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Research Articles

In silico identification and validation of phenolic lipids as potential inhibitor against bacterial and viral strains

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Pages 2525-2538 | Received 22 Mar 2022, Accepted 16 Apr 2023, Published online: 22 May 2023

References

  • Abdelsamed, I. E., Ahmed, M. A. E., Abd, E. N. G. E. G., & Abdulaziz, M. A. (2019). Chemical characterization of euphorbia heterophylla L. Essential oils and their antioxidant activity and allelopathic potential on Cenchrus echinatus L. Chemistry and Biodiversity, 16(5). https://doi.org/10.1002/cbdv.201900051
  • Ahsan, M., Pindi, C., & Senapati, S. (2020). Electrostatics plays a crucial role in HIV-1 protease substrate binding, drugs fail to take advantage. Biochemistry, 59(36), 3316–3331. https://doi.org/10.1021/acs.biochem.0c00341
  • Ahsan, M., Pindi, C., & Senapati, S. (2022). Mechanism of darunavir binding to monomeric HIV-1 protease: A step forward in the rational design of dimerization inhibitors. Physical Chemistry Chemical Physics, 24(11), 7107–7120. DOI https://doi.org/10.1039/d2cp00024e
  • Alireza, T., Vahid, M., Bibi, M. R., & Hossein, H. (2017). Review on clinical trials of black seed (Nigella sativa) and its active constituent, thymoquinone. J. Pharmacopuncture, 20(3), 179–193. https://doi.org/10.3831/KPI.2017.20.021
  • Anuja, G., Sirsendu, B., & Abhay, P. (2020). A glycotherapeutic approach to functionalize biomaterials-based systems. Advanced Functional Materials, 30(44), 1-30. https://doi.org/10.1002/adfm.201910031
  • Asher, M. (2020). Flooded by the torrent: The COVID-19 drug pipeline. Lancet, 395(10232). https://doi.org/10.1016/s0140-6736(20)30894-1
  • Baswa, M., Rath, C. C., Dash, S. K., & Mishra, R. K. (2001). Antibacterial activity of Karanj (Pongamia pinnata) and Neem (Azadirachta indica) seed oil: A preliminary report. Microbios, 105(412), 183–189.
  • Bowden, T. A., Aricescu, A. R., Gilbert, R. J. C., Grimes, J. M., Jones, E. Y., & Stuart, D. I. (2008). Structural basis of Nipah and Hendra virus attachment to their cell-surface receptor ephrin-B2. Nature Structural & Molecular Biology, 15(6), 567–572. https://doi.org/10.1038/nsmb.1435
  • Butt, S. S., Badshah, Y., Shabbir, M., & Rafiq, M. (2020). Molecular docking using chimera and Autodock Vina software for nonbioinformaticians. JMIR Bioinformatics and Biotechnology, 1(1), e14232. https://doi.org/10.2196/14232
  • Carmen, G., Tiziana, G., Ines, M., Vanesa, N., Lucia, B. G., Miguel, A. C. G., Jesus, U., David, R., Covadonga, A., Nuria, E. C., & Ana, M. (2020). COVID-19: Drug targets and potential treatments. Journal of Medicinal Chemistry, 63, 12359–12386. https://doi.org/10.1021/acs.jmedchem.0c00606
  • Chandra, A., Chaudhary, M., Qamar, I., Singh, N., & Nain, V. (2022). In silico identification and validation of natural antiviral compounds as potential inhibitors of SARS-CoV-2 methyltransferase. Journal of Biomolecular Structure & Dynamics, 40(14), 6534–6544. https://doi.org/10.1080/07391102.2021.1886174
  • Luz, C. F., van Niekerk, J. M., Keizer, J., Beerlage-de Jong, N., Braakman-Jansen, L. A., Stein, A., & Glasner, C. (2022). Mapping twenty years of antimicrobial resistance research trends. Artificial intelligence in medicine. 123, 102216–102226.
  • Dame-Teixeira, N., El-Gendy, R., Monici Silva, I., Holanda, C. A., de Oliveira, A. S., Romeiro, L. A. S., & Do, T. (2022). Sustainable multifunctional phenolic lipids as potential therapeutics in dentistry. Scientific Reports, 12(1), 1–12. https://doi.org/10.1038/s41598-022-13292-0
  • David, J. S., Abirami, K., Stephany, L. V., Negin, A. R., Penn, M., Eric, C. R., & Carolyn, M. K. (2018). Transcriptomic response of breast cancer cells to anacardic acid. Scientific Reports, 8(1), 8063. https://doi.org/10.1038/s41598-018-26429-x
  • Dharani, J., Sripathi, R., & Ravi, S. (2018). Chemical composition of Cyanthillium cinereum (L.) H. rob essential oil and its molecular docking study against bacterial proteins. J. Pharm. Sci. Res, 10(9), 2216–2220.
  • Elham, T.-L., Sajad, M., Rahim, R., Mohsen, S., Mehhr, A. M. J., & Samaneh, Z. (2020). Targeting SARS-COV-2 non-structural protein 16: A virtual drug repurposing study. Journal of Biomolecular Structure and Dynamics, 39(13), 4633–4646. https://doi.org/10.1080/07391102.2020.1779133
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
  • Fahmina, Z., Anjali, G., Karthick, T., Kavita, K., Ali, A. S., Anujit, G., Poonam, T., & Nishat, N. (2020). Physicochemical and pharmacokinetic analysis of anacardic acid derivatives. ACS Omega, 5(11), 6021–6030. https://doi.org/10.1021/acsomega.9b04398
  • Fahmina, Z., Anujit, G., Sharmin, E., & Nishat, N. (2019). Cashew nut shell liquid (phenolic lipid) based coatings: polymers to nanocomposites. Integrating Green Chemistry and Sustainable Engineering, 255–289. https://doi.org/10.1002/9781119509868.ch9
  • Geeta, A., Nikita, S., Mankamna, R., & Surendra, N. (2019). Antimicrobial silver nanoparticles: Future of nanomaterials. Microbial Nanobionics, 2, 89–119. https://doi.org/10.1007/978-3-030-16534-5_6
  • 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
  • Houk, K. N., Leach, A. G., Kim, S. P., & Zhang, X. (2003). Binding affinities of host-guest, protein-ligand and protein-transition-state complexes. Angewandte Chemie (International ed. in English), 42(40), 4872–4897. https://doi.org/10.1002/anie.200200565
  • 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
  • Ipek, S. (2020). Importance of ethnopharmacological studies in drug discovery: Role of medicinal plants. Phytochemistry Reviews, 19, 1199-1209. https://doi.org/10.1007/s11101-019-09629-9
  • Jagbir, S., Mahesh, K., Rani, M., Ganesha, C. S., & Aakash, D. (2016). Inhibitor designing, virtual screening and docking studies for methyltransferase: A potential target against dengue virus. Journal of Pharmacy and Bioallied Sciences, 8(3), 188–194. https://doi.org/10.4103/0975-7406.171682
  • Kate, E. J., Nikkita, G. P., Marc, A. L., Adam, S., Deborah, B., John, L. G., & Peter, D (2008). Global trends in emerging infectious diseases. Nature, 451, 990–993. https://doi.org/10.1038/nature06536
  • Kulkarni, S. A., & Ingale, K. (2022). In silico approaches for drug repurposing for SARS-CoV-2 infection.
  • 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
  • Malela, M. W., Zhiyu, L., & Randy, Z. (2014). Computer-aided identification of novel 3, 5-substituted rhodanine derivatives with activity against Staphylococcus aureus DNA gyrase. J. Bioorganic and Medicinal Chemistry, 22(7), 2176–2187.
  • Marco, S., Niclas, F., Knut, O., Franziska, F., Nelson, M., Kristin, K., Ulrike, H., & Lorenz, M. (2020). Antibacterial anacardic acid derivatives. ACS Infectious Diseases, 6(7), 1674–1685. https://doi.org/10.1021/acsinfecdis.9b00378
  • Masaki, H., & Isao, K. (1991). Antibacterial agents from the cashew Anacardium occidentale (Anacardiaceae) nut shell oil. Journal of Agricultural and Food Chemistry, 39(2), 418–421. https://doi.org/10.1021/jf00002a039
  • Mongan, J., Simmerling, C., McCammon, J. A., Case, D. A., & Onufriev, A. (2007). Generalized born model with a simple, robust molecular volume correction. Journal of Chemical Theory and Computation, 3(1), 156–169. https://doi.org/10.1021/ct600085e
  • Muftah, A. M. S., Faizul, A., & Ulrike, L. (2013). Oxasetin from Lophiostoma sp. of the Baltic Sea: Identification, in silico binding mode prediction and antibacterial evaluation against fish pathogenic bacteria. Natural Products Communications, 8(9), 1223–1226. https://doi.org/10.1177/1934578x1300800909
  • Muñoz-Cazares, N., García-Contreras, R., Pérez-López, M., & Castillo-Juárez, I. (2017). Phenolic compounds with anti-virulence properties. Phenolic Compounds-Biological Activity, 139–167. https://doi.org/10.5772/66367
  • Omrani, M., Keshavarz, M., Nejad Ebrahimi, S., Mehrabi, M., McGaw, L. J., Ali Abdalla, M., & Mehrbod, P. (2021). Potential natural products against respiratory viruses: A perspective to develop anti-COVID-19 medicines. Frontiers in Pharmacology, 11, 586993. https://doi.org/10.3389/fphar.2020.586993
  • Onwudiwe, D. C., Ekennia, A. C., Mogwase, B. M., Olubiyi, O. O., & Hosten, E. (2016). Palladium (II) and platinum (II) complexes of N-butyl-N-phenyldithiocarbamate: Synthesis, characterization, biological activities and molecular docking studies. Inorganica Chimica Acta, 450, 69–80. https://doi.org/10.1016/j.ica.2016.05.023
  • Patil, S. M., Martiz, R. M., Ramu, R., Shirahatti, P. S., Prakash, A., Chandra S, J., & Ranganatha, V. L. (2021). In silico identification of novel benzophenone–coumarin derivatives as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibitors. Journal of Biomolecular Structure and Dynamics, 40(23), 13032–13048. https://doi.org/10.1080/07391102.2021.1978322
  • Pradeep, K. Y., Amit, J., & Rajiv, K. S. (2021). In silico study on spice-derived antiviral phytochemicals against SARS-CoV-2 TMPRSS2 target. Journal of Biomolecular Structure and Dynamics, 40(22), 11874-11884. https://doi.org/10.1080/07391102.2021.1965658
  • Roe, D. R., & Cheatham, T. E. III, (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/10.1021/ct400341p
  • Qi, K., Yue, W., Yu, G., Qi, L., Feifei, Q., Shuran, G., & Xiuping, C. (2020). Analysis of the molecular mechanism of Pudilan (PDL) treatment for COVID-19 by network pharmacology tools. Biomedicine & Pharmacotherapy, 128, 110316. https://doi.org/10.1016/j.biopha.2020.110316
  • Richard, R. W., Marisa, H., & Michael, Z. D. (2019). Antimicrobial resistance in methicillin-resistant staphylococcus aureus to newer antimicrobial agents. Antimicrobial Agents and Chemotherapy, 63(12), e01216–e01219. https://doi.org/10.1128/AAC.01216-19
  • Saika, T., Saira, W., Waseem, R., Khushboo, S., Muzzaffar, A. B., Anil, P., Aabid, H. S., & Manzoor, A. R. (2019). A comprehensive review of the antibacterial, antifungal and antiviral potential of essential oils and their chemical constituents against drug-resistant microbial pathogens. Microbial Pathogenesis, 134, 103580. https://doi.org/10.1016/j.micpath.2019.103580
  • Sargis, D., & Arthur, J. O. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology. 1263, 243–250. https://doi.org/10.1007/978-1-4939-2269-7_19
  • Sepehr, T., Wallace, G., Schroeder, A., Stellacci, F., & Conde, J. (2020). Nanotechnology-based disinfectants and sensors for SARS-CoV-2. Nature Nanotechnology, 15(8), 618–621. https://doi.org/10.1038/s41565-020-0751-0
  • Shobha, N., Nanda, N., Giresha, A. S., Praveen, M., Sophiya, P., Dharmappa, K. K., & Nagabhushana, B. M. (2019). Synthesis and characterization of Zinc oxide nanoparticles utilizing seed source of Ricinus communis and study of its antioxidant, antifungal and anticancer activity. Materials Science & Engineering. C, Materials for Biological Applications, 97, 842–850. https://doi.org/10.1016/j.msec.2018.12.023
  • Singh, K., Coopoosamy, R. M., Gumede, N. J., & Sabiu, S. (2022). Computational Insights and In vitro validation of antibacterial potential of Shikimate pathway-derived phenolic acids as NorA Efflux pump inhibitors. Molecules, 27(8), 2601. https://doi.org/10.3390/molecules27082601
  • Smerkova, K., Dolezelikova, K., Bozdechova, L., Heger, Z., Zurek, L., & Adam, V. (2020). Nanomaterials with active targeting as advanced antimicrobials. Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology, 12(5), e1636. https://doi.org/10.1002/wnan.1636
  • Stefan, H. E. K., Anca, D., Richard, S. H., & Ralf, B. (2018). Host-directed therapies for bacterial and viral infections. Nature Reviews Drug Discovery, 17(1), 35–56. https://doi.org/10.1038/nrd.2017.162
  • Tapio, P., Antti, A., Sami, P., Sushil, S., Agnieszka, S., Jing, T., & Tero, A. (2015). Toward more realistic drug-target interaction predictions. Briefings in Bioinformatics, 16(2), 325–337. https://doi.org/10.1093/bib/bbu010
  • Tatiana, F. V., & Sergio, F. S. (2019). Comparing AutoDock and Vina in ligand/decoy discrimination for virtual screening. Applied Sciences, 9(21), 4538. https://doi.org/10.3390/app9214538
  • Terstappen, G. C., & Reggiani, A. (2001). In silico research in drug discovery. Trends in Pharmacological Sciences, 22(1), 23–26. https://doi.org/10.1016/s0165-6147(00)01584-4
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein–ligand interactions. Protein Engineering, Design and Selection, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
  • WHO. (2021). Coronavirus (COVID-19) Dashboard. WHO coronavirus (COVID-19) dashboard with vaccination data. https://covid19.who.int.
  • WHO. (2014). Antimicrobial resistance: Global report on surveillance. World Health Organization.
  • Zaki, H., Belhassan, A., Aouidate, A., Lakhlifi, T., Benlyas, M., & Bouachrine, M. (2019). Antibacterial study of 3-(2-amino-6-phenylpyrimidin-4-yl)-N-cyclopropyl-1-methyl-1H-indole-2-carboxamide derivatives: CoMFA, CoMSIA analyses, molecular docking and ADMET properties prediction. Journal of Molecular Structure, 1177, 275–285. https://doi.org/10.1016/j.molstruc.2018.09.073

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