Solvophobic forces and molecular surface area changes in drug-biomolecule associations as with actinomycin-deoxyguanosine in a wide range of methanol/water mixtures

A method is given to predict the unitary free energies of complexation between drug-like and nucleoside-like biomolecules in a range of mixed solvent compositions. A stability maximum for the actinomycin (A)-deoxyguanosine (D) complex at 8% MeOH (v/v) in methanol/water mixtures is correctly predicted by the theory in agreement with existing experimental data. The molecular surface areas of A and D exposed to the solvent are found to diminish by 36.4 A(2) upon association. The 'microthermodynamic differential surface tension' of the solvophobic theory obtained for nucleoside-like and organic molecules in contact with MeOH/H2O can be used to predict the solvent effect free energies in other such molecular or biopolymeric associations in solution.     

Tolerance of β-diketone hydrolases as representatives of the crotonase superfamily towards organic solvents

Crotonase superfamily enzymes catalyze a wide variety of reactions, including hydrolytic C–C bond cleavage in symmetrical β‐diketones by 6‐oxo camphor hydrolase (OCH) from Rhodococcus sp. The organic solvent tolerance and temperature stability of OCH and its structurally related ortholog Anabaena β‐diketone hydrolase have been investigated. Both enzymes showed excellent tolerance toward organic solvents; for instance, even in the presence of 80% (v/v) THF or dioxane, OCH was still active. In most solvent mixtures, except methanol, the stereospecificity was conserved (>99% e.e. of product), hence neither the type of solvent nor its concentration appeared to have an effect on the stereoselectivity of the enzyme. Attempts to correlate the observed activities with log P, functional solvent group or denaturing capacity (DC) of the solvent were only successful in the case of DC for water miscible solvents. This study represents the first investigation of organic solvent stability for members of the crotonase superfamily. Biotechnol. Bioeng. 2011;108: 2815–2822. © 2011 Wiley Periodicals, Inc.     

A kinetic study of 1H leads to 3H exchange in C(8) H-groups of purinic residues in DNA.

The kinetic study of 1H leads to 3H exchange in C(8) H-groups of purinic residues of DNAs with different G-C content as well as in corresponding dNMP mixtures have been carried out. The present results show that 1H--3H exchange in DNA is retarded (as compared to the exchange in dNMP mixtures) to a lesser extent (Kret =2.4-2.8) than in RNA (Kret=6-8). The degree of retardation in these polymers is practically independent of their nucleotide composition. Assuming the ylide mechanism of exchange reaction it is suggested that the lower rate of 1H leads to 3H exchange in C(8) H-groups of purinic residues in polynucleotides of A-form (RNA and other polyribonucleotides) as compared to those of B-form (DNA and other polydeoxyribonucleotides) might be accounted for by decreased availability of C(8) H-groups for OH-ions of the solvent due to a different microenviroment of these groups in A- and B-type helixes.     

Semi-rational engineering of an amino acid racemase that is stabilized in aqueous/organic solvent mixtures

Enzymes are industrially applied under increasingly diverse environmental conditions that are dictated by the efforts to optimize overall process efficiency. Engineering the operational stability of biocatalysts to enhance their half-lives under the desired process conditions is a widely applied strategy to reduce costs. Here, we present a simple method to enhance enzyme stability in the presence of monophasic aqueous/organic solvent mixtures based on the concept of strengthening the enzyme's surface hydrogen-bond network by exchanging surface-located amino acid residues for arginine. Suitable residues are identified from sequence comparisons with homologous enzymes from thermophilic organisms and combined using a shuffling approach to obtain an enzyme variant with increased stability in monophasic aqueous/organic solvent mixtures. With this approach, we increase the stability of the broad-spectrum amino acid racemase of Pseudomonas putida DSM 3263 eightfold in mixtures with 40% methanol and sixfold in mixtures with 30% acetonitrile.     

Whole cell biocatalysis in nonconventional media

Summary In this paper biocatalytic reactions carried out by whole cells in nonconventional media are reviewed. Similar relationships are observed between solvent hydrophobicity and catalytic activity in reactions carried out by isolated enzymes and whole cells. In addition to the effect of organic solvent on biocatalyst stability, microbial cells are susceptible to damaging effects caused by the organic phase. In general, more hydrophobic solvents manifest lower toxicity towards the cells. Whole cell biocatalysts require more water than isolated enzymes and two-phase systems have been most widely used to study whole cell biocatalysis. Immobilization makes cell biocatalysts more resistant to organic solvents and helps achieve homogeneous biocatalyst dispersion. Cell entrapment methods have been widely used with organic solvent systems and mixtures of natural and/or synthetic polymers allow adjustment of the hydrophobicity-hydrophilicity balance of the support matrix. Some examples of stereoselective catalysis using microbial cells in organic solvent media are presented.     

A hydrophilic and hydrophobic organic solvent mixture enhances enzyme stability in organic media

Binary mixtures of hydrophilic and hydrophobic solvents were assessed for their ability to balance enzyme activity with the conservation of enzyme stability in organic media. Acetone, dioxane and dodecane were chosen as model organic solvents, and subtilisin Carlsberg and horseradish peroxidase (HRP) were chosen as model enzymes. Residual enzyme activities were measured to monitor enzyme stability, and the fluorescence intensity of HRP was monitored to investigate structural changes due to the presence of an organic solvent. Enzyme stability increased with the increasing hydrophobicity of the solvent mixture used, and a solvent mixture with a high log P value (~ >4) was capable of conserving enzyme stability. Enzyme stability in organic media can be conserved therefore with a mixture of hydrophilic and hydrophobic solvents: this approach might be used as a general and practical strategy for optimizing enzyme activity and stability for industrial applications.     

Structural motifs in the maturation process of peptide hormones. The somatostatin precursor. I. A CD conformational study.

Synthetic peptides reproducing both the native domain around the dibasic cleavage site of prosomatostatin, and mutated sequences there of, previously assayed in site-directed mutagenesis experiments, have been studied by CD in different solvent systems, such as water, TFE/H2O, MeCN/H2O and aqueous SDS, in order to ascertain the ability of each solvent to stabilize secondary structural motifs. A combination of deconvolution methods and empirical calculations, that allow subtraction of the contributions due to unordered structures from the spectra, suggests that mainly two distinct families of ordered conformers containing alpha-helix and/or structurally different beta-turns are present in solution, the relative stability of the different conformers depending on the nature of the solvent. The presence of beta-turns is in line with a previous NMR study in DMSO and DMSO/H2O. Comparison of the CD spectra in aqueous SDS of peptides undergoing processing with a sequence not processed in vivo shows that only the latter possesses a stable and detectable alpha-helix population. This observation suggests that the structuration involving beta-turns but no alpha-helix, which was observed by CD both in SDS and organic solvent/H2O mixtures at high water contents, might be of biological significance. The similarity of this structuration to molecular models obtained from NMR data in DMSO and DMSO/H2O is discussed.     

Template-directed extension of a guanosine 5′-phosphate covalently attached to an oligodeoxycytidylate template

We have prepared molecules in which a guanosine 5'-phosphate (pG) residue is attached to the 3' terminus of a decadeoxycytidylate (pdC)10 template via diamine linkers H2N(CH2)nNH2, n = 4-7. The pG residue acts as a primer and is extended very efficiently by incubation with activated pG derivatives to give products containing 6-9 G residues in greater than 80% yield. The detailed nature of the product distribution is discussed.     

Lipase-catalyzed synthesis of xylitol monoesters: solvent engineering approach

A solvent engineering strategy was applied to the lipase-catalyzed synthesis of xylitol-oleic acid monoesters. The different esterification degrees for this polyhydroxylated molecule were examined in different organic solvent mixtures. In this context, conditions for high selectivity towards monooleoyl xylitol synthesis were enhanced from 6 mol% in pure n-hexane to 73 mol% in 2-methyl-2-propanol/dimethylsulfoxide (DMSO) 80:20 (v/v). On the contrary, the highest production of di- and trioleoyl xylitol, corresponding to 94 mol%, was achieved in n-hexane. Changes in polarity of the reaction medium and in the molecular interactions between solvents and reactants were correlated with the activity coefficients of products. Based on experimental results and calculated thermodynamic activities, the effect of different binary mixtures of solvents on the selective production of xylitol esters is reported. From this analysis, it is concluded that in the more polar conditions (100% dimethylsulfoxide (DMSO)), the synthesis of xylitol monoesters is favored. However, these conditions are unfavorable in terms of enzyme stability. As an alternative, binary mixtures of solvents were proposed. Each mixture of solvents was characterized in terms of the quantitative polarity parameter E(T)(30) and related with the activity coefficients of xylitol esters. To our knowledge, the characterization of solvent mixtures in terms of this polarity parameter and its relationship with the selectivity of the process has not been previously reported.     

A combined spectroscopic and TDDFT investigation of the solute‐solvent interactions of two coumarin derivatives

The UV/Vis absorption and fluorescence characteristics of 3‐cyano‐7‐hydroxycoumarin [ CHC ] and 7‐amino‐4‐methyl‐3‐coumarinylacetic acid [ AMCA‐H ] were studied at room temperature in several neat solvents and binary solvent mixtures of 1,4‐dioxane/acetonitrile. The effects of solvent on the spectral properties are analyzed using single and multi‐parameter solvent polarity scales. Both general solute/solvent interactions and hydrogen bond interactions are operative in these systems. The solvation of CHC and AMCA‐H dyes in 1,4‐dioxane/acetonitrile solvent mixtures has been studied. The solutes CHC and AMCA‐H are preferentially solvated by acetonitrile and a synergistic effect is observed for both molecules in dioxane/acetonitrile solvent mixtures. In addition, using the solvatochromic method the ground‐ and the excited‐state dipole moments of both the dyes were calculated. The ground‐ and excited‐state dipole moments, absorption and emission maxima and HOMO–LUMO gap were also estimated theoretically using B3LYP/6–311+ G (d,p) level of theory in the gaseous phase, dioxane and acetonitrile solvents. Furthermore, changes in dipole moment values were also calculated using the variation of Stokes shift with the molecular–microscopic empirical solvent polarity parameter ( ). The observed excited‐state dipole moments are larger than their ground‐state counterparts, indicating a substantial redistribution of the electron densities in a more dipolar excited state for both coumarins investigated.     

Solvent effect on lipase enantioselectivity. Evidence for the presence of two thermodynamic states

The enantioselectivity of lipase-catalyzed kinetic resolutions has been measured at various temperatures in binary mixtures of solvents. Varying the solvent composition and temperature had a profound effect on the enantiomeric ratio. The values for delta delta H(R-S)(#) and delta delta S(R-S)(#), calculated from the E values measured at various temperatures, were estimated as a function of the solvent composition. By plotting delta delta H(R-S)(#) versus delta delta S(R-S)(#) as a function of the solvent composition, an extreme was observed. The resulting "hairpin-type" enthalpy-entropy compensation plots can be described by assuming the presence of two thermodynamically distinct physical states, displaying different enantioselectivities, that are in equilibrium with one another. Changing the solvent composition results in a change in the equilibrium constant K(eq) for the two states. The intriguing bell-shaped curves of the enantioselectivity versus solvent composition observed for lipase-catalyzed kinetic resolutions can be described assuming a linear correlation for the logarithm of K(eq) and the solvent composition. Thus, a simulation of the two-state model adequately describes the solvent effects found for lipase-catalyzed kinetic resolutions in binary mixtures of solvents and possibly in series of homologous organic solvents.     

Effects of solvent molecular toxicity and microenvironment composition on the Delta(1) dehydrogenataon activity of Arthrobacter simplex cells

Solvent selection tests were carried out for the Delta(1) dehydrogenation of 6-alpha-methylhydrocortisone-21-acetate by Arthrobacter simplex cells in the presence of organic solvents. Solubility limits were determined for substrate and product in dry and water-saturated solvents and solvent mixtures. Molecular toxicity levels were estimated by measuring the dehydrogenation activity decay of freely suspended cells incubated in solvent-saturated aqueous media. Chloroform and n-decan-1-ol were the best choice of solvent, for both solubility and catalytic stability. High concentrations of water-soluble additives, such as monosodium glutamate, were found to greatly improve the retention of activity in chloroform-saturated media.     

A new polymorphic locus, D7S411, isolated by cloning from preparative pulse-field gels is close to the mutation causing cystic fibrosis

The mutation causing cystic fibrosis (CF) has been localized to the DNA sequence of 700 kb bounded by the loci identified by the markers pMP6d-9 (D7S399) and pJ3.11 (D7S8). A 560-kb fragment obtained after SacII digestion of DNA from a cell line containing this region of human chromosome 7 in a mouse background was separated using pulse-field gel electrophoresis and isolated from the gel. The DNA was digested with BamHI prior to cloning into lambda EMBL3. Approximately 0.1% of the resulting clones contained human repetitive sequences, and 24 such recombinants were studied. Of these, 23 are on chromosome 7; 8 clones were duplicated, and of the 15 different recombinants, 7 are between MET and INT1L1, and a further 7 are between INT1L1 and pMP6d-9, leaving a single marker, pG2, which is between pMP6d-9 and pJ3.11. pG2 recognizes an RFLP with XbaI. A cosmid walk from pG2 has generated a further marker, H80, which recognizes an RFLP with PstI. This new locus (D7S411) divides the remaining region between the CF flanking markers, thereby making it more accessible to fine pulse-field mapping and allowing the precise localization of further clones to this region. Although it is not possible to position the CF locus unequivocally with respect to D7S411, both polymorphic markers at this locus exhibit low but significant linkage disequilibrium with CF, placing the emphasis for the search for the gene on the D7S399 to D7S411 interval of 250 kb.     

Identification of a collagen-binding protein from Necator americanus by using a cDNA-expression phage display library.

A phage display library was made starting from a cDNA library from the hematophagous human parasite Necator americanus. The cDNA library was transferred by polymerase chain reaction (PCR) cloning into phage display vectors (phagemids), using specially designed primers such that proteins would be expressed as fusions with the C-terminal part of the phage coat protein pVI. The vectors used are multicloning site variants of the original pDONG vectors described by Jespers et al. (1995). Electroporation of the ligation mixtures into electrocompetent Escherichia coli TGI cells yielded 3 x 10(8) pG6A, 1.9 x 10(8) pG6B, and 1 x 10(8) pG6C transfectants for N. americanus. The final libraries consisted of a mix of equal numbers of insert-containing phages from the A, B, and C libraries. Selection of phages for binding to human collagen was performed. Four rounds of panning on human collagens I and III resulted in a significant enrichment of collagen-binding phages from the N. americanus libraries. PCR analysis revealed various insert lengths; however, sequence determination indicated that all phages contained the same protein, albeit with different poly-A tail lengths. The encoded protein itself is a 135-amino acid protein (15 kDa), with no apparent homology to any other known protein. Next the protein was recloned into E. coli using the pET-15b-vector. Upon isopropyl-1-thio-beta-D-galactopyranoside induction, the recombinant protein, rNecH1, could be recovered by urea treatment from inclusion bodies. The rNecH1 protein binds to different collagens: human I > rat I > human III = calf skin I in a specific, dose-dependent, and saturable manner.     

Conformational transition of hyaluronic acid: carboxylic group participation and thermal effect

The chiroptical, viscosity and titration studies of hyaluronic acid in mixed organic/water solvent show a reversible conformational transition of the molecule depending upon pH, solvent composition, temperature, and molecular weight. Neither methylhyaluronate nor chondroitin undergoes conformational transition of this type. These results indicate that hydrogen bonding between the protonated carboxylic group and carbonyl oxygen of the acetamido group is directly involved in the conformational change. Results with chondroitin provide further support for the 4-fold helical structure that we have proposed for hyaluronic acid in mixed organic/water solvent. The thermal stability of the conformation has been studied under various pH values and solvent compositions.     

Effect of organic solvents on the activity and stability of an extracellular protease secreted by the haloalkaliphilic archaeon <Emphasis Type="Italic">Natrialba magadii</Emphasis>

The effect of various organic solvents on the activity and stability of an extracellular protease produced by the haloalkaliphilic archaeon Natrialba magadii was tested. This protease was active and stable in aqueous-organic solvent mixtures containing 1.5 M NaCl and glycerol, dimethylsulfoxide (DMSO), N,N-dimethyl formamide, propylenglycol, and dioxane. Among the solvents tested, DMSO, propylenglycol, and glycerol were effective in preserving enzyme stability in suboptimal NaCl concentrations. The stabilizing effect of DMSO on this haloalkaliphilic protease was more efficient at pH 8 than at pH 10, suggesting that DMSO may not substitute for salt to allow halophilic proteins to withstand the effect of high pH values. These results show that Nab. magadii extracellular protease is a solvent tolerant enzyme and suggest a potential application of this haloalkaliphilic protease in aqueous-organic solvent biocatalysis.     

Infrared spectroscopic studies of solvent-induced conformational changes in globular proteins.

Infrared absorption spectroscopy has been used to study the effect of organic solvents on the conformation of myoglobin, apomyoglobin, hemoglobin, lysozyme and ribonuclease. Beta structure can easily be induced by specific solvent effects. Films prepared from a 50% (v/v) mixture of alcohol, acetone, pyridine, tetrahydrofuran or dimethylsulfoxide/water mixtures show a high proportion of beta structure. The degree of induction of beta structure depends on the hydrocarbon content of the alcohol in the order methanol greater than ethanol greater than butanol. No beta structure was observed in films prepared from aqueous octanol solutions. Lyophilization tends to decrease secondary structure. The conformation of the proteins depends on the particular solvent system and the solvent composition. Solution studies of myoglobin in pure dimethylsulfoxide show that the conformation is a mixture of random and beta forms while in dimethylsulfoxide/2H2O mixtures the conformation is a mixture of alpha-helical and beta forms.     

Free and immobilized Aspergillus niger epoxide hydrolase-catalyzed hydrolytic kinetic resolution of racemic p-chlorostyrene oxide in a neat organic solvent medium

An enantio- and regioselective hydrolytic kinetic resolution (HKR) of racemic p-chlorostyrene oxide (rac-pCSO) was achieved by epoxide hydrolase (EH) from recombinant Aspergillus niger in a selected neat organic solvent medium. The solid free EH was reused four times in repeated-batch reactors; however, the relative activity as well as the enantiomeric ratio (E-value) of this EH decreased from 100 to 20% and from 68 to 23, respectively. In order to overcome the diffusion hindrance, due to the accumulation of the hydrophilic diol in the enzyme micro-environment, and thereby to improve the operational stability of EH after recycling, strategies consisting of the immobilization of EH and the use of a binary organic solvent as the reaction medium were successfully applied. Although the highest protein immobilization yield (82%) and retention of EH activity (142%) in heptane were obtained upon the immobilization of EH on Accurel EP, the E-value and the operational stability of the resulted EH immobilizate after recycling were reduced as compared to the free EH. In contrast, the nonporous DEAE-cellulose improved the operational stability of EH by more than twofold. On the other hand, both the HKR efficiency and the operational stability of A. niger EH were found to be modest to excellent in various binary organic solvent mixtures of heptane and dioxane, depending on their ratio resulting in different Log P.     

Aspects Of Biocatalyst Stability In Organic Solvents

The stability of biocatalysis in systems containing organic solvents is reviewed. Among the examples presented are homogeneous mixtures of water and water-miscible organic solvents, aqueous/organic two-phase systems, solid biocatalysts suspended in organic solvents, enzymes in reverse micelles and modified enzymes soluble in water immiscible solvents. The stability of biocatalysts in organic solvents depends very much on the conditions. The hydrophobicity or the polarity of the solvent is clearly of great importance. More hydrophobic solvents (higher log P values) are less harmful to enzymes than less hydrophobic solvents. The water content of the system is a very important parameter. Some water is essential for enzymatic activity; however, the stability of enzymes decreases with increasing water content. Mechanisms of enzyme inactivation are discussed.     

Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal alpha-helices

Conformational changes in the light illuminated intermediate (pB) of photoactive yellow protein (PYP) were studied from a viewpoint of the diffusion coefficient (D) change of several N-truncated PYPs, which lacked the N-terminal 6, 15, or 23 amino acid residues (T6, T15, and T23, respectively). For intact PYP (i-PYP), D of pB (D(pB)) was approximately 11% lower than that (D(pG)) of the ground state (pG) species. The difference in D (D(pG) - D(pB)) decreased upon cleavage of the N-terminal region in the order of i-PYP>T6>T15>T23. This trend clearly showed that conformational change in the N-terminal group is the main reason for the slower diffusion of pB. This slower diffusion was interpreted in terms of the unfolding of the two alpha-helices in the N-terminal region, increasing the intermolecular interactions due to hydrogen bonding with water molecules. The increase in friction per one residue by the unfolding of the alpha-helix was estimated to be 0.3 x 10(-12) kg/s. The conformational change in the N-terminal group upon photoillumination is discussed.