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Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy

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Abstract

Staphylococcus sciuri (also currently Mammaliicoccus sciuri) are anaerobic facultative and non-motile bacteria that cause significant human pathogenesis such as endocarditis, wound infections, peritonitis, UTI, and septic shock. Methicillin-resistant S. sciuri (MRSS) strains also infects animals that include healthy broilers, cattle, dogs, and pigs. The emergence of MRSS strains thereby poses a serious health threat and thrives the scientific community towards novel treatment options. Herein, we investigated the druggable genome of S. sciuri by employing subtractive genomics that resulted in seven genes/proteins where only three of them were predicted as final targets. Further mining the literature showed that the ArgS (WP_058610923), SecY (WP_058611897), and MurA (WP_058612677) are involved in the multi-drug resistance phenomenon. After constructing and verifying the 3D protein homology models, a screening process was carried out using a library of Traditional Chinese Medicine compounds (consisting of 36,043 compounds). The molecular docking and simulation studies revealed the physicochemical stability parameters of the docked TCM inhibitors in the druggable cavities of each protein target by identifying their druggability potential and maximum hydrogen bonding interactions. The simulated receptor-ligand complexes showed the conformational changes and stability index of the secondary structure elements. The root mean square deviation (RMSD) graph showed fluctuations due to structural changes in the helix-coil-helix and beta-turn-beta changes at specific points where the pattern of the RMSD and root mean square fluctuation (RMSF) (< 1.0 Å) support any major domain shifts within the structural framework of the protein–ligand complex and placement of ligand was well complemented within the binding site. The β-factor values demonstrated instability at few points while the radius of gyration for structural compactness as a time function for the 100-ns simulation of protein–ligand complexes showed favorable average values and denoted the stability of all complexes. It is assumed that such findings might facilitate researchers to robustly discover and develop effective therapeutics against S. sciuri alongside other enteric infections.

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Data is derived/used from the public domain (https://www.ncbi.nlm.nih.gov) for this work.

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Acknowledgements

We would like to acknowledge the mutual research/academic collaboration of authors from different institutions including JRC Genome Research, ICCBS, University of Karachi, Karachi-Pakistan, Department of Chemistry, Islamia College Peshawar–Pakistan, Department of Chemistry and CDTS_Oswaldo Fiocruz, RJ—CAPES, Brazil (Finance Code 001).

Funding

The authors also express their appreciation to the Deanship of Scientific Research at King Khalid University, Saudi Arabia, (Research Group Program under funding grant number: RGP. 2/370/44).

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Author notes

  1. Aafareen Khan, Saman Sohail, Seerat Yaseen, Sareen Fatima, Ayesha Wisal, Sufyan Ahmed, Mahrukh Nasir, Muhammad Irfan, Asad Karim, Zarrin Basharat, Yasmin Khan, Muhammad Aurongzeb, Syed Kashif Raza, Mohammad Y. Alshahrani, Carlos M. Morel, and Syed S. Hassan contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan

    Aafareen Khan, Saman Sohail & Ayesha Wisal

  2. Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan

    Seerat Yaseen & Sufyan Ahmed

  3. Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan

    Sareen Fatima

  4. Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan

    Mahrukh Nasir, Muhammad Irfan, Asad Karim, Yasmin Khan & Syed S. Hassan

  5. Alpha Genomics (Private) Limited, Islamabad, 44710, Pakistan

    Zarrin Basharat

  6. Faculty of Engineering Sciences & Technology, Hamdard University, Karachi, 74600, Pakistan

    Muhammad Aurongzeb

  7. Faculty of Rehabilitation and Allied Health Sciences (FRAHS), Riphah International University, Faisalabad, Pakistan

    Syed Kashif Raza

  8. Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha, 9088, Saudi Arabia

    Mohammad Y. Alshahrani

  9. Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building “Expansão”, 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil

    Carlos M. Morel & Syed S. Hassan

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  1. Aafareen Khan
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  15. Carlos M. Morel
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Conceptualization, Syed S Hassan and Aafareen Khan. Data curation, Syed S Hassan, Saman Sohail, and Aafareen Khan. Formal analysis, investigation, Zarrin Basharat. Methodology, Syed S Hassan, Saman Sohail, Muhammad Irfan. Project administration, Syed S Hassan, Mohammad Y. Alshahrani, and Carlos M. Morel. Resources, Carlos M. Morel. Software, Aafareen Khan and Saman Sohail. Supervision, Syed S Hassan. Validation, Asad Karim; Sareen Fatima, Syed Kashif Raza. Visualization, Aafareen Khan, Saman Sohail, Zarrin Basharat, Mohammad Y. Alshahrani. Writing—original draft, Aafareen Khan, Saman Sohail, Ayesha Wisal. writing—review and editing, Seerat Yaseen, Mahrukh Nasir, Sufyan Ahmed, Muhammad Aurongzeb, Muhammad Irfan, Mohammad Y. Alshahrani and Carlos M. Morel. The final manuscript was reviewed and approved by all authors.

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Correspondence to Carlos M. Morel or Syed S. Hassan.

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Khan, A., Sohail, S., Yaseen, S. et al. Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy. Funct Integr Genomics 23, 254 (2023). https://doi.org/10.1007/s10142-023-01179-w

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  • DOI: https://doi.org/10.1007/s10142-023-01179-w

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