Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability

Cyclization: A potential effective modification strategy for umami peptides

Cyclization enhances various properties of peptides and has been widely used in life sciences, but it has not been explored in taste peptides. Our study found that cyclization of the N/C termini of the peptides (head-to-tail) via amide bond is a potentially effective modification strategy for umami peptides to improve their properties. This is the first report on umami cyclic peptides. Umami peptides were downloaded from TastePeptidesDB and linear/cyclic structures were generated for docking with umami receptors, of which 138 groups completed docking. The lower-scoring group was chosen for contact matrix analysis, yielding three representative umami peptides after dimensionality reduction and clustering. Sensory evaluation of the three groups (chemically synthesized linear and cyclic peptides) revealed that the umami intensity of DPLRGGY was significantly increased after cyclization, with recognition threshold dropped from 0.186 to 0.051 mM; while the umami intensity of RGEPNND decreased. Applying molecular fingerprints and descriptors analysis, it was found that polarity and threshold differences were correlated (|Corr| ≥0.5). DFT calculations were applied to analyze the electron cloud structure and found that electrostatic rearrangement was the main reason for the difference in umami intensity after cyclization. This study proposed a potential cyclization strategy for the development of novel umami peptides and explained the essential reasons for the cyclization effect, providing a new strategy for further expanding the application to explore more efficient umami peptide structural derivatives.

Structure-Based Design of "Head-to-Tail" Macrocyclic PROTACs

Macrocyclization is a compelling strategy for conventional drug design for improving biological activity, target specificity, and metabolic stability, but it was rarely applied to the design of PROTACs possibly due to the mechanism and structural complexity. Herein, we report the rational design of the first series of "Head-to-Tail" macrocyclic PROTACs. The resulting molecule SHD913 exhibited pronounced Brd4 protein degradation with low nM DC50 values while almost totally dismissing the "hook effect", which is a general character and common concern of a PROTAC, in multiple cancer cell lines. Further biological evaluation revealed that the compound exhibited positive cooperativity and induced de novo protein-protein interactions (PPIs) in both biophysical and cellular NanoBRET assays and outperformed macroPROTAC-1 that is the first reported macrocyclic Brd4 PROTAC, in cellular assays. In vitro liver microsomal stability evaluation suggested that SHD913 demonstrated improved metabolic stability in different species compared with the linear counterpart. The co-crystal structure of Brd4BD2: SHD913: VCB (VHL, Elongin C and Elongin B) complex determination and molecular dynamics (MD) simulation also elucidated details of the chemical-induced PPIs and highlighted the crucial contribution of restricted conformation of SHD913 to the ternary complex formation. These results collectively support that macrocyclization could be an attractive and feasible strategy for a new PROTAC design.

Illuminating the multiple Lewis acidity of triaryl-boranes via atropisomeric dative adducts

Using the principle that constrained conformational spaces can generate novel and hidden molecular properties, we challenged the commonly held perception that a single-centered Lewis acid reacting with a single-centered Lewis base always forms a single Lewis adduct. Accordingly, the emergence of single-centered but multiple Lewis acidity among sterically hindered and non-symmetric triaryl-boranes is reported. These Lewis acids feature several diastereotopic faces providing multiple binding sites at the same Lewis acid center in the interaction with Lewis bases giving rise to adducts with diastereomeric structures. We demonstrate that with a proper choice of the base, atropisomeric adduct species can be formed that interconvert via the dissociative mechanism rather than conformational isomerism. The existence of this exotic and peculiar molecular phenomenon was experimentally confirmed by the formation of atropisomeric piperidine-borane adducts using state-of-the-art NMR techniques in combination with computational methods.

Taming Conformational Heterogeneity on Ion Racetrack to Unveil Principles that Drive Membrane Permeation of Cyclosporines

Our study reveals the underlying principles governing the passive membrane permeability in three large N-methylated macrocyclic peptides (N-MeMPs): cyclosporine A (CycA), Alisporivir (ALI), and cyclosporine H (CycH). We determine a series of conformers required for robust passive membrane diffusion and those relevant to other functions, such as binding to protein targets or intermediates, in the presence of solvent additives. We investigate the conformational interconversions and establish correlations with the membrane permeability. Nuclear magnetic resonance (NMR) and cyclic ion-mobility spectrometry-mass spectrometry (cIMS-MS) are employed to characterize conformational heterogeneity and identify cis-amides relevant for good membrane permeability. In addition, ion mobility selected cIMS-MS and infrared (IR) multiple-photon dissociation (IRMPD) spectroscopy experiments are conducted to evaluate the energy barriers between conformations. We observe that CycA and ALI, both cyclosporines with favorable membrane permeabilities, display multiple stable and well-defined conformers. In contrast, CycH, an epimer of CycA with limited permeability, exhibits fewer and fewer stable conformers. We demonstrate the essential role of the conformational shift from the aqueous cis MeVal11-MeBmt1 state (A1) to the closed conformation featuring cis MeLeu9-MeLeu10 (C1) in facilitating membrane permeation. Additionally, we highlight that the transition from A1 to the all-trans open conformation (O1) is specifically triggered by the presence of CaCl2. We also capture a set of conformers with cis Sar3-MeLeu4, MeLeu9-MeLeu10, denoted as I. Conformationally selected cIMS-MS and IRMPD data of [CycA+Ca]2+ show immediate repopulation of the original population distribution, suggesting that CaCl2 smooths out the energy barriers. Finally, our work presents an improved sampling molecular dynamics approach based on a refined force field that not only consistently and accurately captures established conformers of cyclosporines but also exhibits strong predictive capabilities for novel conformers.