Recently, Professor Zhan Peng and Associate Research Fellow Gao Shenghua of the School of Pharmaceutical Sciences, Shandong University, together with collaborators from several research institutions, published an original research article in Nature entitled “Structures and inhibition of the Crimean–Congo haemorrhagic fever virus polymerase.” The study provides the first comprehensive three-dimensional structural characterization of Crimean–Congo haemorrhagic fever virus (CCHFV) polymerase across multiple functional states, systematically delineates the regulatory principles governing viral RNA replication, and elucidates the mechanisms of action of two distinct classes of inhibitors. These findings establish a critical structural framework for the development of next-generation antiviral agents targeting CCHFV polymerase.

Xiong Xiaoli of the Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Chen Xinwen of the Guangzhou National Laboratory; Zhan Peng of Shandong University; and Wang Manli and Deng Zengqin of the Wuhan Institute of Virology, Chinese Academy of Sciences, are co-corresponding authors. Associate Research Fellow Xue Lu and graduate students Gui Jiacheng and Pan Hainei of the Guangzhou Institutes of Biomedicine and Health; Dr Wu Fan and Associate Research Fellow Kuang Wenhua of the Wuhan Institute of Virology; Associate Research Fellow Gao Shenghua of the School of Pharmaceutical Sciences, Shandong University; and graduate student Chang Tiancai of Guangzhou Medical University are co-first authors.

CCHFV is a highly pathogenic, tick-borne orthonairovirus that can cause fatal haemorrhagic fever, with reported case fatality rates of up to 40%. It has been designated by the World Health Organization as a priority pathogen, yet no widely approved vaccine or specific antiviral therapy is currently available. The viral L protein is the core catalytic machinery for genome replication and an important therapeutic target. However, its enormous molecular size and pronounced conformational complexity have long impeded atomic-level structural analysis, substantially constraining rational drug discovery. Using cryo-electron microscopy, the collaborative team determined structures of the apo enzyme and complexes representing 5′/3′ RNA-bound and RNA-elongating states, providing a systematic view of the structural transitions that accompany the progression from RNA recognition to elongation. The study also identified, for the first time, a critical zinc-binding site that regulates enzymatic activity, defined how the template–product RNA duplex and incoming NTP substrate are recognized within the active site, and established a comprehensive molecular model of viral RNA synthesis. In addition, the team resolved the structural and functional basis of the cap-snatching endonuclease (Endo). Collectively, these findings precisely delineate two druggable sites—the Endo pocket and the catalytic centre of the RNA-dependent RNA polymerase (RdRp)—and provide a rational basis for improving the affinity of future lead compounds.

Building on the complete polymerase structures, the team conducted systematic inhibitor screening and mechanistic studies. Drawing on its previous work in anti-influenza drug discovery, the team found that the investigational anti-influenza agent WXSH0208 exhibited favourable anti-CCHFV activity and a promising safety profile. A co-crystal structure of WXSH0208 with the endonuclease of the closely related Kasokero virus (KASV) showed that the compound occupies the Endo domain through a two-metal-ion chelation mechanism. It competitively prevents the host mRNA substrate from binding to the endonuclease and thereby suppresses viral transcription initiation by blocking cap snatching. The team also identified the nucleoside analogue 2′-deoxy-2′-fluorocytidine (2FC) as a potent inhibitor of CCHFV, with an EC₅₀of 75.7 nM. The study establishes for the first time that 2FC acts at the RdRp catalytic centre through a post-translocation chain-termination mechanism. In its active triphosphate form, 2FC is recognized by the polymerase, incorporated into the nascent RNA strand, and translocated normally. Its 2′-fluoro substituent subsequently disrupts the spatial orientation of the 3′-OH by key residues in the catalytic site, preventing formation of the next phosphodiester bond and thereby terminating RNA-chain elongation.

The medicinal chemistry team at the School of Pharmaceutical Sciences contributed throughout the discovery, synthesis, characterization, and activity evaluation of the bioactive small molecules, providing the essential chemical matter required to elucidate the inhibitors’ molecular mechanisms. The team also optimized a preparative route for the active triphosphate metabolite of 2FC, overcoming a critical material bottleneck in the biochemical assays and preparation of cryo-EM complexes. By resolving both the replication mechanism of CCHFV polymerase and the modes of action of two inhibitor classes, this work addresses two major barriers in the field: limited structural information on the therapeutic target and the scarcity of potent lead compounds. It creates a translational path from target structure to candidate-molecule development and establishes a broadly applicable interdisciplinary paradigm that integrates structural biology with medicinal chemistry for antiviral discovery against bunyaviruses.

This work was supported by the State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine and the Innovative Research Group Project of the National Natural Science Foundation of China. It represents another important advance by the School of Pharmaceutical Sciences in leveraging its strengths in medicinal chemistry to support national priorities in the prevention and control of major infectious diseases.

Professor Liu Xinyong, Dean of the Institute of Innovative Drugs at Shandong University, and Professor Rong Lijun of the University of Illinois Chicago provided important guidance for this work.