Exploring a new phyto-derived nanoparticle for targeting bacterial protein EF-Tu: an integrated approach to develop antimicrobial drug

References

• Reygaert WC. An overview of the antimicrobial resistance mechanisms of bacteria. AIMS Microbiol. 2018;4(3):482–501. doi: 10.3934/microbiol.2018.3.482
   PubMed Web of Science ®Google Scholar
• Dadgostar P. Antimicrobial resistance: implications and costs. Infect Drug Resist. 2019;12:3903–3910. doi: 10.2147/IDR.S234610
   PubMed Web of Science ®Google Scholar
• Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health. 2015;109(7):309–318. doi: 10.1179/2047773215Y.0000000030
   PubMed Web of Science ®Google Scholar
• Bhikha RAH, Glynn J. Tibb training manual. African traditional healing and tibb institute. Johannesburg: Ibn Sina Institute of Tibb; 2013.
   Google Scholar
• Siddiqui AA, Iram F, Siddiqui S, et al. Role of natural products in drug discovery process. Int J Drug Dev Res. 2014;6:172–204.
   Google Scholar
• Parimala M, Shoba FG. In vitro antimicrobial activity and HPTLC analysis of hydroalcoholic seed extract of nymphaea nouchali burm. BMC Complement Alt Med. 2014;14(1):361. doi: 10.1186/1472-6882-14-361
   PubMedGoogle Scholar
• Watkins R, Wu L, Zhang C, et al. Natural product-based nanomedicine: recent advances and issues. Int J Nanomed. 2015;10:6055. doi: 10.2147/IJN.S92162
   PubMed Web of Science ®Google Scholar
• Bonifácio BV, da Silva PB, dos Santos Ramos MA, et al. Nanotechnology-based drug delivery systems and herbal medicines: a review. Int J Nanomed. 2014;9:1. doi: 10.2147/IJN.S52634
   PubMed Web of Science ®Google Scholar
• Fischbach MA, Walsh CT. Antibiotics for emerging pathogens. Science. 2019;325(5944):1089–1093. doi: 10.1126/science.1176667
   Google Scholar
• de Villiers MM, Aramwit P, Kwon GS. Nanotechnology in drug delivery. New York (NY): Springer; 2008.
   Google Scholar
• Mirza AZ, Siddiqui FA. Nanomedicine and drug delivery: a mini review. Int Nano Lett. 2014;4(1):94. doi: 10.1007/s40089-014-0094-7
   Google Scholar
• Liu Y, Zhang Y, Zhong H. Application of molecular docking for the degradation of organic pollutants in the environmental remediation: a review. Chemosphere. 2018;203:139–150. doi: 10.1016/j.chemosphere.2018.03.179
   PubMed Web of Science ®Google Scholar
• Torres PHM, Sodero ACR, Jofily P, et al. Key topics in molecular docking for drug design. Int J Mol Sci. 2019;20(18):4574. doi: 10.3390/ijms20184574
   PubMed Web of Science ®Google Scholar
• Alappat B, Alappat J. Anthocyanin pigments: Beyond aesthetics. Molecules. 2020;25(23):5500. doi: 10.3390/molecules25235500
   PubMed Web of Science ®Google Scholar
• Dey R, Nandi S, Samadder A. Pelargonidin mediated selective activation of p53 and parp proteins in preventing food additive induced genotoxicity: an in vivo coupled in silico molecular docking study. Eur J Pharm Sci. 2021;156:105586. doi: 10.1016/j.ejps.2020.105586
   PubMed Web of Science ®Google Scholar
• Yaqoob P, Calder PC. The immune and inflammatory systems. In: Lanham-New, SA, Macdonald IA, Roche HM, editors. Nutrition and metabolism. Nutrition Society textbook series. 2nd ed. Chichester: Wiley-Blackwell; 2010. p. 312–338.
   Google Scholar
• Bub A, Watzl B, Blockhaus M, et al. Fruit juice consumption modulates antioxidative status, immune status and DNA damage. J Nutr Biochem. 2003;14(2):90–98. doi: 10.1016/S0955-2863(02)00255-3
   PubMed Web of Science ®Google Scholar
• Amini AM, Muzs K, Spencer JP, et al. Pelargonidin-3-O-glucoside and its metabolites have modest anti-inflammatory effects in human whole blood cultures. Nutr Res. 2017;46:88–95. doi: 10.1016/j.nutres.2017.09.006
   PubMed Web of Science ®Google Scholar
• Mohamed SM. Anthocyanins and fatty acids from the flowers of Lathyrus odoratus L. and their antimicrobial activity. Planta Med. 2009;75(9): PJ175. doi: 10.1055/s-0029-1234980
   PubMed Web of Science ®Google Scholar
• Harvey KL, Jarocki VM, Charles IG, et al. The diverse functional roles of elongation factor Tu (EF-Tu) in microbial pathogenesis. Front Microbiol. 2019;10:2351. doi: 10.3389/fmicb.2019.02351
   PubMed Web of Science ®Google Scholar
• Fu J, I M, Prasad PVV. Roles of protein synthesis elongation factor ef-tu in heat tolerance in plants. J Bot. 2012;2012:1–8. doi: 10.1155/2012/835836
   Google Scholar
• Kitchen DB, Decornez H, Furr JR, et al. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov. 2004;3(11):935–949. doi: 10.1038/nrd1549
   PubMed Web of Science ®Google Scholar
• Teague SJ. Implications of protein flexibility for drug discovery. Nat Rev Drug Discov. 2003;2(7):527–541. doi: 10.1038/nrd1129
   PubMed Web of Science ®Google Scholar
• Nandi S, Bagchi MC. 3D-QSAR and molecular docking studies of 4anilinoquinazolinederivatives: a rational approach to anticancer drug design. Mol Divers. 2010;14(1):27–38. doi: 10.1007/s11030-009-9137-9
   PubMed Web of Science ®Google Scholar
• Saxena M, Nandi S, Saxena AK. QSAR and molecular docking studies of lethal factor protease inhibitors against bacillus anthracis. SAR QSAR Environ Res. 2019;30(10):715–731. doi: 10.1080/1062936X.2019.1658219
   PubMed Web of Science ®Google Scholar
• Talavera A, Hendrix J, Versees W, et al. Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors. Sci Adv. 2018;4(3):1–14. doi: 10.1126/sciadv.aap9714
   Web of Science ®Google Scholar
• Parasuraman P. Prediction of activity spectra for substances. J Pharmacol Pharmacother. 2011;2(1):52–53. doi: 10.4103/0976-500X.77119
   PubMedGoogle Scholar
• Prasetyo WE, Purnomo H, Sadrini M, et al. Identification of potential bioactive natural compounds from indonesian medicinal plants against 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2: molecular docking, ADME/T, molecular dynamic simulations, and DFT analysis. J Biomol Struct Dyn. 2023;41(10):4467–4484. doi: 10.1080/07391102.2022.2068071
   PubMed Web of Science ®Google Scholar
• Gfeller D, Grosdidier A, Wirth M, et al. SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res. 2014;42(W1):W32–W38. doi: 10.1093/nar/gku293
   PubMed Web of Science ®Google Scholar
• Samadder A, Abraham SK, Khuda-Bukhsh AR. Nanopharmaceutical approach using pelargonidin towards enhancement of efficacy for prevention of alloxan-induced DNA damage in L6 cells via activation of PARP and p53. Environ Toxicol Pharmacol. 2016;43:27–37. doi: 10.1016/j.etap.2016.02.010
   PubMed Web of Science ®Google Scholar
• Das J, Samadder A, Das S, et al. Nanopharmaceutical approach for enhanced anti-cancer activity of betulinic acid in lung-cancer treatment via activation of PARP: interaction with dna as a target: -anti-cancerpotential of nano-betulinic acid in lung cancer. J Pharmacopunct. 2016;19(1):37–44. doi: 10.3831/KPI.2016.19.005
   PubMedGoogle Scholar
• Fessi H, Puisieux F, Devissaguet JP, et al. Nanocapsuleformation by interfacial polymer deposition following solvent displacement. Int J Pharm. 1989;55(1):R1–R4. doi: 10.1016/0378-5173(89)90281-0
   Web of Science ®Google Scholar
• Sow P, Dey S, Dey R, et al. Poly lactide-co-glycolide encapsulated nano-curcumin promoting antagonistic interactions between HSP 90 and XRCC1 proteins to preventcypermethrin-induced toxicity: An in silico predicted in vitro and in vivo approach. Colloids Surf B. 2022;220:112905. doi: 10.1016/j.colsurfb.2022.112905
   PubMed Web of Science ®Google Scholar
• Samadder A, Das J, Das S, et al. Poly(lactic-co-glycolic) acid loaded nano-insulin has greater potentials of combating arsenic induced hyperglycemia in mice: some novel findings. Toxicol Appl Pharmacol. 2013;267(1):57–73. doi: 10.1016/j.taap.2012.12.018
   PubMed Web of Science ®Google Scholar
• Horcas I, Fern´andez R, G´omez-Rodríguez JM, et al. WSXM: a software for scanning probe microscopy and a tool for nanotechnology. Rev Sci Instrum. 2017;78(1):013705. doi: 10.1063/1.2432410
   Google Scholar
• Ghosh K, Tarafdar D, Majumdar A, et al. Dipicolylamine coupled rhodamine dyes: new clefts for highly selective naked eye sensing of Cu 2+ and CN− ions. RSC Adv. 2016;6(53):47802–47812. doi: 10.1039/C6RA05036K
   Web of Science ®Google Scholar
• Samadder A, Tarafdar D, Abraham SK, et al. Nano-pelargonidin protects hyperglycemic-induced l6 cells against mitochondrial dysfunction. Planta Med. 2017;83(5):468–475. doi: 10.1055/s-0043-100017
   PubMed Web of Science ®Google Scholar
• Samadder A, Tarafdar D, Das R, et al. Efficacy of nanoencapsulated pelargonidin in ameliorating pesticide toxicity in fish and L6 cells: modulation of oxidative stress and signalling cascade. Sci Total Environ. 2019;671:466–473. doi: 10.1016/j.scitotenv.2019.03.381
   PubMed Web of Science ®Google Scholar
• Bauer AWMM, Kirby WMM, Sherris JCT, et al. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol. 1966;45:493. doi: 10.1093/ajcp/45.4_ts.493
   PubMed Web of Science ®Google Scholar
• CLSI. Performance standards for antimicrobial susceptibility testing. 30th ed. Wayne; PA: Clinical and Laboratory Standards Institute; 2020.
   Google Scholar
• Ehsan R, Alam M, Akter T, et al. Enterococcus faecalis involved in streptococcosis like infection in silver barb (Barbonymus gonionotus). Aquacult Rep. 2021;21:100868. doi: 10.1016/j.aqrep.2021.100868
   Web of Science ®Google Scholar
• EUCAST. The European committee on antimicrobial susceptibility testing. Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0. 2019;1–100.
   Google Scholar
• Dey S, Nagpal I, Sow P, et al. Morroniside interaction with poly (ADP-ribose) polymerase accentuates metabolic mitigation of alloxan-induced genotoxicity and hyperglycaemia: a molecular docking based in vitro and in vivo experimental therapeutic insight. J Biomol Struct Dyn. 2023;1–18. doi: 10.1080/07391102.2023.2246585
   Web of Science ®Google Scholar
• Mishra MP, Rath S, Swain SS, et al. In vitro antibacterial activity of crude extracts of 9 selected medicinal plants against UTI causing MDR bacteria. J King Saud Univ Sci. 2017;29(1):84–95. doi: 10.1016/j.jksus.2015.05.007
   Web of Science ®Google Scholar
• Rahman M, Rahman MM, Deb SC, et al. Molecular identification of multiple antibiotic resistant fish pathogenic Enterococcus faecalis and their control by medicinal herbs. Sci Rep. 2017;7(1):3747. doi: 10.1038/s41598-017-03673-1
   PubMedGoogle Scholar
• Malik A, Afaq S, Gamal BE, et al. Molecular docking and pharmacokinetic evaluation of natural compounds as targeted inhibitors against Crz1 protein in Rhizoctonia solani. Bioinformation. 2019;15(4):277–286. doi: 10.6026/97320630015277
   PubMed Web of Science ®Google Scholar
• Mishra M. Daphnia magna as a model organism to predict the teratogenic effect of different compounds. Methods Mol Biol. 2024;2753:261–281. doi: 10.1007/978-1-0716-3625-1_13
   PubMedGoogle Scholar
• Beceiro A, Tomás M, Bou G. Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? Clin Microbiol Rev. 2013;26(2):185–230. doi: 10.1128/cmr.00059-12
   PubMed Web of Science ®Google Scholar