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Computational Pharmacology in Drug Discovery

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pharmacology".

Deadline for manuscript submissions: closed (20 February 2024) | Viewed by 1295

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Schmid College of Science and Technology, Computational and Data Science, School of Pharmacy, Chapman University, Orange, CA 92866, USA
Interests: computational biology; structural bioinformatics; computational virology; computational systems biology; theoretical and computational approaches for studies of protein dynamics; mechanisms of allosteric regulation; network modeling of biomolecular systems; machine learning; allosteric drug discovery and engineering of allosteric functions; AI and machine learning approaches for exploring allosteric landscapes and drug design
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Special Issue Information

Dear Colleagues,

Computational pharmacology is an interdisciplinary field that uses computational techniques to study the behavior of drugs in the human body. It combines knowledge from physics, biology, chemistry, pharmacology, and computer science to better understand the complex interactions between drugs and their receptors in the body. Computational pharmacology is an invaluable tool for pharmacological research, providing a level of accuracy and detail that cannot be achieved with traditional methods. It has been used to identify new drug candidates, predict drug–drug interactions, and to better understand the mechanisms of drug action. Computational pharmacology is based on mathematical and computer models that allow researchers to simulate the behavior of drugs and their interactions with other molecules. It can be used to predict and analyze the safety and efficacy of a drug before it is tested in clinical trials. The primary benefit of computational pharmacology is the ability to quickly and accurately predict the pharmacological effects of a drug, enabling researchers to reduce the time and costs associated with drug development. Computational models are used to simulate drug–receptor interactions and to analyze the structure and function of biomolecules. This allows researchers to identify potential drug targets and better understand the pharmacological effects of a drug. In addition to aiding in drug discovery and development, computational pharmacology can also be used to analyze the potential toxicity of a drug. By simulating the behavior of drugs and their interactions in the body, researchers can identify potential side effects and safety risks before a drug is tested in humans.

Computational pharmacology and AI are two powerful tools that have revolutionized the way drugs are discovered and developed. The combination of these two technologies has allowed researchers to develop powerful algorithms and computer models to simulate the effects of potential drugs on the human body. This has enabled them to rapidly identify potential drug candidates and develop them much more efficiently than ever before. In addition, AI has allowed for the development of more accurate and detailed models of how drugs interact with their targets, which can help scientists better understand the mechanisms of action of new drugs. For instance, AI can be used to predict the potential side effects of a drug, allowing researchers to adjust the formulation of the drug before it is tested in clinical trials. AI can also be used to analyze large datasets of clinical data to identify potential biomarkers for drug efficacy and safety, allowing researchers to make informed decisions about which drugs should be developed.

Prof. Dr. Gennady Verkhivker
Guest Editor

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Published Papers (1 paper)

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Research

31 pages, 6806 KiB  
Article
Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking
by Grace Gupta and Gennady Verkhivker
Int. J. Mol. Sci. 2024, 25(9), 4955; https://doi.org/10.3390/ijms25094955 - 1 May 2024
Viewed by 524
Abstract
Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike [...] Read more.
Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and machine-learning-based binding pocket detection with the ensemble-based ligand docking and binding free energy analysis to characterize the potential allosteric binding sites and determine structural and energetic determinants of allosteric inhibition for a series of experimentally validated allosteric molecules. The results demonstrate a good agreement between computational and experimental binding affinities, providing support to the predicted binding modes and suggesting key interactions formed by the allosteric ligands to elicit the experimentally observed inhibition. We establish structural and energetic determinants of allosteric binding for the experimentally known allosteric molecules, indicating a potential mechanism of allosteric modulation by targeting the hinges of the inter-protomer movements and blocking conformational changes between the closed and open spike trimer forms. The results of this study demonstrate that combining ensemble-based ligand docking with conformational states of spike protein and rigorous binding energy analysis enables robust characterization of the ligand binding modes, the identification of allosteric binding hotspots, and the prediction of binding affinities for validated allosteric modulators, which is consistent with the experimental data. This study suggested that the conformational adaptability of the protein allosteric sites and the diversity of ligand bound conformations are both in play to enable efficient targeting of allosteric binding sites and interfere with the conformational changes. Full article
(This article belongs to the Special Issue Computational Pharmacology in Drug Discovery)
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