Dynamics of (Hetero)aryl Motifs: An Integrative Approach To Study the Conformational Landscape in Macrocycles

Area of Science:

• Medicinal Chemistry
• Structural Biology
• Computational Chemistry

Background:

• Macrocyclic peptides are a promising therapeutic class with potential for oral delivery and targeting difficult proteins.
• Incorporating aromatic heterocycles into macrocycles offers unique structural and conformational properties.
• Precisely determining the solution-state structures and dynamics of these complex molecules is a significant challenge.

Purpose of the Study:

• To develop and apply an integrated NMR-computational framework for characterizing the conformational ensembles of aryl- and heterobiaryl-containing macrocycles.
• To investigate how aryl and heterobiaryl motifs influence macrocycle conformation and dynamics in various solvents.
• To provide a general strategy for structure-based design of novel peptide therapeutics.

Main Methods:

• Integration of isotropic and anisotropic Nuclear Magnetic Resonance (NMR) observables, including residual dipolar couplings (RDCs) and nuclear Overhauser effects (NOEs).
• Enhanced sampling simulations to explore conformational space.
• Density functional theory (DFT) calculations to refine structural models and energetics.
• Analysis of conformational dynamics across different solvent systems.

Main Results:

• The integrative NMR-computational approach accurately captures macrocycle solution-state ensembles, extending beyond conventional NMR.
• Residual dipolar coupling (RDC) measurements provided crucial insights into conformational dynamics.
• Up to three interconverting backbone conformers were necessary to reconcile experimental data, highlighting complex dynamics.
• Aryl and heterobiaryl motifs were identified as key modulators of the conformational landscape, influencing hydrogen-bonding networks and backbone geometries.

Conclusions:

• The developed integrative NMR-computational framework offers a precise and general strategy for resolving complex conformational ensembles in macrocycles.
• This methodology enhances the understanding of macrocycle dynamics and structure-activity relationships.
• The findings will guide synthetic modifications and facilitate the structure-based rational design of next-generation peptide therapeutics.