Molecular docking as a popular tool in drug design, an in silico travel

Ruyck, Jérôme de; Brysbaert, Guillaume; Blossey, Ralf; Lensink, Marc F.

doi:10.2147/aabc.s105289

Cited by 230 publications

(141 citation statements)

References 139 publications

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“…The CAPRI community‐wide protein‐docking experiment has catalyzed the development of computational protein docking for more than 15 years and has led to the emergence of now wide‐spread protein docking algorithms and fully automatic web servers . We decided to use an ensemble of four consistently‐performing docking programs (see section 2.2) to model the interaction between ETS and BRCT or SAP domains.…”

Section: Resultsmentioning

confidence: 99%

Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes

et al. 2018

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The Ets‐1 oncoprotein is a transcription factor that promotes target gene expression in specific biological processes. Typically, Ets‐1 activity is low in healthy cells, but elevated levels of expression have been found in cancerous cells, specifically related to tumor progression. Like the vast majority of the cellular effectors, Ets‐1 does not act alone but in association with partners. Given the important role that is attributed to Ets‐1 in major human diseases, it is crucial to identify its partners and characterize their interactions. In this context, two DNA‐repair enzymes, PARP‐1 and DNA‐PK, have been identified recently as interaction partners of Ets‐1. We here identify their binding mode by means of protein docking. The results identify the interacting surface between Ets‐1 and the two DNA‐repair enzymes centered on the α‐helix H1 of the ETS domain, leaving α‐helix H3 available to bind DNA. The models highlight a hydrophobic patch on Ets‐1 at the center of the interaction interface that includes three tryptophans (Trp338, Trp356, and Trp361). We rationalize the binding mode using a series of computational analyses, including alanine scanning, molecular dynamics simulation, and residue centrality analysis. Our study constitutes a first but important step in the characterization, at the molecular level, of the interaction between an oncoprotein and DNA‐repair enzymes.

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Section: Resultsmentioning

confidence: 99%

Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes

et al. 2018

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“…[31,52] Today, researchers from every field taking the support of docking to understand mode and strength of interaction at molecular level. [31,32,[53][54][55][56] In the present work, shape-based cholinium ion was docked with DNA duplex of sequence d(CGCGAATTCGCG)2 dodecamer (PDB ID: 1BNA) to predict the binding site and preferred orientation.…”

Section: Docking Studiesmentioning

confidence: 99%

Interaction studies of cholinium-based ionic liquids with calf thymus DNA: Spectrophotometric and computational methods

Haque

Khan

Hassan

et al. 2017

Journal of Molecular Liquids

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“…The complex with the most negative binding energy (kcal/mol) was subjected to molecular dynamic simulations. A greater expansion of molecular docking can be found in the referenced articles …”

Section: Methodsmentioning

confidence: 99%

A panoptic uncovering of the dynamical evolution of the Zika Virus NS5 methyltransferase binding site loops—zeroing in on the molecular landscape

Devnarain

Soliman

2018

Chem Biol Drug Des

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The global threat of the Zika virus to humanity is real. Innovative and potent anti-Zika virus drugs are still at large, due to the lack of anti-Zika virus drugs that have passed phase 1 trials. Experimental research has revealed novel inhibitors of Zika virus NS5 methyltransferase enzyme. This study has taken a step further to provide insight into the molecular dynamics of Zika virus and inhibitor binding, which have not been established experimentally. Movements of the methyltransferase binding site loops have a large role to play in the methylation of the viral mRNA cap, which is essential for Zika virus replication. Here, we pinpoint the binding interactions between each potential inhibitor and the methyltransferase, residues that are responsible for binding, as well as which inhibitor-bound complex renders the methyltransferase more stable. We also highlight the conformational changes that occur within the methyltransferase to accommodate binding of inhibitors and consequences of those changes upon the RNA- and cap-binding sites in the methyltransferase. This research will improve the understanding of the Zika virus NS5 methyltransferase enzyme, and will be beneficial in driving the development of anti-Zika virus drugs.

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Molecular docking as a popular tool in drug design, an in silico travel

Cited by 230 publications

References 139 publications

Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes

Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes

Interaction studies of cholinium-based ionic liquids with calf thymus DNA: Spectrophotometric and computational methods

A panoptic uncovering of the dynamical evolution of the Zika Virus NS5 methyltransferase binding site loops—zeroing in on the molecular landscape

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