Binding of the antitumor drug nogalamycin and its derivatives to DNA: structural comparison

The three-dimensional molecular structures of the complexes between a novel antitumor drug nogalamycin and its derivative U-58872 with a modified DNA hexamer d[m5CGT(pS)Am5CG] have been determined at 1.7- and 1.8-A resolution, respectively, by X-ray diffraction analyses. Both structures (in space group P6(1)) have been refined with constrained refinement procedure to final R factors of 0.208 (3386 reflections) and 0.196 (2143 reflections). In both complexes, two nogalamycins bind to the DNA hexamer double helix in a 2:1 ratio with the elongated aglycon chromophore intercalated between the CpG steps at both ends of the helix. The aglycon chromophore spans across the GC Watson-Crick base pairs with its nogalose lying in the minor groove and the aminoglucose lying in the major groove of the distorted B-DNA double helix. Most of the sugars remain in the C2'-endo pucker family, except three deoxycytidine residues (terminal C1, C7, and internal C5). All nucleotides are in the anti conformation. Specific hydrogen bonds are found in the complex between the drug and guanine-cytosine bases in both grooves of the helix. One hydroxyl group of the aminoglucose donates a hydrogen bond to the N7 of guanine, while the other receives a hydrogen bond from the N4 amino group of cytosine. The orientation of these two hydrogen bonds suggests that nogalamycin prefers a GC base pair with its aglycon chromophore intercalating at the 5'-side of a guanine (between NpG), or at the 3'-side of a cytosine (between CpN) with the sugars pointing toward the GC base pair. The binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through, suggesting that nogalamycin prefers GC sequences embedded in a stretch of AT sequences.     

Natural products as leads to antitumor drugs

The discussion in this short review emphasizes that the main and future source of novel natural products as leads to antitumor agents is probably in the areas of biology that cannot be seen, i.e. the microbial world. The review discusses the role of microbes in the production of secondary metabolites that were initially thought to be from marine invertebrates and goes on to discuss the potential for a number of well-known anticancer agents isolated from plant sources to actually be the products of a microbe-plant interaction and finishes with a discussion of the potential of microbial “cryptic clusters” as sources of novel agents/leads to anti-tumor treatments.     

Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G

The antitumor antibiotic netropsin has been co-crystallized with a double-helical B-DNA dodecanucleotide of sequence: C-G-C-G-A-A-T-T-BrC-G-C-G, and the structure of the complex has been solved by X-ray diffraction at a resolution of 2.2 A. The structure has been refined independently by Jack-Levitt and Hendrickson-Konnert least-squares methods, leading to a final residual error of 0.257 by the Jack-Levitt approach (0.211 for two-sigma data) or 0.248 by the Hendrickson-Konnert approach, with no significant difference between refined structures. The netropsin molecule displaces the spine of hydration and fits snugly within the minor groove in the A-A-T-T center. It widens the groove slightly and bends the helix axis back by 8 degrees, but neither unwinds nor elongates the double helix. The drug molecule is held in place by amide NH hydrogen bonds that bridge adenine N-3 and thymine O-2 atoms, exactly as with the spine of hydration. The requirement of A X T base-pairs in the binding site arises because the N-2 amino group of guanine would demand impermissibly close contacts with netropsin. It is proposed that substitution of imidazole for pyrrole in netropsin should create a family of "lexitropsins" capable of reading G X C-containing base sequences.     

Interaction of a bisquaternary ammonium compound with the peripheral organophosphorus (POP) site on acetylcholinesterase

O-ethyl-S (2 diisopropylaminoethyl) methyl phosphorothiolate (MPT) is an active site-directed inhibitor of acetylcholinesterase (AChE). The inhibition of mouse muscle AChE by MPT as well as the inhibition of its individual molecular forms do not proceed as simple irreversible bimolecular reactions. The insolubilization of AChE into a semisolid matrix allows to characterize, after dialysis of all unbound ligand, a partially reversible phase of the inhibition by MPT. These results can be explained in terms of two different modes of inhibition by MPT: the classical irreversible phosphorylation of the active site and an inhibition phase involving the reversible binding of MPT at a site peripheral to the active site, the peripheral organophosphorus site (POP-site). We now find that BW 284 C 51, a reversible specific inhibitor of AChE which protects the active site against irreversible inhibition by low MPT concentrations, can prevent the occurrence of the partially reversible inhibition phase. Hence, BW may bind to a peripheral site that either overlaps or is linked to the POP-site.     

Interactions of antitumor drugs and DNA: crystallographic studies

Several antitumor drugs complexed to DNA double helical fragments have been crystallized and their structures solved by single crystal X-ray diffraction analysis at high resolution. These studies show in great detail the manner in which the planar aromatic components of the drugs intercalate between base pairs from the minor groove side of B-DNA, as well as hydrogen bonding components which anchor the drug to DNA through its interaction with base pairs on either side of the intercalative site. Analysis at this level makes it possible to contemplate the rational design of antitumor drugs that might bind more strongly or interact more specifically with certain nucleic acid sequences.     

Binding of amphipathic drugs and probes to biological membranes

Bouvardain is an antitumor drug that inhibits protein synthesis in intact eukaryotic cells and cell-free systems. Our present studies have shown that bouvardin acts at the level of the 80 S ribosome in a site somehow involved with the interaction of EF1 and EF2. Indeed bouvardin inhibits EF1-dependent binding of aminoacyl-tRNA and EF2-dependent translocation of peptidyl-tRNA but does not affect the non-enzymic translocation since this relation does not require EF2. The site of the 80 S ribosome involved in the interaction with bouvardin appears to be independent from the cycloheximide and the cryptopleurine binding sites since yeast mutants resistant to cycloheximide or cryptopleurine are sensitive to bouvardin.     

Potential antitumor mechanisms of phenothiazine drugs

In this study, three kinds of phenothiazine drugs were analyzed to explore their potential antitumor mechanisms. First, target proteins that could interact with chlorpromazine, fluphenazine and trifluoperazine were predicted. Then, the target proteins of the three drugs were intersected. Cell signaling pathway enrichment and related disease enrichment were conducted for the intersected proteins to extract the enrichment categories associated with tumors. By regulation network analysis of the protein interactions, the mechanisms of action of these target proteins in tumor tissue were clarified, thus confirming the potential antitumor mechanisms of the phenothiazine drugs. The final results of cell signaling pathway enrichment and related disease enrichment showed that the categories with the highest score were all found in tumors. Target proteins belonging to the tumor category included signaling pathway members such as Wnt, MAPK and retinoic acid receptor. Moreover, another target protein, MAPK8, could indirectly act on target proteins CDK2, IGF1R, GSK3B, RARA, FGFR2 and MAPK10, thereby affecting tumor cell division and proliferation. Therefore, phenothiazine drugs may have potential antitumor effects, and tumor-associated target proteins play important roles in the process of cell signaling transduction cascades.     

Binding of antitumor antibiotic daunomycin to histones in chromatin and in solution

Daunomycin is an anticancer drug that is well-known to interact with DNA in chromatin. Using a compositionally defined chicken erythrocyte chromatin fraction, we have obtained conclusive evidence that the drug is also able to interact with chromatin-bound linker histones without any noticeable binding to core histones. The drug can interact in an equal fashion with both histone H1 and H5 and to a greater extent with core histones H3/H4 and H2A/H2B as free proteins in solution. Thus, the binding of daunomycin to linker histones in the chromatin fiber is most likely due to the well-known higher accessibility of these histones to the surrounding environment of the fiber. Binding of daunomycin to linker histones appears to primarily involve the trypsin-resistant (winged-helix) domain of these proteins. The studies described here reveal the occurrence of a previously undisclosed mechanism for the antitumor activity of anthracycline drugs at the chromatin level.     

Microbial natural products: molecular blueprints for antitumor drugs

Microbes from two of the three domains of life, the Prokarya, and Eukarya, continue to serve as rich sources of structurally complex chemical scaffolds that have proven to be essential for the development of anticancer therapeutics. This review describes only a handful of exemplary natural products and their derivatives as well as those that have served as elegant blueprints for the development of novel synthetic structures that are either currently in use or in clinical or preclinical trials together with some of their earlier analogs in some cases whose failure to proceed aided in the derivation of later compounds. In every case, a microbe has been either identified as the producer of secondary metabolites or speculated to be involved in the production via symbiotic associations. Finally, rapidly evolving next-generation sequencing technologies have led to the increasing availability of microbial genomes. Relevant examples of genome mining and genetic manipulation are discussed, demonstrating that we have only barely scratched the surface with regards to harnessing the potential of microbes as sources of new pharmaceutical leads/agents or biological probes.     

Biologically active bisquaternary ammonium chlorides: physico-chemical properties of long chain amphiphiles and their evaluation as non-viral vectors for gene delivery

The biological properties of bisquaternary ammonium salts, which are derivatives of N,N-bisdimethyl-1,2-ethanediamine (bis-C(n)BEC), of general formula /C(n)H(2n+1)OOCCH2(CH3)2N(+)CH2CH2N(+)(CH3)2CH2COOC(n)H(2n+1)/2Cl-, were investigated (n=10, 12, 14). The interaction with model membrane was studied by differential scanning calorimetry experiments, and the apparent adiabatic molar compressibility of their solution as a function of concentration was obtained by sound velocity measurements. Their biological activities were assayed by Electrophoresis Mobility Shift, MTT proliferation, and transient transfection. All the investigated compounds interact with the DNA and are able to transfect DNA, when they are co-formulated with DOPE, with an efficiency significantly greater than that of a standard commercial transfection reagent. Bis-C(14)BEC is the only molecule able to deliver DNA inside the cells without a helper lipid, as shown by EGFP expression, albeit with a low efficiency in comparison with a standard commercial transfection reagent. This may be due to a slightly different interaction of bis-C14BEC from bis-C10BEC and bis-C12BEC with phospholipid bilayers. Bis-C10BEC and bis-C12BEC show a slight fluidizing effect, while bis-C14BEC increases stability of both the gel and the rippled gel phases.     

Synthesis and in vitro antimicrobial and antitumor activity of some nitrogen heterocycles

5-Phenyl-2-[(3,4,5-trimethoxybenzylidene)hydrazino]-thiazole and 3-[(3,4,5-trimethoxybenzylidene)amino]-4-oxoimidazolidin-2-thione were prepared by cyclization of 1-[(3,4,5-trimethoxybenzyliden)amino]-thiourea with phenacyl bromide and ethyl chloroacetate in the presence of fused sodium acetate. Acetylation of the synthesized compounds with acetic anhydride gave corresponding N-acetyl derivatives. Condensation of the synthesized thione with aromatic aldehydes yielded two 3-substituted 5-arylidene-4oxo-imidazolidin-2-thiones. Acetylation of the latter compounds with acetic anhydride afforded the corresponding N-acetyl-4-oxo-imidazolidin-2-thiones. Some of the synthesized compounds exhibited antimicrobial activity. The cytotoxic activity of the prepared thiazole and imidazolidin-2-thione derivatives was studied on several tumor cell lines.     

The improved effects of specific active immunotherapy on a rat fibrosarcoma by antitumor drugs

Summary We have tried to find out if the combination of a xenogenized tumor cell vaccine and antitumor drugs is able to induce a synergistic increase in the antitumor therapeutic effect. The degree of increase in the LTD₅₀ (50% lethal tumor dose) is expressed numerically, as a quantitative index designed to compare degrees of transplantation resistance to tumor cell challenge. A LTD₅₀ was achieved by an intradermal (i. d.) immunization with xenogenized tumor cells when challenged with tumor cells implanted intraperitoneally 2 weeks after the immunization: this LTD₅₀ value was 527 000 times higher than that of the non-immunized group. When we combined this type of immunization with appropriate doses of bleomycin (BLM) or cyclophosphamide (CY), which are able to augment antitumor immunity, the LTD₅₀ was 723 000–1190 000 times higher than that of the non-immunized group. This increase in the LTD₅₀ is definitely higher than that achieved by a single immunization with irradiated tumor cells (× 33 000) and combined with either BLM (× 93 000) or CY (×140 000). We also studied the therapeutic effect of a tumor cell vaccine combined with antitumor drugs BLM or CY in tumor-bearing rats. We observed a synergistic effect caused by BLM or CY after i. d. immunization with xenogenized tumor cells: this showed a significant increase when compared with the therapeutic effects obtained by chemotherapy alone (P <0.01). Nevertheless, there was no evidence that the above antitumor effects is superior to the effect achieved by irradiated tumor cells.     

Interaction of the nonintercalative antitumour drugs SN-6999 and SN-18071 with DNA: influence of ligand structure on the binding specificity

Binding to DNA's of the non-intercalative ligands SN-6999 and SN-18071 has been studied by means of circular dichroism, UV absorption, thermal melting and for SN-6999 by viscosity measurements. Both antitumour drugs show a preference for dA.dT rich DNA's, but the base pair selectivity of SN-18071 is lower as indicated by some affinity to dG.dC containing duplex DNA. The dA.dT base pair specificity of SN-6999 is comparable to that of netropsin. It forms very stable complexes with dA.dT containing duplex DNA and competes with netropsin binding on DNA. The ligands SN-18071 and pentamidine are totally released from their complexes with poly(dA-dT).poly(dA-dT) by competitive netropsin binding. The results demonstrate that hydrogen bonding capacity of the ligand in addition to other factors strongly contribute to the base sequence specificity in the recognition process of the ligand with DNA. A binding model of SN-6999 with five dA.dT pairs in the minor groove of B-DNA is suggested.     

质子泵抑制剂与肿瘤耐药研究

恶性肿瘤对抗癌药物的耐药性是肿瘤患者治疗失败的主要原因。肿瘤细胞外微环境的高度酸化是肿瘤细胞对化疗药物产生耐药的机制之一。改变肿瘤细胞内外的pH梯度是逆转耐药的一种有效方法。作为抗酸剂治疗胃病的质子泵抑制剂能够通过抑制质子泵的功能,改变pH梯度而阻断肿瘤微环境的酸化,达到提高肿瘤对化疗药物敏感性的目的。     

Binding of mithramycin to DNA in the presence of second drugs

Comparative DNA equilibrium binding studies with mithramycin (MTR) and ethidium bromide in the presence and in the absence of second drugs were investigated by spectral titrations. Unusual curvatures (in contrast to those due to neighbor exclusion or anticooperativity) are found in the Scatchard plots of MTR-DNA titrations in the presence of netropsin, a minor-groove binder. Parallel studies with ethidium bromide indicate that although the presence of netropsin significantly reduces the binding ability of ethidium, no unusually curved Scatchard plots are obtained. The unusual curvature exhibited by the Scatchard plots of MTR titrations in the presence of netropsin indicates that the binding of netropsin greatly affects the MTR binding to DNA and can be simulated by an explicit incorporation of the second drug-DNA interaction in the binding formalism. Since netropsin is a minor-groove binder, its interference with the binding of MTR is in accord with the notion that MTR also binds at this groove. The observation of negligible effects on the DNA binding ability of MTR in the presence of either a major-groove or a phosphate group binder lends further support to this conclusion. Consistent with its guanine specificity, studies with synthetic polynucleotides suggest that MTR exhibits negligible affinity for poly(dA-dT).poly(dA-dT) or poly(dA).poly(dT).(ABSTRACT TRUNCATED AT 250 WORDS)     

Binding of the hemopressin peptide to the cannabinoid CB1 receptor: structural insights

Hemopressin, a bioactive nonapeptide derived from the α1 chain of hemoglobin, was recently shown to possess selective antagonist activity at the cannabinoid CB(1) receptor [Heimann, A. S., et al. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 20588-20593]. CB(1) receptor antagonists have been extensively studied for their possible therapeutic use in the treatment of obesity, drug abuse, and heroin addiction. In particular, many compounds acting as CB(1) receptor antagonists have been synthesized and subjected to experiments as possible anti-obesity drugs, but their therapeutic application is still complicated by important side effects. Using circular dichroism and nuclear magnetic resonance spectroscopy, this work reports the conformational analysis of hemopressin and its truncated, biologically active fragment hemopressin(1-6). The binding modes of both hemopressin and hemopressin(1-6) are investigated by molecular docking calculations. Our conformational data indicate that regular turn structures in the central portion of hemopressin and hemopressin(1-6) are critical for an effective interaction with the receptor. The results of molecular docking calculations, indicating similarities and differences in comparison to the most accepted CB(1) pharmacophore model, suggest the possibility of new chemical scaffolds for the design of new CB(1) antagonist lead compounds.     

Intercalative and nonintercalative binding of large cationic porphyrin ligands to polynucleotides

The interactions of two positional isomers and one analogue of meso-tetra (4-N-methylpyridyl) porphine, with the synthetic polynucleotides poly[d(A-T)] . poly[d(A-T)] and poly[d(G-C)] . poly[d(G-C)] have been investigated by circular dichroism. All four porphyrins were found to bind to the polynucleotides as shown by the induction of circular dichroism in their Soret bands. Furthermore, the sign of the induced ellipticity reflects selective occupation of binding sites by the porphyrin ligands. The conformational lability of poly[d(A-T)] X poly[d(A-T)] was found to be appreciable as micromolar amounts of meso-substituted 4-N-methylpyridyl, 3-N-methylpyridyl, and p-N-trimethylanilinium porphines induced a CD spectrum similar but not identical to that of DNA in the Z-form, i.e. a negative band at 280 nm and a positive band at 259 nm. The effect of porphyrin binding to poly[d(G-C)] X poly[d(G-C)] was less pronounced and dissimilar to that seen in the AT polymer.