Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B

Abstract

There is an increasing realization that structure-based drug design may show improved success by understanding the ensemble of conformations and sub-states accessible to an enzyme and how the environment affects this ensemble. Human monoamine oxidase B (MAO-B) catalyzes the oxidation of amines and is inhibited for the treatment of both Parkinson's disease and depression. Despite its clinical importance, its catalytic mechanism remains unclear and routes to drugging this target would be valuable. Evidence of a radical in either the transition state or resting state of MAO-B is present throughout the literature, and is suggested to be a flavin semiquinone, a tyrosyl radical or both. Here we see evidence of a resting state flavin semiquinone, via absorption redox studies and electron paramagnetic resonance, suggesting that the anionic semiquinone is biologically relevant. Based on enzyme kinetic studies, enzyme variants and molecular dynamics simulations we find evidence for the importance of the membrane environment in mediating the activity of MAO-B and that this mediation is related to the protein dynamics of MAO-B. Further, our MD simulations identify a hitherto undescribed entrance for substrate binding, membrane modulated substrate access, and indications for half-site reactivity: only one active site is accessible to binding at a time. Our study combines both experimental and computational evidence to illustrate the subtle interplay between enzyme activity, protein dynamics and the immediate membrane environment. Understanding key biomedical enzymes to this level of detail will be crucial to inform strategies (and binding sites) for rational drug design for these targets.

Potential involvement of monoamine oxidase activity in delirium onset and SARS-COV2 infection

“…Potential energy of binding between spike proteins and two MAOB chains is calculated using OPLS3 force field -13424.67 kcal/mol (chain B) and -19073.44 kcal/mol (chain A). Resulting structure shows possible interference of spike protein with the recently presented membrane mediated substrate entrances to MAOB active site (Jones et al 2019).…”

“…Computational modeling defines a mechanism by which the spike protein directly binds to MAOB thereby interfering with its normal function and particularly affecting patients with increased MAOB expression. Detailed computational docking analysis shows strongest binding of spike protein to the region of MAOB recently proposed as the membrane mediated substrate entrance to the active site of MAOB (Jones et al 2019).…”

“…Computational modeling defines a mechanism by which the spike protein directly binds to MAOB thereby interfering with its normal function and particularly affecting patients with increased MAOB expression. Detailed computational docking analysis shows strongest binding of spike protein to the region of MAOB recently proposed as the membrane mediated substrate entrance to the active site of MAOB (Jones et al 2019). Further analysis is currently under way to explore in greater detail the role of MAOB in delirium and SARS-CoV-2 infection with further exploration of the effects of sex and other demographic, medical or drug utilization on the delirium related metabolic changes.…”

Rigidity, normal modes and flexible motion of a SARS-CoV-2 (COVID-19) protease structure

“…Secondly, the global low-frequency motion couples to variations in the binding site/active site geometry [5,6]. Knowledge of the range of flexible variation here is potentially useful for structurebased drug design and/or fragment screening, since attention can be focussed on candidate molecules that interact robustly with the binding site and tolerate its flexibility, in preference to molecules that interact well only with the crystal structure and not with its flexible variations.…”

“…These simplified methods are strongly complementary to both computational MD investigations and experimental biophysical/biochemical studies of protein behaviour. enzyme active site geometry [5][6][7][8]; and, crucially, that a structure generated from geometric simulation of a large amplitude motion can be used as input for further MD investigation [9], as the geometric simulation retains the local bonding geometry and constraint network of the input crystal structure and forbids major bonding distortions and steric clashes.…”