaran, Julie Charles, and Jayaprakash Ramesh, “Molecular Structure, Vibrational Spectra, UV–Vis, NBO, and NMR Analyses on Nevirapine Using ab Initio DFT Methods,” Journal of Theoretical and Applied Physics 7, no. 1 (2013): 51–14.
   Google Scholar
• S. C. Oyaga, J. C. Valdes, S. B. Paez, and K. H. Marquez, “DFT Description of Intermolecular Forces between 9-Aminoacridines and DNA Base Pairs,” Journal of Theoretical Chemistry 2013 (2013): 1-8. https://doi.org/https://doi.org/10.1155/2013/526569.
   Google Scholar
• P. Sharma, A. Mitra, S. Sharma, and H. Singh, “Base Pairing in RNA Structures: A Computational Analysis of Structural Aspects and Interaction Energies,” Journal of Chemical Sciences 119, no. 5 (2007): 525–31.
   Web of Science ®Google Scholar
• A. Frish, A.B. Nielson, and A.J. Holder, Gaussian View user Manuals (Pittsburg, PA: Gaussian Inc), 2000.
   Google Scholar
• R. Lu, W. Gan, B. Wu, Z. Zhang, Y. Guo, and H. Wang, “ C-H stretching vibrations of methyl, methylene and methine groups at the vapor/alcohol (N = 1-8) interfaces ,”The Journal of Physical Chemistry. B 109, no. 29 (2005): 14118–29.
   PubMed Web of Science ®Google Scholar
• G. Socrates, Infrared and Raman Characteristic Group Frequencies: Tables and Charts, 3rd ed. (New York: John Wiley, 2004).
   Google Scholar
• J. G. Grasselli, M. Mehicic, and J. R. Mooney, “Applications of Infrared and Raman Spectroscopy in Industry,” Fresenius' Zeitschrift für analytische Chemie 324, no. 6 (1986): 537–43.
   Google Scholar
• N.B. Colthup, L.H. Daly and S.E.Wiberely, Introducation to IR and Raman Spectroscopy, 3rd ed. (New York: Academic Press Inc., 1990).
   Google Scholar
• M.D. Fayer, Ultrafast Infrared and Raman Spectroscopy, Practical Spectroscopy Series, vol. 26 (Marcel Dekker, Inc., New York, 2001).
   Google Scholar
• R. J. Meier, “Vibrational Spectroscopy: A 'vanishing' discipline??,”Chemical Society Reviews 34no. 9 (2005): 743–52.
   PubMed Web of Science ®Google Scholar
• F. Adar, G. Le Bourdon, J. Reffner, and A. Whitley, “FT-IR and Raman Microscopy on a United Platform: A Technology Whose Time Has Come,” Spectroscopy Magazine 18 (2003): 34–40.
   Web of Science ®Google Scholar
• V. Barone, M. Cossi, and J. Tomasi, “A New Definition of Cavities for the Computation of Solvation Free Energies by the Polarizable Continuum Model,” The Journal of Chemical Physics 107no. 8 (1997): 3210–21.
   Web of Science ®Google Scholar
• I. Fleming, Frontier Orbitals and Organic Chemical Rections (New York: John Willey and Sons, 1976).
   Google Scholar
• J. S. Murray and K. Sen, Molecular Electrostatic Potential Concepts and Applications (Amsterdam, Netherland: Elsevier, 1996).
   Google Scholar
• F. Weinhold and C. R. Landis, "What is a hydrogen bond? Resonance covalency in the supramolecular domain", Chemistry Education: Research and Practice 15 (2014): 276–85.
   Web of Science ®Google Scholar
• J. P. Foster and F. Weinhold, “Natural Hybrid Orbitals,” Journal of the American Chemical Society 102, no. 24 (1980): 7211–8.
   Web of Science ®Google Scholar
• E. D. Glendening and F. Weinhold, “Natural Resonance Theory: I. General Formalism,” Journal of Computational Chemistry 19, no. 6 (1998): 593–609.
   Web of Science ®Google Scholar
• N. Gonohe, H. Abe, N. Mikami, and M. Ito, “Two-Color Photoionization of Van Der Waals Complexes of Fluorobenzene and Hydrogen-Bonded Complexes of Phenol in Supersonic Jets,” The Journal of Physical Chemistry 89, no. 17 (1985): 3642–8.
   Web of Science ®Google Scholar
• M. Gutowski, J. G. C. M. van Duijneveldt‐van de Rijdt, J. H. van Lenthe, and F. B. van Duijneveldtand, “Accuracy of the Boys and Bernardi Function Counterpoise Method,”The Journal of Chemical Physics 98, no. 6 (1993): 4728–37.
   Web of Science ®Google Scholar
• G. Lober and G. Achtert, “On the Complex Formation of Acridine Dyes with DNA. VII. Dependence of the Binding on the Dye Structure,” Biopolymers 8, no. 5 (1969): 595–608.
   PubMed Web of Science ®Google Scholar
• A. Grosdidier, V. Zoete, and O. Michielin, “SwissDock, a Protein-Small Molecule Docking Web Service Based on EADock DSS,”Nucleic Acids Research 39, no. Web Server issue (2011): W270–W277.
   PubMed Web of Science ®Google Scholar
• https://www.rcsb.org/structure/2yng
   Google Scholar