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Updated: Jun 26, 2026
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
Published on: May 9, 2025
An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription
Katherine V Wendelsdorf1, Zhuo Song, Yang Cao
1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Virginia, United States of America.
Abstract:
Nucleoside analogs used in antiretroviral treatment have been associated with mitochondrial toxicity. The polymerase-gamma hypothesis states that this toxicity stems from the analogs' inhibition of the mitochondrial DNA polymerase (polymerase-gamma) leading to mitochondrial DNA (mtDNA) depletion. We have constructed a computational model of the interaction of polymerase-gamma with activated nucleoside and nucleotide analog drugs, based on experimentally measured reaction rates and base excision rates, together with the mtDNA genome size, the human mtDNA sequence, and mitochondrial dNTP concentrations. The model predicts an approximately 1000-fold difference in the activated drug concentration required for a 50% probability of mtDNA strand termination between the activated di-deoxy analogs d4T, ddC, and ddI (activated to ddA) and the activated forms of the analogs 3TC, TDF, AZT, FTC, and ABC. These predictions are supported by experimental and clinical data showing significantly greater mtDNA depletion in cell culture and patient samples caused by the di-deoxy analog drugs. For zidovudine (AZT) we calculated a very low mtDNA replication termination probability, in contrast to its reported mitochondrial toxicity in vitro and clinically. Therefore AZT mitochondrial toxicity is likely due to a mechanism that does not involve strand termination of mtDNA replication.
Insights
Antiretroviral nucleoside analogs can cause mitochondrial toxicity. A computational model shows di-deoxy analogs are more likely to deplete mitochondrial DNA (mtDNA) than other analogs, explaining observed toxicity.
Area of Science:
- Biochemistry
- Molecular Biology
- Pharmacology
Background:
- Nucleoside analogs are key antiretroviral drugs.
- Mitochondrial toxicity, including mitochondrial DNA (mtDNA) depletion, is a known side effect.
- The polymerase-gamma hypothesis links this toxicity to inhibition of mitochondrial DNA polymerase (polymerase-gamma).
Purpose of the Study:
- To computationally model the interaction between polymerase-gamma and activated antiretroviral nucleoside analogs.
- To predict the likelihood of mtDNA strand termination by different analogs.
- To investigate the mechanism of mitochondrial toxicity associated with these drugs.
Main Methods:
- Constructed a computational model of polymerase-gamma interaction with activated nucleoside/nucleotide analogs.
- Incorporated experimental reaction rates, base excision rates, mtDNA genome size, human mtDNA sequence, and mitochondrial dNTP concentrations.
- Calculated the probability of mtDNA strand termination for various activated analogs.
Main Results:
- The model predicted a ~1000-fold difference in required drug concentration for 50% mtDNA strand termination probability between di-deoxy analogs and other analogs.
- Predictions align with experimental and clinical data showing greater mtDNA depletion by di-deoxy analogs.
- Zidovudine (AZT) showed a low predicted probability of mtDNA replication termination, contrasting with its known toxicity.
Conclusions:
- Di-deoxy nucleoside analogs are significantly more prone to causing mtDNA depletion via polymerase-gamma inhibition.
- The mechanism of zidovudine (AZT) mitochondrial toxicity likely involves pathways other than direct mtDNA replication strand termination.
