References

Click Chemistry

Sørensen, R. S., Okholm, A. H., Schaffert, D., Kodal, A. L. B., Gothelf, K. V., & Kjems, J. (2013). Enzymatic ligation of large biomolecules to DNA. Acs Nano, 7(9), 8098-8104.

Aptamers, Binding Strength

Teng, I. T., Li, X., Yadikar, H. A., Yang, Z., Li, L., Lyu, Y., ... & Tan, W. (2018). Identification and characterization of DNA aptamers specific for phosphorylation epitopes of tau protein. Journal of the American Chemical Society, 140(43), 14314- 14323. Aptamer Sequences
Lakhin, A. V., Tarantul, V. Z., & Gening, L. (2013). Aptamers: problems, solutions and prospects. Acta Naturae (англоязычная версия), 5(4 (19)), 34-43.
Slavkovic, S., & Johnson, P. E. (2023). Analysis of Aptamer-Small Molecule Binding Interactions Using Isothermal Titration Calorimetry. Methods in molecular biology (Clifton, N.J.), 2570, 105–118.

SELEX and EP-PCR

Zaccolo, M., Williams, D. M., Brown, D. M., & Gherardi, E. (1996). An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. Journal of molecular biology, 255(4), 589–603.
Lee, S. O., & Fried, S. D. (2021). An error prone PCR method for small amplicons. Analytical Biochemistry, 628, 114266.
Sefah, K., Shangguan, D., Xiong, X., O'donoghue, M. B., & Tan, W. (2010). Development of DNA aptamers using Cell-SELEX. Nature protocols, 5(6), 1169- 1185.
Wilson, D. S., & Keefe, A. D. (2000). Random mutagenesis by PCR. Current protocols in molecular biology, 51(1), 8-3.
Keefe, A. D., & Cload, S. T. (2008). SELEX with modified nucleotides. Current opinion in chemical biology, 12(4), 448-456.

Alzheimer’s Disease and Tau

Jarek DJ, Mizerka H, Nuszkiewicz J, Szewczyk-Golec K. Evaluating p-tau217 and p- tau231 as Biomarkers for Early Diagnosis and Differentiation of Alzheimer's Disease: A Narrative Review. Biomedicines. 2024; 12(4):786.
Sui, D., Liu, M., & Kuo, M. H. (2015). In vitro aggregation assays using hyperphosphorylated tau protein. Journal of visualized experiments: JoVE, (95).
Szabo, L., Eckert, A., & Grimm, A. (2020). Insights into disease-associated tau impact on mitochondria. International journal of molecular sciences, 21(17), 6344.
Karikari, T. K., Ashton, N. J., Brinkmalm, G., Brum, W. S., Benedet, A. L., Montoliu- Gaya, L., ... & Zetterberg, H. (2022). Blood phospho-tau in Alzheimer disease: analysis, interpretation, and clinical utility. Nature Reviews Neurology, 18(7), 400- 418.
Silva, M. C., Ferguson, F. M., Cai, Q., Donovan, K. A., Nandi, G., Patnaik, D., ... & Haggarty, S. J. (2019). Targeted degradation of aberrant tau in frontotemporal dementia patient-derived neuronal cell models. elife, 8, e45457.
Milà-Alomà, M., Ashton, N. J., Shekari, M., Salvadó, G., Ortiz-Romero, P., Montoliu- Gaya, L., ... & Blennow, K. (2022). Plasma p-tau231 and p-tau217 as state markers of amyloid-β pathology in preclinical Alzheimer’s disease. Nature Medicine, 28(9), 1797-1801.
Erten-Lyons, D., Jacobson, A., Kramer, P., Grupe, A., & Kaye, J. (2010). The FAS gene, brain volume, and disease progression in Alzheimer's disease. Alzheimer's & Dementia, 6(2), 118-124.
Laxton, A. W., Stone, S., & Lozano, A. M. (2014). The neurosurgical treatment of Alzheimer's disease: a review. Stereotactic and functional neurosurgery, 92(5), 269- 281.
White, K. E., & Cummings, J. L. (1996). Schizophrenia and Alzheimer's disease: clinical and pathophysiologic analogies. Comprehensive psychiatry, 37(3), 188-195.

Phosphomimetics

Paleologou, K. E., Schmid, A. W., Rospigliosi, C. C., Kim, H. Y., Lamberto, G. R., Fredenburg, R. A., ... & Lashuel, H. A. (2008). Phosphorylation at Ser-129 but not the phosphomimics S129E/D inhibits the fibrillation of α-synuclein. Journal of Biological Chemistry, 283(24), 16895-16905.
Xia, Y., Prokop, S., Gorion, K. M. M., Kim, J. D., Sorrentino, Z. A., Bell, B. M., ... & Giasson, B. I. (2020). Tau Ser208 phosphorylation promotes aggregation and reveals neuropathologic diversity in Alzheimer’s disease and other tauopathies. Acta Neuropathologica Communications, 8, 1-17.
Wu, L., Gilyazova, N., Ervin, J. F., Wang, S. H. J., & Xu, B. (2022). Site-specific phospho-tau aggregation-based biomarker discovery for AD diagnosis and differentiation. ACS Chemical Neuroscience, 13(23), 3281-3290.

Proteosome, PROTAC for AD like model and Ligases

Wang, W., Zhou, Q., Jiang, T., Li, S., Ye, J., Zheng, J., Wang, X., Liu, Y., Deng, M., Ke, D., Wang, Q., Wang, Y., & Wang, J. Z. (2021). A novel small-molecule PROTAC selectively promotes tau clearance to improve cognitive functions in Alzheimer-like models. Theranostics, 11(11), 5279–5295.
Kim, J. H., Lee, J., Choi, W. H., Park, S., Park, S. H., Lee, J. H., ... & Lee, M. J. (2021). CHIP-mediated hyperubiquitylation of tau promotes its self-assembly into the insoluble tau filaments. Chemical Science, 12(15), 5599-5610.
Li, L., Jiang, Y., Wang, J. Z., Liu, R., & Wang, X. (2022). Tau ubiquitination in Alzheimer's disease. Frontiers in Neurology, 12, 786353
Lu, M., Liu, T., Jiao, Q., Ji, J., Tao, M., Liu, Y., ... & Jiang, Z. (2018). Discovery of a Keap1-dependent peptide PROTAC to knockdown Tau by ubiquitination-proteasome degradation pathway. European journal of medicinal chemistry, 146, 251-259.
An, S., & Fu, L. (2018). Small-molecule PROTACs: An emerging and promising approach for the development of targeted therapy drugs. EBioMedicine, 36, 553– 562. https://doi.org/10.1016/j.ebiom.2018.09.005
Potjewyd, F. M., & Axtman, A. D. (2021). Exploration of aberrant E3 ligases implicated in Alzheimer’s disease and development of chemical tools to modulate their function. Frontiers in Cellular Neuroscience, 15, 768655.
Wei, J., Meng, F., Park, K. S., Yim, H., Velez, J., Kumar, P., ... & Jin, J. (2021). Harnessing the E3 ligase KEAP1 for targeted protein degradation. Journal of the American Chemical Society, 143(37), 15073-15083.
Bonet-Costa, V., Pomatto, L. C. D., & Davies, K. J. (2016). The proteasome and oxidative stress in Alzheimer's disease. Antioxidants & redox signaling, 25(16), 886- 901.
Tsujimura, H., Naganuma, M., Ohoka, N., Inoue, T., Naito, M., Tsuji, G., & Demizu, Y. (2023). Development of DNA Aptamer-Based PROTACs That Degrade the Estrogen Receptor. ACS Medicinal Chemistry Letters, 14(6), 827-832.

Failure of UPR mechanism in AD like models

Ajoolabady, A., Lindholm, D., Ren, J., & Pratico, D. (2022). ER stress and UPR in Alzheimer’s disease: mechanisms, pathogenesis, treatments. Cell death & disease, 13(8), 706.

Q.D Related and Diagnostics

Yadav, R., Bhattacharyya, B., Saha, S. K., Dutta, P., Roy, P., Rajasekar, G. P., ... & Pandey, A. (2021). Electronic Structure Insights into the Tunable Luminescence of CuAl x Fe1–x S2/ZnS Nanocrystals. The Journal of Physical Chemistry C, 125(4), 2511-2518.
Sakudo, A. (2016). Near-infrared spectroscopy for medical applications: Current status and future perspectives. Clinica Chimica Acta, 455, 181-188.
Therriault, J., Pascoal, T. A., Lussier, F. Z., Tissot, C., Chamoun, M., Bezgin, G., ... & Rosa-Neto, P. (2022). Biomarker modeling of Alzheimer’s disease using PET-based Braak staging. Nature aging, 2(6), 526-535.
Brum, W. S., Cullen, N. C., Therriault, J., Janelidze, S., Rahmouni, N., Stevenson, J., ... & Hansson, O. (2024). A blood-based biomarker workflow for optimal tau-PET referral in memory clinic settings. Nature Communications, 15(1), 2311.

Delivery

Salmaso, S., & Caliceti, P. (2013). Stealth properties to improve therapeutic efficacy of drug nanocarriers. Journal of drug delivery, 2013(1), 374252.

Other General References

Govindaraju, T. (Ed.). (2022). Alzheimer's Disease. Royal Society of Chemistry.

Compiled by P.K. Harrishnarayanan