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Research Articles

Targeting α-amylase enzyme through multi-fold structure-based virtual screening and molecular dynamic simulation

, , , , , & ORCID Icon show all
Pages 5617-5630 | Received 12 May 2023, Accepted 14 Jun 2023, Published online: 28 Jun 2023

References

  • Abadan, S., Saglam, M. F., Koca, M. S., Bingul, M., Sahin, H., Zorlu, Y., & Sengul, I. F. (2023). Synthesis and molecular modeling studies of naphthazarin derivatives as novel selective inhibitors of α-glucosidase and α-amylase. Journal of Molecular Structure, 1278, 134954. https://doi.org/10.1016/j.molstruc.2023.134954
  • Akshatha, J. V., SantoshKumar, H. S., Prakash, H. S., & Nalini, M. S. (2021). In silico docking studies of α-amylase inhibitors from the anti-diabetic plant Leucas ciliata Benth. and an endophyte, Streptomyces longisporoflavus. 3 Biotech, 11(2), 1–16. https://doi.org/10.1007/s13205-020-02547-0
  • Alagesan, K., Raghupathi, P. K., & Sankarnarayanan, S. (2012). Amylase inhibitors: Potential source of anti-diabetic drug discovery from medicinal plants. International Journal of Pharmacy and Life Sciences, 3(2), 1407–1412.
  • Al-Asri, J., Fazekas, E., Lehoczki, G., Perdih, A., Gorick, C., Melzig, M. F., Gyemant, G., Wolber, G., & Mortier, J. (2015). From carbohydrates to drug-like fragments: Rational development of novel alpha-amylase inhibitors. Bioorganic & Medicinal Chemistry, 23(20), 6725–6732. https://doi.org/10.1016/j.bmc.2015.09.007
  • Ali, S., Ali, M., Khan, A., Ullah, S., Waqas, M., Al-Harrasi, A., Latif, A., Ahmad, M., & Saadiq, M. (2022). Novel 5-(arylideneamino)-1 H-benzo [d] imidazole-2-thiols as potent anti-diabetic agents: synthesis, in vitro α-glucosidase inhibition, and molecular docking studies. ACS Omega, 7(48), 43468–43479. https://doi.org/10.1021/acsomega.2c03854
  • Avula, S. K., Ullah, S., Halim, S. A., Khan, A., Anwar, M. U., Csuk, R., & Al-Harrasi, A. (2023). Synthesis of novel substituted quinoline derivatives as diabetics II inhibitors and along with their in-silico studies. Journal of Molecular Structure, 1274, 134560. https://doi.org/10.1016/j.molstruc.2022.134560
  • B.O. Community. (2018). Blender - a 3D modelling and rendering package.
  • Basnet, S., Ghimire, M. P., Lamichhane, T. R., Adhikari, R., & Adhikari, A. (2023). Identification of potential human pancreatic α-amylase inhibitors from natural products by molecular docking, MM/GBSA calculations, MD simulations, and ADMET analysis. Plos One, 18(3), e0275765. https://doi.org/10.1371/journal.pone.0275765
  • Brayer, G. D., Luo, Y., & Withers, S. G. (1995). The structure of human pancreatic α‐amylase at 1.8 Å resolution and comparisons with related enzymes. Protein Science: A Publication of the Protein Society, 4(9), 1730–1742. https://doi.org/10.1002/pro.5560040908
  • Brayer, G. D., Sidhu, G., Maurus, R., Rydberg, E. H., Braun, C., Wang, Y., Nguyen, N. T., Overall, C. M., & Withers, S. G. (2000). Subsite mapping of the human pancreatic α-amylase active site through structural, kinetic, and mutagenesis techniques. Biochemistry, 39(16), 4778–4791. https://doi.org/10.1021/bi9921182
  • Case, D. A., Belfon, K., Ben-Shalom, I. Y., Berryman, J. T., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., III, Cisneros, G. A., Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Giambasu, G., Gilson, M. K., Gohlke, H., Goetz, A. W., Harris, R., Izadi, S., Izmailov, S. A., Kasavajhala, K., Kaymak, M. C., King, E., Kovalenko, A., Kurtzman, T., Lee, T. S., LeGrand, S., Li, P., Lin, C., Liu, J., Luchko, T., Luo, R., Machado, M., Man, V., Manathunga, M., Merz, K. M., Miao, Y., Mikhailovskii, O., Monard, G., Nguyen, H., O'Hearn, K. A., Onufriev, A., Pan, F., Pantano, S., Qi, R., Rahnamoun, A., Roe, D. R., Roitberg, A., Sagui, C., Schott-Verdugo, S., Shajan, A., Shen, J., Simmerling, C. L., Skrynnikov, N. R., Smith, J., Swails, J., Walker, R. C., Wang, J., Wang, J., Wei, H., Wolf, R. M., Xiong, Y., Xue, Y., York, D. M., Zhao, S., … Kollman, P. A. (2022). Amber 2022. University of California.
  • Clark, A. M., Labute, P., & Santavy, M. (2006). 2D structure depiction. Journal of Chemical Information and Modeling, 46(3), 1107–1123. https://doi.org/10.1021/ci050550m
  • de Souza, P. M., & de Oliveira Magalhaes, P. (2010). Application of microbial alpha-amylase in industry - A review. Brazilian Journal of Microbiology : [Publication of the Brazilian Society for Microbiology], 41(4), 850–861. https://doi.org/10.1590/S1517-83822010000400004
  • Dhital, S., Warren, F. J., Butterworth, P. J., Ellis, P. R., & Gidley, M. J. (2017). Mechanisms of starch digestion by alpha-amylase-structural basis for kinetic properties. Critical Reviews in Food Science and Nutrition, 57(5), 875–892. https://doi.org/10.1080/10408398.2014.922043
  • Gerber, P. R., & Muller, K. (1995). MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. Journal of Computer-Aided Molecular Design, 9(3), 251–268. https://doi.org/10.1007/BF00124456
  • Gregory, G. A., Robinson, T. I. G., Linklater, S. E., Wang, F., Colagiuri, S., de Beaufort, C., Donaghue, K. C., International Diabetes Federation Diabetes Atlas Type, G., Diabetes, 1., Adults Special Interest, i., Magliano, D. J., Maniam, J., Orchard, T. J., Rai, P., & Ogle, G. D. (2022). Global incidence, prevalence, and mortality of type 1 diabetes in 2021 with projection to 2040: A modelling study. The Lancet. Diabetes & Endocrinology, 10(10), 741–760. https://doi.org/10.1016/S2213-8587(22)00218-2
  • Gumucio, D. L., Wiebauer, K., Caldwell, R. M., Samuelson, L. C., & Meisler, M. H. (1988). Concerted evolution of human amylase genes. Molecular and Cellular Biology, 8(3), 1197–1205. https://doi.org/10.1128/MCB.8.3.1197
  • Halim, S. A., Jabeen, S., Khan, A., & Al-Harrasi, A. (2021). Rational design of novel inhibitors of alpha-glucosidase: An application of quantitative structure activity relationship and structure-based virtual screening. Pharmaceuticals (Basel), 14(5), 482. https://doi.org/10.3390/ph14050482
  • Homoki, J. R., Nemes, A., Fazekas, E., Gyemant, G., Balogh, P., Gal, F., Al-Asri, J., Mortier, J., Wolber, G., Babinszky, L., & Remenyik, J. (2016). Anthocyanin composition, antioxidant efficiency, and alpha-amylase inhibitor activity of different Hungarian sour cherry varieties (Prunus cerasus L.). Food Chemistry, 194, 222–229. https://doi.org/10.1016/j.foodchem.2015.07.130
  • Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. https://doi.org/10.1021/ci100275a
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Jakalian, A., Bush, B. L., Jack, D. B., & Bayly, C. I. (2000). Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method. Journal of Computational Chemistry, 21(2), 132–146. https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
  • Khan, A., Waqas, M., Khan, M., Halim, S. A., Rehman, N. U., & Al-Harrasi, A. (2022). Identification of novel prolyl oligopeptidase inhibitors from resin of Boswellia papyrifera (Del.) Hochst. and their mechanism: Virtual and biochemical studies. International Journal of Biological Macromolecules, 213, 751–767. https://doi.org/10.1016/j.ijbiomac.2022.06.001
  • Khan, S., Iqbal, S., Rahim, F., Shah, M., Hussain, R., Alrbyawi, H., Rehman, W., Dera, A. A., Rasheed, L., Somaily, H. H., Pashameah, R. A., Alzahrani, E., & Farouk, A.-E. (2022). New biologically hybrid pharmacophore thiazolidinone-based indole derivatives: synthesis, in vitro alpha-amylase and alpha-glucosidase along with molecular docking investigations. Molecules, 27(19), 6564. https://doi.org/10.3390/molecules27196564
  • Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. 3rd https://doi.org/10.1021/ar000033j
  • Kräutler, V., van Gunsteren, W. F., & Hünenberger, P. H. (2001). A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. Journal of Computational Chemistry, 22(5), 501–508. https://doi.org/10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V
  • Li, C., Begum, A., Numao, S., Park, K. H., Withers, S. G., & Brayer, G. D. (2005). Acarbose rearrangement mechanism implied by the kinetic and structural analysis of human pancreatic α-amylase in complex with analogues and their elongated counterparts. Biochemistry, 44(9), 3347–3357. https://doi.org/10.1021/bi048334e
  • Li, W. L., Zheng, H. C., Bukuru, J., & De Kimpe, N. (2004). Natural medicines used in the traditional Chinese medical system for therapy of diabetes mellitus. Journal of Ethnopharmacology, 92(1), 1–21. https://doi.org/10.1016/j.jep.2003.12.031
  • Lovic, D., Piperidou, A., Zografou, I., Grassos, H., Pittaras, A., & Manolis, A. (2020). The growing epidemic of diabetes mellitus. Current Vascular Pharmacology, 18(2), 104–109. https://doi.org/10.2174/1570161117666190405165911
  • Madeswaran, A., Asokkumar, K., Umamaheswari, M., Sivashanmugam, T., Subhadradevi, V., & Jagannath, P. (2014). Computational drug design of potential α-amylase inhibitors using some commercially available flavonoids. Bangladesh Journal of Pharmacology, 9(1), 72–76. ǁ| https://doi.org/10.3329/bjp.v9i1.17502
  • Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
  • Maurus, R., Begum, A., Williams, L. K., Fredriksen, J. R., Zhang, R., Withers, S. G., & Brayer, G. D. (2008). Alternative catalytic anions differentially modulate human alpha-amylase activity and specificity. Biochemistry, 47(11), 3332–3344. https://doi.org/10.1021/bi701652t
  • Molecular Operating Environment (MOE). (2022). Computational Chemistry group.
  • Najafian, M., Ebrahim-Habibi, A., Hezareh, N., Yaghmaei, P., Parivar, K., & Larijani, B. (2011). Trans-chalcone: A novel small molecule inhibitor of mammalian alpha-amylase. Molecular Biology Reports, 38(3), 1617–1620. https://doi.org/10.1007/s11033-010-0271-3
  • Nguyen, T. H., Wang, S. L., Nguyen, A. D., Doan, M. D., Tran, T. N., Doan, C. T., & Nguyen, V. B. (2022). Novel alpha-amylase inhibitor hemi-pyocyanin produced by microbial conversion of chitinous discards. Mar Drugs, 20(5), 283. https://doi.org/10.3390/md20050283
  • Nikitkova, A. E., Haase, E. M., & Scannapieco, F. A. (2013). Taking the starch out of oral biofilm formation: Molecular basis and functional significance of salivary alpha-amylase binding to oral streptococci. Applied and Environmental Microbiology, 79(2), 416–423. https://doi.org/10.1128/AEM.02581-12
  • Oellien, F., Cramer, J., Beyer, C., Ihlenfeldt, W.-D., & Selzer, P. M. (2006). The impact of tautomer forms on pharmacophore-based virtual screening. Journal of Chemical Information and Modeling, 46(6), 2342–2354. https://doi.org/10.1021/ci060109b
  • Onufriev, A., Bashford, D., & Case, D. A. (2004). Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins, 55(2), 383–394. https://doi.org/10.1002/prot.20033
  • OriginLab-Corporation. (2021). Origin(Pro).
  • 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
  • Press, W. H., Flannery, B. P., Teukolsky, S. A., Vetterling, W. T., & Kramer, P. B. (1987). Numerical recipes: The art of scientific computing. Physics Today, 40(10), 120–122. https://doi.org/10.1063/1.2820230
  • Proenca, C., Rufino, A. T., Ferreira de Oliveira, J. M. P., Freitas, M., Fernandes, P. A., Silva, A. M. S., & Fernandes, E. (2022). Inhibitory activity of flavonoids against human sucrase-isomaltase (alpha-glucosidase) activity in a Caco-2/TC7 cellular model. Food & Function, 13(3), 1108–1118. https://doi.org/10.1039/d1fo02995a
  • Ramasubbu, N., Paloth, V., Luo, Y., Brayer, G. D., & Levine, M. J. (1996). Structure of human salivary α-amylase at 1.6 Å resolution: Implications for its role in the oral cavity. Acta Crystallographica. Section D, Biological Crystallography, 52(Pt 3), 435–446. https://doi.org/10.1107/S0907444995014119
  • Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. 3rd https://doi.org/10.1021/ct400341p
  • Salomon-Ferrer, R., Gotz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. Journal of Chemical Theory and Computation, 9(9), 3878–3888. https://doi.org/10.1021/ct400314y
  • Scheen, A. J. (2003). Is there a role for α-glucosidase inhibitors in the prevention of type 2 diabetes mellitus? Drugs, 63(10), 933–951. https://doi.org/10.2165/00003495-200363100-00002
  • Schrödinger, L. (2018). The PyMOL molecular graphics system. Version 1.8.2015.
  • Sharma, P., Mondal, K., Mondal, K. C., & Thakur, N. (2022). Hunt for alpha-amylase from metagenome and strategies to improve its thermostability: A systematic review. World Journal of Microbiology & Biotechnology, 38(11), 203. https://doi.org/10.1007/s11274-022-03396-0
  • Sindhikara, D. J., Kim, S., Voter, A. F., & Roitberg, A. E. (2009). Bad seeds sprout perilous dynamics: stochastic thermostat induced trajectory synchronization in biomolecules. Journal of Chemical Theory and Computation, 5(6), 1624–1631. https://doi.org/10.1021/ct800573m
  • Tian, C., Kasavajhala, K., Belfon, K. A. A., Raguette, L., Huang, H., Migues, A. N., Bickel, J., Wang, Y., Pincay, J., Wu, Q., & Simmerling, C. (2020). ff19SB: Amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. Journal of Chemical Theory and Computation, 16(1), 528–552. https://doi.org/10.1021/acs.jctc.9b00591
  • van der Maarel, M. J., van der Veen, B., Uitdehaag, J. C., Leemhuis, H., & Dijkhuizen, L. (2002). Properties and applications of starch-converting enzymes of the alpha-amylase family. Journal of Biotechnology, 94(2), 137–155. https://doi.org/10.1016/s0168-1656(01)00407-2
  • Vassetti, D., Pagliai, M., & Procacci, P. (2019). Assessment of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE, and OPC3 for the solvation free energy of druglike organic molecules. Journal of Chemical Theory and Computation, 15(3), 1983–1995. https://doi.org/10.1021/acs.jctc.8b01039
  • Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2001). Antechamber: an accessory software package for molecular mechanical calculations. Journal of the American Chemical Society, 222, U403.
  • Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20(2), 217–230. https://doi.org/10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
  • Wen, J., Scoles, D. R., & Facelli, J. C. (2017). Molecular dynamics analysis of the aggregation propensity of polyglutamine segments. PLoS One, 12(5), e0178333. https://doi.org/10.1371/journal.pone.0178333
  • Yang, T., Wu, J. C., Yan, C., Wang, Y., Luo, R., Gonzales, M. B., Dalby, K. N., & Ren, P. (2011). Virtual screening using molecular simulations. Proteins, 79(6), 1940–1951. https://doi.org/10.1002/prot.23018
  • Zhang, J., Ding, W., Tang, Z., Kong, Y., Liu, J., & Cao, X. (2022). Identification of the effective α-amylase inhibitors from Dalbergia odorifera: Virtual screening, spectroscopy, molecular docking, and molecular dynamic simulation. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 280, 121448. https://doi.org/10.1016/j.saa.2022.121448

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