5T2P

Hepatitis B virus core protein Y132A mutant in complex with sulfamoylbenzamide (SBA_R01)

Summary for 5T2P

• Entry DOI: 10.2210/pdb5t2p/pdb
• Descriptor: Core protein, 4-fluoranyl-3-(4-oxidanylpiperidin-1-yl)sulfonyl-~{N}-[3,4,5-tris(fluoranyl)phenyl]benzamide, ISOPROPYL ALCOHOL, ... (7 entities in total)
• Functional Keywords: hepatitis b virus, hbv, core protein, capsid, y132a dimer, y132a hexamer, sulfamoylbenzamide, sba_r01, viral protein
• Biological source: Hepatitis B virus (HBV)
• Total number of polymer chains: 6
• Total formula weight: 108726.59

Authors

Zhou, Z.,Xu, Z.H. (deposition date: 2016-08-24, release date: 2017-02-22, Last modification date: 2024-11-13)

Primary citation

Zhou, Z.,Hu, T.,Zhou, X.,Wildum, S.,Garcia-Alcalde, F.,Xu, Z.,Wu, D.,Mao, Y.,Tian, X.,Zhou, Y.,Shen, F.,Zhang, Z.,Tang, G.,Najera, I.,Yang, G.,Shen, H.C.,Young, J.A.,Qin, N.
Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms.
Sci Rep, 7:42374-42374, 2017

PubMed Abstract: Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer. The striking difference lies in a unique hydrophobic subpocket that is occupied by the thiazole group of HAP_R01, but is unperturbed by SBA_R01. Photoaffinity labeling confirms the HAP_R01 binding pose at the dimer-dimer interface on capsid and suggests a new mechanism of HAP-induced mis-assembly. Based on the common features in crystal structures we predict that T33 mutations generate similar susceptibility changes to both compounds. In contrast, mutations at positions in close contact with HAP-specific groups (P25A, P25S, or V124F) only reduce susceptibility to HAP_R01, but not to SBA_R01. Thus, HAP and SBA are likely to have distinctive resistance profiles. Notably, P25S and V124F substitutions exist in low-abundance quasispecies in treatment-naïve patients, suggesting potential clinical relevance.

PubMed: 28205569
DOI: 10.1038/srep42374

Experimental method

X-RAY DIFFRACTION (1.693 Å)