5ETX

Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-Linear (MK-5172 linear analogue)

Summary for 5ETX

• Entry DOI: 10.2210/pdb5etx/pdb
• Related: 3SUD 3SUE 3SUG 5EPN 5EPY 5EQQ 5EQR 5EQS 5ESB
• Descriptor: NS3 protease, ZINC ION, ~{tert}-butyl ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[(1~{R},2~{R})-1-(cyclopropylsulfonylcarbamoyl)-2-ethyl-cyclopropyl]carbamoyl]-4-(3-ethyl-7-methoxy-quinoxalin-2-yl)oxy-pyrrolidin-1-yl]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate, ... (5 entities in total)
• Functional Keywords: macrocyclization, mk-5172 analogue, grazoprevir, hcv protease inhibitor resistance, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Hepatitis C virus
• Total number of polymer chains: 4
• Total formula weight: 85862.02

Authors

Soumana, D.,Yilmaz, N.K.,Ali, A.,Prachanronarong, K.L.,Aydin, C.,Schiffer, C.A. (deposition date: 2015-11-18, release date: 2016-01-13, Last modification date: 2023-09-27)

Primary citation

Soumana, D.I.,Kurt Yilmaz, N.,Prachanronarong, K.L.,Aydin, C.,Ali, A.,Schiffer, C.A.
Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.
Acs Chem.Biol., 11:900-909, 2016

PubMed Abstract: Recent advances in direct-acting antivirals against Hepatitis C Virus (HCV) have led to the development of potent inhibitors, including MK-5172, that target the viral NS3/4A protease with relatively low susceptibility to resistance. MK-5172 has a P2-P4 macrocycle and a unique binding mode among current protease inhibitors where the P2 quinoxaline packs against the catalytic residues H57 and D81. However, the effect of macrocyclization on this binding mode is not clear, as is the relation between macrocyclization, thermodynamic stabilization, and susceptibility to the resistance mutation A156T. We have determined high-resolution crystal structures of linear and P1-P3 macrocyclic analogs of MK-5172 bound to WT and A156T protease and compared these structures, their molecular dynamics, and experimental binding thermodynamics to the parent compound. We find that the "unique" binding mode of MK-5172 is conserved even when the P2-P4 macrocycle is removed or replaced with a P1-P3 macrocycle. While beneficial to decreasing the entropic penalty associated with binding, the constraint exerted by the P2-P4 macrocycle prevents efficient rearrangement to accommodate the A156T mutation, a deficit alleviated in the linear and P1-P3 analogs. Design of macrocyclic inhibitors against NS3/4A needs to achieve the best balance between exerting optimal conformational constraint for enhancing potency, fitting within the substrate envelope and allowing adaptability to be robust against resistance mutations.

PubMed: 26682473
DOI: 10.1021/acschembio.5b00647

Experimental method

X-RAY DIFFRACTION (2.35 Å)