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Interaction of dihydrofolate reductase and aminoglycoside adenyltransferase enzyme from Klebsiella pneumoniae multidrug resistant strain DF12SA with clindamycin: a molecular modelling and docking study

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Abstract

Klebsiella pneumoniae strain DF12SA (HQ114261) was isolated from diabetic foot wounds. The strain showed resistance against ampicillin, kanamycin, gentamicin, streptomycin, spectinomycin, trimethoprim, tetracycline, meropenem, amikacin, piperacillin/tazobactam, augmentin, co-trimoxazole, carbapenems, penicillins and cefoperazone, and was sensitive to clindamycin. Molecular characterization of the multidrug-resistance phenotype revealed the presence of a class 1 integron containing two genes, a dihydrofolate reductase (DHFR) (PF00186), which confers resistance to trimethoprim; and aminoglycoside adenyltransferase (AadA) (PF01909), which confers resistance to streptomycin and spectinomycin. A class 1 integron in K. pneumoniae containing these two genes was present in eight (18.18 %) out of 44 different diabetic foot ulcer (DFU) patients. Hence, there is a need to develop therapeutics that inhibit growth of multidrug resistant K. pneumoniae in DFU patients and still achieve amputation control. Am attempt was made to create a 3D model and find a suitable inhibitor using an in silico study. Rational drug design/testing requires crystal structures for DHFR and AadA. However, the structures of DHFR and AadA from K. pneumoniae are not available. Modelling was performed using Swiss Model Server and Discovery Studio 3.1. The PDBSum server was used to check stereo chemical properties using Ramachandran plot analysis of modeled structures. Clindamycin was found to be suitable inhibitor of DHFR and AadA. A DockingServer based on Autodock & Mopac was used for docking calculations. The amino acid residues Ser32, Ile46, Glu53, Gln54, Phe57, Thr72, Met76, Val78, Leu79, Ser122, Tyr128, Ile151 in case of DHFR and Phe34, Asp60, Arg63, Gln64, Leu68, Glu87, Thr89, Val90 for AadA were found to be responsible for positioning clindamycin into the active site. The study identifies amino acid residues crucial to ‘DHFR and AadA -drug’ and ‘DHFR and AadA -inhibitor’ interactions that might be useful in the ongoing search for a versatile DHFR and AadA -inhibitor.

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References

  1. Gadepalli R, Dhawan B, Sreenivas V, Kapil A, Ammini AC, Chaudhry R (2006) A clinico-microbiological study of diabetic foot ulcers in an Indian tertiary care hospital. Diabetes Care 29:1727–1732

    Article  Google Scholar 

  2. Pinzur MS, Slovenkai MP, Trepman E, Shields NN (2005) Guidelines for diabetic foot care: recommendations endorsed by the diabetes committee of the American orthopaedic foot and ankle society. Foot Ankle Int 26:113–119

    Google Scholar 

  3. Lipsky BA, Berendt AR, Deery HG, Embi JM, Joseph WS, Karchmer AW, LeFrock JL, Lew DP, Mader JT, Norden C, Tan JS (2004) Diagnosis and treatment of diabetic foot infections. Clin Infect Diseases 39:885–910

    Article  Google Scholar 

  4. Chincholikar DA, Pal RB (2002) Study of fungal and bacterial infections of the diabetic foot. Indian J Pathol Microbiol 45:15–22

    Google Scholar 

  5. Umadevi S, Kumar S, Joseph NM, Easow JM, Kandhakumari G, Srirangaraj S, Raj S, Stephen S (2011) Microbiological study of diabetic foot infections. Indian J Med Specialit 2:12–17

    Google Scholar 

  6. Kawai T (2006) Hypermucoviscosity: an extremely sticky phenotype of Klebsiella pneumoniae associated with emerging destructive tissue abscess syndrome. Clin Infect Dis 42:1359–1361

    Article  CAS  Google Scholar 

  7. Jones ME, Peters E, Weersink AM, Fluit A, Verhoef J (1997) Widespread occurrence of integrons causing multiple antibiotic resistances in bacteria. Lancet 349:1742–1743

    Article  CAS  Google Scholar 

  8. El-Najjar NG, Farah MJ, Hashwa FA, Tokajian ST (2010) Antibiotic resistance patterns and sequencing of class I integron from uropathogenic Escherichia coli in Lebanon. Lett Appl Microbiol 51:456–461

    Article  CAS  Google Scholar 

  9. Mazel D (2006) Integrons: agents of bacterial evolution. Nat Rev Microbiol 4:608–620

    Article  CAS  Google Scholar 

  10. Gebreyes WA, Altier C (2002) Molecular characterization of multidrug-resistant Salmonella enterica subsp. enterica serovar Typhimurium isolates from swine. J Clin Microbiol 40:2813–2822

    Article  CAS  Google Scholar 

  11. Holger C, Smith DEC, Blom H, Blau N, Bode H, Holzmann K, Pannicke U, Hopfner KP, Rump EM, Ayric Z, Kohne E, Debatin KM, Smulders Y, Schwarz K (2011) Dihydrofolate reductase deficiency due to a homozygous DHFR mutation causes megaloblastic anemia and cerebral folate deficiency leading to severe neurologic disease. Am Soc Human Genet 88:226–231

    Article  Google Scholar 

  12. Schnell JR, Dyson HJ, Wright PE (2004) Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu Rev Biophys Biomol Struct 33:119–140

    Article  CAS  Google Scholar 

  13. Thomas D, Guenter A, Gerd B, Uwe J, Tarmo P, Robert H, Rainer J (2000) The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability. J Mol Biol 297:659–672

    Article  Google Scholar 

  14. Azucena E, Grapsas I, Mobashery S (1997) Properties of a bifunctional bacterial antibiotic resistance enzyme that catalyzes ATP dependent 2″-phosphorylation and acetyl-CoA dependent 6′-acetylation of aminoglycosides. J Am Chem Soc 119:2317–2318

    Article  CAS  Google Scholar 

  15. Ferretti JJ, Gilmore KS, Courvallin P (1986) Nucleotide sequence analysis of the gene specifying the bifunctional 6′-aminoglycoside acetyltransferase 2″-aminoglycoside phosphotransferase enzyme in Streptococcus faecalis and identification and cloning of gene regions specifying the two activities. J Bacteriol 167:631–638

    CAS  Google Scholar 

  16. Wagner FW (1981) The dysvascular foot: a system for diagnosis and treatment. Foot Ankle 2:64–122

    Google Scholar 

  17. Bauer AW, Kirby WM, Sherris JC, Turck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Patholo 45:493–496

    CAS  Google Scholar 

  18. Clinical and Laboratory Standards Institute (2007) Performance standards for antimicrobial susceptibility testing: Seventeenth informational supplement. Wayne, PA, pp M100–S17

  19. Levesque C, Piche L, Larose C, Roy P (1995) PCR mapping of integrons reveals several novel combinations of resistance genes. Antimicrob Agents Chemother 39:185–191

    Article  CAS  Google Scholar 

  20. Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7:1–10

    Article  Google Scholar 

  21. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:116–120

    Article  Google Scholar 

  22. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  Google Scholar 

  23. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biol Evol 24:1596–1599

    Article  CAS  Google Scholar 

  24. Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14:48–54

    Article  CAS  Google Scholar 

  25. Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:369–373

    Article  Google Scholar 

  26. Gao YD, Huang JF (2011) An extension strategy of Discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level (in Chinese). Zool Res 32:262–266

    CAS  Google Scholar 

  27. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL Workspace: a web-based environment for protein structure homology modeling. Bioinformatics 22:195–201

    Article  CAS  Google Scholar 

  28. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31:3381–3385

    Article  CAS  Google Scholar 

  29. Laskowski RA, Chistyakov VV, Thornton JM (2005) D266-8 PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33:266–268

    Article  Google Scholar 

  30. Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004) SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res 1(2):W590–W594

    Article  Google Scholar 

  31. Bikadi Z, Hazai E (2009) Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. J Chem Inf 11:1–15

    Google Scholar 

  32. Solis FJ, Wets RJB (1981) Minimization by random search techniques. Math Operations Res 6:19–30

    Article  Google Scholar 

  33. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Arthur JO (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639–1662

    Article  CAS  Google Scholar 

  34. Rice LB, Sahm D, Bonomo RA (2003) Mechanisms of resistance to antibacterial agents. In: Murray PR, Baron EJ, Pfaller MA, Jorgensen JH, Yolken RH (eds) Manual of clinical microbiology, 8th edn. ASM Press, Washington DC, pp 1074–1101

    Google Scholar 

  35. Lee J, Yennawar NH, Gam J, Benkovic SJ (2010) Kinetic and structural characterization of dihydrofolate reductase from Streptococcus pneumoniae. Biochemistry 49:195–206

    Article  CAS  Google Scholar 

  36. She Q, Singh RK, Confalonieri F et al. (2007) Crystal structure of a putative nucleotidyltransferase (AAK41883.1) from Sulfolobus solfataricus at 1.40 Å resolution. Joint Center for Structural Genomics Submitted to the PDB data bank, doi:10.2210/pdb2rff/pdb

  37. Feeney J, Birdsall B, Kovalevskaya NV, Smurnyy YD, Navarro Peran EM, Polshakov VI (2011) NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions. Biochemistry 50:3609–3620

    Article  CAS  Google Scholar 

  38. Cody V, Galitsky N, Rak D, Luft JR, Pangborn W, Queener SF (1999) Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+. Biochemistry 38:4303–4312

    Article  CAS  Google Scholar 

  39. Gargaro AR, Soteriou A, Frenkiel TA, Bauer CJ, Birdsall B, Polshakov VI, Barsukov IL, Roberts GC, Feeney J (1998) The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate. J Mol Biol 20:119–134

    Article  Google Scholar 

  40. Vidya N, Vadivukkarasi B, Manivannan G, Anbarasu K (2008) Molecular modeling and docking studies of glutamate racemase in Vibrio vulnificus CMCP6. Silico Biol 8:471–483

    CAS  Google Scholar 

  41. Pedersen LC, Benning MM, Holden HM (1995) Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase. Biochemistry 34:13305–13311

    Article  CAS  Google Scholar 

Download references

Acknowledgments

S.K.S. is grateful to the Indian Council of Medical Research, New Delhi (India), for the award of Senior Research Fellowship (80/622/2009-ECD-1). This work is partially supported by a research grant sanctioned to A.K. by the Indian Agricultural Research Institute (No. NBAIM/AMAAS/MD (19)/AK/BG), New Delhi. The facilities provided by Department of Biotechnology (DBT)-funded Sub-Distributed Information Centre (SUB-DIC), Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University (BHU), Varanasi, is gratefully acknowledged.

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Authors and Affiliations

  1. School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi, 221005, India

    Shailesh K. Shahi, Vinay K. Singh & Ashok Kumar

  2. Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India

    Sanjeev K. Gupta

  3. Department of Endocrinology and Metabolism, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India

    Surya K. Singh

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  1. Shailesh K. Shahi
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Correspondence to Ashok Kumar.

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Shahi, S.K., Singh, V.K., Kumar, A. et al. Interaction of dihydrofolate reductase and aminoglycoside adenyltransferase enzyme from Klebsiella pneumoniae multidrug resistant strain DF12SA with clindamycin: a molecular modelling and docking study. J Mol Model 19, 973–983 (2013). https://doi.org/10.1007/s00894-012-1635-5

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