Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component

Nayek, Upendra; Ahamed, Syed Ibrahim Basheer; Halilunnisa, Ummul; Unnikrishnan, M.K.; Salam, Abdul Ajees Abdul

doi:10.1016/j.compbiolchem.2022.107776

Cited by 4 publications

(5 citation statements)

References 51 publications

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“…Authoritatively, the principal component analysis (PCA) was mainly engaged to identify the movements and transformations of pure proteins or complex molecules through dynamics trajectory data 37–39 . Helicase‐Rutaecarpine or helicase‐Acyclovir system PCA [principal component one (PC1) was Gyrate, while principal component two (PC2) was RMSD] were calculated using the gmx covar module.…”

Section: Resultsmentioning

confidence: 99%

“…3.9 Gibbs energy landscape and the MM-GBSA analysis Authoritatively, the principal component analysis (PCA) was mainly engaged to identify the movements and transformations of pure proteins or complex molecules through dynamics trajectory data. [37][38][39] Helicase-Rutaecarpine or helicase-Acyclovir system PCA [principal component one (PC1) was Gyrate, while principal component two (PC2) was RMSD] were calculated using the gmx covar module. Combining the system Gibbs energy, Gyrate, and RMSD parameters, the Gibbs energy landscape of the complex was established to evaluate their energy stable states.…”

Section: Dynamic Simulationmentioning

confidence: 99%

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Identification of natural Rutaecarpine as a potent tobacco mosaic virus (TMV) helicase candidate for managing intractable plant viral diseases

Li,

Hu,

Luo

et al. 2023

Pest Management Science

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BackgroundNaturally occurring alkaloids are particularly suitable for use as pesticide precursors and further modifications due to their cost‐effectiveness, unique mechanism of action, tolerable degradation, and environmental friendliness. The famous tobacco mosaic virus (TMV) is a persistent plant pathogenic virus that can parasitize many plants and severely reduce crop production. To treat TMV disease, TMV helicase acts as a crucial target by hydrolyzing ATP to provide energy for double‐stranded RNA unwinding.ResultsTo seek novel framework alkaloid leads targeting TMV helicase, this work successfully established an efficient screening platform for TMV helicase inhibitors based on natural alkaloids. In vivo activity screening, enzyme activity detection, and binding assays showed that Rutaecarpine from Evodia rutaecarpa (Juss.) Benth exhibited excellent TMV helicase inhibitory properties (Kd = 1.1 μM, IC50 = 227.24 μM) and excellent anti‐TMV ability. Molecular docking and dynamic simulations depicted that Rutaecarpine could stably bind in active pockets of helicase with low binding energy (ΔGbind = ‐17.8 kcal/mol) driven by hydrogen bonding and hydrophobic interactions.ConclusionGiven Rutaecarpine's laudable bioactivity and structural modifiability, it can serve as a privileged building block for further pesticide discovery.This article is protected by copyright. All rights reserved.

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Section: Resultsmentioning

confidence: 99%

Section: Dynamic Simulationmentioning

confidence: 99%

Identification of natural Rutaecarpine as a potent tobacco mosaic virus (TMV) helicase candidate for managing intractable plant viral diseases

Li,

Hu,

Luo

et al. 2023

Pest Management Science

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show abstract

“…The most similar redocked and crystal conformation was used to calculate the root mean square deviation (RMSD) between structures. This method of validation through redocking has been executed recently [48] , [49] . To calculate the RMSD, DockRMSD was utilized [50] .…”

Section: Methodsmentioning

confidence: 99%

Investigation of the relationship between ergocristinine and vascular receptors

2023

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“…Cereblon is a component of the E3 ubiquitin ligase complex involved in this process (Nayek et al, 2022). Park et al generated a Cereblon-based PROTAC that induces the proteasomal degradation of KEAP1, leading to the activation of NRF2 (Park et al, 2023).…”

Section: Nrf2 and Detoxificationmentioning

confidence: 99%

Deciphering Acetaminophen-Induced Hepatotoxicity: The Crucial Role of Transcription Factors like Nuclear Factor Erythroid 2–Related Factor 2 as Genetic Determinants of Susceptibility to Drug-Induced Liver Injury

Laddha,

Wu,

Manautou

2024

Drug Metab Dispos

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Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component

Cited by 4 publications

References 51 publications

Identification of natural Rutaecarpine as a potent tobacco mosaic virus (TMV) helicase candidate for managing intractable plant viral diseases

Identification of natural Rutaecarpine as a potent tobacco mosaic virus (TMV) helicase candidate for managing intractable plant viral diseases

Investigation of the relationship between ergocristinine and vascular receptors

Deciphering Acetaminophen-Induced Hepatotoxicity: The Crucial Role of Transcription Factors like Nuclear Factor Erythroid 2–Related Factor 2 as Genetic Determinants of Susceptibility to Drug-Induced Liver Injury

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