Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function

The efficacy of antibiotics to treat bacterial infections declines rapidly due to antibiotic resistance. This problem has stimulated the development of novel antibiotics, but most attempts have failed. Consequently, the idea of mining uncharacterized genes of pathogens to identify potential targets for entirely new classes of antibiotics was proposed. Without knowing the biochemical function of a protein, it is difficult to validate its potential for drug targeting; therefore, the functional characterization of bacterial proteins of unknown function must be accelerated. Here, we present a paradigm for comprehensively predicting the biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied to the set of 2103 P. aeruginosa proteins encoded by hypothetical genes. The >21000 homology modelling results obtained and available biological and biochemical information about several thousand templates were scrutinized to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning one or often multiple putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P. aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets that participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved in other WHO priority pathogens but not in humans; therefore, they represent high-potential targets for preclinical studies. These and many more biochemical functions assigned to uncharacterized proteins of P. aeruginosa, made available as PaPUF database, may guide the design of experimental screening of inhibitors, which is a crucial step towards the validation of the highest-potential targets for the development of novel drugs against P. aeruginosa and other high-priority pathogens.

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Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function

10.1101/2021.06.15.448521 ◽

2021 ◽

Author(s):

Nikolina Babic ◽

Filip Kovacic

Keyword(s):

Antibiotic Resistance ◽

Unknown Function ◽

Drug Targets ◽

Bacterial Infections ◽

Homology Modelling ◽

Host Recognition ◽

Large Set ◽

Human Pathogens ◽

Functional Characterisation ◽

Hypothetical Genes

Efficacies of antibiotics to treat bacterial infections rapidly decline due to antibiotic resistance. This stimulated the development of novel antibiotics, but most attempts failed. As a response, the idea of mining uncharacterised genes of pathogens to identify potential targets for entirely new classes of antibiotics raised. Without knowing the biochemical function of a protein it is difficult to validate its potential for drug targeting; therefore progress in the functional characterisation of bacterial proteins of an unknown function must be accelerated. Here we present a paradigm for comprehensively predicting biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens, to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied on the set of 2103 P. aeruginosa proteins encoded by hypothetical genes. Obtained >21000 homology modelling results and available biological and biochemical information about several thousand templates was scrutinised to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning, one or often multiple, putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P. aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets which participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved among other WHO priority pathogens but not in humans, therefore they represent high-potential targets for pre-clinical studies. These and many more biochemical functions assigned to uncharacterised proteins of P. aeruginosa, available as PaPUF database may guide the design of experimental screening of inhibitors which is a crucial step toward validation of the most potential targets for the development of novel drugs against P. aeruginosa and other high-priority pathogens.

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Sprouts as functional food- an approach towards the identification of natural antibiotic resistance breakers

Journal of Drug Delivery and Therapeutics ◽

10.22270/jddt.v9i1-s.2240 ◽

2019 ◽

Vol 9 (1-s) ◽

pp. 23-35

Author(s):

Valli. S Abiraami ◽

S. Uma Gowrie

Keyword(s):

Antibiotic Resistance ◽

Bioactive Compounds ◽

Bacterial Infections ◽

Shigella Flexneri ◽

Health Concern ◽

Human Pathogens ◽

Topoisomerase Iv ◽

In Silico Docking ◽

Horse Gram ◽

Macrotyloma Uniflorum

Antibiotics are medicines used to prevent and treat bacterial infections. Antibiotic resistance occurs when bacteria change in response to the use of these medicines. Investigation studies related to discovery of novel antibiotics to deal with antibacterial resistance from natural edible food products have been one of the significant research interests in recent years. The main objective of the study is to identify the bioactive compounds having the natural antibiotic resistance breaking property, by giving scientific validation to the existing bioactive compounds present in the sprouts and recommending the horse gram and mixed sprouts as a natural dietary supplement, a measure for the management of the disease, Shigellosis. Qualitative screening of the phytoconstituents (using different solvent extracts) and quantitative analysis of the primary and secondary phytoconstituents were carried out in methanol and aqueous extracts of the horse gram and mixed sprouts (fresh and dried) using standard protocols in two different samples- horse gram sprouts (Macrotyloma uniflorum (Lam.) Verdc.) and mixed sprouts of combination (Cicer arietinum L. (Chick pea), Macrotyloma uniflorum (Lam.) Verdc. (horse gram) and Vigna radiata (L.). Antibacterial activity of both the samples against human pathogens namely Staphylococcus aureus, Escherichia coli, Salmonella typhi, Klebsiella pneumoniae and Shigella flexneri were studied. In horse gram and mixed sprouts, maximum zone of inhibitions were shown by Shigella flexneri, a food and water borne pathogen leading to outbreaks of Shigellosis, a major public health concern. Ciprofloxacin is a broad spectrum of antimicrobial carboxyfluoroquinolones. The bactericidal action of Ciprofloxacin is by inhibiting DNA gyrase, a type II topoisomerase and topoisomerase IV, which are required for bacterial DNA replication. Phytochemical characterization (FTIR and GC-MS) and antibacterial studies proved the presence of essential phytoconstituents like terpenoids, fatty acids, proteins, carbohydrates and vitamins. Several bioactive compounds obtained from GC-MS analysis were screened for Ciprofloxacin antibiotic resistance. The specific phytoconstituents, DL-Proline from horse gram sprouts and Geranyl geraniol from mixed sprouts was tend to act as novel antibiotic resistance breakers which was proved through in silico docking.

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Rapid resistome mapping using nanopore sequencing

10.1101/067652 ◽

2016 ◽

Cited By ~ 1

Author(s):

Eric van der Helm ◽

Lejla Imamovic ◽

Mostafa M Hashim Ellabaan ◽

Willem van Schaik ◽

Anna Koza ◽

...

Keyword(s):

Antibiotic Resistance ◽

Antibiotic Treatment ◽

Bacterial Infections ◽

Antibiotic Resistance Genes ◽

Modern Medicine ◽

Nanopore Sequencing ◽

Human Pathogens ◽

Major Threat ◽

Gene Acquisition ◽

Collateral Effects

AbstractThe emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by the composition of the gut resistome either by enabling resistance gene acquisition of infecting pathogens or by modulating the collateral effects of antibiotic treatment on the commensal microbiome. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU patient. The accuracy of the poreFUME pipeline is >97 % sufficient for the reliable annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.

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The gut microbiota resistome provides development of drug resistance in causative agents of human infectious diseases

Nauchno-prakticheskii zhurnal «Patogenez» ◽

10.25557/gm.2017.3.8494 ◽

2017 ◽

pp. 20-32 ◽

Cited By ~ 1

Author(s):

Е.Н. Ильина ◽

Е.И. Олехнович ◽

А.В. Павленко

Keyword(s):

Drug Resistance ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Integrated Approach ◽

Modern Medicine ◽

Pathogenic Microorganisms ◽

Human Pathogens ◽

Potential Source ◽

Causative Agents ◽

Bacterial Genes

С течением времени подходы к изучению резистентности к антибиотикам трансформировались от сосредоточения на выделенных в виде чистой культуры патогенных микроорганизмах к исследованию резистентности на уровне микробных сообществ, составляющих биотопы человека и окружающей среды. По мере того, как продвигается изучение устойчивости к антибиотикам, возникает необходимость использования комплексного подхода для улучшения информирования мирового сообщества о наблюдаемых тенденциях в этой области. Все более очевидным становится то, что, хотя не все гены резистентности могут географически и филогенетически распространяться, угроза, которую они представляют, действительно серьезная и требует комплексных междисциплинарных исследований. В настоящее время резистентность к антибиотикам среди патогенов человека стала основной угрозой в современной медицине, и существует значительный интерес к определению ниши, в которых бактерии могут получить гены антибиотикорезистентности, и механизмов их передачи. В данном обзоре мы рассматриваем проблемы, возникшие на фоне широкого использования человечеством антибактериальных препаратов, в свете формирования микрофлорой кишечника резервуара генов резистентности. Over the time, studies of antibiotic resistance have transformed from focusing on pathogenic microorganisms isolated as a pure culture to analysis of resistance at the level of microbial communities that constitute human and environmental biotopes. Advancing studies of antibiotic resistance require an integrated approach to enhance availability of information about observed tendencies in this field to the global community. It becomes increasingly obvious that, even though not all resistance genes can geographically and phylogenetically spread, the threat they pose is indeed serious and requires complex interdisciplinary research. Currently, the antibiotic resistance of human pathogens has become a challenge to modern medicine, which is now focusing on determining a potential source for bacterial genes of drug resistance and mechanisms for the gene transmission. In this review, we discussed problems generated by the widespread use of antibacterial drugs in the light of forming a reservoir of resistance genes by gut microflora.

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Identification of New Drug Targets in Multi-Drug Resistant Bacterial Infections

10.21236/ada610780 ◽

2013 ◽

Author(s):

Andrew M. Gulick ◽

Thomas A. Russo ◽

L. W. Schultz ◽

Timothy C. Umland

Keyword(s):

Drug Targets ◽

Bacterial Infections ◽

Drug Resistant ◽

New Drug

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Bacteriophages as drivers of bacterial virulence and their potential for biotechnological exploitation

FEMS Microbiology Reviews ◽

10.1093/femsre/fuaa041 ◽

2020 ◽

Author(s):

Kaat Schroven ◽

Abram Aertsen ◽

Rob Lavigne

Keyword(s):

Small Molecules ◽

Bacterial Infections ◽

Bacterial Virulence ◽

Arms Race ◽

Control Mechanisms ◽

Human Pathogens ◽

Vaccine Candidates ◽

Cargo Proteins ◽

Genes Encoding ◽

Mutualistic Relationship

ABSTRACT Bacteria-infecting viruses (phages) and their hosts maintain an ancient and complex relationship. Bacterial predation by lytic phages drives an ongoing phage-host arms race, whereas temperate phages initiate mutualistic relationships with their hosts upon lysogenization as prophages. In human pathogens, these prophages impact bacterial virulence in distinct ways: by secretion of phage-encoded toxins, modulation of the bacterial envelope, mediation of bacterial infectivity and the control of bacterial cell regulation. This review builds the argument that virulence-influencing prophages hold extensive, unexplored potential for biotechnology. More specifically, it highlights the development potential of novel therapies against infectious diseases, to address the current antibiotic resistance crisis. First, designer bacteriophages may serve to deliver genes encoding cargo proteins which repress bacterial virulence. Secondly, one may develop small molecules mimicking phage-derived proteins targeting central regulators of bacterial virulence. Thirdly, bacteria equipped with phage-derived synthetic circuits which modulate key virulence factors could serve as vaccine candidates to prevent bacterial infections. The development and exploitation of such antibacterial strategies will depend on the discovery of other prophage-derived, virulence control mechanisms and, more generally, on the dissection of the mutualistic relationship between temperate phages and bacteria, as well as on continuing developments in the synthetic biology field.

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Phage-Encoded Endolysins

Antibiotics ◽

10.3390/antibiotics10020124 ◽

2021 ◽

Vol 10 (2) ◽

pp. 124

Author(s):

Fatma Abdelrahman ◽

Maheswaran Easwaran ◽

Oluwasegun I. Daramola ◽

Samar Ragab ◽

Stephanie Lynch ◽

...

Keyword(s):

Clinical Trials ◽

Cell Wall ◽

Antibiotic Resistance ◽

Bacterial Infections ◽

Therapeutic Strategies ◽

Therapeutic Application ◽

Significant Evidence ◽

Crucial Information

Due to the global emergence of antibiotic resistance, there has been an increase in research surrounding endolysins as an alternative therapeutic. Endolysins are phage-encoded enzymes, utilized by mature phage virions to hydrolyze the cell wall from within. There is significant evidence that proves the ability of endolysins to degrade the peptidoglycan externally without the assistance of phage. Thus, their incorporation in therapeutic strategies has opened new options for therapeutic application against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology sectors. While endolysins show promising results within the laboratory, it is important to document their resistance, safety, and immunogenicity for in-vivo application. This review aims to provide new insights into the synergy between endolysins and antibiotics, as well as the formulation of endolysins. Thus, it provides crucial information for clinical trials involving endolysins.

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Silencing Antibiotic Resistance with Antisense Oligonucleotides

Biomedicines ◽

10.3390/biomedicines9040416 ◽

2021 ◽

Vol 9 (4) ◽

pp. 416

Author(s):

Saumya Jani ◽

Maria Soledad Ramirez ◽

Marcelo E. Tolmasky

Keyword(s):

Antibiotic Resistance ◽

Nucleic Acids ◽

Antisense Oligonucleotides ◽

Bacterial Infections ◽

Genetic Disorders ◽

Antibiotic Resistance Genes ◽

Short Review ◽

Rnase H ◽

Biological Processes ◽

Locked Nucleic Acids

Antisense technologies consist of the utilization of oligonucleotides or oligonucleotide analogs to interfere with undesirable biological processes, commonly through inhibition of expression of selected genes. This field holds a lot of promise for the treatment of a very diverse group of diseases including viral and bacterial infections, genetic disorders, and cancer. To date, drugs approved for utilization in clinics or in clinical trials target diseases other than bacterial infections. Although several groups and companies are working on different strategies, the application of antisense technologies to prokaryotes still lags with respect to those that target other human diseases. In those cases where the focus is on bacterial pathogens, a subset of the research is dedicated to produce antisense compounds that silence or reduce expression of antibiotic resistance genes. Therefore, these compounds will be adjuvants administered with the antibiotic to which they reduce resistance levels. A varied group of oligonucleotide analogs like phosphorothioate or phosphorodiamidate morpholino residues, as well as peptide nucleic acids, locked nucleic acids and bridge nucleic acids, the latter two in gapmer configuration, have been utilized to reduce resistance levels. The major mechanisms of inhibition include eliciting cleavage of the target mRNA by the host’s RNase H or RNase P, and steric hindrance. The different approaches targeting resistance to β-lactams include carbapenems, aminoglycosides, chloramphenicol, macrolides, and fluoroquinolones. The purpose of this short review is to summarize the attempts to develop antisense compounds that inhibit expression of resistance to antibiotics.

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Structures of the surface exposed proteins of Gram positive bacteria

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314095679 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C432-C432

Author(s):

George Minasov ◽

Salvatore Nocadello ◽

Ekaterina Filippova ◽

Andrei Halavaty ◽

Wayne Anderson

Keyword(s):

Cell Wall ◽

Infectious Diseases ◽

Bacillus Anthracis ◽

Structural Genomics ◽

Drug Targets ◽

Morphological Changes ◽

Target Selection ◽

Surface Proteins ◽

Human Pathogens ◽

Gram Positive

The Center for Structural Genomics for Infectious Diseases (CSGID) applies structural genomics approaches to biomedically important proteins from human pathogens. It also provides the infectious disease community with a high throughput pipeline for structure determination that carries out all steps of the process, from target selection through structure deposition. Target proteins include drug targets, essential enzymes, virulence factors and vaccine candidates. The CSGID has deposited over 680 structures in the Protein Data Bank. The proteins that are exposed on the surface of Gram positive bacterial pathogens (including Staphylococcus aureus, Bacillus anthracis, Listeria monocytogenes, Streptococcus species and Clostridium species) have been one focus area for the CSGID. So far, the structures of more than 55 of these proteins have been determined. The surface proteins are important in the interactions between the pathogen and its host, but many of them are as yet functionally uncharacterized. Among the examples that will be presented is the Bacillus anthracis SpoIID protein. SpoIID is part of a coordinated cell wall degradation machine that is essential for sporulation and the morphological changes involved. It represents a new family of lytic transglycosylases that degrade the glycan strands of the peptidoglycan cell wall. The two active site clefts in the dimeric enzyme include residues from both subunits, suggesting that the dimer is required for activity. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contracts No. HHSN272200700058C and HHSN272201200026C.

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Proteomic analysis of the colistin-resistant E. coli clinical isolate: Explorations of the resistome

Protein and Peptide Letters ◽

10.2174/0929866528666211129095001 ◽

2021 ◽

Vol 28 ◽

Author(s):

Divakar Sharma ◽

Manisha Aswal ◽

Nayeem Ahmad ◽

Manish Kumar ◽

Asad U Khan

Keyword(s):

Clinical Isolate ◽

Protein Interaction ◽

Functional Annotation ◽

Drug Targets ◽

Bacterial Infections ◽

Sugar Metabolism ◽

Colistin Resistance ◽

Phosphotransferase System ◽

E Coli ◽

Protein Protein Interaction

Background: Antimicrobial resistance is a worldwide problem after the emergence of colistin resistance since it was the last option left to treat carbapenemase-resistant bacterial infections. The mcr gene and its variants are one of the causes for colistin resistance. Besides mcr genes, some other intrinsic genes are also involved in colistin resistance but still need to be explored. Objective: The aim of this study was to investigate differential proteins expression of colistin-resistant E. coli clinical isolate and to understand their interactive partners as future drug targets. Methods: In this study, we have employed the whole proteome analysis through LC-MS/MS. The advance proteomics tools were used to find differentially expressed proteins in the colistin-resistant Escherichia coli clinical isolate compared to susceptible isolate. Gene ontology and STRING were used for functional annotation and protein-protein interaction networks, respectively. Results: LC-MS/MS analysis showed overexpression of 47 proteins and underexpression of 74 proteins in colistin-resistant E. coli. These proteins belong to DNA replication, transcription and translational process; defense and stress related proteins; proteins of phosphoenol pyruvate phosphotransferase system (PTS) and sugar metabolism. Functional annotation and protein-protein interaction showed translational and cellular metabolic process, sugar metabolism and metabolite interconversion. Conclusion: We conclude that these protein targets and their pathways might be used to develop novel therapeutics against colistin-resistant infections. These proteins could unveil the mechanism of colistin resistance.

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