Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement

The oxy-Cope rearrangement reaction in the antibody AZ28 is investigated using ab initio molecular orbital calculations and molecular mechanical molecular dynamics simulations. This antibody, AZ28, is known as one of the few systems where the mature catalytic antibody shows a negative correlation between the transition state analogue (TSA) binding affinity and the catalytic rate of the oxy-Cope rearrangement compared to the germ line catalytic antibody. The ab initio optimized structure shows that the transition state structure has a more planar configuration than the TSA. The favorable electrostatic interactions between AZ28 and the transition state analogue overcome the unfavorable van der Waals interactions; thus, AZ28 shows higher binding affinity for the TSA than the germ line. However, the AZ28 is not flexible enough to accept the relatively planar transition state structure. Because the lower flexibility causes poorer antibody-hapten interaction energies, the activation free energy of the oxy-Cope rearrangement becomes larger in the mature antibody than the germ line. We show that the differences in flexibility between the germ line and the mature form and the differences in structure between TSA and the transition state are the origin of the negative correlation in AZ28-catalyzed oxy-Cope rearrangement. The mutation of residue 34 of the light chain, 34(L), affects the binding free energies through the interresidue interaction because it is the closest to the hapten among the six mutatable residues. However, it does not affect the negative correlation.     

Production and characterization of monoclonal antibodies against urea derivatives

A panel of monoclonal antibodies was generated against the ureabased haptenN-(2-N-chloroacetylaminobenzyl)-N′-4-chlorophenylurea as a tool for building up sensitive immune assays to detect urea derivatives and to screen them for catalytic antibodies (Abs). Eleven hybridomas were obtained that produced Abs reactive to the hapten. All Abs were of IgG class. Crossreactivities of the Abs to different haptens were examined, especially to a possible transition-state analog. Only four of the hybridomas (R2-DA10/F7, R2-GE7/H2, R2-HC2/A5, R2-HD6/F7) produced Abs crossreactive with the transition-state analog. From the 11 hybridomas, hybridoma B76-BF5 was chosen for further characterization. Compared to the other Abs, B76-BF5 showed the strongest binding and had a rather restricted specificity. These Abs could be used to build up a sensitive enzyme immunoassay for the detection of the hapten. All Abs were screened for crossreactivity with the pesticides monuron and diuron. No reactivity could be detected. In addition, the nucleotide sequences of the variable light and heavy chain genes of the similarly reactive Abs B76-BF5, B76-BB3, R2-DA10/F7, and R2-GA6/G3 were determined to clarify whether structure and binding specificity of these Abs showed any correlation.     

A spectroscopic study of the inclusion of azulene by beta- and gamma-cyclodextrins

The inclusion of azulene (AZ) inside the cavities of beta-cyclodextrin (beta-CD) and gamma-cyclodextrin (gamma-CD) was studied using absorption, fluorescence and induced-circular dichroism spectroscopy. The inclusion of AZ into the cavity of beta-CD has a stoichiometry of 1:1, whereas that of AZ/gamma-CD complex is 1:2. The equilibrium constants for the formation of the two complexes were calculated to be 780+/-150 M(-1) for AZ:beta-CD and (4.5+/-0.86)x10(5) M(-2) for AZ:(gamma-CD)(2). The latter is due to a stepwise equilibrium mechanism in which a 1:1 complex is formed with a binding constant of 775 M(-1), followed by the formation of a 1:2 complex with a binding constant of 580 M(-1). The difference between the two binding constant values is slight, indicating an almost equal contribution from each of the gamma-CD molecules to the overall binding in AZ:(gamma-CD)(2). From the induced-circular dichroism spectra, the inclusion of AZ was found to be axial in AZ:beta-CD and nearly axial in AZ:(gamma-CD)(2).     

Theozyme for antibody aldolases. Characterization of the transition-state analogue

A theozyme for antibody aldolases has been studied at the MP2/6-31G** computational level. Formation of two cooperative hydrogen-bonds between the acidic hydrogen atoms of the enamine and of a methanol molecule with the oxygen atom of the aldol acceptor markedly favors the C-C bond-formation associated with the aldol reaction. A comparative analysis of the geometry, the charge distribution and the shape of the molecular electrostatic potential of the transition structure (TS) with the covalent adduct, resulting from the reaction of methylamine and the beta-diketone used as a hapten allows us to characterize the transition-state analogue (TSA) generated at immunization. This finding allows us to propose a hapten based on a chiral beta-ketosulfoxide that could give the formation of a TSA that addresses the tetrahedral geometry of the TS.     

Binding position of azathioprine with bovine serum albumin determined by measuring nuclear magnetic resonance relaxation time.

The interaction between azathioprine (AZ) and bovine serum albumin (BSA) is mainly due to hydrophobic binding according to the dependence of the binding constant on the ionic strength obtained by equilibrium dialysis. The binding constant and partition coefficient of AZ were smaller than those of warfarin, phenylbutazone and ibuprofen. Little variation in the proton chemical shift of AZ was observed whether there was an absence or presence of BSA (7.25 x 10(-5) M). The spin-lattice relaxation time (T1) of AZ decreased in the presence of BSA to 6-22%. The spin-spin relaxation rate (1/T2) of AZ increased 16-24 times for the methyl group and the imidazole ring and 8-13 times for the purine ring in the presence of BSA. The ratio of the spin-spin relaxation rate of the free AZ to the bound AZ ((1/T2)b/(1/T2)f) of the methyl group and the imidazole ring was 2-3 times larger than that of the purine ring. The binding of AZ to BSA was concluded to be mainly at the methyl group on the imidazole ring of AZ.     

Appended corrole manganese complexes:Catalysis and axial-ligand effect

A series of N-base appended corroles and their manganese complexes were synthesized and their binding constants with three different nitrogenous ligands, triethylamine, N-methylimidazole and pyridine, were evaluated by spectroscopy. Kinetic studies indicated that the presence of appended N- donor ligands may cause a significant enhancement of the rate of oxygen atom transfers （OAT） from （oxo）manganese（V） corrole to alkene, and the stronger axial ligand binding has impact on the rate of the oxidation reaction. Turnover frequency （TOF） for the catalytic oxidation of alkenes by appended manganese corroles varies with the following ligand order： acetamido 〈 pyridyl 〈 imidazolyl. The influence of the external axial ligands on the catalytic epoxidation was investigated by using appended acetamido manganese corrole as catalyst, with the results revealing that N-methylimidazole gave the best enhancement on the yields of total oxidation products among the investigated nitrogenous ligands.     

The effect of the axial ligand on distinct reaction tunneling for methane hydroxylation by nonheme iron(iv)-oxo complexes

Comprehensive density functional theory computations on substrate hydroxylation by a range of nonheme iron(iv)-oxo model systems [Fe(IV)(O)(NH(3))(4)L](+) (where L = CF(3)CO(2)(-), F(-), Cl(-), N(3)(-), NCS(-), NC(-), OH(-)) have been investigated to establish the effects of axial ligands with different degrees of electron donor ability on the reactivity of the distinct reaction channels. The results show that the electron-pushing capability of the axial ligand can exert a considerable influence on the different reaction channels. The σ-pathway reactivity decreases as the electron-donating ability of the axial ligand strengthens, while the π-pathway reactivity follows an opposite trend. Moreover, the apparently antielectrophilic trend observed for the energy gap between the triplet π- and quintet σ-channel (ΔG(T-Q)) stems from the fact that the reaction reactivity can be fine-controlled by the interplay between the exchange-stabilization benefiting from the (5)TS(H) relative to the (3)TS(H) by most nonheme enzymes and the destabilization effect of the orbital by the anionic axial ligand. When the former counteracts the latter, the quintet σ-pathway will be more effective than the other alternatives. Nevertheless, when the dramatic destabilization effect of the orbital by a strong binding axial σ-donor ligand like OH(-) counteracts but does not override the exchange-stabilization, the barrier in the quintet σ-pathway will remain identical to the triplet π-pathway barrier. Indeed, the axial ligand does not change the intrinsic reaction mechanism in its respective pathway; however, it can affect the energy barriers of different reaction channels for C-H activation. As such, the tuning of the reactivity of the different reaction channels can be realised by increasing/decreasing the electron pushing ability.     

A virtual screening approach for thymidine monophosphate kinase inhibitors as antitubercular agents based on docking and pharmacophore models

Docking and pharmacophore screening tools were used to examine the binding of ligands in the active site of thymidine monophosphate kinase of Mycobacterium tuberculosis. Docking analysis of deoxythymidine monophosphate (dTMP) analogues suggests the role of hydrogen bonding and other weak interactions in enzyme selectivity. Water-mediated hydrogen-bond networks and a halogen-bond interaction seem to stabilize the molecular recognition. A pharmacophore model was developed using 20 dTMP analogues. The pharmacophoric features were complementary to the active site residues involved in the ligand recognition. On the basis of these studies, a composite screening model that combines the features from both the docking analysis and the pharmacophore model was developed. The composite model was validated by screening a database spiked with 47 known inhibitors. The model picked up 42 of these, giving an enrichment factor of 17. The validated model was used to successfully screen an in-house database of about 500,000 compounds. Subsequent screening with other filters gave 186 hit molecules.     

Molecular Docking,Molecular Dynamics Simulations,Computational Screening to Design Quorum Sensing Inhibitors Targeting LuxP of <Emphasis Type="Italic">Vibrio harveyi</Emphasis> and Its Biological Evaluation

Quorum sensing (QS) plays an important role in the biofilm formation, production of virulence factors and stress responses in Vibrio harveyi. Therefore, interrupting QS is a possible approach to modulate bacterial behavior. In the present study, three docking protocols, such as Rigid Receptor Docking (RRD), Induced Fit Docking (IFD), and Quantum Polarized Ligand Docking (QPLD) were used to elucidate the binding mode of boronic acid derivatives into the binding pocket of LuxP protein in V. harveyi. Among the three docking protocols, IFD accurately predicted the correct binding mode of the studied inhibitors. Molecular dynamics (MD) simulations of the protein-ligand complexes indicates that the inter-molecular hydrogen bonds formed between the protein and ligand complex remains stable during the simulation time. Pharmacophore and shape-based virtual screening were performed to find selective and potent compounds from ChemBridge database. Five hit compounds were selected and subjected to IFD and MD simulations to validate the binding mode. In addition, enrichment calculation was performed to discriminate and separate active compounds from the inactive compounds. Based on the computational studies, the potent Bicyclo [2.2.1] hept-5-ene-2,3-dicarboxylic acid-2,6-dimethylpyridine 1-oxide (ChemBridge_5144368) was selected for in vitro assays. The compound exhibited dose dependent inhibition in bioluminescence and also inhibits biofilm formation in V. harveyi to the level of 64.25 %. The result from the study suggests that ChemBridge_5144368 could serve as an anti-quorum sensing molecule for V. harveyi.     

Pd-catalyzed inter- and intramolecular carbene transfer from group 6 metal-carbene complexes.

The use of group 6 metal-carbene complexes in inter- and intramolecular carbene transfer reactions has been studied. Thus, pentacarbonyl[(aryl)(methoxy)carbene]chromium(0) and tungsten complexes, 10, efficiently dimerize at room temperature in the presence of diverse Pd(0) and Pd(II)/Et(3)N catalysts. The effect of additives (PPh(3), AsPh(3), or SbPh(3)) on the nature and the isomeric ratio of the reaction products is negligible. The nature of the reaction products is more catalyst-dependent for metal carbenes 12 bearing alkyl groups attached to the carbene carbon. In these cases, either carbene ligand dimerization or beta-hydrogen elimination reactions are observed, depending on the catalyst. The carbene ligand dimerization reaction can be used to prepare conjugated polyenes, including those having metal moieties at both ends of the polyene system, as well as enediyne derivatives. The intramolecular carbene ligand dimerization of chromium bis-carbene complexes 28 and 30 allows the preparation of mono- and bicyclic derivatives, with ring sizes from six to nine members. For bis-carbene derivatives the beta-hydrogen elimination reaction is inhibited, provided that both metal centers are tethered by an o-xylylene group. Other alkyl complexes 32 form new mononuclear carbene complexes 37 or decompose to complex reaction mixtures. The results obtained in these reactions may be explained by transmetalation from Cr(0) to Pd(0) and the intermediacy of Pd-carbene complexes. Aminocarbene-chromium(0) complexes 15, need harsher reaction conditions to transfer the carbene ligand, and this transfer occurs only in the presence of deactivated olefins. The corresponding insertion/hydrolysis products 48 resulted in these cases. A catalytic cycle involving transmetalation from a chromacyclobutane to a palladacyclobutane is proposed to explain these results.     

Hydrolysis of organophosphorus nerve agent soman by the monoclonal antibodies elicited against an oxyphosphorane hapten.

The antibody-mediated hydrolysis of the nerve agent O-1,2,2-trimethylpropyl methylphosphonofluoridate (soman) 1 has now been established with two monoclonal antibodies raised against the cyclic pentacovalent methyloxyphosphorane hapten 10 that mimics the pentacoordinated trigonal bipyramidal transition-state of the reaction. The hydrolysis reaction was studied using molecular orbital methods at the MP2/6-31 + G*/(/)HF/6-31 + G* level of accuracy. According to the ab initio calculations, the reaction seems to proceed via three separate transition-states. The calculations are in good agreement with the experimental results. The 1,3-dioxabenzophosphole hapten 10 was synthesized, coupled to the carrier protein and the antibodies were obtained by the hybridoma technique. Two antibodies, DB-108P and DB-108Q were found to enhance the rate of soman hydrolysis and they were kinetically characterised.     

Vectorized ferrocenes with estrogens and vitamin D2: synthesis, cytotoxic activity and docking studies

Three ferrocene complexes vectorized with estrogens and vitamin D(2) were synthesized and fully characterized by spectroscopic, electrochemical and computational methods. The synthesis of these esters was accomplished by reacting ferrocenoyl chloride with the corresponding ROH groups (R = ergocalciferol, estradiol, estrone). The cytotoxicity of these complexes in HT-29 colon cancer and MCF-7 breast cancer cell lines was investigated in vitro. Only ferrocenoyl 17β-hydroxy-estra-1,3,5(10)-trien-3-olate showed good cytotoxic activity in both cell lines, exceeding those of ferrocenium and ferrocene. In MCF-7, ferrocenoyl 17β-hydroxy-estra-1,3,5(10)-trien-3-olate exhibited remarkable IC(50), in the low micromolar range. This may be attributed to the presence of the estradiol vector. Docking studies between alpha-estrogen receptor ligand binding site and ferrocenoyl 17β-hydroxy-estra-1,3,5(10)-trien-3-olate revealed some key hydrophobic interactions that might explain the cytotoxic activity of this ester.     

Enantioselectivity in Ruthenium-Catalyzed Propargylic Substitution Reactions of Propargylic Alcohols with Acetone: A DFT Study

The enantioselectivity in the propargylic substitution reactions of propargylic alcohols with acetone catalyzed by optically active thiolate-bridged diruthenium complexes was examined via ωB97X-D level DFT calculations. Some structures with intramolecular dispersion interactions between ligands were found for the ruthenium-allenylidene complex, which is the key intermediate in the catalytic reaction, and it was determined that the structure corresponding to the X-ray crystal structure, which had provided the transition state model for the enantioselectivity in previous studies, was not the most stable among the obtained structures. Then, a variety of transition-state structures for the nucleophilic attack of prop-1-ene-2-ol, which is the enol isomer of acetone, on the γ-carbon of the ruthenium-allenylidene complex were explored. Among the transition-state structures with lower energies, the number of structures leading to the major (R) product was found to be larger than that of structures leading to the minor (S) product, providing enantioselectivity in terms of probability distributions. The introduction of a phenyl group in the thiolate ligand was suggested to increase the selectivity. Thus, we propose the novel transition state model for the asymmetric catalytic reaction system.     

Effect of the axial ligand on the reactivity of the oxoiron(IV) porphyrin π-cation radical complex: higher stabilization of the product state relative to the reactant state

The proximal heme axial ligand plays an important role in tuning the reactivity of oxoiron(IV) porphyrin π-cation radical species (compound I) in enzymatic and catalytic oxygenation reactions. To reveal the essence of the axial ligand effect on the reactivity, we investigated it from a thermodynamic viewpoint. Compound I model complexes, (TMP(+?))Fe(IV)O(L) (where TMP is 5,10,15,20-tetramesitylporphyrin and TMP(+?) is its π-cation radical), can be provided with altered reactivity by changing the identity of the axial ligand, but the reactivity is not correlated with spectroscopic data (ν(Fe═O), redox potential, and so on) of (TMP(+?))Fe(IV)O(L). Surprisingly, a clear correlation was found between the reactivity of (TMP(+?))Fe(IV)O(L) and the Fe(II)/Fe(III) redox potential of (TMP)Fe(III)L, the final reaction product. This suggests that the thermodynamic stability of (TMP)Fe(III)L is involved in the mechanism of the axial ligand effect. Axial ligand-exchange experiments and theoretical calculations demonstrate a linear free-energy relationship, in which the axial ligand modulates the reaction free energy by changing the thermodynamic stability of (TMP)Fe(III)(L) to a greater extent than (TMP(+?))Fe(IV)O(L). The linear free energy relationship could be found for a wide range of anionic axial ligands and for various types of reactions, such as epoxidation, demethylation, and hydrogen abstraction reactions. The essence of the axial ligand effect is neither the electron donor ability of the axial ligand nor the electron affinity of compound I, but the binding ability of the axial ligand (the stabilization by the axial ligand). An axial ligand that binds more strongly makes (TMP)Fe(III)(L) more stable and (TMP(+?))Fe(IV)O(L) more reactive. All results indicate that the axial ligand controls the reactivity of compound I (the stability of the transition state) by the stability of the ground state of the final reaction product and not by compound I itself.     

Photoinduced axial ligation and deligation dynamics of nonplanar nickel dodecaarylporphyrins

The ground- and excited-state metal-ligand dynamics of nonplanar nickel(II) 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (NiDPP) and two fluorinated analogues (NiF(20)DPP and NiF(28)DPP) have been investigated using static and time-resolved absorption spectroscopy in toluene and in ligating media that differ in basicity, aromaticity, and steric encumbrance. Because of the electronic and steric consequences of nonplanarity, NiDPP does not bind axial ligands in the ground state, but metal coordination does occur after photoexcitation with multistep dynamics that depend on the properties of the ligand. Following the structural relaxations that occur in all nickel porphyrins within approximately 10 ps, ligand binding to photoexcited NiDPP is progressively longer in pyridine, piperidine, and 3,5-lutidine (25-100 ps) but does not occur at all in 2,6-lutidine in which the ligating nitrogen is sterically encumbered. The transient intermediate that is formed, which nominally could be either a five- or six-coordinate species, also has a ligand-dependent lifetime (200-550 ps). Decay of this intermediate occurs partially via ligand release to re-form the uncoordinated species, in competition with binding of the second axial ligand and/or conformational/electronic relaxations (of a six-coordinate intermediate) to give the ground state of the bis-ligated photoproduct. The finding that the photoproduct channel principally depends on ligand characteristics along with the time-evolving spectra suggests that the transient intermediate may involve a five-coordinate species. In contrast to NiDPP, the fluorinated analogues NiF(20)DPP and NiF(28)DPP do coordinate axial ligands in the ground state but eject them after photoexcitation. Collectively, these results demonstrate the sensitivity with which the electronic and structural characteristics of the macrocycle, substituents, and solvent (ligands) can govern the photophysical and photochemical properties of nonplanar porphyrins and open new avenues for exploring photoinduced ligand association and dissociation behavior.     

Avidin and streptavidin ligands based on the glycoluril bicyclic system

Glycoluril derivatives with a carboxylic acid side chain have been synthesized and shown to bind to both avidin and streptavidin. Introduction of a valerate side chain in glycoluril led to an increased binding to both proteins only when the valerate group was bound to a N atom and with the proper stereochemistry [(+)-enantiomer]. On the other hand, introduction of the valerate side chain either on the bridgehead carbon or on the N atom with the opposite stereochemistry [(-)-enantiomer] led to a decrease in binding constant compared with unsubstituted glycoluril. Direct spectrophotometric competitive titration of each protein with a racemic ligand allowed measurement of the enantioselectivity of the ligand-protein complexation, together with the binding constant of the two enantiomers. In the case of the N-substituted glycoluril, the extension of the side chain by one methylene group, from valerate to caproate, led to an increase in the binding constant to both proteins. Docking studies using AutoDock 3.05 have been performed in order to predict the binding modes of these ligands to streptavidin. The effect of the stereochemistry and the position of the side chain on the binding constant to streptavidin is discussed in view of the predicted binding modes.     

Supervised consensus scoring for docking and virtual screening

Docking programs are widely used to discover novel ligands efficiently and can predict protein-ligand complex structures with reasonable accuracy and speed. However, there is an emerging demand for better performance from the scoring methods. Consensus scoring (CS) methods improve the performance by compensating for the deficiencies of each scoring function. However, conventional CS and existing scoring functions have the same problems, such as a lack of protein flexibility, inadequate treatment of salvation, and the simplistic nature of the energy function used. Although there are many problems in current scoring functions, we focus our attention on the incorporation of unbound ligand conformations. To address this problem, we propose supervised consensus scoring (SCS), which takes into account protein-ligand binding process using unbound ligand conformations with supervised learning. An evaluation of docking accuracy for 100 diverse protein-ligand complexes shows that SCS outperforms both CS and 11 scoring functions (PLP, F-Score, LigScore, DrugScore, LUDI, X-Score, AutoDock, PMF, G-Score, ChemScore, and D-score). The success rates of SCS range from 89% to 91% in the range of rmsd < 2 A, while those of CS range from 80% to 85%, and those of the scoring functions range from 26% to 76%. Moreover, we also introduce a method for judging whether a compound is active or inactive with the appropriate criterion for virtual screening. SCS performs quite well in docking accuracy and is presumably useful for screening large-scale compound databases before predicting binding affinity.     

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

Docking is one of the most commonly used techniques in drug design. It is used for both identifying correct poses of a ligand in the binding site of a protein as well as for the estimation of the strength of protein–ligand interaction. Because millions of compounds must be screened, before a suitable target for biological testing can be identified, all calculations should be done in a reasonable time frame. Thus, all programs currently in use exploit empirically based algorithms, avoiding systematic search of the conformational space. Similarly, the scoring is done using simple equations, which makes it possible to speed up the entire process. Therefore, docking results have to be verified by subsequent in vitro studies. The purpose of our work was to evaluate seven popular docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) on the extensive dataset composed of 1300 protein–ligands complexes from PDBbind 2007 database, where experimentally measured binding affinity values were also available. We compared independently the ability of proper posing [according to Root mean square deviation (or Root mean square distance) of predicted conformations versus the corresponding native one] and scoring (by calculating the correlation between docking score and ligand binding strength). To our knowledge, it is the first large‐scale docking evaluation that covers both aspects of docking programs, that is, predicting ligand conformation and calculating the strength of its binding. More than 1000 protein–ligand pairs cover a wide range of different protein families and inhibitor classes. Our results clearly showed that the ligand binding conformation could be identified in most cases by using the existing software, yet we still observed the lack of universal scoring function for all types of molecules and protein families. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011