Synthesis, virtual screening and computational approach of a quinoxaline derivative as potent anti-HIV agent targeting the reverse transcriptase enzyme

References

• Abbasi, S., Raza, S., Azam, S. S., Liedl, K. R., & Fuchs, J. E. (2016). Interaction mechanisms of a melatonergic inhibitor in the melatonin synthesis pathway. Journal of Molecular Liquids, 221, 507–517. https://doi.org/10.1016/j.molliq.2016.06.034
   Web of Science ®Google Scholar
• Akram, M., Lal, H., Shakya, S., Varshney, R., & Ud-Din, K. (2022). Molecular engineering of complexation between RNA and biodegradable cationic Gemini surfactants: Role of the hydrophobic chain length. Molecular Systems Design & Engineering, 7, 487–506. https://doi.org/10.1039/D1ME00147G
   Web of Science ®Google Scholar
• Akram, M., Lal, H., Shakya, S., & Kabir-ud-Din. (2020). Multispectroscopic and computational analysis insight into the interaction of cationic diester-bonded gemini surfactants with serine protease α-chymotrypsin. ACS Omega, 5(7), 3624–3637.
   PubMed Web of Science ®Google Scholar
• Alinezhad, H., Tajbakhsh, M., Norouzi, M., & Baghery, S. (2013). An efficient and green protocol for the synthesis of 1, 5-benzodiazepine and quinoxaline derivatives using protic pyridinium ionic liquid as a catalyst. World Applied Sciences Journal, 22(12), 1711–1717.
   Google Scholar
• Besler, B. H., Merz, K. M., Jr, & Kollman, P. A. (1990). Atomic charges derived from semiempirical methods. Journal of Computational Chemistry, 11(4), 431–439. https://doi.org/10.1002/jcc.540110404
   Web of Science ®Google Scholar
• Burguete, A., Pontiki, E., Hadjipavlou-Litina, D., Ancizu, S., Villar, R., Solano, B., Moreno, E., Torres, E., Pérez, S., Aldana, I., & Monge, A. (2011). Synthesis and biological evaluation of new quinoxaline derivatives as antioxidant and anti-inflammatory agents. Chemical Biology & Drug Design, 77(4), 255–267. https://doi.org/10.1111/j.1747-0285.2011.01076.x
   PubMed Web of Science ®Google Scholar
• Case, D. A., Babin, V., Berryman, J. T., Betz, R. M., Cai, Q., Cerutti, D. S., Cheatham, I. I. I., Darden, T. E., Duke, T. A., Gohlke, R. E., & others, H. (2014). The FF14SB force field. Amber, 14, 29–31.
   Google Scholar
• Case, D., Ben-Shalom, I., Brozell, S., Cerutti, D., Cheatham, I. I. I. T., Cruzeiro, V., Darden, T., Duke, R., Ghoreishi, D., & Gilson, M. & others. (2018). AMBER (vol. 18). University of California, San Francisco.
   Google Scholar
• Cousins, K. R. (2011). Computer review of ChemDraw ultra 12.0. ACS Publications.
   Google Scholar
• Dennington, R., Keith, T., & Millam, J. (2009). GaussView, version 5.
   Google Scholar
• Domingo, L. R., Aurell, M. J., Pérez, P., & Contreras, R. (2002). Quantitative characterization of the global electrophilicity power of common diene/dienophile pairs in Diels–Alder reactions. Tetrahedron, 58(22), 4417–4423. https://doi.org/10.1016/S0040-4020(02)00410-6
   Web of Science ®Google Scholar
• Elhelby, A. A., Ayyad, R. R., & Zayed, M. F. (2011). Synthesis and biological evaluation of some novel quinoxaline derivatives as anticonvulsant agents. Arzneimittel-Forschung, 61(7), 379–381. https://doi.org/10.1055/s-0031-1296214
   PubMed Web of Science ®Google Scholar
• Fabian, L., Porro, M. T., Gomez, N., Salvatori, M., Turk, G., Estrin, D., & Moglioni, A. (2020). Design, synthesis and biological evaluation of quinoxaline compounds as anti-HIV agents targeting reverse transcriptase enzyme. European Journal of Medicinal Chemistry, 188, 111987. https://doi.org/10.1016/j.ejmech.2019.111987
   PubMed Web of Science ®Google Scholar
• Fernández-Montero, J. V., Vispo, E., & Soriano, V. (2014). Emerging antiretroviral drugs. Expert Opinion on Pharmacotherapy, 15(2), 211–219. https://doi.org/10.1517/14656566.2014.863277
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Petersson, G. A., & Nakatsuji, H. (2016). Gaussian 16. Gaussian, Inc.
   Google Scholar
• Galal, S. A., Abdelsamie, A. S., Tokuda, H., Suzuki, N., Lida, A., ElHefnawi, M. M., Ramadan, R. A., Atta, M. H. E., & El Diwani, H. I. (2011). Part I: Synthesis, cancer chemopreventive activity and molecular docking study of novel quinoxaline derivatives. European Journal of Medicinal Chemistry, 46(1), 327–340. https://doi.org/10.1016/j.ejmech.2010.11.022
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (1996). Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94. Journal of Computational Chemistry, 17(5–6), 553–586. https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<553::AID-JCC3>3.0.CO;2-T
   Web of Science ®Google Scholar
• Haq, F. U., Abro, A., Raza, S., Liedl, K. R., & Azam, S. S. (2017). Molecular dynamics simulation studies of novel β-lactamase inhibitor. Journal of Molecular Graphics and Modelling, 74, 143–152. https://doi.org/10.1016/j.jmgm.2017.03.002
   PubMed Web of Science ®Google Scholar
• Hossain, M. M., Hossain, M. M., Muhib, M. H., Mia, M. R., Kumar, S., & Wadud, S. A. (2012). In vitro antioxidant potential study of some synthetic quinoxalines. Bangladesh Medical Research Council Bulletin, 38(2), 47–50. https://doi.org/10.3329/bmrcb.v38i2.12880
   PubMedGoogle Scholar
• Huey, R., & Morris, G. M. (2008). Using AutoDock 4 with AutoDocktools: a tutorial (pp. 54–56). The Scripps Research Institute, USA.
   Google Scholar
• Islam, M. R., Shakya, S., Selim, A., Alam, M. S., & Ali, M. (2019). Solvatochromic absorbance and fluorescence probe behavior within ionic liquid+ γ-butyrolactone mixture. Journal of Chemical & Engineering Data, 64(9), 4169–4180. https://doi.org/10.1021/acs.jced.9b00576
   Web of Science ®Google Scholar
• Izaguirre, J. A., Catarello, D. P., Wozniak, J. M., & Skeel, R. D. (2001). Langevin stabilization of molecular dynamics. The Journal of Chemical Physics, 114(5), 2090–2098. https://doi.org/10.1063/1.1332996
   Web of Science ®Google Scholar
• Khan, I. M., Islam, M., Shakya, S., Alam, N., Imtiaz, S., & Islam, M. R. (2021). Synthesis, spectroscopic characterization, antimicrobial activity, molecular docking and DFT studies of proton transfer (H-bonded) complex of 8-aminoquinoline (donor) with chloranilic acid (acceptor). Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/10.1080/07391102.2021.1969280
   Web of Science ®Google Scholar
• Khan, I. M., Shakya, S., Islam, M., Khan, S., & Najnin, H. (2021). Synthesis and spectrophotometric studies of CT complex between 1, 2-dimethylimidazole and picric acid in different polar solvents: exploring antimicrobial activities and molecular (DNA) docking. Physics and Chemistry of Liquids, 59(5), 753–769. https://doi.org/10.1080/00319104.2020.1810250
   Web of Science ®Google Scholar
• Khan, M. D., Shakya, S., Vu, H. H. T., Habte, L., & Ahn, J. W. (2021). Low concentrated phosphorus sorption in aqueous medium on aragonite synthesized by carbonation of seashells: Optimization, kinetics, and mechanism study. Journal of Environmental Management, 280, 111652. https://doi.org/10.1016/j.jenvman.2020.111652
   PubMed Web of Science ®Google Scholar
• Kouetcha, D. N., Ramézani, H., & Cohaut, N. (2017). Ultrafast scalable parallel algorithm for the radial distribution function histogramming using MPI maps. The Journal of Supercomputing, 73(4), 1629–1653. https://doi.org/10.1007/s11227-016-1854-0
   Web of Science ®Google Scholar
• Krause, L., Herbst–Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). Comparison of silver and molybdenum microfocus X-ray sources for single-crystal structure determination. J. Appl. Cryst., 48, 3–10. https://doi.org/10.1107/S1600576714022985
   PubMed Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N. S., & Galzitskaya, O. V. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Loriga, M., Vitale, G., & Paglietti, G. (1998). Quinoxaline chemistry Part 9. Quinoxaline analogues of trimetrexate (TMQ) and 10-propargyl-5, 8-dideazafolic acid (CB 3717) and its precursors. Synthesis and evaluation of in vitro anticancer activity. Farmaco (Societa Chimica Italiana: 1989), 53(2), 139–149. https://doi.org/10.1016/S0014-827X(98)00002-0
   PubMedGoogle Scholar
• Maiorov, V. N., & Crippen, G. M. (1994). Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. Journal of Molecular Biology, 235(2), 625–634. https://doi.org/10.1006/jmbi.1994.1017
   PubMed Web of Science ®Google Scholar
• Marella, A., Tanwar, O. P., Saha, R., Ali, M. R., Srivastava, S., Akhter, M., Shaquiquzzaman, M., & Alam, M. M. (2013). Quinoline: A versatile heterocyclic. Saudi Pharmaceutical Journal : SPJ: The Official Publication of the Saudi Pharmaceutical Society, 21(1), 1–12. https://doi.org/10.1016/j.jsps.2012.03.002
   PubMed Web of Science ®Google Scholar
• Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Montana, M., Montero, V., Khoumeri, O., & Vanelle, P. (2020). Quinoxaline derivatives as antiviral agents: a systematic review. Molecules, 25(12), 2784. https://doi.org/10.3390/molecules25122784
   PubMed Web of Science ®Google Scholar
• Natarajan, R., Subramani, A., Kesavan, S. K., & Selvaraj, D. (2013). Biological evaluation of some novel quinoxaline bearing azetidinones including leptospirocidal study. Journal of Pharmacy Research, 1(8), 775–780.
   Google Scholar
• Parr, R. G., Szentpály, L. v., & Liu, S. (1999). Electrophilicity index. Journal of the American Chemical Society, 121(9), 1922–1924. https://doi.org/10.1021/ja983494x
   Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular. Dynamics Trajectory Data, 9(7), 3084–3095.
   Google Scholar
• Roy, D. R., Parthasarathi, R., Maiti, B., Subramanian, V., & Chattaraj, P. K. (2005). Electrophilicity as a possible descriptor for toxicity prediction. Bioorganic & Medicinal Chemistry, 13(10), 3405–3412. https://doi.org/10.1016/j.bmc.2005.03.011
   PubMed Web of Science ®Google Scholar
• Sepkowitz, K. A. (2001). AIDS-the first 20 years. The New England Journal of Medicine, 344(23), 1764–1772. https://doi.org/10.1056/NEJM200106073442306
   PubMed Web of Science ®Google Scholar
• Shekhar, A. C., Rao, P. S., Narsaiah, B., Allanki, A. D., & Sijwali, P. S. (2014). Emergence of pyrido quinoxalines as new family of antimalarial agents. European Journal of Medicinal Chemistry, 77, 280–287. https://doi.org/10.1016/j.ejmech.2014.03.010
   PubMed Web of Science ®Google Scholar
• Sheldrick, G. M. (2015). SHELXT - Integrated space-group and crystal-structure determination. Acta Crystallographica. Section A, Foundations and Advances, 71(Pt 1), 3–8. https://doi.org/10.1107/S2053273314026370
   PubMed Web of Science ®Google Scholar
• Shen, J., Wang, X., Lin, X., Yang, Z., Cheng, G., & Cui, X. (2016). One-Pot regiospecific synthesis of quinoxalines via a CH2-extrusion reaction. Organic Letters, 18(6), 1378–1381. https://doi.org/10.1021/acs.orglett.6b00309
   PubMed Web of Science ®Google Scholar
• Singh, D. C. P., Hashim, S. R., & Singhal, R. G. (2011). Synthesis and antimicrobial activity of some new thioether derivatives of quinoxaline. E-Journal of Chemistry, 8(2), 635–642. https://doi.org/10.1155/2011/482831
   Google Scholar
• Spackman, M. A., & Jayatilaka, D. (2009). Hirshfeld surface analysis. CrystEngComm, 11(1), 19–32. https://doi.org/10.1039/B818330A
   Web of Science ®Google Scholar
• Stash, A. I., & Tsirelson, V. G. (2014). Developing WinXPRO: a software for determination of the multipole-model-based properties of crystals. Journal of Applied Crystallography, 47(6), 2086–2089. https://doi.org/10.1107/S1600576714021566
   Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Turner, P. (2005). XMGRACE, Version 5.1. 19. Cent Coast Land-Margin Res Oregon Grad Inst Sci Technol Beavert.
   Google Scholar
• Usach, I., Melis, V., & Peris, J. (2013). Non-nucleoside reverse transcriptase inhibitors: a review on pharmacokinetics, pharmacodynamics, safety and tolerability. Journal of the International AIDS Society, 16(1), 1–14. https://doi.org/10.7448/IAS.16.1.18567
   PubMed Web of Science ®Google Scholar
• Vahdat, S. M., & Baghery, S. (2013). Sulfonated organic salts: recyclable green catalysts for the facile and rapid route synthesis of 2, 3-dissubstituted quinoxaline derivatives in water. World Applied Science Journal 21, 394–401.
   Google Scholar
• Vieira, M., Pinheiro, C., Fernandes, R., Noronha, J. P., & Prudêncio, C. (2014). Antimicrobial activity of quinoxaline 1,4-dioxide with 2- and 3-substituted derivatives. Microbiological Research, 169(4), 287–293. https://doi.org/10.1016/j.micres.2013.06.015
   PubMed Web of Science ®Google 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. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Yang, F., Yang, J., Zhang, Z., Tu, G., Yao, X., Xue, W., & Zhu, F. (2022). Recent advances in computer-aided antiviral drug design targeting HIV-1 integrase and reverse transcriptase associated ribonuclease H. Current Medicinal Chemistry, 29(10), 1664–1676. https://doi.org/10.2174/0929867328666210708090123
   PubMed Web of Science ®Google Scholar
• Yang, F., Zheng, G., Fu, T., Li, X., Tu, G., Li, Y. H., Yao, X., Xue, W., & Zhu, F. (2018). Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H. Physical Chemistry Chemical Physics: PCCP, 20(37), 23873–23884. https://doi.org/10.1039/c8cp01843j
   PubMed Web of Science ®Google Scholar