A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants

The strategy for estrogen receptor mediated-risk assessment in environmental water: A combination of species sensitivity distributions and in silico approaches

Risk assessment for molecular toxicity endpoints of environmental matrices may be a pressing issue. Here, we combined chemical analysis with species sensitivity distributions (SSD) and in silico docking for multi-species estrogen receptor mediated-risk assessment in water from Dongjiang River, China. The water contains high levels of phenolic endocrine-disrupting chemicals (PEDCs) and phthalic acid esters (PAEs). The concentration of ∑₄PEDCs and ∑₆PAEs ranged from 2202 to 3404 ng/L and 834-4368 ng/L, with an average of 3241 and 2215 ng/L, respectively. The SSD approach showed that 4-NP, BPA, E2 of PEDCs, and DBP, DOP, and DEHP could severely threaten the aquatic ecosystems, while most other target compounds posed low-to-medium risks. Moreover, binding affinities from molecular docking among PEDCs, PAEs, and estrogen receptors (ERα, Erβ, and GPER) were applied as toxic equivalency factors. Estrogen receptor-mediated risk suggested that PEDCs were the main contributors, containing 53.37-69.79% of total risk. They potentially pose more severe estrogen-receptor toxicity to zebrafish, turtles, and frogs. ERβ was the major contributor, followed by ERα and GPER. This study is the first attempt to assess the estrogen receptor-mediated risk of river water in multiple aquatic organisms. The in silico simulation approach could complement toxic effect evaluations in molecular endpoints.

Ecological and AhR-mediated risk assessment of polycyclic aromatic hydrocarbons and polybrominated diphenyl ethers on multiple aquatic species in river water: A combined chemical analysis and in silico approach

Assessing the adverse health risks at molecular endpoints to various aquatic organisms could be an urgent issue. In this manuscript, the ecological and AhR-mediated risk of sixteen polycyclic aromatic hydrocarbons (PAHs) and six polybrominated diphenyl ethers (PBDEs) in surface water of Dongjiang River, Southern China was evaluated using chemical analysis and in silico approaches. Average concentrations of ∑₁₆PAHs and ∑₆PBDEs were 586.3 ng/L and 2.672 ng/L in the dry season (DS), and 366.8 ng/L and 2.554 ng/L in the wet season (WS). Concentrations of PAHs during the DS were significantly higher than that in the WS, while no obvious seasonal distribution was observed for PBDEs. Only Ant and BaP in all congers of PAHs posed low to medium ecological risks, and PBDEs posed a low ecological risk. Moreover, AhR-mediated risk from PAHs was two orders of magnitude higher that from PBDEs, and the AhR-mediated toxicity on frog and eel were higher than those on other aquatic organisms in Dongjiang River. Phe and BDE209 were the significant contributor to the AhR-mediated risk induced by PAHs and PBDEs, respectively. This study is the first attempt to assess AhR-mediated risk of river water in multiple aquatic organisms.

Modulating the Coupling Efficiency of P450 BM3 by Controlling Water Diffusion through Access Tunnel Engineering

Cytochromes P450 have gained much interest for their broad substrate scope in the catalysis of oxidation reactions for pharmaceuticals, plastics, and hormones. However, achieving high coupling efficiency by the engineering of P450s is still a big challenge. The presence of extra water around the active site is deemed to be related to uncoupling. In this study, the access tunnels of P450 BM3 from Bacillus megaterium are engineered to control water access from bulk solvent to the active site. Nine residues located in tunnels are investigated by site-saturation mutagenesis to reduce water diffusion, thereby improving the coupling efficiency. The recombined variant N319L/T411V/T436A shows improved coupling efficiency (from 31.2 % to 52.6 %). Tunnel polarity analysis and molecular dynamics simulation further indicate that reduced water molecules around the active site lead to higher coupling efficiency. Overall, this study provides valuable insight on improving coupling efficiency by controlling water diffusion through tunnel engineering.

A Promiscuous Bacterial P450: The Unparalleled Diversity of BM3 in Pharmaceutical Metabolism

CYP102A1 (BM3) is a catalytically self-sufficient flavocytochrome fusion protein isolated from Bacillus megaterium, which displays similar metabolic capabilities to many drug-metabolizing human P450 isoforms. BM3's high catalytic efficiency, ease of production and malleable active site makes the enzyme a desirable tool in the production of small molecule metabolites, especially for compounds that exhibit drug-like chemical properties. The engineering of select key residues within the BM3 active site vastly expands the catalytic repertoire, generating variants which can perform a range of modifications. This provides an attractive alternative route to the production of valuable compounds that are often laborious to synthesize via traditional organic means. Extensive studies have been conducted with the aim of engineering BM3 to expand metabolite production towards a comprehensive range of drug-like compounds, with many key examples found both in the literature and in the wider industrial bioproduction setting of desirable oxy-metabolite production by both wild-type BM3 and related variants. This review covers the past and current research on the engineering of BM3 to produce drug metabolites and highlights its crucial role in the future of biosynthetic pharmaceutical production.

Assessment of epigenotoxic profiles of Dongjiang River: A comprehensive of chemical analysis, in vitro bioassay and in silico approach

This research explored the occurrence, epigenetic toxic profiling and main toxic pollutants of POPs in surface water of Dongjiang River, southern China. The concentrations of selected POPs including polycyclic aromatic hydrocarbons (PAHs), endocrine disrupting chemicals (EDCs), phthalate esters (PAEs) and polybrominated diphenyl ethers (PBDEs) of surface water from 18 sites were investigated. ∑₁₆PAHs and ∑₄EDCs were at a moderate level, while ∑₆PAEs and ∑₆PBDEs had low pollution levels. PAHs, EDCs and PAEs showed higher concentrations in dry season than those in wet season, and the loading of selected POPs in tributaries was higher than those in mainstream due to intensive manufactures and lower runoff volume. Moreover, activities of DNA methyltransferase (DNMT)1, histone deacetylase (HDAC2, HDAC8) were confirmed to be sensitive indicators for epigenetic toxicity. The DNMT1-mediated epigenetic equivalency toxicity of organic extracts in Dongjiang River were more serious than those of HDAC2 and HDAC8. Correlation analysis shown binding affinity between POPs and DNMT1, HDAC2 and HDAC8 could be regarded as toxic equivalency factors. Risk assessment suggested that 4-nonylphenol and bisphenol A were the largest contributors to epigenetic risk. This study is the first attempt to quantify epigenetic toxicity and epigenetic risk evaluation of river water.

New insight into the role of glutathione reductase in glutathione peroxidase-like activity determination by coupled reductase assay: Molecular Docking Study

Previously we have shown that among 15 substituted salicyloyl (2-hydroxybenzoyl) 5-seleninic acids (SSAs) 4 compounds with longer side chains or a cyclohexyl group exhibit no glutathione peroxidase (GPx)-like activity in the coupled reductase assay. Experimental inhibition of glutathione reductase (GR) by the selenenylsulfide (a main intermediate in the catalytic cycle for GPx-like activity determination) of one of the inactive compounds led us to assess the interactions between 15 selenenylsulfide compounds and the active site of GR by molecular docking. Docking results showed that S and Se atoms in selenenylsulfides of the compounds with no GPx-like activity were beyond 5 Å from S atom of Cys-58 or N atom of imidazole ring of His-467 (Root Mean Square Distances for general assessment of 3 major distances were over 4.8 Å) in the active site, so that they could not be catalyzed to be reduced by GR. Furthermore, their docking scores over 89 Kcal/mol meant that the selenenylsulfides were bound too strongly to the active site to leave it, leading eventually to inhibition of GR. We also applied the molecular docking to other GPx mimics such as ebselen, cyclic seleninate esters and di(propylaminomethylphenyl) diselenides to explain the differences in their GPx-like activity depending to the assays used. Our results suggest that the reduction of a selenenylsulfide by GR plays a positive role in GPx-like activity of GPx mimics in the coupled assay and recommended the prediction of possibility and strength of GPx-like activity by molecular docking before entering experimental research.

A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion

The regio- (and stereo-)selectivity and specific activity of cytochrome P450s are determined by the accessibility of potential sites of metabolism (SOMs) of the bound substrate relative to the heme, and the activation barrier of the regioselective oxidation reaction(s). The accessibility of potential SOMs depends on the relative binding free energy (ΔΔGbind ) of the catalytically active substrate-binding poses, and the probability of the substrate to adopt a transition-state geometry. An established experimental method to measure activation energies of enzymatic reactions is the analysis of reaction rate constants at different temperatures and the construction of Arrhenius plots. This is a challenge for multistep P450-catalyzed processes that involve redox partners. We introduce a modified Arrhenius approach to overcome the limitations in studying P450 selectivity, which can be applied in multiproduct enzyme catalysis. Our approach gives combined information on relative activation energies, ΔΔGbind values, and collision entropies, yielding direct insight into the basis of selectivity in substrate conversion.

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation

Binding free energy (ΔGbind) computation can play an important role in prioritizing compounds to be evaluated experimentally on their affinity for target proteins, yet fast and accurate ΔGbind calculation remains an elusive task. In this study, we compare the performance of two popular end-point methods, i.e., linear interaction energy (LIE) and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), with respect to their ability to correlate calculated binding affinities of 27 thieno[3,2-d]pyrimidine-6-carboxamide-derived sirtuin 1 (SIRT1) inhibitors with experimental data. Compared with the standard single-trajectory setup of MM/PBSA, our study elucidates that LIE allows to obtain direct ("absolute") values for SIRT1 binding free energies with lower compute requirements, while the accuracy in calculating relative values for ΔGbind is comparable (Pearson's r = 0.72 and 0.64 for LIE and MM/PBSA, respectively). We also investigate the potential of combining multiple docking poses in iterative LIE models and find that Boltzmann-like weighting of outcomes of simulations starting from different poses can retrieve appropriate binding orientations. In addition, we find that in this particular case study the LIE and MM/PBSA models can be optimized by neglecting the contributions from electrostatic and polar interactions to the ΔGbind calculations.

Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol

The bacterial Cytochrome P450 (CYP) BM3 (CYP102A1) is one of the most active CYP isoforms. BM3 mutants can serve as a model for human drug-metabolizing CYPs and/or as biocatalyst for selective formation of drug metabolites. Hence, molecular and computational biologists have in the last two decades shown strong interest in the discovery and design of novel BM3 variants with optimized activity and selectivity for substrate conversion. This led e.g. to the discovery of mutant M11 that is able to metabolize a variety of drugs and drug-like compounds with relatively high activity. In order to further improve our understanding of CYP binding and reactions, we performed a co-crystallization study of mutant M11 and report here the three-dimensional structure M11 in complex with dithiothreitol (DTT) at a resolution of 2.16 Å. The structure shows that DTT can coordinate to the Fe atom in the heme group. UV/Vis spectroscopy and molecular dynamics simulation studies underline this finding and as first structure of the CYP BM3 mutant M11 in complex with a ligand, it offers a basis for structure-based design of novel mutants.

The Effect of Cofactor Binding on the Conformational Plasticity of the Biological Receptors in Artificial Metalloenzymes: The Case Study of LmrR

The design of Artificial Metalloenzymes (ArMs), which result from the incorporation of organometallic cofactors into biological structures, has grown steadily in the last two decades and important new-to-Nature reactions have been reached. These type of exercises could greatly benefit from an understanding of the structural impact that the inclusion of organometallic moieties may have on the biological host. To date though, our understanding of this phenomenon is highly partial. This lack of knowledge is one of the elements that condition that first-generation ArMs generally display relatively poor catalytic profiles. In this work, we approach this matter by assessing the dynamics and stability of a series of ArMs resulting from the inclusion, via different anchoring strategies, of a variety of organometallic cofactors into the Lactococcal multidrug resistance regulator (LmrR) protein. To this aim, we coupled standard force field-based techniques such as Protein-Ligand Docking and Molecular Dynamics simulations with a variety of trajectory convergence analyses, capable of assessing both the stability and flexibility of the different systems under study upon the binding of cofactors. Together with the experimental evidence obtained in other studies, we provide an overview on how these changes can affect the catalytic outcomes obtained from the different ArMs. Fundamentally, our results show that the convergence analysis used in this work can assess how the inclusion of synthetic metallic cofactors in proteins can condition different structural modulations of their host. Those conformational modifications are key to the success of the desired catalytic activity and their proper identification can be wisely used to improve the quality and the rate of success of the ArMs.

Characterization of kinetics of human cytochrome P450s involved in bioactivation of flucloxacillin: inhibition of CYP3A-catalysed hydroxylation by sulfaphenazole

Background and Purpose

The aim of this study was to characterize the human cytochrome P450s (CYPs) involved in oxidative bioactivation of flucloxacillin to 5‐hydroxymethyl flucloxacillin, a metabolite with high cytotoxicity towards biliary epithelial cells.

Experimental Approach

The CYPs involved in hydroxylation of flucloxacillin were characterized using recombinant human CYPs, pooled liver microsomes in the presence of CYP‐specific inhibitors and by correlation analysis using a panel of liver microsomes from 16 donors.

Key Results

Recombinant CYPs showing the highest specific activity were CYP3A4, CYP3A7 and to lower extent CYP2C9 and CTP2C8. Michaelis–Menten enzyme kinetics were determined for pooled human liver microsomes, recombinant CYP3A4, CYP3A7 and CYP2C9. Surprisingly, sulfaphenazole appeared to be a potent inhibitor of 5′‐hydroxylation of flucloxacillin by both recombinant CYP3A4 and CYP3A7.

Conclusions and Implications

The combined results show that the 5′‐hydroxylation of flucloxacillin is primarily catalysed by CYP3A4, CYP3A7 and CYP2C9. The large variability of the hepatic expression of these enzymes could affect the formation of 5′‐hydroxymethyl flucloxacillin, which may determine the differences in susceptibility to flucloxacillin‐induced liver injury. Additionally, the strong inhibition in CYP3A‐catalysed flucloxacillin metabolism by sulfaphenazole suggests that unanticipated drug–drug interactions could occur with coadministered drugs.