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Rodríguez Serrano AF, Hsing IM. Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:4799-4809. [PMID: 36134737 DOI: 10.1021/acs.jcim.2c00734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding aptamer-ligand interactions is necessary to rationally design aptamer-based systems. Commonly used in silico tools have proven to be accurate to predict RNA and DNA oligonucleotide tertiary structures. However, given the complexity of nucleic acids, the most thermodynamically stable conformation is not necessarily the one with the highest affinity for a specific ligand. Because many metastable states may coexist, it remains challenging to predict binding sites through molecular docking simulations using available computational pipelines. In this study, we used independent simulations to broaden the conformational diversity sampled from DNA initial models of distinct stability and assessed the binding affinity of selected metastable representative structures. In our results, utilizing multiple metastable conformations for molecular docking analysis helped identify structures favorable for ligand binding and accurately predict the binding sites. Our workflow was able to correctly identify the binding sites of the characterized adenosine monophosphate and l-argininamide aptamers. Additionally, we demonstrated that our pipeline can be used to aid the design of competition assays that are conducive to aptasensing strategies using an uncharacterized aflatoxin B1 aptamer. We foresee that this approach may help rationally design effective and truncated aptamer sequences interacting with protein biomarkers or small molecules of interest for drug design and sensor applications.
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Affiliation(s)
- Alan Fernando Rodríguez Serrano
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
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Ly LC, Yang Y, Li F, Crossley M, Shi Y, Quinlan KGR. Protocols for protein-DNA binding analysis of a zinc finger transcription factor bound to its cognate promoter. STAR Protoc 2022; 3:101598. [PMID: 35928006 PMCID: PMC9344028 DOI: 10.1016/j.xpro.2022.101598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lana C Ly
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Yang Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yunyu Shi
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China.
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Evolution of biophysical tools for quantitative protein interactions and drug discovery. Emerg Top Life Sci 2021; 5:1-12. [PMID: 33739398 DOI: 10.1042/etls20200258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
With millions of signalling events occurring simultaneously, cells process a continuous flux of information. The genesis, processing, and regulation of information are dictated by a huge network of protein interactions. This is proven by the fact that alterations in the levels of proteins, single amino acid changes, post-translational modifications, protein products arising out of gene fusions alter the interaction landscape leading to diseases such as congenital disorders, deleterious syndromes like cancer, and crippling diseases like the neurodegenerative disorders which are often fatal. Needless to say, there is an immense effort to understand the biophysical basis of such direct interactions between any two proteins, the structure, domains, and sequence motifs involved in tethering them, their spatio-temporal regulation in cells, the structure of the network, and their eventual manipulation for intervention in diseases. In this chapter, we will deliberate on a few techniques that allow us to dissect the thermodynamic and kinetic aspects of protein interaction, how innovation has rendered some of the traditional techniques applicable for rapid analysis of multiple samples using small amounts of material. These advances coupled with automation are catching up with the genome-wide or proteome-wide studies aimed at identifying new therapeutic targets. The chapter will also summarize how some of these techniques are suited either in the standalone mode or in combination with other biophysical techniques for the drug discovery process.
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Ratanabunyong S, Aeksiri N, Yanaka S, Yagi-Utsumi M, Kato K, Choowongkomon K, Hannongbua S. Characterization of New DNA Aptamers for Anti-HIV-1 Reverse Transcriptase. Chembiochem 2020; 22:915-923. [PMID: 33095511 DOI: 10.1002/cbic.202000633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/22/2020] [Indexed: 11/09/2022]
Abstract
HIV-1 RT is a necessary enzyme for retroviral replication, which is the main target for antiviral therapy against AIDS. Effective anti-HIV-1 RT drugs are divided into two groups; nucleoside inhibitors (NRTI) and non-nucleoside inhibitors (NNRTI), which inhibit DNA polymerase. In this study, new DNA aptamers were isolated as anti-HIV-1 RT inhibitors. The selected DNA aptamer (WT62) presented with high affinity and inhibition against wild-type (WT) HIV-1 RT and gave a KD value of 75.10±0.29 nM and an IC50 value of 84.81±8.54 nM. Moreover, WT62 decreased the DNA polymerase function of K103 N/Y181 C double mutant (KY) HIV-1 RT by around 80 %. Furthermore, the ITC results showed that this aptamer has small binding enthalpies with both WT and KY HIV-1 RTs through which the complex might form a hydrophobic interaction or noncovalent bonding. The NMR result also suggested that the WT62 aptamer could bind with both WT and KY mutant HIV-1 RTs at the connection domain.
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Affiliation(s)
- Siriluk Ratanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Niran Aeksiri
- Department of Agricultural Sciences, Naresuan University, Phitsanlolok, 65000, Thailand
| | - 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
| | - 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
| | - 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
- Department of Chemistry, Faculty of Science, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand.,Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Bangkok, 10900, Thailand
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