Comparative modeling of HGPRT enzyme of L. donovani and binding affinities of different analogs of GMP

Ansari, Yousuf; Dikhit, Manas Ranjan; Sahoo, Ganesh Chandra; Das, Pradeep

doi:10.1016/j.ijbiomac.2012.01.010

Cited by 31 publications

(15 citation statements)

References 42 publications

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“…At both time points Hprt, which has previously been recommended for isolated TBI and ischemic 22,41 , showed a high expression stability in the hypothalamus. Hprt, a hypoxanthine-phosphoribosyltransferase (Table 1), is essential for the synthesis of purine nucleotides 42 . The mRNA expression of Hprt seems to stay unaffected by the induction of TBI.…”

Section: Discussionmentioning

confidence: 99%

Validation of reference genes for expression analysis in a murine trauma model combining traumatic brain injury and femoral fracture

Otto

Köhli

Appelt

et al. 2020

Sci Rep

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Systemic and local posttraumatic responses are often monitored on mRNA expression level using quantitative real-time PCR (qRT-PCR), which requires normalisation to adjust for confounding sources of variability. Normalisation requests reference (housekeeping) genes stable throughout time and divergent experimental conditions in the tissue of interest, which are crucial for a reliable and reproducible gene expression analysis. Although previous animal studies analysed reference genes following isolated trauma, this multiple-trauma gene expression analysis provides a notable study analysing reference genes in primarily affected (i.e. bone/fracture callus and hypothalamus) and secondarily affected organs (i.e. white adipose tissue, liver, muscle and spleen), following experimental long bone fracture and traumatic brain injury. We considered tissue-specific and commonly used top-ranked reference candidates from different functional groups that were evaluated applying the established expression stability analysis tools NormFinder, GeNorm, BestKeeper and RefFinder. In conclusion, reference gene expression in primary organs is highly time point as well as tissue-specific, and therefore requires careful evaluation for qRT-PCR analysis. Furthermore, the general application of Ppia, particularly in combination with a second reference gene, is strongly recommended for the analysis of systemic effects in the case of indirect trauma affecting secondary organs through local and systemic pathophysiological responses.

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Section: Discussionmentioning

confidence: 99%

Validation of reference genes for expression analysis in a murine trauma model combining traumatic brain injury and femoral fracture

Otto

Köhli

Appelt

et al. 2020

Sci Rep

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“…Subsequently, the six energy‐minimized SSRIs were docked into the S1 pocket of the hSERT using the CDOCKER program embedded in DS 3.0. For each inhibitor, 30 docking poses were generated and ranked using piecewise linear potential 1 (PLP1) scoring function , which was shown to have a high predictive power in estimating the ligand binding affinity . The highest‐scoring pose according to the PLP1 for each inhibitor was selected as the most appropriate pose, followed by a visual inspection of the preservation of the interactions with the pivotal residues found in the hSERT‐inhibitor complex .…”

Section: Methodsmentioning

confidence: 99%

Combining Structure‐Based Pharmacophore andIn SilicoApproaches to Discover Novel Selective Serotonin Reuptake Inhibitors

Zhou

Liu

et al. 2013

Chem Biol Drug Des

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Inhibition of human serotonin transporter (hSERT) has been reported to be a potent strategy for the treatment for depression. To discover novel selective serotonin reuptake inhibitors (SSRIs), a structure-based pharmacophore model (SBPM) was developed using the docked conformations of six highly active SSRIs. The best SBPM, consisting of four chemical features: two ring aromatics (RAs), one hydrophobic (HY), and one positive ionizable (PI), was further validated using Gunner-Henry (GH) scoring and receiver operating characteristic (ROC) curve methods. This well-validated SBPM was then used as a 3D-query in virtual screening to identify potential hits from National Cancer Institute (NCI) database. These hits were subsequently filtered by absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction and molecular docking, and their binding stabilities were validated by 20-ns MD simulations. Finally, only two compounds (NSC175176 and NSC705841) were identified as potential leads, which exhibited higher binding affinities in comparison with the paroxetine. Our results also suggest that cation-π interaction plays a crucial role in stabilizing the hSERT-inhibitor complex. To our knowledge, the present work is the first structure-based virtual screening study for new SSRI discovery, which should be a useful guide for the rapid identification of novel therapeutic agents from chemical database.

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“…For docking, the downloaded 3D structure of the 2NY1 protein in PDB selected from the HIV envelope protein (Wang, Xiao et al 2009). Its inhibitor BMS-378806 was also taken from PubChem and their docking was processed in Discovery Studios (Ansari, Dikhit et al 2012). Discovery Studio (DS) is a commercial molecular modeling program for biological macromolecules (proteins, nucleic acid).…”

Section: Molecular Dockingmentioning

confidence: 99%

Next Generation Sequence Analysis of Sequences From Sra File of Hiv-1 Envelope Protein.

Sinha¹,

Saho²,

Rana³

et al. 2018

IJAR

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Comparative modeling of HGPRT enzyme of L. donovani and binding affinities of different analogs of GMP

Cited by 31 publications

References 42 publications

Validation of reference genes for expression analysis in a murine trauma model combining traumatic brain injury and femoral fracture

Validation of reference genes for expression analysis in a murine trauma model combining traumatic brain injury and femoral fracture

Combining Structure‐Based Pharmacophore andIn SilicoApproaches to Discover Novel Selective Serotonin Reuptake Inhibitors

Next Generation Sequence Analysis of Sequences From Sra File of Hiv-1 Envelope Protein.

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