A Computational Model for Anthracycline Binding to DNA: Tuning Groove-Binding Intercalators for Specific Sequences

Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment

Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.

HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham

A long-lasting goal of computational biochemists, medicinal chemists, and structural biologists has been the development of tools capable of deciphering the molecule-molecule interaction code that produces a rich variety of complex biomolecular assemblies comprised of the many different simple and biological molecules of life: water, small metabolites, cofactors, substrates, proteins, DNAs, and RNAs. Software applications that can mimic the interactions amongst all of these species, taking account of the laws of thermodynamics, would help gain information for understanding qualitatively and quantitatively key determinants contributing to the energetics of the bimolecular recognition process. This, in turn, would allow the design of novel compounds that might bind at the intermolecular interface by either preventing or reinforcing the recognition. HINT, hydropathic interaction, was a model and software code developed from a deceptively simple idea of Donald Abraham with the close collaboration with Glen Kellogg at Virginia Commonwealth University. HINT is based on a function that scores atom-atom interaction using LogP, the partition coefficient of any molecule between two phases; here, the solvents are water that mimics the cytoplasm milieu and octanol that mimics the protein internal hydropathic environment. This review summarizes the results of the extensive and successful collaboration between Abraham and Kellogg at VCU and the group at the University of Parma for testing HINT in a variety of different biomolecular interactions, from proteins with ligands to proteins with DNA.

Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects

Doxorubicin (DOX) is a cancer drug that binds to dsDNA through intercalation. A comprehensive microsecond timescale molecular dynamics study is performed for DOX with 16 tetradecamer dsDNA sequences in explicit aqueous solvent, in order to investigate the intercalation process at both binding stages (conformational change and insertion binding stages). The molecular mechanics generalized Born surface area (MM-GBSA) method is adapted to quantify and break down the binding free energy (BFE) into its thermodynamic components, for a variety of different solution conditions as well as different DNA sequences. Our results show that the van der Waals interaction provides the largest contribution to the BFE at each stage of binding. The sequence selectivity depends mainly on the base pairs located downstream from the DOX intercalation site, with a preference for (AT)₂ or (TA)₂ driven by the favorable electrostatic and/or van der Waals interactions. Invoking the quartet sequence model proved to be most successful to predict the sequence selectivity. Our findings also indicate that the aqueous bathing solution (i.e., water and ions) opposes the formation of the DOX-DNA complex at every binding stage, thus implying that the complexation process preferably occurs at low ionic strength and is crucially dependent on solvent effects.

Molecular mechanism and binding free energy of doxorubicin intercalation in DNA

The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramolecular electrostatic interactions (ΔGele) and electrostatic polar solvation interactions (ΔGpolar-PB/GB) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the standard concentration dependent free energies of DOX (ΔGcon) and the ionic solution (ΔGion). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX-DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. We have calculated the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX-DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1 : 1 complex is -9.1 and -5.1 kcal mol-1 respectively. The same quantities from the modified MM-PBSA method are -12.74 and -8.35 kcal mol-1 respectively. The value of the total BFE ΔGt-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of -7.7 ± 0.3 kcal mol-1.

TEMPO-Catalyzed Direct Conversion of Primary Alcohols to α-Chloroacetals with TCCA Both as an Oxidant and a Chlorination Reagent

Multistep reactions are often required for the transformation of alcohols to α-chloroacetals via the unstable intermediates aldehydes or α-halo aldehydes. Herein, we report a simplified procedure for practical synthesis of α-chloroacetals using 2,2,6,6-tetramethylpiperidine-1-oxyl as a catalyst and trichloroisocyanuric acid both as an oxidant and a chlorination reagent. The reaction is one-pot, solvent-free and high-yielding. In addition, the α-chloroacetals have been transformed to enol ethers through the elimination reaction in the presence of sodium.

Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study

The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.

Synthesis and antitumor activities of novel rhein α-aminophosphonates conjugates

Several rhein α-aminophosphonates conjugates (5a-5q) were synthesized and evaluated for in vitro cytotoxicity against HepG-2, CNE, Spca-2, Hela and Hct-116 cell lines. Some compounds showed relatively high cytotoxicity. Especially, compound 5i exhibited the strongest cytotoxicity against Hct-116 cells (IC50 was 5.32 μM). All the synthesized compounds exhibited low cytotoxicity against HUVEC cells. The mechanism of compound 5i was preliminarily investigated by Hoechst 33258 staining, JC-1 mitochondrial membrane potential staining and flow cytometry, which indicated that the compound 5i induced apoptosis in Hct-116 cancer cells. Cell cycle analysis showed that these compound 5i mainly arrested Hct-116 cells in G1 stage. The effects of 5i on the activation of caspases expression indicated that 5i might induce apoptosis via the membrane death receptor pathways. In addition, the binding properties of a model analog 5i to DNA were investigated by methods (UV-vis, fluorescence, CD spectroscopy and FRET-melting) in compare with that of rhein. Results indicated that 5i showed moderate ability to interact ct-DNA.

Synthesis, cytotoxicity, DNA binding and apoptosis of rhein-phosphonate derivatives as antitumor agents

Several rhein-phosphonate derivatives (5a-c) were synthesized and evaluated for in vitro cytotoxicity against HepG-2, CNE, Spca-2, Hela and Hct-116 cell lines. Some compounds showed relatively high cytotoxicity. Especially compounds 5b exhibited the strongest cytotoxicity against HepG-2 and Spca-2 cells (IC50 was 8.82 and 9.01 µM), respectively. All the synthesized compounds exhibited low cytotoxicity against HUVEC cells. Further experiments proved that 5b could disturb the cell cycle in HepG-2 cells and induce apoptosis. In addition, the binding properties of a model conjugate 5b to DNA were investigated by methods (UV-Vis, fluorescence, CD spectroscopy). Results indicated that 5b showed moderate ability to interact ct-DNA.

Anthracyclines as effective anticancer drugs

Anthracyclines have received significant attention due to their effectiveness and extensive use as anticancer agents. At present, the clinical use of these drugs is offset by drug resistance in tumours and cardiotoxicity. Therefore, a relentless search for the 'better anthracycline' has been ongoing since the inception of these drugs > 30 years ago. This review focuses on the most recent pharmacology and medicinal chemistry developments on the design and use of anthracyclines. Based on their crystal structures as well as molecular modelling, a more detailed mechanism of topoisomerase poisoning by these new anthracyclines has emerged. Chemical modifications of anthracyclines have been found to possibly change the target selectivity among various topoisomerases and, thus, vary their anticancer activity. Additionally, recent sugar modifications of anthracyclines have also been found to overcome P-glycoprotein-mediated drug resistance in cancer therapy. The continued improvement of anthracycline clinical applications so far and the clinical trials of the 'third generation' of anthracyclines (such as sabarubicin) are also discussed. To finally find the 'better' anthracycline, further areas of research still need to be explored such as: the elucidation of the topoisomerase and P-glycoprotein crystal structures, molecular modelling based on crystal structure in order to design the next generation of better anthracycline drugs, the continued modifications of the anthracycline sugar moieties, and the further improvement of anthracycline drug delivery methods.

Computational analysis of structure-based interactions and ligand properties can predict efflux effects on antibiotics

AcrA-AcrB-TolC efflux pumps extrude drugs of multiple classes from bacterial cells and are a leading cause for antimicrobial resistance. Thus, they are of paramount interest to those engaged in antibiotic discovery. Accurate prediction of antibiotic efflux has been elusive, despite several studies aimed at this purpose. Minimum inhibitory concentration (MIC) ratios of 32 β-lactam antibiotics were collected from literature. 3-Dimensional Quantitative Structure-Activity Relationship on the β-lactam antibiotic structures revealed seemingly predictive models (q(2)=0.53), but the lack of a general superposition rule does not allow its use on antibiotics that lack the β-lactam moiety. Since MIC ratios must depend on interactions of antibiotics with lipid membranes and transport proteins during influx, capture and extrusion of antibiotics from the bacterial cell, descriptors representing these factors were calculated and used in building mathematical models that quantitatively classify antibiotics as having high/low efflux (>93% accuracy). Our models provide preliminary evidence that it is possible to predict the effects of antibiotic efflux if the passage of antibiotics into, and out of, bacterial cells is taken into account--something descriptor and field-based QSAR models cannot do. While the paucity of data in the public domain remains the limiting factor in such studies, these models show significant improvements in predictions over simple LogP-based regression models and should pave the path toward further work in this field. This method should also be extensible to other pharmacologically and biologically relevant transport proteins.

Synthesis, biological evaluation, and molecular docking studies of 2,6-dinitro-4-(trifluoromethyl)phenoxysalicylaldoxime derivatives as novel antitubulin agents

A series of 2,6-dinitro-4-(trifluoromethyl)phenoxysalicylaldoxime derivatives (1h-20h) have been designed and synthesized, and their biological activities were also evaluated as potential antiproliferation and tubulin polymerization inhibitors. Among all the compounds, 2h showed the most potent activity in vitro, which inhibited the growth of MCF-7, Hep-G2 and A549 cell lines with IC(50) values of 0.70 ± 0.05, 0.68 ± 0.02 and 0.86 ± 0.05 μM, respectively. Compound 2h also exhibited significant tubulin polymerization inhibitory activity (IC(50)=3.06 ± 0.05 μM). The result of flow cytometry (FCM) demonstrated that compound 2h induced cell apoptosis. Docking simulation was performed to insert compound 2h into the crystal structure of tubulin at colchicine binding site to determine the probable binding model. Based on the preliminary results, compound 2h with potent inhibitory activity in tumor growth may be a potential anticancer agent.

Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT

A public web server performing computational titration at the active site in a protein-ligand complex has been implemented. This calculation is based on the Hydropathic interaction noncovalent force field. From 3D coordinate data for the protein, ligand and bridging waters (if available), the server predicts the best combination of protonation states for each ionizable residue and/or ligand functional group as well as the Gibbs free energy of binding for the ionization-optimized protein-ligand complex. The 3D structure for the modified molecules is available as output. In addition, a graph depicting how this energy changes with acidity, i.e., as a function of added protons, can be obtained. This data may prove to be of use in preparing models for virtual screening and molecular docking. A few illustrative examples are presented. In beta secretase (2va7) computational titration flipped the amide groups of Gln12 and Asn37 and protonated a ligand amine yielding an improvement of 6.37 kcal mol(-1) in the protein-ligand binding score. Protonation of Glu139 in mutant HIV-1 reverse transcriptase (2opq) allows a water bridge between the protein and inhibitor that increases the protein-ligand interaction score by 0.16 kcal mol(-1). In human sialidase NEU2 complexed with an isobutyl ether mimetic inhibitor (2f11) computational titration suggested that protonating Glu218, deprotonating Arg237, flipping the amide bond on Tyr334, and optimizing the positions of several other polar protons would increase the protein-ligand interaction score by 0.71 kcal mol(-1).

Energy-based prediction of amino acid-nucleotide base recognition

Despite decades of investigations, it is not yet clear whether there are rules dictating the specificity of the interaction between amino acids and nucleotide bases. This issue was addressed by determining, in a dataset consisting of 100 high-resolution protein-DNA structures, the frequency and energy of interaction between each amino acid and base, and the energetics of water-mediated interactions. The analysis was carried out using HINT, a non-Newtonian force field encoding both enthalpic and entropic contributions, and Rank, a geometry-based tool for evaluating hydrogen bond interactions. A frequency- and energy-based preferential interaction of Arg and Lys with G, Asp and Glu with C, and Asn and Gln with A was found. Not only favorable, but also unfavorable contacts were found to be conserved. Water-mediated interactions strongly increase the probability of Thr-A, Lys-A, and Lys-C contacts. The frequency, interaction energy, and water enhancement factors associated with each amino acid-base pair were used to predict the base triplet recognized by the helix motif in 45 zinc fingers, which represents an ideal case study for the analysis of one-to-one amino acid-base pair contacts. The model correctly predicted 70.4% of 135 amino acid-base pairs, and, by weighting the energetic relevance of each amino acid-base pair to the overall recognition energy, it yielded a prediction rate of 89.7%.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

New computational strategy to analyze the interactions of ERalpha and ERbeta with different ERE sequences

The importance of computational methods for the simulation and analysis of biological systems has increased during the last years. In particular, methods to predict binding energies are developing not only with the aim of ranking the affinities between two or more complexes, but also to quantify the contribution of different types of interaction. In this work, we present the application of HINT, a non Newtonian force field, to rank the affinities of complexes formed by estrogen receptors (ER) alpha and beta and different estrogen responsive elements (ERE) near the estrogen-regulated genes. We used the crystallographic coordinates of the DNA binding domain of ERalpha complexed to a consensus ERE as a starting point to simulate several complexes in which some nucleotides in the ERE sequence were mutated. Moreover, we used homology modeling methods to create the structure of the complexes between the DNA binding domain of ERbeta (for which no experimental structures are currently available) and the same ERE sequences. Our results show that HINT is able to rank the affinities of ERalpha and ERbeta for different ERE sequences, and to correctly identify the positions on the DNA sequence that are most important for binding affinity. Moreover, the HINT output gives us the opportunity to identify and quantify the role played by each single atom of amino acids and nucleotides in the binding event, as well as to predict the effect on the binding affinity for other nucleotide mutations.

Synthesis of daunorubicin analogues containing truncated aromatic cores and unnatural monosaccharide residues

The anthracycline antibiotics daunorubicin and doxorubicin have been used widely as anticancer drugs, but their cardiotoxicity limits their clinical use. We describe here the preparation of a small panel of daunorubicin analogues in which the anthraquinone core is replaced with simpler aromatic moieties that lack a quinone functionality. The targets consist of a functionalized 1,2,3,4-tetrahydro-naphthalene or 1,2,3,4-tetrahydro-anthracene core bound to one of three monosaccharides: daunosamine, acosamine, or 4-amino-2,3,6-trideoxy-l-threo-hexopyranose. Key steps in the synthesis included an enantioselective ring opening of benzo-fused norbornene derivatives for the preparation of the core structures and the use of silver hexafluorophosphate-promoted thioglycoside activation in the glycosylation of these cores. Evaluation of these compounds against the MCF-7 cancer cell line demonstrated that the identity of the carbohydrate moiety appeared to have little influence on the cytotoxicity. Moreover, the analogues with the 1,2,3,4-tetrahydro-naphthalene core showed no cytotoxicity, while those possessing the 1,2,3,4-tetrahydro-anthracene moiety were more active. The IC50 values for the latter group of compounds were in the range of 94-134 microM, compared to 17 microM for doxorubicin and 5 microM for daunorubicin.

Energetics of the protein-DNA-water interaction

Background

To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species.

Results

An initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r² of 0.21 and standard error of ± 1.71 kcal mol^-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r² of 0.56 and standard error of ± 1.28 kcal mol^-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts.

Conclusion

This study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation) mostly cancel.

Anthracycline glycosides of 2,6-dideoxy-2-fluoro-alpha-L-talopyranose

The methyl beta-glycoside of the title sugar, obtained from 2-deoxy-2-fluoro-beta-D-glucopyranose tetraacetate by a sequence with detailed characterization of all intermediates, was converted by acetolysis-bromination into 3,4-di-O-acetyl-2,6-dideoxy-2-fluoro-alpha-L-talopyranosyl bromide, coupling of which with (7S,9S)-4-demethoxydaunomycinone afforded the 3,4-diacetate of 4-demethoxy-9-O-(2,6-dideoxy-2-fluoro-alpha-L-talopyranosyl)daunomycinone (19). The antitumor-active 19 was converted by way of its 14-bromo derivative into the 14-hydroxy analogue, the antitumor-active 4-demethoxyadriamycinone glycoside 21.

In vitro study of drug accumulation in cancer cells via specific association with CdS nanoparticles

We report a novel approach to enhance the efficient accumulation and utilization of anticancer drug daunorubicin on cancer cells through the combination with CdS nanoparticles. Our observations using confocal fluorescence scanning microscopy as well as electrochemical analysis methods demonstrate that CdS nanoparticles can readily bind with daunorubicin on the external membrane of the targeted cells and facilitate the uptake of drug molecules in the human leukemia K562 cells. Besides, our results also indicate that the competitive binding of CdS nanoparticles with accompanying anticancer drug to the membrane of leukemia K562 cells could efficiently prevent the drug release by the drug-sensitive and drug-resistant leukemia cells and thus inhibit the possible multidrug resistance of cancer cells, which could be further utilized to improve the future drug efficiency in respective tumor chemotherapies.

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

The energetics and hydrogen bonding pattern of water molecules bound to proteins were mapped by analyzing structural data (resolution better than 2.3A) for sets of uncomplexed and ligand-complexed proteins. Water-protein and water-ligand interactions were evaluated using hydropatic interactions (HINT), a non-Newtonian forcefield based on experimentally determined logP(octanol/water) values. Potential water hydrogen bonding ability was assessed by a new Rank algorithm. The HINT-derived binding energies and Ranks for second shell water molecules were -0.04 kcal mol(-1) and 0.0, respectively, for first shell water molecules -0.38 kcal mol(-1) and 1.6, for active site water molecules -0.45 kcal mol(-1) and 2.3, for cavity water molecules -0.55 kcal mol(-1) and 3.3, and for buried water molecules -0.56 kcal mol(-1) and 4.4. For the last four classes, similar energies indicate that internal and external water molecules interact with protein almost equally, despite different degrees of hydrogen bonding. The binding energies and Ranks for water molecules bridging ligand-protein were -1.13 kcal mol(-1) and 4.5, respectively. This energetic contribution is shared equally between protein and ligand, whereas Rank favors the protein. Lastly, by comparing the uncomplexed and complexed forms of proteins, guidelines were developed for prediction of the roles played by active site water molecules in ligand binding. A water molecule with high Rank and HINT score is unlikely to make further interactions with the ligand and is largely irrelevant to the binding process, while a water molecule with moderate Rank and high HINT score is available for ligand interaction. Water molecule displaced for steric reasons were characterized by lower Rank and HINT score. These guidelines, tested by calculating HINT score and Rank for 50 water molecules bound in the active site of four uncomplexed proteins (for which the structures of the liganded forms were also available), correctly predicted the ultimate roles (in the complex) for 76% of water molecules. Some failures were likely due to ambiguities in the structural data.

A new bisintercalating anthracycline with picomolar DNA binding affinity

A new bisintercalating anthracycline (WP762) has been designed, in which monomeric units of daunorubicin have been linked through their amino groups on the daunosamine moieties using an m-xylenyl linker. Differential scanning calorimetry and UV melting experiments were used to measure the ultratight binding of WP762 to DNA. The binding constant for the interaction of WP762 with herring sperm DNA was determined to be 7.3 (+/-0.2) x 10(12) M(-1) at 20 degrees C. The large favorable binding free energy of -17.3 kcal mol(-1) was found to result from a large negative enthalpic contribution of -33.8 kcal mol(-1) and an opposing entropic term (-TDeltaS = +16.5 kcal mol(-1)). A comparative molecular modeling study rationalized the increased binding by the m-xylenyl linker of WP762 positioning in the DNA minor groove compared to the p-xylenyl linker found in WP631, the first bis-anthracycline of this type. The cytotoxicity of WP762 was compared to that of other anthracyclines in Jurkat T lymphocytes. These studies, together with an analysis of the cell-cycle traverse in the presence of WP762, suggest that in these cells the new drug is more cytotoxic than the structurally related WP631.

Docking, triggering, and biological activity of dynemicin A in DNA: a computational study

The triggering and biological activity of the naturally occurring enediyne dynemicin A (1) was investigated, both inside and outside the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG).d(CCAGTAGTAG), using density functional theory (B3LYP with the 3-21G and 6-31G(d) basis set), BD(T)/cc-pVDZ (Brueckner doubles with a perturbative treatment of triple excitations), and the ONIOM approach. Enediyne 1 is triggered by NADPH in a strongly exothermic reaction (-88 kcal/mol), which involves a number of intermediate steps. Untriggered 1 has a high barrier for the Bergman cyclization (52 kcal/mol) that is lowered after triggering to 16.7 kcal/mol due to an epoxide opening and the accompanying strain relief. The Bergman reaction of triggered 1 is slightly exothermic by 2.8 kcal/mol. The singlet biradical formed in this reaction is kinetically stable (activation enthalpies of 19.5 and 21.8 kcal/mol for retro-Bergman reactions) and is as reactive as para-benzyne. The activity-relevant docking mode is an edge-on insertion into the minor groove, whereas the intercalation between base pairs, although leading to larger binding energies, excludes a triggering of 1 and the development of its biological activity. Therefore, an insertion-intercalation model is developed, which can explain all known experimental observations made for 1. On the basis of the insertion-intercalation model it is explained why large intercalation energies suppress the biological activity of dynemicin and why double-strand scission can be achieved only in a two-step mechanism that involves two enediyne molecules, explaining thus the high ratio of single-strand to double-strand scission observed for 1.

Synthesis and biological evaluation of new 1,5-diazaanthraquinones with cytotoxic activity

A series of 1,5-diazaanthraquinone derivatives was synthesized and their in vitro cytotoxic activities were evaluated against several human cancer cell lines. The 1,5-diazaanthraquinone chromophore has been synthesized either on the basis of hetero Diels-Alder reactions involving different quinoline-5,8-diones and alpha,beta-unsaturated aldehyde N,N-dimethylhydrazones or by thermolysis of different arylaminomethylene Meldrum's acid derivatives. Some of these compounds showed cytotoxic activity comparable to that of mitoxantrone against most of the cell lines tested. Compounds 20, 30, 31 and 37 were 4-54 times more potent that mitoxantrone against A549, H116, PSN1 and T98G cancer cell lines but, interestingly, they were 3-16 times less potent against the human breast carcinoma SKBR3. Some structure-activity relationships are described, the most significant one being the increase in cytotoxicity resulting from the introduction of a halogen atom at the C-4 position.

A computational tool to optimize ligand selectivity between two similar biomacromolecular targets

Algorithms for a new computer program designed to increase ligand-receptor selectivity between two proteins are described. In this program ligand-receptor selectivity is increased by functional modifications to the ligand so as to increase the calculated binding affinity of it to one protein and/or decrease the calculated binding affinity of it to the other protein. The structure of the ligand is modified by selective replacement of atoms and/or functional groups in silico based on a specific set of steric and/or hydropathic complementarity rules involving atoms and functional groups. Relative binding scores are calculated with simple grid-based steric penalty, hydrogen bond complementarity, and with the HINT score model. Two examples are shown. First, modifying the structure of the ligand CB3717 is illustrated in a number of ways such that the binding selectivity to wild type L. casei thymidylate synthase or its E60Q mutant may be improved. Second, starting with a non-selective lead compound that had been co-crystallized with both plant and mammalian 4-hydroxyphenylpyruvate dioxygenases, new compounds (similar to selective ligands discovered by screening) to improve the selectivity of (herbicidal) inhibitors for the plant enzyme were designed by the program.

Cooperative effects on the formation of intercalation sites

Daunomycin is one of the most important agents used in anticancer chemotherapy. It interacts with DNA through intercalation of its planar chromophore between successive base pairs. The effect of intercalation on structure, dynamics and energetics is the topic of a wealth of scientific studies. In the present study, we report a computational examination of the energetics of the intercalation process. In detail, we concentrate on the energetic penalty that intercalation of daunomycin introduces into DNA by disturbing it from its unbound conformation. For these means, we are analyzing already published molecular dynamics simulations of daunomycin-DNA complexes and present novel simulations of a bisdaunomycin-DNA and a 9-dehydroxydaunomycin-DNA intercalated complex using the MM-GBSA module implemented in the AMBER suite of programs. Using this molecular dynamics based, continuum solvent method we were able to calculate the energy required to form an intercalation site. Consequently, we compare the free energy of the duplex d(CGCGCGATCGCGCG)(2) in the B-form conformation with the respective conformations when intercalated with daunomycin and a bisintercalating analog. Our results show that the introduction of one single intercalation site costs approximately 32 kcal/mol. For double intercalation, or intercalation of the bisintercalator, the respective value for one intercalation site decreases to 27 and 24 kcal/mol, respectively, at a theoretical salt concentration of 0.15 M. This proposes that at least in these cases, a synergistic effect takes place. Although it is well known that intercalation leads to substantial disturbance of the DNA conformation, already performed investigations suggest a lower energetic penalty. Nevertheless to the best of our knowledge the calculations presented here are the most complete ones and consider hydration effects for the first time. The interaction energy between the ligand and the DNA certainly over-compensates this penalty for introducing the intercalation site and thus favors complexation. Such analyses are helpful for the description of allosteric effects in protein ligand binding.