Effective interaction studies for inhibition of DNA ligase protein from Staphylococcus aureus.

Staphylococcus aureus has been recognized as an important human pathogen for more than 100 years. It is among the most important causative agent of human infections in the twenty-first century. DNA ligase is the main protein responsible for the replication of S. aureus. In order to control the replication mechanism, DNA ligase is a successive drug target, hence we have chosen this protein for this study. We performed virtual screening using ZINC database for identification of potent inhibitor against DNA ligase. Based on the scoring methods, we have selected best five compounds from the ZINC database. In order to improve the accuracy, selected compounds were subjected into Quantum Polarized Ligand Docking (QPLD) docking, for which the results showed high docking score, compared to glide docking score. QPLD is more accurate as it includes charges in the scoring function, which was not available in the glide docking. Binding energy calculation results also indicated that selected compounds have good binding capacity with the target protein. In addition, these compounds on screening have good absorption, distribution, metabolism, excretion and toxicity property. In this study, we identified few compounds that particularly work against DNA ligase protein, having better interaction phenomenon and it would help further the experimental analysis.

Ligand-based pharmacophore modelling and screening of DNA minor groove binders targeting Staphylococcus aureus.

The recognition of DNA by small molecules is of special importance in the design of new drugs. Many natural and synthetic compounds have the ability to interact with the minor groove of DNA. In the present study, identification of minor groove binding compounds was attained by the combined approach of pharmacophore modelling, virtual screening and molecular dynamics approach. Experimentally reported 32 minor groove binding compounds were used to develop the pharmacophore model. Based on the fitness score, best three pharmacophore hypotheses were selected and used as template for screening the compounds from drug bank database. This pharmacophore-based screening provides many compounds with the same pharmacological properties. All these compounds were subjected to four phases of docking protocols with combined Glide-quantum-polarized ligand docking approach. Molecular dynamics results indicated that selected compounds are more active and showed good interaction in the binding site of DNA. Based on the scoring parameters and energy values, the best compounds were selected, and antibacterial activity of these compounds was identified using in vitro antimicrobial techniques.

Prevalence of extended-spectrum ß-lactamase-producing multidrug-resistant Escherichia coli among isolates from community-acquired infections and in silico structural modeling of an ESBL protein.

Escherichia coli is a common major cause of bacterial infections in tea tribe patients of the northeast region of Assam, India. In this study, we documented multidrug resistance (MDR) and the prevalence of extended-spectrum ß-lactamases (ESBLs) among 148 E. coli strains that were isolated from bacterial infections in tea tribe patients who had a history of self-medication. High prevalence of resistance to ampicillin (82%), amoxicillin (68%), cefixime (60%), norfloxacin (60%), nalidixic acid (60%), and co-trimoxazole (53%) was observed. Of 148 E. coli isolates, 38 (26%) were confirmed as ESBL producers. The ESBL genes were sequenced from highly resistant ESBL producing E. coli isolates. Molecular modeling was performed using MODELLER 9v10 software to determine the three-dimensional structure of a protein. This result indicates that the prevailing reason for the high prevalence of antibiotic resistance in this community is prior exposure to low-quality antibiotics, hence MDR in E. coli is increasing. ESBLs are enzymes that are produced by resistant bacteria that hydrolyze advanced generations of cephalosporin antibiotics and cause resistance, even in patients with community-acquired infections. So our results provide a framework for understanding the structure and possible binding sites of ESBL proteins for drug targeting, and the results were found to be reliable.

Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM docking and molecular dynamics simulation.

DNA binding ligands (DBL) were reported to bind the minor groove of bacterial DNA. In the present study, DBL were analyzed and screened for their Staphylococcus inhibitory activity by inhibiting the Staphylococcal DNA replication. The orientation and the ligand-receptor interactions of DBL within the DNA-binding pocket were investigated applying a multi-step docking protocol using Glide and QM/MM docking. The polarization of ligands with QM/MM for DNA-ligand docking with Staphylococcal DNA minor groove was performed in order to understand their possible interactions. Molecular dynamics simulation techniques were employed to obtain the dynamic behavior of the DBL with Staphylococcal DNA. Computational docking and simulation represented a promising alternative to bridge the gap, and so that DNA and gyrase interactions were blocked by DBL. The results revealed the importance of the DBL for strong interactions with the DNA minor groove region and blocking the bacterial replication.

A database for the predicted pharmacophoric features of medicinal compounds.

UNLABELLED: Pharmacophore feature is defined by a set of chemical structure patterns having the active site of drug like molecule. Pharmacophore can be used to assist in building hypothesis about desirable chemical properties in drug molecule and hence it can be used to refine and modify drug candidates. We predicted the pharmacophoric features of 150 medicinal compounds from plants for anti-cancer, anti-carcinogenic, anti-diabetic, anti-microbial, and anti-oxidant. Estimation of pharmacophoric feature is necessary to ensure the optimal supramolecular interaction with a biological target and to trigger or block its biological response. We subsequently make this data available to open access using a database at the URL: http://www.hccbif.info/index.htm AVAILABILITY: The database is available for free at http://www.hccbif.info/index.htm.

Normo-glycemic and hypolipidemic effect of costunolide isolated from Costus speciosus (Koen ex. Retz.)Sm. in streptozotocin-induced diabetic rats.

Diabetes mellitus is the most common and serious metabolic disorder among people all over the world. Many plants have successfully been used to overcome this problem. Costus speciosus is widely used in Indian medicine to treat various diseases including diabetes. Bioassay guided fractionation was followed to isolate costunolide from the hexane extract of C. speciosus root. The structure was elucidated using X-ray crystallography. Costunolide was administered to streptozotocin (STZ) (50 mg/kg bw)-induced diabetic male wistar rats at different doses (5, 10, 20 mg/kg bw) for 30 days to assess its effect on fasting plasma glucose and cholesterol levels. It was found that plasma glucose was significantly (p<0.05) reduced in a dose-dependent manner when compared to the control. In addition, oral administration of costunolide (20 mg/kg bw) significantly decreased glycosylated hemoglobin (HbA(1c)), serum total cholesterol, triglyceride, LDL cholesterol and at the same time markedly increased plasma insulin, tissue glycogen, HDL cholesterol and serum protein. Also costunolide restored the altered plasma enzyme (aspartate aminotransferase, alanine aminotrasferase, lactate dehydrogenase, alkaline phosphatase and acid phosphatase) levels to near normal. Costunolide might have stimulated the beta islets to secrete insulin by inhibiting the expression of nitric oxide synthase. The results of this experimental study indicated that costunolide possessed normo-glycemic and hypolipidemic activity and hence it could be used as a drug for treating diabetes.

A novel dihydroxy gymnemic triacetate isolated from Gymnema sylvestre possessing normoglycemic and hypolipidemic activity on STZ-induced diabetic rats.

AIM OF THE STUDY: Gymnema sylvestre (Asclepiadaceae) is emerging as a potential treatment for the management of diabetes. The leaves are used in herbal medicine preparations. The present study was carried out to isolate and identify the putative antidiabetic compound based on bioassay-guided fractionation. MATERIALS AND METHODS: An active compound dihydroxy gymnemic triacetate has been isolated from Gymnema sylvestre acetone extract and its optimum dose has been determined and patented. An optimum dose of dihydroxy gymnemic triacetate (20mg/kg body weight) was orally administered for 45 days to streptozotocin diabetic rats for the assessment of plasma glucose, insulin, glycated hemoglobin (HbA1c), tissue glycogen, lipid parameters such as triglycerides, total cholesterol, LDL-cholesterol, HDL-cholesterol and activities of hepatic marker enzymes, such as aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP) and acid phosphatase (ACP) in normal and streptozotocin diabetic rats. RESULTS: Dihydroxy gymnemic triacetate at 20mg dose produced significant effects on all biochemical parameters studied compared to diabetic control group. CONCLUSIONS: These results indicate that dihydroxy gymnemic triacetate, the compound from Gymnema sylvestre, possessed hypoglycemic and hypolipidemic activity in long-term treatment and hence it could be used as a drug for treating diabetes.