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Almowallad S, Al-Massabi R. Berberine modulates cardiovascular diseases as a multitarget-mediated alkaloid with insights into its downstream signals using in silico prospective screening approaches. Saudi J Biol Sci 2024; 31:103977. [PMID: 38510527 PMCID: PMC10951604 DOI: 10.1016/j.sjbs.2024.103977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Atherosclerosis is potentially correlated with several cardiac disorders that are greatly associated with cellular oxidative stress generation, inflammation, endothelial cells dysfunction, and many cardiovascular complications. Berberine is a natural isoquinoline alkaloid compound that widely modulates pathogenesis of atherosclerosis through its different curative potentials. This in silico screening study was designed to confirm the potent restorative properties of berberine chloride as a multitarget-mediated alkaloid against the CVDs and their complications through screening, identifying, visualizing, and evaluating its binding models, affinities, and interactions toward several CVDs-related targets as direct and/or indirect-mediated signals via inhibiting cellular ER stress and apoptotic signals and activating autophagy pathway. The drug-likeness properties of berberine were predicted using the computational QSAR/ADMET and Lipinski's RO5 analyses as well as in silico molecular docking simulations. The potent berberine-binding modes, residues-interaction patterns, and free energies of binding scores towards several CVDs-related targets were estimated using molecular docking tools. Furthermore, the pharmacokinetic properties and toxicological features of berberine were clearly determined. According to this in silico virtual screening study, berberine chloride could restore cardiac function and improve pathogenic features of atherosclerotic CVDs through alleviating ER stress and apoptotic signals, activating autophagy, improving insulin sensitivity, decreasing hyperglycemia and dyslipidemia, increasing intracellular RCT signaling, attenuating oxidative stress and vascular inflammation, and upregulating cellular antioxidant defenses in many cardiovascular tissues. In this in silico study, berberine chloride greatly modulated several potent CVDs-related targets, including SIGMAR1, GRP78, CASP3, BECN1, PIK3C3, SQSTM1/p62, LC3B, GLUT3, INSR, LDLR, LXRα, PPARγ, IL1β, IFNγ, iNOS, COX-2, MCP-1, IL10, GPx1, and SOD3.
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Affiliation(s)
- Sanaa Almowallad
- Assistant Professor of Medical Biochemistry, Department of Biochemistry, Faculty of Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Rehab Al-Massabi
- Assistant Professor of Medical Biochemistry, Department of Biochemistry, Faculty of Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
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Ballav S, Lokhande KB, Yadav RS, Ghosh P, Swamy KV, Basu S. Exploring binding mode assessment of novel kaempferol, resveratrol, and quercetin derivatives with PPAR-α as potent drug candidates against cancer. Mol Divers 2023; 27:2867-2885. [PMID: 36544031 DOI: 10.1007/s11030-022-10587-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Peroxisome proliferator-activated receptors (PPAR)-α, a ligand-activated transcription factor stands out to be a valuable protein target against cancer. Given that ligand binding is the crucial process for the activation of PPAR-α, fibrate class of synthetic compounds serves as potent agonist for the receptor. However, their serious side effects limit the long-term application in cancer. This emphasizes the dire need to identify new candidates that would exert desired activation by abrogating the adverse effects caused by synthetic agonists. Natural dietary products serve as an important source of drug discovery. Hence, the present study encompasses the investigation of the role of natural plant phenolic compounds: kaempferol, resveratrol, and quercetin and their 8708 derivatives by the means of computational pipeline comprising molecular docking and molecular dynamic (MD) simulation techniques. Docking calculations shortlisted potential candidates, namely 6-cinnamylchrysin (6-CC), resveratrol potassium-4-sulfate (RPS) and 6-[2-(3,4-Dihydroxyphenyl)-5-hydroxy-4-oxochromen-7-yl]oxyhexyl nitrate (DHOON), and derivatives of kaempferol, resveratrol, and quercetin, respectively. 6-CC, RPS, and DHOON manifested better affinities of - 32.83 kcal/mol (Ala333, Lys358, His440), - 27.22 kcal/mol (Tyr314, Met355), and - 30.18 kcal/mol (Ser280, Tyr314, Ala333), respectively, and were found to act as good stimulants for PPAR-α. Among these three compounds, 6-CC caused relatively least deviations and fluctuations analyzed through MD simulation which judiciously held responsible to attain most favorable interaction with PPAR-α. Followed by the binding free energy (ΔG) calculations using MM-GBSA confirmed the key role of 6-CC toward PPAR-α. The compound 6-CC also achieved high drug-likeness and pharmacokinetic properties. Thus, these findings stipulate new drug leads for PPAR-α receptor which abets a way to develop new anti-cancer drugs.
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Affiliation(s)
- Sangeeta Ballav
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, 201314, India
| | - Rohit Singh Yadav
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - K V Swamy
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
- Bioinformatics Research Group, MIT School of Bioengineering Science & Research, MIT Art, Design and Technology University, Pune, Maharashtra, 412201, India
| | - Soumya Basu
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India.
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Zhuang X, Zhao M, Ji X, Yang S, Yin H, Zhao L. Chitobiose exhibited a lipid-lowering effect in ob/ob -/- mice via butyric acid enrolled liver-gut crosstalk. BIORESOUR BIOPROCESS 2023; 10:79. [PMID: 38647627 PMCID: PMC10991647 DOI: 10.1186/s40643-023-00696-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/14/2023] [Indexed: 04/25/2024] Open
Abstract
Chitobiose (COS2) efficiently lowers lipids in vivo and facilitates butyric acid enrichment during human fecal fermentation. However, whether COS2 can interact with butyric acid to generate a hypolipidemic effect remains unclear. This study examined the hypolipidemic mechanism of COS2 involving butyric acid, which could alleviate non-alcoholic fatty liver disease (NAFLD). The results revealed that COS2 administration modulated the β-oxidation pathway in the liver and restructured the short chain fatty acids in the fecal of ob/ob-/- mice. Moreover, the hypolipidemic effect of COS2 and its specific accumulated metabolite butyric acid was verified in sodium oleate-induced HepG2 cells. Butyric acid was more effective to reverse lipid accumulation and up-regulate β-oxidation pathway at lower concentrations. Furthermore, structural analysis suggested that butyric acid formed hydrogen bonds with key residues in hydrophilic ligand binding domains (LBDs) of PPARα and activated the transcriptional activity of the receptor. Therefore, the potential mechanism behind the lipid-lowering effect of COS2 in vivo involved restoring hepatic lipid disorders via butyric acid accumulation and liver-gut axis signaling.
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Affiliation(s)
- Xinye Zhuang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Mengyao Zhao
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai, 200237, China
| | - Xiaoguo Ji
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Sihan Yang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Hao Yin
- Organ Transplant Center, Shanghai Changzheng Hospital, Shanghai, 200003, China.
| | - Liming Zhao
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
- Organ Transplant Center, Shanghai Changzheng Hospital, Shanghai, 200003, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai, 200237, China.
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Sales PF, do Nascimento AL, Pinheiro FC, Alberto AKM, Teixeira dos Santos AVTDL, Carvalho HDO, de Souza GC, Carvalho JCT. Effect of the Association of Fixed Oils from Abelmoschus esculentus (L.) Moench, Euterpe oleracea Martius, Bixa orellana Linné and Chronic SM ® on Atherogenic Dyslipidemia in Wistar Rats. Molecules 2023; 28:6689. [PMID: 37764465 PMCID: PMC10534590 DOI: 10.3390/molecules28186689] [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: 07/19/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Dyslipidemia presents high levels of serum cholesterol and is characterized as a risk factor for cardiovascular diseases, especially for the development of atherosclerosis. E. oleracea oil (OFEO), A. esculentus oil (OFAE), B. orellana oil (OFBO), and Chronic SM® granules (CHR) are rich in bioactive compounds with the potential to treat changes in lipid metabolism. This study investigated the effects of treatments with oils from A. esculentus, E. oleracea, B. orellana, and Chronic SM® on Cocos nucifera L. saturated-fat-induced dyslipidemia. The chromatographic profile showed the majority presence of unsaturated fatty acids in the tested oils. The quantification of tocotrienols and geranylgeraniol in OFBO and CHR was obtained. Treatments with OFEO, OFAE, OFBO, and CHR were able to significantly reduce glycemia, as well as hypertriglyceridemia, total cholesterol, and LDL-cholesterol, besides increasing HDL-cholesterol. The treatments inhibited the formation of atheromatous plaques in the vascular endothelium of the treated rats. The obtained results suggest that the OFEO, OFAE, OFBO, and CHR exhibit antidyslipidemic effects and antiatherogenic activity.
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Affiliation(s)
- Priscila Faimann Sales
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
| | - Aline Lopes do Nascimento
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
| | - Fernanda Cavalcante Pinheiro
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
| | - Andressa Ketelem Meireles Alberto
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
| | - Abrahão Victor Tavares de Lima Teixeira dos Santos
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
| | - Helison de Oliveira Carvalho
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
| | - Gisele Custódio de Souza
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
| | - José Carlos Tavares Carvalho
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, Km 02, Amapá, Macapá 68902-280, Brazil; (P.F.S.); (A.L.d.N.); (F.C.P.); (A.K.M.A.); (A.V.T.d.L.T.d.S.); (H.d.O.C.); (G.C.d.S.)
- University Hospital of Federal University of Amapá, Rodovia Josmar Chaves Pinto, Macapá 68903-419, Brazil
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Krishnamoorthi S, Iyaswamy A, Sreenivasmurthy SG, Thakur A, Vasudevan K, Kumar G, Guan XJ, Lu K, Gaurav I, Su CF, Zhu Z, Liu J, Kan Y, Jayaraman S, Deng Z, Chua KK, Cheung KH, Yang Z, Song JX, Li M. PPARɑ Ligand Caudatin Improves Cognitive Functions and Mitigates Alzheimer's Disease Defects By Inducing Autophagy in Mice Models. J Neuroimmune Pharmacol 2023; 18:509-528. [PMID: 37682502 DOI: 10.1007/s11481-023-10083-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023]
Abstract
The autophagy-lysosomal pathway (ALP) is a major cellular machinery involved in the clearance of aggregated proteins in Alzheimer disease (AD). However, ALP is dramatically impaired during AD pathogenesis via accumulation of toxic amyloid beta (Aβ) and phosphorylated-Tau (phospho-Tau) proteins in the brain. Therefore, activation of ALP may prevent the increased production of Aβ and phospho-Tau in AD. Peroxisome proliferator-activated receptor alpha (PPARα), a transcription factor that can activate autophagy, and transcriptionally regulate transcription factor EB (TFEB) which is a key regulator of ALP. This suggests that targeting PPARα, to reduce ALP impairment, could be a viable strategy for AD therapy. In this study, we investigated the anti-AD activity of Caudatin, an active constituent of Cynanchum otophyllum (a traditional Chinese medicinal herb, Qing Yang Shen; QYS). We found that Caudatin can bind to PPARα as a ligand and augment the expression of ALP in microglial cells and in the brain of 3XTg-AD mice model. Moreover, Caudatin could activate PPARα and transcriptionally regulates TFEB-augmented lysosomal degradation of Aβ and phosphor-Tau aggregates in AD cell models. Oral administration of Caudatin decreased AD pathogenesis and ameliorated the cognitive dysfunction in 3XTg-AD mouse model. Conclusively, Caudatin can be a potential AD therapeutic agent via activation of PPARα-dependent ALP.
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Affiliation(s)
- Senthilkumar Krishnamoorthi
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Centre for Trans-disciplinary Research, Department of Pharmacology, Saveetha Dental College and Hospitals, Chennai, Tamil Nadu, India
| | - Ashok Iyaswamy
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, India
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | | | - Abhimanyu Thakur
- Pritzker School of Molecular Engineering, Ben May Department for Cancer Research, The University of Chicago, Illinois, USA
| | | | - Gaurav Kumar
- Department of Clinical Research, School of Biological and Biomedical Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Xin-Jie Guan
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Kejia Lu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Isha Gaurav
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
| | - Cheng-Fu Su
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Zhou Zhu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Jia Liu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Yuxuan Kan
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine, Department of Biochemistry, Saveetha Dental College and Hospitals, Chennai, Tamil Nadu, India
| | - Zhiqiang Deng
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Ka Kit Chua
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - King-Ho Cheung
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
| | - Zhijun Yang
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China
| | - Ju-Xian Song
- Medical College of Acupuncture-Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Min Li
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong , SAR, China.
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China.
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Wu J, Wang X, Zhang M, Mathews P, Kang Y. RXR Agonists Enhance Lenalidomide Anti-Myeloma Activity and T Cell Functions while Retaining Glucose-Lowering Effect. Cells 2023; 12:1993. [PMID: 37566072 PMCID: PMC10417536 DOI: 10.3390/cells12151993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Retinoid X receptor (RXR) heterodimerizes with the PPAR nuclear hormone receptor and regulates its downstream events. We investigated the effects of RXR agonists (LG100754, bexarotene, AGN194204, and LG101506) on lenalidomide's anti-myeloma activity, T cell functions, and the level of glucose and lipids in vivo. Genetic overexpression and CRISPR/Cas9 knockout experiments were conducted in multiple myeloma (MM) cell lines and Jurkat T cell lines to determine the roles of CRBN in RXR-agonist mediated effects. A xenograft mouse model of MM was established to determine the combination effect of LG100754 and lenalidomide. The combination of RXR agonists and lenalidomide demonstrated synergistic activity in increasing CRBN expression and killing myeloma cells. Mechanistically, the RXR agonists reduced the binding of PPARs to the CRBN promoter, thereby relieving the repressor effect of PPARs on CRBN transcription. RXR agonists downregulated the exhaustion markers and increased the activation markers of Jurkat T cells and primary human T cells. Co-administration of LG100754 and lenalidomide showed enhanced anti-tumor activity in vivo. LG100754 retained its glucose- and lipid-lowering effects. RXR agonists demonstrate potential utility in enhancing drug sensitivity and T-cell function in the treatment of myeloma.
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Affiliation(s)
| | | | | | | | - Yubin Kang
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (J.W.); (X.W.)
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Powers AS, Pham V, Burger WAC, Thompson G, Laloudakis Y, Barnes NW, Sexton PM, Paul SM, Christopoulos A, Thal DM, Felder CC, Valant C, Dror RO. Structural basis of efficacy-driven ligand selectivity at GPCRs. Nat Chem Biol 2023; 19:805-814. [PMID: 36782010 PMCID: PMC10299909 DOI: 10.1038/s41589-022-01247-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/21/2022] [Indexed: 02/15/2023]
Abstract
A drug's selectivity for target receptors is essential to its therapeutic utility, but achieving selectivity between similar receptors is challenging. The serendipitous discovery of ligands that stimulate target receptors more strongly than closely related receptors, despite binding with similar affinities, suggests a solution. The molecular mechanism of such 'efficacy-driven selectivity' has remained unclear, however, hindering design of such ligands. Here, using atomic-level simulations, we reveal the structural basis for the efficacy-driven selectivity of a long-studied clinical drug candidate, xanomeline, between closely related muscarinic acetylcholine receptors (mAChRs). Xanomeline's binding mode is similar across mAChRs in their inactive states but differs between mAChRs in their active states, with divergent effects on active-state stability. We validate this mechanism experimentally and use it to design ligands with altered efficacy-driven selectivity. Our results suggest strategies for the rational design of ligands that achieve efficacy-driven selectivity for many pharmaceutically important G-protein-coupled receptors.
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Affiliation(s)
- Alexander S Powers
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vi Pham
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Yianni Laloudakis
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Nicholas W Barnes
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | | | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Neuromedicines Discovery Center, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | | | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
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8
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He W, Yang H, Pu Q, Li Y. Novel control strategies for the endocrine-disrupting effect of PAEs to pregnant women in traffic system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158269. [PMID: 36029816 DOI: 10.1016/j.scitotenv.2022.158269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Traffic-related air pollution has become a global issue, and scientific regulation measures are urgently needed to reduce traffic pollution. Phthalates (PAEs) have been widely detected in the traffic environment; thus, they were chosen as target pollutants because of their endocrine-disrupting effects. The pathways of action and mechanisms of PAEs' endocrine-disrupting effects in pregnant women through inhalation were deduced. A novel whole-process 1C + 3D + 5R regulation system was developed to control the endocrine-disrupting effect of PAEs on pregnant women based on the cleaning production concept. (1) For source reduction, the 2D-QSAR model of endocrine-disrupting effects of PAEs in pregnant women was constructed to screen out the key influencing factors as hydrogen bond interaction and hydrophobic interaction. Based on this, a designed PAE substitute molecule with low volatility and endocrine-disrupting effects and no developmental toxicity was screened. The substitute molecule could reduce the volatilization amount of PAEs at the source by 41.76 %; (2) For process interception, selecting C-band UV light to eliminate PAEs molecules in the traffic environment can slow down 19.99 % of the endocrine-disrupting effect of PAEs molecules. The homology modeling method was used to design four kinds of green belt plant proteins with high PAEs absorption efficiency to absorb PAEs molecules in the traffic environment. Compared with the original green belt plant proteins, the absorption amount of PAEs increased by up to 96.08 %, and (3) For terminal prevention, dietary food schemes were designed to regulate PAEs' endocrine-disrupting effect on pregnant women. The optimal dietary food scheme was the simultaneous intake of glutamate, catechin and folic acid, which could reduce the adverse effect of PAEs on maternal and infants by 32.51 %. This study presents theoretical support for regulating PAE exposure to specific populations in the traffic environment and treating other pollutants in the future.
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Affiliation(s)
- Wei He
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Hao Yang
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Qikun Pu
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Yu Li
- MOE Key Laboratory of Resources Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
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9
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Mandal SK, Kumar BK, Sharma PK, Murugesan S, Deepa P. In silico and in vitro analysis of PPAR – α / γ dual agonists: Comparative evaluation of potential phytochemicals with anti-obesity drug orlistat. Comput Biol Med 2022; 147:105796. [DOI: 10.1016/j.compbiomed.2022.105796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/28/2022] [Accepted: 06/26/2022] [Indexed: 11/03/2022]
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10
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Oyama T, Takiguchi K, Miyachi H. Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor δ in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative. Acta Crystallogr F Struct Biol Commun 2022; 78:81-87. [PMID: 35102897 PMCID: PMC8805212 DOI: 10.1107/s2053230x22000449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/12/2022] [Indexed: 11/10/2022] Open
Abstract
Peroxisome proliferator-activated receptor δ (PPARδ) is a member of the nuclear receptor family and regulates glucose and lipid homeostasis in a ligand-dependent manner. Numerous phenylpropanoic acid derivatives targeting three PPAR subtypes (PPARα, PPARγ and PPARδ) have been developed towards the treatment of serious diseases such as lipid-metabolism disorders. In spite of the increasing attraction of PPARδ as a pharmaceutical target, only a limited number of protein-ligand complex structures are available. Here, four crystal structures of the ligand-binding domain of PPARδ in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative are described, including an updated, higher resolution version of a previous studied structure and three novel structures. These structures showed that the ligands were bound in the ligand-binding pocket of the receptor in a similar manner but with minor variations. The results could provide variable structural information for the further design and development of ligands targeting PPARδ.
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Affiliation(s)
- Takuji Oyama
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Japan
| | - Kazuki Takiguchi
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Japan
| | - Hiroyuki Miyachi
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, Japan
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11
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Kamata S, Ishii I. [PPARα-Ligand Binding Modes Revealed by X-ray Crystallography]. YAKUGAKU ZASSHI 2021; 141:1267-1274. [PMID: 34719550 DOI: 10.1248/yakushi.21-00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are nuclear receptor-type transcription factors that consist of three subtypes (α, γ, and β/δ) with distinct physiological functions and ligand recognition. PPARs regulate energy metabolism and therefore become therapeutic targets for various metabolic diseases. While PPARα agonists are used as anti-dyslipidemia drugs and PPARγ agonists as anti-type 2 diabetes drugs, PPAR dual/pan agonists (that acts on two or three subtypes) are expected to treat non-alcoholic steatohepatitis (NASH), pulmonary fibrosis, etc. Structural analyses of PPAR-ligand-binding domain (LBD)-ligand co-crystals using X-ray crystallography have been done mainly on PPARγ, in which ligand-free apocrystals were prepared; however, the information on PPARα-LBD and PPARδ-LBD is limited. Recently, we succeeded to obtain 34 novel co-crystal structures of PPARα-LBD and various PPARα ligands (including fibrates) using various co-crystallization techniques. This procedure is applicable to preparation of PPARδ-LBD co-crystals, and contributes to molecular design of new PPAR targeted drugs based on all three PPAR-LBD structures.
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Affiliation(s)
- Shotaro Kamata
- Laboratory of Health Chemistry, Showa Pharmaceutical University
| | - Isao Ishii
- Laboratory of Health Chemistry, Showa Pharmaceutical University
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12
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Oyama T, Kamata S, Ishii I, Miyachi H. Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR)α Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method. Biol Pharm Bull 2021; 44:1202-1209. [PMID: 34471048 DOI: 10.1248/bpb.b21-00220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisome proliferator-activated receptor (PPAR)α, a member of the nuclear receptor family, is a transcription factor that regulates the expression of genes related to lipid metabolism in a ligand-dependent manner, and has attracted attention as a target for hypolipidemic drugs. We have been developing phenylpropaonic acid derivatives as PPARα-targeted drug candidates for the treatment of metabolic diseases. Recently, we have developed the "ligand-exchange soaking method," which crystallizes the recombinant PPARα ligand-binding domain (LBD) as a complex with intrinsic fatty acids derived from an expression host Escherichia (E.) coli and thereafter replaces them with other higher-affinity ligands by soaking. Here we applied this method for preparation of cocrystals of PPARα LBD with its ligands that have not been obtained with the conventional cocrystallization method. We revealed the high-resolution structures of the cocrystals of PPARα LBD and the three synthetic phenylpropaonic acid derivatives: TIPP-703, APHM19, and YN4pai, the latter two of which are the first observations. The overall structures of cocrystals obtained from the two methods are identical and illustrate the close interaction between these ligands and the surrounding amino acid residues of PPARα LBD. This ligand-exchange soaking method could be applicable to high throughput preparations of co-crystals with another subtype PPARδ LBD for high resolution X-ray crystallography, because it also crystallizes in complex with intrinsic fatty acid(s) while not in the apo-form.
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Affiliation(s)
- Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi
| | - Shotaro Kamata
- Laboratory of Health Chemistry, Showa Pharmaceutical University
| | - Isao Ishii
- Laboratory of Health Chemistry, Showa Pharmaceutical University
| | - Hiroyuki Miyachi
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo
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13
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Miyachi H. Structural Biology-Based Exploration of Subtype-Selective Agonists for Peroxisome Proliferator-Activated Receptors. Int J Mol Sci 2021; 22:ijms22179223. [PMID: 34502131 PMCID: PMC8430769 DOI: 10.3390/ijms22179223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022] Open
Abstract
Progress in understanding peroxisome proliferator-activated receptor (PPAR) subtypes as nuclear receptors that have pleiotropic effects on biological responses has enabled the exploration of new subtype-selective PPAR ligands. Such ligands are useful chemical biology/pharmacological tools to investigate the functions of PPARs and are also candidate drugs for the treatment of PPAR-mediated diseases, such as metabolic syndrome, inflammation and cancer. This review summarizes our medicinal chemistry research of more than 20 years on the design, synthesis, and pharmacological evaluation of subtype-selective PPAR agonists, which has been based on two working hypotheses, the ligand superfamily concept and the helix 12 (H12) holding induction concept. X-ray crystallographic analyses of our agonists complexed with each PPAR subtype validate our working hypotheses.
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Affiliation(s)
- Hiroyuki Miyachi
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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14
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Tahri-Joutey M, Andreoletti P, Surapureddi S, Nasser B, Cherkaoui-Malki M, Latruffe N. Mechanisms Mediating the Regulation of Peroxisomal Fatty Acid Beta-Oxidation by PPARα. Int J Mol Sci 2021; 22:ijms22168969. [PMID: 34445672 PMCID: PMC8396561 DOI: 10.3390/ijms22168969] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 12/12/2022] Open
Abstract
In mammalian cells, two cellular organelles, mitochondria and peroxisomes, share the ability to degrade fatty acid chains. Although each organelle harbors its own fatty acid β-oxidation pathway, a distinct mitochondrial system feeds the oxidative phosphorylation pathway for ATP synthesis. At the same time, the peroxisomal β-oxidation pathway participates in cellular thermogenesis. A scientific milestone in 1965 helped discover the hepatomegaly effect in rat liver by clofibrate, subsequently identified as a peroxisome proliferator in rodents and an activator of the peroxisomal fatty acid β-oxidation pathway. These peroxisome proliferators were later identified as activating ligands of Peroxisome Proliferator-Activated Receptor α (PPARα), cloned in 1990. The ligand-activated heterodimer PPARα/RXRα recognizes a DNA sequence, called PPRE (Peroxisome Proliferator Response Element), corresponding to two half-consensus hexanucleotide motifs, AGGTCA, separated by one nucleotide. Accordingly, the assembled complex containing PPRE/PPARα/RXRα/ligands/Coregulators controls the expression of the genes involved in liver peroxisomal fatty acid β-oxidation. This review mobilizes a considerable number of findings that discuss miscellaneous axes, covering the detailed expression pattern of PPARα in species and tissues, the lessons from several PPARα KO mouse models and the modulation of PPARα function by dietary micronutrients.
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Affiliation(s)
- Mounia Tahri-Joutey
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
- Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Faculty of Sciences & Techniques, University Hassan I, BP 577, 26000 Settat, Morocco;
| | - Pierre Andreoletti
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
| | - Sailesh Surapureddi
- Office of Pollution Prevention and Toxics, United States Environmental Protection Agency, Washington, DC 20460, USA;
| | - Boubker Nasser
- Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Faculty of Sciences & Techniques, University Hassan I, BP 577, 26000 Settat, Morocco;
| | - Mustapha Cherkaoui-Malki
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
| | - Norbert Latruffe
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
- Correspondence:
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15
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Gogoi B, Gogoi D, Gogoi N, Mahanta S, Buragohain AK. Network pharmacology based high throughput screening for identification of multi targeted anti-diabetic compound from traditionally used plants. J Biomol Struct Dyn 2021; 40:8004-8017. [PMID: 33769188 DOI: 10.1080/07391102.2021.1905554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The incurable Type 2 diabetes mellitus (T2DM) has now been considered a pandemic with only supportive care in existence. Due to the adverse effects of available anti-diabetic drugs, there arises a great urgency to develop new drug molecules. One of the alternatives that can be considered for the treatment of T2DM are natural compounds from traditionally used herbal medicine. The present study undertakes, an integrated multidisciplinary concept of Network Pharmacology to evaluate the efficacy of potent anti-diabetic compound from traditionally used anti-diabetic plants of north east India and followed by DFT analysis. In the course of the study, 22 plant species were selected on the basis of their use in traditional medicine for the treatment of T2DM by various ethnic groups of the north eastern region of India. Initially, a library of 1053 compounds derived from these plants was generated. This was followed by network preparation between compounds and targets based on the docking result. The compounds having the best network property were considered for DFT analysis. We have identified that auraptene, a monoterpene coumarin for its activity in the management of Type 2 diabetes mellitus and deciphered its unexplored probable mechanisms. Molecular dynamics simulation of the ligand-protein complexes also reveals the stable binding of auraptene with the target proteins namely, Protein Kinase C θ, Glucocorticoid receptor, 11-β hydroxysteroid dehydrogenase 1 and Aldose Reductase, all of which form uniform interactions throughout the MD simulation trajectory. Therefore, this finding could provide new insights for the development of a new anti-diabetic drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhaskarjyoti Gogoi
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India.,Department of Biotechnology, Royal Global University, Guwahati, Assam, India
| | - Dhrubajyoti Gogoi
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India
| | - Neelutpal Gogoi
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati, Assam, India
| | - Alak K Buragohain
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India.,Department of Biotechnology, Royal Global University, Guwahati, Assam, India
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16
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Kamata S, Oyama T, Ishii I. Preparation of co-crystals of human PPAR α-LBD and ligand for high-resolution X-ray crystallography. STAR Protoc 2021; 2:100364. [PMID: 33718889 PMCID: PMC7933539 DOI: 10.1016/j.xpro.2021.100364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are nuclear receptor-type transcription factors with three subtypes (α, δ, and γ) that regulate cell differentiation and metabolism. Co-crystals of human PPARα-ligand-binding domain (LBD)-PPARα ligand for X-ray crystallography have been difficult to obtain. Recombinant human PPARα-LBD proteins contain intrinsic fatty acids (iFAs of Escherichia coli origin) and may be unstable without ligands during crystallization. To circumvent these limitations, we have successfully applied various crystallization techniques, including co-crystallization, cross-seeding, soaking, delipidation, and coactivator peptide supplementation. For complete details on the use and execution of this protocol, please refer to Kamata et al. (2020). Protocols for recombinant PPARα ligand-binding domain protein purification Techniques to prepare PPARα-ligand co-crystals for high-resolution X-ray crystallography Strategy to obtain PPARα co-crystals with low-affinity PPARα ligands
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Affiliation(s)
- Shotaro Kamata
- Department of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi 400-8510, Japan
| | - Isao Ishii
- Department of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
- Corresponding author
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17
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Hartmann M, Bibli SI, Tews D, Ni X, Kircher T, Kramer JS, Kilu W, Heering J, Hernandez-Olmos V, Weizel L, Scriba GKE, Krait S, Knapp S, Chaikuad A, Merk D, Fleming I, Fischer-Posovszky P, Proschak E. Combined Cardioprotective and Adipocyte Browning Effects Promoted by the Eutomer of Dual sEH/PPARγ Modulator. J Med Chem 2021; 64:2815-2828. [PMID: 33620196 DOI: 10.1021/acs.jmedchem.0c02063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The metabolic syndrome (MetS) is a constellation of cardiovascular and metabolic symptoms involving insulin resistance, steatohepatitis, obesity, hypertension, and heart disease, and patients suffering from MetS often require polypharmaceutical treatment. PPARγ agonists are highly effective oral antidiabetics with great potential in MetS, which promote adipocyte browning and insulin sensitization. However, the application of PPARγ agonists in clinics is restricted by potential cardiovascular adverse events. We have previously demonstrated that the racemic dual sEH/PPARγ modulator RB394 (3) simultaneously improves all risk factors of MetS in vivo. In this study, we identify and characterize the eutomer of 3. We provide structural rationale for molecular recognition of the eutomer. Furthermore, we could show that the dual sEH/PPARγ modulator is able to promote adipocyte browning and simultaneously exhibits cardioprotective activity which underlines its exciting potential in treatment of MetS.
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Affiliation(s)
- Markus Hartmann
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Sofia-Iris Bibli
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, D-60596 Frankfurt am Main, Germany
| | - Daniel Tews
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, Ulm University Medical Centre, D-89075 Ulm, Germany
| | - Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Theresa Kircher
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Whitney Kilu
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Jan Heering
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Victor Hernandez-Olmos
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Gerhard K E Scriba
- Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University Jena, Philosophenweg 14, D-07743 Jena, Germany
| | - Sulaiman Krait
- Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University Jena, Philosophenweg 14, D-07743 Jena, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, D-60438 Frankfurt, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, D-60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, D-60596 Frankfurt am Main, Germany
| | - Pamela Fischer-Posovszky
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, Ulm University Medical Centre, D-89075 Ulm, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
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18
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Kamata S, Oyama T, Saito K, Honda A, Yamamoto Y, Suda K, Ishikawa R, Itoh T, Watanabe Y, Shibata T, Uchida K, Suematsu M, Ishii I. PPARα Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. iScience 2020; 23:101727. [PMID: 33205029 PMCID: PMC7653058 DOI: 10.1016/j.isci.2020.101727] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/08/2020] [Accepted: 10/20/2020] [Indexed: 12/03/2022] Open
Abstract
Most triacylglycerol-lowering fibrates have been developed in the 1960s–1980s before their molecular target, peroxisome proliferator-activated receptor alpha (PPARα), was identified. Twenty-one ligand-bound PPARα structures have been deposited in the Protein Data Bank since 2001; however, binding modes of fibrates and physiological ligands remain unknown. Here we show thirty-four X-ray crystallographic structures of the PPARα ligand-binding domain, which are composed of a “Center” and four “Arm” regions, in complexes with five endogenous fatty acids, six fibrates in clinical use, and six synthetic PPARα agonists. High-resolution structural analyses, in combination with coactivator recruitment and thermostability assays, demonstrate that stearic and palmitic acids are presumably physiological ligands; coordination to Arm III is important for high PPARα potency/selectivity of pemafibrate and GW7647; and agonistic activities of four fibrates are enhanced by the partial agonist GW9662. These results renew our understanding of PPARα ligand recognition and contribute to the molecular design of next-generation PPAR-targeted drugs. X-ray crystallography reveals 34 high-resolution human PPARα-ligand structures Stearic acid and palmitic acid are presumably physiological PPARα ligands Coordination to Arm III domain is important for high PPARα potency/selectivity Agonistic activities of four fibrates are enhanced by the partial agonist GW9662
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Affiliation(s)
- Shotaro Kamata
- Laboratory of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi 400-8510, Japan
| | - Kenta Saito
- Laboratory of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Akihiro Honda
- Laboratory of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Yume Yamamoto
- Laboratory of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Keisuke Suda
- Laboratory of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Ryo Ishikawa
- Laboratory of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Yasuo Watanabe
- Laboratory of Pharmacology, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Takahiro Shibata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Koji Uchida
- Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Isao Ishii
- Laboratory of Health Chemistry, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
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19
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Kadayat TM, Shrestha A, Jeon YH, An H, Kim J, Cho SJ, Chin J. Targeting Peroxisome Proliferator-Activated Receptor Delta (PPARδ): A Medicinal Chemistry Perspective. J Med Chem 2020; 63:10109-10134. [DOI: 10.1021/acs.jmedchem.9b01882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tara Man Kadayat
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Aarajana Shrestha
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Yong Hyun Jeon
- Laboratory Animal Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu 41404, Republic of Korea
| | - Hongchan An
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Jina Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Sung Jin Cho
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu 41404, Republic of Korea
| | - Jungwook Chin
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
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20
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Salazar JR, Loza-Mejía MA, Soto-Cabrera D. Chemistry, Biological Activities and In Silico Bioprospection of Sterols and Triterpenes from Mexican Columnar Cactaceae. Molecules 2020; 25:molecules25071649. [PMID: 32260146 PMCID: PMC7180492 DOI: 10.3390/molecules25071649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
The Cactaceae family is an important source of triterpenes and sterols. The wide uses of those plants include food, gathering, medicinal, and live fences. Several studies have led to the isolation and characterization of many bioactive compounds. This review is focused on the chemistry and biological properties of sterols and triterpenes isolated mainly from some species with columnar and arborescent growth forms of Mexican Cactaceae. Regarding the biological properties of those compounds, apart from a few cases, their molecular mechanisms displayed are not still fully understand. To contribute to the above, computational chemistry tools have given a boost to traditional methods used in natural products research, allowing a more comprehensive exploration of chemistry and biological activities of isolated compounds and extracts. From this information an in silico bioprospection was carried out. The results suggest that sterols and triterpenoids present in Cactaceae have interesting substitution patterns that allow them to interact with some bio targets related to inflammation, metabolic diseases, and neurodegenerative processes. Thus, they should be considered as attractive leads for the development of drugs for the management of chronic degenerative diseases.
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Affiliation(s)
- Juan Rodrigo Salazar
- Correspondence: (J.R.S.); (M.A.L.-M.); Tel.: +52-55-5278-9500 (J.R.S. & M.A.L.-M.)
| | - Marco A. Loza-Mejía
- Correspondence: (J.R.S.); (M.A.L.-M.); Tel.: +52-55-5278-9500 (J.R.S. & M.A.L.-M.)
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21
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Keita H, dos Santos CBR, Ramos MM, Padilha EC, Serafim RB, Castro AN, Amado JRR, da Silva GM, Ferreira IM, Giuliatti S, Carvalho JCT. Assessment of the hypoglycemic effect of Bixin in alloxan-induced diabetic rats: in vivo and in silico studies. J Biomol Struct Dyn 2020; 39:1017-1028. [DOI: 10.1080/07391102.2020.1724567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hady Keita
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
- Division of Post-Grade, University of the Sierra, Ixtlán de Juárez, México
| | - Cleydson Breno Rodrigues dos Santos
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapa, Macapá, Brazil
| | - Matheus Mercês Ramos
- Research Group Biocatalysis and Apllied Organic Synthesis, Federal University of Amapa, Macapá, Brazil
| | - Elias Carvalho Padilha
- Department of Natural Active Principles and Toxicology, Faculty of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Rodolfo Bortolozo Serafim
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Andres Navarrete Castro
- Laboratory of Pharmacology of Natural Products, Faculty of Chemistry, Department of Pharmacy, Universidad Autonoma Nacional de Mexico, Ciudad de Mexico, Mexico
| | - Jesus Rafael Rodriguez Amado
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
| | - Gabriel Monteiro da Silva
- Bioinformatics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Irlon Maciel Ferreira
- Research Group Biocatalysis and Apllied Organic Synthesis, Federal University of Amapa, Macapá, Brazil
| | - Silvana Giuliatti
- Bioinformatics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - José Carlos Tavares Carvalho
- Laboratory of Drugs Discovery, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapa, Macapá, Brazil
- Research Group Biocatalysis and Apllied Organic Synthesis, Federal University of Amapa, Macapá, Brazil
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22
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Kawasaki M, Kambe A, Yamamoto Y, Arulmozhiraja S, Ito S, Nakagawa Y, Tokiwa H, Nakano S, Shimano H. Elucidation of Molecular Mechanism of a Selective PPARα Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations. Int J Mol Sci 2020; 21:E361. [PMID: 31935812 PMCID: PMC6981837 DOI: 10.3390/ijms21010361] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 01/05/2023] Open
Abstract
The selective PPARα modulator (SPPARMα) is expected to medicate dyslipidemia with minimizing adverse effects. Recently, pemafibrate was screened from the ligand library as an SPPARMα bearing strong potency. Several clinical pieces of evidence have proved the usefulness of pemafibrate as a medication; however, how pemafibrate works as a SPPARMα at the molecular level is not fully known. In this study, we investigate the molecular mechanism behind its novel SPPARMα character through a combination of approaches of X-ray crystallography, isothermal titration calorimetry (ITC), and fragment molecular orbital (FMO) analysis. ITC measurements have indicated that pemafibrate binds more strongly to PPARα than to PPARγ. The crystal structure of PPARα-ligand binding domain (LBD)/pemafibrate/steroid receptor coactivator-1 peptide (SRC1) determined at 3.2 Å resolution indicates that pemafibrate binds to the ligand binding pocket (LBP) of PPARα in a Y-shaped form. The structure also reveals that the conformation of the phenoxyalkyl group in pemafibrate is flexible in the absence of SRC1 coactivator peptide bound to PPARα; this gives a freedom for the phenoxyalkyl group to adopt structural changes induced by the binding of coactivators. FMO calculations have indicated that the accumulation of hydrophobic interactions provided by the residues at the LBP improve the interaction between pemafibrate and PPARα compared with the interaction between fenofibrate and PPARα.
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Affiliation(s)
- Mayu Kawasaki
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
| | - Akira Kambe
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
| | - Yuta Yamamoto
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; (Y.Y.); (S.A.); (H.T.)
| | - Sundaram Arulmozhiraja
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; (Y.Y.); (S.A.); (H.T.)
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
| | - Yoshimi Nakagawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan;
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan; (Y.Y.); (S.A.); (H.T.)
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
- Research Center for Smart Molecules, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.K.); (A.K.); (S.I.)
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
| | - Hitoshi Shimano
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo 100-1004, Japan
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan;
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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23
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Scotti L, Monteiro AFM, de Oliveira Viana J, Mendonça Junior FJB, Ishiki HM, Tchouboun EN, Santos R, Scotti MT. Multi-Target Drugs Against Metabolic Disorders. Endocr Metab Immune Disord Drug Targets 2020; 19:402-418. [PMID: 30556507 DOI: 10.2174/1871530319666181217123357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/18/2018] [Accepted: 06/27/2018] [Indexed: 01/13/2023]
Abstract
BACKGROUND Metabolic disorders are a major cause of illness and death worldwide. Metabolism is the process by which the body makes energy from proteins, carbohydrates, and fats; chemically breaking these down in the digestive system towards sugars and acids which constitute the human body's fuel for immediate use, or to store in body tissues, such as the liver, muscles, and body fat. OBJECTIVE The efficiency of treatments for multifactor diseases has not been proved. It is accepted that to manage multifactor diseases, simultaneous modulation of multiple targets is required leading to the development of new strategies for discovery and development of drugs against metabolic disorders. METHODS In silico studies are increasingly being applied by researchers due to reductions in time and costs for new prototype synthesis; obtaining substances that present better therapeutic profiles. DISCUSSION In the present work, in addition to discussing multi-target drug discovery and the contributions of in silico studies to rational bioactive planning against metabolic disorders such as diabetes and obesity, we review various in silico study contributions to the fight against human metabolic pathologies. CONCLUSION In this review, we have presented various studies involved in the treatment of metabolic disorders; attempting to obtain hybrid molecules with pharmacological activity against various targets and expanding biological activity by using different mechanisms of action to treat a single pathology.
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Affiliation(s)
- Luciana Scotti
- Teaching and Research Management - University Hospital, Federal University of Paraíba, João Pessoa, PB, Brazil.,Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, PB, Brazil
| | - Alex France Messias Monteiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, PB, Brazil
| | - Jéssika de Oliveira Viana
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, PB, Brazil
| | - Francisco Jaime Bezerra Mendonça Junior
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, PB, Brazil.,Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Hamilton M Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente, SP, Brazil
| | | | - Rodrigo Santos
- Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, PB, Brazil
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24
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Liu YY, Ding TT, Feng XY, Xu WR, Cheng XC. Virtual identification of novel peroxisome proliferator-activated receptor (PPAR) α/δ dual antagonist by 3D-QSAR, molecule docking, and molecule dynamics simulation. J Biomol Struct Dyn 2019; 38:4143-4161. [PMID: 31556349 DOI: 10.1080/07391102.2019.1673211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The therapeutic potential of PPARs antagonists extends beyond diabetes. PPARs antagonists represent a new drug class that holds promise as a broadly applicable therapeutic approach for cancer treatment. Thus, there is a strong need to develop a rational design strategy for creating PPARs antagonists. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) models of PPARα receptor (CoMFA-1, q 2 = 0.636, r 2 = 0.953; CoMSIA-1, q 2 = 0.779, r 2 = 0.999) and PPARδ receptor (CoMFA-2, q 2 = 0.624, r 2 = 0.906; CoMSIA-2, q 2 = 0.627, r 2 = 0.959) were successfully constructed using 35 triazolone ring derivatives. Contour map analysis revealed that the electrostatic and hydrophobic fields played vital roles in the bioactivity of dual antagonists. Molecular docking studies suggested that the hydrogen bonding, electrostatic and hydrophobic interactions all influenced the binding of receptor-ligand complex. Based on the information obtained above, we designed a series of compounds. The docking results were mutually validated with 3D-QSAR results. Three-dimensional-QSAR and absorption, distribution, metabolism, excretion and toxicity (ADMET) predictions indicated that 19 newly designed compounds possessed excellent biological activity and physicochemical properties. In summary, this research could provide theoretical guidance for the structural optimization of novel PPARα and δ dual antagonists. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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25
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Da'adoosh B, Marcus D, Rayan A, King F, Che J, Goldblum A. Discovering highly selective and diverse PPAR-delta agonists by ligand based machine learning and structural modeling. Sci Rep 2019; 9:1106. [PMID: 30705343 PMCID: PMC6355875 DOI: 10.1038/s41598-019-38508-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
PPAR-δ agonists are known to enhance fatty acid metabolism, preserving glucose and physical endurance and are suggested as candidates for treating metabolic diseases. None have reached the clinic yet. Our Machine Learning algorithm called "Iterative Stochastic Elimination" (ISE) was applied to construct a ligand-based multi-filter ranking model to distinguish between confirmed PPAR-δ agonists and random molecules. Virtual screening of 1.56 million molecules by this model picked ~2500 top ranking molecules. Subsequent docking to PPAR-δ structures was mainly evaluated by geometric analysis of the docking poses rather than by energy criteria, leading to a set of 306 molecules that were sent for testing in vitro. Out of those, 13 molecules were found as potential PPAR-δ agonist leads with EC50 between 4-19 nM and 14 others with EC50 below 10 µM. Most of the nanomolar agonists were found to be highly selective for PPAR-δ and are structurally different than agonists used for model building.
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Affiliation(s)
- Benny Da'adoosh
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - David Marcus
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Anwar Rayan
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
- Institute of Applied Research, Galilee Society, Shefa-Amr, 20200, Israel
- Drug Discovery Informatics Lab, Qasemi-Research Center, Al-Qasemi Academic College, Baka El-Garbiah, 30100, Israel
| | - Fred King
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr., San Diego, CA, 92121, USA
| | - Jianwei Che
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr., San Diego, CA, 92121, USA.
- Department of Chem. & Biochem., University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Amiram Goldblum
- Molecular Modeling Laboratory, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
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Bansal T, Chatterjee E, Singh J, Ray A, Kundu B, Thankamani V, Sengupta S, Sarkar S. Arjunolic acid, a peroxisome proliferator-activated receptor α agonist, regresses cardiac fibrosis by inhibiting non-canonical TGF-β signaling. J Biol Chem 2017; 292:16440-16462. [PMID: 28821620 DOI: 10.1074/jbc.m117.788299] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/11/2017] [Indexed: 12/16/2022] Open
Abstract
Cardiac hypertrophy and associated heart fibrosis remain a major cause of death worldwide. Phytochemicals have gained attention as alternative therapeutics for managing cardiovascular diseases. These include the extract from the plant Terminalia arjuna, which is a popular cardioprotectant and may prevent or slow progression of pathological hypertrophy to heart failure. Here, we investigated the mode of action of a principal bioactive T. arjuna compound, arjunolic acid (AA), in ameliorating hemodynamic load-induced cardiac fibrosis and identified its intracellular target. Our data revealed that AA significantly represses collagen expression and improves cardiac function during hypertrophy. We found that AA binds to and stabilizes the ligand-binding domain of peroxisome proliferator-activated receptor α (PPARα) and increases its expression during cardiac hypertrophy. PPARα knockdown during AA treatment in hypertrophy samples, including angiotensin II-treated adult cardiac fibroblasts and renal artery-ligated rat heart, suggests that AA-driven cardioprotection primarily arises from PPARα agonism. Moreover, AA-induced PPARα up-regulation leads to repression of TGF-β signaling, specifically by inhibiting TGF-β-activated kinase1 (TAK1) phosphorylation. We observed that PPARα directly interacts with TAK1, predominantly via PPARα N-terminal transactivation domain (AF-1) thereby masking the TAK1 kinase domain. The AA-induced PPARα-bound TAK1 level thereby shows inverse correlation with the phosphorylation level of TAK1 and subsequent reduction in p38 MAPK and NF-κBp65 activation, ultimately culminating in amelioration of excess collagen synthesis in cardiac hypertrophy. In conclusion, our findings unravel the mechanism of AA action in regressing hypertrophy-associated cardiac fibrosis by assigning a role of AA as a PPARα agonist that inactivates non-canonical TGF-β signaling.
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Affiliation(s)
- Trisha Bansal
- From the Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal
| | - Emeli Chatterjee
- From the Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal
| | - Jasdeep Singh
- the Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016
| | - Arjun Ray
- the Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, and
| | - Bishwajit Kundu
- the Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016
| | - V Thankamani
- the Department of Biotechnology, University of Kerala, Thiruvananthapuram 695014, Kerala, India
| | - Shantanu Sengupta
- the Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, and
| | - Sagartirtha Sarkar
- From the Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal,
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27
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Ohashi M, Miyachi H. Design and Synthesis of Peroxisome Proliferator-activated Receptor (PPAR) Gamma Antagonists Based on the Principle of Operation of Nuclear Receptor I. YAKUGAKU ZASSHI 2017; 137:957-967. [DOI: 10.1248/yakushi.17-00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masao Ohashi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Hiroyuki Miyachi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
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28
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Rationally designed PPARδ-specific agonists and their therapeutic potential for metabolic syndrome. Proc Natl Acad Sci U S A 2017; 114:3284-3285. [PMID: 28320957 DOI: 10.1073/pnas.1702084114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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29
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Structural basis for specific ligation of the peroxisome proliferator-activated receptor δ. Proc Natl Acad Sci U S A 2017; 114:E2563-E2570. [PMID: 28320959 PMCID: PMC5380080 DOI: 10.1073/pnas.1621513114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The peroxisome proliferator-activated receptor (PPAR) family comprises three subtypes: PPARα, PPARγ, and PPARδ. PPARδ transcriptionally modulates lipid metabolism and the control of energy homeostasis; therefore, PPARδ agonists are promising agents for treating a variety of metabolic disorders. In the present study, we develop a panel of rationally designed PPARδ agonists. The modular motif affords efficient syntheses using building blocks optimized for interactions with subtype-specific residues in the PPARδ ligand-binding domain (LBD). A combination of atomic-resolution protein X-ray crystallographic structures, ligand-dependent LBD stabilization assays, and cell-based transactivation measurements delineate structure-activity relationships (SARs) for PPARδ-selective targeting and structural modulation. We identify key ligand-induced conformational transitions of a conserved tryptophan side chain in the LBD that trigger reorganization of the H2'-H3 surface segment of PPARδ. The subtype-specific conservation of H2'-H3 sequences suggests that this architectural remodeling constitutes a previously unrecognized conformational switch accompanying ligand-dependent PPARδ transcriptional regulation.
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30
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Understanding PPAR-δ affinity and selectivity using hologram quantitative structure-activity modeling, molecular docking and GRID calculations. Future Med Chem 2016; 8:1913-1926. [PMID: 27689854 DOI: 10.4155/fmc-2016-0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AIM Type 2 diabetes mellitus and metabolic syndrome are two diseases related to disorders of lipid and carbohydrate metabolism and insulin resistance. Peroxisome proliferator-activated receptors (PPARs) are a class of nuclear receptors that control the metabolism of lipids/carbohydrates and are considered targets for both diseases. PPAR affinity and selectivity are critical points to design drug candidates with appropriated pharmacodynamic/kinetic profiles. MATERIALS & METHODS Hologram quantitative structure-activity relationships studies were conducted, as well molecular docking and molecular interaction field calculations, in order to explain affinity and selectivity of selected compounds. RESULTS The constructed hologram quantitative structure-activity relationship models are robust and predictive (values of q2 and r2test above 0.70). CONCLUSION The quantitative structure-activity relationship models and docking/GRID analyses indicated that carboxyl group of indole-sulfonamide derivatives could interact at helix-3 region, being considered important point of PPAR-δ selectivity.
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31
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Egawa D, Itoh T, Akiyama Y, Saito T, Yamamoto K. 17-OxoDHA Is a PPARα/γ Dual Covalent Modifier and Agonist. ACS Chem Biol 2016; 11:2447-55. [PMID: 27337155 DOI: 10.1021/acschembio.6b00338] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
17-Hydroxy docosahexaenoic acid (17-HDHA) is an oxidized form of docosahexaenoic acid (DHA) and known as a specialized proresolving mediator. We found that a further oxidized product, 17-oxodocosahexaenoic acid (17-oxoDHA), activates peroxisome proliferator-activated receptors γ (PPARγ) and PPARα in transcriptional assays and thus can be classified as an α/γ dual agonist. ESI mass spectroscopy and X-ray crystallographic analysis showed that 17-oxoDHA binds to PPARγ and PPARα covalently, making 17-oxoDHA the first of a novel class of PPAR agonists, the PPARα/γ dual covalent agonist. Furthermore, the covalent binding sites were identified as Cys285 for PPARγ and Cys275 for PPARα.
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Affiliation(s)
- Daichi Egawa
- Laboratory of Drug Design
and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Toshimasa Itoh
- Laboratory of Drug Design
and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yui Akiyama
- Laboratory of Drug Design
and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Tomoko Saito
- Laboratory of Drug Design
and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Keiko Yamamoto
- Laboratory of Drug Design
and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
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32
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Zhang J, Liu X, Xie XB, Cheng XC, Wang RL. Multitargeted bioactive ligands for PPARs discovered in the last decade. Chem Biol Drug Des 2016; 88:635-663. [PMID: 27317624 DOI: 10.1111/cbdd.12806] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/20/2016] [Indexed: 12/13/2022]
Abstract
Type 2 diabetes took insulin resistance as the main clinical manifestation. PPARs have been reported to be the therapeutic targets of metabolic disorders, such as obesity, hypertension, diabetes, and cardiovascular disease. Previously, PPARγ agonist rosiglitazone was restricted in clinic due to cardiomyocytes infarction, weight gain, and other serious side-effects, which were mainly due to the single and selective PPARγ agonism. In recent years, multitarget-directed PPAR agonists with synergistic reaction as well as fewer side-effect have been the hot topic in designing promising agents. In this review, we updated and generalized the development of PPARγ partial agonists, PPARγ antagonists, PPARα/γ dual agonists, PPARδ partial agonists, PPARδ antagonists, PPARα/δ dual agonists, PPARγ/δ dual agonists, and PPARα/γ/δ pan-agonists published in recent decade. Most of these molecules were modified from known structures or came from high-throughput screening. Among these molecules, some were expected to be promising drugs against metabolic disorders, while others seemed to provide new insight for designing novel PPAR agents.
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Affiliation(s)
- Jun Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xian-Bin Xie
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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33
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Lewis SN, Garcia Z, Hontecillas R, Bassaganya-Riera J, Bevan DR. Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands. J Comput Aided Mol Des 2015; 29:421-39. [PMID: 25616366 PMCID: PMC4395532 DOI: 10.1007/s10822-015-9831-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/09/2015] [Indexed: 01/28/2023]
Abstract
Peroxisome proliferator-activated receptor-gamma (PPARγ) is a nuclear hormone receptor involved in regulating various metabolic and immune processes. The PPAR family of receptors possesses a large binding cavity that imparts promiscuity of ligand binding not common to other nuclear receptors. This feature increases the challenge of using computational methods to identify PPAR ligands that will dock favorably into a structural model. Utilizing both ligand- and structure-based pharmacophore methods, we sought to improve agonist prediction by grouping ligands according to pharmacophore features, and pairing models derived from these features with receptor structures for docking. For 22 of the 33 receptor structures evaluated we observed an increase in true positive rate (TPR) when screening was restricted to compounds sharing molecular features found in rosiglitazone. A combination of structure models used for docking resulted in a higher TPR (40 %) when compared to docking with a single structure model (<20 %). Prediction was also improved when specific protein-ligand interactions between the docked ligands and structure models were given greater weight than the calculated free energy of binding. A large-scale screen of compounds using a marketed drug database verified the predictive ability of the selected structure models. This study highlights the steps necessary to improve screening for PPARγ ligands using multiple structure models, ligand-based pharmacophore data, evaluation of protein-ligand interactions, and comparison of docking datasets. The unique combination of methods presented here holds potential for more efficient screening of compounds with unknown affinity for PPARγ that could serve as candidates for therapeutic development.
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Affiliation(s)
- Stephanie N Lewis
- Genetics, Bioinformatics, and Computational Biology Program, Virginia Tech, Blacksburg, VA, USA,
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Structure-based virtual screening and discovery of New PPARδ/γ dual agonist and PPARδ and γ agonists. PLoS One 2015; 10:e0118790. [PMID: 25767888 PMCID: PMC4358979 DOI: 10.1371/journal.pone.0118790] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/16/2014] [Indexed: 12/13/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are involved in the control of carbohydrate and lipid metabolism and are considered important targets to treat diabetes mellitus and metabolic syndrome. The available PPAR ligands have several side effects leading to health risks justifying the search for new bioactive ligands to activate the PPAR subtypes, in special PPARδ, the less studied PPAR isoform. Here, we used a structure-based virtual screening protocol in order to find out new PPAR ligands. From a lead-like subset of purchasable compounds, we identified 5 compounds with potential PPAR affinity and, from preliminary in vitro assays, 4 of them showed promising biological activity. Therefore, from our in silico and in vitro protocols, new PPAR ligands are potential candidates to treat metabolic diseases.
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35
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Kahremany S, Livne A, Gruzman A, Senderowitz H, Sasson S. Activation of PPARδ: from computer modelling to biological effects. Br J Pharmacol 2015; 172:754-70. [PMID: 25255770 PMCID: PMC4301687 DOI: 10.1111/bph.12950] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/13/2014] [Accepted: 09/18/2014] [Indexed: 12/18/2022] Open
Abstract
PPARδ is a ligand-activated receptor that dimerizes with another nuclear receptor of the retinoic acid receptor family. The dimers interact with other co-activator proteins and form active complexes that bind to PPAR response elements and promote transcription of genes involved in lipid metabolism. It appears that various natural fatty acids and their metabolites serve as endogenous activators of PPARδ; however, there is no consensus in the literature on the nature of the prime activators of the receptor. In vitro and cell-based assays of PPARδ activation by fatty acids and their derivatives often produce conflicting results. The search for synthetic and selective PPARδ agonists, which may be pharmacologically useful, is intense. Current rational modelling used to obtain such compounds relies mostly on crystal structures of synthetic PPARδ ligands with the recombinant ligand binding domain (LBD) of the receptor. Here, we introduce an original computational prediction model for ligand binding to PPARδ LBD. The model was built based on EC50 data of 16 ligands with available crystal structures and validated by calculating binding probabilities of 82 different natural and synthetic compounds from the literature. These compounds were independently tested in cell-free and cell-based assays for their capacity to bind or activate PPARδ, leading to prediction accuracy of between 70% and 93% (depending on ligand type). This new computational tool could therefore be used in the search for natural and synthetic agonists of the receptor.
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Affiliation(s)
- Shirin Kahremany
- Division of Medicinal Chemistry, Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan UniversityRamat-Gan, Israel
| | - Ariela Livne
- Department of Pharmacology, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of JerusalemJerusalem, Israel
| | - Arie Gruzman
- Division of Medicinal Chemistry, Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan UniversityRamat-Gan, Israel
| | - Hanoch Senderowitz
- Division of Medicinal Chemistry, Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan UniversityRamat-Gan, Israel
| | - Shlomo Sasson
- Department of Pharmacology, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of JerusalemJerusalem, Israel
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Wang XJ, Zhang J, Wang SQ, Xu WR, Cheng XC, Wang RL. Identification of novel multitargeted PPARα/γ/δ pan agonists by core hopping of rosiglitazone. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:2255-62. [PMID: 25422585 PMCID: PMC4232041 DOI: 10.2147/dddt.s70383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The thiazolidinedione class peroxisome proliferator-activated receptor gamma (PPARγ) agonists are restricted in clinical use as antidiabetic agents because of side effects such as edema, weight gain, and heart failure. The single and selective agonism of PPARγ is the main cause of these side effects. Multitargeted PPARα/γ/δ pan agonist development is the hot topic in the antidiabetic drug research field. In order to identify PPARα/γ/δ pan agonists, a compound database was established by core hopping of rosiglitazone, which was then docked into a PPARα/γ/δ active site to screen out a number of candidate compounds with a higher docking score and better interaction with the active site. Further, absorption, distribution, metabolism, excretion, and toxicity prediction was done to give eight compounds. Molecular dynamics simulation of the representative Cpd#1 showed more favorable binding conformation for PPARs receptor than the original ligand. Cpd#1 could act as a PPARα/γ/δ pan agonist for novel antidiabetic drug research.
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Affiliation(s)
- Xue-Jiao Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Jun Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, People's Republic of China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
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37
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Tsakovska I, Al Sharif M, Alov P, Diukendjieva A, Fioravanzo E, Cronin MTD, Pajeva I. Molecular modelling study of the PPARγ receptor in relation to the mode of action/adverse outcome pathway framework for liver steatosis. Int J Mol Sci 2014; 15:7651-66. [PMID: 24857909 PMCID: PMC4057697 DOI: 10.3390/ijms15057651] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 12/14/2022] Open
Abstract
The comprehensive understanding of the precise mode of action and/or adverse outcome pathway (MoA/AOP) of chemicals has become a key step toward the development of a new generation of predictive toxicology tools. One of the challenges of this process is to test the feasibility of the molecular modelling approaches to explore key molecular initiating events (MIE) within the integrated strategy of MoA/AOP characterisation. The description of MoAs leading to toxicity and liver damage has been the focus of much interest. Growing evidence underlines liver PPARγ ligand-dependent activation as a key MIE in the elicitation of liver steatosis. Synthetic PPARγ full agonists are of special concern, since they may trigger a number of adverse effects not observed with partial agonists. In this study, molecular modelling was performed based on the PPARγ complexes with full agonists extracted from the Protein Data Bank. The receptor binding pocket was analysed, and the specific ligand-receptor interactions were identified for the most active ligands. A pharmacophore model was derived, and the most important pharmacophore features were outlined and characterised in relation to their specific role for PPARγ activation. The results are useful for the characterisation of the chemical space of PPARγ full agonists and could facilitate the development of preliminary filtering rules for the effective virtual ligand screening of compounds with PPARγ full agonistic activity.
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Affiliation(s)
- Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Merilin Al Sharif
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Petko Alov
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Elena Fioravanzo
- Soluzioni Informatiche srl, Via Ferrari 14, Vicenza 36100, Italy.
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
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38
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Bernardes A, Souza PCT, Muniz JRC, Ricci CG, Ayers SD, Parekh NM, Godoy AS, Trivella DBB, Reinach P, Webb P, Skaf MS, Polikarpov I. Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization. J Mol Biol 2013; 425:2878-93. [PMID: 23707408 DOI: 10.1016/j.jmb.2013.05.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 04/30/2013] [Accepted: 05/15/2013] [Indexed: 01/01/2023]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPARα in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPARα in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPARα was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPARα ligands.
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Affiliation(s)
- Amanda Bernardes
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos, SP 13560-970, Brazil
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39
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SAR and Computer-Aided Drug Design Approaches in the Discovery of Peroxisome Proliferator-Activated Receptor γ Activators: A Perspective. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/406049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Activators of PPARγ, Troglitazone (TGZ), Rosiglitazone (RGZ), and Pioglitazone (PGZ) were introduced for treatment of Type 2 diabetes, but TGZ and RGZ have been withdrawn from the market along with other promising leads due cardiovascular side effects and hepatotoxicity. However, the continuously improving understanding of the structure/function of PPARγ and its interactions with potential ligands maintain the importance of PPARγ as an antidiabetic target. Extensive structure activity relationship (SAR) studies have thus been performed on a variety of structural scaffolds by various research groups. Computer-aided drug discovery (CADD) approaches have also played a vital role in the search and optimization of potential lead compounds. This paper focuses on these approaches adopted for the discovery of PPARγ ligands for the treatment of Type 2 diabetes. Key concepts employed during the discovery phase, classification based on agonistic character, applications of various QSAR, pharmacophore mapping, virtual screening, molecular docking, and molecular dynamics studies are highlighted. Molecular level analysis of the dynamic nature of ligand-receptor interaction is presented for the future design of ligands with better potency and safety profiles. Recently identified mechanism of inhibition of phosphorylation of PPARγ at SER273 by ligands is reviewed as a new strategy to identify novel drug candidates.
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40
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Jia Y, Kim JY, Jun HJ, Kim SJ, Lee JH, Hoang MH, Kim HS, Chang HI, Hwang KY, Um SJ, Lee SJ. Cyanidin is an agonistic ligand for peroxisome proliferator-activated receptor-alpha reducing hepatic lipid. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:698-708. [DOI: 10.1016/j.bbalip.2012.11.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/15/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022]
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41
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Ohashi M, Oyama T, Putranto EW, Waku T, Nobusada H, Kataoka K, Matsuno K, Yashiro M, Morikawa K, Huh NH, Miyachi H. Design and synthesis of a series of α-benzyl phenylpropanoic acid-type peroxisome proliferator-activated receptor (PPAR) gamma partial agonists with improved aqueous solubility. Bioorg Med Chem 2013; 21:2319-2332. [DOI: 10.1016/j.bmc.2013.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 11/16/2022]
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42
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Nevin DK, Peters MB, Carta G, Fayne D, Lloyd DG. Integrated virtual screening for the identification of novel and selective peroxisome proliferator-activated receptor (PPAR) scaffolds. J Med Chem 2012; 55:4978-89. [PMID: 22582973 DOI: 10.1021/jm300068n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We describe a fully customizable and integrated target-specific "tiered" virtual screening approach tailored to identifying and characterizing novel peroxisome proliferator activated receptor γ (PPARγ) scaffolds. Built on structure- and ligand-based computational techniques, a consensus protocol was developed for use in the virtual screening of chemical databases, focused toward retrieval of novel bioactive chemical scaffolds for PPARγ. Consequent from application, three novel PPAR scaffolds displaying distinct chemotypes have been identified, namely, 5-(4-(benzyloxy)-3-chlorobenzylidene)dihydro-2-thioxopyrimidine-4,6(1H,5H)-dione (MDG 548), 3-((4-bromophenoxy)methyl)-N-(4-nitro-1H-pyrazol-1-yl)benzamide (MDG 559), and ethyl 2-[3-hydroxy-5-(5-methyl-2-furyl)-2-oxo-4-(2-thienylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]-4-methyl-1,3-thiazole-5-carboxylate (MDG 582). Fluorescence polarization(FP) and time resolved fluorescence resonance energy transfer (TR-FRET) show that these compounds display high affinity competitive binding to the PPARγ-LBD (EC(50) of 215 nM to 5.45 μM). Consequent characterization by a TR-FRET activation reporter assay demonstrated agonism of PPARγ by all three compounds (EC(50) of 467-594 nM). Additionally, differential PPAR isotype specificity was demonstrated through assay against PPARα and PPARδ subtypes. This work showcases the ability of target specific "tiered screen" protocols to successfully identify novel scaffolds of individual receptor subtypes with greater efficacy than isolated screening methods.
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Affiliation(s)
- Daniel K Nevin
- Molecular Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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43
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Ban S, Oyama T, Kasuga JI, Ohgane K, Nishio Y, Morikawa K, Hashimoto Y, Miyachi H. Bidirectional fluorescence properties of pyrene-based peroxisome proliferator-activated receptor (PPAR) α/δ dual agonist. Bioorg Med Chem 2012; 20:3460-4. [PMID: 22551628 DOI: 10.1016/j.bmc.2012.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 04/05/2012] [Accepted: 04/06/2012] [Indexed: 10/28/2022]
Abstract
Based on X-ray crystallographic analysis of a peroxisome proliferator-activated receptor (PPAR) α/δ dual agonist complexed with human PPARs ligand binding domain (LBD), we previously reported the design and synthesis of a pyrene-based fluorescent PPARα/δ co-agonist 2. Here, we found that the fluorescence intensity of 2 increased upon binding to hPPARα-LBD, in a manner dependent upon the concentration of the LBD. But, surprisingly, the fluorescence intensity of 2 decreased concentration-dependently upon binding to hPPRδ-LBD. Site-directed mutagenesis of the two hPPAR subtypes clearly indicated that Trp264 of hPPARδ-LBD, located between H2' helix and H3 helix (omega loop), is critical for the concentration-dependent decrease in fluorescence intensity, which is suggested to be due to fluorescence resonance energy transfer (FRET) from the pyrene moiety of bound 2 to the nearby side-chain indole moiety of Trp264 in the hPPARδ-LBD.
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Affiliation(s)
- Shintaro Ban
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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44
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Kuwabara N, Oyama T, Tomioka D, Ohashi M, Yanagisawa J, Shimizu T, Miyachi H. Peroxisome Proliferator-Activated Receptors (PPARs) Have Multiple Binding Points That Accommodate Ligands in Various Conformations: Phenylpropanoic Acid-Type PPAR Ligands Bind to PPAR in Different Conformations, Depending on the Subtype. J Med Chem 2012; 55:893-902. [DOI: 10.1021/jm2014293] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naoyuki Kuwabara
- Graduate School of Pharmaceutical
Sciences, Faculty of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takuji Oyama
- Institute for Protein Research, Osaka University, 6-2-3 Furuedai, Suita, Osaka 565-0874,
Japan
| | - Daisuke Tomioka
- Graduate School of
Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Masao Ohashi
- Graduate School of Medicine,
Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Junn Yanagisawa
- Graduate School of Life and
Environmental Sciences, University of Tsukuba, Tsukuba Science City, Ibaraki 305-8577, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical
Sciences, Faculty of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Miyachi
- Graduate School of Medicine,
Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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45
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Structure-based design, synthesis, and nonalcoholic steatohepatitis (NASH)-preventive effect of phenylpropanoic acid peroxisome proliferator-activated receptor (PPAR) α-selective agonists. Bioorg Med Chem 2011; 19:3183-91. [DOI: 10.1016/j.bmc.2011.03.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/26/2011] [Accepted: 03/30/2011] [Indexed: 11/19/2022]
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46
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Jeong HW, Lee JW, Kim WS, Choe SS, Kim KH, Park HS, Shin HJ, Lee GY, Shin D, Lee H, Lee JH, Choi EB, Lee HK, Chung H, Park SB, Park KS, Kim HS, Ro S, Kim JB. A newly identified CG301269 improves lipid and glucose metabolism without body weight gain through activation of peroxisome proliferator-activated receptor alpha and gamma. Diabetes 2011; 60:496-506. [PMID: 21270261 PMCID: PMC3028349 DOI: 10.2337/db09-1145] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Peroxisome proliferator-activated receptor (PPAR)-α/γ dual agonists have been developed to alleviate metabolic disorders. However, several PPARα/γ dual agonists are accompanied with unwanted side effects, including body weight gain, edema, and tissue failure. This study investigated the effects of a novel PPARα/γ dual agonist, CG301269, on metabolic disorders both in vitro and in vivo. RESEARCH DESIGN AND METHODS Function of CG301269 as a PPARα/γ dual agonist was assessed in vitro by luciferase reporter assay, mammalian one-hybrid assay, and analyses of PPAR target genes. In vitro profiles on fatty acid oxidation and inflammatory responses were acquired by fatty acid oxidation assay and quantitative (q)RT-PCR of proinflammatory genes. In vivo effect of CG301269 was examined in db/db mice. Total body weight and various tissue weights were measured, and hepatic lipid profiles were analyzed. Systemic glucose and insulin tolerance were measured, and the in vivo effect of CG301269 on metabolic genes and proinflammatory genes was examined by qRT-PCR. RESULTS CG301269 selectively stimulated the transcriptional activities of PPARα and PPARγ. CG301269 enhanced fatty acid oxidation in vitro and ameliorated insulin resistance and hyperlipidemia in vivo. In db/db mice, CG301269 reduced inflammatory responses and fatty liver, without body weight gain. CONCLUSIONS We demonstrate that CG301269 exhibits beneficial effects on glucose and lipid metabolism by simultaneous activation of both PPARα and PPARγ. Our data suggest that CG301269 would be a potential lead compound against obesity and related metabolic disorders.
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Affiliation(s)
- Hyun Woo Jeong
- School of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Korea
| | - Joo-Won Lee
- School of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Korea
| | - Woo Sik Kim
- School of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Korea
| | - Sung Sik Choe
- School of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Korea
| | - Kyung-Hee Kim
- Division of Cardiology, Seoul National University College of Medicine, Seoul, Korea
| | - Ho Seon Park
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Jung Shin
- School of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Korea
| | - Gha Young Lee
- School of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Korea
| | - Dongkyu Shin
- Crystal Genomics, Seoul National University, Seoul, Korea
| | - Hanjae Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Jun Hee Lee
- Crystal Genomics, Seoul National University, Seoul, Korea
| | - Eun Bok Choi
- Korea Research Institute of Chemical Technology, Daejeon, Korea
| | - Hyeon Kyu Lee
- Korea Research Institute of Chemical Technology, Daejeon, Korea
| | - Heekyoung Chung
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Korea
| | - Seung Bum Park
- Department of Chemistry, Seoul National University, Seoul, Korea
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, Korea
| | - Kyong Soo Park
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo-Soo Kim
- Division of Cardiology, Seoul National University College of Medicine, Seoul, Korea
| | - Seonggu Ro
- Crystal Genomics, Seoul National University, Seoul, Korea
| | - Jae Bum Kim
- School of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Korea
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, Korea
- Corresponding author: Jae Bum Kim,
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47
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Ohashi M, Oyama T, Nakagome I, Satoh M, Nishio Y, Nobusada H, Hirono S, Morikawa K, Hashimoto Y, Miyachi H. Design, Synthesis, and Structural Analysis of Phenylpropanoic Acid-Type PPARγ-Selective Agonists: Discovery of Reversed Stereochemistry−Activity Relationship. J Med Chem 2010; 54:331-41. [DOI: 10.1021/jm101233f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masao Ohashi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takuji Oyama
- Institute for Protein Research, Osaka University, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Izumi Nakagome
- School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Mayumi Satoh
- Tumor Therapy Project, The Tokyo Metropolitan Institute of Medical Science, Tokyo Metropolitan Organization for Medical Research, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Yoshino Nishio
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hiromi Nobusada
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Shuichi Hirono
- School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kosuke Morikawa
- Institute for Protein Research, Osaka University, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yuichi Hashimoto
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroyuki Miyachi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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48
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Kasuga JI, Ishikawa M, Yonehara M, Makishima M, Hashimoto Y, Miyachi H. Improvement of water-solubility of biarylcarboxylic acid peroxisome proliferator-activated receptor (PPAR) δ-selective partial agonists by disruption of molecular planarity/symmetry. Bioorg Med Chem 2010; 18:7164-73. [DOI: 10.1016/j.bmc.2010.08.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 08/19/2010] [Indexed: 11/25/2022]
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49
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Flexible ligand recognition of peroxisome proliferator-activated receptor-gamma (PPARgamma). Bioorg Med Chem Lett 2010; 20:3344-7. [PMID: 20444603 DOI: 10.1016/j.bmcl.2010.04.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/16/2010] [Accepted: 04/09/2010] [Indexed: 11/21/2022]
Abstract
The peroxisome proliferator-activated receptor-gamma (PPARgamma) is a direct pharmacological target for drugs that enhance insulin sensitivity and are used clinically for the treatment of type II diabetes. Because the specificity of ligand recognition is lower for PPARgamma than for other nuclear receptors, PPARgamma can bind a larger variety of ligand types. In order to elucidate why the ligand recognition of PPARgamma is so flexible, we performed correlated fragment molecular orbital calculations for complexes of PPARgamma and each of two distinctive ligands, rosiglitazone and farglitazar. We found quite different patterns of ligand binding for these two ligands. The ligand-binding system of rosiglitazone, a drug in common clinical use, is based mainly on local electrostatic interactions around the thiazolidine ring, whereas both electrostatic interactions and van der Waals dispersion interactions with hydrophobic residues are required for the binding of farglitazar to PPARgamma. We suggest that the development of novel ligands will require adequately hydrophobic pharmacophores.
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Kasuga JI, Ishida S, Yamasaki D, Makishima M, Doi T, Hashimoto Y, Miyachi H. Novel biphenylcarboxylic acid peroxisome proliferator-activated receptor (PPAR) delta selective antagonists. Bioorg Med Chem Lett 2009; 19:6595-9. [PMID: 19853439 DOI: 10.1016/j.bmcl.2009.10.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/04/2009] [Accepted: 10/06/2009] [Indexed: 11/17/2022]
Abstract
We designed and synthesized novel PPARdelta antagonists based on the crystal structure of the PPARdelta full agonist TIPP-204 bound to the PPARdelta ligand-binding domain, in combination with our nuclear receptor helix 12 folding modification hypothesis. Representative compound 3a exhibits PPARdelta-preferential antagonistic activity.
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Affiliation(s)
- Jun-ichi Kasuga
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
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