Design and Synthesis of an Expanded Porphyrin That Has Selectivity for the c-MYC G-Quadruplex Structure

Abstract

Cationic porphyrins are known to bind to and stabilize different types of G-quadruplexes. Recent studies have shown the biological relevance of the intramolecular parallel G-quadruplex as a transcriptional silencer in the c-MYC promoter. TMPyP4 also binds to this G-quadruplex and most likely converts it to a mixed parallel/antiparallel G-quadruplex with two external lateral loops and one internal propeller loop, suppressing c-MYC transcriptional activation. To achieve therapeutic selectivity by targeting G-quadruplexes, it is necessary to synthesize drugs that can differentiate among the different types of G-quadruplexes. We have designed and synthesized a core-modified expanded porphyrin analogue, 5,10,15,20-[tetra(N-methyl-3-pyridyl)]-26,28-diselenasapphyrin chloride (Se2SAP). Se2SAP converts the parallel c-MYC G-quadruplex into a mixed parallel/antiparallel G-quadruplex with one external lateral loop and two internal propeller loops, resulting in strong and selective binding to this G-quadruplex. A Taq polymerase stop assay was used to evaluate the binding of TMPyP4 and Se2SAP to G-quadruplex DNA. Compared to TMPyP4, Se2SAP shows a greater selectivity for and a 40-fold increase in stabilization of the single lateral-loop hybrid. Surface plasmon resonance and competition experiments with duplex DNA and other G-quadruplexes further confirmed the selectivity of Se2SAP for the c-MYC G-quadruplex. Significantly, Se2SAP was found to be less photoactive and noncytotoxic in comparison to TMPyP4. From this study, we have identified an expanded porphyrin that selectively binds with the c-MYC G-quadruplex in the presence of duplex DNA and other G-quadruplexes.

Deconvoluting the Structural and Drug-Recognition Complexity of the G-Quadruplex-Forming Region Upstream of the bcl-2 P1 Promoter

“…41,68-70 For example, cationic porphyrins and sapphyrins have been shown to bind to and stabilize a number of different types of G-quadruplexes. 41,44,71,72 Specifically, the cationic porphyrin and sapphyrin used in this study, TMPyP4 and Se2SAP, have been shown to have variable selectivity for G-quadruplex structures. TMPyP4 is less discriminating compared to Se2SAP, which has been shown to specifically stabilize one of the c-myc G-quadruplexes, 41 as well as the K + form of the human telomeric G-quadruplex.…”

“…Se2SAP is a synthetic, core-modified, expanded porphyrin that was first synthesized in our laboratory with the specific aim of targeting a subset of G-quadruplex structures. 41 Telomestatin is a natural product, 51 which has been shown to inhibit telomerase through its strong G-quadruplex interaction with the human telomeric sequence. 52 DNA polymerase stop assays were preformed with this series of compounds together with the three individual G-quadruplex-forming sequences (5′G4, MidG4, and 3′G4) to test whether selective stabilization of specific G-quadruplexes was achievable (Figure 7).…”

Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands

“…Owing to the unique secondary motif, G-quadruplex is impervious to be attacked by enzymes targeting normal single-stranded or duplex DNA, and consequently is able to regulate the transcription and replication of specific gene. Therefore, G-quadruplex motif attracts growing interests and the ligands able to stabilize or regulate the formation of specific G-quadruplex motifs have been considered as potential novel anticancer medicines [10][11][12].…”

An important functional group, benzo[1,3]dioxole, of alkaloids induces the formation of the human telomeric DNA G-quadruplex

“…For example, telomestatin, a macrocyclic natural product comprising a similar structure to a G-tetrad, is currently regarded as a good G-quadruplex ligand and is the most efficient in vitro telomerase inhibitor [15][16][17]. Another important feature of G-quadruplex ligands is the central cationic aromatic core.…”