Theoretical Design of a Bistetrapeptide Derivative of Mitoxantrone Targeted Towards the Double-Stranded Hexanucleotide Sequence d(GGCGCC)₂

Abstract

The hexanucleotide d(GGCGCC)2 is encountered in recurrent fashion within transcriptional activating sequences in retroviruses and protooncogenes. Our first theoretical design of novel oligopeptide derivatives of mitoxantrone, MTX (1), had enabled us to predict derivatives depsiGly-Lys(L) and depsiGly-Gly-Orn(D) to preferentially target the tetrameric core d(CCGG)2. Owing to the crucial importance of hexamer d(GGCGCC)2, we have attempted to extend the realm of our approach by now targeting this specific hexanucleotide. For that purpose, we undertook the design of further oligopeptide derivatives of MTX, in which each arm was identically amidated (rather than esterified as in (1)) by tri- or tetrapeptides of varying sequences and individual residue configurations. The binding affinities of these derivatives to the palindromic sequences d(GGCGCC)2, d(CGCGCG)2, d(GCCGGC)2 and d(CCCGGG)2, were compared by energy-minimization. We report here the results obtained with the most promising derivative, having the sequence Arg(L)-Gly-Val(L)-Glu(L), and displaying a considerable energy preference for d(GGCGCC)2 over the other candidate hexameric sites (referred to as I). In the corresponding complexes, the two arms are in two mutually antiparallel directions in the major groove, and adopt a beta-sheet like arrangement stabilized by two H-bonds involving the carbonyl and amide groups of the Gly residues. Each Arg side chain on a given arm chelates O6 and N7 atoms of G1, G2/G1', G2' with its imino and cis amino hydrogen, and is simultaneously bound through two amino hydrogens in a bidentate interaction with the Glu residue.

Rational Design, Synthesis, and DNA Binding Properties of Novel Sequence‐Selective Peptidyl Congeners of Ametantrone

“…In fact, the double charge-dipole interactions mediated by the two lysines seem to guarantee this stable conformation over the entire 2 ns course of simulation. It is also gratifying to observe that such a motif, which had been predicted earlier on the basis of simpler energy minimizations, [17,18] could be retained in the course of the 2 ns simulation.…”

“…To verify these modeling predictions experimentally, [17,18] we synthesized and tested the series of compounds depicted in Figure 1. The substituents are linked to the anthraquinone by esterification of the two arms of AM (3) with Gly or Gly-(l-Lys) (compounds 9 and 15), in which 15 represents the peptidyl-AM predicted to exhibit sequence-selective properties.…”

“…[17][18][19][20] On the basis of computational studies, anthraquinone derivatives were designed, and their binding energies with d(GGCGCC) 2 were compared to those with the other concurrent palindromic sequences containing the CG step. The d(GGCGCC) 2 sequence, a mutational hot spot in DNA, is located in several oncogenes and is also part of the primer binding site (PBS) of the long terminal repeat (LTR) of the HIV-1 retrovirus that is necessary for the initial steps of reverse transcriptase (RT)-mediated cDNA synthesis.…”

“…Our earlier theoretical studies predicted that the peptide backbones of the two arms of the anthraquinone nucleus should adopt an antiparallel b-sheet arrangement, enabling each arm to interact with one distinct strand. [17,18] Their symmetrical disposition with respect to the chromophore is a reflection of the palindromic nature of targeted sequences d(GGCGCC) 2 and d(CCCGGG) 2 that were chosen for our studies.…”

“…[35] The random sequence was obtained annealing FAM-GTG AGA TAC CGA CAG AGG (FAM-random) with CCT CTG TCG TGA TCT CAC-DAB (DAB-random); the second and the third pairs were specific sequences whose core was designed according to theoretical studies, [17,18] namely Z1 by annealing FAM-5'-ACT ATT CCC GGG TAA TGA-3' (FAM-Z1) with 5'-TCA TTA CCC GGG TAA AGT-3'-DAB (DAB-Z1). FAM-5'-ACT ATT GGC GCC TAA TGA-3' (FAM-Z2) and 5'-TCA TTA GGC GCC AAT AGT-3'-DAB (DAB-Z2) oligonucleotide were annealed to give the Z2 oligo.…”