Computational protocol: High throughput evaluation of macrocyclization strategies for conformer stabilization

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Protocol publication

[…] Although generation of conformational ensembles of macrocycles is difficult, many methods have been developed to overcome the particular difficulties of sampling introduced by macrocyclization. Here we use the Prime Macrocycle Conformational Sampling algorithm (Prime-MCS) which can quickly produce accurate, diverse macrocycle conformations. Default calculation parameters were used including unbiased PrimeMCS sampling and OPLS3.0 force field parameters in vacuum. This assumes that unbiased default sampling is sufficient to cover representative conformational space and that the OPLS3 force field can sufficiently represent the compound. It is possible that, depending on the design context, especially the macrocycle topological complexity, that these assumptions will be broken and the sampling protocol should be modified. Some such modifications are discussed in the Discussion section. [...] To properly score the conformational ensemble, a metric for the similarity to the bioactive substructure is required. For many projects, the conserved substructure is obvious since the linker modifications leave the original acyclic molecule largely unchanged. Here, we apply the maximum common substructure (MCS) algorithm, as implemented in Canvas software, to the designed macrocycles and the bioactive linear reference to determine the conserved region. Though this approach may not be optimal for use in prospective projects, the MCS is useful under the assumption that the topological differences between the macrocyclic designs and the reference are purely in the cyclization linker, and thus the bioactive conformation of the remaining substructure is intended to be conserved. We take the RMSD of the heavy atoms in the conserved region, RMSDcons as a simple metric for similarity to the bioactive substructure under the assumption that, for the sets of macrocycles we will be considering, the ability for these atoms to adopt a conserved binding mode is the primary determinant of binding affinity. Alternate structural metrics are discussed below in the Discussion section. When measuring the RMSDcons, we account for symmetry by generating a SMARTS pattern from the MCS atoms in the reference ligand and choosing the minimum RMSD for all matches to the SMARTS patterns in the test compounds. Here, the MCS atoms were calculated using Schrodinger’s canvas_MCS utilitity ($SCHRODINGER/utilities/canvas_MCS) using default settings in Schrodinger release 2017-3. This MCS technique distinguishes atoms by atomic number, bond order, and aromaticity. [...] For this study we use systems from macrocycle design projects taken from the literature. In a related paper submitted recently, seven macrocyclization projects were curated to evaluate free energy perturbation (FEP) technology on affinity calculations for macrocycles. For that article, papers were chosen describing projects which contained macrocyclizations (conversion of linear compounds to macrocyclic), modification of macrocycle linker sizes, or both. Projects were only used if there were no apparent issues with the data that would complicate an evaluation by atom-scale biophysical modeling such as significant missing structural data and insufficient affinity data. Here we select from those seven projects the only three where there were at least two macrocycles within the set. Those systems were Chk1 (PDBID 2E9P), Bace-1 (PDBID 2Q15), and Hsp90 (PDBID 3RKZ), see Table  and Figure . Though protein structures are available, they were not used for any part of these calculations except to confirm that the various modifications to the linker are on the solvent exposed side of the ligand and therefore less likely to be involved in specific protein-ligand interactions that could affect the binding affinities of these molecules.For the calculations here, the experimental structural data for the macrocyclic structures were removed by converting the structures to SMILES then back to 3D. These 3D structures were then inspected to ensure correct stereoisomer states as well as trans amide bonds. These, as well as the linear reference structure, were prepared using LigPrep.Figure 1 […]

Pipeline specifications

Software tools Macrocycles, OPLS3, Canvas, LigPrep
Application Drug design