A combined
            <i>in silico</i>
            approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives

Guendouzi, Abdelmadjid; Belkhiri, Lotfi; Guendouzi, Abdelkrim; Derouiche, Tahar Mohamed Taha; Djekoun, Abdelhamid

doi:10.1080/07391102.2023.2192801

Cited by 5 publications

(2 citation statements)

References 78 publications

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“…Pharmacokinetic pro le refers to how the drug is absorbed, distributed, metabolized, and excreted, while toxicological pro le reveals the potential adverse drug reactions. These parameters, collectively known as ADMET parameters, can be determined by computer models instead of experimental procedures, which save time and reduces the risk of hazards [70,71].…”

Section: Pharmacokinetic and Toxicological Pro Le Analysismentioning

confidence: 99%

Identification of Natural Product Inhibitors Targeting Dengue Capsid Protein Using an Open-Access Artificial Intelligence-Based Drug Discovery Methodology

Khan,

Hasan,

Hasan

2024

Preprint

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Dengue fever, or break-bone fever, is caused by dengue flavivirus transmitted through mosquito bites. To identify a druggable protein target for developing effective antiviral therapies, we studied how proteins from the dengue virus interact with the human body and created a detailed protein-protein interaction network of these interactions. The analysis of molecular functions and biological processes associated with proteins has shown that the capsid protein is crucial in facilitating the interaction between the virus and the host. This finding highlights the significance of the capsid protein as a potential target. We used AutoDockFR to study the binding of 208 natural compounds from Azadirachta indica with capsid protein. We screened the compounds using the X-ray diffraction structure of capsid protein (6vg5) and placed them into the binding pocket of an inhibitor called ST-148. We re-docked the inhibitor ST-148 and considered its docking score (-8.5) as the threshold value for hit selection. After applying these criteria, we obtained 81 hits. The binding mode analysis of the hits revealed that the cyclopentanoperhydrophenathrene ring structure is an essential pharmacophore that fits well into the binding cavity. Further molecular dynamics simulation study of the complexes for the highest affinity and the lowest affinity hits score confirmed the stability of the complex. An exhaustive analysis of the physical and chemical characteristics of potential drug candidates and their pharmacokinetic profiles has revealed that the natural products under consideration hold great potential as a viable treatment option for infections caused by the dengue virus.

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Section: Pharmacokinetic and Toxicological Pro Le Analysismentioning

confidence: 99%

Identification of Natural Product Inhibitors Targeting Dengue Capsid Protein Using an Open-Access Artificial Intelligence-Based Drug Discovery Methodology

Khan,

Hasan,

Hasan

2024

Preprint

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“…The process of molecular docking is a crucial tool in drug discovery as it aids in predicting the binding of a ligand to its target protein [21] . In this study, the technique of molecular docking was employed using the Virtual Molegro Docker software [22] to determine the optimal positioning of four different compounds, namely Apigenin (API), Luteolin (lut), Naringenin (nari) and Quercetin (que) figure 1, with respect to two different prostaglandin proteins (PDB ID: 3DWW Resolution: 3.50 Å and PDB ID: 3LN1 Resolution: 2.40 Å), which were retrieved from the Protein Data Bank (RCSB) (figure 1).…”

Section: Computational Detailsmentioning

confidence: 99%

Identification of Ajuga Iva Extracts as Potential Candidates for Antidysmenorrhea Targeting Human COX2 and PGE2S‐1 through In Vitro and In Silico Drug Repurposing Approach

Djelti,

Berkane,

Alharbi

et al. 2024

ChemistrySelect

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Ajuga Iva, renowned in ethnomedicine, possesses various pharmacological properties, attributed to its diverse phytochemical profile. Despite its therapeutic potential, little research has examined the efficacy of Ajuga Iva in the treatment of dysmenorrhea, a prevalent inflammatory disorder that affects a significant number of adult women around the world, This study aims to explore the anti‐inflammatory properties of Ajuga Iva in the context of treating dysmenorrhea through a combined in vitro and in silico drug repurposing approach. In vitro assays evaluated the anti‐inflammatory efficacy of the plant extracts, revealing significant activity in inhibiting protein denaturation and heat‐induced haemolysis. Molecular docking studies identified potential bioactive phytochemicals, including Apigenin, Luteolin, Naringenin, and Quercetin, interacting with COX‐2 and PGES‐1, key enzymes in dysmenorrhea‐associated inflammatory pathways. Molecular dynamics simulations supported these interactions. Ajuga Iva methanolic extract exhibited significant anti‐inflammatory activity, as shown by its ability to inhibit protein denaturation by 80.68% at 1000 (μg/m) and heat induced haemolysis by 83.41% at 2000 (μg/m). Ajuga Iva bioactive phytochemicals showed promising interactions with COX‐2 and PGES‐1, suggesting their role in the plant's anti‐inflammatory mechanism. This research underscores the promising anti‐inflammatory activities of Ajuga Iva by inhibiting COX‐2 and PGE2S‐1, offering valuable insights for future therapeutic applications.

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Comprehensive evaluation and systematic comparison of Gaussian process (GP) modelling applications in peptide quantitative structure-activity relationship

Ye,

Zhang,

et al. 2024

Chemometrics and Intelligent Laboratory Systems

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A combined in silico approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives

Cited by 5 publications

References 78 publications

Identification of Natural Product Inhibitors Targeting Dengue Capsid Protein Using an Open-Access Artificial Intelligence-Based Drug Discovery Methodology

Identification of Natural Product Inhibitors Targeting Dengue Capsid Protein Using an Open-Access Artificial Intelligence-Based Drug Discovery Methodology

Identification of Ajuga Iva Extracts as Potential Candidates for Antidysmenorrhea Targeting Human COX2 and PGE2S‐1 through In Vitro and In Silico Drug Repurposing Approach

Comprehensive evaluation and systematic comparison of Gaussian process (GP) modelling applications in peptide quantitative structure-activity relationship

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