Biomolecular Talks—Part 2: Applications and Challenges of Molecular Docking Approaches

Amutha, R.; Balasubramanian, Sangeetha; Rajagopalan, Muthukumaran

doi:10.1016/b978-0-12-822312-3.00024-2

Cited by 3 publications

(1 citation statement)

References 156 publications

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“…The creation of molecular complexes via intermolecular interactions is extensively investigated using the computer approach known as molecular docking. Computer-aided drug design has shown the effectiveness of molecular docking in studying molecular recognition by predicting the affinity and binding mode between the interacting molecules, such as protein–ligand interactions [ 43 ].…”

Section: Resultsmentioning

confidence: 99%

In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4

Cabral

Cruz

Sato

et al. 2022

IJERPH

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Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) are widespread across the globe, existing in the environment in complex mixtures potentially capable of initiating respiratory illnesses. Here, we use an in silico approach to evaluate the potential pro-inflammatory effects of various carcinogenic PAHs and VOCs through their binding affinity towards the human toll-like receptor 4 (TLR4). For receptors and ligands, RCSB Protein Data Bank and PubChem were used in obtaining their 3D structures, respectively. Autodock Vina was utilized to obtain the best docking poses and binding affinities of each PAH and VOC. Out of the 14 PAHs included in this study, indeno(1,2,3-cd)pyrene, benzo(ghi)perylene, and benzo[a]pyrene had the highest binding affinity values of −10, −9, and −8.9 kcal/mol, respectively. For the VOCs, out of the 10 compounds studied, benzene, 1,4-dichlorobenzene, and styrene had the highest binding affinity values of −3.6, −3.9, and −4.6 kcal/mol, respectively. Compounds with higher affinity than LPS (−4.1 kcal/com) could potentially induce inflammation, while compounds with lower affinity would be less likely to induce an inflammatory response. Meanwhile, molecular dynamics simulation and RMSF statistical analysis proved that the protein, TLR4, stably preserve its conformation despite ligand interactions. Overall, the structure of the TLR4 was considered inflexible.

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Section: Resultsmentioning

confidence: 99%

In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4

Cabral

Cruz

Sato

et al. 2022

IJERPH

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Repurposing of Serotonin Pathway Influencing Drugs for Potential Cancer Therapy and Antimicrobial Functions

Ray

Kumar

2023

Drug Repurposing for Emerging Infectious Diseases and Cancer

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In vitro inhibitor effect and molecular docking of thiamine (vitamin B ₁ ), riboflavin (vitamin B ₂ ), and reference inhibitor captopril on angiotensin-converting enzyme purified from sheep plasma

Ciftci,

Turkoglu,

Bas

et al. 2024

Archives of Physiology and Biochemistry

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Biomolecular Talks—Part 2: Applications and Challenges of Molecular Docking Approaches

Cited by 3 publications

References 156 publications

In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4

In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4

Repurposing of Serotonin Pathway Influencing Drugs for Potential Cancer Therapy and Antimicrobial Functions

In vitro inhibitor effect and molecular docking of thiamine (vitamin B ₁ ), riboflavin (vitamin B ₂ ), and reference inhibitor captopril on angiotensin-converting enzyme purified from sheep plasma

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Biomolecular Talks—Part 2: Applications and Challenges of Molecular Docking Approaches

Cited by 3 publications

References 156 publications

In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4

In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4

Repurposing of Serotonin Pathway Influencing Drugs for Potential Cancer Therapy and Antimicrobial Functions

In vitro inhibitor effect and molecular docking of thiamine (vitamin B 1 ), riboflavin (vitamin B 2 ), and reference inhibitor captopril on angiotensin-converting enzyme purified from sheep plasma

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Product

Resources

About

In vitro inhibitor effect and molecular docking of thiamine (vitamin B ₁ ), riboflavin (vitamin B ₂ ), and reference inhibitor captopril on angiotensin-converting enzyme purified from sheep plasma