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Mechanistic Approach of Effective Combination of Antibiotics Against Clinical Bacterial Strains Having New Delhi Metallo-Beta-Lactamase Variants and Functional Gain Laboratory Mutant

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Abstract

Antimicrobial resistance has emerged as a serious issue for physicians and health-care workers treating infections that could lead to the next pandemic. One of the key resistance mechanisms is beta-lactamases. Although several beta-lactamase inhibitors in combination with antibiotics have been created and are being utilized in clinical settings, resistance to these formulations has also been evolving in the bacterial population due to their distinct targets. In this study we used effective combination of antibiotic as an approach to inhibit multidrug resistance bacteria. We used four combinations and checked its efficacy against NDM (New Delhi Metallo-beta-lactamase) variants and functional gain laboratory mutant by employing FICI, enzyme kinetics, fluorescence and computational biology approaches (Docking and Molecular Dynamics Simulation). FICI values of all the combinations were either less than 0.5 or equal to 0.5. Binding features acquired by spectroscopic techniques showed important interaction and complex formation between drugs and enzymes with decreased ksv and kq values. In steady-state kinetics, a reduction in hydrolytic efficiency of enzymes was shown by cooperative binding behaviour when they were treated with different drugs. We have also tested functional gain laboratory mutant developed in our lab, keeping in view that if in future upcoming variants of this kind be emerged then these mutants could also be subsided by combinational therapy. This study identifies three other combinations better than fluoroquinolones effective against NDM variants and laboratory mutant.

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References

  1. Martinez JL (2014) General principles of antibiotic resistance in bacteria. Drug Discov Today Technol 11:33–39. https://doi.org/10.1016/j.ddtec.2014.02.001

    Article  PubMed  Google Scholar 

  2. Miller WR, Munita JM, Arias CA (2014) Mechanisms of antibiotic resistance in enterococci. Expert Rev Anti Infect Ther 12:1221–1236. https://doi.org/10.1586/14787210.2014.956092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Roca I, Akova M, Baquero F et al (2015) The global threat of antimicrobial resistance: science for intervention. New Microbes New Infect 6:22–29. https://doi.org/10.1016/j.nmni.2015.02.007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Bodi M, Ardanuy C, Rello J (2001) Impact of Gram-positive resistance on outcome of nosocomial pneumonia. Crit Care Med 29:N82–N86. https://doi.org/10.1097/00003246-200104001-00005

    Article  CAS  PubMed  Google Scholar 

  5. Safdar N, Handelsman J, Maki DG (2004) Does combination antimicrobial therapy reduce mortality in Gram-negative bacteraemia? A meta-analysis. Lancet Infect Dis 4:519–527. https://doi.org/10.1016/S1473-3099(04)01108-9

    Article  PubMed  Google Scholar 

  6. Mouton JW (1999) Combination therapy as a tool to prevent emergence of bacterial resistance. Infection 27:S24–S28. https://doi.org/10.1007/BF02561666

    Article  PubMed  Google Scholar 

  7. From the American Association of Neurological Surgeons (AANS), American Society of Neuroradiology (ASNR), Cardiovascular and Interventional Radiology Society of Europe (CIRSE), Canadian Interventional Radiology Association (CIRA), Congress of Neurological and WSO (WSO), Sacks D, Baxter B et al (2018) Multisociety consensus quality improvement revised consensus statement for endovascular therapy of acute ischemic stroke. Int J Stroke 13:612–632. https://doi.org/10.1177/1747493018778713

    Article  Google Scholar 

  8. Paul M, Lador A, Grozinsky-Glasberg S, Leibovici L (2014) Beta lactam antibiotic monotherapy versus beta lactam-aminoglycoside antibiotic combination therapy for sepsis. Cochrane Database Syst Rev. https://doi.org/10.1002/14651858.CD003344.pub3

    Article  PubMed  PubMed Central  Google Scholar 

  9. Tamma PD, Cosgrove SE, Maragakis LL (2012) Combination therapy for treatment of infections with gram-negative bacteria. Clin Microbiol Rev 25:450–470. https://doi.org/10.1128/CMR.05041-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Paul M, Carmeli Y, Durante-Mangoni E et al (2014) Combination therapy for carbapenem-resistant Gram-negative bacteria. J Antimicrob Chemother 69:2305–2309. https://doi.org/10.1093/jac/dku168

    Article  CAS  PubMed  Google Scholar 

  11. Ali A, Gupta D, Srivastava G et al (2019) Molecular and computational approaches to understand resistance of New Delhi metallo β-lactamase variants (NDM-1, NDM-4, NDM-5, NDM-6, NDM-7)-producing strains against carbapenems. J Biomol Struct Dyn 37:2061–2071. https://doi.org/10.1080/07391102.2018.1475261

    Article  CAS  PubMed  Google Scholar 

  12. Ali A, Azam MW, Khan AU (2018) Non-active site mutation (Q123A) in New Delhi metallo-β-lactamase (NDM-1) enhanced its enzyme activity. Int J Biol Macromol 112:1272–1277. https://doi.org/10.1016/j.ijbiomac.2018.02.091

    Article  CAS  PubMed  Google Scholar 

  13. Farhat N, Gupta D, Ali A et al (2022) Broad-spectrum inhibitors against class A, B, and C Type β-lactamases to block the hydrolysis against antibiotics: kinetics and structural characterization. Microbiol Spectr. https://doi.org/10.1128/spectrum.00450-22

    Article  PubMed  PubMed Central  Google Scholar 

  14. Farhat N, Ali A, Waheed M et al (2022) Chemically synthesised flavone and coumarin based isoxazole derivatives as broad spectrum inhibitors of serine β-lactamases and metallo-β-lactamases: a computational, biophysical and biochemical study. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2022.2099977

    Article  PubMed  Google Scholar 

  15. Galleni M, Franceschini N, Quinting B et al (1994) Use of the chromosomal class A beta-lactamase of Mycobacterium fortuitum D316 to study potentially poor substrates and inhibitory beta-lactam compounds. Antimicrob Agents Chemother 38:1608–1614. https://doi.org/10.1128/AAC.38.7.1608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Farhat N, Khan AU (2021) Repurposing drug molecule against SARS-Cov-2 (COVID-19) through molecular docking and dynamics: a quick approach to pick FDA-approved drugs. J Mol Model 27:1–11. https://doi.org/10.1007/s00894-021-04923-w

    Article  CAS  Google Scholar 

  17. Kim S, Chen J, Cheng T et al (2019) PubChem 2019 update: improved access to chemical data. Nucleic Acids Res 47:D1102–D1109. https://doi.org/10.1093/nar/gky1033

    Article  PubMed  Google Scholar 

  18. Biasini M, Bienert S, Waterhouse A et al (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258. https://doi.org/10.1093/nar/gku340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Benkert P, Künzli M, Schwede T (2009) QMEAN server for protein model quality estimation. Nucleic Acids Res 37:W510–W514. https://doi.org/10.1093/nar/gkp322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291. https://doi.org/10.1107/S0021889892009944

    Article  CAS  Google Scholar 

  21. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–W410. https://doi.org/10.1093/nar/gkm290

    Article  PubMed  PubMed Central  Google Scholar 

  22. Sievers F, Wilm A, Dineen D et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. https://doi.org/10.1038/msb.2011.75

    Article  PubMed  PubMed Central  Google Scholar 

  23. Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245:43–53. https://doi.org/10.1016/S0022-2836(95)80037-9

    Article  CAS  PubMed  Google Scholar 

  24. Beg AZ, Farhat N, Khan AU (2021) Designing multi-epitope vaccine candidates against functional amyloids in Pseudomonas aeruginosa through immunoinformatic and structural bioinformatics approach. Infect Genet Evol 93:104982. https://doi.org/10.1016/j.meegid.2021.104982

    Article  CAS  PubMed  Google Scholar 

  25. Schüttelkopf AW, van Aalten DMF (2004) PRODRG : a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr Sect D Biol Crystallogr 60:1355–1363. https://doi.org/10.1107/S0907444904011679

    Article  CAS  Google Scholar 

  26. Sharma M, Farhat N, Khan AU et al (2023) Studies on the interaction of 2,4-dibromophenol with human hemoglobin using multi-spectroscopic, molecular docking and molecular dynamics techniques. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2023.2264975

    Article  PubMed  Google Scholar 

  27. Chen Z, Xu H, Zhu Y et al (2014) Understanding the fate of an anesthetic, nalorphine upon interaction with human serum albumin: a photophysical and mass-spectroscopy approach. RSC Adv 4:25410–25419. https://doi.org/10.1039/C4RA03541K

    Article  CAS  Google Scholar 

  28. Palm GJ, Lederer T, Orth P et al (2008) Specific binding of divalent metal ions to tetracycline and to the Tet repressor/tetracycline complex. JBIC J Biol Inorg Chem 13:1097–1110. https://doi.org/10.1007/s00775-008-0395-2

    Article  CAS  PubMed  Google Scholar 

  29. Hancock RE, Farmer SW, Li ZS, Poole K (1991) Interaction of aminoglycosides with the outer membranes and purified lipopolysaccharide and OmpF porin of Escherichia coli. Antimicrob Agents Chemother 35:1309–1314. https://doi.org/10.1128/AAC.35.7.1309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Dalhoff A (2021) Selective toxicity of antibacterial agents—still a valid concept or do we miss chances and ignore risks? Infection 49:29–56. https://doi.org/10.1007/s15010-020-01536-y

    Article  CAS  PubMed  Google Scholar 

  31. Michalak K, Sobolewska-Włodarczyk A, Włodarczyk M et al (2017) Treatment of the fluoroquinolone-associated disability: the pathobiochemical implications. Oxid Med Cell Longev 2017:1–15. https://doi.org/10.1155/2017/8023935

    Article  CAS  Google Scholar 

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Acknowledgements

We acknowledge the facility and support provided by the Department of Biotechnology, Ministry of science and technology, Government of India.

Funding

We acknowledge funding from the DBT, Government of India, Grant No. BT/PR40148/BTIS/137/20/2021, Tata Innovation Fellowship, BT/HRD/TIF/09/04/2021-22 and NNP DBT GRANT: BT/PR40180/BTIS/137/59/2023. NF is also recipient of senior research fellow from mentioned project.

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Authors and Affiliations

  1. Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India

    Nabeela Farhat, Sameera Mujahid & Asad U. Khan

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  1. Nabeela Farhat
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  2. Sameera Mujahid
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  3. Asad U. Khan
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NF, performed all experiments and wrote manuscript, SM, performed some of the experiments, AUK, conceived problem and guided the study provided resources and checked first draft of manuscript.

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Correspondence to Asad U. Khan.

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Farhat, N., Mujahid, S. & Khan, A.U. Mechanistic Approach of Effective Combination of Antibiotics Against Clinical Bacterial Strains Having New Delhi Metallo-Beta-Lactamase Variants and Functional Gain Laboratory Mutant. Curr Microbiol 81, 41 (2024). https://doi.org/10.1007/s00284-023-03553-0

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