13ND | pdb_000013nd

Crystallographic fragment screening discovers novel micromolar active inhibitors and druggable hotspots of SARS-CoV-2 PL pro.

(2026) Int J Biol Macromol 347: 150689-150689

• PubMed: 41638277 Search on PubMed
• DOI: https://doi.org/10.1016/j.ijbiomac.2026.150689
• Primary Citation of Related Structures:  
  13MI, 13MJ, 13MK, 13ML, 13MM, 13MN, 13MO, 13MP, 13MQ, 13MR, 13MS, 13MT, 13MU, 13MV, 13MW, 13MX, 13MY, 13MZ, 13NA, 13NB, 13NC, 13ND, 13NE, 13NF, 13NG, 13NH, 13NI, 13NJ, 13NK, 13NL, 13NM, 13NN, 13NO, 13NP, 13NQ, 13NR, 13NS, 13NT, 13NU, 13NV, 13NW, 13NX, 13NY, 13NZ, 13OA, 13OB, 13OC, 13OD, 13OE, 13OF


• PubMed Abstract: 
  

  The COVID-19 pandemic has highlighted the need to develop broad-spectrum antiviral therapeutics targeting rapidly evolving coronaviruses. This research focuses on SARS-CoV-2 PL ^pro , a conserved viral protease that plays dual roles in viral polyprotein processing and host immune suppression. Using an integrated fragment-based drug discovery (FBDD) approach that combines high-throughput X-ray crystallography and biochemical assays, we systematically screened a diverse library of 800 fragment compounds. Structural characterization identified 129 validated binders occupying 12 distinct binding sites on PL ^pro . Remarkably, two fragments demonstrated potent micromolar inhibitory activity. Fr12895 inhibited SARS-CoV-2 PL ^pro protease activity (IC ₅₀  = 8.013 μM), as measured using the fluorogenic substrate RLRGG-AMC, while Fr12338 showed inhibition against PL ^pro deISGylase activity (IC ₅₀  = 4.5 μM), as determined with the substrate Ac-ISG15prox-Rh110MP. This provides a case for directly obtaining micromolar-active compounds through crystallographic fragment screening of a small number of random compounds. Detailed structural analysis revealed these fragments engage key functional regions including the blocking loop 2 (BL2) and ubiquitin/ISG15 binding interface through extensive hydrogen-bond networks and hydrophobic interactions. Our study reveals novel micromolar active inhibitors and druggable sites of SARS-CoV-2 PL ^pro by crystallographic fragment screening, provides crucial scaffold and a structural roadmap for developing broad-spectrum antivirals against coronaviruses.

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Organizational Affiliation: 
• Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
Jiangxi Province Key Laboratory of Pharmacology of Traditional Chinese Medicine, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China. Electronic address: rmsl_2040@163.com.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China. Electronic address: wangqs@sari.ac.cn.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China; Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China. Electronic address: yufeng@sari.ac.cn.
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