Towardin vivo-relevant hERG safety assessment and mitigation strategies based on relationships between non-equilibrium blocker binding, three-dimensional channel-blocker interactions, dynamic occupancy, dynamic exposure, and cellular arrhythmia

Abstract

The human ether-a-go-go-related voltage-gated cardiac ion channel (commonly known as hERG) conducts the rapid outward repolarizing potassium current in cardiomyocytes (IKr). Inadvertent blockade of this channel by drug-like molecules represents a key challenge in pharmaceutical R&D due to frequent overlap between the structure-activity relationships of hERG and many primary targets. Building on our previous work, together with recent cryo-EM structures of hERG, we set about to better understand the energetic and structural basis of promiscuous blocker-hERG binding in the context of Biodynamics theory. We propose a two-step blocker binding process consisting of: 1) Diffusion of a single fully solvated blocker copy into a large cavity lined by the intracellular cyclic nucleotide binding homology domain (the initial capture step). Occupation of this cavity is a necessary but insufficient condition for ion current disruption.2) Translocation of the captured blocker along the channel axis (the IKr disruption step), such that:a) The head group, consisting of a quasi-linear moiety, projects into the open pore, accompanied by partial de-solvation of the binding interface. b) One tail moiety packs along a kink between the S6 helix and proximal C-linker helix adjacent to the intra-cellular entrance of the pore, likewise accompanied by mutual de-solvation of the binding interface (noting that the association barrier is comprised largely of the total head + tail group de-solvation cost). c) Blockers containing a highly planar moiety that projects into a putative constriction zone within the closed channel become trapped upon closing, as do blockers terminating prior to this region. d) A single captured blocker molecule may associate and dissociate from the pore many times before exiting the CNBHD cavity.Lastly, we highlight possible flaws in the current hERG safety index (SI) and propose an alternate in vivo-relevant strategy factoring in: 1) Benefit/risk.2) The predicted arrhythmogenic fractional hERG occupancy (based on action potential simulations of the undiseased human ventricular cardiomyocyte).3) Alteration of the safety threshold due to underlying disease. 4) Risk of exposure escalation toward the predicted arrhythmic limit due to patient-to-patient pharmacokinetic variability, drug-drug interactions, overdose, and use for off-label indications in which the hERG safety parameters may differ from their on-label counterparts.As is widely appreciated throughout the pharmaceutical industry, the risk of torsade de pointes arrhythmia (TdP) is promoted by drug-induced loss of function of the human ether-a-go-go gene product (hERG) [1][2][3][4] in proportion to the concomitant fractional decrease in the outward repolarizing hERG current (denoted IKr) due to dynamic blocker occupancy. TdP arises at a threshold level of IKr reduction, which may auto-extinguish spontaneously or progress to ventricular fibrillation and death [5][6][7][8]. The causal relationship between acquired loss of hERG function and TdP was deduced in the l...

Probing cellular arrhythmogenesis using the O’Hara-Rudy model of the undiseased human ventricular cardiomyocyte

“…The AP-generation system responds to increasing levels of perturbation, as follows: Slow quasi-linear growth in APD, accompanied by decreasing d (Δ ψ m ( t ))/ dt within the shoulder region. T 1 is approached more rapidly for trappable versus non-trappable blockers exhibiting slower k on , consistent with our earlier argument against a one-size-fits-all safety margin [12] (further addressed in [18]). Large swings in successive APD (Figure 7) (short-long-short QT sequences are known to precede TdP). Such behavior, reflecting high instability of the system, is attributable to oscillations in d (Δ ψ m ( t ))/ dt , APD, and ion channel activity on approach to the T 1 tipping point. Abrupt crossing of the T 1 tipping point. …”

“…1) Slow quasi-linear growth in APD, accompanied by decreasing (∆ ( ))/ within the shoulder region. T1 is approached more rapidly for trappable versus non-trappable blockers exhibiting slower kon, consistent with our earlier argument against a one-size-fits-all safety margin [12] (further addressed in [18]).…”

“…Our results reiterate our previous claim that significantly greater exposure is required to achieve pre-arrhythmic occupancy for non-trappable blockers exhibiting slower k on , versus trappable blockers or non-trappable blockers with faster k on (at equivalent IC 50 ) (Figure 23). Revision of the hERG safety margin may be warranted based on our simulated mechanism-based dose-response results (further addressed in [18]), which furthermore, could facilitate more straightforward consideration of benefit/risk criteria in the hERG safety equation.…”

General structure-free energy relationships of hERG blocker binding under native cellular conditions

“…ii. Projection of a single quasi-rod-shaped blocker moiety (denoted as "BP") into the open pore (denoted as "P") [4]. The on-rate is described by kb…”

Probing the dynamic structure-function and structure-free energy relationships of the corona virus main protease with Biodynamics theory

“…In this work, we break from traditional screening and structure-based drug design approaches, and examine M pro inhibition from a theoretical , in vivo -relevant perspective, based on multi-scale Biodynamics principles described in our previous work [1,2]. Our theory addresses the fundamental nature of dynamic structure-free energy relationships under aqueous cellular conditions (powered principally by de-solvation and re-solvation costs [2,3]), and the general means by which cellular function is derived from interacting molecular species undergoing time-dependent cycles of exponential buildup and decay. As such, enzyme structure-function is necessarily considered in the overall context of cellular function and dysfunction (consisting of viral infection in this case), and in particular: Synchrony between substrate k 1 , k cat , and k -1 , in which the bound substrate lifetime (t 1/2 ) is comparable to 1/k cat (a general kinetic paradigm that was first described by van Slyke and Cullen [4,5]), and product inhibition is circumvented via fast leaving group dissociation. Synchrony between the rates of enzyme and substrate buildup and product formation. …”