Structure-based drug design: exploring the proper filling of apolar pockets at enzyme active sites

The proper filling of apolar pockets at enzyme active sites is central for increasing binding activity and selectivity of hits and leads in medicinal chemistry. In our structure-based design approach toward the generation of potent enzyme inhibitors, we encountered a variety of challenges in gaining suitable binding affinity from the occupation of such pockets. We summarize them here for the first time. A fluorine scan of tricyclic thrombin inhibitors led to the discovery of favorable orthogonal dipolar C-F...CO interactions. Efficient cation-pi interactions were established in the S4 pocket of factor Xa, another serine protease from the blood coagulation cascade. Changing from mono- to bisubstrate inhibitors of catechol O-methyltransferase, a target in the L-Dopa-based treatment of Parkinson's disease, enabled the full exploitation of a previously unexplored hydrophobic pocket. Conformational preorganization of a pocket at an enzyme active site is crucial for harvesting binding affinity. This is demonstrated for two enzymes from the nonmevalonate pathway of isoprenoid biosynthesis, IspE and IspF, which are pursued as antimalarial targets. Disrupting crystallographically defined water networks on the way into a pocket might cost all of the binding free enthalpy gained from its occupation, as revealed in studies with tRNA-guanine transglycosylase, a target against shigellosis. Investigations of the active site of plasmepsin II, another antimalarial target, showed that principles for proper apolar cavity filling, originally developed for synthetic host-guest systems, are also applicable to enzyme environments.     

Structure rationalization and topology prediction of two-distinct-component organic crystals: the role of volume fraction and interface topology

We consider here small-length-scale crystal structures with two clearly different molecular components (e.g., hydrophobic and hydrophilic). Using a perspective developed by studies on large-length-scale block copolymers and liquid crystals, we focus on the crystalline interface between the two components. We examine four types of two-component crystals: aromatic ammonium carboxylates, aromatic oligo(ethylene oxides), cyclohexylammonium carboxylates, and ether-thioether compounds. Of the 111 crystal structures found in the Cambridge Structure Database (CSD), 108 adopt one of the five generic topologies found in diblock copolymers: spheres, columns, perforated layers, layers, and bicontinuous structures. As in diblock copolymers, a key factor controlling the interfacial topology is shown to be the volume ratio of the two components. When the volume fraction of one component is less than 30% of the whole, more than five-sixths of the examined crystal structures are of columnar or spherical type. For volume fractions between 40 and 50% more than three-quarters are of lamellar or bicontinuous type. We use this model to predict the topologies of small-length-scale two-component crystals. We predict the crystal topolgies of six new crystal structures: three are predicted to be columnar, and the other three, lamellar or bicontinuous. The crystal structures of these systems were then determined by single-crystal X-ray methods. Five of the structures form in topologies consistent with the predictions: three in columns and two in layers. The remaining one forms as a perforated layer instead of the predicted columnar structure. Such predictive accuracy is consistent with the statistics of the CSD investigation.     

The prediction of nucleophilic attacking sites via determinants of ‘active’ frontier and near-frontier orbitals

A method for computing the most favourable initial attacking site for a nucleophile on a transition metal complex is described, and applied to the nucleophilic substitution and addition reactions of fluoromethane, and the cationic complexes [BFe(CO)₃]⁺ (B = C₆H₇ and C₇H₉). The reactions considered are classified according to whether they are frontier or non-frontier orbitally or charge controlled. It is found that initial attack on the (polyenyl)M(CO)₃ cations is always predicted to occur at the M(CO)₃ moiety, in agreement with the experimental observation of intermediates in several such reactions and suggesting that the existence of these species is a general phenomenon.     

Influence of the number of active sites on kinetic characteristics

The possibility for a complicated dependence of the steady-state reaction rate on the total number of catalyst active sites is shown for nonlinear mechanisms.

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Structure and nature of active sites on the surface of pyrogenic titanosilica

The structure and nature of active sites on the surface of pyrogenic titanosilica (TS) have been studied. The new acidic centers on TS surface occur with formation of titanosiloxane bridges, their formation seemed to be a result of combination of basic structural units of SiO₂ (tetrahedron) and TiO₂ (octahedron).     

Study of interlayer water on the active sites of mineral sorbent: Thermal analysis

The programmed heating of montmorillonite samples is accompanied by their dehydration and dehydroxilation, this being registered by means of Derivatograph. The form of the endothermal effects within the 80–250°C interval can be of simple or double character depending on the nature of exchange cations. Though this phenomenon has been known for a long time, no satisfactory explanation has been provided so far. The herewith paper contains the results of bound water researches at various forms (Na, Ca, Al, Fe) of montmorillonite by means of thermal analysis as well as other physico-chemical methods. It has been found that the form of dehydration endoeffects depends on the state of the active centers of the mineral. In certain conditions, by means of thermal analysis one can determine corresponding quantities of bound water that are in agreement with various kinds of active centers of the mineral sorbent.This revised version was published online in November 2005 with corrections to the Cover Date.     

Chemical imaging of terrace-based active sites on gold

Scanning tunneling microscopy data of a mixed monolayer comprised of a 40:60 ratio of H8Si8O12 and C6H13-H7Si8O12 clusters on gold are presented. The images display a composite monolayer surface with well-defined domain regions of the individual components. Holes present at face-centered cubic (fcc) sites of the starting Au/H7Si8O12 adsorbate layer indicate the location of active sites for impinging C6H13-H7Si8O12 clusters. Adsorption of a C6H13-H7Si8O12 cluster likely yields a mobile hydrogen atom available to recombine with and desorb an adjacent H8Si8O12 cluster. Hydrogen atom diffusion along substrate [121] directions is the proposed pattern formation mechanism of the mixed monolayer. Imaging of the spherosiloxane cluster domains identifies a novel terrace-based active site located in the fcc regions of the Au(111) 23 x square root3 surface reconstruction.     

A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites

BACKGROUND: An 18-nucleotide DNA oligomer, PS2.M, derived using an in vitro selection method was previously reported to bind hemin (Fe(III)-protoporphyrinIX) with submicromolar affinity. The DNA-hemin complex exhibited DNA-enhanced peroxidative activity. PS2. M is guanine-rich and requires potassium ions to fold to its active conformation, consistent with its forming a guanine-quaduplex. In investigating the specific catalytic features of PS2.M we tested the peroxidative properties of its RNA version (rPS2.M) as well as that of an unrelated DNA guanine-quadruplex, OXY4. RESULTS: The hemin-binding affinity of rPS2.M was found to be 30-fold weaker than that of PS2.M. The UV-visible spectra and kinetics of enzymatic peroxidation of the RNA-hemin complex, however, were nearly identical to those of its DNA counterpart. Both displayed peroxidase activity substantially greater than those of heme proteins such as catalase and Fe(III)-myoglobin. Kinetic analysis suggested that PS2. M and rPS2.M catalyzed the breakdown of the hemin-hydrogen peroxide covalent complex to products. The hemin complex of folded OXY4 (which bound hemin as strongly as did rPS2.M) had a distinct absorption spectrum and only a minor peroxidase activity above the background level. CONCLUSIONS: The results indicated that it is possible for RNA and DNA of the same sequence to fold to form comparable cofactor-binding sites, and to show comparable catalytic behavior. The results further suggest that only a subset of cofactor-binding sites formed within folded nucleic acids might be able to function as active sites, by providing the appropriate chemical environments for catalysis.     

Simulations of the active transport of a neutral solute based on a kinase-channel-phosphatase topology

Simulations of coupled interactions involving two opposite enzymatic reactions, solute diffusions, and electrostatic interactions between membrane charges and charged solutes were conducted under a fixed kinase-channel-phosphatase (KCP) topology oriented from the outside to the inside of a porous membrane structure. Depending on the kinase and phosphatase locations, we recently demonstrated that an active transport of a phosphorylated substrate may occur via the opposite topology, that is, a PCK topology. The present analysis demonstrates that, under a KCP membrane topology, which also behaves as a specific ATP-dependent transporter, the active transport of a neutral substrate may occur. This analogous active transport appears to be dependent on the phosphatase location and on the membrane surface potentials. A broad analysis of the role played by the main parameters taken into account in the model was conducted in order to define precisely the physico-chemical conditions and the membrane topology needed for the highest active transports within the shortest time.     

Probing the active sites for CO dissociation on ruthenium nanoparticles

The active sites for CO dissociation were probed on mass-selected Ru nanoparticles on a HOPG support by temperature programmed desorption spectroscopy using isotopically labelled CO. Combined with transmission electron microscopy we gain insight on how the size and morphology of the nanoparticles affect the CO dissociation activity. The Ru nanoparticles were synthesized in a UHV chamber by gas-aggregation magnetron sputtering in the size range from 3 to 15 nm and the morphology was investigated in situ by scanning tunneling microscopy and ex situ by high resolution transmission electron microscopy. Surprisingly, it was found that larger particles were more active per surface area for CO dissociation. It is suggested that this is due to larger particles exposing a more rough surface than the smaller particles, giving rise to a higher relative amount of under-coordinated adsorption sites on the larger particles. The induced surface roughness is proposed to be a consequence of the growth processes in the gas-aggregation chamber.     

Nanocrystalline gold and gold-palladium alloy oxidation catalysts: a personal reflection on the nature of the active sites

The discoveries that supported gold nanoparticles are exceptionally efficient catalysts for a whole range of reactions is one of the most surprising revelations in the recent history of chemistry. For many years gold was considered too noble to be chemically interesting. However, when divided to the nano-scale, small gold nanoparticles comprising relatively few atoms, are very efficient in catalysing a range of redox and chemical synthesis reactions. In this perspectives article some of the recent research in this rapidly evolving field is highlighted, and the nature of the active site for oxidation reactions is commented on.     

Investigation of the effect of active diluents on the molecular mobility and topology of cross-linked amine epoxy-adamantane polymers

Using the framework of the concepts about the nature of large-scale mobility of kinetic units, the interconnection between kinetic and structural heterogeneity of molecules of the epoxy polymers based on diglycidyl ester of diphenylolpropane cured with diaminomethyladamantane upon dilution with monofunctional reactive compounds is studied by the example of phenylglycidyl ester. The possibility of controlling the changes in structural heterogeneity of the polymers is shown, which is important for achieving optimal properties of novel materials under development (adhesives, sealants, and so on).     

Structure and nuclearity of active sites in Fe-zeolites: comparison with iron sites in enzymes and homogeneous catalysts

Fe-ZSM-5 and Fe-silicalite zeolites efficiently catalyse several oxidation reactions which find close analogues in the oxidation reactions catalyzed by homogeneous and enzymatic compounds. The iron centres are highly dispersed in the crystalline matrix and on highly diluted samples, mononuclear and dinuclear structures are expected to become predominant. The crystalline and robust character of the MFI framework has allowed to hypothesize that the catalytic sites are located in well defined crystallographic positions. For this reason these catalysts have been considered as the closest and best defined heterogeneous counterparts of heme and non heme iron complexes and of Fenton type Fe(2+) homogeneous counterparts. On this basis, an analogy with the methane monooxygenase has been advanced several times. In this review we have examined the abundant literature on the subject and summarized the most widely accepted views on the structure, nuclearity and catalytic activity of the iron species. By comparing the results obtained with the various characterization techniques, we conclude that Fe-ZSM-5 and Fe-silicalite are not the ideal samples conceived before and that many types of species are present, some active and some other silent from adsorptive and catalytic point of view. The relative concentration of these species changes with thermal treatments, preparation procedures and loading. Only at lowest loadings the catalytically active species become the dominant fraction of the iron species. On the basis of the spectroscopic titration of the active sites by using NO as a probe, we conclude that the active species on very diluted samples are isolated and highly coordinatively unsaturated Fe(2+) grafted to the crystalline matrix. Indication of the constant presence of a smaller fraction of Fe(2+) presumably located on small clusters is also obtained. The nitrosyl species formed upon dosing NO from the gas phase on activated Fe-ZSM-5 and Fe-silicalite, have been analyzed in detail and the similarities and differences with the cationic, heme and non heme homogeneous counterparts have been evidenced. The same has been done for the oxygen species formed by N(2)O decomposition on isolated sites, whose properties are more similar to those of the (FeO)(2+) in cationic complexes (included the [(H(2)O)(5)FeO](2+)"brown ring" complex active in Fenton reaction) than to those of ferryl groups in heme and non heme counterparts.     

Steric effects-II: Relationship between topology and the steric parameter. E's—topology as a tool for the correlation and prediction of steric effects

The steric effect of alkyl groups as characterized by the revised Taft E'_s parameter is analysed using an approach based on the DARC topological system and its PELCO correlation method. This approach involves an analysis of the systemativ variation of E'_s in a topological dequencing of alkyl groups and shows the existence of three regions of distinct behaviour: R I, a “normal” behaviour region (ca 6 E'_s units) in which the contribution of the introduction of successive Me groups to the overall steric effect _{increases monotonically} (groups with 1 to 7 carbons); R II, a region, in which a “levelling” effect is observed, i.e. the contribution diminishes and becomes nil (groups with 8 and 9 carbons); and R III, where this contribution changes sign, “inversion” effect (groups with 10 carbons).Using a series of successive approximations, topological models are developed and tested. The conditions under which the topology may be used to represent the topography (i.e. the real 3-dimensional structure) are considered. The correlation of existing E'_s values and the reliable prediction of experimentally unavailable steric effects are direct consequences of this treatment.     

Enzyme active sites: bioinformatics,architecture, and mechanisms of action

A comparative analysis of the amino acid sequences of some enzymes which comprise superfamilies of enzymes belonging to different classes was carried out. Based on the amino acid sequence alignment for enzymes belonging to different classes with the use of the information entropy as a criterion, the amino acid residues involved in the catalytic portion of the active site are demonstrated to be most conservative. The rating scale for conservativeness of amino acids in enzymes is created. Glycine and aspartic acid are the most commonly occurring conservative amino acids essential for the catalysis. The role of aspartic acid and histidine in the mechanism of molecule activation in the catalytic site is considered using hydrolases as examples. The role of glycine, proline, and cysteine in the structural organization of the active sites is discussed.     

Electrochemical interfaces on chalcogenides: Some structural perspectives and synergistic effects of single-surface active sites

The use of single-atom metals (SAM) as catalysts of energy conversion reactions is a recent topic, which has gained popularity in the last two decades. Transition metal dichalcogenides emerged as important electrocatalysts since it was discovered that their chalcogenide edge sites are active towards the electrocatalytic hydrogen evolution reaction (HER) and could also serve as supports for other metals within the same applications. Currently, several groups have reported a novel metal?chalcogenide arrangement, with the possibility of isolating metals at specific sites on chalcogenides to enhance their properties resulting in a synergistic effect in which both chalcogenide and single-atom metal features are exploited, either as promoters or active sites. Theoretical studies have been the basis of these reports.     

Nature of active sites in the cobalt-zirconium oxide catalyst

The temperature-programmed reduction, powder X-ray diffraction, and oxygen adsorption methods were applied to study the phase composition and the nature of the active surface of the catalyst Co(10%)/ZrO₂. The results of the physicochemical studies were compared with the data on the activity and selectivity of the catalysts in the synthesis of hydrocarbons from CO and H₂. The mechanism for the reduction of the cobalt phases in the Co(10%)/ZrO₂ system was proposed. The main features governing the formation of active sites of the synthesis of high-molecular-weight hydrocarbons were considered.