Cyclic peptide natural products have served as important drug molecules, with several examples used clinically. Enzymatic or chemical macrocyclization is the key transformation for constructing these chemotypes. Methods to generate new and diverse cyclic peptide scaffolds enabling the modular and predictable synthesis of peptide libraries are desirable in drug discovery platforms. Here we identify a suite of post-translational modifying enzymes from bacteria that install single or multiple strained cyclophane macrocycles. The crosslinking occurs on three-residue motifs that include tryptophan or phenylalanine to form indole- or phenyl-bridged cyclophanes. The macrocycles display restricted rotation of the aromatic ring and induce planar chirality in the asymmetric indole bridge. The biosynthetic gene clusters originate from a broad range of bacteria derived from marine, terrestrial and human microbiomes. Three-residue cyclophane-forming enzymes define a new and significant natural product family and occupy a distinct region in sequence–function space.

环肽天然产物已作为重要的药物分子，有几个临床使用的例子。酶促或化学大环化是构建这些化学型的关键转化。在药物发现平台中，需要生成新的和多样化的环状肽支架的方法，使肽库的模块化和可预测的合成成为可能。在这里，我们从细菌中鉴定出一套翻译后修饰酶，这些酶安装了单个或多个应变的环烷大环化合物。交联发生在包括色氨酸或苯丙氨酸的三个残基基序上以形成吲哚或苯基桥联的环烷。大环显示芳环的有限旋转并在不对称吲哚桥中诱导平面手性。生物合成基因簇来源于来自海洋、陆地和人类微生物组的广泛细菌。三残基环烷形成酶定义了一个新的重要天然产物家族，并在序列功能空间中占据了一个不同的区域。