The denaturation maxima of proteins and of drug-biomolecule complex formation in a wide range of methanol/water mixtures. Solvophobic theory predictions as compared to experiments

Independent experiments have shown that both protein folding (G. Velicelebi and J.M. Sturtevant, Biochemistry 18 (1979) 1180) and drug-biomolecule complexation (D.M. Crothers and D.I. Ratner, Biochemistry 7 (1968) 1823) in a wide range of compositions of methanol/water mixed solvents exhibit a maximum at 8% (v/v) MeOH. This hitherto unexplained phenomenon is shown to be given a priori by the 'solvophobic theory' developed earlier by Sinanoglu which had related the solvent effects including water in biochemistry to the then introduced 'molecular surface areas' and to 'microthermodynamic cavity inner surface tensions' and in a different version to interfacial microtensions between side chains and the solvent. Both analyses carried out in the present paper in detail for MeOH/water mixtures show how the denaturation or complexation free energies are predicted for the entire range of MeOH/water compositions from only data at one point. The molecular surface area changes for the conformational processes are obtained as well as the free energies in the hypothetical but theoretically important in vacuo limits with no solvent present.     

Denaturation of proteins in methanol/water mixtures

The solvophobic theory developed earlier by Sinanoglu introducing the use of molecular surface areas and microthermodynamic surface and interfacial tensions at molecular dimensions is applied to the interpretation of calorimetric data on denaturation of lysozyme in a wide range of methanol/water mixtures. The experimental values of standard unitary free energies of denaturation correlate well with our predictions. The molecular surface area change of the protein upon denaturation is evaluated using the solvophobic theory. The maximum in the stability of the native form of the protein is predicted to occur at 8% (v/v) methanol. This is found to be in agreement with the experimental results.     

ESI-MS investigation of solvent effects on the chiral recognition capacity of tartar emetic towards neutral side-chain amino acids

The effect of solvent systems on previously-reported ESI-MS based proton-assisted enantioselective molecular recognition phenomena of tartar emetic, L-antimony(III)-tartrate, was evaluated. This was achieved by carrying out a series of competitive binding experiments using chiral selectors, bis(sodium) D- and -L-antimony(III)-tartrates with chiral selectands, neutral side-chain amino acid enantiomeric isotopomers of alanine (Ala), valine (Val), leucine (Leu) and phenylalanine (Phe), in three different solvent systems, ACN/H(2)O (75/25 v/v), H(2)O (100%) and H(2)O/MeOH (25/75 v/v). Observations from these experiments suggest that the effect of solvent systems on previously reported proton-assisted chiral recognition capacity of D,L-antimony(III)-tartrates is small, but not negligible. It was observed that an ACN/H(2)O (75/25 v/v) solvent system facilitates and enhances the chiral discrimination capacity of protonated {[D,L-Sb(2)-tar(2)][H]}(-) ionic species. Further, amino acid enantiomers showed a general trend of increasing selectivity order, Val ≤ Ala < Leu ≈ Phe towards the protonated {[D,L-Sb(2)-tar(2)][H]}(-) ionic species which was independent of the solvent system employed. The lack of enantioselective binding for {[D,L-Sb(2)-tar(2)]}(2-) ionic species was consistently recorded in respective mass spectra from all performed experiments, which suggests that ESI-friendly solvent systems have no effect and do not influence this phenomenon.     

ZL-DHP lignin model compound at the air-water interface

In this paper we present our surface chemistry studies of enzymatically polymerized, poly-coniferyl alcohol lignin model compound (dehydrogenate polymer a.k.a. ZL-DHP) at the air-water interface. Using the CHCl(3)/MeOH (5:1 v/v) spreading solvent, we found an average molecular area of ZL-DHP of approximately 1200 A(2). The monolayer expresses a high compressibility with a collapsed area of 500 A(2) and collapsed surface pressure of 28 mN m(-1). In the range of applied surface pressures, ZL-DHP polymer have no phase changes, as shown by the very high linearity (R=0.994) of absorbance vs. surface pressure cure. There was no symmetry transitions observed as shown by absence of shifts of absorption peak maximums.     

Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site

In drug optimization calculations, the molecular mechanics Poisson‐Boltzmann surface area (MM‐PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature. To assess the effect of the force field on the calculation of binding energies, in this article we use large‐scale density functional theory (DFT) calculations as an alternative method to evaluate the energies of the configurations in a “QM‐PBSA” approach. Our DFT calculations are performed with a near‐complete basis set and a minimal parameter implicit solvent model, within the self‐consistent calculation, using the ONETEP program on protein–ligand complexes containing more than 2600 atoms. We apply this approach to the T4‐lysozyme double mutant L99A/M102Q protein, which is a well‐studied model of a polar binding site, using a set of eight small aromatic ligands. We observe that there is very good correlation between the MM and QM binding energies in vacuum but less so in the solvent. The relative binding free energies from DFT are more accurate than the ones from the MM calculations, and give markedly better agreement with experiment for six of the eight ligands. Furthermore, in contrast to MM‐PBSA, QM‐PBSA is able to correctly predict a nonbinder. Proteins 2014; 82:3335–3346. © 2014 Wiley Periodicals, Inc.     

Excluded volume in solvation: sensitivity of scaled-particle theory to solvent size and density

Changes in solvent environment greatly affect macromolecular structure and stability. To investigate the role of excluded volume in solvation, scaled-particle theory is often used to calculate delta G(tr)(ev), the excluded-volume portion of the solute transfer free energy, delta G(tr). The inputs to SPT are the solvent radii and molarities. Real molecules are not spheres. Hence, molecular radii are not uniquely defined and vary for any given species. Since delta G(tr)(ev) is extremely sensitive to solvent radii, uncertainty in these radii causes a large uncertainty in delta G(tr)(ev)-several kcal/mol for amino acid solutes transferring from water to aqueous mixtures. This uncertainty is larger than the experimental delta G(tr) values. Also, delta G(tr)(ev) can be either positive or negative. Adding neutral crowding molecules may not necessarily reduce solubility. Lastly, delta G(tr)(ev) is very sensitive to solvent density, rho. A few percent error in rho may even cause qualitative deviations in delta G(tr)(ev). For example, if rho is calculated by assuming the hard-sphere pressure to be constant, then delta G(tr)(ev) values and uncertainties are now only tenths of a kcal/mol and are positive. Because delta G(tr)(ev) values calculated by scaled-particle theory are strongly sensitive to solvent radii and densities, determining the excluded-volume contribution to transfer free energies using SPT may be problematic.     

Computational modelling of the open-state Kv 1.5 ion channel block by bupivacaine

Binding of R(+)-bupivacaine to open-state homology models of the mammalian K(v)1.5 membrane ion channel is studied using automated docking and molecular dynamics (MD) methods. Homology models of K(v)1.5 are built using the 3D structures of the KcsA and MthK channels as a template. The packing of transmembrane (TM) alpha-helices in the KcsA structure corresponds to a closed channel state. Opening of the channel may be reached by a conformational transition yielding a bent structure of the internal S6 helices. Our first model of the K(v) open state involves a PVP-type of bending hinge in the internal helices, while the second model corresponds to a Gly-type of bending hinge as found in the MthK channel. Ligand binding to these models is probed using the common local anaesthetic bupivacaine, where blocker binding from the intracellular side of the channel is considered. Conformational properties and partial atomic charges of bupivacaine are determined from quantum mechanical HF/6-31G* calculations with inclusion of solvent effects. The automated docking and MD calculations for the PVP-bend model predict that bupivacaine could bind either in the central cavity or in the PVP region of the channel pore. Linear interaction energy (LIE) estimates of the binding free energies for bupivacaine predict strongest binding to the PVP region. Surprisingly, no binding is predicted for the Gly-bend model. These results are discussed in light of electrophysiological data which show that the K(v)1.5 channel is unable to close when bupivacaine is bound.     

Macromolecular solvation energies derived from small molecule crystal morphology.

The morphology of small molecule crystals provides a model for evaluating surface solvation energies in a system with similar packing density to that observed for amino acid residues in proteins. The solvation energies associated with the transfer of methylene and carboxyl groups between vacuum and aqueous phases are estimated to be approx. $40 and -260 cal/A2, respectively, from an analysis of the morphology of succinic acid crystals. These solvation energies predict values for contact angles in reasonable agreement with measurements determined from macroscopic monolayer surfaces. Transfer free energies between vapor and water phases for a series of carboxylic acids are also predicted reasonably well by these solvation energies, provided the surface exposure of different groups is quantitated with the molecular surface area rather than the more traditional accessible surface area. In general, molecular surfaces and molecular surface areas are seen to have important advantages for characterizing the structure and energetics of macromolecular surfaces. Crystal faces of succinic acid with the lowest surface energies in aqueous solution are characteristically smooth. Increasing surface roughness and apolarity are associated with higher surface energies, which suggests an approach for modifying the surface properties of proteins and other macromolecules.     

Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations

Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson–Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors.     

Application of the Free Energy Calculations to Study Drug-enzyme and Drug-dna Complexes

Applications of two free energy calculation approaches are presented to study drug-biomolecule complexes. The first method, the free energy perturbation (FEP) method and molecular dynamics simulations has been applied to study the JG-365 inhibitor bound to the HIV-aspartic protease. The FEP method has been applied to predict the consequence of replacing each of the seven peptide bonds in the JG-365 by trans-ethylene or fluoroethylene units. The necessary initial conformations of the inhibitor for "in water" perturbations have been found using neural network clustering approach applied to the long molecular dynamics trajectory of the inhibitor in water solution. The second method is applied to study binding free energies of some DNA-drug complexes and is based on analysis of long molecular dynamics trajectories by continuum solvent approach (MM/PBSA).     

An extended aqueous solvation model based on atom-weighted solvent accessible surface areas: SAWSA v2.0 model

A new method is proposed for calculating aqueous solvation free energy based on atom-weighted solvent accessible surface areas. The method, SAWSA v2.0, gives the aqueous solvation free energy by summing the contributions of component atoms and a correction factor. We applied two different sets of atom typing rules and fitting processes for small organic molecules and proteins, respectively. For small organic molecules, the model classified the atoms in organic molecules into 65 basic types and additionally. For small organic molecules we proposed a correction factor of hydrophobic carbon to account for the aggregation of hydrocarbons and compounds with long hydrophobic aliphatic chains. The contributions for each atom type and correction factor were derived by multivariate regression analysis of 379 neutral molecules and 39 ions with known experimental aqueous solvation free energies. Based on the new atom typing rules, the correlation coefficient (r) for fitting the whole neutral organic molecules is 0.984, and the absolute mean error is 0.40 kcal mol^–1, which is much better than those of the model proposed by Wang et al. and the SAWSA model previously proposed by us. Furthermore, the SAWSA v2.0 model was compared with the simple atom-additive model based on the number of atom types (NA). The calculated results show that for small organic molecules, the predictions from the SAWSA v2.0 model are slightly better than those from the atom-additive model based on NA. However, for macromolecules such as proteins, due to the connection between their molecular conformation and their molecular surface area, the atom-additive model based on the number of atom types has little predictive power. In order to investigate the predictive power of our model, a systematic comparison was performed on seven solvation models including SAWSA v2.0, GB/SA_1, GB/SA_2, PB/SA_1, PB/SA_2, AM1/SM5.2R and SM5.0R. The results showed that for organic molecules the SAWSA v2.0 model is better than the other six solvation models. For proteins, the model classified the atoms into 20 basic types and the predicted aqueous free energies of solvation by PB/SA were used for fitting. The solvation model based on the new parameters was employed to predict the solvation free energies of 38 proteins. The predicted values from our model were in good agreement with those from the PB/SA model and were much better than those given by the other four models developed for proteins.Figure The definition of hydrophobic carbons. Here CA, CB and CD are three carbon atoms; X represents a heteroatom. According to our definition, CB is a hydrophobic carbon, CA is not a hydrophobic carbon because a heteroatom is within four atoms and CD is not a hydrophobic carbon because CD is sp²- hydridized and in a six-member ring.Electronic Supplementary Material Supplementary material is available for this article at     

High-yield purification of lung surfactant proteins sp-b and sp-c and the effects on surface activity

Several protocols for purification of milligram quantities of lung surfactant proteins (SP)-B and SP-C were studied for separation efficiency and surface activity of the isolated proteins recombined with synthetic phospholipids (SPL). SP-B and SP-C were obtained from calf lung surfactant extract by C8 chromatography with isocratic elution by either of three solvent systems: 7:1:0.4 MeOH/CHCl(3)/5% 0.1 M HCl (solvent A), 7:1 MeOH/CHCl(3)+ 0.1% TFA (solvent B), and 7:1:0.4 MeOH/CHCl(3)/H(2)O + 0.1% TFA (solvent C). Solvents A and C yielded pure apoprotein in a single pass, with estimated total protein recoveries of >85 and >90%, respectively. Solvent B was less effective in purifying SP-B and SP-C, had a lower recovery efficiency, and gave isolates with less surface activity. Mixtures of SPL plus SP-B eluted with solvents A and C adsorbed to equilibrium surface tensions of 21-22 mN/m and reached minimum surface tensions <1 mN/m during dynamic cycling. Mixtures of SPL with SP-C obtained with solvents A and C had equilibrium surface tensions of 26-27 mN/m and minimum dynamic values of 2-7 mN/m. The ability to obtain milligrams of virtually lipid-free SP-B and SP-C in a single column pass will facilitate research on their biological, structural, and biophysical properties.     

Use of electrospray ionization liquid chromatography-mass spectrometry to study the role of CYP2D^ in the in vitro metabolism of 5-hydroxytryptamine receptor antagonists

An electrospray ionization liquid chromatographic-mass spectrometric (ESI-LC-MS) method has been developed to study the involvement of the cytochrome P450 isoenzyme CYP2D6 in the in vitro metabolism of the indole containing 5-hydroxytryptamine (5-HT₃) receptor antagonists tropisetron, ondansetron and dolasetron in human liver microsomes. Compounds were eluted using linear gradients of acetonitrile-20 mM ammonium acetate, solvent A, (10:90, v/v) (ph 6.0) and solvent B, (60:40, v/v) (pH 6.0) and a Nucleosil C₄ column. Microsomal incubations were analysed using selected ion monitoring of the molecular ion of parent drug and the molecular ion of hydroxylated metabolites. The involvement of CYP2D6 in drug metabolism was assessed by inhibition studies using quinidine (5 μM), a specific inhibitor of human CYP2D6, as well as by incubating compounds with microsomes prepared from celss transfected with cDNA encoding human CYP2D6. Results showed that the oxidation of all three compounds involved CYP2D6, but only that of tropisetron was inhibited by over 90% in the presence of quinidine. The present method can be applied to pre-clinical compounds, at an early stage of drug discovery, to assess the involvement of CYP2D6 in their metabolism and to screen for those compounds where CYP2D6 is the only isoenzyme implicated in the formation of major metabolites.     

Diffusion and saponification inside porous cellulose triacetate fibers

Cellulose triacetate (CTA) fibers were partially hydrolyzed in 0.054 N solutions of NaOH/H(2)O and NaOMe/MeOH. The surface concentration of acetyl groups was determined using ATR-FTIR. Total acetyl content was determined by the alkaline hydrolysis method. Fiber cross-sections were stained with Congo red in order to examine the interface between reacted and unreacted material; these data were used to estimate the rate constant k and effective diffusivity D(B) for each reagent during the early stages of reaction by means of a volume-based unreacted core model. For NaOH/H(2)O, k = 0.37 L mol(-1) min(-1) and D(B) = 6.2 x 10(-7) cm(2)/sec; for NaOMe/MeOH, k = 4.0 L mol(-1) min(-1) and D(B) = 5.7 x 10(-6) cm(2)/sec. The NaOMe/MeOH reaction has a larger rate constant due to solvent effects and the greater nucleophilicity of MeO(-) as compared to OH(-); the reaction has a larger effective diffusivity because CTA swells more in MeOH than it does in water. Similarities between calculated concentration profiles for each case indicate that the relatively diffuse interface seen in fibers from the NaOMe/MeOH reaction results from factors not considered in the model; shrinkage of stained fiber cross-sections suggests that increased disruption of intermolecular forces may be the cause.     

Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors

Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein / ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1) / inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann / surface area (MM / PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects.     

Effects of organic solvents on the enzyme activity of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase in calorimetric assays

In drug discovery programs, dimethyl sulfoxide (DMSO) is a standard solvent widely used in biochemical assays. Despite the extensive use and study of enzymes in the presence of organic solvents, for some enzymes the effect of organic solvent is unknown. Macromolecular targets may be affected by the presence of different solvents in such a way that conformational changes perturb their active site structure accompanied by dramatic variations in activity when performing biochemical screenings. To address this issue, in this work we studied the effects of two organic solvents, DMSO and methanol (MeOH), in the isothermal titration calorimetry (ITC) kinetic assays for the catalyzed reaction of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Trypanosoma cruzi. The solvent effects on T. cruzi GAPDH had not yet been studied. This enzyme was shown here to be affected by the organic solvents content up to 5.0% for MeOH and up to 7.5% for DMSO. The results show that when GAPDH is assayed in the presence of DMSO (5%, v/v) using the ITC experiment, the enzyme exhibits approximately twofold higher activity than that of GAPDH with no cosolvent added. When MeOH (5%, v/v) is the cosolvent, the GAPDH activity is sixfold higher. The favorable effects of the organic solvents on the Michaelis-Menten enzyme-substrate complex formation ensure the consistency of the biological assays, structural integrity of the protein, and reproducibility over the measurement time. The reaction was also kinetically monitored by standard spectrophotometric assays to establish a behavioral performance of T. cruzi GAPDH when used for screening of potential inhibitors.     

Intermembrane distance in multilamellar vesicles of phosphatidylcholine depends on the interaction free energy between solvents and the hydrophilic segments of the membrane surface

To investigate the interaction of the surface of biomembranes with solvents systematically, we have studied the structure and phase behavior of multilamellar vesicles of dipalmitoylphosphatidylcholine (DPPC) and 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) in dimethylformamide (DMF)-water mixture by X-ray diffraction and differential scanning calorimetry. The solubility of phosphorylcholine, which is the same molecular structure as the head-group of phosphatidylcholine (PC), decreased with an increase in DMF concentration. This result indicates that DMF is a poor solvent for the hydrophilic segments of the surface of the PC membrane, and interaction free energy of the hydrophilic segments of the membrane surface with solvents increases with an increase in DMF concentration. X-ray diffraction data indicated that DPPC-MLVs were in the bilayer gel phase from 0 to 80% (v/v) DMF, and that the spacing (lamellar repeat period) and intermembrane distance of DPPC-MLV decreased with an increase in DMF concentration. Main transition temperature and pre-transition temperature of DPPC-MLV increased with an increase in DMF concentration, and above 50% (v/v) DMF there was no pre-transition. In the interaction of POPC-MLV with DMF, X-ray diffraction data indicated that POPC-MLVs were in L(alpha) phase (liquid-crystalline phase) from 0 to 80% (v/v) DMF, and that the spacing and intermembrane distance of POPC-MLV decreased with an increase in DMF concentration. These results are discussed by the change of the interaction free energy between the hydrophilic segments of the membrane surface and solvents. As DMF concentration increases, this interaction free energy may increase, resulting in the decrease of the intermembrane distance of PC-MLVs.     

Pseudo-dynamic contact surface areas: estimation of apolar bonding

A new Monte Carlo based algorithm has been written for the computation of pseudo-dynamic contact surface areas. The linear correlation of this contact area with solute transfer free energies (water leads to organic liquid) is established for apolar amino acid side chains. The slope of these linear plots, deltaGosp, is a unitary free energy which has potential use in the estimation of apolar bond free energies in proteins. The magnitude of deltaGosp is dependent upon the nature of the organic solvent involved in the transfer process, varying from 86 to 130 cal/A2. Analogues linear correlations with the same range of deltaGosp values are observed for inhibitors of protein-catalyzed reactions.     

Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins

Potentials of mean force (PMFs) of three-body hydrophobic association are investigated to gain insight into similar processes in protein folding. Free energy landscapes obtained from explicit simulations of three methanes in water are compared with that predicted by popular implicit-solvent effective potentials for the study of proteins. Explicit-water simulations show that for an extended range of three-methane configurations, hydrophobic association at 25 degrees C under atmospheric pressure is mostly anti-cooperative, that is, less favorable than if the interaction free energies were pairwise additive. Effects of free energy nonadditivity on the kinetic path of association and the temperature dependence of additivity are explored by using a three-methane system and simplified chain models. The prevalence of anti-cooperativity under ambient conditions suggests that driving forces other than hydrophobicity also play critical roles in protein thermodynamic cooperativity. We evaluate the effectiveness of several implicit-solvent potentials in mimicking explicit water simulated three-body PMFs. The favorability of the contact free energy minimum is found to be drastically overestimated by solvent accessible surface area (SASA). Both the SASA and a volume-based Gaussian solvent exclusion model fail to predict the desolvation barrier. However, this barrier is qualitatively captured by the molecular surface area model and a recent "hydrophobic force field." None of the implicit-solvent models tested are accurate for the entire range of three-methane configurations and several other thermodynamic signatures considered.