Allosteric Mechanism Of Cyclopropylindolobenzazepine Inhibitors For HCV NS5B RdRp Via Dynamic Correlation Network

Inhibitor induced allosteric regulation is associated with signaling event a protein generate through inhibitor binding and transmitted to a second site via long-range intra-molecular communication that causes a change in the structural conformation at a distal site and leads to a change in function(e.g.catalytic efficiency or binding affinity),likewisethe cellular protein allosteric regulation that respond to changes in concentrations of small molecules.Following the same phenomena of cellular protein regulation,Compound M2,a cyclopropylindolobenzazepine derivative among the HCV RNA dependent RNA polymerase(RdRp)nonstructural protein 5B(NS5B)targeted drugs,bind to site 1 of thumb domain distant from catalytic site and allosterically inhibit HCV NS5 B RdRp activity prior to elongation.In vitro and crystallographic studies evidenced the potency of inhibitory activity and structural changes the M2 and similar inhibitors produced in HCV NS5 B at distal sites.However,the experimental methods are not enough to explain the detailed allosteric mechanism for these derivatives and similar inhibitors at molecular level.With continuous improvements in field of computations,molecular dynamics simulations along with algorithm design are likely to play an increasingly important role to overcome such limitations.In this study fluctuation correlation networks were constructed based on all-atom molecular dynamics simulations to elucidate the allosteric mechanism of M2 bound to NS5 B.The fluctuation correlation networks between free and M2 bound NS5 B are significantly different.The information can better transfer from the allosteric site to the catalytic site for bound NS5 B than for free NS5 B.Thus,the hypothesis of “binding induced allosteric regulation” is proposed to link the enzyme inactivation and inhibitor binding and then confirmed by mutant network.Finally,one possible allosteric pathway was identified with the shortest path and evaluated by the perturbation of the network.These methods will be helpful to identify the allosteric pathway of other proteins and to design drug targeting on the pathway.