Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib

Covalent inhibitors represent a promising class of therapeutic compounds. Nonetheless, rationally designing covalent inhibitors to achieve a right balance between selectivity and reactivity remains extremely challenging. To better understand the covalent binding mechanism, a computational study is carried out using the irreversible covalent inhibitor of Bruton tyrosine kinase (BTK) ibrutinib as an example. A multi-μs classical molecular dynamics trajectory of the unlinked inhibitor is generated to explore the fluctuations of the compound associated with the kinase binding pocket. Then, the reaction pathway leading to the formation of the covalent bond with the cysteine residue at position 481 via a Michael addition is determined using the string method in collective variables on the basis of hybrid quantum mechanical-molecular mechanical (QM/MM) simulations. The reaction pathway shows a strong correlation between the covalent bond formation and the protonation/deprotonation events taking place sequentially in the covalent inhibition reaction, consistent with a 3-step reaction with transient thiolate and enolates intermediate states. Two possible atomistic mechanisms affecting deprotonation/protonation events from the thiolate to the enolate intermediate were observed: a highly correlated direct pathway involving proton transfer to the Cα of the acrylamide warhead from the cysteine involving one or a few water molecules and a more indirect pathway involving a long-lived enolate intermediate state following the escape of the proton to the bulk solution. The results are compared with experiments by simulating the long-time kinetics of the reaction using kinetic modeling.

Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex

The cytochrome bc₁ complex is a transmembrane enzymatic protein complex that plays a central role in cellular energy production and is present in both photosynthetic and respiratory chain organelles. Its reaction mechanism is initiated by the binding of a quinol molecule to an active site, followed by a series of charge transfer reactions between the quinol and protein subunits. Previous work hypothesized that the primary reaction was a concerted proton-coupled electron transfer (PCET) reaction because of the apparent absence of intermediate states associated with single proton or electron transfer reactions. In the present study, the kinetics of the primary bc₁ complex PCET reaction is investigated with a vibronically nonadiabatic PCET theory in conjunction with all-atom molecular dynamics simulations and electronic structure calculations. The computed rate constants and relatively high kinetic isotope effects are consistent with experimental measurements on related biomimetic systems. The analysis implicates a concerted PCET mechanism with significant hydrogen tunneling and nonadiabatic effects in the bc₁ complex. Moreover, the employed theoretical framework is shown to serve as a general strategy for describing PCET reactions in bioenergetic systems.

Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc1 Complex

The bc₁ complex is a critical enzyme for the ATP production in photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q-cycle, which is well established and operates via quinol substrates that bind inside the protein complex. Despite decades of research, the quinol-protein interaction, which initiates the Q-cycle, has not yet been completely described. Furthermore, the initial charge transfer reactions of the Q-cycle lack a physical description. The present investigation utilizes classical molecular dynamics simulations in tandem with quantum density functional theory calculations, to provide a complete and consistent quantitative description of the primary events that occur within the bc₁ complex upon quinol binding. In particular, the electron and proton transfer reactions that trigger the Q-cycle in the bc₁ complex from Rhodobacter capsulatus are studied. The coupled nature of these charge transfer reactions was revealed by obtaining the transition energy path connecting configurations of the Q_o-site prior and after the transfers. The analysis of orbitals and partial charge distribution of the different states of the Q_o-site has further supported the conclusion. Finally, key structural elements of the bc₁ complex that trigger the charge transfer reactions were established, manifesting the importance of the environment in the process, which is furthermore evidenced by free energy calculations.

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2

Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to their redox partners and integral membrane proteins and exchanging electrons. Diffusive search, recognition, binding, and unbinding of these proteins often amount to kinetic bottlenecks in cellular energy conversion, but despite the availability of structures and intense study, the physical mechanisms controlling redox partner interactions remain largely unknown. The present molecular dynamics study provides an all-atom description of the cytochrome c2-docked bc1 complex in Rhodobacter sphaeroides in terms of an ensemble of favorable docking conformations and reveals an intricate series of conformational changes that allow cytochrome c2 to recognize the bc1 complex and bind or unbind in a redox state-dependent manner. In particular, the role of electron transfer in triggering a molecular switch and in altering water-mediated interface mobility, thereby strengthening and weakening complex formation, is described. The results resolve long-standing discrepancies between structural and functional data.

Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex

Enzymes of the bc₁ complex family power the biosphere through their central role in respiration and photosynthesis. These enzymes couple the oxidation of quinol molecules by cytochrome c to the transfer of protons across the membrane, to generate a proton-motive force that drives ATP synthesis. Key for the function of the bc₁ complex is the initial redox process that involves a bifurcated electron transfer in which the two electrons from a quinol substrate are passed to different electron acceptors in the bc₁ complex. The electron transfer is coupled to proton transfer. The overall mechanism of quinol oxidation by the bc₁ complex is well enough characterized to allow exploration at the atomistic level, but details are still highly controversial. The controversy stems from the uncertain binding motifs of quinol at the so-called Q_o active site of the bc₁ complex. Here we employ a combination of classical all atom molecular dynamics and quantum chemical calculations to reveal the binding modes of quinol at the Q_o-site of the bc₁ complex from Rhodobacter capsulatus. The calculations suggest a novel configuration of amino acid residues responsible for quinol binding and support a mechanism for proton-coupled electron transfer from quinol to iron–sulfur cluster through a bridging hydrogen bond from histidine that stabilizes the reaction complex.

Configurable spatiotemporal properties in a photon-pair source based on spontaneous four-wave mixing with multiple transverse modes

We present an experimental and theoretical study of photon pairs generated by spontaneous four-wave mixing (SFWM), based on birefringent phasematching, in a fiber that supports more than one transverse mode. We present SFWM spectra, obtained through single-channel and coincidence photon counting, which exhibit multiple peaks shown here to be the result of multiple SFWM processes associated with different combinations of transverse modes for the pump, signal, and idler waves.