Exhaustive Exploration of the Conformational Landscape of Small Cyclic Peptides Using a Robotics Approach

Cyclotides: The next generation in biopesticide development for eco-friendly agriculture

Chemical pesticides remain the predominant method for pest management in numerous countries. Given the current landscape of agriculture, the development of biopesticides has become increasingly crucial. The strategy empowers farmers to efficiently manage pests and diseases, while prioritizing minimal adverse effects on the environment and human health, hence fostering sustainable management. In recent years, there has been a growing interest and optimism surrounding the utilization of peptide biopesticides for crop protection. These sustainable and environmentally friendly substances have been recognized as viable alternatives to synthetic pesticides due to their outstanding environmental compatibility and efficacy. Numerous studies have been conducted to synthesize and identify peptides that exhibit activity against significant plant pathogens. One of the peptide classes is cyclotides, which are cyclic cysteine-rich peptides renowned for their wide range of sequences and functions. In this review, we conducted a comprehensive analysis of cyclotides, focusing on their structural attributes, developmental history, significant biological functions in crop protection, techniques for identification and investigation, and the application of biotechnology to enhance cyclotide synthesis. The objective is to emphasize the considerable potential of cyclotides as the next generation of plant protection agents on the global scale.

Benchmarking quantum chemical methods for accurate gas-phase structure predictions of carbonyl compounds: the case of ethyl butyrate

High-resolution spectroscopy techniques play a pivotal role to validate and efficiently benchmark available methods from quantum chemistry. In this work, we analyzed the microwave spectrum of ethyl butyrate within the scope of a systematic investigation to benchmark state-of-the-art exchange-correlation functionals and ab initio methods, to accurately predict the lowest energy conformers of carbonyl compounds in their isolated state. Under experimental conditions, we observed two distinct conformers, one of Cs and one of C1 symmetry. As reported earlier in the cases of some ethyl and methyl alkynoates, structural optimizations of the most abundant conformer that exhibits a C1 symmetry proved extremely challenging for several quantum chemical levels. To probe the sensitivity of different methods and basis sets, we use the identified soft-degree of freedom in proximity to the carbonyl group as an order parameter. The results of our study provide useful insight for spectroscopists to select an adapted method for structure prediction of carbonyl compounds based on their available computational resources, suggesting a reasonable trade-off between accuracy and CPU cost. At the same time, our observations and the resulting sets of highly accurate experimental constants from high-resolution spectroscopy experiments give an appeal to theoretical groups to look further into this seemingly simple family of chemical compounds, which may prove useful for the further development and parametrization of theoretical methods in computational chemistry.

Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock

Macrocycles are interesting molecules with unique features due to their conformationally constrained yet flexible ring structure. This characteristic poses a difficult challenge for computational modeling studies since they rely on accurate structural descriptions. In particular, molecular docking calculations suffer from the lack of ring flexibility during pose generation, which is often compensated by using pregenerated ligand conformer ensembles. Moreover, receptor structures are mainly treated rigidly, which limits the use of many docking tools. In this study, we optimized our previous molecular dynamics-based sampling and docking pipeline specifically designed for the accurate prediction of macrocyclic compounds. We developed a dihedral classification procedure for in-depth conformational analysis of the macrocyclic rings and extracted structural ensembles that were subsequently docked in both bound and unbound protein structures employing a fully flexible approach. Our results suggest that including a ring conformer close to the bound state in the starting ensemble increases the chance of successful docking. The bioactive conformations of a diverse set of ligands could be predicted with high and decent accuracy in bound and unbound protein structures, respectively, due to the incorporation of full molecular flexibility in our approach. The remaining unsuccessful docking calculations were mainly caused by large flexible substituents that bind to surface-exposed binding sites, rather than the macrocyclic ring per se and could be further improved by explicit molecular dynamics simulations of the docked complex.

Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond

Cyclic peptides formed by disulfide bonds have been one large group of common drug candidates in drug development. Structural information of a peptide is essential to understand its interaction with its target. However, due to the high flexibility of peptides, it is difficult to sample the near-native conformations of a peptide. Here, we have developed an extended version of our MODPEP approach, named MODPEP2.0, to fast generate the conformations of cyclic peptides formed by a disulfide bond. MODPEP2.0 builds the three-dimensional (3D) structures of a cyclic peptide from scratch by assembling amino acids one by one onto the cyclic fragment based on the constructed rotamer and cyclic backbone libraries. Being tested on a data set of 193 diverse cyclic peptides, MODPEP2.0 obtained a considerable advantage in both accuracy and computational efficiency, compared with other sampling algorithms including PEP-FOLD, ETKDG, and modified ETKDG (mETKDG). MODPEP2.0 achieved a high sampling accuracy with an average C\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\alpha$$\end{document}α RMSD of 2.20 Å and 1.66 Å when 10 and 100 conformations were considered, respectively, compared with 3.41 Å and 2.62 Å for PEP-FOLD, 3.44 Å and 3.16 Å for ETKDG, 3.09 Å and 2.72 Å for mETKDG. MODPEP2.0 also reproduced experimental peptide structures for 81.35% of the test cases when an ensemble of 100 conformations were considered, compared with 54.95%, 37.50% and 50.00% for PEP-FOLD, ETKDG, and mETKDG. MODPEP2.0 is computationally efficient and can generate 100 peptide conformations in one second. MODPEP2.0 will be useful in sampling cyclic peptide structures and modeling related protein-peptide interactions, facilitating the development of cyclic peptide drugs.

Distance geometry and protein loop modeling

Due to the role of loops in protein function, loop modeling is an important problem in computational biology. We present a new approach to loop modeling based on a combinatorial version of distance geometry, where the search space of the associated problem is represented by a binary tree and a branch-and-prune method is defined to explore it, following an atomic ordering previously given. This ordering is used to calculate the coordinates of atoms from the positions of its predecessors. In addition to the theoretical development, computational results are presented to illustrate the advantage of the proposed method, compared with another approach of the literature. Our algorithm is freely available at https://github.com/michaelsouza/bpl.

Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations

Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.

Steering New Drug Discovery Campaigns: Permeability, Solubility, and Physicochemical Properties in the bRo5 Chemical Space

An increasing number of drug discovery programs concern compounds in the beyond rule of 5 (bRo5) chemical space, such as cyclic peptides, macrocycles, and degraders. Recent results show that common paradigms of property-based drug design need revision to be applied to larger and more flexible compounds. A virtual event entitled "Solubility, permeability and physico-chemical properties in the bRo5 chemical space" was organized to provide preliminary guidance on how to make the discovery of oral drugs in the bRo5 space more effective. The four speakers emphasized the importance of the bRo5 space as a source of new oral drugs and provided examples of experimental and computational methods specifically tailored for design and optimization in this chemical space.

Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A

In this work, we investigate the conformational properties of unguisin A, a natural macrocyclic heptapeptide that incorporates a γ-aminobutyric acid (Gaba), and four of its difluorinated stereoisomers at the Gaba residue. According to nuclear magnetic resonance (NMR) experiments, their secondary structure depends dramatically on the stereochemistry of the fluorinated carbon atoms. However, many molecular details of the structure and flexibility of these systems remain unknown, so that a rationale of the conformational changes induced by the fluorine atoms in the macrocycle is still missing. To fill this gap, we apply enhanced molecular dynamics (MD) techniques to explore the peptide conformational space in dimethyl sulfoxide solution followed by 4-8 μs of conventional MD simulations that provide extensive equilibrium sampling. The simulations, which compare reasonably well with the NMR-based observations, show that the secondary structure of the macrocycle is altered substantially upon fluorination, except for the (S,S) diastereomer. It also turns out that the conformations of the fluorinated peptides are visited during the enhanced MD simulation of natural unguisin A, suggesting thus that conformations accessible to the unsubstituted macrocyclic peptide may be selected by fluorination. Therefore, computational characterization of the macrocyclic peptides could be helpful in the rational design of stereoselective fluorinated peptides with fine-tuned conformation and activity.

Quantifying soft degrees of freedom in volatile organic compounds: insight from quantum chemistry and focused single molecule experiments

Sampling of the vast conformational landscape of organic compounds remains a challenging task in computational chemistry, especially when it comes to the characterization of soft-degrees of freedom and relatively small energy barriers between different local minima. Therefore, studying the intrinsic properties of isolated molecules using focused experiments such as high-resolution molecular spectroscopy provides a powerful approach to validate and improve available quantum chemical methods. Here, we report on the most abundant gas-phase structure of ethyl 2-methyl pentanoate under molecular jet conditions, which we used to benchmark several exchange-correlation functionals and ab initio methods at the quantum chemical level. The observed conformer of ethyl 2-methyl pentanoate in the gas-phase is of C1 symmetry and exhibits a large amplitude motion around the C-C bond in proximity to the carbonyl moiety, which, unlike in the case of its structural isomer ethyl 2-ethyl butyrate, is very sensitive to the applied quantum chemical method and basis set. Depending on the applied quantum chemical method, the dihedral angle of the lowest energy conformer is optimized to absolute values of ±20°. This is far above the usual convergence error of the theoretical methods and has a tremendous impact on the rotational constants of this conformer, which complicates the prediction of rotational spectra and the assignment of experimental data. We show that the loss of symmetry in the aliphatic chain bound to the carboxylic moiety of ethyl esters results in a shift of the dihedral angle value due to a flat potential well around the corresponding C-C bond. Our benchmark calculations further indicate the potential relevance of the wB97X-D functional for this ethyl pentanoate and other related ethyl esters.

Strategies for Fine-Tuning the Conformations of Cyclic Peptides

Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.

Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4

The D3R Grand Challenge 4 provided a brilliant opportunity to test macrocyclic docking protocols on a diverse high-quality experimental data. We participated in both pose and affinity prediction exercises. Overall, we aimed to use an automated structure-based docking pipeline built around a set of tools developed in our team. This exercise again demonstrated a crucial importance of the correct local ligand geometry for the overall success of docking. Starting from the second part of the pose prediction stage, we developed a stable pipeline for sampling macrocycle conformers. This resulted in the subangstrom average precision of our pose predictions. In the affinity prediction exercise we obtained average results. However, we could improve these when using docking poses submitted by the best predictors. Our docking tools including the Convex-PL scoring function are available at https://team.inria.fr/nano-d/software/.

Conformation and Permeability: Cyclic Hexapeptide Diastereomers

Conformational ensembles of eight cyclic hexapeptide diastereomers in explicit cyclohexane, chloroform, and water were analyzed by multicanonical molecular dynamics (McMD) simulations. Free-energy landscapes (FELs) for each compound and solvent were obtained from the molecular shapes and principal component analysis at T = 300 K; detailed analysis of the conformational ensembles and flexibility of the FELs revealed that permeable compounds have different structural profiles even for a single stereoisomeric change. The average solvent-accessible surface area (SASA) in cyclohexane showed excellent correlation with the cell permeability, whereas this correlation was weaker in chloroform. The average SASA in water correlated with the aqueous solubility. The average polar surface area did not correlate with cell permeability in these solvents. A possible strategy for designing permeable cyclic peptides from FELs obtained from McMD simulations is proposed.