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Kim K, Chen P, Li C, Li B. Novel Inhibitor of Glutamate-Cysteine Ligase Catalytic Subunit against Tribolium castaneum: High-Throughout Virtual Screening, Molecular Docking and Dynamics Simulation, and Bioassay. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17813-17823. [PMID: 39080857 DOI: 10.1021/acs.jafc.4c02089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
The enzyme glutamate-cysteine ligase catalytic subunit (Gclc) is a rate-limiting enzyme in the biosynthesis of glutathione that is involved in antioxidant defense, detoxification of xenobiotics, and/or its metabolites and regulates the cell cycle and immune function. Therefore, Gclc presents an appealing target for the development of novel insecticides. In this study, we conducted high-throughput virtual screening from the ZINC20 database and identified three compounds with high binding affinity to the Tribolium castaneum Gclc (TcGclc). Ultimately, we selected ZINC000032992384 due to its superior stability and lowest binding energy, as determined through molecular dynamics simulations. Bioassay results revealed that the IC50 value of ZINC000032992384 was 19.70 μM lower than that of BSO (49.67 μM). Furthermore, the larval mortality in the ZINC000032992384 treated group was 63.8%, significantly higher than that of the controls (29.1% in the dichlorvos group and 6.4% in the acetone group). This study provides novel insights for the development of a Gclc-targeted inhibitor as a potent insecticide based on the interaction between receptors and ligands.
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Affiliation(s)
- KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
- Department of Life-Science, University of Science, Pyongyang 999093, Democratic People's Republic of Korea
| | - Peng Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Chengjun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Kim K, Zhang W, Chen P, Li C, Li B. Identification of potent inhibitors targeting Tribolium castaneum GSTe2 via structure-based screening and molecular dynamics simulation. J Biomol Struct Dyn 2024:1-12. [PMID: 38268222 DOI: 10.1080/07391102.2024.2306499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024]
Abstract
Red flour beetle, Tribolium castaneum, has a major negative impact during storage of agricultural products and reveals the negative impacts on human health. Insect-specific epsilon glutathione S-transferase (GSTs) which requires reduced glutathione (GSH) as an essential substrate not only develop insecticide resistance but also play important role in insect metamorphosis. Inhibition of the insect metamorphosis and the development of insecticide resistance could play an important role in pest control, so T. castaneum GSTe2 (TcGSTe2) in our previous study could be an important target protein for this purpose. This study aimed to find a potential TcGSTe2 inhibitors through in silico mothods, including molecular modeling, molecular docking, ADMET assay, followed by molecular dynamics (MD) simulation, principal component analysis and MM/PBSA analysis. The results showed that ZINC000169293362 and ZINC000095566957 were selected as potential TcGSTe2 inhibitors with high-binding affinity and without any toxicity from 3618 of GSH-like compounds obtained from ZINC database. MD simulation results revealed that TcGSTe2-ZINC000169293362 had more stability than that of reference GSH. Moreover, TcGSTe2-ZINC000169293362 and TcGSTe2-ZINC000095566957 showed lower binding free energy (-27.53 ± 0.16 kcal/mol and -18.83 ± 0.15 kcal/mol, respectively) compared with TcGSTe2-GSH (-8.90 ± 0.30 kcal/mol). This study could provide new insight into reduction of insecticide resistance and be used to design new inhibitors of insect GSTs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Department of Life Science, University of Science, Pyongyang, Democratic People's Republic of Korea
| | - Wenjing Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Peng Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chengjun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Coveñas R, Rodríguez FD, Robinson P, Muñoz M. The Repurposing of Non-Peptide Neurokinin-1 Receptor Antagonists as Antitumor Drugs: An Urgent Challenge for Aprepitant. Int J Mol Sci 2023; 24:15936. [PMID: 37958914 PMCID: PMC10650658 DOI: 10.3390/ijms242115936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
The substance P (SP)/neurokinin-1 receptor (NK-1R) system is involved in cancer progression. NK-1R, activated by SP, promotes tumor cell proliferation and migration, angiogenesis, the Warburg effect, and the prevention of apoptosis. Tumor cells overexpress NK-1R, which influences their viability. A typical specific anticancer strategy using NK-1R antagonists, irrespective of the tumor type, is possible because these antagonists block all the effects mentioned above mediated by SP on cancer cells. This review will update the information regarding using NK-1R antagonists, particularly Aprepitant, as an anticancer drug. Aprepitant shows a broad-spectrum anticancer effect against many tumor types. Aprepitant alone or in combination therapy with radiotherapy or chemotherapy could reduce the sequelae and increase the cure rate and quality of life of patients with cancer. Current data open the door to new cancer research aimed at antitumor therapeutic strategies using Aprepitant. To achieve this goal, reprofiling the antiemetic Aprepitant as an anticancer drug is urgently needed.
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Affiliation(s)
- Rafael Coveñas
- Laboratory of Neuroanatomy of the Peptidergic Systems, Institute of Neurosciences of Castilla y León (INCYL), University of Salamanca, 37007 Salamanca, Spain;
- Group GIR-BMD (Bases Moleculares del Desarrollo), University of Salamanca, 37007 Salamanca, Spain;
| | - Francisco D. Rodríguez
- Group GIR-BMD (Bases Moleculares del Desarrollo), University of Salamanca, 37007 Salamanca, Spain;
- Department of Biochemistry and Molecular Biology, Faculty of Chemical Sciences, University of Salamanca, 37007 Salamanca, Spain
| | - Prema Robinson
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
| | - Miguel Muñoz
- Pediatric Intensive Care Unit, Research Laboratory on Neuropeptides (IBIS), Virgen del Rocío University Hospital, 41013 Seville, Spain;
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Torrens-Fontanals M, Stepniewski TM, Aranda-García D, Morales-Pastor A, Medel-Lacruz B, Selent J. How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs. Int J Mol Sci 2020; 21:E5933. [PMID: 32824756 PMCID: PMC7460635 DOI: 10.3390/ijms21165933] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 01/08/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are implicated in nearly every physiological process in the human body and therefore represent an important drug targeting class. Advances in X-ray crystallography and cryo-electron microscopy (cryo-EM) have provided multiple static structures of GPCRs in complex with various signaling partners. However, GPCR functionality is largely determined by their flexibility and ability to transition between distinct structural conformations. Due to this dynamic nature, a static snapshot does not fully explain the complexity of GPCR signal transduction. Molecular dynamics (MD) simulations offer the opportunity to simulate the structural motions of biological processes at atomic resolution. Thus, this technique can incorporate the missing information on protein flexibility into experimentally solved structures. Here, we review the contribution of MD simulations to complement static structural data and to improve our understanding of GPCR physiology and pharmacology, as well as the challenges that still need to be overcome to reach the full potential of this technique.
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Affiliation(s)
- Mariona Torrens-Fontanals
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
- InterAx Biotech AG, PARK innovAARE, 5234 Villigen, Switzerland
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - David Aranda-García
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Adrián Morales-Pastor
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Brian Medel-Lacruz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
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Elmezayen AD, Yelekçi K. Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes. J Biomol Struct Dyn 2020; 39:6396-6414. [PMID: 32715940 DOI: 10.1080/07391102.2020.1798812] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have no crystal structures, such as HDAC5 and HDAC9. Lacking proper and suitable crystal structure is obstructing the designing of appropriate isoform selective inhibitors. Here in this study, we constructed human HDAC5 and HDAC9 protein models using human HDAC4 (PDB:2VQM_A) as a template by the means of homology modeling approach. Based on the Z-score of the built models, model M0014 of HDAC5 and model M0020 of HDAC9 were selected. The models were verified by MODELLER and validated using the Web-based PROCHECK server. All selected known inhibitors displayed reasonable binding modes and equivalent predicted Ki values in comparison to the experimental binding affinities (Ki/IC50). The known inhibitor Rac26 showed the best binding affinity for HDAC5, while TMP269 showed the best binding affinity for HDAC9. The best two compounds, CHEMBL2114980 and CHEMBL217223, had relatively similar inhibition constants against HDAC5 and HDAC9. The built models and their complexes were subjected to molecular dynamic simulations (MD) for 100 ns. Examining the MD simulation results of all studied structures, including the RMSD, RMSF, radius of gyration and potential energy suggested the stability and reliability of the built models. Accordingly, the results obtained in this study could be used for designing de novo inhibitors against HDAC5 and HDAC9. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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Shan C, Li H, Zhang Y, Li Y, Chen Y, He W. Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study. PeerJ 2019; 7:e7329. [PMID: 31404433 PMCID: PMC6686837 DOI: 10.7717/peerj.7329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/19/2019] [Indexed: 11/24/2022] Open
Abstract
Epididymal protease inhibitor (EPPIN) that is located on the sperm surface and specific to the male reproductive system is a non-hormonal contraceptive target, since the binding of EPPIN with the seminal plasma protein semenogelin-1 (SEMG1) causes a loss of sperm function. Here, we investigated the binding interactions between EPPIN and SEMG1 by homology modeling, docking and molecular dynamics simulation. Since no crystal structure was reported for EPPIN, its 3D structure was constructed by homology modeling and refined by dynamics simulation, illustrating the C-terminus domain of EPPIN could bind with its N-terminus domain through the residues 30–32 and 113–116. The binding interaction of SEMG110-8 peptide and EPPIN was investigated by Z-DOCK and dynamics simulation. After evaluating the models according to the calculated binding free energies, we demonstrated that C-terminus domain of EPPIN was important for the binding of SEMG1 via residues Tyr107, Gly112, Asn116, Gln118 and Asn122, while residue Arg32 in N-terminus domain also had contribution for their binding interaction. Additionally, the binding pocket of EPPIN was defined according to these key residues and verified by molecular docking with reported inhibitor EP055, suggesting that the pocket formed by Arg32, Asn114, Asn116, Phe117 and Asn122 could be important for the design of new ligands. This study might be helpful for the understanding of biological function of EPPIN and would encourage the discovery of non-hormonal contraceptive leads/drugs in the future.
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Affiliation(s)
- Changyu Shan
- Department of Pharmaceutical Chemistry, The Third Military Medical University, Chongqing, China
| | - Hongwei Li
- Department of Pharmaceutical Chemistry, The Third Military Medical University, Chongqing, China
| | - Yuping Zhang
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Yuyan Li
- Department of Obstetrics and Gynecology, Southwest Hospital, The Third Military Medical University, Chongqing, China
| | - Yingchun Chen
- Department of Pharmaceutical Chemistry, The Third Military Medical University, Chongqing, China
| | - Wei He
- Department of Obstetrics and Gynecology, Southwest Hospital, The Third Military Medical University, Chongqing, China
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