title: The effect of pyridyl substituents on the thermodynamics of porphyrin binding to G-quadruplex DNA.
abstract: Most of the G-quadruplex interactive molecules reported to date contain extended aromatic flat ring systems and are believed to bind principally by π-π stacking on the end G-tetrads of the quadruplex structure. One such molecule, TMPyP4, (5,10,15,20-tetra(N-methyl-4-pyridyl)porphyrin), exhibits high affinity and some selectivity for G-quadruplex DNA over duplex DNA. Although not a realistic drug candidate, TMPyP4 is used in many nucleic acid research laboratories as a model ligand for the study of small molecule G-quadruplex interactions. Here we report on the synthesis and G-quadruplex interactions of four new cationic porphyrin ligands having only 1, 2, or 3 (N-methyl-4-pyridyl) substituents. The four new ligands are: P(5) (5-(N-methyl-4-pyridyl)porphyrin), P(5,10) (5,10-di(N-methyl-4-pyridyl)porphyrin), P(5,15) (5,15-di(N-methyl-4-pyridyl)porphyrin), and P(5,10,15) (5,10,15-tri(N-methyl-4-pyridyl)porphyrin). Even though these compounds have been previously synthesized, we report alternative synthetic routes that are more efficient and that result in higher yields. We have used ITC, CD, and ESI-MS to explore the effects of the number of N-methyl-4-pyridyl substituents and the substituent position on the porphyrin on the G-quadruplex binding energetics. The relative affinities for binding these ligands to the WT Bcl-2 promoter sequence G-quadruplex are: K(TMPyP4)≈K(P)(5,15)>KP(5,10,15)>>>KP(5,10), KP(5). The saturation stoichiometry is 2:1 for both P(5,15) and P(5,10,15), while neither P(5) nor P(5,10) exhibit significant complex formation with the WT Bcl-2 promoter sequence G-quadruplex. Additionally, binding of P(5,15) appears to interact by an 'intercalation mode' while P(5,10,15) appears to interact by an 'end-stacking mode'.
authors.affiliation: Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States. Electronic address: growland@chemistry.msstate.edu.
authors.forename: Gerald B
authors.initials: GB
authors.lastname: Rowland
authors.forename: Kerry
authors.initials: K
authors.lastname: Barnett
authors.forename: Jesse I
authors.initials: JI
authors.lastname: Dupont
authors.forename: Gopalakrishna
authors.initials: G
authors.lastname: Akurathi
authors.forename: Vu H
authors.initials: VH
authors.lastname: Le
authors.forename: Edwin A
authors.initials: EA
authors.lastname: Lewis
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D054856:G-Quadruplexes / Q000187:drug effects*; D008958:Models, Molecular; D011166:Porphyrins / Q000737:chemistry* / Q000494:pharmacology*; D013816:Thermodynamics
chemical_list: D011166:Porphyrins; C021096:tetra(4-N-methylpyridyl)porphine; D004247:DNA
keywords: Binding; DNA; G-quadruplex; ITC; Ligands; Porphyrins