Phytochemical Moieties From Indian Traditional Medicine for Targeting Dual Hotspots on SARS-CoV-2 Spike Protein: An Integrative in-silico Approach.

SARS-CoV-2 infection across the world has led to immense turbulence in the treatment modality, thus demanding a swift drug discovery process. Spike protein of SARS-CoV-2 binds to ACE2 receptor of human to initiate host invasion. Plethora of studies demonstrate the inhibition of Spike-ACE2 interactions to impair infection. The ancient Indian traditional medicine has been of great interest of Virologists worldwide to decipher potential antivirals. Hence, in this study, phytochemicals (1,952 compounds) from eight potential medicinal plants used in Indian traditional medicine were meticulously collated, based on their usage in respiratory disorders, along with immunomodulatory and anti-viral potential from contemporary literature. Further, these compounds were virtually screened against Receptor Binding Domain (RBD) of Spike protein. The potential compounds from each plant were prioritized based on the binding affinity, key hotspot interactions at ACE2 binding region and glycosylation sites. Finally, the potential hits in complex with spike protein were subjected to Molecular Dynamics simulation (450 ns), to infer the stability of complex formation. Among the compounds screened, Tellimagrandin-II (binding energy of -8.2 kcal/mol and binding free energy of -32.08 kcal/mol) from Syzygium aromaticum L. and O-Demethyl-demethoxy-curcumin (binding energy of -8.0 kcal/mol and binding free energy of -12.48 kcal/mol) from Curcuma longa L. were found to be highly potential due to their higher binding affinity and significant binding free energy (MM-PBSA), along with favorable ADMET properties and stable intermolecular interactions with hotspots (including the ASN343 glycosylation site). The proposed hits are highly promising, as these are resultant of stringent in silico checkpoints, traditionally used, and are documented through contemporary literature. Hence, could serve as promising leads for subsequent experimental validations.

Mutation spectrum in BBS genes guided by homozygosity mapping in an Indian cohort.

Bardet-Biedl syndrome (BBS), a ciliopathy disorder with pleiotropic effect manifests primarily as retinal degeneration along with renal insufficiency, polydactyly and obesity. In this study, we have performed homozygosity mapping using NspI 250K affymetrix gene chip followed by mutation screening of the candidate genes located in the homozygous blocks. These regions are prioritized based on the block length and candidature of the genes in BBS and other ciliopathies. Gene alterations in known BBS (22) and other ciliopathy genes such as ALMS1 (2) were seen in 24 of 30 families (80%). Mutations in BBS3 gene, inclusive of a novel recurrent mutation (p.I91T) accounted for 18% of the identified variations. Disease associated polymorphisms p.S70N (BBS2), rs1545 and rs1547 (BBS6) were also observed. This is the first study in Indian BBS patients and homozygosity mapping has proved to be an effective tool in prioritizing the candidate genes in consanguineous pedigrees. The study reveals a different mutation profile in the ciliopathy genes in Indian population and implication of novel loci/genes in 20% of the study group.

Structural studies on AIPL1 and its functional interactions with NUB1 to identify key interacting residues in LCA4.

Leber congenital amaurosis (LCA) is an autosomal recessive disorder that causes visual impairment in children due to fifteen different gene mutations. Of these, mutations in Aryl-Hydrocarbon Receptor Interacting Protein-like 1 (AIPL1) cause the most severe form of LCA (LCA4) leading to the degeneration of photoreceptor cells. NEDD8 Ultimate Buster 1 (NUB1), a protein that regulates cell cycle progression, interacts with AIPL1 to prevent the over expression of NUB1. In the case of over expression, cell cycle progression is disrupted and may lead to LCA. The studies on interactions between these two proteins will aid in identifying potential modulators for this condition. Since no three-dimensional structure is currently available for these two proteins, in this study we predicted the structures of these two proteins by molecular modelling methods. Moreover, we also modelled the three proven significant mutant forms of AIPL1 spanning the tetratricopeptide domain. Finally, both the modelled wild and mutant structures of AIPL1 (A197P, C239R and G262S) were computationally docked to NUB1, so as to map the potential molecular interactions. This is the first study on modelling the structure-function relationship of AIPL1-NUB1 interactions which shall aid in discovery of novel therapeutic agents.

Chemical inhibition of fatty acid synthase: molecular docking analysis and biochemical validation in ocular cancer cells.

Fatty acid biosynthesis is an attractive target for anti-cancer therapeutics. The ocular cancer, retinoblastoma cells were treated with fatty acid synthase (FASN) enzyme inhibitors: cerulenin, triclosan and orlistat. The IC(50) and dose-dependent sensitivity of cancer cells to FASN inhibitors decrease in biologic enzyme activity, and cell morphology alterations were analysed. Molecular interactions of enzyme-inhibitor complexes were studied by molecular modelling and docking simulations. The crystal structures of ketoacyl synthase (PDB ID:3HHD) (cerulenin) and thioesterase (PDB ID:2PX6) (orlistat) domains of human FASN were utilized for docking, while for the non-crystallised human FASN enoyl reductase domain (triclosan), homology model was built and used for docking. All three inhibitors showed significant binding energy indicating stable complex formation with their respective FASN subunits. The predicted Ki value of the FASN inhibitors corroborated well with their corresponding anti-cancer effects.

Simultaneous separation and preconcentration of trace elements in water samples by coprecipitation on manganese dioxide using D-glucose as reductant for KMnO(4).

A field oriented and economical method of coprecipitation of trace elements like Al, Au, Bi, Cd, Co, Cu, Fe, Mo, Ni, Pb, Pd, Ti, V, W, Zn and REE has been developed. A novel reductant D-glucose, reduces KMnO(4) in solution to form a precipitate of MnO(2.) Two liters of clear natural water sample is adjusted to pH 3.5-4.0, and is treated with 10 ml of 1% KMnO(4) and 20 ml of 0.1% D-glucose. The sample is heated at a temperature of 75-80 degrees C, MnO(2) is formed which coprecipitates the above trace elements. The precipitate is separated by filtration, dissolved in 2 ml of 50% HCl and 2 ml of 30% H(2)O(2) and diluted to 25 ml for analysis using AAS and ICP-AES. The recoveries were found to be 96-105%. The preconcentration factor is 80. Limits of determination by the proposed method in natural waters are 1 mug l(-1) for Al, Cd, Mo, V, W, Ti and Zn, 5 mug l(-1) for Au, Bi, Co, Cu, Fe, Ni, Pb and Pd and 8 mug l(-1) for REE. The RSD of the present procedure (n=5) is 8% at approximately 5 mug l(-1) level. Twenty water samples can be analyzed by an analyst in an 8-h day.

Cold dissolution method for the determination of uranium in various geological materials at trace levels by laser fluorimetry.

A cold dissolution procedure for the determination of uranium in various geological materials like rocks, minerals, soils etc., has been described. Samples are allowed to react with HF and HNO(3) at room temperature overnight. Boric acid is added to complex excess fluoride ions. From the clear solution thus obtained, uranium is determined directly in laser fluorimeter after the addition of fluorescence enhancing reagents. The results of few standard reference materials analysed by the present method agree with the certified values. This methodology does not require platinum or teflon ware, exhaust system and time consuming solvent extraction step. Hazardous acid vapours are not left in air, so there is no air pollution. Chemicals consumption is minimal. Therefore the method is economical. The method can be employed for high sample throughput which is the prerequisite for exploration geochemists.