INVESTIGATION OF THE INHIBITORY POTENTIAL OF SOME ANTIVIRAL AGENTS ON HUMAN TELOMERASE BY MOLECULAR DOCKING AND MOLECULAR DYNAMICS SIMULATION STUDIES

Öz

Objective: This study investigated the anticancer effects of nucleoside and non-nucleoside reverse transcriptase inhibitors drugs by computational methods. The study aimed to evaluate the binding capacity of these drugs on the telomerase essential N-terminal (TEN) domain of telomerase reverse transcriptase (TERT). Molecular docking was used to assess the drugs' binding potential to the TEN domain. The stability of the protein-drug combination obtained from the docking method was assessed using molecular dynamics (MD) simulation. Material and Method: The TEN domain of TERT's crystal structure was obtained from the Protein Data Bank (PDB). The crystal structure identified by the PDB code 2B2A has a resolution of 2.2 Å. The molecular docking was performed using AutoDock Vina. The complexes were visualized using Biovia Discovery Studio. The MD simulation was conducted using GROMACS 2020 as indicated. An MD simulation was conducted for 200 ns on both the complexes and the free protein. The RMSD (root mean square deviation) of the backbone protein and the molecules in relation to the backbone protein, RMSF (root mean square fluctuation), and Rg (radius of gyration) were shown via Qt Grace. Result and Discussion: Doravirine, Etravirine, Rilpivirine showed higher binding affinity to the TEN domain compared to the reference TERT inhibitor, BIBR1532, based on the docking investigation. The MD simulation analysis showed that the protein-Doravirine complex had the highest stability in remaining within the protein's binding pocket. On the contrary, the protein-Rilpivirine complex decreased stability, potentially causing the ligand to not to stay within the binding site. Doravirine was found to inhibit the TEN domain in the computational study. Therefore, the design and synthesis of novel doravirin derivatives is being considered because of the potential anticancer activity of doravirin in inhibiting the TEN domain of TERT.

Anahtar Kelimeler

• MD simulation
• molecular docking
• NNRTI
• NRTI
• TERT

BAZI ANTİVİRAL AJANLARIN İNSAN TELOMERAZ ENZİMİ ÜZERİNDEKİ İNHİBİTÖR POTANSİYELİNİN MOLEKÜLER KENETLENME VE MOLEKÜLER DİNAMİK SİMÜLASYON ÇALIŞMALARI İLE ARAŞTIRILMASI

Öz

Amaç: Bu çalışmada, nükleozid ve non-nükleozid ters transkriptaz inhibitörü ilaçların, antikanser etki potansiyeli hesaplamalı yaklaşımlar kullanılarak araştırılmıştır. Bu amaçla, bu ilaçların telomeraz ters transkirptaz (TERT)'ın telomeraz temel N-terminal (TEN) alanına bağlanma potansiyeli araştırılmıştır. İlaçların TEN alanına bağlanma potansiyeli için moleküler yerleştirme çalışması yapılmıştır. Moleküler yerleştirme sonucu elde edilen protein-ilaç kompleksinin kararlılığı moleküler dinamik (MD) simülasyonu ile değerlendirilmiştir. Gereç ve Yöntem: TERT'in TEN alanı kristal yapısı için Protein Veri Bankası (PDB) kullanılmıştır. 2,2 Å çözünürlüğe sahip PDB kodu 2B2A kristal yapı kullanımıştır. Moleküler yerleştirme çalışması için AutoDock Vina programı kullanılmıştır. Kompleksler Biovia Discovery Studio kullanılarak görselleştirilmiştir. MD simülasyonu GROMACS 2020 kullanılarak gerçekleştirilmiştir. Hem kompleksler hem de serbest protein üzerinde 200 ns boyunca bir MD simülasyonu gerçekleştirilmiştir. Omurga protein ve moleküllerin, omurga yapısına göre RMSD (kök ortalama kare sapması), RMSF (kök ortalama kare dalgalanması) ve Rg (dönme yarıçapı), Qt Grace ile gösterilmiştir. Sonuç ve Tartışma: Moleküler yerleştirme çalışması sonucunda, Doravirin (bileşik 3), Etravirin (bileşik 6) ve Rilpivirin’in (bileşik 9) referans TERT inhibitörü BIBR1532'ye kıyasla TEN alanına daha yüksek bağlanma potansiyeli ile bağlandığını ortaya koymuştur. MD simülasyon çalışması ile, protein-Doravirin kompleksinin proteinin bağlanma cebindeki en yüksek stabiliteye sahip olduğu gösterilmiştir. Öte yandan, protein-Rilpivirin kompleksinin kararlı olmaması nedeniyle bağlanma cebinde kalmama ihtimali bulunmaktadır. Yapılan çalışma, Doravirin’in TEN’i inhibe edebileceğini göstermiştir. Bu nedenle, Doravirin'in TERT'in TEN alanını inhibe ederek antikanser potansiyel gösterebilme ihtimali nedeniyle Doravirin türevi yeni bileşiklerin tasarlanması ve sentezlenmesi düşünülmektedir.

Anahtar Kelimeler

• MD simülasyon
• moleküler yerleştirme
• NNRTI
• NRTI
• TERT

Kaynakça

1. 1. High, K.P., Brennan-Ing, M., Clifford, D.B., Cohen, M.H., Currier, J., Deeks, S.G., Deren, S., Effros, R. B., Gebo, K., Goronzy, J.J., Justice, A.C., Landay, A., Levin, J., Miotti, P.G., Munk, R. J., Nass, H., Rinaldo, C.R., Jr, Shlipak, M.G., Tracy, R., Valcour, V. (2012). HIV and aging: State of knowledge and areas of critical need for research. A report to the NIH Office of AIDS Research by the HIV and Aging Working Group. Journal of Acquired Immune Deficiency Syndromes, 60(1), S1-S18. [CrossRef]
2. 2. Rasmussen, L.D., May, M.T., Kronborg, G., Larsen, C.S., Pedersen, C., Gerstoft, J., Obel, N. (2015). Time trends for risk of severe age-related diseases in individuals with and without HIV infection in Denmark: A nationwide population-based cohort study. The Lancet, 2(7), 288-298. [CrossRef]
3. 3. Bollmann, F.M. (2013). Telomerase inhibition may contribute to accelerated mitochondrial aging induced by anti-retroviral HIV treatment. Medical Hypotheses, 81(2), 285-287. [CrossRef]
4. 4. Haycock, P.C., Heydon, E.E., Kaptoge, S., Butterworth, A.S., Thompson, A., Willeit, P. (2014). Leucocyte telomere length and risk of cardiovascular disease: Systematic review and meta-analysis. BMJ, 349, 4227. [CrossRef]
5. 5. Honig, L.S., Kang, M.S., Schupf, N., Lee, J.H., Mayeux, R. (2012). Association of shorter leukocyte telomere repeat length with dementia and mortality. Archives of Neurology, 69(10), 1332-1339. [CrossRef]
6. 6. Blackburn, E.H., Collins, K. (2011). Telomerase: An RNP enzyme synthesizes DNA. Cold Spring Harbor Perspectives in Biology, 3(5), a003558. [CrossRef]
7. 7. Nakamura, T.M., Morin, G.B., Chapman, K.B., Weinrich, S.L., Andrews, W.H., Lingner, J., Harley, C.B., Cech, T.R. (1997). Telomerase catalytic subunit homologs from fission yeast and human. Science, 277(5328), 955-959. [CrossRef]
8. 8. Feng, J., Funk, W.D., Wang, S.S., Weinrich, S.L., Avilion, A.A., Chiu, C.P., Adams, R.R., Chang, E., Allsopp, R.C., Yu, J. (1995). The RNA component of human telomerase. Science, 269(5228), 1236-1241. [CrossRef]

9. 9. Strahl, C., Blackburn, E.H. (1996). Effects of reverse transcriptase inhibitors on telomere length and telomerase activity in two immortalized human cell lines. Molecular and Cellular Biology, 16(1), 53-65. [CrossRef]
10. 10. Peng, Y., Mian, I.S., Lue, N.F. (2001). Analysis of telomerase processivity: Mechanistic similarity to HIV-1 reverse transcriptase and role in telomere maintenance. Molecular Cell, 7(6), 1201-1211. [CrossRef]
11. 11. Ji, H.J., Rha, S.Y., Jeung, H.C., Yang, S.H., An, S.W., Chung, H.C. (2005). Cyclic induction of senescence with intermittent AZT treatment accelerates both apoptosis and telomere loss. Breast Cancer Research and Treatment, 93(3), 227-236. [CrossRef]
12. 12. Brown, T., Sigurdson, E., Rogatko, A., Broccoli, D. (2003). Telomerase inhibition using azidothymidine in the HT-29 colon cancer cell line. Annals of Surgical Oncology, 10(8), 910-915. [CrossRef]
13. 13. Liu, X., Takahashi, H., Harada, Y., Ogawara, T., Ogimura, Y., Mizushina, Y., Saneyoshi, M., Yamaguchi, T. (2007). 3'-Azido-2',3'-dideoxynucleoside 5'-triphosphates inhibit telomerase activity in vitro, and the corresponding nucleosides cause telomere shortening in human HL60 cells. Nucleic Acids Research, 35(21), 7140-7149. [CrossRef]
14. 14. Fang, J.L., Beland, F.A. (2009). Long-term exposure to zidovudine delays cell cycle progression, induces apoptosis, and decreases telomerase activity in human hepatocytes. Toxicological Sciences: An Official Journal of the Society of Toxicology, 111(1), 120-130. [CrossRef]
15. 15. Gomez, D.E., Tejera, A.M., Olivero, O.A. (1998). Irreversible telomere shortening by 3'-azido-2',3'-dideoxythymidine (AZT) treatment. Biochemical and Biophysical Research Communications, 246(1), 107-110. [CrossRef]
16. 16. Jacobs, S.A., Podell, E.R., Cech, T.R. (2006). Crystal structure of the essential N-terminal domain of telomerase reverse transcriptase. Nature Structural Molecular Biology, 13(3), 218-225. [CrossRef]
17. 17. Tian, W., Chen, C., Lei, X., Zhao, J., Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(1), 363-367. [CrossRef]
18. 18. Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B.A., Thiessen, P.A., Yu, B., Zaslavsky, L., Zhang, J., Bolton, E.E. (2021). PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Research, 49(1), 1388-1395. [CrossRef]
19. 19. Trott, O., Olson, A.J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461. [CrossRef]
20. 20. Muhammed, M.T., Aki-Yalcin, E. (2024). Computational insight into the mechanism of action of DNA gyrase inhibitors; revealing a new mechanism. Current Computer-Aided Drug Design, 20(3), 224-235. [CrossRef]
21. 21. Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX 1-2, 19-25. [CrossRef]
22. 22. Muhammed, M.T., Kokbudak, Z., Akkoc, S. (2023). Cytotoxic activities of the pyrimidine-based acetamide and isophthalimide derivatives: An in vitro and in silico studies, Molecular Simulation, 49(10), 982-992. [CrossRef]
23. 23. Wang, Y., Cheng, F.X., Yuan, X.L., Tang, W.J., Shi, J.B., Liao, C.Z., Liu, X.H. (2016). Dihydropyrazole derivatives as telomerase inhibitors: Structure-based design, synthesis, SAR and anticancer evaluation in vitro and in vivo. European Journal of Medicinal Chemistry, 112, 231-251. [CrossRef]
24. 24. Fragkiadaki, P., Renieri, E., Kalliantasi, K., Kouvidi, E., Apalaki, E., Vakonaki, E., Mamoulakis, C., Spandidos, D.A., Tsatsakis, A. (2022). Τelomerase inhibitors and activators in aging and cancer: A systematic review. Molecular Medicine Reports, 25(5), 158. [CrossRef]
25. 25. Sherin, D.R., Manojkumar, T.K., Prakash, R.C., Sobha, V.N. (2020). Molecular docking and dynamics simulation study of telomerase inhibitors as potential anti-cancer agents. Materials Today: Proceedings, 46, 2898-2905. [CrossRef]
26. 26. Muhammed, M.T., Er, M., Akkoç, S. (2023). Molecular modeling and in vitro antiproliferative activity studies of some imidazole and isoxazole derivatives. Journal of Molecular Structure, 1282, 135066. [CrossRef]
27. 27. Işık, A., Çevik, U.A., Celik, I., Erçetin, T., Koçak, A., Özkay, Y., Kaplancıklı, Z.A. (2022). Synthesis, characterization, molecular docking, dynamics simulations, and in silico absorption, distribution, metabolism, and excretion (ADME) studies of new thiazolylhydrazone derivatives as butyrylcholinesterase inhibitors. Zeitschrift fur Naturforschung C, 77(11-12), 447-457. [CrossRef]
28. 28. Gökçe, B., Muhammed, M.T. (2023). Evaluation of in vitro effect, molecular docking, and molecular dynamics simulations of some dihydropyridine-class calcium channel blockers on human serum paraoxonase 1 (hPON1) enzyme activity. Biotechnology and Applied Biochemistry, 70(5), 1707-1719. [CrossRef]