Dielectric studies of molecular complexes ofDDT with some compounds of biological interest

The molecular complexation ofDDT (acceptor) with some compounds of biological interest as donors (e.g. indole, 2-methylindole, 3-methylindole, benzene and naphthalene) have been studied using refractive index,Guggenheim and dielectric titration plot methods. The interaction between these donors with solvents (CCl₄ and C₆H₆) have also been observed by calculating _ind through _ind=_sol–_inert. These data have shown that the molecular interaction between polar solutes and non-polar aromatics is governed by dipole-induced dipole electrostatic attraction. The dipole moment obtained due to charge transfer (_DA) has also been calculated and found that its value increases with the increase in the extent of interaction between donor and acceptor. These data support the charge-transfer complex formation hypothesis for the mode of action ofDDT on molecular level.

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Dielektrizitäts-Untersuchungen an Molekülkomplexen von DDT mit einigen biologisch relevanten Verbindungen

Zusammenfassung Es wurden Molekülkomplexe vonDDT (als Acceptor) mit einigen Verbindungen von biologischem Interesse (als Donoren: Indol, 2-Methyl-indol, 3-Methyl-indol, Benzol und Naphthalin) mittels Brechungsindex,Guggenheim-Methode und dielektrischer Titration untersucht. Dipolmomentberechnungen ergaben, daß die intermolekulare Wechselwirkung von einer Anziehung induzierter Dipol-Dipol bestimmt wird; es wurde auch der charge-transfer-Anteil des Dipolmoments abgeschätzt. Alle diese Daten unterstützen die Annahme der charge-transfer-Komplexierung vonDDT.

     

A molecular model for the active site of S-adenosyl-l-homocysteine hydrolase

Summary S-adenosyl-l-homocysteine hydrolase (AdoHcy hydrolase, EC 3.3.1.1.), a specific target for antiviral drug design, catalyzes the hydrolysis of AdoHcy to adenosine (Ado) and homocysteine (Hcy) as well as the synthesis of AdoHcy from Ado and Hcy. The enzyme isolated from different sources has been shown to contain tightly bound NAD⁺.Based on the 2.0 Å-resolution X-ray crystal structure of dogfish lactate dehydrogenase (LDH), which is functionally homologous to AdoHcy hydrolase, and the primary sequence of rat liver AdoHcy hydrolase, we have derived a molecular model of an extended active site for AdoHcy hydrolase. The computational mutation was performed using the software MUTAR (Yeh et al., University of Kansas, Lawrence), followed by molecular mechanics optimizations using the programs AMBER (Singh et al., University of California, San Francisco) and YETI (Vedani, University of Kansas). Solvation of the model structure was achieved by use of the program SOLVGEN (Jacober, University of Kansas); 56 water molecules were explicitly included in all refinements. Some of these may be involved in the catalytic reaction.We also studied a model of the complex of AdoHcy hydrolase with NAD⁺, as well as the ternary complexes of the redox reaction catalyzed by AdoHcy hydrolase and has been used to differentiate the relative binding strength of inhibitors.     

Potentiometric studies on the complex formation of lanthanides with proline and hydroxyproline

The formation of the lanthanide (La, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Lu) complexes with proline and hydroxyproline has been investigated by potentiometric methods as well as by a turbidimetric one which has provided some additional conclusions. It has been found that 11 and a slight amount of 21 complexes are formed. The deviation from the typical course of the formation function is discussed. It is suggested that the perturbations of complex formation in the systems are caused by hydrolysis. The stability constants of the complexes are reported.

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Potentiometrische Untersuchungen an Lanthanid-Komplexen von Prolin und Hydroxyprolin

Zusammenfassung Die Bildung von Lanthanid-Komplexen (La, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Lu) mit Prolin und Hydroxyprolin wurde potentiometrisch und mit Hilfe von Trübungsmessungen untersucht. Es wurde festgestellt, daß sich Komplexe der Zusammensetzung 11 und in kleiner Menge auch 21 bilden. Die Abweichung von typischem Verlauf der Bildungskurven wurde untersucht. Es wurde dabei festgestellt, daß für die Störungen in der Komplexbildung die Hydrolyse verantwortlich ist. Die Stabilitätskonstanten wurden bestimmt.

     

Molecular modeling studies on the urease active site and the enzyme-catalyzed urea hydrolysis

Summary These studies are an attempt to gain better insight into the pharmacophore requirements of urease. On the basis of published information on this enzyme (EXAFS, amino acid sequence, essential groups at the active site) a hypothetical nickel-tripeptide complex, as preliminary substitute for the urease active site was modeled using computer-aided molecular modeling techniques. The results suggest two alternative docking modes of urea and reaction intermediates, corresponding to two different reaction mechanisms. Both binding modes are compatible with the docking of known potent inhibitors such as selected hydroxamic acids and phosphorodiamides. The results can be used to help in the design of new potential inhibitors of urease.     

A fluorine scan of non-peptidic inhibitors of neprilysin: Fluorophobic and fluorophilic regions in an enzyme active site

This article describes the synthesis and in vitro biological affinities of (poly)fluorinated neprilysin inhibitors. Two series of inhibitors with F-substitution of the central benzimidazole platform of the ligands and the benzylic vector to fill the S1’ pocket of NEP were investigated. The S1’ pocket was found to be highly fluorophobic, and F-substitution led to significantly decreased binding affinities of inhibitors. This result is explained by electrostatically unfavorable close contacts of organic fluorine with the negatively polarized π-surfaces of surrounding aromatic amino acid side chains. In contrast, the protein environment around the benzimidazole platform, with three electropositive guanidinium side chains of Arg residues, was found to provide a fluorophilic environment. Overall, the data support that organic fluorine, with its high negative charge density prefers to orient into electropositive regions of receptor sites. pK_a measurements of fluorinated ligands provided several simple patterns for the prediction of pK_a values of benzimidazoles, important building blocks in medicinal chemistry.     

Refractometric studies of molecular complexes ofDDT with some compounds of biological interest

Formation of molecular complexes betweenDDT as acceptor and indole, 2-methylindole, 3-methylindole, benzene and naphthalene as donors have been studied in carbon tetrachloride using refractometric and differential refractometric measurements. Titration techniques through these measurements have indicated11 stoichiometry of these complexes. Equilibrium constants (K ₁) and extent of electronic polarization were calculated. Two types of complexes were observed, one association involving primarily the benzhydryltrichloromethyl grouping ofDDT with a polar complexing agents, and the other interaction of theDDT aromatic -electron system with -electrons of donors in the complexing molecule. These data support the charge-transfer complex formation hypothesis for the mode of action ofDDT on molecular level.

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Refraktometrische Untersuchungen an Molekülkomplexen von DDT mit einigen biologisch relevanten Verbindungen

Zusammenfassung Es wurde die Bildung von Molekülkomplexen zwischenDDT als Acceptor und Indol, 2-Methyl-indol, 3-Methyl-indol, Benzol und Naphthalin als Donor in CCl₄ mittels Refraktometrie und differenzieller Refraktometrie untersucht. Es wurde11-Stöchiometrie der Komplexe festgestellt, Gleichgewichtskonstanten und das Ausmaß der Elektronenpolarisation wurden berechnet. Zwei Typen von Komplexen wurden beobachtet; in einem Fall erfolgt die Assoziation primär über die Benzhydryltrichlormethyl-Gruppierung desDDT, im anderen Fall über -Elektronenwechselwirkungen. Die Daten unterstützen ein chargetransfer-Modell der Komplexbildung vonDDT mit geeigneten Donormolekülen.

     

Spectral studies on the reaction of chromium (VI) compounds with aminophosphonic esters

The studies on reaction of newly obtained aminophosphonic acid diethyl ester derivatives of fluorene with Cr₂O₇ ^2–, CrO₄ ^2–, CrO₃Cl^– and CrO₃ have been investigated using electronic, infrared,Raman and NMR spectral methods. It has been found that the resulting compounds are of the type (AH)₂Cr₂O₇, whereA stands for the organic part of the molecule. The organic cation and solvent effects on the electronic states of pseudotetrahedrally arranged Cr(VI) anions are discussed.

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Spektroskopische Untersuchungen über Reaktionen von Chrom(VI)-Verbindungen mit Aminophosphonsäure-Estern

Zusammenfassung Es wurden Elektronen-, Ultrarot-,Raman- und NMR-spektroskopische Untersuchungen beschrieben, die an neuen Verbindungen durchgeführt wurden, welche als Reaktionsprodukte von Cr₂O₇ ^2–, CrO₄ ^2–, CrO₃Cl^– und CrO₃ mit Aminophosphonsäurediethylesterderivaten von Fluorene synthetisiert worden waren. Es wurde festgestellt, daß diese Verbindungen mit einer allgemeinen Formel (AH)₂Cr₂O₇ beschrieben können werden, in derA den organischen Teil der Verbindungen bedeutet. Der Einfluß des organischen Kations wie auch der von Lösungsmitteln auf die Elektronenzustände des pseudotetraedrischen Cr(VI)-Anions wurde gleichfalls untersucht.

     

Density functional studies of the dipole polarizabilities of the linear polyacenes benzene through nonacene

We report Ab Initio studies of the electric dipole polarizability of the linear polyacene series benzene through nonacene. A number of Ab Initio studies were done at different levels of theory for benzene, with all remaining Ab Initio calculations being at the B3LYP/6-311G(2d, 1p)//B3LYP/6-311+G(2d, 1p) level of theory. We find that the NN tensor component shows a constant increment of 20 atomic units per ring. AM1 and QSAR-quality empirical calculations show poor absolute agreement with the Ab Initio results but given excellent statistical correlation coefficients with the Ab Initio values. This implies that the results of such cheaper calculations can be suitably scaled for predictive purposes.     

Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

The W191G cavity of cytochrome c peroxidase is useful as a model system for introducing small molecule oxidation in an artificially created cavity. A set of small, cyclic, organic cations was previously shown to bind in the buried, solvent-filled pocket created by the W191G mutation. We docked these ligands and a set of non-binders in the W191G cavity using AutoDock 3.0. For the ligands, we compared docking predictions with experimentally determined binding energies and X-ray crystal structure complexes. For the ligands, predicted binding energies differed from measured values by +/- 0.8 kcal/mol. For most ligands, the docking simulation clearly predicted a single binding mode that matched the crystallographic binding mode within 1.0 A RMSD. For 2 ligands, where the docking procedure yielded an ambiguous result, solutions matching the crystallographic result could be obtained by including an additional crystallographically observed water molecule in the protein model. For the remaining 2 ligands, docking indicated multiple binding modes, consistent with the original electron density, suggesting disordered binding of these ligands. Visual inspection of the atomic affinity grid maps used in docking calculations revealed two patches of high affinity for hydrogen bond donating groups. Multiple solutions are predicted as these two sites compete for polar hydrogens in the ligand during the docking simulation. Ligands could be distinguished, to some extent, from non-binders using a combination of two trends: predicted binding energy and level of clustering. In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.     

Small-angle X-ray scattering studies on the X-ray induced aggregation of malate synthase I. Structural and kinetic studies

Small-angle X-ray scattering measurements on malate synthase in aqueous solution revealed a continuous increase of the intensity in the innermost portion of the scattering curve with increasing measuring time. We have definite evidence that this increase reflects an X-ray induced aggregation of the enzyme particles in the course of the small-angle X-ray scattering experiment. Obviously this aggregation is a consequence of a radiation damage of the particles by the primary beam used in the scattering experiment.The aggregation process of malate synthase was monitoredin situ by smallangle X-ray scattering. For this purpose scattering curves were taken at various stages of aggregation. The analysis of these curves established the increase of the particle dimensions, the retention of the pseudo thickness factor of the native enzyme and the occurrence of one and later on of two pseudo cross-section factors. These results suggest the way how the aggregation might proceed. The results led to a tentative model of the aggregation process in which a one-dimensional side-by-side association of the oblate enzyme particles is followed by a two-dimensional aggregation. An aggregation in the third dimension was not observed during the time covered by our experiment.The time dependence of molecular parameters, for instance of the apparent mean radius of gyration, was used to compare the aggregation of enzyme samples that were irradiated under different experimental conditions. The addition of dithiothreitol to the enzyme solutions as well as the presence of the substrates or of a substrate analogue or of ethanol were found to reduce the rate of aggregation.

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Röntgenkleinwinkeluntersuchungen der durch Röntgenstrahlen induzierten Aggregation der Malatsynthase. I. Strukturuntersuchungen und kinetische Messungen

Zusammenfassung Röntgenkleinwinkeluntersuchungen an wäßrigen Lösungen von Malatsynthase zeigten eine mit der Meßdauer ansteigende Zunahme der Streuintensität im Innenteil der Streukurve. Dieser Intensitätsanstieg spiegelt zweifelsohne eine durch die Röntgenbestrahlung induzierte Aggregation der Enzymteilchen während der Röntgenkleinwinkelmessung wider. Diese Aggregation ist offensichtlich auf einen durch die Primärstrahlung verursachten Strahlenschaden zurückzuführen.Das Fortschreiten der Aggregation der Malatsynthase wurde mit Hilfe der Röntgenkleinwinkelstreuungin situ verfolgt. Zu diesem Zweck wurden Streukurven bei verschiedenen Aggregationsstadien aufgenommen. Die Analyse dieser Kurven zeigte die Zunahme der Teilchendimensionen, das Beibehalten des Pseudodickenfaktors des nativen Enzyms und das Auftreten eines und später zweier Pseudoquerschnittsfaktoren an. Diese Ergebnisse lieferten Hinweise, wie die Aggregation ablaufen könnte, und führten zu einem möglichen Modell für den Aggregationsvorgang. Demnach sollte auf eine eindimensionale, laterale Aggregation der oblaten Enzymteilchen eine zweidimensionale Aggregation folgen. Ein Fortschreiten der Aggregation in der dritten Dimension konnte während der Dauer des Experimentes nicht beobachtet werden.Die zeitliche Abhängigkeit molekularer Parameter, z. B. des apparenten mittleren Streumassenradius, wurde für den Vergleich der Aggregation von Enzymproben, die unter verschiedenen experimentellen Bedingungen bestrahlt wurden, herangezogen. Durch Zugabe von Dithiothreitol oder Ethanol zu den Enzymlösungen oder durch die Anwesenheit der Substrate oder eines Substratanalogen konnte die Aggregationsgeschwindigkeit herabgesetzt werden.

     

Dehydrogenation studies of dihydronicotinamide adenine dinucleotide (NADH) with methylene blue in the presence of the copper hexcyanoferrate(II) complex and light

The effects of copper ferrocyanide and light on the dehydrogenation rate of NADH by methylene blue is studied. The results suggest that the dehydrogenation rate of NADH with methylene blue is enhanced by copper ferrocyanide. Light also affects the reaction rate.     

Physico-chemical studies on the chelation behaviour of biologically active 2-hydroxy-1-naphthaldehyde semicarbazone (HNAS) with some lanthanons

Summary The chelation behaviour of the complexes of La³⁺, Ce³⁺, Pr³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Y³⁺, Tb³⁺, Dy³⁺, Ho³⁺ with biologically active 2-Hydroxy-1-naphthaldehyde semicarbazone (HNAS) has been studied potentiometrically in 75% (v/v) dioxane-water medium at various ionic strengths. The method of Bjerrum and Calvin, as modified by Irving and Rossotti has been used to find out the values of n andpL. The formation constants of metal chelates and the values ofS _min have been calculated. The order of formation constants of chelates was found to be: La³⁺3+3+3+3+3+3+3+3+3+3+.

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Physikochemische Untersuchungen zur Komplexierung von biologisch aktivem 2-Hydroxy-1-naphthaldehyd-Semicarbazon (HNAS) mit Lanthanoiden

Zusammenfassung Das Chelierungsverhalten von La³⁺, Ce³⁺, Pr³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Y³⁺, Tb³⁺, Dy³⁺ und Ho³⁺ mit 2-Hydroxy-1-naphthaldehydsemicarbazon (HNAS) wurde potentiometrisch in 75% (v/v) Dioxan-Wasser bei verschiedenen Ionenstärken untersucht. Die Werte für n undpL wurden nach der Methode von Bjerrum und Calvin in der Modifikation von Irving und Rossotti bestimmt. Die Komplexbildungskonstanten der Metallchelate und die WerteS _min wurden ermittelt. Die Reihung der Komplexbildungskonstanten war La³⁺3+3+3+3+3+3+3+3+33+.

     

Efficient identification of inhibitors targeting the closed active site conformation of the HPRT from Trypanosoma cruzi

Background: Currently, only two drugs are recommended for treatment of infection with Trypanosoma cruzi, the etiologic agent of Chagas’ disease. These compounds kill the trypomastigote forms of the parasite circulating in the bloodstream, but are relatively ineffective against the intracellular stage of the parasite life cycle. Neither drug is approved by the FDA for use in the US. The hypoxanthine phosphoribosyltransferase (HPRT) from T. cruzi is a possible new target for antiparasite chemotherapy. The crystal structure of the HPRT in a conformation approximating the transition state reveals a closed active site that provides a well-defined target for computational structure-based drug discovery.Results: A flexible ligand docking program incorporating a desolvation correction was used to screen the Available Chemicals Directory for inhibitors targeted to the closed conformation of the trypanosomal HPRT. Of 22 potential inhibitors identified, acquired and tested, 16 yielded K_i’s between 0.5 and 17 μM versus the substrate phosphoribosylpyrophosphate. Surprisingly, three of eight compounds tested were effective in inhibiting the growth of parasites in infected mammalian cells.Conclusions: This structure-based docking method provided a remarkably efficient path for the identification of inhibitors targeting the closed conformation of the trypanosomal HPRT. The inhibition constants of the lead inhibitors identified are unusually favorable, and the trypanostatic activity of three of the compounds in cell culture suggests that they may provide useful starting points for drug design for the treatment of Chagas’ disease.     

A theoretical study of Zn++ interacting with models of ligands present at the thermolysin active site

Summary The binding energy and the geometrical arrangements of the complexes formed by the zinc dication with OH^–, one, four, five or six water molecules, SH^–, H₂S, formic acid, the formate anion, imidazole, its anion and formamide are calculated using the MNDO method. The comparison of the results obtained with those of ab initio computations on the same complexes induced us to propose for Zn⁺⁺ a set of parameters different from the one determined by Dewar for the neutral metal atom. Using the two MNDO parametrizations, similar calculations are carried out for Zn⁺⁺ interacting with two molecules of 2-aminoethanethiol and with models of the four ligands which are present at the thermolysin active site, in order to evaluate the possibilities and limitations of this semiempirical method for theoretical studies concerning zinc metalloenzymes. In the last case, the results obtained suggest that, in the crystal state, the water molecule could be deprotonated. This finding is discussed in relation with the mechanism of action of the enzyme which has been proposed.This laboratory is part of UA 506 of the C.N.R.S.     

Solvation of the active site of cytochrome P450-cam

Summary Energetically favorable water binding sites in the substrate pocket of cytochrome P450-cam have been predicted by a molecular mechanics method. Binding sites corresponding to all the experimentally observed water sites in this region of the enzyme were located. The calculations also indicate the presence of two further water binding sites. One of these is located in a hydrophobic region of the protein where a water molecule would not bind tightly to the substrate-free enzyme. However, in the substrate-bound enzyme, a water molecule in this region could donate a hydrogen bond of optimum geometry to the carbonyl oxygen atom of the camphor substrate and could therefore contribute to the correct positioning of the comphor substrate for 5-exo-hydroxylation. These calculations also suggest that a steric analogue of camphor, containing an alkyl group which could prevent a water molecule from binding in this region, might inhibit cytochrome P450-cam by forming a more stable enzyme-ligand complex than camphor itself.     

Thermodynamics of the isopropanol/n-hexane and isopropanol/n-heptane systems part II. NMR studies

The nuclear magnetic resonance spectra of the systems isopropanol/n-hexane and isopropanol/n-heptane are recorded to deduce thermodynamic functions. A discussion ofSaroléa-Mathot's methods follows.Für die im Titel genannten Systeme werden aus den NMR-Spektren thermodynamische Funktionen abgeleitet. Eine Diskussion derSaroléa-Mathot-Methode wird präsentiert.

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Zur Thermodynamik des Isopropanol/n-Hexan und Isopropanol/n-Heptan Systems, II. NMR-Untersuchungen

     

A molecular model of the folate binding site of Pneumocystis carinii dihydrofolate reductase

Summary The inhibition of Pneumocystis carinii dihydrofolate reductase (DHFR) continues to be the major treatment strategy for P. carinii pneumonia (PCP). The design of new anti-pneumocystis agents would be significantly enhanced by the availability of a 3D model of the methotrexate (MTX) binding site of the P. carinii DHFR. However, an X-ray crystal structure of the P. carinii DHFR is not yet available. Alignment of the amino acid sequences of P. carinii and Lactobacillus casei DHFRs indicates that the two proteins show approximately 80% homology among MTX binding-site residues. This high level of homology suggests that the L. casei DHFR MTX binding-site structure could serve as a structural template in developing a model of the P. carinii DHFR MTX binding site. Therefore, the X-ray crystal structure of L. casei DHFR was used to develop a 3D model of the methotrexate binding site of P. carinii DHFR. The molecular modeling and dynamics software QUANTA/CHARMm was used. Amino acid residue mutations and deletions were performed using QUANTA and macromolecular minimizations were achieved with CHARMm. The MTX binding-site residues of L. casei DHFR were mutated to the corresponding residues of the P. carinii DHFR sequence. The resulting structure was extensively minimized. The resulting P. carinii MTX binding-site model showed significant differences in hydrogen-bonding patterns from the L. casei MTX binding site. Also, the P. carinii site is more hydrophobic than the corresponding L. casei site. Analysis of atom-to-atom close contacts between methotrexate and protein binding-site residues indicates that the P. carinii MTX binding-site complex is primarily stabilized by hydrophobic interactions, while the L. casei complex is mostly stabilized by electrostatic interactions. The model is consistent with the observed increased sensitivity of P. carinii DHFR to lipid-soluble inhibitors and provides a rational basis for the design of new anti-pneumocystis agents.     

Thermodynamics of the isopropanol/n-hexane and isopropanol/n-heptane systems. Part I. Infrared studies

The association equilibria for different conglomerates are calculated for the isopropanol/n-Hexane, isopropanol/n-Heptane systems from the infrared spectra.

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Zur Thermodynamik des Isopropanol/n-Hexan und Isopropanol/n-Heptan Systems, I. Untersuchungen mittels IR-Spektroskopie

Zusammenfassung Es werden die Assoziationsgleichgewichte für verschiedene Konglomerate im Isopropanol/n-Hexan- bzw.-/n-Heptan-System aus den IR-Spektren abgeleitet.

     

Synthesis and studies of organic nitrates of the heterofunctional series

N-Nicotinoyltris(hydroxymethy)aminomethane trinitrate hydronitrate, an analog ofN-nicotinoylethanolamine nitrate (the active principle of the antianginal drug nicorandil), was prepared byO-nitration of the corresponding triol with concentrated HNO₃. The structure of the reaction product was established by X-ray structural analysis. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2224–2227, December, 1997.