Exploiting the Carboxylate-Binding Pocket of β‑Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library

β-Lactamase enzymes hydrolyze
and thereby provide bacterial
resistance to the important β-lactam class of antibiotics. The
OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort
β-lactams, carbapenems, leading to a serious public health threat.
Here, we utilized DNA-encoded chemical library (DECL) technology to
discover novel β-lactamase inhibitors. We exploited the β-lactamase
enzyme–substrate binding interactions and created a DECL targeting
the carboxylate-binding pocket present in all β-lactamases.
A library of 106 compounds, each containing a carboxylic
acid or a tetrazole as an enzyme recognition element, was designed,
constructed, and used to identify OXA-48 and NDM-1 inhibitors with
micromolar to nanomolar potency. Further optimization led to NDM-1
inhibitors with increased potencies and biological activities. This
work demonstrates that the carboxylate-binding pocket-targeting DECL,
designed based on substrate binding information, aids in inhibitor
identification and led to the discovery of novel non-β-lactam
pharmacophores for the development of β-lactamase inhibitors
for enzymes of different structural and mechanistic classes.

β-内酰胺酶（β-Lactamase）可通过水解反应使细菌对重要的β-内酰胺类抗生素产生耐药性。其中OXA-48与NDM-1型β-内酰胺酶可介导细菌对作为临床最后一线治疗药物的β-内酰胺类碳青霉烯类抗生素产生耐药性，进而构成严重的公共卫生威胁。本研究利用DNA编码化合物库（DNA-encoded chemical library, DECL）技术发掘新型β-内酰胺酶抑制剂。研究团队基于β-内酰胺酶与底物的结合相互作用机制，针对所有β-内酰胺酶共有的羧酸结合口袋构建了靶向DNA编码化合物库。我们设计并构建了包含106个化合物的库，每个化合物均以羧酸或四唑作为酶识别元件，并通过该库筛选得到了对OXA-48与NDM-1具有微摩尔至纳摩尔级抑制活性的抑制剂。后续的优化工作进一步提升了NDM-1抑制剂的活性与生物学效能。本研究证实，基于底物结合信息设计的靶向羧酸结合口袋的DNA编码化合物库可有效助力抑制剂的发掘，并成功发现了新型非β-内酰胺类药效团，可用于开发针对不同结构与作用机制分类的β-内酰胺酶抑制剂。