All-Atom Simulations Disclose How Cytochrome Reductase Reshapes the Substrate Access/Egress Routes of Its Partner CYP450s

Ritacco, Ida; Saltalamacchia, Andrea; Spinello, Angelo; Ippoliti, Emiliano; Magistrato, Alessandra

doi:10.1021/acs.jpclett.9b03798

Cited by 19 publications

(21 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[6] Molecular dynamics (MD) simulations have given insights into the dynamici nteractions between CYP450 and CPR, its redox partner. [14][15][16] Ac lose approach betweent he CPR flavin mononucleotide (FMN) and CYP450 heme (8.8 )t riggers the first electron transfer. [14] Often, the second-coordination sphere in heme andn onheme iron enzymes plays ac rucial role in determining the selectivity and activity of enzymes through either substrate and oxidant positioning or long-range electrostatic perturbations.…”

Section: Introductionmentioning

confidence: 99%

How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions?

Dixit

Warwicker

Visser

2020

Chemistry A European J

View full text Add to dashboard Cite

Cytochrome P450 (CYP450)e nzymes play important roles in maintaining human health andt heir reaction rates are dependento nt he first electron transfer from the reduction partner.I nterestingly,e xperimental work has shown that this step is highly influenced by the addition of metal ions. To understand the effect of externalp erturbations on the CYP450 first reduction step, we have performed ac omputational studyw ith model complexes in the presence of metal and organic ions, solvent molecules, and an electricf ield. The results show that these medium-rangei nteractions affect the driving force as well as electron-transfer rates dramatically.Based on the location, distance, and direction of the ions/electric field, the catalytic reaction rates are enhanced or impaired. Calculations on al arge crystal structure with bonded alkali metal ions indicated inhibition patterns of the ions. Therefore, we predict that the activef orms of the naturalC YP450i sozymes will not have more than one alkali metal ion bound in the second-coordination sphere. As such, this study provides an insighti nto the activity of CYP450 enzymes and the effects of ions and electric field perturbations on their activity.

show abstract

Section: Introductionmentioning

confidence: 99%

How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions?

Dixit

Warwicker

Visser

2020

Chemistry A European J

View full text Add to dashboard Cite

show abstract

“…An alteration in ligand tunnels due to CPR binding has also recently been observed in conventional MD simulations of the CYP 19A1-CPR complex in a membrane. 67 Our results indicate, however, that more extensive studies of substrate access and product release would be necessary to confirm the effect of CPR.…”

Section: Cpr Affects Cyp Ligand Tunnels Due To Cyp Reorientation and mentioning

confidence: 68%

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

Mukherjee

Nandekar

Wade

2020

Preprint

View full text Add to dashboard Cite

Cytochrome P450 (CYP) enzymes are heme monooxygenases that require two electrons for their catalytic cycle. For the mammalian microsomal CYPs, key enzymes for xenobiotic metabolism and steroidogenesis and important drug targets and biocatalysts, the electrons are transferred by NADPH-cytochrome P450 oxidoreductase (CPR). CYP and CPR each attach to the membrane of the endoplasmic reticulum by a single transmembrane helix with their catalytic domains in the cytosol. No structure of a mammalian CYP-CPR complex has been solved experimentally, hindering a detailed understanding of the determinants of electron transfer (ET), which is often rate-limiting for CYP reactions. Here, we investigated the structure and dynamics of the interactions between membrane-bound CYP 1A1, an antitumor drug target, and CPR by a multiresolution computational approach, combining Brownian dynamics, coarse-grained and allatom molecular dynamics simulations. We find that upon binding to CPR, the CYP 1A1 catalytic domain becomes less embedded in the membrane and reorients, indicating that CPR may affect ligand passage between the membrane and the CYP active site. Despite the constraints imposed by membrane binding, we identify several arrangements of CPR around CYP 1A1 that are compatible with ET. In the complexes, the interactions of the CPR FMN domain with the proximal side of CYP 1A1 are supplemented by more transient interactions of the CPR NADP domain with the distal side of CYP 1A1. Computed ET rates and pathways agree well with available experimental data and suggest why the CYP-CPR ET rates are low compared to those of soluble bacterial CYPs. TOC GRAPHICS

show abstract

“…Grounding on recent evidence demonstrating the existence of allosteric binding sites [50] and their possible exploitation for a non-competitive/mixed inhibition mechanism [54] we docked glyphosate into the two allosteric cavities. Namely, we docked it to Site 1, which lies along the most relevant access channel to the enzyme active site [77] and to Site 2, which instead lies at the interface with the cytochrome P450 reductase (CPR), supplying the electrons necessary for catalysis ( Figure 3) [78]. In the docking pose in Site 1 and during MD simulations glyphosate engages a salt bridge interaction with its phosphate group and Arg192, as well as the formation of a hydrogen (H)-bond between Gln218 and the carboxylic group of the pesticide.…”

Section: Molecular Dynamics Simulations On Aromatasementioning

confidence: 99%

Molecular Basis for Endocrine Disruption by Pesticides Targeting Aromatase and Estrogen Receptor

Zhang

Schilirò²,

Gea³

et al. 2020

IJERPH

Self Cite

View full text Add to dashboard Cite

The intensive use of pesticides has led to their increasing presence in water, soil, and agricultural products. Mounting evidence indicates that some pesticides may be endocrine disrupting chemicals (EDCs), being therefore harmful for the human health and the environment. In this study, three pesticides, glyphosate, thiacloprid, and imidacloprid, were tested for their ability to interfere with estrogen biosynthesis and/or signaling, to evaluate their potential action as EDCs. Among the tested compounds, only glyphosate inhibited aromatase activity (up to 30%) via a non-competitive inhibition or a mixed inhibition mechanism depending on the concentration applied. Then, the ability of the three pesticides to induce an estrogenic activity was tested in MELN cells. When compared to 17β-estradiol, thiacloprid and imidacloprid induced an estrogenic activity at the highest concentrations tested with a relative potency of 5.4 × 10−10 and 3.7 × 10−9, respectively. Molecular dynamics and docking simulations predicted the potential binding sites and the binding mode of the three pesticides on the structure of the two key targets, providing a rational for their mechanism as EDCs. The results demonstrate that the three pesticides are potential EDCs as glyphosate acts as an aromatase inhibitor, whereas imidacloprid and thiacloprid can interfere with estrogen induced signaling.

show abstract

All-Atom Simulations Disclose How Cytochrome Reductase Reshapes the Substrate Access/Egress Routes of Its Partner CYP450s

Cited by 19 publications

References 18 publications

How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions?

How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions?

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

Molecular Basis for Endocrine Disruption by Pesticides Targeting Aromatase and Estrogen Receptor

Contact Info

Product

Resources

About