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Jana A, Naga R, Saha S, Griñán-Ferré C, Banerjee DR. Integration of ligand and structure-based pharmacophore screening for the identification of novel natural leads against Euchromatic histone lysine methyltransferase 2 (EHMT2/G9a). J Biomol Struct Dyn 2024; 42:3535-3562. [PMID: 37216299 DOI: 10.1080/07391102.2023.2213346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/08/2023] [Indexed: 05/24/2023]
Abstract
Herein, we report a blended ligand and structure-based pharmacophore screening approach to identify new natural leads against the Protein Lysine Methyltransferase 2 (EHMT2/G9a). The EHMT2/G9a has been associated with Cancer, Alzheimer's, and aging and is considered an emerging drug target having no clinically passed inhibitor. Purposefully, we developed the ligand-based pharmacophore (Pharmacophore-L) based on the common features of known inhibitors and the structure-based pharmacophore (Pharmacophore-S) based on the interaction profile of available crystal structures. The Pharmacophore-L and Pharmacophore-S were subjected to multiple tiers of validations and utilized in combination for the screening of total 741543 compounds coming from multiple databases. Additional layers of stringency were applied in the screening process to test drug-likeness (using Lipinski's rule, Veber's rule, SMARTS and ADMET filtration), to rule out any toxicity (TOPKAT analysis). The interaction profiles, stabilities, and comparative analysis against the reference were carried out by flexible docking, MD simulation, and MM-GBSA analysis, which finally led to three leads as potential inhibitors of G9a.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhisek Jana
- Department of Chemistry, National Institute of Technology Durgapur, Durgapur, India
| | - Rahul Naga
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Sougata Saha
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Deb Ranjan Banerjee
- Department of Chemistry, National Institute of Technology Durgapur, Durgapur, India
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Wu C, Wong AR, Chen Q, Yang S, Chen M, Sun X, Zhou L, Liu Y, Yang AWH, Bi J, Hung A, Li H, Zhao X. Identification of inhibitors from a functional food-based plant Perillae Folium against hyperuricemia via metabolomics profiling, network pharmacology and all-atom molecular dynamics simulations. Front Endocrinol (Lausanne) 2024; 15:1320092. [PMID: 38435751 PMCID: PMC10905266 DOI: 10.3389/fendo.2024.1320092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction Hyperuricemia (HUA) is a metabolic disorder caused by purine metabolism dysfunction in which the increasing purine levels can be partially attributed to seafood consumption. Perillae Folium (PF), a widely used plant in functional food, has been historically used to mitigate seafood-induced diseases. However, its efficacy against HUA and the underlying mechanism remain unclear. Methods A network pharmacology analysis was performed to identify candidate targets and potential mechanisms involved in PF treating HUA. The candidate targets were determined based on TCMSP, SwissTargetPrediction, Open Targets Platform, GeneCards, Comparative Toxicogenomics Database, and DrugBank. The potential mechanisms were predicted via Gene Ontology (GO) and Kyoto Gene and Genome Encyclopedia (KEGG) analyses. Molecular docking in AutoDock Vina and PyRx were performed to predict the binding affinity and pose between herbal compounds and HUA-related targets. A chemical structure analysis of PF compounds was performed using OSIRIS DataWarrior and ClassyFire. We then conducted virtual pharmacokinetic and toxicity screening to filter potential inhibitors. We further performed verifications of these inhibitors' roles in HUA through molecular dynamics (MD) simulations, text-mining, and untargeted metabolomics analysis. Results We obtained 8200 predicted binding results between 328 herbal compounds and 25 potential targets, and xanthine dehydrogenase (XDH) exhibited the highest average binding affinity. We screened out five promising ligands (scutellarein, benzyl alpha-D-mannopyranoside, elemol, diisobutyl phthalate, and (3R)-hydroxy-beta-ionone) and performed MD simulations up to 50 ns for XDH complexed to them. The scutellarein-XDH complex exhibited the most satisfactory stability. Furthermore, the text-mining study provided laboratory evidence of scutellarein's function. The metabolomics approach identified 543 compounds and confirmed the presence of scutellarein. Extending MD simulations to 200 ns further indicated the sustained impact of scutellarein on XDH structure. Conclusion Our study provides a computational and biomedical basis for PF treating HUA and fully elucidates scutellarein's great potential as an XDH inhibitor at the molecular level, holding promise for future drug design and development.
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Affiliation(s)
- Chuanghai Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Ann Rann Wong
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora, VIC, Australia
| | - Qinghong Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Shuxuan Yang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Meilin Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Xiaomin Sun
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Lin Zhou
- Endocrinology Department, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanyan Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Angela Wei Hong Yang
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora, VIC, Australia
| | - Jianlu Bi
- Endocrinology Department, Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, China
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, Australia
| | - Hong Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
- School of Science, STEM College, RMIT University, Melbourne, VIC, Australia
| | - Xiaoshan Zhao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
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Li LP, Li HX, Zhou H, Li WY, Wang RL, Zhang YC, Ma Y. Exploring the mechanism of C473D mutation on CDC25B causing weak binding affinity with CDK2/CyclinA by molecular dynamics study. J Biomol Struct Dyn 2023; 41:12552-12564. [PMID: 36655391 DOI: 10.1080/07391102.2023.2166995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023]
Abstract
CDC25B belongs to the CDC25 family, and it plays an important part in regulating the activity of CDK/CyclinA. Studies have shown that CDC25B is closely related to cancer development. When CYS473 on CDC25B is mutated into ASP, the affinity between CDC25B and CDK2/CyclinA weakens, and their dissociation speed is greatly improved. However, the mechanism by which the CDC25BC473D mutant weakens its binding to CDK2/CyclinA is unclear. In order to study the effect of CDC25BC473D mutants on CDK2/CyclinA substrates, we constructed and verified the rationality of the CDC25BWT:CDK2/CyclinA system and CDC25BC473D:CDK2/CyclinA system and conducted molecular dynamics (MD) simulation analysis. In the post-analysis, the fluctuations of residues ARG488-SER499, LYS541-TRP550 on CDC25B and residues ASP206-ASP210 on CDK2 were massive in the mutant CDC25BC473D:CDK2/CyclinA system. And the interactions between residue ARG492 and residue GLU208, residue ARG544 and residue GLU42, residue ARG544 and TRP550 were weakened in the mutant CDC25BC473D:CDK2/CyclinA system. The results showed that when CYS473 on CDC25B was mutated into ASP473, the mutant CDC25BC473D:CDK2/CyclinA system was less stable than the wild-type CDC25BWT:CDK2/CyclinA system. Finally, active site CYS473 of CDC25B was speculated to be the key residue, which had great effects on the binding between CDC25BCYS473 and CDK2 in the CDC25BC473D:CDK2/CyclinA system. Consequently, overall analyses appeared in this study ultimately provided a useful understanding of the weak interactions between CDC25BCYS473D and CDK2/CyclinA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Li-Peng Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Hao-Xin Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Hui Zhou
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Wei-Ya Li
- China Department of Pharmacy, Tianjin Medical University, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Run-Ling Wang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Ying-Chi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
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Wang Y, Zhang H, Li J, Niu MM, Zhou Y, Qu Y. Discovery of potent and noncovalent KRAS G12D inhibitors: Structure-based virtual screening and biological evaluation. Front Pharmacol 2022; 13:1094887. [PMID: 36618907 PMCID: PMC9815544 DOI: 10.3389/fphar.2022.1094887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
KRASG12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of pancreatic cancer. Herein, we identified four potent and noncovalent KRASG12D inhibitors (hits 1-4) by using structure-based virtual screening and biological evaluation. The in vitro assays indicated that the four compounds had sub-nanomolar affinities for KRASG12D and showed a dose-dependent inhibitory effect on human pancreatic cancer cells. In particular, the hit compound 3 was the most promising candidate and significantly inhibited the tumor growth of pancreatic cancer in tumor-bearing mice. The hit compound 3 represented a promising starting point for structural optimization in hit-to-lead development. This study shows that hit compound 3 provides a basis for the development of the treatment of cancer driven by KRASG12D.
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Affiliation(s)
- Yuting Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Hai Zhang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jindong Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Yang Zhou
- Department of Pathology, Department of Gastrointestinal Surgery, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China,*Correspondence: Yang Zhou, ; Yuanqian Qu,
| | - Yuanqian Qu
- Department of Pathology, Department of Gastrointestinal Surgery, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou, China,*Correspondence: Yang Zhou, ; Yuanqian Qu,
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Zhang G, Zhu M, Liao Y, Gong D, Hu X. Action mechanisms of two key xanthine oxidase inhibitors in tea polyphenols and their combined effect with allopurinol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:7195-7208. [PMID: 35727856 DOI: 10.1002/jsfa.12085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Tea polyphenols have been reported to have the effect of lowering uric acid. However, there are few studies on the inhibitory effects and molecular mechanisms of specific catechins on the urate-metabolizing enzyme xanthine oxidase (XO). In this research, multiple spectroscopic methods and computer simulations were used to determine the inhibitory ability and mechanisms of epigallocatechin gallate (EGCG) and gallocatechin gallate (GCG) on XO. RESULTS Herein, EGCG and GCG reversibly inhibited XO activity in a mixed manner, with IC50 values of 40.50 ± 0.32 and 33.60 ± 0.53 μmol L-1 , and also decreased the superoxide anion radical (O2 - ) of the catalytic system by reducing the XO molecule and inhibiting the formation of uric acid. The combination of EGCG or GCG with allopurinol showed synergistic inhibition on XO. The binding of EGCG or GCG to XO with moderate affinity formed a stable complex by hydrogen bonds and van der Waals forces. The presence of EGCG and GCG made the structure of XO more stable and compact. The two inhibitors bound to the vicinity of flavin adenine dinucleotide (FAD) in XO, hindering the entry of substrate; thus the activity of XO was suppressed. CONCLUSION Both EGCG and GCG are excellent natural XO inhibitors, and inhibited the activity of XO by occupying the channel of the substrate to enter the active center and interfering with the dual substrate reaction catalyzed by XO. These findings provide a scientific basis for the application of catechins in dietary supplements and medicines with lowering uric acid effects. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Miao Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Yijing Liao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Deming Gong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Xing Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
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Salarizadeh N, Aallaei MR, Zarei A, Malekshah RE, Molaakbari E, Farajnezhadi A. Docking and Molecular Dynamics Simulations of Flavonoids as Inhibitors of Infectious Agents: Rutin as a Coronavirus Protease Inhibitor. ChemistrySelect 2022. [DOI: 10.1002/slct.202202043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Navvabeh Salarizadeh
- Department of Cell & Molecular Biology School of Biology College of Science University of Tehran Tehran Iran
- School of Medicine Baqyatallah University of Medical Sciences Tehran Iran
| | | | - Ali Zarei
- School of Medicine Baqyatallah University of Medical Sciences Tehran Iran
| | | | - Elaheh Molaakbari
- Department of Chemistry Shahid Bahonar University of Kerman Kerman Iran
| | - Amirreza Farajnezhadi
- School of Chemical Engineering College of Engineering University of Tehran Tehran Iran
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7
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Zhai N, Chen Y, Wang C, Wu F, Luo X, Ju X, Liu H, Liu G. A multiscale screening strategy for the identification of novel xanthine oxidase inhibitors based on the pharmacological features of febuxostat analogues. NEW J CHEM 2022. [DOI: 10.1039/d2nj00115b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two compounds as potential XOI hits were identified by a novel screening strategy based on the pharmacophores of well-known scaffolds.
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Affiliation(s)
- Na Zhai
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Yanming Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Chenchen Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Fengshou Wu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Xiaogang Luo
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, Henan Province, P. R. China
| | - Xiulian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Hui Liu
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, P. R. China
| | - Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
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8
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Zhai N, Wang C, Wu F, Xiong L, Luo X, Ju X, Liu G. Exploration of Novel Xanthine Oxidase Inhibitors Based on 1,6-Dihydropyrimidine-5-Carboxylic Acids by an Integrated in Silico Study. Int J Mol Sci 2021; 22:8122. [PMID: 34360886 PMCID: PMC8348919 DOI: 10.3390/ijms22158122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Xanthine oxidase (XO) is an important target for the effective treatment of hyperuricemia-associated diseases. A series of novel 2-substituted 6-oxo-1,6-dihydropyrimidine-5-carboxylic acids (ODCs) as XO inhibitors (XOIs) with remarkable activities have been reported recently. To better understand the key pharmacological characteristics of these XOIs and explore more hit compounds, in the present study, the three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) studies were performed on 46 ODCs. The constructed 3D-QSAR models exhibited reliable predictability with satisfactory validation parameters, including q2 = 0.897, R2 = 0.983, rpred2 = 0.948 in a CoMFA model, and q2 = 0.922, R2 = 0.990, rpred2 = 0.840 in a CoMSIA model. Docking and MD simulations further gave insights into the binding modes of these ODCs with the XO protein. The results indicated that key residues Glu802, Arg880, Asn768, Thr1010, Phe914, and Phe1009 could interact with ODCs by hydrogen bonds, π-π stackings, or hydrophobic interactions, which might be significant for the activity of these XOIs. Four potential hits were virtually screened out using the constructed pharmacophore model in combination with molecular dockings and ADME predictions. The four hits were also found to be relatively stable in the binding pocket by MD simulations. The results in this study might provide effective information for the design and development of novel XOIs.
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Affiliation(s)
- Na Zhai
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Chenchen Wang
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Fengshou Wu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Liwei Xiong
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xiaogang Luo
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
- School of Materials Science and Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Xiulian Ju
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Genyan Liu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
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Ding TT, Liu YY, Zhang LM, Shi JR, Xu WR, Li SY, Cheng XC. Exploring dual agonists for PPARα/γ receptors using pharmacophore modeling, docking analysis and molecule dynamics simulation. Comb Chem High Throughput Screen 2021; 25:1450-1461. [PMID: 34182904 DOI: 10.2174/1386207324666210628114216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors belonging to the nuclear receptor family. The roles of PPARα in fatty acid oxidation and PPARγ in adipocyte differentiation and lipid storage have been widely characterized. Compounds with dual PPARα/γ activity have been proposed, combining the benefits of insulin sensitization and lipid-lowering into one drug, allowing a single drug to reduce hyperglycemia and hyperlipidemia while preventing the development of cardiovascular complications. METHODS The new PPARα/γ agonists were screened through virtual screening of pharmacophores and molecular dynamics simulations. First, in the article, the constructed pharmacophore was used to screen the Ligand Expo Components-pub database to obtain the common structural characteristics of representative PPARα/γ agonist ligands. Then, the obtained ligand structure was modified and replaced to obtain 12 new compounds. Using molecular docking, ADMET and molecular dynamics simulation methods, the designed 12 ligands were screened, their docking scores were analyzed when they bound to the PPARα/γ dual targets, and also their stability and pharmacological properties were assessed when they were bound to the PPARα/γ dual targets. RESULTS We performed pharmacophore-based virtual screening for 22949 molecules in the Ligand Expo Components-pub database. Structural analysis and modification were performed on the compounds that were superior to the original ligand , and a series of compounds with novel structures were designed. Using precise docking, ADMET prediction and molecular dynamics methods, newly designed compounds were screened and verified, and the above compounds showed higher docking scores and lower side effects. CONCLUSION 9 new PPARα/γ agonists were obtained by pharmacophore modeling, docking analysis and molecule dynamics simulation.
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Affiliation(s)
- Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Li-Ming Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Jia-Rui Shi
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Shao-Yong Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
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10
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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11
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Bou-Salah L, Benarous K, Linani A, Rabhi F, Chaib K, Chine I, Bensaidane H, Yousfi M. Anti-inflammatory drugs as new inhibitors to xanthine oxidase: In vitro and in silico approach. Mol Cell Probes 2021; 58:101733. [PMID: 33957269 DOI: 10.1016/j.mcp.2021.101733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/06/2023]
Abstract
The two important targets to treat gout disease are (1) control the hyperuricemia by the inhibition of Xanthine Oxidase (XO) and (2) treatment of acute attacks of gout by the use of anti-inflammatory drugs. It is important to distinguish between therapy to manage hyperuricemia and to reduce acute inflammation. While reducing hyperuricemia is resolved very slowly with available drugs, gout symptoms like pain and inflammation may become persistent. The objective of this study is to find a relevant treatment with a beneficial double effect. (1) As an anti-inflammatory, analgesic, and antipyretic effect and (2) as XO inhibitory effect, which is the main objective of this study. We investigated the effect of five non-steroidal anti-inflammatory drugs (NSAIDs) against human and bovine milk xanthine oxidases (HXO and BXO) using the double enzyme detection method (DED) and molecular docking with the Autodock vina program. in vitro results show that the NSAIDs give an important inhibition to HXO and BXO with an IC50 of 2.04 ± 0.13 μg/ml, 2.75 ± 0.23 μg/ml, 1.45 ± 0.19 μg/ml, 0.31 ± 0.13 μg/ml and 1.27 ± 0.11 μg/ml, for HXO, and 2.96 ± 0.27 μg/ml, 9.46 ± 0.13 μg/ml, 6.21 ± 1.17 μg/ml, 0.83 ± 0.11 μg/ml, and 3.48 ± 0.13 μg/ml, for BXO, for respectively, Naproxen, Ibuprofen, Diclofenac, Indomethacin, and Celecoxib. Testing the inhibitory activity of these drugs on both XOs shows an important inhibition, especially from Indomethacin, which could be a promising lead compound for reducing acute inflammation and at the same time controlling hyperuricemia.
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Affiliation(s)
- Leila Bou-Salah
- Laboratory of Fundamental Sciences, University of Amar Telidji, Laghouat, Algeria.
| | - Khedidja Benarous
- Laboratory of Fundamental Sciences, University of Amar Telidji, Laghouat, Algeria; Biology Department, University of Amar Telidji, Laghouat, Algeria
| | - Abderahmane Linani
- Laboratory of Fundamental Sciences, University of Amar Telidji, Laghouat, Algeria
| | - Faiza Rabhi
- Biology Department, University of Amar Telidji, Laghouat, Algeria
| | - Kheira Chaib
- Biology Department, University of Amar Telidji, Laghouat, Algeria
| | - Imane Chine
- Biology Department, University of Amar Telidji, Laghouat, Algeria
| | | | - Mohamed Yousfi
- Laboratory of Fundamental Sciences, University of Amar Telidji, Laghouat, Algeria
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12
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Sippl W, Ntie-Kang F. Editorial to Special Issue-"Structure-Activity Relationships (SAR) of Natural Products". Molecules 2021; 26:E250. [PMID: 33418945 PMCID: PMC7825126 DOI: 10.3390/molecules26020250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 11/17/2022] Open
Abstract
The topic of structure-activity-relationships (SAR) has recently drawn a lot of attention, and there is increasing interest in natural products (NPs) as a "source of inspiration" for the discovery of new lead compounds [...].
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Affiliation(s)
- Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Kurt-Mothes-Str. 3, 06122 Halle, Germany;
| | - Fidele Ntie-Kang
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Kurt-Mothes-Str. 3, 06122 Halle, Germany;
- Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea CM-00237, Cameroon
- Institute of Botany, Technical University of Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
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13
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Benarous K, Bou-Salah L, Linani A, Yousfi M, Kostova I, Saso L. Lanthanide (III) complexes of bis-coumarins as strong inhibitors of bovine xanthine oxidase - molecular docking and SAR studies. J Biomol Struct Dyn 2020; 40:2733-2739. [PMID: 33146077 DOI: 10.1080/07391102.2020.1842247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The gout disease is spreading worldwide and its drug target is the human xanthine oxidase. Through this work, we investigated the inhibitory effect of the ten lanthanide(III) complexes of biologically active bis-coumarins on xanthine oxidase. We achieved molecular docking studies using GOLD software to study the formed interactions in the enzyme-inhibitor complex. The results confirm the inhibitory effect of the lanthanide complexes showing the best Nd(III) complex with IC50 of 12.91 nM. The docking results confirm this inhibition. We saved nearly the same interactions between the two inhibitors allopurinol and the Nd(III) complex according to the docking results. No further studies have been found in this context. The ADMET analysis show that the three complexes are nontoxic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khedidja Benarous
- Laboratoire des sciences fondamentales, Université Amar Telidji, Laghouat, Algérie
| | - Leila Bou-Salah
- Laboratoire des sciences fondamentales, Université Amar Telidji, Laghouat, Algérie
| | - Abderrahmane Linani
- Laboratoire des sciences fondamentales, Université Amar Telidji, Laghouat, Algérie
| | - Mohamed Yousfi
- Laboratoire des sciences fondamentales, Université Amar Telidji, Laghouat, Algérie
| | - Irena Kostova
- Faculty of Pharmacy, Department of Chemistry, Medical University, Bulgaria
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Italy
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14
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Xin T, Lv W, Liu D, Jing Y, Hu F. Opa1 Reduces Hypoxia-Induced Cardiomyocyte Death by Improving Mitochondrial Quality Control. Front Cell Dev Biol 2020; 8:853. [PMID: 32984338 PMCID: PMC7483501 DOI: 10.3389/fcell.2020.00853] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction contributes to cardiovascular disorders, especially post-infarction cardiac injury, through incompletely characterized mechanisms. Among the latter, increasing evidence points to alterations in mitochondrial quality control, a range of adaptive responses regulating mitochondrial morphology and function. Optic atrophy 1 (Opa1) is a mitochondrial inner membrane GTPase known to promote mitochondrial fusion. In this study, hypoxia-mediated cardiomyocyte damage was induced to mimic post-infarction cardiac injury in vitro. Loss- and gain-of-function assays were then performed to evaluate the impact of Opa1 expression on mitochondrial quality control and cardiomyocyte survival and function. Hypoxic stress reduced cardiomyocyte viability, impaired contractile/relaxation functions, and augmented the synthesis of pro-inflammatory mediators. These effects were exacerbated by Opa1 knockdown, and significantly attenuated by Opa1 overexpression. Mitochondrial quality control was disturbed by hypoxia, as reflected by multiple mitochondrial deficits; i.e., increased fission, defective fusion, impaired mitophagy, decreased biogenesis, increased oxidative stress, and blunted respiration. By contrast, overexpression of Opa1 normalized mitochondrial quality control and sustained cardiomyocyte function. We also found that ERK, AMPK, and YAP signaling can regulate Opa1 expression. These results identify Opa1 as a novel regulator of mitochondrial quality control and highlight a key role for Opa1 in protecting cardiomyocytes against post-infarction cardiac injury.
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Affiliation(s)
- Ting Xin
- Department of Cardiology, Tianjin First Center Hospital, Tianjin, China
| | - Wei Lv
- Department of Cardiology, Tianjin First Center Hospital, Tianjin, China
| | - Dongmei Liu
- Department of Cardiology, Tianjin First Center Hospital, Tianjin, China
| | - Yongle Jing
- Department of Cardiology, Tianjin First Center Hospital, Tianjin, China
| | - Fang Hu
- Department of Cardiology, Tianjin First Center Hospital, Tianjin, China
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15
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Sharma M, Mittal A, Singh A, Jainarayanan AK, Sharma S, Paliwal S. Pharmacophore-driven identification of N-methyl-D-receptor antagonists as potent neuroprotective agents validated using in vivo studies. Biol Methods Protoc 2020; 5:bpaa013. [PMID: 32913897 PMCID: PMC7474860 DOI: 10.1093/biomethods/bpaa013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 01/18/2023] Open
Abstract
Alzheimer's disease (AD), apparently the most widespread reason behind dementia, is delineated by a continuous cognitive weakening in the aged. During its progression, N-methyl-D-aspartate receptor (NMDAR) antagonists are known to play a pivotal part in the mechanisms of learning and memory. Since there is an unmet medical need for the treatment of AD, we aim to identify possible chemical compounds targeted toward N-methyl-D-aspartate receptors. Three-dimensional models are developed to unveil some of the essential characteristics of the N-methyl-D-aspartate receptors by using a collection of already discovered N-methyl-D-aspartate receptor inhibitors. This is followed by virtual screening, which results in novel chemical compounds having the potential to inhibit N-methyl-D-aspartate receptors. Molecular docking studies and analysis promulgated two lead compounds with a high LibDock score. The compounds are shortlisted based on high estimated activity, fit values, LibDock score, no violation of Lipinski's, and availability for procuring. Finally, the shortlisted compounds are tested by employing in vivo studies, which we further propose as potential NMDA inhibitors for treating AD.
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Affiliation(s)
- Mukta Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Anupama Mittal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Aarti Singh
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | | | - Swapnil Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, Rajasthan, India
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16
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Wang J, Toan S, Zhou H. New insights into the role of mitochondria in cardiac microvascular ischemia/reperfusion injury. Angiogenesis 2020; 23:299-314. [PMID: 32246225 DOI: 10.1007/s10456-020-09720-2] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
As reperfusion therapies have become more widely used in acute myocardial infarction patients, ischemia-induced myocardial damage has been markedly reduced, but reperfusion-induced cardiac injury has become increasingly evident. The features of cardiac ischemia-reperfusion (I/R) injury include microvascular perfusion defects, platelet activation and sequential cardiomyocyte death due to additional ischemic events at the reperfusion stage. Microvascular obstruction, defined as a no-reflow phenomenon, determines the infarct zone, myocardial function and peri-operative mortality. Cardiac microvascular endothelial cell injury may occur much earlier and with much greater severity than cardiomyocyte injury. Endothelial cells contain fewer mitochondria than other cardiac cells, and several of the pathological alterations during cardiac microvascular I/R injury involve mitochondria, such as increased mitochondrial reactive oxygen species (mROS) levels and disturbed mitochondrial dynamics. Although mROS are necessary physiological second messengers, high mROS levels induce oxidative stress, endothelial senescence and apoptosis. Mitochondrial dynamics, including fission, fusion and mitophagy, determine the shape, distribution, size and function of mitochondria. These adaptive responses modify extracellular signals and orchestrate intracellular processes such as cell proliferation, migration, metabolism, angiogenesis, permeability transition, adhesive molecule expression, endothelial barrier function and anticoagulation. In this review, we discuss the involvement of mROS and mitochondrial morphofunction in cardiac microvascular I/R injury.
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Affiliation(s)
- Jin Wang
- Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China
| | - Sam Toan
- Department of Chemical Engineering, University of Minnesota-Duluth, Duluth, MN, 55812, USA
| | - Hao Zhou
- Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, 100853, China. .,Department of Cardiology, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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17
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Xin T, Lu C. Irisin activates Opa1-induced mitophagy to protect cardiomyocytes against apoptosis following myocardial infarction. Aging (Albany NY) 2020; 12:4474-4488. [PMID: 32155590 PMCID: PMC7093202 DOI: 10.18632/aging.102899] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Myocardial infarction is characterized by sudden ischemia and cardiomyocyte death. Mitochondria have critical roles in regulating cardiomyocyte viability and can sustain damage under ischemic conditions. Mitophagy is a mechanism by which damaged mitochondria are removed by autophagy to maintain mitochondrial structure and function. We investigated the role of the dynamin-like GTPase optic atrophy 1 (Opa1) in mitophagy following myocardial infarction. Opa1 expression was downregulated in infarcted hearts in vivo and in hypoxia-treated cardiomyocytes in vitro. We found that Opa1 overexpression protected cardiomyocytes against hypoxia-induced damage and enhanced cell viability by inducing mitophagy. Opa1-induced mitophagy was activated by treatment with irisin, which protected cardiomyocytes from further damage following myocardial infarction. Opa1 knockdown abolished the cardioprotective effects of irisin resulting in an enhanced inflammatory response, increased oxidative stress, and mitochondrial dysfunction in cardiomyocytes. Our data indicate that Opa1 plays an important role in maintaining cardiomyocyte viability and mitochondrial function following myocardial infarction by inducing mitophagy. Irisin can activate Opa1-induced mitophagy and protect against cardiomyocyte injury following myocardial infarction.
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Affiliation(s)
- Ting Xin
- The First Center Clinic College of Tianjin Medical University, Tianjin First Center Hospital, Tianjin, China.,Department of Cardiology, Tianjin First Center Hospital, Tianjin, China
| | - Chengzhi Lu
- Department of Cardiology, Tianjin First Center Hospital, Tianjin, China
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18
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Tomovic K, Ilic BS, Smelcerovic Z, Miljkovic M, Yancheva D, Kojic M, Mavrova AT, Kocic G, Smelcerovic A. Benzimidazole-based dual dipeptidyl peptidase-4 and xanthine oxidase inhibitors. Chem Biol Interact 2020; 315:108873. [DOI: 10.1016/j.cbi.2019.108873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/08/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022]
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19
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Zhou Y, Peng J, Li P, Du H, Li Y, Li Y, Zhang L, Sun W, Liu X, Zuo Z. Discovery of novel indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors by virtual screening. Comput Biol Chem 2018; 78:306-316. [PMID: 30616156 DOI: 10.1016/j.compbiolchem.2018.11.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/17/2018] [Accepted: 11/25/2018] [Indexed: 02/04/2023]
Abstract
In this study, a combination of virtual screening methods were utilized to identify novel potential indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. A series of IDO1 potential inhibitors were identified by a combination of following steps: Lipinski's Rule of Five, Veber rules filter, molecular docking, HipHop pharmacophores, 3D-Quantitative structure activity relationship (3D-QSAR) studies and Pan-assay Interference Compounds (PAINS) filter. Three known categories of IDO1 inhibitors were used to constructed pharmacophores and 3D-QSAR models. Four point pharmacophores (RHDA) of IDO1 inhibitors were generated from the training set. The 3D-QSAR models were obtained using partial least squares (PLS) analyze based on the docking conformation alignment from the training set. The leave-one-out correlation (q2) and non-cross-validated correlation coefficient (r2pred) of the best CoMFA model were 0.601 and 0.546, and the ones from the best CoMSIA model were 0.506 and 0.541, respectively. Six hits from Specs database were identified and analyzed to confirm their binding modes and key interactions to the amino acid residues in the protein. This work may provide novel backbones for new generation of inhibitors of IDO1.
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Affiliation(s)
- Yeheng Zhou
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China; State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiale Peng
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China
| | - Penghua Li
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China
| | - Haibo Du
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China
| | - Yaping Li
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China
| | - Yingying Li
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China
| | - Li Zhang
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China
| | - Wei Sun
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Xingyong Liu
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China.
| | - Zhili Zuo
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, China; State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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