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PubMed2001

Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach.

Determination of potential drug toxicity and side effect in early stages of drug development is important in reducing the cost and time of drug discovery. In this work, we explore a computer method for predicting potential toxicity and side effect protein targets of a small molecule. A ligand-protein inverse docking approach is used for computer-automated search of a protein cavity database to identify protein targets. This database is developed from protein 3D structures in the protein data bank (PDB). Docking is conducted by a procedure involving multiple conformer shape-matching alignment of a molecule to a cavity followed by molecular-mechanics torsion optimization and energy minimization on both the molecule and the protein residues at the binding region. Potential protein targets are selected by evaluation of molecular mechanics energy and, while applicable, further analysis of its binding competitiveness against other ligands that bind to the same receptor site in at least one PDB entry. Our results on several drugs show that 83% of the experimentally known toxicity and side effect targets for these drugs are predicted. The computer search successfully predicted 38 and missed five experimentally confirmed or implicated protein targets with available structure and in which binding involves no covalent bond. There are additional 30 predicted targets yet to be validated experimentally. Application of this computer approach can potentially facilitate the prediction of toxicity and side effect of a drug or drug lead.

Ascorbic Acid↗

PubMed1998

Similarity studies on guanidinium, imidazolinium, and imidazolium cations: toward new bradykinin antagonists.

Bradykinin (BK) is a potent nociceptive agent and its antagonists show analgesic activity. In the search for new antagonists of BK, the design of nonpeptidic derivatives with different terminal cations has been considered. Among these new antagonists, the guanidinium cations, which appear not only in the terminal arginine residues of BK but also in several nonpeptidic antagonists, will be substituted by groups with characteristics similar in terms of electrostatic potential, electron density, shape, etc. Several similarity indexes have been calculated for guanidinium, 2-aminoimidazolinium, and 2-aminoimidazolium cations and their corresponding neutral species to design new nonpeptidic BK antagonists. The geometric and electronic characteristics of the molecules were compared by means of: (1) the Carbo index, (2) the Hodgkin index, and (3) a shape similarity index based on the volume of each molecule as defined by a certain electron density. Molecular geometries and energies were optimized by ab initio calculations at the B3LYP/6311+2G** level. The molecular electrostatic potential (MEP) and the electron density (rho) were then computed in a cubic grid of points around each molecule. These molecular properties were used to calculate similarity indexes with the guanidinium cation or guanidine as the reference molecule in each family. In addition, three-dimensional similarity maps were generated to localize those molecular areas more alike in each of the sets.

Bradykinin↗

PubMed1997

On the theory of folding kinetics for short proteins.

BACKGROUND: Recent data have suggested two principles that are central to the work we describe here. First, proteins are the result of evolutionary 'sequence selection' to optimize the energy of the native state. Second, the overlap with the native state is a qualitatively suitable reaction coordinate for modeling folding kinetics. The former principle is bolder and better established. RESULTS: Employing only these two principles, we have constructed a non-phenomenological, correlated energy landscape theory that predicts single barrier protein folding kinetics. Moreover, we are able to analytically describe the nature of the free energetic barrier between the denatured and native states of a protein and to detail the nature of folding kinetics for short proteins. Our model predicts Hammond behavior and also describes how mutations can lead to drastic differences in folding times. CONCLUSIONS: We find that folding and unfolding kinetics can be characterized by a single thermodynamic parameter and, moreover, that Monte Carlo simulation data on folding and unfolding rates with different temperatures and mutations collapse with this characterization. Our results also delineate a regime in which kinetics may proceed via a single unique nucleus.

Computer Simulation↗

PubMed2005

Desorption/ionization on silicon nanowires.

Dense arrays of single-crystal silicon nanowires (SiNWs) have been used as a platform for laser desorption/ionization mass spectrometry of small molecules, peptides, protein digests, and endogenous and xenobiotic metabolites in biofluids. Sensitivity down to the attomole level has been achieved on the nanowire surfaces by optimizing laser energy, surface chemistry, nanowire diameter, length, and growth orientation. An interesting feature of the nanowire surface is that it requires lower laser energy as compared to porous silicon and MALDI to desorb/ionize small molecules, therefore reducing background ion interference. Taking advantage of their high surface area and fluid wicking capabilities, SiNWs were used to perform chromatographic separation followed by mass analysis of the separated molecules providing a unique platform that can integrate separation and mass spectrometric detection on a single surface.

Chromatography↗

PubMed1992

Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state.

In order to quantitate the contributions of the polar, uncharged amino acids to the stability of the native state of staphylococcal nuclease, each of the 13 alanines, 9 glycines, 9 threonines, 6 prolines, 6 glutamines, 6 asparagines, and 3 serines was substituted, either with both alanine and glycine or with 1 of these 2 amino acids plus valine. For each mutant, the stability to reversible denaturation (delta GH2O) was quantitated by determining the Kapp for this reaction as a function of guanidine hydrochloride concentration. In addition, the parameter mGuHCl (= d(delta G)/d[GuHCl]) was calculated from the data. To identify the local structural features responsible for the relatively large and variable changes in delta GH2O and mGuHCl observed for the same type of substitution at different locations in nuclease, statistical correlations were sought between delta GH2O, mGuHCl, and a number of descriptors of the local structure. As with substitutions of the large hydrophobic amino acids [Shortle, D., Stites, W. E., & Meeker, A. K. (1990) Biochemistry 29, 8033-8041], mutation of polar, uncharged residues to Gly leads to a change in stability that, on average, correlates well with the degree to which the wild-type residue is buried. This correlation is especially significant for threonine, an amino acid with both polar and hydrophobic character, but is not demonstrated for the more typically hydrophobic residue alanine. As reported in the previous study of alanine/glycine substitutions of hydrophobic residues, a significant correlation between changes in stability and changes in the value of mGuHCl is again observed, strengthening the conclusion that the putative structural changes in the denatured state which lead to increases or decreases in mGuHCl are responsible for a significant fraction of the stability loss for an average mutant. The existence of this correlation is consistent with the denatured state of wild-type staphylococcal nuclease having evolved to a relatively high free energy via optimization of a balance between a maximal exposure of hydrophobic surface and a minimal gain in chain entropy. On average, mutations are less stable in proportion to the extent of which they perturb this balance. A new and puzzling correlation is reported between the extent of buriedness of a residue in the wild-type native state versus the difference in mGuHCl between the Ala mutation and the Gly mutation at that position.

Alanine↗

PubMed2001

CO(2) fixation by Rubisco: computational dissection of the key steps of carboxylation, hydration, and C-C bond cleavage.

Despite intensive experimental and computational studies, some important features of the mechanism of the photosynthetic CO(2)-fixing enzyme, Rubisco, are still not understood. To complement our previous investigation of the first catalytic step, the enolization of D-ribulose-1,5-bisphosphate (King et al., Biochemistry 1998, 44, 15414-15422), we present the first complete computational dissection of subsequent steps of the carboxylation reaction that includes the roles of the central magnesium ion and modeled residues of the active site. We investigated carboxylation, hydration, and C-C bond cleavage using the density functional method and the B3LYP/6-31G(d) level to perform geometry optimizations. The energies were determined by B3LYP/6-311+G(2d,p) single-point calculations. We modeled a fragment of the active site and substrate, taking into account experimental findings that the residues coordinated to the Mg ion, especially the carbamylated Lys-201, play critical roles in this reaction sequence. The carbamate appears to act as a general base, not only for enolization but also for hydration of the beta ketoacid formed by addition of CO(2) and, as well, cleavage of the C2-C3 bond of the hydrate. We show that CO(2) is added directly, without assistance of a Michaelis complex, and that hydration of the resultant beta ketoacid occurs in a separate subsequent step with a discrete transition state. We suggest that two conformations of the hydrate (gem-diol), with different metal coordination, are possible. The step with the highest activation energy during the carboxylation cycle is the C-C bond cleavage. Depending on the conformations of the gem-diol, different pathways are possible for this step. In either case, special arrangements of the metal coordination result in bond breaking occurring at remarkably low activation energies (between 28 and 37 kcal mol(-1)) which might be reduced further in the enzyme environment.

Binding Sites↗

PubMed2002

The ene reactions of nitroso compounds involve polarized diradical intermediates.

The ene reactions of nitroso compounds were studied with B3LYP/6-31G* geometry optimizations and energy calculations, along with single point energy evaluations using CASPT2/6-31G** and UCCSD(T)/6-311+G* methods. Reactions of HNO with propene and of MeNO and p-NO2C6H4NO with propene or substituted alkenes were also studied. The reaction mechanism is stepwise and involves a polarized diradical intermediate. The electronic structure of this intermediate is between that of a closed shell polar species and that of a pure diradical, and it is stabilized by polar solvents. A weak C-N bonding interaction combined with a CH-O hydrogen bond leads to heightened barriers to rotation about formally single bonds compared to conventional diradicals. Consequently, rotation is slower than hydrogen abstraction and cyclization to form an aziridine N-oxide. This aziridine N-oxide does not lead to ene products without subsequent ring opening but provides a mechanism for the RNO moiety to translate from one end of the alkene to the other. B3LYP calculations are also able to reproduce kinetic isotope effects and regioselectivity.

Journal Article↗

PubMed2003

Benzoxazine oligomers: evidence for a helical structure from solid-state NMR spectroscopy and DFT-based dynamics and chemical shift calculations.

A combination of molecular modeling, DFT calculations, and advanced solid-state NMR experiments is used to elucidate the supramolecular structure of a series of benzoxazine oligomers. Intramolecular hydrogen bonds are characterized and identified as the driving forces for ring-shape and helical conformations of trimeric and tetrameric units. In fast MAS (1)H NMR spectra, the resonances of the protons forming the hydrogen bonds can be assigned and used for validating and refining the structure by means of DFT-based geometry optimizations and (1)H chemical-shift calculations. Also supporting these proposed structures are homonuclear (1)H[bond](1)H double-quantum NMR spectra, which identify the local proton-proton proximities in each material. Additionally, quantitative (15)N[bond](1)H distance measurements obtained by analysis of dipolar spinning sideband patterns confirm the optimized geometry of the tetramer. These results clearly support the predicted helical geometry of the benzoxazine polymer. This geometry, in which the N...H...O and O...H...O hydrogen bonds are protected on the inside of the helix, can account for many of the exemplary chemical properties of the polybenzoxazine materials. The combination of advanced experimental solid-state NMR spectroscopy with computational geometry optimizations, total energy, and NMR spectra calculations is a powerful tool for structural analysis. Its results provide significantly more confidence than the individual measurements or calculations alone, in particular, because the microscopic structure of many disordered systems cannot be elucidated by means of conventional methods due to lack of long-range order.

Journal Article↗

PubMed1993

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds.

The directional properties of hydrogen bonds play a major role in determining the specificity of intermolecular interactions. An energy function which takes explicit account of these properties has been developed for use in the determination of energetically favorable ligand binding sites on molecules of known structure by the GRID method (Goodford, P.J.J. Med. Chem. 1985, 28, 849. Boobbyer, D.N.A.; Goodford, P.J.; McWhinnie, P.M.; Wade, R.C.J. Med. Chem. 1989, 32, 1083). In this method, the interaction energy between a target molecule and a small chemical group (a probe), which may be part of a larger ligand, was calculated using an energy function consisting of Lennard-Jones, electrostatic, and hydrogen bond terms. The latter term was a function of the length of the hydrogen bond, its orientation at the hydrogen-bonding atoms, and their chemical nature. We now describe hydrogen bond energy functions which take account of the spatial distribution of the hydrogen bonds made by probes with the ability to form two hydrogen bonds. These functions were designed so as to model the experimentally observed angular dependence of the hydrogen bonds. We also describe the procedure to locate the position and orientation of the probe at which the interaction energy is optimized. The use of this procedure is demonstrated by examples of biological and pharmacological interest which show that it can produce results that are consistent with other theoretical approaches and with experimental observations.

Binding Sites↗

PubMed2005

Theoretical study of the addition patterns of C60 fluorination: C60Fn (n = 1-60).

A systematic study is presented of addition patterns occurring upon fluorination of C60. We use the program SACHA, which increments the number of fluorine addends, tests all available addition sites within a given cutoff radius, and selects the most energetically stable structure for further addition on the basis of full AM1 optimizations for every isomer. The lowest energy structures are optimized at HF/3-21G level of theory. A number of distinct addition routes are predicted, based on octahedral, 'S', and 'T' addition patterns, leading both to experimentally observed C60F(n) isomers and to isomers not previously described in the literature. Furthermore the main addition routes were analyzed for C60F2n isomers, using ab initio global and local aromaticity calculations. For this, magnetizability and NICS calculations have been carried out at HF/3-21G level of theory. We show the possibility of using NICS to predict the next preferential addition site, matching the above-described addition routes.

Journal Article↗

PubMed2005

Computational study on the reaction CH2CH2 + F --> CH2CHF + H.

Previous ab initio studies on reactions involving radical addition to alkenes showed that such reactions are very sensitive to theoretical levels, and thus are difficult to deal with. This motivates us to theoretically reexamine the title reaction thoroughly, which has been studied only at several low levels of theory. In the present work, the geometry optimizations and energy calculations for all species involved in the title reaction were performed at several high levels of theory. The reaction mechanism of the title reaction is discussed at the CCSD(T)/aug-cc-pVDZ//CCSD/6-31G(d,p) theoretical level. According to our study, the fluorine addition to ethylene occurs via the formation of a prereaction complex with C2v symmetry, which is pointed out for the first time. The prereaction complex evolves into a fluoroethyl radical almost without a barrier, with an exothermicity of 41.49 kcal/mol. The fluoroethyl radical can further decompose into a hydrogen atom and fluoroethylene, with an energy release of 10.33 kcal/mol. Besides the direct departure of the hydrogen atom from the fluoroethyl radical, an indirect decomposition pathway may also be open, which has not been reported before. In addition, the formation of a fluoroethyl radical from a separate fluorine atom and ethylene is described pictorially via the molecular intrinsic characteristic contour (MICC) and the electron density mapped on it. Thereby, strong interpolarization and evident electron transfer between the fluorine atom and ethylene are observed as they approach each other. The transition structure for the fluorine addition to ethylene is clearly shown to be reactant-like. This provides new and intuitional insight into the title reaction.

Journal Article↗

PubMed2005

DFT investigation of CO adsorption on Pt(211) and Pt(311) surfaces from low to high coverage.

Adsorption of CO on Pt(211) and Pt(311) surfaces has been investigated by the density functional theory (DFT) method (periodic DMol3) with full geometry optimization. Adsorption energies, structures, and C-O stretching vibrational frequencies are studied by considering multiple possible adsorption sites and comparing them with the experimental data. The calculated C-O stretching frequencies agree well with the experimental ones, and precise determination of adsorption sites can be carried out. For Pt(211), CO adsorbs at the atop site on the step edge at low coverage, but CO adsorbs at the atop and bridge sites simultaneously on both the step edge and the terrace with further increasing CO coverage. The present results interpret the reflection adsorption infrared (RAIR) spectra of Brown and co-workers very well from low to high coverage. For Pt(311), CO adsorbs also at the atop site on the step edge at low coverage. The lifting of reconstruction by CO adsorption occurs also for Pt(311), whereas the energy gain for lifting the reconstruction of the Pt(311) surface is smaller than that for Pt(110). The largest difference between the stepped Pt(211)/Pt(311) and Pt(110) surfaces is the occupation on the edge sites at higher coverage. For the stepped surfaces, the bridge site begins to be occupied at higher coverage, whereas the atop site is always occupied for the Pt(110) surface.

Journal Article↗

PubMed2005

On the origin of the ultrafast internal conversion of electronically excited pyrimidine bases.

The ultrafast radiationless decay of photoexcited uracil and cytosine has been investigated by ab initio quantum chemical methods based on CIS and CR-EOM-CCSD(T) electronic energy calculations at optimized CIS geometries. The calculated potential energy profiles indicate that the S(1) --> S(0) internal conversion of the pyrimidine bases occurs through a barrierless state switch from the initially excited (1)pipi state to the out-of-plane deformed excited state of biradical character, which intersects the ground state at a lower energy. This three-state nonradiative decay mechanism predicts that replacement of the C5 hydrogen by fluorine introduces an energy barrier for the initial state switch, whereas replacement of the C6 hydrogen by fluorine does not. These predictions are borne out by the very different fluorescence yields of 5-fluorinated bases relative to the corresponding 6-fluorinated bases. It is concluded from these results that the origin of the ultrafast radiationless decay is the same for the two pyrimidine bases.

Cytosine↗

PubMed2001

Mechanical effects of liriodenine on the left ventricular-arterial coupling in Wistar rats: pressure-stroke volume analysis.

1. In a recent in vivo study, liriodenine, an aporphine alkaloid, has been identified as a prominent anti-arrhythmic agent that can prevent rats' sudden deaths, even at the dose as low as 10(-7) g kg(-1). The aim of this study was to determine whether liriodenine at its effective anti-arrhythmic dose of 10(-7) g kg(-1) had effects on the left ventricular (LV)-arterial coupling in Wistar rats. 2. LV pressure and ascending aortic flow signals were recorded to construct the ventricular and arterial end-systolic pressure-stroke volume relationships to calculate LV end-systolic elastance (E(es)) and effective arterial volume elastance (E(a)), respectively. The optimal afterload (Q(load)) determined by the ratio of E(a) to E(es) was used to measure the optimality of energy transmission from the left ventricle to the arterial system. 3. Liriodenine at the dose of 10(-7) g kg(-1) showed no significant changes in basal heart rate (HR), cardiac output (CO), LV end-systolic pressure (P(es)), E(a), E(es), and Q(load). 4. By contrast, liriodenine at the dose of 10(-6) g kg(-1) produced a significant fall of 2.0% in HR and a significant rise of 5.8% in CO, but no significant change in P(es). Moreover, liriodenine administration of 10(-6) g kg(-1) to rats significantly decreased E(es) by 8.5% and E(a) by 10.6%, but did not change Q(load). 5. We conclude that liriodenine at the dose of 10(-7) g kg(-1) has no effects on the mechanical properties of the heart and the vasculature and the matching condition for the left ventricle coupled to its vasculature in rats. Even at 10 times the effective anti-arrhythmic dose, liriodenine shows no effects on the efficiency of energy transferred from the left ventricle to the arterial system.

Analysis of Variance↗

PubMed1991

Mechanism of acyl transfer by the class A serine beta-lactamase of Streptomyces albus G.

Optimization by energy minimization of stable complexes occurring along the pathway of hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase has highlighted a proton shuttle that may explain the catalytic mechanism of the beta-lactamases of class A. Five residues, S70, S130, N132, T235 and A237, are involved in ligand binding. The gamma-OH group of T235 and, in the case of benzylpenicillin, the gamma-OH group of S130 interact with the carboxylate group, on one side of the ligand molecule. The side-chain NH2 group of N132 and the carbonyl backbone of A237 interact with the exocyclic CONH amide bond, on the other side of the ligand. The backbone NH groups of S70 and A237 polarize the carbonyl group of the scissile beta-lactam amide bond. Four residues, S70, K73, S130 and E166, and two water molecules, W1 and W2, perform hydrolysis of the bound beta-lactam compound. E166, via W1, abstracts the proton from the gamma-OH group of S70. While losing its proton, the O-gamma atom of S70 attacks the carbonyl carbon atom of the beta-lactam ring and, concomitantly, the proton is delivered back to the adjacent nitrogen atom via W2, K73 and S130, thus achieving formation of the acyl-enzyme. Subsequently, E166 abstracts a proton from W1. While losing its proton, W1 attacks the carbonyl carbon atom of the S70 ester-linked acyl-enzyme and, concomitantly, re-entry of a water molecule W'1 replacing W1 allows E166 to deliver the proton back to the same carbonyl carbon atom, thus achieving hydrolysis of the beta-lactam compound and enzyme recovery. The model well explains the differences found in the kcat. values for hydrolysis of benzylpenicillin and cephalosporin C by the Streptomyces albus G beta-lactamase. It also explains the effects caused by site-directed mutagenesis of the Bacillus cereus beta-lactamase I [Gibson, Christensen & Waley (1990) Biochem J. 272, 613-619].

Amino Acid Sequence↗

PubMed2003

Structure-activity relationship: analyses of p-glycoprotein substrates and inhibitors.

OBJECTIVE: A large number of structurally and functionally diverse compounds act as substrates or modulators of p-glycoprotein (p-gp). Some of them possess multiple drug resistance (MDR)-reversing activity, but only a small number of them have entered clinical study. In order to uncover the factors which exert a significant impact on the interaction between substrates/modulators and p-gp, we have performed structure-activity relationship (SAR) analyses, including molecular modelling, two-dimensional (2D) and three-dimensional (3D) parameter-frame-setting analysis, quantitative structure activity relationship (QSAR) analysis among substrates/modulators, as well as clinically promising MDR-reversing agents. METHODS: The physicochemical parameters C log P, CMR and all regression equations were derived by using C log P version 4.0 and the latest CQSAR software, respectively. Molecular modelling and all other parameter calculations were performed by using HyperChem version 5.0 program, after geometry optimization and energy minimization using the AM1 semiempirical method. RESULTS: SAR analyses indicate that MDR reversal activity is correlated with the lipophilicity (C log P), molecular weight (log Mw), longest chain (Nlc) of the molecule and the energy of the highest occupied orbital (Ehomo). In addition, the presence of a basic tertiary nitrogen atom in the structure is also an important contributor to p-gp inhibitory activity. Some separation in space is achieved for different subsets of p-gp substrates and inhibitors using Nlc, C log P and Ehomo as three independent parameters in the 3D-parameter-frame setting. CONCLUSION: A highly effective p-gp modulator candidate should possess a log P value of 2.92 or higher, 18-atom-long or longer molecular axis, and a high Ehomo value, as well as at least one tertiary basic nitrogen atom. The results obtained may be useful in explaining drug-p-gp interactions for different compounds, including drug interactions and the development of new MDR chemosensitizers.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed1975

[Theoretical investigations for optimising the quantum in radiodiagnosis (author's transl)].

On the basis of the present calculations, it is possible to determine the optimal exposure energies for any object of combination of materials. The results of the present investigation contradict present day practice. Calculated energies are sometimes much higher than those employed at present. This has certain definite advantages; reduced radiation dose to the object; a less sharp decline of contrast with high kilovoltage. Unfortunately it is only possible to guess at the causes of this difference. Further investigations, dealing particularly with the effect of spectral energy distribution under certain conditions, are in progress. Investigations into the sensitivity of intensifiers and film/screen combinations, combined with a comparison with calculated energies would be valuable.

Radiation Dosage↗

PubMed2005

(G-H)-C and G-(C-H) radicals derived from the guanine.cytosine base pair cause DNA subunit lesions.

The radicals generated by the homolytic cleavage of an X-H bond from the guanine.cytosine (G.C) base pair were studied by using carefully calibrated theoretical methods. The gradient-corrected density functional B3LYP was applied in conjunction with double-zeta plus polarization and diffuse function basis sets. Optimized geometries, energies, and vibrational frequencies were obtained for all of the radicals considered. Structural perturbations along with energy relaxation due to radical formation were investigated. Dissociation energies of the G.C base pair and all of the radicals are predicted and compared with the dissociation energy of neutral G.C. The three lowest-energy base pair radicals all involve removal of an H atom from one of the N atoms in G.C. The lowest-energy base pair radical has the hydrogen atom removed from the guanine nitrogen atom used for the sugar phosphate linkage in DNA. This (G-H)(*)-C radical has a dissociation energy (to G-H(*) + C) of 30 kcal/mol, which may be compared with 27 kcal/mol for G.C. All of the radicals that are possible outcomes of direct ionizing radiation or oxidizing species were investigated for the presence of local minima with significant structural changes. Major structural deformations cause strain in the interstrand hydrogen bonding in the DNA double helix. Severe geometry changes were observed when the hydrogen was abstracted from interstrand hydrogen bonding sites, along with sizeable energy changes, indicating the potentially serious consequences to the G.C base pair.

Base Pairing↗