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Computational mapping identifies the binding sites of organic solvents on proteins

Computational mapping places molecular probes—small molecules or functional groups—on a protein surface to identify the most favorable binding positions. Although x-ray crystallography and NMR show that organic solvents bind to a limited number of sites on a protein, current mapping methods result in hundreds of energy minima and do not reveal why some sites bind molecules with different sizes and polarities. We describe a mapping algorithm that explains the origin of this phenomenon. The algorithm has been applied to hen egg-white lysozyme and to thermolysin, interacting with eight and four different ligands, respectively. In both cases the search finds the consensus site to which all molecules bind, whereas other positions that bind only certain ligands are not necessarily found. The consensus sites are pockets of the active site, lined with partially exposed hydrophobic residues and with a number of polar residues toward the edge. These sites can accommodate each ligand in a number of rotational states, some with a hydrogen bond to one of the nearby donor/acceptor groups. Specific substrates and/or inhibitors of hen egg-white lysozyme and thermolysin interact with the same side chains identified by the mapping, but form several hydrogen bonds and bind in unique orientations.

Algorithms for computational solvent mapping of proteins

Computational mapping methods place molecular probes (small molecules or functional groups) on a protein surface to identify the most favorable binding positions by calculating an interaction potential. We have developed a novel computational mapping program called CS‐Map (computational solvent mapping of proteins), which differs from earlier mapping methods in three respects: (i) it initially moves the ligands on the protein surface toward regions with favorable electrostatics and desolvation, (ii) the final scoring potential accounts for desolvation, and (iii) the docked ligand positions are clustered, and the clusters are ranked on the basis of their average free energies. To understand the relative importance of these factors, we developed alternative algorithms that use the DOCK and GRAMM programs for the initial search. Because of the availability of experimental solvent mapping data, lysozyme and thermolysin are considered as test proteins. Both DOCK and GRAMM speed up the initial search, and the combined algorithms yield acceptable mapping results. However, the DOCK‐based approaches place the consensus site farther from its experimentally determined position than CS‐Map, primarily because of the lack of a solvation term in the initial search. The GRAMM‐based program also finds the correct consensus site for thermolysin. We conclude that good sampling is the most important requirement for successful mapping, but accounting for desolvation and clustering of ligand positions also help to reduce the number of false positives. Proteins 2003;51:340–351.

Correlation between retention indices and quantum-chemical descriptors of ketones and aldehydes on stationary phases of different polarity

Abstract Kovats retention indices determined on four different capillary columns (OV-1, HP-50, DB-210 and HP-Innowax) were correlated with molecular structural parameters calculated by a semiempirical quantum-chemical method PM3. Multivariate techniques: principal component analysis and cluster analysis were applied to extract the data structure. Multiple linear regression was made in forward stepwise manner to select suitable variables in the model. Basic correlations were found between the retention indices on different columns and the molecular surface, energies of highest occupied and lowest unoccupied molecular orbitals { E (HOMO) and E (LUMO)}, polarizability, and dipole moments. These correlations provide insights into the mechanism of chromatographic retention on a molecular level. They support the view: the more polar is the stationary phase, the greater is the effect of the polarity (polarizability and dipole moment) of solute molecules on the retention phenomena.

Insights into a surprising reaction: The microwave-assisted direct esterification of phosphinic acids

It is well-known that phosphinic acids do not undergo direct esterifications with alcohols under thermal conditions. However, the esterifications take place under microwave (MW) irradiation due to the beneficial effect of MW. As a comparison, maximum 12-15% conversions were observed on traditional heating. It was proved experimentally that the MW-assisted esterifications are not reversible under the conditions applied that may be the consequence of the hydrophobic medium established by the long chain alcohol/phosphinic ester. Neither the thermodynamic, nor the kinetic data obtained by high level quantum chemical calculations justify the direct esterification of phosphinic acids under thermal conditions. The thermodynamic data show that there is no driving force for the reactions under discussion. As a consequence of the relatively high values of activation enthalpy (102-161 kJ mol(-1)), these esterifications are controlled kinetically. Comparing the energetics of the esterification of phosphinic acids and the preparative results obtained under MW conditions, one can see the potential of the MW technique in the synthesis of phosphinates. During our study, a series of new cyclic phosphinates with lipophilic alkyl groups was synthesized.

Mapping of Possible Binding Sequences of Two Beta-Sheet Breaker Peptides on Beta Amyloid Peptide of Alzheimer's Disease

Aggregation of amyloid peptide (Abeta) has been identified as a major feature of the pathogenesis of Alzheimers disease. Increased risk for disease is associated with increased formation of polymerized Abeta. Inhibition of formation of toxic (aggregated) form of Abeta is one of the therapeutic possibilities. Beta sheet breaker peptides (BSBs) fulfill the requirements of an effective inhibitor. After having attached to the Abeta molecules, BSBs can prevent aggregation of Abeta to polymeric forms (aggregates). In the present study, we performed molecular modelling of complex formation between Abeta and two BSB peptides. Our aim was to find proper binding sequences for the BSB peptides on Abeta and characterize them. A dimeric model of Abeta was also used to study the interaction of BSBs with the aggregated forms of Abeta and find the sequences responsible for the polymerization process. A fast and efficient computational method: molecular docking was used for the afore-mentioned purposes.

Penetratin and derivatives acting as antifungal agents

The synthesis, in vitro evaluation, and conformational study of RQIKIWFQNRRMKWKK-NH(2) (penetratin) and related derivatives acting as antifungal agents are reported. Penetratin and some of its derivatives displayed antifungal activity against the human opportunistic pathogenic standardized ATCC strains Candida albicans and Cryptococcus neoformans as well as clinical isolates of C. neoformans. Among the compounds tested, penetratin along with the nonapeptide RKWRRKWKK-NH(2) and the tetrapeptide RQKK-NH(2) exhibited significant antifungal activities against the Cryptococcus species. A comprehensive conformational analysis on the peptides reported here using three different approaches, molecular mechanics, simulated annealing and molecular dynamics simulations, was carried out. The experimental and theoretical results allow us to identify a topographical template which may provide a guide for the design of new compounds with antifungal characteristics against C. neoformans.

Hydrogen bonding interactions of benzylidene type Schiff bases studied by vibrational spectroscopic and computational methods

The structural features of four benzylidene type Schiff bases [(E)-benzaldehyde-N-phenyl imine, (A) (E)-2-hydroxybenzaldehyde-N-phenyl imine (B) (E)-benzaldehyde-N-2-hydroxyphenyl imine (C) (E)-2-hydroxybenzaldehyde-N-2-hydroxyphenyl imine (D)] were studied by FT-IR spectroscopy in solution, photoacoustic and Raman spectroscopies in the solid state and quantum chemical calculations. It was found that molecule D dimerised in the solid state with concomitant loss of aromaticity in the benzylidene ring. Beside the intermolecular C=O...HO hydrogen bonds, intramolecular N-H...C=O hydrogen bonds could be found experimentally as well as computationally. Spectra taken in solution and ab initio quantum chemical calculation helped to identify hydrogen bonding interactions occurring for compounds B and C. Intramolecular OH...N hydrogen bond predominated in molecule B, while this interaction, although it existed, was weaker.

Improved mapping of protein binding sites

Computational mapping methods place molecular probes – small molecules or functional groups – on a protein surface in order to identify the most favorable binding positions by calculating an interaction potential. Mapping is an important step in a number of flexible docking and drug design algorithms. We have developed improved algorithms for mapping protein surfaces using small organic molecules as molecular probes. The calculations reproduce the binding of eight organic solvents to lysozyme as observed by NMR, as well as the binding of four solvents to thermolysin, in good agreement with x-ray data. Application to protein tyrosine phosphatase 1B shows that the information provided by the mapping can be very useful for drug design. We also studied why the organic solvents bind in the active site of proteins, in spite of the availability of alternative pockets that can very tightly accommodate some of the probes. A possible explanation is that the binding in the relatively large active site retains a number of rotational states, and hence leads to smaller entropy loss than the binding elsewhere else. Indeed, the mapping reveals that the clusters of the ligand molecules in the proteins active site contain different rotational-translational conformers, which represent different local minima of the free energy surface. In order to study the transitions between different conformers, reaction path and molecular dynamics calculations were performed. Results show that most of the rotational states are separated by low free energy barriers at the experimental temperature, and hence the entropy of binding in the active site is expected to be high.

Correlation of retention indices with van der Waals' volumes and surface areas: Alkanes and azo compounds

SummaryVan der Waals’ volumes (VW) and surface areas (SW) of alkanes, (E)-azoalkanes and structurally similar alkenes (R1-X=X-R2, X=N, CH) were calculated by a semiempirical quantum-chemical method (AM1). The calculated data are in reasonable agreement with the experimental values of Bondi and good correlations were found between the calculated data and Kovats’ retention indices (IR). While theVWs of alkanes with the same carbon number are very close to one another, theSWs follow the scatter of theIR values for branched alkanes. The difference in theIR of (E)-azo compounds and the structurally similar alkenes can be explained by the difference inVWs.

Harmonic vibrational frequency scaling factors for the new NDDO Hamiltonians: RM1 and PM6

Scaling factors have been derived to obtain fundamental vibrational frequencies with the recently introduced semiempirical molecular orbital methods RM1 and PM6, implemented in MOPAC2007. A least-squares approach is used with a training set comprised of 90 singlet-state molecules and 922 distinct vibrations, extracted from the NIST Computational Chemistry Comparison and Benchmark Database (CCCBDB). Results are presented both for the conventional Scott-Radom type single-factor fitting, and for a multi-factor linear model: Semiempirical Semiglobal Self-consistently Scaled Quantum Mechanical (S4QM). The new NDDO methods in conjunction with the multi-linear fitting are shown to yield improved prediction of vibrational frequencies. To demonstrate the performance of S4QM//PM6 for calculating vibrational spectra, the examples of indene, indazole and four tetrachlorinated p-dibenzodioxins are presented.