Hina Shahid, Muhammad Ibrahim, Wadi B Alonazi, Zhanyou Chi
{"title":"利用计算机辅助药物设计解码鞣花丹宁先导化合物治疗非酒精性脂肪肝的诀窍。","authors":"Hina Shahid, Muhammad Ibrahim, Wadi B Alonazi, Zhanyou Chi","doi":"10.2174/0115734099325555240927054614","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>The prevalence of nonalcoholic fatty liver disease (NAFLD) is increasing globally, impacting individuals in Western nations and rapid growing in Asian countries due to sedentary lifestyles; thus, NAFLD has emerged as a significant worldwide health concern. Presently, lifestyle changes represent the primary approach to managing NAFLD.</p><p><strong>Methods: </strong>This research aimed to identify the potential drug targets for treating NAFLD through comprehensive in silico computational analysis. These include the prediction of the three-dimensional structure of the protein, the prediction of inhibitors by PubChem and ZINC, molecular docking by Autodcok, pharmacophore modeling, molecular dynamics simulation by the OPLS_2005 force field, and the orthorhombic box solvent model Intermolecular Interaction Potential 3 Points Transferable to the selected compound. The toxicity of the lead compounds was analyzed through AdmetSAR software.</p><p><strong>Results: </strong>The protein associated with the PNPLA3 gene, whose overall three-dimensional structure was 95% accurate, were retrieved following inhibitor selection via PubChem and ZINC. Among the selected inhibitors and docked compounds with ID 10033935 (ellagitannin) showed a minimum E-Score of -17.266. In docking and pharmacophore modeling the compound ellagitannin shows promise as a potential drug candidate. Moreover, the molecular dynamics and structural stability of the protein-ligand complex were evaluated with several metrics such as as root mean square fluctuation and root mean square deviation and resulted in the stability not only of PNPLA3-10033935 (ellagitannin) but also of compound PNPLA3-71448940 and PNPLA3-5748394 complexed proteins at 400 ns with very slight variation.</p><p><strong>Conclusion: </strong>Overall, ellagitannin was identified as the best druggable target with the best therapeutics profile. The findings of our study can pave the way for the development of a new drug against NALFD.</p>","PeriodicalId":93961,"journal":{"name":"Current computer-aided drug design","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Decoding the Knacks of Ellagitannin Lead Compounds to Treat Nonalcoholic Fatty Liver Disease using Computer-aided Drug Designing.\",\"authors\":\"Hina Shahid, Muhammad Ibrahim, Wadi B Alonazi, Zhanyou Chi\",\"doi\":\"10.2174/0115734099325555240927054614\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>The prevalence of nonalcoholic fatty liver disease (NAFLD) is increasing globally, impacting individuals in Western nations and rapid growing in Asian countries due to sedentary lifestyles; thus, NAFLD has emerged as a significant worldwide health concern. Presently, lifestyle changes represent the primary approach to managing NAFLD.</p><p><strong>Methods: </strong>This research aimed to identify the potential drug targets for treating NAFLD through comprehensive in silico computational analysis. These include the prediction of the three-dimensional structure of the protein, the prediction of inhibitors by PubChem and ZINC, molecular docking by Autodcok, pharmacophore modeling, molecular dynamics simulation by the OPLS_2005 force field, and the orthorhombic box solvent model Intermolecular Interaction Potential 3 Points Transferable to the selected compound. The toxicity of the lead compounds was analyzed through AdmetSAR software.</p><p><strong>Results: </strong>The protein associated with the PNPLA3 gene, whose overall three-dimensional structure was 95% accurate, were retrieved following inhibitor selection via PubChem and ZINC. Among the selected inhibitors and docked compounds with ID 10033935 (ellagitannin) showed a minimum E-Score of -17.266. In docking and pharmacophore modeling the compound ellagitannin shows promise as a potential drug candidate. Moreover, the molecular dynamics and structural stability of the protein-ligand complex were evaluated with several metrics such as as root mean square fluctuation and root mean square deviation and resulted in the stability not only of PNPLA3-10033935 (ellagitannin) but also of compound PNPLA3-71448940 and PNPLA3-5748394 complexed proteins at 400 ns with very slight variation.</p><p><strong>Conclusion: </strong>Overall, ellagitannin was identified as the best druggable target with the best therapeutics profile. The findings of our study can pave the way for the development of a new drug against NALFD.</p>\",\"PeriodicalId\":93961,\"journal\":{\"name\":\"Current computer-aided drug design\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-10-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Current computer-aided drug design\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.2174/0115734099325555240927054614\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current computer-aided drug design","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.2174/0115734099325555240927054614","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Decoding the Knacks of Ellagitannin Lead Compounds to Treat Nonalcoholic Fatty Liver Disease using Computer-aided Drug Designing.
Background: The prevalence of nonalcoholic fatty liver disease (NAFLD) is increasing globally, impacting individuals in Western nations and rapid growing in Asian countries due to sedentary lifestyles; thus, NAFLD has emerged as a significant worldwide health concern. Presently, lifestyle changes represent the primary approach to managing NAFLD.
Methods: This research aimed to identify the potential drug targets for treating NAFLD through comprehensive in silico computational analysis. These include the prediction of the three-dimensional structure of the protein, the prediction of inhibitors by PubChem and ZINC, molecular docking by Autodcok, pharmacophore modeling, molecular dynamics simulation by the OPLS_2005 force field, and the orthorhombic box solvent model Intermolecular Interaction Potential 3 Points Transferable to the selected compound. The toxicity of the lead compounds was analyzed through AdmetSAR software.
Results: The protein associated with the PNPLA3 gene, whose overall three-dimensional structure was 95% accurate, were retrieved following inhibitor selection via PubChem and ZINC. Among the selected inhibitors and docked compounds with ID 10033935 (ellagitannin) showed a minimum E-Score of -17.266. In docking and pharmacophore modeling the compound ellagitannin shows promise as a potential drug candidate. Moreover, the molecular dynamics and structural stability of the protein-ligand complex were evaluated with several metrics such as as root mean square fluctuation and root mean square deviation and resulted in the stability not only of PNPLA3-10033935 (ellagitannin) but also of compound PNPLA3-71448940 and PNPLA3-5748394 complexed proteins at 400 ns with very slight variation.
Conclusion: Overall, ellagitannin was identified as the best druggable target with the best therapeutics profile. The findings of our study can pave the way for the development of a new drug against NALFD.
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