Interaction of Aldehyde dehydrogenase with acetaminophen as examined by spectroscopies and molecular docking

Binding of flavonoids to yeast aldehyde dehydrogenase: a molecular mechanism and computational approach

The interaction of three flavonoids, apigenin, fisetin and quercetin with yeast aldehyde dehydrogenase, ALDH was studied by spectroscopic and molecular docking methods. A combination of both static and dynamic processes interaction mechanism for the binding of flavonoids with ALDH was found. The interaction takes place with moderate binding and the interaction was driven by hydrophobic contacts. The microenvironments of the fluorescent amino acids changed upon flavonoids binding. The distances between ALDH and flavonoids determined by Förster Resonant Energy Transfer (FRET) confirmed the results obtained by fluorescence. The structure of ALDH against thermal denaturation was stabilized by apigenin and destabilized by fisetin and quercetin. Molecular docking simulation showed that all flavonoids bind to the same site of ALDH and confirmed the moderate binding straight found in fluorescence.Communicated by Ramaswamy H. Sarma.

Investigating Paracetamol's Role as a Potential Treatment for Parkinson's Disease: Ab Initio Analysis of Dopamine, l-DOPA, Paracetamol, and NAPQI Interactions with Enzymes Involved in Dopamine Metabolism

Recently, it was found that paracetamol can extend the therapeutic window of l-DOPA treatment for Parkinson's disease [Golding (2019) BJPharm, 4(2), Article 619]. It has been posited that the effect could be due to paracetamol and its metabolite, NAPQI, inhibiting pain signals in the spinal column. In this work, we examine the possibility that the therapeutic effect of the paracetamol for the Parkinson's disease patient may be due to an inhibition of the enzymes that metabolize dopamine and/or l-DOPA, thus effectively extending the lifetime of the l-DOPA treatment. In this work, we use the M062X/6-311+G* level of theory to calculate the electronic binding energies (including explicit desolvation) of several ligands (paracetamol, NAPQI, dopamine, and l-DOPA) with a series of enzymes important to the production and metabolism of dopamine and compare them to calculated binding energy values for the natural substrates for those enzymes in order to predict possible inhibition. Benchmark interaction energies for a subset of the systems studied are calculated using the more accurate second-order Møller-Plesset perturbation (MP2) method in order to calibrate the accuracy of the M062X method. If we assume that the interaction energies calculated here can serve as a proxy for in vivo inhibition, then we can predict that paracetamol and NAPQI should not inhibit the natural production of dopamine and may in fact inhibit the metabolism of l-DOPA and dopamine, thus extending the length of l-DOPA treatments.

Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation

Styrene is a nonpolar organic compound used in very high volume for the industrial scale production of commercially important polymers such as polystyrene resins as well as copolymers like acrylonitrile butadiene styrene, latex, and rubber. These resins are widely used in the manufacturing of various products including single-use plastics such as disposable cups and containers, protective packaging, heat insulation, and so forth. The large-scale utilization leads to the over-accumulation of styrene waste in the environment causing deleterious health risks including cancer, neurological impairment, dysbiosis of central nervous system, and respiratory problems. To eliminate the accumulating waste. Microbial enzyme-based system represents the most environmental friendly and sustainable approach for elimination of styrene waste. However, comprehensive understanding of the enzyme-substrate interaction and associated pathways would be crucial for developing large-scale disposal systems. This study aims to understand the molecular interaction between the protein-ligand complexes of the styrene catabolic reactions by bacterial enzymes of sty operon. Molecular docking analysis for catalytic enzymes namely, styrene monooxygenase (SMO), styrene oxide isomerase (SOI), and phenylacetaldehyde dehydrogenase (PAD) of the bacterial sty operon was carried out with their individual substrates, that is, styrene, styrene oxide, and phenylacetic acid, respectively. The binding energy, amino acids forming binding cavity, and binding interactions between the protein-ligand binding sites were calculated for each case. The obtained binding energies showed a stable association of these complexes indicating the future scope of their utilization for large-scale bioremediation of styrene, and its commercially used polymers and copolymers.

Investigations of the molecular mechanism of diltiazem binding to human serum albumin in the presence of metal ions, glucose and urea

The molecular mechanism and thermodynamic properties of the interaction between diltiazem (DTZ) and human serum albumin (HSA), has been studied in vitro using spectroscopic techniques (UV-Vis, fluorescence, FTIR), and molecular docking methods. The effect of acidic and basic pH, glucose, urea, and metal ions on the DTZ-HSA binding has been investigated as well. According to the results, there is a 1:1 interaction between DTZ and HSA, while the quenching mechanism is static up to 313 K. The apparent binding constant was 2.09 × 10⁶ M^-1 that indicates a strong binding between DTZ and HSA. DTZ binding was increased in acidic pH while its binding was slowly decreased in the presence of glucose, urea, and metal ions. Thermodynamic studies showed that DTZ binds to HSA via an exothermic and spontaneous reaction via hydrogen bonding and electrostatic interactions. The conformational alteration of HSA is obvious according to the FTIR study. The site marker competitive study confirmed the binding of DTZ to the warfarin binding site. Molecular docking studies showed that DTZ binds to subdomain IB (-9.22 kcal mol^-1) and subdomain IIIA (-9.03 kcal mol^-1) with a higher tendency. Also, the results showed that the oxygen and nitrogen atoms of hydroxyl and amino functional groups of DTZ facilitate hydrogen bond formation. HighlightsStrong binding of diltiazem to HSA was studied and confirmed by fluorescence quenching titrations.Diltiazem binding to HSA reduces in the presence of metal ions, glucose, urea and alkaline pH.Diltiazem binding to HSA is exothermic and spontaneous.