HIV Drug Resistance Mutations in Patients with HIV and HIV-TB Coinfection After Failure of First-Line Therapy: A Prevalence Study in a Resource-Limited Setting

Sequence-based drug design as a concept in computational drug design

Drug development based on target proteins has been a successful approach in recent decades. However, the conventional structure-based drug design (SBDD) pipeline is a complex, human-engineered process with multiple independently optimized steps. Here, we propose a sequence-to-drug concept for computational drug design based on protein sequence information by end-to-end differentiable learning. We validate this concept in three stages. First, we design TransformerCPI2.0 as a core tool for the concept, which demonstrates generalization ability across proteins and compounds. Second, we interpret the binding knowledge that TransformerCPI2.0 learned. Finally, we use TransformerCPI2.0 to discover new hits for challenging drug targets, and identify new target for an existing drug based on an inverse application of the concept. Overall, this proof-of-concept study shows that the sequence-to-drug concept adds a perspective on drug design. It can serve as an alternative method to SBDD, particularly for proteins that do not yet have high-quality 3D structures available.

Torque Teno Virus plasma level as novel biomarker of retained immunocompetence in HIV-infected patients

PURPOSE

To predict the course of immune recovery (IR) in HIV-1-infected patients after initiation of combined antiretroviral therapy (cART) by determination of the plasma concentration of Torque Teno Virus (TTV). TTV has been identified as marker for risk assessment in immunosuppressed patients after transplantation procedures. Here, TTV was analyzed in HIV-1-infected therapy-naïve patients to evaluate its use as predictor of the course of IR for guidance of individualized treatment.

METHODS

TTV DNA was quantified in plasma samples of 301 therapy-naïve HIV-1-infected patients and correlated to CD4⁺ cell count, HIV viral load, presence of the herpes viruses CMV, EBV and HHV-8, age and sex. Patients were classified according to their initial CD4⁺ cell count and to the extent of CD4⁺ T-cell increase within the first year of cART.

RESULTS

TTV DNA was detectable in 96% of the patients' plasma samples with a median TTV plasma concentration of 5.37 log₁₀ cop/ml. The baseline CD4⁺ cell count was negatively correlated with TTV plasma concentration (p = 0.003). In patients with a CD4⁺ cell recovery < 50 cells/µl, the median TTV plasma concentration was significantly higher compared to patients with a CD4⁺ cell recovery of > 200 CD4⁺ cells/µl (5.68 log₁₀ cop/ml versus 4.99 log₁₀ cop/ml; p = 0.011). TTV plasma concentration in combination with baseline CD4⁺ cell count were significantly correlated to CD4⁺ cell recovery (p = 0.004). For all other parameters considered, no significant correlation for CD4⁺ cell recovery was found.

CONCLUSION

Within the cohort, the significantly elevated TTV plasma concentration in patients with diminished CD4⁺ cell recovery indicates a more profound immune defect. Baseline TTV plasma concentrations and CD4⁺ cell count are predictive for the course of immune recovery in HIV-1-infected patients with severe immunodeficiency.