Unveiling the Influence of Glutathione in Suppressing the Conversion of Aspirin to Salicylic Acid: A Fluorescence and DFT Study.

Aspirin is a commonly used nonsteroidal anti-inflammatory drug, associated with many adverse effects. The adverse effects of aspirin such as tinnitus, Reye's syndrome and gastrointestinal bleeding are caused due to conversion of aspirin into its active metabolite salicylic acid after oral intake. Glutathione is a naturally occurring antioxidant produced by the liver and nerve cells in the central nervous system. It helps to metabolize toxins, break down free radicles, and support immune function. This study aims to investigate and explore the possibility of inhibiting aspirin to salicylic acid conversion in presence of glutathione at a molecular level using spectroscopic techniques such as UV-Visible absorption, time-Resolved and time-dependent fluorescence and theoretical DFT/ TD-DFT calculations. The results of steady state fluorescence spectroscopy and time-dependent fluorescence indicated that the aspirin to salicylic acid conversion is considerably inhibited in presence of glutathione. Further, the results presented here might have significant clinical implications for individuals with variations in glutathione level.

Revisiting the Use of Quantum Chemical Calculations in LogPoctanol-water Prediction.

The partition coefficients of drug and drug-like molecules between an aqueous and organic phase are an important property for developing new therapeutics. The predictive power of computational methods is used extensively to predict partition coefficients of molecules. The application of quantum chemical calculations is used to develop methods to develop structure-activity relationship models for such prediction, either based on molecular fragment methods, or via direct calculation of solvation free energy in solvent continuum. The applicability, merits, and shortcomings of these developments are revisited here.

Octanol-Water Partition Coefficients of Fluorinated Drug Molecules with Continuum Solvation Models.

In this work, we have examined the efficiency of continuum solvation models, used with density functional theory methods, in calculating octanol-water partition coefficients (logP) of 56 fluorine containing drug molecules. The solvation model based on density model computed logP values that are in good agreement with the benchmark values. The conductor-like polarizable continuum models computed results have issues in predicting correct trend, often with reversal of sign from benchmark. The choice of basis set does not show significant effect, and the selection of atomic radii affects geometry convergence during calculations.

Diagnostic and prognostic application of Raman spectroscopy in carcinoma cervix: A biomolecular approach.

Blood serum samples from 63 cervical cancer patients and 30 controls were collected at three different phases of the treatment (i.e. before, during, and at follow up). The spectra of serum samples from control as well as patients were classified into different groups using principal component analysis (PCA) and linear discriminant analysis (LDA) based on different phases of treatment using R software. The spectra of blood serum samples have shown the distinct changes and differences compared with each other in the profile of various biochemical parameters. The sensitivity (92.5%) and specificity (85%) were observed maximum between control and cervical cancer patients (before treatment). Between different phases of treatment, the sensitivity and specificity were less but, all accuracies of detection and classification reached above 50%. This method can be considered as a screening method for detection and treatment monitoring.

Activation mechanism of plasmepsins, pepsin-like aspartic proteases from Plasmodium, follows a unique trans-activation pathway.

Plasmodium parasites that cause malaria produce plasmepsins (PMs), pepsin-like aspartic proteases that are important antimalarial drug targets due to their role in host hemoglobin degradation. The enzymes are synthesized as inactive zymogens (pro-PMs), and the mechanism of their conversion to the active, mature forms has not been clearly elucidated. Our structural investigations of vacuolar pro-PMs with truncated prosegment (pro-tPMs) reveal that the formation of the S-shaped dimer is their innate property. Further structural studies, biochemical analysis, and molecular dynamics simulations indicate that disruption of the Tyr-Asp loop (121p-4), coordinated with the movement of the loop L1 (237-247) and helix H2 (101p-113p), is responsible for the extension of the pro-mature region (harboring the cleavage site). Consequently, under acidic pH conditions, these structural changes result in the dissociation of the dimers to monomers and the protonation of the residues in the prosegment prompts its unfolding. Subsequently, we demonstrated that the active site of the monomeric pro-tPMs with the unfolded prosegment is accessible for peptide substrate binding; in contrast, the active site is blocked in folded prosegment form of pro-tPMs. Thus, we propose a novel mechanism of auto-activation of vacuolar pro-tPMs that under acidic conditions can form a catalytically competent active site. One monomer cleaves the prosegment of the other one through a trans-activation process, resulting in formation of mature enzyme. As a result, once a mature enzyme is generated, it leads to the complete conversion of all the inactive pro-tPMs to their mature form. DATABASE: Atomic coordinates and structure factors have been submitted in the Protein Data Bank (PDB) under the PDB IDs 6KUB, 6KUC, and 6KUD.

Optical coherence tomography of racemose angioma.

Wyburn-Mason syndrome is associated with racemose angioma of the retina and arteriovenous malformation of the brain. Optical coherence tomography and MRI angiography may be used to document the vascular lesion of the retina and brain, respectively.

Mechanism and reactivity in the Morita-Baylis-Hillman reaction: the challenge of accurate computations.

A systematic density functional theory exploration of various reactive steps together with benchmark coupled cluster results are used to propose an accurate model of the mechanism of the Morita-Baylis-Hillman (MBH) reaction in organic chemistry. This reaction has attracted considerable interest from the synthetic and mechanistic points of view in recent years, with both computational and experimental mechanistic studies. It has recently (R. E. Plata and D. A. Singleton, J. Am. Chem. Soc., 2015, 137, 3811-3826) been correctly pointed out that previous computational studies failed to reproduce known mechanistic features of the reaction. The same study argued that computation is simply not able at the present time to provide accurate models for such reactions. This second claim is shown by our present work to overstate the problem: by using current 'state of the art' methodology, our results are fully consistent with observed behavior within the expected error bars of 1-5 kcal mol-1, far smaller than the errors reported in Plata and Singleton's study. On the basis of exhaustive calculations reported here, we suggest that our proposed approaches for modeling electronic structure, solvation, and entropy should be able to provide accurate predictions for many more reactions. We also suggest that reactions like the MBH reaction, where solvation and entropy effects are particularly large, are among the hardest for computational mechanistic studies.

Understanding the structural basis of substrate recognition by Plasmodium falciparum plasmepsin V to aid in the design of potent inhibitors.

Plasmodium falciparum plasmepsin V (PfPMV) is an essential aspartic protease required for parasite survival, thus, considered as a potential drug target. This study reports the first detailed structural analysis and molecular dynamics simulation of PfPMV as an apoenzyme and its complexes with the substrate PEXEL as well as with the inhibitor saquinavir. The presence of pro-peptide in PfPMV may not structurally hinder the formation of a functionally competent catalytic active site. The structure of PfPMV-PEXEL complex shows that the unique positions of Glu179 and Gln222 are responsible for providing the specificity of PEXEL substrate with arginine at P3 position. The structural analysis also reveals that the S4 binding pocket in PfPMV is occupied by Ile94, Ala98, Phe370 and Tyr472, and therefore, does not allow binding of pepstatin, a potent inhibitor of most pepsin-like aspartic proteases. Among the screened inhibitors, the HIV-1 protease inhibitors and KNI compounds have higher binding affinities for PfPMV with saquinavir having the highest value. The presence of a flexible group at P2 and a bulky hydrophobic group at P3 position of the inhibitor is preferred in the PfPMV substrate binding pocket. Results from the present study will aid in the design of potent inhibitors of PMV.

Structure, dynamics, and interactions of a C4'-oxidized abasic site in DNA: a concomitant strand scission reverses affinities.

Apurinic/apyrimidinic (AP) sites constitute the most frequent form of DNA damage. They have proven to produce oxidative interstrand cross-links, but the structural mechanism of cross-link formation within a DNA duplex is poorly understood. In this work, we study three AP-containing d[GCGCGCXCGCGCG]·d[CGCGCGKGCGCGC] duplexes, where X = C, A, or G and K denotes an α,ß-unsaturated ketoaldehyde derived from elimination of a C4'-oxidized AP site featuring a 3' single-strand break. We use explicit solvent molecular dynamics simulations, complemented by quantum chemical density functional theory calculations on isolated X:K pairs. When X = C, the K moiety in the duplex flips around its glycosidic bond to form a stable C:K pair in a near-optimal geometry with two hydrogen bonds. The X = A duplex shows no stable interaction between K and A, which contrasts with AP sites lacking a strand scission that present a preferential affinity for adenine. Only one, transient G:K hydrogen bond is formed in the X = G duplex, although the isolated G:K pair is the most stable one. In the duplex, the stable C:K pair induces unwinding and sharp bending into the major groove at the lesion site, while the internal structure of the flanking DNA remains unperturbed. Our simulations also unravel transient hydrogen bonding between K and the cytosine 5' to the orphan base X = A. Taken together, our results provide a mechanistic explanation for the experimentally proven high affinity of C:K sites in forming cross-links in DNA duplexes and support experimental hints that interstrand cross-links can be formed with a strand offset.

What singles out the G[8-5]C intrastrand DNA cross-link? Mechanistic and structural insights from quantum mechanics/molecular mechanics simulations.

Naturally occurring intrastrand oxidative cross-link lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalently bonded to the C5 atom of a nearby cytosine belonging to the same strand) occurs with a low incidence yet takes on special importance because of its high mutagenicity. Hybrid Car-Parrinello molecular dynamics simulations, rooted in density functional theory and coupled to molecular mechanics, have been performed to shed light on the cyclization process. The activation free energy of the reacting subsystem embedded in a solvated dodecamer is estimated to be ∼12.4 kcal/mol, which is ∼3 kcal/mol higher than the value for the prototypical G[8-5m]T lesion inferred employing the same theoretical framework [Garrec, J., Patel, C., Rothlisberger, U., and Dumont, E. (2012) J. Am. Chem. Soc.134, 2111-2119]. This study also situates the G[8-5m]mC lesion at an intermediate activation free energy (∼10.5 kcal/mol). The order of reactivity in DNA (T(•) > mC(•) > C(•)) is reversed compared to that in the reacting subsystems in the gas phase (C(•) > mC(•) > T(•)), stressing the crucial role of the solvated B-helix environment. The results of our simulations also characterize a more severe distortion for G[8-5]C than for methylene-bridged intrastrand cross-links.

Insights into intrastrand cross-link lesions of DNA from QM/MM molecular dynamics simulations.

DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linked dinucleotides. The detailed structure of the damaged DNA macromolecule has remained elusive. In this study we generated in silico the most frequent oxidative intrastrand cross-link adduct, G[8,5-Me]T, embedded in a solvated DNA dodecamer by means of quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations. The free energy of activation required to bring the reactant close together and to form the C-C covalent-bond is estimated to be ~10 kcal/mol. We observe that the G[8,5-Me]T tandem lesion is accommodated with almost no perturbation of the Watson-Crick hydrogen-bond network and induces bend and unwinding angles of ~20° and 8°, respectively. This rather small structural distortion of the DNA macromolecule compared to other well characterized intrastrand cross-links, such as cyclobutane pyrimidines dimers or cisplatin-DNA complex adduct, is a probable rationale for the known lack of efficient repair of oxidative damages.

Improved DFT description of intrastrand cross-link formation by inclusion of London dispersion corrections.

The formation of covalent linkages between two vicinal nucleotides has been proved experimentally to constitute a particularly deleterious class of DNA lesions. These tandem lesions by essence present a competitive chemistry. The density functional theory with dispersion (DFT-D) method is shown to dramatically improve the theoretical description of the formation of a prototypical intrastrand cross-link, when compared to pure or hybrid GGA functionals which strongly deviate from the π-π self-stacking mode, as dinucleotides are artificially stabilized by the formation of unrealistic intramolecular hydrogen bonds (HBs). Inclusion of London dispersion correction restores a more realistic picture of the reactant structure and also of geometries and energies along the reaction profile. This paves the way toward a robust insilico screening of intrastrand cross-link DNA defects.

TiCl4-promoted Baylis-Hillman reaction: mechanistic rationale toward product distribution and stereoselectivity.

The mechanism of TiCl(4)-promoted Baylis-Hillman reaction between methyl vinyl ketone (MVK) and acetaldehyde, in the absence of any base, is studied using the mPW1K density functional theory. The study focuses on several mechanistic intricacies as well as selectivity issues at each step of the reaction. The minimum energy pathway for this reaction involves three major steps such as a chloride transfer resulting in a chloro-enolate, titanium-mediated aldol reaction, and elimination of HCl or HOTiCl(3). Both s-cis and s-trans conformers of MVK are considered along with various modes of chloride transfer involving different complexes between TiCl(4), aldehyde, and MVK. Chloride transfer is found to be kinetically more favored for s-cis-MVK than for s-trans-MVK. The diastereoselectivity in the next step, i.e., Ti-mediated aldol reaction between the enolate and aldehyde, is found to be dependent on the geometry of the enolate, wherein anti and syn BH products are predicted for Z and E enolates, respectively. An interesting secondary orbital interaction between the oxygen atoms of the enolate and aldehyde moieties in the transition states for the C-C bond formation is identified as one of the contributing factors toward the predicted diastereoselectivity in the formation of the alpha-chloromethyl aldol product (P2). It has earlier been reported that under different experimental conditions, any of the three products such as (i) a normal BH product (P1), (ii) 2-(chloromethyl)vinyl ketones (P3), and (iii) alpha-chloro methyl aldol could be generated (Scheme 1 ). The present study offers valuable insights toward rationalizing the observed product distribution as well as diastereoselectivity in TiCl(4)-promoted BH reaction under base-free conditions. The computed energetics indicate that when MVK is employed as the Michael acceptor, the formation of 2-(choromethyl)vinyl ketone is the preferred product rather than the corresponding normal BH product, consistent with the known experimental reports.

Mechanistic insights and the role of cocatalysts in Aza-Morita-Baylis-hillman and Morita-Baylis-Hillman reactions.

The mechanism of the trimethylamine or trimethylphosphine catalyzed aza-Morita-Baylis-Hillman (MBH) reaction between acrolein and mesyl imine is investigated by using ab initio and density functional methods. All key transition states are located at the CBS-4M as well as at the mPW1K/6-31+G** levels of theories. To account for the experimentally known rate enhancements through the use of polar protic cocatalysts, transition state models with explicit cocatalysts are considered. Inclusion of polar protic cocatalysts is found to have a profound influence in decreasing the activation barriers associated with the key elementary steps. The protic cocatalysts such as water, methanol, and formic acid are identified as effective in promoting a relay proton transfer. Interestingly, the efficiency of the relay mechanism results in relatively better stabilization of the proton transfer transition state as compared to the addition of enolate to the electrophile (C-C bond formation). The cocatalyst bound models suggest that the proton transfer could become the rate-determining step in the aza-MBH reaction under polar protic conditions. A comparison of the aza-MBH reaction with the analogous MBH reaction is also attempted to bring out the subtle differences between these two reactions. Enhanced kinetic advantages arising from the nature of the activated electrophile are noticed for the aza-MBH reaction. The difference in the relative energies between the transition states for the proton transfer and the C-C bond formation steps with bound cocatalyst(s) is found to be more pronounced in the aza-MBH reaction. In general, the reported results underscore the importance of considering explicit solvents/cocatalysts in order to account for the likely role of the specific interactions between reactants and solvents/cocatalysts.

Probing intramolecular interactions in arylselenides using a property descriptor based approach.

Although a large volume of experimental evidence is available on the existence of intramolecular nonbonding interactions between chalcogen atoms in main group organometallic compounds, the primary focus has been on the contact distances involving the chalcogen atoms. The important class of intramolecular Se...X (where X is O, S, N) nonbonding interaction in a series of organoselenium compounds is quantified using a new scheme based on a molecular property descriptor. In the present study, we have employed the nucleus-independent chemical shift [NICS(0)] values, as a property descriptor to evaluate the strength of exocyclic nonbonding interactions in a series of aryl selenides. The ab initio MP2 as well as density functional theory methods have been used in conjunction with Dunning's cc-pVDZ basis set. The quantified values of Se...X nonbonding interactions are compared with other schemes based on thermochemical equations such as homodesmic and ortho-para methods. The changes in NICS(0) values at the aryl ring center are found to be sensitive to the strength of exocyclic Se...X interaction.