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In silico evaluation of natural compounds to confirm their anti-DNA gyrase activity

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title In silico evaluation of natural compounds to confirm their anti-DNA gyrase activity
 
Creator Kumar, Reetesh
Srivastava, Yogesh
Maji, Somnath
Siddiqui, Seemab
Tyagi, Rajeev Kumar
Muthuramalingam, Pandiyan
Singh, Sunil Kumar
Tiwari, Savitri
Verma, Geetika
Thomazella, Daniela Paula de Toledo
Shin, Hyunsuk
Prajapati, Dinesh Kumar
Rai, Pankaj Kumar
Beura , Samir Kumar
Panigrahi, Abhishek Ramachandra
Moraes , Fabio Rogerio de
Rao , Pasupuleti Visweswara
 
Subject QR Microbiology
 
Description The slow clearance of bacteria owing to drug resistance to the currently available antibiotics has been a global public health issue. The development of antibiotic resistance in Staphylococcus aureus has become prevalent in community-acquired infections, posing a significant challenge. DNA gyrase, an enzyme essential in all bacteria but absent in higher eukaryotes, emerges as an attractive target for novel antibacterial agents. This type II topoisomerase introduces negative supercoils in double-stranded DNA, at the expense of ATP, during DNA replication. In this study, we conducted a comprehensive screening of natural compound libraries from the ZINC database using different computational approaches targeting DNA gyrase activity. We identified five promising compounds following a detailed screening of drug-like compounds using pharmacokinetic-based studies, including the determination of the compound absorption, distribution, metabolism, excretion, and toxicity. Furthermore, based on protein–ligand docking studies, we showed the position, orientation, and binding affinity of the selected compounds within the active site of DNA gyrase. Overall, our study provides a primary reference to explore the molecular mechanisms associated with the antibacterial activity of the selected compounds, representing an important step toward the discovery of novel DNA gyrase inhibitors. Further investigation involving structural optimization as well as comprehensive in vivo and in vitro evaluations are necessary to fully explore the potential of these chemicals as effective antibacterial agents.
 
Publisher SPRINGER LINK
 
Date 2023-06-03
 
Type Article
PeerReviewed
 
Relation https://link.springer.com/article/10.1007/s13237-023-00426-6
http://crdd.osdd.net/open/3188/
 
Identifier Kumar, Reetesh and Srivastava, Yogesh and Maji, Somnath and Siddiqui, Seemab and Tyagi, Rajeev Kumar and Muthuramalingam, Pandiyan and Singh, Sunil Kumar and Tiwari, Savitri and Verma, Geetika and Thomazella, Daniela Paula de Toledo and Shin, Hyunsuk and Prajapati, Dinesh Kumar and Rai, Pankaj Kumar and Beura , Samir Kumar and Panigrahi, Abhishek Ramachandra and Moraes , Fabio Rogerio de and Rao , Pasupuleti Visweswara (2023) In silico evaluation of natural compounds to confirm their anti-DNA gyrase activity. Nucleus India, 66. pp. 167-182.