Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania

Dihydrofolate reductase has successfully been used as a drug target in the area of anti-cancer, anti-bacterial and anti-malarial chemotherapy. Little has been done to evaluate it as a drug target for treatment of the trypanosomiases and leishmaniasis. A crystal structure of Leishmania major dihydrofolate reductase has been published. In this paper, we describe the modelling of Trypanosoma cruzi and Trypanosoma brucei dihydrofolate reductases based on this crystal structure. These structures and models have been used in the comparison of protozoan, bacterial and human enzymes in order to highlight the different features that can be used in the design of selective anti-protozoan agents. Comparison has been made between residues present in the active site, the accessibility of these residues, charge distribution in the active site, and the shape and size of the active sites. Whilst there is a high degree of similarity between protozoan, human and bacterial dihydrofolate reductase active sites, there are differences that provide potential for selective drug design. In particular, we have identified a set of residues which may be important for selective drug design and identified a larger binding pocket in the protozoan than the human and bacterial enzymes.     

Efforts Toward the Direct Experimental Characterization of Enzyme Microenvironments: Tyrosine100 in Dihydrofolate Reductase

State secrets : Site‐specific deuteration and FTIR studies reveal that Tyr100 in dihydrofolate reductase plays an important role in catalysis, with a strong electrostatic coupling occuring between Tyr100 and the charge that develops in the hydride‐transfer transition state (see picture, NADP⁺ purple, Tyr100 green). However, relaying correlated motions that facilitate catalysis from distal sites of the protein to the hydride donor may also be involved.

     

Comparative structural analysis of a histone-like protein from Spiroplasma melliferum in the crystalline state and in solution

A solution of a histone-like protein from Spiroplasma melliferum (HUSpm) was examined by small-angle X-ray scattering (SAXS). The experimental SAXS curve was compared with those calculated for the HUSpm structures from the PDB databank obtained by both X-ray diffraction analysis and nuclear magnetic resonance spectroscopy. The model of the HUSpm structure in solution, which best agrees with the experimental SAXS data, has a shorter distance between the centers of mass of the HUSpm monomers compared to the crystal structure, indicating that the HUSpm monomers can be located closer to each other in solution than in the crystalline state.     

Mechanism of the cyclization of dimethyl diethynyl silane with selenium tetrabromide: Computational and structural studies, and monitoring

The structure of 2,4-dibromo-2-dibromomethyl-3,3-dimethyl-1-selena-3-silacyclopentene-4, formed by regioselective electrophilic addition of SeBr₄ to dimethyl diethynyl silane, has been determined using X-ray analysis technique. Quantum chemistry methods were used to study elementary stages of the reaction. It was found that the first stage consisted of SeBr₄ conversion into bimolecular complex Br₂?SeBr₂, initiated by dimethyl diethynyl silane. Possible formation of five-membered and six-membered heterocycles involves different cyclization mechanisms. The formation of only five-membered heterocycle is explained by kinetically preferable ring closure through four-center transition state. The conclusions obtained by calculations were confirmed by monitoring of the reaction using ¹H NMR method.     

The chemistry of trityl isoselenocyanate revisited: A preparative and structural investigation

The reaction of trityl chloride with KSeCN gives trityl isoselenocyanate which was structurally characterised by X-ray diffraction. Trityl isoselenocyanate reacts with hydrazine to give trityl selenosemicarbazide and with primary amines to give selenourea derivatives. However, with secondary amines mixtures of selenoureas and substitution products are formed. Trityl selenosemicarbazide undergoes a condensation reaction with salicylaldehyde to give the corresponding trityl selenosemicarbazone. In the case of 2-pyridinecarboxaldehyde, the analogous selenosemicarbazone cannot be isolated, instead a small quantity of the diselenide was isolated from the reaction mixture. The compounds prepared here were fully characterised spectroscopically and several also by X-ray diffraction.     

Tri-n-butyltin carboxylate derivatives of para-substituted phenyl-ethanoic acids: synthesis, characterization and X-ray structure determination

The tributyltin esters of 4-(ethyl)-phenyl-ethanoic acid and 4-(isopropyl)-phenyl-ethanoic acid have been prepared as model compounds of the repeating unit of the related stannylated polystyrenic derivatives. Both the products were fully characterized by proton and carbon NMR two-dimensional techniques. FT-IR spectra show in the solid state carboxylated moieties bridging R₃Sn groups with the metal atom expanding its coordination number, this structure being destroyed in solution. The supramolecular arrangement of the products in the solid state has been investigated by X-ray diffraction, which confirms the pentacoordination at tin in both the products, and indicates a different spatial arrangement of the alkylated aryl groups, as evidenced also by the slightly different thermal properties.     

Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters

The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental ¹⁹F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the ¹⁹F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein–ligand recognition.     

Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations

Solvent effects play a crucial role in mediating the interactions between proteins and their ligands. Implicit solvent models offer some advantages for modeling these interactions, but they have not been parameterized on such complex problems, and therefore, it is not clear how reliable they are. We have studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models. The solvation free energy calculations are more than 10³ faster using the Surface Generalized Born implicit solvent model compared to FEP simulations with explicit solvent. For some of the electrostatic calculations needed to estimate the binding free energy, there is near quantitative agreement between the explicit and implicit solvent model results; overall, the qualitative trends in the binding predicted by the explicit solvent FEP simulations are reproduced by the implicit solvent model. With an appropriate choice of reference system based on the binding of the discharged ligand, electrostatic interactions are found to enhance the binding affinity because the favorable Coulomb interaction energy between the ligand and protein more than compensates for the unfavorable free energy cost of partially desolvating the ligand upon binding. Some of the effects of protein flexibility and thermal motions on charging the peptide in the solvated complex are also considered. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 591–607, 2001     

The asymmetric ONNO complexes of dioxouranium(VI) with N,N-diarylidene-S-propyl-thiosemicarbazones derived from 3,5-dichlorosalicylaldehyde: Synthesis, spectroscopic and structural studies

Two uranyl complexes having the composition [UO₂(L)DMSO] were synthesized using salicyl- and 3,5-dichlorosalicylaldehyde-S-propyl-thiosemicarbazones as starting materials. The S-propyl-thiosemicarbazidato structures in the complexes are N¹-3,5-dichlorosalicylidene-N⁴-salicylidene and N¹-salicylidene-N⁴-3,5-dichlorosalicylidene. The stable solid complexes were characterized by means of elemental analysis, IR and ¹H NMR spectroscopies, and the single crystal X-ray diffraction technique. The two complexes, with the same formula, crystallize in different space groups. In the title complexes, the uranium atom is seven-coordinated in a distorted pentagonal-bipyramidal geometry involving an ONNO donor set of the thiosemicarbazidato ligand and an oxygen atom of a DMSO molecule. The two apical positions of the pentagonal bipyramid are occupied by the two oxygen atoms of the trans-dioxouranium group. The relative orientations of the DMSO and S-propyl groups in both complexes are somewhat different due to different crystal packing.     

Binuclear and polynuclear transition metal complexes with macrocyclic ligands. 2. New macrocyclic Schiff"s base in the reaction of 4-tert-butyl-2,6-diformylphenol with 1,2-diaminobenzene. Synthesis and structural,spectroscopic, and theoretical study

Condensation of 4-tert-butyl-2,6-diformylphenol with 1,2-diaminobenzene in ethanol is accompanied by partial reduction of the azomethine double bonds to form symmetrical macrocyclic Schiff"s base containing the alternating >C=N and >CH—NH fragments. In solution, this compound exists as the only isomer in which two endocyclic hydrogen atoms are bound to the oxygen atoms of the phenol groups and two other endocyclic H atoms are attached to the nitrogen atoms of the CH₂—NH fragments. All endocyclic protons are involved in hydrogen bonding and undergo rapid exchange with each other at room temperature. In the crystal, the planar macrocyclic molecules are arranged in closely packed stacks. The steric hindrances resulting from overlapping of the bulky tert-butyl groups are eliminated through rotation of the molecules with respect to each other in the adjacent layers. Study of the potential energy surface for the Schiff"s base under consideration by the DFT method demonstrated that the structure corresponding to the global minimum is similar to that found in solution. However, the isolated molecule is nonplanar, its macrocycle adopting a ladder conformation. The local minimum on the potential energy surface whose energy is 2.6 kcal mol^–1 higher than that of the global minimum corresponds to the zwitterionic structure in which all four endocyclic hydrogen atoms are attached to the nitrogen atoms and the macrocycle adopts a tub conformation. Flattening of the ring is considered as a consequence of stacking interactions between the molecules in the crystal.     

Acylation of phosphoryl- and thiophosphorylacetonitriles under phase transfer catalysis conditions and the keto-enol tautomerism of phosphorus-substituted acylacetonitriles

A procedure was developed for acylation of phosphoryl- and thiophosphorylacetonitriles under phase transfer catalysis conditions. The reaction in the solid KOH/MeCN system affordedC-acylation products in high yields. In the individual state and in aprotic solvents, these products exist in the enol form (Z isomers) stabilizedvia a strong intramolecular hydrogen bond. In hydroxyl-containing media and in aprotic bipolar solvents, these compounds exist as a mixture of two geometric isomers (E andZ) of the corresponding enols. In this case, theZ isomer exists in two forms, namely, in the cyclic form with an intramolecular hydrogen bond and in the open form stabilized by intermolecular hydrogen bonds with the solvent. The results of X-ray diffraction analysis of both forms ofZ isomers of the compounds containing the phosphoryl and thiophosphoryl groups are discussed. Deceased. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1687–1694, September, 1998.     

1-Methylimidazol-2-yl-functionalized cyclopentadienyl titanium and zirconium complexes. Crystal structure of [η 5:η1-C5H4CPh2CH2-(1-MeC3H2N2)]TiCl3

The new side-chain functionalized cyclopentadienyl ligand LiC₅H₄CPh₂CH₂R (R is 1-methylimidazol-2-yl) as lithium salt 2, the trimethylsilyl derivative Me₃SiC₅H₄CPh₂CH₂R (3), and the ligand in the CH form (4) were prepared starting from 6,6-diphenylfulvene and 1,2-dimethylimidazole lithiated at the 2-Me group (1) and then characterized. The half-sandwich complexes (η⁵:η ¹-C₅H₄CPh₂CH₂R)TiCl₃ (5) and (η⁵:η ¹-C₅H₄CPh₂CH₂R)ZrCl₃ (6) were synthesized. The molecular structure of complex 5 was established by X-ray diffraction. Complexes 5 and 6 exhibit dynamic behavior in solution associated with degenerate interconversion of the pseudo-six-membered metallacycle. For titanium complex 5 in a solvating solvent, a dynamic process due to intramolecular dissociation—coordination of the imidazole fragment was observed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1518–1524, September, 2006.     

Thiocyanate complexes of the group 12 metals with pyridine-2-carboxamide: Synthesis and structural characterization

Three complexes of picolinamide (pyridine-2-carboxamide, pia) and metal thiocyanates, M(SCN)₂, (M = Zn, Cd, Hg), namely two polymorphs of bis(picolinamide-N,O)-bis-(thiocyanato-N)zinc(II) (1a and 1b), catena-[bis(μ-thiocyanato-S,N)-picolinamide-N,O-cadmium(II)] (2) and bis[(μ₂-thiocyanato-S-thiocyanato-S-picolinamide-N,O)mercury(II)] (3) have been prepared and characterized by spectroscopic, thermal and X-ray crystallographic methods. The IR and thermal data correlate with the structures of the complexes in the solid state. The vibration bands of diagnostic value are compared to the values of the free ligands.