PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

2006 ◽  
Vol 20 (10-11) ◽  
pp. 647-671 ◽  
Author(s):  
Steven L. Dixon ◽  
Alexander M. Smondyrev ◽  
Eric H. Knoll ◽  
Shashidhar N. Rao ◽  
David E. Shaw ◽  
...  
Keyword(s):  
Model Development ◽  
3D Qsar ◽  
Qsar Model ◽  
Preliminary Results ◽  
3D Database ◽  
Database Screening

Generation of Pharmacophore and Atom Based 3D-QSAR Model of Novel Isoquinolin-1-one and Quinazolin-4-one-type Inhibitors of TNFα

2012 ◽  
Vol 8 (3) ◽  
pp. 436-451 ◽  
Author(s):  
Pradeep Hanumanthappa ◽  
Mahesh K. Teli ◽  
Rajanikant G. Krishnamurthy
Keyword(s):  
3D Qsar ◽  
Qsar Model

Computational Atom-based Three-Dimensional Quantitative Structure-Activity Relationship (3D QSAR) Model for Predicting Anti-Dengue Agents

2021 ◽  
Vol 16 (10) ◽  
pp. 50-58
Author(s):  
Ali Qusay Khalid ◽  
Vasudeva Rao Avupati ◽  
Husniza Hussain ◽  
Tabarek Najeeb Zaidan
Keyword(s):  
Dengue Fever ◽  
Three Dimensional ◽  
3D Qsar ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Activity Relationship ◽  
Quantitative Structure ◽  
Contour Maps ◽  
Structure Activity ◽  
Bioactive Ligands

Dengue fever is a viral infection spread by the female mosquito Aedes aegypti. It is a virus spread by mosquitoes found all over the tropics with risk levels varying depending on rainfall, relative humidity, temperature and urbanization. There are no specific medications that can be used to treat the condition. The development of possible bioactive ligands to combat Dengue fever before it becomes a pandemic is a global priority. Few studies on building three-dimensional quantitative structure-activity relationship (3D QSAR) models for anti-dengue agents have been reported. Thus, we aimed at building a statistically validated atom-based 3D-QSAR model using bioactive ligands reported to possess significant anti-dengue properties. In this study, the Schrodinger PhaseTM atom-based 3D QSAR model was developed and was validated using known anti-dengue properties as ligand data. This model was also tested to see if there was a link between structural characteristics and anti-dengue activity of a series of 3-acyl-indole derivatives. The established 3D QSAR model has strong predictive capacity and is statistically significant [Model: R2 Training Set = 0.93, Q2 (R2 Test Set) = 0.72]. In addition, the pharmacophore characteristics essential for the reported anti-dengue properties were explored using combined effects contour maps (coloured contour maps: blue: positive potential and red: negative potential) of the model. In the pathway of anti-dengue drug development, the model could be included as a virtual screening method to predict novel hits.

scholarly journals STRUCTURAL EXPLORATION AND PHARMACOPHORIC INVESTIGATION OF PYRAZOLE BASED ANALOGS AS NOVEL HISTONE DEACETYLASE 1 INHIBITOR USING COMBINATORIAL STUDIES

2018 ◽  
Vol 10 (3) ◽  
pp. 90
Author(s):  
Avineesh Singh ◽  
Harish Rajak
Keyword(s):  
Molecular Docking ◽  
Histone Deacetylase ◽  
Histone Deacetylase Inhibitors ◽  
Research Work ◽  
3D Qsar ◽  
Qsar Model ◽  
Docking Studies ◽  
Inhibition Activity ◽  
Design Strategies ◽  
Histone Deacetylase 1

Objective: Histone deacetylase inhibitors (HDACi) have four essential pharmacophores as cap group, connecting unit, a linker moiety and zinc binding group for their anticancer and histone deacetylase (HDAC) inhibition activity. On the basis of this fact, the objective of this research was to evaluate the exact role of pyrazole nucleus as connecting unit and its role in the development of newer HDACi.Methods: Ligand and structure-based computer-aided drug design strategies such as pharmacophore and atom based 3D QSAR modelling, molecular docking and energetic based pharmacophore mapping have been frequently applied to design newer analogs in a precise manner. Herein, we have applied these combinatorial approaches to develop the structure-activity correlation among novel pyrazole-based derivatives.Results: the Pharmacophore-based 3D-QSAR model was developed employing Phase module and e-pharmacophore on compound 1. This 3D-QSAR model provides fruitful information regarding favourable and unfavourable substitution on pyrazole-based analogs for HDAC1 inhibition activity. Molecular docking studies indicated that all the pyrazole derivatives bind with HDAC1 proteins and showed critical hydrophobic interaction with 5ICN and 4BKX HDAC1 proteins.Conclusion: The outcome of the present research work clearly indicated that pyrazole nucleus added an essential hydrophobic feature in cap group and could be employed to design the ligand molecules more accurately.

Approach to thiazole-containing tetrahydropyridines via Aza–Rauhut–Currier reaction and their potent fungicidal and insecticidal activity

RSC Advances ◽  
2016 ◽  
Vol 6 (113) ◽  
pp. 112704-112711 ◽  
Author(s):  
Yu-Jie Zhu ◽  
Xiao-Feng Guo ◽  
Zhi-Jin Fan ◽  
Lai Chen ◽  
Liu-Yong Ma ◽  
...  
Keyword(s):  
Insecticidal Activity ◽  
3D Qsar ◽  
Qsar Model ◽  
Fumarate Reductase ◽  
Cross Resistance

Insecticidal and fungicidal active thiazole-containing tetrahydropyridine derivatives with accurately predicted 3D QSAR model againstAphis LaburniKaltenbach and predicted potential anti-fungus target of fumarate reductase without cross resistance were synthesized.

scholarly journals FABP4 inhibitors 3D-QSAR model and isosteric replacement of BMS309403 datasets

Data in Brief ◽  
2019 ◽  
Vol 22 ◽  
pp. 471-483 ◽  
Author(s):  
Giuseppe Floresta ◽  
Agostino Cilibrizzi ◽  
Vincenzo Abbate ◽  
Ambra Spampinato ◽  
Chiara Zagni ◽  
...  
Keyword(s):  
3D Qsar ◽  
Qsar Model
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