A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation

We describe an efficient solvation model for proteins. In this model atomic solvation parameters imitating the hydrocarbon core of a membrane, water, and weak polar solvent (octanol) were developed. An optimal number of solvation parameters was chosen based on analysis of atomic hydrophobicities and fitting experimental free energies of gas-cyclohexane, gas-water, and octanol-water transfer for amino acids. The solvation energy term incorporated into the ECEPP/2 potential energy function was tested in Monte Carlo simulations of a number of small peptides with known energies of bilayer-water and octanol-water transfer. The calculated properties were shown to agree reasonably well with the experimental data. Furthermore, the solvation model was used to assess membrane-promoting alpha-helix formation. To accomplish this, all-atom models of 20-residue homopolypeptides-poly-Leu, poly-Val, poly-Ile, and poly-Gly in initial random coil conformation-were subjected to nonrestrained Monte Carlo conformational search in vacuo and with the solvation terms mimicking the water and hydrophobic parts of the bilayer. All the peptides demonstrated their largest helix-forming tendencies in a nonpolar environment, where the lowest-energy conformers of poly-Leu, Val, Ile revealed 100, 95, and 80% of alpha-helical content, respectively. Energetic and conformational properties of Gly in all environments were shown to be different from those observed for residues with hydrophobic side chains. Applications of the solvation model to simulations of peptides and proteins in the presence of membrane, along with limitations of the approach, are discussed.     

Photophysics, photochemistry, and reactivity: molecular aspects of perylenequinone reactions.

Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) were used to elucidate the photochemistry and photophysics of eight different perylenequinones (PQ). The objective of this work has been to quantitatively investigate the photodynamic therapeutic potential of this family of compounds and give an overview of their photoreactivity. The effects of solvation were evaluated through single-point calculations using the integral equation formalism of the polarised continuum model. It is concluded that the eight studied perylenequinones can generate singlet oxygen (in aqueous solution) and superoxide radical anions, and that the autoionisation of two nearby PQ molecules is possible.     

Correlation between octanol/water and liposome/water distribution coefficients and drug absorption of a set of pharmacologically active compounds

Abstract

Absorption and consequent therapeutic action are key issues in the development of new drugs by the pharmaceutical industry. In this sense, different models can be used to simulate biological membranes to predict the absorption of a drug. This work compared the octanol/water and the liposome/water models. The parameters used to relate the two models were the distribution coefficients between liposomes and water and octanol and water and the fraction of drug orally absorbed. For this study, 66 drugs were collected from literature sources and divided into four groups according to charge and ionization degree: neutral; positively charged; negatively charged; and partially ionized/zwitterionic. The results show a satisfactory linear correlation between the octanol and liposome systems for the neutral (R^2?=?0.9324) and partially ionized compounds (R^2?=?0.9367), contrary to the positive (R^2?=?0.4684) and negatively charged compounds (R^2?=?0.1487). In the case of neutral drugs, results were similar in both models because of the high fraction orally absorbed. However, for the charged drugs (positively, negatively, and partially ionized/zwitterionic), the liposomal model has a more-appropriate correlation with absorption than the octanol model. These results show that the neutral compounds only interact with membranes through hydrophobic bonds, whereas charged drugs favor electrostatic interactions established with the liposomes. With this work, we concluded that liposomes may be a more-appropriate biomembrane model than octanol for charged compounds.     

Prediction of the aqueous solvation free energy of organic compounds by using autocorrelation of molecular electrostatic potential surface properties combined with response surface analysis

Several quantitative structure-property relationship (QSPR) approaches have been explored for the prediction of aqueous solubility or aqueous solvation free energies, DeltaG(sol), as crucial parameter affecting the pharmacokinetic profile and toxicity of chemical compounds. It is mostly accepted that aqueous solvation free energies can be expressed quantitatively in terms of properties of the molecular surface electrostatic potentials of the solutes. In the present study we have introduced autocorrelation molecular electrostatic potential (autoMEP) vectors in combination with nonlinear response surface analysis (RSA) as alternative 3D-QSPR strategy to evaluate the aqueous solvation free energy of organic compounds. A robust QSPR model (r(cv)=0.93) has been obtained by using a collection of 248 organic chemicals. An external test set based on 23 molecules confirmed the good predictivity of the autoMEP/RSA model suggesting its further applicability in the in silico prediction of water solubility of large organic compound libraries.     

Combined theoretical studies on solvation and hydrogen bond interactions in glycine tripeptide

The theoretical conformational analysis of glycine tripeptide (GT) has been carried out by molecular dynamics (MD) method in order to find minimum energy conformations. The MD studies on GT with water have been carried out for over 10 ns with a time step of 2 fs using fixed charge force field (AMBER ff03). By adding the solvation effect using water as a solvent, the GT conformers identified in this study exhibit α-helical conformation. Compared with the earlier reports, this MD study is able to identify the energetically favourable GT conformations. The obtained geometry of the five most stable GT conformations was optimised using the density functional theory method at B3LYP/6-311G** level of theory. Subsequently, the effects of solvation on the conformational characteristics of five most stable GT conformers with four water molecules (the number of water molecules in the first solvation shell of GT obtained from MD study) were investigated using the same method and the same level of theory. The effect of microsolvation on the fifth GT conformer has been studied with a cluster of 11 water molecules as the first hydration shell which generates folded structure. The interaction energies of all the complexes are calculated by correcting the basis set superposition error. The strong hydrogen bond mainly contributes to the interaction energies. The atoms in molecules theory and natural bond orbital analysis were used to study the origin of H-bonds. A good correlation between the structural parameters and the properties of charge density is found. NMR calculations show that the C = O carbons of the amine groups of the first and middle glycine fragments have maximum chemical shifts.     

Some physicochemical properties of the antitumor drug thiotepa and its metabolite tepa as obtained by density functional theory (DFT) calculations

Density functional theory (DFT) using the B3LYP functional was applied to elucidate the molecular properties of the antitumor drug thiotepa and its main metabolite tepa. Aqueous solvent effects were introduced using the conductor-like polarizable continuum model (CPCM). The protocol for calculating the pK _a values obtained with different cavity models was tested on a series of aziridine and phosphoramide compounds. An efficient computational scheme has been identified that uses the CPCM model of solvation with a universal force field (UFF) cavity. The method has been used to evaluate the basicities of thiotepa and its metabolite. Our calculations show that the basicities of the aziridine moiety of thiotepa and tepa are dramatically reduced compared to free aziridine, indicating that highly acidic media are needed to produce substantial yields of the N-protonated form of the drug. Finally, the mechanisms of reaction of the drug and its metabolite are discussed based on our theoretical results. The calculations reproduce the experimental trends very satisfactorily.     

Theoretical proton affinities of alpha1 adrenoceptor ligands

A systematic study has been performed of the proton affinity of a large family of agonists and antagonists of the alpha1-adrenoceptor at the B3LYP/6-31G* level of theory. After a conformational search, all the N atoms were considered as protonation sites and protonation energy values were determined. The inclusion of solvation by means of the Onsager model yielded stabilization in the proton affinity values obtained. In addition, a good correlation was found between the proton affinity values corresponding to the first protonation in gas phase of some of the compounds and their corresponding experimental affinity constants K(i) for the alpha1A adrenergic receptor.     

Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study

Background

Novel pentacycloundecane (PCU)-lactone-CO-EAIS peptide inhibitors were designed, synthesized, and evaluated against wild-type C-South African (C-SA) HIV-1 protease. Three compounds are reported herein, two of which displayed IC₅₀ values of less than 1.00 μM. A comparative MM-PB(GB)SA binding free energy of solvation values of PCU-lactam and lactone models and their enantiomers as well as the PCU-lactam-NH-EAIS and lactone-CO-EAIS peptide inhibitors and their corresponding diastereomers complexed with South African HIV protease (C-SA) was performed. This will enable us to rationalize the considerable difference between inhibitory concentration (IC₅₀) of PCU-lactam-NH-EAIS and PCU-lactone-CO-EAIS peptides.

Results

The PCU-lactam model exhibited more negative calculated binding free energies of solvation than the PCU-lactone model. The same trend was observed for the PCU-peptide inhibitors, which correspond to the experimental activities for the PCU-lactam-NH-EAIS peptide (IC₅₀ = 0.076 μM) and the PCU-lactone-CO-EAIS peptide inhibitors (IC₅₀ = 0.850 μM). Furthermore, a density functional theory (DFT) study on the natural atomic charges of the nitrogen and oxygen atoms of the three PCU-lactam, PCU-lactim and PCU-lactone models were performed using natural bond orbital (NBO) analysis. Electrostatic potential maps were also used to visualize the electron density around electron-rich regions. The asymmetry parameter (η) and quadrupole coupling constant (χ) values of the nitrogen and oxygen nuclei of the model compounds were calculated at the same level of theory. Electronic molecular properties including polarizability and electric dipole moments were also calculated and compared. The Gibbs theoretical free solvation energies of solvation (∆G_solv) were also considered.

Conclusions

A general trend is observed that the lactam species appears to have a larger negative charge distribution around the heteroatoms, larger quadrupole constant, dipole moment and better solvation energy, in comparison to the PCU-lactone model. It can be argued that these characteristics will ensure better eletronic interaction between the lactam and the receptor, corresponding to the observed HIV protease activities in terms of experimental IC₅₀ data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-015-0115-5) contains supplementary material, which is available to authorized users.     

Theoretical studies on solvation contribution to the thermodynamic stability of mutants of lysozyme T4

Atomic solvation parameters (ASPs) are widely used to estimate the solvation contribution to the thermodynamic stability of proteins as well as the free energy of association for protein-ligand complexes. In view of discrepancies in the results of free energies of solvation of folding for various proteins obtained using different atomic solvation parameter sets, systematic studies have been carried out for the calculation of accessible surface area and the changes in free energy of solvation of folding (deltaG(s,f)) for mutants of lysozyme T4 where threonine 157 is replaced by amino acids: cysteine, aspartate, glutamate, phenylalanine, glycine, histidine, isoleucine, leucine, asparagine, arginine, serine and valine. The deviations of the calculated results from the experimental results are discussed to highlight the discrepancies in the atomic solvation parameter sets and possible reasons for them. The results are also discussed to throw light on the effect of chain free energy and hydrogen bonding on the stability of mutants. The octanol to water-based ASP sets 'Sch1' and 'EM' perform better than the vacuum to water-based ASP sets. The vacuum to water-based ASP sets 'Sch3' and 'WE' can be used to predict the stability of mutants if a proper method to calculate the hydrogen bond contribution to overall stability is in place.     

Binding measurements of indolocarbazole derivatives to immobilised human serum albumin by high-performance liquid chromatography

The binding properties of six indolocarbazole derivatives have been measured using immobilised human serum albumin (HSA) in an HPLC column. The compounds showed very strong binding to HSA which necessitated the application of a 30 to 40% concentration of 2-propanol in the mobile phase. This represents a much higher concentration than is recommended by the column manufacturers. This HSA column had not changed its binding property when it was used again with 4% 2-propanol and 96% phosphate buffer. The binding parameters were estimated by extrapolation to 0% 2-propanol and were above 99% for each indolocarbazole derivative. The correlation analysis, including the calculated octanol/water partition coefficient (logP),pK_a values as well as measured reversed-phase retention data of the compounds, revealed that the extremely strong binding can be explained by the hydrophobic and acidic properties of the compounds.     

Accurate Aqueous Proton Dissociation Constants Calculations for Selected Angiotensin-Converting Enzyme Inhibitors

Abstract

Studies that allow computing values of aqueous proton dissociation constants (pK_a), gas phase proton affinities, and the free energy of solvation have been performed for six members of angiotensin-I-converting enzyme (ACE) inhibitor family (captopril, enalaprilat, imidaprilat, ramiprilat, perindoprilat, and spiraprilat). Density functional theory (DFT) calculations using PBE1PBE functional on optimized molecular geometries have been carried out to investigate the thermodynamics of gas-phase protonation. The conductor-like polarizable continuum model (CPCM) solvation method at various levels of theory was applied to calculate the free energy of solvation for the ACE inhibitors and their respective anions. The CPCM solvation calculations were performed on both gas-phase and solvent-phase optimized structures. The combination of gas-phase and solvation energies according to the thermodynamic cycle enabled us to compute accurate pK_a values for the all studied molecules.     

Synthesis and Cytotoxicity Assessment against Human Colorectal Cancer Cell Lines of Quaternary 8-Dichloromethyl Protoberberine Alkaloids

Twenty-two quaternary 8-dichloromethylprotoberberine alkaloids were synthesized from unmodified quaternary protoberberine alkaloids (QPAs) to improve their physical and chemical properties and to obtain selectively anticancer derivatives. The synthesized derivatives showed more appropriate octanol/water partition coefficients by up to values 3–4 compared to unmodified QPA substrates. In addition, these compounds exhibited significant antiproliferative activity against colorectal cancer cells and lower toxicity on normal cells, resulting in more significant selectivity indices than unmodified QPA compounds in vitro. The IC₅₀ values of antiproliferative activity of quaternary 8-dichloromethyl-pseudoberberine 4-chlorobenzenesulfonate and quaternary 8-dichloromethyl-pseudopalmatine methanesulfonate against colorectal cancer cells are 0.31 μM and 0.41 μM, respectively, significantly stronger than those of other compounds and positive control 5-fluorouracil. These findings suggest that 8-dichloromethylation can be used as one of the modification strategies to guide the structural modification and subsequent investigation of anticancer drugs for CRC based on QPAs.     

Amino acid side-chain partition energies and distribution of residues in soluble proteins

Energies required to transfer amino acid side chains from water to less polar environments were calculated from results of several studies and compared with several statistical analyses of residue distributions in soluble proteins. An analysis that divides proteins into layers parallel with their surfaces is more informative than those that simply classify residues as exposed or buried. Most residues appear to be distributed as a function of the distance from the protein-water interface in a manner consistent with partition energies calculated from partitioning of amino acids between water and octanol phases and from solubilities of amino acids in water, ethanol, and methanol. Lys, Arg, Tyr, and Trp residues tend to concentrate near the water-protein interface where their apolar side-chain components are more buried than their polar side-chain components. Residue distributions calculated in this manner do not correlate well with side-chain solvation energies calculated from vapor pressures of side-chain analogs over a water phase. Results of statistical studies that classify residues as exposed to solvent or buried inside the protein interior appear to depend on the method used to classify residues. Data from some of these studies correlate better with solvation energies, but other data correlate better with partition energies. Most other statistical methods that have been used to evaluate effects of water on residue distributions yield results that correlate better with partition energies than with solvation energies.     

Experimental determination and calculations of redox potential descriptors of compounds directed against retroviral zinc fingers: Implications for rational drug design.

A diverse set of electrophilic compounds that react with cysteine thiolates in retroviral nucleocapsid (NC) proteins and abolish virus infectivity has been identified. Although different in chemical composition, these compounds are all oxidizing agents that lead to the ejection of Zn(II) ions bound to conserved structural motifs (zinc fingers) present in retroviral NC proteins. The reactivity of a congeneric series of aromatic disulfides toward the NC protein of the human immunodeficiency virus type 1 (HIV-1), NCp7, has been characterized by HPLC separation of starting reagents from reaction products. We calculated the absolute redox potentials of these compounds in the gas phase and in aqueous solvent, using a density functional theory method and a continuum solvation model. Pulsed polarography experiments were performed and showed a direct correlation between calculated and experimentally determined redox propensities. A dependence between protein reactivity and redox potential for a specific compound was shown: Reaction with NCp7 did not take place below a threshold value of redox potential. This relationship permits the distinction between active and nonactive compounds targeted against NCp7, and provides a theoretical basis for a scale of reactivity with retroviral zinc fingers. Our results indicate that electrophilic agents with adequate thiophilicity to react with retroviral NC fingers can now be designed using known or calculated electrochemical properties. This may assist in the design of antiretroviral compounds with greater specificity for NC protein. Such electrophilic agents can be used in retrovirus inactivation with the intent of preparing a whole-killed virus vaccine formulation that exhibits unaffected surface antigenic properties.     

Effects of electric field on alamethicin bound at the lipid-water interface: a molecular mechanics study.

A systematic molecular mechanics study of the alamethicin molecule was made to determine a set of low-energy conformers in vacuo and in aqueous environment. The behavior of these conformers was investigated at the phase boundary which was modeled as a plane dividing two compartments with solvation properties of water and octanol with a constant electric field applied normal to the boundary. The calculations were performed with a molecular mechanics program for calculation of stable conformations at the phase boundary utilizing the Empiric Conformational Energy Program for Peptides force field and the Hopfinger-Scheraga solvation model. 371 minimum energy conformers of alamethicin, determined in vacuo with the build-up procedure, were used as starting conformations for energy minimization in aqueous environment and at the phase boundary. Only 49 interphase-bound structures were within 12 kcal/mol of the minima which was found. No helical structures having values close to the canonical parameters for an alpha- or 3(10)-helix were found despite the presence of eight alpha-methylalanine residues which favor the formation of these helices; four helix-like structures were found, having all negative phi, psi values. All the helical conformers have very high energies in water (approximately 14 kcal/mol), but are quite stable at the phase boundary (3.7-6.8 kcal/mol above the lowest minima found). The implications of these results for proposed mechanisms for membrane-binding and voltage-dependent gating are considered.     

Reactivity of nitro-thiophene derivatives with electron and oxygen radicals studied by pulse radiolysis and polarographic techniques

Summary A new series of nitrothiophene derivatives have been synthetized and some of the physico-chemical parameters which can influence both their radiosensitizing efficiency and toxicity have been investigated. These include octanol/water partition coefficient (P), one-electron reduction potential (E ₇ ¹ ) and reactivity of the drugs towards primary radical species. For these studies, pulse radiolysis techniques and conventional polarography have been extensively used. Biological responses (both sensitization and toxicity) have been tested towards Chinese Hamster cells in vitro. The results are valuable in selecting, among the tested compounds, 5-NTMA, 5-NTM, 4- and 5-NTCA as the nitrothiophenes promising for in vivo applications.     

Distinctive Solvation Patterns Make Renal Osmolytes Diverse

The kidney uses mixtures of five osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, including solubility data for scyllo-inositol. It turns out that renal osmolytes fall into three distinct classes with respect to their solvation. Trimethyl-amines (GPC and glycine-betaine) are characterized by strong hard-sphere-like self-exclusion; urea, taurine, and myo-inositol have a tendency toward self-association; sorbitol and most other nonrenal osmolytes have a relatively constant, intermediate solvation that has components of both exclusion and association. The data presented here show that renal osmolytes are quite diverse with respect to their solvation patterns, and they can be further differentiated based on observations from experiments examining their effect on macromolecules. It is expected, based on the available surface groups, that each renal osmolyte has distinct effects on various classes of biomolecules. This likely allows the kidney to use specific combinations of osmolytes independently to fine-tune the chemical activities of several types of molecules.     

Molecular dynamics and quantum chemical studies of solvent effects on cyclo glycylglycine and glycylalanine dipeptides

Hydrogen bond (H-bond) interactions between the two cyclo dipeptides, cyclo(glycyl-glycine) (CGG) and cyclo(glycyl-alanine) (CGA), and water have been studied using molecular dynamics (MD) and quantum chemical methods. The MD studies have been carried out on CGG and CGA in water using fixed charge force field (AMBER ff03) for over 10 ns with a MD time step of 2 fs. The results of this study show that the solvation pattern influences the conformations of the cyclo dipeptides. Following molecular simulations, post Hartree–Fock and density functional theory methods have been used to explore the molecular properties of the cyclo dipeptides in gaseous and aqueous phase environments. The self-consistent reaction field theory has been used to optimise the cyclopeptides in diethyl ether (? = 4.3) and water (? = 78.5), and the solvent effects have been analysed. A cluster of eight water molecules leads to the formation of first solvation shell of CGG and CGA and the strong H-bonding mainly contributes to the interaction energies. The H-bond interactions have been analysed by the calculation of electron density ρ(r) and its Laplacian ▽²ρ(r) at bond critical points using atoms in molecules theory. The natural bond orbital analysis was carried out to reveal the nature of H-bond interactions. In the solvated complexes, the keto carbons registered the maximum NMR chemical shifts.