Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery

K Sato, M Hamada - Briefings in Bioinformatics, 2023 - academic.oup.com
Computational analysis of RNA sequences constitutes a crucial step in the field of RNA
biology. As in other domains of the life sciences, the incorporation of artificial intelligence …

Fragment-based approaches to identify RNA binders

BM Suresh, A Taghavi, JL Childs-Disney… - Journal of medicinal …, 2023 - ACS Publications
Although fragment-based drug discovery (FBDD) has been successfully implemented and
well-explored for protein targets, its feasibility for RNA targets is emerging. Despite the …

Low-molecular weight small molecules can potently bind RNA and affect oncogenic pathways in cells

BM Suresh, Y Akahori, A Taghavi… - Journal of the …, 2022 - ACS Publications
RNA is challenging to target with bioactive small molecules, particularly those of low
molecular weight that bind with sufficient affinity and specificity. In this report, we developed …

Fragment‐based drug discovery for RNA targets

KP Lundquist, V Panchal, CH Gotfredsen… - …, 2021 - Wiley Online Library
Rapid development within the fields of both fragment‐based drug discovery (FBDD) and
medicinal targeting of RNA provides possibilities for combining technologies and methods in …

Machine learning approaches to optimize small-molecule inhibitors for RNA targeting

H Grimberg, VS Tiwari, B Tam, L Gur-Arie… - Journal of …, 2022 - Springer
In the era of data science, data-driven algorithms have emerged as powerful platforms that
can consolidate bioisosteric rules for preferential modifications on small molecules with a …

Ribosome‐targeting antibacterial agents: Advances, challenges, and opportunities

L Zhang, J He, L Bai, S Ruan, T Yang… - Medicinal Research …, 2021 - Wiley Online Library
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of
bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria …

Fragment-sized thiazoles in fragment-based drug discovery campaigns: friend or foe?

M Proj, M Hrast, D Knez, K Bozovičar… - ACS medicinal …, 2022 - ACS Publications
Thiazoles exhibit a wide range of biological activities and therefore represent useful and
attractive building blocks. To evaluate their usefulness and pinpoint their liabilities in …

[HTML][HTML] Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis

ADH Kingdon, LJ Alderwick - Computational and Structural Biotechnology …, 2021 - Elsevier
Mycobacterium tuberculosis is the causative agent of TB and was estimated to cause 1.4
million death in 2019, alongside 10 million new infections. Drug resistance is a growing …

Structure-Informed Design of an Ultra Bright RNA-activated Fluorophore

JS Schneekloth Jr, M Yang, P Prestwood… - Research …, 2024 - pmc.ncbi.nlm.nih.gov
Fluorogenic RNAs such as the Mango aptamers are uniquely powerful tools for imaging
RNA. A central challenge has been to develop brighter, more specific, and higher affinity …

Fluorescent indicator displacement assay for the discovery of UGGAA repeat-targeted small molecules

T Shibata, Y Matsumoto, A Iihara, K Yamada… - Chemical …, 2023 - pubs.rsc.org
We report that a selective fluorescent indicator NBD-NCD for UGGAA repeats resulted in
fluorescence quenching upon binding to RNA and recovered the fluorescence by displacing …