In silico exploration of the potential inhibitory activities of in-house and ZINC database lead compounds against alpha-glucosidase using structure-based virtual screening and molecular dynamics simulation approach

References

• Alrefai, H., Allababidi, H., Levy, S., & Levy, J. (2002). The endocrine system in diabetes mellitus. Endocrine, 18(2), 105–119. https://doi.org/10.1385/ENDO:18:2:105
   PubMed Web of Science ®Google Scholar
• Association, A. D. (2014). Standards of medical care in diabetes–2014. Diabetes Care, 37, S14–S80.
   PubMed Web of Science ®Google Scholar
• Bae, J. H., Han, K.-D., Ko, S.-H., Yang, Y. S., Choi, J. H., Choi, K. M., Kwon, H.-S., & Won, K. C. (2022). Diabetes fact sheet in Korea 2021. Diabetes & Metabolism Journal, 46(3), 417–426. https://doi.org/10.4093/dmj.2022.0106
   PubMed Web of Science ®Google Scholar
• Bello, N. A., Pfeffer, M. A., Skali, H., McGill, J. B., Rossert, J., Olson, K. A., Weinrauch, L., Cooper, M. E., de Zeeuw, D., Rossing, P., McMurray, J. J. V., & Solomon, S. D. (2014). Retinopathy and clinical outcomes in patients with type 2 diabetes mellitus, chronic kidney disease, and anemia. BMJ Open Diabetes Research & Care, 2(1), e000011. https://doi.org/10.1136/bmjdrc-2013-000011
   PubMedGoogle Scholar
• Bibi, S., & Sakata, K. (2016). Current status of computer-aided drug design for type 2 diabetes. Current Computer Aided-Drug Design, 12(2), 167–177. https://doi.org/10.2174/1573409912666160426120709
   Web of Science ®Google Scholar
• Chaudhury, A., Duvoor, C., Reddy Dendi, V. S., Kraleti, S., Chada, A., Ravilla, R., Marco, A., Shekhawat, N. S., Montales, M. T., Kuriakose, K., Sasapu, A., Beebe, A., Patil, N., Musham, C. K., Lohani, G. P., & Mirza, W. (2017). Clinical review of antidiabetic drugs: Implications for type 2 diabetes mellitus management. Frontiers in Endocrinology, 8, 6. https://doi.org/10.3389/fendo.2017.00006
   PubMed Web of Science ®Google Scholar
• Chen, X., Zheng, Y., & Shen, Y. (2006). Voglibose (Basen®, AO-128), one of the most important α-glucosidase inhibitors. Current Medicinal Chemistry, 13(1), 109–116. https://doi.org/10.2174/092986706789803035
   PubMed Web of Science ®Google Scholar
• Chiasson, J.-L. (2006). Acarbose for the prevention of diabetes, hypertension, and cardiovascular disease in subjects with impaired glucose tolerance: The study to prevent non-insulin-dependent diabetes mellitus (STOP-NIDDM) trial. Endocrine Practice: Official Journal of the American College of Endocrinology and the American Association of Clinical Endocrinologists, 12 Suppl 1, 25–30. https://doi.org/10.4158/EP.12.S1.25
   PubMedGoogle Scholar
• Damsud, T., Chanwun, T., & Kaewpiboon, C. (2017). Antidiabetic agents with α-glucosidase inhibition and antioxidant capacity from the shoots of Clausena cambodiana Guill. Int. J. Agric. Technol, 13(4), 449–456.
   Google Scholar
• Daud, Saima, Abid, Obaid-ur-Rahman, Sardar, Asma, Shah, Basit Ali, Rafiq, Muhammad, Wadood, Abdul, Ghufran, Mehreen, Rehman, Wajid, Iftikhar, Fatima, Sultana, Rifhat, Daud, Habiba, Niaz, Basit, Zain-ul-Wahab, (2022). Design, synthesis, in vitro evaluation, and docking studies on ibuprofen derived 1, 3, 4-oxadiazole derivatives as dual α-glucosidase and urease inhibitors. Medicinal Chemistry Research, 2, 31316–336. https://doi.org/10.1007/s00044-021-02814-6
   Web of Science ®Google Scholar
• Dong, Y., Zhang, B., Sun, W., & Xing, Y. (2019). Intervention of Prediabetes by Flavonoids from Oroxylum indicum Bioactive Food as Dietary Interventions for Diabetes. (pp. 559–575): Elsevier.
   Google Scholar
• Esser, N., Paquot, N., & Scheen, A. J. (2015). Anti-inflammatory agents to treat or prevent type 2 diabetes, metabolic syndrome and cardiovascular disease. Expert Opinion on Investigational Drugs, 24(3), 283–307. https://doi.org/10.1517/13543784.2015.974804
   PubMed Web of Science ®Google Scholar
• Ferreira, S. B., Sodero, A. C., Cardoso, M. F., Lima, E. S., Kaiser, C. R., Silva, F. P., Jr,., & Ferreira, V. F. (2010). Synthesis, biological activity, and molecular modeling studies of 1 h-1, 2, 3-triazole derivatives of carbohydrates as α-glucosidases inhibitors. Journal of Medicinal Chemistry, 53(6), 2364–2375. https://doi.org/10.1021/jm901265h
   PubMed Web of Science ®Google Scholar
• Ghufran, M., Khan, H. A., Ullah, M., Ghufran, S., Ayaz, M., Siddiq, M., Hassan, S. S. U., & Bungau, S. (2022). In silico strategies for designing of peptide inhibitors of oncogenic K-Ras G12V mutant: Inhibiting cancer growth and proliferation. Cancers, 14(19), 4884. https://doi.org/10.3390/cancers14194884
   PubMed Web of Science ®Google Scholar
• Ghufran, M., Rehman, A. U., Ayaz, M., Ul-Haq, Z., Uddin, R., Azam, S. S., & Wadood, A. (2023). New lead compounds identification against KRas mediated cancers through pharmacophore-based virtual screening and in vitro assays. Journal of Biomolecular Structure & Dynamics, 41(16), 8053–8067. https://doi.org/10.1080/07391102.2022.2128878
   PubMed Web of Science ®Google Scholar
• Ghufran, M., Ullah, M., Khan, H. A., Ghufran, S., Ayaz, M., Siddiq, M., Abbas, S. Q., Hassan, S. S. U., & Bungau, S. (2023). In-silico lead druggable compounds identification against SARS COVID-19 main protease target from in-house, chembridge and zinc databases by structure-based virtual screening, molecular docking and molecular dynamics simulations. Bioengineering, 10(1), 100. https://doi.org/10.3390/bioengineering10010100
   PubMedGoogle Scholar
• Halim, S. A., Jabeen, S., Khan, A., & Al-Harrasi, A. (2021). Rational design of novel inhibitors of α-glucosidase: An application of quantitative structure activity relationship and structure-based virtual screening. Pharmaceuticals, 14(5), 482. https://doi.org/10.3390/ph14050482
   Web of Science ®Google Scholar
• Hardy, K., Brand-Miller, J., Brown, K. D., Thomas, M. G., & Copeland, L. (2015). The importance of dietary carbohydrate in human evolution. The Quarterly Review of Biology, 90(3), 251–268. https://doi.org/10.1086/682587
   PubMed Web of Science ®Google Scholar
• Hassan, S. S., Tiwari, S., Guimarães, L. C., Jamal, S. B., Folador, E., Sharma, N. B., de Castro Soares, S., Almeida, S., Ali, A., Islam, A., Póvoa, F. D., de Abreu, V. A. C., Jain, N., Bhattacharya, A., Juneja, L., Miyoshi, A., Silva, A., Barh, D., Turjanski, A. G., Azevedo, V., & Ferreira, R. S. (2014). Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics, 15 Suppl 7(Suppl 7), S3. https://doi.org/10.1186/1471-2164-15-S7-S3
   PubMedGoogle Scholar
• Hoang, T. X., Trovato, A., Seno, F., Banavar, J. R., & Maritan, A. (2004). Geometry and symmetry presculpt the free-energy landscape of proteins. Proceedings of the National Academy of Sciences of the United States of America, 101(21), 7960–7964. https://doi.org/10.1073/pnas.0402525101
   PubMed Web of Science ®Google Scholar
• Jiao, Y., Hua, D., Huang, D., Zhang, Q., & Yan, C. (2018). Characterization of a new heteropolysaccharide from green guava and its application as an α-glucosidase inhibitor for the treatment of type II diabetes. Food & Function, 9(7), 3997–4007. https://doi.org/10.1039/c8fo00790j
   PubMed Web of Science ®Google Scholar
• Kashtoh, H., & Baek, K.-H. (2022). Recent updates on phytoconstituent alpha-glucosidase inhibitors: An approach towards the treatment of type two diabetes. Plants, 11(20), 2722. https://doi.org/10.3390/plants11202722
   Google Scholar
• Li, M., Song, L. J., & Qin, X. Y. (2014). Advances in the cellular immunological pathogenesis of type 1 diabetes. Journal of Cellular and Molecular Medicine, 18(5), 749–758. https://doi.org/10.1111/jcmm.12270
   PubMed Web of Science ®Google Scholar
• Li, W., Yuan, G., Pan, Y., Wang, C., & Chen, H. (2017). Network pharmacology studies on the bioactive compounds and action mechanisms of natural products for the treatment of diabetes mellitus: A review. Frontiers in Pharmacology, 8, 74. https://doi.org/10.3389/fphar.2017.00074
   PubMed Web of Science ®Google Scholar
• Li, X., & Tan, X. (2022). Exploring the mechanism of the cystic fibrosis transmembrane conductance regulator-ATP binding through molecular dynamics and potential of mean force simulations.
   Google Scholar
• Lipinski, C. A. (2000). Drug-like properties and the causes of poor solubility and poor permeability. Journal of Pharmacological and Toxicological Methods, 44(1), 235–249. https://doi.org/10.1016/s1056-8719(00)00107-6
   PubMed Web of Science ®Google Scholar
• Liu, M., Zhang, W., Wei, J., & Lin, X. (2011). Synthesis and α-glucosidase inhibitory mechanisms of bis (2, 3-dibromo-4, 5-dihydroxybenzyl) ether, a potential marine bromophenol α-glucosidase inhibitor. Marine Drugs, 9(9), 1554–1565. https://doi.org/10.3390/md9091554
   PubMed Web of Science ®Google Scholar
• Liu, S.-K., Hao, H., Bian, Y., Ge, Y.-X., Lu, S., Xie, H.-X., Wang, K.-M., Tao, H., Yuan, C., Zhang, J., Zhang, J., Jiang, C.-S., & Zhu, K. (2021). Discovery of new α-glucosidase inhibitors: Structure-based virtual screening and biological evaluation. Frontiers in Chemistry, 9, 639279. https://doi.org/10.3389/fchem.2021.639279
   PubMed Web of Science ®Google Scholar
• Mahnashi, M. H., Alqahtani, Y. S., Alyami, B. A., Alqarni, A. O., Alqahl, S. A., Ullah, F., Sadiq, A., Zeb, A., Ghufran, M., Kuraev, A., Nawaz, A., & Ayaz, M. (2022). HPLC-DAD phenolics analysis, α-glucosidase, α-amylase inhibitory, molecular docking and nutritional profiles of Persicaria hydropiper L. BMC Complementary Medicine and Therapies, 22(1), 26. https://doi.org/10.1186/s12906-022-03510-7
   PubMedGoogle Scholar
• Moelands, S. V., Lucassen, P. L., Akkermans, R. P., De Grauw, W. J., & Van de Laar, F. A, Cochrane Metabolic and Endocrine Disorders Group. (2018). Alpha‐glucosidase inhibitors for prevention or delay of type 2 diabetes mellitus and its associated complications in people at increased risk of developing type 2 diabetes mellitus. Cochrane Database of Systematic Reviews, 2018(12). https://doi.org/10.1002/14651858.CD005061.pub3
   Google Scholar
• Patel, S. (2016). Cerebrovascular complications of diabetes: Alpha glucosidase inhibitor as potential therapy. Hormone and Metabolic Research = Hormon- Und Stoffwechselforschung = Hormones et Metabolisme, 48(2), 83–91. https://doi.org/10.1055/s-0035-1565181
   PubMed Web of Science ®Google Scholar
• Pili, R., Chang, J., Partis, R. A., Mueller, R. A., Chrest, F. J., & Passaniti, A. (1995). The α-glucosidase I inhibitor castanospermine alters endothelial cell glycosylation, prevents angiogenesis, and inhibits tumor growth. Cancer Research, 55(13), 2920–2926.
   PubMed Web of Science ®Google Scholar
• Proença, C., Freitas, M., Ribeiro, D., Oliveira, E. F. T., Sousa, J. L. C., Tomé, S. M., Ramos, M. J., Silva, A. M. S., Fernandes, P. A., & Fernandes, E. (2017). α-Glucosidase inhibition by flavonoids: An in vitro and in silico structure–activity relationship study. Journal of Enzyme Inhibition and Medicinal Chemistry, 32(1), 1216–1228. https://doi.org/10.1080/14756366.2017.1368503
   PubMed Web of Science ®Google Scholar
• Rashid, K., Chowdhury, S., Ghosh, S., & Sil, P. C. (2017). Curcumin attenuates oxidative stress induced NFκB mediated inflammation and endoplasmic reticulum dependent apoptosis of splenocytes in diabetes. Biochemical Pharmacology, 143, 140–155. https://doi.org/10.1016/j.bcp.2017.07.009
   PubMed Web of Science ®Google Scholar
• Sakulkeo, O., Wattanapiromsakul, C., Pitakbut, T., & Dej-Adisai, S. (2022). Alpha-glucosidase inhibition and molecular docking of isolated compounds from traditional thai medicinal plant, Neuropeltis racemosa Wall. Molecules (Basel, Switzerland), 27(3), 639. https://doi.org/10.3390/molecules27030639
   PubMed Web of Science ®Google Scholar
• Saltos, M. B. V., Puente, B. F. N., Faraone, I., Milella, L., De Tommasi, N., & Braca, A. (2015). Inhibitors of α-amylase and α-glucosidase from Andromachia igniaria Humb. & Bonpl. Phytochemistry Letters, 14, 45–50. https://doi.org/10.1016/j.phytol.2015.08.018
   Web of Science ®Google Scholar
• Shimada, Y., Nishimura, E., Hoshina, H., Kobayashi, H., Higuchi, T., Eto, Y., … Ohashi, T. (2015). Proteasome inhibitor Bortezomib enhances the activity of multiple mutant forms of lysosomal α-glucosidase in Pompe disease. JIMD Reports, 18, 33–39. volume
   PubMedGoogle Scholar
• Sosa-Peinado, A., León-Cruz, E., Velázquez-López, I., Matuz-Mares, D., Cano-Sánchez, P., & González-Andrade, M. (2022). Theoretical-experimental studies of calmodulin-peptide interactions at different calcium equivalents. Journal of Biomolecular Structure & Dynamics, 40(6), 2689–2700. https://doi.org/10.1080/07391102.2020.1841679
   PubMed Web of Science ®Google Scholar
• Stein, S. A., Lamos, E. M., & Davis, S. N. (2013). A review of the efficacy and safety of oral antidiabetic drugs. Expert Opinion on Drug Safety, 12(2), 153–175. https://doi.org/10.1517/14740338.2013.752813
   PubMed Web of Science ®Google Scholar
• Tripathi, B. K., & Srivastava, A. K. (2006). Diabetes mellitus: Complications and therapeutics. Medical Science Monitor. 12(7), 130–147.
   Web of Science ®Google Scholar
• Tundis, R., Loizzo, M., & Menichini, F. (2010). Natural products as α-amylase and α-glucosidase inhibitors and their hypoglycaemic potential in the treatment of diabetes: An update. Mini Reviews in Medicinal Chemistry, 10(4), 315–331. https://doi.org/10.2174/138955710791331007
   PubMed Web of Science ®Google Scholar
• Wei-Ya, L., Yu-Qing, D., Yang-Chun, M., Xin-Hua, L., Ying, M., & Wang, R.-L. (2019). Exploring the cause of the inhibitor 4AX attaching to binding site disrupting protein tyrosine phosphatase 4A1 trimerization by molecular dynamic simulation. Journal of Biomolecular Structure & Dynamics, 37(18), 4840–4851. https://doi.org/10.1080/07391102.2019.1567392
   PubMed Web of Science ®Google Scholar
• Wilcox, G. (2005). Insulin and insulin resistance. Clinical Biochemist Reviews, 26(2), 19.
   PubMedGoogle Scholar
• Wu, P.-P., Zhang, B.-J., Cui, X.-P., Yang, Y., Jiang, Z.-Y., Zhou, Z.-H., Zhong, Y.-Y., Mai, Y.-Y., Ouyang, Z., Chen, H.-S., Zheng, J., Zhao, S.-Q., & Zhang, K. (2017). Synthesis and biological evaluation of novel ursolic acid analogues as potential α-glucosidase inhibitors. Scientific Reports, 7(1), 45578. https://doi.org/10.1038/srep45578
   PubMedGoogle Scholar
• Zimmet, P., Alberti, K., & Shaw, J. (2001). Global and societal implications of the diabetes epidemic. Nature, 414(6865), 782–787. https://doi.org/10.1038/414782a
   PubMed Web of Science ®Google Scholar
• Zwanzig, R. (1973). Nonlinear generalized Langevin equations. Journal of Statistical Physics, 9(3), 215–220. https://doi.org/10.1007/BF01008729
   Google Scholar