1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Zhang T, Wei D. Recent progress on structural bioinformatics research of cytochrome P450 and its impact on drug discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 827:327-39. [PMID: 25387973 DOI: 10.1007/978-94-017-9245-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Cytochrome P450 is predominantly responsible for human drug metabolism, which is of critical importance for drug discovery and development. Structural bioinformatics focuses on analysis and prediction of three-dimentional structure of biological macromolecules and elucidation of structure-function relationship as well as identification of important binding interactions. Rapid advancement of structural bioinformatics has been made over the last decade. With more information available for CYP structures, the methods of structural bioinformatics may be used in the CYP field. In this review, we demonstrate three previous studies on CYP using the methods of structural bioinformatics, including the investigation of reasons for decrease of enzymatic activity of CYP1A2 caused by a peripheral mutation, the construction of a pharmacophore model specific to active site of CYP1A2 and the prediction of the functional consequences of single residue mutation in CYP. By illustrating these studies we attempt to show the potential role of structural bioinformatics in CYP research and help better understanding the importance of structural bioinformatics in drug designing.
Collapse
Affiliation(s)
- Tao Zhang
- State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,
| | | |
Collapse
|
3
|
Abstract
Efforts from the TB Structural Genomics Consortium together with those of tuberculosis structural biologists worldwide have led to the determination of about 350 structures, making up nearly a tenth of the pathogen's proteome. Given that knowledge of protein structures is essential to obtaining a high-resolution understanding of the underlying biology, it is desirable to have a structural view of the entire proteome. Indeed, structure prediction methods have advanced sufficiently to allow structural models of many more proteins to be built based on homology modeling and fold recognition strategies. By means of these approaches, structural models for about 2,877 proteins, making up nearly 70% of the Mycobacterium tuberculosis proteome, are available. Knowledge from bioinformatics has made significant inroads into an improved annotation of the M. tuberculosis genome and in the prediction of key protein players that interact in vital pathways, some of which are unique to the organism. Functional inferences have been made for a large number of proteins based on fold-function associations. More importantly, ligand-binding pockets of the proteins are identified and scanned against a large database, leading to binding site-based ligand associations and hence structure-based function annotation. Near proteome-wide structural models provide a global perspective of the fold distribution in the genome. New insights about the folds that predominate in the genome, as well as the fold combinations that make up multidomain proteins, are also obtained. This chapter describes the structural proteome, functional inferences drawn from it, and its applications in drug discovery.
Collapse
|
4
|
Kumar S, Farmer R, Turnbull AP, Tripathy NK, Manjasetty BA. Structural and functional conservation profiles of novel cathepsin L-like proteins identified in the Drosophila melanogaster genome. J Biomol Struct Dyn 2012; 31:1481-9. [PMID: 23256878 DOI: 10.1080/07391102.2012.745379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cathepsin L is a cysteine protease which degrades connective tissue proteins including collagen, elastin, and fibronectin. In this study, five well-characterized cathepsin L proteins from different arthropods were used as query sequences for the Drosophila genome database. The search yielded 10 cathepsin L-like sequences, of which eight putatively represent novel cathepsin L-like proteins. To understand the phylogenetic relationship among these cathepsin L-like proteins, a phylogenetic tree was constructed based on their sequences. In addition, models of the tertiary structures of cathepsin L were constructed using homology modeling methods and subjected to molecular dynamics simulations to obtain reasonable structure to understand its dynamical behavior. Our findings demonstrate that all of the potential Drosophila cathepsin L-like proteins contain at least one cathepsin propeptide inhibitor domain. Multiple sequence alignment and homology models clearly highlight the conservation of active site residues, disulfide bonds, and amino acid residues critical for inhibitor binding. Furthermore, comparative modeling indicates that the sequence/structure/function profiles and active site architectures are conserved.
Collapse
Affiliation(s)
- Sunil Kumar
- a An Autonomous Institute of Department of Biotechnology, Government of India , Institute of Life Sciences , Nalco Square, Bhubaneswar , 751023 , India
| | | | | | | | | |
Collapse
|