Molecular Characterization of Wheat Genotypes Using SSR Markers

Wheat (Triticum aestivum L.) rusts are the most destructive and widespread among all other diseases of wheat because of their wide distribution, and their capacity to form new races that can attack previously resistant cultivars which result in serious yield losses. The molecular characterization and genetic diversity of 20 wheat genotypes was investigated using 34 polymorphic Simple Sequence Repeats (SSR) screened primers. About thirty-one loci were found. Lr-19 gene was present in all 20 wheat genotypes that cause resistance against wheat rust. Shalimar-86 and Chakwal-86 showed the highest genetic diversity with SH-02 and Ufaq respectively, giving a 98.94% genetic similarity and a minimum genetic diversity was observed between Chakwal-50 and Bhakar which showed that they are 74% similar. The current research found that SSR makers could distinguish and characterize all of the genotypes, more screened primers could be used for study and for saturation of different regions in further research. The identification of rust resistant genes in Pakistani wheat germplasm will help in accelerating the breeding program in future, including pyramiding of different wheat resistant genes in wheat genotypes and varieties

In silico elucidation of potential drug target sites of the Thumb Index Fold Protein, Wnt-8b

Purpose: The involvement of Wnt-8b in Wnt signaling pathway leads to various  cancers. The purpose of this study was to determine the therapeutic compounds from the available library by targeting Wnt-8b using molecular docking analyses.Methods: Threading and comparative modeling approaches were employed to predict the 3D structure of Wnt-8b. Sixty-eight models were evaluated using molprobity, ERRAT and rampage evaluation tools and the model having 82.456 % overall quality value was selected for further analyses. The acyl group was added to the suitable model to satisfy the hydrophobic nature of the Wnt-8b. Literature-derivedcompounds were selected for comparative molecular docking studies using GOLD, AutoDock and AutoDock Vina. Furthermore, docked complexes were analyzed and visualized using Chimera and Ligplot.Results: The compound ZINC04029462 exhibited high binding potential with Wnt-8b and palmitoleic acid and was found common among top 20 compounds of each tool. His-183, Val-185, Ser-186, Gly-187, Ser-188 and Thr-190 residues commonly interacted with compounds and palmitoleic acid and considered as potential interacting residues.Conclusion: Common interacting residues from top 20 compounds of each tool suggest that these compounds may be utilized to inhibit aberrant expression of Wnt-8b. The common inhibitor ZINC04029462 may act as a lead compound for further drug designing against Wnt family.Keywords: Wnt-8b, Cancer, Homology modeling, Molecular docking, AutoDoc

Pharmacoinformatics, Adaptive Evolution, and Elucidation of Six Novel Compounds for Schizophrenia Treatment by Targeting DAOA (G72) Isoforms

Studies on Schizophrenia so far reveal a complex picture of neurological malfunctioning reported to be strongly associated with DAOA. Detailed sequence analyses proved DAOA as a primate specific gene having conserved gene desert region on both upstream and downstream region. The analyses of 10 MB chromosomal region of primates, birds, rodents, and reptiles having DAOA evidenced the conserved part in primates and in the rest of species, while DAOA is only present in primates. DAOA has four isoforms having one interaction partner DAO. Protein-protein analyses of four DAOA isoforms with DAO were performed individually and find potential interacting residues computationally. It was observed that molecular docking of approved FDA drugs revealed efficient results but there was no common drug with effective binding to all DAOA isoforms. Library of compounds was constructed by virtual screening of 2D similarity search against recommended SZ drugs in conjunction with their physiochemical properties. Molecular docking resulted in six novel compounds exhibiting maximum binding affinity with selected four DAOA isoforms. However not the entire schizophrenic population responds to the single drug and interestingly in this study six novel compounds having promising results and same binding site to that DAOA that may be used to interact with DAO against four DAOA isoforms were observed

In silico Comparative Modeling of PapA1 and PapA2 Proteins Involved in Mycobacterium Tuberculosis Sulfolipid-1 Biosynthesis Pathway

Tuberculosis is one of the most serious health problems, as globally; around 2 billion or one third of the world's total population has been infected with Mycobacterium tuberculosis. Mycobacterium tuberculosis is a unique among bacterial pathogens in that it displays a wide array of complex lipids and lipoglycans on its cell surface. One such glycolipid, sulfolipid-1 (SL-1), is the most sulfatide, consists of a trehalose core, four fatty acyl groups, and a sulfate ester. Several proteins involved in SL-1 biosynthesis have been identified, the enzymes that acylate the T2S core to form SL1278 and SL-1, and the biosynthetic order of these acylation reactions, are unknown. Here we studied the in silico identification of PapA2 and PapA1, proteins responsible for the sequential acylation of T2S to form SL1278 and are essential for SL-1 biosynthesis, by applying different bioinformatics tools. Benchmark, of 3 different homology modeling programs Modeller, Swiss-Model (Deep View), and ESyPred3D, has been performed used to transform the alignment to a 3D model. The 3D structures of targeted proteins were evaluated by evaluation tools, ANOLEA and Verify3D. It is concluded that in SL-1 biosynthesis pathway, PapA1 and PapA2 proteins could be used as drug target, drug lead design and to find out the other proteins involved in this pathway that not yet have been identified and may be used to the cure of tuberculosis infection

<i>In silico</i> elucidation of potential drug target sites of the Thumb Index Fold Protein, Wnt-8b

International audienc

Current Therapeutic Molecules and Targets in Neurodegenerative Diseases Based on in silico Drug Design

International audienc

Comprehensive in silico analyses of flavonoids elucidating the drug properties against kidney disease by targeting AIM2.

Kidney disorders are among the most common diseases and there is a scarcity of effective treatments for chronic kidney disease. There has been a progressive improvement in specific flavonoids for protective effects against kidney diseases. Flavonoids inhibit the regulatory enzymes to control inflammation-related diseases. In the present study, a hybrid approach of molecular docking analyses and molecular dynamic simulation was followed by principal component analyses and a dynamics cross-correlation matrix. In the present study, the top-ranked five flavonoids were reported, and the maximum binding affinity was observed against AIM2. Molecular docking analyses revealed that Glu_186, Phe_187, Lys_245, Glu_248, Ile_263, and Asn_265 are potent residues against AIM2 for ligand-receptor interactions. Extensive in silico analyses suggested that procyanidin is a potential molecule against AIM2. Moreover, the site-directed mutagenesis for the reported interacting residues of AIM2 could be important for further in vitro analyses. The observed novel results based on extensive computational analyses may be significant for potential drug design against renal disorders by targeting AIM2

In silico elucidation of potential drug targets against oxygenase domain of Human eNOS Dysfunction.

Nitric Oxide (NO) signaling pathway plays a vital role in various physiological and pathophysiological processes including vasodilation, neurogenesis, inflammation, translation and protein regulation. NO signaling pathway is associated with various diseases such as cardiovascular diseases, vision impairment, hypertension and Alzheimer's disease. Human Endothelial Nitric Oxide Synthase (eNOS) bound with calcium regulatory protein (calmodulin (CaM)) to produce NO which initiates cGMP pathway. The current study employs to screen the novel compounds against human eNOS independent of calcium regulatory protein (CaM). The current effort emphasized that the deficiency of CaM leads to dysfunction of cGMP signaling pathway. In this work, a hybrid approach of high-throughput virtual screening and comparative molecular docking studies followed by molecular dynamic simulation analyses were applied. The screening of top ranked two novel compounds against eNOS were reported that showed effective binding affinity, retrieved through the DrugBank and ZINC database libraries. Comparative molecular docking analyses revealed that Val-104, Phe-105, Gln-247, Arg-250, Ala-266, Trp-330, Tyr-331, Pro-334, Ala-335, Val-336, Tyr-357, Met-358, Thr-360, Glu-361, Ile-362, Arg-365, Asn-366, Asp-369, Arg-372, Trp-447 and Tyr-475 are potent residues for interactional studies. High-throughput virtual screening approach coupled with molecular dynamic simulation and drug likeness rules depicted that ZINC59677432 and DB00456 are potent compounds to target eNOS. In conclusion, the proposed compounds are potent against eNOS based on extensive in silico analyses. Overall, the findings of this study may be helpful to design therapeutic targets against eNOS