scholarly journals Intracellular Expression of Peptide Fusions for Demonstration of Protein Essentiality in Bacteria

2003 ◽  
Vol 47 (9) ◽  
pp. 2875-2881 ◽  
Author(s):  
R. Edward Benson ◽  
Elizabeth B. Gottlin ◽  
Dale J. Christensen ◽  
Paul T. Hamilton
Keyword(s):  
Cell Growth ◽  
Phage Display ◽  
Drug Targets ◽  
Antimicrobial Agents ◽  
Specific Interaction ◽  
Screening Tools ◽  
Peptide Sequence ◽  
Essential Proteins ◽  
Intracellular Expression ◽  
Protein Essentiality

ABSTRACT We describe a “protein knockout” technique that can be used to identify essential proteins in bacteria. This technique uses phage display to select peptides that bind specifically to purified target proteins. The peptides are expressed intracellularly and cause inhibition of growth when the protein is essential. In this study, peptides that each specifically bind to one of seven essential proteins were identified by phage display and then expressed as fusions to glutathione S-transferase in Escherichia coli. Expression of peptide fusions directed against E. coli DnaN, LpxA, RpoD, ProRS, SecA, GyrA, and Era each dramatically inhibited cell growth. Under the same conditions, a fusion with a randomized peptide sequence did not inhibit cell growth. In growth-inhibited cells, inhibition could be relieved by concurrent overexpression of the relevant target protein but not by coexpression of an irrelevant protein, indicating that growth inhibition was due to a specific interaction of the expressed peptide with its target. The protein knockout technique can be used to assess the essentiality of genes of unknown function emerging from the sequencing of microbial genomes. This technique can also be used to validate proteins as drug targets, and their corresponding peptides as screening tools, for discovery of new antimicrobial agents.

scholarly journals Antibacterial Activities of Rhodamine B-Conjugated Gelsolin-Derived Peptides Compared to Those of the Antimicrobial Peptides Cathelicidin LL37, Magainin II, and Melittin

2004 ◽  
Vol 48 (5) ◽  
pp. 1526-1533 ◽  
Author(s):  
Robert Bucki ◽  
Jennifer J. Pastore ◽  
Paramjeet Randhawa ◽  
Rolands Vegners ◽  
Daniel J. Weiner ◽  
...  
Keyword(s):  
Rhodamine B ◽  
Antimicrobial Agents ◽  
Specific Binding ◽  
Specific Interaction ◽  
Phospholipid Composition ◽  
Antibacterial Properties ◽  
Peptide Sequence ◽  
Resistant Bacteria ◽  
Bacterial Killing ◽  
Bacterial Proteins

ABSTRACT The growing number of antibiotic-resistant bacteria necessitates the search for new antimicrobial agents and the principles by which they work. We report that cell membrane-permeant rhodamine B (RhB)-conjugated peptides based on the phosphatidylinositol-4,5-bisphosphate binding site of gelsolin can kill the gram-negative organisms Escherichia coli and Pseudomonas aeruginosa and the gram-positive organism Streptococcus pneumoniae. RhB linkage to the QRLFQVKGRR sequence in gelsolin was essential for the antibacterial function, since the unconjugated peptide had no effect on the bacteria tested. Because RhB-QRLFQVKGRR (also termed PBP10), its scrambled sequence (RhB-FRVKLKQGQR), and PBP10 synthesized from d-isomer amino acids show similar antibacterial properties, the physical and chemical properties of these derivatives appear to be more important than specific peptide folding for their antibacterial functions. The similar activities of PBP10 and all-d-amino-acid PBP10 also indicate that a specific interaction between RhB derivatives and bacterial proteins is unlikely to be involved in the bacterial killing function of PBP10. By using a phospholipid monolayer system, we found a positive correlation between the antibacterial function of PBP10, as well as some naturally occurring antibacterial peptides, and the intrinsic surface pressure activity at the hydrophobic-hydrophilic interface. Surprisingly, we observed little or no dependence of the insertion of these peptides into lipid monolayers on the phospholipid composition. These studies show that an effective antimicrobial agent can be produced from a peptide sequence with specificity to a phospholipid not found in bacteria, and comparisons with other antimicrobial agents suggest that the surface activities of these peptides are more important than specific binding to bacterial proteins or lipids for their antimicrobial functions.

A Survey on Computational Methods for Essential Proteins and Genes Prediction

2019 ◽  
Vol 14 (3) ◽  
pp. 211-225 ◽  
Author(s):  
Ming Fang ◽  
Xiujuan Lei ◽  
Ling Guo
Keyword(s):  
Computational Methods ◽  
Drug Targets ◽  
Disease Genes ◽  
Essential Proteins ◽  
Experimental Identification ◽  
Cellular Life ◽  
Different Types ◽  
The Stability ◽  
Human Disease Genes ◽  
Biology Research

Background: Essential proteins play important roles in the survival or reproduction of an organism and support the stability of the system. Essential proteins are the minimum set of proteins absolutely required to maintain a living cell. The identification of essential proteins is a very important topic not only for a better comprehension of the minimal requirements for cellular life, but also for a more efficient discovery of the human disease genes and drug targets. Traditionally, as the experimental identification of essential proteins is complex, it usually requires great time and expense. With the cumulation of high-throughput experimental data, many computational methods that make useful complements to experimental methods have been proposed to identify essential proteins. In addition, the ability to rapidly and precisely identify essential proteins is of great significance for discovering disease genes and drug design, and has great potential for applications in basic and synthetic biology research. Objective: The aim of this paper is to provide a review on the identification of essential proteins and genes focusing on the current developments of different types of computational methods, point out some progress and limitations of existing methods, and the challenges and directions for further research are discussed.

scholarly journals DGAT1 is a lipid metabolism oncoprotein that enables cancer cells to accumulate fatty acid while avoiding lipotoxicity

2020 ◽  
Author(s):  
Daniel J. Wilcock ◽  
Andrew P. Badrock ◽  
Rhys Owen ◽  
Melissa Guerin ◽  
Andrew D. Southam ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Cell Growth ◽  
Cancer Cells ◽  
Melanoma Cell ◽  
Drug Targets ◽  
Lipid Peroxides ◽  
Acid Oxidation ◽  
Growth Factor Signaling ◽  
Bona Fide

ABSTRACTDysregulated cellular metabolism is a hallmark of cancer. As yet, few druggable oncoproteins directly responsible for this hallmark have been identified. Increased fatty acid acquisition allows cancer cells to meet their membrane biogenesis, ATP, and signaling needs. Excess fatty acids suppress growth factor signaling and cause oxidative stress in non-transformed cells, but surprisingly not in cancer cells. Molecules underlying this cancer adaptation may provide new drug targets. Here, we identify Diacylglycerol O-acyltransferase 1 (DGAT1), an enzyme integral to triacylglyceride synthesis and lipid droplet formation, as a frequently up-regulated oncoprotein allowing cancer cells to tolerate excess fatty acids. DGAT1 over-expression alone induced melanoma in zebrafish melanocytes, and co-operated with oncogenic BRAF or NRAS for more rapid melanoma formation. Mechanistically, DGAT1 stimulated melanoma cell growth through sustaining mTOR kinase–S6 kinase signaling and suppressed cell death by tempering fatty acid oxidation, thereby preventing accumulation of reactive oxygen species including lipid peroxides.SIGNIFICANCEWe show that DGAT1 is a bona fide oncoprotein capable of inducing melanoma formation and co-operating with other known drivers of melanoma. DGAT1 facilitates enhanced fatty acid acquisition by melanoma cells through suppressing lipototoxicity. DGAT1 is also critical for maintaining S6K activity required for melanoma cell growth.

scholarly journals QSYP Peptide Sequence Is Selected from Phage Display Libraries by Bovine IgG Contaminants in Monoclonal Antibody Preparations

BioTechniques ◽  
2003 ◽  
Vol 34 (1) ◽  
pp. 132-141 ◽  
Author(s):  
J.M. Jacobs ◽  
B.W. Bailey ◽  
J.B. Burritt ◽  
S.G. Morrison ◽  
R.P. Morrison ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Phage Display ◽  
Peptide Sequence ◽  
Phage Display Libraries ◽  
Antibody Preparations

scholarly journals Blocking the Trigger: Inhibition of the Initiation of Bacterial Chromosome Replication as an Antimicrobial Strategy

Antibiotics ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 111
Author(s):  
Julia E. Grimwade ◽  
Alan C. Leonard
Keyword(s):  
Drug Targets ◽  
Antimicrobial Agents ◽  
Current Knowledge ◽  
Chromosome Replication ◽  
Bacterial Chromosome ◽  
Resistant Bacteria ◽  
Bacterial Cells ◽  
Drug Resistant Bacteria ◽  
New Antibiotics ◽  
Novel Drug

All bacterial cells must duplicate their genomes prior to dividing into two identical daughter cells. Chromosome replication is triggered when a nucleoprotein complex, termed the orisome, assembles, unwinds the duplex DNA, and recruits the proteins required to establish new replication forks. Obviously, the initiation of chromosome replication is essential to bacterial reproduction, but this process is not inhibited by any of the currently-used antimicrobial agents. Given the urgent need for new antibiotics to combat drug-resistant bacteria, it is logical to evaluate whether or not unexploited bacterial processes, such as orisome assembly, should be more closely examined for sources of novel drug targets. This review will summarize current knowledge about the proteins required for bacterial chromosome initiation, as well as how orisomes assemble and are regulated. Based upon this information, we discuss current efforts and potential strategies and challenges for inhibiting this initiation pharmacologically.

scholarly journals Application of the Subtractive Genomics and Molecular Docking Analysis for the Identification of Novel Putative Drug Targets against Salmonella enterica subsp. enterica serovar Poona

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Tanvir Hossain ◽  
Mohammad Kamruzzaman ◽  
Talita Zahin Choudhury ◽  
Hamida Nooreen Mahmood ◽  
A. H. M. Nurun Nabi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Salmonella Enterica ◽  
Drug Targets ◽  
Subcellular Location ◽  
Essential Genes ◽  
Scoring Functions ◽  
Essential Proteins ◽  
Cellular Processes ◽  
Subtractive Genomics ◽  
Resistance Patterns

The emergence of novel pathogenic strains with increased antibacterial resistance patterns poses a significant threat to the management of infectious diseases. In this study, we aimed at utilizing the subtractive genomic approach to identify novel drug targets against Salmonella enterica subsp. enterica serovar Poona strain ATCC BAA-1673. We employed in silico bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted proteome was further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We carried out metabolic pathway and subcellular location analysis of the essential proteins of the pathogen to elucidate the involvement of these proteins in important cellular processes. We found 52 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we investigated these proteins in the DrugBank databases and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. Molecular docking analyses of the novel druggable targets with the drugs were carried out by AutoDock Vina option based on scoring functions. The results showed promising candidates for novel drugs against Salmonella infections.

scholarly journals CYP51 as drug targets for fungi and protozoan parasites: past, present and future

Parasitology ◽  
2018 ◽  
Vol 145 (14) ◽  
pp. 1820-1836 ◽  
Author(s):  
Galina I. Lepesheva ◽  
Laura Friggeri ◽  
Michael R. Waterman
Keyword(s):  
Cell Growth ◽  
Drug Targets ◽  
Mortality Rates ◽  
Phenotypic Screening ◽  
Protozoan Parasites ◽  
First Line ◽  
Fungal Cell ◽  
History Of ◽  
Actual Target ◽  
Human Infections

AbstractThe efficiency of treatment of human infections with the unicellular eukaryotic pathogens such as fungi and protozoa remains deeply unsatisfactory. For example, the mortality rates from nosocomial fungemia in critically ill, immunosuppressed or post-cancer patients often exceed 50%. A set of six systemic clinical azoles [sterol 14α-demethylase (CYP51) inhibitors] represents the first-line antifungal treatment. All these drugs were discovered empirically, by monitoring their effects on fungal cell growth, though it had been proven that they kill fungal cells by blocking the biosynthesis of ergosterol in fungi at the stage of 14α-demethylation of the sterol nucleus. This review briefs the history of antifungal azoles, outlines the situation with the current clinical azole-based drugs, describes the attempts of their repurposing for treatment of human infections with the protozoan parasites that, similar to fungi, also produce endogenous sterols, and discusses the most recently acquired knowledge on the CYP51 structure/function and inhibition. It is our belief that this information should be helpful in shifting from the traditional phenotypic screening to the actual target-driven drug discovery paradigm, which will rationalize and substantially accelerate the development of new, more efficient and pathogen-oriented CYP51 inhibitors.

Isolation of Peptide Ligands that Inhibit Glutamate Racemase Activity from a Random Phage Display Library

2000 ◽  
Vol 5 (6) ◽  
pp. 435-440 ◽  
Author(s):  
Woo-Chang Kim ◽  
Hae-Ik Rhee ◽  
Boo-Kil Park ◽  
Kyoung-Ho Suk ◽  
Sang-Hoon Cha
Keyword(s):  
Cell Wall ◽  
Phage Display ◽  
Antibacterial Agents ◽  
Bacterial Resistance ◽  
Phage Display Library ◽  
Peptide Sequence ◽  
Membrane Function ◽  
Glutamate Racemase ◽  
Positive Phage

Several new antibacterial agents are currently being developed in response to the emergence of bacterial resistance to existing antibiotic substances. The new agents include compounds that interfere with bacterial membrane function. The peptidoglycan component of the bacterial cell wall is synthesized by glutamate racemase, and this enzyme is responsible for the biosynthesis of d-glutamate, which is an essential component of cell wall peptidoglycan. In this study, we screened a phage display library expressing random dodecapeptides on the surface of bacteriophage against an Escherichia coli glutamate racemase, and isolated specific peptide sequences that bind to the enzyme. Twenty-seven positive phage clones were analyzed, and seven different peptide sequences were obtained. Among them, the peptide sequence His-Pro-Trp-His-Lys-Lys-His-Pro-Asp-Arg-Lys-Thr was found most frequently, suggesting that this peptide might have the highest affinity to glutamate racemase. The positive phage clones and HPWHKKHPDRKT synthetic peptide were able to inhibit glutamate racemase activity in vitro, implying that our peptide inhibitors may be utilized for the molecular design of new potential antibacterial agents targeting cell wall synthesis.

scholarly journals Mapping the substrate specificity of the Plasmodium M1 and M17 aminopeptidases.

2021 ◽  
Author(s):  
Tess R Malcolm ◽  
Karolina W. Swiderska ◽  
Brooke K Hayes ◽  
Chaille T Webb ◽  
Marcin Drag ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Drug Targets ◽  
Protein Production ◽  
Turnover Rate ◽  
Plasmodium Species ◽  
Peptide Sequence ◽  
Sequence Specificity ◽  
Model Species ◽  
Hydrophobic Residues ◽  
Digestion Process

During malarial infection, Plasmodium parasites digest human hemoglobin to obtain free amino acids for protein production and maintenance of osmotic pressure. The Plasmodium M1 and M17 aminopeptidases are both postulated to have an essential role in the terminal stages of the hemoglobin digestion process and are validated drug targets for the design of new dual-target anti-malarial compounds. In this study, we profiled the substrate specificity fingerprints and kinetic behaviors of M1 and M17 aminopeptidases from Plasmodium falciparum and Plasmodium vivax, and the mouse model species, Plasmodium berghei. We found that although the Plasmodium M1 aminopeptidases share a largely similar, broad specificity at the P1 position, the P. falciparum M1 displays the greatest diversity in specificity and P. berghei M1 showing a preference for charged P1 residues. In contrast, the Plasmodium M17 aminopeptidases share a highly conserved preference for hydrophobic residues at the P1 position. The aminopeptidases also demonstrated intra-peptide sequence specificity, particularly the M1 aminopeptidases, which showed a definitive preference for peptides with fewer negatively charged intrapeptide residues. Overall, the P. vivax and P. berghei enzymes had a faster substrate turnover rate than the P. falciparum enzymes, which we postulate is due to subtle differences in structural dynamicity. Together, these results build a kinetic profile that allows us to better understand the catalytic nuances of the M1 and M17 aminopeptidases from different Plasmodium species.

scholarly journals Mapping the substrate sequence and length of the Plasmodium M1 and M17 aminopeptidases

2020 ◽  
Author(s):  
Tess R Malcolm ◽  
Karolina W. Swiderska ◽  
Brooke K Hayes ◽  
Marcin Drag ◽  
Nyssa Drinkwater ◽  
...  
Keyword(s):  
Drug Targets ◽  
Protein Production ◽  
Behavioral Responses ◽  
Peptide Sequence ◽  
Sequence Specificity ◽  
Model Species ◽  
Hydrophobic Residues ◽  
Digestion Process ◽  
Malarial Infection ◽  
Peptide Length

AbstractDuring malarial infection, Plasmodium parasites digest human hemoglobin to obtain free amino acids for protein production and maintenance of osmotic pressure. The Plasmodium M1 and M17 aminopeptidases are both postulated to have an essential role in the terminal stages of the hemoglobin digestion process and are validated drug targets for the design of new dualtarget anti-malarial compounds. In this study, we profiled the substrate specificity fingerprints and kinetic behaviors of M1 and M17 aminopeptidases from Plasmodium falciparum and Plasmodium vivax, and the mouse model species, Plasmodium berghei. We found that although the Plasmodium M1 aminopeptidases share a largely similar, broad specificity at the P1 position, the P. falciparum M1 displays the greatest diversity in specificity and P. berghei M1 showing a preference for charged P1 residues. In contrast, the Plasmodium M17 aminopeptidases share a highly conserved preference for hydrophobic residues at the P1 position. The aminopeptidases also demonstrated intra-peptide sequence specificity, particularly the M1 aminopeptidases, which showed a definitive preference for peptides with fewer negatively charged intrapeptide residues. When tested with a panel of peptides of increasing length, each aminopeptidase exhibited unique catalytic behavioral responses to the increase in peptide length, although all six aminopeptidases exhibited an increase in cooperativity as peptide length increased. Overall the P. vivax and P. berghei enzymes were generally faster than the P. falciparum enzymes, which we postulate is due to subtle differences in structural dynamicity. Together, these results build a kinetic profile that allows us to better understand the catalytic nuances of the M1 and M17 aminopeptidases from different Plasmodium species.

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