分子动力学模拟研究质子化态在HIV-1 Protease-Indinavir复合物中的作用

I 型人体免疫缺陷病毒(HIV-1)蛋白酶中Asp25/Asp25'的质子化对于理论研究HIV-1 蛋白酶和抑制剂的作用机制
以及氨基酸变异对抗药性的影响有重要意义. 分别对Protease-Indinavir (PR-IDV)复合物的六种可能的质子化态进行了
5 ns 的分子动力学模拟, 分析了不同状态对动力学特征和结构的影响, 用molecular mechanics/Possion-Boltzman surface
area (MM-PBSA)方法计算了PR 和IDV 在各种状态下的结合自由能. 计算结果说明A 链Asp25 的OD2 的质子化是最
为可能的状态. 对PR-IDV 复合物中起到媒介作用的水分子与PR-IDV 复合物形成的氢键进行了分析, 分析结果说明不
同的质子化态对水分子在PR-IDV 复合物中所起的媒介作用没有影响, 这一结果与我们先前对PR-BEA369 复合物的研
究不同. 我们的研究结果为更高效的PR 抑制剂的设计以及PR 氨基酸变异对药物抗药性的研究提供了理论上的指导.     

Constant pH molecular dynamics in generalized Born implicit solvent

A new method is proposed for constant pH molecular dynamics (MD), employing generalized Born (GB) electrostatics. Protonation states are modeled with different charge sets, and titrating residues sample a Boltzmann distribution of protonation states as the simulation progresses, using Monte Carlo sampling based on GB-derived energies. The method is applied to four different crystal structures of hen egg-white lysozyme (HEWL). pK(a) predictions derived from the simulations have root-mean-square (RMS) error of 0.82 relative to experimental values. Similarity of results between the four crystal structures shows the method to be independent of starting crystal structure; this is in contrast to most electrostatics-only models. A strong correlation between conformation and protonation state is noted and quantitatively analyzed, emphasizing the importance of sampling protonation states in conjunction with dynamics.     

Aluminum speciation in biological environments. The deprotonation of free and aluminum bound citrate in aqueous solution

Citrate is the main low mass molecule chelator of aluminum in serum, and knowledge of the interaction mode of this organic molecule with this cation is necessary to understand aluminum speciation in biosystems. However, the 1?∶?1 complexation of citric acid to Al(iii) is a complex process due to the myriad of coordination sites and protonation states of this molecule. Moreover, due to the acidic character of the complex, its entire experimental characterization is elusive. The system is also challenging from a computational point of view, due to the difficulties in getting a balanced estimation of the large range of solvation free energies encountered for the different protonation states of a multiprotic acid in both situations, complexed and uncomplexed with a trivalent cation. Herein, the deprotonation process of the free citric acid in solution and that interacting with Al(iii) have been investigated considering all possible coordination modes and protonation states of the citric acid. All the structures were optimized in solution combining the B3LYP density function method with the polarizable continuum IEFPCM model. In addition, different schemes have been employed to obtain reliable solvation energies. Taking into account the most stable isomer of each protonation state, the pK(a) values were computationally estimated for the free citric acid and that interacting with Al(iii), showing a good agreement with the experimental data. All these results shed light on how the deprotonation process of the citric acid takes place, and show that Al(iii) not only increases the acidity of the molecule, but also changes qualitatively the deprotonation pattern of the citric acid. This information is highly relevant to understand aluminum speciation in biological environments, for which citrate is the main low molecular weight chelator, and responsible for its cellular in-take.     

Structure-function relationship of amino acid-[2]rotaxanes

Synthetic methodology was developed to construct amino acid-[2]rotaxanes that have phenylalanine and 3,5-di-tert-butylbenzene as blocking groups and dibenzo-24-crown-8, derivatized with either N-acetylargininyl or a carboxylic group, as the ring. A relative measure of the intramolecular interaction energies between the functional groups in DMSO/water mixtures is obtained by comparing their pK(a) values. Rotaxane structures were investigated through 2D NMR analysis and molecular dynamics simulations. Association constants for complexes of amino acids and rotaxanes in various protonation states were determined in a variety of solvent systems by (1)H NMR analysis. The unique intracomponent interactions that exist in the rotaxanes and their ability to act as artificial receptors are discussed.     

Effect of temperature on the chromatographic retention of ionizable compounds. III. Modeling retention of pharmaceuticals as a function of eluent pH and column temperature in RPLC

We propose a general simple equation for accurately predicting the retention factors of ionizable compounds upon simultaneous changes in mobile phase pH and column temperature at a given hydroorganic solvent composition. Only four independent experiments provide the input data: retention factors measured in two pH buffered mobile phases at extreme acidic and basic pH values (e. g., at least +/- 2 pH units far from the analyte pK(a)) and at two column temperatures. The equations, derived from the basic thermodynamics of the acid-base equilibria, additionally require the knowledge of the solute pK(a )and enthalpies of acid-base dissociation of both the solute and the buffer components in the hydroorganic solvent mixture. The performance of the predictive model is corroborated with the comparison between theoretical and experimental retention factors of several weak acids and bases of important pharmacological activity, in mobile phases containing different buffer solutions prepared in 25% w/w ACN in water and at several temperatures.     

First-principles prediction of the pK(a)s of anti-inflammatory oxicams

The gas- and aqueous-phase acidities of a series of oxicams have been computed by combining M05-2X/6-311+G(3df,2p) gas-phase free energies with solvation free energies from the CPCM-UAKS, COSMO-RS, and SMD solvent models. To facilitate accurate gas-phase calculations, a benchmarking study was further carried out to assess the performance of various density functional theory methods against the high-level composite method G3MP2(+). Oxicams are typically diprotic acids, and several tautomers are possible in each protonation state. The direct thermodynamic cycle and the proton exchange scheme have been employed to compute the microscopic pK(a)s on both solution- and gas-phase equilibrium conformers, and these were combined to yield the macroscopic pK(a) values. Using the direct cycle of pK(a) calculation, the CPCM-UAKS model delivered reasonably accurate results with MAD ~ 1, whereas the SMD and COSMO-RS models' performance was less satisfactory with MAD ~ 3. Comparison with experiment also indicates that direct cycle calculations based on solution conformers generally deliver better accuracy. The proton exchange cycle affords further improvement for all solvent models through systematic error cancellation and therefore provides better reliability for the pK(a) prediction of compounds of these types. The latter approach has been applied to predict the pK(a)s of several recently synthesized oxicam derivatives.     

DFT/electrostatic calculations of pK(a) values in cytochrome c oxidase

Using classical electrostatic calculations, earlier we examined the dependence of the protonation state of bovine cytochrome c oxidase (CcO) on its redox state. Based on these calculations, we have proposed a model of CcO proton pumping that involves His291, one of the Cu(B) histidine ligands, which was found to respond to redox changes of the enzyme Fe(a)(3)-Cu(B) catalytic center. In this work, we employ combined density functional and continuum electrostatic calculations to evaluate the pK(a)() values of His291 and Glu242, two key residues of the model. The pK(a) values are calculated for different redox states of the enzyme, and the influence of different factors on the pK(a)'s is analyzed in detail. The calculated pK(a)() values of Glu242 are between 9.4 and 12.0, depending on the redox state of the protein, which is in excellent agreement with recent experimental measurements. Assuming the reduced state of heme a(3), His291 of the oxidized Cu(B) center possesses a pK(a)() between 2.1 and 4.0, while His291 of the reduced Cu(B) center has a pK(a) above 17. The obtained results support the proposal that the His291 ligand of the Cu(B) center in CcO is a proton pump element.     

Chemistry of covalent inhibition of the gastric (H+, K+)-ATPase by proton pump inhibitors

Proton pump inhibitors (PPIs), drugs that are widely used for treatment of acid related diseases, are either substituted pyridylmethylsulfinyl benzimidazole or imidazopyridine derivatives. They are all prodrugs that inhibit the acid-secreting gastric (H(+), K(+))-ATPase by acid activation to reactive thiophiles that form disulfide bonds with one or more cysteines accessible from the exoplasmic surface of the enzyme. This unique acid-catalysis mechanism had been ascribed to the nucleophilicity of the pyridine ring. However, the data obtained here show that their conversion to the reactive cationic thiophilic sulfenic acid or sulfenamide depends mainly not on pyridine protonation but on a second protonation of the imidazole component that increases the electrophilicity of the C-2 position on the imidazole. This protonation results in reaction of the C-2 with the unprotonated fraction of the pyridine ring to form the reactive derivatives. The relevant PPI pK(a)'s were determined by UV spectroscopy of the benzimidazole or imidazopyridine sulfinylmethyl moieties at different medium pH. Synthesis of a relatively acid stable analogue, N(1)-methyl lansoprazole, (6b), allowed direct determination of both pK(a) values of this intact PPI allowing calculation of the two pK(a) values for all the PPIs. These values predict their relative acid stability and thus the rate of reaction with cysteines of the active proton pump at the pH of the secreting parietal cell. The PPI accumulates in the secretory canaliculus of the parietal cell due to pyridine protonation then binds to the pump and is activated by the second protonation on the surface of the protein to allow disulfide formation.     

Preparative separation of isomeric and stereoisomeric dicarboxylic acids by pH-zone-refining counter-current chromatography

This work involves the preparative separation of some isomeric dicarboxylic acids using pH-zone-refining counter-current chromatography (CCC), a relatively new preparative technique for the separation of ionizable compounds. The paper concentrates especially on the separation of a synthetic mixture of closely related cis and trans pairs of 1-methyl- and 1,3-dimethyl-1,3-cyclohexanedicarboxylic acids. The elution sequence of the isomers is discussed in terms of their relative acidities (pK(a) values) in solution and gas phase, hydrophobicities, and steric configuration. Two possible explanations are suggested for the mechanism of separation. They both involve the amount of retainer acid used, as it affects the separation and plays a role in the chemohydrodynamic equilibrium of the dicarboxylic acids in the column.     

Diprotonation process of meso-tetraphenylporphyrin derivatives designed for photodynamic therapy of cancers: from multivariate curve resolution to predictive QSPR modeling

Tetrapyrrole rings possess four nitrogen atoms, two of which act as Br?ndsted bases in acidic media. The two protonation steps occur on a close pH range, particularly in the case of meso-tetraphenylporphyrin (TPP) derivatives. If the cause of this phenomenon is well known--a protonation-induced distortion of the porphyrin ring--data on stepwise protonation constants and on electronic absorption spectra of monoprotonated TPPs are sparse. A multivariate approach has been systematically applied to a series of glycoconjugated and hydroxylated TPPs, potential anticancer drugs usable in Photodynamic Therapy. The dual purpose was determination of protonation constants and linking substitution with basicity. Hard-modeling version of MCR-ALS (Multivariate Curve Resolution Alternating Least Squares) has given access to spectra and distribution profile of pure components. Spectra of monoprotonated species (H(3)TPP(+)) in solution resemble those of diprotonated species (H(4)TPP(2+)), mainly differing by a slight blue-shift of bands. Overlap of H(3)TPP(+) and H(4)TPP(2+) spectra reinforces the difficulty to evidence an intermediate form only present in low relative abundance. Depending on macrocycle substitution, pK values ranged from 3.5±0.1 to 5.1±0.1 for the first protonation and from 3.2±0.2 to 4.9±0.1 for the second one. Inner nitrogens' basicity is affected by position, number and nature of peripheral substituents depending on their electrodonating character. pK values have been used to establish a predictive Multiple Linear Regression (MLR) model, relying on atom-type electrotopological indices. This model accurately describes our results and should be applied to new TPP derivatives in a drug-design perspective.     

Superoxide radical anion adduct of 5,5-dimethyl-1-pyrroline n-oxide (DMPO). 1. The thermodynamics of formation and its acidity

The nitrone 5,5-dimethyl-1-pyrroline N-oxide (DMPO) has been the most widely used spin trap for the detection of transient free radicals in chemical, biological, and biomedical research using electron paramagnetic resonance (EPR) spectroscopy. A density functional theory (DFT) approach was used to predict the thermodynamics of formation of the superoxide anion/hydroperoxyl radical (O2*-/*O2H) adduct of DMPO as well as its pK(a) in aqueous systems. At the B3LYP/6-31+G(d,p)//B3LYP/6-31G(d) level, we predicted (in the gas phase and with a polarizable continuum model (PCM) for water) three conformational minima for both the DMPO-O2- and DMPO-O2H adducts. Using DFT and the PCM solvation method, the pK(a) of DMPO-O2H was predicted to be 14.9 +/- 0.5. On the basis of free energy considerations, the formation of DMPO-O2H at neutral pH proceeds via initial addition of O2*- to DMPO to form the DMPO-O2- adduct and then subsequent protonation by water (or other acidic sources) to form DMPO-O2H. Under acidic conditions, the addition of *O2H to DMPO is predicted to be more exoergic than the addition of O2*- and is consistent with available experimental kinetic data.     

The active site of a zinc-dependent metalloproteinase influences the computed pK(a) of ligands coordinated to the catalytic zinc ion

TNF-alpha converting enzyme (TACE) is a multidomain, membrane-anchored protein that includes a Zn-dependent protease domain. It releases the soluble form of cytokine tumor necrosis factor-alpha (TNF-alpha) from its membrane-bound precursor. TACE is a metalloprotease containing a catalytic glutamic acid, Glu-406, and a Zn(2+) ion ligated to three imidazoles. The protonation states of the active site glutamic acid and inhibitors are important factors in understanding the potency of inhibitors with acidic zinc-ligating groups such as hydroxamic and carboxylic acids. Density functional methods were utilized to compute pK(a) values using a model of the catalytic site of TACE and to predict a concomitant mechanism of binding, consistent with lowering the pK(a) of the bound ligand and raising the pK(a) of the active site Glu-406. Weak acids, such as hydroxamic acids, bind in their neutral form and then transfer an acidic proton to Glu-406. Stronger acids, such as carboxylic acids, bind in their anionic form and require preprotonation of Glu-406. Similar binding events would be expected for other zinc-dependent proteases.     

Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and (15)N NMR

The acid/base character of nucleobases affects phenomena such as self-association, interaction with metal ions, molecular recognition by proteins, and nucleic acid base-pairing. Therefore, the investigation of proton-transfer equilibria of natural and synthetic nucleos(t)ides is of great importance to obtain a deeper understanding of these phenomena. For this purpose, a set of ATP prototypes was investigated using (15)N NMR spectroscopy, and the corresponding adenine bases were investigated by theoretical calculations. (15)N NMR measurements provided not only acidity constants but also information on the protonation site(s) on the adenine ring and regarding the ratio of the singly protonated species in equilibrium. Substituents of different nature and position on the adenine ring did not change the preferred protonation site, which remained N1. However, for 2-thioether-ATP derivatives a mixed population of N1 and N7 singly protonated species was observed. Reduction of basicity of 0.4-1 pK(a) units relative to ATP was also observed for all evaluated ATP derivatives, except for 2-Cl-ATP, for which K(a) was ca. 10,000-fold lower. To explain the substitution-dependent variations in the experimental pK(a) values of the ATP analogues, gas-phase proton affinities (PA), Delta Delta G(hyd), and pK(a) values of the corresponding adenine bases were calculated using quantum mechanical methods. The computed PA and Delta Delta G(hyd) values successfully explained the experimental pK(a) values. A computational procedure for the prediction of accurate pK(a) values was developed using density functional theory and polarizable continuum model calculations. In this procedure, we developed a set of parameters for the polarizable continuum model that was fitted to reproduce experimental pK(a) values of nitrogen heterocycles. This method is proposed for the prediction of pK(a) values and protonation site(s) of purine analogues that have not been synthesized or analyzed.     

A reliable and efficient first principles-based method for predicting pKa values. III. Adding explicit water molecules: Can the theoretical slope be reproduced and pKa values predicted more accurately?

A popular method for predicting pK(a) values for organic molecules in aqueous solution is to establish empirical linear least-squares fits between calculated deprotonation energies and known experimental pK(a) values. In virtually all such calculations, the empirically observed slope of the pK(a) vs. ΔE fit is significantly less than the theoretical value, 1/(2.303RT) (which is 0.73 mol/kcal at room temperature). In our own continuum solvation calculations (Zhang et al., J Phys Chem A 2010, 114, 432), the empirical slope for carboxylic acids was only 0.23 mol/kcal, despite the excellent fit to the experimental pK(a) values. There has been much speculation about the reason for this phenomenon. Although the ΔE - pK(a) relation neglects entropic effects, these are expected to largely cancel. The most likely cause for the strange behavior of the fitted slope is explicit solute-solvent (water) interactions, especially involving the ions, which cannot be described accurately by continuum solvation models. We used our previously developed pK(a) protocol (OLYP/6-311+G(d,p)//3-21G(d) with the COSMO solvation model) to investigate the effect of adding one or two explicit water molecules to the system. The slopes for organic acids (especially carboxylic acids) are much closer to the theoretical value when explicit water molecules are added to both the neutral molecule and the anion. However, explicit water molecules have almost no effect on the slopes for organic bases. Adding explicit water molecules to the ions only produces intermediate results. Unfortunately, linear fits involving explicit water molecules have much larger errors than with continuum solvation models alone and are also much more expensive. Consequently, they are not suitable for large-scale pK(a) calculations. The results compared with literature values showed that our predicted pK(a) s are more accurate.     

Density Functional Theory Study of Hypoxanthine Tautomerism in Both the Isolated State and a Modeled-Ideal Aqueous Solution at Several Heterocyclic Protonation Levels

In order to advance the knowledge of prototropic tautomerism from the physicochemical point of view, the purine derivative hypoxanthine has been selected and studied. The overall purpose has been to explore thermodynamic aspects of the heterocycle tautomerism under the influence of both its protonation level and the surrounding dielectric constant. A Density Functional Theory study (at the B3LYP/6-31++G** level) was performed, in which the energetic and thermodynamic stabilities, the electric dipole moment values, the tautomeric equilibrium constants and the tautomeric populations were obtained for several hypoxanthine tautomers under systematically modified heterocyclic protonation levels, considering both isolated and ideal aqueous solution states. Among the interesting results obtained are changes in the tautomeric populations for several heterocyclic protonation states and with the increase of the dielectric constant. Several of the predictions made for an aqueous solution show good agreement with recently reported experimental conclusions. Also, the ionizable groups that contribute to the different hypoxanthine ionization steps in the main tautomers have been established. These and other related results are presented and discussed. Finally, the confidence developed in the predicted tautomeric populations in a modeled-ideal aqueous solution allows us to propose that the methodology applied here can be used for the study of prototropic tautomerism in heterocycles belonging to this class, particularly when the experimental work is challenging in both performance and physicochemical data analysis.     

DFT and AIM study of the protonation of nitrous acid and the pKa of nitrous acidium ion

The gas phase and aqueous thermochemistry, NMR chemical shifts, and the topology of chemical bonding of nitrous acid (HONO) and nitrous acidium ion (H(2)ONO(+)) have been investigated by ab initio methods using density functional theory. By the same methods, the dissociation of H(2)ONO(+) to give the nitrosonium ion (NO(+)) and water has also been investigated. We have used Becke's hybrid functional (B3LYP), and geometry optimizations were performed with the 6-311++G(d,p) basis set. In addition, highly accurate ab initio composite methods (G3 and CBS-Q) were used. Solvation energies were calculated using the conductor-like polarizable continuum model, CPCM, at the B3LYP/6-311++G(d,p) level of theory, with the UAKS cavity model. The pK(a) value of H(2)ONO(+) was calculated using two different schemes: the direct method and the proton exchange method. The calculated pK(a) values at different levels of theory range from -9.4 to -15.6, showing that H(2)ONO(+) is a strong acid (i.e., HONO is only a weak base). The equilibrium constant, K(R), for protonation of nitrous acid followed by dissociation to give NO(+) and H(2)O has also been calculated using the same methodologies. The pK(R) value calculated by the G3 and CBS-QB3 methods is in best (and satisfactory) agreement with experimental results, which allows us to narrow down the likely value of the pK(a) of H(2)ONO(+) to about -10, a value appreciably more acidic than literature values.     

Formation and stability of enolates of acetamide and acetate anion: an Eigen plot for proton transfer at alpha-carbonyl carbon

Second-order rate constants were determined in D(2)O for deprotonation of acetamide, N,N-dimethylacetamide, and acetate anion by deuterioxide ion and for deprotonation of acetamide by quinuclidine. The values of k(B) = 4.8 x 10(-8) M(-1) s(-1) for deprotonation of acetamide by quinuclidine (pK(BH) = 11.5) and k(BH) = 2-5 x 10(9) M(-1) s(-1) for the encounter-limited reverse protonation of the enolate by protonated quinuclidine give pK(a)(C) = 28.4 for ionization of acetamide as a carbon acid. The limiting value of k(HOH) = 1 x 10(11) s(-1) for protonation of the enolate of acetate anion by solvent water and k(HO) = 3.5 x 10(-9) M(-1) s(-1) for deprotonation of acetate anion by HO(-) give pK(a)(C) approximately 33.5 for acetate anion. The change in the rate-limiting step from chemical proton transfer to solvent reorganization results in a downward break in the slope of the plot of log k(HO) against carbon acid pK(a) for deprotonation of a wide range of neutral alpha-carbonyl carbon acids by hydroxide ion, from -0.40 to -1.0. Good estimates are reported for the stabilization of the carbonyl group relative to the enol tautomer by electron donation from alpha-SEt, alpha-OMe, alpha-NH(2), and alpha-O(-) substituents. The alpha-NH(2) and alpha-OMe groups show similar stabilizing interactions with the carbonyl group, while the interaction of alpha-O(-) is only 3.4 kcal/mol more stabilizing than for alpha-OH. We propose that destabilization of the enolate intermediates of enzymatic reactions results in an increasing recruitment of metal ions by the enzyme to provide electrophilic catalysis of enolate formation.     

Atypical protonation states in the active site of HIV-1 protease: a computational study

The HIV protease (HIVP) is a prominent example for successful structure-based drug design. Besides its pharmaceutical impact, it is a well-studied system for which, as experimentally evidenced, protonation changes in the active site occur upon ligand binding. Therefore, it serves as an ideal candidate for a case study using our newly developed partial charge model, which was optimized toward the application of Poisson-Boltzmann based pK(a) calculations. The charge model suggests reliably experimentally determined protonation states in the active site of HIVP. Furthermore, we perform pKa calculations for two HIVP complexes with novel types of inhibitors developed and synthesized in our group. For these complexes, no experimental knowledge about the protonation states is given. For one of the compounds, containing a central pyrrolidine ring, the calculations predict that both catalytic aspartates should be deprotonated upon ligand binding.     

Electronic structure studies on deprotonation of dithiophosphinic acids in water clusters

We report herein a computational study of proton transfer reactions between dithiophosphinic acids (HAs) and water clusters using B3LYP and MP2 methods. The ground-state and transition-state structures of HA-(H(2)O)(n) (n = 1, 2, 3) cluster complexes have been calculated. The influence of water molecules on energy barrier heights of proton transfer reactions has been examined in the gas phase and solution for bis[o-(trifluoromethyl)phenyl]- and bis(2,4,4-trimethylpentyl)dithiophosphinic acids (HA1 and HA2, respectively). Gas-phase calculations indicate that electron-withdrawing substituents and trifluoromethyl groups in the ortho position favor deprotonation of HA1 when three water molecules are included in the cluster. This suggests that at least three water molecules are necessary to solvate the abstracted proton in the presence of the anion. In the case of HA2, the electron-donating groups favor the reverse proton transfer reaction, namely, protonation of dithiophosphinate anion. Bulk solvent effects have been modeled for aqueous and organic media with the CPCM model. The calculated results show that polar solvents can lower the activation energy for less energetically stable transition states that have more localized charges.     

Electric-Field Effects in 13-Demethyl-11,14-Epoxyretinal-Bacteriorhodopsin Films

Abstract— We report the results of experiments on the application of electric fields across thin, dry Alms of a bacteriorho-dopsin (BR) analog pigment in which the retinal chro-mophore has been replaced with 13-demethyl-11,14-epoxyretinal. As previously observed in other BR variants with low Schiff-base pK values, this pigment exhibits protonation and deprotonation of the Schiff base under an applied electric field, depending on the initial Schiff-base protonation state or effective pH. At low effective pH, a fast (<200 μs) deprotonation reaction dominates. At high pH, an apparently different mechanism leads to Schiff-base protonation on the time scale of seconds. Comparison of our results with a simple model suggests that the external field causes a shift in the pK of the Schiff base by1–2 pH units.