Contributions of pocket depth and electrostatic interactions to affinity and selectivity of receptors for methylated lysine in water

Abstract

Dynamic combinatorial chemistry was used to generate a set of receptors for peptides containing methylated lysine (KMen, n = 0-3) and study the contribution of electrostatic effects and pocket depth to binding affinity and selectivity. We found that changing the location of a carboxylate resulted in an increase in preference for KMe2, presumably based on ability to form a salt bridge with KMe2. The number of charged groups on either the receptor or peptide guest systematically varied the binding affinities to all guests by approximately 1-1.5 kcal mol(-1), with little influence on selectivity. Lastly, formation of a deeper pocket led to both increased affinity and selectivity for KMe3 over the lower methylation states. From these studies, we identified that the tightest binder was a receptor with greater net charge, with a Kd of 0.2 μM, and the receptor with the highest selectivity was the one with the deepest pocket, providing 14-fold selectivity between KMe3 and KMe2 and a Kd for KMe3 of 0.3 μM. This work provides key insights into approaches to improve binding affinity and selectivity in water, while also demonstrating the versatility of dynamic combinatorial chemistry for rapidly exploring the impact of subtle changes in receptor functionality on molecular recognition in water.

Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin

“…Efforts to approximate protein surfaces with supramolecular ligands have involved calixarenes, crown ethers, curcurbiturils, foldamers, porphyrins and tweezers . Recent attention has focused on the cationic side chains of lysine and arginine as potential targets that protrude invitingly from the protein surface . Ligands for lysine and arginine typically possess one or more of the attributes: anionic, aromatic and cavity‐containing, thus enabling the formation of salt‐bridge, CH–π and cation–π interactions.…”

Fluorogenic sensor platform for the histone code using receptors from dynamic combinatorial libraries

“…2). 21–24 These receptors were developed and synthesized using dynamic combinatorial chemistry (DCC), which is a reversible process that relies on the thermodynamic templation of building blocks into favorable receptors due to binding to guests. 29–31 Importantly, it allows for rapid variation of each building block in the receptor, therefore easily generating a number of host molecules.…”

“…Moreover, each receptor has a distinct pattern of binding affinities and selectivities, and is sensitive to the neighboring charge. 23,24,41 …”

“…All four receptors, A 2 B , A 2 D , A 2 G , and A 2 N , bind Kme3 in the context of a histone tail sequence (Ac-WGGG-QTAR-Kme3-STG-NH2) with affinities in the low micromolar to high nanomolar range, and selectivities over unmodified Lys of 8-fold to >40-fold. 21–24 Additionally, receptor A 2 D binds Rme2a with low micromolar affinity and with 12-fold selectivity over Arg. To develop a sensor platform for modified histone tails, indicator displacement assays were established for each receptor.…”

Synthetic Receptors for the Recognition and Discrimination of Post‐Translationally Methylated Lysines

“…To increase and vary the binding affinities and selectivity of receptor 32 , the group of Waters used the DCL approach to generate macrocycles 33 – 38 (Scheme ) They have impressively high affinities to histone peptide H3K9 in its different methylation forms, ranging from 0.13–2.6 (trimethylation) to 0.18–13.2 (dimethylation), 1.0–40 (monomethylation) and 1.8–58 μ m (unmethylated peptide; Table S6). For a broad application of disulfide receptors as trimethyllysine sensors, a late‐stage modification has been suggested .…”