1
|
Kumar S, Dubey R, Mishra R, Gupta S, Dwivedi VD, Ray S, Jha NK, Verma D, Tsai LW, Dubey NK. Repurposing of SARS-CoV-2 compounds against Marburg Virus using MD simulation, mm/GBSA, PCA analysis, and free energy landscape. J Biomol Struct Dyn 2024:1-20. [PMID: 38450706 DOI: 10.1080/07391102.2024.2323701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/22/2024] [Indexed: 03/08/2024]
Abstract
The significant mortality rate associated with Marburg virus infection made it the greatest hazard among infectious diseases. Drug repurposing using in silico methods has been crucial in identifying potential compounds that could prevent viral replication by targeting the virus's primary proteins. This study aimed at repurposing the drugs of SARS-CoV-2 for identifying potential candidates against the matrix protein VP40 of the Marburg virus. Virtual screening was performed where the control compound, Nilotinib, showed a binding score of -9.99 kcal/mol. Based on binding scores, hit compounds 9549298, 11960895, 44545852, 51039094, and 89670174 were selected that had a lower binding score than the control. Subsequent molecular dynamics (MD) simulation revealed that compound 9549298 consistently formed a hydrogen bond with the residue Gln290. This was observed both in molecular docking and MD simulation poses, indicating a strong and significant interaction with the protein. 11960895 had the most stable and consistent RMSD pattern exhibited in 100 ns simulation, while 9549298 had the most identical RMSD plot compared to the control molecule. MM/PBSA analysis showed that the binding free energy (ΔG) of 9549298 and 11960895 was lower than the control, with -30.84 and -38.86 kcal/mol, respectively. It was observed by the PCA (principal component analysis) and FEL (free energy landscape) analysis that compounds 9549298 and 11960895 had lesser conformational variation. Overall, this study proposed 9549298 and 11960895 as potential binders of VP40 MARV that can cause its inhibition, however it inherently lacks experimental validation. Furthermore, the study proposes in-vitro experiments as the next step to validate these computational findings, offering a practical approach to further explore these compounds' potential as antiviral agents.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, UP, India
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei City, Taiwan
| | - Richa Mishra
- Department of Computer Engineering, Parul University, Vadodara, Gujarat, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Bioinformatics Research Division, Greater Noida, UP, India
| | - Subhasree Ray
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
| | - Niraj Kumar Jha
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, India
- Centre of Research Impact and Outreach, Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
| | - Devvret Verma
- Department of Biotechnology, Graphic Era (Deemed to Be University), Dehradun, Uttarakhand, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, Taiwan
| | | |
Collapse
|
2
|
Rabaan AA, Almansour ZH, Al Bshabshe A, Halwani MA, Al-Subaie MF, Al Kaabi NA, Alshamrani SA, Alshehri AA, Nahari MH, Alqahtani AS, Alhajri M, Alissa M. Application of temperature-dependent and steered molecular dynamics simulation to screen anti-dengue compounds against Marburg virus. J Biomol Struct Dyn 2024:1-20. [PMID: 38234048 DOI: 10.1080/07391102.2024.2303386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Marburg virus infections are extremely fatal with a fatality range of 23% to 90%, therefore there is an urgent requirement to design and develop efficient therapeutic molecules. Here, a comprehensive temperature-dependent molecular dynamics (MD) simulation method was implemented to identify the potential molecule from the anti-dengue compound library that can inhibit the function of the VP24 protein of Marburg. Virtual high throughput screening identified five effective binders of VP24 after screening 484 anti-dengue compounds. These compounds were treated in MD simulation at four different temperatures: 300, 340, 380, and 420 K. Higher temperatures showed dissociation of hit compounds from the protein. Further, triplicates of 100 ns MD simulation were conducted which showed that compounds ID = 118717693, and ID = 5361 showed strong stability with the protein molecule. These compounds were further validated using Δ G binding free energies and they showed: -30.38 kcal/mol, and -67.83 kcal/mol binding free energies, respectively. Later, these two compounds were used in steered MD simulation to detect its dissociation. Compound ID = 5361 showed the maximum pulling force of 199.02 kcal/mol/nm to dissociate the protein-ligand complex while ID = 118717693 had a pulling force of 101.11 kcal/mol/nm, respectively. This ligand highest number of hydrogen bonds with varying occupancies at 89.93%, 69.80%, 57.93%, 52.33%, and 50.63%. This study showed that ID = 5361 can bind with the VP24 strongly and has the potential to inhibit its function which can be validated in the in-vitro experiment.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Zainab H Almansour
- Biological Science Department, College of Science, King Faisal University, Hofuf, Saudi Arabia
| | - Ali Al Bshabshe
- Adult critical care Department of Medicine, Division of adult critical care, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Saudi Arabia
| | - Maha F Al-Subaie
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh, Saudi Arabia
| | - Nawal A Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, United Arab Emirates
| | - Saleh A Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed H Nahari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ali S Alqahtani
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| |
Collapse
|
3
|
Wang N, Gu Y, Li L, Chi J, Liu X, Xiong Y, Zhong C. Development and Validation of a Prognostic Classifier Based on Lipid Metabolism-Related Genes for Breast Cancer. J Inflamm Res 2022; 15:3477-3499. [PMID: 35726216 PMCID: PMC9206459 DOI: 10.2147/jir.s357144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Background The changes of lipid metabolism have been implicated in the development of many tumors, but its role in breast invasive carcinoma (BRCA) remains to be fully established. Here, we attempted to ascertain the prognostic value of lipid metabolism-related genes in BRCA. Methods We obtained RNA expression data and clinical information for BRCA and normal samples from public databases and downloaded a lipid metabolism-related gene set. Ingenuity Pathway Analysis (IPA) was applied to identify the potential pathways and functions of Differentially Expressed Genes (DEGs) related to lipid metabolism. Subsequently, univariate and multivariate Cox regression analyses were utilized to construct the prognostic gene signature. Functional enrichment analysis of prognostic genes was achieved by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Kaplan-Meier analysis, Receiver Operating Characteristic (ROC) curves, clinical follow-up results were employed to assess the prognostic potency. Potential compounds targeting prognostic genes were screened by Connectivity Map (CMap) database and a prognostic gene-drug interaction network was constructed using Comparative Toxicogenomics Database (CTD). Furthermore, we separately validated the selected marker genes in BRCA samples and human breast cancer cell lines (MCF-7, MDA-MB-231). Results IPA and functional enrichment analysis demonstrated that the 162 lipid metabolism-related DEGs we obtained were involved in many lipid metabolism and BRCA pathological signatures. The prognostic classifier we constructed comprising SDC1 and SORBS1 can serve as an independent prognostic marker for BRCA. CMap filtered 37 potential compounds against prognostic genes, of which 16 compounds could target both two prognostic genes were identified by CTD. The functions of the two prognostic genes in breast cancer cells were verified by cell function experiments. Conclusion Within this study, we identified a novel prognostic classifier based on two lipid metabolism-related genes: SDC1 and SORBS1. This result highlighted a new perspective on the metabolic exploration of BRCA.
Collapse
Affiliation(s)
- Nan Wang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Yuanting Gu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Lin Li
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Jiangrui Chi
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Xinwei Liu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Youyi Xiong
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Chaochao Zhong
- Department of Plastic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| |
Collapse
|
4
|
Zhang S. Abrine Elicits Liver Carcinoma Immunity and Enhances Antitumor Efficacy of Immune Checkpoint Blockade by Modulating PD-L1 Signaling. J Oncol 2022; 2022:7609676. [PMID: 35602291 DOI: 10.1155/2022/7609676] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 12/21/2022]
Abstract
Background Liver cancer is the most malignant type of human malignancies. In recent years, immune therapy that targets the immune check points such as programmed cell death ligand 1 (PD-L1) has achieve great success. Abrine is the dominant alkaloid in Abrus cantoniensis and Abrus precatorius Linn. that exhibited anticancer effect. This work is aimed at studying the effects of abrine in immunity of liver cancer. Methods Cell viability, proliferation, and migration were assessed by CCK-8, Edu, and Transwell assay. Cell apoptosis was checked by flow cytometry. Tumor growth was determined by an in vivo xenograft model. Quantitative real-time PCR assay was conducted to evaluate the levels of KAT5 and PD-L1. T cells and liver cancer cells were cocultured in a Transwell system, and the levels of PD-L1 and PD-1 was checked by flow cytometry. The interaction between KAT5 and PD-L1 was determined by ChIP assay. Results Abrine treatment suppressed liver tumor growth both in vitro and in vivo and simultaneously decreased the level of PD-L1 and KAT5. In the coculture system, treatment with abrine inhibited proliferation and activity of cocultured T cell. KAT5 epigenetically elevated recruitment of H3k27ac and RNA polymerase II to PD-L1 promoter region. Ectopic expression of KAT5 and PD-L1 reversed the function of abrine on tumor growth and T cell function. Conclusion Abrine modulated growth and apoptosis of liver cancer cells and regulated proliferation and activation of T cells through the KAT5/PD-L1 axis.
Collapse
|
5
|
Yang Z, Dan Wang, Li Y, Zhou X, Liu T, Shi C, Li R, Zhang Y, Zhang J, Yan J, Zhu X, Li Y, Gong M, Wang C, Yuan C, Cui Y, Wu X. Untargeted metabolomics analysis of the anti-diabetic effect of Red ginseng extract in Type 2 diabetes Mellitus rats based on UHPLC-MS/MS. Biomed Pharmacother 2022; 146:112495. [PMID: 34891123 DOI: 10.1016/j.biopha.2021.112495] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 11/27/2022] Open
Abstract
Red ginseng is a traditional Chinese herbal medicine that has long been used to treat diabetes, and its blood sugar-lowering activity has been confirmed. However, the mechanism of action of red ginseng on type 2 diabetes mellitus (T2DM) at the metabolic level is still unclear. The purpose of this study is to investigate the effect of red ginseng extract in the treatment of T2DM rats based on untargeted metabolomics. The rat model of T2DM was induced by a high-fat diet (HFD) combined with streptozotocin (STZ), and serum samples were collected after four weeks of treatment. The ultra-high-performance liquid chromatography coupled with Q Exactive HF-X Mass Spectrometer was used to analyze the level of metabolites in serum to evaluate the differences in metabolic levels between different groups. The results of biochemical analysis showed that red ginseng extract intervention significantly improved the levels of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), serum glucose (GLU), and fasting insulin (FINS) after four weeks. Orthogonal partial least squares discriminant analysis was used to study the overall changes of rat metabolomics. After the intervention of red ginseng extract, 50 biomarkers showed a callback trend. Metabolic pathway enrichment analysis showed that the regulated pathways were D-arginine and D-ornithine metabolism, D-glutamine and D-glutamate metabolism, taurine and hypotaurine metabolism, arginine biosynthesis, and tryptophan metabolism. Generally, the results demonstrated that red ginseng extract had beneficial effects on T2DM, which could be mediated via ameliorating the metabolic disorders.
Collapse
MESH Headings
- Amino Acids/metabolism
- Animals
- Biomarkers/blood
- Chromatography, High Pressure Liquid
- Diabetes Mellitus, Experimental/blood
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 2/blood
- Diabetes Mellitus, Type 2/drug therapy
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Hypoglycemic Agents/pharmacology
- Hypoglycemic Agents/therapeutic use
- Lipid Metabolism
- Male
- Metabolic Networks and Pathways/drug effects
- Metabolomics
- Panax
- Pancreas/drug effects
- Pancreas/pathology
- Phytotherapy
- Plant Extracts/pharmacology
- Plant Extracts/therapeutic use
- Rats, Sprague-Dawley
- Tandem Mass Spectrometry
- Rats
Collapse
Affiliation(s)
- Zijun Yang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Dan Wang
- Department of Pharmacy, Chu Hisen-I Memorial Hospital, Tianjin Medical University, Tianjin 300134, China
| | - Yuanyuan Li
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China; Department of Pharmacy, Tianjin Fourth Central Hospital, Tianjin 300140, China
| | - Xinfeng Zhou
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Tiantian Liu
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Chang Shi
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Rongshan Li
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yanwen Zhang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Jun Zhang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Jiuxing Yan
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Xuehui Zhu
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ying Li
- Tianjin Neurological Institute, Tianjin Medical University, Tianjin 300052, China
| | - Min Gong
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Chongzhi Wang
- Tang Center for Herbal Medicine Research, University of Chicago, Illinois 60637, USA
| | - Chunsu Yuan
- Tang Center for Herbal Medicine Research, University of Chicago, Illinois 60637, USA
| | - Yan Cui
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
| | - Xiaohui Wu
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| |
Collapse
|
6
|
Meng Y, Yin D, Qiu S, Zhang X. Abrine promotes cell proliferation and inhibits apoptosis of interleukin-1β-stimulated chondrocytes via PIM2/VEGF signalling in osteoarthritis. Phytomedicine 2022; 96:153906. [PMID: 35026522 DOI: 10.1016/j.phymed.2021.153906] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Osteoarthritis (OA), a common joint disorder with an increasing incidence worldwide, severely affects the quality of life of patients. In Chinese herbal medicine, Abrus cantoniensis Hance is considered to exert protective effects on the liver and to have beneficial effects on the gallbladder; additionally, it has antibacterial and anti-inflammatory properties, as well as the ability to enhance immunity, scavenge free radicals, regulate smooth muscle function, and improve endurance. Abrine extracted from A. cantoniensis Hance has been reported as a main functional compound capable of treating chronic inflammation. PURPOSE In this study, we explored the effect of abrine on OA progression. STUDY DESIGN Bioinformatics analysis was performed on abrine and its potential targets in OA, using the Comparative Toxicogenomics Database, GSE1919 dataset from the Gene Expression Omnibus database, Gene Set Enrichment Analysis, and docking interaction analysis. METHODS The effect of abrine in vitro was analysed by Cell Counting Kit 8 assays, colony formation assays, enzyme-linked immunosorbent assay, flow cytometry analysis, quantitative real-time PCR, and western blotting using human transformed chondrocyte cell line C28/I2. The effect of abrine was evaluated in vivo using the anterior cruciate ligament transection (ACLT) Sprague-Dawley rat OA model. RESULTS Abrine enhanced the proliferation of interleukin (IL)-1β-stimulated C28/I2 cells in a dose-dependant manner. Expression of pro-inflammatory cytokines was induced by IL-1β treatment, whereas abrine treatment repressed the induction of C28/I2 cells in a dose dependant manner (p < 0.05). Abrine induced cell proliferation and inhibited apoptosis in IL-1β-stimulated C28/I2 cells (p < 0.05). Abrine also inhibited Proviral Integrations of Moloney virus 2 (PIM2) expression in IL-1β-stimulated C28/I2 cells (p < 0.05). The expression of vascular endothelial growth factor (VEGF), p-VEGFR2, and p-eNOS was induced by IL-1β treatment in C28/I2 cells, while abrine inhibited this induction in a dose dependant manner. Treatment with abrine decreased the expression levels of PIM2 and VEGF in IL-1β-stimulated C28/I2 cells (p < 0.05). Overexpression of PIM2 induced cell proliferation and inhibited apoptosis in IL-1β-stimulated C28/I2 cells, while VEGF silencing reversed this effect (p < 0.05). Finally, abrine prevented cartilage degradation in the ACLT model. CONCLUSION We demonstrated that abrine promoted cell proliferation and inhibited apoptosis in IL-1β-stimulated C28/I2 cells through PIM2/VEGF signalling. These findings indicate PIM2 to be a potential drug target. Moreover, abrine has potential applicability as a therapeutic agent against OA.
Collapse
Affiliation(s)
- Yong Meng
- Department of Orthopaedics, Weihai Municipal Hospital, Weihai, Shandong 264200, PR China; Department of Orthopaedics, The Fifth Affiliated Hospital (Heyuan Shenhe People's Hospital) Jinan University, Heyuan, Guangdong 517000, PR China
| | - Dezhen Yin
- Department of Spine Surgery, Weihai Municipal Hospital, Weihai, Shandong 264200, PR China
| | - Siqiang Qiu
- Department of Spine Surgery, The Fourth People's Hospital of Jinan, Jinan, Shandong 250031, PR China
| | - Xin Zhang
- Department of Orthopeadic Surgery, Zhucheng people's hospital, Zhucheng, Shandong 262200, PR China.
| |
Collapse
|
7
|
Sellami A, Réau M, Montes M, Lagarde N. Review of in silico studies dedicated to the nuclear receptor family: Therapeutic prospects and toxicological concerns. Front Endocrinol (Lausanne) 2022; 13:986016. [PMID: 36176461 PMCID: PMC9513233 DOI: 10.3389/fendo.2022.986016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Being in the center of both therapeutic and toxicological concerns, NRs are widely studied for drug discovery application but also to unravel the potential toxicity of environmental compounds such as pesticides, cosmetics or additives. High throughput screening campaigns (HTS) are largely used to detect compounds able to interact with this protein family for both therapeutic and toxicological purposes. These methods lead to a large amount of data requiring the use of computational approaches for a robust and correct analysis and interpretation. The output data can be used to build predictive models to forecast the behavior of new chemicals based on their in vitro activities. This atrticle is a review of the studies published in the last decade and dedicated to NR ligands in silico prediction for both therapeutic and toxicological purposes. Over 100 articles concerning 14 NR subfamilies were carefully read and analyzed in order to retrieve the most commonly used computational methods to develop predictive models, to retrieve the databases deployed in the model building process and to pinpoint some of the limitations they faced.
Collapse
|
8
|
Wang L, Wang Z, Yu Y, Ren Z, Jia Y, Wang J, Li S, Jiang T. Metabolomics analysis of stool in rats with type 2 diabetes mellitus after single-anastomosis duodenal-ileal bypass with sleeve gastrectomy. Front Endocrinol (Lausanne) 2022; 13:1013959. [PMID: 36204098 PMCID: PMC9530139 DOI: 10.3389/fendo.2022.1013959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Single-anastomosis duodenal-ileal bypass with sleeve gastrectomy (SADI-S) is one of the most effective bariatric procedures in the treatment of type 2 diabetes mellitus (T2DM). However, the mechanisms by which SADI-S improves T2DM are not well-known. OBJECTIVE To explore the effects of SADI-S on metabolites in the stool of rats with T2DM. METHODS Twenty rats were fed on high-fat diet and administered with a low-dose (30mg/kg) of streptozotocin to establish T2DM models. The rats were then randomly assigned to the SADI-S group (n=10) and sham operation group (n=9). Stool samples were collected from all rats at 8 weeks after surgery and stored at -80 °C. Metabolomics analysis was performed to identify differential metabolites through ultra- performance liquid chromatography-mass spectrometry. RESULTS At 8-week after surgery, rats of the SADI-S group showed significantly decreased fasting blood glucose, glucose tolerance test 2-hour, glycated haemoglobin, and body weight compared with those of the sham group. A total of 245 differential metabolites were identified between the two groups. Among them, 16 metabolites such as branched-chain amino acids (valine), aromatic amino acid (phenylalanine), bile acid (cholic acid, lithocholic acid, and β-muricholic acid), short-chain fatty acid (isobutyric acid), and phospholipid [lysoPE(17:0), lysoPE(20:3) and lysoPS(16:0)] were associated to the T2DM remission after SADI-S. CONCLUSION SADI-S improves T2DM in rats by regulating phenylalanine biosynthesis, valine, phenylalanine, alanine, glutamate, proline, bile acid, and phospholipid metabolism pathways.
Collapse
|
9
|
Ahsan W. The Journey of Thiazolidinediones as Modulators of PPARs for the Management of Diabetes: A Current Perspective. Curr Pharm Des 2020; 25:2540-2554. [PMID: 31333088 DOI: 10.2174/1381612825666190716094852] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/04/2019] [Indexed: 01/06/2023]
Abstract
Peroxisome Proliferator-Activated Receptors (PPARs) also known as glitazone receptors are a family of receptors that regulate the expression of genes and have an essential role in carbohydrate, lipid and protein metabolism apart from other functions. PPARs come in 3 sub-types: PPAR-α, PPAR-β/δ and PPAR-γ - with PPAR-γ having 2 isoforms - γ1 and γ2. Upon activation, the PPARs regulate the transcription of various genes involved in lipid and glucose metabolism, adipocyte differentiation, increasing insulin sensitivity, prevention of oxidative stress and to a certain extent, modulation of immune responses via macrophages that have been implicated in the pathogenesis of insulin resistance. Hence, PPARs are an attractive molecular target for designing new anti-diabetic drugs. This has led to a boost in the research efforts directed towards designing of PPAR ligands - particularly ones that can selectively and specifically activate one or more of the PPAR subtypes. Though, PPAR- γ full agonists such as Thiazolidinediones (TZDs) are well established agents for dyslipidemia and type 2 diabetes mellitus (T2D), the side effect profile associated with TZDs has potentiated an imminent need to come up with newer agents that act through this pathway. Several newer derivatives having TZD scaffold have been designed using structure based drug designing technique and computational tools and tested for their PPAR binding affinity and efficacy in combating T2D and some have shown promising activities. This review would focus on the role of PPARs in the management of T2D; recently reported TZD derivatives which acted as agonists of PPAR- γ and its subtypes and are potentially useful in the new drug discovery for the disease.
Collapse
Affiliation(s)
- Waquar Ahsan
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P. Box No. 114, Jazan, Saudi Arabia
| |
Collapse
|
10
|
Sullivan HJ, Wang X, Nogle S, Liao S, Wu C. To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations. PPAR Res 2020; 2020:5314187. [PMID: 32308671 DOI: 10.1155/2020/5314187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/25/2020] [Accepted: 03/03/2020] [Indexed: 02/06/2023] Open
Abstract
Chiglitazar is a promising new-generation insulin sensitizer with low reverse effects for the treatment of type II diabetes mellitus (T2DM) and has shown activity as a nonselective pan-agonist to the human peroxisome proliferator-activated receptors (PPARs) (i.e., full activation of PPARγ and a partial activation of PPARα and PPARβ/δ). Yet, it has no high-resolution complex structure with PPARs and its detailed interactions and activation mechanism remain unclear. In this study, we docked chiglitazar into three experimentally resolved crystal structures of hPPAR subtypes, PPARα, PPARβ/δ, and PPARγ, followed by 3 μs molecular dynamics simulations for each system. Our MM-GBSA binding energy calculation revealed that chiglitazar most favorably bound to hPPARγ (-144.6 kcal/mol), followed by hPPARα (-138.0 kcal/mol) and hPPARβ (-135.9 kcal/mol), and the order is consistent with the experimental data. Through the decomposition of the MM-GBSA binding energy by residue and the use of two-dimensional interaction diagrams, key residues involved in the binding of chiglitazar were identified and characterized for each complex system. Additionally, our detailed dynamics analyses support that the conformation and dynamics of helix 12 play a critical role in determining the activities of the different types of ligands (e.g., full agonist vs. partial agonist). Rather than being bent fully in the direction of the agonist versus antagonist conformation, a partial agonist can adopt a more linear conformation and have a lower degree of flexibility. Our finding may aid in further development of this new generation of medication.
Collapse
|
11
|
Vijayakumar S, Das P. Recent progress in drug targets and inhibitors towards combating leishmaniasis. Acta Trop 2018; 181:95-104. [PMID: 29452111 DOI: 10.1016/j.actatropica.2018.02.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/24/2018] [Accepted: 02/11/2018] [Indexed: 12/22/2022]
Abstract
Lesihmaniasis is one of the major neglected tropical disease caused by the parasite of the genus Leishmania. The disease has more than one clinical forms and the visceral form is considered fatal. With the lack of potential vaccine, chemotherapy is the major treatment source considered for the control of the disease in the infected people. Drugs including amphotericin B and miltefosine are widely used for the treatment, however, development of resistance by the parasite towards the administered drug and high-toxicity of the drug are of major concern. Hence, more attention has been shown on identifying new targets, effective inhibitors, and better drug delivery system against the disease. This review deals with recent studies on drug targets and exploring their essentiality for the survival of Leishmania. Further, new inhibitors for those targets, novel anti-leishmanial peptides and vaccines against leishmaniasis were discussed. We believe that this pool of information will ease the researchers to gain knowledge and help in choosing right targets and design of new inhibitors against Leishmaniasis.
Collapse
|
12
|
Singh S, Mohanty A. In silico identification of potential drug compound against Peroxisome proliferator-activated receptor-gamma by virtual screening and toxicity studies for the treatment of Diabetic Nephropathy. J Biomol Struct Dyn 2017; 36:1776-1787. [PMID: 28539091 DOI: 10.1080/07391102.2017.1334596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Diabetic Nephropathy is a serious complication of diabetes mellitus. Current therapeutic strategies of Diabetic Nephropathy are based on control of modifiable risks like hypertension, glucose levels, and dyslipidemia. Peroxisome proliferator activated receptor-gamma (PPAR-γ) is implicated in several metabolic syndromes including Diabetic Nephropathy, besides obesity, insulin insensitivity, dislipidemia, inflammation, and hypertension. In the present study, virtual screening of 617 compounds from two different public databases was done against PPAR-γ with an objective to find a possible lead compound. Two softwares, PyRx and iGEMDOCK, were used to achieve the docking accuracy in order to avoid loss of candidate compounds. Rosiglitazone (used to treat Diabetic Nephropathy) was taken as the standard compound. A total of 30 compounds with good binding affinity with PPAR-γ were selected for further filtering, on the basis of absorption, distribution, metabolism, excretion, and toxicity (ADMET). The interaction profiling of these 30 compounds, showed a minimum of one and maximum of three interactions with reference to rosiglitazone (SER-289, HIS-449, HIS-323, TYR-473). The fulfilling of ADMET analysis criteria of 30 compounds led to the selection of four compounds (ZINC ID 00181552, 00276456, 00298314, 00448009). Molecular dynamics simulation of these lead compounds in complex with PPAR-γ revealed that three of the four compounds formed a stable complex in the ligand-binding pocket of PPAR-γ during 20-ns simulation. Hence, these three (ZINC ID 00181552, 00276456, 00298314) of the four compounds are potential candidates for experimental validation of biological activity against PPAR-γ in future drug discovery studies.
Collapse
Affiliation(s)
- Smrita Singh
- a Bioinformatics Infrastructure Facility , Gargi College, University of Delhi , New Delhi , 110049 , India
| | - Aparajita Mohanty
- b Department of Botany , Gargi College, University of Delhi , New Delhi , 110049 , India
| |
Collapse
|
13
|
Cannizzaro L, Rossoni G, Savi F, Altomare A, Marinello C, Saethang T, Carini M, Payne DM, Pisitkun T, Aldini G, Leelahavanichkul A. Regulatory landscape of AGE-RAGE-oxidative stress axis and its modulation by PPARγ activation in high fructose diet-induced metabolic syndrome. Nutr Metab (Lond) 2017; 14:5. [PMID: 28101123 PMCID: PMC5237238 DOI: 10.1186/s12986-016-0149-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/29/2016] [Indexed: 12/26/2022] Open
Abstract
Background The AGE-RAGE-oxidative stress (AROS) axis is involved in the onset and progression of metabolic syndrome induced by a high-fructose diet (HFD). PPARγ activation is known to modulate metabolic syndrome; however a systems-level investigation looking at the protective effects of PPARγ activation as related to the AROS axis has not been performed. The aim of this work is to simultaneously characterize multiple molecular parameters within the AROS axis, using samples taken from different body fluids and tissues of a rat model of HFD-induced metabolic syndrome, in the presence or absence of a PPARγ agonist, Rosiglitazone (RGZ). Methods Rats were fed with 60% HFD for the first half of the treatment duration (21 days) then continued with either HFD alone or HFD plus RGZ for the second half. Results Rats receiving HFD alone showed metabolic syndrome manifestations including hypertension, dyslipidemia, increased glucose levels and insulin resistance, as well as abnormal kidney and inflammatory parameters. Systolic blood pressure, plasma triglyceride and glucose levels, plasma creatinine, and albuminuria were significantly improved in the presence of RGZ. The following molecular parameters of the AROS axis were significantly upregulated in our rat model: carboxymethyl lysine (CML) in urine and liver; carboxyethyl lysine (CEL) in urine; advanced glycation end products (AGEs) in plasma; receptor for advanced glycation end products (RAGE) in liver and kidney; advanced oxidation protein products (AOPP) in plasma; and 4-hydroxynonenal (HNE) in plasma, liver, and kidney. Conversely, with RGZ administration, the upregulation of AOPP and AGEs in plasma, CML and CEL in urine, RAGE in liver as well as HNE in plasma and liver was significantly counteracted/prevented. Conclusions Our data demonstrate (i) the systems-level regulatory landscape of HFD-induced metabolic syndrome involving multiple molecular parameters, including HNE, AGEs and their receptor RAGE, and (ii) attenuation of metabolic syndrome by PPARγ modulation. Electronic supplementary material The online version of this article (doi:10.1186/s12986-016-0149-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luca Cannizzaro
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ; Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Giuseppe Rossoni
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Vanvitelli 32, 20129 Milan, Italy
| | - Federica Savi
- Pathological Anatomy Unit (U.O.C. Anatomia Patologica), ASST Santi Paolo e Carlo, Via di Rudinì 8, 20142 Milan, Italy
| | - Alessandra Altomare
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Cristina Marinello
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Thammakorn Saethang
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Marina Carini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - D Michael Payne
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Trairak Pisitkun
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Asada Leelahavanichkul
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| |
Collapse
|
14
|
Karthick V, Nagasundaram N, Doss CGP, Chakraborty C, Siva R, Lu A, Zhang G, Zhu H. Virtual screening of the inhibitors targeting at the viral protein 40 of Ebola virus. Infect Dis Poverty 2016; 5:12. [PMID: 26888469 PMCID: PMC4757971 DOI: 10.1186/s40249-016-0105-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Ebola virus is highly pathogenic and destructive to humans and other primates. The Ebola virus encodes viral protein 40 (VP40), which is highly expressed and regulates the assembly and release of viral particles in the host cell. Because VP40 plays a prominent role in the life cycle of the Ebola virus, it is considered as a key target for antiviral treatment. However, there is currently no FDA-approved drug for treating Ebola virus infection, resulting in an urgent need to develop effective antiviral inhibitors that display good safety profiles in a short duration. METHODS This study aimed to screen the effective lead candidate against Ebola infection. First, the lead molecules were filtered based on the docking score. Second, Lipinski rule of five and the other drug likeliness properties are predicted to assess the safety profile of the lead candidates. Finally, molecular dynamics simulations was performed to validate the lead compound. RESULTS Our results revealed that emodin-8-beta-D-glucoside from the Traditional Chinese Medicine Database (TCMD) represents an active lead candidate that targets the Ebola virus by inhibiting the activity of VP40, and displays good pharmacokinetic properties. CONCLUSION This report will considerably assist in the development of the competitive and robust antiviral agents against Ebola infection.
Collapse
Affiliation(s)
- V Karthick
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - N Nagasundaram
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - C George Priya Doss
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong.,Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Chiranjib Chakraborty
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong.,Department of Bioinformatics, School of Computer and Information Sciences, Galgotias University, Noida, India
| | - R Siva
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Aiping Lu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ge Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Hailong Zhu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| |
Collapse
|
15
|
|
16
|
Cheang WS, Tian XY, Wong WT, Huang Y. The peroxisome proliferator-activated receptors in cardiovascular diseases: experimental benefits and clinical challenges. Br J Pharmacol 2015; 172:5512-22. [PMID: 25438608 DOI: 10.1111/bph.13029] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/24/2014] [Accepted: 11/20/2014] [Indexed: 12/13/2022] Open
Abstract
The peroxisome proliferator-activated receptors, PPARα, PPARβ/δ and PPARγ, are ligand-activated transcriptional factors belonging to the nuclear receptors superfamily and they are known to play important roles in glucose and lipid metabolism. Experimental studies in animal models of metabolic diseases have also revealed that activation of PPARs protects against the vascular complications of diabetes, hypertension, atherosclerosis, myocardial infarction and stroke, through exerting their anti-inflammatory, anti-atherogenic and antioxidant effects. In clinical trials and post-market surveillance, agonists of PPARs have been shown to effectively prevent cardiovascular events. However, adverse effects, particularly for PPARγ agonists, are also observed with the use of investigational PPAR agonists and even some approved drugs. Further exploration of underlying mechanisms is needed to develop novel ways of PPAR activation without causing serious side effects. This article reviews the cardiovascular effects of PPARs, with emphasis on the therapeutic potential of PPAR agonists in combating metabolic vascular diseases.
Collapse
Affiliation(s)
- Wai San Cheang
- Shenzhen Research Institute, Institute of Vascular Medicine and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Xiao Yu Tian
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Wing Tak Wong
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Yu Huang
- Shenzhen Research Institute, Institute of Vascular Medicine and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|