Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization

Secondary Structure Stabilization of Macrocyclic Antimicrobial Peptides via Cross-Link Swapping

Lactam cross-links have been employed to stabilize the helical secondary structure and enhance the activity and physiological stability of antimicrobial peptides; however, stabilization of β-sheets via lactamization has not been observed. In the present study, lactams between the side chains of C- and N-terminal residues have been used to stabilize the β-sheet conformation in a short ten-residue analogue of chicken angiogenin-4. Designed using a combination of molecular dynamics simulations and Markov state models, the lactam cross-linked peptides are shown to adopt stabilized β-sheet conformations consistent with simulated structures. Replacement of the peptide side-chain Cys-Cys disulfide by a lactam cross-link enhanced the broad-spectrum antibacterial activity compared to the parent peptide and exhibited greater propensity to induce proinflammatory activity in macrophages. The combination of molecular simulations and conformational and biological analyses of the synthetic peptides provides a useful paradigm for the rational design of therapeutically active peptides with constrained β-sheet structures.

Kinetic Analysis of Lanthipeptide Cyclization by Substrate-Tolerant ProcM

Lanthipeptides are ribosomally synthesized and post-translationally modified peptides characterized by the presence of thioether crosslinks. Class II lanthipeptide synthetases are bifunctional enzymes responsible for the multistep chemical modification of these natural products. ProcM is a class II lanthipeptide synthetase known for its remarkable substrate tolerance and ability to install diverse (methyl)lanthionine rings with high accuracy. Previous studies suggested that the final ring pattern of the lanthipeptide product may be determined by the substrate sequence rather than by ProcM, and that ProcM operates by a kinetically controlled mechanism, wherein the ring pattern is dictated by the relative rates of the individual cyclization reactions. This study utilizes kinetic assays to determine if rates of isolated modifications can predict the final ring pattern present in prochlorosins. Changes in the core substrate sequence resulted in changes to the reaction rates of ring formation as well as a change in the order of modifications. Additionally, individual chemical reaction rates were significantly impacted by the presence of other modifications on the peptide. These findings indicate that the rates of isolated modifications are capable of predicting the final ring pattern but are not necessarily a good predictor of the order of modification in WT ProcA3.3 and its variants.

Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method

New psychoactive substances (NPS) targeting cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabinoids have been linked to the higher downstream β-arrestin signaling. Thus, understanding the mechanism of differential signaling will reveal important structure-activity relationship essential for identifying and potentially regulating NPS molecules. In this study, we simulate the slow (un)binding process of NPS MDMB-Fubinaca and classical cannabinoid HU-210 from CB1 using multi-ensemble simulation to decipher the effects of ligand binding dynamics on downstream signaling. The transition-based reweighing method is used for the estimation of transition rates and underlying thermodynamics of (un)binding processes of ligands with nanomolar affinities. Our analyses reveal major interaction differences with transmembrane TM7 between NPS and classical cannabinoids. A variational autoencoder-based approach, neural relational inference (NRI), is applied to assess the allosteric effects on intracellular regions attributable to variations in binding pocket interactions. NRI analysis indicate a heightened level of allosteric control of NPxxY motif for NPS-bound receptors, which contributes to the higher probability of formation of a crucial triad interaction (Y7.53-Y5.58-T3.46) necessary for stronger β-arrestin signaling. Hence, in this work, MD simulation, data-driven statistical methods, and deep learning point out the structural basis for the heightened physiological side effects associated with NPS, contributing to efforts aimed at mitigating their public health impact.

Promiscuity of Omphalotin A Biosynthetic Enzymes Allows de novo Production of Non-Natural Multiply Backbone N-Methylated Peptide Macrocycles in Yeast

Multiple backbone N-methylation and macrocyclization improve the proteolytic stability and oral availability of therapeutic peptides. Chemical synthesis of such peptides is challenging, in particular for the generation of peptide libraries for screening purposes. Enzymatic backbone N-methylation and macrocyclization occur as part of both non-ribosomal and ribosomal peptide biosynthesis, exemplified by the fungal natural products cyclosporin A and omphalotin A, respectively. Omphalotin A, a 9fold backbone N-methylated dodecamer isolated from the agaricomycete Omphalotus olearius, can be produced in Pichia pastoris by coexpression of the ophMA and ophP genes coding for the peptide precursor protein harbouring an autocatalytic peptide α-N-methyltransferase domain, and a peptide macrocyclase, respectively. Since both OphMA and OphP were previously shown to be relatively promiscuous in terms of peptide substrates, we expressed mutant versions of ophMA, encoding OphMA variants with altered core peptide sequences, along with wildtype ophP and assessed the production of the respective peptide macrocycles by the platform by high-performance liquid chromatography, coupled with tandem mass spectrometry (HPLC-MS/MS). Our results demonstrate the successful production of fifteen non-natural omphalotin-derived macrocycles, containing polar, aromatic and charged residues, and, thus, suggest that the system may be used as biotechnological platform to generate libraries of non-natural multiply backbone N-methylated peptide macrocycles.

The conformationally dynamic structural biology of lanthipeptide biosynthesis

Lanthipeptide synthetases are fascinating biosynthetic enzymes that install intramolecular thioether bridges into genetically encoded peptides, typically endowing the peptide with therapeutic properties. The factors that control the macrocyclic topology of lanthipeptides are numerous and remain difficult to predict and manipulate. The key challenge in this endeavor derives from the vast conformational space accessible to the disordered precursor lanthipeptide, which can be manipulated in subtle ways by interaction with the cognate synthetase. This review explores the unique strategies employed by each of the five phylogenetically divergent classes of lanthipeptide synthetase to manipulate and exploit the dynamic lanthipeptide conformational ensemble, collectively enabling these biosynthetic enzymes to guide peptide maturation along specific trajectories to products with distinct macrocyclic topology and biological activity.