Computational protocol: Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA

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Protocol publication

[…] The inhibitors BMS-790052 and AZD7295 were constructed and geometrically optimised within SYBYL-X 2.0 (Certara, L. P., http://www.tripos.com) using the MMFF94s forcefield and partial atomic charges, conjugate gradient convergence method. Termination of the optimisation was achieved when the gradient difference of successive steps was < 0.05 kcals/mol•Å. Since residues 26–32, located on a flexible loop connecting the Zn2+ binding domain (residues 33–213) to the amphipathic helix (residues 1–25), is a site of many resistance mutations, we decided to include this region and the amphipathic helix in our models. To construct the 3FQQ dimer model for NS5A1–191, residues 1–27 of the NMR structure 1R7G were combined with the 3FQQ A and B chains (residues 33–191). The loops containing residues 26–32 were built manually in a conformation that would allow the amphipathic helices (residues 1–25) to interact with the cell membrane and for L28 and L31 to point towards the putative compound binding pocket (, , ). The side-chains of the NS5A1–191 3FQQ dimer model were geometry optimised for 1,000 iterations (or until the gradient of successive iterations was < 0.05 kcal/mol•Å) using the same protocol as above. The 1ZH1 dimer model (, ) was generated in an analogous fashion. The inhibitors were then docked into each of the NS5A1–191 dimer models using the docking algorithm Surflex (within SYBYL-X 2.0, Certara L. P., http://tripos.com). For both the 3FQQ and 1ZH1 dimer models, the protomol was generated by manually selecting the residues lining the pocket at the monomer-monomer interface, a threshold of 0.50 and a bloat value of 2. The docking mode used for both NS5A1–191 dimer models was GeomX and protein flexibility was allowed, all other parameters were at default values. The C-Score scoring function was used and the top 100 ranked poses of each inhibitor were retained for examination. Both BMS-790052 and AZD7295 are conformationally flexible and can adopt a range of orientations within the docking sites of both dimers. The orientations shown in and are selected examples. , and were produced using PyMOL (http://pymol.org). […]

Pipeline specifications

Software tools Sybyl-X, Surflex-Dock, PyMOL
Application Protein interaction analysis
Organisms Hepacivirus C, Homo sapiens, Classical swine fever virus
Diseases Hepatitis C