Small molecule inhibitor of the RPA70 N-terminal protein interaction domain discovered using in silico and in vitro methods

The pharmacological suppression of the DNA damage response and DNA repair can increase the therapeutic indices of conventional chemotherapeutics. Replication Protein A (RPA), the major single-stranded DNA binding protein in eukaryotes, is required for DNA replication, DNA repair, DNA recombination, and DNA damage response signaling. Through the use of high-throughput screening of 1500 compounds, we have identified a small molecule inhibitor, 15-carboxy-13-isopropylatis-13-ene-17,18-dioic acid (NSC15520), that inhibited both the binding of Rad9-GST and p53-GST fusion proteins to the RPA N-terminal DNA binding domain (DBD), interactions that are essential for robust DNA damage signaling. NSC15520 competitively inhibited the binding of p53-GST peptide with an IC(50) of 10 μM. NSC15520 also inhibited helix destabilization of a duplex DNA (dsDNA) oligonucleotide, an activity dependent on the N-terminal domain of RPA70. NSC15520 did not inhibit RPA from binding single-stranded oligonucleotides, suggesting that the action of this inhibitor is specific for the N-terminal DBD of RPA, and does not bind to DBDs essential for single-strand DNA binding. Computer modeling implicates direct competition between NSC15520 and Rad9 for the same binding surface on RPA. Inhibitors of protein-protein interactions within the N-terminus of RPA are predicted to act synergistically with DNA damaging agents and inhibitors of DNA repair. Novel compounds such as NSC15520 have the potential to serve as chemosensitizing agents.

Diphenic acid as a general conformational lock in the design of bihelical structures

The bihelical (figure of "infinity") topology was examined from vantages of design, crystal structures, chirality, circular dichroism (CD) studies and molecular-orbital calculations. The minimalistic design envisaged the sequential linking of cystine to the anchor diphenic acid, which proved to be a general conformational lock. The bihelical compound 4 was obtained in two steps from diphenic anhydride 1 and cystine di-OMe. The chirality of 4 arises largely from the L-cystine. The bihelical compound 5 obtained from D-cystine di-OMe was found, by X-ray crystallography, CD studies, and optical rotation, to be the perfect mirror image of 4 prepared from L-cystine. The crystal structure of prototype 8, prepared by protocols used for 4 from the achiral cystine analogue cystamine, had a "U"-shaped conformation held together by intramolecular hydrogen bonds. Analysis of 4 and 5 show that the pairs of nine-membered beta-turn-like constructs made compact through hydrogen bonding with DMSO hold the key for the bihelical conformation. Another factor is the need for the presence of a ligand at the Calpha position. The absence of this, as in 8, allows major flexibility in the torsional angles around this critical region, promoting flexible alternatives. The CD analysis of 4, confirmed to be bihelical by X-ray crystallography, showed a typical negative band at about 210 A attributed to the beta-turn-like motif, and in the positive-band region a peak at about 227 A, generally related to the twist of the biphenyl unit. The cystamine analogue 8, which showed a "U"-type structure, presented a CD spectrum with no typical features. The total energy, derived from theoretical calculations by using the X-ray structure data, support the bihelical structure for 4 and a "U"-shaped one for 8. The limited utility of such calculations was tested with composite 9. Composite 9, in which the anchor diphenic acid is linked to cystamine on the one hand and to cystine on the other, showed a CD spectrum similar to that of 4, and this coupled with molecular-orbital calculations, using data from 4 and 8, predict a bihelical structure for this compound.

α,β-Unsaturated Ketoximes Carrying a Terminal Pyridine or Quinoline Subunit as Building Blocks for Supramolecular Syntheses

[Structure: see text]. The crystal structures of a new series of alpha,beta-unsaturated ketoximes, 8-14, carrying the terminal 4-pyridinyl, 3-pyridinyl, or 4-quinolinyl subunit have been investigated by X-ray structural analysis. The dominating intermolecular interaction in all structures, except 11, is the head-tail OH...N hydrogen bond between the oxime moiety and the nitrogen atom of the heterocyclic unit. This intermolecular interaction generates infinite chains, which are cross-linked by CH...O/N/Cl or CH...pi interactions. Compound 10 has been shown to adopt a double-helical structure in the crystalline state. Compound 11 represents the only case where the unexpected head-head NOH...N(OH) hydrogen bonds determine the crystal packing. Both hydrogen-bonding and aromatic interactions stabilize the crystal structures of 8-14.