Integrated Computational Exploration of Pyrimidine-2,4-dione Derivatives as Dual HIV-1 RT/RNase H Inhibitor

Introduction. Continuous efforts to uncover new antiviral entities targeting HIV RT RNase H stem from the suffering of affected individuals and the relentless increase in death cases. The present study focused on ten molecules based on the pyrimidine-2,4-dione scaffold, which were discovered to have potent antiviral activity against HIV RT RNase H and acceptable bioavailability and pharmacokinetic properties.

Aim. The main goal of this study is to discover and evaluate promising pyrimidine-2,4-dione-derived molecules as potential inhibitors of HIV.

Materials and methods. A docking protocol was executed to investigate the binding mechanisms of the designed compounds within RNase H's active site using the AutoDock Vina program. The molecular dynamics simulation analysis for 100 ns was carried out using Desmond, and the complexes were constructed using the OPLS3-2005 force field. The frontier molecular orbital energies and related reactivity factors of the best antiviral agents were determined using the DFT-B3LYP/6-31G (d,p) calculations performed with the Gaussian program.

Results and discussion. Two molecules, Pyr06 and Pyr07, displayed a higher docking score (–10.7 kcal/mol) than the control compound (MPD: –9.8 kcal/mol) and the other designed compounds (with affinities ranging from –9.6 to –10.4 kcal/mol). On the other hand, it was noted that these two molecules formed significant hydrogen bonds and hydrophobic contacts with active site residues. Furthermore, our analysis through MD simulations for 100 ns validated the binding stability and conformation of molecules Pyr06 and Pyr07 in complexes with the 5J1E receptor. The DFT findings for both molecules, Pyr06 and Pyr07, also confirmed their docking scores and their ability to form stable complexes with RNase H.

Conclusion. The results obtained could be highly beneficial for designing and developing Pyr06 and Pyr07 as potential therapeutic drugs to combat HIV RT RNase H.

1. Centers for Disease Control (CDC). Update: acquired immunodeficiency syndrome (AIDS) – United States. Morbidity and Mortality Weekly Report. 1984;32(52):688–691.

2. Takasawa A., Morimoto I., Wake A., Haratake J., Fujii K., Okada Y., Oda S., Hashimoto H., Eto S. Autopsy findings of Addison’s disease caused by systemic cytomegalovirus infection in a patient with acquired immunodeficiency syndrome. Internal Medicine. 1995;34(6):533–536. DOI: 10.2169/internalmedicine.34.533.

3. Février M., Dorgham K., Rebollo A. CD4+ T cell depletion in human immunodeficiency virus (HIV) infection: role of apoptosis. Viruses. 2011;3(5):586–612. DOI: 10.3390/v3050586.

4. Woodham A. W., Skeate J. G., Sanna A. M., Taylor J. R., Da Silva D. M., Cannon P. M., Kast W. M. Human immunodeficiency virus immune cell receptors, coreceptors, and cºfactors: implications for prevention and treatment. AIDS Patient Care and STDs. 2016;30(7):291–306. DOI: 10.1089/apc.2016.0100.

5. Singh A. K., Das K. Insights into HIV-1 reverse transcriptase (RT) inhibition and drug resistance from thirty years of structural studies. Viruses. 2022;14(5):1027. DOI: 10.3390/v14051027.

6. Arts E. J., Hazuda D. J. HIV-1 antiretroviral drug therapy. Cold Spring Harbor Perspectives in Medicine. 2012;2(4):a007161. DOI: 10.1101/cshperspect.a007161.

7. Cihlar T., Fordyce M. Current status and prospects of HIV treatment. Current Opinion in Virology. 2016;18:50–56. DOI: 10.1016/j.coviro.2016.03.004.

8. Wang L., Tang J., Huber A. D., Casey M. C., Kirby K. A., Wilson D. J., Kankanala J., Xie J., Parniak M. A., Sarafianos S. G., Wang Z. 6-Arylthio-3-hydroxypyrimidine-2,4-diones potently inhibited HIV reverse transcriptase-associated RNase H with antiviral activity. European Journal of Medicinal Chemistry. 2018;156:652–665. DOI: 10.1016/j.ejmech.2018.07.039.

9. Chen A. Y., Adamek R. N., Dick B. L., Credille C. V., Morrison C. N., Cohen S. M. Targeting metalloenzymes for therapeutic intervention. Chemical Reviews. 2019;119(2):1323–1455. DOI: 10.1021/acs.chemrev.8b00201.

10. Ilina T. V., Brosenitsch T., Sluis-Cremer N., Ishima R. Retroviral RNase H: structure, mechanism, and inhibition. In: Cameron C. E., Arnold J. J., editors. The Enzymes. Viral Replication Enzymes and their Inhibitors Part B. Volume 50. New York: Academic Press; 2021. P. 227–247. DOI: 10.1016/bs.enz.2021.07.007.

11. Sluis-Cremer N. Retroviral reverse transcriptase: structure, function and inhibition. In: Cameron C. E., Arnold J. J., editors. The Enzymes. Viral Replication Enzymes and their Inhibitors Part B. Volume 50. New York: Academic Press; 2021. P. 179–194. DOI: 10.1016/bs.enz.2021.06.006.

12. Hu W.-S., Hughes S. H. HIV-1 reverse transcription. Cold Spring Harbor Perspectives in Medicine. 2012;2(10):a006882. DOI: 10.1101/cshperspect.a006882.

13. Julias J. G., McWilliams M. J., Sarafianos S. G., Arnold E., Hughes S. H. Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo. Proceedings of the National Academy of Sciences. 2002;99(14):9515–9520. DOI: 10.1073/pnas.142123199.

14. Gerbouin O., Grellet J. Virus de l’immunodéficience humaine: cycle viral et épidémiologie. Actualités Pharmaceutiques. 2017;56(564):1–2. DOI: 10.1016/j.actpha.2016.12.001.

15. Spence R. A., Kati W. M., Anderson K. S., Johnson K. A. Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors. Science. 1995;267(5200):988–993. DOI: 10.1126/science.7532321.

16. Hang J. Q., Li Y., Yang Y., Cammack N., Mirzadegan T., Klumpp K. Substrate-dependent inhibition or stimulation of HIV RNase H activity by non-nucleoside reverse transcriptase inhibitors (NNRTIs). Biochemical and Biophysical Research Communications. 2007;352(2):341–350. DOI: 10.1016/j.bbrc.2006.11.018.

17. Cihlar T., Ray A. S. Nucleoside and nucleotide HIV reverse transcriptase inhibitors: 25 years after zidovudine. Antiviral Research. 2010;85(1):39–58. DOI: 10.1016/j.antiviral.2009.09.014.

18. El Masaoudy Y., Tabti K., Koubi Y., Maghat H., Lakhlifi T., Bouachrine M. In silico design of new pyrimidine-2,4-dione derivatives as promising inhibitors for HIV reverse transcriptase-associated RNase H using 2D-QSAR modeling and (ADME/Tox) properties. Moroccan Journal of Chemistry. 2023;11(2):300–337. DOI: 10.48317/IMIST.PRSM/morjchem-v11i2.35455.

19. Lipinski C. A., Lombardo F., Dominy B. W., Feeney P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews. 1997;23(1–3):3–25. DOI: 10.1016/S0169-409X(96)00423-1.

20. Pires D. E. V., Blundell T. L., Ascher D. B. pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry. 2015;58(9):4066–4072. DOI: 10.1021/acs.jmedchem.5b00104.

21. Yang C., Chen E. A., Zhang Y. Protein–ligand docking in the machine-learning era. Molecules. 2022;27(14):4568. DOI: 10.3390/molecules27144568.

22. Kamal I. M., Chakrabarti S. MetaDOCK: a combinatorial molecular docking approach. ACS Omega. 2023;8(6):5850–5860. DOI: 10.1021/acsomega.2c07619.

23. Trott O., Olson A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry. 2010;31(2):455–461. DOI: 10.1002/jcc.21334.

24. Wang L., Tang J., Huber A. D., Casey M. C., Kirby K. A., Wilson D. J., Kankanala J., Parniak M. A., Sarafianos S. G., Wang Z. 6-Biphenylmethyl-3-hydroxypyrimidine-2,4-diones potently and selectively inhibited HIV reverse transcriptase-associated RNase H. European Journal of Medicinal Chemistry. 2018;156:680–691. DOI: 10.1016/j.ejmech.2018.07.035.

25. Morris G. M., Huey R., Lindstrom W., Sanner M. F., Belew R. K., Goodsell D. S., Olson A. J. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. Journal of Computational Chemistry. 2009;30(16):2785–2791. DOI: 10.1002/jcc.21256.

26. Desmond Molecular Dynamics System. D. E. Shaw Research. Maestro-Desmond Interoperability Tools. New York: Schrödinger; 2023.

27. El Masaoudy Y., Lakhlifi T., Maghat H., Bouachrine M. 4-Oxoquinoline Ribonucleosides as HIV-1 Reverse Transcriptase Inhibitors: A combination of DFT, QSAR Study, Docking Simulation, and ADMET Prediction. RHAZES: Green and Applied Chemistry. 2025;21:12–31. DOI: 10.48419/IMIST.PRSM/rhazes-v21.55495.