Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations

Noureddine, Olfa; Issaoui, Noureddine; Medimagh, Mouna; Aldossary, Omar M.; Marouani, Houda

doi:10.1016/j.jksus.2020.101334

Cited by 114 publications

(28 citation statements)

References 33 publications

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“…A docking score indicates binding potentiality, and various methods of fitting the ligand into the binding site are investigated [71]. Flexible-ligand search docking and flexible-protein docking are the two major forms of molecular docking [72]. In the case of flexible-ligand search docking, three techniques are generally used, namely the systematic approach, the stochastic method, and the simulation method, while flexible-protein docking typically uses Monte Carlo (MC) and molecular dynamics (MD) methods [73].…”

Section: Molecular Dockingmentioning

confidence: 99%

Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

Hasan

Alsaiari

Fakhurji³

et al. 2022

Molecules

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The conventional drug discovery approach is an expensive and time-consuming process, but its limitations have been overcome with the help of mathematical modeling and computational drug design approaches. Previously, finding a small molecular candidate as a drug against a disease was very costly and required a long time to screen a compound against a specific target. The development of novel targets and small molecular candidates against different diseases including emerging and reemerging diseases remains a major concern and necessitates the development of novel therapeutic targets as well as drug candidates as early as possible. In this regard, computational and mathematical modeling approaches for drug development are advantageous due to their fastest predictive ability and cost-effectiveness features. Computer-aided drug design (CADD) techniques utilize different computer programs as well as mathematics formulas to comprehend the interaction of a target and drugs. Traditional methods to determine small-molecule candidates as a drug have several limitations, but CADD utilizes novel methods that require little time and accurately predict a compound against a specific disease with minimal cost. Therefore, this review aims to provide a brief insight into the mathematical modeling and computational approaches for identifying a novel target and small molecular candidates for curing a specific disease. The comprehensive review mainly focuses on biological target prediction, structure-based and ligand-based drug design methods, molecular docking, virtual screening, pharmacophore modeling, quantitative structure–activity relationship (QSAR) models, molecular dynamics simulation, and MM-GBSA/MM-PBSA approaches along with valuable database resources and tools for identifying novel targets and therapeutics against a disease. This review will help researchers in a way that may open the road for the development of effective drugs and preventative measures against a disease in the future as early as possible.

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Section: Molecular Dockingmentioning

confidence: 99%

Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

Hasan

Alsaiari

Fakhurji³

et al. 2022

Molecules

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“…Distinct colors indicate different electrostatic potential values at the surface; red and blue regions in the MEP signify electron-rich and electron-poor regions, respectively; green represents the neutral electrostatic potential [63]. The electrophilic attack region is red (P=S group in ax.…”

Section: Molecular Electrostatic Potential (Mep) and Density Of State...mentioning

confidence: 99%

Structural, Electronic, Reactivity, and Conformational Features of 2,5,5-Trimethyl-1,3,2-diheterophosphinane-2-sulfide, and Its Derivatives: DFT, MEP, and NBO Calculations

et al. 2022

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In this study, we used density functional theory (DFT) and natural bond orbital (NBO) analysis to determine the structural, electronic, reactivity, and conformational features of 2,5,5-trimethyl-1,3,2-di-heteroatom (X) phosphinane-2-sulfide derivatives (X = O (compound 1), S (compound 2), and Se (compound 3)). We discovered that the features improve dramatically at 6-31G** and B3LYP/6-311+G** levels. The level of theory for the molecular structure was optimized first, followed by the frontier molecular orbital theory development to assess molecular stability and reactivity. Molecular orbital calculations, such as the HOMO–LUMO energy gap and the mapping of molecular electrostatic potential surfaces (MEP), were performed similarly to DFT calculations. In addition, the electrostatic potential of the molecule was used to map the electron density on a surface. In addition to revealing molecules’ size and shape distribution, this study also shows the sites on the surface where molecules are most chemically reactive.

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“…Determination of molecular geometries, with the most stable minimum energy of ligands having the potential to bind to the active protein sites of targets, enables calculations to give more successful results in the molecular docking process. DFT-based optimized geometry allows for the study of frontier molecular orbitals that play an important role in understanding the interaction mechanisms between drugs and their receptors in determining the hit ligands against SARS-CoV-2 [86][87][88][89][90]. The difference between HOMO (highest-energy molecular orbital occupied by electrons) and LUMO (lowest-energy molecular orbital not occupied by electrons) energy values plays a critical role in determining the chemical reactivity, charge transfer capabilities, and bioactivity potential of molecular systems [91][92][93][94][95].…”

Section: Computer Aided Drug Designmentioning

confidence: 99%

A Multidisciplinary Approach to Coronavirus Disease (COVID-19)

Ertürk

Şahin

et al. 2021

Molecules

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Since December 2019, humanity has faced an important global threat. Many studies have been published on the origin, structure, and mechanism of action of the SARS-CoV-2 virus and the treatment of its disease. The priority of scientists all over the world has been to direct their time to research this subject. In this review, we highlight chemical studies and therapeutic approaches to overcome COVID-19 with seven different sections. These sections are the structure and mechanism of action of SARS-CoV-2, immunotherapy and vaccine, computer-aided drug design, repurposing therapeutics for COVID-19, synthesis of new molecular structures against COVID-19, food safety/security and functional food components, and potential natural products against COVID-19. In this work, we aimed to screen all the newly synthesized compounds, repurposing chemicals covering antiviral, anti-inflammatory, antibacterial, antiparasitic, anticancer, antipsychotic, and antihistamine compounds against COVID-19. We also highlight computer-aided approaches to develop an anti-COVID-19 molecule. We explain that some phytochemicals and dietary supplements have been identified as antiviral bioproducts, which have almost been successfully tested against COVID-19. In addition, we present immunotherapy types, targets, immunotherapy and inflammation/mutations of the virus, immune response, and vaccine issues.

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Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations

Cited by 114 publications

References 33 publications

Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

Structural, Electronic, Reactivity, and Conformational Features of 2,5,5-Trimethyl-1,3,2-diheterophosphinane-2-sulfide, and Its Derivatives: DFT, MEP, and NBO Calculations

A Multidisciplinary Approach to Coronavirus Disease (COVID-19)

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