Synthesis, X-ray crystallography, computational investigation on quinoxaline derivatives as potent against adenosine receptor A2AAR

References

• Abad, N., El Bakri, Y., Lai, C.-H., Karthikeyan, S., Ramli, Y., Ferfra, S., Mague, J. T., & Essassi, E. M. (2022). Insights into the crystal structure of two newly synthesized quinoxalines derivatives as potent inhibitor for c-Jun N-terminal kinases. Journal of Biomolecular Structure & Dynamics, 40(6), 2797–2814. https://doi.org/10.1080/07391102.2020.1844049
   PubMed Web of Science ®Google Scholar
• Abdel-Rahman, L. H., Mohamed, S. K., El Bakri, Y., Ahmad, S., Lai, C.-H., Amer, A. A., Mague, J. T., & Abdalla, E. M. (2021). Synthesis, crystal structural determination and in silico biological studies of 3,3′-ethane-1,2-diylbis (2-benzylidene-1,3-thiazolidin-4-one. Journal of Molecular Structure, 1245, 130997. https://doi.org/10.1016/j.molstruc.2021.130997
   Web of Science ®Google Scholar
• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Agarwal, S., & Mehrotra, R. (2016). An overview of molecular docking. JSM Chemistry, 4(2), 1024–1028.
   Google Scholar
• Ahmad, B., Saeed, A., Castrosanto, M. A., Amir Zia, M., Farooq, U., Abbas, Z., & Khan, S. (2023). Identification of natural marine compounds as potential inhibitors of CDK2 using molecular docking and molecular dynamics simulation approach. Journal of Biomolecular Structure & Dynamics, 41(17), 8506–8516. https://doi.org/10.1080/07391102.2022.2135594
   PubMed Web of Science ®Google Scholar
• Ahmed, E. A., Mohamed, M. F. A., Omran, A., & Salah, H. (2020). Synthesis, EGFR-TK inhibition and anticancer activity of new quinoxaline derivatives. Synthetic Communications, 50(19), 2924–2940. https://doi.org/10.1080/00397911.2020.1787448
   Web of Science ®Google Scholar
• Allouche, A. (2012). Gabedit—A graphical user interface for computational chemistry softwares. Journal of Computational Chemistry, 32(1), 174–182. https://doi.org/10.1002/jcc
   Web of Science ®Google Scholar
• Arjun, H. A., Rajan, R. K., Elancheran, R., Ramanathan, M., Bhattacharjee, A., & Kabilan, S. (2020). Crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies on benzohydrazide derivatives as potential inhibitors of prostate cancer. Chemical Data Collections, 26, 100350. https://doi.org/10.1016/j.cdc.2020.100350
   Google Scholar
• Ayoub, B. M., Michel, H. E., Mowaka, S., Hendy, M. S., & Tadros, M. M. (2021). Repurposing of omarigliptin as a neuroprotective agent based on docking with A2A adenosine and AChE receptors, brain GLP-1 response and its brain/plasma concentration ratio after 28 days multiple doses in rats using LC-MS/MS. Molecules (Basel, Switzerland), 26(4), 889. https://doi.org/10.3390/molecules26040889
   PubMed Web of Science ®Google Scholar
• Babar, A., Khalid, H., Ayub, K., Saleem, S., Waseem, A., Mahmood, T., Munawar, M. A., Abbas, G., & Khan, A. F. (2014). Synthesis, characterization and density functional theory study of some new 2-anilinothiazoles. Journal of Molecular Structure, 1072, 221–227. https://doi.org/10.1016/j.molstruc.2014.05.009
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P. A., Crichlow, G. V., Dalenberg, K., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., Flatt, J. W., Ganesan, S., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., … Zardecki, C. (2023). RCSB Protein Data Bank (RCSB.org): Delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Research, 51(D1), D488–D508. https://doi.org/10.1093/nar/gkac1077
   PubMed Web of Science ®Google Scholar
• Chen, J.-F., Eltzschig, H. K., & Fredholm, B. B. (2013). Adenosine receptors as drug targets—What are the challenges? Nature Reviews. Drug Discovery, 12(4), 265–286. https://doi.org/10.1038/nrd3955
   PubMed Web of Science ®Google Scholar
• Chen, J., Wang, J., Zhang, Q., Chen, K., & Zhu, W. (2015). Probing origin of binding difference of inhibitors to MDM2 and MDMX by polarizable molecular dynamics simulation and QM/MM-GBSA calculation. Scientific Reports, 5(1), 17421. https://doi.org/10.1038/srep17421
   PubMed Web of Science ®Google Scholar
• Cieślak, M., Komoszyński, M., & Wojtczak, A. (2008). Adenosine A 2A receptors in Parkinson’s disease treatment. Purinergic Signalling, 4(4), 305–312. https://doi.org/10.1007/s11302-008-9100-8
   PubMed Web of Science ®Google Scholar
• Coen, D. M., & Schaffer, P. A. (2003). Antiherpesvirus drugs: A promising spectrum of new drugs and drug targets. Nature Reviews. Drug Discovery, 2(4), 278–288. https://doi.org/10.1038/nrd1065
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2014). iLOGP: A simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. Journal of Chemical Information and Modeling, 54(12), 3284–3301. https://doi.org/10.1021/ci500467k
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Daina, A., & Zoete, V. (2016). A BOILED-Egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem. 11(11), 1117–1121. https://doi.org/10.1002/cmdc.201600182
   PubMed Web of Science ®Google Scholar
• Dennington, R., Keith, T. A., & Millam, J. M. (2016). GaussView. Version 6.0.16. Semichem Inc.
   Google Scholar
• Dhasmana, D., Singh, A., Shukla, R., Tripathi, T., & Garg, N. (2018). Targeting nucleotide binding domain of multidrug resistance-associated protein-1 (MRP1) for the reversal of multi drug resistance in cancer. Scientific Reports, 8(1), 11973. https://doi.org/10.1038/s41598-018-30420-x
   PubMedGoogle Scholar
• Doré, A. S., Robertson, N., Errey, J. C., Ng, I., Hollenstein, K., Tehan, B., Hurrell, E., Bennett, K., Congreve, M., Magnani, F., Tate, C. G., Weir, M., & Marshall, F. H. (2011). Structure of the adenosine A 2A receptor in complex with ZM241385 and the xanthines XAC and caffeine. Structure (London, England: 1993), 19(9), 1283–1293. https://doi.org/10.1016/j.str.2011.06.014
   PubMed Web of Science ®Google Scholar
• Drwal, M. N., Banerjee, P., Dunkel, M., Wettig, M. R., & Preissner, R. (2014). ProTox: A web server for the in silico prediction of rodent oral toxicity. Nucleic Acids Research, 42(Web Server issue), W53–8. https://doi.org/10.1093/nar/gku401
   PubMed Web of Science ®Google Scholar
• Edwards, A. J., Mackenzie, C. F., Spackman, P. R., Jayatilaka, D., & Spackman, M. A. (2017). Intermolecular interactions in molecular crystals: What’s in a name? Faraday Discussions, 203, 93–112. https://doi.org/10.1039/c7fd00072c
   PubMed Web of Science ®Google Scholar
• El Bakri, Y., Ahmad, B., Saravanan, K., Ahmad, I., Bakhite, E. A., Younis, O., Al-Waleedy, S. A. H., Ibrahim, O. F., Nafady, A., Mague, J. T., & Mohamed, S. K. (2023). Insight into crystal structures and identification of potential styrylthieno [2,3-b] pyridine-2-carboxamidederivatives against COVID-19 Mpro through structure-guided modeling and simulation approach. Journal of Biomolecular Structure & Dynamics, 1–19. https://doi.org/10.1080/07391102.2023.2220799
   Web of Science ®Google Scholar
• El Bakri, Y., Anouar, E. H., Marmouzi, I., Sayah, K., Ramli, Y., El Abbes Faouzi, M., Essassi, E. M., & Mague, J. T. (2018). Potential antidiabetic activity and molecular docking studies of novel synthesized 3.6-dimethyl-5-oxo-pyrido[3,4-f][1,2,4]triazepino[2,3-a]benzimidazole and 10-amino-2-methyl-4-oxo pyrimido[1,2-a]benzimidazole derivatives. Journal of Molecular Modeling, 24(7), 179. https://doi.org/10.1007/s00894-018-3705-9
   PubMed Web of Science ®Google Scholar
• El Bakri, Y., Karthikeyan, S., Anouar, E. H., Sebhaoui, J., Ben Ali, A., El Ghayati, L., Essassi, E. M., & Mague, J. T. (2020). A newly synthesized 6-methyl-7H,8H,9H-[1,2,4]triazolo[4,3-b][1,2,4]triazepin-8-one for potential inhibitor of adenosine A1 receptor: A combined experimental and computational studies. Journal of Biomolecular Structure & Dynamics, 38(12), 3578–3586. https://doi.org/10.1080/07391102.2019.1662848
   PubMed Web of Science ®Google Scholar
• El Bakri, Y., Kurbanova, M., Ahsin, A., Ramazanzade, N., & Al-Salahi, R. (2023). A probe to surface reactivity, crystal structure, and DFT investigations for newly synthesized 4,5-bis(4-nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione: A combined theoretical and experimental study. Crystals, 13(6), 942. https://doi.org/10.3390/cryst13060942
   Web of Science ®Google Scholar
• El Bakri, Y., Kurbanova, M. M., Siddique, S. A., Ahmad, S., & Goumri-Said, S. (2022). One-pot synthesis, X-ray crystal structure, and identification of potential molecules against COVID-19 main protease through structure-guided modeling and simulation approach. Arabian Journal of Chemistry, 15(11), 104230. https://doi.org/10.1016/j.arabjc.2022.104230
   PubMed Web of Science ®Google Scholar
• El Bakri, Y., Kurbanova, M., Siddique, S. A., Karthikeyan, S., Maharramov, A., & Ramazanzade, N. (2023). Synthesis, virtual screening, and computational approach of 6-(4-metoxyphenyl)-4-phenyl-1, 2-dihydropyrimidin-2-one as a potential target for thioredoxin glutathione reductase (TGR). Journal of Molecular Structure, 1286, 135623. https://doi.org/10.1016/j.molstruc.2023.135623
   Web of Science ®Google Scholar
• El Bakri, Y., Marmouzi, I., El Jemli, M., Anouar, E. H., Karthikeyan, S., Harmaoui, A., Faouzi, M. E. A., Mague, J. T., & Essassi, E. M. (2019). Synthesis, biological activity and molecular modeling of a new series of condensed 1,2,4-triazoles. Bioorganic Chemistry, 92, 103193. https://doi.org/10.1016/j.bioorg.2019.103193
   PubMed Web of Science ®Google Scholar
• Flores-Holguín, N., Frau, J., & Glossman-Mitnik, D. (2021). Computational pharmacokinetics report, ADMET study and conceptual DFT-based estimation of the chemical reactivity properties of marine cyclopeptides. ChemistryOpen, 10(11), 1142–1149. https://doi.org/10.1002/open.202100178
   PubMed Web of Science ®Google Scholar
• Foster, A J. P., & Weinhold, F. (1980). Natural hybrid orbitals. Journal of the American Chemical Society, 102(24), 7211–7218. https://doi.org/10.1021/ja00544a007
   Web of Science ®Google Scholar
• Fredholm, B. B. (2014). Adenosine—A physiological or pathophysiological agent? Journal of Molecular Medicine (Berlin, Germany), 92(3), 201–206. https://doi.org/10.1007/s00109-013-1101-6
   PubMed Web of Science ®Google Scholar
• Fredholm, B. B., IJzerman, A. P., Jacobson, K. A., Klotz, K.-N., & Linden, J. (2001). International Union of Pharmacology. XXV. Nomenclature and classification of adenosine receptors. Pharmacological Reviews, 53(4), 527–552.
   PubMed Web of Science ®Google Scholar
• Frisch, A., Nielson, A. B., & Holder, A. J. (2000). Gaussview user manual. Gaussian, Inc., p. 556.
   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
• Garadi, W. A., Bakri, Y. E., Lai, C., Karthikeyan, S., Ghayati, L. E., Mague, J. T., & Essassi, E. M. (2020). Synthesis, crystal structure and computational investigation of new 4‐phenyl‐decahydro‐1H‐1, 5‐benzodiazepin‐2‐one as potent inhibitor of Mu‐opioid receptor. ChemistrySelect, 5(15), 4601–4607. https://doi.org/10.1002/slct.202000356
   Web of Science ®Google Scholar
• Gentry, P. R., Sexton, P. M., & Christopoulos, A. (2015). Novel allosteric modulators of G protein-coupled receptors. The Journal of Biological Chemistry, 290(32), 19478–19488. https://doi.org/10.1074/jbc.R115.662759
   PubMed Web of Science ®Google Scholar
• Glendening, E. D., Reed, A. E., Carpenter, J. E., & Weinhold, F. (1998). NBO Version 3.1. TCI, University of Wisconsin.
   Google Scholar
• Glukhova, A., Thal, D. M., Nguyen, A. T., Vecchio, E. A., Jörg, M., Scammells, P. J., May, L. T., Sexton, P. M., & Christopoulos, A. (2017). Structure of the adenosine A1 receptor reveals the basis for subtype selectivity. Cell, 168(5), 867–877.e13. https://doi.org/10.1016/j.cell.2017.01.042
   PubMed Web of Science ®Google Scholar
• Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17. https://doi.org/10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Jacobson, K. A., & Gao, Z.-G. (2006). Adenosine receptors as therapeutic targets. Nature Reviews. Drug Discovery, 5(3), 247–264. https://doi.org/10.1038/nrd1983
   PubMed Web of Science ®Google Scholar
• Jang, C., Yadav, D. K., Subedi, L., Venkatesan, R., Venkanna, A., Afzal, S., Lee, E., Yoo, J., Ji, E., Kim, S. Y., & Kim, M.-H. (2018). Identification of novel acetylcholinesterase inhibitors designed by pharmacophore-based virtual screening, molecular docking and bioassay. Scientific Reports, 8(1), 14921. https://doi.org/10.1038/s41598-018-33354-6
   PubMedGoogle Scholar
• Kawsar, S. M. A., Hosen, M. A., Ahmad, S., El Bakri, Y., Laaroussi, H., Hadda, T. B., Almalki, F. A., Ozeki, Y., & Goumri-Said, S. (2022). Potential SARS-CoV-2 RdRp inhibitors of cytidine derivatives: Molecular docking, molecular dynamic simulations, ADMET, and POM analyses for the identification of pharmacophore sites. PLoS One, 17(11), e0273256. https://doi.org/10.1371/JOURNAL.PONE.0273256
   PubMed Web of Science ®Google Scholar
• Kenakin, T., & Christopoulos, A. (2013). Signalling bias in new drug discovery: Detection, quantification and therapeutic impact. Nature Reviews. Drug Discovery, 12(3), 205–216. https://doi.org/10.1038/nrd3954
   PubMed Web of Science ®Google Scholar
• Khan, S., Irfan, M., Hameed, A. R., Ullah, A., Abideen, S. A., Ahmad, S., Haq, M. U., El Bakri, Y., Al-Harbi, A. I., Ali, M., & Haleem, A. (2022). Vaccinomics to design a multi-epitope-based vaccine against monkeypox virus using surface-associated proteins. Journal of Biomolecular Structure & Dynamics, 41(20), 10859–10868. https://doi.org/10.1080/07391102.2022.2158942
   PubMedGoogle Scholar
• Kleinman, D. A. (1962). Nonlinear dielectric polarization in optical media. Physical Review, 126(6), 1977–1979. https://doi.org/10.1103/PhysRev.126.1977
   Web of Science ®Google Scholar
• Lee, M. R., Baker, D., & Kollman, P. A. (2001). 2.1 and 1.8 Å average Cα RMSD structure predictions on two small proteins, HP-36 and S15. Journal of the American Chemical Society, 123(6), 1040–1046. https://doi.org/10.1021/ja003150i
   PubMed Web of Science ®Google Scholar
• Lee, J., Cheng, X., Jo, S., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Biophysical Journal, 110(3), 641A. https://doi.org/10.1016/j.bpj.2015.11.3431
   Web of Science ®Google Scholar
• Lipinski, C. (2003). Chris Lipinski discusses life and chemistry after the Rule of Five. Drug Discovery Today, 8, 12–16. https://doi.org/10.1016/S1359-6446(02)02556-4
   PubMed Web of Science ®Google Scholar
• Lu, T., & Chen, F. (2012). Multiwfn: A multifunctional wavefunction analyzer. Journal of Computational Chemistry, 33(5), 580–592. https://doi.org/10.1002/jcc.22885
   PubMed Web of Science ®Google Scholar
• Mackenzie, C. F., Spackman, P. R., Jayatilaka, D., & Spackman, M. A. (2017). CrystalExplorer model energies and energy frameworks: Extension to metal coordination compounds, organic salts, solvates and open-shell systems. IUCrJ, 4(Pt 5), 575–587. https://doi.org/10.1107/S205225251700848X
   PubMedGoogle Scholar
• MacKerell, A. D., Jr., Banavali, N., & Foloppe, N. (2000). Development and current status of the CHARMM force field for nucleic acids. Biopolymers, 56(4), 257–265. https://doi.org/10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
   PubMed Web of Science ®Google Scholar
• Müller, C. E., & Jacobson, K. A. (2011). Recent developments in adenosine receptor ligands and their potential as novel drugs. Biochimica et Biophysica Acta, 1808(5), 1290–1308. https://doi.org/10.1016/j.bbamem.2010.12.017
   PubMed Web of Science ®Google Scholar
• Muthu, S., & Prabhakaran, A. (2014). Vibrational spectroscopic study and NBO analysis on tranexamic acid using DFT method. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 129, 184–192. https://doi.org/10.1016/j.saa.2014.03.050
   PubMed Web of Science ®Google Scholar
• Nazish, M., Legendre, C. M., Graw, N., Herbst-Irmer, R., Muhammed, S., Parameswaran, P., Stalke, D., & Roesky, H. W. (2023). Compounds with alternating single and double bonds of antimony and silicon; isoelectronic to ethane-1,2-diimine. Inorganic Chemistry, 62(24), 9306–9313. https://doi.org/10.1021/acs.inorgchem.2c03695
   PubMed Web of Science ®Google Scholar
• Novelli, F., Chen, K., Buchmann, A., Ockelmann, T., Hoberg, C., Head-Gordon, T., & Havenith, M. (2023). The birth and evolution of solvated electrons in the water. Proceedings of the National Academy of Sciences of the United States of America, 120(8), e2216480120. https://doi.org/10.1073/pnas.2216480120
   PubMed Web of Science ®Google Scholar
• Okulik, N., & Jubert, A. H. (2005). Theoretical analysis of the reactive sites of non-steroidal anti-inflammatory drugs. Internet Electronic Journal of Molecular Design, 4(1), 17–30.
   Google Scholar
• Sawynok, J. (2016). Adenosine receptor targets for pain. Neuroscience, 338, 1–18. https://doi.org/10.1016/j.neuroscience.2015.10.031
   PubMed Web of Science ®Google Scholar
• Sheldrick, G. M. (2015a). Crystal structure refinement with SHELXL. Acta Crystallographica. Section C, Structural Chemistry, 71(Pt 1), 3–8. https://doi.org/10.1107/S2053229614024218
   PubMed Web of Science ®Google Scholar
• Sheldrick, G. M. (2015b). 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
• Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D., & Spackman, M. A. (2021). CrystalExplorer: A program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. Journal of Applied Crystallography, 54(Pt 3), 1006–1011. https://doi.org/10.1107/S1600576721002910
   PubMedGoogle Scholar
• Turner, M. J., Thomas, S. P., Shi, M. W., Jayatilaka, D., & Spackman, M. A. (2015). Energy frameworks: Insights into interaction anisotropy and the mechanical properties of molecular crystals. Chemical Communications (Cambridge, England), 51(18), 3735–3738. https://doi.org/10.1039/c4cc09074h
   PubMed Web of Science ®Google Scholar
• Vanitha, U., Elancheran, R., Manikandan, V., Kabilan, S., & Krishnasamy, K. (2021). Design, synthesis, characterization, molecular docking and computational studies of 3-phenyl-2-thioxoimidazolidin-4-one derivatives. Journal of Molecular Structure, 1246, 131212. https://doi.org/10.1016/j.molstruc.2021.131212
   Web of Science ®Google Scholar
• Yaraguppi, D., Bagewadi, Z., Deshpande, S., & Chandramohan, V. (2022). In silico study on the inhibition of UDP-N-acetylglucosamine 1-carboxy vinyl transferase from Salmonella typhimurium by the lipopeptide produced from Bacillus aryabhattai. International Journal of Peptide Research and Therapeutics, 28(3), 80. https://doi.org/10.1007/s10989-022-10388-z
   Web of Science ®Google Scholar