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Research Articles

A computational odyssey: uncovering classical β-lactamase inhibitors in dry fruits

ORCID Icon & ORCID Icon
Pages 4578-4604 | Received 29 Jan 2023, Accepted 29 May 2023, Published online: 08 Jun 2023

References

  • Adekunle, O. C., Idris, O. J., Sule, I. O., Olorunfemi, A. R., & Adekunle, A. S. (2022). Phytochemicals combating antibiotics resistance: Updated review. Alexandria Journal for Veterinary Sciences, 75(1), 41-52.
  • Adelusi, T. I., Oyedele, A.-Q K., Boyenle, I. D., Ogunlana, A. T., Adeyemi, R. O., Ukachi, C. D., Idris, M. O., Olaoba, O. T., Adedotun, I. O., Kolawole, O. E., Xiaoxing, Y., & Abdul-Hammed, M. (2022). Molecular modeling in drug discovery. Informatics in Medicine Unlocked, 29, 100880. https://doi.org/10.1016/j.imu.2022.100880
  • Akhtar, A., Fatima, N., & Khan, H. M. (2022). Beta-lactamases and their classification: An overview. In Shahid, M., Singh, A., & Sami, H. (Eds.), Beta-lactam resistance in gram-negative bacteria (pp. 25–33). Springer.
  • Alasalvar, C., & Shahidi, F. (2013). Composition, phytochemicals, and beneficial health effects of dried fruits: An overview. In Alasalvar, C. & Shahidi, F. (Eds.), Dried fruits: Phytochemicals Health Effects (pp. 1–18). John Wiley & Sons.
  • Al-Khafaji, K., Al-Duhaidahawi, D., & Taskin Tok, T. (2021). Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 39(9), 3387–3395. https://doi.org/10.1080/07391102.2020.1764392
  • Al-Khafaji, K., & Tok, T. T. (2020). Molecular dynamics simulation, free energy landscape and binding free energy computations in exploration the anti-invasive activity of amygdalin against metastasis. Computer Methods and Programs in Biomedicine, 195, 105660. https://doi.org/10.1016/j.cmpb.2020.105660
  • Amanat, M., Daula, A. S. U., & Islam, F. (2022). Potential usage of Zerumbone to suppress inflammation: An in silico study. https://doi.org/10.17812/ajsmr.2021.741
  • Ambarwati, N. S. S., Azminah, A., & Ahmad, I. (2022). Molecular docking, physicochemical and drug-likeness properties of isolated compounds from Garcinia latissima Miq. on elastase enzyme: In-silico analysis. Pharmacognosy Journal, 14(2), 282–288. https://doi.org/10.5530/pj.2022.14.35
  • Annunziato, G. (2019). Strategies to overcome antimicrobial resistance (AMR) making use of non-essential target inhibitors: A review. International Journal of Molecular Sciences, 20(23), 5844. https://doi.org/10.3390/ijms20235844
  • Arslan, H., Ondul Koc, E., Ozay, Y., Canli, O., Ozdemir, S., Tollu, G., & Dizge, N. (2023). Antimicrobial and antioxidant activity of phenolic extracts from walnut (Juglans regia L.) green husk by using pressure-driven membrane process. Journal of Food Science and Technology, 60(1), 73–83. https://doi.org/10.1007/s13197-022-05588-w
  • Ayaz, M., Ullah, F., Sadiq, A., Ullah, F., Ovais, M., Ahmed, J., & Devkota, H. P. (2019). Synergistic interactions of phytochemicals with antimicrobial agents: Potential strategy to counteract drug resistance. Chemico-Biological Interactions, 308, 294–303. https://doi.org/10.1016/j.cbi.2019.05.050
  • Aydemir, E., Sarıyer, E., Akyıldız, E., Özad Düzgün, A., Camadan, Y., & Saral Sarıyer, A. (2022). In-vitro and in-silico evaluation of some plant extracts and phytocompounds against multidrug-resistant Gram-negative bacteria. Advances in Traditional Medicine, 22(4), 749–759. https://doi.org/10.1007/s13596-021-00602-6
  • Baammi, S., Daoud, R., & El Allali, A. (2023). In-silico protein engineering shows that novel mutations affecting NAD + binding sites may improve phosphite dehydrogenase stability and activity. Scientific Reports, 13(1), 1878. https://doi.org/10.1038/s41598-023-28246-3
  • Baer-Dubowska, W., Szaefer, H., Majchrzak-Celińska, A., & Krajka-Kuźniak, V. (2020). Tannic acid: Specific form of tannins in cancer chemoprevention and therapy-old and new applications. Current Pharmacology Reports, 6(2), 28–37. https://doi.org/10.1007/s40495-020-00211-y
  • Bahr, G., Gonzalez, L. J., & Vila, A. J. (2021). Metallo-β-lactamases in the age of multidrug resistance: From structure and mechanism to evolution, dissemination, and inhibitor design. Chemical Reviews, 121(13), 7957–8094. https://doi.org/10.1021/acs.chemrev.1c00138
  • Bahrani, H. M. H., Ghobeh, M., & Homayouni Tabrizi, M. (2023). The anticancer, anti-oxidant, and antibacterial activities of chitosan-lecithin-coated parthenolide/tyrosol hybrid nanoparticles. Journal of Biomaterials Science, Polymer Edition, 1–15. https://doi.org/10.1080/09205063.2023.2177473
  • Baidya, A. T., Kumar, A., Kumar, R., & Darreh-Shori, T. (2022). Allosteric binding sites of Aβ peptides on the acetylcholine synthesizing enzyme ChAT as deduced by in silico molecular modeling. International Journal of Molecular Sciences, 23(11), 6073. https://doi.org/10.3390/ijms23116073
  • Bashir, I., Ikhlaq, A., Ali, Y., Ali, B., Riaz, H., Aziz, A., Ijaz, D. F., & Aftab, D. K. (2021). Drug-like properties analysis and in-silico anti-antibiotic resistant Klebsiella pneumoniae activity of extracts of Nigella sativa and Cassia angustifolia in comparison with Sulbactam-a novel anti-drug resistance drug. Clinical Case Reports and Clinical Study, 3(4), 1-4.
  • Basu, S., Joshi, S. M., Ramaiah, S., & Anbarasu, A. (2022). Designing anti-microbial peptides against major β-lactamase enzymes in clinically important gram-negative bacterial pathogens: An in-silico study. Probiotics and Antimicrobial Proteins, 14(2), 263–276. https://doi.org/10.1007/s12602-022-09929-1
  • Benmaghnia, S., Meddah, B., Tir-Touil, A., & Hernandez, J. A. G. (2019). Phytochemical analysis, antioxidant and antimicrobial activities of three samples of dried figs (Ficus carica L.) from the region of Mascara. Journal of Microbiology, Biotechnology and Food Sciences, 9(2), 208–215. https://doi.org/10.15414/jmbfs.2019.9.2.208-215
  • Bhat, M. A., Kumar, V., Ahmed, M. Z., Alqahtani, A. S., Alqahtani, M. S., Jan, A. T., Rahman, S., Tiwari., & A., Hemlata. (2021). Screening of natural compounds for identification of novel inhibitors against β-lactamase CTX-M-152 reported among Kluyvera georgiana isolates: An in-vitro and in-silico study. Microbial Pathogenesis, 150, 104688. https://doi.org/10.1016/j.micpath.2020.104688
  • Brink, A. J., Coetzee, J., Richards, G. A., Feldman, C., Lowman, W., Tootla, H. D., Miller, M. G. A., Niehaus, A. J., Wasserman, S., Perovic, O., Govind, C. N., Schellack, N., & Mendelson, M. (2022). Best practices: Appropriate use of the new β-lactam/β-lactamase inhibitor combinations, ceftazidime-avibactam and ceftolozane-tazobactam in South Africa. Southern African Journal of Infectious Diseases, 37(1), 453. https://doi.org/10.4102/sajid.v37i1.453
  • Carcione, D., Siracusa, C., Sulejmani, A., Leoni, V., & Intra, J. (2021). Old and new beta-lactamase inhibitors: Molecular structure, mechanism of action, and clinical Use. Antibiotics, 10(8), 995. https://doi.org/10.3390/antibiotics10080995
  • Castanheira, M., Simner, P. J., & Bradford, P. A. (2021). Extended-spectrum β-lactamases: An update on their characteristics, epidemiology and detection. JAC-Antimicrobial Resistance, 3(3), dlab092. https://doi.org/10.1093/jacamr/dlab092
  • Cavallo, L., Kleinjung, J., & Fraternali, F. (2003). POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Research, 31(13), 3364–3366. https://doi.org/10.1093/nar/gkg601
  • Cheesman, M. J., Ilanko, A., Blonk, B., & Cock, I. E. (2017). Developing new antimicrobial therapies: Are synergistic combinations of plant extracts/compounds with conventional antibiotics the solution? Pharmacognosy Reviews, 11(22), 57–72. https://doi.org/10.4103/phrev.phrev_21_17
  • Cherak, Z., Loucif, L., Moussi, A., Bendjama, E., Benbouza, A., & Rolain, J.-M. (2022). Emergence of metallo-β-lactamases and oxa-48 carbapenemase producing gram-negative bacteria in hospital wastewater in Algeria: A potential dissemination pathway into the environment. Microbial Drug Resistance (Larchmont, N.Y.), 28(1), 23–30. https://doi.org/10.1089/mdr.2020.0617
  • Chiang, Y. C., Wong, M. T., & Essex, J. W. (2020). Molecular dynamics simulations of antibiotic ceftaroline at the allosteric site of penicillin‐binding protein 2a (PBP2a). Israel Journal of Chemistry, 60(7), 754–763. https://doi.org/10.1002/ijch.202000012
  • Dai, Q., Yan, Y., Ning, X., Li, G., Yu, J., Deng, J., Yang, L., & Li, G.-B. (2021). AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-β-lactamases and indoleamine/tryptophan 2, 3-dioxygenases. Acta Pharmaceutica Sinica. B, 11(7), 1931–1946. https://doi.org/10.1016/j.apsb.2021.01.018
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
  • Dalal, V., Dhankhar, P., Singh, V., Singh, V., Rakhaminov, G., Golemi-Kotra, D., & Kumar, P. (2021). Structure-based identification of potential drugs against FmtA of Staphylococcus aureus: Virtual screening, molecular dynamics, MM-GBSA, and QM/MM. The Protein Journal, 40(2), 148–165. https://doi.org/10.1007/s10930-020-09953-6
  • Das, P., Majumder, R., Mandal, M., & Basak, P. (2021). In-silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis. Journal of Biomolecular Structure & Dynamics, 39(16), 6265–6280. https://doi.org/10.1080/07391102.2020.1796799
  • Davari, K., Nowroozi, J., Hosseini, F., Sepahy, A. A., & Mirzaie, S. (2017). Structure-based virtual screening to identify the beta-lactamase CTX-M-9 inhibitors: An in-silico effort to overcome antibiotic resistance in E. coli. Computational Biology and Chemistry, 67, 174–181. https://doi.org/10.1016/j.compbiolchem.2017.01.009
  • de Azevedo, E. C., & Nascimento, A. S. (2022). The β-lactam Ticarcillin is a Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase binder. Biochimie, 197, 1–8. https://doi.org/10.1016/j.biochi.2022.01.016
  • de Bruijn, W. J., Araya-Cloutier, C., Bijlsma, J., de Swart, A., Sanders, M. G., de Waard, P., Gruppen, H., & Vincken, J.-P. (2018). Antibacterial prenylated stilbenoids from peanut (Arachis hypogaea). Phytochemistry Letters, 28, 13–18. https://doi.org/10.1016/j.phytol.2018.09.004
  • DeLano, W. L. (2002). The PyMOL molecular graphics system. http://www.pymol.org/.
  • Dhiman, P., Soni, K., & Singh, S. (2014). Nutritional value of dry fruits and their vital significance – A review. PharmaTutor, 2, 102–108.
  • Durham, E., Dorr, B., Woetzel, N., Staritzbichler, R., & Meiler, J. (2009). Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Journal of Molecular Modeling, 15(9), 1093–1108. https://doi.org/10.1007/s00894-009-0454-9
  • Ejaz, H., Younas, S., Abosalif, K. O., Junaid, K., Alzahrani, B., Alsrhani, A., Abdalla, A. E., Ullah, M. I., Qamar, M. U., & Hamam, S. S. (2021). Molecular analysis of blaSHV, blaTEM, and blaCTX-M in extended-spectrum β-lactamase producing Enterobacteriaceae recovered from fecal specimens of animals. PloS One, 16(1), e0245126. https://doi.org/10.1371/journal.pone.0245126
  • Etehadpour, M. (2021). Bioinformatics evaluation of the compounds effect of medicinal plants Hyssopus officinalis L., Tragopogon graminifolius and Avicennia marina L. on the inhibition of effective proteins against antibiotic resistance in Acinetobacter baumannii. Agricultural Biotechnology Journal, 13, 147–170. https://doi.org/10.22103/jab.2021.17570.1315
  • Findlay, J., Poirel, L., Juhas, M., & Nordmann, P. (2021). KPC-mediated resistance to ceftazidime-avibactam and collateral effects in Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy, 65(9), e00890–00821. https://doi.org/10.1128/AAC.00890-21
  • Gao, H., Liu, Y., Wang, R., Wang, Q., Jin, L., & Wang, H. (2020). The transferability and evolution of NDM-1 and KPC-2 co-producing Klebsiella pneumoniae from clinical settings. EBioMedicine, 51, 102599. https://doi.org/10.1016/j.ebiom.2019.102599
  • Ghenea, A. E., Zlatian, O. M., Cristea, O. M., Ungureanu, A., Mititelu, R. R., Balasoiu, A. T., Vasile, C. M., Salan, A.-I., Iliuta, D., Popescu, M., Udriștoiu, A.-L., & Balasoiu, M. (2022). TEM, CTX-M, SHV genes in ESBL-producing Escherichia coli and Klebsiella pneumoniae isolated from clinical samples in a county clinical emergency hospital romania-predominance of CTX-M-15. Antibiotics, 11(4), 503. https://doi.org/10.3390/antibiotics11040503
  • Gill, C. M., Aktaþ, E., Alfouzan, W., Bourassa, L., Brink, A., Burnham, C.-A D., Canton, R., Carmeli, Y., Falcone, M., Kiffer, C., Marchese, A., Martinez, O., Pournaras, S., Satlin, M., Seifert, H., Thabit, A. K., Thomson, K. S., Villegas, M. V., & Nicolau, D. P, ERACE-PA Global Study Group. (2021). The ERACE-PA global surveillance program: Ceftolozane/tazobactam and ceftazidime/avibactam in-vitro activity against a global collection of carbapenem-resistant Pseudomonas aeruginosa. European Journal of Clinical Microbiology & Infectious Diseases: Official Publication of the European Society of Clinical Microbiology, 40(12), 2533–2541. https://doi.org/10.1007/s10096-021-04308-0
  • Granata, D., Baftizadeh, F., Habchi, J., Galvagnion, C., De Simone, A., Camilloni, C., Laio, A., & Vendruscolo, M. (2015). The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments. Scientific Reports, 5, 15449. https://doi.org/10.1038/srep15449
  • Gupta, S., Singh, A. K., Kushwaha, P. P., Prajapati, K. S., Shuaib, M., Senapati, S., & Kumar, S. (2021). Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies. Journal of Biomolecular Structure & Dynamics, 39(12), 4334–4345. https://doi.org/10.1080/07391102.2020.1776157
  • Gurung, S., Kafle, S., Dhungel, B., Adhikari, N., Shrestha, U. T., Adhikari, B., Banjara, M. R., Rijal, K. R., & Ghimire, P. (2020). Detection of OXA-48 gene in carbapenem-resistant Escherichia coli and Klebsiella pneumoniae from urine samples. Infection and Drug Resistance, 13, 2311–2321. https://doi.org/10.2147/IDR.S259967
  • Guzmán-Puche, J., Jenayeh, R., Pérez-Vázquez, M., Asma, F., Jalel, B., Oteo-Iglesias, J., Martínez-Martínez, & L., Manuel-Causse. (2021). Characterization of OXA-48-producing Klebsiella oxytoca isolates from a hospital outbreak in Tunisia. Journal of Global Antimicrobial Resistance, 24, 306–310., https://doi.org/10.1016/j.jgar.2021.01.008
  • Haider, S., Parkinson, G. N., & Neidle, S. (2008). Molecular dynamics and principal components analysis of human telomeric quadruplex multimers. Biophysical Journal, 95(1), 296–311. https://doi.org/10.1529/biophysj.107.120501
  • Halder, S. K., Mim, M. M., Alif, M. M. H., Shathi, J. F., Alam, N., Shil, A., & Himel, M. K. (2022). Oxa-376 and Oxa-530 variants of β-lactamase: Computational study uncovers potential therapeutic targets of Acinetobacter baumannii. RSC Advances, 12(37), 24319–24338. https://doi.org/10.1039/D2RA02939A
  • Han, M. S., Park, K. S., Jeon, J. H., Lee, J. K., Lee, J. H., Choi, E. H., & Lee, S. H. (2020). SHV hyperproduction as a mechanism for piperacillin–tazobactam resistance in extended-spectrum cephalosporin-susceptible Klebsiella pneumoniae. Microbial Drug Resistance (Larchmont, N.Y.), 26(4), 334–340. https://doi.org/10.1089/mdr.2019.0079
  • Haq, F. U., Abro, A., Raza, S., Liedl, K. R., & Azam, S. S. (2017). Molecular dynamics simulation studies of novel β-lactamase inhibitor. Journal of Molecular Graphics & Modelling, 74, 143–152. https://doi.org/10.1016/j.jmgm.2017.03.002
  • Hayes, J. M., Skamnaki, V. T., Archontis, G., Lamprakis, C., Sarrou, J., Bischler, N., Skaltsounis, A. L., Zographos, S. E., & Oikonomakos, N. G. (2011). Kinetics, in-silico docking, molecular dynamics, and MM‐GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP‐binding site inhibitors: The role of water molecules examined. Proteins, 79(3), 703–719. https://doi.org/10.1002/prot.22890
  • Huang, Y., Li, J., Wang, Q., Tang, K., Cai, X., & Li, C. (2023). Detection of carbapenem-resistant hypervirulent Klebsiella pneumoniae ST11-K64 co-producing NDM-1 and KPC-2 in a tertiary hospital in Wuhan. The Journal of Hospital Infection, 131, 70–80. https://doi.org/10.1016/j.jhin.2022.09.014
  • Ijaz, S., Akhtar, N., Khan, M. S., Hameed, A., Irfan, M., Arshad, M. A., Ali, S., & Asrar, M. (2018). Plant derived anticancer agents: A green approach towards skin cancers. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 103, 1643–1651. https://doi.org/10.1016/j.biopha.2018.04.113
  • Jaidhan, B., Rao, P. S., & Apparao, A. (2014). Energy minimization and conformation analysis of molecules using steepest descent method. International Journal of Computer Science and Information Technologies, 5, 3525–3528.
  • Jha, V., Matharoo, D. K., Kasbe, S., Gharat, K., Rathod, M., Sonawane, N., & Kanade, T. (2021). Computational screening of phytochemicals to discover potent inhibitors against chinkungunya virus. Vegetos, 34(3), 515–527. https://doi.org/10.1007/s42535-021-00227-9
  • Jing, W., Xiaolan, C., Yu, C., Feng, Q., & Haifeng, Y. (2022). Pharmacological effects and mechanisms of tannic acid. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 154, 113561. https://doi.org/10.1016/j.biopha.2022.113561
  • Joël, T. E., Bernardin, A. A., Karine, G. K. M., Nathalie, G. K., & Simon-Pierre, N. A. (2022). Detection and dissemination of extented-spectrum beta-lactamases genes (CTX-M-15 and SHV-187) isolated in multi-drug resistant uropathogenic Klebsiella pneumoniae and Escherichia coli in Cote D'ivoire. Journal of Advances in Biology & Biotechnology, 25, 20–29. https://doi.org/10.9734/jabb/2022/v25i7586
  • Joji, R. M., Al-Mahmeed, A., Dar, F. K., & Shahid, M. (2022). Trends in βeta-lactamase classification. In Shahid, M., Singh, A. & Sami, H. (Eds.), Beta-lactam resistance in gram-negative bacteria (pp. 17–24). Springer.
  • Jolliffe, I. T., & Cadima, J. (2016). Principal component analysis: A review and recent developments. Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences, 374(2065), 20150202. https://doi.org/10.1098/rsta.2015.0202
  • Kar, B., Kundu, C. N., Pati, S., & Bhattacharya, D. (2023). Discovery of phyto-compounds as novel inhibitors against NDM-1 and VIM-1 protein through virtual screening and molecular modelling. Journal of Biomolecular Structure and Dynamics, 41(4), 1267–1280. https://doi.org/10.1080/07391102.2021.2019125
  • Kato, K., Nakayoshi, T., Fukuyoshi, S., Kurimoto, E., & Oda, A. (2017). Validation of molecular dynamics simulations for prediction of three-dimensional structures of small proteins. Molecules, 22(10), 1716. https://doi.org/10.3390/molecules22101716
  • Khairy, A., Hammoda, H. M., Celik, I., Zaatout, H. H., & Ibrahim, R. S. (2022). Discovery of potential natural dihydroorotate dehydrogenase inhibitors and their synergism with brequinar via integrated molecular docking, dynamic simulations and in-vitro approach. Scientific Reports, 12(1), 19037. https://doi.org/10.1038/s41598-022-23006-1
  • Khalifa, H. O., Soliman, A. M., Ahmed, A. M., Shimamoto, T., Nariya, H., Matsumoto, T., & Shimamoto, T. (2019). High prevalence of antimicrobial resistance in Gram-negative bacteria isolated from clinical settings in Egypt: Recalling for judicious use of conventional antimicrobials in developing nations. Microbial Drug Resistance (Larchmont, N.Y.), 25(3), 371–385. https://doi.org/10.1089/mdr.2018.0380
  • Kim, I. J., & Na, H. (2022). An efficient algorithm calculating common solvent accessible volume. PloS One, 17(3), e0265614. https://doi.org/10.1371/journal.pone.0265614
  • 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. https://doi.org/10.1021/ar000033j
  • Kongkham, B., Yadav, A., Ojha, M. D., Prabakaran, D., & P, H. (2022). In-vitro and computational studies of the β-lactamase inhibition and β-lactam potentiating properties of plant secondary metabolites. Journal of Biomolecular Structure and Dynamics, 1–21. https://doi.org/10.1080/07391102.2022.2154843
  • Krzysztoforska, K., Mirowska-Guzel, D., & Widy-Tyszkiewicz, E. (2019). Pharmacological effects of protocatechuic acid and its therapeutic potential in neurodegenerative diseases: Review on the basis of in-vitro and in-vivo studies in rodents and humans. Nutritional Neuroscience, 22(2), 72–82. https://doi.org/10.1080/1028415X.2017.1354543
  • Kushwaha, P. P., Singh, A. K., Bansal, T., Yadav, A., Prajapati, K. S., Shuaib, M., & Kumar, S. (2021). Identification of natural inhibitors against SARS-CoV-2 drugable targets using molecular docking, molecular dynamics simulation, and MM-PBSA approach. Frontiers in Cellular and Infection Microbiology, 11, 728. https://doi.org/10.3389/fcimb.2021.730288
  • Laddach, A., Chung, S. S., & Fraternali, F. (2018). Prediction of protein-protein interactions: Looking through the kaleidoscope. In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics (pp. 834–848). Elsevier.
  • Laganà, A., Visalli, G., Corpina, F., Ferlazzo, M., Di Pietro, A., & Facciolà, A. (2023). Antibacterial activity of nanoparticles and nanomaterials: A possible weapon in the fight against healthcare-associated infections. European Review for Medical and Pharmacological Sciences, 27(8), 3645–3663. https://doi.org/10.26355/eurrev_202304_32151
  • Lans, C., & van Asseldonk, T. (2020). Dr. Duke’s phytochemical and ethnobotanical databases, a cornerstone in the validation of ethnoveterinary medicinal plants, as demonstrated by data on pets in British Columbia. In Medicinal and aromatic plants of North America (pp. 219–246). Springer.
  • Lebreton, F., Corey, B. W., McElheny, C. L., Iovleva, A., Preston, L., Margulieux, K. R., Cybulski, R. J., Mc Gann, P., Doi, Y., & Bennett, J. W. (2021). Characterization of KPC-82, a KPC-2 variant conferring resistance to ceftazidime-avibactam in a carbapenem-nonsusceptible clinical isolate of Citrobacter koseri. Antimicrobial Agents and Chemotherapy, 65(7), e00150–00121. https://doi.org/10.1128/AAC.00150-21
  • Lewies, A., Du Plessis, L. H., & Wentzel, J. F. (2019). Antimicrobial peptides: The Achilles’ heel of antibiotic resistance? Probiotics and Antimicrobial Proteins, 11(2), 370–381. https://doi.org/10.1007/s12602-018-9465-0
  • Li, S., Shen, S., Ding, L., Han, R., Guo, Y., Yin, D., Guan, M., & Hu, F. (2022). First report of blaCTX–M–167, blaSHV–1, and blaTEM–1B carrying Klebsiella pneumonia showing high-level resistance to carbapenems. Frontiers in Microbiology, 13, 916304. https://doi.org/10.3389/fmicb.2022.916304
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1–3), 3–26. https://doi.org/10.1016/S0169-409X(00)00129-0
  • Liu, Z., Gu, Y., Li, X., Liu, Y., Ye, Y., Guan, S., & Li, J. (2019). Identification and characterization of NDM-1-producing hypervirulent (hypermucoviscous) Klebsiella pneumoniae in China. Annals of Laboratory Medicine, 39(2), 167–175. https://doi.org/10.3343/alm.2019.39.2.167
  • Lobanov, M. Y., Bogatyreva, N., & Galzitskaya, O. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
  • Londhe, A. M., Gadhe, C. G., Lim, S. M., & Pae, A. N. (2019). Investigation of molecular details of Keap1-Nrf2 inhibitors using molecular dynamics and umbrella sampling techniques. Molecules, 24(22), 4085. https://doi.org/10.3390/molecules24224085
  • López-López, E., Naveja, J. J., & Medina-Franco, J. L. (2019). DataWarrior: An evaluation of the open-source drug discovery tool. Expert Opinion on Drug Discovery, 14(4), 335–341. https://doi.org/10.1080/17460441.2019.1581170
  • Loqman, S., Soraa, N., Diene, S. M., & Rolain, J.-M. (2021). Dissemination of carbapenemases (OXA-48, NDM and VIM) producing Enterobacteriaceae isolated from the Mohamed VI University Hospital in Marrakech, Morocco. Antibiotics, 10(5), 492. https://doi.org/10.3390/antibiotics10050492
  • Lu, S., Hu, L., Lin, H., Judge, A., Rivera, P., Palaniappan, M., Sankaran, B., Wang, J., Prasad, B. V., & Palzkill, T. (2022). An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M β-lactamase drug-resistance enzymes. Nature Communications, 13(1), 6726. https://doi.org/10.1038/s41467-022-34564-3
  • Maheshwari, M., Abul Qais, F., Althubiani, A. S., Abulreesh, H. H., & Ahmad, I. (2019). Bioactive extracts of Carum copticum and thymol inhibit biofilm development by multidrug-resistant extended spectrum β-lactamase producing enteric bacteria. Biofouling, 35(9), 1026–1039. https://doi.org/10.1080/08927014.2019.1688305
  • Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology, 385(1), 312–329. https://doi.org/10.1016/j.jmb.2008.10.018
  • Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2010). Relation between free energy landscapes of proteins and dynamics. Journal of Chemical Theory and Computation, 6(2), 583–595. https://doi.org/10.1021/ct9005745
  • Makabenta, J. M. V., Nabawy, A., Li, C.-H., Schmidt-Malan, S., Patel, R., & Rotello, V. M. (2021). Nanomaterial-based therapeutics for antibiotic-resistant bacterial infections. Nature Reviews Microbiology, 19(1), 23–36. https://doi.org/10.1038/s41579-021-00680-y
  • Makepeace, K. A., Brodie, N. I., Popov, K. I., Gudavicius, G., Nelson, C. J., Petrotchenko, E. V., Dokholyan, N. V., & Borchers, C. H. (2020). Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations. Journal of Proteomics, 211, 103544. https://doi.org/10.1016/j.jprot.2019.103544
  • Martínez, L. (2015). Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PloS One, 10(3), e0119264. https://doi.org/10.1371/journal.pone.0119264
  • Mesentean, S., Fischer, S., & Smith, J. C. (2006). Analyzing large‐scale structural change in proteins: Comparison of principal component projection and sammon mapping. Proteins, 64(1), 210–218. https://doi.org/10.1002/prot.20981
  • Mingrou, L., Guo, S., Ho, C. T., & Bai, N. (2022). Review on chemical compositions and biological activities of peanut (Arachis hypogeae L.). Journal of Food Biochemistry, 46(7), e14119. https://doi.org/10.1111/jfbc.14119
  • Mishra, N., Dubey, A., Mishra, R., & Barik, N. (2010). Study on antioxidant activity of common dry fruits. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 48(12), 3316–3320. https://doi.org/10.1016/j.fct.2010.08.029
  • Mishra, A., Maurya, S. K., Singh, A., Siddique, H., Samanta, S. K., & Mishra, N. (2023). Neolamarckia cadamba (Roxb.) Bosser (Rubiaceae) extracts: Promising prospects for anticancer and antibacterial potential through in-vitro and in-silico studies. Medical Oncology, 40(3), 99. https://doi.org/10.1007/s12032-023-01971-5
  • Moharana, M., Pattanayak, S. K., & Khan, F. (2023). Molecular recognition of bio-active triterpenoids from Swertia chirayita towards hepatitis Delta antigen: A mechanism through docking, dynamics simulation, Gibbs free energy landscape. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2023.2184173
  • Morris, G., Huey, R., Lindstrom, W., Sanner, M., Belew, R., Goodsell, D., & Olson, A. (2009). Autodock4 and AutoDockTools4: Automated docking with selective receptor flexiblity. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Mukerjee, N., Das, A., Maitra, S., Ghosh, A., Khan, P., Alexiou, A., Dey, A., Baishya, D., Ahmad, F., Sachdeva, P., & Al-Muhanna, M. K. (2022). Dynamics of natural product Lupenone as a potential fusion inhibitor against the spike complex of novel Semliki Forest Virus. PloS One, 17(2), e0263853. https://doi.org/10.1371/journal.pone.0263853
  • Mukherjee, S. K., Mukherjee, M., & Mishra, P. P. (2021). Impact of mutation on the structural stability and the conformational landscape of inhibitor-resistant TEM β-Lactamase: A high-performance molecular dynamics simulation study. The Journal of Physical Chemistry. B, 125(40), 11188–11196. https://doi.org/10.1021/acs.jpcb.1c05988
  • Murugan, N. A., Priya, G. R., Sastry, G. N., & Markidis, S. (2022). Artificial intelligence in virtual screening: Models versus experiments. Drug Discovery Today, 27(7), 1913–1923. https://doi.org/10.1016/j.drudis.2022.05.013
  • Nandhini, P., Gupta, P. K., Mahapatra, A. K., Das, A. P., Agarwal, S. M., Mickymaray, S., Alothaim, A. S., & Rajan, M. (2023). In-silico molecular screening of natural compounds as a potential therapeutic inhibitor for methicillin-resistant Staphylococcus aureus inhibition. Chemico-Biological Interactions, 374, 110383. https://doi.org/10.1016/j.cbi.2023.110383
  • Nguyen, T. H., & Vu, D. C. (2023). A review on phytochemical composition and potential health-promoting properties of walnuts. Food Reviews International, 39(1), 397–423. https://doi.org/10.1080/87559129.2021.1912084
  • Nicu, A. I., Pirvu, L., Stoian, G., & Vamanu, A. (2018). Antibacterial activity of ethanolic extracts from Fagus sylvatica L. and Juglans regia L. leaves. FARMACIA, 66(3), 483–486. https://doi.org/10.31925/farmacia.2018.3.13
  • Papaleo, E., Mereghetti, P., Fantucci, P., Grandori, R., & De Gioia, L. (2009). Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case. Journal of Molecular Graphics & Modelling, 27(8), 889–899. https://doi.org/10.1016/j.jmgm.2009.01.006
  • Parida, P., Bhowmick, S., Saha, A., & Islam, M. A. (2021). Insight into the screening of potential beta-lactamase inhibitors as anti-bacterial chemical agents through pharmacoinformatics study. Journal of Biomolecular Structure & Dynamics, 39(3), 923–942. https://doi.org/10.1080/07391102.2020.1720819
  • Pathak, R. K., Seo, Y.-J., & Kim, J.-M. (2022). Structural insights into inhibition of PRRSV Nsp4 revealed by structure-based virtual screening, molecular dynamics, and MM-PBSA studies. Journal of Biological Engineering, 16(1), 4. https://doi.org/10.1186/s13036-022-00284-x
  • Patra, M., Hyvönen, M. T., Falck, E., Sabouri-Ghomi, M., Vattulainen, I., & Karttunen, M. (2007). Long-range interactions and parallel scalability in molecular simulations. Computer Physics Communications, 176(1), 14–22. https://doi.org/10.1016/j.cpc.2006.07.017
  • Prada-Gracia, D., Gómez-Gardeñes, J., Echenique, P., & Falo, F. (2009). Exploring the free energy landscape: From dynamics to networks and back. PLoS Computational Biology, 5(6), e1000415. https://doi.org/10.1371/journal.pcbi.1000415
  • Pradeep, S., Patil, S. M., Dharmashekara, C., Jain, A., Ramu, R., Shirahatti, P. S., Mandal, S. P., Reddy, P., Srinivasa, C., Patil, S. S., Ortega-Castro, J., Frau, J., Flores-Holgúın, N., Shivamallu, C., Kollur, S. P., & Glossman-Mitnik, D. (2022). Molecular insights into the in silico discovery of corilagin from Terminalia chebula as a potential dual inhibitor of SARS-CoV-2 structural proteins. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2022.2158943
  • Prakash, A., Nithyanand, P., & Vadivel, V. (2018). In-vitro antibacterial activity of nut by-products against foodborne pathogens and their application in fresh-cut fruit model. Journal of Food Science and Technology, 55(10), 4304–4310. https://doi.org/10.1007/s13197-018-3373-x
  • Qais, F. A., Ahmad, & I., Samreen. (2023). In-silico screening and in-vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli. Journal of Biomolecular Structure and Dynamics, 41(6), 2189–2201. https://doi.org/10.1080/07391102.2022.2029564
  • Qamar, M. U., Walsh, T. R., Toleman, M. A., Tyrrell, J. M., Saleem, S., Aboklaish, A., & Jahan, S. (2019). Dissemination of genetically diverse NDM-1,-5,-7 producing-Gram-negative pathogens isolated from pediatric patients in Pakistan. Future Microbiology, 14, 691–704. https://doi.org/10.2217/fmb-2019-0012
  • Rehman, N., Azam, S., Ali, A., Khan, I., Asghar, M., Ali, M., Waqas, M., Ullah, F., & Sehra, G. E. (2021). Molecular epidemiology of antibiotic-resistant genes and potent inhibitors against TEM, CTX-M-14, CTX-M-15, and SHV-1 proteins of Escherichia coli in district Peshawar, Pakistan. Saudi Journal of Biological Sciences, 28(11), 6568–6581. https://doi.org/10.1016/j.sjbs.2021.07.028
  • Richter, D. C., Heininger, A., Chiriac, U., Frey, O. R., Rau, H., Fuchs, T., Röhr, A. C., Brinkmann, A., & Weigand, M. A. (2022). Antibiotic stewardship and therapeutic drug monitoring of β-lactam antibiotics: Is there a link? An opinion paper. Therapeutic Drug Monitoring, 44(1), 103–111. https://doi.org/10.1097/FTD.0000000000000949
  • Robert Frost, H. (2022). Eigenvectors from eigenvalues sparse principal component analysis. Journal of Computational and Graphical Statistics: A Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America, 31(2), 486–501. https://doi.org/10.1080/10618600.2021.1987254
  • Ruemke, S., Rubalskii, E., Salmoukas, C., Hermes, K., Natanov, R., Kaufeld, T., Gryshkov, O., Mutsenko, V., Rubalsky, M., Burgwitz, K., Glasmacher, B., Haverich, A., Rustum, S., & Kuehn, C. (2023). Combination of bacteriophages and antibiotics for prevention of vascular graft infections—An in-vitro study. Pharmaceuticals, 16(5), 744. https://doi.org/10.3390/ph16050744
  • Sabanés Zariquiey, F., Jacoby, E., Vos, A., van Vlijmen, H. W. T., Tresadern, G., & Harvey, J. (2022). Divide and conquer. Pocket-opening mixed-solvent simulations in the perspective of docking virtual screening applications for drug discovery. Journal of Chemical Information and Modeling, 62(3), 533–543. https://doi.org/10.1021/acs.jcim.1c01164
  • Savojardo, C., Manfredi, M., Martelli, P. L., & Casadio, R. (2020). Solvent accessibility of residues undergoing pathogenic variations in humans: From protein structures to protein sequences. Frontiers in Molecular Biosciences, 7, 626363. https://doi.org/10.3389/fmolb.2020.626363
  • Schreiner, W., Karch, R., Knapp, B., & Ilieva, N. (2012). Relaxation estimation of RMSD in molecular dynamics immunosimulations. Computational and Mathematical Methods in Medicine, 2012, 173521. https://doi.org/10.1155/2012/173521
  • Schrodinger, LLC. (2015). The PyMOL Molecular Graphics System, Version 2.5.
  • Schüttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/s0907444904011679
  • Seca, A. M., & Pinto, D. C. (2019). Biological potential and medical use of secondary metabolites. MDPI, 6(2), 66. https://doi.org/10.3390/medicines6020066
  • Sen, A. (2020). Prophylactic and therapeutic roles of oleanolic acid and its derivatives in several diseases. World Journal of Clinical Cases, 8(10), 1767–1792. https://doi.org/10.12998/wjcc.v8.i10.1767
  • Shahrajabian, M. H., & Sun, W. (2023). The important nutritional and wonderful health benefits of Cashew (Anacardium occidentale L.). The Natural Products Journal, 13(4), 2–10. https://doi.org/10.2174/2210315512666220427113702
  • Sharma, S., Fatima, A., Manhas, F. M., Agarwal, N., Singh, M., Muthu, S., Siddiqui, N., & Javed, S. (2022). Experimental spectroscopic, quantum chemical, molecular docking, and molecular dynamic simulation studies on hydantoin (monomer and dimer). Polycyclic Aromatic Compounds, 1–27. https://doi.org/10.1080/07391102.2021.1970024
  • Singh, H., & Bharadvaja, N. (2021). Treasuring the computational approach in medicinal plant research. Progress in Biophysics and Molecular Biology, 164, 19–32. https://doi.org/10.1016/j.pbiomolbio.2021.05.004
  • Singh, M. B., Vishvakarma, V. K., Lal, A. A., Chandra, R., Jain, P., & Singh, P. (2022). A comparative study of 5-fluorouracil, doxorubicin, methotrexate, paclitaxel for their inhibition ability for Mpro of nCoV: Molecular docking and molecular dynamics simulations. Journal of the Indian Chemical Society, 99(12), 100790. https://doi.org/10.1016/j.jics.2022.100790
  • Sohaib, A. K., Ain, Q.-U., Madiha, K., Mudassir, A. K., Khan, M. S. G., & Rabia, G. (2017). Dry fruits and diabetes mellitus. International Journal of Medical Research Health Sciences, 6, 116–119.
  • Song, J., He, Y., Luo, C., Feng, B., Ran, F., Xu, H., Ci, Z., Xu, R., Han, L., & Zhang, D. (2020). New progress in the pharmacology of protocatechuic acid: A compound ingested in daily foods and herbs frequently and heavily. Pharmacological Research, 161, 105109. https://doi.org/10.1016/j.phrs.2020.105109
  • Souhila, B., Asma, B., Boumediene, M., & Aicha, T.-T. (2021). Antimicrobial activity of dried fig (Ficus carica L.) extracts from the region of Mascara (Western Algeria) on Enterobacter cloacae identified by MALDI-TOF/MS. European Journal of Biological Research, 11, 234–241. https://doi.org/10.5281/zenodo.4641370
  • Stewart, A., Harris, P., Henderson, A., & Paterson, D. (2018). Treatment of infections by OXA-48-producing Enterobacteriaceae. Antimicrobial Agents and Chemotherapy, 62(11), e01195–01118. https://doi.org/10.1128/AAC.01195-18
  • Sun, N., Li, D., Chen, X., Wu, P., Lu, Y.-J., Hou, N., Chen, W.-H., & Wong, W.-L. (2019). New applications of oleanolic acid and its derivatives as cardioprotective agents: A review of their therapeutic perspectives. Current Pharmaceutical Design, 25(35), 3740–3750. https://doi.org/10.2174/1381612825666191105112802
  • Surya Ulhas, R., & Malaviya, A. (2022). In-silico validation of novel therapeutic activities of withaferin A using molecular docking and dynamics studies. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/10.1080/07391102.2022.2078410
  • Sutrisno, S., Hidayah, S. W., Sukarianingsih, D., Rachman, I. B., & Retnosari, R. (2021). Antibacterial activity of peanut oil (Arachis hypogaea Linn) and its derivatives (K-soap, FFAs, and FAMEs) against Staphylococcus aureus and Escherichia coli. AIP Conference Proceedings (pp. 030040). AIP Publishing LLC.
  • Talukder, S., Ahmed, K. S., Hossain, H., Hasan, T., Liya, I. J., Amanat, M., Nahar, N., Shuvo, M. S. R., & Daula, A. S. U. (2022). Fimbristylis aestivalis Vahl: A potential source of cyclooxygenase-2 (COX-2) inhibitors. Inflammopharmacology, 30(6), 2301–2315. https://doi.org/10.1007/s10787-022-01057-0
  • Temel, H., Atlan, M., Türkmenoğlu, B., Ertaş, A., Erdönmez, D., & Çalışkan, U. K. (2023). In-silico and biological activity evaluation of quercetin-boron hybrid compounds, anti-quorum sensing effect as alternative potential against microbial resistance. Journal of Trace Elements in Medicine and Biology: Organ of the Society for Minerals and Trace Elements (GMS), 77, 127139. https://doi.org/10.1016/j.jtemb.2023.127139
  • Thawabteh, A. M., Swaileh, Z., Ammar, M., Jaghama, W., Yousef, M., Karaman, R., A. Bufo, S., & Scrano, L. (2023). Antifungal and antibacterial activities of isolated marine compounds. Toxins, 15(2), 93. https://doi.org/10.3390/toxins15020093
  • Tooke, C. L., Hinchliffe, P., Bonomo, R. A., Schofield, C. J., Mulholland, A. J., & Spencer, J. (2021). Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl–enzyme conformational dynamics to extend antibiotic resistance. Journal of Biological Chemistry, 296, 100126. https://doi.org/10.1074/jbc.RA120.016461
  • Tooke, C. L., Hinchliffe, P., Bragginton, E. C., Colenso, C. K., Hirvonen, V. H., Takebayashi, Y., & Spencer, J. (2019). β-lactamases and β-lactamase inhibitors in the 21st century. Journal of Molecular Biology, 431(18), 3472–3500. https://doi.org/10.1016/j.jmb.2019.04.002
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
  • Tsoulfidis, L., & Athanasiadis, I. (2022). A new method of identifying key industries: A principal component analysis. Journal of Economic Structures, 11(1), 1–23. https://doi.org/10.1186/s40008-022-00261-z
  • Tumskiy, R. S., & Tumskaia, A. V. (2021). Multistep rational molecular design and combined docking for discovery of novel classes of inhibitors of SARS-CoV-2 main protease 3CLpro. Chemical Physics Letters, 780, 138894. https://doi.org/10.1016/j.cplett.2021.138894
  • Vakayil, R., Kabeerdass, N., Murugesan, K., Shanmugam, G., Ramasamy, S., & Mathanmohun, M. (2022). Antibacterial activity and molecular characteristics of Indian Olibanum (Boswellia serrata) Phytochemicals: An in silico approach. Applied Ecology and Environmental Research, 20(2), 919–929. https://doi.org/10.15666/aeer/2002_919929
  • Vakayil, R., Kabeerdass, N., Srinivasan, R., Shanmugam, G., Ramasamy, S., & Mathanmohun, M. (2021). In-vitro and in-silico studies on antibacterial potentials of phytochemical extracts. Materials Today: Proceedings, 47, 453–460. https://doi.org/10.1016/j.matpr.2021.05.017
  • Vasudevan, A., Kesavan, D. K., Wu, L., Su, Z., Wang, S., Ramasamy, M. K., Hopper, W., & Xu, H. (2022). In-silico and in-vitro screening of natural compounds as broad-spectrum β-lactamase inhibitors against Acinetobacter baumannii New Delhi metallo-β-lactamase-1 (NDM-1). BioMed Research International, 2022, 4230788. https://doi.org/10.1155/2022/4230788
  • Velázquez-Libera, J. L., Durán-Verdugo, F., Valdés-Jiménez, A., Núñez-Vivanco, G., & Caballero, J. (2020). LigRMSD: A web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking. Bioinformatics (Oxford, England), 36(9), 2912–2914. https://doi.org/10.1093/bioinformatics/btaa018
  • Venkata, K. C. N., Ellebrecht, M., & Tripathi, S. K. (2021). Efforts towards the inhibitor design for New Delhi metallo-beta-lactamase (NDM-1). European Journal of Medicinal Chemistry, 225, 113747. https://doi.org/10.1016/j.ejmech.2021.113747
  • Wang, L., Shen, W., Zhang, R., & Cai, J. (2022). Identification of a novel ceftazidime-avibactam-resistant KPC-2 variant, KPC-123, in Citrobacter koseri following ceftazidime-avibactam treatment. Frontiers in Microbiology, 13, 930777. https://doi.org/10.3389/fmicb.2022.930777
  • Wang, T., Xu, K., Zhao, L., Tong, R., Xiong, L., & Shi, J. (2021). Recent research and development of NDM-1 inhibitors. European Journal of Medicinal Chemistry, 223, 113667. https://doi.org/10.1016/j.ejmech.2021.113667
  • Wilson, G. M., Fitzpatrick, M., Walding, K., Gonzalez, B., Schweizer, M. L., Suda, K. J., & Evans, C. T. (2021). Meta-analysis of clinical outcomes using ceftazidime/avibactam, ceftolozane/tazobactam, and meropenem/vaborbactam for the treatment of multidrug-resistant Gram-negative infections. Open Forum Infectious Diseases, 8(2), ofaa651. https://doi.org/10.1093/ofid/ofaa651
  • Ya, G., Ye, M., & John, Z. H. Z. (2015). Treatment of hydrogen bonds in protein simulations. In Jianjun, L. (Ed.), Advanced materials for renewable hydrogen production, storage and utilization. IntechOpen.
  • Yu, W., & Chen, Z. (2021). Computer aided drug design based on artificial intelligence algorithm. Journal of Physics: Conference Series, 2066(1), 012012. https://doi.org/10.1088/1742-6596/2066/1/012012
  • Zaki, A. A., Ashour, A., Elhady, S. S., Darwish, K. M., & Al-Karmalawy, A. A. (2022). Calendulaglycoside A showing potential activity against SARS-CoV-2 main protease: Molecular docking, molecular dynamics, and SAR studies. Journal of Traditional and Complementary Medicine, 12(1), 16–34. https://doi.org/10.1016/j.jtcme.2021.05.001
  • Zhang, S., Gai, Z., Gui, T., Chen, J., Chen, Q., & Li, Y. (2021). Antioxidant effects of protocatechuic acid and protocatechuic aldehyde: Old wine in a new bottle. Evidence-Based Complementary and Alternative Medicine: eCAM, 2021, 6139308. https://doi.org/10.1155/2021/6139308
  • Zia, Q., Rehman, M. T., Hashmi, M. A., Siddiqui, S., Bin Dukhyil, A., Ahmed, M. Z., Jamal, A., Banawas, S., Almalki, S. G., Owais, M., Aldhafeeri, H. Q., Ibrahim, I. M., Alturaiki, W., AlAjmi, M. F., Alsieni, M., & Alqurashi, Y. E. (2022). Effect of date palm (Phoenix dactylifera) phytochemicals on Aβ1-40 amyloid formation: An in-silico analysis. Frontiers in Neuroscience, 16, 1124. https://doi.org/10.3389/fnins.2022.915122
  • Ziani, B. E., Carocho, M., Abreu, R. M., Bachari, K., Alves, M. J., Calhelha, R. C., Talhi, O., Barros, L., & Ferreira, I. C. (2020). Phenolic profiling, biological activities and in silico studies of Acacia tortilis (Forssk.) Hayne ssp. raddiana extracts. Food Bioscience, 36, 100616. https://doi.org/10.1016/j.fbio.2020.100616

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