3D-QSAR (CoMFA, CoMSIA, HQSAR and topomer CoMFA), MD simulations and molecular docking studies on purinylpyridine derivatives as B-Raf inhibitors for the treatment of melanoma cancer

Chavda, Jaydeepsinh; Bhatt, Hardik

doi:10.1007/s11224-019-01334-9

Cited by 22 publications

(9 citation statements)

References 18 publications

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“…Moreover, to validate the predictive abilities of QSAR models, the predicted R 2 ( R 2 pred ) was calculated using the test set and its formula was expressed by the following equation (Golbraikh & Tropsha, 2002; Chavda & Bhatt, 2019),

R_{pred}^{2} = 1 ‐ false(PRESS false/ SD false)

…”

Section: Methodsmentioning

confidence: 99%

“…The higher R 2 pred is, the higher the predictive power of the generated QSAR model is. The ideal value of R 2 pred is more than 0.5, which indicated that the model is qualified for prediction (Chavda & Bhatt, 2019).…”

Section: Methodsmentioning

confidence: 99%

“…In the CoMFA model, steric and electrostatic fields of a set of aligned compounds are calculated based on principles of Columbia potential and Lenard–Jones potential; then, their biological activities over a lattice of point are predicted (Abdizadeh et al ., 2020). In the CoMSIA analysis, a probe atom is used to calculate similarity indices (including steric, electrostatic, HBD, HBA and hydrophobic parameters) at regularly placed grid points for the aligned molecules, then build the correlation between bioactive capacity and structural feature (Chavda & Bhatt, 2019; Abdizadeh et al ., 2020). HQSAR uses the fragment fingerprints of molecular holograms and other molecular descriptors (Atoms, connections, bonds, hydrogen atoms, chirality, donor and acceptor) to predict the biological activity of a set of aligned compounds (Aswathy et al ., 2018; Abdizadeh et al ., 2020).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structure–activity relationship and molecular docking analysis of cysteine‐containing dipeptides as antioxidant and ACE inhibitory

Lü

Jia

Gao

et al. 2020

Int J of Food Sci Tech

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R_{pred}^{2} = 1 ‐ false(PRESS false/ SD false)

…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Structure–activity relationship and molecular docking analysis of cysteine‐containing dipeptides as antioxidant and ACE inhibitory

Lü

Jia

Gao

et al. 2020

Int J of Food Sci Tech

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“…Skin cancer/melanoma is rising in current years due to exposure to UV radiation. Almost the aggressiveness of skin cancer caused by exposure to an excess of UV radiation from the sun [6].…”

Section: Introductionmentioning

confidence: 99%

Molecular Docking Study of Nutmeg (Myristica Fragrans) Constituents as Anti-Skin Cancer Agents

Fitriani

Ansory

2021

JKPK

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<p>Molecular docking analysis was carried out to understand better the interaction between DHODH and inhibitor from nutmeg in this series. The nutmeg constituent binding orientations in the active site of DHODH was seen in a molecular docking analysis and helped design a potentially new inhibitor. This work aimed to study the molecular docking of nutmeg constituents with the DHODH inhibitor using a computer-aided drug design. Molecular docking using AutoDock 4.2 was done to explore the models of binding complexes. The 3D structure was derived using Discovery Studio to investigate the essential chemical interaction of complex structures. Dihydroguaiaretic acid was the most potent ligand having a docking score of -9.3 kcal/mol. This value was better than the standard drug 5-FU. The dihydroguaiaretic acid structure interacted with Tyr365 and Thr63 through a hydrogen bond similar to the native ligand. These results suggest that nutmeg seed could serve as the lead compound for potent DHODH inhibitors against skin.</p>

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“…Molecular descriptors (MDs) are the support of several bio‐chem‐informatics applications, such as quantitative structure–activity/property/toxicity relationships (QSAR/QSPR/QSTR), and similarity/dissimilarity analyses . Several commercial and noncommercial software have been developed to compute the MDs (and fingerprints) defined to date.…”

Section: Introductionmentioning

confidence: 99%

Distributed and multicore QuBiLS‐MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

et al. 2020

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Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 (http://tomocomd.com/qubils-midas) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute

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3D-QSAR (CoMFA, CoMSIA, HQSAR and topomer CoMFA), MD simulations and molecular docking studies on purinylpyridine derivatives as B-Raf inhibitors for the treatment of melanoma cancer

Cited by 22 publications

References 18 publications

Structure–activity relationship and molecular docking analysis of cysteine‐containing dipeptides as antioxidant and ACE inhibitory

Structure–activity relationship and molecular docking analysis of cysteine‐containing dipeptides as antioxidant and ACE inhibitory

Molecular Docking Study of Nutmeg (Myristica Fragrans) Constituents as Anti-Skin Cancer Agents

Distributed and multicore QuBiLS‐MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

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