Computed interactions of berenil with restricted foldamers of c-MYC DNA G-quadruplexes

G-quadruplexes (G4s) are secondary four-stranded DNA helical structures made up of guanine-rich nucleic acids that can assemble in the promoter regions of multiple genes under the appropriate conditions. Stabilization of G4 structures by small molecules can regulate transcription in non-telomeric regions, including in proto-oncogenes and promoter regions, contributing to anti-proliferative and anti-tumor activities. Because G4s are detectable in cancer cells but not in normal cells, they make excellent drug discovery targets. Diminazene, DMZ (or berenil), has been shown to be an efficient G-quadruplex binder. Due to the stability of the folding topology, G-quadruplex structures are frequently found in the promotor regions of oncogenes and may play a regulatory role in gene activation. Using molecular docking and molecular dynamics simulations on several different binding poses, we have studied DMZ binding toward multiple G4 topologies of the c-MYC G-quadruplex. DMZ binds preferentially to G4s that have extended loops and flanking bases. This preference arises from its interactions with the loops and the flanking nucleotides, which were not found in the structure lacking extended regions. The binding to the G4s with no extended regions instead occurred mostly through end stacking. All binding sites for DMZ were confirmed by 100 ns molecular dynamics simulations and through binding enthalpies calculated using the MM-PBSA method. The primary driving forces were electrostatic, as the cationic DMZ interacts with the anionic phosphate backbone, and through van der Waals interactions, which primarily contributed in end stacking interactions.Communicated by Ramaswamy H. Sarma.

Biochemical responses of Anticarsia gemmatalis (Lepidoptera: Noctuidae) in soybean cultivars sprayed with the protease inhibitor berenil

The damage caused by Anticarsia gemmatalis motivates this study on the adaptive mechanisms of the insect to soybean. The lipoxygenase pathway produces and releases jasmonic acid, involved in the regulation of the plant defense genes, which encodes protease inhibitor (PI) production. Three soybean cultivars IAC-18, IAC-24, and Foscarin-31 were sprayed with water and berenil, a synthetic inhibitor, at 0.60 and 1.0% (w/v) and then infested with A. gemmatalis larvae. The lipoxygenase (LOX) activity increased in the leaves of Foscarin-31, IAC-18, and IAC-24 by 87, 81, and 78%, respectively, after 24 h of A. gemmatalis damage. IAC-18 revealed the lowest increase in PI when compared to the other cultivars. Protease, amidase, and esterase activities in soybean larvae dropped drastically after berenil application. PIs may be included in the control strategies of A. gemmatalis in soybean by lowering the digestive enzyme activity in the larval midgut, thus affecting insect growth and development.

The trypanocide diminazene aceturate is accumulated predominantly through the TbAT1 purine transporter: additional insights on diamidine resistance in african trypanosomes

Resistance to diminazene aceturate (Berenil) is a severe problem in the control of African trypanosomiasis in domestic animals. It has been speculated that resistance may be the result of reduced diminazene uptake by the parasite. We describe here the mechanisms by which [(3)H]diminazene is transported by Trypanosoma brucei brucei bloodstream forms. Diminazene was rapidly accumulated through a single transporter, with a K(m) of 0.45 +/- 0.11 micro M, which was dose dependently inhibited by pentamidine and adenosine. The K(i) values for these inhibitors were consistent with this transporter being the P2/TbAT1 adenosine transporter. Yeast expressing TbAT1 acquired the ability to take up [(3)H]diminazene and [(3)H]pentamidine. TbAT1-null mutants had lost almost all capacity for [(3)H]diminazene transport. However, this cell line still displayed a small but detectable rate of [(3)H]diminazene accumulation, in a nonsaturable manner. We conclude that TbAT1 mediates [(3)H]diminazene transport almost exclusively and that this explains the observed diminazene resistance phenotypes of TbAT1-null mutants and field isolates.

Lipid–drug conjugate nanoparticles of the hydrophilic drug diminazene—cytotoxicity testing and mouse serum adsorption

Sleeping sickness is a widely distributed disease in great parts of Africa. It is caused by Trypanosoma brucei gambiense and rhodiense, transmitted by the Tse-Tse fly. After a hemolymphatic stage, the parasites enter the central nervous system where they cannot be reached by hydrophilic drugs. To potentially deliver the hydrophilic antitrypanosomal drug diminazene diaceturate to the brain of infected mice, the drug was formulated as lipid-drug conjugate (LDC) nanoparticles (NP) by combination with stearic- (SA) and oleic acid (OA). To estimate the in vivo compatibility, the particles were incubated with human granulocytes. Because as potential delivery mechanism the absorption of specific serum proteins (ApoE, Apo AI and Apo AIV) was found to be responsible for the delivery of nanoparticles to the brain, demonstrated using PBCA nanoparticles coated with polysorbate 80 (LDL uptake mechanism) the nanoparticles were incubated with mouse serum and the adsorption pattern was determined using the 2-D PAGE technique. As a result of this study, the cytotoxic potential was shown to decrease when diminazene is part of the particle matrix compared to pure fatty acid nanoparticles and the mouse serum protein adsorption pattern differs from the samples studied earlier in human serum. Especially, the fact concerning Apo-E that could be detected when the particles were incubated in human serum is absent after the mouse serum incubation, potentially, is a critical point for the delivery via the LDL-uptake mechanism but the data demonstrate that LDC nanoparticles, with 33% (wt/wt) drug loading capacity possess the potential to act as a delivery system for hydrophilic drugs like diminazene diaceturate and that further studies have to demonstrate the usability as a brain delivery system.

The effect of inducing agents on the metabolism of trypanocidal diamidines by isolated rat hepatocytes

This study has investigated the effect of phenobarbitone (PB), 3-methylcholanthrene (3-MC), and deltamethrin (DM) on the metabolism of two trypanocidal diamidines; pentamidine isethionate and diminazene aceturate in freshly isolated Sprague-Dawley rat hepatocytes. There were significant increases in the total cytochrome p450 content of hepatocytes obtained from rats pre-treated with PB and 3-MC, whereas pre-treatment with DM did not produce any significant induction of cytochrome p450. However, pre-treatment of rats with each of the three agents led to inhibition of pentamidine metabolism following a 3h incubation of pentamidine (100 microM) with freshly isolated rat hepatocytes (5 x 10(6) cells ml(-1)). Pre-treatment with 3-MC caused the highest inhibitory effect on pentamidine metabolism (8-fold inhibition), compared with PB (4.8-fold) and DM (2.2-fold). Six previously reported phase I metabolites of pentamidine were identified in cells from all the pre-treated animals as well as controls. When compared to the control group, there were significant differences between the profiles of the three major metabolites of pentamidine, 1,5-di(4'-amidinophenoxy)-2-pentanol, 1,5-di(4'-amidinophenoxy)-3-pentanol and 5-(4'-amidinophenoxy) pentanoic acid, in hepatocytes from the DM and 3-MC pre-treated rats, whereas no significant differences were observed in the cells from the PB pre-treated group. In contrast, diminazene was not metabolised with the same experimental conditions. Differences in the metabolic profiles of pentamidine and its metabolites as a result of concomitant exposure to environmental xenobiotics could have important toxicological and pharmacological implications for patients that receive the drug.

Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry

Electrospray mass spectrometry was evaluated regarding the reliability of the determination of the stoichiometries and equilibrium association constants from single spectra. Complexes between minor groove binders (Hoechst 33258, Hoechst 33342, DAPI, netropsin and berenil) and 12mer oligonucleotide duplexes with a central sequence (A/T)4 flanked by G/C base pairs were chosen as model systems. To validate the electrospray ionization mass spectrometry (ESI-MS) method, comparisons were made with circular dichroism and fluorescence spectroscopy measurements. ESI-MS allowed the detection of minor (2 drug + DNA) species for Hoechst 33258, Hoechst 33342, DAPI and berenil with duplex d(GGGG(A/T)4GGGG). d(CCCC(A/T)4CCCC), which were undetectable with the other techniques. Assuming that the duplexes and the complexes have the same electrospray response factors, the equilbrium association constants of the 1:1 and 2:1 complexes were determined by ESI-MS, and the values show a good quantitative agreement with fluorescence determined constants for Hoechst 33258 and Hoechst 33342. It is also shown that ESI-MS can quickly give reliable information on the A/T sequence selectivity of a drug: the signal of a complex is directly related to the affinity of the drug for that particular duplex. The potential of ESI-MS as a qualitative and quantitative affinity screening method is emphasized.

Heterogeneous DNA binding modes of berenil

Isothermal titration calorimetry (ITC) profiles of berenil bound to different DNAs show that, despite the strong preference of berenil for AT-rich regions in DNA, it can bind to other DNA sequences significantly. The ITC results were used to quantify the binding of berenil, and the thermodynamic profiles were obtained using natural DNAs as well as synthetic polynucleotides. ITC binding isotherms cannot be simply described when a single set of identical binding sites is considered, except for poly[d(A-T)2]. Ultraviolet melting of DNA and differential scanning calorimetry were also used to quantify several aspects of the binding of berenil to salmon testes DNA. We present evidence for secondary binding sites for berenil in DNA, corresponding to G+C rich sites. Berenil binding to poly[d(G-C)2] is also observed. Circular dichroism experiments showed that binding to GC-rich sites involves drug intercalation. Using a molecular modeling approach we demonstrate that intercalation of berenil into CpG steps is sterically feasible.

Phosphatase-triggered guest release from a cyclodextrin complex

[reaction: see text] A synthetic supramolecular system is described that models the effect of phosphoryl transfer in molecular recognition. beta-Cyclodextrin-6A-phosphate (pCD), which is shown to be a substrate of alkaline phosphatase, binds cationic aromatic guests, including anticancer agents, up to 100-fold better than native beta-CD. The above observations demonstrate that pCD is capable of releasing the guests from its cavity upon hydrolysis with the phosphatase, as also confirmed by monitoring the hydrolysis in the presence of a guest.

DNA multimode interaction with berenil and pentamidine; double helix stiffening, unbending and bending

The antitrypanosomal drugs berenil (Ber) and pentamidine (Pm) preferentially bind to DNA in the minor groove of A.T-rich domains. The properties of A.T clusters are essential for sequence-mediated helix bending. Groove binding drugs locally stiffen the DNA helix but may also change intrinsic helix bends or may bend straight DNA. Ligand binding to randomly distributed sites alters the apparent DNA persistence length, a. Criteria permit the distinction of the underlying mechanism(s). Helix bends, if phased with the helix screw, however, generate solenoidal superhelix components mediating an apparent change of the hydrodynamically effective DNA contour length, L. The measurement of relative changes of both, a and L, as induced by Ber or Pm is performed by titration rotational viscometry. The determination of the two quantities requires two independent measurements: the relative change of DNA intrinsic viscosity, deltay, for short (tending to rod-like) DNA molecules and for comparably long (almost coil-like) ones as a function of r, the bound drug molecules per DNA-P, and this under conditions effectively excluding intramolecular DNA-DNA crosslinking effects. At least at r< or =0.05 and < or =0.03, respectively, the two drugs virtually bind completely to a eukaryotic DNA. r ranges of different drug binding strength and, concomitantly, of different specific conformational response, could be resolved. They represent (sub)modes of different DNA sequences... Whereas the mode-specific elongation effects are fairly similar for both systems, there are pronounced quantitative differences in the relative change of DNA persistence length. The sites of highest Ber-binding strength are correlated to unbent alternating helical A.T segments followed by bent and by less bent or unbent dAn.dTn tracts straightened on Ber-binding. For Pm-DNA interaction the ligand bends the sites of highest Pm affinity. Generally, ligand induced and sequence mediated local DNA-bend removal or DNA bending, as observed for several modes of interaction with A.T rich DNA, are considered to be of gene regulatory relevance.

The berenil ligand directs the DNA binding of the cytotoxic drug Pt-berenil

To determine the affinity towards DNA sequences of novel antitumor drugs in comparison with their parental compounds may lead to the design of new analogous drugs with improved antitumor activity. Thus, the affinities of Pt-berenil towards different DNA sites relative to cis-DDP and berenil drugs were analysed using DNase I footprinting and restriction endonuclease analysis. The data show that the Pt-berenil drug inhibits the cutting activity of Hind III enzyme to the same extent as the berenil ligand. In contrast, inhibition by Pt-berenil of the cutting activity of Bam HI enzyme is significantly lower than that of cis-DDP. These results indicate that although the cis-Pt(II) centres of Pt-berenil maintain certain affinity toward G + C regions, which are the main binding sequences of cis-DDP, however, the berenil ligand seems to direct the Pt-berenil molecule towards A + T regions, which are the binding sequences preferred by berenil. In fact, 1H- and 195Pt-NMR spectra of Pt-berenil:nucleoside complexes show that Pt-berenil not only covalently binds to N7 of guanosine but also to N1/N7 of adenosine.

Anthraquinone photonucleases: a surprising role for chloride in the sequence-neutral cleavage of DNA and the footprinting of minor groove-bound ligands

Irradiation of water-soluble anthraquinone (AQ) reagents in the presence of chloride ions results in the spontaneous, sequence-neutral cleavage of DNA. Mechanistic studies indicate that cleavage is initiated by chlorine atoms, produced by charge transfer interaction between chloride anion and AQ triplet states. High-resolution gel electrophoresis suggests that cleavage arises from abstraction of a hydrogen atom from C-4' of deoxyribose units. The targeting of this hydrogen, which is located in the minor groove of duplex DNA, can be effectively blocked by netropsin and, to a lesser degree, berenil, leading to photofootprinting of these minor groove-binding drugs.

The influence of the exocyclic amino group characteristic of GC base pairs on molecular recognition of specific nucleotide sequences in DNA by berenil and DAPI

The expedient of preparing homologous DNA samples substituted with inosine for guanosine residues, 2,6-diaminopurine (DAP) for adenine residues, or both, has been used to investigate the role of the purine 2-amino group in determining the preferred binding sites for the drugs berenil [1,3-bis(4-phenylamidinium) triazene] and DAPI (4',6-diamidino-2-phenyl indole) on DNA. The selectivity of these two minor groove binders for AT-rich sequences is seen to be radically altered in the substituted DNA molecules. Neither berenil nor DAPI bind to DAP-substituted DNA where all purine residues bear a 2-amino group. By contrast, they bind to AT-rich, IC-rich and even mixed sequences of the inosine DNA where all purine residues lack the 2-amino group. With the inosine and DAP double substituted DNA, both berenil and DAPI bind preferentially to IC-rich clusters instead of their canonical tracts endowed with an extra 2-amino group through substitution with DAP. These results establish that the location of the purine 2-amino group represents a critical determinant for recognition of DNA nucleotide sequences by the two drugs.

The binding mode of drugs to the TAR RNA of HIV-1 studied by electric linear dichroism

For the first time, the interaction between a series of small molecules and the TAR RNA of HIV-1 has been investigated by electric linear dichroism (ELD). The compounds tested include the DNA intercalating drugs proflavine and ethidium bromide and an amsacrine-4-carboxamide DNA-threading intercalator as well as the AT-specific DNA minor groove binders netropsin, Hoechst 33258, berenil and DAPI. In all cases except for netropsin, negative reduced dichroism signals were measured in the drug absorption band. In agreement with previous studies, the results indicate that both classical and threading intercalation can occur with the TAR RNA. The ELD data show that the mode of binding of the drugs Hoechst 33258, berenil and DAPI to the TAR RNA is similar to their binding mode in GC-rich regions of DNA and likely involves intercalation into the A-form TAR RNA helix. The wide and shallow minor groove of the TAR RNA is apparently not accessible to DNA minor groove binding drugs such as netropsin. The ELD technique appears uniquely valuable as a means of investigating the interaction of drugs with the TAR RNA.

Berenil [1,3-bis(4'-amidinophenyl)triazene] binding to DNA duplexes and to a RNA duplex: evidence for both intercalative and minor groove binding properties

Berenil is an antitrypanosomal agent that binds to nucleic acid duplexes. The generally accepted mode of berenil binding is via complexation into the minor groove of AT-rich domains of DNA double helices. We find that berenil can bind to RNA as well as DNA duplexes, while exhibiting properties characteristic of both intercalation as well as minor groove binding. More specifically, we use spectroscopic, calorimetric, and hydrodynamic techniques to characterize berenil binding to four DNA duplexes and to one RNA duplex. Our results reveal the following features: (i) Berenil binding to the poly[d(A-T)]2, poly(dA).poly(dT), poly[d(I-C)]2, poly[d(G-C)]2, and poly(rA).poly(rU) duplexes exhibits intercalative as well as minor groove binding characteristics. (ii) The apparent "site sizes" associated with berenil binding to these five duplexes range from 1 to 13 base pairs per bound berenil and depend, in part, on the host duplex. One of the site sizes common to all five duplexes is consistent with berenil binding to the minor groove. (iii) The apparent berenil binding affinity follows the hierarchy: poly(dA).poly(dT) > poly-[d(A-T)]2 approximately poly[d(I-C)]2 >> poly(rA).poly(rU) > poly[d(G-C)]2. (iv) Viscometric data reveal properties characteristic of a significant contribution from an intercalative mode of binding when berenil interacts with the poly[d(A-T)]2, poly[d(I-C)]2, poly[d(G-C)]2, and poly(rA).poly(rU) duplexes, while revealing an apparent nonintercalative mode when the drug binds to the poly(dA).poly(dT) duplex. (v) Berenil binding unwinds negative supercoils in the pBR322 plasmid, an observation consistent with an intercalative mode of binding to duplex DNA. (vi) Salt-dependent melting data suggest that both positively charged amidino groups of berenil participate in the complexation of the drug to the poly[d(I-C)]2, poly[d(A-T)]2, poly(dA).poly(dT), and poly(rA).poly(rU) duplexes, while also suggesting that the binding event is site-specific. In the aggregate, our results suggest that, in contrast to the conventional wisdom, berenil can exhibit intercalative as well as minor groove binding properties when it binds to both DNA and RNA duplexes, while also exhibiting a preference for DNA duplexes with unobstructed minor grooves. We comment on the potential correlation between drugs, such as berenil, that exhibit "mixed" binding motifs and those that express anticancer activity via inhibition of topoisomerase I activity.

Berenil complexation with a nucleic acid triple helix

The interaction of berenil molecule, a minor groove binding drug, with T-A-T triple helix and A-T double helix was studied using circular dichroism spectroscopy and thermal denaturation. The triple helix was made by an oligonucleotide (dA)12-X-(dT)12-X-(dT)12, where x is a hexaethylene glycol chain bridged between the 3' phosphate of one strand and the 5' phosphate of the following strand. This oligonucleotide is able to fold back on itself to form a very stable triplex. Circular dichroism spectroscopy demonstrates that berenil can bind to the triple helical structure. Spectral analysis shows that in the same ionic strength the drug bound to a double-stranded structure exhibits a conformation and an environment close to those observed in triple-stranded structure. The influence of the ionic strength on the interaction between the berenil molecule and the 36-mer is clearly demonstrated. We showed that when no NaCl salt is added in the buffer the triplex form of (dA)12-X-(dT)12-X-(dT)12 is stabilized by berenil whereas it is destabilized slightly by the dye when NaCl concentration is 1 M.

A thermodynamic and spectroscopic study on the binding of berenil to poly d(AT) and to poly (dA) x poly (dT)

The complete thermodynamic profile for the non-intercalative binding of berenil to the alternating copolymer poly d(AT) and to the homopolymer poly (dA) x poly (dT) was investigated. Differential Scanning Calorimetry (DSC) and UV absorbance spectroscopy have been used to characterize and to compare the binding of berenil to the different synthetic polymers. Both double stranded DNA's show two types of binding; one stronger binding mode at low berenil concentrations and a weaker, in the case of poly d(AT)-berenil complexes slightly cooperative binding mode at higher drug to base pair ratios. For the interaction of berenil with poly d(AT) the thermodynamic data delta G(bind)0 = -33 kJ/mol drug, delta H(bind)0 = -29 kJ/mol of drug and delta S(bind)0 = +13 J/Kmol of drug were calculated. For the minor groove binding of berenil to poly (dA) x poly (dT) the following values were obtained: delta G(bind)0 = -34 kJ/mol of drug, delta H(bind)0 = -25 kJ/mol of drug and delta S(bind)0 = +30 J/Kmol of drug. Temperature-dependent UV absorbance spectroscopy revealed for both duplexes a biphasic "melting" behavior. However, the saturated nucleic acids (drug to base pair ratio 0.33) "melted" monophasically and with a decreased length of the cooperative unit. The obtained apparent equilibrium constants K(app) for the complexation with the discharged drug molecule showed to be a sensitive function of the ionic environment. But in contradiction to the expected release of two counterions into the solvent only a value of 1.0 was observed for the alternating copolymer poly d(AT). The complexation of berenil with poly (dA) x poly (dT) is followed by a release of 1.4 ions indicating stronger electrostatic interactions. For both polynucleotides the predicted release of two ions is not achieved. This is due to the presence of a binding mode, which involves less electrostatic interactions. From the complete data set it is proposed that the mode of binding is closely related to that found for the analogue minor groove binders DAPI and netropsin.

Berenil recognizes and changes the characteristics of adenine and thymine polynucleotide structures

Using circular dichroism, differential scanning calorimetry and susceptibility to DNAse I cleavage assays, we show that the interaction of berenil, a minor-groove binding drug, with poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT) involves important changes in the polynucleotide conformation. The effect of berenil on poly(dA-dT).poly(dA-dT) comprises a clear alteration in CD spectra even at drug/DNA ratios smaller than the stoichiometric value. Berenil recognizes and binds to the alternating-B conformation of DNA changing it to a new conformation which appears to show some of the peculiarities of poly(dA).poly(dT), possibly through a modification in the helical parameters at the TpA and ApT steps. Such alteration is accompanied by a small calorimetric enthalpy change. Moreover, the calorimetric enthalpy does not change significantly whatever the input ratio of drug to poly(dA-dT).poly(dA-dT), indicating that berenil binding does not substantially alters the enthalpy of transition. In addition to increasing the melting temperature of the polynucleotide, berenil reduces the cooperativity of the poly(dA-dT).poly(dA-dT) transition slightly more than either distamycin or netropsin.

DNA minor groove-binding ligands: a different class of mammalian DNA topoisomerase I inhibitors

A number of DNA minor groove-binding ligands (MGBLs) are known to exhibit antitumor and antimicrobial activities. We show that DNA topoisomerase (Topo) I may be a pharmacological target of MGBLs. In the presence of calf thymus Topo I, MGBLs induced limited but highly specific single-strand DNA breaks. The 3' ends of the broken DNA strands are covalently linked to Topo I polypeptides. Protein-linked DNA breaks are readily reversed by a brief heating to 65 degrees C or the addition of 0.5 M NaCl. These results suggest that MGBLs, like camptothecin, abort Topo I reactions by trapping reversible cleavable complexes. The sites of cleavage induced by MGBLs are distinctly different from those induced by camptothecin. Two of the major cleavage sites have been sequenced and shown to be highly A + T-rich, suggesting the possible involvement of a Topo I-drug-DNA ternary complex at the sites of cleavage. Different MGBLs also exhibit varying efficiency in inducing Topo I-cleavable complexes, and the order of efficiency is as follows: Hoechst 33342 and 33258 >> distamycin A > berenil > netropsin. The lack of correlation between DNA binding and cleavage efficiency suggest that, in addition to binding to the minor grooves of DNA, MGBLs must also interact with Topo I in trapping Topo I-cleavable complexes.

NMR and molecular modeling studies of the interaction of berenil and pentamidine with d(CGCAAATTTGCG)2

The interaction of two anti-trypanosomal agents, berenil and pentamidine, with the A+T-rich dodecamer d(CGCAAATTTGCG)2 has been examined by high-resolution 1H-NMR, optical spectroscopy, and molecular modeling. Proton assignments for the free DNA and each DNA-ligand complex were obtained using nuclear Overhauser enhancement spectroscopy and total correlation spectroscopy. Complexation induces large changes in chemical shift for protons in the DNA minor groove for the A5-T9 segment, and intermolecular NOEs reveal contacts between the DNA bases and each ligand. The asymmetric binding site for berenil indicated by the NMR data suggests that at least two overlapping sites are involved. Rapid exchange between symmetrically-equivalent binding sites, via dissociative rearrangement, is consistent with retention of twofold degeneracy for both the ligand and the DNA host. Calculations of binding energy confirm that this DNA duplex contains overlapping sites of similar binding affinity. In contrast, the larger pentamidine molecule occupies a site that spans four or five bp, with asymmetric binding to the minor-groove 5'-ATTT sequence. The B-type conformation of the DNA is not altered substantially by either ligand.

Metabolic N-hydroxylation of diminazene in vitro

The two N-hydroxylated derivatives (amide oximes) and the corresponding amides of the trypanocidal diamidine diminazene (Berenil, CAS 536-71-0) have been synthesized. These reference compounds made it possible to investigate the in vitro metabolism of the amidine functionalities of diminazene. Diminazene metabolites were detected for the first time, in the form of the corresponding mono- and di(amide oxime), after incubation with 12000 g supernatants from rabbit liver homogenates and careful workup (freeze drying). The identification was based on the behavior in thin-layer chromatography and on comparison of the mass spectral data for the metabolites with those for synthetic material. The N-hydroxylation of diminazene showed the properties typical of a reaction catalyzed by a microsomal monoxygenase. Diminazene amides did not occur as metabolites. The di(amide oxime) of diminazene was tested for its trypanocidal and leishmanicidal activity on various laboratory strains of trypanosomes in mice and on Leishmania donovani in hamsters. The studies showed that the di(amide oxime) has a trypanocidal effect on various strains of trypanosomes (T. brucei, T. vivax, T. congolense and T. evansi), but this is distinctly weaker than that of diminazene. A diminazene-resistant strain of T. rhodesiense is also unaffected by the di(amide oxime). The di(amide oxime) also has a leishmanicidal effect, but this again is distinctly less than that of diminazene.

H-NMR studies on d(GCTTAAGC)2 and its complex with berenil

Two-dimensional (2D) 1H-NMR spectroscopy has been used to analyze the structure of d(GCTTAAGC)2 and its interaction with berenil in solution. Nuclear Overhauser enhancement connectivities enabled sequential assignments of nearly all proton resonances in the self-complementary octamer duplex and demonstrated that the oligonucleotide is primarily in a B-type conformation. No major conformational changes were observed by the addition of berenil, but proton resonances of the two adenosine nucleotides shifted substantially. Intermolecular nuclear Overhauser effects between berenil and the DNA duplex revealed that the drug binds via the minor groove of d(GCTTAAGC)2 in the A.T-base-pair region. At 18 degrees C the twofold symmetry of the duplex is preserved on berenil binding. However, strongly shifted proton resonances broadened significantly. A model is proposed for the berenil-d(GCTTAAGC)2 complex involving fast exchange of berenil between two equivalent symmetry-related binding sites, which span the 5'-TAA-3' region and are asymmetrically disposed with respect to the dyad axis of the duplex. These results are compared with previous studies on the berenil-d(GCAATTGC)2 complex.

Interaction of berenil with the tyrT DNA sequence studied by footprinting and molecular modelling. Implications for the design of sequence-specific DNA recognition agents

We have developed a technique of partially-restrained molecular mechanics enthalpy minimisation which enables the sequence-dependence of the DNA binding of a non-intercalating ligand to be studied for arbitrary sequences of considerable length (greater than = 60 base-pairs). The technique has been applied to analyse the binding of berenil to the minor groove of a 60 base-pair sequence derived from the tyrT promoter; the results are compared with those obtained by DNAse I and hydroxyl radical footprinting on the same sequence. The calculated and experimentally observed patterns of binding are in good agreement. Analysis of the modelling data highlights the importance of DNA flexibility in ligand binding. Further, the electrostatic component of the interaction tends to favour binding to AT-rich regions, whilst the van der Waals interaction energy term favours GC-rich ones. The results also suggest that an important contribution to the observed preference for binding in AT-rich regions arises from lower DNA perturbation energies and is not accompanied by reduced DNA structural perturbations in such sequences. It is therefore concluded that those modes of DNA distortion favourable to binding are probably more flexible in AT-rich regions. The structure of the modelled DNA sequence has also been analysed in terms of helical parameters. For the DNA energy-minimised in the absence of berenil, certain helical parameters show marked sequence-dependence. For example, purine-pyrimidine (R-Y) base pairs show a consistent positive buckle whereas this feature is consistently negative for Y-R pairs. Further, CG steps show lower than average values of slide while GC steps show lower than average values of rise. Similar analysis of the modelling data from the calculations including berenil highlights the importance of DNA flexibility in ligand binding. We observe that the binding of berenil induces characteristic responses in different helical parameters for the base-pairs around the binding site. For example, buckle and tilt tend to become more negative to the 5'-side of the binding site and more positive to the 3'-side, while the base steps at either side of the centre of the site show increased twist and decreased roll.

Netropsin, distamycin and berenil interact differentially with a high-affinity binding site for the high mobility group protein HMG-I

Netropsin, distamycin, berenil and the chromosomal protein HMG-I share the ability to bind preferentially to AT-rich regions of DNA. We studied the binding behaviour of the chemical agents towards a high-affinity binding site for HMG-I by DNase I and MPE footprinting and analyzed their ability to challenge HMG-I-DNA complexes by competition experiments. Significant differences in the binding affinities and in the efficiencies to abolish HMG-I-DNA complexes were observed for the three drugs. Netropsin proved to be the most avidly binding compound and the most efficient competitor raising the interesting possibility that netropsin affects cell growth by interfering with HMG-I-DNA interaction.

The binding of nonintercalative drugs to alternating DNA sequences

Molecular mechanics methods have been applied to suggest possible models for netropsin and related compounds binding to two different sequences of DNA, namely poly[d(AT)].poly[d(AT)] and poly[d(GC)].poly[d(GC)], and to evaluate the different contributions to the binding affinities of these compounds in the ethidium displacement assay. The geometries found after energy refinement suggest that one of the reasons for the selectivity of binding of these agents to A + T-rich DNA regions could be the different widths of the minor groove of the double strand of DNA found in the complexes of these drugs with both DNA sequences.

The effect of structural changes in a polyamine backbone on its DNA-binding properties

A novel analog of spermine, compound 1, 2, 6 bis(N-3-aminopropylmethanamine)-1-methoxy-4-methylbenzene, has been prepared which shows DNA binding which is altered from spermine in its base pair selectivity. A fluorescence spectroscopic assay is used to compare the complexation properties of compound 1, spermine, spermidine, putrescine, and berenil binding to calf thymus DNA, poly d(AT), and poly d(GC). The results are interpreted in terms of a major groove binding motif and compared with literature values for DNA dissociation constants.

Comparison of binding sites in DNA for berenil, netropsin and distamycin. A footprinting study

Techniques of DNase I and micrococcal nuclease footprinting have been used to compare the binding sites for berenil, netropsin and distamycin on two different DNA fragments. Each ligand binds to the A + T-rich zones which contain clusters of at least four A.T base pairs. Neither guanosine nor cytidine nucleotides appear to be allowed within the A + T-rich runs which constitute the preferred binding sites, although they are sometimes protected from DNase I cleavage in neighbouring regions. Berenil and netropsin share with distamycin the property of causing enhanced rates of cleavage at certain sequences flanking their binding sites. There are significant differences in the concentrations of each ligand required to produce defined patterns of protection, seemingly dependent upon the nature (and possibly the gross base composition) of the piece of DNA being used in the experiment.

The crystal structure of the DNA-binding drug berenil: molecular modelling studies of berenil-DNA complexes

The crystal structure of the DNA minor-groove DNA-binding drug berenil has been determined. Molecular-modelling techniques have been used to establish plausible binding modes of the structure to A-T sequences. These have shown that specific hydrogen bonds are possible between the amidine groups of the drug molecule and 02 atoms of thymine, although global energy minimisations tended to emphasise electrostatic interactions with phosphate groups rather than these hydrogen bonds with bases.

DNA structure and perturbation by drug binding

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Studies in cattle on the disposition of the anti-trypanosomal drug diminazene diaceturate (Berenil)

After intramuscular injection of ca. 3.5 mg kg-1 diminazene diaceturate-(bis-phenyl-U-14C) to two healthy male calves weighing 185 and 180 kg, levels of radioactivity were determined in blood, plasma, urine, faeces, and in edible tissues. The maximal blood level of 4.6 micrograms and 4.7 micrograms equivalents of diminazene diaceturate ml-1 (calculated from total radioactivity) occurred 15 min (calf C1) and 45 min (calf C2) after administration. The decrease in concentration followed a biphasic process with half lives of 2 and 188 hours. Seven days after treatment 47.1% of the dose had been excreted in the urine and 7.1% in the faeces. The respective values were 72.2% and 10.3% after 20 days. The half lives were similar to those in blood. The main product in urine was unchanged diminazene. Distribution studies showed concentrations which were low in general in edible tissues, i.e. in skeletal musculature and fat (below 1 microgram equivalent g-1), but higher in organs with excretory functions. There were 75.5 micrograms equivalents g-1, corresponding to 22% of the dose, in the liver 7 days after injection. This had decreased to 24.4 micrograms equivalents g-1, corresponding to 15% of the dose, at day 20. Only unchanged deminazene was detected in the liver extracts by thin-layer chromatography. Relay-bioavailability studies showed that the total liver residues were only partially available (mean = 23% of the dose) when fed to rats.

Pharmacokinetics of diminazene in sheep

The pharmacokinetic behavior of diminazene in plasma after administration of 2 mg/kg i.v. and 3.5 mg/kg i.m. was studied in four healthy Dala x Ryggja rams. Following i.v. injection, the data were satisfactorily described by a tri-exponential equation; the apparent volume of distribution at the steady-state was 0.56 +/- 0.04 L/Kg (mean +/- SD; n = 4); total body clearance averaged 1.1 +/- 0.09 ml/kg/min and elimination half-life was 9.30 +/- 1.40 hr. After intramuscular administration peak plasma levels of 6.30-7.57 micrograms/ml were reached in 20 to 45 min and the mean absorption time averaged 5.83 +/- 1.61 hr. Systemic availability relative to the intravenous dose was 95.10 +/- 23.21% and mean residence time averaged 14.16 +/- 1.55 hr. The partition of diminazene between erythrocytes and plasma averaged 0.64 +/- 0.10; plasma protein binding was high (65-85%) and concentration-dependent. Based on the experimental data obtained, an initial i.m. dose of 2.5 mg/kg followed by 2 mg/kg 24 hr later should be safe and effective in cases of babesiosis and trypanosomiasis sensitive to diminazene. A preslaughter withdrawal period of 14-26 days was estimated.

Studies in rabbits on the disposition and trypanocidal activity of the anti-trypanosomal drug, diminazene aceturate (Berenil)

After intramuscular injection of 3.5 mg kg-1 to rabbits, diminazene aceturate shows biphasic pharmacokinetics with maximum blood and interstitial fluid concentrations occurring after 15 min and 3 h respectively. Seven days after treatment, 40-50% of the dose had been excreted in the urine and 8-20% in faeces. Highest diminazene residues were determined in liver: 7 days after dosage, residues of 40.53 +/- 4.00 micrograms g-1 were present, corresponding to 35-50% of the dose. The recommended dose of 3.5 mg kg-1 was not curative for Trypanosoma congolense infections of rabbit but did cause the parasitaemia to become subpatent. A limited prophylactic effect was observed.

The binding of berenil to Escherichia coli ribosome

The binding of the nonintercalating dye berenil to the 70S ribosome of Escherichia coli has been demonstrated by spectrophotometric measurements and gel filtration through Biogel P100 column. The berenil spectrum is gradually shifted towards the red region with the increasing amount of ribosome added, the isosbestic point being at 375 nm. There is positive cooperativity in the binding of berenil to the ribosome as demonstrated by the equilibrium dialysis. On binding with berenil, the ribosome is degraded faster by RNase I especially at low Mg++ concentration and its capacity to inhibit RNase I catalysed hydrolysis of ribopolymers is decreased. These indicate the unfolding of the structure of the ribosome.

Trypanocidal activity of blood and tissue fluid from normal and infected rabbits treated with curative drugs

A new technique for determining the trypanocidal activity of body fluids has been devised, using very small quantities in the wells of plastic microtest plates. The activities of blood and tissue fluid of rabbits have been measured after the infection of melarsoprol, suramin, diminazene aceturate and isometamidium chloride. Activity against Trypanosoma (Trypanozoon) brucei persisted in body fluids for a shorter time in treated normal rabbits than in treated rabbits infected with the trypanosome. The difference was caused by the participation of the immune response of the infected animals. The new technique was sensitive enough to detect these interactions of chemotherapy and immunology and should be of use in the study of new trypanocidal compounds.