Search

The term “privileged structure” refers to a single molecular substructure or scaffold that can serve as a starting point for high‐affinity ligands for more than one receptor type. In this report, a hitherto overlooked group of privileged substructures is addressed, namely aromatic oligoamides, for which there are natural models in the form of cystobactamids, albicidin, distamycin A, netropsin, and others. The aromatic and heteroaromatic core, together with a flexible selection of substituents, form conformationally well‐defined scaffolds capable of specifically binding to conformationally well‐defined regions of biomacromolecules such as helices in proteins or DNA often by acting as helices mimics themselves. As such, these aromatic oligoamides have already been employed to inhibit protein–protein and nucleic acid–protein interactions. This article is the first to bring together the scattered knowledge about aromatic oligoamides in connection with biomedical applications., Privileged! Aromatic oligoamides based on pyrroles, pyridines, and p‐aminobenzoic acids are presented as privileged structures that efficiently target nucleic acids and proteins as well as complexes derived therefrom. Their design can be related to natural products such distamycin A and the cystobactamids.

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.

Context: Natural oligopeptide antibiotic distamycin A (Dst) biosynthesized by Streptomyces distallicus is traditionally used in medical practice as an anti-inflammatory and antitumour drug. Objective: Dst was investigated for its effect on the structural components of native chromatin directly within isolated rat liver nuclei in the presence of physiologically significant cations (magnesium or spermine and spermidine). Materials and methods: Differential scanning calorimetry (DSC) was used to study the Dst action at molar ratio Dst/DNA = 0.1 and 0.15 mM Dst on the melting profile of nuclei suspension in different conditions. Results: Results showed that the thermodynamic parameters of control nuclei in the presence of polyamines or Mg2+ were different. The incubation of nuclei with Dst raised transition temperatures of relaxed (peak II) and topologically constrained DNA (peak III) by 6–8 °C and decreased by 2–4 °C that of core-histones (peak I). The total excess transition enthalpy (ΔHexc) in buffer with polyamines (24.7 kJ/mol DNA nucleotides) increased by1.5 times versus control but in buffer with Mg2+, the value of ΔHexc (35.8 kJ/mol DNA nucleotides) remained unchanged. Conclusions: The association of Dst with chromatin in the nucleus weakens histone-DNA contacts and causes additional strengthening of interaction between two complementary DNA chains. Our results contribute towards validation of DSC to test drug ability to modulate chromatin structure in the physiological environment and to clarify the mechanism of these modulations.

A de novo 14/21 Robertsonian translocation and a familially inherited Y/15 translocation were observed in a male infant with anomalies of the external genitalia. The Y/15 translocation was confirmed by cultivating lymphocytes in a medium containing distamycin A and by determining the occurrence of the Y-specific DNA sequences by means of Hae III restriction endonuclease analysis. Any connection between the structural chromosomal abnormalities and the symptoms of the infant is highly improbable.

Distamycin A and netropsin are basic oligopeptide antibiotics. Though the chemical structure of both antibiotics is very similar, the action on grampositive and gramnegative bacteria is quite different. Distamycin A acts only on grampositive bacteria, while netropsin inhibits grampositive as well as gramnegative bacteria. Our experiments with the normal rod form and the stable protoplast type L-form of E. coli W1655F+ have shown that distamycin A inhibits gramnegative bacteria to the same extent as netropsin, when wall-less L-form-ells were used. The normal rod cells were inhibited by netropsin only. That means that the wall prevents the penetration of distamycin A as reported earlier for the macrolid antibiotics, actinomycin C and kirromycin.

The frequency and distribution of fragile sites by different concentration of distamycin-A were studied in the blood cultures of buffalo lymphocyte. The percentage of total aberrant cells, total breaks, total gaps, total structure abnormalities, deletion and polyploid were detected in the treated and control cultures. The results revealed that the treated cultures showed increases in the chromosomal abnormalities particularly in breaks and gaps at 50 and 100 μg/ml of distamycin-A concentrations compared with control cultures. Metaphases affected with chromosomal aberrations were destained and reexamined after G-banding to allow the identification of fragile sites involved. The fragile sites were identified as a site of non-staining gaps or breaks at specific points on chromosomes and their frequencies more than 3% per individual. The distamycin-A inducible fragile sites expressed as 1q22, 1q35, 4q26, 4q35, 6q36 and Xq22.In conclusion, the fragile sites are unique chromosomal regions and hot spots for establish break points maps and integration of foreign genomes.

DNA minor groove binders constitute an important class of derivatives in anticancer therapy. Some of these compounds form noncovalent complexes with DNA (e.g., distamycin A, Hoechst 33258, and pentamidine) while others DNA-binding compounds (such as CC-1065) cause cleavages in the DNA backbone. In this article, we have reviewed the minor groove binders currently in preclinical evaluation in the last years. Diarylamidines such as DAPI, berenil, and pentamidine; bis-benzimidazoles such as Hoechst 33258; ecteinascidins, pyrrololo [2,1-c]-[1,4]-benzodiazepines (PBDs), CC-1065, and distamycins are the classes discussed in this review article. A special section has been dedicated to hybrid molecules resulted by the combination of two minor groove binders, especially for derivatives of naturally occurring antitumor agents, such as anthramycin or the alkylating unit of the antibiotic CC-1065, and distamycin frames.

This article describes the production and characterization of two liposome formulations containing antitumor drugs, namely distamycin A (Dist) and a new alkyl derivative of distamycin A (C16-Dist). Egg-PC/cholesterol liposomes (4:1 mol/mol) were prepared by reverse phase evaporation technique followed by extrusion through polycarbonate filters. The encapsulation efficiency was found to be almost complete for C16-Dist (99.8%), while native distamycin A showed a lower yield (19.0%). The in vitro antiproliferative activity of the distamycins-containing liposomes determined on human leukaemic K562 cells, was 11-fold and 8-fold higher for native and alkyl derivative distamycin A, respectively, compared with that of the corresponding free drugs. Liposomal formulations show an increase in the activity and specificity of distamycins in experimental antitumor therapy.

Liposomes containing Distamycin A (DA) may be clinically useful in the treatment of ocular HSV infections, especially in acyclovir-resistant HSV keratitis. This study evaluated the in vitro and in vivo performance of a topical controlled release liposomal formulation containing DA (DA-Lipo) aimed at reducing the toxicity of the encapsulated active agent and improving drug uptake by ocular tissues. The bioavailability of DA in the tear fluid and the DA uptake into the cornea were increased after instillation of DA-Lipo in rabbits, reaching the DA corneal concentration corresponding to IC50 values against HSV without any sign of transcorneal permeation of drug. DA-Lipo was definitely less cytotoxic then plain DA in rabbit corneal epithelial cells. These results provide new insights into the correlation between the in vitro data and the drug kinetics following ocular applications of liposomal vesicles.

A series of novel thiazole-containing oligopeptides (oligo-1,3-thiazolecarboxamides) interesting specifically with the minor groove of DNA was shown to inhibit human DNA topoisomerase I (topo I). Inhibitory effects of thiazole-containing oligopeptides (TCO) increase with the number of thiazole units in such compounds. Inhibitory properties of TCO containing 3 or 4 thiazole units were shown to be 3-10 times better than those of the well-known natural antibiotic, distamycin A containing pyrrole rings. The structure of various additional groups attached to the N-terminus and C-terminus of TCO had no significant effect on TCO interaction with the complex of DNA and topo I. TCO were shown to be capable of binding with double-stranded DNA (dsDNA), and the majority of TCO analyzed were more effective in binding with dsDNA than distamycin A. Possible reasons for the different effects of distamycin A and TCO on the reaction of relaxation catalyzed by topo I are discussed.

The solution-phase synthesis of two 1000-membered positional scanning libraries of distamycin A analogues is described enlisting acid/base liquid-liquid extractions for isolation and purification of all intermediates and final products. The results of their screening for functional activity (L1210 cytotoxic potency) and DNA binding affinity were compared with those derived from libraries containing the same compound members but prepared in a smaller 10-compound mixture format. The positional scanning libraries, which are substantially less demanding to prepare, allowed the accurate detection of the global observations and the clearly more potent activities, but more subtle discoveries and less distinguishable activities were not detected. This is a natural consequence of testing the larger 100-compound mixtures and the relative insensitivity of the assays to the contribution of any single, uniquely acting compound in the mixture. Thus, the disadvantages associated with the loss of some information contained within the library must be balanced against the advantages of the ease of library synthesis and judged in light of the library screening objectives.

The development of a solution-phase synthesis of distamycin A and its extension to the preparation of 2640 analogues are described. Thus, solution-phase synthesis techniques with reaction workup an...

This review surveys the crystal structures between minor groove drugs and oligonucleotides, of which over thirty have now been determined. The various factors that are involved in the observed A/T sequence selectivity of these drugs are examined in structural terms. The roles of, in particular, hydrogen-bond recognition and sequence-dependent groove width, are assessed, and as a consequence the minor groove drugs have been classified into two categories, dependent on the relative roles played by these two factors in sequence recognition. Implications for the recognition of non-A/T sequences are discussed. © 1997 John Wiley & Sons, Inc. Biopoly 44: 105–121, 1997

The transition of the 14-meric deoxyoligonucleotide duplex d-(ACCCCCTTTTTTTG).d-(CAAAAAAAGGGGGT) from the B- to the A-conformation in water/trifluorethanol (TFE) solution was studied with the use of circular dichroism. An increase in the fraction of TFE induces a two-step B-A transition. In the first step, up to 73% TFE, the A-form is generated from the GC-rich part; in the second step, 73–82% TFE, the AT-rich part shifts to the A-form. By this we suggest the existence of a B/A junction near 73% TFE. Emergence of the B/A junction has been directly confirmed with the use of distamycin A and netropsin, ligands known to selectively bind to AT stretches of B-DNA. It can be shown that both ligands suppress formation of the A-form in the B-philic part. The free energy value for the B/A junction was estimated to be 2.1 kcal/mol, which agrees well with known data for polymeric DNAs. The obtained results may have biological relevance in connection with recently published x-ray data about the occurrence of the B/A junction in the complex of DNA with reverse transcriptase of HIV.

The acid-base properties of eight 3-aminopropionamidine derivatives R1R2N(CH2)2C((DOUBLE BOND)NH)NR3R4 (1, R1 = R2 = R3 = R4 = H; 2, R1 = R3 = R4 = H, R2 = Me; 3, R1 = R2 = R4 = H, R3 = Me; 4, R1 = R2 = H, R3 = R4 = Me; 5, R1 = Tos, R2 = R3 = R4 = H; 6, R1 = Tos, R2 = Me R3 = R4 = H; 7, R1 = Tos, R2 = R4 = H, R3 = Me; 8, R1 = Tos, R2 = H, R3 = R4 = Me; Tos = 4-toluenesulphonyl) related to the antiviral natural product distamycin A were investigated in water and dimethyl sulphoxide (DMSO). The measured pKa values for the ammonium function in 1–4 in water ranged between 7·48 and 7·73, whereas the corresponding values in DMSO were 9·4 ± 0·3. The amidinium moiety of these compounds displayed pKa values in the range 11·4–12·0 and 13·4–13·6 in water and DMSO, respectively. The tosylamide group in compounds 5–8 was deprotonated in the expected pH region and exhibited pKa values between 9·49 and 10·02 in water, but was considerably less acidic in DMSO (14·5 ≤ pKa ≤ 15·7). The behaviour of the amidinium cation of 5–8 in water and DMSO resembled that of 1–4. The measured pKa values are discussed and the solvent-induced pKa shifts are explained in terms of solvent and substituent effects. The observed pKa differences between the ammonium and the amidinium functions in 1–4 render these compounds suitable intermediates in an alternative synthesis of distamycin A.

Poly(dA-dT)•poly(dA-dT) which adopts the Z-form at 5 M NaCl in presence of 95 mM Ni2+ions is reversed to the B-conformation by the nonintercalating drugs netropsin (Nt) and distamycin A (Dst). The drug-induced reversal from the Z-to B-form of poly(dA- dT)•poly(dA-dT) is evidenced by CD spectral changes at characteristic wavelengths around 295 nm and 248 nm. The drug-induced conformational transition is accompanied by a slow kinetic process. The results suggest the preference of these AT-specific drugs for the B-form and the inability of Nt and Dst to form a stable complex with the Z-form of poly(dA-dT)•poly(dA-dT).

The interaction of the minor groove binding drug distamycin with the T-A-T triple helix and the A-T double helix was studied using circular dichroism spectroscopy and thermal denaturation. The triple helix was made by the 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. Changing the conditions allows the same oligonucleotide to be in a duplex form with a dangling arm. Circular dichroism spectroscopy demonstrates that the distamycin A molecule can bind to the triple-stranded form of this oligonucleotide. Spectral analysis shows that the bound distamycin exhibits a conformation and an environment slightly different from those which are observed when the drug is bound to the corresponding double-stranded structure. Furthermore, a second type of complex which is observed in the double-strand binding (two stacked distamycins in the minor groove) is not observed with the triple-stranded host. When distamycin is added to the triplex made of unbridged chains (dA)12 + 2(dT)12, the triplex dissociates to give a double-stranded structure. Thermal denaturation experiments demonstrate that distamycin binding destabilizes the triplex whereas it stabilizes the duplex. These results are compared with those obtained by the same experimental approaches on other minor groove binding drugs.

Background: Human papillomavirus (HPV) is the main causative agent of cervical cancer, particularly high risk strains such us HPV-16, -18 and -31. The viral encoded E2 protein acts as a transcriptional modulator and exerts a key role in viral DNA replication. Thus, E2 constitutes an attractive target for developing antiviral agents. E2 is a homodimeric protein that interacts with the DNA target through an α-helix of each monomer. However, a peptide corresponding to the DNA recognition helix of HPV-16 E2 binds DNA with lower affinity than its full-length DNA binding domain. Therefore, in an attempt to promote the DNA binding of the isolated peptide, we have designed a conjugate compound of the E2 α-helix peptide and a derivative of the antibiotic distamycin, which involves simultaneous minor- and major-groove interactions. Methodology/Principal Findings: An E2 α-helix peptide-distamycin conjugate was designed and synthesized. It was characterized by NMR and CD spectroscopy, and its DNA binding properties were investigated by CD, DNA melting and gel shift experiments. The coupling of E2 peptide with distamycin does not affect its structural properties. The conjugate improves significantly the affinity of the peptide for specific DNA. In addition, stoichiometric amounts of specific DNA increase meaningfully the helical population of the peptide. The conjugate enhances the DNA binding constant 50-fold, maintaining its specificity. Conclusions/Significance: These results demonstrate that peptide-distamycin conjugates are a promising tool to obtain compounds that bind the E2 target DNA-sequences with remarkable affinity and suggest that a bipartite major/minor groove binding scaffold can be a useful approach for therapeutic treatment of HPV infection. © 2011 Wetzler et al. Fil:Wetzler, D.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Comin, M.J. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Gallo, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.

The design, synthesis, and in vitro and in vivo activities of novel benzoyl and cinnamoyl nitrogen mustard and half-mustard derivatives of distamycin A, in which the amidino moiety has been replaced by moieties of different physico-chemical features, are described and structure-activity relationships are discussed. Some amidino-modified derivatives show significant cytotoxicity and antileukemic activity.

Distamycin A (Dst) is an antibiotic which binds to the minor groove of double-stranded DNA at A/T-rich regions. We have examined the affinity and mode of Dst binding to DNA duplexes containing a conserved A/T core and variable terminal A/T regions by using circular dichroism spectroscopy. The observed circular dichroism spectra were analyzed by singular value decomposition and fitted to a two-step binding model. The result clearly shows a correlation between the affinity for Dst and the preference for Dst-DNA 1:1 binding over 2:1 binding. The A/T stretches that prefer 1:1 binding form high-affinity 1:1 complexes, whereas those preferring 2:1 binding form stable 2:1 complex with low overall affinities. The terminal A/T residues of the Dst binding region play an important role in the stabilization/destabilization of the 1:1 and 2:1 complexes, resulting in a terminal residue-dependent variation of the binding affinity and the binding mode preference.

Pyrrolepolyamide-2′-deoxyguanosine hybrids (Hybrid2and Hybrid3) incorporating the 3-aminopropionyl or 3-aminopropyl linker were designed and synthesized on the basis of previously reported results of a pyrrolepolyamide-adenosine hybrid (Hybrid1). Evaluation of the DNA binding sequence selectivity of pyrrolepolyamide-2′-deoxyguanosine hybrids was performed by CD spectral andTmanalyses. It was shown that Hybrid3possessed greater binding specificity than distamycin A, Hybrid1and Hybrid2.

The present article describes a comparative study of the performances of liposomes and ethosomes as specialized delivery systems for distamycin A (DA) and two of its derivatives. Liposomes and ethosomes were prepared by classical methods, extruded through polycarbonate filters, and characterized in terms of dimensions, morphology, and encapsulation efficiency. It was found that DA was associated with vesicles (either liposomes or ethosomes) by around 16.0%, while both derivatives of DA showed a percentage of association around 80% in the case of liposomes and around 50% in the case of ethosomes. In vitro antiproliferative activity experiments performed on cultured human and mouse leukemic cells demonstrated that vesicles were able to increase the activity of both derivatives of DA. In addition, it was demonstrated that the aging of both liposomes- and ethosomes-associated distamycin suspensions did not heavily influence the vesicle size, while all samples showed a relevant drug leakage with time. Moreover, according to the different physicochemical characteristics of DA and its derivatives (i.e., log P), vesicle-associated DA showed the highest loss of drug with respect to both its derivatives. In conclusion, the enhancement of drug activity expressed by these specialized delivery systems-associated DD could be interesting to obtain an efficient therapeutic effect aimed at reducing or minimizing toxic effects occurring with distamycins administration.

The study of DNA G-quadruplex stabilizers has enjoyed a great momentum in the late years due to their application as anticancer agents. The recognition of the grooves of these structural motifs is expected to result in a higher degree of selectivity over other DNA structures. Therefore, to achieve an enhanced knowledge on the structural and conformational requisites for quadruplex groove recognition, distamycin A, the only compound for which a pure groove binding has been proven, has been chemically modified. Surprisingly, structural and thermodynamic studies revealed that the absence of Coulombic interactions results in an unprecedented binding position in which both the groove and the 3' end of the DNA are occupied. This further contribution adds another piece to the so far elusive puzzle of the recognition between ligands and DNA quadruplexes and will serve as a platform for a rational design of new groove binders.

Differential pulse voltammetry (DPV) was used to study the interaction of distamycin A (Dis) with the manganese(III) complex of meso-tetrakis(N-methyl-4-pyridiniumyl)porphine (Mn III P) and that of this complex with calf thymus (CT) DNA. The addition of distamycin to Mn III caused a diminution in the peak current and a positive shift in the peak potential of the DPV wave for the reduction of Mn III P

The synthesis of a novel amidine-linked analogue 1 of the phenyl-containing congener 2 of distamycin A and its DNA binding properties are described. The amidine group in 1 improves its water solubility while retaining the minor groove and AT sequence binding selectively. A phenyl-containing and amidine-linked analogue 1 of distamycin A has improved water solubility while retaining the minor groove and AT sequence binding selectivity to DNA.

Objective(s): Herpes simplex virus (HSV) infections in immunocompromised individuals may require prolonged antiviral therapy resulting in the emergence of viral strains resistant to the currently employed antiviral drugs. Distamycin A (DA), a basic antibiotic belonging to the lexitropsin DNA minor groove binding drugs, exhibits antiviral properties. In this study we evaluated the in vitro cytotoxicity and antiviral activity of DA against HSV type 1 and HSV type 2 clinical isolates from transplanted patients and compared them with those of acyclovir (ACV) in search of alternative antiviral drugs. Methods: Viral detection and typing was performed by multiplex PCR and immunofluorescence assay; the in vitro cytotoxicity of DA and the antiviral activity of ACV and DA was evaluated respectively by neutral red uptake assay and plaque reduction assay for HSV2 isolates and fluorescence reduction assay for HSV1 isolates. Results: Tissue culture 50% cytotoxic concentration of DA was 58 µM. Tissue culture 50% inhibitory concentration values ranged from 0.16 to 7.4 µM for the ACV-sensitive and from 5.4 to 32 µM for the ACV-resistant viral strains. Conclusions: In spite of the lower activity against ACV-resistant strains, DA may be used as an antiherpetic drug.

The use of small molecules that bind and stabilize G-quadruplex structures is emerging as a promising way to inhibit telomerase activity in tumor cells. In this paper, isothermal titration calorimetry (ITC) and 1H NMR studies have been conducted to examine the binding of distamycin A and its two carbamoyl derivatives (compounds 1 and 2) to the target [d(TGGGGT)]4 and d[AG3(T2AG3)3] quadruplexes from the Tetrahymena and human telomeres, respectively. The interactions were examined using two different buffered solutions containing either K+ or Na+ at a fixed ionic strength, to evaluate any influence of the ions present in solution on the binding behaviour. Experiments reveal that distamycin A and compound 1 bind the investigated quadruplexes in both solution conditions; conversely, compound 2 appears to have a poor affinity in any case. Moreover, these studies indicate that the presence of different cations in solution affects the stoichiometry and thermodynamics of the interactions.

The complex between distamycin A and the parallel DNA quadruplex [d(TGGGGT)]4 has been studied by 1H NMR spectroscopy and isothermal titration calorimetry (ITC). To unambiguously assert that distamycin A interacts with the grooves of the quadruplex [d(TGGGGT)]4, we have analyzed the NMR titration profile of a modified quadruplex, namely [d(TGGMeGGT)]4, and we have applied the recently developed differential frequency-saturation transfer difference (DF-STD) method, for assessing the ligand-DNA binding mode. The three-dimensional structure of the 4:1 distamycin A/[d(TGGGGT)]4 complex has been determined by an in-depth NMR study followed by dynamics and mechanics calculations. All results unequivocally indicate that distamycin molecules interact with [d(TGGGGT)]4 in a 4:1 binding mode, with two antiparallel distamycin dimers that bind simultaneously two opposite grooves of the quadruplex. The affinity between distamycin A and [d(TGGGGT)]4 enhances ( approximately 10-fold) when the ratio of distamycin A to the quadruplex is increased. In this paper we report the first three-dimensional structure of a groove-binder molecule complexed to a DNA quadruplex structure.