Unveiling Berberine analogues as potential inhibitors of Escherichia coli FtsZ through machine learning molecular docking and molecular dynamics approach
Abstract The bacterial cell division protein FtsZ, a crucial GTPase, plays a vital role in the formation of the contractile Z-ring, which is essential for bacterial cytokinesis. Consequently, inhibiting FtsZ could prevent the formation of proto-filaments and interfere with the cell division machiner...
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| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-04-01
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| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-98835-x |
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| Summary: | Abstract The bacterial cell division protein FtsZ, a crucial GTPase, plays a vital role in the formation of the contractile Z-ring, which is essential for bacterial cytokinesis. Consequently, inhibiting FtsZ could prevent the formation of proto-filaments and interfere with the cell division machinery. The remarkable conservation of FtsZ across diverse bacterial species makes it a promising drug target for combating drug resistance. In the present study, 1072 berberine analogues were screened for favorable pharmacokinetic properties. A total of 60 compounds that fulfilled the drug-likeliness criteria and were found to be non-toxic were selected for virtual screening against Escherichia coli FtsZ protein (PDB ID: 8GZY). Molecular docking revealed a strong binding affinity of ZINC000524729297 (− 8.73 kcal/mol) and ZINC000604405393 (and − 8.55 kcal/mol) with FtsZ by strong intermolecular hydrogen bonds and hydrophobic interactions. Subsequently, the docking profiles were validated through a 500 ns MD simulation and MMPBSA analysis of the FtsZ-ligand complexes. The analysis revealed the FtsZ- ZINC524729297 and FtsZ-ZINC000604405393 complexes had the lowest root-mean-square deviation with lowest binding energy and enhanced conformational stability in a dynamic environment. These findings suggest that ZINC524729297 and ZINC000604405393 are the potent lead compound that targets FtsZ and requires further experimental validation. |
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| ISSN: | 2045-2322 |