New Inhibitors of Bacterial Protein Synthesis from a Combinatorial Library of Macrocycles

Abstract

A mixture-based combinatorial library of 14-membered macrocycles was synthesized to target ribosomal RNA and uncover a new class of antibacterial agents. High-throughput screening identified a macrocyclic mixture that inhibited cell-free-coupled transcription/translation in Escherichia coli-derived extracts, with an IC(50) value in the 25-50 microM range. In a follow-up library of 64 single macrocycles, 8 gave IC(50) values ranging from 12 to 50 microM in the cell-free protein synthesis inhibition assay. Some of the macrocycles were screened in a translation inhibition assay, and IC(50) values generally paralleled those obtained in the uncoupled transcription/translation assay. Additional analogues were prepared in a preliminary structure-activity relationship study, and more potent macrocycles were identified with low micromolar activity (IC(50) values = 2-3 microM). Some of these macrocycles displayed antibacterial activity against lipopolysaccharide mutant E. coli bacterial cells (IC(50) values = 12-50 microM).

MacroEvoLution: A New Method for the Rapid Generation of Novel Scaffold‐Diverse Macrocyclic Libraries

“…Sphere‐like conformations are reported to have a higher probability of penetrating biological membranes . This result is comparable to analyses of other macrocylic libraries …”

“…One of the main reasons evidently is the difficult chemical access, especially the challenges being faced with the generation of high numbers of biologically relevant diverse compounds required for HTS (high throughput screening) and the potential for rapid optimization. Even though remarkable efforts have been made in the past to overcome these difficulties, rapid access to macrocyclic libraries is still an unsolved problem . The SICLOPPS represents an alternative approach to purely synthetic methodologies and relies on the split‐intein mediated circular ligation, which delivers cyclic peptides in a range of 10 6 to 10 7 different systems.…”

Real-time assay for testing components of protein synthesis

“…Protein synthesis is being studied intensively with a variety of motivations, ranging from practical needs for the development of efficient methods of cell-free protein synthesis (CFPS) for production of proteins that are difficult to express in cells (1–3), for the identification of new antibiotics (4,5), and toward achieving understanding of basic mechanisms of individual steps of the translation cycle and of overall protein synthesis (6,7). Many mechanistic studies employ fluorescent-labeled constituents of the protein synthesis machinery.…”

The Synthesis of Macrocycles for Drug Discovery

“…For example, a combinatorial library of 12,000 macrocycles was synthesized on solid phase capitalizing on this approach for the cyclization step (284, Figure 11.23, site of ring closure indicated). 377 Compounds that inhibited bacterial protein synthesis were identified from this collection. Similarly, antibacterial lead compounds were identified from a library of 1,350 compounds possessing a quinolone pharmacophore (285) 378 and a DOS approach gave a variety of macro-heterocycles, 379 such as shown in general structures 286 and 287, each of which relied on an intramolecular S N Ar process for cyclization.…”