Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: a molecular mechanics investigation.

On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7 belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N-methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.

Joint molecular modeling and spectroscopic studies of DNA complexes of a bis(arginyl) conjugate of a tricationic porphyrin designed to target the major groove.

To target selectively the major groove of double-stranded B DNA, we have designed and synthesized a bis(arginyl) conjugate of a tricationic porphyrin (BAP). Its binding energies with a series of double-stranded dodecanucleotides, having in common a central d(CpG)2 intercalation site were compared. The theoretical results indicated a significant energy preference favoring major groove over minor groove binding and a preferential binding to a sequence encompassing the palindrome GGCGCC encountered in the Primary Binding Site of the HIV-1 retrovirus. Spectroscopic studies were carried out on the complexes of BAP with poly(dG-dC) and poly(dA-dT) and a series of oligonucleotide duplexes having either a GGCGCC, CCCGGG, or TACGTA sequence. The results of UV-visible and circular dichroism spectroscopies indicated that intercalation of the porphyrin takes place in poly(dG-dC) and all the oligonucleotides. Thermal denaturation studies showed that BAP increased significantly the melting temperature of the oligonucleotides having the GGCGCC sequence, whereas it produced only a negligible stabilization of sequences having CCCGGG or TACGTA in place of GGCGCC. This indicates a preferential binding of BAP to GGCGCC, fully consistent with the theoretical predictions. IR spectroscopy on d(GGCGCC)2 indicated that the guanine absorption bands, C6=O6 and N7-C8-H, were shifted by the binding of BAP, indicative of the interactions of the arginine arms in the major groove. Thus, the de novo designed compound BAP constitutes one of the very rare intercalators which, similar to the antitumor drugs mitoxantrone and ditercalinium, binds DNA in the major groove rather than in the minor groove.

Structure and energetics in the complexes of a double-stranded B-DNA dodecamer with netropsin derivatives of a tricationic water-soluble porphyrin: a theoretical investigation.

The structural and energetical characteristics of the complexes formed between two auto-complementary DNA dodecamers, d(CGCGAATTCGCG)2, and d(GCGCAATTGCGC)2, and two novel netropsin (I) and glycine-netropsin (II) conjugates of a tricationic water-soluble porphyrin are investigated in detail by means of theoretical computations. This study was prompted by the successful chemical synthesis of II, which was recently reported (Anneheim-Herbelin, G., Perrée-Fauvet, M., Gaudemer, A., Hélissey, P., Giorgi-Renault, S. and Gresh, N., Tetrahedron Lett. 34, 7263 (1993)). The results indicate that: a) Intercalative binding of II does not entail significant distortions of the DNA backbone, and the Net moiety can bind tightly to the core of the minor groove. b) Intercalative binding of I is computed to energetically weaker than that of II. This is a consequence of the reduced length of the oligopeptide arm, such that the terminal propionamidinium group interacts less favorably with the fourth A-T base-pair than is the case with II. c) Nonintercalative binding of II produces considerable conformational distortions of the DNA. These results in a break of the DNA axis in between the fourth and the fifth base-pairs, namely, at the level where the long axis of the chromophore and of the oligopeptide intersect.

Structural studies of metalloporphyrins. Part XIa: Complexes of water-soluble zinc(II) porphyrins with amino acids: influence of ligand-ligand interactions on the stability of the complexes.

The stability constants of a series of complexes of the cationic water-soluble porphyrin ZnTMPyP with various amino acids have been determined by 1H NMR spectroscopy at pH 10.5. The following stability order has been observed: Tyr greater than Phe, Glu greater than Asp greater than Ile greater than Val greater than Gly. These results can be best rationalized by invoking complex stabilization due to ligand-ligand (e.g., stacking or electrostatic) interactions. Evidence for stacking interactions between the porphyrin ring and the aromatic ring of phenylalanine, tyrosine, and tryptophan was further provided by study of the complexation of these amino acids with the free-base porphyrin TMPyPH2. In this case, complexation constants increased in the order: Phe less than Tyr less than Trp. Attempts to form complexes of the amino acids with the anionic porphyrin ZnTCPP proved unsuccessful, indicating that electrostatic interactions play a major role in the stability of the zinc porphyrin-amino acids complexes.

Molecular complexes of nucleosides and nucleotides with a monomeric cationic porphyrin and some of its metal derivatives.

Tetrakis(4-7V-methylpyridyl)porphine (H2TMpyP) and a number of its metal derivatives interact extensively with mononucleotides and mononucleosides in aqueous solution. The complexes formed are of a stacking-type involving extensive overlap of the -systems of the porphyrin and purine or pyrimidine bases. Coulombic attractions help stabilize the complexes but there is no evidence for ligation of the bases to axial sites of the metalloporphyrins. Stability constants determined via NMR and spectrophotometric titrations are larger for purine bases than pyrimidines with a given porphyrin derivative. More dramatic influences on stability result from changing porphyrins. Porphyrins having no axial ligands (e.g., metal-free copper(II), palladium(II), and nickel(II) derivatives) or one axial ligand (Zn(II)) produce much larger interactions with a given nucleotide or nucleoside than do metalloporphyrins having two axial ligands (e.g., Mn(III), Fe(III), or Co(III)). The kinetics of the interaction of H2TMpyP with 2'-deoxyadenosine S'-monophosphate (dAMP) were studied via the laser raman temperature-jump method. The measured rate constants are consistent with a simple stacking model for the interaction.