Ring Size as an Independent Variable in Cyclooligomeric Depsipeptide Antiarrhythmic Activity

Abstract

Hit-to-lead studies employ a variety of strategies to optimize binding to a target of interest. When a structure for the target is available, hypothesis-driven structure–activity relationships (SAR) are a powerful strategy for refining the pharmacophore to achieve robust binding and selectivity characteristics necessary to identify a lead compound. Recrafting the three-dimensional space occupied by a small molecule, optimization of hydrogen bond contacts, and enhancing local attractive interactions are traditional approaches in medicinal chemistry. Ring size, however, is rarely able to be leveraged as an independent variable because most hits lack the symmetry required for such a study. Our discovery that the cyclic oligomeric depsipeptide ent-verticilide inhibits mammalian cardiac ryanodine receptor calcium release channels with submicromolar potency provided an opportunity to explore ring size as a variable, independent of other structural or functional group changes. We report here that ring size can be a critical independent variable, suggesting that modest conformational changes alone can dramatically affect potency.

Structure–Activity Relationships for the N-Me- Versus N-H-Amide Modification to Macrocyclic ent-Verticilide Antiarrhythmics

“…Sunazuka has reported several pathways to nat -verticilide using fragment couplings in both solution and solid phases, but our enantioselective synthesis of the α-oxyacid provided the most effective means to access the N -methyl amide series for ent -verticilide described here. As outlined in Scheme , hexanal was converted into α-hydroxy ester 8 in 47% yield as previously described. , Coupling of alcohol 8 with either N- Me or N -H alanine provided didepsipeptides 9 & 10 in consistently high yield. In this manner, both N -H and N -Me didepsipeptide analogues could be accessed at a 15 g scale.…”

“…The extent to which this high degree of methylation is required for activity is not yet known. Our recent finding that the 18-membered macrocyclic oligomer ( ent -verticilide B1) exhibits a similar effect to that of ent -verticilide provided a second platform with which to examine the importance of each N -methyl amide . In this study, we show that N -methylation is critical for activity in both hit compounds but that some residual activity can be observed in certain cases.…”

“…Unlike other cases where N -methyl → N -H replacements will either modify receptor engagement directly or through a remote effect, the oligomeric nature of ent -verticilide was attractive as a template that would likely retain some form of the pharmacophore despite a single N -Me → N -H replacement. This hypothesis was validated in a ring-size oligomer study wherein the 18-membered oligomer exhibited only a modest loss of activity despite the dramatic change in ring size . Decreasing ring size further, or extending to larger ring sizes, led to inactive compounds.…”

“…Analogues 2 , 3 , and 5 were not readily prepared by partial methylation, so we turned to a traditional approach to their synthesis that used conventional amide bond formation as outlined in Scheme . Sunazuka has reported several pathways to nat -verticilide using fragment couplings in both solution and solid phases, but our enantioselective synthesis of the α-oxyacid provided the most effective means to access the N -methyl amide series for ent -verticilide described here. As outlined in Scheme , hexanal was converted into α-hydroxy ester 8 in 47% yield as previously described. , Coupling of alcohol 8 with either N- Me or N -H alanine provided didepsipeptides 9 & 10 in consistently high yield.…”

“…We recently reported that ent -verticilide B1 ( 27 ), the 18-membered oligomer of ent -verticilide, inhibited calcium sparks similar to ent -verticilide . This provided a second series (Figure ) with which to investigate the degree of N -methylation and its effect on activity.…”