Precision Elimination: Proof-of-Concept In Silico Testing of a Novel Construct for Optimizing HIV-1 Eradication

Background/Objectives: Human immunodeficiency virus type 1 (HIV-1) persists in individuals on combination antiretroviral therapy (cART) due to the existence of latent reservoirs that evade immune detection. Although shock-and-kill strategies utilizing latency-reversing agents (LRAs) aim to reactivate and eliminate these reservoirs, their effectiveness is limited by cART's lack of cytotoxicity, which means LRA treatments fail to eliminate the infected cell population. As a result, treatment cessation results in rapid viral rebound. This study introduces and evaluates a novel HIV-1 LTR-driven therapeutic construct that reactivates latent HIV-1 cells and directly eliminates both latent and active infected cells, independent of immune clearance. Methods: We employed a dual computational modeling approach to assess the efficacy of the HIV-1 LTR-driven therapeutic construct. A system of SBML-based ODE models was used to analyze population-level trends in viral suppression and reservoir reduction over time. Additionally, ABMs implemented in NetLogo provided insights into spatial and stochastic interactions between infected cells and therapeutic agents. Both models compared the novel construct to conventional cART and LRA-based shock-and-kill strategies by tracking changes in both detectable and total active, reactivated, and latent HIV-1 reservoirs. Results: The novel treatment monotherapy reduced the HIV-1 population by 96.26% (p < 0.0001), with a cytotoxic efficacy of 99.27% (p < 0.0001). This resulted in a 93.17% greater reduction in the viral reservoir compared to the cART-LRA polytherapy. Sensitivity analyses highlighted the role of key kinetic parameters in treatment efficacy. Variations in k₃ and kLRA in the novel treatment model showed a consistent reduction in the viral reservoir, with higher values leading to greater efficacy. ABM results demonstrated that in the experimental group, treatment resulted in a 1.39% increase in healthy CD4+ T cells, a 12.00% reduction in latent HIV-1 cells, and a statistically significant decline in active HIV-1 cells. Conclusions: This study demonstrates that the novel HIV-1 LTR-driven therapeutic construct significantly improves upon current shock-and-kill strategies by directly eliminating both latent and active HIV-1-infected cells with high cytotoxic efficacy. By utilizing the diphtheria toxin A (DTA) suicide gene, this construct overcomes the limitations of cART and LRA polytherapies, which fail to eradicate infected cells, rather depending on suppression. Computational modeling results show that the construct substantially reduces both detectable and total viral reservoirs, providing a promising adjunct to existing HIV-1 treatment strategies. These findings serve as a foundation for future in vitro and in vivo research and contribute to the development of a functional cure for HIV-1.