Structure-Based Design of "Head-to-Tail" Macrocyclic PROTACs

Chungen Li; Yihan Chen; Weixue Huang; Yudi Qiu; Shengjie Huang; Yang Zhou; Fengtao Zhou; Jian Xu; Xiaomei Ren; Jinwei Zhang; Zhen Wang; Ming Ding; Ke Ding

doi:10.1021/jacsau.4c00831

Structure-Based Design of "Head-to-Tail" Macrocyclic PROTACs

JACS Au. 2024 Nov 21;4(12):4866-4882. doi: 10.1021/jacsau.4c00831. eCollection 2024 Dec 23.

Authors

Chungen Li¹, Yihan Chen^{1

2}, Weixue Huang¹, Yudi Qiu³, Shengjie Huang⁴, Yang Zhou⁴, Fengtao Zhou⁴, Jian Xu⁵, Xiaomei Ren¹, Jinwei Zhang¹, Zhen Wang¹, Ming Ding⁶, Ke Ding¹

Affiliations

¹ State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No. 345 Lingling Road, Shanghai 200032, China.
² University of Chinese Academy of Sciences, No. 1 Yanxihu Road, Huairou District, Beijing 101408, China.
³ Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shengyang Pharmaceutical University, Shenyang 110016, China.
⁴ International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, No. 855 Xingye Avenue East, Guangzhou 511400, China.
⁵ Livzon Research Institute, Livzon Pharmaceutical Group Inc., No. 38, Chuangye North Road, Jinwan District, Zhuhai 519000, China.
⁶ School of Life Science and Technology, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing 211198, China.

Abstract

Macrocyclization is a compelling strategy for conventional drug design for improving biological activity, target specificity, and metabolic stability, but it was rarely applied to the design of PROTACs possibly due to the mechanism and structural complexity. Herein, we report the rational design of the first series of "Head-to-Tail" macrocyclic PROTACs. The resulting molecule SHD913 exhibited pronounced Brd4 protein degradation with low nM DC₅₀ values while almost totally dismissing the "hook effect", which is a general character and common concern of a PROTAC, in multiple cancer cell lines. Further biological evaluation revealed that the compound exhibited positive cooperativity and induced de novo protein-protein interactions (PPIs) in both biophysical and cellular NanoBRET assays and outperformed macroPROTAC-1 that is the first reported macrocyclic Brd4 PROTAC, in cellular assays. In vitro liver microsomal stability evaluation suggested that SHD913 demonstrated improved metabolic stability in different species compared with the linear counterpart. The co-crystal structure of Brd4^BD2: SHD913: VCB (VHL, Elongin C and Elongin B) complex determination and molecular dynamics (MD) simulation also elucidated details of the chemical-induced PPIs and highlighted the crucial contribution of restricted conformation of SHD913 to the ternary complex formation. These results collectively support that macrocyclization could be an attractive and feasible strategy for a new PROTAC design.