Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations

<p>The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of –46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X–H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent’s rule is verified for the C–H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (<i>ρ</i>) and Laplacian of electron density (∇²<i>ρ</i>) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)₄ with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.</p

Theoretical studies on the interaction between the nitrile-based inhibitors and the catalytic triad of Cathepsin K

<p>Computational studies on the interaction of novel inhibitor compounds with the Cathepsin K protease have been performed to study the inhibition properties of the inhibitor compounds. The quantum chemical calculations have been performed to analyze the molecular geometries, structural stability, reactivity, nature of interaction, and the charge transfer properties using B3LYP level of theory by implementing 6-311g(d,p) basis set. The calculated C–S and N–H…N bond lengths of the inhibitor-triad complexes are found to agree well with the previous literature results. The chemical reactivity of the inhibitors and catalytic triad are analyzed through frontier molecular orbital analysis and found that the inhibitors are subjected to nucleophilic attack by the catalytic triad. The nature of inhibition of the inhibitor compounds is examined using the quantum theory of Atoms in Molecules analysis and found to be partially covalent. The NBO stabilization energy for the Cys – inhibitor are found to be most stable than the other interactions. The molecular dynamic simulations were performed to study the influence of dynamic of the active site on the QM results. The many body decomposition interaction energy calculated for the final results of MD simulation reveals that the dynamic of the active site induces significant changes in the interaction energy and occupancy of H-bonds plays a major role in the stabilizing the active site inhibitor interactions. The present study reveals that the inhibitor compounds can inhibit the proteolytic activity of the proteases on binding with the catalytic active site.</p

Mechanism and kinetics of the atmospheric degradation of 2-formylcinnamaldehyde with O₃ and hydroxyl OH radicals – a theoretical study

<p>In the present investigation, the reaction mechanism and kinetics of 2-<b>f</b>ormylcinnamaldehyde (2-FC) with O₃ and hydroxyl OH radicals were studied. The reaction of 2-FC with O₃ radical are initiated by the formation of primary ozonide, whereas the reaction of 2-FC with the hydroxyl OH radical are initiated by two different ways: (1). H-atom abstraction by hydroxyl OH radical from the –CHO and –CH = CHCHO group of 2-FC (2). Hydroxyl OH addition to the –CH = CHCHO group to the ring-opened 2-FC. These reactions lead to the formation of an alkyl radical. The reaction pathways corresponding to the reactions between 2-FC with O₃ and hydroxyl OH radicals have been analysed using density functionals of B3LYP and M06-2X level of methods with the 6-31+G(d,p) basis set. Single-point energy calculations for the most favourable reactive species are determined by B3LYP/6-311++G(d,p) and CCSD(T)/6-31+G(d,p) levels of theory. From the obtained results, the hydroxyl OH addition at C8 position of 2-FC are most favourable than the C9 position of 2-FC. The subsequent reactions of the alkyl radicals, formed from the hydroxyl OH addition at C8 position, are analysed in detail. The individual and overall rate constant for the most favourable reactions are calculated by canonical variational transition theory with small-curvature tunnelling corrections over the temperature range of 278–350 K. The calculated theoretical rate constants are in good agreement with the available experimental data. The Arrhenius plot of the rate constants with the temperature are fitted and the atmospheric lifetimes of the 2-FC with hydroxyl OH radical reaction in the troposphere calculate for the first time, which can be applied to the study on the atmospheric implications. The condensed Fukui function has been verified for the most favourable reaction sites. This study can be regarded as an attempt to investigate the O₃-initiated and hydroxyl OH-initiated reaction mechanisms of 2-FC in the atmosphere.</p

A theoretical study on the reaction mechanism and kinetics of allyl alcohol (CH₂ = CHCH₂OH) with ozone (O₃) in the atmosphere

<p>Volatile organic compounds (VOCs) play a major role in the physical and chemical process of the tropospheric chemical reactions in both polluted and remote environments. A theoretical work has been presented on the VOC of allyl alcohol with O₃ molecule is investigated using density functional theory methods. The reaction profile is initiated through the cycloaddition of ozone which leads to the formation of primary ozonide with minimal relative energy barrier of 1.31 kcal/mol which decomposes to form carbonyl molecule and carbonyl oxide. Carbonyl oxide, i.e. criegee intermediates reacts with various atmospheric species to produce more hazardous and toxic end products to the environment. The condensed form of Fukui function was calculated to predict reactive sites of the primary and secondary reaction profile. The rate coefficient using CVT with SCT over the temperature range of 258–358K is analysed and also to study the atmospheric effects of allyl alcohol in the atmosphere. The predicted rate coefficient for the favourable reaction pathway of <i>k</i>_p1 found to be 1.190 ×10⁻¹⁵ cm³/molecule/sec and comparable with the experimental result at 298 K. The atmospheric lifetime of allyl alcohol was found to be around 10 hours in addition to that global warming potentials are compared with the CO₂.</p

Additional file 3: Table S1. of An open-label clinical trial to investigate the efficacy and safety of corifollitropin alfa combined with hCG in adult men with hypogonadotropic hypogonadism

Summary of Adverse Events in the Combined Treatment Phase. (DOCX 29 kb

Additional file 1: Figure S1. of An open-label clinical trial to investigate the efficacy and safety of corifollitropin alfa combined with hCG in adult men with hypogonadotropic hypogonadism

Study design. (EPS 1160 kb