Probing the mechanism of peptide binding to REV response element RNA of HIV-1; MD simulations and free energy calculations.

Ribonucleic acid (RNA) of HIV-1 contains a 350 nucleotide, highly structured, cis-acting element called RRE (REV-response-element RNA), essential for virus replication. REV is a natural peptide that binds to RRE and transports it from the nucleus to cytoplasm where it is expressed into a new virus. The synthetic peptide known as RSG-1.2 also binds the RRE element and competes with REV. The purpose of study is to rationally design novel peptides such as RSG peptide with improved binding affinity to prevent the transport of HIV-1 RNA and so replication of virus. Herein, we performed MD simulation and free energy calculations to evaluate the interactions and binding free energies of REV (PDB ID: 4PMI) and RSGs peptides (PDB IDs: 1G70 and 1I9F) with RRE. The protein-RNA interactions were analyzed using the MM-PBSA method. Results suggest that REV has more binding free energy -188.41 kcal/mol than two RSG peptides with total binding free energy -120.97 and -141.46 kcal/mol. The ARG and ASN were found to be important residues of REV. In the RRE sequence, the nucleotides 62-67 and 78-84 were found to be important contributors in binding free energy. This study play a major role in elaboration of binding REV and RSG1-2 with RRE element and pave the way for further synthesis of peptide that can bind with RRE element and can be selected as therapeutic agent for HIV.Communicated by Ramaswamy H. Sarma.

Anti-hyperglycemic and anti-hyperlipidemic effects of rhinacanthins-rich extract from Rhinacanthus nasutus leaves in nicotinamide-streptozotocin induced diabetic rats.

Rhinacanthus nasutus has traditionally been used in the treatment of various disorders including diabetes mellitus. Rhinacanthins-rich extract (RRE) is a semipurified R. nasutus leaf extract that contains 60% w/w of rhinacanthin-C (RC) obtained by a green extraction process. The purpose of this study was to investigate the anti-hyperglycemic and anti-hyperlipidemic activity of RRE (15 mg/kg equivalent to RC content) in comparison to its marker compound RC (15 mg/kg) and the standard drug glibenclamide (Glb) (600 µg/kg) in nicotinamide-streptozotocin induced diabetic rats for 28 days. In addition, the in silico pharmacokinetic and toxicity analysis of RC was also performed. RRE, RC and Glb significantly reduced the FBG, HbA1c and food/water intake while increasing the insulin level and body weight in diabetic rats without affecting the normal rats. The serum lipid, liver and kidney biomarkers were markedly normalized by RRE, RC and Glb in diabetic rats without affecting the normal rats. Moreover, the histopathology of the pancreas revealed that RRE, RC and Glb evidently restored the islets of Langerhans in diabetic rats. The overall results indicated that RRE has equivalent antidiabetic potential to that of RC. Moreover, the in silico pharmacokinetic and toxicity analysis predicts that RC is orally non-toxic, non-carcinogenic and non-mutagenic with a decent bioavailability. The undertaken study suggests that RRE could be used as an effective natural remedy in the treatment of diabetes.

Characterization of cryptic allosteric site at IL-4Rα: New paradigm towards IL-4/IL-4R inhibition.

Interleukin-4(IL-4), an anti-inflammatory cytokine, plays significant role in pathogenesis of various diseases such as asthma, tumors, and HIV infections. These responses are mediated by expression of IL-4R (receptor) on various hematopoietic and non-hematopoietic cells surfaces. To date, the X-ray crystal structure of unbound (i.e. free) IL-4R is not reported which hampers active research on the molecular interaction mechanism between IL-4 and IL-4R. To investigate the missing gaps about stable binding mode of IL-4 and drug-ability of IL-4R active site, modelling and molecular dynamics (MD) simulation of IL-4/IL-4R complex was performed. Drug-ability of the target protein changed after modelling the loop region near C-terminal of IL-4R protein. This led to the identification of a novel druggable site other than the reported interfacial site. Our analysis showed that the modelled residues Ser111 and Ser164-Lys167 are part of newly discovered allosteric site, which underwent major fluctuation after association with its ligand protein (IL-4). The results indicated possible role of this cryptic allosteric site in IL-4/IL-4R signaling pathway that might help us to block IL-4/IL-4R association to prevent various allergic and malignant diseases.

Synthesis of pyrimidine-2,4,6-trione derivatives: Anti-oxidant, anti-cancer, α-glucosidase, ß-glucuronidase inhibition and their molecular docking studies.

This paper describes a facile protocol, efficient, and environmentally benign for the synthesis a series of barbiturate acid substituted at C5 position 3a-o. The desired compounds subjected in vitro for different set of bioassays including against anti-oxidant (DPPH and super oxide scavenger assays), anti-cancer, α-glucosidase and ß-glucuronidase inhibitions. Compound 3m (IC50=22.9±0.5µM) found to be potent α-glucosidase enzyme inhibitors and showed more activity than standard acarbose (IC50=841±1.73µM). Compound 3f (IC50=86.9±4.33µM) found to be moderate ß-Glucuronidase enzyme inhibitors and showed activity comparatively less than the standard d-saccharic acid 1,4-lactone (IC50=45.75±2.16µM). Furthermore, in sillico investigation was carried out to investigate bonding mode of barbiturate acid derivatives.