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Kim J, Jin H, Kim J, Cho SY, Moon S, Wang J, Mao J, No KT. Leveraging the Fragment Molecular Orbital and MM-GBSA Methods in Virtual Screening for the Discovery of Novel Non-Covalent Inhibitors Targeting the TEAD Lipid Binding Pocket. Int J Mol Sci 2024; 25:5358. [PMID: 38791396 PMCID: PMC11121470 DOI: 10.3390/ijms25105358] [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: 04/04/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The Hippo pathway controls organ size and homeostasis and is linked to numerous diseases, including cancer. The transcriptional enhanced associate domain (TEAD) family of transcription factors acts as a receptor for downstream effectors, namely yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ), which binds to various transcription factors and is essential for stimulated gene transcription. YAP/TAZ-TEAD facilitates the upregulation of multiple genes involved in evolutionary cell proliferation and survival. TEAD1-4 overexpression has been observed in different cancers in various tissues, making TEAD an attractive target for drug development. The central drug-accessible pocket of TEAD is crucial because it undergoes a post-translational modification called auto-palmitoylation. Crystal structures of the C-terminal TEAD complex with small molecules are available in the Protein Data Bank, aiding structure-based drug design. In this study, we utilized the fragment molecular orbital (FMO) method, molecular dynamics (MD) simulations, shape-based screening, and molecular mechanics-generalized Born surface area (MM-GBSA) calculations for virtual screening, and we identified a novel non-covalent inhibitor-BC-001-with IC50 = 3.7 μM in a reporter assay. Subsequently, we optimized several analogs of BC-001 and found that the optimized compound BC-011 exhibited an IC50 of 72.43 nM. These findings can be used to design effective TEAD modulators with anticancer therapeutic implications.
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Affiliation(s)
- Jongwan Kim
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Haiyan Jin
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (J.K.); (J.W.); (J.M.)
| | - Jinhyuk Kim
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (J.K.); (J.W.); (J.M.)
- Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea; (S.Y.C.); (S.M.)
| | - Seon Yeon Cho
- Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea; (S.Y.C.); (S.M.)
| | - Sungho Moon
- Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea; (S.Y.C.); (S.M.)
| | - Jianmin Wang
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (J.K.); (J.W.); (J.M.)
| | - Jiashun Mao
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (J.K.); (J.W.); (J.M.)
| | - Kyoung Tai No
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (J.K.); (J.W.); (J.M.)
- Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea; (S.Y.C.); (S.M.)
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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Wu Y, Bashir MA, Shao C, Wang H, Zhu J, Huang Q. Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages. Food Funct 2024; 15:4207-4222. [PMID: 38512055 DOI: 10.1039/d4fo00610k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Numerous natural compounds are recognized for their anti-inflammatory properties attributed to antioxidant effects and the modulation of key inflammatory factors. Among them, astaxanthin (AST), a potent carotenoid antioxidant, remains relatively underexplored regarding its anti-inflammatory mechanisms and specific molecular targets. In this study, human monocytic leukemia cell-derived macrophages (THP-1) were selected as experimental cells, and lipopolysaccharides (LPS) served as inflammatory stimuli. Upon LPS treatment, the oxidative stress was significantly increased, accompanied by remarkable cellular damage. Moreover, LPSs escalated the expression of inflammation-related molecules. Our results demonstrate that AST intervention could effectively alleviate LPS-induced oxidative stress, facilitate cellular repair, and significantly attenuate inflammation. Further exploration of the anti-inflammatory mechanism revealed AST could substantially inhibit NF-κB translocation and activation, and mitigate inflammatory factor production by hindering NF-κB through the antioxidant mechanism. We further confirmed that AST exhibited protective effects against cell damage and reduced the injury from inflammatory cytokines by activating p53 and inhibiting STAT3. In addition, utilizing network pharmacology and in silico calculations based on molecular docking, molecular dynamics simulation, we identified interleukin-6 (IL-6) as a prominent core target of AST anti-inflammation, which was further validated by the RNA interference experiment. This IL-6 binding capacity actually enabled AST to curb the positive feedback loop of inflammatory factors, averting the onset of possible inflammatory storms. Therefore, this study offers a new possibility for the application and development of astaxanthin as a popular dietary supplement of anti-inflammatory or immunomodulatory function.
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Affiliation(s)
- Yahui Wu
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
| | - Mona A Bashir
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
| | - Changsheng Shao
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Han Wang
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
| | - Jianxia Zhu
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China
| | - Qing Huang
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
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Yu F, Wu X, Chen W, Yan F, Li W. Computer-assisted discovery and evaluation of potential ribosomal protein S6 kinase beta 2 inhibitors. Comput Biol Med 2024; 172:108204. [PMID: 38484695 DOI: 10.1016/j.compbiomed.2024.108204] [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: 11/23/2023] [Revised: 02/11/2024] [Accepted: 02/19/2024] [Indexed: 03/26/2024]
Abstract
S6K2 is an important protein in mTOR signaling pathway and cancer. To identify potential S6K2 inhibitors for mTOR pathway treatment, a virtual screening of 1,575,957 active molecules was performed using PLANET, AutoDock GPU, and AutoDock Vina, with their classification abilities compared. The MM/PB(GB)SA method was used to identify four compounds with the strongest binding energies. These compounds were further investigated using molecular dynamics (MD) simulations to understand the properties of the S6K2/ligand complex. Due to a lack of available 3D structures of S6K2, OmegaFold served as a reliable 3D predictive model with higher evaluation scores in SAVES v6.0 than AlphaFold, AlphaFold2, and RoseTTAFold2. The 150 ns MD simulation revealed that the S6K2 structure in aqueous solvation experienced compression during conformational relaxation and encountered potential energy traps of about 19.6 kJ mol-1. The virtual screening results indicated that Lys75 and Lys99 in S6K2 are key binding sites in the binding cavity. Additionally, MD simulations revealed that the ligands remained attached to the activation cavity of S6K2. Among the compounds, compound 1 induced restrictive dissociation of S6K2 in the presence of a flexible region, compound 8 achieved strong stability through hydrogen bonding with Lys99, compound 9 caused S6K2 tightening, and the binding of compound 16 was heavily influenced by hydrophobic interactions. This study suggests that these four potential inhibitors with different mechanisms of action could provide potential therapeutic options.
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Affiliation(s)
- Fangyi Yu
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Xiaochuan Wu
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - WeiSong Chen
- Department of Respiratory Medicine, Jinhua Municipal Central Hospital, Jinhua, Zhejiang, 321000, China
| | - Fugui Yan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
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Evsen L, Morris PJ, Thomas CJ, Ceribelli M. Comparative Assessment and High-Throughput Drug-Combination Profiling of TEAD-Palmitoylation Inhibitors in Hippo Pathway Deficient Mesothelioma. Pharmaceuticals (Basel) 2023; 16:1635. [PMID: 38139762 PMCID: PMC10747288 DOI: 10.3390/ph16121635] [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: 09/29/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 12/24/2023] Open
Abstract
The hippo signaling pathway is a central tumor suppressor cascade frequently inactivated in selected human cancers, leading to the aberrant activation of TEAD transcription factors. Whereas several TEAD auto-palmitoylation inhibitors are currently in development, a comprehensive assessment of this novel drug-modality is missing. Here, we report a comparative analysis among six TEADi(s) using cell-based and biochemical assays in Hippo pathway deficient mesothelioma. Our analysis revealed varying potency and selectivity across TEADi, also highlighting their limited efficacy. To overcome this limitation, we performed an unbiased, quantitative high-throughput drug screening by combining the TEADi VT-103 with a library of approximately 3000 oncology-focused drugs. By exploiting this library's mechanistic redundancy, we identified several drug-classes robustly synergized with TEADi. These included glucocorticoid-receptor (GR) agonists, Mek1/2 inhibitors, mTOR inhibitors, and PI3K inhibitors, among others. Altogether, we report a coherent single-agent dataset informing on potency and selectivity of TEAD-palmitoylation inhibitors as single-agents. We also describe a rational pipeline enabling the systematic identification of TEAD druggable co-dependencies. This data should support the pre-clinical development of drug combination strategies for the treatment of Hippo-deficient mesothelioma, and more broadly, for other cancers dependent on the oncogenic activity of YAP/TEAD.
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Affiliation(s)
| | | | | | - Michele Ceribelli
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
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Song S, Zhang Q, Yang H, Guo J, Xu M, Yang N, Yi J, Wang Z, Chen C. A combined application of molecular docking technology and indirect ELISA for the serodiagnosis of bovine tuberculosis. J Vet Sci 2022; 23:e50. [PMID: 35618322 PMCID: PMC9149502 DOI: 10.4142/jvs.21270] [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: 10/19/2021] [Revised: 03/18/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND There is an urgent need to find reliable and rapid bovine tuberculosis (bTB) diagnostics in response to the rising prevalence of bTB worldwide. Toll-like receptor 2 (TLR2) recognizes components of bTB and initiates antigen-presenting cells to mediate humoral immunity. Evaluating the affinity of antigens with TLR2 can form the basis of a new method for the diagnosis of bTB based on humoral immunity. OBJECTIVES To develop a reliable and rapid strategy to improve diagnostic tools for bTB. METHODS In this study, we expressed and purified the sixteen bTB-specific recombinant proteins in Escherichia coli. The two antigenic proteins, MPT70 and MPT83, which were most valuable for serological diagnosis of bTB were screened. Molecular docking technology was used to analyze the affinity of MPT70, MPT83, dominant epitope peptide of MPT70 (M1), and dominant epitope peptide MPT83 (M2) with TLR2, combined with the detection results of enzyme-linked immunosorbent assay to evaluate the molecular docking effect. RESULTS The results showed that interaction surface Cα-atom root mean square deviation of proteins (M1, M2, MPT70, MPT83)-TLR2 protein are less than 2.5 A, showing a high affinity. It is verified by clinical serum samples that MPT70, MPT83, MPT70-MPT83 showed good diagnostic potential for the detection of anti-bTB IgG and M1, M2 can replace the whole protein as the detection antigen. CONCLUSIONS Molecular docking to evaluate the affinity of bTB protein and TLR2 combined with ELISA provides new insights for the diagnosis of bTB.
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Affiliation(s)
- Shengnan Song
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Collaborative Innovation Center for Prevention and Control of High Incidence Zoonotic Infectious Diseases in Western China, Shihezi 832003, China
| | - Qian Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832003, China
| | - Hang Yang
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Agriculture and Rural Affairs Bureau of Manas County, Hui Autonomous Prefecture of Changji 832200, China
| | - Jia Guo
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Collaborative Innovation Center for Prevention and Control of High Incidence Zoonotic Infectious Diseases in Western China, Shihezi 832003, China
| | - Mingguo Xu
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Collaborative Innovation Center for Prevention and Control of High Incidence Zoonotic Infectious Diseases in Western China, Shihezi 832003, China
| | - Ningning Yang
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Collaborative Innovation Center for Prevention and Control of High Incidence Zoonotic Infectious Diseases in Western China, Shihezi 832003, China
| | - Jihai Yi
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Collaborative Innovation Center for Prevention and Control of High Incidence Zoonotic Infectious Diseases in Western China, Shihezi 832003, China
| | - Zhen Wang
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Collaborative Innovation Center for Prevention and Control of High Incidence Zoonotic Infectious Diseases in Western China, Shihezi 832003, China.
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.,Collaborative Innovation Center for Prevention and Control of High Incidence Zoonotic Infectious Diseases in Western China, Shihezi 832003, China.
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