Kinetics and Computational Evaluation of Eugenol and Vanillic Acid on Inhibition of a Potential Enzyme of a Nosocomial Pathogen that Promotes Struvite Formation

Author(s): Venkataseshan Jagannathan, Arthi Venkatesan, Pragasam Viswanathan*

Journal Name: Current Enzyme Inhibition

Volume 16 , Issue 2 , 2020

DOI : 10.2174/1573408016999200415115754

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Abstract:

Background: Struvite/infection stone is one of the major clinical burdens in urinary tract infections that is caused by the ureolytic behavior of pathogenic bacteria.

Objective: The current strategy for treating infective stones is mostly antibiotic therapy, which ends in promoting resistance to the organisms. Hence in the present study, we investigated two phytocompounds, eugenol (an allyl-substituted guaiacol) and vanillic acid (a phenolic acid) that are found to be effective in inhibiting the urease enzyme of a nosocomial pathogen Proteus mirabilis.

Methods: The enzyme was purified to apparent homogeneity and the kinetic parameters were studied in the presence and in the absence of eugenol and vanillic acid. Molecular docking and simulation were done to understand the level of protein-ligand interactions and the interacting residues.

Results: Kinetic parameters obtained from the Michaelis-Menten plot show that both eugenol and vanillic acid exhibit non-competitive inhibition of urease enzyme in a dose-dependent manner. In silico studies showed that eugenol and vanillic acid have almost similar binding affinities to the regulatory pocket of the modeled protein. Dynamics and simulation results indicate that the interaction of ligands with the ARG373 residue of the protein provides a stable bound conformation.

Conclusion: Overall, our results suggest that both the phytocompounds eugenol and vanillic acid have a potential application as a new therapy for the inhibition of urease enzyme that could possibly replace the complexions related to struvite stone formation.

Keywords: Dynamics and simulation, eugenol, struvite, urease inhibition kinetics, vanillic acid.

[1]
Tan, L.; Su, J.; Wu, D.; Yu, X.; Su, Z.; He, J.; Su, Z. Kinetics and mechanism study of competitive inhibition of jack-bean urease by baicalin. Sci.World J.,, 2013, ,2013,879501.
[http://dx.doi.org/10.1155/2013/879501]
[2]
Burne, R.A.;; Chen, Y.Y.M. Bacterial ureases in infectious diseases. Microbes Infect., .,2000, ,2(5), ,533-542.
[http://dx.doi.org/10.1016/S1286-4579(00)00312-9] [PMID: 10865198]
[3]
Krajewska,, B.;; Zaborska, W. Jack bean urease: The effect of active-site binding inhibitors on the reactivity of enzyme thiol groups. Bioorg. Chem.,, 2007,, 35(5), 355-365.
[http://dx.doi.org/10.1016/j.bioorg.2007.02.002] [PMID: 17418881]
[4]
Karlowsky, J.A.; Lagacé-Wiens, P.R.; Simner,, P.J.;; DeCorby,, M.R.;; Adam,, H.J.;; Walkty,, A.;; Hoban,, D.J.;; Zhanel,, G.G.; Antimicrobial resistance in urinary tract pathogens in Canada from 2007 to 2009: CANWARD surveillance study. Antimicrob.Agents Chemother.,, 2011, 55(7), 3169-3175.
[http://dx.doi.org/10.1128/AAC.00066-11] [PMID: 21537027]
[5]
Nicolosi,, D.;; Tempera,, G.;; Genovese,, C.;; Furneri,, P.M.; Antiadhesion activity of A2-type proanthocyanidins (a cranberry major component) on uropathogenic E. coli and P. mirabilis strains. Antibiotics (Basel), 2014,, 3,(2), ,143-154.
[http://dx.doi.org/10.3390/antibiotics3020143] [PMID: 27025740]
[6]
Schaffer,, J. N.;; Pearson,, M. M.; Proteus mirabilis and urinary tract infections. Urinary Tract Infections : Molecular Pathogenesis and Clinical Management,, 2017,, 383-433.
[http://dx.doi.org/10.1128/9781555817404.ch17]
[7]
Bichler,, K.H.;; Eipper,, E.;; Naber,, K.;; Braun,, V.;; Zimmermann,, R.;; Lahme,, S.; Urinary infection stones. Int.J.Antimicrob.Agents, 2002,, 19(6), ,488-498.
[http://dx.doi.org/10.1016/S0924-8579(02)00088-2] [PMID: 12135839]
[8]
Jagannathan,, V.;; Viswanathan,, P.; Proanthocyanidins-Will they effectively restrain conspicuous bacterial strains devolving on urinary tract infection? J. Basic Microbiol., 2018, 58(7), 567-578.
[http://dx.doi.org/10.1002/jobm.201800131] [PMID: 29775211]
[9]
Devi,, K.P.;; Sakthivel,, R.;; Nisha,, S.A.;; Suganthy,, N.;; Pandian,, S.K.; Eugenol alters the integrity of cell membrane and acts against the nosocomial pathogen Proteus mirabilis. Arch. Pharm. Res., 2013, 36(3), 282-292.
[http://dx.doi.org/10.1007/s12272-013-0028-3] [PMID: 23444040]
[10]
Rathinam,, P.;; Vijay Kumar,, H.S.;; Viswanathan,, P.; Eugenol exhibits anti-virulence properties by competitively binding to quorum sensing receptors. Biofouling,, 2017,, 33(8), ,624-639.
[http://dx.doi.org/10.1080/08927014.2017.1350655] [PMID: 28792229]
[11]
Duke,, J.A.; Duke's handbook of medicinal plants of Latin America;; crc press,, 2008.
[12]
Torzewska,, A.;; Rozalski,, A.; Inhibition of crystallization caused by Proteus mirabilis during the development of infectious urolithiasis by various phenolic substances. Microbiol. Res., 2014, 169(7-8), 579-584.
[http://dx.doi.org/10.1016/j.micres.2013.09.020] [PMID: 24239192]
[13]
Wang,, W.B.;; Lai,, H.C.;; Hsueh,, P.R.;; Chiou,, R.Y.Y.;; Lin,, S.B.;; Liaw,, S.J.; Inhibition of swarming and virulence factor expression in Proteus mirabilis by resveratrol. J. Med. Microbiol., 2006, 55(Pt 10), 1313-1321.
[http://dx.doi.org/10.1099/jmm.0.46661-0] [PMID: 17005777]
[14]
Das,, N.;; Kayastha,, A.M.;; Srivastava,, P.K.; Purification and characterization of urease from dehusked pigeonpea (Cajanus cajan L) seeds. Phytochemistry, 2002, 61(5), 513-521.
[http://dx.doi.org/10.1016/S0031-9422(02)00270-4] [PMID: 12409017]
[15]
Bradford,, M.M.; A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 1976, 72(1-2), 248-254.
[http://dx.doi.org/10.1016/0003-2697(76)90527-3] [PMID: 942051]
[16]
The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res., 2017, 45(D1), D158-D169.
[http://dx.doi.org/10.1093/nar/gkw1099] [PMID: 27899622]
[17]
Altschul,, S.F.;; Gish,, W.;; Miller,, W.;; Myers,, E.W.;; Lipman,, D.J.; Basic local alignment search tool. J. Mol. Biol., 1990, 215(3), 403-410.
[http://dx.doi.org/10.1016/S0022-2836(05)80360-2] [PMID: 2231712]
[18]
Berman,, H.M.;; Westbrook,, J.;; Feng,, Z.;; Gilliland,, G.;; Bhat,, T.N.;; Weissig,, H.;; Shindyalov,, I.N.;; Bourne,, P.E.; RCSB Protein Data Bank: Structural biology views for basic and applied research. Nucleic Acids Res., 2000, 28(1), 235-242.
[http://dx.doi.org/10.1093/nar/28.1.235] [PMID: 10592235]
[19]
Bienert,, S.;; Waterhouse,, A.;; de Beer,, T.A.;; Tauriello,, G.;; Studer,, G.;; Bordoli,, L.;; Schwede,, T.; The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Res., 2017, 45(D1), D313-D319.
[http://dx.doi.org/10.1093/nar/gkw1132] [PMID: 27899672]
[20]
Laskowski,, R.A.;; MacArthur,, M.W.;; Moss,, D.S.;; Thronton,, J.M.; PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 1993, 26, 283-291.
[http://dx.doi.org/10.1107/S0021889892009944]
[21]
Morris,, G.M.;; Huey,, R.;; Lindstrom,, W.;; Sanner,, M.F.;; Belew,, R.K.;; Goodsell,, D.S.;; Olson,, A.J. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem., 2009, 30(16), 2785-2791.
[http://dx.doi.org/10.1002/jcc.21256] [PMID: 19399780]
[22]
Guex,, N.; Peitsch,, M.C.; Schwede,, T. Automated comparative protein structure modeling with SWISSMODEL and Swiss PdbViewer: a historical perspective. Electrophoresis, 2009, S162.
[http://dx.doi.org/10.1002/elps.200900140]
[23]
Kim,, S.;; Thiessen,, P.A.;; Bolton,, E.E.;; Chen,, J.;; Fu,, G.;; Gindulyte,, A.;; Wang,, J. BS The PubChem Project. Nucleic Acids Res., 2016, 44(D1), D1202-D1213.
[http://dx.doi.org/10.1093/nar/gkv951] [PMID: 26400175]
[24]
Pronk,, S.;; Páll,, S.;; Schulz,, R.;; Larsson,, P.;; Bjelkmar,, P.;; Apostolov,, R.;; Shirts,, M.R.;; Smith,, J.C.;; Kasson,, P.M.;; van der Spoel,, D.;; Hess,, B.;; Lindahl,, E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 2013, 29(7), 845-854.
[http://dx.doi.org/10.1093/bioinformatics/btt055] [PMID: 23407358]
[25]
Braun,, A.R.;; Sachs,, J.N.;; Nagle,, J.F. Comparing simulations of lipid bilayers to scattering data: the GROMOS 43A1-S3 force field. J. Phys. Chem. B, 2013, 117(17), 5065-5072.
[http://dx.doi.org/10.1021/jp401718k] [PMID: 23560979]
[26]
van Aalten,, D.M.;; Bywater,, R.;; Findlay,, J.B.;; Hendlich,, M.;; Hooft,, R.W.;; Vriend,, G. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des., 1996, 10(3), 255-262.
[http://dx.doi.org/10.1007/BF00355047] [PMID: 8808741]
[27]
Mohammed,, S. O.; Elshahaby,, O.; Hafez,, E. E.; Mohammed,, A. K.; Ahmed,, E. Characterization and purification of urease enzyme from new proteus mirabilis strain. J. Adv. Sci. Res.,, 2014,, 5(4), 08-11.
[28]
Jones,, B.D.;; Mobley,, H.L. Genetic and biochemical diversity of ureases of Proteus, Providencia, and Morganella species isolated from urinary tract infection. Infect. Immun., 1987, 55(9), 2198-2203.
[http://dx.doi.org/10.1128/IAI.55.9.2198-2203.1987] [PMID: 3623698]
[29]
Du,, N.;; Chen,, M.;; Liu,, Z.;; Sheng,, L.;; Xu,, H.;; Chen,, S. Kinetics and mechanism of jack bean urease inhibition by Hg2+. Chem. Cent. J., 2012, 6(1), 154.
[http://dx.doi.org/10.1186/1752-153X-6-154] [PMID: 23228101]
[30]
Yu,, X.D.;; Zheng,, R.B.;; Xie,, J.H.;; Su,, J.Y.;; Huang,, X.Q.;; Wang,, Y.H.;; Zheng,, Y.F.;; Mo,, Z.Z.;; Wu;, X.L.,; Wu, D.W.; Liang, Y.E.; Zeng, H.F.; Su, Z.R.; Huang, P. Biological evaluation and molecular docking of baicalin and scutellarin as Helicobacter pylori urease inhibitors. J. Ethnopharmacol., 2015, 162, 69-78.
[http://dx.doi.org/10.1016/j.jep.2014.12.041] [PMID: 25557028]
[31]
Plaggenborg, R.; Overhage, J.; Loos, A.; Archer, J.A.; Lessard, P.; Sinskey, A.J.; Steinbüchel, A.; Priefert, H. Potential of Rhodococcus strains for biotechnological vanillin production from ferulic acid and eugenol. Appl. Microbiol. Biotechnol., 2006, 72(4), 745-755.
[http://dx.doi.org/10.1007/s00253-005-0302-5] [PMID: 16421716]
[32]
Krajewska, B.; Zaborska, W.; Leszko, M. Inhibition of chitosan-immobilized urease by slow-binding inhibitors: Ni2+, F− and acetohydroxamic acid. J. Mol. Catal., B Enzym., 2001, 14(4-6), 101-109.
[http://dx.doi.org/10.1016/S1381-1177(00)00243-5]
[33]
Kot, M.; Zaborska, W. Inhibition of jack bean urease by tetrachloro-o-benzoquinone and tetrachloro-p-benzoquinone. J. Enzyme Inhib. Med. Chem., 2006, 21(5), 537-542.
[http://dx.doi.org/10.1080/14756360600720903] [PMID: 17194024]
[34]
Krajewska, B.; van Eldik, R.; Brindell, M. Temperature- and pressure-dependent stopped-flow kinetic studies of jack bean urease. Implications for the catalytic mechanism. J. Biol. Inorg. Chem., 2012, 17(7), 1123-1134.
[http://dx.doi.org/10.1007/s00775-012-0926-8] [PMID: 22890689]
[35]
Maroney, M.J.; Ciurli, S. Nonredox nickel enzymes. Chem. Rev., 2014, 114(8), 4206-4228.
[http://dx.doi.org/10.1021/cr4004488] [PMID: 24369791]
[36]
Krajewska, B. A combined temperature-pH study of urease kinetics. Assigning pKa values to ionizable groups of the active site involved in the catalytic reaction. J. Mol. Catal., B Enzym., 2016, 124, 70-76.
[http://dx.doi.org/10.1016/j.molcatb.2015.11.021]


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Article Details

VOLUME: 16
ISSUE: 2
Year: 2020
Published on: 30 June, 2020
Page: [162 - 171]
Pages: 10
DOI: 10.2174/1573408016999200415115754
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