Investigation of RT1t49 aptamer binding to human immunodeficiency virus 1 reverse transcriptase

Siriluk  Ratanabunyong; Maho  Yagi-Utsumi; Saeko  Yanaka; Koichi  Kato; Kiattawee  Choowongkomon; Supa  Hannongbua

Authors

Siriluk Ratanabunyong Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand and Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
Maho Yagi-Utsumi Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, 12 Okazaki, Aichi 444-8787, Japan
Saeko Yanaka Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, 12 Okazaki, Aichi 444-8787, Japan
Koichi Kato Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, 12 Okazaki, Aichi 444-8787, Japan
Kiattawee Choowongkomon Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
Supa Hannongbua Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand and Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10990, Thailand and Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Bangkok 10900, Thailand

Keywords:

aptamer, HIV-1 RT, human immunodeficiency virus 1, K103N/Y181C, NNRTI, RT1t49, reverse transcriptase

Abstract

HIV is the causative agent of AIDS. UNAIDS reported in 2020 that 1.7 million people were newly infected with HIV, 38 million people were living with HIV and 690,000 people died of AIDS-related illnesses. The HIV genome includes essential proteins especially reverse transcriptase (RT) that enables synthesis of the viral DNA, and its integration into the host genome. The RT1t49 is a DNA aptamer that can inhibit RT. This study aimed to clarify the activity of RT1t49 on wild-type (WT) and K103N/Y181C double mutant (KY) HIV-1 RTs function and characterize HIV-1 RTs-RT1t49 aptamer complex. The biophysical characterizations of complexes of RT1t49 with both WT and KY HIV-1 RTs were done by surface plasmon resonance (SPR), isothermal calorimetry (ITC), and nuclear magnetic resonance (NMR). The RT1t49 aptamer showed IC₅₀ values of 3.39±0.60 and 4.82±0.45 nM on the WT and KY HIV-1 RTs, respectively. This RT1t49 aptamer bound to the WT and KY HIV-1 RTs with K_D values of 52.8±0.22 and 65.8±0.52 nM, respectively, as determined by SPR. Furthermore, the thermodynamic properties of the complexes were analyzed by ITC. The results showed a slightly different enthalpy change on the complex of HIV-1 RTs-RT1t49. Additionally, the spectral changes of the RT1t49-HIV-1 RTs were studied by NMR. The results showed the RT1t49 effect on M16, M184, M230, and M357 residues at the NNRTI drug binding site. All of the results displayed the RT1t49 bound to HIV-1 RTs at the NNRTI drug binding site which resulted in suppression of the DNA polymerase function.

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