Examination of the reduced affinity of the thymidylate synthase G52S mutation for FdUMP by ab initio and semi-empirical studies.

BACKGROUND: The G52S mutation in the Arg50 loop of thymidylate synthase leads to decreased binding of FdUMP. It has been suggested that the mutation affects the Arg50 residue (within the Arg50 loop) responsible for binding the phosphate of FdUMP. The binding of the methylguanidinium moiety as a model for Arg50 to a methylphosphate entity as a model for FdUMP was investigated with theoretical calculations, as well as the structure of the Arg50-Thr51-Gly52 tripeptide in comparison with the Arg50-Thr51-Ser52 tripeptide. METHODS: Gaussian-98 and PC Spartan programs were used to perform Hartree-Fock and Post-Hartree-Fock quantum chemical calculations as well as MNDO (semi-empirical calculations). RESULTS: It was found that the strongest binding occurs between the negative methylphosphate ion and methylguanidine. The replacement of Gly52 by Ser52 leads to a significant displacement of Arg50, which may be responsible for the decreased binding to FdUMP. CONCLUSION: The arginine-phosphate binding appears to be geometry dependent. Thus, the displacement of the Arg50 residue, as observed in these calculated models, upon mutation of Gly52 to Ser may contribute to decreased binding of FdUMP to mTS (G52S).

Ab initio studies of the reaction of hydrogen transfer from DNA to the calicheamicinone diradical.

BACKGROUND: The biological activity of enediyne chemotherapeutic (anti-cancer) agents is attributed to their ability to cleave duplex DNA. Part of the reaction of cleavage is the abstraction of hydrogens from the deoxyribose moiety of DNA by the biradical formed via a Bergman rearrangement. METHODS: The mechanism of the reaction of abstraction of two hydrogen atoms from two deoxyribophosphate molecules by the calicheamicinone biradical is studied with ab initio calculations at Hartree-Fock and post-Hartree-Fock level. The Titan program is used to perform the calculations. RESULTS: It is found that the reactions are exothermic and thus thermodynamically reasonable. CONCLUSIONS: The mechanism of DNA cleavage by the enediyne-containing drugs is likely to proceed by the abstraction of the hydrogens from deoxyribose by the biradical formed by the drug. Further studies should determine in which way the modification of the drug's structure would make this reaction even more exothermic and, thus, more likely to occur.

Ab initio calculations on (-)-calicheamicinone and some of its reactions involved in its activation and interaction with DNA.

Ab initio calculations were performed on (-)-calicheamicinone, and on the product (Z or E) of the Michael addition via a reaction with methanethiol. It is found that the sulfur moiety position versus the rest of the molecule is quite flexible. The Michael adduct featuring the carbamate group E to the sulfur moiety is more stable than the Z isomer. The Bergman reaction of the diradical formation is strongly exothermic.

Semi-empirical, ab initio and molecular modeling studies on the DNA binding of a calicheamicinone-polyamide conjugate.

AM1 semi-empirical and ab initio calculations were performed on certain synthetic polyamide conjugates of the aglycone of the minor groove binding antibiotic calicheamicin. Geometry optimized conformations and heats of formation were obtained. The binding of the optimized conformations of the drug to both alternating and non-alternating (AT)n and to (G)n x (C)n sequences were studied and the energies of binding were compared to each other. The results can be utilized in the design of novel enediyne-based drugs.

Ab initio studies of some amino acid residue complexes with 4-mercaptopyridine as a model for thymitaq (AG337), an inhibitor of thymidylate synthase.

The complex formed by isopentane, as a model for the isoleucine residue present in the wild-type thymidylate synthase, with 4-mercaptopyridine as a fragment of the thymidylate synthase inhibitor Thymitaq (AG337) is investigated with ab initio quantum chemical calculations at Hartree-Fock and MP2 levels, using the 3-21G* basis set. The binding energy is compared with the binding energies of 4-mercaptopyridine with amino acid residues found in mutant thymidylate synthase enzymes. As compared with isoleucine, alanine and glycine do not show binding, in agreement with enzyme-inhibition results.

Models of F.H contacts relevant to the binding of fluoroaromatic inhibitors to carbonic anhydrase II.

[formula: see text] Complexes formed between fluorobenzene and N-methylformamide or benzene have been used as models of the interaction of fluoroaromatic drugs with carbonic anhydrase II. These structures have been investigated via ab initio and density functional methods, including HF, B3LYP, and MP2 procedures. The results of the calculations are consistent with the hypothesis, suggested originally by experimental X-ray crystal structures of the drug-receptor complexes, that favorable fluorine-hydrogen interactions affect binding affinity.

Theoretical studies employing an ab initio and molecular modeling combination method on the DNA binding of bis-benzimidazoles designed for bioreductive activation.

Ab initio calculations (Hartree-Fock) using the 3-21G and the STO-3G Gaussian basis sets were performed on synthetic analogues of the minor groove binding bis-benzimidazole Hoechst 33258 designed to be subject to bioreductive activation. Such compounds have been shown experimentally to react with DNA to exhibit sequence dependent inhibition of human placental helicase and display significant anticancer properties. Geometry optimized conformations and energies were derived. The binding of the optimized conformations of the drugs to both alternating and non-alternating (AT)n and to (G)n-(C)n sequences were studied. The energetics of reaction at alternative DNA base sites are calculated and compared.

Theoretical studies using an ab initio and molecular modelling combination method on the binding of sequence recognition altered bis-benzimidazoles to the minor groove of DNA.

Ab initio calculations (Hartree-Fock) using the 3-21G and the STO-3G Gaussian basis sets were performed on synthetic analogues of the minor groove binding bis-benzimidazole Hoechst 33258 designed to exhibit altered sequence recognition. Geometry optimized conformations, energies and distribution of electrostatic charges within the molecule were derived. The binding of the optimized conformations of the drug to both alternating and non-alternating (AT)n and (GC)n sequences were studied.

Quantum chemical studies employing an ab initio combination approach on the binding of the bis-benzimidazole Hoechst 33258 to the minor groove of DNA.

Ab initio calculations (Hartree-Fock) using the 3-21G and the STO-3G Gaussian basis sets were performed on the sequence selective minor groove binding bis-benzimidazole Hoechst 33258. Geometry optimized conformations, energies and distribution of electrostatic charges within the molecule were derived. The binding of the optimized conformations of the drug to both alternating and non-alternating (AT)n sequences was studied.

Ab initio studies of 2,4-diamino triazine and its complexes with ligands: a model for inhibitor-active site interactions of dihydrofolate reductase.

The protonation energies of 2,4-diamino triazine, an inhibitor of the therapeutic target dihydrofolate reductase, has been calculated using ab initio (Hartree-Fock) calculations. It is found that N1 (see Fig. 1) exhibits the highest proton affinity (261.6 kcal/mol) by comparison with other inhibitor protonation sites. The energies of binding of the formate ion and formamide (as models for the amino acid residues in the active site of dihydrofolate reductase) to neutral and protonated 2,4-diamino triazine are also obtained. The highest binding energies are featured by the complex formed from a formate attached to the N4 and N1 protonated forms of the triazine. However, as N4 has a comparatively low proton affinity (195.0 kcal/mol), it is unlikely that an interaction of this nature would prevail. On the other hand, the formate-protonated N1 interaction is similar to the structures identified by X-ray crystallography of enzyme-triazine complexes.

Quantum chemical and molecular mechanics studies on the binding of stereoisomers of the oligopeptide antibiotics amidinomycin and noformycin to the minor groove of B-DNA.

Ab initio calculations (Hartree-Fock) using the 6-31G basis set have been performed on two chiral oligopeptide antitumor antibiotics amidinomycin 5 and noformycin 6. The latter are DNA minor groove binding agents related to the A.T recognizing netropsin 4 and distamycin 3 but, unlike the latter, bear stereocenters (two for 5 and one for 6) that may be expected to affect binding to the B-DNA receptor. Geometry optimized conformations, energies and distribution of electrostatic charges within the molecules were derived. The rotational barrier for bond C3-C6 in 6 was calculated to be ca. 6 kcal.mole-1 and the dipole moment for 6 was 7.69D and for 5 was 5.58D. The ab initio derived parameters of the geometry optimized conformations of the different possible stereoisomeric forms of 5 and 6 were used to interpret their different interactions with the minor groove of DNA at both A.T and G.C sequences and the results were compared with molecular mechanics calculations. The order of binding of the four stereoisomers of 5 at the preferred (A.T)n sequences by both ab initio and molecular mechanics calculations is 1S,3R > RR > RS > SS. The predicted energy differences for complexation with DNA of the other stereoisomers from that of 1S,3R are: RR (4.2%); RS (6.7%) and SS (21.5%). In the case of noformycin the 4R structure binds more effectively than the enantiomer. Considerations of phasing in the computed distances between hydrogen bond donating sites in the DNA-bound antibiotics provide further insight into the binding processes. In the complexes of noformycin 6 the N-N1-N4 and N1-N5 distances (9.05 and 9.15 A respectively for 4R-6 and 9.23 and 9.26 A respectively for 4S-6) are close to the optimum value of 9.1 A for effective binding. In the case of amidinomycin 5 the best agreement with the optimum value occurs with the strongest binding diastereomer 1S,3R (N1-N3 = 8.91, N1-N4 = 9.41 A). The unexpected result, consistent in both ab initio and molecular mechanics treatments, is that, in contrast to the cases of kikumycin 1 and anthelvencin 2, the natural 3S configuration of 5 and 4S of 6 do not confer maximal binding efficiency. This suggests that biogenetic factors in the generation of the oligopeptide antibiotics lead to maximum DNA binding in the cases of kikumycin and anthelvencin but not in the cases of amidinomycin and noformycin.

Ab initio studies of aromatic-aromatic and aromatic-polar interactions in the binding of substrate and inhibitor to dihydrofolate reductase.

Aromatic-aromatic and aromatic-polar interactions are investigated by performing ab initio Hartree-Fock calculations. Binding energies and optimum distances between subsystems are obtained. It is found that the binding energy between two benzene rings is of 3.1 kcal/mol when correlation effects are included, while the serine aromatic complexes energies of binding range from 1.9 to 3.1 kcal/mol.

Amide isosteres of lexitropsins: synthesis, DNA binding characteristics and sequence selectivity of thioformyldistamycin.

The synthesis and properties of an amide isostere of the antibiotic distamycin, thioformyldistamycin 3 is described. Compound 3 exists predominantly in the E conformation of the thioamide group in freshly prepared DMSO solution but is converted into the Z form, predicted by molecular mechanics to be more stable, on standing for 24 h. The coalescence temperature in DMSO is 110 degrees C by 1H-NMR. The thioformyl moiety of 3 is resistant to both peptidase action and acid treatment. Complementary strand MPE footprinting on a EcoRI/Hind III restriction fragment of pBR322 DNA demonstrated that either E or Z forms of 3 give a single set of footprints very similar to that of the parent antibiotic with strongest protection at TAAG and TATTAT with moderately strong protection at ATTT and AAAA. The strength of binding of 3 and distamycin from delta Tm measurements to either poly.d(AT) or calf thymus DNA is comparable. Molecular modeling predicted a preferred conformation for 3 wherein the C = S bond has a torsional angle of 110 degrees with the pyrrole ring. The energy difference between this conformation and the E form is less than 1 kcal/mole. In contrast the E-form has an energy 17.3 kcal/mole greater than the Z and a value of 26.3 kcal/mole was calculated for the energy barrier between the two isomers.

The binding of prototype lexitropsins to the minor groove of DNA: quantum chemical studies.

Ab initio calculations (Hartree-Fock) using the 6-31 G basis set have been performed on two prototype lexitropsins or information-reading molecules. The latter are DNA minor groove binding agents related to the A.T recognizing netropsin in which each of the two N-methylpyrrole moieties is replaced in turn by 1-methylimidazole and which thereby confers the property of recognizing G.C sites.Ab initio treatment was possible by examining composities of separate non-conjugated segments of the molecules. Geometry optimized conformations, energies and distribution of electrostatic charges within the molecules were derived. The ab initio derived parameters of the geometry optimized conformations of these lexitropsins were used to interpret their interaction with different sequences within the minor groove of B-DNA.

Molecular recognition and binding of a GC site-avoiding thiazole-lexitropsin to the decadeoxyribonucleotide d-[CGCAATTGCG]2: 1H-NMR evidence for thiazole intercalation.

The structural and dynamic aspects of the interaction of the thiazole containing lexitropsin (1) with an oligodeoxyribonucleotide were studied by high field 1H-NMR spectroscopy. Complete assignment of the 1H-NMR resonances of lexitropsin 1 was accomplished by 2D-NMR techniques. The complexation-induced chemical shifts and NOE cross peaks in the NOESY map of the 1:1 complex of lexitropsin (1) and d-[CGCAATTGCG]2 reveal that the thiazole ring of the lexitropsin (1) intercalates between dA4.A5 bases and the rest of the ligand resides in the minor groove of the AT rich core of decamer, thus occupying the 5'-AATT sequence on the DNA. Intercalation of the thiazole moiety of the drug has been detected by the presence of intermolecular NOEs both in the major and the minor groove of the decamer helix. The absence of intranucleotide NOEs between base protons and H1'/H2' protons suggested local unwinding of the binding site on the DNA. From COSY and NOESY methods of 2D-NMR, it was established that the N-formyl (amino) terminus of the thiazole lexitropsin (1) is projecting into the major groove towards A5H8 while the amidinium terminus lies in the minor groove towards the T7G8 base pairs of the opposite strand. The expected intranucleotide NOEs confirmed that the decadeoxyribonucleotide in the 1:1 complex exists in a right handed B-conformation. The presence of exchange signals along the binding site 5'-AATT indicated an exchange of the bound drug process wherein the rate of exchange between the two equivalent sites was estimated to be congruent to 130 s-1 at 30 degrees C and with delta G degrees of 62.4 kJ mol-1. Force field and Pi calculations permitted a rationalization of the experimentally observed binding mode in terms of preferred conformation of the ligand and repeat length in lexitropsins compared with the DNA receptor.

Ab initio studies of the decomposition of nitrosourea in the presence of cations.

Self-consistent (Hartree-Fock) calculations of the process of decomposition of protonated and lithiated syn-N-nitrosourea show that the presence of cations perturbs the electron distribution significantly. The decomposition of nitrosourea is facilitated when a proton or lithium ion is positioned at the oxygen of the nitroso group. These results may suggest clinical experimentation with nitrosoureas used in conjunction with lithium salts.

Mechanism of interstrand cross-linking of DNA by anticancer 2-haloethylnitrosoureas.

E and Z-2-haloethyldiazotates, which have been postulated as the ultimate electrophiles responsible for the biological activity of 2-haloethylnitrosoureas (HENUs), have been synthesized and characterized by 15N-nmr. Their stability and solubility in organic solvents are increased by forming crown ether complexes. While E and Z forms are configurationally stable in solution the Z form cyclizes at greater than or equal to -20 degrees C to a 1,2,3-oxadiazoline. The E isomers cross-link DNA, in contrast to the Z isomers. However, both E and Z (2'chloroethyl)thioethyldiazotates (neither of which may cyclize) cross-link DNA extremely efficiently. The cross-linking by these agents is a two-step process and increases with the (G + C) content of the DNA. E-2-chloroethyldiazotate exhibits activity against P388 leukaemia in vivo, lending credence to the suggestion that it is the ultimate electrophile from HENUs. Ab initio calculations predicted the optimized geometry, LUMO energies and atom contributions and the net atomic charges for the diazohydroxides and the HOMO energies and atom contributions for the alternative DNA base sites. An analysis based on Frontier Orbital methods invoking the Hard and Soft Acids and Bases theory permitted an interpretation of the formation of a cross-link site and several modified bases isolated from the reaction of HENUs with DNA.

Isolation and characterization of electrophiles from 2-haloethylnitrosoureas forming cytotoxic DNA cross-links and cyclic nucleotide adducts and the analysis of base site-selectivity by ab initio calculations.

E- and Z-2-haloethyldiazotates--electrophilic species hitherto suggested as intermediates in the reactions of 2-haloethylnitrosoureas (HENUs) under physiological conditions--were synthesized and characterized by 1H-, 15N- and 13C-NMR (nuclear magnetic resonance). They were stabilized and solubilized in organic solvents as their 18-crown-6 ether complexes. Characterization of the Z-2-fluoroethyldiazotate by 19F- and 13C-NMR, and comparison with the Z-2-chloroethyl compound, confirmed facile cyclization to the 1,2,3-oxadiazoline and subsequent decomposition to nitrogen and ethylene oxide. The E-2-haloethyldiazotates form DNA interstrand cross-links at a rate, and to an extent, and with a DNA base dependence, which parallels the behaviour of the parent HENUs, while the Z isomers alkylate DNA but show minimal cross-linking. Both E-and Z-(2'-chloroethyl)thioethyldiazotates, neither of which can undergo cyclization, cross-link DNA efficiently. Self-consistent-field (SCF) ab initio calculations provided optimized geometries, atomic charges and LUMO (Lowest Unoccupied Molecular Orbital) atom contributions for the E- and Z-2-haloethyldiazohydroxides. The HSAB (Hard and Soft Acids and Bases) theory, in conjunction with HOMO (Highest Occupied Molecular Orbital) values on key DNA base sites, accounted for the observed site-selectivity in the formation of identified cross-links produced by 1,3-bis-(2-chloroethyl)-1-nitrosourea. Independent chemical studies on cytosine derivatives corroborated the predicted site selectivity of attack by electrophiles and the formation of ethanocytidine cyclic adducts.

Ab initio studies of the antiviral drug 1-(2-fluoro-2-deoxy-beta-D-arabinofuranosyl) thymine.

The antiviral drug 1-(2-fluoro-2-deoxy-beta-D-arabinofuranosyl) thymine (FMAU) exhibits a high therapeutic index against a number of herpesviruses. As with other drugs which are nucleoside analogs, such as 1-(2-fluoro-2-deoxy-beta-D-arabinofuranosyl)-5-iodocytosine and others, the activity seems to be strongly related to the presence of a fluorine atom in the sugar moiety, in the arabino position. Theoretical calculations, using quantum-chemical methods, are used to elucidate the role of the fluorine in the arabino position and to provide information about the sugar puckering. The results seem to indicate that the fluorine atom prevents the rotation of the base around the sugar-base bond, locking it into an anti structure (Fig. 2,A3) which might be related to its exposure to enzymatic attack. The sugar study confirms the endo position (above the plane) of the C'2 carbon as opposed to the endo position of the C'3 carbon.