Targeting MYC G-quadruplexes by virtual screening of their dynamic ensembles for drug development

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Guanine-rich DNA sequences can form the four-stranded G-quadruplexes (G4s), which are found in promoter regions of oncogenes. For example, the G4 formation down-regulates the transcription of the prominent MYC oncogene and thereby suppresses the Myc protein, which is indispensable in many cancer cells. Therefore, drug-induced stabilization of the MYC G4s has been proposed as future cancer therapy. Most G4-interactive compounds stack upon the rigid G-core and this binding pocket is complemented by different combination of flexible loop and flanking sequences, almost unique for each G4 sequence. This enormous variability of binding pockets allows the development of highly-selective drugs for MYC G4s. In principle, computational docking can identify promising small molecules through virtual screening, based on their specific molecular interactions. However, the reliability of virtual screening is limited for G4s since conventional approaches cannot correctly capture the conformational landscape of their dynamic binding sites. Thus, interesting compounds are overlooked and false-positives occur. In this project, I want to overcome this limitation with an improved MYC G4-specific virtual screening approach that determines and accounts for the dynamic nature of binding sites. This will be accomplished by the first determination of G4 dynamic ensembles, which represent the relevant conformations of the flexible binding sites. The determination of residual dipolar couplings (RDCs) by nuclear magnetic resonance spectroscopy will measure the dynamics of two selected MYC G4s with atomic resolution. Possible conformations of the MYC G4s will be sampled by molecular dynamics calculations and the conformers of the dynamic ensembles will be selected based on the RDC data. Subsequently, the use of the G4 dynamic ensembles in virtual screenings will be examined to find novel, highly-selective ligands. Finally, in vitro and in vivo tests of the identified compounds will validate their selection from virtual screenings and determine their value for future studies.