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When perylenequinonoid pigments were irradiated with visible light, semiquinone radicals, singlet oxygen, superoxide anion radical, hydroxyl radical and hydrogen peroxide were detected. The formation of the semiquinone radicals and activated oxygen species and the transformations and competitions between them depend on the quinone and oxygen concentrations, time and intensity of irradiation and the nature of the substrate. In anaerobic solution, the semiquinone radicals, which exhibit well-defined electron paramagnetic resonance (EPR) spectra at room temperature, are predominantly photoproduced via the self-electron transfer between the excited and ground species. The EPR spectra of the semiquinone radicals were assigned by reference to simulated spectra. The presence of electron donors significantly promotes the production of the semiquinone radicals. The EPR hyperfine splittings of the semiquinone radicals mainly originate from the coupling interactions of the aromatic, phenolic hydroxyl and methoxyl protons with the unpaired spin. An exception is hypocrellin B in which the two methylene protons of the side-ring are also involved in the hyperfine splitting to a minor extent because the double bond of the side-ring conjugates with the perylenequinonoid chromophore. In addition, compared with cercosporin, the EPR spectra of the hypocrellin semiquinone radicals are further complicated by tautomerizations at ambient temperature. Therefore EPR spectroscopy can also be utilized to study the tautomerization together with nuclear magnetic resonance (NMR), absorption spectroscopy and some specific chemical trapping reactions. In aerobic solution, singlet oxygen is the principal product in the photosensitization of perylenequinonoid pigments. In addition to singlet oxygen, superoxide anion radical is also generated, to a lesser extent, by the quinones on illumination in aerobic solution via the reduction of oxygen by the semiquinone radicals, and this process is significantly enhanced by the presence of electron donors.

Contrary to theoretical predictions on the basis of a discrete hetaryne intermediate (frontier orbitals, total atomic charges on C-3 and C-4, and activation energies for the concerted process) from the MO calculations, reactions of dicyanomethylides with 3-(3′,3′-dimethyltriazene-1-yl)pyridine-4-carboxylic acid, a formal precursor of 3,4-didehydropyridine, afforded exclusively the pyrido[4,3-a]indolizines. The results are better in accord with a mechanism involving a zwitterionic hetaryne precursor.

The synthesis of several aminoanthraquinone derivatives (AAQs), designed to suppress the dark toxicity and to promote more efficient cancer cell photosensitization for potential use in photodynamic therapy (PDT), is described. The following AAQs were synthesized: 1-NH 2 -4,5-(MeO) 2 -AQ ( 1 ), 1,5-(NH 2 ) 2 -4,8-(MeO) 2 -AQ ( 2 ), 1,8-(NH 2 ) 2 -4,5-(MeO) 2 -AQ ( 3 ), and 1,5-(NHPhMe) 2 -4,8-(MeO) 2 -AQ ( 8 ). The agents exhibit strong absorption in the region 480–620 nm. Possible mechanisms of photosensitization were studied by measuring 1 O 2 phosphorescence at 1270 nm, detecting superoxide radicals employing an electron paramagnetic resonance (EPR)-spin trapping technique, and measuring oxygen consumption during the photo-oxidation of a representative biological electron donor, NADH. Strong phosphorescence from 1 O 2 was observed upon illumination of 2 and 3 in C 6 H 6 (quantum yield of 0.25 and 0.5 respectively), and in EtOH (quantum yield of 0.23 and 0.34). The 1-amino-AQ ( 1 ) was the weakest 1 O 2 sensitizer, with quantum yield of 0.13 in benzene. No phosphorescence was observed in EtOH. A superoxide radical was detected as a spin adduct of 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) in irradiated benzene solutions of 1 , 2 or 3 and DMPO. AAQs 2 and 3 sensitized photo-oxidation of NADH in H 2 O/EtOH mixture with the intermediacy of singlet oxygen as judged by the effect of sodium azide on the photostimulated oxygen consumption. Evolution of O 2 upon addition of catalase to the illuminated solution confirmed the ultimate formation of hydrogen peroxide. These findings suggested that the (di)amino-dimethoxyanthraquinones might exert photosensitization via both Type I and Type II mechanisms. The AAQs were tested for their ability to photosensitize K562 human chronic myeloid leukemic cells in culture. Viability was measured using the 3,4,5-diethylthiazol-2,5-diphenyl tetrazolium blue assay, and DNA and possible membrane damage were assessed. The results from illuminating cells with light > 475 nm show that for the 1,5-compounds, the presence of methoxy substituents at 4,8 positions reduces the dark toxicity from ID 50 of 23 to 250 μM and for the 1,8-compounds correspondingly from ID 50 of 53 to > 300 μM. In the 1,5-series,this decrease of the dark toxicity is accompanied by an increase in light-induced dose modification from 8.85 to 14.4.Differences exist in the mechanisms of cytotoxicity between the prototype phenolic AAQs and their methoxy counterparts. It appears that the cytotoxic action of the latter causes cell damage by the formation of a high proportion of alkali labile sites in addition to frank strand breaks. No evidence for membrane damage, as determined by transport of the model amino acid cycloleucine, could be observed even at supralethal doses.

The interaction of thioformyldistamycin, an amide isostere of the naturally occurring antibiotic distamycin A, with a self-complementary decadeoxynucleotide duplex, d(CGCAATTGCG)2, has been examined using a variety of high-field 1H-NMR techniques. The ligand exhibits two forms in solution arising from geometric isomerism due to restricted rotation around the thioformamide bond. Only the thermodynamically more stable Z-form is shown to bind to the oligonucleotide along its minor groove at the central 5'-AATT segment with the end groups of the ligand extending into the flanking GC regions but without any close contact at the amidinium terminus. Cross-peaks involving characteristic intra- and interresidue proton connectivities in the 2D experiments (COSY and NOESY) were employed to assign individual resonances of both strands in the asymmetric DNA-drug complex. The solution structure of the complex was constructed by molecular mechanics calculations based upon initial estimates of drug-DNA NOE contacts and further refined through energy minimization. These results complement previous structural studies on distamycin and other lexitropsins with oligonucleotides. The exchange of the ligand between two equivalent binding sites on the DNA sequence was estimated to occur at 40 s-1 with a free energy of activation of 16.5 kcal.mol-1 at 321-326 K. There was no evidence of formation of a 2:1 drug-oligomer complex, in contrast to the case of the natural product, which is attributed to steric demands of the larger sulfur atom.

An oligopeptide has been synthesized in which an imidazole ring is substituted for the central pyrrole ring of distamycin A. Two-dimensional NMR spectroscopy was used to characterize the complex formed between 3-[1-methyl-4-[1-methyl-4-[1-methyl-4-(formylamino)pyrrole-2-carboxamido]imidazole-2-carboxamido]pyrrole-2-carboxamido]propionamidine hydrochloride (2-ImD) and d(CGCAAGTTGGC).d(GCCAACTTGCG). Titration of the AAGTT duplex with 2-ImD yielded a single complex with a ligand:DNA stoichiometry of 2:1

Perylenequinonoid pigments have several advantages as photodynamic therapy (PDT) agents compared with the commonly used hematoporphyrin derivatives. Certain new halogenated and metal-ion chelated perylenequinonoid pigments have been prepared, and their halogenation and chelation reactions are discussed. In addition, the photophysical and photochemical properties of these halogenated and metal-ion chelated perylenequinonoid pigments have been investigated. Their significantly enhanced red absorptivities and strong 1 O 2 -generating functions may qualify them as promising PDT photosensitizers.

The marked photosensitizing properties of perylene quinonoid pigments, a promising class of agents for photodynamic therapy of human tumors, have been recognized, but quantitative information on their excited states is lacking. For the first time, some fundamental photophysical parameters of hypocrellins A and B; and cercosporin in benzene have been determined. For hypocrellin A, kF = 1.4 × 108 s−1, ΦF = 0.14, τS = 0.98 ns, ES = 48.5 kcal mol−1, ΦST = 0.86, kST = 8.6 × 108 s−1 and ET = 41.0 kcal mol−. For hypocrellin B, kF = 9.1 × 107 s−1, kC = 2.7 × 109 s−1, kST = 1.1 × 1010 s−1, ΦF = 0.058, ΦIC = 0.18, τS = 0.66 ns, ES = 47.7 kcal mol−1, ΦST = 0.76 and ET = 40.2 kcal mol−1. For cercosporin, kF = 8.3 × 107 s−1, kIC = 1.7 × 109 s−1, kST = 1.1 × 1010 s−1, ΦF = 0.061, ΦIC = 0.13, τS = 0.75 ns, ES = 48.0 kcal mol−1, ΦST = 0.81 and ET = 40.5 kcal mol−1. The quantum yields of singlet oxygen formation by these agents were also determined: ΦO2(hypocrellin A) = 0.83, Φ1O2(hypocrellin B) = 0.76 and Φ1O2(cercosporin) = 0.81. Finally, these perylene quinonoid agents have been shown to act as excellent singlet oxygen sensitizers with several advantages over existing sensitizers, including large molar extinction coefficients, wide UV—visible absorption bands, high quantum yields of singlet oxygen generation, good stability, good solubility and small solvent and concentration effects.

The design and synthesis of several hybrid intercalator-linked porphyrins and their corresponding metalloporphyrin derivatives designed as cellular DNA targetted anticancer agents is described. 9-Chloro-7-methylimidazo[4,5-f]quinoline was condensed with ethylenediamine, 1,4-phenylenediamine and 2,5-toluenediamine to give compounds Ia–c. Naphtho[2,1-b]thiophene-4-carboxylic acid was condensed with 1,6-hexanediamine, 1,10-decanediamine, and 1,12-dodecanediamine to give compounds IIa–c and IIIa–c. Compounds Ia–c and IIa-c were condensed with deuterioporphyrin monomethyl ester and deuterioporphyrin to yield compounds IVa–j. Compounds IVa–h were refluxed with MnCl2 or CoCl2 in DMF to give metalloporphyrins Va–j. Compounds Ia–c, IIa–c, IIIa–c, IVa–j, and Va–j were characterized by IR, NMR, and MS (FAB) spectral data. Kassoc value for intercalative binding of these porphyrin derivatives to calf thymus DNA is in the range 1.9−3.0 × 106 L M−1.

Selective INEPT (INAPT) experiments were used to correlate the nitrogen- and carbon-bound hydrogens of nucleosides with 13C resonances via 2J(C, H) and 3J(C, H). Such experiments are useful as part of a strategy to distinguish the imino hydrogens of uridine and thymidine, which cannot be accomplished on the basis of chemical shift. The strategy involves correlation of the imino hydrogen with C-5 using INAPT and testing whether or not the C-5 resonance is quaternary. Polarization transfer is ineffecient for most positions in nucleosides owing to the small long-range couplings, except the H-6C-5 transfer in adenosine, which results in enhancement of the 13C resonance over its equilibrium value. The efficiency of polarization transfer from H-3 to C-5 of thymidine depends on the base-paired status of the nucleoside indicating a change in the 3J(C, H) on base-pair formation. This sensitivity to electronic reorganization on base-pair formation makes the INAPT experiment a useful probe for the base-paired status of nucleosides and of the electronic properties of uridine and thymidine analogues.

The transformation from 1,2-naphthoquinone to perylenequinone, which usually requires several steps, is stereo- selectivity realized via one step in excellent yield by a newly developed, double coupling method. The possible mechanism for this novel reaction and the properties of the resulting perylenequinone are discussed. Moreover, an improved procedure for the preparation of a 5-bromo-1,2-naphtalenediol, a reported coupling precursor to perylenequinone, is also described. These synthetic procedures open convenient ways to perlenequinone structures of significant biological potential.

The synthesis and characterization are described of trifluorothymidine groups incorporated into an antisense 21 mer designed to target gene sequences that encode serine proteases in T-lymphocytes. i H NMR titration studies on 3',5'-O-TPDS-trifluorothymidine (3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)trifluorothymidine) with 3',5'-O-TPDS-2'-deoxyadenosine provided clear evidence of normal Watson-Crick base pairing via detection of the imino proton signals

The synthesis of a series of 1,2,4-triazole-containing oligopeptide lexitropsins related to the natural antitumor antibiotic distamycin is described. The binding properties of these new agents to both native DNAs and synthetic polydeoxyribonucleotides were determined by UV absorption and circular dichroism studies. The DNA binding and sequence selectivity of these agents have been determined by complementary strand MPE footprinting on two restriction fragments of pBR322 DNA. The lexitropsins bearing one 1,2,4-triazole moiety bind to AT sequences like distamycin but also tolerate GC sites. However, 3, which contains two contiguous 1,2,4-triazole moieties, appears not to recognize AT stretches and demands two consecutive GC bases in the middle of a four-base recognition site. The triazole lexitropsins avoid ATTT (4264-4267) and AAAA (4273-4276) to which distamycin binds strongly to the EcoRI/Hind III fragment. Determination of pKa values indicates the 1,2,4-triazole units are protonated under physiological conditions. The avoidance of AT stretches and the recognition of GC base sites by 3 suggest molecular recognition in these cases is determined, not by electrostatic effects, but rather by invoking a hydrogen bond between the triazole 4-nitrogen and G-2NH2 in the minor groove.

An efficient procedure is presented for the introduction of a 6- N -(2-cholesteroloxycarboaminoethyl)-or 6- N -[2-(9-fluorenylmethoxycarboamino)ethyl]moieties into adenosine, which is compatible with solid phase incorporation into antisense oligodeoxyribonucleotides and has the further advantage of lack of diastereomer formation.

Various substituted oxazolo[5,4-b]pyridines 5a-d have been synthesized by condensation of appropriate hydroxyaminopyridines and aldehydes followed by oxidative cyclization of the resulting Schiff's bases with lead tetraacetate. This method has been extended to the synthesis of the DNA minor groove binding ligands 5e and 5f related to Hoechst 33258 1.

Various substituted benzimidazoles and imidazolo[4,5-b] pyridines 5a-c have been prepared by condensation of appropriate diamines and aldehydes in nitrobenzene. This method has been utilized to synthesize compounds 5f-h, which are analogues of the DNA binding fluorochrome Hoechst 33258.

The utility of sodium borohydride in the presence of acetic acid in efficiently and selectively cleaving substituted benzoxazoles to o-hydroxy-N-substituted anilines in the presence of other functional groups is described. These conditions offer practical advantages over existing ring opening procedures with normally resistant benzoxazoles.

The synthesis of novel thiazole-bearing oligopeptides related to the antibiotic distamycin is described. These lexitropsins, or information reading agents, are designed to test the principle of DNA base site exclusion or avoidance as well as base pair acceptance in molecular recognition of oligopeptides for DNA. The first group of compounds, therefore, has the sulfur atom aligned inward to the DNA minor groove, whereas the second group of agents has the sulfur atom directed away from the DNA minor groove. All six compounds synthesized bind to double helical DNA, and their binding constants to calf thymus DNA and relative to distamycin and netropsin are reported

The design, synthesis and biological evaluation of novel pyrrolo [2,1][1,4] benzodiazepine (PBD) dimers 38–43 linked with pyrrole and imidazole polyamides from either side by a flexible methylene chain of variable length are described, which involved mercuric chloride mediated cyclization of the corresponding amino diethyl thioacetals. The compounds were prepared with varying numbers of pyrrole and imidazole containing polyamides to determine the structural requirements for optimal in vitro antitumor activity. These compounds were tested against a panel of 60 human cancer cells by the National Cancer Institute, and demonstrated that, of the compounds bis-PBD-pyrrole polyamides (38–40) and bis-PBD-imidazole polyamides (41–43) certain of the bis-PBD-pyrrole and imidazole polyamide conjugates are active for individual cancer cell lines ( Table 1 ). However, this study found that bis-PBD-pyrrole and imidazole polyamide conjugates 38–43 in general are potent against many human cancer cell lines. Download : Download full-size image

The synthesis and biological evaluation of novel L-tryptophan pyrrole, imidazole polyamide conjugates (16-21), L-tryptophan-glycosylated pyrrole polyamide conjugates (28-30), L-tryptophan dimers (37-42) with straight carbon links of varying length, and L-tryptophan dimers (68-73) linked with pyrrole and imidazole polyamide from both sides by a flexible methylene chain of variable length are described. The compounds were prepared with varying numbers of pyrrole- and/or imidazole-containing polyamides and glycosylated pyrrole polyamides to determine the structural requirements for optimal in vitro antitumor activity. The compounds listed in Table 1 have been evaluated in a three cell line, one dose primary anticancer assay. The compounds listed in Table 2 have been evaluated against nine panels of 60 human cancer cell lines including leukemia, non-small cell lung cancer, colon cancer, CNS cancer, melanoma, ovarian cancer, renal cancer, prostate cancer, and breast cancer. It is observed from the initial cytotoxic data (Table 1) that compounds 16-19, 28-30, 68-69, and 71-73 have varying cytotoxic potencies against the three cancer cell lines. It is also observed, from the biological data from Table 2 for compounds 20-21, 37-42, and 70 against the 60 different tumor cells, that the L-tryptophan dimers 37-42 linked by a different number of carbon chains are more active than the L-tryptophan dimers linked by pyrrole or imidazole polyamides. The cytotoxic potency in tryptophan dimers, linked by a different number of carbon atoms increased the number of carbons between the two L-tryptophan rings.

The design, synthesis and biological evaluation of novel pyrrolo [2,1][1,4] benzodiazepine-water insoluble 31-38 and water soluble 39-46 glycosylated pyrrole and imidazole polyamide conjugates are described that involved mercuric chloride mediated cyclization of the corresponding amino diethyl thioacetals. The compounds were prepared with varying numbers of pyrrole and imidazole containing polyamides and incorporating glucose moieties in order to improve the water solubility of PBD-polyamide conjugates and probe the structural requirements for optimal in vitro antitumor activity. These compounds were tested against a panel of 60 human cancer cells by the National Cancer Institute, and demonstrated that the water soluble PBD-polyamide compounds exhibited a higher level of cytotoxic activity than the existing natural and synthetic pyrrolo [2,1-c][1,4] benzodiazepines. The cytotoxic activities of these compounds dramatically increase after hydrolysis of their acetylated counterparts. The activity data summarized in Table 1 and Table 2 show that the solubility of the PBD-polyamides and also the type of heterocycle play important roles influencing the cytotoxic activity of the PBD-polyamide conjugates. The PBD-glycosylated polyamide (water soluble) conjugates 39-46 are highly cytotoxic against many human cancer cell lines in comparison with the PBD-polyamide (water insoluble version) conjugates.

The C7–C7, C7–N3 and N3–N3 dimers of 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benzo[e]indole (seco-CBI) with pyrrole and imidazole polyamides were synthesized and preliminary anti-cancer evaluation carried out by NCI against three types of cancer cells.

Clinical use of non-steroidal anti-inflammatory drugs (NSAIDs) is associated with significant toxicity particularly in the gastrointestinal tract and kidney. Various approaches such as formulation co-administration (of agents to protect the stomach), chemical manipulation and synthesis of new safer anti-inflammatory drugs reported in the literature to overcome the toxicity of NSAIDs have been summarized. As far as synthesis of new more effective and safer anti-inflammatory drugs is concerned, we have reported recent findings in the area of synthesis of heterocyclic compounds such as pyrimidines, imidazole, benzimidazole, thiazole, thiazolidine, acridine, thiourea, alkanoic acid derivatives and other related heterocyclic compounds and their role as inflammation inhibitors.

The design, synthesis, and biological evaluation of novel C-8 linked pyrrolo[2,1-c][1,4]benzodiazepine (PBD)-imidazole polyamide conjugates (1-5) are described that involve mercuric chloride-mediated cyclization of the corresponding amino diethyl thioacetals. The compounds were prepared with varying numbers of imidazole- and pyrrole-containing polyamides in order to probe the structural requirements for optimal in vitro antitumor activity. These compounds were tested against a panel of human cancer cells by the National Cancer Institute, demonstrating that the compounds exhibited a higher level of cytotoxic activity than the existing natural and synthetic pyrrolo[2,1-c][1,4]benzodiazepines. The data presented show that the length of the polyamides and also the type of heterocycle play important roles in this series of compounds for anticancer activity. Compounds 1, 2, 3, and 5 have significant cytotoxic activity against the various types of cancer cell lines. It appears that cytotoxic activity is related to both the length and the heterocycles of the polyamides. Compound 1 exhibited a wide spectrum of anticancer activities against all cell lines in nine cancer panels and was especially effective against colon cancer, melanoma, and renal cancer and breast cancer, however, compound 4 did not exhibit any significant anticancer activity. This study found that PBD-imidazole polyamide conjugates are highly cytotoxic against many human cancer cell lines in comparison with the PBD-pyrrole polyamide conjugates.

Two DNA minor-groove binding polyamides 1 and 2 were designed and synthesized and evaluated for inhibition of FIV-34TF10 replication. Both 1 and 2 decreased the replication of FIV-34TF10 by 75% by acting at the level of the virus but outside of the LTR or env region.

A family of naturally occurring oligopeptides includes netropsin, distamycin, anthelvencin, kikumycin B, amidinomycin, and norformycin. Netropsin (I) and distamycin (II) express their biological activities by targeting specific sequences of chemical functionalities in the minor groove of DNA. Both netropsin and distamycin can be regarded as polyamide chains in which each alpha-carbon has been replaced by a five-membered pyrrole ring. The repeat distance in such an augmented polyamide chain is almost the same as the distance from one base pair to the next along the floor of a minor groove within beta-DNA. In this paper we report the synthesis of 16-21 cross-linked polyamides containing a thiazole heterocyclic ring bearing the active functionalites NH(2), NHCHO, or H. 16 and 17 were synthesized by DCC and HOBt catalyzed reaction of 5 with 14 and 15, while the formylation products 18 and 19 were obtained by coupling the formylated 4-methyl-thiazolated acid 6 with 14 and 15. The deaminated compounds 20 and 21 were obtained by the coupling of 5-trichloroacetyl-4-methylthiazole 7 synthesized from 4-methylthiazole. All the six cross-linked polyamides 16-21 were tested for their DNA gyrase inhibition. The studies have shown these polyamides have better sequence recognition and a greater percentage of inhibition than the corresponding monomers. The compound 17 shows complete inhibition of gyrase at 0.5 microM concentration as compared to the naturally occurring distamycin at 1.0 microM.

Recent progress in synthetic and computational chemistry has made it possible to develop certain novel drug candidates. Drug candidates for genetic diseases, such as cancer, may also be designed on the basis of structural information obtained using X-ray analysis and NMR, as well as evidence from biological techniques applied to natural products–DNA (or RNA) complexes and conjugates. The resulting designed drug candidates exhibit promising performance based on the recognition on nucleic acid sequences.

Abstract: Marine organisms are a rich source for natural products. Pyrrolo[4,3,2-de]quinolines and pyrido[4,3,2-mn]acridines are of major interest as metabolites in sponges and ascidians. Many of these compounds have generated interest both as challenging problems for structure elucidation and synthesis as well as for their cytotoxicities. The isolation, structure proof, biological activities, chemical properties and synthesis have attracted the attention of chemists, biologists and pharmacists. The principal structural feature of these alkaloids is the core of a planar iminoquinone moiety which can intercalate into DNA and cleave the DNA double helix or inhibit the action of topoisomerase II. Of the makaluvamines, rhakaluvamine F and A are the most cytotoxic to the HCT 116 cell line. The enhanced toxicity of the makaluvamines towards xrs-6 cells shows that all of the makaluvamines, except makaluvamine B, act like m-AMSA and etoposide in inhibiting topoisomerases via cleavable complex formation, or via the direct induction of DNA double-strand breaks. They are also amongst the most potent inhibitors of topoisomerase II. Both makaluvamine A and C can decrease tumor size in a solid human tumor model. Discorhabdin A and C in contrast are of high cytotoxicity, but they exhibit no inhibition of topoisomerase II. As representatives of the derivatives of pyrido[4,3,2-mn]acridine, cystodytins, kuanoniamines and diplamine are the most potent to inhibit HCT replication. Eilatin, as a 1,10-phenanthroline derivative, can form complexes with metal ions. It has been shown that these metal complexes can bind to DNA by intercalation. The new members of the pyrrolo[4,3,2-de]quinolines and pyrido[4,3,2- mn]acridines, such as veiutamine, discorhabdin G, tsitsikammamines, epinartins, arnoamines as well as sagitol are reviewed. Some successful syntheses of pyrrolo[4,3,2- de]quinoline ring system and pyrido[4,3,2-mn]acridine ring system are also reviewed in this article.

Alignment of the available human immunodeficiency virus type 1 (HIV-1) viral DNA termini [U5 and U3 long terminal repeats (LTRs)] shows a high degree of conservation and the presence of a stretch of five or six consecutive adenine and thymine (AT) sequences approximately 10 nucleotides away from each LTR end. A series of AT-selective minor-groove binders, including distamycin and bisdistamycins, bisnetropsins, novel lexitropsins, and the classic monomeric DNA binders Hoechst 33258, 4'-diamino-2-phenylindole, pentamidine, berenil, spermine, and spermidine, were tested for their inhibitory activities against HIV-1 integrase (IN). Although netropsin, distamycin, and all other monomeric DNA binders showed weak activities in the range of 50-200 microM, some of the polyamides, bisdistamycins, and lexitropsins were remarkably active at nanomolar concentrations. Bisdistamycins were 200 times less potent when the conserved AAAAT stretch present in the U5 LTR was replaced with GGGGG, consistent with the preferred binding of these drugs to AT sequences. DNase I footprinting of the U5 LTR further demonstrated the selectivity of these bisdistamycins for the conserved AT sequence. The tested compounds were more potent in Mg+2 than in Mn+2 and inhibited IN50-212 deletion mutant in disintegration assays and the formation of IN/DNA complexes. The lexitropsins also were active against HIV-2 IN. Some of the synthetic polyamides exhibited significant antiviral activity. Taken together, these data suggest that selective targeting of the U5 and U3 ends of the HIV-1 LTRs can inhibit IN function. Polyamides might represent new leads for the development of antiviral agents against acquired immune deficiency syndrome.

Publisher Summary Recently it has become evident that DNA sequence selectivity is an important component contributing to the cytotoxic potency of several chemotherapeutic agents derived from natural sources. This chapter examines factors that have been uncovered that contribute to the molecular recognition processes between groove-binding ligands and nucleic acid receptors and that may consequently be incorporated into drug design. Additional incentive to pursue this approach of rationally altered DNA sequence recognition of small molecules is provided by the observation of biological responses attributable to sequence specific effects in the cases of both lexitropsins and bis-benzimidazoles. Sequence selectivity of the bis-benzimidazoles also appears to play a role in the cytotoxic potency. The stage is now set for the further development of therapeutically useful agents based on the bis-benzimidazole structure.