Pyrrolidine in Drug Discovery: A Versatile Scaffold for Novel Biologically Active Compounds

The five-membered pyrrolidine ring is one of the nitrogen heterocycles used widely by medicinal chemists to obtain compounds for the treatment of human diseases. The great interest in this saturated scaffold is enhanced by (1) the possibility to efficiently explore the pharmacophore space due to sp3-hybridization, (2) the contribution to the stereochemistry of the molecule, (3) and the increased three-dimensional (3D) coverage due to the non-planarity of the ring—a phenomenon called “pseudorotation”. In this review, we report bioactive molecules with target selectivity characterized by the pyrrolidine ring and its derivatives, including pyrrolizines, pyrrolidine-2-one, pyrrolidine-2,5-diones and prolinol described in the literature from 2015 to date. After a comparison of the physicochemical parameters of pyrrolidine with the parent aromatic pyrrole and cyclopentane, we investigate the influence of steric factors on biological activity, also describing the structure–activity relationship (SAR) of the studied compounds. To aid the reader’s approach to reading the manuscript, we have planned the review on the basis of the synthetic strategies used: (1) ring construction from different cyclic or acyclic precursors, reporting the synthesis and the reaction conditions, or (2) functionalization of preformed pyrrolidine rings, e.g., proline derivatives. Since one of the most significant features of the pyrrolidine ring is the stereogenicity of carbons, we highlight how the different stereoisomers and the spatial orientation of substituents can lead to a different biological profile of drug candidates, due to the different binding mode to enantioselective proteins. We believe that this work can guide medicinal chemists to the best approach in the design of new pyrrolidine compounds with different biological profiles.

Crystal structure and Hirshfeld surface analysis of (3aR,4S,7S,7aS)-4,5,6,7,8,8-hexachloro-2-{6-[(3aR,4R,7R,7aS)-4,5,6,7,8,8-hexachloro-1,3-dioxo-1,3,3a,4,7,7a-hexahydro-2H-4,7-methanoisoindol-2-yl]hexyl}-3a,4,7,7a-tetrahydro-1H-4,7-methanoisoindole-1,3(2H)-dione

The molecule of the title compound, C24H16Cl12N2O4, is generated by a crystallographic inversion centre at the midpoint of the central C—C bond. A kink in the molecule is defined by a torsion angle of −169.86 (15)° about this central bond of the alkyl bridge. The pyrrolidine ring is essentially planar [max. deviation = 0.014 (1) Å]. The cyclohexane ring has a boat conformation, while both cyclopentane rings adopt an envelope conformation. In the crystal structure, molecules are linked by intermolecular C—H...O, C—H...Cl and C—Cl...π interactions, and short intermolecular Cl...O and Cl...Cl contacts, forming a three-dimensional network.

Acyltransferase AniI as tailoring enzyme with broad substrate tolerance for high-level production of anisomycin

Anisomycin (1), a pyrrolidine antibiotic, exhibits diverse biological and pharmacologic activities. The biosynthetic gene cluster of 1 has been identified previously and the multistep assembly of the core benzylpyrrolidine scaffold was characterized. However, enzymatic modifications, such as acylation involved in 1 biosynthesis are unknown. In this study, the genetic manipulation of aniI proved that it encoded indispensable acetyltransferase for 1 biosynthesis. Bioinformatics analysis suggested AniI as a member of LbH-MAT-GAT sugar O-acetyltransferase, but the biochemical assay identified that its target site was the hydroxyl group of the pyrrolidine ring. AniI was found to be tolerant of acyl donors with different chain length for the biosynthesis of 1 and derivatives 12 and 13 with butyryl and isovaleryl groups, respectively. Meanwhile, it showed comparable activity towards biosynthetic intermediates and synthesized analogues, suggesting promiscuity to the pyrrolidine ring structure of 1. These data may inspire new viable synthetic routes for the construction of more complex pyrrolidine ring scaffolds in 1. Finally, the overexpression of aniI under the control of strong promoters contributed to the higher productivities of 1 and its analogues. These findings reported here not only improved the understanding of anisomycin biosynthesis but also expand the substrate scope of O-acetyltransferase working on the pyrrolidine ring and pave the way for future metabolic engineering construction of high-yield strain. IMPORTANCE Acylation is an important tailoring reaction during natural products biosynthesis. Acylation could increase the structural diversity, affect the chemical stability, volatility, biological activity and even the cellular localization of specialized compounds. Many acetyltransferases have been reported in natural product biosynthesis. The typical example of LbH-MAT-GAT sugar O-acetyltransferase subfamily was reported to catalyze the CoA-dependent acetylation of the 6-hydroxyl group of sugars. However, no protein of this family has been characterized to acetylate non-sugar secondary metabolic product. Here, AniI was found to catalyze the acylation of the hydroxyl group of the pyrrolidine ring and be tolerant of diverse acyl donors and acceptors, which made the biosynthesis more efficient and exclusive for 1 and its derivatives biosynthesis. Moreover, the overexpression of aniI serves as a successful example of genetic manipulation of a modification gene for the high production of final products and might set the stage for future metabolic engineering.

Crystal structure and Hirshfeld surface analysis of 4,5-dibromo-6-methyl-2-phenyl-2,3,3a,4,5,6,7,7a-octahydro-3a,6-epoxy-1H-isoindol-1-one

In the title compound, C15H15Br2NO2, two bridged tetrahydrofuran rings adopt envelope conformations with the O atom as the flap. The pyrrolidine ring also adopts an envelope conformation with the spiro C atom as the flap. In the crystal, the molecules are linked into dimers by pairs of C—H...O hydrogen bonds, thus generating R 2 2(18) rings. The crystal packing is dominated by H...H, Br...H, H...π and Br...π interactions. One of the Br atoms is disordered over two sites with occupation ratio of 0.833 (8):0.167 (8).

Crystal structure and Hirshfeld surface analysis of ethyl (4R,4aS)-2-methyl-5,8-dioxo-6-phenyl-4a,5,6,7,7a,8-hexahydro-4H-furo[2,3-f]isoindole-4-carboxylate

In the title compound, C20H19NO5, the central six-membered ring has a slightly distorted half-chair conformation, with puckering parameters of Q T = 0.3387 (11) Å, θ = 49.11 (19)° and φ = 167.3 (2)°. The conformation of the fused pyrrolidine ring is that of an envelope. Molecules are connected by intermolecular C—H...O hydrogen bonds, C—H...π interactions and π–π stacking interactions [centroid-to-centroid distance = 3.9536 (11) Å, with a slippage of 2.047 Å], forming a three-dimensional network. The most important contributions to the surface contacts are from H...H (46.3%), O...H/H...O (31.5%) and C...H/H...C (17.3%) interactions, as concluded from a Hirshfeld surface analysis.

Conformer-Dependent VUV Photodynamics and Chiral Asymmetries in Pure Enantiomers of Gas Phase Proline

Proline is a unique amino-acid, with a secondary amine fixed within a pyrrolidine ring providing specific structural properties to proline-rich biopolymers. Gas-phase proline possesses four main H-bond stabilized conformers differing by the ring puckering and carboxylic acid orientation. The latter defines two classes of conformation, whose large ionization energy difference allows a unique conformer-class tagging via electron spectroscopy. Photoelectron circular dichroism (PECD) is an intense chiroptical effect sensitive to molecular structures, hence theorized to be highly conformation-dependent. Here, besides a conformer-dependant cation fragmentation behaviour, we present experimental evidence of an intense and striking conformer-specific PECD, measured in the VUV photoionization of proline. This finding, combined with theoretical modelling, allows a refinement of the conformational landscape and energetic ordering, that proves inaccessible to current molecular electronic structure calculations. Additionally, astrochemical implications regarding a possible link of PECD to the origin of life’s homochirality are considered in terms of plausible temperature constraints.

Crystal structure of (1′S,2′S,3S)-1′-benzoyl-2′-(4-methoxyphenyl)-1-methyl-2′,5′,6′,10b′-tetrahydro-1′H-spiro[indoline-3,3′-pyrrolo[2,1-a]isoquinolin]-2-one

In the title spiro compound, C34H30N2O3, the central pyrrolidine ring is fused with the tetrahydroisoquinoline ring, both having distorted envelope conformations, with the flap atoms being C and N, respectively. The methoxyphenyl group is attached to the pyrrolidine ring, and is disordered over two positions, with refined occupancies of 0.638 (6):0.362 (6) Å. The central pyrrolidine ring is inclined relative to the tetrahydroisoquinoline group, such that the dihedral between the non-flap atoms of each ring system is 11.29 (7)°. The spiro-linkage creates a dihedral angle of 83.26 (5)° between the indolinone ring and the non-flap atoms of the pyrrolidine ring. In the crystal, molecules are linked via C—H...O hydrogen bonds. For the major disorder component, these form C(11) chains that propagate parallel to the a axis.

1-Ethyl 2-methyl 3,4-bis(acetyloxy)pyrrolidine-1,2-dicarboxylate: crystal structure, Hirshfeld surface analysis and computational chemistry

The title compound, C13H19NO8, is based on a tetra-substituted pyrrolidine ring, which has a twisted conformation about the central C—C bond; the Cm—Ca—Ca—Cme torsion angle is 38.26 (15)° [m = methylcarboxylate, a = acetyloxy and me = methylene]. While the N-bound ethylcarboxylate group occupies an equatorial position, the remaining substituents occupy axial positions. In the crystal, supramolecular double-layers are formed by weak methyl- and methylene-C—H...O(carbonyl) interactions involving all four carbonyl-O atoms. The two-dimensional arrays stack along the c axis without directional interactions between them. The Hirshfeld surface is dominated by H...H (55.7%) and H...C/C...H (37.0%) contacts; H...H contacts are noted in the inter-double-layer region. The interaction energy calculations point to the importance of the dispersion energy term in the stabilization of the crystal.

6,7-Dihydro-5H-pyrrolo[1,2-a]imidazole

The crystal structure of 6,7-dihydro-5H-pyrrolo[1,2-a]imidazole, C6H8N2, at 100 K has monoclinic (P21/n) symmetry. The molecule adopts an envelope conformation of the pyrrolidine ring, which might help for the relief torsion tension. The crystal cohesion is achieved by C—H...N hydrogen bonds. Interestingly, this fused ring system provides protection of the α-C atom (attached to the non-bridging N atom of the imidazole ring), which provides stability that is of interest with respect to electrochemical properties as electrolytes for fuel cells and batteries, and electrodeposition.