The Synthesis of Some Head to Head Linked DNA Minor Groove Binders

Novel distamycin analogues that block the cell cycle of African trypanosomes with high selectivity and potency

Polyamides-based compounds related to the Streptomycetal distamycin and netropsin are potent cytostatic molecules that bind to AT-rich regions of the minor groove of the DNA, hence interfering with DNA replication and transcription. Recently, derivatives belonging to this scaffold have been reported to halt the proliferation of deadly African trypanosomes by different and unrelated mechanisms. Here we describe the synthesis and preliminary characterization of the anti-trypanosomal mode of action of new potent and selective distamycin analogues. Two tri-heterocyclic derivatives containing a central N-methyl pyrrole ring (16 and 17) displayed high activity (EC₅₀ < 20 nM) and selectivity (selectivity index >5000 with respect to mammalian macrophages) against the infective form of T. brucei. Both compounds caused cell cycle arrest by blocking the replication of the mitochondrial DNA but without affecting its integrity. This mode of action clearly differs from that reported for classical minor groove binder (MGB) drugs, which induce the degradation of the mitochondrial DNA. In line with this, in vitro assays suggest that 16 and 17 have a comparatively lower affinity for different template DNAs than the MGB drug diminazene. Therapeutic efficacy studies and stability assays suggest that the pharmacological properties of the hits should be optimized. The compounds can be rated as excellent scaffolds for the design of highly potent and selective anti-T. brucei agents.

Synthesis of Novel Dna Binding Agents: Indole-Containing Analogues of Bis-Netropsin

Molecular modelling studies showed that indole dicarboxylic acids are potential linkers for the synthesis of bis-netropsin analogues with a good fit to the minor groove of DNA. To test this hypothesis, 2-carboxyindole-6-acetic acid, indole-2,6-dicarboxylic acid, 6-(2-carboxyethyl)indole-2-carboxylic acid, 6-(2-carboxy-1-ethenyl)indole-2-carboxylic acid were prepared and coupled to 3-[1-methyl-4-(1-methyl-4-aminopyrrole-2-carboxamido)pyrrole-2-carboxamido]dimethylaminopropane. Similarly indole-2,5-dicarboxylic acid was prepared and coupled to 3-[1-methyl-4-(1-methyl-4-aminopyrrple-2-carboxamido)pyrrole-2-carboxamido]propionamidine hydrochloride. The derivatives of 26–28 showed especially strong binding to AT rich regions as shown by footprinting studies.

Deformative transition of the Menschutkin reaction and helical atropisomers in a congested polyheterocyclic system

A 4,7-phenanthroline polycyclic 1A designed for probing the limits of the Menschutkin reaction was synthesized in a six-step sequence. The rotational barrier of the phenyl ring nearby the N-methyl group in rac-2A was estimated to be ≫ 18.1 kcal/mol from VT-NMR experiments, making them a new type of helical atropisomer. The methylation rate constants of 9 and 1A with MeI was found to be 2.22 × 10(-4) and 9.62 × 10(-6) s(-1) mol(-1) L, respectively; thus, the formation rate of (P/M)-2A is one of the slowest rates ever reported for a Menschutkin reaction. The N-methyl protons in (P/M)-2A exhibit a significant upfield shift (Δδ 1.0 ppm) in its (1)H NMR, compared to those without a nearby phenyl, indicating a strong CH-π interaction is involved. Conformational flexibility in dipyridylethene 9 is clearly shown by its complexation with BH3 to form helical atropisomers (P,P/M,M)-10. The pKa values of the conjugate acids of 1A and 9 in acetonitrile were determined to be 4.65 and 5.07, respectively, which are much smaller compared to that of pyridine 14a (pKa = 12.33), implying that the basicity, nucleophilicity, and amine alkylation rates of 1A and 9 are markedly decreased by the severe steric hindrance of the flanking phenyl rings in the polyheterocycles.

Synthesis of cell-permeable stapled BH3 peptide-based Mcl-1 inhibitors containing simple aryl and vinylaryl cross-linkers

We report the synthesis of a series of distance-matching aryl and vinylaryl cross-linkers for constructing stapled peptides containing cysteines at i,i+7 positions. Langevin dynamics simulation studies helped to classify these cross-linkers into two categories: the rigid cross-linkers with narrower S-S distance distribution and the flexible cross-linkers with wider S-S distance distribution. The stapled Noxa BH3 peptides with the flexible distance-matching cross-linkers gave the highest degree of helicity as well as the most potent inhibitory activity against Mcl-1. However, the stapled peptides with the highest hydrophobicity showed the most efficient cellular uptake. Together, this work illustrates the divergent nature of binding affinity and cellular uptake, and the vital importance of choosing appropriate cross-linkers in constructing stapled peptides with the drug-like properties.

The effects of conformational constraints in the polyamine moiety of philanthotoxins on AMPAR inhibition

Philanthotoxin-433 (PhTX-433) is a known potent inhibitor of ionotropic glutamate receptors, and analogues have been synthesised to identify more potent and selective antagonists. Herein we report the synthesis of four PhTXs with a cyclopropane moiety introduced into their polyamine chain, and their inhibition of an α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subtype by using two-electrode voltage-clamp assays on Xenopus oocytes expressing the GluA1flop subunit. All analogues were found to be more potent than PhTX-343, with trans-cyclopropyl-PhTX-343 being the most potent (∼28-fold) and cis-cyclopropyl-PhTX-343 least potent (∼4-fold). Both cis- and trans-cyclopropyl-PhTX-444 had intermediate potency (both∼12-fold). Molecular modelling indicates that a cyclopropane moiety confers a favourable steric constraint to the polyamine part, but this is compromised by a cis conformation due to enhanced intramolecular folding. Elongated PhTX-444 analogues alleviate this to some extent, but optimal positioning of the amines is not permitted.

Recognition of the DNA minor groove by thiazotropsin analogues

Solution-phase self-association characteristics and DNA molecular-recognition properties are reported for three close analogues of minor-groove-binding ligands from the thiazotropsin class of lexitropsin molecules; they incorporate isopropyl thiazole as a lipophilic building block. Thiazotropsin B (AcImPy(iPr) ThDp) shows similar self-assembly characteristics to thiazotropsin A (FoPyPy(iPr) ThDp), although it is engineered, by incorporation of imidazole in place of N-methyl pyrrole, to swap its DNA recognition target from 5'-ACTAGT-3' to 5'-ACGCGT-3'. Replacement of the formamide head group in thiazotropsin A by nicotinamide in AIK-18/51 results in a measureable difference in solution-phase self-assembly character and substantially enhanced DNA association characteristics. The structures and associated thermodynamic parameters of self-assembled ligand aggregates and their complexes with their respective DNA targets are considered in the context of cluster targeting of DNA by minor-groove complexes.

From multiply active natural product to candidate drug? Antibacterial (and other) minor groove binders for DNA

Natural products that bind to DNA in the minor groove are valuable templates for drug design. Examples include distamycin, netropsin, duocarmycin and anthramycin. Anticancer and anti-infective drugs feature strongly amongst their derivatives. The structures and activities of chemotypes with various therapeutic actions are discussed in the context of the broader field of therapeutically active minor groove binders. The evolution of a series of exceptionally potent and nontoxic antibacterial compounds is discussed using the general design principle of introducing additional hydrophobicity into the distamycin template to increase the strength of binding to DNA. As well as potent antibacterial compounds, antifungal and antiparasitic compounds with exceptional cellular activity against trypanosomes have been identified. Possible mechanisms of action including gene regulation and topoisomerase inhibition are discussed with the need in mind to understand selective toxicity in the series to support future drug discovery.

Amide isosteres in structure-activity studies of antibacterial minor groove binders

Antibacterial minor groove binders related to the natural product, distamycin, are development candidates for novel antibiotics. Alkenes have been found to be effective substitutes for the isosteric amide links in some positions and alkyl groups larger than methyl have been found to increase binding to DNA in both selectivity and affinity. However the impact of other isosteres such as diazenes and the position of an alkyl group with respect to DNA binding and antibacterial activity are not known. The effects of some systematic variations in the structure of polyamide minor groove binders are investigated. Isosteres of the amide link (alkenes and diazenes) are compared: it is shown that all three are competent for binding to DNA but that alkene links give the tightest binding and highest antibacterial activity; no significant antibacterial activity was found for compounds with a diazene link. Within a series of alkene linked compounds, the effect of branched N-alkyl substituents on binding to DNA and antibacterial activity is investigated: it was found that C3 and C4 branched chains are acceptable at the central pyrrole residue but that at the pyrrole ring adjacent to the basic tail group, a C4 branched chain was too large both for DNA binding and for antibacterial activity. The active branched alkyl chain compounds were found to be especially active against Mycobacterium aurum, a bacterium related to the causative agent of tuberculosis.

Photochemical oxidative cyclisation of stilbenes and stilbenoids--the Mallory-reaction

After Mallory described in 1964 the use of iodine as catalyst for the photochemical cyclisation of stilbenes, this reaction has proven its effectiveness in the synthesis of phenanthrenes, other PAHs and phenacenes with a surprisingly large selection of substituents. The "early age" of the reaction was reviewed by Mallory in 1984 in a huge chapter in the Organic Reactions series, but the development has continued. Alternative conditions accommodate more sensitive substituents, and isomers can be favoured by sacrificial substituents. Herein the further developments and applications of this reaction after 1984 are discussed and summarized.

A new synthesis of alkene-containing minor-groove binders and essential hydrogen bonding in binding to DNA and in antibacterial activity

A practical synthesis of alkene-containing minor-groove binders for DNA, related to distamycin, with potential for wide structural diversity is described, based upon the Wittig chemistry of N-alkylpyrrole aldehydes. The compounds prepared have been evaluated for binding to DNA by physical methods (melting temperature and NMR) and for their antibacterial activity. Significantly, it was found that alkenes linking the aryl head group of the minor-groove binder promote strong binding to DNA and high antibacterial activity against Gram-positive bacteria. Conversely, a minor-groove binder containing an alkene located towards the alkylamino tail group has a low affinity for DNA and does not show antibacterial activity. These observations suggest an important role for specific hydrogen bonds in the binding of compounds of this type to DNA, and in their antibacterial activity.

Surface-assisted coordination chemistry and self-assembly

This article discusses different approaches to build up supramolecular nanoarchitectures on surfaces, which were simultaneously investigated by scanning tunneling microscopy (STM) on the single-molecule level. Following this general road map, first, the hydrogen-bonding guided self-assembly of two different, structural-equivalent molecular building blocks, azobenzene dicarboxylic acid and stilbene dicarboxylic acid, was studied. Secondly, the coordination chemistry of the same building blocks, now acting as ligands in metal coordination reactions, towards co-sublimed Fe atoms was studied under near surface-conditions. Extended two-dimensional tetragonal network formation with unusual Fe2L(4/2)-dimers at the crossing points was observed on copper surfaces. Complementary to the first two experiments, a two-step approach based on the solution-based self-assembly of square-like tetranuclear complexes of the M4L4-type with subsequent deposition on graphite surfaces was investigated. One- and two-dimensional arrangements as well as single molecules of the M4L4-complexes could be observed. Moreover, the local electronic properties of a single M4L4-complexes could be probed with submolecular resolution by means of scanning tunnelling spectroscopy (STS).

Programming supramolecular assembly and chirality in two-dimensional dicarboxylate networks on a Cu(100) surface

We report a comparative study on the 2D self-assembly of two related ditopic benzoic acid species, which have similar shape and endgroups but different backbone symmetry. High-resolution scanning tunneling microscopy data reveal how the symmetry information of molecular building blocks is readily expressed in the resulting chiral or nonchiral supramolecular networks. The underlying square Cu(100) surface steers network orientation and accounts for carboxylate formation, resulting in an unusual intermolecular hydrogen bond motif. Our results demonstrate that symmetry and chiral resolution in 2D supramolecular assembly can be controlled via the design of functional molecules and choice of substrate.