The Nonequilibrium Mechanism of Noise Enhancer synergizing with Activator in HIV Latency Reactivation

Reactivating HIV latency and then simultaneously eliminating it by antiretroviral therapy has become a leading strategy in curing HIV. Recently, single-cell screening experiments have shown the drug synergy between two categories of biomolecules, Activators (AC) and Noise Enhancers (NE): NE can amplify the reactivation of latent HIV induced by AC, although NE itself cannot reactivate HIV latency. Based on an established LTR-two-state effective model, we uncover two necessary conditions for this type of drug synergy: The decreasing of the turning-on rate of LTR induced by NE is highly inhibited when presented with AC; The timescale of LTR turning off without AC/NE presented should be no slower than the timescale of Tat transactivation. Then we propose a detailed LTR-four-state mechanistic model with both AC/NE regulation kinetics and Tat transactivation circuit. We show that, in order to achieve drug synergy, the system of HIV gene state transition must operate out of thermodynamic equilibrium, which is caused by energy input. The direction of energy input determines whether the inhibition of NE upon the reactivation rate of LTR-off states (unbinding of RNAP) can be successfully prevented in the presence of AC. The drug synergy can also be significantly enhanced if the energy input is appropriately distributed to more than one reaction. Our model reveals a generic nonequilibrium mechanism underpinning the noise enhanced drug synergy, which may apply to identify the same drug synergy on reactivating a diverse class of lentivirus latency. Significance StatementThe "kick and kill" strategy has become a promising way to cure HIV by eliminating latent HIV reservoirs, the main barrier to a clinical cure. Two categories of biomolecules, Activators (AC) and Noise Enhancers (NE), have been found to have synergy on reactivating latent HIV (kick strategy). We uncover the underlying non-equilibrium mechanism of such drug synergy by developing mathematical models based on genetic regulatory kinetics. We find that controlling the magnitude and direction of energy input into genetic regulatory kinetics can prevent NE from reducing the turn-on rate of the inactivated gene state in the presence of AC, which produces the synergy. This general nonequilibrium mechanism can be useful for identifying other drug synergies on lentivirus latency reactivation.