1887

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Volume 69, Issue 8

Molecular docking, dynamics and free energy analyses of OXA class enzymes with carbapenems investigating their hydrolytic mechanisms Free

Abstract

is a critical priority pathogen listed by the World Health Organization due to increasing levels of resistance to carbapenem classes of antibiotics. It causes wound and other nosocomial infections, which can be life-threatening. Hence, there is an urgent need for the development of new classes of antibiotics.

To study the interaction of carabapenems with class D beta-lactamases (oxacillinases) and analyse drug resistance by studying enzyme–substrate complexes using modelling approaches as a means of establishing correlations with the phenotypic data.

The three-dimensional structures of carbapenems (doripenem, ertapenem, imipenem and meropenem) were obtained from DrugBank and screened against class D beta-lactamases. Further, the study was extended with their variants. The variants’ structure was homology-modelled using the Schrödinger Prime module (Schrödinger LLC, NY, USA).

The first discovered intrinsic beta-lactamase of , OXA-51, had a binding energy value of −40.984 kcal mol, whereas other OXA-51 variants, such as OXA-64, OXA-110 and OXA-111, have values of −60.638, –66.756 and −67.751 kcal mol, respectively. The free energy values of OXA-51 variants produced better results than those of other groups.

Imipenem and meropenem showed MIC values of 2 and 8 µg ml, respectively against OXA-51 in earlier studies, indicating that these are the most effective drugs for treatment of infection. According to our results, OXA-51 is an active enzyme that shows better interactions and is capable of hydrolyzing carbapenems. When correlating the hydrogen-bonding interaction with MIC values, the predicted results are in good agreement and might provide initial insights into performing similar studies related to OXA variants or other antibiotic–enzyme-based studies.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Acinetobacter baumannii , antibiotic resistance , carbapenems , class D beta lactams , Gram-negative bacteria , life-threatening disease and OXA-51
Funding
This study was supported by the:
  • DST Indo Taiwan project (Award GITA/DST/TWN/P-86/2019 Dated: 04/03/2020)
    • Principle Award Recipient: Jeyakanthan Jeyaraman
  • MHRD-RUSA 2.0, New Delhi (Award F.24-51/2014-U, Policy (TNMulti-Gen), Dept. of Edn. Govt. of India, Dt. 09.10.2018)
    • Principle Award Recipient: Jeyakanthan Jeyaraman
  • Department of Science and Technology, Ministry of Science and Technology (IN) (Award File No. EMR/2016/000498 dated: 26.09.2016)
    • Principle Award Recipient: Jeyakanthan Jeyaraman
  • Research Grants Council, University Grants Committee (HK) (Award UGC-RA-2016-18-OB-AM-7124 dated: 18.04.2016)
    • Principle Award Recipient: Jeyakanthan Jeyaraman
  • DST – Promotion of University Research and Scientific Excellence (PURSE) (Award No. SR/PURSE Phase2/38)
    • Principle Award Recipient: Jeyakanthan Jeyaraman
  • DST – FIST (Award SR/FST/LSI-667/2016)
© 2020 The Authors
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2020-08-10
2024-12-07
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Molecular docking, dynamics and free energy analyses of Acinetobacter baumannii OXA class enzymes with carbapenems investigating their hydrolytic mechanisms
J. Med. Microbiol. 69, 1062 (2020); https://doi.org/10.1099/jmm.0.001233
/content/journal/jmm/10.1099/jmm.0.001233
/content/journal/jmm/10.1099/jmm.0.001233
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