760
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Synthesis, antimicrobial activity, molecular docking, molecular dynamics simulation, and ADMET properties of the mannopyranoside derivatives as antimicrobial agents

, , , & ORCID Icon
Article: 2327101 | Received 30 Dec 2023, Accepted 03 Mar 2024, Published online: 13 Mar 2024

References

  • Naika HR, Lingaraju K, Chandramohan V, et al. Evaluation of phytoconstituents and molecular docking against NS3 protease of hepatitis C virus. J Pharm Sci Pharmacol. 2016;2:96–103. doi:10.1166/jpsp.2015.1057
  • Choo QL, Kuo G, Weiner AJ, et al. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science. 1989;244:359–362. doi:10.1126/science.2523562
  • Bisceglie AD. Hepatitis C–related hepatocellular carcinoma in the United States: influence of ethnic status. Am J Gastroenterol. 2003;98:2060–2063. doi:10.1111/j.1572-0241.2003.t01-1-07641.x
  • Pately PD, Pately MR, Kaushik-Basu N, et al. 3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors. J Chem Inf Model. 2008;48:42–55. doi:10.1021/ci700266z
  • Sears P, Wong CH. Intervention of carbohydrate recognition by proteins and nucleic acids. Proc Natl Acad Sci. USA. 1996;93:12086–12093. doi:10.1073/pnas.93.22.12086
  • Seeberger PH, Werz DB. Synthesis and medical applications of oligosaccharides. Nature. 2007;446:1046–1051. doi:10.1038/nature05819
  • Chen S, Fukuda M. Cell type-specific roles of carbohydrates in tumor metastasis. Meth Enzymol. 2006;416:371–380. doi:10.1016/S0076-6879(06)16024-3
  • Kawsar SMA, Hosen MA, El Bakri Y, et al. In silico approach for potential antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetic and bioactivity predictions of galactopyranoside derivatives. Arab J Basic Appl Sci. 2022;29:99–112. doi:10.1080/25765299.2022.2068275
  • Qais FA, Khan MS, Ahmad I, et al. Plumbagin inhibits quorum sensing-regulated virulence and biofilms of gram-negative bacteria: in vitro and in silico investigations. Biofouling. 2021;37:724–739. doi:10.1080/08927014.2021.1955250
  • Kabir AKMS, Kawsar SMA, Bhuiyan MMR, et al. Antimicrobial screening studies of some derivatives of methyl α-D-glucopyranoside. Pakistan J Sci Ind Res. 2009;52:138–142.
  • Kawsar SMA, Hamida AA, Sheikh AU, et al. Chemically modified uridine molecules incorporating acyl residues to enhance antibacterial and cytotoxic activities. Int J Org Chem. 2015;5:232–245. doi:10.4236/ijoc.2015.54023
  • Hosen MA, Alam A, Islam M, et al. Geometrical optimization, PASS prediction, molecular docking, and in silico ADMET studies of thymidine derivatives against FimH adhesin of escherichia coli. Bulg Chem Commun. 2021;53:327–342.
  • Varki A. Biological roles of oligosaccharides: all of the theories are correct. Glycobiology. 1993;3:97–130. doi:10.1093/glycob/3.2.97
  • Chtita S, Larif M, Ghamali M, et al. Quantitative structure–activity relationship studies of dibenzo [a,d] cycloalkenimine derivatives for non-competitive antagonists of N-methyl-D-aspartate based on density functional theory with electronic and topological descriptors. J Taibah Univ Sci. 2015;9:143–154. doi:10.1016/j.jtusci.2014.10.006
  • Ghamali M, Chtita S, Aouidate A, et al. Combining DFT and QSAR computation to predict the interaction of flavonoids with the GABA (A) receptor using electronic and topological descriptors. J Taibah Univ Sci. 2017;11:422–433. doi:10.1016/j.jtusci.2016.06.005
  • Tabti K, Sbai A, Maghat H, et al. Computational assessment of the reactivity and pharmaceutical potential of novel triazole derivatives: an approach combining DFT calculations, molecular dynamics simulations, and molecular docking. Arabian J Chem. 2024;17:105376, doi:10.1016/j.arabjc.2023.105376
  • Nour H, Daoui O, Abchir O, et al. Combined computational approaches for developing new anti-Alzheimer drug candidates: 3D-QSAR, molecular docking and molecular dynamics studies of liquiritigenin derivatives. Heliyon. 2022;8:e11991, doi:10.1016/j.heliyon.2022.e11991
  • Abdessadak O, Alaqarbeh M, Zaki H, et al. Computational approaches to discover a kaempferol derivative extracted from senna alexandrina as escherichia coli enzyme (MurF) inhibitor by molecular docking, molecular dynamics simulation, and ADME-Tox. Struct Chem. 2023;34:1173–1187. doi:10.1007/s11224-022-02068-x
  • Chtita S, Hmamouchi R, Larif M, et al. QSPR studies of 9-aniliioacridine derivatives for their DNA drug binding properties based on density functional theory using statistical methods: model, validation and influencing factors. J Taibah Univ Sci. 2016;10:868–876. doi:10.1016/j.jtusci.2015.04.007
  • Belhassan A, Chtita S, Lakhlifi T, et al. QSPR study of the retention/release property of odorant molecules in pectin gels using statistical methods. J Taibah Univ Sci. 2017;11:1030–1046. doi:10.1016/j.jtusci.2017.05.004
  • Nour H, Abchir O, Belaidi S, et al. 2D-QSAR and molecular docking studies of carbamate derivatives to discover novel potent anti-butyrylcholinesterase agents for Alzheimer’s disease treatment. Bull Korean Chem Soc. 2022;43:277–292. doi:10.1002/bkcs.12449
  • Dearden JC. The history and development of quantitative structure-activity relationships (QSARs). Int J Quant Struct Relation. 2017;2:36–46. doi:10.4018/IJQSPR.2016010101
  • Chtita S, Belhassan A, Bakhouch M, et al. QSAR study of unsymmetrical aromatic disulfides as potent avian SARS-CoV main protease inhibitors using quantum chemical descriptors and statistical methods. Chemometr Intell Lab Sys. 2021;210:104266, doi:10.1016/j.chemolab.2021.104266
  • Nour H, Hashmi MA, Belaidi S, et al. Design of acetylcholinesterase inhibitors as promising anti-Alzheimer’s agents based on QSAR, molecular docking, and molecular dynamics studies of liquiritigenin derivatives. ChemistrySelect. 2023;8:e202301466, doi:10.1002/slct.202301466
  • Abchir O, Daoui O, Nour H, et al. Exploration of cannabis constituents as potential candidates against diabetes mellitus disease using molecular docking, dynamics simulations and ADMET investigations. Sci Afr. 2023;21:e01745, doi:10.1016/j.sciaf.2023.e01745
  • Hassan SA, Aziz DM, Abdullah MN, et al. In vitro and in vivo evaluation of the antimicrobial, antioxidant, cytotoxic, hemolytic activities and in silicoPOM/DFT/DNA-binding and pharmacokinetic analyses of new sulfonamide bearing thiazolidin-4-ones. J Biomol Struct Dyn. 2023: 1–17. doi:10.1080/07391102.2023.2226713
  • Bhat AR, Dongre RS, Almalki FA, et al. Synthesis, Biological activity and POM/DFT/docking analyses of annulated pyrano[2,3-d]pyrimidine derivatives: identification of antibacterial and antitumor pharmacophore sites. Bioorg Chem. 2021;106:104480, doi:10.1016/j.bioorg.2020.104480
  • Nour H, Abdou A, Belaidi S, et al. Discovery of promising cholinesterase inhibitors for Alzheimer’s disease treatment through DFT, docking, and molecular dynamics studies of eugenol derivatives. J Chinese Chem Soc. 2022;69:1534–1551. doi:10.1002/jccs.202200195
  • Rana KM, Maowa J, Alam A, et al. In silico DFT study, molecular docking, and ADMET predictions of cytidine analogs with antimicrobial and anticancer properties. In Silico Pharmacol. 2021;9:42, doi:10.1007/s40203-021-00102-0
  • Ahmed S, Bhat AR, Rahiman AK, et al. Green synthesis, antibacterial and antifungal evaluation of new thiazolidine-2,4-dione derivatives: molecular dynamic simulation, POM study and identification of antitumor pharmacophore sites. J Biomol Struct Dyn. 2023: 1–17. doi:10.1080/07391102.2023.2258404
  • Bauer AW, Kirby WMM, Sherris JC. Antibiotic susceptibility testing by a standardized single disc method. Am J Clin Pathol. 1966;45:439–476. doi:10.1093/ajcp/45.4_ts.493
  • Clinical Laboratory Standards Institute (CLSI). Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically; Approved Standard-Ninth Edition. Wayne (PA): Clinical and Laboratory Standards Institute. CLSI Documents M07-A9; 2012.
  • Grover RK, Moore JD. In-vitro efficacy of certain essential oils and plant extracts against three major pathogens of jatropha curcas L. Phytopathology. 1962;52:876–879.
  • Kawsar SMA, Huq E, Nahar N. Cytotoxicity assessment of the aerial parts of macrotyloma uniflorum linn. Int J Pharmacol. 2008;4:297–300. doi:10.3923/ijp.2008.297.300
  • Hunt WA. The effects of aliphatic alcohols on the biophysical and biochemical correlates of membrane function. Adv Exp Med Biol. 1975;56:195–210. doi:10.1007/978-1-4684-7529-6_9
  • Kim YM, Farrah S, Baney RH. Structure–antimicrobial activity relationship for silanols, a new class of disinfectants, compared with alcohols and phenols. Int J Antimicrob Agents. 2007;29:217–222. doi:10.1016/j.ijantimicag.2006.08.036
  • Mourik T, Bühl M, Marie-Pierre G. Density functional theory across chemistry, physics and biology. Philos Trans A Math Phys Eng Sci. 2011;372:20120488, doi:10.1098/rsta.2012.0488
  • Gaussian RA, Frisch MJ, Trucks GW, et al. Gaussian, Inc, Wallingford CT. 2009.
  • Lee C, Yang W, Parr RG. Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Phys Rev B. 1988;37:785–789. doi:10.1103/PhysRevB.37.785
  • Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A. 1988;38:3098–3100. doi:10.1103/PhysRevA.38.3098
  • Hadni H, Elhallaoui M. 2D and 3D-QSAR, molecular docking and ADMET properties in silico studies of azaaurones as antimalarial agents. New J Chem. 2020;44:6553–6565. doi:10.1039/C9NJ05767F
  • Yakovenko O, Sharma S, Forero M. Fimh forms catch bonds that are enhanced by mechanical force due to allosteric regulation. J Biol Chem. 2008;283:11596, doi:10.1074/jbc.M707815200
  • Abchir O, Yamari I, Nour H, et al. Structure-based virtual screening, ADMET analysis, and molecular dynamics simulation of Moroccan natural compounds as candidates α-amylase inhibitors. ChemistrySelect. 2023;8:e202301092, doi:10.1002/slct.202301092
  • Trott O, Olson AJ. Autodock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31:455–461. doi:10.1002/jcc.21334
  • Onodera K, Satou K, Hirota H. Evaluations of molecular docking programs for virtual screening. J Chem Inf Model. 2007;47:1609–1618. doi:10.1021/ci7000378
  • Hadni H, Elhallaoui M. 3D-QSAR, docking and ADMET properties of aurone analogues as antimalarial agents. Heliyon. 2020;6:e03580, doi:10.1016/j.heliyon.2020.e03580
  • Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem. 2005;26:1781–1802. doi:10.1002/jcc.20289
  • Jo S, Kim T, Iyer VG, et al. Charmm-Gui: a web-based graphical user interface for Charmm. J Comput Chem. 2008;29:1859–1865. doi:10.1002/jcc.20945
  • Im W, Seefeld S, Roux B. A grand canonical monte carlo–Brownian dynamics algorithm for simulating ion channels. Biophys J. 2000;79:788–801. doi:10.1016/S0006-3495(00)76336-3
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–38. doi:10.1016/0263-7855(96)00018-5
  • En-nahli F, Baammi S, Hajji H, et al. High-throughput virtual screening approach of natural compounds as target inhibitors of plasmepsin-II. J Biomol Struct Dyn. 2022: 1–11. doi:10.1080/07391102.2022.2152871
  • Pires DEV, Blundell TL, Ascher DB. pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem.
  • Farhana Y, Amin MR, Hosen A, et al. Bromobenzoylation of methyl α-D-mannopyranoside: synthesis and spectral characterization. J Sib Fed Univ Chem. 2021;14:171–183. doi:10.17516/1998-2836-0226
  • Islam S, Hosen MA, Ahmad S, et al. Synthesis, antimicrobial, anticancer activities, PASS prediction, molecular docking, molecular dynamics and pharmacokinetic studies of designed methyl α-D-glucopyranoside esters. J Mol Struct. 2022;1260:132761, doi:10.1016/j.molstruc.2022.132761
  • Tamokou JDD, Kuiate JR, Tene M, et al. The antimicrobial activities of extract and compounds isolated from brillantaisia lamium. Iran J Med Sci. 2011;36:24–31.
  • Maowa J, Alam A, Rana KM, et al. Synthesis, characterization, synergistic antimicrobial properties and molecular docking of sugar modified uridine derivatives. Ovidius Univ Ann Chem. 2021;32:6–21. doi:10.2478/auoc-2021-0002
  • Matsumoto R, Fujii Y, Kawsar SMA, et al. Cytotoxicity and glycan-binding properties of an 18 kDa lectin isolated from the marine sponge halichondria okada. Toxins (Basel). 2012;4:323–338.
  • Sribalan R, Banuppriya G, Kirubavathi M. Synthesis, biological evaluation and in silico studies of tetrazole-heterocycle hybrids. J Mol Struct. 2019;1175:577–586.
  • Li WR, Xie XB, Shi QS, et al. Antibacterial activity and mechanism of silver nanoparticles on escherichia coli. Appl Microbiol Biotechnol. 2010;85:1115–1122. doi:10.1007/s00253-009-2159-5
  • Judge V, Narasimhan B, Ahuja M, et al. Synthesis, antimycobacterial, antiviral, antimicrobial activity and QSAR studies of N(2)-acyl isonicotinic acid hydrazide derivatives. Med Chem. 2013;9:53–76. doi:10.2174/157340613804488404
  • Marinescu M, Emandi A, Marton G, et al. Structural studies and optical nonlinear response of some pyrazole-5-ones. Nanosci Nanotechnol Lett. 2015;7:846–854. doi:10.1166/nnl.2015.2032
  • Parr RG, Donnelly RA, Levy M, et al. Electronegativity: the density functional viewpoint. J Chem Phys. 1978;68:3801–3807. doi:10.1063/1.436185
  • Aihara J. Reduced HOMO−LUMO gap as an index of kinetic stability for polycyclic aromatic hydrocarbons. J Phys Chem A. 1999;103:7487–7495. doi:10.1021/jp990092i
  • Khedraoui M, Nour H, Yamari I, et al. Design of a new potent Alzheimer’s disease inhibitor based on QSAR, molecular docking and molecular dynamics investigations. Chem Phys Impact. 2023;7:100361, doi:10.1016/j.chphi.2023.100361
  • Hadni H, Fitri A, Benjelloun AT, et al. Identification of terpenoids as potential inhibitors of SARS-CoV-2 (main protease) and spike (RBD) via computer-aided drug design. J Biomol Struct Dyn. 2023: 1–14. doi:10.1080/07391102.2023.2245051
  • Hasan AH, Shakya S, Hussain FHS, et al. Design, synthesis, anti-ecetylcholinesterase evaluation and molecular modelling studies of novel coumarin-chalcone hybrids. J Biomol Struct Dyn. 2023;41:11450–11462. doi:10.1080/07391102.2022.2162583
  • Hussen NH, Hasan AH, Jamalis J, et al. Potential inhibitory activity of phytoconstituents against black fungus: in silico ADMET, molecular docking and MD simulation studies. Comput Toxicol. 2022;100247; doi:10.1016/j.comtox.2022.100247
  • Kawsar SMA, Kumer A, Munia NS, et al. Chemical descriptors, PASS, molecular docking, molecular dynamics and ADMET predictions of glucopyranoside derivatives as inhibitors to bacteria and fungi growth. Org Commun. 2022;15:184–203. doi:10.25135/acg.oc.122.2203.2397
  • Amin MR, Yasmin F, Dey S, et al. Methyl β-D-galactopyranoside esters as potential inhibitors for SARS-CoV-2 protease enzyme: synthesis, antimicrobial, PASS, molecular docking, molecular dynamics simulations and quantum computations. Glycoconjugate J. 2021;39:261–290. doi:10.1007/s10719-021-10039-3
  • Hasan AH, Yusof FSM, Kamarudin NA, et al. Synthesis, anti-ecetylcholinesterase evaluation, molecular docking and molecular dynamics simulation of novel psoralen derivatives. Curr Org Synth. 2023; doi:10.2174/1570179420666230328121554
  • Devasia J, Chinnam S, Khatana K, et al. Synthesis, DFT and in silico anti-COVID evaluation of novel tetrazole analogues. Polycyclic Arom Comp. 2023;43:1941–1956. doi:10.1080/10406638.2022.2036778
  • Yamari I, Mouhib A, Es-Sounni B, et al. Oxidative functionalization of triterpenes isolated from euphorbia resinifera latex: semisynthesis, ADME-Tox, molecular docking, and molecular dynamics simulations. Chem Phys Impact. 2023;7:100372, doi:10.1016/j.chphi.2023.100372