共查询到20条相似文献,搜索用时 46 毫秒
1.
Laura?E. Batten Alice?E. Parnell Neil?J. Wells Amber?L. Murch Petra C.?F. Oyston Peter?L. Roach 《Bioscience reports》2016,36(1)
The metabolism of polyphosphate is important for the virulence of a wide range of pathogenic bacteria and the enzymes of polyphosphate metabolism have been proposed as an anti-bacterial target. In the intracellular pathogen Francisella tularensis, the product of the gene FTT1564 has been identified as a polyphosphate kinase from the polyphosphate kinase 2 (PPK2) family. The isogenic deletion mutant was defective for intracellular growth in macrophages and was attenuated in mice, indicating an important role for polyphosphate in the virulence of Francisella. Herein, we report the biochemical and structural characterization of F. tularensis polyphosphate kinase (FtPPK2) with a view to characterizing the enzyme as a novel target for inhibitors. Using an HPLC-based activity assay, the substrate specificity of FtPPK2 was found to include purine but not pyrimidine nts. The activity was also measured using 31P-NMR. FtPPK2 has been crystallized and the structure determined to 2.23 Å (1 Å=0.1 nm) resolution. The structure consists of a six-stranded parallel β-sheet surrounded by 12 α-helices, with a high degree of similarity to other members of the PPK2 family and the thymidylate kinase superfamily. Residues proposed to be important for substrate binding and catalysis have been identified in the structure, including a lid-loop and the conserved Walker A and B motifs. The ΔFTT1564 strain showed significantly increased sensitivity to a range of antibiotics in a manner independent of the mode of action of the antibiotic. This combination of biochemical, structural and microbiological data provide a sound foundation for future studies targeting the development of PPK2 small molecule inhibitors. 相似文献
2.
Pramod C Bhasme Mahantesh M Kurjogi Rajeshwari D Sanakal Rohit B Kaliwal Basappa B Kaliwal 《Bioinformation》2013,9(7):339-344
The bovine mastitis caused by coagulase negative staphylococci (CNS) has increased in many herds of urban and rural areas of
India. Emergence of multi drug resistant bacteria has further made its management more complex and serious. Therefore,
innovation of novel specific drug for the treatment of disease caused by particular organism remained to be a challenge. Hence, in
the present study a bacterium was isolated from milk of the cow with bovine mastitis and was identified as S. saprophyticus, 44
pathways of S. saprophyticus retrieved (KEGG) from web server were found to be non homologous to the host Bos taurus, out of
which 39 pathways were found to be in cytoplasm, 2 in cell wall and 3 in the cell membrane. The knowledge of the present study
could make the drug discovery easier which have high affinity to the target site of the causative organism. 相似文献
3.
Martins M Pluvinage B Li de la Sierra-Gallay I Barbault F Dairou J Dupret JM Rodrigues-Lima F 《Journal of molecular biology》2008,383(3):549-560
Arylamine N-acetyltransferase (NAT) enzymes are found in a broad range of eukaryotes and prokaryotes. There is increasing evidence that NAT enzymes could contribute to antibiotic resistance in pathogenic bacteria such as Mycobacterium tuberculosis. Nocardia farcinica is an opportunistic human pathogen that causes pulmonary infections (nocardiosis) with clinical manifestations that resemble tuberculosis. While the genomic sequence of this prokaryote has been determined, studies of N. farcinica proteins remain almost nonexistent. In particular, N. farcinica proteins putatively involved in antibiotic resistance mechanisms have not been described structurally or functionally. Here, we have characterized a new NAT enzyme (NfNAT) from N. farcinica at the structural and functional level. NfNAT is the first N. farcinica protein for which a 3D structure is reported. We showed that this novel prokaryotic isoform is structurally and functionally related to the mycobacterial NAT enzymes. In particular, NfNAT was found to display high N-acetyltransferase activity towards several known NAT substrates including the antitubercular drug isoniazid. Interestingly, isoniazid is not used for the treatment of nocardiosis and has been shown to be poorly active against several nocardial species. On the contrary, NfNAT was found to be poorly active towards sulfamethoxazole, a sulfonamide drug considered as the treatment of choice for the treatment of nocardiosis. The functional and structural data reported in this study will help to develop our understanding of the role of NAT enzymes in nocardia and mycobacteria and may help in the rational design of NAT antagonists for a range of clinical applications. 相似文献
4.
Plasmodium falciparum alanine M1-aminopeptidase (PfA-M1) is a validated target for anti-malarial drug development. Presence of
significant similarity between PfA-M1 and human M1-aminopeptidases, particularly within regions of enzyme active site leads to
problem of non-specificity and off-target binding for known aminopeptidase inhibitors. Molecular docking based in silico screening
approach for off-target binding has high potential but requires 3D-structure of all human M1-aminopeptidaes. Therefore, in the
present study 3D structural models of seven human M1-aminopeptidases were developed. The robustness of docking parameters
and quality of predicted human M1-aminopeptidases structural models was evaluated by stereochemical analysis and docking of
their respective known inhibitors. The docking scores were in agreement with the inhibitory concentrations elucidated in enzyme
assays of respective inhibitor enzyme combinations (r2≈0.70). Further docking analysis of fifteen potential PfA-M1 inhibitors
(virtual screening identified) showed that three compounds had less docking affinity for human M1-aminopeptidases as compared
to PfA-M1. These three identified potential lead compounds can be validated with enzyme assays and used as a scaffold for
designing of new compounds with increased specificity towards PfA-M1. 相似文献
5.
Francesca Spyrakis Paolo Felici Alexander S. Bayden Enea Salsi Riccardo Miggiano Glen E. Kellogg Pietro Cozzini Paul F. Cook Andrea Mozzarelli Barbara Campanini 《Biochimica et Biophysica Acta - Proteins and Proteomics》2013,1834(1):169-181
O-acetylserine sulfhydrylase (OASS) catalyzes the synthesis of l-cysteine in the last step of the reductive sulfate assimilation pathway in microorganisms. Its activity is inhibited by the interaction with serine acetyltransferase (SAT), the preceding enzyme in the metabolic pathway. Inhibition is exerted by the insertion of SAT C-terminal peptide into the OASS active site. This action is effective only on the A isozyme, the prevalent form in enteric bacteria under aerobic conditions, but not on the B-isozyme, the form expressed under anaerobic conditions. We have investigated the active site determinants that modulate the interaction specificity by comparing the binding affinity of thirteen pentapeptides, derived from the C-terminal sequences of SAT of the closely related species Haemophilus influenzae and Salmonella typhimurium, towards the corresponding OASS-A, and towards S. typhimurium OASS-B. We have found that subtle changes in protein active sites have profound effects on protein–peptide recognition. Furthermore, affinity is strongly dependent on the pentapeptide sequence, signaling the relevance of P3–P4–P5 for the strength of binding, and P1–P2 mainly for specificity. The presence of an aromatic residue at P3 results in high affinity peptides with Kdiss in the micromolar and submicromolar range, regardless of the species. An acidic residue, like aspartate at P4, further strengthens the interaction and results in the higher affinity ligand of S. typhimurium OASS-A described to date. Since OASS knocked-out bacteria exhibit a significantly decreased fitness, this investigation provides key information for the development of selective OASS inhibitors, potentially useful as novel antibiotic agents. 相似文献
6.
The Mur E enzyme of Mur pathway of Mycobacterium tuberculosis is an attractive drug target as it is unique to bacteria and is absent
in mammalian cells. The virtual screening of large libraries of drug like molecules against a protein target is a common strategy
used to identify novel inhibitors. However, the method has a large number of pitfalls, with large variations in accuracy caused in
part by inaccurate protocols, use of improper standards and libraries, and system dependencies such as the potential for nonspecific
docking from large active-site cavities. The screening of drug-like small molecules from diversity sets can, however, be
used to short-list potential fragments as building blocks to generate leads with improved specificity. We describe a protocol to
implement this strategy, which involves an analysis of the active site and known inhibitors to identify orthospecific determinants,
virtual screening of a drug-like diversity library to identify potential drug primitives, and inspection of the potential docked
fragments for both binding potential and toxicity. The protocol is implemented on the M.tb Mur E protein which has a large active
site with poor enrichment of known positives and a set of drug-like molecules that meets this criteria is presented for further
analysis.
Abbreviations
MTB - Mycobacterium tuberculosis, NCI - National Cancer Institute, PDB - Protein Databank. 相似文献7.
A great challenge is posed to the treatment of tuberculosis due to the evolution of multidrug-resistant (MDR) and extensively drugresistant
(XDR) strains of Mycobacterium tuberculosis in recent times. The complex cell envelope of the bacterium contains unusual
structures of lipids which protects the bacterium from host enzymes and escape immune response. To overcome the drug
resistance, targeting “drug targets” which have a critical role in growth and virulence factor is a novel approach for better
tuberculosis treatment. The enzyme Phosphopantetheinyl transferase (PptT) is an attractive drug target as it is primarily involved
in post translational modification of various types-I polyketide synthases and assembly of mycobactin, which is required for lipid
virulence factors. Our in silico studies reported that the structural model of M.tuberculosis PptT characterizes the structure-function
activity. The refinement of the model was carried out with molecular dynamics simulations and was analyzed with root mean
square deviation (RMSD), and radius of gyration (Rg). This confirmed the structural behavior of PptT in dynamic system.
Molecular docking with substrate coenzyme A (CoA) identified the binding pocket and key residues His93, Asp114 and Arg169
involved in PptT-CoA binding. In conclusion, our results show that the M.tuberculosis PptT model and critical CoA binding pocket
initiate the inhibitor design of PptT towards tuberculosis treatment. 相似文献
8.
Strategic genome-scale prioritization of unique drug targets: A case study of Streptococcus gordonii
Sandeep Telkar Hulikal shivashankara Santosh Kumar Nagaraja Deeplanaik Riaz Mahmood 《Bioinformation》2013,9(19):983-987
The current reach of genomics extends facilitated identification of microbial virulence factors, a primary objective for antimicrobial
drug and vaccine design. Many putative proteins are yet to be identified which can act as potent drug targets. There is lack and
limitation of methods which appropriately combine several omics ways for putative and new drug target identification. The study
emphasizes a combined bioinformatic and theoretical method of screening unique and putative drug targets, lacking similarity
with experimentally reported essential genes and drug targets. Synteny based comparison was carried out with 11 streptococci
considering S. gordonii as reference genome. It revealed 534 non-homologous genes of which 334 were putative. Similarity search
against host proteome, metabolic pathway annotation and subcellular localization predication identified 16 potent drug targets.
This is a first attempt of several combinational approaches of similarity search with target protein structural features for screening
drug targets, yielding a pipeline which can be substantiated to other human pathogens. 相似文献
9.
Reporter bacteria are beneficial for the rapid and sensitive screening of cultures producing peptide antibiotics, which can be an addition or alternative to the established antibiotics. This study was carried out to validate the usability of specific reporter strains for the target mediated identification of antibiotics produced by native Bacillus spp. isolated from different food sources. During preliminary classification, cell wall stress causing Bacillus isolates were screened by using reporter strain Bacillus subtilis BSF2470. The isolates which induced cell wall stress were further characterized for their specific mode of action by using other B. subtilis reporter strains (TMB 488, TMB 299 and TMB 279). The isolate B. licheniformis N12 was found to produce bacitracin confirmed by the response to reporter strain B. subtilis TMB 279 and by putative identification of bacitracin biosynthetic loci. The other isolate B. subtilis EC1 also induced B. subtilis TMB 279, but does not possess the bacitracin gene cluster indicating that it can be a novel, bacitracin like antibiotic. The different but related subsets of peptide antibiotics that bind the pyrophosphate moiety of the lipid carrier of cell wall biosynthesis can be identified using this whole cell based reporter strains. 相似文献
10.
Meenu Kesarwani Erika Huber Zachary Kincaid Mohammad Azam 《Journal of visualized experiments : JoVE》2014,(94)
The discovery of BCR/ABL as a driver oncogene in chronic myeloid leukemia (CML) resulted in the development of Imatinib, which, in fact, demonstrated the potential of targeting the kinase in cancers by effectively treating the CML patients. This observation revolutionized drug development to target the oncogenic kinases implicated in various other malignancies, such as, EGFR, B-RAF, KIT and PDGFRs. However, one major drawback of anti-kinase therapies is the emergence of drug resistance mutations rendering the target to have reduced or lost affinity for the drug. Understanding the mechanisms employed by resistant variants not only helps in developing the next generation inhibitors but also gives impetus to clinical management using personalized medicine. We reported a retroviral vector based screening strategy to identify the spectrum of resistance conferring mutations in BCR/ABL, which has helped in developing the next generation BCR/ABL inhibitors. Using Ruxolitinib and JAK2 as a drug target pair, here we describe in vitro screening methods that utilizes the mouse BAF3 cells expressing the random mutation library of JAK2 kinase. 相似文献
11.
The rise in antibiotic resistance has led to an increased research focus on discovery of new antibacterial candidates. While broad-spectrum antibiotics are widely pursued, there is evidence that resistance arises in part from the wide spread use of these antibiotics. Our group has developed a system to produce protein affinity agents, called synbodies, which have high affinity and specificity for their target. In this report, we describe the adaptation of this system to produce new antibacterial candidates towards a target bacterium. The system functions by screening target bacteria against an array of 10,000 random sequence peptides and, using a combination of membrane labeling and intracellular dyes, we identified peptides with target specific binding or killing functions. Binding and lytic peptides were identified in this manner and in vitro tests confirmed the activity of the lead peptides. A peptide with antibacterial activity was linked to a peptide specifically binding Staphylococcus aureus to create a synbody with increased antibacterial activity. Subsequent tests showed that this peptide could block S. aureus induced killing of HEK293 cells in a co-culture experiment. These results demonstrate the feasibility of using the synbody system to discover new antibacterial candidate agents. 相似文献
12.
Sudha Karumuri Puneet Kumar Singh Pratyoosh Shukla 《Indian journal of microbiology》2015,55(3):333-340
The diseases caused by dermatophytes are common among several other infections which cause serious threat to human health. It is evident that enzyme squalene epoxidase is responsible for prolonged dermatophyte infection and it is appealing to note that this enzyme is also responsible for fatty acid synthesis in these groups of fungi. In the present study, terbinafine drug which targets enzyme squalene epoxidase has been explored to design its various novel analogues. The present study suggests that many more prominent drug analogues could be constituted which may be crucial towards designing new drug candidates. In the present study, we have designed a series of such analogues viz. [(2E)-6,6-dimethylhept-2-en-4-yn-1-yl](methyl)(naphthalen-1-ylmethyl)amine, N-[8-({[(2E)-6,6-dimethylhept-2-en-4-yn-1-yl](methyl)amino}methyl)naphthalen-1-yl]-2-(sulfoamino) acetamide, {[4-(dihydroxyamino)-8-({[(2E)-6,6-dimethylhept-2-en-4-yn-1-yl](methyl)amino}methyl)naphthalen-1-yl]sulfanyl}methanol and (R)-{[4-({[(2E,6R)-6,7-dimethyloct-2-en-4-yn-1-yl](methyl)amino}methyl)-5-[(hydroxysulfamoyl)amino]naphthalen-1-yl]amino}sulfinic acid. Moreover, further by molecular docking approach the binding between enzyme and designed analogues was further analysed. The present preliminary report suggested a considerably good docking interaction score of −338.75 kcal/mol between terbinafine and squalene epoxidase from Trichophyton rubrum. This preliminary study implies that few designed candidate ligands can be effectual towards the activity of this enzyme and can play crucial role in pathogenesis control of T. rubrum. 相似文献
13.
Roberto C. Molina-Quiroz Cecilia A. Silva Cristian F. Molina Lorenzo E. Leiva Sebastián Reyes-Cerpa Inés Contreras Carlos A. Santiviago 《Open biology》2015,5(10)
It has been proposed that sub-inhibitory concentrations of antibiotics play a role in virulence modulation. In this study, we evaluated the ability of Salmonella enterica serovar Typhimurium (hereafter S. Typhimurium) to colonize systemically BALB/c mice after exposure to a sub-inhibitory concentration of cefotaxime (CTX). In vivo competition assays showed a fivefold increase in systemic colonization of CTX-exposed bacteria when compared to untreated bacteria. To identify the molecular mechanisms involved in this phenomenon, we carried out a high-throughput genetic screen. A transposon library of S. Typhimurium mutants was subjected to negative selection in the presence of a sub-inhibitory concentration of CTX and genes related to anaerobic metabolism, biosynthesis of purines, pyrimidines, amino acids and other metabolites were identified as needed to survive in this condition. In addition, an impaired ability for oxygen consumption was observed when bacteria were cultured in the presence of a sub-inhibitory concentration of CTX. Altogether, our data indicate that exposure to sub-lethal concentrations of CTX increases the systemic colonization of S. Typhimurium in BALB/c mice in part by the establishment of a fitness alteration conducive to anaerobic metabolism. 相似文献
14.
A. hydrophila, a ubiquitous gram-negative bacterium present in aquatic environments, has been implicated in illness in humans, fish and amphibians.
Lipopolysaccharides (LPS), a surface component of the outer membrane, are one of the main virulent factors of gram-negative bacteria.
UDP-galactose 4-epimerase (GalE) catalyses the last step in the Leloir pathway of galactose metabolism and provides precursor for the biosynthesis
of extracellular LPS and capsule. Due to its key role in LPS biosynthesis, it is a potential drug target. The present study describes cloning, sequence
analysis and prediction of three dimensional structure of the deduced amino acid sequence of the galE of A. hydrophila AH17. The cloned galE
consists of the putative promoter-operator region, and an open reading frame of 338 amino acid residues. Sequence alignment and predicted 3Dstructure
revealed that the GalE of A. hydrophila consists of the signature sequences of the epimerase super family. The present study reports the
molecular modeling / 3D-structure prediction of GalE of A. hydrophila. Further, the potential regions of the enzyme that can be targeted for drug
design are identified. 相似文献
15.
Conventionally, drugs are discovered by testing chemically synthesized compounds against a battery of in vivo biological screens.
Information technology and Omic science enabled us for high throughput screening of compound libraries against biological
targets and hits are then tested for efficacy in cells or animals. Chancroid, caused by Haemophilus ducreyi is a public health problem
and has been recognized as a cofactor for Human Immunodeficiency Virus (HIV) transmission. It facilitates HIV transmission by
providing an accessible portal entry, promoting viral shedding, and recruiting macrophages as well as CD4 cells to the skin. So,
there is a requirement to develop an efficient drug to combat Chancroid that can also diminish HIV infection. In-silico screening of
potential inhibitors against the target may facilitate in detection of the novel lead compounds for developing an effective chemo
preventive strategy against Haemophilus ducreyi. The present study has investigated the effects of approximately 1100 natural
compounds that inhibit three vital enzymes viz. Phosphoenolpyruvate phosphotransferase, Acetyl-coenzyme A carboxylase and
Fructose 1, 6-bisphosphatase of Haemophilus ducreyi in reference to a commercial drug Rifabutin. Results reveal that the lead
compound uses less energy to bind to target. The lead compound parillin has also been predicted as less immunogenic in
comparison to Rifabutin. Further, better molecular dynamics, pharmacokinetics, pharmacodynamics and ADME-T properties
establish it as an efficient chancroid preventer. 相似文献
16.
Yuan H Chai SC Lam CK Howard Xu H Ye QZ 《Bioorganic & medicinal chemistry letters》2011,21(11):3395-3398
Drug resistance in Gram-negative bacteria, such as Acinetobacter baumannii, is emerging as a significant healthcare problem. New antibiotics with a novel mechanism of action are urgently needed to overcome the drug resistance. Methionine aminopeptidase (MetAP) carries out an essential cotranslational methionine excision in many bacteria and is a potential target to develop such novel antibiotics. Two putative MetAP genes were identified in A. baumannii genome, but whether they actually function as MetAP enzymes was not known. Therefore, we established an efficient E. coli expression system for their production as soluble and metal-free proteins for biochemical characterization. We demonstrated that both could carry out the metal-dependent catalysis and could be activated by divalent metal ions with the order Fe(II) ≈ Ni(II) > Co(II) > Mn(II) for both. By using a set of metalloform-selective inhibitors discovered on other MetAP enzymes, potency and metalloform selectivity on the A. baumannii MetAP proteins were observed. The similarity of their catalysis and inhibition to other MetAP enzymes confirmed that both may function as competent MetAP enzymes in A. baumannii and either or both may serve as the potential drug target. 相似文献
17.
Inhibition of α-amylase is an important strategy to control post-prandial hyperglycemia.
The present study on Ruellia tuberosa, known as traditional anti-diabetic agent, is being provided in silico
study to identify compounds inhibiting α-amylase in rat and human. Compounds were explored from PubChem database.
Molecular docking was studied using the autodock4. The interactions were further visualized and analyzed using
the Accelrys Discovery Studio version 3.5. Binding energy of compounds to α-amylase was varying between -1.92
to -6.66 kcal/mol in rat pancreatic alpha amylase and -3.06 to -8.42kcal/mol in human pancreatic alpha amylase,
and inhibition konstanta (ki) was varying between 13.12- 39460µM in rat and 0.67-5600µM in human. The docking
results verify that betulin is the most potential inhibitor of all towards rat model alpha amylase and human
alpha amylase. Further analysis reveals that betulin could be a potential inhibitor with non-competitive pattern
like betulinic acid. In comparison, betulin has smaller Ki (0.67µM) than acarbose (2.6 µM), which suggesting
that betulin is more potential as inhibitor than acarbose, but this assumption must be verified in vitro. 相似文献
18.
Linear polyphosphate chains have been found to play a key role in bacterial responses to stresses and nutritional depletion, and are necessary for host infection of various pathogens. Polyphosphate kinase (PPK) is a critical enzyme responsible for polyphosphate synthesis in bacteria. PPK knockout mutations in several Gram-negative pathogens identify PPK as an ideal drug target for the development of a new class of antibacterial drugs. To reveal the catalytic mechanism and provide a structural basis for drug discovery, we have purified and crystallized full-length Escherichia coli PPK and its complex with AMP-PNP. The crystals diffract to a resolution of 2.5A and belong to the space group P4(2)2(1)2 with unit-cell parameters a=152.0, b=152.0, and c=150.0 A. Crystal structure of PPK is being determined by the Se-Met MAD experiment. 相似文献
19.
《Saudi Journal of Biological Sciences》2022,29(10):103424
Antibiotics are drugs that are used to treat or prevent bacterial infections. They work by either killing or stopping bacteria from spreading. Nevertheless, it appeared in the last decade, Antibiotic-resistant bacteria are bacteria resistant to antibiotics and cannot be controlled or killed by them. In the presence of an antibiotic, they can live and even reproduce. The Neisseria gonorrhoeae bacteria is appearing to be a multidrug-resistant pathogen. Many factors contribute to antibiotic resistance, including unfettered access to antimicrobials, incorrect drug selection, misuse, and low-quality antibiotics. Here, we investigated in-silico docking screening and analysis for ten natural marine fungus extracted compounds. The resulted data were examined for the best binding affinity, toxicity, and chemical interactions. The most superior compound was elipyrone A with six hydrogen bonds, ?8.5 of binding affinity, and preferable results in the SWISS-ADME examination. It is well known that “Declining corporate investment and a lack of innovation in the development of new antibiotics are weakening efforts to battle drug-resistant illnesses,” according to the World Health Organization (WHO). So, we extended our effort to predict a new natural compound to overcome the resistance of this bacteria. 相似文献
20.
Kees van Frankenhuyzen Yuehong Liu Amanda Tonon 《Journal of invertebrate pathology》2010,103(2):124-131
We examined interaction between Bacillus thuringiensis subsp. kurstaki HD-1 (Foray 48B) and larval midgut bacteria in two lepidopteran hosts, Lymantria dispar and Choristoneura fumiferana. The pathogen multiplied in either moribund (C. fumiferana) or dead (L. dispar) larvae, regardless of the presence of midgut bacteria. Inoculation of L. dispar resulted in a pronounced proliferation of enteric bacteria, which did not contribute to larval death because B. thuringiensis was able to kill larvae in absence of midgut bacteria. Sterile, aureomycin- or ampicillin-treated larvae were killed in a dose-dependent manner but there was no mortality among larvae treated with the antibiotic cocktail used by
[Broderick et al., 2006] and [Broderick et al., 2009]. These results do not support an obligate role of midgut bacteria in insecticidal activity of HD-1. The outcome of experiments on the role of midgut bacteria may be more dependent on which bacterial species are dominant at the time of experimentation than on host species per se. The L. dispar cohorts used in our study had a microflora, that was dominated by Enterococcus and Staphylococcus and lacked Enterobacter. Another factor that can confound experimental results is the disk-feeding method for inoculation, which biases mortality estimates towards the least susceptible portion of the test population. 相似文献