Computational Prediction of 3,5-Diaryl-1H-Pyrazole and spiropyrazolines derivatives as potential acetylcholinesterase inhibitors for alzheimer disease treatment by 3D-QSAR, molecular docking, molecular dynamics simulation, and ADME-Tox

References

• Agrahari, A. K., Sneha, P., George Priya Doss, C., Siva, R., & Zayed, H. (2018). A profound computational study to prioritize the disease-causing mutations in PRPS1 gene. Metabolic Brain Disease, 33(2), 589–600. https://doi.org/10.1007/s11011-017-0121-2
   PubMed Web of Science ®Google Scholar
• Bagherzadeh, K., Shirgahi Talari, F., Sharifi, A., Ganjali, M. R., Saboury, A. A., & Amanlou, M. (2015). A new insight into mushroom tyrosinase inhibitors: Docking, pharmacophore-based virtual screening, and molecular modeling studies. Journal of Biomolecular Structure & Dynamics, 33(3), 487–501. https://doi.org/10.1080/07391102.2014.893203
   PubMed Web of Science ®Google Scholar
• Bharadwaj, S., Rao, A. K., Dwivedi, V. D., Mishra, S. K., & Yadava, U. (2021). Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation. Journal of Biomolecular Structure & Dynamics, 39(7), 2338–2351. https://doi.org/10.1080/07391102.2020.1747545
   PubMed Web of Science ®Google Scholar
• Corbett, A., Pickett, J., Burns, A., Corcoran, J., Dunnett, S. B., Edison, P., Hagan, J. J., Holmes, C., Jones, E., Katona, C., Kearns, I., Kehoe, P., Mudher, A., Passmore, A., Shepherd, N., Walsh, F., & Ballard, C. (2012). Drug repositioning for Alzheimer’s disease. Nature Reviews. Drug Discovery, 11(11), 833–846. https://doi.org/10.1038/nrd3869
   PubMed Web of Science ®Google Scholar
• Cramer, R. D., Patterson, D. E., & Bunce, J. D. (1988). Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. Journal of the American Chemical Society, 110(18), 5959–5967. https://doi.org/10.1021/ja00226a005
   PubMed Web of Science ®Google Scholar
• Cui, Q., Sulea, T., Schrag, J. D., Munger, C., Hung, M.-N., Naïm, M., Cygler, M., & Purisima, E. O. (2008). Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex. Journal of Molecular Biology, 379(4), 787–802. https://doi.org/10.1016/j.jmb.2008.04.035
   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
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N ⋅log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• de Azevedo Junior, W. F., Bitencourt-Ferreira, G., Godoy, J. R., Adriano, H. M. A., dos Santos Bezerra, W. A., & dos Santos Soares, A. M. (2021). Protein-Ligand Docking Simulations with AutoDock4 Focused on the Main Protease of SARS-CoV-2. Current Medicinal Chemistry, 28(37), 7614–7633. https://doi.org/10.2174/0929867328666210329094111
   PubMed Web of Science ®Google Scholar
• Dowlati Beirami, A., Hajimahdi, Z., & Zarghi, A. (2019). Docking-based 3D-QSAR (CoMFA, CoMFA-RG, CoMSIA) study on hydroquinoline and thiazinan-4-one derivatives as selective COX-2 inhibitors. Journal of Biomolecular Structure and Dynamics, 37(11), 2999–3006. https://doi.org/10.1080/07391102.2018.1502687
   PubMed Web of Science ®Google Scholar
• El Aissouq, A., Chedadi, O., Bouachrine, M., Ouammou, A., & Khalil, F. (2023). Development of novel monoamine oxidase B (MAO-B) inhibitors by combined application of docking-based alignment, 3D-QSAR, ADMET prediction, molecular dynamics simulation, and MM_GBSA binding free energy. Journal of Biomolecular Structure & Dynamics, 41(10), 4667–4680. https://doi.org/10.1080/07391102.2022.2071341
   PubMed Web of Science ®Google Scholar
• El Khatabi, K., Aanouz, I., El-Mernissi, R., Khaldan, A., Ajana, M. A., Bouachrine, M., & Lakhlifi, T. (2020). 3D-QSAR and Molecular Docking Studies of p-Aminobenzoic Acid Derivatives to Explore the Features Requirements of Alzheimer Inhibitors. Orbital: The Electronic Journal of Chemistry, 12(4), 172–181. https://doi.org/10.17807/orbital.v12i4.1467
   Web of Science ®Google Scholar
• Elzupir, A. O. (2022). Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 40(5), 2113–2120. https://doi.org/10.1080/07391102.2020.1835732
   PubMed Web of Science ®Google Scholar
• Gao, Y., Wang, H., Wang, J., & Cheng, M. (2020). In silico studies on p21-activated kinase 4 inhibitors: Comprehensive application of 3D-QSAR analysis, molecular docking, molecular dynamics simulations, and MM-GBSA calculation. Journal of Biomolecular Structure & Dynamics, 38(14), 4119–4133. https://doi.org/10.1080/07391102.2019.1673823
   PubMed Web of Science ®Google Scholar
• Goudzal, A., El Aissouq, A., El Hamdani, H., Hadaji, E. G., Ouammou, A., & Bouachrine, M. (2023). 3D-QSAR modeling and molecular docking studies on a series of 2, 4, 5-trisubstituted imidazole derivatives as CK2 inhibitors. Journal of Biomolecular Structure & Dynamics, 41(1), 234–248. https://doi.org/10.1080/07391102.2021.2014360
   PubMed Web of Science ®Google Scholar
• Grest, G. S., & Kremer, K. (1986). Molecular dynamics simulation for polymers in the presence of a heat bath. Physical Review. A, General Physics, 33(5), 3628–3631. https://doi.org/10.1103/PhysRevA.33.3628
   PubMedGoogle Scholar
• Gu, X., Wang, Y., Wang, M., Wang, J., & Li, N. (2021). Computational investigation of imidazopyridine analogs as protein kinase B (Akt1) allosteric inhibitors by using 3D-QSAR, molecular docking and molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 39(1), 63–78. https://doi.org/10.1080/07391102.2019.1705185
   PubMed Web of Science ®Google Scholar
• Gutti, G., Kumar, D., Paliwal, P., Ganeshpurkar, A., Lahre, K., Kumar, A., Krishnamurthy, S., & Singh, S. K. (2019). Development of pyrazole and spiropyrazoline analogs as multifunctional agents for treatment of Alzheimer’s disease. Bioorganic Chemistry, 90, 103080. https://doi.org/10.1016/j.bioorg.2019.103080
   PubMed Web of Science ®Google Scholar
• Iqbal, K., del C. Alonso, A., Chen, S., Chohan, M. O., El-Akkad, E., Gong, C.-X., Khatoon, S., Li, B., Liu, F., Rahman, A., Tanimukai, H., & Grundke-Iqbal, I. (2005). Tau pathology in Alzheimer disease and other tauopathies. Biochimica Et Biophysica Acta, 1739(2-3), 198–210. https://doi.org/10.1016/j.bbadis.2004.09.008
   PubMed Web of Science ®Google Scholar
• Islam, M. S., Al-Majid, A. M., Azam, M., Verma, V. P., Barakat, A., Haukka, M., Elgazar, A. A., Mira, A., & Badria, F. A. (2021). Construction of Spirooxindole Analogues Engrafted with Indole and Pyrazole Scaffolds as Acetylcholinesterase Inhibitors. ACS Omega, 6(47), 31539–31556. https://doi.org/10.1021/acsomega.1c03978
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L. (2004). The Many Roles of Computation in Drug Discovery. Science (New York, N.Y.), 303(5665), 1813–1818. https://doi.org/10.1126/science.1096361
   PubMed Web of Science ®Google Scholar
• Khaldan, A., Bouamrane, S., El-Mernissi, R., Maghat, H., Ajana, M. A., Sbai, A., Bouachrine, M., & Lakhlifi, T. (2021). 3D-QSAR modeling, molecular docking and ADMET properties of benzothiazole derivatives as α-glucosidase inhibitors. Materials Today: Proceedings, 45, 7643–7652. https://doi.org/10.1016/j.matpr.2021.03.114
   Google Scholar
• Khalid, D., M, L., N.n, M., M, E., & M, E. H. (2020). QSAR studies on 2-arylethenylquinoline derivatives as multifunctional agents for the treatment of Alzheimer’s disease via CoMFA and CoMSIA analysis. Maghrebian Journal of Pure and Applied Science, 6, 51–59. Pages https://doi.org/10.48383/IMIST.PRSM/MJPAS-V6I1.20944
   Google Scholar
• Klebe, G., Abraham, U., & Mietzner, T. (1994). Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity. Journal of Medicinal Chemistry, 37(24), 4130–4146. https://doi.org/10.1021/jm00050a010
   PubMed Web of Science ®Google Scholar
• Kumar, S., Paul, P., Yadav, P., Kaul, R., Maitra, S. S., Jha, S. K., & Chaari, A. (2022). A multi-targeted approach to identify potential flavonoids against three targets in the SARS-CoV-2 life cycle. Computers in Biology and Medicine, 142, 105231. https://doi.org/10.1016/j.compbiomed.2022.105231
   PubMed Web of Science ®Google Scholar
• LaFerla, F. M., Green, K. N., & Oddo, S. (2007). Intracellular amyloid-β in Alzheimer’s disease. Nature Reviews. Neuroscience, 8(7), 499–509. https://doi.org/10.1038/nrn2168
   PubMed Web of Science ®Google Scholar
• Liu, Y., Grimm, M., Dai, W., Hou, M., Xiao, Z.-X., & Cao, Y. (2020). CB-Dock: A web server for cavity detection-guided protein–ligand blind docking. Acta Pharmacologica Sinica, 41(1), 138–144. https://doi.org/10.1038/s41401-019-0228-6
   PubMed Web of Science ®Google Scholar
• Mattson, M. P., Tomaselli, K. J., & Rydel, R. E. (1993). Calcium-destabilizing and neurodegenerative effects of aggregated β-amyloid peptide are attenuated by basic FGF. Brain Research, 621(1), 35–49. https://doi.org/10.1016/0006-8993(93)90295-X
   PubMed Web of Science ®Google Scholar
• Moharana, M., Pattanayak, S. K., & Khan, F. (2023). Molecular recognition of bio-active triterpenoids from Swertia chirayita towards hepatitis Delta antigen: A mechanism through docking, dynamics simulation, Gibbs free energy landscape. Journal of Biomolecular Structure & Dynamics, 14, 1–14. https://doi.org/10.1080/07391102.2023.2184173
   Google Scholar
• Nosé, S. (1984). A molecular dynamics method for simulations in the canonical ensemble. Molecular Physics, 52(2), 255–268. https://doi.org/10.1080/00268978400101201
   Web of Science ®Google Scholar
• O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/10.1002/jcc.20289
   PubMed Web of Science ®Google Scholar
• Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Safavi, A., Ghodousi, E. S., Ghavamizadeh, M., Sabaghan, M., Azadbakht, O., Veisi, A., Babaei, H., Nazeri, Z., Darabi, M. K., & Zarezade, V. (2021). Computational investigation of novel farnesyltransferase inhibitors using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking and molecular dynamics simulation studies: A new insight into cancer treatment. Journal of Molecular Structure, 1241, 130667. https://doi.org/10.1016/j.molstruc.2021.130667
   Web of Science ®Google Scholar
• Sarma, R. H. (1997). Journal of Biomolecular Structure and Dynamics. Journal of Biomolecular Structure & Dynamics, 15(3), 634–634. https://doi.org/10.1080/07391102.1997.10508975
   PubMed Web of Science ®Google Scholar
• Sen, D., Debnath, P., Debnath, B., Bhaumik, S., & Debnath, S. (2022). Identification of potential inhibitors of SARS-CoV-2 main protease and spike receptor from 10 important spices through structure-based virtual screening and molecular dynamic study. Journal of Biomolecular Structure & Dynamics, 40(2), 941–962. https://doi.org/10.1080/07391102.2020.1819883
   PubMed Web of Science ®Google Scholar
• Sharma, A., Vora, J., Patel, D., Sinha, S., Jha, P. C., & Shrivastava, N. (2022). Identification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches. Journal of Biomolecular Structure & Dynamics, 40(7), 3296–3311. https://doi.org/10.1080/07391102.2020.1846624
   PubMed Web of Science ®Google Scholar
• Shaw, A. Y., Liau, H.-H., Lu, P.-J., Yang, C.-N., Lee, C.-H., Chen, J.-Y., Xu, Z., & Flynn, G. (2010). 3,5-Diaryl-1H-pyrazole as a molecular scaffold for the synthesis of apoptosis-inducing agents. Bioorganic & Medicinal Chemistry, 18(9), 3270–3278. https://doi.org/10.1016/j.bmc.2010.03.016
   PubMed Web of Science ®Google Scholar
• Shirvani, P., & Fassihi, A. (2022). In silico design of novel FAK inhibitors using integrated molecular docking, 3D-QSAR and molecular dynamics simulation studies. Journal of Biomolecular Structure & Dynamics, 40(13), 5965–5982. https://doi.org/10.1080/07391102.2021.1875880
   PubMed Web of Science ®Google Scholar
• Shrivastava, S. K., Sinha, S. K., Srivastava, P., Tripathi, P. N., Sharma, P., Tripathi, M. K., Tripathi, A., Choubey, P. K., Waiker, D. K., Aggarwal, L. M., Dixit, M., Kheruka, S. C., Gambhir, S., Shankar, S., & Srivastava, R. K. (2019). Design and development of novel p-aminobenzoic acid derivatives as potential cholinesterase inhibitors for the treatment of Alzheimer’s disease. Bioorganic Chemistry, 82, 211–223. https://doi.org/10.1016/j.bioorg.2018.10.009
   PubMed Web of Science ®Google Scholar
• Shuaib, S., Saini, R. K., Goyal, D., & Goyal, B. (2020). Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β 42 peptide in Alzheimer’s disease: Key insights from molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 38(3), 708–721. https://doi.org/10.1080/07391102.2019.1586587
   PubMed Web of Science ®Google Scholar
• Stitou, M., Toufik, H., Bouachrine, M., & Lamchouri, F. (2021). Quantitative structure–activity relationships analysis, homology modeling, docking and molecular dynamics studies of triterpenoid saponins as Kirsten rat sarcoma inhibitors. Journal of Biomolecular Structure & Dynamics, 39(1), 152–170. https://doi.org/10.1080/07391102.2019.1707122
   PubMed Web of Science ®Google Scholar
• Sultana, R., Perluigi, M., & Butterfield, D. A. (2009). Oxidatively modified proteins in Alzheimer’s disease (AD), mild cognitive impairment and animal models of AD: Role of Abeta in pathogenesis. Acta Neuropathologica, 118(1), 131–150. https://doi.org/10.1007/s00401-009-0517-0
   PubMed Web of Science ®Google Scholar
• Vora, J., Patel, S., Sinha, S., Sharma, S., Srivastava, A., Chhabria, M., & Shrivastava, N. (2019). Structure based virtual screening, 3D-QSAR, molecular dynamics and ADMET studies for selection of natural inhibitors against structural and non-structural targets of Chikungunya. Journal of Biomolecular Structure & Dynamics, 37(12), 3150–3161. https://doi.org/10.1080/07391102.2018.1509732
   PubMed Web of Science ®Google Scholar
• Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
   PubMed Web of Science ®Google Scholar
• Wu, H.-Q., Yao, J., He, Q.-Q., & Chen, F.-E. (2014). Docking-based CoMFA and CoMSIA studies on naphthyl-substituted diarylpyrimidines as NNRTIs. SAR and QSAR in Environmental Research, 25(10), 761–775. https://doi.org/10.1080/1062936X.2014.955054
   PubMed Web of Science ®Google Scholar
• Xiao, Z., Xiao, Y.-D., Feng, J., Golbraikh, A., Tropsha, A., & Lee, K.-H. (2002). Antitumor Agents. 213. Modeling of Epipodophyllotoxin Derivatives Using Variable Selection k Nearest Neighbor QSAR Method. Journal of Medicinal Chemistry, 45(11), 2294–2309. https://doi.org/10.1021/jm0105427
   PubMed Web of Science ®Google Scholar
• Xu, Y., He, Z., Liu, H., Chen, Y., Gao, Y., Zhang, S., Wang, M., Lu, X., Wang, C., Zhao, Z., Liu, Y., Zhao, J., Yu, Y., & Yang, M. (2020). 3D-QSAR, molecular docking, and molecular dynamics simulation study of thieno[3,2- b] pyrrole-5-carboxamide derivatives as LSD1 inhibitors. RSC Advances, 10(12), 6927–6943. https://doi.org/10.1039/C9RA10085G
   PubMed Web of Science ®Google Scholar
• Zaki, H., Belhassan, A., Benlyas, M., Lakhlifi, T., & Bouachrine, M. (2021). New dehydroabietic acid (DHA) derivatives with anticancer activity against HepG2 cancer cell lines as a potential drug targeting EGFR kinase domain. CoMFA study and virtual ligand-based screening. Journal of Biomolecular Structure & Dynamics, 39(8), 2993–3003. https://doi.org/10.1080/07391102.2020.1759452
   PubMed Web of Science ®Google Scholar
• Zhang, C., Li, Q., Meng, L., & Ren, Y. (2020). Design of novel dopamine D 2 and serotonin 5-HT 2A receptors dual antagonists toward schizophrenia: An integrated study with QSAR, molecular docking, virtual screening and molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 38(3), 860–885. https://doi.org/10.1080/07391102.2019.1590244
   PubMed Web of Science ®Google Scholar