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Kurmi A, Sen P, Dash M, Ray SK, Satapathy SS. Differentially used codons among essential genes in bacteria identified by machine learning-based analysis. Mol Genet Genomics 2024; 299:72. [PMID: 39060647 DOI: 10.1007/s00438-024-02163-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-expression and low-expression genes in several bacteria. In this article, we have extended codon usage study considering gene essentiality as a feature. Using machine learning (ML) based approaches, we have analysed Relative Synonymous Codon Usage (RSCU) values between essential and non-essential genes in Escherichia coli and thirty-four other bacterial genomes whose gene essentiality features were available in public databases. We observed significant differences in codon usage patterns between essential and non-essential genes for majority of the bacterial genomes and accordingly, ML based classifiers achieved high area under curve (AUC) scores, with a minimum score of 70.0 across twenty-eight organisms. Further, importance of the codons towards classifying genes found to differ among the codons in each genome. Arg codon CGT and Gly codon GGT were observed to be the most preferred codons among essential genes in Escherichia coli. Interestingly, some of the codons like CGT, ATA, GGT and GGG observed to be contributing consistently towards classifying essential genes across thirty-five bacteria genomes studied. In other hand, codons TGY and CAY encoding amino acids Cys and His respectively were among the least contributing codons towards classification among all these bacteria. This study demonstrates the gene essentiality based differences in synonymous codon usage in bacteria genomes and presents a common codon usage pattern across bacteria.
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Affiliation(s)
- Annushree Kurmi
- Department of Computer Science and Engineering, Tezpur University, Napaam, Assam, 784028, India
- Department of Computer Science and Engineering, The Assam Kaziranga University, Jorhat, Assam, 785006, India
| | - Piyali Sen
- Department of Computer Science and Engineering, Tezpur University, Napaam, Assam, 784028, India
| | - Madhusmita Dash
- Department of Electronics and Communication Engineering, NIT, Jote, Arunachal Pradesh, 791113, India
| | - Suvendra Kumar Ray
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Assam, 784028, India
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2
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Wirtz L, Casanova F, Schaffrath U, Wegner A. Development of a telomere vector-based approach to overcome limitations caused by lethal phenotypes in the study of essential genes in Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2024; 25:e13460. [PMID: 38695626 PMCID: PMC11064798 DOI: 10.1111/mpp.13460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Reverse genetic approaches are common tools in genomics for elucidating gene functions, involving techniques such as gene deletion followed by screening for aberrant phenotypes. If the generation of gene deletion mutants fails, the question arises whether the failure stems from technical issues or because the gene of interest (GOI) is essential, meaning that the deletion causes lethality. In this report, we introduce a novel method for assessing gene essentiality using the phytopathogenic ascomycete Magnaporthe oryzae. The method is based on the observation that telomere vectors are lost in transformants during cultivation without selection pressure. We tested the hypothesis that essential genes can be identified in deletion mutants co-transformed with a telomere vector. The M. oryzae gene MoPKC, described in literature as essential, was chosen as GOI. Using CRISPR/Cas9 technology transformants with deleted GOI were generated and backed up by a telomere vector carrying a copy of the GOI and conferring fenhexamid resistance. Transformants in which the GOI deletion in the genome was not successful lost the telomere vector on media without fenhexamid. In contrast, transformants with confirmed GOI deletion retained the telomere vector even in absence of fenhexamid selection. In the latter case, the maintenance of the telomere indicates that the GOI is essential for the surveillance of the fungi, as it would have been lost otherwise. The method presented here allows to test for essentiality of genes when no mutants can be obtained from gene deletion approaches, thereby expanding the toolbox for studying gene function in ascomycetes.
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Affiliation(s)
- Louisa Wirtz
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | - Florencia Casanova
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | - Ulrich Schaffrath
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
| | - Alex Wegner
- Department of Molecular Plant PhysiologyRWTH Aachen UniversityAachenGermany
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3
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Vemula D, Maddi DR, Bhandari V. Homology modeling, virtual screening, molecular docking, and dynamics studies for discovering Staphylococcus epidermidis FtsZ inhibitors. Front Mol Biosci 2023; 10:1087676. [PMID: 36936991 PMCID: PMC10020519 DOI: 10.3389/fmolb.2023.1087676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Staphylococcus epidermidis is the most common cause of medical device-associated infections and is an opportunistic biofilm former. Among hospitalized patients, S. epidermidis infections are the most prevalent, and resistant to most antibiotics. In order to overcome this resistance, it is imperative to treat the infection at a cellular level. The present study aims to identify inhibitors of the prokaryotic cell division protein FtsZ a widely conserved component of bacterial cytokinesis. Two substrate binding sites are present on the FtsZ protein; the nucleotide-binding domain and the inter-domain binding sites. Molecular modeling was used to identify potential inhibitors against the binding sites of the FtsZ protein. One hundred thirty-eight chemical entities were virtually screened for the binding sites and revealed ten molecules, each with good binding affinities (docking score range -9.549 to -4.290 kcal/mol) compared to the reference control drug, i.e., Dacomitinib (-4.450 kcal/mol) and PC190723 (-4.694 kcal/mol) at nucleotide and inter-domain binding sites respectively. These top 10 hits were further analyzed for their ADMET properties and molecular dynamics simulations. The Chloro-derivative of GTP, naphthalene-1,3-diyl bis(3,4,5-trihydroxybenzoate), Guanosine triphosphate (GTP), morpholine and methylpiperazine derivative of GTP were identified as the lead molecules for nucleotide binding site whereas for inter-domain binding site, 1-(((amino(iminio)methyl)amino)methyl)-3-(3-(tert-butyl)phenyl)-6,7-dimethoxyisoquinolin-2-ium, and Chlorogenic acidwere identified as lead molecules. Molecular dynamics simulation and post MM/GBSA analysis of the complexes revealed good protein-ligand stability predicting them as potential inhibitors of FtsZ (Figure 1). Thus, identified FtsZ inhibitors are a promising lead compounds for S. epidermidis related infections.
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Song D, Zhang N, Ma Y, Zhang S, Chen W, Guo T, Ma S. Acridinium-conjugated aromatic heterocycles as highly potent FtsZ inhibitors: Design, synthesis, and biological evaluation. Arch Pharm (Weinheim) 2022; 355:e2100400. [PMID: 35267210 DOI: 10.1002/ardp.202100400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/05/2022]
Abstract
The epidemic of multidrug resistance (MDR) is a serious threat to public health, and new classes of antibiotics with novel mechanisms of action are in critical need. We rationally designed and efficiently synthesized three series of new chemical entities with potential antibacterial activity targeting filamenting temperature-sensitive mutant Z (FtsZ). Evaluation of these compounds against a panel of Gram-positive bacteria including MDR and vancomycin-resistant Enterococcus strains indicated that most compounds showed enhanced antibacterial efficacy, comparable or even superior to the reference drugs. The newly synthesized compounds proved to be substrates of the Escherichia coli efflux pump AcrB, thus affecting the activity. Their structure-activity relationships were summarized in detail. The most potent compound 10f quickly eliminated bacteria in a bactericidal mode, with low susceptibility to induce bacterial resistance. Further mechanistic studies with the BsFtsZ protein revealed that 10f functioned as an effective FtsZ inhibitor through altering the dynamics of FtsZ self-polymerization via a stimulatory mechanism, which leads to inhibition of cell division and cell death. Besides, 10f not only displayed no obvious cytotoxicity to mammalian cells but also had a high efficacy in a murine model of bacteremia in vivo. Regarded as a whole, our findings highlight 10f as a promising new FtsZ-targeting bactericidal agent.
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Affiliation(s)
- Di Song
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Nan Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yangchun Ma
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shenyan Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Weijin Chen
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ting Guo
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shutao Ma
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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Chelliah R, Banan-MwineDaliri E, Khan I, Wei S, Elahi F, Yeon SJ, Selvakumar V, Ofosu FK, Rubab M, Ju HH, Rallabandi HR, Madar IH, Sultan G, Oh DH. A review on the application of bioinformatics tools in food microbiome studies. Brief Bioinform 2022; 23:6533500. [PMID: 35189636 DOI: 10.1093/bib/bbac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.
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Affiliation(s)
- Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Eric Banan-MwineDaliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Imran Khan
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Department of Biotechnology, University of Malakand, Khyber Pakhtunkhwa Pakistan
| | - Shuai Wei
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea.,Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fazle Elahi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Su-Jung Yeon
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Vijayalakshmi Selvakumar
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Momna Rubab
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Hum Hun Ju
- Department of Biological Environment, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Harikrishna Reddy Rallabandi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
| | - Inamul Hasan Madar
- Department of Biochemistry, School of Life Science, Bharathidasan, University, Thiruchirappalli, Tamilnadu, India
| | - Ghazala Sultan
- Department of Computer Science, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Deog Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Korea
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Liu X, Luo Y, He T, Ren M, Xu Y. Predicting essential genes of 37 prokaryotes by combining information-theoretic features. J Microbiol Methods 2021; 188:106297. [PMID: 34343487 DOI: 10.1016/j.mimet.2021.106297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
Essential genes are required for the reproduction and survival of an organism. Rapid identification of essential genes has practical application value in biomedicine. Information theory is a discipline that studies information transmission. Based on the similarity between heredity and information transmission, measures derived from information theory can be applied to genetic sequence analysis on different scales. In this study, we employed 114 features extracted by information theory methods to construct an essential gene prediction model. We applied a backpropagation neural network to construct a classifier and employed it to predict essential genes of 37 prokaryotes. The performance of the classifier was evaluated by applying intra-organism prediction and leave-one-species-out prediction. Among 37 prokaryotes, intra-organism prediction and leave-one-species-out prediction yielded average AUC scores of 0.791 and 0.717, respectively. Considering the potential redundancy in the feature set, we performed feature selection and constructed a key feature subset. In the above two prediction methods, the average AUC scores of 37 organisms obtained by using key features were 0.786 and 0.714, respectively. The results show the potential and universality of information-theoretic features in the study of prokaryotic essential gene prediction.
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Affiliation(s)
- Xiao Liu
- School of Microelectronics and Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing 400044, China.
| | - Yachuan Luo
- School of Microelectronics and Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing 400044, China
| | - Ting He
- School of Microelectronics and Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing 400044, China
| | - Meixiang Ren
- School of Microelectronics and Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing 400044, China
| | - Yuqiao Xu
- School of Microelectronics and Communication Engineering, Chongqing University, 174 ShaPingBa District, Chongqing 400044, China
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7
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FtsZ inhibitors as a new genera of antibacterial agents. Bioorg Chem 2019; 91:103169. [PMID: 31398602 DOI: 10.1016/j.bioorg.2019.103169] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 11/21/2022]
Abstract
The continuous emergence and rapid spread of a multidrug-resistant strain of bacterial pathogens have demanded the discovery and development of new antibacterial agents. A highly conserved prokaryotic cell division protein FtsZ is considered as a promising target by inhibiting bacterial cytokinesis. Inhibition of FtsZ assembly restrains the cell-division complex known as divisome, which results in filamentation, leading to lysis of the cell. This review focuses on details relating to the structure, function, and influence of FtsZ in bacterial cytokinesis. It also summarizes on the recent perspective of the known natural and synthetic inhibitors directly acting on FtsZ protein, with prominent antibacterial activities. A series of benzamides, trisubstituted benzimidazoles, isoquinolene, guanine nucleotides, zantrins, carbonylpyridine, 4 and 5-Substituted 1-phenyl naphthalenes, sulindac, vanillin analogues were studied here and recognized as FtsZ inhibitors that act either by disturbing FtsZ polymerization and/or GTPase activity. Doxorubicin, from a U.S. FDA, approved drug library displayed strong interaction with FtsZ. Several of the molecules discussed, include the prodrugs of benzamide based compound PC190723 (TXA-709 and TXA707). These molecules have exhibited the most prominent antibacterial activity against several strains of Staphylococcus aureus with minimal toxicity and good pharmacokinetics properties. The evidence of research reports and patent documentations on FtsZ protein has disclosed distinct support in the field of antibacterial drug discovery. The pressing need and interest shall facilitate the discovery of novel clinical molecules targeting FtsZ in the upcoming days.
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Nigatu D, Sobetzko P, Yousef M, Henkel W. Sequence-based information-theoretic features for gene essentiality prediction. BMC Bioinformatics 2017; 18:473. [PMID: 29121868 PMCID: PMC5679510 DOI: 10.1186/s12859-017-1884-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/26/2017] [Indexed: 11/10/2022] Open
Abstract
Background Identification of essential genes is not only useful for our understanding of the minimal gene set required for cellular life but also aids the identification of novel drug targets in pathogens. In this work, we present a simple and effective gene essentiality prediction method using information-theoretic features that are derived exclusively from the gene sequences. Results We developed a Random Forest classifier and performed an extensive model performance evaluation among and within 15 selected bacteria. In intra-organism predictions, where training and testing sets are taken from the same organism, AUC (Area Under the Curve) scores ranging from 0.73 to 0.90, 0.84 on average, were obtained. Cross-organism predictions using 5-fold cross-validation, pairwise, leave-one-species-out, leave-one-taxon-out, and cross-taxon yielded average AUC scores of 0.88, 0.75, 0.80, 0.82, and 0.78, respectively. To further show the applicability of our method in other domains of life, we predicted the essential genes of the yeast Schizosaccharomyces pombe and obtained a similar accuracy (AUC 0.84). Conclusions The proposed method enables a simple and reliable identification of essential genes without searching in databases for orthologs and demanding further experimental data such as network topology and gene-expression. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1884-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dawit Nigatu
- Transmission Systems Group, Jacobs University Bremen, Campus Ring 1, Bremen, D-28759, Germany.
| | - Patrick Sobetzko
- Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, Mehrzweckgebäude, Marburg, 35043, Germany
| | - Malik Yousef
- Community Information Systems, Zefat Academic College, Zefat, 13206, Israel
| | - Werner Henkel
- Transmission Systems Group, Jacobs University Bremen, Campus Ring 1, Bremen, D-28759, Germany
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Kucková L, Bučinský L, Kožíšek J. Copper atom representation in charge density analysis of (5-chlorosalicylate)-(2,9-dimethylphenanthroline)-(aqua) copper complex: Experimental and theoretical study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.01.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Bem AE, Velikova N, Pellicer MT, Baarlen PV, Marina A, Wells JM. Bacterial histidine kinases as novel antibacterial drug targets. ACS Chem Biol 2015; 10:213-24. [PMID: 25436989 DOI: 10.1021/cb5007135] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial histidine kinases (HKs) are promising targets for novel antibacterials. Bacterial HKs are part of bacterial two-component systems (TCSs), the main signal transduction pathways in bacteria, regulating various processes including virulence, secretion systems and antibiotic resistance. In this review, we discuss the biological importance of TCSs and bacterial HKs for the discovery of novel antibacterials, as well as published TCS and HK inhibitors that can be used as a starting point for structure-based approaches to develop novel antibacterials.
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Affiliation(s)
- Agnieszka E. Bem
- Host−Microbe
Interactomics, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Nadya Velikova
- Instituto
de Biomedicina
de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Jaume Roig 11, 46010-Valencia, Spain
| | - M. Teresa Pellicer
- R&D Department Interquim, Ferrer HealthTech, Joan Buscalla 10, 08137-Sant Cugat del Valles Barcelona, Spain
| | - Peter van Baarlen
- Host−Microbe
Interactomics, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Alberto Marina
- Instituto
de Biomedicina
de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Jaume Roig 11, 46010-Valencia, Spain
- Centro de Investigacion
Biomedica en Red de Enfermedades Raras (CIBER-ISCIII), Jaume Roig 11, 46010-Valencia, Spain
| | - Jerry M. Wells
- Host−Microbe
Interactomics, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
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Lu Y, Deng J, Rhodes JC, Lu H, Lu LJ. Predicting essential genes for identifying potential drug targets in Aspergillus fumigatus. Comput Biol Chem 2014; 50:29-40. [PMID: 24569026 DOI: 10.1016/j.compbiolchem.2014.01.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND Aspergillus fumigatus (Af) is a ubiquitous and opportunistic pathogen capable of causing acute, invasive pulmonary disease in susceptible hosts. Despite current therapeutic options, mortality associated with invasive Af infections remains unacceptably high, increasing 357% since 1980. Therefore, there is an urgent need for the development of novel therapeutic strategies, including more efficacious drugs acting on new targets. Thus, as noted in a recent review, "the identification of essential genes in fungi represents a crucial step in the development of new antifungal drugs". Expanding the target space by rapidly identifying new essential genes has thus been described as "the most important task of genomics-based target validation". RESULTS In previous research, we were the first to show that essential gene annotation can be reliably transferred between distantly related four Prokaryotic species. In this study, we extend our machine learning approach to the much more complex Eukaryotic fungal species. A compendium of essential genes is predicted in Af by transferring known essential gene annotations from another filamentous fungus Neurospora crassa. This approach predicts essential genes by integrating diverse types of intrinsic and context-dependent genomic features encoded in microbial genomes. The predicted essential datasets contained 1674 genes. We validated our results by comparing our predictions with known essential genes in Af, comparing our predictions with those predicted by homology mapping, and conducting conditional expressed alleles. We applied several layers of filters and selected a set of potential drug targets from the predicted essential genes. Finally, we have conducted wet lab knockout experiments to verify our predictions, which further validates the accuracy and wide applicability of the machine learning approach. CONCLUSIONS The approach presented here significantly extended our ability to predict essential genes beyond orthologs and made it possible to predict an inventory of essential genes in Eukaryotic fungal species, amongst which a preferred subset of suitable drug targets may be selected. By selecting the best new targets, we believe that resultant drugs would exhibit an unparalleled clinical impact against a naive pathogen population. Additional benefits that a compendium of essential genes can provide are important information on cell function and evolutionary biology. Furthermore, mapping essential genes to pathways may also reveal critical check points in the pathogen's metabolism. Finally, this approach is highly reproducible and portable, and can be easily applied to predict essential genes in many more pathogenic microbes, especially those unculturable.
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Affiliation(s)
- Yao Lu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, 24/1400 Beijing (W) Road, Shanghai 200040, PR China
| | - Jingyuan Deng
- Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC7024, Cincinnati, OH 45229, USA
| | - Judith C Rhodes
- Department of Pathology and Laboratory Medicine, University of Cincinnati, 2600 Clifton Avenue, Cincinnati, OH 45221, USA
| | - Hui Lu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, 24/1400 Beijing (W) Road, Shanghai 200040, PR China; Department of Bioengineering (MC 063), University of Illinois at Chicago, 851 S Morgan St, 218 SEO, Chicago, IL 60607, USA.
| | - Long Jason Lu
- Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC7024, Cincinnati, OH 45229, USA; Division of Epidemiology and Biostatistics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC7024, Cincinnati, OH 45229, USA; Department of Computer Science, University of Cincinnati, 2600 Clifton Avenue, Cincinnati, OH 45221, USA; Department of Environmental Health, University of Cincinnati, 2600 Clifton Avenue, Cincinnati, OH 45221, USA; Department of Biomedical Engineering, University of Cincinnati, 2600 Clifton Avenue, Cincinnati, OH 45221, USA.
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12
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Cheng J, Xu Z, Wu W, Zhao L, Li X, Liu Y, Tao S. Training set selection for the prediction of essential genes. PLoS One 2014; 9:e86805. [PMID: 24466248 PMCID: PMC3899339 DOI: 10.1371/journal.pone.0086805] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/13/2013] [Indexed: 01/23/2023] Open
Abstract
Various computational models have been developed to transfer annotations of gene essentiality between organisms. However, despite the increasing number of microorganisms with well-characterized sets of essential genes, selection of appropriate training sets for predicting the essential genes of poorly-studied or newly sequenced organisms remains challenging. In this study, a machine learning approach was applied reciprocally to predict the essential genes in 21 microorganisms. Results showed that training set selection greatly influenced predictive accuracy. We determined four criteria for training set selection: (1) essential genes in the selected training set should be reliable; (2) the growth conditions in which essential genes are defined should be consistent in training and prediction sets; (3) species used as training set should be closely related to the target organism; and (4) organisms used as training and prediction sets should exhibit similar phenotypes or lifestyles. We then analyzed the performance of an incomplete training set and an integrated training set with multiple organisms. We found that the size of the training set should be at least 10% of the total genes to yield accurate predictions. Additionally, the integrated training sets exhibited remarkable increase in stability and accuracy compared with single sets. Finally, we compared the performance of the integrated training sets with the four criteria and with random selection. The results revealed that a rational selection of training sets based on our criteria yields better performance than random selection. Thus, our results provide empirical guidance on training set selection for the identification of essential genes on a genome-wide scale.
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Affiliation(s)
- Jian Cheng
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhao Xu
- College of Science, Northwest A&F University, Yangling Shaanxi, China
| | - Wenwu Wu
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Li Zhao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiangchen Li
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanlin Liu
- College of Wine, Northwest A&F University, Yangling Shaanxi, China
- * E-mail: (YL); (ST)
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
- Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (YL); (ST)
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Cheng J, Wu W, Zhang Y, Li X, Jiang X, Wei G, Tao S. A new computational strategy for predicting essential genes. BMC Genomics 2013; 14:910. [PMID: 24359534 PMCID: PMC3880044 DOI: 10.1186/1471-2164-14-910] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/29/2013] [Indexed: 12/17/2022] Open
Abstract
Background Determination of the minimum gene set for cellular life is one of the central goals in biology. Genome-wide essential gene identification has progressed rapidly in certain bacterial species; however, it remains difficult to achieve in most eukaryotic species. Several computational models have recently been developed to integrate gene features and used as alternatives to transfer gene essentiality annotations between organisms. Results We first collected features that were widely used by previous predictive models and assessed the relationships between gene features and gene essentiality using a stepwise regression model. We found two issues that could significantly reduce model accuracy: (i) the effect of multicollinearity among gene features and (ii) the diverse and even contrasting correlations between gene features and gene essentiality existing within and among different species. To address these issues, we developed a novel model called feature-based weighted Naïve Bayes model (FWM), which is based on Naïve Bayes classifiers, logistic regression, and genetic algorithm. The proposed model assesses features and filters out the effects of multicollinearity and diversity. The performance of FWM was compared with other popular models, such as support vector machine, Naïve Bayes model, and logistic regression model, by applying FWM to reciprocally predict essential genes among and within 21 species. Our results showed that FWM significantly improves the accuracy and robustness of essential gene prediction. Conclusions FWM can remarkably improve the accuracy of essential gene prediction and may be used as an alternative method for other classification work. This method can contribute substantially to the knowledge of the minimum gene sets required for living organisms and the discovery of new drug targets.
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Affiliation(s)
| | | | | | | | | | - Gehong Wei
- College of Life Science, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
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14
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Gladki A, Kaczanowski S, Szczesny P, Zielenkiewicz P. The evolutionary rate of antibacterial drug targets. BMC Bioinformatics 2013; 14:36. [PMID: 23374913 PMCID: PMC3598507 DOI: 10.1186/1471-2105-14-36] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 01/29/2013] [Indexed: 11/17/2022] Open
Abstract
Background One of the major issues in the fight against infectious diseases is the notable increase in multiple drug resistance in pathogenic species. For that reason, newly acquired high-throughput data on virulent microbial agents attract the attention of many researchers seeking potential new drug targets. Many approaches have been used to evaluate proteins from infectious pathogens, including, but not limited to, similarity analysis, reverse docking, statistical 3D structure analysis, machine learning, topological properties of interaction networks or a combination of the aforementioned methods. From a biological perspective, most essential proteins (knockout lethal for bacteria) or highly conserved proteins (broad spectrum activity) are potential drug targets. Ribosomal proteins comprise such an example. Many of them are well-known drug targets in bacteria. It is intuitive that we should learn from nature how to design good drugs. Firstly, known antibiotics are mainly originating from natural products of microorganisms targeting other microorganisms. Secondly, paleontological data suggests that antibiotics have been used by microorganisms for million years. Thus, we have hypothesized that good drug targets are evolutionary constrained and are subject of evolutionary selection. This means that mutations in such proteins are deleterious and removed by selection, which makes them less susceptible to random development of resistance. Analysis of the speed of evolution seems to be good approach to test this hypothesis. Results In this study we show that pN/pS ratio of genes coding for known drug targets is significantly lower than the genome average and also lower than that for essential genes identified by experimental methods. Similar results are observed in the case of dN/dS analysis. Both analyzes suggest that drug targets tend to evolve slowly and that the rate of evolution is a better predictor of drugability than essentiality. Conclusions Evolutionary rate can be used to score and find potential drug targets. The results presented here may become a useful addition to a repertoire of drug target prediction methods. As a proof of concept, we analyzed GO enrichment among the slowest evolving genes. These may become the starting point in the search for antibiotics with a novel mechanism.
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Affiliation(s)
- Arkadiusz Gladki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, Poland
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15
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Giorgi FM, Del Fabbro C, Licausi F. Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana. ACTA ACUST UNITED AC 2013; 29:717-24. [PMID: 23376351 DOI: 10.1093/bioinformatics/btt053] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MOTIVATION Coexpression networks are data-derived representations of genes behaving in a similar way across tissues and experimental conditions. They have been used for hypothesis generation and guilt-by-association approaches for inferring functions of previously unknown genes. So far, the main platform for expression data has been DNA microarrays; however, the recent development of RNA-seq allows for higher accuracy and coverage of transcript populations. It is therefore important to assess the potential for biological investigation of coexpression networks derived from this novel technique in a condition-independent dataset. RESULTS We collected 65 publicly available Illumina RNA-seq high quality Arabidopsis thaliana samples and generated Pearson correlation coexpression networks. These networks were then compared with those derived from analogous microarray data. We show how Variance-Stabilizing Transformed (VST) RNA-seq data samples are the most similar to microarray ones, with respect to inter-sample variation, correlation coefficient distribution and network topological architecture. Microarray networks show a slightly higher score in biology-derived quality assessments such as overlap with the known protein-protein interaction network and edge ontological agreement. Different coexpression network centralities are investigated; in particular, we show how betweenness centrality is generally a positive marker for essential genes in A.thaliana, regardless of the platform originating the data. In the end, we focus on a specific gene network case, showing that although microarray data seem more suited for gene network reverse engineering, RNA-seq offers the great advantage of extending coexpression analyses to the entire transcriptome.
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16
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Ng NS, Leverett P, Hibbs DE, Yang Q, Bulanadi JC, Jie Wu M, Aldrich-Wright JR. The antimicrobial properties of some copper(ii) and platinum(ii) 1,10-phenanthroline complexes. Dalton Trans 2013; 42:3196-209. [DOI: 10.1039/c2dt32392c] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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17
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Ma J, Zhang X, Ung CY, Chen YZ, Li B. Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes. MOLECULAR BIOSYSTEMS 2012; 8:1179-86. [DOI: 10.1039/c2mb05376d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Amini S, Tavazoie S. Antibiotics and the post-genome revolution. Curr Opin Microbiol 2011; 14:513-8. [PMID: 21816663 DOI: 10.1016/j.mib.2011.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 12/28/2022]
Abstract
The emergence of pathogenic bacteria resistant to multiple antimicrobial agents is turning into a major crisis in human and veterinary medicine. This necessitates a serious re-evaluation of our approaches toward antibacterial drug discovery and use. Concurrent advances in genomics including whole-genome sequencing, genotyping, and gene expression profiling have the potential to transform our basic understanding of antimicrobial pathways and lead to the discovery of novel targets and therapeutics.
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Affiliation(s)
- Sasan Amini
- Department of Molecular Biology & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
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19
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Barker CA, Farha MA, Brown ED. Chemical Genomic Approaches to Study Model Microbes. ACTA ACUST UNITED AC 2010; 17:624-32. [DOI: 10.1016/j.chembiol.2010.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 12/15/2022]
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20
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Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. Nat Chem Biol 2009; 5:849-56. [PMID: 19783991 DOI: 10.1038/nchembio.221] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 07/23/2009] [Indexed: 01/18/2023]
Abstract
One of the most significant hurdles to developing new chemical probes of biological systems and new drugs to treat disease is that of understanding the mechanism of action of small molecules discovered with cell-based small-molecule screening. Here we have assembled an ordered, high-expression clone set of all of the essential genes from Escherichia coli and used it to systematically screen for suppressors of growth inhibitory compounds. Using this chemical genomic approach, we demonstrate that the targets of well-known antibiotics can be identified as high copy suppressors of chemical lethality. This approach led to the discovery of MAC13243, a molecule that belongs to a new chemical class and that has a unique mechanism and promising activity against multidrug-resistant Pseudomonas aeruginosa. We show that MAC13243 inhibits the function of the LolA protein and represents a new chemical probe of lipoprotein targeting in bacteria with promise as an antibacterial lead with Gram-negative selectivity.
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21
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Kapoor S, Panda D. Targeting FtsZ for antibacterial therapy: a promising avenue. Expert Opin Ther Targets 2009; 13:1037-51. [DOI: 10.1517/14728220903173257] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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22
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23
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Hwang YC, Lin CC, Chang JY, Mori H, Juan HF, Huang HC. Predicting essential genes based on network and sequence analysis. MOLECULAR BIOSYSTEMS 2009; 5:1672-8. [DOI: 10.1039/b900611g] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Relationship between insertion/deletion (indel) frequency of proteins and essentiality. BMC Bioinformatics 2007; 8:227. [PMID: 17598914 PMCID: PMC1925122 DOI: 10.1186/1471-2105-8-227] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 06/28/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such indels may provide sufficient spatial differences between the pathogenic protein and human proteins to allow for selective targeting. In one example, an indel difference was targeted via large scale in-silico screening. This resulted in selective antibodies and small compounds which were capable of binding to the deletion-bearing essential pathogen protein without any cross-reactivity to the highly similar human protein. The objective of the current study was to investigate whether indels were found more frequently in essential than non-essential proteins. RESULTS We have investigated three species, Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae, for which high-quality protein essentiality data is available. Using these data, we demonstrated with t-test calculations that the mean indel frequencies in essential proteins were greater than that of non-essential proteins in the three proteomes. The abundance of indels in both types of proteins was also shown to be accurately modeled by the Weibull distribution. However, Receiver Operator Characteristic (ROC) curves showed that indel frequencies alone could not be used as a marker to accurately discriminate between essential and non-essential proteins in the three proteomes. Finally, we analyzed the protein interaction data available for S. cerevisiae and observed that indel-bearing proteins were involved in more interactions and had greater betweenness values within Protein Interaction Networks (PINs). CONCLUSION Overall, our findings demonstrated that indels were not randomly distributed across the studied proteomes and were likely to occur more often in essential proteins and those that were highly connected, indicating a possible role of sequence insertions and deletions in the regulation and modification of protein-protein interactions. Such observations will provide new insights into indel-based drug design using bioinformatics and cheminformatics tools.
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25
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von Nussbaum F, Brands M, Hinzen B, Weigand S, Häbich D. Antibacterial natural products in medicinal chemistry--exodus or revival? Angew Chem Int Ed Engl 2007; 45:5072-129. [PMID: 16881035 DOI: 10.1002/anie.200600350] [Citation(s) in RCA: 467] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To create a drug, nature's blueprints often have to be improved through semisynthesis or total synthesis (chemical postevolution). Selected contributions from industrial and academic groups highlight the arduous but rewarding path from natural products to drugs. Principle modification types for natural products are discussed herein, such as decoration, substitution, and degradation. The biological, chemical, and socioeconomic environments of antibacterial research are dealt with in context. Natural products, many from soil organisms, have provided the majority of lead structures for marketed anti-infectives. Surprisingly, numerous "old" classes of antibacterial natural products have never been intensively explored by medicinal chemists. Nevertheless, research on antibacterial natural products is flagging. Apparently, the "old fashioned" natural products no longer fit into modern drug discovery. The handling of natural products is cumbersome, requiring nonstandardized workflows and extended timelines. Revisiting natural products with modern chemistry and target-finding tools from biology (reversed genomics) is one option for their revival.
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Affiliation(s)
- Franz von Nussbaum
- Bayer HealthCare AG, Medicinal Chemistry Europe, 42096 Wuppertal, Germany.
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26
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Lerner CG, Hajduk PJ, Wagner R, Wagenaar FL, Woodall C, Gu YG, Searle XB, Florjancic AS, Zhang T, Clark RF, Cooper CS, Mack JC, Yu L, Cai M, Betz SF, Chovan LE, McCall JO, Black-Schaefer CL, Kakavas SJ, Schurdak ME, Comess KM, Walter KA, Edalji R, Dorwin SA, Smith RA, Hebert EJ, Harlan JE, Metzger RE, Merta PJ, Baranowski JL, Coen ML, Thornewell SJ, Shivakumar AG, Saiki AY, Soni N, Bui M, Balli DJ, Sanders WJ, Nilius AM, Holzman TF, Fesik SW, Beutel BA. From Bacterial Genomes to Novel Antibacterial Agents: Discovery, Characterization, and Antibacterial Activity of Compounds that Bind to HI0065 (YjeE) from Haemophilus influenzae. Chem Biol Drug Des 2007; 69:395-404. [PMID: 17581233 DOI: 10.1111/j.1747-0285.2007.00521.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of a fully integrated and comprehensive strategy to discover novel antibacterial agents, NMR- and mass spectrometry-based affinity selection screens were performed to identify compounds that bind to protein targets uniquely found in bacteria and encoded by genes essential for microbial viability. A biphenyl acid lead series emerged from an NMR-based screen with the Haemophilus influenzae protein HI0065, a member of a family of probable ATP-binding proteins found exclusively in eubacteria. The structure-activity relationships developed around the NMR-derived biphenyl acid lead were consistent with on-target antibacterial activity as the Staphylococcus aureus antibacterial activity of the series correlated extremely well with binding affinity to HI0065, while the correlation of binding affinity with B-cell cytotoxicity was relatively poor. Although further studies are needed to conclusively establish the mode of action of the biphenyl series, these compounds represent novel leads that can serve as the basis for the development of novel antibacterial agents that appear to work via an unprecedented mechanism of action. Overall, these results support the genomics-driven hypothesis that targeting bacterial essential gene products that are not present in eukaryotic cells can identify novel antibacterial agents.
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Affiliation(s)
- Claude G Lerner
- Abbott Global Pharmaceutical Research and Development, Abbott Park, IL 60064-6098, USA
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27
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Hernick M, Fierke CA. Molecular recognition by Escherichia coli UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase is modulated by bound metal ions. Biochemistry 2007; 45:14573-81. [PMID: 17144651 DOI: 10.1021/bi061625y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The metal-dependent enzyme UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) catalyzes the conversion of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine to UDP-3-O-(R-3-hydroxymyristoyl)glucosamine and acetate. This is the committed step in the biosynthesis of lipid A, and for this reason, LpxC is a target for the development of antibiotics in the treatment of Gram-negative bacterial infections. Here we examine the importance of bound metal ion(s) and fatty acids for molecular recognition of ligands by LpxC. The KDproduct value increases >1000-fold with the loss of the hydroxymyristoyl moiety, indicating that the enhanced catalytic efficiency of substrates containing this acyl group is mainly due to increased binding affinity. New fluorescent binding assays for measuring the affinity of LpxC for fatty acids indicate that myristate binds to LpxC 10-fold less tightly than palmitate and that fatty acid affinity is only modestly dependent on pH. Furthermore, LpxC homologues from different species have similar affinities for fatty acids despite alterations in protein sequence. In contrast, the affinity of LpxC for both product and fatty acids is significantly influenced (< or =40-fold) by changes in the number and identity of metal ions bound to the LpxC active site. Therefore, interactions with these metal ions are critical for molecular recognition of ligands by LpxC and may mimic similar contacts with active site inhibitors. These data indicate that the potency of LpxC inhibitors in vitro can be altered by assay conditions used in screening and/or development of LpxC inhibitors and that the metal ion status of LpxC in vivo will likely influence the effectiveness of LpxC inhibitors as antibiotics.
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Affiliation(s)
- Marcy Hernick
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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28
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Gallagher LA, Ramage E, Jacobs MA, Kaul R, Brittnacher M, Manoil C. A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate. Proc Natl Acad Sci U S A 2007; 104:1009-14. [PMID: 17215359 PMCID: PMC1783355 DOI: 10.1073/pnas.0606713104] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Francisella tularensis, the causative agent of tularemia, is one of the most infectious bacterial pathogens known and is a category A select agent. We created a sequence-defined, near-saturation transposon mutant library of F. tularensis novicida, a subspecies that causes a tularemia-like disease in rodents. The library consists of 16,508 unique insertions, an average of >9 insertions per gene, which is a coverage nearly twice that of the greatest previously achieved for any bacterial species. Insertions were recovered in 84% (1,490) of the predicted genes. To achieve high coverage, it was necessary to construct transposons carrying an endogenous Francisella promoter to drive expression of antibiotic resistance. An analysis of genes lacking (or with few) insertions identified nearly 400 candidate essential genes, most of which are likely to be required for growth on rich medium and which represent potential therapeutic targets. To facilitate genome-scale screening using the mutant collection, we assembled a sublibrary made up of two purified mutants per gene. The library provides a resource for virtually complete identification of genes involved in virulence and other nonessential processes.
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Affiliation(s)
- Larry A. Gallagher
- *Department of Genome Sciences, University of Washington, Campus Box 355065, 1705 NE Pacific Street, Seattle, WA 98195; and
| | - Elizabeth Ramage
- *Department of Genome Sciences, University of Washington, Campus Box 355065, 1705 NE Pacific Street, Seattle, WA 98195; and
| | - Michael A. Jacobs
- Department of Medicine, University of Washington, Campus Box 352145, 1705 NE Pacific Street, Seattle, WA 98195
| | - Rajinder Kaul
- Department of Medicine, University of Washington, Campus Box 352145, 1705 NE Pacific Street, Seattle, WA 98195
| | - Mitchell Brittnacher
- *Department of Genome Sciences, University of Washington, Campus Box 355065, 1705 NE Pacific Street, Seattle, WA 98195; and
| | - Colin Manoil
- *Department of Genome Sciences, University of Washington, Campus Box 355065, 1705 NE Pacific Street, Seattle, WA 98195; and
- To whom correspondence should be addressed. E-mail:
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29
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Rokem JS, Lantz AE, Nielsen J. Systems biology of antibiotic production by microorganisms. Nat Prod Rep 2007; 24:1262-87. [DOI: 10.1039/b617765b] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Predicting essential genes in fungal genomes. Genome Res 2006; 16:1126-35. [PMID: 16899653 PMCID: PMC1557763 DOI: 10.1101/gr.5144106] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Essential genes are required for an organism's viability, and the ability to identify these genes in pathogens is crucial to directed drug development. Predicting essential genes through computational methods is appealing because it circumvents expensive and difficult experimental screens. Most such prediction is based on homology mapping to experimentally verified essential genes in model organisms. We present here a different approach, one that relies exclusively on sequence features of a gene to estimate essentiality and offers a promising way to identify essential genes in unstudied or uncultured organisms. We identified 14 characteristic sequence features potentially associated with essentiality, such as localization signals, codon adaptation, GC content, and overall hydrophobicity. Using the well-characterized baker's yeast Saccharomyces cerevisiae, we employed a simple Bayesian framework to measure the correlation of each of these features with essentiality. We then employed the 14 features to learn the parameters of a machine learning classifier capable of predicting essential genes. We trained our classifier on known essential genes in S. cerevisiae and applied it to the closely related and relatively unstudied yeast Saccharomyces mikatae. We assessed predictive success in two ways: First, we compared all of our predictions with those generated by homology mapping between these two species. Second, we verified a subset of our predictions with eight in vivo knockouts in S. mikatae, and we present here the first experimentally confirmed essential genes in this species.
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Affiliation(s)
- Michael Seringhaus
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Alberto Paccanaro
- Department of Computer Science, Royal Holloway University of London, Egham, TW20 0EX, United Kingdom
- Corresponding author.E-mail ; fax (360) 838-7861
| | - Anthony Borneman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Michael Snyder
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
- Corresponding author.E-mail ; fax (360) 838-7861
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von Nussbaum F, Brands M, Hinzen B, Weigand S, Häbich D. Antibakterielle Naturstoffe in der medizinischen Chemie – Exodus oder Renaissance? Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600350] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Bacterial resistance: a sensitive issue complexity of the challenge and containment strategy in Europe. Drug Resist Updat 2006; 9:123-33. [PMID: 16807066 PMCID: PMC7185659 DOI: 10.1016/j.drup.2006.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Revised: 05/29/2006] [Accepted: 06/01/2006] [Indexed: 12/03/2022]
Abstract
The development of antimicrobial agents has been a key achievement of modern medicine. However, their overuse has led to an increasing incidence of infections due to antibiotic-resistant microorganisms. Quantitative figures on the current economic and health impact of antimicrobial resistance are scant, but it is clearly a growing challenge that requires timely action. That action should be at the educational, ethical, economic and political level. An important first step would be to increase public awareness and willingness to take the necessary measures to curb resistance. Hence, studies are needed that would provide solid, quantitative data on the societal impact of antibiotic resistance. This review discusses the complexity of resistance, identifies its main drivers and proposes measures to contain it on a European scale.
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Prakash Singh M. Rapid test for distinguishing membrane-active antibacterial agents. J Microbiol Methods 2006; 67:125-30. [PMID: 16631264 DOI: 10.1016/j.mimet.2006.03.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 02/09/2006] [Accepted: 03/09/2006] [Indexed: 11/30/2022]
Abstract
In the search for antibacterial agents with a novel mode-of-action (MOA) many targeted cellular and cell-free assays are developed and used to screen chemical and natural product libraries. Frequently, hits identified by the primary screens include compounds with nonspecific activities that can affect the integrity and function of bacterial membrane. For a rapid dereplication of membrane-active compounds, a simple method was established using a commercially available Live/Dead(R) Bacterial Viability Kit. This method utilized two fluorescent nucleic acid stains, SYTO9 (stains all cells green) and propidium iodide (stains cells with damaged membrane red) for the drug-treated bacterial cells. The cells were then either examined visually by fluorescence microscopy or their fluorescence emissions were recorded using a multi-label plate reader set to measure emissions at two different wavelengths. The ratio of green versus red was compared to a standard curve indicating the percentage of live versus dead bacteria. Nine known antibiotics and 14 lead compounds from various antibacterial screens were tested with results consistent with their MOA.
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Affiliation(s)
- Maya Prakash Singh
- Chemical and Screening Sciences, Wyeth Research, 401 N. Middletown Road, Pearl River, NY 10965, USA.
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34
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Pucci MJ. Use of genomics to select antibacterial targets. Biochem Pharmacol 2006; 71:1066-72. [PMID: 16412986 DOI: 10.1016/j.bcp.2005.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 11/29/2005] [Accepted: 12/06/2005] [Indexed: 01/08/2023]
Abstract
The problem of antibiotic resistance has eroded the usefulness of our arsenal of effective antibiotics. There is a need for new strategies to discover and develop new, effective drugs. The advent of the microbial genomics era has provided a wealth of information on a variety of microorganisms. This has allowed the identification and/or validation of a number of gene products that could serve as targets for the discovery of novel antibacterial agents. New genetic techniques and approaches have arisen in an attempt to exploit this newly available genomic data. Both random and targeted gene disruption efforts have proven effective in this process. Many of these methods would have been difficult to accomplish without DNA sequence and bioinformatics analyses. Several targets have been selected to further characterize and screen for inhibitors and one has yielded two clinical candidates.
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Affiliation(s)
- Michael J Pucci
- Achillion Pharmaceuticals, Inc., 300 George Street, New Haven, CT 06511, USA.
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Barrett JF. Overview of anti-infective drug development. CURRENT PROTOCOLS IN PHARMACOLOGY 2006; Chapter 13:Unit13A.1. [PMID: 21953396 DOI: 10.1002/0471141755.ph13a01s31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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36
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Pucci MJ. Overview of antibacterial target selection. CURRENT PROTOCOLS IN PHARMACOLOGY 2006; Chapter 13:Unit13A.2. [PMID: 21953397 DOI: 10.1002/0471141755.ph13a02s31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Michael J Pucci
- Achillion Pharmaceuticals, Inc., New Haven, Connecticut, USA
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37
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Abstract
Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knockouts in rich media. Comparing 55 genomes of Firmicutes and Gamma-proteobacteria to identify the genes which, while persistent among genomes, do not lead to a lethal phenotype when inactivated, we show that the characteristics of persistence, conservation, expression, and location are shared between persistent nonessential (PNE) genes and experimentally essential genes. PNE genes show an overrepresentation of genes related to maintenance and stress response. This outlines the limits of current experimental techniques to define gene essentiality and highlights the essential role of genes implicated in maintenance which, although dispensable for growth, are not dispensable from an evolutionary point of view. Firmicutes and Gamma-proteobacteria are mostly differing in the construction of the cell envelope, DNA replication and proofreading, and RNA degradation. In addition to suggesting functions for persistent genes that had until now resisted identification, we show that these genes have many characters in common with experimentally identified essential genes. They should then be regarded as truly essential genes.
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Affiliation(s)
- Gang Fang
- Unité Génétique des Génomes Bactériens, Institut Pasteur, Paris Cedex, France
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Abstract
Modern chemotherapy has played a major role in our control of tuberculosis. Yet tuberculosis still remains a leading infectious disease worldwide, largely owing to persistence of tubercle bacillus and inadequacy of the current chemotherapy. The increasing emergence of drug-resistant tuberculosis along with the HIV pandemic threatens disease control and highlights both the need to understand how our current drugs work and the need to develop new and more effective drugs. This review provides a brief historical account of tuberculosis drugs, examines the problem of current chemotherapy, discusses the targets of current tuberculosis drugs, focuses on some promising new drug candidates, and proposes a range of novel drug targets for intervention. Finally, this review addresses the problem of conventional drug screens based on inhibition of replicating bacilli and the challenge to develop drugs that target nonreplicating persistent bacilli. A new generation of drugs that target persistent bacilli is needed for more effective treatment of tuberculosis.
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Affiliation(s)
- Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA.
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Han C, Wang Q, Dong L, Sun H, Peng S, Chen J, Yang Y, Yue J, Shen X, Jiang H. Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori. Biochem Biophys Res Commun 2004; 319:1292-8. [PMID: 15194508 DOI: 10.1016/j.bbrc.2004.05.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Indexed: 11/26/2022]
Abstract
Helicobacter pylori is a gram-negative pathogenic bacterium, which is associated with peptic ulcer disease and gastric cancer. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. In bacteria, peptide deformylase (PDF) catalyzes the removal of a formyl group from the N-termini of nascent polypeptides. Due to its essentiality and absence in mammalian cells, PDF has been considered as an attractive target for the discovery of novel antibiotics. In this work, a new PDF gene (def) from H. pylori strain SS1 was cloned, expressed, and purified in Escherichia coli system. Sequence alignment shows that H. pylori PDF (HpPDF) shares about 40% identity to E. coli PDF (EcPDF). The enzymatic properties of HpPDF demonstrate its relatively high activity toward formyl-Met-Ala-Ser, with K(cat) of 3.4s(-1), K(m) of 1.7 mM, and K(cat) / K(m) of 2000M(-1)s(-1). HpPDF enzyme appears to be fully active at pH between 8.0 and 9.0, and temperature 50 degrees C. The enzyme activity of Co(2+)-containing HpPDF is apparently higher than that of Zn(2+)-containing HpPDF. This present work thereby supplies a potential platform that facilitates the discovery of novel HpPDF inhibitors and further of possible antimicrobial agents against H. pylori.
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Affiliation(s)
- Cong Han
- Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 201203, China
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O'Brien TP. Management of bacterial keratitis: beyond exorcism towards consideration of organism and host factors. Eye (Lond) 2004; 17:957-74. [PMID: 14631403 DOI: 10.1038/sj.eye.6700635] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- T P O'Brien
- The Wilmer Ophthalmological Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Abstract
Although bioinformatics achieved prominence because of its central role in genome data storage, management and analysis, its focus has shifted as the life sciences exploit these data. In pharmacology, genomic, transcriptomic and proteomic data are being used in the quest for drugs that fulfill unmet medical needs, are disease modifying or curative and are more effective and safer than current drugs. Bioinformatics is used in drug target identification and validation and in the development of biomarkers and toxicogenomic and pharmacogenomic tools to maximize the therapeutic benefit of drugs. Now that the 'parts list' of cellular signalling pathways is available, integrated computational and experimental programmes are being developed, with the goal of enabling in silico pharmacology by linking the genome, transcriptome and proteome to cellular pathophysiology.
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Affiliation(s)
- Paul A Whittaker
- Novartis Respiratory Research Centre, Wimblehurst Road, Horsham, West Sussex RH12 5AB, UK.
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Abstract
To address the worsening problem of antibiotic-resistant bacteria there is an urgent need to develop new antibiotics. Comparative genomics and molecular genetics are being applied to produce lists of essential new targets for compound screening programmes. Combinatorial chemistry and structural biology are being applied to rapidly explore and optimize the interactions between lead compounds and their biological targets. Several compounds that have been identified from target-based screens are now in development, but technical and economic constraints might result in a trickle, rather than a flood, of new antibiotics onto the market in the near future.
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Affiliation(s)
- Diarmaid Hughes
- Department of Cell and Molecular Biology, Box 596, The Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden.
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Abstract
The availability of genome sequences is revolutionizing the field of microbiology. Genetic methods are being modified to facilitate rapid analysis at a genome-wide level and are blossoming for human pathogens that were previously considered intractable. This revolution coincided with a growing concern about the emergence of microbial drug resistance, compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of the new technologies, combined with many genetic strategies, has changed the way that researchers approach antibacterial drug discovery.
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Affiliation(s)
- Lynn Miesel
- Department of Antimicrobial Therapy, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033-0530, USA.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2447381 DOI: 10.1002/cfg.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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