Discrete Dynamics of Warhead Modulation on Covalent Inhibition of Oxyr: A QM/MM Study

The bacterial transcriptional factor OxyR, a peroxide sensor conserved in bacterial virulence pathways, has the capability to exhibit exceptional reactivity toward hydrogen peroxide (H₂O₂). H₂O₂ is essential for oxidizing cysteine thiolates to maintain cellular redox homeostasis and is dispensable for bacterial growth that can potentially mitigate drug resistance, thus underlining OxyR as a valuable target. We employ quantum mechanics/molecular mechanics (QM/MM) umbrella sampling (US) simulations at the DFTB3/MM level of theory and propose a reaction mechanism with four potential covalent inhibitors. The potential of mean force reveals the direct role of intrinsic reactivity of inhibitors, for instance, benzothiophenes and modified experimental inhibitors with methyl oxo-enoate warhead-activated carbonyl samples in the first step of reaction, which shed light on the significance of proton transfer indispensable for full inhibition, whereas the nitrile inhibitor undergoes a stepwise mechanism with a small proton-transfer energy barrier and lower imaginary frequencies that materialize instantly after nucleophilic attack. To unveil the molecular determinants of respective binding affinities, transition states along the reaction path are optimized and characterized with B3LYP 6-31+G(d,p). Furthermore, the post-simulation analysis indicates the catalytic triad (His130/Cys199/Thr129), thermodynamically favored for inhibition, which restricts water molecules from acting as the potential source of protonation/deprotonation. This study thus serves as a preamble to add variation in the proposed structures and unveils the impact of functional groups lying in warheads that modulate the kinetics of proton transfer, which will certainly aid to design more selective and efficient irreversible inhibitors of OxyR.

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations

The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a simulation study of the inhibition of the SARS-CoV-2 main protease (Mpro), a cysteine hydrolase essential for the life cycle of the virus. The free energy landscape for the mechanism of the inhibition process is explored by QM/MM umbrella sampling and free energy perturbation simulations at the M06-2X/MM level of theory for two proposed peptidyl covalent inhibitors that share the same recognition motif but feature distinct cysteine-targeting warheads. Regardless of the intrinsic reactivity of the modeled inhibitors, namely a Michael acceptor and a hydroxymethyl ketone activated carbonyl, our results confirm that the inhibitory process takes place by means of a two-step mechanism, in which the formation of an ion pair C145/H41 dyad precedes the protein-inhibitor covalent bond formation. The nature of this second step is strongly dependent on the functional groups in the warhead: while the nucleophilic attack of the C145 sulfur atom on the Cα of the double bond of the Michael acceptor takes place concertedly with the proton transfer from H41 to Cβ, in the compound with an activated carbonyl, the sulfur attacks the carbonyl carbon concomitant with a proton transfer from H41 to the carbonyl oxygen via the hydroxyl group. An analysis of the free energy profiles, structures along the reaction path, and interactions between the inhibitors and the different pockets of the active site on the protein shows a measurable effect of the warhead on the kinetics and thermodynamics of the process. These results and QM/MM methods can be used as a guide to select warheads to design efficient irreversible and reversible inhibitors of SARS-CoV-2 Mpro.

Dimethyl fumarate alters intracellular Ca2+ handling in immune cells by redox-mediated pleiotropic effects

Dimethyl fumarate (DMF) is widely used to treat the human autoimmune diseases multiple sclerosis (MS) and psoriasis. DMF causes short-term oxidative stress and activates the antioxidant response via the transcription factor Nrf2 but its immunosuppressive effect is not well understood. Immune cell activation depends on calcium signaling which itself is influenced by the cellular redox state. We therefore measured calcium, reactive oxygen species levels and glutathione content in lymphocytes from immunized mice before onset of experimental autoimmune encephalomyelitis, in peripheral blood mononuclear cells from MS patients treated with DMF, and in mouse splenocytes treated ex vivo with DMF. This demonstrated altered redox states and increased lymphocytic calcium levels in all model systems. DMF caused an immediate influx of calcium from the extracellular space, long-term increased cytosolic calcium levels and reduced calcium stored in intracellular stores. The DMF-elicited current had the electrophysiological characteristics of a transient receptor potential channel and the intracellular calcium levels were normalized by antagonists of TRPA1. Interestingly, the sarco/endoplasmic reticulum Ca²⁺-ATPase SERCA2b was downregulated but more active due to glutathionylation of the redox-sensitive cysteine 674. DMF therefore causes pleiotropic changes in cellular calcium homeostasis which are likely caused by redox-sensitive post-translational modifications. These changes probably contribute to its immunosuppressive effects.