Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscle and Structure Activity Relationship

Abstract

Despite large investments from academia and industry, heart failure, which results from a disruption of the contractile apparatus, remains a leading cause of death. Cardiac muscle contraction is a calcium-dependent mechanism, which is regulated by the troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium binding subunit (cNTnC). There is an increasing need for the development of small molecules that increase calcium sensitivity without altering systolic calcium concentration, thereby strengthening cardiac function. Here, we examined the effect of our previously identified calcium sensitizing small molecule, ChemBridge compound 7930079, in the context of several homologous muscle systems. The effect of this molecule on force generation in isolated cardiac trabeculae and slow skeletal muscle fibers was measured. Furthermore, we explored the use of Gaussian accelerated molecular dynamics in sampling highly predictive receptor conformations based on NMR derived starting structures. Additionally, we took a rational computational approach for lead optimization based on lipophilic diphenyl moieties. This led to the identification of three novel low affinity binders, which had similar binding affinities to known positive inotrope trifluoperazine. The most potent identified calcium sensitizer was compound 16 with an apparent affinity of 117±17 μM.

Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations

“…Dvornikov et al explored the effect of the R145W mutation on myofilament length-dependent activation (LDA) and found that the mutation does not affect LDA but does increase the sensitivity of the myofilament to Ca 2+ . Moreover, biochemical assays and functional experiments on the R145G mutation converged on the finding that this mutation causes an increase in myofilament Ca 2+ -sensitivity , and reduces the ability of cTnI to inhibit activation of cardiac muscle. , Computational efforts have also explored the effect that these cTnI mutations can have on the thermodynamics of the cTnC HP opening event. ,− Our lab and others have successfully shown the potential of computational tools as a viable option for studying cTn dynamics for the purpose of computationally aided drug discovery − and Ca 2+ -binding simulations. − …”

Unraveling the Behavior of Intrinsically Disordered Protein c-Myc: A Study Utilizing Gaussian-Accelerated Molecular Dynamics

“…MD simulation is a computational method that is used to explore conformational spaces for proteins and ligands and is widely used in studying the behavior of IDPs. 26,27 These in silico approaches are well suited for conformational analysis as they can provide insight into the atomic-level detail of IDPs, other proteins, and complex systems that allow for predicting and understanding biological pathways and their activity. 28 A limitation of using conventional MD is the presence of energy barriers that hinder molecules and residues from transitioning between conformational states.…”