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Lin Y, Zhang Y, Wang D, Yang B, Shen YQ. Computer especially AI-assisted drug virtual screening and design in traditional Chinese medicine. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 107:154481. [PMID: 36215788 DOI: 10.1016/j.phymed.2022.154481] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/14/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Traditional Chinese medicine (TCM), as a significant part of the global pharmaceutical science, the abundant molecular compounds it contains is a valuable potential source of designing and screening new drugs. However, due to the un-estimated quantity of the natural molecular compounds and diversity of the related problems drug discovery such as precise screening of molecular compounds or the evaluation of efficacy, physicochemical properties and pharmacokinetics, it is arduous for researchers to design or screen applicable compounds through old methods. With the rapid development of computer technology recently, especially artificial intelligence (AI), its innovation in the field of virtual screening contributes to an increasing efficiency and accuracy in the process of discovering new drugs. PURPOSE This study systematically reviewed the application of computational approaches and artificial intelligence in drug virtual filtering and devising of TCM and presented the potential perspective of computer-aided TCM development. STUDY DESIGN We made a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Then screening the most typical articles for our research. METHODS The systematic review was performed by following the PRISMA guidelines. The databases PubMed, EMBASE, Web of Science, CNKI were used to search for publications that focused on computer-aided drug virtual screening and design in TCM. RESULT Totally, 42 corresponding articles were included in literature reviewing. Aforementioned studies were of great significance to the treatment and cost control of many challenging diseases such as COVID-19, diabetes, Alzheimer's Disease (AD), etc. Computational approaches and AI were widely used in virtual screening in the process of TCM advancing, which include structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS). Besides, computational technologies were also extensively applied in absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction of candidate drugs and new drug design in crucial course of drug discovery. CONCLUSIONS The applications of computer and AI play an important role in the drug virtual screening and design in the field of TCM, with huge application prospects.
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Affiliation(s)
- Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - You Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dongyang Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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2
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Deng C, Yan H, Wang J, Liu K, Liu BS, Shi YM. Current scenario on non-nucleoside reverse transcriptase inhibitors (2018-present). ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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3
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Anand AV, Balamuralikrishnan B, Kaviya M, Bharathi K, Parithathvi A, Arun M, Senthilkumar N, Velayuthaprabhu S, Saradhadevi M, Al-Dhabi NA, Arasu MV, Yatoo MI, Tiwari R, Dhama K. Medicinal Plants, Phytochemicals, and Herbs to Combat Viral Pathogens Including SARS-CoV-2. Molecules 2021; 26:1775. [PMID: 33809963 PMCID: PMC8004635 DOI: 10.3390/molecules26061775] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2), is the most important health issue, internationally. With no specific and effective antiviral therapy for COVID-19, new or repurposed antiviral are urgently needed. Phytochemicals pose a ray of hope for human health during this pandemic, and a great deal of research is concentrated on it. Phytochemicals have been used as antiviral agents against several viruses since they could inhibit several viruses via different mechanisms of direct inhibition either at the viral entry point or the replication stages and via immunomodulation potentials. Recent evidence also suggests that some plants and its components have shown promising antiviral properties against SARS-CoV-2. This review summarizes certain phytochemical agents along with their mode of actions and potential antiviral activities against important viral pathogens. A special focus has been given on medicinal plants and their extracts as well as herbs which have shown promising results to combat SARS-CoV-2 infection and can be useful in treating patients with COVID-19 as alternatives for treatment under phytotherapy approaches during this devastating pandemic situation.
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Affiliation(s)
- Arumugam Vijaya Anand
- Medical Genetics and Epigenetics Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India; (M.K.); (K.B.); (A.P.)
| | | | - Mohandass Kaviya
- Medical Genetics and Epigenetics Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India; (M.K.); (K.B.); (A.P.)
| | - Kathirvel Bharathi
- Medical Genetics and Epigenetics Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India; (M.K.); (K.B.); (A.P.)
| | - Aluru Parithathvi
- Medical Genetics and Epigenetics Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, India; (M.K.); (K.B.); (A.P.)
| | - Meyyazhagan Arun
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, India;
| | - Nachiappan Senthilkumar
- Institute of Forest Genetics and Tree Breeding (IFGTB), Forest Campus, Cowley Brown Road, RS Puram, Coimbatore 641002, India;
| | | | | | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (N.A.A.-D.); (M.V.A.)
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (N.A.A.-D.); (M.V.A.)
- Xavier Research Foundation, St. Xavier’s College, Palayamkottai, Thirunelveli 627002, India
| | - Mohammad Iqbal Yatoo
- Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar 190006, India;
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura 281001, India;
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India
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4
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Choengpanya K, Ratanabunyong S, Seetaha S, Tabtimmai L, Choowongkomon K. Anti-HIV-1 reverse transcriptase property of some edible mushrooms in Asia. Saudi J Biol Sci 2021; 28:2807-2815. [PMID: 34012322 PMCID: PMC8116966 DOI: 10.1016/j.sjbs.2021.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022] Open
Abstract
Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS), which is a serious health threat worldwide. One of its core enzymes, reverse transcriptase (RT), is a target for HIV inhibition. A number of bioactive compounds have been successfully used for HIV treatment. However, HIV rapidly mutates, and long-term treatment can cause drug-resistant strains. Therefore, new inhibitors are required to overcome this problem. In this study, the aqueous, ethanolic and hexane crude extracts of 19 edible and medicinal mushrooms, which are widely grown and available commercially in Thailand, were screened against HIV-1 RT. The results showed that the water extracts of A. blazei and I. obliquus, the ethanol extracts of I. obliquus and P. igniarius and the hexane extract of I. obliquus exhibited strong anti-HIV-1 RT activity with IC50 values of 1.92 ± 0.15, 4.39 ± 0.79, 6.17 ± 0.76 and 7.75 ± 246 µg/ml, respectively. These mushrooms have the potential for HIV treatment, and further study on identification of the bioactive compounds against HIV-1 RT should be performed.
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Affiliation(s)
| | - Siriluk Ratanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.,Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Supaphorn Seetaha
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.,Department of Companion Animals Clinical Sciences, Faculty of Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand.,Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
| | - Lueacha Tabtimmai
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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5
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Ali SI, Sheikh WM, Rather MA, Venkatesalu V, Muzamil Bashir S, Nabi SU. Medicinal plants: Treasure for antiviral drug discovery. Phytother Res 2021; 35:3447-3483. [PMID: 33590931 PMCID: PMC8013762 DOI: 10.1002/ptr.7039] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022]
Abstract
The pandemic of viral diseases like novel coronavirus (2019-nCoV) prompted the scientific world to examine antiviral bioactive compounds rather than nucleic acid analogous, protease inhibitors, or other toxic synthetic molecules. The emerging viral infections significantly associated with 2019-nCoV have challenged humanity's survival. Further, there is a constant emergence of new resistant viral strains that demand novel antiviral agents with fewer side effects and cell toxicity. Despite significant progress made in immunization and regenerative medicine, numerous viruses still lack prophylactic vaccines and specific antiviral treatments that are so often influenced by the generation of viral escape mutants. Of importance, medicinal herbs offer a wide variety of therapeutic antiviral chemotypes that can inhibit viral replication by preventing viral adsorption, adhering to cell receptors, inhibiting virus penetration in the host cell, and competing for pathways of activation of intracellular signals. The present review will comprehensively summarize the promising antiviral activities of medicinal plants and their bioactive molecules. Furthermore, it will elucidate their mechanism of action and possible implications in the treatment/prevention of viral diseases even when their mechanism of action is not fully understood, which could serve as the base for the future development of novel or complementary antiviral treatments.
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Affiliation(s)
- Sofi Imtiyaz Ali
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | - Wajid Mohammad Sheikh
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | - Muzafar Ahmad Rather
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | | | - Showkeen Muzamil Bashir
- Biochemistry & Molecular Biology Lab, Division of veterinary Biochemistry, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
| | - Showkat Ul Nabi
- Large Animal Diagnostic Laboratory, Department of Clinical Veterinary Medicine, Ethics & Jurisprudence, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Srinagar, India
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6
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vonRanke NL, Ribeiro MMJ, Miceli LA, de Souza NP, Abrahim-Vieira BA, Castro HC, Teixeira VL, Rodrigues CR, Souza AMT. Structure-activity relationship, molecular docking, and molecular dynamic studies of diterpenes from marine natural products with anti-HIV activity. J Biomol Struct Dyn 2020; 40:3185-3195. [PMID: 33183161 DOI: 10.1080/07391102.2020.1845977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
HIV-1 infection is a global epidemic whose treatment is limited majorly by viral resistance and adverse effects. Natural products from algae have been studied for many years, including antiviral, being an alternative to anti-HIV drug design. Since the isolation of natural products can be a hurdle, molecular modeling is an important tool to study these compounds. Herein, structure-activity relationship, molecular docking, and molecular dynamic studies were performed to direct the studies of ten marine natural products with anti-HIV activity. In the structure-activity relationship, descriptors were identified associating the anti-HIV activity of five diterpenes with possible action on the reverse transcriptase allosteric site. These diterpenes were evaluated by molecular docking, and it was identified that only dolabelladienetriol interacted in the allosteric site. Molecular dynamics suggested that the dolabelladienetriol might interfere with the viral RNA binding to HIV-1 RT by inducing a conformational change of the enzyme. Also, in silico ADMET simulations predicts that the dolabelladienetriol present a high potential to be successfully developed as a drug. Thus, applying in silico approaches was possible to suggest potential anti-HIV compounds derived from marine natural products.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N L vonRanke
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M M J Ribeiro
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - L A Miceli
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Biology Institute, Federal Fluminense University, Niteroi, Brazil
| | - N P de Souza
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - B A Abrahim-Vieira
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - H C Castro
- Laboratory of Antibiotics, Biochemistry, Education and Molecular Modeling (LABiEMol), Biology Institute, Federal Fluminense University, Niteroi, Brazil
| | - V L Teixeira
- Center for Biological Sciences and Health (CCBS), Rectory, Federal University of Rio de Janeiro State, Rio de Janeiro, Brazil
| | - C R Rodrigues
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A M T Souza
- Laboratory of Molecular Modeling and QSAR (ModMolQSAR), Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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7
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Kammarabutr J, Mahalapbutr P, Okumura H, Wolschann P, Rungrotmongkol T. Structural dynamics and susceptibility of anti-HIV drugs against HBV reverse transcriptase. J Biomol Struct Dyn 2020; 39:2502-2511. [PMID: 32308149 DOI: 10.1080/07391102.2020.1751715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hepatitis B virus (HBV), a small enveloped DNA virus, attacks the human liver causing both acute and chronic diseases. Current therapeutic drugs use the nucleos(t)ide analogues (NAs) as a competitive inhibitor against HBV reverse transcriptase (HBV-RT), an essential enzyme pivotally involved in viral replication. Unfortunately, this treatment still causes the development of resistant variants of HBV against NAs. As HBV-RT is homologous to the human immunodeficiency virus reverse transcriptase (HIV-RT), it is reasonable to treat HBV-RT with anti-HIV drugs. In the present study, we aimed to investigate the structural dynamics and susceptibility of the known anti-HIV drugs (stavudine [d4T], didanosine [DDI], and zidovudine [ZDV]) against HBV-RT enzyme in comparison to the anti-HBV drug lamivudine (3TC) and deoxythymidine triphosphate (dTTP) substrate using several computational approaches. The ΔGbindresidue calculations revealed that seven polar residues (K32, R41, D83, S85, D205, N236, and K239) and three hydrophobic residues (A86, A87, and F88) of HBV-RT as well as the adjacent DNA strands play an important role in the ligand binding. In addition, the H-bond pattern of d4T is similar to that of 3TC, especially at the residues A86 and A87. Such interactions promote the favorable conformation of ligand in the HBV-RT binding pocket, while the several different conformations of ligand are found in the unbound state. The predicted binding free energy results based on QM/MM-GBSA and MM/GB(PB)SA methods suggested that the susceptibility towards HBV-RT of d4T and ZDV is higher than that of 3TC and dTTP. Altogether, this work sheds light on the potentiality of d4T and ZDV as a promising drug for HBV-infected patients harboring 3TC resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jirayu Kammarabutr
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Panupong Mahalapbutr
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Hisashi Okumura
- Institute for Molecular Science, Research Center for Computational Science, Okazaki, Japan.,Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Peter Wolschann
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand.,Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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8
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Singh VK, Srivastava R, Gupta PSS, Naaz F, Chaurasia H, Mishra R, Rana MK, Singh RK. Anti-HIV potential of diarylpyrimidine derivatives as non-nucleoside reverse transcriptase inhibitors: design, synthesis, docking, TOPKAT analysis and molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:2430-2446. [DOI: 10.1080/07391102.2020.1748111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vishal K. Singh
- Department of Chemistry, Bioorganic Research Laboratory, University of Allahabad, Prayagraj, India
| | - Ritika Srivastava
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Parth Sarthi Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Farha Naaz
- Department of Chemistry, Bioorganic Research Laboratory, University of Allahabad, Prayagraj, India
| | - Himani Chaurasia
- Department of Chemistry, Bioorganic Research Laboratory, University of Allahabad, Prayagraj, India
| | - Richa Mishra
- Department of Chemistry, Bioorganic Research Laboratory, University of Allahabad, Prayagraj, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Ramendra K. Singh
- Department of Chemistry, Bioorganic Research Laboratory, University of Allahabad, Prayagraj, India
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9
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Lignans and Their Derivatives from Plants as Antivirals. Molecules 2020; 25:molecules25010183. [PMID: 31906391 PMCID: PMC6982783 DOI: 10.3390/molecules25010183] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022] Open
Abstract
Lignans are widely produced by various plant species; they are a class of natural products that share structural similarity. They usually contain a core scaffold that is formed by two or more phenylpropanoid units. Lignans possess diverse pharmacological properties, including their antiviral activities that have been reported in recent years. This review discusses the distribution of lignans in nature according to their structural classification, and it provides a comprehensive summary of their antiviral activities. Among them, two types of antiviral lignans—podophyllotoxin and bicyclol, which are used to treat venereal warts and chronic hepatitis B (CHB) in clinical, serve as examples of using lignans for antivirals—are discussed in some detail. Prospects of lignans in antiviral drug discovery are also discussed.
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10
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Wang Y, Wang X, Xiong Y, Li CD, Xu Q, Shen L, Chandra Kaushik A, Wei DQ. An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. Int J Mol Sci 2019; 20:ijms20246226. [PMID: 31835584 PMCID: PMC6940937 DOI: 10.3390/ijms20246226] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/19/2019] [Accepted: 12/04/2019] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptor 15 (GPR15, also known as BOB) is an extensively studied orphan G protein-coupled receptors (GPCRs) involving human immunodeficiency virus (HIV) infection, colonic inflammation, and smoking-related diseases. Recently, GPR15 was deorphanized and its corresponding natural ligand demonstrated an ability to inhibit cancer cell growth. However, no study reported the potential role of GPR15 in a pan-cancer manner. Using large-scale publicly available data from the Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases, we found that GPR15 expression is significantly lower in colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) than in normal tissues. Among 33 cancer types, GPR15 expression was significantly positively correlated with the prognoses of COAD, neck squamous carcinoma (HNSC), and lung adenocarcinoma (LUAD) and significantly negatively correlated with stomach adenocarcinoma (STAD). This study also revealed that commonly upregulated gene sets in the high GPR15 expression group (stratified via median) of COAD, HNSC, LUAD, and STAD are enriched in immune systems, indicating that GPR15 might be considered as a potential target for cancer immunotherapy. Furthermore, we modelled the 3D structure of GPR15 and conducted structure-based virtual screening. The top eight hit compounds were screened and then subjected to molecular dynamics (MD) simulation for stability analysis. Our study provides novel insights into the role of GPR15 in a pan-cancer manner and discovered a potential hit compound for GPR15 antagonists.
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Affiliation(s)
- Yanjing Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.W.); (X.W.); (Y.X.); (C.-D.L.); (Q.X.)
| | - Xiangeng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.W.); (X.W.); (Y.X.); (C.-D.L.); (Q.X.)
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.W.); (X.W.); (Y.X.); (C.-D.L.); (Q.X.)
| | - Cheng-Dong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.W.); (X.W.); (Y.X.); (C.-D.L.); (Q.X.)
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.W.); (X.W.); (Y.X.); (C.-D.L.); (Q.X.)
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China;
| | - Aman Chandra Kaushik
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
- Correspondence: (A.C.K.); (D.-Q.W.)
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.W.); (X.W.); (Y.X.); (C.-D.L.); (Q.X.)
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen 518055, China
- Correspondence: (A.C.K.); (D.-Q.W.)
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