Identification of Inhibitors for Flagellar Assembly Protein FliN of Uropathogenic Escherichia coli using Virtual Screening and Molecular Dynamics Simulation Study

Atanasov AG, Zotchev SB, Dirsch VM, Orhan IE, Banach M, Rollinger JM, Barreca D, Weckwerth W, Bauer R, Bayer EA, Majeed M, Bishayee A, Bochkov V, Bonn GK, Braidy N, Bucar F, Cifuentes A, D’Onofrio G, Bodkin M, Supuran CT (2021) Natural products in drug discovery: advances and opportunities. Nat Rev Drug Disc 20:200–216. https://doi.org/10.1038/s41573-020-00114-z

Article  CAS  Google Scholar 

Brown PN, Mathews MAA, Joss LA, Hill CP, Blair DF (2005) Crystal structure of the flagellar rotor protein FliN from thermotoga maritima. J Bacteriol 187:2890–2902. https://doi.org/10.1128/JB.187.8.2890-2902.2005/SUPPL_FILE/TWO_FLIN_S.JPG

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cowan MM (1999) Plant products as antimicrobial agents. Clin Microbiol Rev 12:564. https://doi.org/10.1128/CMR.12.4.564

Article  CAS  PubMed  PubMed Central  Google Scholar 

Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:42717. https://doi.org/10.1038/srep42717

Article  PubMed  PubMed Central  Google Scholar 

Dallakyan S, Olson AJ (2015) Small-molecule library screening by docking with PyRx. Mol Biol 1263:243–250. https://doi.org/10.1007/978-1-4939-2269-7

Article  CAS  Google Scholar 

Drake D, Montie TC (1988) Flagella, motility and invasive virulence of Pseudomonas aeruginosa. J Gen Microbiol 134:43–52. https://doi.org/10.1099/00221287-134-1-43/CITE/REFWORKS

Article  CAS  PubMed  Google Scholar 

Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Research 34:116–118. https://doi.org/10.1093/nar/gkl282

Article  CAS  Google Scholar 

Emody L, Kerényi M, Nagy G (2003) Virulence factors of uropathogenic Escherichia coli. Int J Antimicrob Agents 22:29–33. https://doi.org/10.1016/s0924-8579(03)00236-x

Article  PubMed  Google Scholar 

Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ (2015) Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol 13:269–284. https://doi.org/10.1038/nrmicro3432

Article  CAS  PubMed  PubMed Central  Google Scholar 

Flores-mireles AL, Walker JN, Caparon M, Hultgren SJ (2016) UTIs. Nat Rev Microbiol 13:269–284. https://doi.org/10.1038/nrmicro3432.Urinary

Article  Google Scholar 

Gupta R, Verma R, Pradhan D, Jain AK, Umamaheswari A, Rai CS (2019) An in silico approach towards identification of novel drug targets in pathogenic species of Leptospira. PLoS ONE. https://doi.org/10.1371/JOURNAL.PONE.0221446

Article  PubMed  PubMed Central  Google Scholar 

Islam MI, Bae JH, Ishida T, Ridone P, Lin J, Kelso MJ, Sowa Y, Buckley BJ, Baker MAB (2021) Novel amiloride derivatives that inhibit bacterial motility across multiple strains and stator types. J Bacteriol 203:367–388. https://doi.org/10.1128/JB.00367-21/SUPPL_FILE/JB.00367-21-S0003.MP4

Article  Google Scholar 

Ivanović V, Rančić M, Arsić B, Pavlović A (2020) Lipinski’s rule of five, famous extensions and famous exceptions. Pop Sci Art 3:171–177

Google Scholar 

Josenhans C, Suerbaum S (2002) The role of motility as a virulence factor in bacteria. Int J Med Microbiol 291:605–614. https://doi.org/10.1078/1438-4221-00173

Article  CAS  PubMed  Google Scholar 

Kalia M, Singh PK, Yadav VK, Yadav BS, Sharma D, Narvi SS, Mani A, Agarwal V (2017) Structure based virtual screening for identification of potential quorum sensing inhibitors against LasR master regulator in Pseudomonas aeruginosa. Microb Pathog 107:136–143. https://doi.org/10.1016/J.MICPATH.2017.03.026

Article  CAS  PubMed  Google Scholar 

Kao CY, Lin WH, Tseng CC, Wu AB, Wang MC, Wu JJ (2014) The complex interplay among bacterial motility and virulence factors in different Escherichia coli infections. Eur J Clin Microbiol Infect Dis 33:2157–2162. https://doi.org/10.1007/S10096-014-2171-2/METRICS

Article  CAS  PubMed  Google Scholar 

Kao CY, Sheu BS, Wu JJ (2016) Helicobacter pylori infection: an overview of bacterial virulence factors and pathogenesis. Biomed J 39:14–23. https://doi.org/10.1016/J.BJ.2015.06.002

Article  PubMed  PubMed Central  Google Scholar 

Kaper JB, Nataro JP, Mobley HL (2004) Pathogenic Escherichia coli. Nat Rev Microbiol 2:123–140. https://doi.org/10.1038/nrmicro818

Article  CAS  PubMed  Google Scholar 

Kaur H, Singh V, Kalia M, Mohan B, Taneja N (2022) Identification and functional annotation of hypothetical proteins of uropathogenic Escherichia coli strain CFT073 towards designing antimicrobial drug targets. J Biomol Struct Dyn 40:14084–14095. https://doi.org/10.1080/07391102.2021.2000499

Article  CAS  PubMed  Google Scholar 

Kaza P, Mahindroo J, Veeraraghavan B, Mavuduru RS (2019) Evaluation of risk factors for colistin resistance among uropathogenic isolates of Escherichia coli and Klebsiella Pneumoniae : a case – control study. J med microbiol. https://doi.org/10.1099/jmm.0.000986

Article  PubMed  Google Scholar 

Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845–858. https://doi.org/10.1038/nprot.2015.053

Article  CAS  PubMed  PubMed Central  Google Scholar 

Köhler CD, Dobrindt U (2011) What defines extraintestinal pathogenic Escherichia coli? Int J Med Microbiol 301:642–647. https://doi.org/10.1016/j.ijmm.2011.09.006

Article  PubMed  Google Scholar 

Kulis-Horn RK, Persicke M, Kalinowski J (2014) Histidine biosynthesis, its regulation and biotechnological application in Corynebacterium glutamicum. Microb Biotechnol 7:5–25. https://doi.org/10.1111/1751-7915.12055

Article  CAS  PubMed  Google Scholar 

Liao S, Sun A, Ojcius DM, Wu S, Zhao J, Yan J (2009) Inactivation of the FliY gene encoding a flagellar motor switch protein attenuates mobility and virulence of Leptospira interrogans strain Lai. BMC Microbiol 9:1–10. https://doi.org/10.1186/1471-2180-9-253/FIGURES/8

Article  Google Scholar 

López-Blanco JR, Aliaga JI, Quintana-Ortí ES, Chacón P (2014) IMODS: internal coordinates normal mode analysis server. Nucleic Acids Res 42:271–276. https://doi.org/10.1093/nar/gku339

Article  CAS  Google Scholar 

López-Blanco JR, Aliaga JI, Quintana-Ortí ES, Chacón P (2014) iMODS: internal coordinates normal mode analysis server. Nucleic Acids Res 42:271. https://doi.org/10.1093/NAR/GKU339

Article  Google Scholar 

Maunz A, Gütlein M, Rautenberg M, Vorgrimmler D, Gebele D, Helma C, Travis KZ (2013) lazar: a modular predictive toxicology framework. Front Pharmacol 4:1–10. https://doi.org/10.3389/fphar.2013.00038

Article  CAS  Google Scholar 

McCarter LL (2001) Polar flagellar motility of the vibrionaceae. Microbiol Mol Biol Rev 65:445–462. https://doi.org/10.1128/MMBR.65.3.445-462.2001/ASSET/12F0560B-5A64-4193-9058-A2782DEB274F/ASSETS/GRAPHIC/MR0310015007.JPEG

Article  CAS  PubMed  PubMed Central  Google Scholar 

Navinraj S, Boopathi NM, Balasubramani V, Nakkeeran S, Raghu R, Gnanam R, Saranya N, Santhanakrishnan VP (2023) Molecular docking of nimbolide extracted from leaves of azadirachta indica with protein targets to confirm the antifungal, antibacterial and insecticidal activity. Indian J Microbiol 63:494–512. https://doi.org/10.1007/S12088-023-01104-6

Article  CAS  PubMed  Google Scholar 

O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an Open chemical toolbox. J Cheminf. https://doi.org/10.1186/1758-2946-3-33

Article  Google Scholar 

Paul K, Blair DF (2006) Organization of FliN subunits in the flagellar motor of Escherichia coli. J bacteriol 188:2502–2511. https://doi.org/10.1128/JB.188.7.2502

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peirano G, Schreckenberger PC, Pitout JDD (2011) Characteristics of NDM-1-producing Escherichia coli isolates that belong to the successful and virulent clone ST131. Antimicrob Agents Chemother 55:2986–2988. https://doi.org/10.1128/AAC.01763-10

Article  CAS  PubMed  PubMed Central  Google Scholar 

Singhal L, Shrivastava A, Kumar N, Shekhar Sharma C (2023) Screening of Zinc database to identify MurB enzyme inhibitors for Staphylococcus aureus pathogen. Eur Chem Bull 12:11450–11463

CAS  Google Scholar 

Steffen C, Thomas K, Huniar U, Hellweg A, Rubner O, Schroer A (2010) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J Comput Chem 31:2967–2970. https://doi.org/10.1002/jcc

Article  CAS  PubMed  Google Scholar 

Sterling T, Irwin JJ (2015) ZINC 15 - Ligand discovery for everyone. J Chem Inf Model 55:2324–2337. https://doi.org/10.1021/acs.jcim.5b00559

Article  CAS 

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