{"title":"A comprehensive computer-based assessment of Deacetylnomilin as an inhibitor for antibiotic-resistant genes identified from the whole genome sequence of the multidrug-resistant Enterobacter cloacae isolate 1382.","authors":"Shubhi Singh, Sahithya Selvakumar, Priya Swaminathan","doi":"10.1007/s11030-024-11077-3","DOIUrl":"https://doi.org/10.1007/s11030-024-11077-3","url":null,"abstract":"<p><p>The twenty-first century presents a serious threat to public health due to the growth in antibiotic resistance among opportunistic bacteria, particularly within the ESKAPE group, which includes Enterobacter species with high morbidity, mortality, virulence, and nosocomial dissemination rates. Enterobacter species, especially Enterobacter cloacae, bacteria have developed resistance to multiple antibiotics through mechanisms, such as continuous production of AmpC beta-lactamase. In this study, a comprehensive bioinformatics approach was employed to analyze the genome of Enterobacter cloacae, utilizing sequence data from GenBank (ID: OW968328.1). The AbritAMR and ResFinder tools were utilized to identify antibiotic-resistant genes, which included the presence of blaOXA-48, blaCMH, FosA, OqxA, and OqxB each conferring resistance to specific antibiotics such as β-lactams and fluoroquinolones. These proteins were analyzed using bioinformatics tools such as ProtParam, SOPMA, Robetta, I-TASSER, AlphaFold, and PROCHECK to investigate different structural models and their properties. The models from AlphaFold had the best quality in terms of structural accuracy, providing valuable insights into the 3D conformations of these resistant proteins. Based on the Molecular docking studies, these constructed targets were docked with 20 natural compounds known for their activity against Gram-negative bacteria. Among them, Deacetylnomilin showed the highest docking score and passed their ADMET properties. Molecular dynamic (MD) simulation was conducted for 100 ns for Deacetylnomilin with different resistant proteins. Deacetylnomilin exhibited more favorable binding free energies compared to the reference compounds across all five proteins, indicating higher stability and affinity. These results suggest that Deacetylnomilin could be an effective inhibitor against the resistant proteins of Enterobacter cloacae, making it a promising candidate for further drug development.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142862507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohammed Alissa, Abdullah Alghamdi, Suad A Alghamdi, Muhammad Suleman
{"title":"Immunoinformatic based designing of highly immunogenic multi-epitope subunit vaccines to stimulate an adaptive immune response against Junin virus.","authors":"Mohammed Alissa, Abdullah Alghamdi, Suad A Alghamdi, Muhammad Suleman","doi":"10.1007/s11030-024-11082-6","DOIUrl":"https://doi.org/10.1007/s11030-024-11082-6","url":null,"abstract":"<p><p>The Junin virus causes Argentine hemorrhagic fever, leading to severe complications such as high fever, malaise, muscle pain, and bleeding disorders, including hemorrhages in the skin and mucous membranes. Neurological issues like confusion, seizures, and coma can also occur. Without prompt and effective treatment, the disease can be fatal, with mortality rates reaching up to 30%. Taking serious measures is essential to mitigate the spread of the disease. Vaccination is the most effective choice to neutralize the Junin virus in the current situation. Consequently, to design the highly immunogenic and non-allergenic multi-epitope subunit vaccine against the Junin virus, we employed the immunoinformatic approach to screen the glycoprotein, nucleoprotein, and RDRP protein for potential immunogenic CTL (Cytotoxic T Lymphocyte), HTL (Helper T Lymphocyte) and B (B Lymphocyte) cell epitopes. Afterward, the predicted epitopes were subjected to 3D modeling and validation. The strong binding affinity of the constructed vaccines with the human TLR3 was confirmed through molecular docking, with scores of - 333 kcal/mol for glycoprotein, - 297 kcal/mol for nucleoprotein, - 308 kcal/mol for RDRP, and - 305 kcal/mol for combined vaccines. Additionally, the binding free energies recorded were - 63.54 kcal/mol, - 64.16 kcal/mol, - 56.81 kcal/mol, and - 51.52 kcal/mol, respectively. Furthermore, the dynamic stability, residual fluctuation, and compactness of vaccine-TLR-3 complexes were confirmed by the molecular dynamic simulation. The codon adaptation index (CAI) values and high GC content confirmed the stable expression of constructed vaccines in the pET-28a ( +) expression vector. The immune simulation analysis demonstrated that administering booster doses of the developed vaccines resulted in a notable increase in IgG, IgM, interleukins, and cytokines levels, indicating effective antigen clearance over time. In conclusion, our study provides preclinical evidence for designing a highly effective Junin virus vaccine, necessitating further in-vitro and in-vivo experiments.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ahmed Alobaida, Amr S Abouzied, A Taslim Ahmed, Bader Huwaimel
{"title":"Potential VEGFR2 inhibitors for managing metastatic cervical cancer: insights from molecular dynamics and free energy landscape studies.","authors":"Ahmed Alobaida, Amr S Abouzied, A Taslim Ahmed, Bader Huwaimel","doi":"10.1007/s11030-024-11080-8","DOIUrl":"https://doi.org/10.1007/s11030-024-11080-8","url":null,"abstract":"<p><p>Metastatic cervical cancer, the advanced stage where the cancer spreads beyond the cervix to other parts of the body, poses significant treatment challenges and is associated with poor survival rates. Vascular Endothelial Growth Factor Receptor 2 (VEGFR2), a critical angiogenic mediator, is upregulated in metastatic cervical cancer, driving the formation of new blood vessels that fuel tumor growth and spread, making it an attractive target for anti-angiogenic therapies aimed at halting metastasis. This study aims to determine the anti-angiogenic effects of natural compounds to identify new VEGFR2 inhibitors for managing metastatic cervical cancer. The potential effect of these compounds as VEGFR2 inhibitors at the structural level was assessed using various methods such as virtual screening, docking, MD simulations (1000 ns), binding free energy calculations, and free energy landscape analysis. Four compounds, including IMPHY007574, IMPHY004129, IMPHY008783, and IMPHY004928, were found to be potential VEGFR2 inhibitors. Among the structures analyzed in the present work, IMPHY007574 revealed the highest binding stability with VEGFR2 and the most favorable interaction pattern, thus proving the possibility of its use as an effective anti-angiogenic compound. The other three compounds also demonstrated a reasonably good promise in VEGFR2 inhibition. These findings provide a foundation for developing novel therapeutic strategies for metastatic cervical cancer, potentially overcoming drug resistance and improving patient survival rates.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structural aspects of HIV-1 integrase inhibitors: SAR studies and synthetic strategies.","authors":"Pallavi Barik, Shankar Gupta, Gurpreet Singh, Sanjay Kumar Bharti, Vivek Asati","doi":"10.1007/s11030-024-11068-4","DOIUrl":"https://doi.org/10.1007/s11030-024-11068-4","url":null,"abstract":"<p><p>Acquired immunodeficiency syndrome (AIDS) poses a significant threat to life. Antiretroviral therapy is employed to diminish the replication of the human immunodeficiency virus (HIV), extending life expectancy and improving the quality of patients' lives. These HIV-1 integrase inhibitors form robust covalent interactions with Mg<sup>2+</sup> ions, contributing to their tight binding, thereby inhibiting the integration of viral DNA into the CD4 cell DNA. The second-generation INSTIs, the most recently approved, exhibit a higher genetic barrier compared to first-generation drugs. Hence, there is a need to develop novel and safe compounds as inhibitors of HIV-1 integrase. This article presents an overview of the current landscape of anti-HIV-1 integrase inhibitors, emphasizing the structure-activity relationship (SAR) of small molecules. The molecules discussed include monocyclic rings consisting of triazoles moiety, and pyrimidine analog along with bicyclic rings with nitrogen-containing moieties. Researchers are exploring anti-HIV-1 integrase inhibitors from natural sources like marine environments, plant extracts, and microbial products, emphasizing the importance of diverse bioactive compounds in combating the virus, which have also been included in the manuscript. The current manuscript will be helpful to the scientific community engaged in the manipulation of small molecules as anti-HIV integrase inhibitors for designing newer leads.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Manisha Yadav, Baddipadige Raju, Gera Narendra, Jasveer Kaur, Manoj Kumar, Om Silakari, Bharti Sapra
{"title":"Leveraging machine learning to predict drug permeation: impact of menthol and limonene as enhancers.","authors":"Manisha Yadav, Baddipadige Raju, Gera Narendra, Jasveer Kaur, Manoj Kumar, Om Silakari, Bharti Sapra","doi":"10.1007/s11030-024-11062-w","DOIUrl":"https://doi.org/10.1007/s11030-024-11062-w","url":null,"abstract":"<p><p>The present study aimed to develop robust machine learning (ML) models to predict the skin permeability of poorly water-soluble drugs in the presence of menthol and limonene as penetration enhancers (PEs). The ML models were also applied in virtual screening (VS) to identify hydrophobic drugs that exhibited better skin permeability in the presence of permeation enhancers i.e. menthol and limonene. The drugs identified through ML-based VS underwent experimental validation using in vitro skin penetration studies. The developed model predicted 80% probability of permeability enhancement for Sumatriptan Succinate (SS), Voriconazole (VCZ), and Pantoprazole Sodium (PS) with menthol and limonene. The in vitro release studies revealed that menthol increased penetration by approximately 2.49-fold, 2.25-fold, and 4.96-fold for SS, VCZ, and PS, respectively, while limonene enhanced permeability by approximately 1.32-fold, 2.27-fold, and 3.7-fold for SS, VCZ, and PS. The results from in silico and in vitro studies were positively correlated, indicating that the developed ML models could effectively reduce the need for extensive in vitro and in vivo experimentation.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fawaz M Almufarriji, Bader S Alotaibi, Ahlam Saleh Alamri, Samia S Alkhalil, Nada Alkhorayef
{"title":"Structure-guided identification of potential inhibitors of MurB from S. typhimurium LT2 strain: towards therapeutic development against multidrug resistance.","authors":"Fawaz M Almufarriji, Bader S Alotaibi, Ahlam Saleh Alamri, Samia S Alkhalil, Nada Alkhorayef","doi":"10.1007/s11030-024-11069-3","DOIUrl":"https://doi.org/10.1007/s11030-024-11069-3","url":null,"abstract":"<p><p>MurB or UDP-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) is involved in the synthesis of bacterial cell walls of Salmonella typhimurium LT2 as it catalyzes one of the reactions in the formation of peptidoglycan. Since the enzyme is required for bacterial survival and is not present in humans, this makes it an ideal drug target, for multidrug resistance (MDR) strains. Thus, we proceeded with the identification of novel inhibitors of MurB that could overcome the existing resistance. The potential leads were identified from the PubChem library by selecting compounds with high structural similarity to the known inhibitors of MurB. These compounds were then taken through molecular docking studies and were further assessed based on physicochemical and ADMET characteristics. Regarding binding efficiency and drug-likeliness, two hit molecules with PubChem CID:10416900 and CID:14163894 were identified against MurB. Both compounds were closely bound to the MurB active site and did not induce any substantial structural changes in the MurB structure during all-atom molecular dynamics (MD) simulations and MM-PBSA studies. These compounds showed higher potential than the existing inhibitors and stood out as promising leads for the development of therapeutic inhibitors of MurB. The findings of the study, therefore, point to the viability of these compounds in the treatment of bacterial infections, thus enhancing the quality of patient care and disease management. More studies and experimental validation are required to explore their clinical use to the optimum.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Synthesis, anticancer evaluation, preliminary mechanism study of novel 1, 2, 3-triazole-piperlongumine derivatives.","authors":"Nianlin Feng, Xuemei Qiu, Fulian Li, Yue Zhou, Chengpeng Li, Bingqian Liu, Jiao Meng, Song Bai, Zhurui Li, Danping Chen, Zhenchao Wang","doi":"10.1007/s11030-024-11021-5","DOIUrl":"https://doi.org/10.1007/s11030-024-11021-5","url":null,"abstract":"<p><p>Piperlongumine, a natural product from traditional Chinese medicine, shows promising antitumor effects but suffers from high toxicity. In this study, X and Q series Piperlongumine derivatives containing 1, 2, 3-triazole were designed and synthesized using the principle of molecular hybridization. The antitumor activity of these target compounds was evaluated, revealing significant activity compared to piperlongumine across four cancer cell lines. The structure-activity relationship of these compounds was analyzed using 3D-QSAR. Among these derivatives, compound 6Q demonstrated the highest antitumor activity against human chronic myeloid leukemia (K562) cells, with an IC<sub>50</sub> value of 0.31 μM, low toxicity to normal cells, and a selectivity index (SI) of 11.2. Further in vitro experiments confirmed that 6Q induced apoptosis in K562 cells by disrupting mitochondrial membrane potential, activating the MAPK signaling pathway, and causing cell cycle arrest in the G2/M phase. These findings underscored the potential of the natural product derivative 6Q as a promising candidate for further development in cancer therapy.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rajat Nandi, Anupama Sharma, Ananya Priya, Diwakar Kumar
{"title":"Integrating traditional QSAR and read-across-based regression models for predicting potential anti-leishmanial azole compounds.","authors":"Rajat Nandi, Anupama Sharma, Ananya Priya, Diwakar Kumar","doi":"10.1007/s11030-024-11070-w","DOIUrl":"https://doi.org/10.1007/s11030-024-11070-w","url":null,"abstract":"<p><p>Leishmaniasis, a neglected tropical disease caused by various Leishmania species, poses a significant global health challenge, especially in resource-limited regions. Visceral Leishmaniasis (VL) stands out among its severe manifestations, and current drug therapies have limitations, necessitating the exploration of new, cost-effective treatments. This study utilized a comprehensive computational workflow, integrating traditional 2D-QSAR, q-RASAR, and molecular docking to identify novel anti-leishmanial compounds, with a focus on Glycyl-tRNA Synthetase (LdGlyRS) as a promising drug target. A feature selection process combining Genetic Function Approximation (GFA)-Lasso with Multiple Linear Regression (MLR) was used to characterize 99 azole compounds across ten structural classes. The baseline MLR model (MOD1), containing seven simple and interpretable 2D features, exhibited robust predictive capabilities, achieving an R<sup>2</sup><sub>train</sub> value of 0.82 and an R<sup>2</sup><sub>test</sub> value of 0.87. To further enhance prediction accuracy, three qualified single models (two MLR and one q-RASAR) were used to construct three consensus models (CMs), with CM2 (MAE<sub>test</sub> = 0.127) demonstrating significantly higher prediction accuracy for test compounds than the MOD1. Subsequently, Support Vector Regression (SVR) and Boosting yielded 0.88 (R<sup>2</sup><sub>train</sub>), 0.86 (R<sup>2</sup><sub>test</sub>), 0.92 (R<sup>2</sup><sub>train</sub>), and 0.82 (R<sup>2</sup><sub>test</sub>), respectively. Molecular docking highlighted interactions of potent azoles within the QSAR dataset with critical residues in the LdGlyRS active site (Arg226 and Glu350), emphasizing their inhibitory potential. Furthermore, the pIC50 values of an accurate external set of 2000 azole compounds from the ZINC20 database were simultaneously predicted by CM2 + SVR + Boosting models and docked against the LdGlyRS, which identified Bazedoxifene, Talmetacin, Pyrvinium, Enzastaurin as leading FDA candidates, whereas three novel compounds with the database code ZINC000001153734, ZINC000011934652, and ZINC000009942262 displayed stable docked interactions and favourable ADMET assessments. Subsequently, Molecular Dynamics (MD) simulations for 100 ns were conducted to validate the findings further, offering enhanced insights into the stability and dynamic behaviour of the ligand-protein complexes. The integrated approach of this study underscores the efficacy of 2D-QSAR modelling. It identifies LdGlyRS as a promising leishmaniasis target, offering a robust strategy for discovering and optimizing anti-leishmanial compounds to address the critical need for improved treatments.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jovana S Marjanović, Jovana D Matić, Žiko Milanović, Vera M Divac, Marijana M Kosanić, Miloš R Petković, Marina D Kostić
{"title":"Molecular modeling studies, in vitro antioxidant and antimicrobial assay and BSA affinity of novel benzyl-amine derived scaffolds as CYP51B inhibitors.","authors":"Jovana S Marjanović, Jovana D Matić, Žiko Milanović, Vera M Divac, Marijana M Kosanić, Miloš R Petković, Marina D Kostić","doi":"10.1007/s11030-024-11074-6","DOIUrl":"https://doi.org/10.1007/s11030-024-11074-6","url":null,"abstract":"<p><p>New scaffolds derived from benzylamine were prepared, characterized, and tested for their antimicrobial, antioxidant activities and binding interactions with BSA. Structure-activity relationship analysis revealed that compounds incorporating both benzylamine and quinoline or pyridine moieties (specifically 3a and 3d) demonstrated potent antifungal activity, surpassing that of the standard drug Ketoconazole against Penicillium italicum. Molecular docking studies confirmed significant inhibitory activity against the CYP51B enzyme-an essential component of fungal cell walls. In addition, compounds 3h, 3d and 3b displayed promising DPPH radical scavenging activity, indicating its strong potential as an antioxidant source. Thermodynamic parameters of standard antiradical mechanisms confirmed antiradical capacity expressed via formal hydrogen atom transfer (FHT). The results of spectrofluorometric assays and molecular docking studies on the affinity of the tested compounds for the BSA enzyme confirmed that all compounds show significant binding affinity for active site III, with compound 3d demonstrating the highest binding affinity. Key pharmacokinetic parameters were assessed using ADMET analysis, ensuring the viability of these compounds for potential therapeutic applications.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaokai Fan, Le Xin, Xuan Yu, Maoxuan Liu, Joong Sup Shim, Gui Yang, Liang Chen
{"title":"Identify critical genes of breast cancer and corresponding leading natural product compounds of potential therapeutic targets.","authors":"Xiaokai Fan, Le Xin, Xuan Yu, Maoxuan Liu, Joong Sup Shim, Gui Yang, Liang Chen","doi":"10.1007/s11030-024-11035-z","DOIUrl":"https://doi.org/10.1007/s11030-024-11035-z","url":null,"abstract":"<p><p>Breast cancer is a leading cause of cancer mortality among women globally, with over 2.26 million new cases annually, according to GLOBOCAN 2020. This accounts for approximately 25% of all new female cancers and 15.5% of female cancer deaths. To address this critical public health challenge, we conducted a multi-omics study aimed at identifying hub genes, therapeutic targets, and potential natural product-based therapies. We employed weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis to pinpoint hub genes in breast cancer. Regulatory networks for these genes were constructed by re-analyzing chromatin immunoprecipitation sequencing (ChIP-seq) data from breast cancer cell lines. Additionally, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) were utilized to characterize hub gene expression profiles and their relationships with immune cell clusters and tumor microenvironments. Survival analysis based on mRNA and protein expression levels identified prognostic factors and potential therapeutic targets. Lastly, large-scale virtual screening of natural product compounds revealed leading compounds that target squalene epoxidase (SQLE). Our multi-omics analysis paves the way for more effective clinical treatments for breast cancer.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}