Elucidating structural basis of benzofuran pyrrolidine pyrazole derivatives for enhancing potency against both the InhA enzyme and intact M. tuberculosis cells: a combined MD simulations and 3D-QSAR study

RSC Advances ◽  
2015 ◽  
Vol 5 (65) ◽  
pp. 52926-52937 ◽  
Author(s):  
Pharit Kamsri ◽  
Auradee Punkvang ◽  
Supa Hannongbua ◽  
Patchreenart Saparpakorn ◽  
Pornpan Pungpo
Keyword(s):  
3D Qsar ◽  
Md Simulations ◽  
Structural Basis ◽  
Pyrazole Derivatives ◽  
Qsar Study ◽  
Structural Concept

The structural concept for enhancing both IC50 and MIC90 activities summarized from MD simulations and CoMSIA results.

ChemInform Abstract: Synthesis, Antitubercular Evaluation and 3D-QSAR Study of N-Phenyl-3-(4-fluorophenyl)-4-substituted Pyrazole Derivatives.

ChemInform ◽  
2012 ◽  
Vol 43 (22) ◽  
pp. no-no
Author(s):  
R. C. Khunt ◽  
V. M. Khedkar ◽  
R. S. Chawda ◽  
N. A. Chauhan ◽  
A. R. Parikh ◽  
...  
Keyword(s):  
3D Qsar ◽  
Pyrazole Derivatives ◽  
Qsar Study

scholarly journals Computational Approaches for the Design of Novel Anticancer Compounds Based on Pyrazolo[3,4-d]pyrimidine Derivatives as TRAP1 Inhibitor

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 5932
Author(s):  
Amena Ali ◽  
Magda H. Abdellattif ◽  
Abuzer Ali ◽  
Ola AbuAli ◽  
Mohd Shahbaaz ◽  
...  
Keyword(s):  
3D Qsar ◽  
Md Simulations ◽  
Docking Study ◽  
Qsar Model ◽  
Computational Techniques ◽  
Amino Acid Residues ◽  
Molecular Docking Study ◽  
Qsar Study ◽  
Screening Study ◽  
Leave One Out

In the present in-silico study, various computational techniques were applied to determine potent compounds against TRAP1 kinase. The pharmacophore hypothesis DHHRR_1 consists of important features required for activity. The 3D QSAR study showed a statistically significant model with R2 = 0.96 and Q2 = 0.57. Leave one out (LOO) cross-validation (R2 CV = 0.58) was used to validate the QSAR model. The molecular docking study showed maximum XP docking scores (−11.265, −10.532, −10.422, −10.827, −10.753 kcal/mol) for potent pyrazole analogs (42, 46, 49, 56, 43), respectively, with significant interactions with amino acid residues (ASP 594, CYS 532, PHE 583, SER 536) against TRAP1 kinase receptors (PDB ID: 5Y3N). Furthermore, the docking results were validated using the 100 ns MD simulations performed for the selected five docked complexes. The selected inhibitors showed relatively higher binding affinities than the TRAP1 inhibitor molecules present in the literature. The ZINC database was used for a virtual screening study that screened ZINC05297837, ZINC05434822, and ZINC72286418, which showed similar binding interactions to those shown by potent ligands. Absorption, distribution, metabolism, and excretion (ADME) analysis showed noticeable results. The results of the study may be helpful for the further development of potent TRAP1 inhibitors

Novel 5-chloro-pyrazole derivatives containing a phenylhydrazone moiety as potent antifungal agents: synthesis, crystal structure, biological evaluation and a 3D-QSAR study

2019 ◽  
Vol 43 (16) ◽  
pp. 6350-6360 ◽  
Author(s):  
Jian Jiao ◽  
An Wang ◽  
Min Chen ◽  
Meng-Qi Wang ◽  
Chun-Long Yang
Keyword(s):  
Crystal Structure ◽  
Structural Optimization ◽  
Fungicidal Activity ◽  
Antifungal Agents ◽  
3D Qsar ◽  
Biological Evaluation ◽  
Pyrazole Derivatives ◽  
Qsar Study

Novel 5-chloro-pyrazole derivatives containing a phenylhydrazone moiety were designed and synthesized. Some of the target compounds showed potent fungicidal activity. A 3D-QSAR study provides information for structural optimization.

Synthesis, antitubercular evaluation and 3D-QSAR study of N-phenyl-3-(4-fluorophenyl)-4-substituted pyrazole derivatives

2012 ◽  
Vol 22 (1) ◽  
pp. 666-678 ◽  
Author(s):  
R.C. Khunt ◽  
V.M. Khedkar ◽  
R.S. Chawda ◽  
N.A. Chauhan ◽  
A.R. Parikh ◽  
...  
Keyword(s):  
3D Qsar ◽  
Pyrazole Derivatives ◽  
Qsar Study

A 3D-QSAR Study on Betulinic Acid Derivatives as Anti-Tumor Agents and the Synthesis of Novel Derivatives for Modeling Validation

2017 ◽  
Vol 17 (4) ◽  
pp. 566-575 ◽  
Author(s):  
Weimin Ding ◽  
Sheng Zhang ◽  
Meixuan Zhu ◽  
Shaoming Wang ◽  
Tao Xu ◽  
...  
Keyword(s):  
Betulinic Acid ◽  
3D Qsar ◽  
Qsar Study

scholarly journals Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher Agnew ◽  
Pelin Ayaz ◽  
Risa Kashima ◽  
Hanna S. Loving ◽  
Prajakta Ghatpande ◽  
...  
Keyword(s):  
Md Simulations ◽  
Kinase Domain ◽  
Structural Basis ◽  
Type I ◽  
Type Ii ◽  
Exchange Mass Spectrometry ◽  
Receptor Complexes ◽  
Bmp Receptors ◽  
Morphogenetic Protein ◽  
Smad Proteins

AbstractUpon ligand binding, bone morphogenetic protein (BMP) receptors form active tetrameric complexes, comprised of two type I and two type II receptors, which then transmit signals to SMAD proteins. The link between receptor tetramerization and the mechanism of kinase activation, however, has not been elucidated. Here, using hydrogen deuterium exchange mass spectrometry (HDX-MS), small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations, combined with analysis of SMAD signaling, we show that the kinase domain of the type I receptor ALK2 and type II receptor BMPR2 form a heterodimeric complex via their C-terminal lobes. Formation of this dimer is essential for ligand-induced receptor signaling and is targeted by mutations in BMPR2 in patients with pulmonary arterial hypertension (PAH). We further show that the type I/type II kinase domain heterodimer serves as the scaffold for assembly of the active tetrameric receptor complexes to enable phosphorylation of the GS domain and activation of SMADs.

3D-QSAR Study on Apicidin Inhibit Histone Deacetylase

2010 ◽  
Vol 21 (12) ◽  
pp. 1596-1607 ◽  
Author(s):  
Hai-Feng Chen ◽  
Jiu-Hong Kang ◽  
Qiang Li ◽  
Bao-Shan Zeng ◽  
Xiao-Jun Yao ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
3D Qsar ◽  
Qsar Study
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