Bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of Leclercia sp. QAU-66

Naveed, Muhammad; Ahmed, Iftikhar; Khalid, Nauman; Mumtaz, Abdul Samad

doi:10.1590/s1517-83822014000200031

Cited by 29 publications

(20 citation statements)

References 35 publications

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“…Two strong hydrogen bonds were established with Asp-2357 and Tyr-2225 ( Figure 5). Hydrogen bonding with these residues is a cause of increase in potency as reported by [23,30,31].…”

Section: Docking Analysis Of Azd 2014mentioning

confidence: 86%

“…The phosphate groups of ATP extend towards the area of lower hydrophobicity and methyl-morpholine moiety of AZD2014 and AZD8055 extend towards the other edge of low hydrophobicity area. Hydrophobic interactions enhance the binding affinity between ligand and protein [30,45]. The chemical structure of the inhibitors can be optimized for increasing drug efficacy and specificity based on hydrophobic interactions.…”

Section: Comparison Of Highly Specific Binding Modesmentioning

confidence: 99%

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Molecular Docking and Pharmacokinetic of Highly Specific Novel Pan-Mtor Inhibitors against Solid Tumors

Naveed¹

2017

MOJPB

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Mechanistic/mammalian target of rapamycin (mTOR) a serine/threonine kinase belonging to PI3K/Akt/mTOR pathway is involved in different cellular functions cell survival, metabolism, growth, proliferation, apoptosis and autophagy. PanmTOR inhibitors are targeted towards mTOR dysregulation, inhibiting the kinase domain of both mTORC1 and mTORC2. The present study analyzes the binding modes and molecular interactions of highly specific mTOR inhibitors, AZD8055 and its sister compoundAZD2014using computational approach. Both inhibitors proved to be effective against solid tumors in vitro and in vivo. Docking analysis was performed using Auto Dock Vina, conformations were scored based upon their binding energy (kcal/mol) and illustrated using Discovery Studio Visualizer 4.5 version. Inhibitors fit between N-and C-lobes of mTOR kinase domain into the inner hydrophobic core. The results indicated interactions with distinctive mTOR residues Trp-2239, Leu-2185 and newly developed interactions with Asp-2375 for AZD2014 and with Ala-2248, His-2247, Thr-2245 for AZD8055. The binding pattern of both inhibitors was slightly different, responsible for better pharmacokinetic profile of AZD2014 and 5 fold increase in efficacy of AZD8055. The binding energy of best docking score for AZD8055 was -8.0 kcal/mol however AZD20144 showed best binding affinity at -8.2kcal/mol (RMSD l.b. 0.908, RMSD u.b. 1.075). Highly specific, less toxic and potent inhibitors can be designed or optimized based upon the docking results.

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“…Two strong hydrogen bonds were established with Asp-2357 and Tyr-2225 ( Figure 5). Hydrogen bonding with these residues is a cause of increase in potency as reported by [23,30,31].…”

Section: Docking Analysis Of Azd 2014mentioning

confidence: 86%

Section: Comparison Of Highly Specific Binding Modesmentioning

confidence: 99%

Molecular Docking and Pharmacokinetic of Highly Specific Novel Pan-Mtor Inhibitors against Solid Tumors

Naveed¹

2017

MOJPB

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“…Various studies for gene and protein like MBL2 gene, GDH protein and TAGAP gene have been carried out using in silico tools (Naveed, Ahmed, Khalid, & Mumtaz, , Kalia, Sharma, Kaur, Kamboj, & Singh, and Arshad et al, ). Novel therapeutic sites can be found by such studies.…”

Section: Discussionmentioning

confidence: 99%

Identification of most damaging nsSNPs in human CCR6 gene: In silico analyses

Akhtar

Jamal

Jamal³

et al. 2019

Int J Immunogenetics

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Single nucleotide polymorphisms in CCR6 (C–C chemokine receptor type 6) gene have been found to be the possible cause of many diseases like rheumatoid arthritis, psoriasis, lupus nephritis and systemic sclerosis and other autoimmune diseases. Therefore, identification of structurally and functionally important polymorphisms in CCR6 is important in order to study its potential malfunctioning and discovering therapeutic targets. Several bioinformatics tools were used to identify most damaging nsSNPs that might be vital for CCR6 structure and function. The in silico tools included PROVEAN, SIFT, SNP&GO and PolyPhen2 followed by I‐Mutant MutPred and ConSurf. Phyre2 and I‐TASSER were used for protein 3‐D Modelling while gene–gene interaction was predicted by STRING and GeneMANIA. Our study suggested that three nsSNPs https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1376162684, https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=751102128 and https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1185426631 are the most damaging in CCR6 gene while 7 missense SNPs https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1438637216, https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=139697820, https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=768420505, https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1282264186, https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1394647982, https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=769360638 and https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1263402382 are found to revert into stop codons. Prediction of post‐transcriptional modifications highlighted the significance of https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1376162684 because it effected potential phosphorylation site. Gene–gene interactions showed relation of CCR6 with other genes depicting its importance in several pathways and co‐expressions. In future, studying diseases related to CCR6 should include investigation of these 10 nsSNPs. Being the first of its type, this study also proposes future perspectives that will help in precision medicines. For such purposes, CCR6 proteins from patients of autoimmune diseases should be explored. Animal models can also be of significance find out the effects of CCR6 in diseases.

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“…We used the ExPASy-ProtParam tool (https:// www.expasy.org/tools/protparam.html) and EMBOSSPepstats (https://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/) to investigate the physical and chemical properties of PCNXL2 for its functional validation in the lab. 16 We submitted protein queries in the form of a SWISS ID or protein sequence. 17,18 The server directly calculated the values of pI/MW (isoelectric point, molecular weight), percentage of each amino acid, extinction coefficient (EC), instability index (II), aliphatic index (AI) and GRAVY (Grand Average of Hydrophobicity) of the key protein query.…”

Section: Prediction Of Physiochemical Parametersmentioning

confidence: 99%

In silicofunctional and tumor suppressor role of hypothetical protein PCNXL2 with regulation of the Notch signaling pathway

et al. 2018

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Bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of Leclercia sp. QAU-66

Cited by 29 publications

References 35 publications

Molecular Docking and Pharmacokinetic of Highly Specific Novel Pan-Mtor Inhibitors against Solid Tumors

Molecular Docking and Pharmacokinetic of Highly Specific Novel Pan-Mtor Inhibitors against Solid Tumors

Identification of most damaging nsSNPs in human CCR6 gene: In silico analyses

In silicofunctional and tumor suppressor role of hypothetical protein PCNXL2 with regulation of the Notch signaling pathway

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