PREDICTION OF PUTATIVE BINDING POCKET FOR CARBOHYDRATES DOCKING IN COMPUTED MODEL OF AN INSECTICIDAL LECTIN-LIKE PROTEIN, ARCELIN FROM INDIAN WILD PULSE LABLAB PURPUREUS

ABSTRACT: Protein-carbohydrate recognition is a most important form of inter-cell communication that performs key role in many biologically significant processes. The legume lectin family has served as a model system for proteincarbohydrate interactions for several decades. Although there were extensive studies in the protein-carbohydrate recognition using legume lectin molecules, specific studies are not available for legume lectin-like proteins called arcelin. In this study, an attempt was made to reveal the identification of potential carbohydrate binding pocket using different carbohydrates in refined computed model of arcelin isolated from wild legume seed, Lablab purpureus. The four methods viz., LIGSITEcs, PASS, Q-SiteFinder and SURFNET through Meta Pocket Server was used to identify the potential carbohydrate binding pocket for suitable ligand docking. The docking studies revealed that chitotriose (-11.37Kcal/Mol) produced more affinity towards the computed model of L. purpureus arcelin. The identified ligand-chitotriose would thus act as inducer for the molecular action of arcelin. This prediction provides development of potential transgenic L.purpureus plant with arcelin and Chitotriose synthesizing gene for Integrated Pest Management Programme (IPM) against bruchid larvae. Keywords: Lablab purpureus arcelin; carbohydrate binding moiety; computed model; potential pockets; MEDock Server, Integrated Pest Management. [I] NTRODUCTION Insecticides are widely used to protect crop plants against their natural insect predators. Nevertheless, the extensive use of these synthetic chemicals has given rise to widespread concern about insecticide resistance among insect pests and of soil pollution. This has prompted active investigation into new protective strategies, and the development of genetically engineered crops expressing insecticidal proteins appears attractive PREDICTION OF PUTATIVE BINDING POCKET FOR CARBOHYDRATES DOCKING IN COMPUTED MODEL Sundaram Janarthanan, et al. 218 protein, whereas Minney et al. [6] consider arcelin to be an indigestible protein which induces starvation of the larvae and leads to death. The mechanism of arcelin toxicity in insects is speculative. Paes et al. Ligands Preparation The twenty different carbohydrates Cellobiose, Chitotriose, Fructose, Fucose, Galacturonic Acid, Glucosamine -6-Phosphate, Glucosamine, Glucose-6-Phosphate, Beta D Glucose, Lactose, Lactulose, L-arabinose, Maltose, N-Acetyl-D-glucosamine, Rhamnose, Ribose, Sorbital, Sucrose, Xylose. These all 3D structures are approved by FDA were retrieved from Drug Bank http://www.drugbank.ca for docking studies. The atomic co-ordinate and quality of structures were verified by CORINA -SMILES notations 2.3. Prediction of putative active site We subjected the refined model which is obtained from PMDB, to META POCKET active site prediction server. Based on output of Meta pocket server and combination of all 8 algorithms showed that, the computed model of arcelin has one potential carbohydrate binding (cluster) pocket with the distance of PCS(Pocassa) 0.220 nm, FPK(F-pocket) 0.228 nm, CON (Concavity) 0.103 nm, SFN (Surfnet) 0.578 nm, LCS (Ligsite) 0.458 nm , GHE (Ghecom) 0.720 nm and Q-site fider 0.331 from MPT. This result clearly stating that, base method Predicted pockets are present one adjacent another with in the short distance in computed model of L. purpureus arcelin. The amino acids involved in the formation of active clusters and it chains are tabulated. Hence, the selected amino acids were considered for refined docking study to find the interaction with various carbohydrate moieties Docking In MeDock Server The docking simulations aim to mimic the biochemical process of a ligand approaching the active site of its receptor using computational methodologies. Docking analysis of different carbohydrates with arcelin receptor was carried by MEDock (Maximum Entropy Based) docking server. Docking PREDICTION OF PUTATIVE BINDING POCKET FOR CARBOHYDRATES DOCKING IN COMPUTED MODEL Sundaram Janarthanan, et al. 219 allows virtual screening of a database of compounds and predicts the strongest binders based on various scoring functions which is based on Gaussian distribution. It explores ways in which two molecules, such as ligand and protein or enzyme or receptor fit together and dock to each other like pieces of a threedimensional jigsaw puzzle. The molecules binding to a receptor inhibit or enhance its function and thus act as inhibitor or inducer. The collection of different ligands for arcelin molecular action was identified via docking and their relative stabilities were evaluated using molecular dynamics and their binding affinities, using free energy simulations. The receptors were docked against various carbohydrates via MEDock server by refined dock approach. We assigned the grid spacing 0.375 A 0 and docking run for five for the selection of most stable confirmations of the substrate based on lowest docking energy and their binding mode was analyzed at resulting selected functional site, the remaining parameters are set to be default for all carbohydrate docking process. [III] RESULTS The putative active site clusters in computed L. purpureus arcelin were predicted online by submitting to active cavity prediction server Meta pocket. The server output showed that our predicted model had one potential active cavity cluster at a distance of POCASA 0.221 nm, F-POCKET 0.228 nm, CONCAVITY 0.103 nm, SURFNET 0.578 nm, LIGSITE 0.458 nm and GHECOM 0.720 nm from META POCKET. The amino acids involved in the formation of active clusters and its chains are presented

Analysis on the arcelin expression in bruchid pest resistant wild pulses using real time RT-qPCR

1195-1200Arcelin, the antimetabolic protein from wild pulses is a known natural insecticidal molecule. Wild pulses with high arcelin content could serve as potential source to increase the levels of insect resistance in cultivated pulse crops. In this study, arcelin (Arl) gene expression was screened in seven stored product insect pest resistant wild pulse varieties using real time RT-qPCR. Arcelin gene specific real time PCR primers were synthesized from arcelin mRNA sequence of the wild pulse variety, <i style="mso-bidi-font-style: normal">Lablab purpureus. The results revealed different levels of arcelin gene expression in the tested varieties. Canavalia virosa<span style="font-size:9.0pt;mso-bidi-font-size: 12.0pt" lang="EN-GB"> registered significantly high content indicating its suitability for utilization of arcelin gene in developing stored product insect pest resistance with other cultivated pulses. </span

Evaluation of anti-ulcer activity of Samanea saman (Jacq) merr bark on ethanol and stress induced gastric lesions in albino rats

Objective : To evaluate the antiulcer activity of Samanea saman (Jacq) Merr bark on ethanol and stress induced gastric lesions in albino rats. Materials and Methods : Gastric lesions were induced in rats by oral administration of absolute ethanol (5 ml/kg) and stress induced by water immersion. The antiulcer activity of methanolic extract of Samanea saman (Jacq) Merr bark (100 mg/kg, 200 mg/kg, 400 mg/kg) was compared with standard drugs. The parameters studied were ulcer index, gastric juice volume, pH, free acidity and total acidity. Result : Samanea saman (Jacq) Merr showed a dose dependent curative ratio compared to ulcer control groups. The extract at 400 mg/kg showed significant anti ulcer activity which is almost equal to that of the standard drug in both models. The volume of acid secretion, total and free acidity was decreased and pH of the gastric juice was increased compared to ulcer control group. Conclusions : The present study indicates that Samanea saman (Jacq) Merr bark extracts have potential anti ulcer activity

Prediction of Abrasive Waterjet Machining Parameters of Military-Grade Armor Steel by Semi-Empirical and Regression Models

Rolled homogeneous armor steel (RHA) with a high tensile strength, toughness, and hardness is often used in military combat vehicles. RHA is a high-strength low alloy steel suitable for all battlefield usage in military vehicles. The present work examines the prediction output responses in the material removal rate (MRR), surface roughness (Ra), and kerf angle (Ka) for the AWJM of armor steel using regression and semi-empirical models. The AWJM trials were performed using an L27 factorial design with each process variable set to three levels, namely, the standoff distance (SOD), jet traversing speed (JT), and jet water pressure (P). A regression model was constructed using the response surface method (RSM) and data from the trials. Through dimensional analysis and with Buckingham’s π-theorem, a semi-empirical model was built using both the experimental data and material property data. Predictions made by the models were proportionate with the results of the experiments under the same conditions. Microscopic investigations on MRR and Ra were performed using a scanning electron microscope (SEM). The optimal values of the output responses of the machined armor steel plate were obtained with higher MRR = 298.92 mm3/min, lower Ka = 0.651°, and lower Ra = 2.23 µm. The present work established that semi-empirical models accurately predict the output responses in the AWJM of armor steel

Keratinocytes: An Enigmatic Factor in Atopic Dermatitis

Atopic dermatitis (AD), characterized by rashes, itching, and pruritus, is a chronic inflammatory condition of the skin with a marked infiltration of inflammatory cells into the lesion. It usually commences in early childhood and coexists with other atopic diseases such as allergic rhinitis, bronchial asthma, allergic conjunctivitis, etc. With a prevalence rate of 1–20% in adults and children worldwide, AD is gradually becoming a major health concern. Immunological aspects have been frequently focused on in the pathogenesis of AD, including the role of the epidermal barrier and the consequent abnormal cytokine expressions. Disrupted epidermal barriers, as well as allergic triggers (food allergy), contact allergens, irritants, microbes, aggravating factors, and ultraviolet light directly initiate the inflammatory response by inducing epidermal keratinocytes, resulting in the abnormal release of various pro-inflammatory mediators, inflammatory cytokines, and chemokines from keratinocytes. In addition, abnormal proteinases, gene mutations, or single nucleotide polymorphisms (SNP) affecting the function of the epidermal barrier can also contribute towards disease pathophysiology. Apart from this, imbalances in cholinergic or adrenergic responses in the epidermis or the role played by immune cells in the epidermis such as Langerhans cells or antigen-presenting cells can also aggravate pathophysiology. The dearth of specific biomarkers for proper diagnosis and the lack of a permanent cure for AD necessitate investigation in this area. In this context, the widespread role played by keratinocytes in the pathogenesis of AD will be reviewed in this article to facilitate the opening up of new avenues of treatment for AD

SARS-CoV-2 Infection after Effects: Multi-Organ Damage through Oxygen Radicals

Introduction: SARS-CoV-2 respiratory infection leads to two-layered pathology in time (a) immediate pathology and recovery or fatal ending and (b) long periods of remission followed by unexplained clinical expressions involving one or more systems with various clinical presentations, even leading to loss of lives. Among the common causative factors affecting nearly all organs and systems, oxygen radicals and oxygen-derived species (ROS) should rank conclusively on top. Objective: This clinical report, part of a community screening of unexplained clinical outcomes in post-COVID presentation, carries findings focusing on ROS production and possible ROS-induced damages. Materials and Methods: Flow cytometry was used to quantify the samples' total ROS, superoxide production, and apoptosis quantification. Results: Observations indicate unexplained nearly uniform enhanced ROS production in all these long COVID subjects, although clinical presentations varied from no complaints to the requirement of advanced interventions. Conclusion: Causative factors leading to raised oxygen-derived toxic intermediaries (ROS) in initiating these variable long COVID presentations are ill-understood yet possibly merit mass screenings and possible intense anti-oxidative therapy given that such antioxidant therapy through oral medications led to rapid lowering of ROS production and improvement of clinical presentations

A network pharmacology, molecular docking and <i>in vitro</i> investigation of <i>Picrorhiza kurroa</i> extract for the treatment of diabetic nephropathy

Picrorhiza kurroa Royle ex Benth. (P. kurroa/PK/Kutki), a Himalayan herb belonging to the family Scrophulariaceae, is widely known for its hepatoprotective activity. Traditionally, it is found to be effective for upper respiratory tract disorders, kidney and liver problems, dyspepsia and chronic diarrhoea but the mechanism of action is unclear. In this study, the mode of action of P. kurroa for the treatment of diabetic nephropathy (DN) was investigated by network pharmacology, molecular docking and in vitro assays. Numerous databases have been screened and 33 P. kurroa bioactive compounds and 56 targets were identified. The compounds-targets network, targets-pathways network and compounds-targets-pathways network were constructed. The major bioactive compounds include picrorhizaoside D, scrophuloside A, vanillic acid, arvenin I, cinnamic acid, picein, 6-feruloyl catalpol, picroside V, pikuroside, apocynin, picroside I, picroside IV, androsin, cucurbitacin P, boschnaloside, kutkoside, cucurbitacin O, cucurbitacin K, picracin, etc. The potential protein targets identified in this study were MMP1, PRKCA, MMP7, IL18, IL1, TNF, ACE, ASC, CASP1, NLRP3, MAP, KURROA1, mitogen-activated protein kinase (MAPK)14 and MAPK8. In the Database for annotation visualization and integrated discovery (DAVID) pathways and Gene Ontology enrichment analysis, 14 major DN signalling pathways were identified, including MAPK, renin-angiotensin system (RAS), TNF, signal transducer and activator of transcription (JAK-STAT), TLR, vascular endothelial growth factor (VEGF), mTOR, Wnt, Ras, PPARs, NFB, NOD and phosphatidylinositol signalling pathways. A molecular docking study revealed that 32 bioactive compounds of P. kurroa interacted with 14 significant proteins/genes associated with DN. P. kurroa extract was proven to enhance the survival rate of HEK cells significantly. Protein expression analysis using Western blot demonstrated that P. kurroa extract significantly altered the expression of p47phox, p67phox, gp91phox, IL-1 and TGFβ-1. As a result of network pharmacology and docking work, new concepts for discovering bioactive compounds and effective modes of action could be developed. The potential effect of P. kurroa extract on DN disease was evident in the in-vitro studies aided by network pharmacology and molecular docking. Communicated by Ramaswamy H. Sarma</p