A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds

Abstract

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.

Fig. 1. Chemical structures of some biologically active macrocyclic peptidomimetics. MCP-1 is a potent inhibitor of the menin-mixed lineage leukemia 1 protein–protein interaction, Clicktophycin-52 displays in vitro activity against the multidrug resistant human cervix carcinoma cell line KB-V1 and compound 1 is a motilin antagonist.

Scheme 1. Outline of our advanced DOS strategy towards the combinatorial variation of macrocyclic peptidomimetic scaffolds. The coloured shapes represent major scaffold-defining elements (i.e. areas that can be varied to obtain different macrocyclic ring architectures).

Fig. 2. Building blocks used in library synthesis. Complete experimental procedures for the synthesis of the building blocks are given in the ESI.

Scheme 2. An illustrative example of the synthesis of final macrocyclic peptidomimetics using the B/C/P strategy. The lowest energy conformations (molecular shapes) of two final library compounds 16 and 17 are shown (conformational search by Molecular Operating Environment (MOE) software package). Conditions: (a) EDC·HCl, HOBt, NEt₃, CH₂Cl₂, rt; (b) (i) [Cp*RuCl]₄, toluene, reflux; (ii) HCl–dioxane (4.0 M); (c) (i) CuI, DIPEA, THF, reflux; (ii) HCl–dioxane (4.0 M); (d) AcOH–NMM* (1.25 : 1, molar ratio), 2-Butanol, microwave irradiation (T = 150 °C). NMM*: morpholinomethyl-polystyrene (loading = 3.51 mmol g^–1).

Scheme 3. An illustrative example of the synthesis of some final macrocyclic peptidomimetics using a route incorporating iterative coupling steps (i.e. B/C/C/P and B/C/C/C/P). (a) (i) EDC·HCl, HOBt, Boc-l-Ala-OH (12a), NEt₃, CH₂Cl₂, rt; (ii) TMSCl, MeOH, 0 °C to rt; (b) (i) EDC·HCl, HOBt, Boc-l-Phe-OH (12d), NEt₃, CH₂Cl₂, rt; (ii) TMSCl, MeOH, 0 °C to rt; (c) EDC·HCl, HOBt, 11b, NEt₃, CH₂Cl₂, rt; (d) (i) [Cp*RuCl]₄, toluene, reflux; (ii) HCl–dioxane (4.0 M); (e) (i) CuI, DIPEA, THF, reflux; (ii) HCl–dioxane (4.0 M).

Scheme 4. Illustrative example of the synthesis of some final macrocyclic peptidomimetics using a route incorporating two couple steps (i.e. B/C/C/P). The lowest energy conformations (molecular shapes) of some final library compounds (27, 28, 32–34) are shown (conformational search by MOE software package). Conditions:(a) (i) EDC·HCl, HOBt, Boc-l-Glu-OMe (12b), NEt₃, CH₂Cl₂, rt; (ii) TMSCl, MeOH, 0 °C to rt; (b) (i) EDC·HCl, HOBt, 11i or 11m or 11j, NEt₃, CH₂Cl₂, rt; (c) (i) [Cp*RuCl]₄, toluene, reflux; (ii) HCl–dioxane (4.0 M); (d) AcOH–NMM* (1.25 : 1, molar ratio), 2-Butanol, Microwave irradiation (T = 150 °C). NMM*: morpholinomethyl-polystyrene (loading = 3.51 mmol g^–1).

Fig. 3. Comparative PCA and PMI plots of 219 macrocyclic DOS library compounds (“DOS library”, solid red circles), 40 top-selling brand-name drugs (“Drugs”, solid green squares), 60 diverse natural products (“Natural Products”, solid blue triangles) and 24 macrocyclic natural products (“Macro Natural Products”, empty blue triangles). (a) PCA plot of PC1 versus PC2. (b) PCA plot of PC1 versus PC3. (c) PCA plot of PC3 versus PC2. (d) PMI plot illustrating the molecular shape diversity of the DOS library. The lowest energy conformations (molecular shapes) of representative DOS library compounds 35–37 based on each of the three extremes of molecular shape types are shown (conformational search by MOE software package). See ESI for the structures of 35–37 and more details.