scholarly journals 2D-QSAR model development and analysis on variant groups of anti -tuberculosis drugs

2011 ◽  
Vol 7 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Neeraja Dwivedi ◽  
Bhartendu Nath Mishra ◽  
Vishwa Mohan Katoch
Keyword(s):  
Model Development ◽  
Qsar Model ◽  
2D Qsar

Physicochemical, Interaction & Topological Descriptors vs. hMAO-A Inhibition of Aplysinopsin Analogs: A Boulevard to the Discovery of Semi-Synthetic Anti-Depression Agents

2021 ◽  
Vol 22 ◽  
Author(s):  
Rajeev K. Singla ◽  
Ghulam Md Ashraf ◽  
Magdah Ganash ◽  
Varadaraj Bhat G ◽  
Bairong Shen
Keyword(s):  
Model Development ◽  
Principal Component ◽  
Partial Least Square ◽  
Least Square ◽  
Partial Least Square Regression ◽  
Topological Descriptors ◽  
Good Prediction ◽  
Physicochemical Interaction ◽  
Human Beings ◽  
2D Qsar

Background: Neurological disorder, depression is the globally 4th leading cause of chronic disabilities in human beings. Objective: This study aimed to model a 2D-QSAR equation that can facilitate the researchers to design better aplysinopsin analogs with potent hMAO-A inhibition. Methods: Aplysinopsin analogs dataset were subjected to ADME assessment for drug-likeness suitability using StarDrop software before modeled equation. 2D-QSAR equations were generated using VLife MDS 4.6. Dataset was segregated into training and test set using different methodologies, followed by variable selection. Model development was done using principal component regression, partial least square regression, and multiple regression. Results: The dataset has successfully qualified the drug-likeness criteria in ADME simulation, with more than 90% of molecules cleared the ideal conditions including intrinsic solubility, hydrophobicity, CYP3A4 2C9pKi, hERG pIC50, etc. 112 models were developed using multiparametric consideration of methodologies. The best six models were discussed with their extent of significance and prediction capabilities. ALP97 was emerged out as the most significant model out of all, with ~83% of the variance in the training set, the internal predictive ability of ~74% while having the external predictive capability of ~79%. Conclusion: ADME assessment suggested that aplysinopsin analogs are worth investigating. Interaction among the descriptors in a way of summation or multiplication products, are quite influential and yielding significant 2D-QSAR models with good prediction efficiency. This model can be used for the design of a more potent hMAO-A inhibitor having an aplysinopsin scaffold, which can then contribute to the treatment of depression and other neurological disorders.

scholarly journals An In Silico Model for Predicting Drug-Induced Hepatotoxicity

2019 ◽  
Vol 20 (8) ◽  
pp. 1897 ◽  
Author(s):  
Shuaibing He ◽  
Tianyuan Ye ◽  
Ruiying Wang ◽  
Chenyang Zhang ◽  
Xuelian Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Characteristic Curve ◽  
External Validation ◽  
Model Development ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
New Drugs ◽  
Drug Induced ◽  
Drug Candidates ◽  
External Test

As one of the leading causes of drug failure in clinical trials, drug-induced liver injury (DILI) seriously impeded the development of new drugs. Assessing the DILI risk of drug candidates in advance has been considered as an effective strategy to decrease the rate of attrition in drug discovery. Recently, there have been continuous attempts in the prediction of DILI. However, it indeed remains a huge challenge to predict DILI successfully. There is an urgent need to develop a quantitative structure–activity relationship (QSAR) model for predicting DILI with satisfactory performance. In this work, we reported a high-quality QSAR model for predicting the DILI risk of xenobiotics by incorporating the use of eight effective classifiers and molecular descriptors provided by Marvin. In model development, a large-scale and diverse dataset consisting of 1254 compounds for DILI was built through a comprehensive literature retrieval. The optimal model was attained by an ensemble method, averaging the probabilities from eight classifiers, with accuracy (ACC) of 0.783, sensitivity (SE) of 0.818, specificity (SP) of 0.748, and area under the receiver operating characteristic curve (AUC) of 0.859. For further validation, three external test sets and a large negative dataset were utilized. Consequently, both the internal and external validation indicated that our model outperformed prior studies significantly. Data provided by the current study will also be a valuable source for modeling/data mining in the future.

scholarly journals 2D-QSAR and 3D-QSAR Analyses for EGFR Inhibitors

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Manman Zhao ◽  
Lin Wang ◽  
Linfeng Zheng ◽  
Mengying Zhang ◽  
Chun Qiu ◽  
...  
Keyword(s):  
Correlation Coefficient ◽  
3D Qsar ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Structure Activity Relationship ◽  
Egfr Inhibitors ◽  
Activity Relationship ◽  
Quantitative Structure ◽  
2D Qsar ◽  
Structure Activity

Epidermal growth factor receptor (EGFR) is an important target for cancer therapy. In this study, EGFR inhibitors were investigated to build a two-dimensional quantitative structure-activity relationship (2D-QSAR) model and a three-dimensional quantitative structure-activity relationship (3D-QSAR) model. In the 2D-QSAR model, the support vector machine (SVM) classifier combined with the feature selection method was applied to predict whether a compound was an EGFR inhibitor. As a result, the prediction accuracy of the 2D-QSAR model was 98.99% by using tenfold cross-validation test and 97.67% by using independent set test. Then, in the 3D-QSAR model, the model with q2=0.565 (cross-validated correlation coefficient) and r2=0.888 (non-cross-validated correlation coefficient) was built to predict the activity of EGFR inhibitors. The mean absolute error (MAE) of the training set and test set was 0.308 log units and 0.526 log units, respectively. In addition, molecular docking was also employed to investigate the interaction between EGFR inhibitors and EGFR.

scholarly journals Comprehensive data on a 2D-QSAR model for Heme Oxygenase isoform 1 inhibitors

Data in Brief ◽  
2017 ◽  
Vol 15 ◽  
pp. 281-299 ◽  
Author(s):  
Emanuele Amata ◽  
Agostino Marrazzo ◽  
Maria Dichiara ◽  
Maria N. Modica ◽  
Loredana Salerno ◽  
...  
Keyword(s):  
Heme Oxygenase ◽  
Qsar Model ◽  
2D Qsar ◽  
Comprehensive Data

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

scholarly journals Generation of 2D-QSAR Model for Angiogenin Inhibitors: A Ligand-Based Approach for Cancer Drug Design

2016 ◽  
Vol 9 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Krishnan Sundar ◽  
Joseph Christina Rosy ◽  
Saminathan Balamurali ◽  
John Asnet Mary ◽  
Rajaiah Shenbagara
Keyword(s):  
Drug Design ◽  
Qsar Model ◽  
Cancer Drug ◽  
2D Qsar

scholarly journals QSAR Models for Active Substances Against Pseudomonas aeruginosa Using Disk-diffusion Test Data

2021 ◽  
Author(s):  
Cosmin Alexandru Bugeac ◽  
Robert Ancuceanu ◽  
Mihaela Dinu
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Model Development ◽  
Qsar Model ◽  
Machine Learning Algorithms ◽  
Disk Diffusion ◽  
Support Vector ◽  
Decision Tree Classifier ◽  
K Nearest Neighbors ◽  
Disk Diffusion Test ◽  
Tree Classifier

Pseudomonas aeruginosa is a Gram-negative bacillus included among the six "ESKAPE" microbial species with an outstanding ability to "escape" currently used antibiotics and developing new antibiotics against it is of the highest priority. Whereas minimum inhibitory concentration (MIC) values against Pseudomonas aeruginosa have been used previously for QSAR model development, disk diffusion results (inhibition zones) have not been apparently used for this purpose in the literature, and we decided to explore their use in this sense. We developed multiple QSAR methods using several machine learning algorithms (Support vector classifier, K Nearest Neighbors, Random Forest Classifier, Decision Tree Classifier, AdaBoost Classifier, Logistic Regression, and Naive Bayes Classifier). The main descriptors used in building the models belonged to the families of adjacency matrix, constitutional descriptors, first highest eigenvalue of Burden matrix, centered Moreau-Broto autocorrelation, and averaged and centered Moreau-Broto autocorrelation descriptors. A total of 32 models were built, of which 28 were selected and stacked to create a meta-model. In terms of balanced accuracy, the best performance was provided by KNN, SVM and AdaBoost algorithms, but the ensemble method had slightly superior results in nested cross-validation.

Importance of Applicability Domain of QSAR Models

2015 ◽  
pp. 180-211 ◽  
Author(s):  
Kunal Roy ◽  
Supratik Kar
Keyword(s):  
Environmental Fate ◽  
Interpolation Space ◽  
Model Development ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Applicability Domain ◽  
Property Prediction ◽  
Qsar Models ◽  
Environmental Fate Modeling

Quantitative Structure-Activity Relationship (QSAR) models have manifold applications in drug discovery, environmental fate modeling, risk assessment, and property prediction of chemicals and pharmaceuticals. One of the principles recommended by the Organization of Economic Co-operation and Development (OECD) for model validation requires defining the Applicability Domain (AD) for QSAR models, which allows one to estimate the uncertainty in the prediction of a compound based on how similar it is to the training compounds, which are used in the model development. The AD is a significant tool to build a reliable QSAR model, which is generally limited in use to query chemicals structurally similar to the training compounds. Thus, characterization of interpolation space is significant in defining the AD. An attempt is made in this chapter to address the important concepts and methodology of the AD as well as criteria for estimating AD through training set interpolation in the descriptor space.

Sign in / Sign up

Export Citation Format

Share Document