Literature DB >> 29966734

G-quadruplex virtual drug screening: A review.

Robert C Monsen1, John O Trent2.   

Abstract

Over the past two decades biologists and bioinformaticians have unearthed substantial evidence supporting a role for G-quadruplexes as important mediators of biological processes. This includes telomere damage signaling, transcriptional activity, and splicing. Both their structural heterogeneity and their abundance in oncogene promoters makes them ideal targets for drug discovery. Currently, there are hundreds of deposited DNA and RNA quadruplex atomic structures which have allowed researchers to begin using in silico drug screening approaches to develop novel stabilizing ligands. Here we provide a review of the past decade of G-quadruplex virtual drug discovery approaches and campaigns. With this we introduce relevant virtual screening platforms followed by a discussion of best practices to assist future G4 VS campaigns.
Copyright © 2018 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Entities:  

Keywords:  Docking; Drug discovery; G-quadruplex; Virtual screening

Mesh:

Substances:

Year:  2018        PMID: 29966734      PMCID: PMC6134840          DOI: 10.1016/j.biochi.2018.06.024

Source DB:  PubMed          Journal:  Biochimie        ISSN: 0300-9084            Impact factor:   4.079


  101 in total

1.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Authors:  Richard A Friesner; Jay L Banks; Robert B Murphy; Thomas A Halgren; Jasna J Klicic; Daniel T Mainz; Matthew P Repasky; Eric H Knoll; Mee Shelley; Jason K Perry; David E Shaw; Perry Francis; Peter S Shenkin
Journal:  J Med Chem       Date:  2004-03-25       Impact factor: 7.446

2.  Interaction of distamycin A and netropsin with quadruplex and duplex structures: a comparative 1H-NMR study.

Authors:  Antonio Randazzo; Aldo Galeone; Veronica Esposito; Michela Varra; Luciano Mayol
Journal:  Nucleosides Nucleotides Nucleic Acids       Date:  2002       Impact factor: 1.381

3.  Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

Authors:  W Welch; J Ruppert; A N Jain
Journal:  Chem Biol       Date:  1996-06

4.  Identification of a selective G-quadruplex DNA binder using a multistep virtual screening approach.

Authors:  Jin-Qiang Hou; Shuo-Bin Chen; Li-Peng Zan; Tian-Miao Ou; Jia-Heng Tan; Leonard G Luyt; Zhi-Shu Huang
Journal:  Chem Commun (Camb)       Date:  2015-01-04       Impact factor: 6.222

5.  G-quadruplex structures within the 3' UTR of LINE-1 elements stimulate retrotransposition.

Authors:  Aleksandr B Sahakyan; Pierre Murat; Clemens Mayer; Shankar Balasubramanian
Journal:  Nat Struct Mol Biol       Date:  2017-01-30       Impact factor: 15.369

6.  Novel G-quadruplex stabilizing agents: in-silico approach and dynamics.

Authors:  Rajiv Kumar Kar; Priyanka Suryadevara; Jagannath Jana; Anirban Bhunia; Subhrangsu Chatterjee
Journal:  J Biomol Struct Dyn       Date:  2012-12-17

7.  Quadruplex-interactive agents as telomerase inhibitors: synthesis of porphyrins and structure-activity relationship for the inhibition of telomerase.

Authors:  D F Shi; R T Wheelhouse; D Sun; L H Hurley
Journal:  J Med Chem       Date:  2001-12-20       Impact factor: 7.446

Review 8.  Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?

Authors:  Shankar Balasubramanian; Laurence H Hurley; Stephen Neidle
Journal:  Nat Rev Drug Discov       Date:  2011-04       Impact factor: 84.694

9.  Local epigenetic reprogramming induced by G-quadruplex ligands.

Authors:  Guillaume Guilbaud; Pierre Murat; Bénédicte Recolin; Beth C Campbell; Ahmed Maiter; Julian E Sale; Shankar Balasubramanian
Journal:  Nat Chem       Date:  2017-07-31       Impact factor: 24.427

Review 10.  Molecular dynamics simulations: advances and applications.

Authors:  Adam Hospital; Josep Ramon Goñi; Modesto Orozco; Josep L Gelpí
Journal:  Adv Appl Bioinform Chem       Date:  2015-11-19
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  14 in total

1.  Drug discovery of small molecules targeting the higher-order hTERT promoter G-quadruplex.

Authors:  Robert C Monsen; Jon M Maguire; Lynn W DeLeeuw; Jonathan B Chaires; John O Trent
Journal:  PLoS One       Date:  2022-06-16       Impact factor: 3.752

Review 2.  Modulation of DNA structure formation using small molecules.

Authors:  Imee M A Del Mundo; Karen M Vasquez; Guliang Wang
Journal:  Biochim Biophys Acta Mol Cell Res       Date:  2019-09-03       Impact factor: 4.739

3.  Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes.

Authors:  Jonathan Dickerhoff; Jixun Dai; Danzhou Yang
Journal:  Nucleic Acids Res       Date:  2021-06-04       Impact factor: 16.971

4.  Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences.

Authors:  Robert C Monsen; Lynn W DeLeeuw; William L Dean; Robert D Gray; Srinivas Chakravarthy; Jesse B Hopkins; Jonathan B Chaires; John O Trent
Journal:  Nucleic Acids Res       Date:  2022-04-22       Impact factor: 19.160

5.  Binding Study of the Fluorescent Carbazole Derivative with Human Telomeric G-Quadruplexes.

Authors:  Agata Głuszyńska; Bernard Juskowiak; Błażej Rubiś
Journal:  Molecules       Date:  2018-11-30       Impact factor: 4.411

6.  Exploration of the Structure and Recognition of a G-quadruplex in the her2 Proto-oncogene Promoter and Its Transcriptional Regulation.

Authors:  Xiaojie Cui; Han Chen; Qiang Zhang; Ming Xu; Gu Yuan; Jiang Zhou
Journal:  Sci Rep       Date:  2019-03-08       Impact factor: 4.379

7.  Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives.

Authors:  Jonas Becher; Daria V Berdnikova; Heiko Ihmels; Christopher Stremmel
Journal:  Beilstein J Org Chem       Date:  2020-11-18       Impact factor: 2.883

8.  Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands.

Authors:  Michael P O'Hagan; Susanta Haldar; Juan C Morales; Adrian J Mulholland; M Carmen Galan
Journal:  Chem Sci       Date:  2020-11-26       Impact factor: 9.825

9.  Probing the Importance of the G-Quadruplex Grooves for the Activity of the Anti-HIV-Integrase Aptamer T30923.

Authors:  Veronica Esposito; Francesca Esposito; Antonietta Pepe; Isabel Gomez Monterrey; Enzo Tramontano; Luciano Mayol; Antonella Virgilio; Aldo Galeone
Journal:  Int J Mol Sci       Date:  2020-08-06       Impact factor: 5.923

10.  No G-Quadruplex Structures in the DNA of Parvovirus B19: Experimental Evidence versus Bioinformatic Predictions.

Authors:  Gloria Bua; Daniele Tedesco; Ilaria Conti; Alessandro Reggiani; Manuela Bartolini; Giorgio Gallinella
Journal:  Viruses       Date:  2020-08-25       Impact factor: 5.048

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