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Article

In Vitro and In Silico Approaches for the Evaluation of Antimicrobial Activity, Time-Kill Kinetics, and Anti-Biofilm Potential of Thymoquinone (2-Methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione) against Selected Human Pathogens

1
Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah 51911, Saudi Arabia
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Department of Biosciences, COMSATS University Islamabad, Islamabad 45600, Pakistan
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Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
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Department of Biotechnology, Faculty of Biosciences, Invertis University, Bareilly 243123, India
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Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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Department of Microbiology, KTHM College, Savitribai Phule Pune University (SPPU), Nashik 422002, India
*
Authors to whom correspondence should be addressed.
Academic Editors: Roberta Colicchio, Chiara Pagliuca and Jean-Marc Sabatier
Antibiotics 2022, 11(1), 79; https://doi.org/10.3390/antibiotics11010079
Received: 5 December 2021 / Revised: 30 December 2021 / Accepted: 1 January 2022 / Published: 10 January 2022
Thymoquinone (2-methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione; TQ), a principal bioactive phytoconstituent of Nigella sativa essential oil, has been reported to have high antimicrobial potential. Thus, the current study evaluated TQ’s antimicrobial potential against a range of selected human pathogens using in vitro assays, including time-kill kinetics and anti-biofilm activity. In silico molecular docking of TQ against several antimicrobial target proteins and a detailed intermolecular interaction analysis was performed, including binding energies and docking feasibility. Of the tested bacteria and fungi, S. epidermidis ATCC 12228 and Candida albicans ATCC 10231 were the most susceptible to TQ, with 50.3 ± 0.3 mm and 21.1 ± 0.1 mm zones of inhibition, respectively. Minimum inhibitory concentration (MIC) values of TQ are in the range of 12.5–50 µg/mL, while minimum biocidal concentration (MBC) values are in the range of 25–100 µg/mL against the tested organisms. Time-kill kinetics of TQ revealed that the killing time for the tested bacteria is in the range of 1–6 h with the MBC of TQ. Anti-biofilm activity results demonstrate that the minimum biofilm inhibitory concentration (MBIC) values of TQ are in the range of 25–50 µg/mL, while the minimum biofilm eradication concentration (MBEC) values are in the range of 25–100 µg/mL, for the tested bacteria. In silico molecular docking studies revealed four preferred antibacterial and antifungal target proteins for TQ: D-alanyl-D-alanine synthetase (Ddl) from Thermus thermophilus, transcriptional regulator qacR from Staphylococcus aureus, N-myristoyltransferase from Candida albicans, and NADPH-dependent D-xylose reductase from Candida tenuis. In contrast, the nitroreductase family protein from Bacillus cereus and spore coat polysaccharide biosynthesis protein from Bacillus subtilis and UDP-N-acetylglucosamine pyrophosphorylase from Aspergillus fumigatus are the least preferred antibacterial and antifungal target proteins for TQ, respectively. Molecular dynamics (MD) simulations revealed that TQ could bind to all four target proteins, with Ddl and NADPH-dependent D-xylose reductase being the most efficient. Our findings corroborate TQ’s high antimicrobial potential, suggesting it may be a promising drug candidate for multi-drug resistant (MDR) pathogens, notably Gram-positive bacteria and Candida albicans. View Full-Text
Keywords: antimicrobial activity; anti-biofilm activity; molecular docking; molecular dynamics simulations; time-kill kinetics; thymoquinone antimicrobial activity; anti-biofilm activity; molecular docking; molecular dynamics simulations; time-kill kinetics; thymoquinone
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MDPI and ACS Style

Qureshi, K.A.; Imtiaz, M.; Parvez, A.; Rai, P.K.; Jaremko, M.; Emwas, A.-H.; Bholay, A.D.; Fatmi, M.Q. In Vitro and In Silico Approaches for the Evaluation of Antimicrobial Activity, Time-Kill Kinetics, and Anti-Biofilm Potential of Thymoquinone (2-Methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione) against Selected Human Pathogens. Antibiotics 2022, 11, 79. https://doi.org/10.3390/antibiotics11010079

AMA Style

Qureshi KA, Imtiaz M, Parvez A, Rai PK, Jaremko M, Emwas A-H, Bholay AD, Fatmi MQ. In Vitro and In Silico Approaches for the Evaluation of Antimicrobial Activity, Time-Kill Kinetics, and Anti-Biofilm Potential of Thymoquinone (2-Methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione) against Selected Human Pathogens. Antibiotics. 2022; 11(1):79. https://doi.org/10.3390/antibiotics11010079

Chicago/Turabian Style

Qureshi, Kamal A., Mahrukh Imtiaz, Adil Parvez, Pankaj K. Rai, Mariusz Jaremko, Abdul-Hamid Emwas, Avinash D. Bholay, and Muhammad Qaiser Fatmi. 2022. "In Vitro and In Silico Approaches for the Evaluation of Antimicrobial Activity, Time-Kill Kinetics, and Anti-Biofilm Potential of Thymoquinone (2-Methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione) against Selected Human Pathogens" Antibiotics 11, no. 1: 79. https://doi.org/10.3390/antibiotics11010079

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