br Discussion br Concluding remarks There are potentially hu

Discussion
Concluding remarks There are potentially hundreds or thousands of G-quadruplexes which form within promoters, telomeres, RNA transcripts, and even LINEs and SINES [9,11,121,122]. As articulated previously [27], G-quadruplexes are easily targetable with heterocyclic aromatic compounds because of the common tetrad face. Selectivity, then, must come from groove-interacting ligands or by end-pasting molecules with “built-in” selectivity for loops around the 5′ or 3′ interface. This is best achieved using massive, un-filtered libraries targeted at small pockets in and around the loops and grooves (Fig. 15). The authors have recently used Surflex-Dock version 2.1 to screen the ZINC [50] drug-like libraries (versions 2014 and 2016) for a total of ∼45 million compounds docked to multiple residue-defined loop/groove pockets of a modeled hTERT G-quadruplex (modeled using guanine stacks from the parallel c-myc G4, PDB ID: 1XAV) [113]. The quadruplex was subjected to MD simulations and stripped of waters and ions before docking. Docking was carried out using a computing grid known as the DataseamGrid [123] which utilizes computers across schools in Kentucky. Ligands were used as-is from the ZINC drug-like database. Purchased compounds were chosen by hierarchical clustering of the top 6000 molecules using Tanimoto similarity coefficients. From this analysis, 69 compounds were selected and screened using FRET, CD, ITC, fluorescent intercalator displacement assays, and analytical ultracentrifugation. The initial FRET screen resulted in ∼33/69 G4 interacting compounds. The top 3 were further characterized, resulting in 2 potent groove or loop interacting ligands (unpublished) which are currently undergoing optimization and lead development. Virtual screening of G-quadruplexes and other higher order nucleic SB408124 structures is still in its infancy. As noted here, few VS platforms have been used in G4 drug discovery and even fewer have been used extensively enough with nucleic acids as to permit cross-platform comparisons. Furthermore, like protein systems, nucleic acids remain sensitive (if not more so) to the limitations of VS technologies. As mentioned previously [33,124] receptor flexibility remains difficult to address in a high-throughput manner, and so G4 loops remain a challenge to target. Similarly, while docking algorithms can be very reproducible and rapid, there remains a dire need for accurate, robust scoring approximations [124]. Fortunately, the predictions [125] of hit enrichment from high performance computing and large libraries were correct. So, while the world awaits breakthroughs in scoring, receptor flexibility, and machine learning [33,126], it might be valuable to seek out your nearest computing cluster to carry out your G4 screening.
Funding This work was supported by the National Institute of Health (grants GM077422 and P30GM106396).
Conflicts of interest
Acknowledgements
Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMSP41-GM103311).
Introduction G-quadruplex structures are four stranded architectures held together by guanines bonded to each other by Hoogsteen pairing. [1] DNA G-quadruplex structures play vital roles in genome functions, including transcription, recombination and replication. [2] These structures are also found in crucial regulatory regions of the human genome, such as telomeric regions. [3] The transcription activity of DNA can be inhibited by the stabilization of the corresponding G-quadruplexes with some stabilizers. Due to their biological functions and potential value for drug design, G-quadruplex structures have drawn much attention during recent years. Hence, a large number of organic molecules have been developed as inhibitors to stabilize the formation of these quadruplex DNA structures. 4, 5, 6 In recent years, some ligands with a specificity toward certain G-quadruplex structures over others have been reported. Some of them gained the specificity to particular G-quadruplex DNAs through the recognition of the adjacent DNA sequences. 7, 8, 9, 10, 11