Theoretical Assessment of the Ligand/Metal/Quadruplex Recognition in the Non-Canonical Nucleic Acids Structures.

Quadruplexes (GQs), peculiar DNA/RNA motifs concentrated in specific genomic regions, play a vital role in biological processes including telomere stability and, hence, represent promising targets for anticancer therapy. GQs are formed by folding guanine-rich sequences into square planar G-tetrads which stack onto one another. Metal cations, most often potassium, further stabilize the architecture by coordinating the lone electron pairs of the O atoms. The presence of additional nucleic acid bases, however, has been recently observed experimentally and contributes substantially to the structural heterogeneity of quadruplexes. Therefore, it is of paramount significance to understand the factors governing the underlying complex processes in these structures. The current study employs DFT calculations to model the interactions between metal cations (K+, Na+, Sr2+) and diverse tetrads composed of a guanine layer in combination with a guanine (G)-, adenine (A)-, cytosine (C)-, thymine (T)-, or uracil (U)-based tetrad layer. Moreover, the addition of 4-(3,4-dihydroisoquinolin-2-yl)-2-(quinolin-2-yl)quinazoline to the modeled quadruplexes as a possible mechanism of its well-exerted antitumor effect is assessed. The calculations imply that the metal cation competition and ligand complexation are influenced by the balance between electronic and implicit/explicit solvation effects, the composition of the tetrad layers, as well as by the solvent exposure to the surrounding environment expressed in terms of different dielectric constant values. The provided results significantly enhance our understanding of quadruplex diversity, ligand recognition, and the underlying mechanisms of stabilization at an atomic level.

Small Heterocyclic Ligands as Anticancer Agents: QSAR with a Model G-Quadruplex.

G-quadruplexes (GQs) have become valid targets for anticancer studies in recent decades due to their multifaceted biological function. Herewith, we aim to quantify interactions of potential heterocyclic ligands (Ls) with model GQs. For seven 4-aminoquinazolines and three 2-heteroaryl perimidines, seven of this ten-membered group so far unknown, we use routine quantum chemical modeling. As shown in the literature, a preferred mode of interaction of heterocycles with cellular structures is stacking to exposable faces of G-quadruplexes. To exploit the energy of this interaction as a molecular descriptor and achieve the necessary chemical precision, we use state of the art large-scale density functional theory (DFT) calculations of stacked heterocycles to a GQ. Actually, the GQ has been simplified for the computation by stripping it off all pentose phosphate residues into a naked model of stacked guanine quartets. The described model thus becomes computable. The obtained heterocyclic ligand GQ.L stacking energies, that is, their GQ affinities, are the necessary ligand descriptors. Using the ligand biological inhibitory activities (IC50) on a human malignant melanoma A375 cell line, we obtain a good linear relationship between computed ligand stacking affinities to GQ, and experimental log (IC50) values. Based on the latter relationship, we discuss a putative mechanism of anticancer activity of heterocyclic ligands via stacking interactions with GQs and thereby controlling cell regulatory activity. This mechanism may tentatively be applied to other condensed five- and six-membered small heterocycles as well.

Biological activity of quinazoline analogues and molecular modeling of their interactions with G-quadruplexes.

BACKGROUND: Quinazolines 1 to 6, with an aromatic or aryl-vinyl substituent in position 2 are selected with the aim to compare their structures and biological activity. The selection includes a natural alkaloid, schizocommunin, and the synthetic 2-(2'-quinolyl)-3H-quinazolin-4-one, known to interact with guanine-quadruplex dependent enzymes, respectively telomerase and topoisomerase. METHODS: Breast cancer cells of the MDA cell line have been used to study the bioactivity of the tested compounds by the method of Comet Assay and FACS analyses. We model observed effects assuming stacking interactions of studied heterocycles with a naked skeleton of G-quadruplex, consisting of guanine quartet layers and potassium ions. Interaction energies are computed using a dispersion corrected density functional theory method, and an electron-correlated molecular orbital theory method. RESULTS: Selected compounds do not remarkably delay nor change the dynamics of cellular progression through the cell cycle phases, while changing significantly cell morphology. Our computational models quantify structural effects on heterocyclic G4-complex stabilization energies, which directly correlate with observed biological activity. CONCLUSION: Our computational model of G-quadruplexes is an acceptable tool for the study of interaction energies of G-quadruplexes and heterocyclic ligands, predicting, and allowing design of novel structures. GENERAL SIGNIFICANCE: Genotoxicity of quinazolin-4-one analogues on human breast cancer cells is not related to molecular metabolism but rather to their interference with G-quadruplex regulatory mechanisms. Computed stabilization energies of heterocyclic ligand complexes of G-quadruplexes might be useful in the prediction of novel telomerase / helicase, topoisomerase and NA polymerase dependent drugs.

Solvent induced shifts of electronic spectra IV. Computational study on PRODAN fluorescence and implications to the excited state structure.

Vertical S(1)-S(0) electronic transitions of the highly solvent-sensitive fluorescence label 2-propionyl-6-dimethylamino naphthalene (PRODAN) are modeled by semiempirical CISD AM1 and TD DFT calculations in a large number of solvents of different polarity and hydrogen donating ability. Calculations correctly reproduce the observed solvent induced shifts of the emission maxima. The fluorescence Frank-Condon transition energies in solvent can be predicted quantitatively at the AM1 SM5.42 OPEN(2,2) C.I.=5 CISD level. For the planar PRODAN emitting state at the latter level we obtain a regression with practically unit slope and zero intercept for aprotic solvents. The respective relationship for the O-twisted S(1) state has a slope of 0.59 and intercept of 9100 cm(-1). These results support the concept that no geometry twist in the S(1) state of PRODAN is necessary to explain the observed solvent effects on fluorescence.

Origins of stereoselectivity in the Diels-Alder addition of chiral hydroxyalkyl vinyl ketones to cyclopentadiene: a quantitative computational study.

Modest basis set level MP2/6-31G(d,p) calculations on the Diels-Alder addition of S-1-alkyl-1-hydroxy-but-3-en-2-ones (1-hydroxy-1-alkyl methyl vinyl ketones) to cyclopentadiene correctly reproduce the trends in known experimental endo/exo and diastereoface selectivity. B3LYP theoretical results at the same or significantly higher basis set level, on the other hand, do not satisfactorily model observed endo/exo selectivities and are thus unsuitable for quantitative studies. The same is valid also with regard to subtle effects originating from, for example, conformational distributions of reactants. The latter shortcomings are not alleviated by the fact that observed diastereoface selectivities are well-reproduced by DFT calculations. Quantitative computational studies of large cycloaddition systems would require higher basis sets and better account for electron correlation than MP2, such as, for example, CCSD. Presently, however, with 30 or more non-hydrogen atoms, these computations are hardly feasible. We present quantitatively correct stereochemical predictions using a hybrid layered ONIOM computational approach, including the chiral carbon atom and the intramolecular hydrogen bond into a higher level, MP2/6-311G(d,p) or CCSD/6-311G(d,p), layer. Significant computational economy is achieved by taking account of surrounding bulky (alkyl) residues at 6-31G(d) in a low HF theoretical level layer. We conclude that theoretical calculations based on explicit correlated MO treatment of the reaction site are sufficiently reliable for the prediction of both endo/exo and diastereoface selectivity of Diels-Alder addition reactions. This is in line with the understanding of endo/exo selectivity originating from dynamic electron correlation effects of interacting pi fragments and diastereofacial selectivity originating from steric interactions of fragments outside of the Diels-Alder reaction site.

Correlated MO study of the low-barrier intramolecular motions in donor-acceptor ethenes.

Correlated MP2 and MCSCF MO calculations of several model push-pull ethenes in most cases indicate no great participation of excited singlet and triplet electronic configurations in either the minima or the transition structures for the suggested facilitated intramolecular rotation about the polarized C=C bond. This situation changes significantly only in molecules with sulfur atoms in the molecule as either donors or acceptors. The outstanding contribution of sulfur atoms as either donors or acceptors is a significant increase of push-pull ethene molecular polarizabilities. Thus, within the studied small series of mostly planar push-pull ethenes, polarizability appears a better indicator of rapid intramolecular motions about the C=C bond than straight polarity. Substituents with larger steric demands around the C=C bond are shown to likely preclude its complete turnaround, thus prompting a ramification of the interpretations of dynamic NMR phenomena in sterically constrained push-pull ethenes as large-amplitude librations resulting from strong rovibrational and relatively weak electronic coupling. These librations, as shown by complete vibrational mode analysis of corresponding rotational transition structures, cover in fact certain sectors of the intuitively suggested full rotations similar to those about C-C single bonds.

Kinetic studies and molecular modelling attribute a crucial role in the specificity and stereoselectivity of penicillin acylase to the pair ArgA145-ArgB263.

Kinetic experiments with a substrate series of phenylacetyl-arylamides reveal that at least one polar group in the amine moiety is required for the proper orientation of the substrate in the large nucleophile-binding subsite of penicillin acylase of Escherichia coli. Quantum mechanical molecular modelling of enzyme-substrate interactions in the enzyme active site shows that in the case of substrates lacking local symmetry, the productive binding implies two nonsymmetrical arrangements with respect to the two positively charged guanidinium residues of ArgA145 and ArgB263. This indicates a crucial role of the specified arginine pair in the substrate- and stereoselectivity of penicillin acylase.

Thorpe-Ingold effects in cyclizations to five-membered and six-membered rings containing planar segments. The rearrangement of N(1)-alkyl-substituted dihydroorotic acids to hydantoinacetic acids in base.

While the gem-dimethyl effect (GDME) is quantitatively similar for cyclizations to cyclopentane and cyclohexane rings and their homomorphs, in systems containing planar segments the GDME is stronger for the formation of five-membered rings. Planar pentagons have smaller angles than planar hexagons and their formation is helped by the decrease in the potential internal bond angle caused by substituents, as suggested by Thorpe and Ingold for small rings. The phenomenon is illustrated with crystal structure data on five-membered hydantoins and six-membered dihydrouracils containing four-atom planar segments. Such a Thorpe-Ingold effect explains the rearrangement in base of N-alkyl substituted dihydroorotic acids 1 to hydantoinacetic acids 3. The reaction involves initial hydrolysis to N-(N-alkylcarbamoyl)aspartic acids 2 and their subsequent cyclization. The unsubstituted N-carbamoylaspartic acid 2a is stable in 1 M KOH, the N(1)-methyl and ethyl compounds 2b and 2c are in equilibrium with the hydantoinacetic acids 3, while the cyclization of the N(1)-isopropyl and cyclohexyl derivatives 2d and 2e is irreversible. Experimental data on equilibria and pK(a)s for ionization of the carboxy and NH groups allow equilibria and rates involving the N-unsubstituted compounds to be estimated and compared with those for the N-alkyl derivatives. The strongest effect is observed on the equilibrium [3(2-)]/2[(2-)], where substitution of H by methyl increases K 600-fold. In vitro the kinetic regioselectivity for acid catalyzed cyclization of N-carbamoylaspartic to hydantoinacetic acid against dihydroorotic acid is only 10:1. This, together with the weaker acidity of the remote carboxyl group, favours cyclization to dihydroorotic acid under biological conditions.

Schiff base addition to cyclic dicarboxylic anhydrides: an unusual concerted reaction. An MO and DFT theoretical study.

The existing controversy as to whether dicarboxylic anhydride iminolysis by Schiff bases is a concerted [4 + 2] addition or a stepwise reaction following either a Perkin-like route or occurs as iminolysis via zwitterionic intermediates is solved computationally by DFT and MO theory. Both types of theory favor a concerted mechanism starting as bimolecular addition of imine to the carbonyl carbon of anhydride monoenol, accompanied by simultaneous elimination of carboxylate. The reaction proceeds further without forming any intermediate and completes as intramolecular charge transfer from enol HOMO to imine LUMO with ring closure.

Fluorinated alcohols enable olefin epoxidation by H2O2: template catalysis.

Experimental observations show that direct olefin epoxidation by H(2)O(2), which is extremely sluggish otherwise, occurs in fluorinated alcohol (R(f)OH) solutions under mild conditions requiring no additional catalysts. Theoretical calculations of ethene and propene epoxidation by H(2)O(2) in the gas phase and in the presence of methanol and of two fluorinated alcohols, presented in this paper, show that the fluoro alcohol itself acts as a catalyst for the reaction by providing a template that stabilizes specifically the transition state (TS) of the reaction. Thus, much like an enzyme, the fluoro alcohol provides a complementary charge template that leads to the reduction of the barrier by 5-8 kcal mol(-)(1). Additionally, the fluoro alcohol template keeps the departing OH and hydroxyalkenyl moieties in close proximity and, by polarizing them, facilitates the hydrogen migration from the latter to form water and the epoxide product. The reduced activation energy and structural confinement of the TS over the fluoro alcohol template render the epoxidation reaction observable under mild synthetic conditions.