Interactions of hormonal steroids with nucleic acids. 3. Role of polymer structure

Stereochemical complementarity of progesterone and cavities between base pairs in partially unwound double stranded DNA using computer modeling and energy calculations to determine degree of fit

Computer modeling was applied for the first time to investigate previously reported complementarity of progesterone and cavities formed between base pairs in partially unwound double stranded DNA. Computer graphics enabled a more objective assessment of complementarity; energy calculations provided a rigorous method to evaluate degree of fit. Graphics confirmed that the complementarity was virtually "lock and key", i.e. close contacts were formed between van der Waals surfaces in the progesterone/DNA complexes and hydrogen bonds were formed between the two carbonyl groups on opposite ends of the steroid and phosphate groups on adjacent strands of DNA. Molecular mechanics calculations revealed that insertion of the steroid resulted in a relatively stable complex i.e. both van der Waals and electrostatic energies were lowered due to favorable steric interactions and stereospecific hydrogen bonds, respectively. Three published X-ray crystal structures of progesterone exhibited similar complementarity. Ent-progesterone which does not occur naturally possessed very poor complementarity. These findings confirm that the structure of progesterone is directly reflected in the stereochemistry of DNA. While no mechanistic explanation for these results is proffered, we hypothesize that such complementarity must have played a decisive role in the evolution of steroid hormone structure and function.

Stereochemical complementary of DNA and steroid agonists and antagonists

Modelling studies in our laboratories over the past decade have demonstrated that a variety of natural products exhibit stereochemical complementarity with nucleic acids. In the case of steroid hormones, the basic cyclopentanophenanthrene skeleton fits between base pairs in partially unwound double stranded DNA; heteroatoms on the steroids form stereospecific donor/acceptor linkages to hydrogen bonding heteroatoms on the DNA. Each of the hormones appears to fit best in the site, i.e. 5'-dTdG-3'.5'dCdA-3'; the pattern of donor/acceptor linkages is unique for each type of hormonal activity. Steroid hormone agonists fit into the same site as the parent hormone; degree of fit correlates with degree of hormonal activity. Steroid hormone antagonists (e.g. RU 486; tamoxifen; anandron) fit into the same site as the agonists but possess different donor/acceptor linkages than the parent hormone; these linkages occur within the site between the base pairs or along the outside surface of the DNA helix in the major or minor grooves. A chronological review of the underlying concepts and observations leading to these discoveries is presented. Work in progress and some potential implications of the emerging technology are also discussed.

On the possible mechanism of recognition of DNA base sequence by steroid hormones

Geometry of the complex of a steroid hormone, dexamethasone, with a hexanucleotide sequence from the glucocorticoid responsive element d(TGTTCT)2, is optimised here using computer aided geometry simulation with an energy minimization technique. We have also optimised its geometries with genetically modified and arbitrarily chosen DNA sequences. The drug molecule is considered to have both intercalative as well as non-intercalative binding. Comparison of energetics and stereochemical aspects, as well as the H-bonding scheme, is used here to bring out salient features about the mechanism of DNA sequence recognition by steroid hormones.

The stereochemical complementarity of DNA and reproductive steroid hormones correlates with biological activity

Modeling studies revealed that progesterone, testosterone, and estradiol are stereochemically complementary to the cavity formed between base pairs in the DNA sequence, 5'-dTdG-3' X 5'-dCdA-3'. Each steroid aligned precisely with the topography of the cavity and formed 2 stereospecific hydrogen bonds linking phosphate oxygens on adjacent DNA strands. Hydrogen bonding donor-acceptor relationships were different for each hormone. The remarkable stereochemical specificity of the hormone-DNA complexes was demonstrated by the lack of complementarity of steroid enantiomers and steroid analogs having alternate ring systems and/or changes in the position of functional groups. Fit of molecules into DNA in the manner of the parent hormone correlated with biological activity. Antagonists also fit into the cavity but differed from agonists in their hydrogen bonding linkages to DNA and/or extended out of the cavity beyond the helix. Unlike flat intercalating agents which form stable complexes with DNA, wedge shaped steroids may thus be capable of forming reversible sequence-specific complexes with DNA. We conclude that the stereochemistry of DNA can be used to predict hormonal activity.

Possible role of 4',4''-diethylstilbestrol quinone in diethylstilbestrol carcinogenesis

4',4''-Diethylstilbestrol quinone, an intermediate in diethylstilbestrol metabolism, had previously been postulated to play a role in diethylstilbestrol-induced carcinogenesis. Possible mechanisms by which 4',4''-diethylstilbestrol quinone may participate in the induction of tumors by diethylstilbestrol are discussed. The possibilities of a direct modification of cellular macromolecules by the quinone intermediate and also an indirect involvement via generation of radicals are explored.

The structure of 4',4''-diethylstilbestrol (DES) quinone

The structure of 4',4''-diethylstilbestrol quinone (DES quinone), a short-lived metabolic intermediate of the synthetic estrogen E-diethylstilbestrol (DES), was investigated by 13C- and 1H-nmr. Selected homonuclear decoupling experiments were carried out to identify the carbons and protons with which resonances were associated. The 1H-nmr spectrum of DES quinone remained unchanged in the temperature range from 25 degrees C to 65 degrees C. The spectral results suggested the structure of DES quinone to be planar or time-averaged planar with the exception of the freely rotating ethyl groups. The conformation of this intermediate was found to be transoid without any indication of conversion through a cisoid conformation. The similarity of the 1H-nmr spectrum of 3',3'',-5',5''-tetrafluoro-4',4''-diethylstilbestrol quinone (TF-DES quinone) and that of the non-fluorinated parent suggested a high degree of structural similarity. The planar structures of the quinone intermediates differed from those of DES or Z,Z-dienestrol which were not coplanar with respect to the aromatic ring systems.

On the fidelity of DNA synthesis:effects of steroids and intercalating agents

Studies on the fidelity of DNA synthesis in vitro were extended to pharmacological agents that interact non-covalently to DNA. Several steroids, intercalators and cancer chemotherapeutic agents increased the relative frequency of incorrect deoxynucleotide incorporation in the fidelity assay. The relationship between non-covalent interactions with DNA and the decreased fidelity of DNA synthesis in vitro is considered.

Stereochemical aspects of the interaction between steroidal diamines and DNA

A complete series of stereoisomeric quaternised diaminoandrostanes, differing in their stereochemistry at the 3,5 and 17 positions, has been examined for effects on the thermal denaturation of calf thymus DNA and for the ability to remove and reverse the supercoiling of closed circular duplex PM2 DNA. In both types of test the eight isomers rank in the same order of effectiveness. The preferred stereochemistry for the quaternary substituents at positions 3 and 17 is beta; of these the orientation of the 17- substituent is more critical. Folding of the steroid skeleton between the A and B rings, as in 5beta-androstanes, diminishes effectiveness but does not necessarily abolish the effect on supercoiling. The over-riding importance of the C-D ring end of the steroid nucleus bearing a 17beta-amino substituent is confirmed by a comparison of the effects of five mon-amino androstanes. Relative helix=unwinding angles per bound steroidal diamine molecule have been determined for four of the isomers; for three 17beta compounds the estimated values are similar to that previously reported for irehdiamine A. For a fourth isomer the angle is 0.22 times that of ethidium, the lowest yet determined for any DNA-binding drug. The results lend further support to the argument that intercalation can be reled out, and alternative models for the binding mechanism are discussed.

Interaction of steroids with nucleic acids

17beta-Estradiol and testosterone bind to both native and denatured DNA, and to RNA and poly(A)-poly(U). Binding affinity depends on the conformation of nucleic acid. Lowering the electrolyte concentration and raising the temperature increase the binding of 17beta-estradiol to native DNA and decrease that to denatured DNA. In 0.01 M NaCl and at 37 degrees, more 17beta-estradiol is bound to native DNA than to denatured DNA. Higher binding of steroid to denatured DNA relative to native DNA at low temperature and high ionic strength is related to larger fraction of binding sites per unit nucleotide in denatured DNA. In addition to 17beta-estradiol and testosterone, 17alpha-estradiol, 17beta-estradiol-3-methyl ether and 19-nortestosterone also stabilize the structure of nucleic acids and poly(A)-poly(U) against thermal denaturation. The 17beta-estradiol induced elevation of the T-m of DNA is diminished by methanol or high NaCl concentration. These results indicate the involvement of hydrogen bonding and hydrophobic interactions between steroids and nucleic acids. The results of binding isotherms and optical studies suggest a conformational dependence of the binding of steroids to nucleic acids.