Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens

• Published in: Communications biology Vol. 6; no. 1; p. 195
• Main Authors: Maurya, Vikas, Singh, Raja, Singh, Reman Kumar, Pandey, Stuti, Yadav, Pooja, Parashar, Palak, Gaind, Rajni, Dubey, Kshatresh Dutta, Naresh Patwari, G., Tandon, Vibha
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.02.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 14; 14/63; 631/114/2397; 631/154/556; 631/326/22/1434; 82/29; 82/80; 82/83; 96/31; Animal models; Animals; Apoptosis; Biology; Biomedical and Life Sciences; Bisbenzimidazole; Cell death; Conformation; Deoxyribonucleic acid; DNA; DNA fragmentation; DNA topoisomerase; DNA Topoisomerases, Type I - chemistry; DNA Topoisomerases, Type I - genetics; DNA Topoisomerases, Type I - metabolism; DNA, Single-Stranded; Enzymes; Escherichia coli - genetics; Filamentation; Gram-negative bacteria; Gram-positive bacteria; Life Sciences; Mice; Multidrug resistance; Neutropenia; Toxicity
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-023-04412-1

Type IA topoisomerases maintain DNA topology by cleaving ssDNA and relaxing negative supercoils. The inhibition of its activity in bacteria prevents the relaxation of negative supercoils, which in turn impedes DNA metabolic processes leading to cell death. Using this hypothesis, two bisbenzimidazoles, PPEF and BPVF are synthesized, selectively inhibiting bacterial TopoIA and TopoIII. PPEF stabilizes the topoisomerase and topoisomerase-ssDNA complex, acts as an interfacial inhibitor. PPEF display high efficacy against ~455 multi-drug resistant gram positive and negative bacteria. To understand molecular mechanism of inhibition of TopoIA and PPEF, accelerated MD simulation is carried out, and results suggested that PPEF binds, stabilizes the closed conformation of TopoIA with –6Kcal/mol binding energy and destabilizes the binding of ssDNA. The TopoIA gate dynamics model can be used as a tool to screen TopoIA inhibitors as therapeutic candidates. PPEF and BPVF cause cellular filamentation and DNA fragmentation leading to bacterial cell death. PPEF and BPVF show potent efficacy against systemic and neutropenic mouse models harboring E. coli , VRSA, and MRSA infection without cellular toxicity. Two potent inhibitors PPEF and BPVF of bacterial TopoIA enzymes function by impairing DNA binding and thus DNA cleavage and relaxation activities of bacterial topoisomerase I enzymes.