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Yu X, Cai L, Yao J, Li C, Wang X. Agonists and Inhibitors of the cGAS-STING Pathway. Molecules 2024; 29:3121. [PMID: 38999073 PMCID: PMC11243509 DOI: 10.3390/molecules29133121] [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: 05/31/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is pivotal in immunotherapy. Several agonists and inhibitors of the cGAS-STING pathway have been developed and evaluated for the treatment of various diseases. The agonists aim to activate STING, with cyclic dinucleotides (CDNs) being the most common, while the inhibitors aim to block the enzymatic activity or DNA binding ability of cGAS. Meanwhile, non-CDN compounds and cGAS agonists are also gaining attention. The omnipresence of the cGAS-STING pathway in vivo indicates that its overactivation could lead to undesired inflammatory responses and autoimmune diseases, which underscores the necessity of developing both agonists and inhibitors of the cGAS-STING pathway. This review describes the molecular traits and roles of the cGAS-STING pathway and summarizes the development of cGAS-STING agonists and inhibitors. The information is supposed to be conducive to the design of novel drugs for targeting the cGAS-STING pathway.
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Affiliation(s)
- Xiaoxuan Yu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Linxiang Cai
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jingyue Yao
- Department of Pharmacy, Fourth Military Medical University, Xi’an 710032, China;
| | - Cenming Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaoyong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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2
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Li R, Chen L, He X, Cao D, Zhang Z, Jiang H, Chen K, Cheng X. Loops Mediate Agonist-Induced Activation of the Stimulator of Interferon Genes Protein. J Chem Inf Model 2023; 63:7373-7381. [PMID: 37831484 DOI: 10.1021/acs.jcim.3c00984] [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: 10/14/2023]
Abstract
The stimulator of interferon genes (STING) is an important therapeutic target for cancer diseases. The activated STING recruits downstream tank-binding kinase 1 (TBK1) to trigger several important immune responses. However, the molecular mechanism of how agonist molecules mediate the STING-TBK1 interactions remains elusive. Here, we performed molecular dynamics simulations to capture the conformational changes of STING and TBK1 upon agonist binding. Our simulations revealed that multiple helices (α5-α7) and especially three loops (loop 6, loop 8, and C-terminal tail) of STING participated in the allosteric mediation of the STING-TBK1 interactions. Consistent results were also observed in the simulations of the constitutive activating mutant of STING (R284S). We further identified α5 as a key region in this agonist-induced activation mechanism of STING. Free-energy perturbation calculations of multiple STING agonists demonstrated that an alkynyl group targeting α5 is a determinant for agonist activities. These results not only offer deeper insights into the agonist-induced allosteric mediation of STING-TKB1 interactions but also provide a guidance for future drug development of this important therapeutic target.
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Affiliation(s)
- Rui Li
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Duanhua Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zehong Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Kaixian Chen
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou District, Beijing 101408, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, No.1 Xiangshan Branch Lane, Hangzhou 310024, China
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Chang J, Hou S, Yan X, Li W, Xiao J. Discovery of Novel STING Inhibitors Based on the Structure of the Mouse STING Agonist DMXAA. Molecules 2023; 28:molecules28072906. [PMID: 37049669 PMCID: PMC10095708 DOI: 10.3390/molecules28072906] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/18/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
The stimulator-of-interferon-gene (STING) protein is involved in innate immunity. The drug DMXAA (5,6-dimethylxanthenone-4-acetic acid) proved to be a potent murine-STING (mSTING) agonist but had little effect on human-STING (hSTING). In this paper, we draw upon the comparison of different crystal structures and protein-ligand interaction relationships analysis to venture the hypothesis that the drug design of DMXAA variants has the potential to convert STING agonists to inhibitors. Based on our previous discovery of two DMXAA analogs, 3 and 4 (both could bind to STING), we structurally optimized them and synthesized new derivatives, respectively. In binding assays, we found compounds 11 and 27 to represent STING binders that were superior to the original structures and discussed the structure-activity relationships. All target compounds were inactive in cellular assays for the screening of STING agonistic activity. Gratifyingly, we identified 11 and 27 as STING inhibitors with micromolar activity in both hSTING and mSTING pathways. In addition, 11 and 27 inhibited the induction of interferon and inflammatory cytokines activated by 2'3'-cGAMP without apparent cytotoxicity. These findings break the rigid thinking that DMXAA provides the structural basis specifically for STING agonists and open up more possibilities for developing novel STING agonists or inhibitors.
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Affiliation(s)
- Jiajia Chang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Shi Hou
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Xinlin Yan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Wei Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Junhai Xiao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
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4
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The stimulator of interferon genes (STING) agonists for treating acute myeloid leukemia (AML): current knowledge and future outlook. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 25:1545-1553. [PMID: 36587109 DOI: 10.1007/s12094-022-03065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023]
Abstract
Acute myeloid leukemia (AML) is an aggressive hematologic cancer in adults. Some patients exhibit restricted T cell infiltration and do not respond to routine treatments. This may be prevented by enhancing adaptive immunity by stimulating innate immune cells inside the tumor microenvironment (TME). To activate the adaptive immunological reaction against tumors, type I interferons (IFNs) can promote the presentation of tumor-specific cytotoxic T lymphocyte (CTL) cell recruitment. During the activation of innate immunity, cyclic di-nucleotides (CDNs) bind to and stimulate the stimulator of interferon genes (STING), a protein localized inside the endoplasmic reticulum (ER) membrane, resulting in the expression of type I IFNs. The efficacy of STING agonists as effective stimulators of the anti-tumor response in AML is being investigated in numerous clinical studies. Therefore, the purpose of this investigation was to thoroughly review existing knowledge in this field and provide perspective into the clinical potential of STING agonists in AML.
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Morere J, Hognon C, Miclot T, Jiang T, Dumont E, Barone G, Monari A, Bignon E. How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency. J Chem Inf Model 2022; 62:3096-3106. [PMID: 35675714 DOI: 10.1021/acs.jcim.2c00315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The stimulator of interferon genes (STING) protein is a cornerstone of the human immune response. Its activation by cGAMP in the presence of cytosolic DNA stimulates the production of type I interferons and inflammatory cytokines. In the human population, several STING variants exist and exhibit dramatic differences in their activity, impacting the efficiency of the host defense against infections. Understanding the molecular mechanisms of these variants opens perspectives for personalized medicine treatments against diseases such as viral infections, cancers, or autoinflammatory diseases. Through microsecond-scale molecular modeling simulations, contact analyses, and machine learning techniques, we reveal the dynamic behavior of four STING variants (wild type, G230A, R293Q, and G230A/R293Q) and rationalize the variability of efficiency observed experimentally. Our results show that the decrease in STING activity is linked to a stiffening of key structural elements of the binding cavity together with changes in the interaction patterns within the protein.
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Affiliation(s)
- Jeremy Morere
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
| | - Tom Miclot
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France.,Department of Biological, Chemical and Pharmaceutical Sciences, Universita degli Studi di Palermo, via delle Scienze, 90126 Palermo, Italy
| | - Tao Jiang
- Université de Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F-69342 Lyon, France
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F-69342 Lyon, France.,Institut Universitaire de France, 5 rue Descartes, F-75005 Paris, France
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences, Universita degli Studi di Palermo, via delle Scienze, 90126 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France.,Université Paris Cité and CNRS, ITODYS, F-75006, Paris, France
| | - Emmanuelle Bignon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
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Cherney EC, Zhang L, Lo J, Huynh T, Wei D, Ahuja V, Quesnelle C, Schieven GL, Futran A, Locke GA, Lin Z, Monereau L, Chaudhry C, Blum J, Li S, Fereshteh M, Li-Wang B, Gangwar S, Pan C, Chong C, Zhu X, Posy SL, Sack JS, Zhang P, Ruzanov M, Harner M, Akhtar F, Schroeder GM, Vite G, Fink B. Discovery of Non-Nucleotide Small-Molecule STING Agonists via Chemotype Hybridization. J Med Chem 2022; 65:3518-3538. [PMID: 35108011 DOI: 10.1021/acs.jmedchem.1c01986] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The identification of agonists of the stimulator of interferon genes (STING) pathway has been an area of intense research due to their potential to enhance innate immune response and tumor immunogenicity in the context of immuno-oncology therapy. Initial efforts to identify STING agonists focused on the modification of 2',3'-cGAMP (1) (an endogenous STING activator ligand) and other closely related cyclic dinucleotides (CDNs). While these efforts have successfully identified novel CDNs that have progressed into the clinic, their utility is currently limited to patients with solid tumors that STING agonists can be delivered to intratumorally. Herein, we report the discovery of a unique class of non-nucleotide small-molecule STING agonists that demonstrate antitumor activity when dosed intratumorally in a syngeneic mouse model.
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Affiliation(s)
- Emily C Cherney
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Liping Zhang
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Julian Lo
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Tram Huynh
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Donna Wei
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Vijay Ahuja
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Claude Quesnelle
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gary L Schieven
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Alan Futran
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gregory A Locke
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Zeyu Lin
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Laura Monereau
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Charu Chaudhry
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Jordan Blum
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Sha Li
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mark Fereshteh
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Bifang Li-Wang
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Sanjeev Gangwar
- Bristol Myers Squibb Research and Development, 700 Bay Rd, Redwood City, California 94063, United States
| | - Chin Pan
- Bristol Myers Squibb Research and Development, 700 Bay Rd, Redwood City, California 94063, United States
| | - Colin Chong
- Bristol Myers Squibb Research and Development, 700 Bay Rd, Redwood City, California 94063, United States
| | - Xiao Zhu
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Shana L Posy
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - John S Sack
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Ping Zhang
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Max Ruzanov
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mary Harner
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Fahad Akhtar
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gretchen M Schroeder
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gregory Vite
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Brian Fink
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
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7
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Liu K, Lan Y, Li X, Li M, Cui L, Luo H, Luo L. Development of small molecule inhibitors/agonists targeting STING for disease. Biomed Pharmacother 2020; 132:110945. [PMID: 33254439 DOI: 10.1016/j.biopha.2020.110945] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 01/07/2023] Open
Abstract
Cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) -stimulator of interferon genes (STING) signaling pathway is the primary immune response pathway in the cytoplasm. Pharmacological regulation of the STING pathway has good characteristics in both structure and function, which plays a significant role in the immunotherapy of autoimmune diseases, autoinflammatory diseases, and cancer. In this review, we summarized the activation of STING signaling pathway, the STING-related diseases, the development principle and the latest progress of inhibitors and agonists targeting STING. Our review demonstrates that STING signal pathway is a promising drug target, providing effective clues and correct guidance for the discovery of novel small molecule inhibitors/agonists that targeted STING for cancer, autoimmune, and inflammatory diseases.
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Affiliation(s)
- Kaifeng Liu
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China
| | - Yongqi Lan
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China
| | - Xiaoling Li
- Animal Experiment Center of Guangdong Medical University, Zhanjiang, 524023, China
| | - Mingyue Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Liao Cui
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Hui Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, Guangdong, 524023, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, Guangdong, 524023, China.
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8
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Daei Farshchi Adli A, Jahanban-Esfahlan R, Seidi K, Farajzadeh D, Behzadi R, Zarghami N. Co-Administration of Vadimezan and Recombinant Coagulase-NGR Inhibits Growth of Melanoma Tumor in Mice. Adv Pharm Bull 2020; 11:385-392. [PMID: 33880362 PMCID: PMC8046391 DOI: 10.34172/apb.2021.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/01/2020] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose: Tumor vascular targeting appeared as an appealing approach to fight cancer, though, the results from the clinical trials and drugs in the market were proved otherwise. The promise of anti-angiogenic therapy as the leading tumor vascular targeting strategy was negatively affected with the discovery that tumor vascularization can occur non-angiogenic mechanisms such as co-option. An additional strategy is induction of tumor vascular infarction and ischemia. Methods: Such that we used truncated coagulase (tCoa) coupled to tumor endothelial targeting moieties to produce tCoa-NGR fusion proteins. We showed that tCoa-NGR can bypass coagulation cascade to induce selective vascular thrombosis and infarction of mild and highly proliferative solid tumors in mice. Moreover, combination therapy can be used to improve the potential of cancer vascular targeting modalities. Herein, we report combination of tCoa-NGR with vascular disrupting agent (VDA), vadimezan. Results: Our results show that synergistic work of these two agents can significantly suppress growth of B16-F10 melanoma tumors in C57/BL6 mice. Conclusion: For the first time, we used the simultaneous benefits of two strategies for inducing thrombosis and destruction of tumor vasculature as spatial co-operation. The tCoa-NGR induce thrombosis which reduces blood flow in the peripheral tumor region. And combined with the action of DMXAA, which target inner tumor mass, growth and proliferation of melanoma tumors can be significantly suppressed.
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Affiliation(s)
- Amir Daei Farshchi Adli
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Seidi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Davoud Farajzadeh
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Ramezan Behzadi
- North Research Center, Pasture Institute of Iran, Tehran, Amol, Iran
| | - Nosratollah Zarghami
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Feng H, Gao W, Su L, Liu Y, Sun Z, Chen L. Evolution of diffusion and structure of six n-alkanes in carbon dioxide at infinite dilution over wide temperature and pressure ranges: a molecular dynamics study. J Mol Model 2019; 25:370. [PMID: 31792615 DOI: 10.1007/s00894-019-4229-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/10/2019] [Indexed: 12/17/2022]
Abstract
Over wide temperature and pressure ranges, the molecular dynamics simulation is performed to study the mass transfer of six n-alkanes from n-C5H12 to n-C10H22 in CO2 at infinite dilution by calculating the diffusion coefficients, which have not yet been measured by experiment. Meanwhile, the structural properties of these systems are explored. It is found that under different temperature and pressure conditions, the variation trends of the radial distribution functions of n-alkanes are quite different, while the variation trends of the average coordination number of n-alkanes can be divided into three types. The radius of gyration and the solvent accessible surface area are both affected by temperature and carbon chain length, but their variation trends are different, and it could explain the abnormal variation trends of the radial distribution functions and the average coordination number. Graphical abstract Over wide temperature and pressure ranges, the variation trends of the average coordination number of n-alkanes can be divided into three types.
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Affiliation(s)
- Huajie Feng
- School of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, People's Republic of China
| | - Wei Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Li Su
- Hainan Entry-Exit Inspection and Quarantine Technology Center, Haikou, 570311, People's Republic of China
| | - Yanchun Liu
- School of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, People's Republic of China
| | - Zhenfan Sun
- School of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, People's Republic of China
| | - Liuping Chen
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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10
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Cui X, Zhang R, Cen S, Zhou J. STING modulators: Predictive significance in drug discovery. Eur J Med Chem 2019; 182:111591. [PMID: 31419779 PMCID: PMC7172983 DOI: 10.1016/j.ejmech.2019.111591] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/10/2019] [Accepted: 08/05/2019] [Indexed: 12/19/2022]
Abstract
Cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) - stimulator of interferon genes (STING) signaling pathway plays the critical role in the immune response to DNA. Pharmacological modulation of the STING pathway has been well characterized both from structural and functional perspectives, which paves the way for the drug design of small modulators by medicinal chemists. Here, we outline recent progress in studies on the STING pathway, the structure and biological function of STING, the STING related disease, as well as the rationale and progress in the development of STING modulators. Our review demonstrates that STING is a promising drug target, and providing clues for the discovery of novel STING agonists and antagonists for the potential treatment of various disease including microbial infectious diseases, cancer, and autoimmune disease.
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Affiliation(s)
- Xiangling Cui
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China,Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Rongyu Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China,Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China; Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China; Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321004, PR China.
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11
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Akher FB, Farrokhzadeh A, Ramharack P, Shunmugam L, Van Heerden FR, Soliman MES. Discovery of novel natural flavonoids as potent antiviral candidates against hepatitis C virus NS5B polymerase. Med Hypotheses 2019; 132:109359. [PMID: 31466018 DOI: 10.1016/j.mehy.2019.109359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/28/2019] [Accepted: 08/11/2019] [Indexed: 12/13/2022]
Abstract
The non-structural 5B (NS5B) polymerase of hepatitis C virus (HCV) is an attractive target for antiviral intervention. Quercetagetin (Que) is a natural flavonoid, which has been exhibited to have anti-HCV property through inhibition of RNA binding to NS5B. The last few decades have witnessed a growing interest in the extraction of natural flavonoids with a plethora of different biological activities. Considering the high therapeutic potential of Que, the aim of this study is to explore wide structure entities with potent activity using Que as a prototype. A virtual screen protocol involving docking and molecular dynamics has been performed to examine the potency of forty-three natural flavonoids which recently extracted from plants for inhibition of NS5B. During two screening stages, two compounds 24 and 41 were identified to have more favorable binding affinity to NS5B as compared to Que. The comparative analysis showed that there is a significant difference in the binding free energy of Que and 41 (ΔΔGbind = -11.17 kcal/mol). It was revealed that van der Waals (vdW) interaction drives the binding process of both 24 and 41 and plays an important role in increasing their activities relative to Que. PHE162 serves as a crucial residue in both the NS5B-24 and NS5B-41 systems, contributing the most vdW energy by π-π interaction, suggesting that aromatic interactions are critical for the binding of 24 and 41 to NS5B. Moreover, hydrogen bond analysis indicates that the hydrogen bonds formed by LYS98, THR137, ASP164 and ARG168, can play important roles in the increased binding affinity of 41 to NS5B relative to Que. The findings of this study will provide useful structure-activity relationship (SAR) guidelines for the design of novel inhibitors with improved/enhanced therapeutic activities in the treatment of hepatitis C.
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Affiliation(s)
- Farideh Badichi Akher
- Department of Computer Science, University of Cape Town, Cape Town 7701, South Africa; Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa.
| | - Abdolkarim Farrokhzadeh
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg 3209, South Africa; Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Pritika Ramharack
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Letitia Shunmugam
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Fanie R Van Heerden
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg 3209, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa.
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Dynamic Structural Differences between Human and Mouse STING Lead to Differing Sensitivity to DMXAA. Biophys J 2019; 114:32-39. [PMID: 29320694 DOI: 10.1016/j.bpj.2017.10.027] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 09/29/2017] [Accepted: 10/16/2017] [Indexed: 10/18/2022] Open
Abstract
The stimulator-of-interferon-genes (STING) protein is involved in innate immunity. It has recently been shown that modulation of STING can lead to an aggressive antitumor response. DMXAA is an antitumor agent that had shown great promise in murine models but failed in human clinical trials. The molecular target of DMXAA was subsequently shown to be murine STING (mSTING); however, human STING (hSTING) is insensitive to DMXAA. Molecular dynamics simulations were employed to investigate the differences between hSTING and mSTING that could influence DMXAA binding. An initial set of simulations was performed to investigate a single lid region mutation G230I in hSTING (corresponding residue in mSTING is an Ile), which rendered the protein sensitive to DMXAA. The simulations found that an Ile side chain was enough to form a steric barrier that prevents exit of DMXAA, whereas in WT hSTING, the Gly residue that lacks a side chain formed a porous lid region that allowed DMXAA to exit. A second set of molecular dynamics simulations compared the tendency of STING to be in an open-inactive conformation or a closed-active conformation. The results show that hSTING prefers to be in an open-inactive conformation even with cGAMP, the native ligand, bound. On the other hand, mSTING prefers a closed-active conformation even without a ligand bound. These results highlight the challenges in translating a mouse active STING compound into a human active compound, while also providing avenues to pursue for designing a small-molecule drug targeting human STING.
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Akher FB, Farrokhzadeh A, Soliman MES. Covalent vs. Non-Covalent Inhibition: Tackling Drug Resistance in EGFR - A Thorough Dynamic Perspective. Chem Biodivers 2019; 16:e1800518. [PMID: 30548188 DOI: 10.1002/cbdv.201800518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022]
Abstract
A persistent challenge in the treatment of non-small cell lung cancer (NSCLC) with EGFR is the emergence of drug-resistant caused by somatic mutations. The EGFR L858R/T790 M double mutant (EGFRDM ) was found to be the most alarming variant. Despite the development of a wide range of inhibitors, none of them could inhibit EGFRDM effectively. Recently, 11h and 45a, have been found to be potent inhibitors against EGFRDM through two distinctive mechanisms, non-covalent and covalent binding, respectively. However, the structural and dynamic implications of the two modes of inhibitions remain unexplored. Herein, two molecular dynamics simulation protocols, coupled with free-energy calculations, were applied to gain insight into the atomistic nature of each binding mode. The comparative analysis confirmed that there is a significant difference in the binding free energy between 11h and 45a (ΔΔGbind =-21.17 kcal/mol). The main binding force that governs the binding of both inhibitors is vdW, with a higher contribution for 45a. Two residues ARG841 and THR854 were found to have curtailed role in the binding of 45a to EGFRDM by stabilizing its flexible alcohol chain. The 45a binding to EGFRDM induces structural rearrangement in the active site to allow easier accessibility of 45a to target residue CYS797. The findings of this work can substantially shed light on new strategies for developing novel classes of covalent and non-covalent inhibitors with increased specificity and potency.
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Affiliation(s)
- Farideh Badichi Akher
- Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Abdolkarim Farrokhzadeh
- Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
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Farrokhzadeh A, Akher FB, Soliman MES. Probing the Dynamic Mechanism of Uncommon Allosteric Inhibitors Optimized to Enhance Drug Selectivity of SHP2 with Therapeutic Potential for Cancer Treatment. Appl Biochem Biotechnol 2018; 188:260-281. [DOI: 10.1007/s12010-018-2914-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/05/2018] [Indexed: 01/24/2023]
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