Rafiullah Shirzadi, Abdul Musawer Bayan, Sayed Hussain Mosawi
{"title":"通过结合能量学和结构动力学解读姜黄素对KPC-3、L2和CTX-M-15 β-内酰胺酶的差异抑制作用。","authors":"Rafiullah Shirzadi, Abdul Musawer Bayan, Sayed Hussain Mosawi","doi":"10.1007/s40203-025-00421-6","DOIUrl":null,"url":null,"abstract":"<p><p>The rise of β-lactamase-mediated resistance in Gram-negative pathogens has created an urgent need for novel inhibitors to preserve antibiotic efficacy. This study explores the potential of curcumin, a natural polyphenol with known antimicrobial properties, as a broad-spectrum inhibitor of class A serine-β-lactamases (SBLs) through comprehensive computational analysis. Using molecular docking, 200 ns molecular dynamics simulations, and binding energy calculations, we investigated curcumin's interactions with three clinically important SBLs: KPC-3, CTX-M-15, and L2. Our results demonstrate curcumin's strong binding affinity across all three enzymes, with particularly potent inhibition of L2 (ΔG = - 7.67 kcal/mol) driven by favorable van der Waals interactions (- 115.03 kJ/mol) and an extensive hydrogen bonding network involving catalytic residues Ser70 and Ser130. Molecular dynamics simulations revealed distinct inhibition mechanisms: L2 showed global stabilization with reduced flexibility (15-20% decrease in RMSF); CTX-M-15 exhibited balanced binding with moderate solvation effects; while KPC-3 displayed local active-site stabilization despite overall structural destabilization, evidenced by increased radius of gyration. These findings highlight curcumin's remarkable adaptability as a multi-target β-lactamase inhibitor, capable of employing enzyme-specific strategies while maintaining core inhibitory interactions. The study provides crucial molecular insights that could guide the development of curcumin-derived adjuvants to combat β-lactam resistance, bridging traditional medicine and modern drug discovery approaches to address this critical public health challenge.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-025-00421-6.</p>","PeriodicalId":94038,"journal":{"name":"In silico pharmacology","volume":"13 3","pages":"128"},"PeriodicalIF":0.0000,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411342/pdf/","citationCount":"0","resultStr":"{\"title\":\"Deciphering curcumin's differential inhibition of KPC-3, L2, and CTX-M-15 β-lactamases through binding energetics and structural dynamics.\",\"authors\":\"Rafiullah Shirzadi, Abdul Musawer Bayan, Sayed Hussain Mosawi\",\"doi\":\"10.1007/s40203-025-00421-6\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The rise of β-lactamase-mediated resistance in Gram-negative pathogens has created an urgent need for novel inhibitors to preserve antibiotic efficacy. This study explores the potential of curcumin, a natural polyphenol with known antimicrobial properties, as a broad-spectrum inhibitor of class A serine-β-lactamases (SBLs) through comprehensive computational analysis. Using molecular docking, 200 ns molecular dynamics simulations, and binding energy calculations, we investigated curcumin's interactions with three clinically important SBLs: KPC-3, CTX-M-15, and L2. Our results demonstrate curcumin's strong binding affinity across all three enzymes, with particularly potent inhibition of L2 (ΔG = - 7.67 kcal/mol) driven by favorable van der Waals interactions (- 115.03 kJ/mol) and an extensive hydrogen bonding network involving catalytic residues Ser70 and Ser130. Molecular dynamics simulations revealed distinct inhibition mechanisms: L2 showed global stabilization with reduced flexibility (15-20% decrease in RMSF); CTX-M-15 exhibited balanced binding with moderate solvation effects; while KPC-3 displayed local active-site stabilization despite overall structural destabilization, evidenced by increased radius of gyration. These findings highlight curcumin's remarkable adaptability as a multi-target β-lactamase inhibitor, capable of employing enzyme-specific strategies while maintaining core inhibitory interactions. The study provides crucial molecular insights that could guide the development of curcumin-derived adjuvants to combat β-lactam resistance, bridging traditional medicine and modern drug discovery approaches to address this critical public health challenge.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-025-00421-6.</p>\",\"PeriodicalId\":94038,\"journal\":{\"name\":\"In silico pharmacology\",\"volume\":\"13 3\",\"pages\":\"128\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2025-09-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411342/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"In silico pharmacology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1007/s40203-025-00421-6\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"In silico pharmacology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1007/s40203-025-00421-6","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"","JCRName":"","Score":null,"Total":0}
Deciphering curcumin's differential inhibition of KPC-3, L2, and CTX-M-15 β-lactamases through binding energetics and structural dynamics.
The rise of β-lactamase-mediated resistance in Gram-negative pathogens has created an urgent need for novel inhibitors to preserve antibiotic efficacy. This study explores the potential of curcumin, a natural polyphenol with known antimicrobial properties, as a broad-spectrum inhibitor of class A serine-β-lactamases (SBLs) through comprehensive computational analysis. Using molecular docking, 200 ns molecular dynamics simulations, and binding energy calculations, we investigated curcumin's interactions with three clinically important SBLs: KPC-3, CTX-M-15, and L2. Our results demonstrate curcumin's strong binding affinity across all three enzymes, with particularly potent inhibition of L2 (ΔG = - 7.67 kcal/mol) driven by favorable van der Waals interactions (- 115.03 kJ/mol) and an extensive hydrogen bonding network involving catalytic residues Ser70 and Ser130. Molecular dynamics simulations revealed distinct inhibition mechanisms: L2 showed global stabilization with reduced flexibility (15-20% decrease in RMSF); CTX-M-15 exhibited balanced binding with moderate solvation effects; while KPC-3 displayed local active-site stabilization despite overall structural destabilization, evidenced by increased radius of gyration. These findings highlight curcumin's remarkable adaptability as a multi-target β-lactamase inhibitor, capable of employing enzyme-specific strategies while maintaining core inhibitory interactions. The study provides crucial molecular insights that could guide the development of curcumin-derived adjuvants to combat β-lactam resistance, bridging traditional medicine and modern drug discovery approaches to address this critical public health challenge.
Supplementary information: The online version contains supplementary material available at 10.1007/s40203-025-00421-6.