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1- and 1,5-Aminoalkylamine substituted anthraquinones (AAQs, 1C3 and 1,5C3) were peptide coupled to 1-, 2-, and 3-pyrrole lexitropsins to generate compounds that incorporated both DNA minor groove and intercalating moieties. The corresponding platinum(II) amidine complexes were synthesized through a synthetically facile amine-to-platinum mediated nitrile 'Click' reaction. The precursors as well as the corresponding platinum(II) complexes were biologically evaluated in 2D monolayer cells and 3D tumour cell models. Despite having cellular accumulation levels that were up to five-fold lower than that of cisplatin, the platinum complexes had cytotoxicities that were only three-fold lower. Accumulation was lowest for the complexes with two or three pyrrole groups, but the latter was the most active of the complexes exceeding the activity of cisplatin in the MDA-MB-231 cell line. All compounds showed moderate to good penetration into spheroids of DLD-1 cells with the distributions being consistent with active uptake of the pyrrole containing complexes in regions of the spheroids starved of nutrients.

Complexes incorporating a threading anthraquinone intercalator with pyrrole lexitropsin and platinum(II) moieties attached were developed with the goal of generating novel DNA binding modes, including the targeting of AT-rich regions in order to have high cytotoxicities. The binding of the complexes to DNA has been investigated and profiles surprisingly similar to that for cisplatin were observed; the profiles were different to those for a complex lacking the pyrrole lexitropsin component. The lack of selective binding to AT-rich regions suggests the platinum binding was dominating the sequence selectivity, and is consistent with the pyrrole lexitropsin slowing intercalation. The DNA unwinding profiles following platinum binding were evaluated by gel electrophoresis and suggested that intercalation and platinum binding were both occurring.

Lexitropsins are small molecules that bind to the minor groove of DNA as antiparallel dimers in a specific orientation. These molecules have shown therapeutic potential in the treatment of several diseases; however, the development of these molecules to target particular genes requires revealing the factors that dictate their preferred orientation in the minor grooves, which to date have not been investigated. In this study, a distinct structure (thzC) was carefully designed as an analog of a well-characterized lexitropsin (thzA) to reveal the factors that dictate the preferred binding orientation. Comparative evaluations of the biophysical and molecular modeling results of both compounds showed that the position of the dimethylaminopropyl group and the orientation of the amide links of the ligand with respect to the 5'-3'-ends; dictate the preferred orientation of lexitropsins in the minor grooves. These findings could be useful in the design of novel lexitropsins to selectively target specific genes.

The DNA as the depository of genetic information is a natural target for chemotherapy. A lot of anticancer and antimicrobial agents derive their biological activity from their selective interaction with DNA in the minor groove and from their ability to interfere with biological processes such as enzyme catalysis, replication and transcription. The discovery of the details of minor groove binding drugs, such as netropsin and distamycin A, oligoamides built of 4-amino-1-methylpyrrole-2-carboxylic acid residues, allowed to develop various DNA sequence-reading molecules, named lexitropsins, capable of interacting with DNA precisely, strongly and with a high specificity, and at the same time exhibiting significant cytotoxic potential. Among such compounds, lexitropsins built of carbocyclic sixmembered aromatic rings occupy a quite prominent place in drug research. This work is an attempt to present current findings in the study of carbocyclic lexitropins, their structures, syntheses and biological investigations such as DNA-binding and antiproliferative activity.

Molecular-modeling methods have been used to perform energy analysis of dimeric complex formation between lexitropsins and double-stranded DNA. Stabilization of dimeric complexes by hydrophobic and van der Waals interactions has been demonstrated. Electrostatic interactions and the contributions of hydrogen bonds and changes in the number of degrees of freedom had a destabilizing influence. The energy of monomeric and dimeric binding has been compared.

A critical factor in the design of effective drugs is the specificity of the drug/target interaction. In the case of genome-based drug design, the double helical structure of DNA provides three binding mode opportunities for potential ligands. These are (1) binding in the major groove, (2) binding in the minor groove, and (3) intercalation between nucleotide bases. The naturally occurring compounds, netropsin and distamycin, along with their synthetic derivatives, the lexitropsins, bind in the minor groove of duplex DNA. Netropsin and distamycin specifically bind to A/T-rich sequences, whereas lexitropsins may be designed to bind A/T- or G/G-rich segments. Netropsin forms a 1:1 drug:DNA complex, whereas distamycin may form either 1:1 or 2:1 drug:DNA complexes. Both netropsin and distamycin also bind to G-quadruplex DNA. A single netropsin binds to each of the four quadruplex grooves, resulting in a 4:1 netropsin:quadruplex DNA complex. Distamycin dimers bind to one quadruplex groove forming a 2:1 complex or to opposite grooves resulting in a 4:1 complex. Depending on the nucleotide sequence of the G-quadruplex structure, distamycin dimers may bind to the terminal planes of the quadruplex, also resulting in a 4:1 distamycin:quadruplex structure. Typically, lexitropsins are designed to fit into the minor groove as overlapping molecular dimers or as hairpin structures. Hairpin lexitropsins fold onto themselves; as a result, their binding in the minor groove resembles that of dimeric molecules. Since the fundamental DNA sequence reading feature of netropsin, distamycin, and the lexitropsins is the hydrophobic interaction of their pyrrole/imidazole rings with nearby nucleotide bases, strategies to enhance and extend this interaction have been critical in the design of new minor groove recognizing compounds.

DNA-minor-groove-binding ligands are potent antineoplastic molecules. The antibiotic distamycin A is the prototype of one class of these DNA-interfering molecules that have been largely used in vitro. The affinity of distamycin A for DNA is well known, and the structural details of the complexes with some B-DNA and G-quadruplex-forming DNA sequences have been already elucidated. Here, we show that distamycin A binds S100β, a protein involved in the regulation of several cellular processes. The reported affinity of distamycin A for the calcium(II)-loaded S100β reinforces the idea that some biological activities of the DNA-minor-groove-binding ligands arise from the binding to cellular proteins. Copyright © 2015 John Wiley & Sons, Ltd.

The synthesis and biological activity of a variety of analogues to the naturally occurring antibacterial and antifungal Distamycin A were explored by a number of authors. These compounds were subject to a large array of assays. Some of these compounds showed high activity against a range of Gram-positive, Gram-negative bacteria as well as fungi. To explore the anti-parasitic activity of this class of compounds, specific modifications had to be made. A number of these compounds proved to be active against Trypanosoma brucei. The binding of a number of these compounds to short sequences of DNA were also examined using footprinting assays as well as NMR spectroscopy. Computer modelling was employed on selected compounds to understand the way these compounds bind to specific DNA sequences. A large number of variations were made to the standard structure of Distamycin. These changes involved the replacement of the pyrrole moieties as well as the head and tail groups with a number of heterocyclic compounds. Some of these minor groove binders (MGBs) were also investigated for their capability for the treatment of cancer and in particular lung cancer.