Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase

Lee, Kin Sing Stephen; Henriksen, Niel M.; Ng, Connie J.; Yang, Jun; Jia, Wenbao; Morisseau, Christophe; Andaya, Armann; Gilson, Michael K.; Hammock, Bruce D.

doi:10.1016/j.abb.2016.10.017

Cited by 10 publications

(9 citation statements)

References 64 publications

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“…The protein soluble epoxide hydrolase (sEH) is found in most mammalian tissues and catalyzes the conversion of epoxyeicosatrienoic acid (EETs) to dihydroxyeicosatrienoic acids (DHET) . It plays a physiological role in blood pressure, anti-inflammation, neuroprotection, and cardioprotection, and as well as being a target for treating chronic obstructive pulmonary diseases (COPD), atrial fibrillation, and diabetic neuropathic pain, it has had many drugs in clinical trials . The binding site of sEH [see Figure (C)] is large and deeply buried .…”

Section: Methodsmentioning

confidence: 99%

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions

2018

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Ligand (un)binding kinetics is being recognized as a determinant of drug specificity and efficacy in an increasing number of systems. However, the calculation of kinetics and the simulation of drug unbinding is more difficult than computing thermodynamic quantities, such as binding free energies. Here we present the first full simulations of an unbinding process at pharmacologically relevant time scales (11 min), without the use of biasing forces, detailed prior knowledge, or specialized processors using the weighted ensemble based algorithm, WExplore. These simulations show the inhibitor TPPU unbinding from its enzyme target soluble epoxide hydrolase, which is a clinically relevant target that has attracted interest in kinetics optimization in order to increase efficacy. We make use of conformation space networks that allow us to conceptualize unbinding not just as a linear process, but as a network of interconnected states that connect the bound and unbound states. This allows us to visualize patterns in hydrogen-bonding, solvation, and nonequilibrium free energies, without projection onto progress coordinates. The topology and layout of the network reveal multiple unbinding pathways, and other rare events, such as the reversal of ligand orientation within the binding site. Furthermore, we make a prediction of the transition state ensemble, using transition path theory, and identify protein-ligand interactions which are stabilizing to the transition state. Additionally, we uncover trends in ligand and binding site solvation that corroborate experimental evidence from more classical structure kinetics relationships and generate new questions as to the role of drug modifications in kinetics optimization. Finally, from only 6 μs of simulation time we observed 75 unbinding events from which we calculate a residence time of 42 s, and a standard error range of 23 to 280 s. This nearly encompasses the experimental residence time 11 min (660 s). In addition to the insights to sEH inhibitor unbinding, this study shows that simulations of complex processes on timescales as long as minutes are becoming feasible for more researchers to perform.

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Section: Methodsmentioning

confidence: 99%

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions

2018

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“…12 This observation was further supported from SAR studies (EC5019 vs EC5023 in Table 1). 5,19 Also, Lee et al revealed that the binding pocket of sEH is promiscuous, 30 and the left side of the pocket can tolerate chemical structures of various sizes. 31 The tunnel appears to breathe or even open to accept bulky groups.…”

Section: ■ Biochemcal Mechanism Of Actionmentioning

confidence: 99%

Movement to the Clinic of Soluble Epoxide Hydrolase Inhibitor EC5026 as an Analgesic for Neuropathic Pain and for Use as a Nonaddictive Opioid Alternative

Hammock¹,

McReynolds²,

Wagner³

et al. 2021

J. Med. Chem.

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This report describes the development of an orally active analgesic that resolves inflammation and neuropathic pain without the addictive potential of opioids. EC5026 acts on the cytochrome P450 branch of the arachidonate cascade to stabilize epoxides of polyunsaturated fatty acids (EpFA), which are natural mediators that reduce pain, resolve inflammation, and maintain normal blood pressure. EC5026 is a slow-tight binding transitionstate mimic that inhibits the soluble epoxide hydrolase (sEH) at picomolar concentrations. The sEH rapidly degrades EpFA; thus, inhibiting sEH increases EpFA in vivo and confers beneficial effects. This mechanism addresses disease states by shifting endoplasmic reticulum stress from promoting cellular senescence and inflammation toward cell survival and homeostasis. We describe the synthesis and optimization of EC5026 and its development through human Phase 1a trials with no drug-related adverse events. Additionally, we outline fundamental work leading to discovery of the analgesic and inflammationresolving CYP450 branch of the arachidonate cascade.

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“…The protonation state of the catalytic residue His374 was predicted to be protonated (positively charged). His374 is of particular importance as it lies between Asp192 and Asp348, and it has been previously shown that the protonated form is required for the stability of the complex. ,,, PROPKA suggests that most of the remaining histidine residues in both the WT and LW202 proteins should be deprotonated (neutral); for some, the appropriate protonation state is unclear. We have therefore generated complexes for both WT and LW202 where all histidine residues, with the exception of the protonated His374, are either positively charged or neutral.…”

Section: Methodsmentioning

confidence: 99%

Effect of Binding on Enantioselectivity of Epoxide Hydrolase

Zaugg

Gumulya

Bodén

et al. 2018

J. Chem. Inf. Model.

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Molecular dynamics simulations and free energy calculations have been used to investigate the effect of ligand binding on the enantioselectivity of an epoxide hydrolase (EH) from Aspergillus niger. Despite sharing a common mechanism, a wide range of alternative mechanisms have been proposed to explain the origin of enantiomeric selectivity in EHs. By comparing the interactions of ( R)- and ( S)-glycidyl phenyl ether (GPE) with both the wild type (WT, E = 3) and a mutant showing enhanced enantioselectivity to GPE (LW202, E = 193), we have examined whether enantioselectivity is due to differences in the binding pose, the affinity for the ( R)- or ( S)- enantiomers, or a kinetic effect. The two enantiomers were easily accommodated within the binding pockets of the WT enzyme and LW202. Free energy calculations suggested that neither enzyme had a preference for a given enantiomer. The two substrates sampled a wide variety of conformations in the simulations with the sterically hindered and unhindered carbon atoms of the GPE epoxide ring both coming in close proximity to the nucleophilic aspartic acid residue. This suggests that alternative pathways could lead to the formation of a ( S)- and ( R)-diol product. Together, the calculations suggest that the enantioselectivity is due to kinetic rather than thermodynamic effects and that the assumption that one substrate results in one product when interpreting the available experimental data and deriving E-values may be inappropriate in the case of EHs.

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Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase

Cited by 10 publications

References 64 publications

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions

Movement to the Clinic of Soluble Epoxide Hydrolase Inhibitor EC5026 as an Analgesic for Neuropathic Pain and for Use as a Nonaddictive Opioid Alternative

Effect of Binding on Enantioselectivity of Epoxide Hydrolase

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