1
|
Chaudhary KK, Prasad CVSS. Virtual Screening of compounds to 1-deoxy-Dxylulose 5-phosphate reductoisomerase (DXR) from Plasmodium falciparum. Bioinformation 2014; 10:358-64. [PMID: 25097379 PMCID: PMC4110427 DOI: 10.6026/97320630010358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 12/02/2022] Open
Abstract
The 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) protein (Gen Bank ID AAN37254.1) from Plasmodium falciparum is a
potential drug target. Therefore, it is of interest to screen DXR against a virtual library of compounds (at the ZINC database) for
potential binders as possible inhibitors. This exercise helped to choose 10 top ranking molecules with ZINC00200163 [N-(2,2di
methoxy ethyl)-6-methyl-2, 3, 4, 9-tetrahydro-1H-carbazol-1-amine] a having good fit (-6.43 KJ/mol binding energy) with the target
protein. Thus, ZINC00200163 is identified as a potential molecule for further comprehensive characterization and in-depth
analysis.
Collapse
Affiliation(s)
- Kamal Kumar Chaudhary
- Division of Applied Sciences & IRCB, Systems Biology lab, Indian Institute of Information Technology Allahabad, Deoghat, Jhalwa, Allahabad 211012, India
| | - C V S Siva Prasad
- Division of Applied Sciences & IRCB, Systems Biology lab, Indian Institute of Information Technology Allahabad, Deoghat, Jhalwa, Allahabad 211012, India
| |
Collapse
|
2
|
Huang SH, Wang X, Jong A. The evolving role of infectomics in drug discovery. Expert Opin Drug Discov 2013; 2:961-75. [PMID: 23484816 DOI: 10.1517/17460441.2.7.961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Signatures of infectomes, which are encoded by both host and microbial genomes, and mirror the interplay between pathogens and their hosts, provide invaluable knowledge in the search for novel antimicrobial drugs. Infectomics is the study of infectomes by using systems biology and high-throughput omic approaches. There are three types of infectomic approaches that can be used for drug discovery: ecological infectomics, immunoinfectomics and chemical infectomics. Ecological infectomics, which is the ecological study of infectomes, explores symbiotic solutions to microbial infections. Research on drug discovery using infectomic signatures and immunomic approaches falls within the field of immunoinfectomics. Advances in chemical infectomics will lead to the development of a new generation of chemical drugs for therapeutics for microbial infections.
Collapse
Affiliation(s)
- Sheng-He Huang
- University of Southern California, Division of Infectious Diseases, Childrens Hospital Los Angeles, Department of Pediatrics, School of Medicine, 4650 Sunset Blvd., Mailstop #51, Los Angeles, CA 90027, USA +1 323 669 4160 ; +1 323 660 2661 ;
| | | | | |
Collapse
|
3
|
Wang J, Peng W, Wu FX. Computational approaches to predicting essential proteins: A survey. Proteomics Clin Appl 2013; 7:181-92. [DOI: 10.1002/prca.201200068] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/12/2012] [Accepted: 11/06/2012] [Indexed: 12/13/2022]
Affiliation(s)
- Jianxin Wang
- School of Information Science and Engineering; Central South University; Changsha; China
| | - Wei Peng
- School of Information Science and Engineering; Central South University; Changsha; China
| | - Fang-Xiang Wu
- Department of Mechanical Engineering and Division of Biomedical Engineering; University of Saskatchewan; Saskatoon; SK; Canada
| |
Collapse
|
4
|
Liu Y, Yin Q, Yuan Y, Yang W, Jiang C, Huang C. Infectomics Screening for Novel Antiviral Drug Targets. Drug Dev Res 2012. [PMCID: PMC7163650 DOI: 10.1002/ddr.21027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Copyright 2012 Wiley-Liss, Inc., A Wiley Company Infectomics, a novel way to globally and comprehensively understand the interactions between microbial pathogens and their hosts, has significantly expanded understanding of the microbial infections. The infectomics view of viral–host interactions on the viral perspective principally focuses on gene acquisition, deletion, and point mutation, while traditional antiviral drug discovery concentrates on viral encoding proteins. Recently, high‐throughput technologies, such as mass spectrometry‐based proteomics, activity‐based protein profiling, microarray analysis, yeast two‐hybrid assay, small interfering RNA screening, and micro RNA profiling, have been gradually employed in the research of virus–host interactions. Besides, signaling pathways and cellular processes involved in viral–host interactions provide new insights of infectomics in antiviral drug discovery. In this review, we summarize related infectomics approaches in the studies of virus–host interactions, which shed light on the development of novel antiviral drug targets screening.
Collapse
Affiliation(s)
- Yuan Liu
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Qi Yin
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Yao Yuan
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Wenyong Yang
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Chuangui Jiang
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| | - Canhua Huang
- The State Key Laboratory of Biotherapy; West China Hospital, West China, Sichuan University; Chengdu; 610041; China
| |
Collapse
|
5
|
Hammami R, Fliss I. Current trends in antimicrobial agent research: chemo- and bioinformatics approaches. Drug Discov Today 2010; 15:540-6. [PMID: 20546918 DOI: 10.1016/j.drudis.2010.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 03/23/2010] [Accepted: 05/10/2010] [Indexed: 12/16/2022]
Abstract
Databases and chemo- and bioinformatics tools that contain genomic, proteomic and functional information have become indispensable for antimicrobial drug research. The combination of chemoinformatics tools, bioinformatics tools and relational databases provides means of analyzing, linking and comparing online search results. The development of computational tools feeds on a diversity of disciplines, including mathematics, statistics, computer science, information technology and molecular biology. The computational approach to antimicrobial agent discovery and design encompasses genomics, molecular simulation and dynamics, molecular docking, structural and/or functional class prediction, and quantitative structure-activity relationships. This article reviews progress in the development of computational methods, tools and databases used for organizing and extracting biological meaning from antimicrobial research.
Collapse
Affiliation(s)
- Riadh Hammami
- STELA Dairy Research Center, Nutraceuticals and Functional Foods Institute, Université Laval, Québec, QC, Canada.
| | | |
Collapse
|
6
|
Shanmugam A, Natarajan J. Computational genome analyses of metabolic enzymes in Mycobacterium leprae for drug target identification. Bioinformation 2010; 4:392-5. [PMID: 20975887 PMCID: PMC2951640 DOI: 10.6026/97320630004392] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 03/06/2010] [Indexed: 11/23/2022] Open
Abstract
Leprosy is an infectious disease caused by Mycobacterium leprae. M. leprae has undergone a major reductive evolution leaving a minimal set of functional genes for survival. It remains non-cultivable. As M. leprae develops resistance against most of the drugs, novel drug targets are required in order to design new drugs. As most of the essential genes mediate several biosynthetic and metabolic pathways, the pathway predictions can predict essential genes. We used comparative genome analysis of metabolic enzymes in M. leprae and H. sapiens using KEGG pathway database and identified 179 non-homologues enzymes. On further comparison of these 179 non-homologous enzymes to the list of minimal set of 48 essential genes required for cell-wall biosynthesis of M. leprae reveals eight common enzymes. Interestingly, six of these eight common enzymes map to that of peptidoglycan biosynthesis and they all belong to Mur enzymes. The machinery for peptidoglycan biosynthesis is a rich source of crucial targets for antibacterial chemotherapy and thus targeting these enzymes is a step towards facilitating the search for new antibiotics.
Collapse
Affiliation(s)
- Anusuya Shanmugam
- Department of Bioinformatics, VMKV Engineering College, Vinayaka Missions University, Salem
| | | |
Collapse
|
7
|
Balg C, Huot JL, Lapointe J, Chênevert R. Inhibition of Helicobacter pylori Aminoacyl-tRNA Amidotransferase by Puromycin Analogues. J Am Chem Soc 2008; 130:3264-5. [DOI: 10.1021/ja7100714] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christian Balg
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
| | - Jonathan L. Huot
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
| | - Jacques Lapointe
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
| | - Robert Chênevert
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
| |
Collapse
|
8
|
Ochsner UA, Sun X, Jarvis T, Critchley I, Janjic N. Aminoacyl-tRNA synthetases: essential and still promising targets for new anti-infective agents. Expert Opin Investig Drugs 2007; 16:573-93. [PMID: 17461733 DOI: 10.1517/13543784.16.5.573] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The emergence of resistance to existing antibiotics demands the development of novel antimicrobial agents directed against novel targets. Historically, bacterial cell wall synthesis, protein, and DNA and RNA synthesis have been major targets of very successful classes of antibiotics such as beta-lactams, glycopeptides, macrolides, aminoglycosides, tetracyclines, rifampicins and quinolones. Recently, efforts have been made to develop novel agents against validated targets in these pathways but also against new, previously unexploited targets. The era of genomics has provided insights into novel targets in microbial pathogens. Among the less exploited--but still promising--targets is the family of 20 aminoacyl-tRNA synthetases (aaRSs), which are essential for protein synthesis. These targets have been validated in nature as aaRS inhibition has been shown as the specific mode of action for many natural antimicrobial agents synthesized by bacteria and fungi. Therefore, aaRSs have the potential to be targeted by novel agents either from synthetic or natural sources to yield specific and selective anti-infectives. Numerous high-throughput screening programs aimed at identifying aaRS inhibitors have been performed over the last 20 years. A large number of promising lead compounds have been identified but only a few agents have moved forward into clinical development. This review provides an update on the present strategies to develop novel aaRS inhibitors as anti-infective drugs.
Collapse
Affiliation(s)
- Urs A Ochsner
- Replidyne, Inc., 1450 Infinite Dr, Louisville, CO 80027, USA.
| | | | | | | | | |
Collapse
|
9
|
Oh SJ, Joung JG, Chang JH, Zhang BT. Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. BMC Bioinformatics 2006; 7:284. [PMID: 16753070 PMCID: PMC1534063 DOI: 10.1186/1471-2105-7-284] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Accepted: 06/06/2006] [Indexed: 11/30/2022] Open
Abstract
Background To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. Results To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. Conclusion By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence information. This method may yield further information about biological evolution, such as the history of horizontal transfer of each gene, by studying the detailed structure of the phylogenetic tree constructed by the kernel-based method.
Collapse
Affiliation(s)
- S June Oh
- Department of Pharmacology, Inje University College of Medicine, Busan, 614-735, Korea
| | - Je-Gun Joung
- Center for Bioinformation Technology, Seoul National University, Seoul, 151-742, Korea
- Graduate Program in Bioinformatics, Seoul National University, Seoul, 151-742, Korea
| | - Jeong-Ho Chang
- Biointelligence Laboratory, School of Computer Sci. and Eng., Seoul National University, Seoul, 151-742, Korea
| | - Byoung-Tak Zhang
- Center for Bioinformation Technology, Seoul National University, Seoul, 151-742, Korea
- Graduate Program in Bioinformatics, Seoul National University, Seoul, 151-742, Korea
- Biointelligence Laboratory, School of Computer Sci. and Eng., Seoul National University, Seoul, 151-742, Korea
| |
Collapse
|
10
|
Cherkasov A, Lee SJ, Nandan D, Reiner NE. Large-scale survey for potentially targetable indels in bacterial and protozoan proteins. Proteins 2006; 62:371-80. [PMID: 16315289 DOI: 10.1002/prot.20631] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Our previous results demonstrated that some essential, housekeeping proteins from pathogenic microorganisms may contain sizable insertions-deletions in their sequences (compared to close human homologs) that can be responsible for unexpected virulence properties. For example, we found that indel-bearing elongation factor-1alpha from several pathogenic protozoa can activate a human tyrosine phosphatase SHP-1 leading to deactivation of macrophages. On the one hand, these findings allowed development of a strategy for targeting some indel-containing pathogen proteins that have similar human counterparts. On the other hand, the results raised numerous questions regarding the nature and implications of sequence indels in pathogen proteins. In the present study, we conducted a large-scale survey of indels in proteins from 136 bacterial and protozoan genomes. It has been established that sizable insertions and deletions occur in approximately 5-10% of bacterial proteins with close human homologs, while proteins from the protozoan pathogens such as Trypanosoma cruzi, Plasmodium falciparum, and Leishmania donovani exhibit elevated indel content that can reach up to 25%. The finding suggested that the occurrence of sequence indels may be involved in the evolution of pathogenic mechanisms in these protozoa.
Collapse
Affiliation(s)
- Artem Cherkasov
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Faculty of Medicine, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada.
| | | | | | | |
Collapse
|
11
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2448450 DOI: 10.1002/cfg.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|