scholarly journals QSPR/QSAR Analyses by Means of the CORAL Software

2017 ◽  
pp. 929-955
Author(s):  
Andrey A. Toropov ◽  
Alla P. Toropova ◽  
Emilio Benfenati ◽  
Orazio Nicolotti ◽  
Angelo Carotti ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Molecular Graph ◽  
Qsar Model ◽  
Mathematical Function ◽  
Coral Software ◽  
Structure Property ◽  
Qsar Analysis ◽  
The Monte Carlo Method ◽  
Optimal Descriptor ◽  
New Ideas

In this chapter, the methodology of building up quantitative structure—property/activity relationships (QSPRs/QSARs)—by means of the CORAL software is described. The Monte Carlo method is the basis of this approach. Simplified Molecular Input-Line Entry System (SMILES) is used as the representation of the molecular structure. The conversion of SMILES into the molecular graph is available for QSPR/QSAR analysis using the CORAL software. The model for an endpoint is a mathematical function of the correlation weights for various features of the molecular structure. Hybrid models that are based on features extracted from both SMILES and a graph also can be built up by the CORAL software. The conceptually new ideas collected and revealed through the CORAL software are: (1) any QSPR/QSAR model is a random event; and (2) optimal descriptor can be a translator of eclectic information into an endpoint prediction.

QSPR/QSAR Analyses by Means of the CORAL Software

2015 ◽  
pp. 560-585 ◽  
Author(s):  
Andrey A. Toropov ◽  
Alla P. Toropova ◽  
Emilio Benfenati ◽  
Orazio Nicolotti ◽  
Angelo Carotti ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Molecular Graph ◽  
Qsar Model ◽  
Mathematical Function ◽  
Coral Software ◽  
Structure Property ◽  
Qsar Analysis ◽  
The Monte Carlo Method ◽  
Optimal Descriptor ◽  
New Ideas

In this chapter, the methodology of building up quantitative structure—property/activity relationships (QSPRs/QSARs)—by means of the CORAL software is described. The Monte Carlo method is the basis of this approach. Simplified Molecular Input-Line Entry System (SMILES) is used as the representation of the molecular structure. The conversion of SMILES into the molecular graph is available for QSPR/QSAR analysis using the CORAL software. The model for an endpoint is a mathematical function of the correlation weights for various features of the molecular structure. Hybrid models that are based on features extracted from both SMILES and a graph also can be built up by the CORAL software. The conceptually new ideas collected and revealed through the CORAL software are: (1) any QSPR/QSAR model is a random event; and (2) optimal descriptor can be a translator of eclectic information into an endpoint prediction.

The Monte Carlo Method as a Tool to Build up Predictive QSPR/QSAR

2020 ◽  
Vol 16 (3) ◽  
pp. 197-206 ◽  
Author(s):  
Andrey A. Toropov ◽  
Alla P. Toropova
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Target Function ◽  
Statistical Characteristics ◽  
Mathematical Function ◽  
Coral Software ◽  
Structure Property ◽  
Molecular Features ◽  
The Monte Carlo Method ◽  
Correlation Weights

Background: The Monte Carlo method has a wide application in various scientific researches. For the development of predictive models in a form of the quantitative structure-property / activity relationships (QSPRs/QSARs), the Monte Carlo approach also can be useful. The CORAL software provides the Monte Carlo calculations aimed to build up QSPR/QSAR models for different endpoints. Methods: Molecular descriptors are a mathematical function of so-called correlation weights of various molecular features. The numerical values of the correlation weights give the maximal value of a target function. The target function leads to a correlation between endpoint and optimal descriptor for the visible training set. The predictive potential of the model is estimated with the validation set, i.e. compounds that are not involved in the process of building up the model. Results: The approach gave quite good models for a large number of various physicochemical, biochemical, ecological, and medicinal endpoints. Bibliography and basic statistical characteristics of several CORAL models are collected in the present review. In addition, the extended version of the approach for more complex systems (nanomaterials and peptides), where behaviour of systems is defined by a group of conditions besides the molecular structure is demonstrated. Conclusion: The Monte Carlo technique available via the CORAL software can be a useful and convenient tool for the QSPR/QSAR analysis.

scholarly journals On Ve-Degree and Ev-Degree Topological Properties of Hyaluronic Acid‐Anticancer Drug Conjugates with QSPR

2021 ◽  
Vol 2021 ◽  
pp. 1-23
Author(s):  
Syed Ajaz K. Kirmani ◽  
Parvez Ali ◽  
Faizul Azam ◽  
Parvez Ahmad Alvi
Keyword(s):  
Molecular Structure ◽  
Hyaluronic Acid ◽  
Biological Activities ◽  
Molecular Graph ◽  
Topological Indices ◽  
Structure Property ◽  
Zagreb Index ◽  
Anticancer Properties ◽  
Drug Conjugates ◽  
Molecular Structure Analysis

The design of the quantitative structure-property/activity relationships for drug-related compounds using theoretical methods relies on appropriate molecular structure representations. The molecular structure of a compound comprises all the information required to determine its chemical, biological, and physical properties. These properties can be assessed by employing a graph theoretical descriptor tool widely known as topological indices. Generalization of descriptors may reduce not only the number of molecular graph-based descriptors but also improve existing results and provide a better correlation to several molecular properties. Recently introduced ve-degree and ev-degree topological indices have been successfully employed for development of models for the prediction of various biological activities/properties. In this article, we propose the general ve-inverse sum indeg index ISI α , β ve G and general ve-Zagreb index M α ve G of graph G and compute ISI α , β ve G , M α ve G , and M α ev G (general ev-degree index) of hyaluronic acid-curcumin/paclitaxel conjugates, renowned for its potential anti-inflammatory, antioxidant, and anticancer properties, by using molecular structure analysis and edge partitioning technique. Several ve-degree- and ev-degree-based topological indices are obtained as a special case of ISI α , β ve G , M α ve G , and M α ev G . Furthermore, QSPR analysis of ISI α , β ve G , M α ve G , and M α ev G for particular values of α and β is performed, which reveals their predicting power. These results allow researchers to better understand the physicochemical properties and pharmacological characteristics of these conjugates.

Evolution of Optimal Descriptors

2016 ◽  
Vol 1 (2) ◽  
pp. 52-71
Author(s):  
Alla P. Toropova ◽  
Andrey A. Toropov
Keyword(s):  
Monte Carlo ◽  
Medicinal Chemistry ◽  
Monte Carlo Technique ◽  
Coral Software ◽  
Quantitative Structure ◽  
Structure Property ◽  
Qsar Analysis

The quantitative structure - property / activity relationships (qsprs/qsars) analysis of different substances is an important area in mathematical and medicinal chemistry. The evolution and logic of optimal descriptors which are based on the monte carlo technique in the role of a tool of the qspr/qsar analysis is discussed. A group of examples of application of the optimal descriptors which are calculated with the coral software (http://www.insilico.eu/coral) for prediction of physicochemical and biochemical endpoints of potential therapeutical agents are presented. The perspectives and limitations of the optimal descriptors are listed. The attempt of the systematization of the models calculated with the coral software is the aim of this work.

Graph Neural Networks for Prediction of Fuel Ignition Quality

2020 ◽  
Author(s):  
Artur Schweidtmann ◽  
Jan Rittig ◽  
Andrea König ◽  
Martin Grohe ◽  
Alexander Mitsos ◽  
...  
Keyword(s):  
Neural Networks ◽  
Octane Number ◽  
Molecular Graph ◽  
Chemical Properties ◽  
Graph Representation ◽  
Structure Property ◽  
Oxygenated Hydrocarbons ◽  
Physico Chemical ◽  
Ignition Quality ◽  
Graph Neural Networks

<div>Prediction of combustion-related properties of (oxygenated) hydrocarbons is an important and challenging task for which quantitative structure-property relationship (QSPR) models are frequently employed. Recently, a machine learning method, graph neural networks (GNNs), has shown promising results for the prediction of structure-property relationships. GNNs utilize a graph representation of molecules, where atoms correspond to nodes and bonds to edges containing information about the molecular structure. More specifically, GNNs learn physico-chemical properties as a function of the molecular graph in a supervised learning setup using a backpropagation algorithm. This end-to-end learning approach eliminates the need for selection of molecular descriptors or structural groups, as it learns optimal fingerprints through graph convolutions and maps the fingerprints to the physico-chemical properties by deep learning. We develop GNN models for predicting three fuel ignition quality indicators, i.e., the derived cetane number (DCN), the research octane number (RON), and the motor octane number (MON), of oxygenated and non-oxygenated hydrocarbons. In light of limited experimental data in the order of hundreds, we propose a combination of multi-task learning, transfer learning, and ensemble learning. The results show competitive performance of the proposed GNN approach compared to state-of-the-art QSPR models making it a promising field for future research. The prediction tool is available via a web front-end at www.avt.rwth-aachen.de/gnn.</div>

QSAR Analysis for Antioxidant Activity of Dipicolinic Acid Derivatives

2018 ◽  
Vol 21 (3) ◽  
pp. 204-214 ◽  
Author(s):  
Vesna Rastija ◽  
Maja Molnar ◽  
Tena Siladi ◽  
Vijay Hariram Masand
Keyword(s):  
Antioxidant Activity ◽  
Antioxidant Activities ◽  
Dipicolinic Acid ◽  
External Validation ◽  
Qsar Model ◽  
Internal Validation ◽  
Qsar Analysis ◽  
Dragon Descriptors ◽  
Qsar Models ◽  
New Compounds

Aims and Objectives: The aim of this study was to derive robust and reliable QSAR models for clarification and prediction of antioxidant activity of 43 heterocyclic and Schiff bases dipicolinic acid derivatives. According to the best obtained QSAR model, structures of new compounds with possible great activities should be proposed. Methods: Molecular descriptors were calculated by DRAGON and ADMEWORKS from optimized molecular structure and two algorithms were used for creating the training and test sets in both set of descriptors. Regression analysis and validation of models were performed using QSARINS. Results: The model with best internal validation result was obtained by DRAGON descriptors (MATS4m, EEig03d, BELm4, Mor10p), split by ranking method (R2 = 0.805; R2 ext = 0.833; F = 30.914). The model with best external validation result was obtained by ADMEWORKS descriptors (NDB, MATS5p, MDEN33, TPSA), split by random method (R2 = 0.692; R2 ext = 0.848; F = 16.818). Conclusion: Important structural requirements for great antioxidant activity are: low number of double bonds in molecules; absence of tertial nitrogen atoms; higher number of hydrogen bond donors; enhanced molecular polarity; and symmetrical moiety. Two new compounds with potentially great antioxidant activities were proposed.

Application of the Monte Carlo Method for the Prediction of Behavior of Peptides

2019 ◽  
Vol 20 (12) ◽  
pp. 1151-1157 ◽  
Author(s):  
Alla P. Toropova ◽  
Andrey A. Toropov
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Method ◽  
Natural Sciences ◽  
Monte Carlo Technique ◽  
Quantitative Structure ◽  
Structure Property ◽  
The Monte Carlo Method ◽  
Modern Natural

Prediction of physicochemical and biochemical behavior of peptides is an important and attractive task of the modern natural sciences, since these substances have a key role in life processes. The Monte Carlo technique is a possible way to solve the above task. The Monte Carlo method is a tool with different applications relative to the study of peptides: (i) analysis of the 3D configurations (conformers); (ii) establishment of quantitative structure – property / activity relationships (QSPRs/QSARs); and (iii) development of databases on the biopolymers. Current ideas related to application of the Monte Carlo technique for studying peptides and biopolymers have been discussed in this review.

Applications of Quantitative Structure-Activity Relationships (QSAR) based Virtual Screening in Drug Design: A Review

2020 ◽  
Vol 20 (14) ◽  
pp. 1375-1388 ◽  
Author(s):  
Patnala Ganga Raju Achary
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Virtual Screening ◽  
Model Building ◽  
Chemical Space ◽  
Qsar Model ◽  
Quantitative Structure ◽  
Efficient Manner ◽  
Qsar Analysis ◽  
Structure Activity

The scientists, and the researchers around the globe generate tremendous amount of information everyday; for instance, so far more than 74 million molecules are registered in Chemical Abstract Services. According to a recent study, at present we have around 1060 molecules, which are classified as new drug-like molecules. The library of such molecules is now considered as ‘dark chemical space’ or ‘dark chemistry.’ Now, in order to explore such hidden molecules scientifically, a good number of live and updated databases (protein, cell, tissues, structure, drugs, etc.) are available today. The synchronization of the three different sciences: ‘genomics’, proteomics and ‘in-silico simulation’ will revolutionize the process of drug discovery. The screening of a sizable number of drugs like molecules is a challenge and it must be treated in an efficient manner. Virtual screening (VS) is an important computational tool in the drug discovery process; however, experimental verification of the drugs also equally important for the drug development process. The quantitative structure-activity relationship (QSAR) analysis is one of the machine learning technique, which is extensively used in VS techniques. QSAR is well-known for its high and fast throughput screening with a satisfactory hit rate. The QSAR model building involves (i) chemo-genomics data collection from a database or literature (ii) Calculation of right descriptors from molecular representation (iii) establishing a relationship (model) between biological activity and the selected descriptors (iv) application of QSAR model to predict the biological property for the molecules. All the hits obtained by the VS technique needs to be experimentally verified. The present mini-review highlights: the web-based machine learning tools, the role of QSAR in VS techniques, successful applications of QSAR based VS leading to the drug discovery and advantages and challenges of QSAR.

Discovery of New Phosphoinositide 3-kinase Delta (PI3Kδ) Inhibitors via Virtual Screening using Crystallography-derived Pharmacophore Modelling and QSAR Analysis

2019 ◽  
Vol 15 (6) ◽  
pp. 588-601 ◽  
Author(s):  
Mahmoud A. Al-Sha'er ◽  
Rua'a A. Al-Aqtash ◽  
Mutasem O. Taha
Keyword(s):  
Virtual Screening ◽  
Inflammatory Diseases ◽  
Qsar Model ◽  
Qsar Analysis ◽  
Pharmacophore Modelling ◽  
Physicochemical Descriptors ◽  
Qsar Modelling ◽  
Ic50 Values ◽  
Phosphoinositide 3 Kinase ◽  
Pharmacophore Models

<P>Background: PI3K&#948; is predominantly expressed in hematopoietic cells and participates in the activation of leukocytes. PI3K&#948; inhibition is a promising approach for treating inflammatory diseases and leukocyte malignancies. Accordingly, we decided to model PI3K&#948; binding. </P><P> Methods: Seventeen PI3K&#948; crystallographic complexes were used to extract 94 pharmacophore models. QSAR modelling was subsequently used to select the superior pharmacophore(s) that best explain bioactivity variation within a list of 79 diverse inhibitors (i.e., upon combination with other physicochemical descriptors). </P><P> Results: The best QSAR model (r2 = 0.71, r2 LOO = 0.70, r2 press against external testing list of 15 compounds = 0.80) included a single crystallographic pharmacophore of optimal explanatory qualities. The resulting pharmacophore and QSAR model were used to screen the National Cancer Institute (NCI) database for new PI3Kδ inhibitors. Two hits showed low micromolar IC50 values. </P><P> Conclusion: Crystallography-based pharmacophores were successfully combined with QSAR analysis for the identification of novel PI3K&#948; inhibitors.</P>

scholarly journals Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis

2021 ◽  
Vol 14 (4) ◽  
pp. 357
Author(s):  
Magdi E. A. Zaki ◽  
Sami A. Al-Hussain ◽  
Vijay H. Masand ◽  
Siddhartha Akasapu ◽  
Sumit O. Bajaj ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Virtual Screening ◽  
Simulation Analysis ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Dynamics Simulation ◽  
Multilinear Regression ◽  
Qsar Analysis ◽  
Main Protease

Due to the genetic similarity between SARS-CoV-2 and SARS-CoV, the present work endeavored to derive a balanced Quantitative Structure−Activity Relationship (QSAR) model, molecular docking, and molecular dynamics (MD) simulation studies to identify novel molecules having inhibitory potential against the main protease (Mpro) of SARS-CoV-2. The QSAR analysis developed on multivariate GA–MLR (Genetic Algorithm–Multilinear Regression) model with acceptable statistical performance (R2 = 0.898, Q2loo = 0.859, etc.). QSAR analysis attributed the good correlation with different types of atoms like non-ring Carbons and Nitrogens, amide Nitrogen, sp2-hybridized Carbons, etc. Thus, the QSAR model has a good balance of qualitative and quantitative requirements (balanced QSAR model) and satisfies the Organisation for Economic Co-operation and Development (OECD) guidelines. After that, a QSAR-based virtual screening of 26,467 food compounds and 360 heterocyclic variants of molecule 1 (benzotriazole–indole hybrid molecule) helped to identify promising hits. Furthermore, the molecular docking and molecular dynamics (MD) simulations of Mpro with molecule 1 recognized the structural motifs with significant stability. Molecular docking and QSAR provided consensus and complementary results. The validated analyses are capable of optimizing a drug/lead candidate for better inhibitory activity against the main protease of SARS-CoV-2.

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