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Santos Nascimento IJD, de Aquino TM, da Silva Júnior EF. Computer-Aided Drug Design of Anti-inflammatory Agents Targeting Microsomal Prostaglandin E2 Synthase-1 (mPGES-1). Curr Med Chem 2022; 29:5397-5419. [PMID: 35301943 DOI: 10.2174/0929867329666220317122948] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/22/2022]
Abstract
Inflammation is a natural process in response to external stimuli associated with organism protection. However, this reaction could be exaggerated, leading to severe damages related to physiopathological processes, such as rheumatoid arthritis, cancer, diabetes, allergies, infections, among others. Inflammation is mainly characterized by pain, increased temperature, flushing, and edema, which can be controlled using anti-inflammatory drugs. In this context, prostaglandin E2 (PGE2) inhibition has been targeted for designing new compounds with anti-inflammatory properties. It is a bioactive lipid overproduced during an inflammatory process, in which its increased production is carried out mainly by COX-1, COX-2, and microsomal prostaglandin E2 synthase-1 (mPGES-1). Recently, studies have demonstrated that mPGES-1 inhibition is a safe strategy to develop anti-inflammatory agents, which could protect against pain, acute inflammation, arthritis, autoimmune diseases, and different types of cancers. To decrease production costs and increase the probability of discovering active substances, computer-aided drug design (CADD) approaches have been increasingly used for designing new inhibitors. Thus, this review will cover all aspects involving high-throughput virtual screening, molecular docking, dynamics, fragment-based drug design, quantitative structure-activity relationship in seeking new promising mPGES-1 inhibitors.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Laboratory of Synthesis and Research in Medicinal Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, Brazil.
- Department of Pharmacy, Estácio of Alagoas College, Maceió, Brazil
| | - Thiago Mendonça de Aquino
- Laboratory of Synthesis and Research in Medicinal Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, Brazil.
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, Brazil
| | - Edeildo Ferreira da Silva Júnior
- Laboratory of Synthesis and Research in Medicinal Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, Brazil.
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, Brazil
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Zhang T, Qiao J, Song H, Xu F, Liu X, Xu C, Ma J, Liu H, Sun Z, Chu W. Cu(OAc)2-Mediated benzimidazole-directed C–H cyanation using 2-(4-methylpiperazin-1-yl)acetonitrile as the cyano source. NEW J CHEM 2019. [DOI: 10.1039/c9nj00776h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The C–H activation catalytic system was originally applied to the C(sp2)–H cyanation of aryls/heteroaryls to synthesize 2-(1H-benzo[d]imidazol-2-yl)aryl nitriles.
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Adhikari N, Amin SA, Ghosh B, Jha T. Shedding light on designing potential meprin β inhibitors through ligand-based robust validated computational approaches: A proposal to chemists! J Biomol Struct Dyn 2017; 36:3003-3022. [DOI: 10.1080/07391102.2017.1374210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Balaram Ghosh
- Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
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Amin SA, Adhikari N, Gayen S, Jha T. An integrated ligand-based modelling approach to explore the structure-property relationships of influenza endonuclease inhibitors. Struct Chem 2017. [DOI: 10.1007/s11224-017-0933-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jiang L, Li Y. Modification of PBDEs (BDE-15, BDE-47, BDE-85 and BDE-126) biological toxicity, bio-concentration, persistence and atmospheric long-range transport potential based on the pharmacophore modeling assistant with the full factor experimental design. JOURNAL OF HAZARDOUS MATERIALS 2016; 307:202-212. [PMID: 26785211 DOI: 10.1016/j.jhazmat.2015.12.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 12/15/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
In this study, the properties of AhR binding affinity, bio-concentration factor, half-life and vapor pressure were selected as the typical indicators of biological toxicity, bio-concentration, persistence and atmospheric long-range transport potential for polybrominated diphenyl ethers (PBDEs), respectively. A three-dimensional pharmacophore modeling assistant with a full factor experimental design for each property was used to reveal the significant pharmacophore features and the substituent effects to obtain reasonable modified schemes for the selected target PBDEs. Finally, the performances of the persistent organic pollutant (POP) properties, the synthesis feasibility and the fire resistance of the modified compounds were evaluated. The most influential pharmacophore feature for all POP properties was the hydrophobic group, especially the vinyl and propyl groups. Modified compounds with two additional hydrophobic groups exhibited a better regulatory performance. The average reduction in the proportions of the four POP properties for the modified compounds (except for 3-phenyl-BDE-15) was 70.60%, 52.44%, 47.04% and 70.88%. In addition, the energy and the C-Br bond dissociation enthalpy of the four typical PBDEs were higher than those of the modified compounds (except for 3-phenyl-BDE-15), indicating the synthesis feasibility and the lower energy barrier of the modified compounds to release Br free radicals to provide fire resistance.
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Affiliation(s)
- Long Jiang
- Resources and Environmental Research Academy, North China Electric Power University, Beijing 102206, China; MOE Key Laboratory of Regional Energy Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Yu Li
- Resources and Environmental Research Academy, North China Electric Power University, Beijing 102206, China; MOE Key Laboratory of Regional Energy Systems Optimization, North China Electric Power University, Beijing 102206, China.
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Xu Z, Chen Y, Qiu Y, Gu W, Li Y. Prediction of stability for polychlorinated biphenyls in transformer insulation oil through three-dimensional quantitative structure-activity relationship pharmacophore model and full factor experimental design. Chem Res Chin Univ 2016. [DOI: 10.1007/s40242-016-5461-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Paragi Vedanthi PP, Doble M. Inhibition of microsomal prostaglandin E synthase-1 by phenanthrene imidazoles: a QSAR study. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1290-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Chen KC, Chang SS, Huang HJ, Lin TL, Wu YJ, Chen CYC. Three-in-one agonists for PPAR-α, PPAR-γ, and PPAR-δ from traditional Chinese medicine. J Biomol Struct Dyn 2012; 30:662-83. [DOI: 10.1080/07391102.2012.689699] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Tou WI, Chen CYC. Traditional Chinese medicine as dual guardians against hypertension and cancer? J Biomol Struct Dyn 2012; 30:299-317. [PMID: 22694277 DOI: 10.1080/07391102.2012.680030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study utilizes the comprehensive traditional Chinese medicine database TCM Database@Taiwan ( http://tcm.cmu.edu.tw/ ) in conjunction with structure-based and ligand-based drug design to identify multi-function Src inhibitors. The three potential TCM candidates identified as having suitable docking conformations and bioactivity profiles were Angeliferulate, (3R)-2'-hydroxy-3',4'-dimethoxyisoflavan-7-O-beta-D-glucoside (HMID), and 3-[2',6-dihydroxy-5'-(2-propenyl)[1,1'-biphenyl]3-yl]-(E)-2-propenoic acid (3PA). Molecular dynamics simulation demonstrated that the TCM candidates have more stable interactions with the cleft and in complex with Src kinase compared to Saracatinib. Angeliferulate and HMID, both originated from Angelica sinensis, not only interact with Lys298 and amino acids from different loops in the cleft, but also with Asp407 located on the activation loop. These interactions are important to reduce the opening of the activation loop due to phosphorylation, hence stabilize the Src kinase cleft structure and inhibit activation. The TCM candidates also exhibited high affinity to other cancer-related target proteins (EGFR, HER2, and HSP90). Our observations suggest that the TCM candidates might have multi-targeting effects in hypertension and cancer.
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Affiliation(s)
- Weng Ieong Tou
- School of Medicine, China Medical University, Taichung, Taiwan
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Lee CL, Lin YT, Chang FR, Chen GY, Backlund A, Yang JC, Chen SL, Wu YC. Synthesis and biological evaluation of phenanthrenes as cytotoxic agents with pharmacophore modeling and ChemGPS-NP prediction as topo II inhibitors. PLoS One 2012; 7:e37897. [PMID: 22666407 PMCID: PMC3362575 DOI: 10.1371/journal.pone.0037897] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/28/2012] [Indexed: 11/23/2022] Open
Abstract
In a structure-activity relationship (SAR) study, 3-methoxy-1,4-phenanthrenequinones, calanquinone A (6a), denbinobin (6b), 5-OAc-calanquinone A (7a) and 5-OAc-denbinobin (7b), have significantly promising cytotoxicity against various human cancer cell lines (IC50 0.08–1.66 µg/mL). Moreover, we also established a superior pharmacophore model for cytotoxicity (r = 0.931) containing three hydrogen bond acceptors (HBA1, HBA2 and HBA3) and one hydrophobic feature (HYD) against MCF-7 breast cancer cell line. The pharmacophore model indicates that HBA3 is an essential feature for the oxygen atom of 5-OH in 6a–b and for the carbonyl group of 5-OCOCH3 in 7a–b, important for their cytotoxic properties. The SAR for moderately active 5a–b (5-OCH3), and highly active 6a–b and 7a–b, are also elaborated in a spatial aspect model. Further rational design and synthesis of new cytotoxic phenanthrene analogs can be implemented via this model. Additionally, employing a ChemGPS-NP based model for cytotoxicity mode of action (MOA) provides support for a preliminary classification of compounds 6a–b as topoisomerase II inhibitors.
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Affiliation(s)
- Chia-Lin Lee
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Natural Medicinal Products Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Ying-Ting Lin
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Fang-Rong Chang
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- * E-mail: (YCW); (FRC)
| | - Guan-Yu Chen
- Natural Medicinal Products Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Anders Backlund
- Division of Pharmacognosy, Department of Medicinal Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Juan-Chang Yang
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Li Chen
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yang-Chang Wu
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Natural Medicinal Products Research Center, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan
- * E-mail: (YCW); (FRC)
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Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database against H1N1 virus. J Biomol Struct Dyn 2011; 28:773-86. [PMID: 21294588 DOI: 10.1080/07391102.2011.10508605] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.
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Affiliation(s)
- Tung-Ti Chang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
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12
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Chen KC, Sun MF, Yang SC, Chang SS, Chen HY, Tsai FJ, Chen CYC. Investigation into potent inflammation inhibitors from traditional Chinese medicine. Chem Biol Drug Des 2011; 78:679-88. [PMID: 21801310 DOI: 10.1111/j.1747-0285.2011.01202.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Microsomal prostaglandin E synthase-1 (mPGES-1) is the key enzyme for prostaglandin E2 (PGE2) generation during inflammation and is a potential target for designing anti-inflammatory drugs. Potential inhibitors of m-PGES-1 were selected from traditional Chinese medicine (TCM Database@Taiwan) based on the pharmacophore map generated by the top HypoGen hypothesis and validated using structure- and ligand-based analysis. Key features for potential m-PGES-1 inhibitors include pi-interactions and H-bond donors. TCM compounds, shanciol B, shanciol A, castilliferol, and aurantiamide acetate, contoured to the quantitative structure-activity relationship pharmacophore and exhibited high docking scores and binding stability with m-PGES-1. Bioactivity models multiple linear regression (MLR) and support vector machine also supported activity predictions for the candidate compounds. Our results indicate that the investigated TCM compounds could be of use for development into mPGES-1 inhibitors.
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Affiliation(s)
- Kuan-Chung Chen
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
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Sun MF, Yang SC, Chang KW, Tsai TY, Chen HY, Tsai FJ, Lin JG, Chen CYC. Screening from TCM Database@Taiwan and QSAR model for identifying HER2 inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.569550] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Drug design for mPGES-1 from traditional Chinese medicine database: A screening, docking, QSAR, molecular dynamics, and pharmacophore mapping study. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Chang TT, Sun MF, Chang KW, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database for inhibiting DNA repair protein XRCC4. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.554550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Chang JS. Bioconversion and bioprocess technology for cleaner environment and better life. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2011.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Waltenberger B, Wiechmann K, Bauer J, Markt P, Noha SM, Wolber G, Rollinger JM, Werz O, Schuster D, Stuppner H. Pharmacophore modeling and virtual screening for novel acidic inhibitors of microsomal prostaglandin E₂ synthase-1 (mPGES-1). J Med Chem 2011; 54:3163-74. [PMID: 21466167 PMCID: PMC3088311 DOI: 10.1021/jm101309g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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Microsomal prostaglandin E2 synthase-1 (mPGES-1) catalyzes prostaglandin E2 formation and is considered as a potential anti-inflammatory pharmacological target. To identify novel chemical scaffolds active on this enzyme, two pharmacophore models for acidic mPGES-1 inhibitors were developed and theoretically validated using information on mPGES-1 inhibitors from literature. The models were used to screen chemical databases supplied from the National Cancer Institute (NCI) and the Specs. Out of 29 compounds selected for biological evaluation, nine chemically diverse compounds caused concentration-dependent inhibition of mPGES-1 activity in a cell-free assay with IC50 values between 0.4 and 7.9 μM, respectively. Further pharmacological characterization revealed that also 5-lipoxygenase (5-LO) was inhibited by most of these active compounds in cell-free and cell-based assays with IC50 values in the low micromolar range. Together, nine novel chemical scaffolds inhibiting mPGES-1 are presented that may possess anti-inflammatory properties based on the interference with eicosanoid biosynthesis.
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Affiliation(s)
- Birgit Waltenberger
- Institute of Pharmacy, Pharmacognosy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria
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Lin CH, Chang TT, Sun MF, Chen HY, Tsai FJ, Chang KL, Fisher M, Chen CYC. Potent inhibitor design against H1N1 swine influenza: structure-based and molecular dynamics analysis for M2 inhibitors from traditional Chinese medicine database. J Biomol Struct Dyn 2011; 28:471-82. [PMID: 21142218 DOI: 10.1080/07391102.2011.10508589] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The rapid spread of influenza virus subtype H1N1 poses a great threat to million lives worldwide. To search for new anti-influenza compounds, we performed molecular docking and molecular dynamics simulation to identify potential traditional Chinese medicine (TCM) constituents that could block influenza M2 channel activity. Quinic acid, genipin, syringic acid, cucurbitine, fagarine, and methyl isoferulate all have extremely well docking results as compared to control amantadine. Further de novo drug design suggests that derivatives of genipin and methyl isoferulate could have enhanced binding affinity towards M2 channel. Selected molecular dynamics simulations of M2-derivative complexes show stable hydrogen bond interactions between the derivatives and M2 residues, Ser10 and Ala9. To our best knowledge, this is the first study on the anti-viral activity of the above listed TCM compounds.
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Affiliation(s)
- Chia-Hui Lin
- Department of Chinese Medicine, China Medical University Hospital, Taiwan
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Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Novel hemagglutinin inhibitors for H1N1 influenza virus screening from TCM database. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.543973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tung-Ti Chang
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
- b Department of Chinese Pediatrics , China Medical University Hospital , Taichung, 40402, Taiwan, ROC
| | - Mao-Feng Sun
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
- c Department of Acupuncture , China Medical University Hospital , Taichung, 40402, Taiwan, ROC
| | - Hsin-Yi Chen
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan, ROC
| | - Fuu-Jen Tsai
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan, ROC
- e Department of Medical Genetics , China Medical University , Taichung, 40402, Taiwan, ROC
| | - Mark Fisher
- f Harvard-MIT Division of Health Sciences and Technology , 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jaung-Geng Lin
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
| | - Calvin Yu-Chian Chen
- a Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University , Taichung, 40402, Taiwan, ROC
- d Department of Bioinformatics , Asia University , Taichung, 41354, Taiwan, ROC
- f Harvard-MIT Division of Health Sciences and Technology , 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- g Computational and Systems Biology, Massachusetts Institute of Technology , Cambridge, MA, 02139, USA
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Li CL, Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Chen CYC, Lee CL, Fang WC, Wong YH. Structure-based and ligand-based drug design for microsomal prostaglandin E synthase-1 inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.538054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Bagga V, Silakari O, Ghorela VS, Bahia MS, Rambabu G, Sarma J. A three-dimensional pharmacophore modelling of ITK inhibitors and virtual screening for novel inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:171-190. [PMID: 21391146 DOI: 10.1080/1062936x.2010.510480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Interleukin-2-inducible T-cell kinase (ITK) is a key member of the Tec family of non-receptor tyrosine kinases, and has been found to be a novel target for a number of inflammatory and autoimmune diseases. A three-dimensional pharmacophore model has been generated for protein ITK from its known inhibitors. The best HypoGen model consisted of four pharmacophore features: one hydrogen bond acceptor, one hydrogen bond donor and two hydrophobic rings. This model showed a correlation coefficient of 0.947, a root mean square deviation of 0.914 and a configuration cost of 16.866. The model was validated using test set prediction and Fischer's test. A test set containing 204 compounds showed an r(2) of 0.745 between estimated activity and activity measured experimentally. Fisher's test gave a confidence level of 95%. The best pharmacophore model (Hypo1) was then employed for virtual screening (3D database searching), including Lipinsiki's filter, to obtain a pool of more drug-like molecules. The molecular pool thus retrieved was subjected to docking analysis with a study protein to remove any molecules showing false positive activity for ITK.
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Affiliation(s)
- V Bagga
- Department of Pharmaceutical Science and Drug Research, Punjabi University, Patiala, Punjab, India
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Lai CY, Chang TT, Sun MF, Chen HY, Tsai FJ, Lin JG, Chen CYC. Molecular dynamics analysis of potent inhibitors of M2 proton channel against H1N1 swine influenza virus. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.543972] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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De Simone R, Chini MG, Bruno I, Riccio R, Mueller D, Werz O, Bifulco G. Structure-Based Discovery of Inhibitors of Microsomal Prostaglandin E2 Synthase−1, 5-Lipoxygenase and 5-Lipoxygenase-Activating Protein: Promising Hits for the Development of New Anti-inflammatory Agents. J Med Chem 2011; 54:1565-75. [DOI: 10.1021/jm101238d] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rosa De Simone
- Department of Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
| | - Maria Giovanna Chini
- Department of Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
| | - Ines Bruno
- Department of Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
| | - Raffaele Riccio
- Department of Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
| | - Daniela Mueller
- Department of Pharmaceutical Analytics, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, D-72076 Tuebingen, Germany
| | - Oliver Werz
- Department of Pharmaceutical Analytics, Pharmaceutical Institute, University of Tuebingen, Auf der Morgenstelle 8, D-72076 Tuebingen, Germany
| | - Giuseppe Bifulco
- Department of Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
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Huang HJ, Lee KJ, Yu HW, Chen HY, Tsai FJ, Chen CYC. A novel strategy for designing the selective PPAR agonist by the "sum of activity" model. J Biomol Struct Dyn 2010; 28:187-200. [PMID: 20645652 DOI: 10.1080/07391102.2010.10507352] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Peroxisome proliferator-activated receptors alpha, delta and gamma are a collection of ligand-activated transcription factors crucial in lipid and glucose homeostasis. The involvement of these receptors in lipid metabolism makes them perfect therapeutic target for treating obesity and stroke. In this study, 'sum of activity' model was employed to design multi-target agonists. We used a new strategy to design agonists that fit both alpha and delta but not gamma, to avoid side effect. The CoMFA and CoMSIA models were used to explore the pharmacophore features by constructing three individual models: (a) alpha-model, (b) delta-model and (c) gamma-model, and two sum models: (d) alpha, delta- model, and (e) alpha, delta and gamma-model. The CoMFA model yielded a significant cross validation value, q(2), of 0.729 and non-cross validation value, r(2), of 0.933 in the alpha, delta-model. The CoMSIA studies yielded the best predictive models with q(2) of 0.622 in A+S and with r(2) of 0.911 in the alpha, delta-model. Finally, we proposed that distinct features shown in models (a), (b), (d) but not (c) and (e) should be accounted in designing weight-controlling drugs.
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Affiliation(s)
- Hung-Jin Huang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC
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Huang HJ, Lee KJ, Yu HW, Chen CY, Hsu CH, Chen HY, Tsai FJ, Chen CYC. Structure-based and ligand-based drug design for HER 2 receptor. J Biomol Struct Dyn 2010; 28:23-37. [PMID: 20476793 DOI: 10.1080/07391102.2010.10507341] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Human epidermal growth factor receptor 2, HER2, is a commonly over-expressed tyrosine kinase receptor found in many types of carcinoma. Despite that there are several HER2 inhibitors, namely Iressa, Tarceva and Tykerb, currently in clinical trials, all can cause several side effects. In this study, both structure-based and ligand-based drug design were employed to design novel HER2 inhibitors from traditional Chinese medicine (TCM). The HER2 structure model was built in homology modeling based on known receptors of the same family. Docking and de novo evolution experiments were performed to identify candidates and to build derivatives. A training set of 32 compounds with inhibitory activities to HER2 was used to formulate the pharmacophore hypotheses that were subsequently used to examine candidates obtained from the docking study. Hydrogen bond interactions, salt-bridge formations and pi-stacking were observed between the ligands and Phe731, Lys753, Asp863 and Asp808 of HER2 protein. Combining results from both docking and pharmacophore mapping analysis, CLC015-5, CLC604-11 and CLC604-18 were well accepted and consistent in both approaches and were considered as the most potential HER2 inhibitors.
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Affiliation(s)
- Hung-Jin Huang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC
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Huang HJ, Chen CY, Chen HY, Tsai FJ, Chen CYC. Computational screening and QSAR analysis for design of AMP-activated protein kinase agonist. J Taiwan Inst Chem Eng 2010. [DOI: 10.1016/j.jtice.2009.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Chen CYC. Virtual screening and drug design for PDE-5 receptor from traditional Chinese medicine database. J Biomol Struct Dyn 2010; 27:627-40. [PMID: 20085380 DOI: 10.1080/07391102.2010.10508577] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Erectile dysfunction (ED) is a sexual disorder mainly caused by decrease in cellular concentration of cyclic guanosine monophosphate (cGMP), which is degraded by phosphodiesterase type-5 (PDE-5). As a potent therapeutic target, inhibitors such as Viagra , Cialis, and Levitra have already been developed to target PDE-5 for treating ED; traditional Chinese medicine, Epimedium sagittatum, also has shown prominent results as well. To developed new PDE-5 inhibitors, we performed a virtual screening of traditional Chinese medicine (TCM) database and docking analyses to identify candidates. Known PDE-5 inhibitors were used to construct a three dimensional quantitative structure-activity relationship (3D QSAR) model by HypoGen program. From docking analyses, isochlorogenic acid b was identified as the most potential inhibitory compound. De novo evolution designed 47 derivatives. Of the 47 derivatives, seven were able to map into the pharmacophore model, and these seven compounds were suggested to be the most promising leads for inhibiting PDE-5. An analysis of the hydrogen bond interactions formed between the docked ligands and PDE-5 identified ASN662, SER663 and GLN817 as the most frequently interacting residues. A total of eight novel leading compounds were identified to have favorable interaction with PDE-5. These compounds all had hydrogen bond interactions with three key residues that could be further investigated for understanding of PDE-5 and ligands interaction.
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Affiliation(s)
- Calvin Yu-Chian Chen
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC.
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Chen CYC. Bioinformatics, chemoinformatics, and pharmainformatics analysis of HER2/HSP90 dual-targeted inhibitors. J Taiwan Inst Chem Eng 2010. [DOI: 10.1016/j.jtice.2009.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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