Combinatorial Chemistry & High Throughput Screening - Volume 20, Issue 3, 2017

Background: Regucalcin (RGN), a calcium regulating protein having anti-prolific, antiapoptotic functions, plays important part in the biosynthesis of ascorbic acid. It is a highly conserved protein that has been reported from many tissue types of various vertebrate species. Employing its effect of regulating enzyme activities through reaction with sulfhydryl group (-SH) and calcium, structural level study believed to offer a better understanding of binding properties and regulatory mechanisms of RGN, was performed. Material and method: Using sample from testis of Bubalus bubalis, amplification of regucalcin (RGN) gene was subjected to characterization by performing digestion using different restriction endonucleases (RE). Alongside, cDNA was cloned into pPICZαC vector and transformed in DH5α host for custom sequencing. To get a better insight of its structural characteristics, three dimensional (3D) structure of protein sequence was generated using in silico molecular modelling approach. The full trajectory analysis of structure was achieved by the Molecular Dynamics (MD) that explains the stability, flexibility and robustness of protein during simulation in a time of 50ns. Molecular docking against 1,5-anhydrosorbitol was performed for functional characterization of RGN. Results: Preliminary screening of amplified products on Agarose gel showed expected size of ~893 bp of PCR product corresponding to RGN. Following sequencing, BLASTp search of the target sequence revealed that it shares 91% similarity score with human senescence marker protein-30 (pdb id: 3G4E). Molecular docking of 1,5-anhydrosorbitol reveals information regarding important binding site residues of RGN. 1,5-anhydrosorbitol was found to interact with binding free energy of - 6.01 Kcal/mol. RMSD calculation of subunits A, B and D-F might be responsible for functional and conserved regions of modeled protein. Conclusion: Three dimensional structure of RGN was generated and its interactions with 1,5- anhydrosorbitol, demonstrates the role of key binding residues. Until now, no structural details were available for buffalo RGN proteins, hence this study will broaden the horizon towards understanding the structural and functional aspects of different proteins in cattle.

Background: Cancer-associated metabolites result from cell-wide mechanisms of dysregulation. The field of metabolomics has sought to identify these aberrant metabolites as disease biomarkers, clues to understanding disease mechanisms, or even as therapeutic agents. Objective: This study was undertaken to reliably predict metabolites associated with colorectal, esophageal, and prostate cancers. Metabolite and disease biological action networks were compared in a computational platform called MSD-MAP (Multi Scale Disease-Metabolite Association Platform). Methods: Using differential gene expression analysis with patient-based RNAseq data from The Cancer Genome Atlas, genes up- or down-regulated in cancer compared to normal tissue were identified. Relational databases were used to map biological entities including pathways, functions, and interacting proteins, to those differential disease genes. Similar relational maps were built for metabolites, stemming from known and in silico predicted metabolite-protein associations. The hypergeometric test was used to find statistically significant relationships between disease and metabolite biological signatures at each tier, and metabolites were assessed for multi-scale association with each cancer. Metabolite networks were also directly associated with various other diseases using a disease functional perturbation database. Results: Our platform recapitulated metabolite-disease links that have been empirically verified in the scientific literature, with network-based mapping of jointly-associated biological activity also matching known disease mechanisms. This was true for colorectal, esophageal, and prostate cancers, using metabolite action networks stemming from both predicted and known functional protein associations. Conclusion: By employing systems biology concepts, MSD-MAP reliably predicted known cancermetabolite links, and may serve as a predictive tool to streamline conventional metabolomic profiling methodologies.

Aim and Objective: The population of diabetic patients is rapidly increasing globally. The treatment of these patients is a complex phenomenon due to the use of the different drugs. The present article reports a synchronized fast SPE-UFLC separation of eight antidiabetic drugs in human plasma. Inexpensive solid phase extraction (SPE) and ultra fast liquid chromatography (UFLC) methods were presented for monitoring of eight antidiabetic drugs in human plasma. The separated drugs include metformin HCl, vildagliptin, gliclazide, linagliptin, sitagliptin, pioglitazone, glimepiride and repaglinide plasma sample. Material and Method: The column used was a Sunshell C18 (150 x 4.6 mm, 2.6 μm) with eluent of acetate buffer (0.05% TEA in 0.05 M NH4Ac of pH 7.0 with H 3PO4) - ACN (60 : 40, v/v). The flow rate was 1.0 mL/min with a detection wavelength of 210 nm and column temp. of 45±1ºC. These drugs were extracted from human plasma using Sep-Pac C18 cartridge. Phosphate buffer (25 mM; pH 7.0) containing these drugs were allowed to pass through cartridge at 0.1 mL/min flow rate. The adsorbed drugs on C18 cartridge were eluted by methanol at 1.0 mL/min flow rate. Results: The values for the retention, separation and resolution factors were ranged from 0.072 to 9.140, 1.443 to 4.208 and 2.147 to 18.652, correspondingly. The percent recoveries for these drugs in the standard laboratory samples prepared in water ranged from 77 to 88%. These values in plasma samples ranged from 10 to 22%. Conclusion: The validated method was fruitfully adopted to analyze these drugs in human plasma for the clinical monitoring of these drugs.

Aim and Objective: Kelch like ECH-associated protein 1 (Keap1) and Nuclear factor-E2 related factor 2 (Nrf2) binding is a key step in the ubiquitination and degradation of Nrf2. The compounds inhibiting this binding exert antioxidant actions. Naturally occurring pentacyclic triterpenoids (PTs) and their synthetic derivatives are projected as activators of Nrf2 signalling. The 16-mer Nrf2 peptide binding site on Keap-1 (PDB: 2 FLU) is proposed to be the prospective target where pentacyclic triterpenoid may exert protein-protein interaction. Material and Method: In the present study, seventy seven PTs of natural and synthetic origin are screened for Nrf2 stimulatory activity using online PASS (Prediction of Activity Spectrum of Substances) software followed by in silico molecular docking against 16-mer Nrf2 peptide binding site on Keap-1. This virtual screening reveals that Nrf2 stimulatory PTs dock on the 16-mer peptide binding site on Keap-1 and may exert their biological activities by interfering with the Keap-1 and Nrf2 binding. Results: In the present study shows that the small molecules like PT’s bind to keap 1 pocket where the 16 mer peptide of Neh2 domain of Nrf2. High docking score of -10.53, -9.08, -8.36, -7.94, -7.49 and -7.18 is shown by glycyrrhizin, asiatic acid, medecassic acid, barrigenic acid, rotundic acid, ursolic acid, respectively. Conclusion: The identified hits such as asiatic acid and medecassic acid represent a very promising starting point for the development of potent Nrf2 stimulator. The natural PTs are more promising than the most potent synthetic derivatives of oleanolic acid like CDDO, CDDO-methyl and CDDOimidazol.

Tuberculosis causes around 1.4 million deaths every year remaining to be a major cause of morbidity and mortality. Mycobacterium tuberculosis is adept at surviving the assault of our immune system, which has perplexed many researchers. Not only are they difficult to treat, but also difficult to detect accurately. The current reservoir of drugs and method to diagnose them is depleting faster than we are able to replace them with newer one. The advances made in the field of metabolomic have opened up a window of opportunities such as identification of new drug and druggable site, prediction of drug toxicity and detection of new biomarkers to accurately diagnose the disease. With its short history of less than two decades, metabolomics has shown very promising future to tackle this concern. Equally important developments in analytical techniques and application of data interpretation have further facilitated the scope of this field. The present review discusses the advances in metabolomic research with an emphasis on tuberculosis diagnosis and therapeutics.

Identifying novel bio markers in gastro intestinal disease is a promising method where a comprehensive analysis of the metabolome is performed. Metabolomics has evolved enormously in the past decade, paving a path in gastro intestinal disease research, especially diseases which lead to high morbidity and mortality. Metabolomics involves identifying metabolites such as anti-oxidants, and amino acids etc., which are screened in the urine, feces and tissue samples. Certain cases employ advanced tools like GC-MS, 1HNMR and GC–MS/SPME which reveal valuable information concerning disease severity and differentiation. In light of escalating health care costs and risky invasive procedures, metabolomics can be chosen as a safe yet precise method for screening diseases like ulcerative colitis, Crohns’ disease, celiac disease, and gastro intestinal cancers. The present review focuses on major advancements in gastro intestinal metabolomics, giving attention to which parameters are assessed, and to recent changes in metabolite analysis.

Aim and Objective: Visceral leishmaniasis is a deadly disease left untreated in over 95% of cases. It is characterized by irregular bouts of fever, weight loss, enlargement of the spleen and liver, and anemia. It is highly endemic in the Indian subcontinent. CAAX prenyl protease I of Leishmania donovani is one of the important targets regulating the post translational modification process. Hence identifying potent drug candidate against the target is essential. This study mainly focuses on developing new and potent inhibitors against CAXX prenyl protease I of Leishmania donovani. Materials and Methods: Pharmacophore based virtual screening was carried out using derivatives of bi-substrate analog farnesyl transferase inhibitors reported against CAAX prenyl proteases I. On the basis of ligand based pharmacophore model we have obtained 5 point pharmacophore AAADR with three hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatic ring. The newly identified hits through pharmacophore model were further docked into the active site of the modeled protein. To get further insights of protein ligand interaction we have performed induced fit docking followed by molecular dynamics simulations. The DFT analysis depicts the electronic structure properties of the compounds. These results can be useful for the development of novel and potent CAAX prenyl protease I inhibitors. Results: Initially, we have obtained a large number of newly identified hits by screening four different databases further docked into the active site of the protein and 20 compounds were selected on the basis of docking score. Perhaps Induced fit docking was performed to infer protein ligand interaction in a dynamic state and top 5 compounds 7118044, 7806909, LEG12866807, 9208535, SYN 19867403 were found to have good protein ligand interactions with key amino acid residues such as Glu287, His290 and additional interaction like Ile197, Asn209 Tyr253, Phe254, Gly256, Tyr266 with better binding energy -59.794 Kcal/mol, -66.305 Kcal/mol, -70.467 Kcal/mol, -82.474 Kcal/mol, -64.045. The predicted ADME properties are in desirable range and the HOMO/LUMO gap clearly indicates the electrons behavior of the ligands. Molecular dynamics simulations of the protein ligand complex for 20 ns clearly depicts the compounds are stable throughout the simulation time. Conclusion: The newly identified hits through pharmacophore based screening could be used as potential CAAX prenyl protease I inhibitors of Leishmania donovani.

Background: Heterocyclic scaffold, benzotriazole and its derivatives are potential anaesthetic agents that act locally. Objective: QSAR and docking analysis of previously synthesized benzotriazolyl derivatives were modelled for their local anaesthetic action using computer assisted multiple regression analysis. It provides the insight about the structural requirements for the local anaesthetic action. Method: A training set comprising of 16 molecules and test set of 8 molecules were selected for present investigation by using sphere exclusion method with dissimilarity value of +4.0. The validation of the QSAR models was performed by cross-validation and external test set prediction. Docking studies was performed using GRIP docking methodology. Results & Conclusion: Further GRIP docking with the pentameric ligand gated ion channel, 2XQ3 facilitated the mechanistic analysis of interactions of the test molecules active site residues.