Interaction of steroids with nucleic acids

Testo and testo-Pt(II) bind DNA at different locations

The development of new targeted anticancer agents able to efficiently and specifically destroy cancer cells with minimal toxic side effects is nowadays a subject of intensive research endeavors. We report the conjugation of testo and testo-Pt(II) (two semi-synthetic testosterone derivatives) with calf thymus DNA in aqueous solution at physiological pH. Multiple spectroscopic methods, thermodynamic analysis and modeling were used to determine the binding efficacy of these drugs to DNA duplex. Thermodynamic parameters showed drug-DNA conjugation occurs via ionic interactions with testo-Pt(II) forming more stable DNA adducts than testo with K_testo-DNA = 1.80 (±0.5) x 10⁵ M^-1 and K_{testo-Pt(II)-DNA} = 2.3 (±0.8) x 10⁵ M^-1. Molecular modeling shows that testo and testo-Pt(II) bind DNA at different locations.

Location of multiple binding sites for testo and testo-Pt(II) with tRNA

We report the binding of testo and testo-Pt(II) complexes (testosterone derivatives) with tRNA in aqueous solution at physiological pH. Thermodynamic parameter ΔH₀ -8 to -3 (kJ mol^-1), ΔS₀ 35 to 18 (J mol^-1K^-1) and ΔG₀ -14 to -13 (kJ mol^-1) and other spectroscopic results showed drug-tRNA binding occurs via ionic contacts with testo-Pt(II) forming more stable tRNA complexes in comparison to testo: K_testo-Pt(II)-tRNA= 3.2 (± 0.9) × 10⁵ M^-1 > K_testo-tRNA= 2.1 (± 0.7) × 10⁵ M^-1. Molecular modeling showed multiple binding sites for testo and testo-Pt(II) on tRNA molecule. Some of the useful molecular descriptors are calculated. Major structural changes were observed for biopolymers upon drug complexation, while tRNA remains in the A-family structures.

Testosterone and its dimers alter tRNA morphology

The morphology of tRNA was studied upon conjugation with testosterone and its aliphatic and aromatic dimers, using multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling. Structural analysis showed that testosterone binds tRNA through A62, A64, C60, C61, C63, G51, U50 and U59 bases. The binding affinity was testosterone dimer-aromatic>testosterone dimer-aliphatic>testosterone. The steroid loading efficacy was 35-45%. Transmission electron microscopy showed major changes in tRNA morphology upon testosterone interaction with an increase in the diameter of the tRNA aggregate, indicating encapsulation of testosterone by tRNA.

Effect of testosterone and its aliphatic and aromatic dimers on DNA morphology

Conjugation of DNA with testosterone and it aliphatic dimer (alip) and aromatic dimer (arom) was investigated in aqueous solution at pH 7.4. Multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling were used to characterize steroid-DNA binding and DNA morphology. Spectroscopic analysis showed that testosterone binds DNA via A7, A16, A17, T8, T15 and T18 nucleobases with overall binding constants K_test-DNA=1.8 (±0.4)×10⁴M^-1, K_{test-dimeralip-DNA}=5.7 (±0.7)×10⁴M^-1 and K_{test-dimer-arom-DNA}=7.3 (±0.9)×10⁴M^-1. The binding affinity increases in this order: testosterone dimer-aromatic>testosterone dimer-aliphatic>testosterone. The steroid loading efficacy was 40-50%. Transmission electron microscopy showed major changes in DNA morphology as testosterone-DNA interaction occurred with increase in the diameter of the DNA aggregate, indicating encapsulation of testosterone by DNA. Modeling showed the presence of several nucleobases attached to testosterone with the free binding energy of -4.93Kcal/mol.

Finding potential DNA-binding compounds by using molecular shape

For the first time a general shape-search docking algorithm (DOCK) has been applied to the minor and major grooves of A-, B- and Z-type DNA dodecamers and to an intercalation site in a B-DNA-type hexamer. Both experimentally and theoretically derived geometries for the various DNA fragments were used. The DOCK searches were carried out on a subset of the Cambridge Crystallographic Database, consisting of almost 10,000 molecules. One of the molecules that scored best in terms of the DOCK algorithm was CC-1065, a potent antitumor agent known to (covalently) bind the AT-rich parts of the minor groove of B-DNA. Several known DNA-binding agents also scored highly. Molecules with shapes complementary to A-, B- and Z-type DNA were indicated by DOCK. In addition, compounds were extracted from the database that might be selective for the GC-rich regions of the minor groove of B-DNA. Many of the compounds in the present study may serve as a starting point for further molecular design of novel DNA-binding ligands.

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.

Apparent stereochemical complementarity of estrogens and helical cavities between DNA base pairs: implications for the mechanism of action of steroids

The shape of the space occupied by a model of the estrogenic steroid hormone estradiol-17 beta conforms closely to a helical cavity between neighboring base pairs in partially coiled B-DNA. The orientation of estradiol-17 beta when fitted into DNA allows stereochemically complementary hydrogen bonding of both the 3- and 17 beta-hydroxyl groups to phosphate oxygens of the deoxyribose-phosphate backbone on adjacent strands. Changes in the chirality (handedness) of the steroid skeleton or in the absolute stereochemistry of hydrogen bonding groups prevent formation of complementary fits in the DNA. Synthetic estrogens can also adopt conformations which are stereochemically complementary to the cavities between base pairs. The complementary relationships between active estrogens and nucleic acids may be related to constraints on the evolution of the structure and the biological function of steroids.

Organization of polyoma virus DNA in mouse tumor cell lines

Restriction mapping of polyoma virus DNA in mouse tumor cell lines gave patterns that varied with the cell line examined. These reflected differences in both the organization and the state of integration of virus genomes in the host chromosomes. (The cell lines were derived from tumors induced by polyoma virus in vivo and were propagated continuously in culture.) Two of the cell lines contained multiple copies of tandemly integrated virus genomes as well as free virus DNA molecules. Two other cell lines appeared to contain only integrated virus genomes arranged as tandem repeats. Based on restriction analysis with eleven different endonucleases, the virus DNA in one of the cell lines containing both free and integrated virus genomes was not detectably defective or hypermethylated. This is in contrast to most previously described polyoma virus transformed mouse cells. These virus genomes may, however, contain point mutations or unobserved rearrangements. The second cell line possessing free virus DNA molecules contained both nondefective and defective virus genomes. Most, if not all, defective virus genomes in this line were integrated. The two other cell lines possessing only detectable integrated virus DNA apparently contained only defective virus genomes. The defect in both cases was a small deletion (less than or equal to 0.2 kb) encompassing 0.12 map units on the physical map of polyoma virus DNA, a region coding for the proximal part of the large T antigen. Moreover, in contrast to the cell lines with free and detectably nondefective virus DNA, the virus DNA was extensively methylated in cell lines containing only integrated and defective virus genomes.

Deoxycorticosterone-adenine interactions in a crystalline complex

Deoxycorticosterone-adenine monohydrate is the first complex involving a steroid and a component of DNA to be successfully crystallized and studied by single crystal x-ray analysis. Hydrogen bonds between O(20) and N(6) as well as O(21) and N(1) connect the corticoid side chain to an adenine molecule. The molecules are also packed such that a second adenine moiety is situated over the delta4-3-one region of the steroid. These observations of the solid state suggest ways in which steroids and nucleic acids may interact in vivo.