Structural and Dynamic Aspects of Non-Intercalative (1:1) Binding of a Thiazole-Lexitropsin to the Decadeoxyribonucleotide d-[CGCAATTGCG]₂: An¹H-NMR and Molecular Modeling Study

Abstract

The location, orientation and dynamics of a thiazole-containing analogue of distamycin 1 bound to the decadeoxyribonucleotide d-[CGCAATTGCG]2 have been studied by non-exchangable and imino proton NMR resonances of the 1:1 complex. Using NOE difference, COSY and NOESY experiments, lexitropsin (1) was located in the minor groove of DNA at 5'-CAAT sequence. This was concluded by an intermolecular NOE between the ligand and a minor groove A4H2 proton. The NOE cross-correlations in the NOESY map confirmed that the DNA decamer duplex in the 1:1 complex remains in a right-handed B-conformation similar to that in the free decamer. Experiments on non-exchangeable and exchangeable proton NMR resonances placed the N-formylamino terminus of drug 1 on the 5'-C3 nucleotide, while the rest of the molecule extends onto the 5'-AAT sequence. The structural evidence for sequence preferential binding at 5'CAAT rather than 5'AATT suggests this reflects an attempt on the part of the sterically demanding inward directed sulfur of the thiazole to minimize compression by moving part of the molecule to the somewhat wider CG base site. The lack of evidence for a 2:1 drug:DNA complex, in contrast to distamycin, is in accord with this interpretation. The lexitropsin 1 was found to be in an exchange between the equivalent 5'-CAAT sites at a rate of approximately 35S-1 with a delta G degree of 65 +/- 5 kJ mol-1 at 303 K. The experimental data suggests a slide-swing mechanism for this exchange process.

Thiazole and oxazole peptides: biosynthesis and molecular machinery

“…36 Indeed, thiazole-containing analogues of these molecules bind in the minor groove of DNA with significant sequence bias. 37,38 The pyridinyl bithiazole and terthiazole peptide family of antibiotics can show selectivity of recognition for specific members of two other major classes of biomolecules, RNA and proteins. Thus, in the inhibition of bacterial protein synthesis by thiostrepton 21 14 and GE2270A 23 16, each acts to block a specific and distinct step in polypeptide elongation when aminoacyl-tRNAs deliver their charged amino acids to the growing peptidyl-tRNA intermediate in the peptide synthase cavity of the ribosome.…”

Sequence-Specific DNA Minor Groove Binders. Design and Synthesis of Netropsin and Distamycin Analogues

“…Among the numerous lexitropsins synthesized so far, imidazole lexitropsins such as compounds 8-10 display the most pronounced capacity for binding to GC-containing sequences (68)(69)(70)(71)(72)(73)(74)(75)(76)(77)(78)(79). Thiazole lexitropsins either accept or avoid a G‚C base pair in their binding sites, depending on the position of the sulfur atom (80)(81)(82)(83). For example, the lexitropsin 11 with the sulfur atom directed into the minor groove does not bind to GC-containing sites, whereas the lexitropsin 12 containing two thiazole rings with the sulfur atoms directed outward from the minor groove binds best to alternating purine-pyrimidine sequences such as 5′-TATGAC and 5′-TGCATGC (84).…”

DNA recognition by lexitropsins, minor groove binding agents

“…Decrease in binding affinity, predicted to b? due to the increase in the repeat distance of about 0.9A, causes failure of the amide hydrogen to participate in hydrogen bonding with N3 of A or 0 2 of T (Kumar et al, 1990(Kumar et al, , 1991. Although the presence of a thiazole moiety with a sterically demanding inwarddirected sulfur ensures AT recognition.…”

“…Although the presence of a thiazole moiety with a sterically demanding inwarddirected sulfur ensures AT recognition. Thus a thiazole in the middle of the lexitropsin leads to minor groove binding (Kumar et al, 1991) whereas a thiazole at the end of the molecule demands intercalation of this moiety and simultaneous groove binding of the rest of the molecule (Kumar et al, 1990).…”