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Research Articles

Quantum mechanical, virtual screening, molecular docking, molecular dynamics, ADME and antimicrobial activity studies of some new indole-hydrazone derivatives as potent agents against E. faecalis

, , , , &
Pages 8112-8126 | Received 01 Jul 2021, Accepted 10 Sep 2021, Published online: 18 Oct 2021

References

  • 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
  • Ahmad, A., Ahmad, A., Sudhakar, R., Varshney, H., Subbarao, N., Ansari, S., Rauf, A., & Khan, A. U. (2017). Designing, synthesis, and antimicrobial action of oxazoline and thiazoline derivatives of fatty acid esters. Journal of Biomolecular Structure & Dynamics, 35(15), 3412–3431. https://doi.org/10.1080/07391102.2016.1255260
  • Ahmad, A., Ahmad, A., Varshney, H., Rauf, A., Rehan, M., Subbarao, N., & Khan, A. U. (2013). Designing and synthesis of novel antimicrobial heterocyclic analogs of fatty acids. European Journal of Medicinal Chemistry, 70, 887–900. https://doi.org/10.1016/j.ejmech.2013.10.051
  • Alam, M. S., Jebin, S., Rahman, M. M., Bari, M. L., & Lee, D.-U. (2016). Biological and quantitative-SAR evaluations, and docking studies of (E)-N-benzylidenebenzohydrazide analogues as potential antibacterial agents. EXCLI Journal, 15, 350.
  • Alonso, H., Bliznyuk, A. A., & Gready, J. E. (2006). Combining docking and molecular dynamic simulations in drug design. Medicinal Research Reviews, 26(5), 531–568. https://doi.org/10.1002/med.20067
  • Amine Khodja, I., Boulebd, H., Bensouici, C., & Belfaitah, A. (2020). Design, synthesis, biological evaluation, molecular docking, DFT calculations and in silico ADME analysis of (benz) imidazole-hydrazone derivatives as promising antioxidant, antifungal, and anti-acetylcholinesterase agents. Journal of Molecular Structure, 1218, 128527. https://doi.org/10.1016/j.molstruc.2020.128527
  • Bekker, H., Berendsen, H., Dijkstra, E., Achterop, S., Vondrumen, R., Vanderspoel, D., Sijbers, A., Keegstra, H., & Renardus, M. (1993). Gromacs – A parallel computer for molecular-dynamics simulations. In 4th International Conference on Computational Physics (PC 92) (pp 252–256). World Scientific Publishing.
  • Blair, J. M., Webber, M. A., Baylay, A. J., Ogbolu, D. O., & Piddock, L. J. (2015). Molecular mechanisms of antibiotic resistance. Nature Reviews: Microbiology, 13(1), 42–51. https://doi.org/10.1038/nrmicro3380
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
  • Celı K, I., Onay-Besı Kcı, A., & Ayhan-Kilcigı L, G. (2021). Approach to the mechanism of action of hydroxychloroquine on SARS-CoV-2: A molecular docking study. Journal of Biomolecular Structure & Dynamics, 39(15), 5792–5797. https://doi.org/10.1080/07391102.2020.1792993
  • Celik, I., Erol, M., Temiz Arpaci, O., Sezer Senol, F., & Erdogan Orhan, I. (2020). Evaluation of activity of some 2, 5-disubstituted benzoxazole derivatives against acetylcholinesterase, butyrylcholinesterase and tyrosinase: ADME prediction, DFT and comparative molecular docking studies. Polycyclic Aromatic Compounds, 1–12. https://doi.org/10.1080/10406638.2020.1737827
  • Cihan-Üstündağ, G., Naesens, L., Şatana, D., Erköse-Genç, G., Mataracı-Kara, E., & Çapan, G. (2019). Design, synthesis, antitubercular and antiviral properties of new spirocyclic indole derivatives. Monatshefte Fur Chemie, 150(8), 1533–1544. https://doi.org/10.1007/s00706-019-02457-9
  • Clinical Institute LS (2017). Performance standards for antimicrobial susceptibility testing (Trans Reprinted). Clinical and Laboratory Standards Institute Wayne.
  • Demurtas, M., Baldisserotto, A., Lampronti, I., Moi, D., Balboni, G., Pacifico, S., Vertuani, S., Manfredini, S., & Onnis, V. (2019). Indole derivatives as multifunctional drugs: Synthesis and evaluation of antioxidant, photoprotective and antiproliferative activity of indole hydrazones. Bioorganic Chemistry, 85, 568–576. https://doi.org/10.1016/j.bioorg.2019.02.007
  • Dennington, R., Keith, T., Millam, J., Eppinnett, K., Hovell, W. L., & Gilliland, R. (2003). GaussView, Version 3.09 (Vol. 2003(2.6), p. 1). Semichem. Inc.
  • El-Sharief, A. M. S., Ammar, Y. A., Belal, A., El-Sharief, M. A. S., Mohamed, Y. A., Mehany, A. B., Ali, G. A. E., & Ragab, A. (2019). Design, synthesis, molecular docking and biological activity evaluation of some novel indole derivatives as potent anticancer active agents and apoptosis inducers. Bioorganic Chemistry, 85, 399–412. https://doi.org/10.1016/j.bioorg.2019.01.016
  • Erol, M., Celik, I., Temiz-Arpaci, O., Kaynak-Onurdag, F., & Okten, S. (2021). Design, synthesis, molecular docking, density functional theory and antimicrobial studies of some novel benzoxazole derivatives as structural bioisosteres of nucleotides. Journal of Biomolecular Structure & Dynamics, 39(9), 3012–3080. https://doi.org/10.1080/07391102.2020.1760134
  • Erol, M., Celik, I., Uzunhisarcikli, E., & Kuyucuklu, G. (2020). Synthesis, molecular docking, and DFT studies of some new 2, 5-disubstituted benzoxazoles as potential antimicrobial and cytotoxic agents. Polycyclic Aromatic Compounds, 1–18. https://doi.org/10.1080/10406638.2020.1802305
  • Frisch, M., Trucks, G., Schlegel, H., Scuseria, G., Robb, M., Cheeseman, J., Scalmani, G., Barone, V., Mennucci, B., & Petersson, G. (2009). Gaussian 09 (Revision A. 02) [Computer software]. Gaussian Inc.
  • Gajiwala, K. S., Margosiak, S., Lu, J., Cortez, J., Su, Y., Nie, Z., & Appelt, K. (2009). Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme. FEBS Letters, 583(17), 2939–2946. https://doi.org/10.1016/j.febslet.2009.08.001
  • Guedes, I. A., de Magalhães, C. S., & Dardenne, L. E. (2014). Receptor–ligand molecular docking. Biophysical Reviews, 6(1), 75–87. https://doi.org/10.1007/s12551-013-0130-2
  • Gurkok, G., Altanlar, N., & Suzen, S. (2009). Investigation of antimicrobial activities of indole-3-aldehyde hydrazide/hydrazone derivatives. Chemotherapy, 55(1), 15–19. https://doi.org/10.1159/000166999
  • Homeyer, N., & Gohlke, H. (2012). Free energy calculations by the molecular mechanics Poisson–Boltzmann surface area method. Molecular Informatics, 31(2), 114–122. https://doi.org/10.1002/minf.201100135
  • Huang, Y., Zhang, B., Li, J., Liu, H., Zhang, Y., Yang, Z., & Liu, W. (2019). Design, synthesis, biological evaluation and docking study of novel indole-2-amide as anti-inflammatory agents with dual inhibition of COX and 5-LOX. European Journal of Medicinal Chemistry, 180, 41–50. https://doi.org/10.1016/j.ejmech.2019.07.004
  • Jansen, K. U., Knirsch, C., & Anderson, A. S. (2018). The role of vaccines in preventing bacterial antimicrobial resistance. Nature Medicine, 24(1), 10–19. https://doi.org/10.1038/nm.4465
  • Khan, S. A., Asiri, A. M., Basisi, H. M., Asad, M., Zayed, M. E., Sharma, K., & Wani, M. Y. (2019). Synthesis and evaluation of Quinoline-3-carbonitrile derivatives as potential antibacterial agents. Bioorganic Chemistry, 88, 102968. https://doi.org/10.1016/j.bioorg.2019.102968
  • Khodja, I. A., Bensouici, C., & Boulebd, H. (2020). Combined experimental and theoretical studies of the structure-antiradical activity relationship of heterocyclic hydrazone compounds. Journal of Molecular Structure, 1221, 128858. https://doi.org/10.1016/j.molstruc.2020.128858
  • Kowalska-Krochmal, B., & Dudek-Wicher, R. (2021). The minimum inhibitory concentration of antibiotics: Methods, interpretation, clinical relevance. Pathogens, 10(2), 165. https://doi.org/10.3390/pathogens10020165
  • Kumari, R., Kumar, R., Consortium, O. S. D. D., Lynn, A., & Open Source Drug Discovery Consortium (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information & Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. https://doi.org/10.1021/jm060522a
  • Maestro, S. (2018). LLC. Schrödinger release 2018-1 (Trans Reprinted).
  • Mary, Y. S., Yalcin, G., Mary, Y. S., Resmi, K., Thomas, R., Önkol, T., Kasap, E. N., & Yildiz, I. (2020). Spectroscopic, quantum mechanical studies, ligand protein interactions and photovoltaic efficiency modeling of some bioactive benzothiazolinone acetamide analogs. Chemical Papers, 74(6), 1957–1958. https://doi.org/10.1007/s11696-019-01047-7
  • Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 . Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
  • Pagniez, F., Lebouvier, N., Na, Y. M., Ourliac-Garnier, I., Picot, C., Le Borgne, M., & Le Pape, P. (2020). Biological exploration of a novel 1,2,4-triazole-indole hybrid molecule as antifungal agent. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 398–403. https://doi.org/10.1080/14756366.2019.1705292
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
  • Peters, L., Olson, L., Khu, D. T., Linnros, S., Le, N. K., Hanberger, H., Hoang, N. T., Tran, D. M., & Larsson, M. (2019). Multiple antibiotic resistance as a risk factor for mortality and prolonged hospital stay: A cohort study among neonatal intensive care patients with hospital-acquired infections caused by gram-negative bacteria in Vietnam. PloS One, 14(5), e0215666. https://doi.org/10.1371/journal.pone.0215666
  • Puskullu, M. O., Celik, I., Erol, M., Fatullayev, H., Uzunhisarcikli, E., & Kuyucuklu, G. (2020). Antimicrobial and antiproliferative activity studies of some new quinoline-3-carbaldehyde hydrazone derivatives. Bioorganic Chemistry, 101, 104014. https://doi.org/10.1016/j.bioorg.2020.104014
  • Qin, H.-L., Liu, J., Fang, W.-Y., Ravindar, L., & Rakesh, K. (2020). Indole-based derivatives as potential antibacterial activity against methicillin-resistance Staphylococcus aureus (MRSA). European Journal of Medicinal Chemistry, 194, 112245. https://doi.org/10.1016/j.ejmech.2020.112245
  • Release (2017). 4: QikProp. S. Schrödinger, LLC.
  • Sayed, M., Kamal El-Dean, A. M., Ahmed, M., & Hassanien, R. (2018). Synthesis of some heterocyclic compounds derived from indole as antimicrobial agents. Synthetic Communications, 48(4), 413–421. https://doi.org/10.1080/00397911.2017.1403627
  • Shi, L., Ge, H.-M., Tan, S.-H., Li, H.-Q., Song, Y.-C., Zhu, H.-L., & Tan, R.-X. (2007). Synthesis and antimicrobial activities of Schiff bases derived from 5-chloro-salicylaldehyde. European Journal of Medicinal Chemistry, 42(4), 558–564. https://doi.org/10.1016/j.ejmech.2006.11.010
  • Shirinzadeh, H., Altanlar, N., Yucel, N., Ozden, S., & Suzen, S. (2011). Antimicrobial evaluation of indole-containing hydrazone derivatives. Zeitschrift Fur Naturforschung. C, Journal of Biosciences, 66(7–8), 340–344. https://doi.org/10.1515/znc-2011-7-804
  • Siddiqui, Z. N., Praveen, S., Musthafa, T. M., Ahmad, A., & Khan, A. U. (2012). Thermal solvent-free synthesis of chromonyl chalcones, pyrazolines and their in vitro antibacterial, antifungal activities. Journal of Enzyme Inhibition & Medicinal Chemistry, 27(1), 84–91. https://doi.org/10.3109/14756366.2011.577035
  • Spellberg, B., Bartlett, J. G., & Gilbert, D. N. (2013). The future of antibiotics and resistance. The New England Journal of Medicine, 368(4), 299–302. https://doi.org/10.1056/NEJMp1215093
  • Sravanthi, T., Lulu, S. S., Vino, S., Jayasri, M., Mohanapriya, A., & Manju, S. (2017). Synthesis, docking, and evaluation of novel thiazoles for potent antidiabetic activity. Medicinal Chemistry Research, 26(6), 1306–1315. https://doi.org/10.1007/s00044-017-1851-8
  • Ventola, C. L. (2015). The antibiotic resistance crisis: Part 1: Causes and threats. P & T: A Peer-Reviewed Journal for Formulary Management, 40(4), 277–283.
  • Wang, T., Wallace, O. B., Zhang, Z., Fang, H., Yang, Z., Robinson, B. A., Spicer, T. P., Gong, Y.-F., Blair, W. S., Shi, P.-Y., Lin, P.-F., Deshpande, M., Meanwell, N. A., & Kadow, J. F. (2019). A survey of core replacements in indole-based HIV-1 attachment inhibitors. Bioorganic & Medicinal Chemistry Letters, 29(11), 1423–1429. https://doi.org/10.1016/j.bmcl.2019.03.018
  • Wang, X.-L., Zhang, Y.-B., Tang, J.-F., Yang, Y.-S., Chen, R.-Q., Zhang, F., & Zhu, H.-L. (2012). Design, synthesis and antibacterial activities of vanillic acylhydrazone derivatives as potential β-ketoacyl-acyl carrier protein synthase III (FabH) inhibitors. European Journal of Medicinal Chemistry, 57, 373–382. https://doi.org/10.1016/j.ejmech.2012.09.009
  • Wayne, P. (2008). Clinical and Laboratory Standards Institute: Reference method for broth dilution antifungal susceptibility testing of yeasts; approved standard. CLSI Document M27-A3 & Supplement S, 3, 6–12.
  • Wróbel, M. Z., Chodkowski, A., Herold, F., Marciniak, M., Dawidowski, M., Siwek, A., Starowicz, G., Stachowicz, K., Szewczyk, B., Nowak, G., Belka, M., Bączek, T., Satała, G., Bojarski, A. J., & Turło, J. (2019). Synthesis and biological evaluation of new multi-target 3-(1H-indol-3-yl)pyrrolidine-2,5-dione derivatives with potential antidepressant effect. European Journal of Medicinal Chemistry, 183, 111736. https://doi.org/10.1016/j.ejmech.2019.111736

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