Possible allosteric binding site on Gyrase B, a key target for novel anti-TB drugs: homology modelling and binding site identification using molecular dynamics simulation and binding free energy calculations
30
Citation
64
Reference
10
Related Paper
Citation Trend
Keywords:
Docking (animal)
Binding affinities
Drug Design
Bacterial DNA gyrase is a well-known and validated target in the design of antibacterial drugs. However, inhibitors of its ATP binding subunit, DNA gyrase B (GyrB), have so far not reached clinical use. In the present study, three different series of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides were designed and prepared as potential DNA gyrase B inhibitors. The IC50 values of compounds on DNA gyrase from Escherichia coli were in the low micromolar range, with the best compound, (4-(4,5-dibromo-1H-pyrrole-2-carboxamido)benzoyl)glycine (18a), displaying an IC50 of 450 nM. For this compound, a high-resolution crystal structure in complex with E. coli DNA gyrase B was obtained, revealing details of its binding mode within the active site. The binding affinities of three compounds with GyrB were additionally evaluated by surface plasmon resonance, and the results were in good agreement with the determined enzymatic activities. For the most promising compounds, the inhibitory activities against DNA gyrase from Staphylococcus aureus and topoisomerases IV from E. coli and S. aureus were determined. Antibacterial activities of the most potent compounds of each series were evaluated against two Gram-positive and two Gram-negative bacterial strains. The results obtained in this study provide valuable information on the binding mode and structure–activity relationship of N-phenyl-4,5-dibromopyrrolamides and N-phenylindolamides as promising classes of ATP competitive GyrB inhibitors.
Quinolone
Cite
Citations (52)
Due to the rapid development of antimicrobial resistance, the discovery of new antibacterials is essential in the fight against potentially lethal infections. The DNA gyrase B (GyrB) subunit of bacterial DNA gyrase is an excellent target for the design of antibacterials, as it has been clinically validated by novobiocin. However, there are currently no drugs in clinical use that target GyrB. We prepared a new series of N-phenyl-4,5-dibromopyrrolamides and evaluated them against DNA gyrase and against the structurally and functionally similar enzyme, topoisomerase IV. The most active compound, 28, had an IC50 of 20 nM against Escherichia coli DNA gyrase. The IC50 values of 28 against Staphylococcus aureus DNA gyrase, and E. coli and S. aureus topoisomerase IV were in the low micromolar range. However, the compounds evaluated did not show significant antibacterial activities against selected Gram-positive and Gram-negative bacteria. Our results indicate that for potent inhibition of DNA gyrase, a combination of polar groups on the carboxylic end of the molecule and substituents that reach into the 'lipophilic floor' of the enzyme is required.
Novobiocin
Topoisomerase IV
Cite
Citations (16)
Drug target
Cite
Citations (31)
Bulky, flexible molecules such as peptides and peptidomimetics are often used as lead compounds during the drug discovery process. Pathophysiological events, e.g., the formation of amyloid fibrils in Alzheimer's disease, the conformational changes of prion proteins, or β-secretase activity, may be successfully hindered by the use of rationally designed peptide sequences. A key step in the molecular engineering of such potent lead compounds is the prediction of the energetics of their binding to the macromolecular targets. Although sophisticated experimental and in silico methods are available to help this issue, the structure-based calculation of the binding free energies of large, flexible ligands to proteins is problematic. In this study, a fast and accurate calculation strategy is presented, following modification of the scoring function of the popular docking program package AutoDock and the involvement of ligand-based two-dimensional descriptors. Quantitative structure−activity relationships with good predictive power were developed. Thorough cross-validation tests and verifications were performed on the basis of experimental binding data of biologically important systems. The capabilities and limitations of the ligand-based descriptors were analyzed. Application of these results in the early phase of lead design will contribute to precise predictions, correct selections, and consequently a higher success rate of rational drug discovery.
Binding affinities
Peptidomimetic
Docking (animal)
Rational design
Drug Design
AutoDock
Cite
Citations (31)
There has been an increase in the emergence and spread of drug-resistant pathogens, leading to a steep incline in the cases of antimicrobial resistance. Due to this, there is an imperative need for the development and identification of new antimicrobials to combat this menace of antimicrobial resistance. But this need is not being completely fulfilled by conventional drug discovery focused on a one molecule-one target approach. Polypharmacology, i.e., designing a drug in a way that acts on multiple cellular or molecular targets, a new approach for the identification of antimicrobial compounds, has been gaining attention. DNA gyrase B is one of the critical proteins involved in DNA replication and cell division in E. coli. In this study, the polypharmacological effect of amoxicillin and its analogues was studied on the DNA gyrase B and various other proteins of E. coli, using multiple in silico approaches like molecular docking, structural similarity, DFT, and molecular dynamics simulation. Both amoxicillin and its analogue, Cefaclor, tend to disrupt bacterial cell wall synthesis, but this study, based on in silico analysis, suggests a probable additional mode of action involving DNA gyrase B of E. coli which can be further explored to design novel dual-target inhibitors.
Docking (animal)
Drug Design
Cite
Citations (2)
Advances in protein modeling algorithms and state-of-the-art sequence similarity comparison and fold recognition methods, in combination with growing protein structure information, are facilitating "genome-to-drug lead" approaches in which chemicals are virtually screened against computationally-predicted protein targets. Although the quality of predicted protein structures by homology modeling methods, and thus their applicability to drug discovery initiatives, predominantly depends on the sequence similarity between the protein of known structure and the protein target to be modeled, recent research underscores that this approach can be used to significant advantage in the identification and optimization of lead compounds, as well as for the identification and validation of drug targets. Rational structure-based drug design cycles begin with an iterative procedure that is dependent on the initial determination of the structure of the target protein, followed by the prediction of ligands for the target protein from molecular modeling computation. The structure determination of all proteins encoded by vast genome sequencing efforts appears to be an unrealistic goal with current technologies. Therefore, other approaches based on the development of technology useful for accurately predicting and modeling the structures of proteins have become exceedingly important in certain structure-based drug design efforts. This review provides an overview of the recent method advancements in protein structure prediction by homology modeling and includes an assessment of the application of homology modeling to pharmaceutically relevant questions. In addition, examples of successful applications of homology modeling approaches to genome-to-drug lead investigations are described.
Drug Design
Protein structure database
Loop modeling
Structural genomics
Protein sequencing
Threading (protein sequence)
Cite
Citations (40)
We investigated how cyclothialidine (Ro 09-1437), a novel DNA gyrase inhibitor belonging to a new chemical class of compounds, acts to inhibit Escherichia coli DNA gyrase. Cyclothialidine up to 100 micrograms/ml showed no effect on DNA gyrase when linear DNA was used as a substrate. Under the same conditions, quinolones, which inhibit the resealing reaction of DNA gyrase, caused a decrease in the amount of linear DNA used. No effect of cyclothialidine was observed on the accumulation of the covalent complex of DNA and the A subunit of DNA gyrase induced by ofloxacin in the absence of ATP. The effect of cyclothialidine on the DNA supercoiling reaction was antagonized by ATP, reducing the inhibitory activity 11-fold as the ATP concentration was increased from 0.5 to 5 mM. Cyclothialidine competitively inhibited the ATPase activity of DNA gyrase (Ki = 6 nM). The binding of [14C]benzoyl-cyclothialidine to E. coli gyrase was inhibited by ATP and novobiocin, but not by ofloxacin. These results suggest that cyclothialidine acts by interfering with the ATPase activity of the B subunit of DNA gyrase. Cyclothialidine was active against a DNA gyrase resistant to novobiocin, suggesting that its precise site of action might be different from that of novobiocin.
Novobiocin
Replisome
Cite
Citations (33)
HIV-I protease (HIV-I PR) is aspartic protease enzyme which is essential for the life-cycle of HIV retrovirus. Homology structural model and function relation of HIV-I PR have solved the structure of HIV-I proteases. We created a homology model of HIV-I PR and the 3-D structure as template using with ICMPro software. The ICMPro homology modeling algorithm has demonstrated excellent accuracy in blind predictions. Moreover, recent results show that ICMPro models built with as little as 35% identity can be accurate enough to be successfully used in receptor based rational drug design. The closest homologue with the highest sequence identity of 38.395% was selected as representative model using YASARA tools. The model was validated using protein structure checking tools such as PROCHEK for reliability. A total of two pockets were predicted by the software. Once the pockets were predicted, the ligand was subjected to docking reaction using the docking module of ICMPro software. Based on the RMSD and energy values, the best docking orientation was selected. The better RMSD value of docking is 0.0066288. This study will be used in broad screening of inhibitors of the protein and can be further implemented in future drug designing.
Docking (animal)
Drug Design
Protein–ligand docking
Cite
Citations (7)
Cite
Citations (11)