Abstract
Background: The quantitative structure-activity relationship (QSAR) approach is most widely used for the prediction of biological activity of potential medicinal compounds. A QSAR model is developed by correlating the information obtained from chemical structures (numerical descriptors/ independent variables) with the experimental response values (the dependent variable).
Methods: In the current study, we have developed a QSAR model to predict the inhibitory activity of small molecule carboxamides against severe acute respiratory syndrome coronavirus (SARS-- CoV) 3CLpro enzyme. Due to the structural similarity of this enzyme with SARS-CoV-2, the causative organism of the recent pandemic, the former may be used for the development of therapies against coronavirus disease 19 (COVID-19).
Results: The final multiple linear regression (MLR) model was based on four two-dimensional descriptors with definite physicochemical meaning. The model was strictly validated using different internal and external quality metrics. The model showed significant statistical quality in terms of determination coefficient (R2=0.748, adjusted R2 or R2 adj = 0.700), cross-validated leave-one-out Q2 (Q2=0.628) and external predicted variance R2 pred = 0.723. The final validated model was used for the prediction of external set compounds as well as to virtually design a new library of small molecules. We have also performed a docking analysis of the most active and least active compounds present in the dataset for comparative analysis and to explain the features obtained from the 2D-QSAR model.
Conclusion: The derived model may be useful to predict the inhibitory activity of small molecules within the applicability domain of the model only based on the chemical structure information prior to their synthesis and testing.
Keywords: QSAR, 3CLpro enzyme, Carboxamides, COVID-19, design, respiratory failure.
Combinatorial Chemistry & High Throughput Screening
Title:In Silico Modeling of Small Molecule Carboxamides as Inhibitors of SARS-CoV 3CL Protease: An Approach Towards Combating COVID-19
Volume: 24 Issue: 8
Author(s): Pathan Mohsin Khan, Vinay Kumar and Kunal Roy*
Affiliation:
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032,India
Keywords: QSAR, 3CLpro enzyme, Carboxamides, COVID-19, design, respiratory failure.
Abstract:
Background: The quantitative structure-activity relationship (QSAR) approach is most widely used for the prediction of biological activity of potential medicinal compounds. A QSAR model is developed by correlating the information obtained from chemical structures (numerical descriptors/ independent variables) with the experimental response values (the dependent variable).
Methods: In the current study, we have developed a QSAR model to predict the inhibitory activity of small molecule carboxamides against severe acute respiratory syndrome coronavirus (SARS-- CoV) 3CLpro enzyme. Due to the structural similarity of this enzyme with SARS-CoV-2, the causative organism of the recent pandemic, the former may be used for the development of therapies against coronavirus disease 19 (COVID-19).
Results: The final multiple linear regression (MLR) model was based on four two-dimensional descriptors with definite physicochemical meaning. The model was strictly validated using different internal and external quality metrics. The model showed significant statistical quality in terms of determination coefficient (R2=0.748, adjusted R2 or R2 adj = 0.700), cross-validated leave-one-out Q2 (Q2=0.628) and external predicted variance R2 pred = 0.723. The final validated model was used for the prediction of external set compounds as well as to virtually design a new library of small molecules. We have also performed a docking analysis of the most active and least active compounds present in the dataset for comparative analysis and to explain the features obtained from the 2D-QSAR model.
Conclusion: The derived model may be useful to predict the inhibitory activity of small molecules within the applicability domain of the model only based on the chemical structure information prior to their synthesis and testing.
Export Options
About this article
Cite this article as:
Khan Mohsin Pathan , Kumar Vinay and Roy Kunal *, In Silico Modeling of Small Molecule Carboxamides as Inhibitors of SARS-CoV 3CL Protease: An Approach Towards Combating COVID-19, Combinatorial Chemistry & High Throughput Screening 2021; 24 (8) . https://dx.doi.org/10.2174/1386207323666200914094712
DOI https://dx.doi.org/10.2174/1386207323666200914094712 |
Print ISSN 1386-2073 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5402 |
Call for Papers in Thematic Issues
Artificial Intelligence Methods for Biomedical, Biochemical and Bioinformatics Problems
Recently, a large number of technologies based on artificial intelligence have been developed and applied to solve a diverse range of problems in the areas of biomedical, biochemical and bioinformatics problems. By utilizing powerful computing resources and massive amounts of data, methods based on artificial intelligence can significantly improve the ...read more
Eco-friendly Agents for Biological Control of Pathogenic Diseases
The discovery of an alternative biological approach to disease management includes work on medicinal products derived from natural sources as a starting point for the development of eco-friendly agents for these diseases and the injuries they cause, as well as reducing human contact with hazardous chemicals and their residues. We ...read more
Emerging trends in diseases mechanisms, noble drug targets and therapeutic strategies: focus on immunological and inflammatory disorders
Recently infectious and inflammatory diseases have been a key concern worldwide due to tremendous morbidity and mortality world Wide. Recent, nCOVID-9 pandemic is a good example for the emerging infectious disease outbreak. The world is facing many emerging and re-emerging diseases out breaks at present however, there is huge lack ...read more
Exploring Spectral Graph Theory in Combinatorial Chemistry
Scope of the Thematic Issue: Combinatorial chemistry involves the synthesis and analysis of a large number of diverse compounds simultaneously. Traditional methods rely on brute force experimentation, which can be time-consuming and resource-intensive. Spectral Graph Theory, a branch of mathematics dealing with the properties of graphs in relation to the ...read more
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
Related Articles
-
Non-viral Gene Delivery and Therapeutics Targeting to Brain
Current Nanoscience HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) Inflammatory Network
Inflammation & Allergy - Drug Targets (Discontinued) Single Emulsion-Solvent Evaporation Technique and Modifications for the Preparation of Pharmaceutical Polymeric Nanoparticles
Recent Patents on Drug Delivery & Formulation DNA Repair in Premature Aging Disorders and Neurodegeneration
Current Aging Science The Endocrine Regulation of Stem Cells: Physiological Importance and Pharmacological Potentials for Cell-Based Therapy
Current Stem Cell Research & Therapy Prostaglandin EP Receptor Subtypes Involved in Regulating HCO3- Secretion from Gastroduodenal Mucosa
Current Pharmaceutical Design Scope and Applications of Nanomedicines for the Management of Multiple Sclerosis
Current Drug Metabolism Treatment Options in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorders
Current Pharmaceutical Design The Potential Role of Dysfunctions in Neuron-Microglia Communication in the Pathogenesis of Brain Disorders
Current Neuropharmacology Proteases and Their Role in Chronic Inflammatory Lung Diseases
Current Drug Targets Nanocarriers Conjugated with Cell Penetrating Peptides: New Trojan Horses by Modern Ulysses
Current Pharmaceutical Biotechnology Exploring New CGRP Family Peptides and their Receptors in Vertebrates
Current Protein & Peptide Science Gliogenesis and Glial Pathology in Depression
CNS & Neurological Disorders - Drug Targets Angiogenesis and Vascularization of Uterine Leiomyoma: Clinical Value of Pseudocapsule Containing Peptides and Neurotransmitters
Current Protein & Peptide Science The Role of Antihistamine Drugs in Allergic Disorders
Current Medicinal Chemistry - Anti-Inflammatory & Anti-Allergy Agents Neuroprotective Gene Therapy for Parkinson’s Disease
Current Gene Therapy Impact of COVID-19 Infection on Maternal and Neonatal Outcomes: A Review of 11078 Pregnancies Reported in the Literature
Current Women`s Health Reviews The Interactions Between Diabetes Mellitus and Myelodysplastic Syndromes: Current State of Evidence and Future Directions
Current Diabetes Reviews Once-a-Day (QD) vs Twice-Daily (BID) Nevirapine as Simplification in PITreated Patients After 2 mos. of BID Induction
Current HIV Research Statins, Mevalonate Pathway and its Intermediate Products in Placental Development and Preeclampsia
Current Molecular Pharmacology