Identification of Novel Inhibitors of Bacterial Methionine Aminopeptidase Using In Silico Virtual Screening Approach and In Vitro Validation (original) (raw)
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Identification of novel inhibitors of bacterial surface enzyme Staphylococcus aureus Sortase A
Bioorganic & Medicinal Chemistry Letters, 2008
In-silico virtual screening of bacterial surface enzyme Staphylococcus aureus Sortase A against commercial compound libraries using FlexX software package has led to the identification of novel inhibitors. Inhibition of enzyme catalytic activity was determined by monitoring the steady state cleavage of a model peptide substrate. Preliminary structure activity relationship studies on the lead compound resulted in the identification of compounds with improved activity. The most active compound has an IC50 value of 58 μM against the enzyme.A novel class of inhibitors of Staphylococcus aureus Sortase A is discovered by in-silico virtual screening and structure activity relationship studies.
The Journal of Antibiotics
Staphylococcus aureus is one of the most dangerous pathogens commonly associated with high levels of morbidity and mortality. Sortase A is considered as a promising molecular target for the development of antistaphylococcal agents. Using hybrid virtual screening approach and FRET analysis, we have identified five compounds able to decrease the activity of sortase A by more than 50% at the concentration of 200 µM. The most promising compound was 2-(2-amino-3-chlorobenzoylamino)-benzoic acid which was able to inhibit S. aureus sortase A at the IC 50 value of 59.7 µM. This compound was selective toward sortase A compared to other four cysteine proteasescathepsin L, cathepsin B, rhodesain, and the SARS-CoV2 main protease. Microscale thermophoresis experiments confirmed that this compound bound sortase A with K D value of 189 µM. Antibacterial and antibiofilm assays also confirmed high specificity of the hit compound against two standard and three wild-type, S. aureus hospital infection isolates. The effect of the compound on biofilms produced by two S. aureus ATCC strains was also observed suggesting that the compound reduced biofilm formation by changing the biofilm structure and thickness.
European Journal of Medicinal Chemistry, 2010
Synthetic methods have been developed for lead Sortase A inhibitors identified from previous studies. Several derivatives of the lead inhibitor were synthesized to derive preliminary structure activity relationships (SAR). Different regions of the lead inhibitor that are critical for the enzyme activity have been determined by systematic SAR studies. The E stereochemistry of the lead compound was found to be critical for its activity. Replacement of the E double bond with Z double bond or a rigid triple bond reduced the enzyme inhibitory activity in most cases. Reduction of the double bond to a C–C single bond resulted in complete loss of activity. Amide carbonyl and NH groups were also found to be crucial for the activity of this class of inhibitors, as well. The morpholine ring oxygen atom was also found to be an important factor for the activity of the lead inhibitor. Preliminary SAR studies led to the identification of compounds with improved enzyme inhibition. The most active compound was found to have an IC50 value of 58 μM against the enzyme.Synthesis and structure activity relationship studies of a lead structural template of Staphylococcus aureus Sortase A inhibitor are described.
Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors
Proteins: Structure, Function, and Bioinformatics, 2006
In this article we describe the application of structural biology methods to the discovery of novel potent inhibitors of methionine aminopeptidases. These enzymes are employed by the cells to cleave the N-terminal methionine from nascent peptides and proteins. As this is one of the critical steps in protein maturation, it is very likely that inhibitors of these enzymes may prove useful as novel antibacterial agents. Involvement of crystallography at the very early stages of the inhibitor design process resulted in serendipitous discovery of a new inhibitor class, the pyrazole-diamines. Atomic-resolution structures of several inhibitors bound to the enzyme illuminate a new mode of inhibitor binding. Proteins 2007;66:538-546. V V C 2006 Wiley-Liss, Inc.
Journal of Molecular Graphics and Modelling, 2015
Staphylococcus aureus sortase A is an attractive target of Gram-positive bacteria that plays a crucial role in anchoring of surface proteins to peptidoglycan present in bacterial cell wall. Inhibiting sortase A is an elementary and essential effort in preventing the pathogenesis. In this context, in silico virtual screening of in-house database was performed using ligand based pharmacophore model as a filter. The developed pharmacophore model AAHR 11 consists of two acceptors, one hydrophobic and one ring aromatic feature. Top ranked molecule KKR1 was docked into the active site of the target. After profound analysis, it was analyzed and optimized based on the observations from its binding pose orientation. Upgraded version of KKR1 was KKR2 and has improved docking score, binding interactions and best fit in the binding pocket. KKR1 along with KKR2 were further validated using 100 ns molecular dynamic studies. Both KKR1 and KKR2 contain Indole-thiazolidine moiety and were synthesized. The disk diffusion assay has good initial results (ZI of KKR1, KKR2 were 24, 38 mm at 10 g/mL and ZI of Ampicillin was 22 at 10 g/mL) and calculated MICs of the molecules (KKR1 5.56 ± 0.28 g/mL, KKR2 1.32 ± 0.12 g/mL, Ampicillin 8 ± 1.1 g/mL) were in good agreement with standard drug Ampicillin. KKR1 has shown IC 50 of 1.23 ± 0.14 M whereas the optimized lead molecule KKR2 show IC 50 of 0.008 ± 0.07 M. Results from in silico were validated by in vitro studies and proved that indole-thiazolidine molecules would be useful for future development as lead molecules against S. aureus sortase A.
Structural Analysis of Sortase A Inhibitors
Molecules, 2016
Bacterial sortases are cysteine transpeptidases that regulate the covalent linkage of several surface protein virulence factors in Gram-positive bacteria. Virulence factors play significant roles in adhesion, invasion of host tissues, biofilm formation and immune evasion, mediating the bacterial pathogenesis and infectivity. Therefore, sortases are emerging as important targets for the design of new anti-infective agents. We employed a computational study, based on structure derived descriptors and molecular fingerprints, in order to develop simple classification methods which could allow predicting low active or high active SrtA inhibitors. Our results indicate that a highly active SrtA inhibitor has a molecular weight ranging between 180 and 600, contains one up to four nitrogen atoms, up to three oxygen atoms and under 18 hydrogen atoms. Also the hydrogen acceptor number and the molecular flexibility, as assessed by the number of rotatable bounds, have emerged as the most relevant descriptors for SrtA affinity. The Bemis-Murcko scaffolding revealed favoured scaffolds as containing at least two ring structures bonded directly or merged in a condensed cycle. This data represent a valuable tool for identifying new potent SrtA inhibitors, potential anti-virulence agents targeted against Gram-positive bacteria, including multiresistant strains.
Title : Identification of Small Molecule Inhibitors of the Staphylococcus aureus Sortase
2008
approved: ________________________________ ________________________ Dennis Hruby The Sortase A (SrtA) enzyme is a potential target f or a new class of anti-infective drugs because it is responsible for anchoring virulence f actors to the surface of pathogenic, Gram-positive bacteria such as Staphylococcus aureus. High throughput screening yielded low molecular weight compounds that inhibit purified SrtA from S. aureus. The efficacy of these compounds at targeting SrtA in li ve bacteria was successfully determined by developing sensitive biological assay that measure inhibition of sortasedependent surface protein expression in S. aureus. Fibrinogen-clumping and fibrinogenbinding assays were developed to determine the pres nc of clumping factors (ClfA and B), a fibronectin-binding assay was used to determi ne the presence of fibrinogen-binding proteins (FnBPA and B), and dot blots were develope d to measure protein A on the cell surface. Fifty-six compounds were identified that inhibi...
Chemical Data Collections, 2018
Briefly describe the contentof thisdata article. If data is supplied with the data article, please explicitly state this or indicate the reference number and repository name for the data stored elsewhere. If this article is related to a published full research article, please also directly mention the article in the abstract] Novel molecules were designed against Staphylococcus aureus sortase A, an imperative and vital target involved in the bacterial virulence. Structure guided de novo designing was performed using different chemical fragments. These fragments were extended based on the requirements of the binding cavity. All the compounds in its binding orientation has formed good interaction network with amino acids HIS 120 and ARG 197. Molecules designed contain indole-chroman and indolin-chroman moieties and their docking scores were ranging from-6.92 to-5.67. Designed molecules were selected for synthesis and tested in vitro against Staphylococcus aureus sortase A using Fluorescence resonance energy transfer assay. The highest active molecule KK4 ((Z)-3-((5-nitro-1H-indol-3-yl) methylene) chroman-2,4-dione)
Combined pharmacophore and 3D-QSAR study on a series of Staphylococcus aureus Sortase A inhibitors
Chemical biology & drug design, 2012
Methicillin resistant Staphylococcus aureus has become a major health concern and it requires new therapeutic agents. Staphylococcus aureus Sortase A enzyme contributes in adherence of bacteria with the cell wall of host cell; consequently, inhibition of S. aureus Sortase A by small molecules could be employed as potential antibacterial agents against methicillin resistant S. aureus. Current study focused on the identification of 3D pharmacophoric features within a series of rhodanine, pyridazinone, and pyrazolethione analogs as S. aureus Sortase A inhibitors. Pharmacophore model was constructed employing representative molecules using Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database. The identified pharmacophoric points were then utilized to create alignment hypothesis for three-dimensional quantitative structure-activity relationships. Outcome of comparative molecular field analysis and comparative molecular similarity indices analysis experiments were in good agreement (comparative molecular field analysis: q 2 = 0.562 and r 2 = 0.995, comparative molecular similarity indices analysis: q 2 = 0.549 and r 2 = 0.978) and capable of explaining the variance in biological activities coherently with respect to the structural features of compounds. The results were also found in concurrence with the outcome of pharmacophoric features.
Molecular Docking and Screening Studies of New Natural Sortase A Inhibitors
International journal of molecular sciences, 2017
To date, multi-drug resistant bacteria represent an increasing health threat, with a high impact on mortality, morbidity, and health costs on a global scale. The ability of bacteria to rapidly and permanently acquire new virulence factors and drug-resistance elements requires the development of new antimicrobial agents and selection of new proper targets, such as sortase A. This specific bacterial target plays an important role in the virulence of many Gram-positive pathogens, and its inhibition should produce a mild evolutionary pressure which will not favor the development of resistance. A primary screening using a fluorescence resonance energy transfer assay was used to experimentally evaluate the inhibitory activity of several compounds on sortase A. Using molecular docking and structure-activity relationship analyses, several lead inhibitors were identified, which were further tested for antimicrobial activity using the well diffusion test and minimum inhibitory concentration. ...