Abstract
Nalidixic acid is an antibiotic drug used for treatment of Salmonellosis, a gastrointestinal infection. DNA gyrase subunit A (GyrA) of Salmonella typhimurium is the drug target for nalidixic acid. Resistance of GyrA to nalidixic acid, because of a point mutation in S. typhimurium, was recently reported. Substitution of Phe in place of Ser at locus 83 in GyrA of S. typhimurium has been experimentally associated with nalidixic acid resistance. Despite recent efforts, the mechanism of this resistance is not well understood. In this investigation we used computational techniques to address this shortcoming. Our results showed that contact with residue Arg 91 is certainly important for efficient binding of nalidixic acid to the target protein, and that mutation of this residue results in 180° rotation of the antibiotic in its binding pocket, around its own long axis. It is hoped these findings may enable development of new antibiotics against resistant forms of Salmonella.
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Abrol R, Trzaskowski B, Goddard WA, Nesterov A, Olave I, Irons C (2014) Ligand- and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor. Proc Natl Acad Sci 111:13040–13045
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucl Acids Res 38:529–533
Baucheron S, Monchaux I, Le Hello S, Weill FX, Cloeckaert A (2014) Lack of efflux mediated quinolone resistance in Salmonella enterica serovars typhi and paratyphi A. Front Microbiol 5:12
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucl Acids Res 28:235–242
Bopp CA, Brenner FW, Fields PI, Wells JG, Stockbine NA (2003) Escherichia, shigella, and salmonella. Man Clin Microbiol 1:654–671 (Ed. 8)
Capriotti E, Fariselli P, Casadio R (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucl Acids Res 33:306–310
Cloeckaert A, Chaslus-Dancla E (2001) Mechanisms of quinolone resistance in Salmonella. Vet Res 32:291–300
Crump JA, Mintz ED (2010) Global trends in typhoid and paratyphoid fever. Clin Infect Dis 50:241–246
Dhanik A, McMurray JS, Kavraki L (2012) AUTODOCK-based incremental docking protocol to improve docking of large ligands. In: proceedings of IEEE international conference on bioinformatics and biomedicine workshops (BIBMW) New York IEEE 48–55
Du QS, Huang RB, Wang CH, Li XM, Chou KC (2009) Energetic analysis of the two controversial drug binding sites of the M2 proton channel in influenza A virus. J Theor Biol 259:159–164
Edwards MJ, Flatman RH, Mitchenall LA, Stevenson CE, Le TB, Clarke TA, McKay AR, Fiedler HP, Buttner MJ, Lawson DM, Maxwell A (2009) A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase. Science 326:1415–1418
Esaki H, Morioka A, Ishihara K, Kojima A, Shiroki S, Tamura Y, Takahashi T (2004) Antimicrobial susceptibility of Salmonella isolated from cattle, swine and poultry (2001–2002): report from the Japanese veterinary antimicrobial resistance monitoring program. J Antimicrob Chemother 53:266–270
Fisher IST, Threlfall EJ (2005) The enter-net and salm-gene databases of foodborne bacterial pathogens that cause human infections in Europe and beyond: an international collaboration in surveillance and the development of intervention strategies. Epidemiol Infect 133:1–7
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416
Giraud E, Baucheron S, Cloeckaert A (2006) Resistance to fluoroquinolones in Salmonella: emerging mechanisms and resistance prevention strategies. Microbes Infect 8:1937–1944
Gromiha MM, Saranya N, Selvaraj S, Jayaram B, Fukui K (2011) Sequence and structural features of binding site residues in protein–protein complexes: comparison with protein–nucleic acid complexes. Proteome Sci 1:13
Hartigan JA (1973) Minimum evolution fits to a given tree. Biometrics 29:53–65
Hassing RJ, Goessens WH, Mevius DJ, van Pelt W, Mouton JW, Verbon A, van Genderen PJ (2013) Decreased ciprofloxacin susceptibility in salmonella typhi and paratyphi infections in ill-returned travellers: the impact on clinical outcome and future treatment options. Eur J Clin Microbiol Infect Dis 32:1295–1301
Hassing RJ, Menezes GA, van Pelt W, Petit PL, van Genderen PJ, Goessens WH (2011) Analysis of mechanisms involved in reduced susceptibility to ciprofloxacin in Salmonella enterica serotypes typhi and paratyphi A isolates from travellers to Southeast Asia. Int J Antimicrob Agents 37:240–243
Hearnshaw SJ, Edwards MJ, Stevenson CE, Lawson DM, Maxwell A (2014) A new crystal structure of the bifunctional antibiotic simocyclinone D8 bound to DNA gyrase gives fresh insight into the mechanism of inhibition. J Mol Biol 426:2023–2033
Hess B, Kutzner C, Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447
Huang RB, Du QS, Wang CH, Chou KC (2008) An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochem Biophys Res Commun 377:1243–1247
Jaenicke R (1991) Protein stability and molecular adaptation to extreme conditions. Eur J Biochem 202:715–728
Kumar S, Gadagkar SR (2000) Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. J Mol Evol 51:544–553
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948
Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand–protein interaction diagrams for drug discovery. J Chem Inf Model 51:2778–2786
Li Z, Watanabe T, Hatta M, Watanabe S, Nanbo A, Ozawa M, Kakugawa S, Shimojima M, Yamada S, Neumann G, Kawaoka Y (2009) Mutational analysis of conserved amino acids in the influenza A virus nucleoprotein. J Virol 83:4153–4162
Liu Y, Rao U, McClure J, Konopa P, Manocheewa S, Kim M, Chen L, Troyer RM, Tebit DM, Holte S, Arts EJ, Mullins JI (2014) Impact of mutations in highly conserved amino acids of the HIV-1 Gag-p24 and Env-gp120 proteins on viral replication in different genetic backgrounds. PLoS One 9:e94240
Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O’Brien SJ, Jones TF, Fazil A, Hoekstra RM (2010) The global burden of non typhoidal salmonella gastroenteritis. Clin Infect Dis 50:882–889
Meagher KL, Carlson HA (2005) Solvation influences flap collapse in HIV-1 protease. Proteins 58:119–125
Menezes GA, Harish BN, Khan MA, Goessens WH, Hays JP (2011) Antimicrobial resistance trends in blood culture positive salmonella typhi isolates from Pondicherry, India, 2005–2009. Clin Microbiol Infect 18:239–245
Michael GB, Butaye P, Cloeckaert A, Schwarz S (2006) Genes and mutations conferring antimicrobial resistance in Salmonella: an update. Microbes Infect 8:1898–1914
Mohanty S, Renuka K, Sood S, Das BK, Kapil A (2006) Natural and synthetic compounds such as trimethoprim behave as inhibitors of efflux in gram negative bacteria. Epidemiol Infect 134:961–966
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WEJ (1998) Automated docking using a lamarckian genetic algorithm and empirical binding free energy function. Comput Chem 19:1639–1662
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791
Oteo J, Aracil B, Alos JI, Gomez-Garces JL (2000) High rate of resistance to nalidixic acid in Salmonella enterica: its role as a marker of resistance to fluoroquinolones. Clin Microbiol Infect 6:273–276
Pan XS, Ambler J, Mehtar S, Fisher LM (1996) Involvement of topoisomerase IV and DNA gyrase as ciprofloxacin targets in Streptococcus pneumoniae. Antimicrob Agents Chemother 40:2321–2326
Piddock LJV (2002) Fluoroquinolone resistance in salmonella serovars isolated from humans and food animals. FEMS Microbiol Rev 26:3–16
Piddock LJV, Garvey MI, Rahman MM, Gibbons S (2010) Natural and synthetic compounds such as trimethoprim behave as inhibitors of efflux in gram negative bacteria. J Antimicrob Chemother 65:1215–1223
Pillai PK, Prakash K (1993) Current status of drug resistance and phage types of salmonella typhi in India. Indian J Med Res 97:154–158
Pires DE, Ascher DB, Blundell TL (2014) DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucl Acids Res 42:314–319
Raghav D, Sharma V (2013) An in silico evaluation of deleterious nonsynonymous single nucleotide polymorphisms in the ErbB3 oncogene. Biores Open Access 2:206–211
Rajagopal S, Vishveshwara S (2005) Short hydrogen bonds in proteins. FEBS J 272:1819–1832
Ronald AR, Low DE (2003) Fluroquinolone antibiotics. Milestones in drug theraphy Birkhauser Verlag Switzerland
Robert J, Cambau E, Grenet K, Trystram D, Péan Y, Fiévet MH, Jarlier V (2001) Trends in quinolone susceptibility of enterobacteriaceae among inpatients of a large university hospital: 1992–98. Clin Microbiol Infect 7:553–561
Ruiz J (2003) Mechanisms of resistance to quinolones: target alterations, decreased accumulation and DNA gyrase protection. J Antimicrob Chemother 51:1109–1117
Saha MR, Dutta P, Bhattacharya SK, Rasaily R, Mitra U, Dutta D, Bhattacharya MK, Pal SC (1992) Occurrence of multi-drug resistant salmonella typhi in Calcutta. Indian J Med Res 95:179–180
Sahu SK, Pandeya SN, Pathak AK (2013) In-silico identification and molecular docking studies of quinolone resistance determining region (QRDR) of E.coli DNA gyrase-a with nsubstituted piperazinyl schiff bases of gatifloxacin. Int J Drug Dev Res 5:203–210
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Satish J, Amusa AS, Gopalakrishna P (2012) In vitro activities of fluoroquinolones entrapped in non-ionic surfactant vesicles against ciprofloxacin-resistant bacteria strains. J Pharm Technol Drug Res 1:1–11
Schuttelkopf AW, Van Aalten DM (2004) PRODRG-a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr 60:1355–1363
Soto SM, Ruiz J, Mendoza MC, Vila J (2003) In vitro fluoroquinolone-resistant mutants of Salmonella enterica serotype enteritidis: analysis of mechanisms involved in resistance. Int J Antimicrob Agents 22:537–540
Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718
Sirinavin S, Garner P (2000) Antibiotics for treating salmonella gut infections. Cochrane Database Syst Rev 2:CD001167
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Velge P, Cloeckaert A, Barrow P (2005) Emergence of salmonella epidemics: the problems related to Salmonella enterica serotype enteritidis and multiple antibiotic resistance in other major serotypes. Vet Res 36:267–288
Venselaar H, TeBeek TA, Kuipers RK, Hekkelman ML, Vriend G (2010) Protein structure analysis of mutations causing inheritable diseases. BMC Bioinformat 11:548
Warren LD (2002) The PyMOL molecular graphics system. DeLano Scientific LLC, San Carlos
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucl Acids Res 1:668–672
Wong WC, Pui CF, Chai LC, Tunung R, Jeyaletchumi P, Noor Hidayah MS, Ubong A, Farinazleen MG, Cheah YK, Son R (2011) Review article Salmonella: a foodborne pathogen. Int Food Res J 18:465–473
World Health Organization: Indian Network for Surveillance of Antimicrobial Resistance (2012) Antibiogram of Salmonella enterica serovar typhi and Salmonella enterica serovar paratyphi A: a multi-centre study from India. WHO South-East Asia J Public Heal 1:182–188
Zheng J, Cui S, Meng J (2009) Effect of transcriptional activators RamA and SoxS on expression of multidrug efflux pumps AcrAB and AcrEF in fluoroquinolone-resistant salmonella typhimurium. J Antimicrob Chemother 63:95–102
Acknowledgments
The authors thank the management of VIT University for providing the facilities, support, and constant encouragement to perform this work. The authors also thank Professor M.A. Mohamed Sahul Hameed, English Division, VIT University, for English editing and grammar corrections in our manuscript.
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Preethi, B., Ramanathan, K. Molecular level understanding of resistance to nalidixic acid in Salmonella enteric serovar typhimurium associates with the S83F sequence type. Eur Biophys J 45, 35–44 (2016). https://doi.org/10.1007/s00249-015-1073-2
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DOI: https://doi.org/10.1007/s00249-015-1073-2