Conformational analysis of macrocycles: comparing general and specialized methods

Abstract

Macrocycles represent an important class of medicinally relevant small molecules due to their interesting biological properties. Therefore, a firm understanding of their conformational preferences is important for drug design. Given the importance of macrocycle-protein modelling in drug discovery, we envisaged that a systematic study of both classical and recent specialized methods would provide guidance for other practitioners within the field. In this study we compare the performance of the general, well established conformational analysis methods Monte Carlo Multiple Minimum (MCMM) and Mixed Torsional/Low-Mode sampling (MTLMOD) with two more recent and specialized macrocycle sampling techniques: MacroModel macrocycle Baseline Search (MD/LLMOD) and Prime macrocycle conformational sampling (PRIME-MCS). Using macrocycles extracted from 44 macrocycle-protein X-ray crystallography complexes, we evaluated each method based on their ability to (i) generate unique conformers, (ii) generate unique macrocycle ring conformations, (iii) identify the global energy minimum, (iv) identify conformers similar to the X-ray ligand conformation after Protein Preparation Wizard treatment (X-rayppw), and (v) to the X-rayppw ring conformation. Computational speed was also considered. In addition, conformational coverage, as defined by the number of conformations identified, was studied. In order to study the relative energies of the bioactive conformations, the energy differences between the global energy minima and the energy minimized X-rayppw structures and, the global energy minima and the MCMM-Exhaustive (1,000,000 search steps) generated conformers closest to the X-rayppw structure, were calculated and analysed. All searches were performed using relatively short run times (10,000 steps for MCMM, MTLMOD and MD/LLMOD). To assess the performance of the methods, they were compared to an exhaustive MCMM search using 1,000,000 search steps for each of the 44 macrocycles (requiring ca 200 times more CPU time). Prior to our analysis, we also investigated if the general search methods MCMM and MTLMOD could also be optimized for macrocycle conformational sampling. Taken together, our work concludes that the more general methods can be optimized for macrocycle modelling by slightly adjusting the settings around the ring closure bond. In most cases, MCMM and MTLMOD with either standard or enhanced settings performed well in comparison to the more specialized macrocycle sampling methods MD/LLMOD and PRIME-MCS. When using enhanced settings for MCMM and MTLMOD, the X-rayppw conformation was regenerated with the greatest accuracy. The, MD/LLMOD emerged as the most efficient method for generating the global energy minima. Graphic abstract

Benchmark of Generic Shapes for Macrocycles

“… 34 Some of these algorithms are based on distance geometry (DG), 35 inverse kinematics, 36 genetic algorithms, 37 molecular dynamics (MD) simulations implementing either low-frequency modes 38 or normal-mode search steps plus energy minimization, 39 and, most recently, Monte Carlo multiple minimum/mixed torsional/low mode. 40 …”

“…34 Some of these algorithms are based on distance geometry (DG), 35 inverse kinematics, 36 genetic algorithms, 37 molecular dynamics (MD) simulations implementing either lowfrequency modes 38 or normal-mode search steps plus energy minimization, 39 and, most recently, Monte Carlo multiple minimum/mixed torsional/low mode. 40 Generally, these software programs are distinguished on the basis of the strategy adopted to generate conformations, systematic or stochastic. For example, molecular operating environment (MOE), MacroModel (MM), Cambridge Crystallographic Data Centre (CCDC) conformer generator, and experimental-torsion DG with additional "basic knowledge" (ETKDG) belong to the stochastic search category.…”

Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins

“…10, 97,98 Consequently, significant work has been put into enhanced sampling algorithms towards macrocycle conformation prediction. [97][98][99][100][101][102][103][104][105][106][107][108][109] Additional work has been put into docking or otherwise calculating macrocycle binding free energies. [110][111][112][113][114][115][116] More recently, a structure-based design of peptide macrocycles targeting the interaction site of human adaptor protein 14-3-3 using Free Energy Perturbation (FEP) calculations was proposed.…”

“…Implementation of reliable in silico approaches for an accurate design is therefore needed to guide experimental efforts toward the most promising compounds. ,− To perform rational design, a reliable description of macrocycles’ conformational landscape is essential. Unfortunately, the rugged conformational landscape limits the effectiveness of standard approaches for small molecules to reliably predict macrocycle conformations. ,, Consequently, significant work has been made into enhanced sampling algorithms toward macrocycle conformation prediction. − Additional work has been put into docking or otherwise calculating macrocycle binding free energies. − More recently, a structure-based design of peptide macrocycles targeting the interaction site of human adaptor protein 14-3-3 using free-energy perturbation (FEP) calculations was proposed . Despite the above-mentioned efforts, to the best of our knowledge, there is no computational method available that combines automatic enumeration, evaluation, and ranking of the macrocyclizations based on a list of chemical linkers (derived from available reagents) and the 3D structure of a linear reference.…”

Automated Design of Macrocycles for Therapeutic Applications: from Small Molecules to Peptides and Proteins

“…10,97,98 Consequently, significant work has been put into enhanced sampling algorithms towards macrocycle conformation prediction. [97][98][99][100][101][102][103][104][105][106][107][108][109] Additional work has been put into docking or otherwise calculating macrocycle binding free energies. [110][111][112][113][114][115][116] More recently, a structure-based design of peptide macrocycles targeting the interaction site of human adaptor protein 14-3-3 using Free Energy Perturbation (FEP) calculations was proposed.…”