Srinivasan M , Ismail Y , Irfan N , Mohammed Zaidh S
{"title":"协同抑制细胞生长:通过混合计算方法揭示靶向p53和MDM2的苯咪嗪衍生物。","authors":"Srinivasan M , Ismail Y , Irfan N , Mohammed Zaidh S","doi":"10.1016/j.compbiolchem.2025.108344","DOIUrl":null,"url":null,"abstract":"<div><div>Lung cancer is the leading cause of mortality in both men and women due to genetic and epigenetic modifications. Our study focuses on fabricating phenmiazine ring leads by a functional group-based drug design to inhibit p53 −7A1W and MDM2–7AU9 proteins responsible for cancer cell growth. One hundred molecules are designed and allowed to bind inside the active site of 7A1W and 7AU9 protein using a glide dock platform and subjected to find MMGBSA. The stability and interaction were confirmed by MD simulation analysis at 100 ns and DFTB chemical stability study. The result gave the best binding energy of −8.16 kcal/mol for aminobenzoic acid substituted molecule and the MD simulation head map illustrates that majorly 9 amino acids form hydrophobic and h-bond interactions. DFTB analysis reveals the energy gaps of 0.0508 signifying stability and lower chemical reactivity of the Phenmiazine ring derivatives. These findings conclude that the Phenmiazine ring derivative will be a better lead molecule to eradicate lung cancer.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"115 ","pages":"Article 108344"},"PeriodicalIF":2.6000,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Synergistic suppression of cell growth: Phenmiazine derivatives targeting p53 and MDM2 unveiled through hybrid computational method\",\"authors\":\"Srinivasan M , Ismail Y , Irfan N , Mohammed Zaidh S\",\"doi\":\"10.1016/j.compbiolchem.2025.108344\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Lung cancer is the leading cause of mortality in both men and women due to genetic and epigenetic modifications. Our study focuses on fabricating phenmiazine ring leads by a functional group-based drug design to inhibit p53 −7A1W and MDM2–7AU9 proteins responsible for cancer cell growth. One hundred molecules are designed and allowed to bind inside the active site of 7A1W and 7AU9 protein using a glide dock platform and subjected to find MMGBSA. The stability and interaction were confirmed by MD simulation analysis at 100 ns and DFTB chemical stability study. The result gave the best binding energy of −8.16 kcal/mol for aminobenzoic acid substituted molecule and the MD simulation head map illustrates that majorly 9 amino acids form hydrophobic and h-bond interactions. DFTB analysis reveals the energy gaps of 0.0508 signifying stability and lower chemical reactivity of the Phenmiazine ring derivatives. These findings conclude that the Phenmiazine ring derivative will be a better lead molecule to eradicate lung cancer.</div></div>\",\"PeriodicalId\":10616,\"journal\":{\"name\":\"Computational Biology and Chemistry\",\"volume\":\"115 \",\"pages\":\"Article 108344\"},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2025-01-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computational Biology and Chemistry\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1476927125000040\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Biology and Chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1476927125000040","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOLOGY","Score":null,"Total":0}
Synergistic suppression of cell growth: Phenmiazine derivatives targeting p53 and MDM2 unveiled through hybrid computational method
Lung cancer is the leading cause of mortality in both men and women due to genetic and epigenetic modifications. Our study focuses on fabricating phenmiazine ring leads by a functional group-based drug design to inhibit p53 −7A1W and MDM2–7AU9 proteins responsible for cancer cell growth. One hundred molecules are designed and allowed to bind inside the active site of 7A1W and 7AU9 protein using a glide dock platform and subjected to find MMGBSA. The stability and interaction were confirmed by MD simulation analysis at 100 ns and DFTB chemical stability study. The result gave the best binding energy of −8.16 kcal/mol for aminobenzoic acid substituted molecule and the MD simulation head map illustrates that majorly 9 amino acids form hydrophobic and h-bond interactions. DFTB analysis reveals the energy gaps of 0.0508 signifying stability and lower chemical reactivity of the Phenmiazine ring derivatives. These findings conclude that the Phenmiazine ring derivative will be a better lead molecule to eradicate lung cancer.
期刊介绍:
Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered.
Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered.
Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.