Thiazotropsin aggregation and its relationship to molecular recognition in the DNA minor groove.

Aggregated states have been alluded to for many DNA minor groove binders but details of the molecule-on-molecule relationship have either been under-reported or ignored. Here we report our findings from ITC and NMR measurements carried out with AIK-18/51, a compound representative of the thiazotropsin class of DNA minor groove binders. The free aqueous form of AIK-18/51 is compared with that found in its complex with cognate DNA duplex d(CGACTAGTCG)2. Molecular self-association of AIK-18/51 is consistent with anti-parallel, face-to-face dimer formation, the building block on which the molecule aggregates. This underlying structure is closely allied to the form found in the ligand's DNA complex. NMR chemical shift and diffusion measurements yield a self-association constant Kass=(61±19)×10(3)M(-1) for AIK-18/51 that fits with a stepwise self-assembly model and is consistent with ITC data. The deconstructed energetics of this assembly process are reported with respect to a design strategy for ligand/DNA recognition.

Phytochemical and antimicrobial investigations of stilbenoids and flavonoids isolated from three species of Combretaceae.

The antimicrobial activity and chemistry of the African Combretaceae has been well studied in recent years. The present study aimed to investigate the phytochemistry and antimicrobial activity of lesser known members of this family viz. C. hereroense, C. apiculatum and C. collinum. Pulverized leaves of C. collinum and C. apiculatum, and the fruit of C. hereroense were extracted with organic solvents and subjected to preparative chromatography. Seventeen phenolic constituents including four phenanthrenes from the fruit of C. hereroense and two known bibenzyls (including a combretastatin) from the leaves of C. collinum were isolated. The compounds were then subsequently tested for their antimicrobial activity against Candida albicans, Mycobacterium fortuitum, Staphylococcus aureus, Escherichia coli and Proteus vulgaris. Pinocembrin showed excellent activity against C. albicans (MIC - 6.25 µg/ml), superior to that of the positive control, fluconazole and against S. aureus (MIC - 12.5 mg/ml). The phenanthrenes (compounds 1, 2, 3 and 5) showed some activity against M. fortuitum and S. aureus with a uniform MIC of 25 µg/ml. From this study it was evident that most stilbenoids and flavonoids from the selected Combretaceae have little or no antimicrobial activity.

Quantification of binding data using capillary electrophoresis.

The design of new DNA-targeted molecules, primarily for use in the therapy of diseases such as cancer, relies on the assessment of both affinity for DNA and selectivity of binding to chosen base pair sequences. Capillary electrophoresis, with a polymer added to the running buffer, is very well suited to the separation of oligonucleotides in the range 12-20 base pairs, with the separation based on length rather than base pair sequence. In this way, it is possible to conduct competition experiments using mixtures of up to four oligonucleotides and giving a direct measure of the relative affinity of high-affinity ligands, specifically those binding in the minor groove with slow on-off rates. The relative affinities can be securely quantified, even where the affinities are very high. Working from first principles, it is shown that the measurement of absolute affinities presents various problems, not least that the concentration of DNA and ligand used in the experiment will affect the magnitude of K(d), which is not constant.

Benzylguanidines and other galegine analogues inducing weight loss in mice.

Dimethylallylguanidine, also known as galegine, isolated from Galega officinalis, has been shown to have weight reducing properties in vivo. Substitution of the guanidine group with an N-cyano group and replacement of guanidine with amidine, pyrimidine, pyridine, or the imidazole moieties removed the weight reducing properties when evaluated in BALB/c mice. However, retention of the guanidine and replacement of the dimethylallyl group by a series of functionalized benzyl substituents was shown to exhibit, and in some cases significantly improve, the weight reducing properties of these molecules in BALB/c, ob/ob, and diet induced obesity (DIO) mice models. The lead compound identified, across all models, was 1-(4-chlorobenzyl)guanidine hemisulfate, which gave an average daily weight difference (% from time-matched controls; +/- SEM) of -19.7 +/- 1.0, -11.0 +/- 0.7, and -7.3 +/- 0.8 in BALB/c, ob/ob, and DIO models, respectively.

Antimicrobial lexitropsins containing amide, amidine, and alkene linking groups.

The synthesis and properties of 80 short minor groove binders related to distamycin and the thiazotropsins are described. The design of the compounds was principally predicated upon increased affinity arising from hydrophobic interactions between minor groove binders and DNA. The introduction of hydrophobic aromatic head groups, including quinolyl and benzoyl derivatives, and of alkenes as linkers led to several strongly active antibacterial compounds with MIC for Staphylococcus aureus, both methicillin-sensitive and -resistant strains, in the range of 0.1-5 microg mL-1, which is comparable to many established antibacterial agents. Antifungal activity was also found in the range of 20-50 microg mL-1 MIC against Aspergillus niger and Candida albicans, again comparable with established antifungal drugs. A quinoline derivative was found to protect mice against S. aureus infection for a period of up to six days after a single intraperitoneal dose of 40 mg kg-1.

Capillary electrophoresis for studying drug-DNA interactions.

The development of new drugs to treat disease by binding directly to DNA offers much promise but is reliant on methods to determine the relative affinity of the putative drug for different DNA sequences. Such methods should ideally be rapid and inexpensive as well as reliable. Use of capillary electrophoresis in simple silica columns offers such a method. The development of systems in which the solvent carries a soluble polymer allows the reliable separation of DNA oligomers, of 12-20 bp in length, which can then be titrated with the ligand in competition experiments. The results obtained are comparable with those obtained by footprinting and give direct graphical output, easily analysed for relative binding affinity.

The role of water in drug-receptor interactions.

The idea that liquid water is not a uniform and random arrangement of molecules has been taken very seriously by the scientific community. Many experimental and computational investigations show that clathrate- or ice-like structures probably exist at a short time scale in solution. We have designed a new program to simulate water structure around solutes. Our model is based on the geometrical constraints of hydrogen bonding in order to be capable of producing clathrate-like structures. Simulations with small molecules and bio-molecules, using the new software, produce networks of water with specific patterns made of small water rings. The water structures built are consistent with the classification of molecules in terms of structure breaking and making. This approach may give insight into, and a more accurate description of, drug-receptor interactions. The results also suggest that water structure may impart sufficient energy to modify the conformational space of organic molecules through hydrogen bonding.

DNA sequence recognition by an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B).

We have used DNA footprinting and fluorescence melting experiments to study the sequence specific binding of an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B) to DNA. While the parent compound (thiazotropsin A) binds to the hexanucleotide sequence ACTAGT, changing one of the N-methylpyrrole groups to N-methylimidazole changes the preferred binding sequence to (A/T)CGCG(T/A). Experiments with DNA fragments that contain variants of this sequence suggest that the ligand can also bind, with lower affinity, to sequences which differ from this by 1bp in any position.

In silico footprinting of ligands binding to the minor groove of DNA.

The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by "in silico footprinting". Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting.

Antimalarial benzo[c]phenanthridines.

Analogues of the antimalarial alkaloid nitidine have been prepared with high potency against both chloroquine-sensitive and -resistant strains of Plasmodium falciparum in vitro. Simple modifications, using an established synthetic route, resulted in an analogue with IC(50) below 5ng/mL against a chloroquine-sensitive strain of P. falciparum. N-Ethylethoxidine had IC(50) below 30ng/mL against both chloroquine-sensitive and chloroquine-resistant strains of P. falciparum.

Synthesis and antimicrobial activity of some netropsin analogues.

Nine novel lexitropsins were synthesized by linking two netropsin-like moieties through three different dicarboxylic acids; 9,10-dihydro-2,7-phenanthrenedicarboxylic acid; [(3-[[(carboxymethyl)amino]carbonyl]benzoyl)amino]acetic acid and indole-2,5-dicarboxylic acid. The netropsin residues were modified by the use of N-isopentylpyrrole, 5-methylthiophene or 5-isopropylthiazole heterocyclic building blocks in place of the usual N-methylpyrrole. The compounds were tested against five gram-positive bacteria: Staphylococcus aureus, Streptomyces faecalis, methicillin resistant Staphylococcus aureus, Enterobacter cloacae, Mycobacterium fortuitum, three gram-negative bacteria: Klebsiella aerogenes, Proteus vulgaris, Escherichia coli and three fungi: Aspergillus niger, Candida albicans and Aspergillus nidulans. Some of the compounds showed significant inhibitory effects on the growth of the microorganisms.

Short lexitropsin that recognizes the DNA minor groove at 5'-ACTAGT-3': understanding the role of isopropyl-thiazole.

Isopropyl-thiazole ((iPr)Th) represents a new addition to the building blocks of nucleic acid minor groove-binding molecules. The DNA decamer duplex d(CGACTAGTCG)(2) is bound by a short lexitropsin of sequence formyl-PyPy(iPr)Th-Dp (where Py represents N-methyl pyrrole, (iPr)Th represents thiazole with an isopropyl group attached, and Dp represents dimethylaminopropyl). NMR data indicate ligand binding in the minor groove of DNA to the sequence 5'-ACT(5)AG(7)T-3' at a 2:1 ratio of ligand to DNA duplex. Ligand binding, assisted by the enhanced hydrophobicity of the (iPr)Th group, occurs in a head-to-tail fashion, the formyl headgroups being located toward the 5'-ends of the DNA sequence. Sequence reading is augmented through hydrogen bond formation between the exocyclic amine protons of G(7) and the (iPr)Th nitrogen, which lies on the minor groove floor. The B(I)/B(II) DNA backbone equilibrium is altered at the T(5) 3'-phosphate position to accommodate a B(II) configuration. The ligands bind in a staggered mode with respect to one another creating a six base pair DNA reading frame. The introduction of a new DNA sequence-reading element into the recognition jigsaw, combined with an extended reading frame for a small lexitropsin with enhanced hydrophobicity, holds great promise in the development of new, potentially commercially viable drug lead candidates for gene targeting.

DNA sequence recognition by an isopropyl substituted thiazole polyamide.

We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted thiazole polyamide, to DNA. In one fragment, which contains every tetranucleotide sequence, sub-micromolar concentrations of the ligand generate a single footprint at the sequence ACTAGT. This sequence preference is confirmed in melting experiments with fluorescently labelled oligonucleotides. Experiments with DNA fragments that contain variants of this sequence suggest that the ligand also binds, with slightly lower affinity, to sequences of the type XCYRGZ, where X is any base except C, and Z is any base except G.

Distamycin analogues with enhanced lipophilicity: synthesis and antimicrobial activity.

Forty-eight heterocyclic amino acid trimers, analogues of distamycin, with a number of features that enhance lipophilicity are described. They contain alkyl or cycloalkyl groups larger than methyl; some are N-terminated by acetamide or methoxybenzamide and are C-terminated by dimethylaminopropyl or aliphatic heterocylic aminopropyl substituents. The ability of these compounds to bind principally to AT tracts of DNA has been evaluated using capillary zone electrophoresis. Significant antimicrobial activity against key organisms such as MRSA and Candida albicans is shown by several compounds, especially those containing a thiazole. Moreover, these compounds have low toxicity with respect to several mammalian cell lines.

Cyclobutanes from Combretum albopunctatum.

A dichloromethane extract of the aerial parts of Combretum albopunctatum Suesseng afforded five phenolic compounds-three known flavonoids and two novel cyclobutane chalcone dimers. The chemical structures were determined by standard spectroscopic techniques and the structure and relative stereochemistry of one chalcone dimer, rel-(1 alpha,2 beta)-di-(2,6-dimethoxy-4-hydroxy)-benzoyl-rel-(3 alpha,4 beta)-diphenylcyclobutane, were confirmed by single crystal X-ray diffraction.

DNA binding of a short lexitropsin.

Footprinting, capillary electrophoresis, molecular modelling and NMR studies have been used to examine the binding of a short polyamide to DNA. This molecule, which contains an isopropyl-substituted thiazole in place of one of the N-methylpyrroles, is selective for the sequence 5'-ACTAGT-3' to which it binds with high affinity. Two molecules bind side-by-side in the minor groove, but their binding is staggered so that the molecule reads six base pairs, unlike the related natural products, which tend to bind to four-base-pair sequences. The result suggests that high affinity and selectivity may be gained without resort to very large molecules, which may be difficult to deliver to the site of action.

Synthesis and antiviral effect against herpes simplex type 1 of 12-substituted benzo[c]phenanthridinium salts.

The synthesis of benzo[c]phenanthridine alkaloid derivatives is described. In vitro antiviral activity against herpes simplex type 1 (HSV1) has been investigated. Contrary to the natural product fagaronine, which did not have any activity in the HSV1 antiviral tests, four 12-alkoxy derivatives showed good activity demonstrating the importance of the 12-substitution in the structure-activity relationships.

Two very unusual macrocyclic flavonoids from the water lily Nymphaea lotus.

Three novel flavonols, myricetin-3'-O-(6"-p-coumaroyl)glucoside and two epimeric macrocyclic derivatives, as well as the known myricetin-3-O-rhamnoside and pentagalloyl glucose, have been isolated from the wild water lily Nymphaea lotus L. and identified using 2D NMR. This is the first report of such a macrocycle from any source.

Antimicrobial activity of pentacyclic triterpenes isolated from African Combretaceae.

Four pentacyclic tritepenes were isolated from Combretum imberbe Engl. & Diels, of which two are novel glycosidic derivatives of 1alpha,3beta,23-trihydroxyolean-12-en-29-oic acid (hydroxyimberbic acid). Terminalia stuhlmannii Engl. & Diels stem bark yielded two glycosides of hydroxyimberbic acid, one of which is reported for the first time. The structures of the isolated compounds were elucidated by spectroscopic methods. Several of the compounds had antibacterial activity, imberbic acid showing particularly potent activity against Mycobacterium fortuitum and Staphylococcus aureus.