Multi-targeted molecular docking, pharmacokinetics, and drug-likeness evaluation of coumarin based compounds targeting proteins involved in development of COVID-19

Mun, Chan Sook; Hui, Lok Yong; Sing, Lai Cong; Karunakaran, Rohini; Ravichandran, V.

doi:10.1016/j.sjbs.2022.103458

Cited by 13 publications

(10 citation statements)

References 38 publications

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“…It also helps to predict the types of energy of interaction between ligands and target proteins [45]. In the present study, molecular docking was performed by PyRx (Autodock vina) tools version v0.8 programs [46][47][48]. The docking poses with the least interaction energy was analyzed and visualized by using Discovery Studio Visualizer.…”

Section: Molecular Docking Studymentioning

confidence: 99%

Computational approaches: Atom-based 3D-QSAR, molecular docking, ADME-Tox, MD simulation and DFT to find novel multi-targeted Anti-tubercular agents

Panigrahi,

Sahu

2024

Preprint

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Tuberculosis (TB) has become the biggest threat towards human society due to the rapid rise in resistance of the causative bacteria Mycobacterium tuberculosis (MTB) against the available anti-tubercular drugs. There is an urgent need to design new multi-targeted anti-tubercular agents to overcome the resistance species of MTB through computational design tools. With this aim in the present work, a combination of atom-based three-dimensional quantitative structure-activity relationship (3D-QSAR), six-point pharmacophore (AHHRRR), and molecular docking analysis was performed on a series of fifty-eight anti-tubercular agents. The generated QSAR model showed statistically significant correlation co-efficient R2, Q2, and Pearson r-factor of 0.9521, 0.8589, and 0.8988 respectively indicating good predictive ability. Molecular docking study was performed for the data set of compounds with the two important anti-tubercular target proteins, Enoyl acyl carrier protein reductase (InhA) (PDBID: 2NSD) and Decaprenyl phosphoryl-β-D-Ribose 20-epimerase (DprE1) (PDBID: 4FDO). Using the similarity search principle virtual screening was performed on 237 compounds retrieved from the Pubchem database to identify potent multitargeted anti-tubercular agents. The screened compound, MK3 showed the highest docking score of -9.2 and − 8.3 Kj/mol towards both the target proteins InhA and DprE1 were picked for 100ns molecular dynamic simulation study using GROMACS. From the data generated, the compound MK3 showed thermodynamic stability and effective binding within the active binding pocket of both target proteins without much deviation. The result of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and energy gap analysis predicts the molecular reactivity and stability of the identified molecule. Based on the result of the above studies the proposed compound MK3 can be successfully used for the development of a novel multi-targeted anti-tubercular agent with high binding affinity and favourable ADME-T properties.

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Section: Molecular Docking Studymentioning

confidence: 99%

Computational approaches: Atom-based 3D-QSAR, molecular docking, ADME-Tox, MD simulation and DFT to find novel multi-targeted Anti-tubercular agents

Panigrahi,

Sahu

2024

Preprint

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“…Mun et al, 112 synthesized coumarin derivatives and tested them as anti-COVID-19 agents using a molecular docking analysis. Among them, psoralen 89 showed the highest binding affinity against RdRp (PDB code: 7BV2), PL pro (PDB code: 6W9C), M pro (PDB code: 6W63), and spike glycoprotein (PDB code: 6M0J) of SARS-CoV-2 with values of −6.5, −6.2, −6.6, and −6.4kcal/mol, respectively.…”

Section: In Silico Studies Of Covid-19mentioning

confidence: 99%

A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds

Nazir,

Ahmad,

Aslam

et al. 2024

DDDT

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The Coronavirus disease 2019 (COVID-19) pandemic is one of the most considerable health problems across the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the major causative agent of COVID-19. The severe symptoms of this deadly disease include shortness of breath, fever, cough, loss of smell, and a broad spectrum of other health issues such as diarrhea, pneumonia, bronchitis, septic shock, and multiple organ failure. Currently, there are no medications available for coronavirus patients, except symptom-relieving drugs. Therefore, SARS-CoV-2 requires the development of effective drugs and specific treatments. Heterocycles are important constituents of more than 85% of the physiologically active pharmaceutical drugs on the market now. Several FDA-approved drugs have been reported including molnupiravir, remdesivir, ritonavir, oseltamivir, favipiravir, chloroquine, and hydroxychloroquine for the cure of COVID-19. In this study, we discuss potent anti-SARS-CoV-2 heterocyclic compounds that have been synthesized over the past few years. These compounds included; indole, piperidine, pyrazine, pyrimidine, pyrrole, piperazine, quinazoline, oxazole, quinoline, isoxazole, thiazole, quinoxaline, pyrazole, azafluorene, imidazole, thiadiazole, triazole, coumarin, chromene, and benzodioxole. Both in vitro and in silico studies were performed to determine the potential of these heterocyclic compounds in the fight against various SARS-CoV-2 proteins.

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“…In silico techniques help design bioactive agents and identify anti-SARS-CoV-2 hits [ 118 , 119 ]. Diverse acyclic [ 120 ] and heterocycles [ [121] , [122] , [123] ] of different scaffolds (triazole [ 124 ], oxadiazole [ 125 ], thiadiazole [ 126 ], indole [ 127 ], pyridine [ 128 ], pyrimidine [ 129 ] and coumarin [ 130 ]) were predicated as effective inhibitory agents for SARS-CoV-2 RdRp. However, the lack of experimental in vitro and in vivo observed results hindered the usefulness of these proposed prospective compounds.…”

Section: In Silico Proposed Compoundsmentioning

confidence: 99%

Potential RNA-dependent RNA polymerase (RdRp) inhibitors as prospective drug candidates for SARS-CoV-2

Bekheit

Panda

Girgis

2023

European Journal of Medicinal Chemistry

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Multi-targeted molecular docking, pharmacokinetics, and drug-likeness evaluation of coumarin based compounds targeting proteins involved in development of COVID-19

Cited by 13 publications

References 38 publications

Computational approaches: Atom-based 3D-QSAR, molecular docking, ADME-Tox, MD simulation and DFT to find novel multi-targeted Anti-tubercular agents

Computational approaches: Atom-based 3D-QSAR, molecular docking, ADME-Tox, MD simulation and DFT to find novel multi-targeted Anti-tubercular agents

A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds

Potential RNA-dependent RNA polymerase (RdRp) inhibitors as prospective drug candidates for SARS-CoV-2

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