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Hou R, Xie C, Gui Y, Li G, Li X. Machine-Learning-Based Data Analysis Method for Cell-Based Selection of DNA-Encoded Libraries. ACS OMEGA 2023; 8:19057-19071. [PMID: 37273617 PMCID: PMC10233830 DOI: 10.1021/acsomega.3c02152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is a powerful ligand discovery technology that has been widely adopted in the pharmaceutical industry. DEL selections are typically performed with a purified protein target immobilized on a matrix or in solution phase. Recently, DELs have also been used to interrogate the targets in the complex biological environment, such as membrane proteins on live cells. However, due to the complex landscape of the cell surface, the selection inevitably involves significant nonspecific interactions, and the selection data are much noisier than the ones with purified proteins, making reliable hit identification highly challenging. Researchers have developed several approaches to denoise DEL datasets, but it remains unclear whether they are suitable for cell-based DEL selections. Here, we report the proof-of-principle of a new machine-learning (ML)-based approach to process cell-based DEL selection datasets by using a Maximum A Posteriori (MAP) estimation loss function, a probabilistic framework that can account for and quantify uncertainties of noisy data. We applied the approach to a DEL selection dataset, where a library of 7,721,415 compounds was selected against a purified carbonic anhydrase 2 (CA-2) and a cell line expressing the membrane protein carbonic anhydrase 12 (CA-12). The extended-connectivity fingerprint (ECFP)-based regression model using the MAP loss function was able to identify true binders and also reliable structure-activity relationship (SAR) from the noisy cell-based selection datasets. In addition, the regularized enrichment metric (known as MAP enrichment) could also be calculated directly without involving the specific machine-learning model, effectively suppressing low-confidence outliers and enhancing the signal-to-noise ratio. Future applications of this method will focus on de novo ligand discovery from cell-based DEL selections.
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Affiliation(s)
- Rui Hou
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology LimitedHealth@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Chao Xie
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhan Gui
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Gang Li
- Institute
of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaoyu Li
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology LimitedHealth@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
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2
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Gui Y, Wong CS, Zhao G, Xie C, Hou R, Li Y, Li G, Li X. Converting Double-Stranded DNA-Encoded Libraries (DELs) to Single-Stranded Libraries for More Versatile Selections. ACS OMEGA 2022; 7:11491-11500. [PMID: 35415338 PMCID: PMC8992267 DOI: 10.1021/acsomega.2c01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is an efficient high-throughput screening technology platform in drug discovery and is also gaining momentum in academic research. Today, the majority of DELs are assembled and encoded with double-stranded DNA tags (dsDELs) and has been selected against numerous biological targets; however, dsDELs are not amendable to some of the recently developed selection methods, such as the cross-linking-based selection against immobilized targets and live-cell-based selections, which require DELs encoded with single-stranded DNAs (ssDELs). Herein, we present a simple method to convert dsDELs to ssDELs using exonuclease digestion without library redesign and resynthesis. We show that dsDELs could be efficiently converted to ssDELs and used for affinity-based selections either with purified proteins or on live cells.
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Affiliation(s)
- Yuhan Gui
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Clara Shania Wong
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Chao Xie
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Rui Hou
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK,
Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology
Parks, New Territories, Hong Kong SAR , China
| | - Yizhou Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Gang Li
- Institute
of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Xiaoyu Li
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK,
Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology
Parks, New Territories, Hong Kong SAR , China
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3
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Keijzer JF, Firet J, Albada B. Site-selective and inducible acylation of thrombin using aptamer-catalyst conjugates. Chem Commun (Camb) 2021; 57:12960-12963. [PMID: 34792071 DOI: 10.1039/d1cc05446e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two acyl-transfer catalysts were conjugated to thrombin-binding DNA aptamers to acylate thrombin. Modification occurred site-selectively on Lys (≫Ser) residues proximal to the respective aptamer-thrombin interface, was selective for thrombin in the presence of other proteins, and the activity of both DNA-catalysts could be controlled by an external trigger.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE, Wageningen, The Netherlands.
| | - Judith Firet
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE, Wageningen, The Netherlands.
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE, Wageningen, The Netherlands.
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Yan Y, Zhang Y, Xia S, Wan S, Vohs T, Tanasova M, Luck RL, Liu H. Ratiometric Near-Infrared Fluorescent Probes Based on Hemicyanine Dyes Bearing Dithioacetal and Formal Residues for pH Detection in Mitochondria. Molecules 2021; 26:molecules26072088. [PMID: 33917350 PMCID: PMC8038704 DOI: 10.3390/molecules26072088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/02/2022] Open
Abstract
Ratiometric near-infrared fluorescent probes (AH+ and BH+) have been prepared for pH determination in mitochondria by attaching dithioacetal and formal residues onto a hemicyanine dye. The reactive formyl group on probe BH+ allows for retention inside mitochondria as it can react with a protein primary amine residue to form an imine under slightly basic pH 8.0. Probes AH+ and BH+ display ratiometric fluorescent responses to pH changes through the protonation and deprotonaton of a hydroxy group in hemicyanine dyes with experimentally determined pKa values of 6.85 and 6.49, respectively. Calculated pKa values from a variety of theoretical methods indicated that the SMDBONDI method of accounting for solvent and van der Waals radii plus including a water molecule located near the site of protonation produced the closest overall agreement with the experimental values at 7.33 and 6.14 for AH+ and BH+ respectively.
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Affiliation(s)
- Yunnan Yan
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Yibin Zhang
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- Correspondence: (Y.Z.); (R.L.L.); (H.L.)
| | - Shuai Xia
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Shulin Wan
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Tara Vohs
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Marina Tanasova
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Rudy L. Luck
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- Correspondence: (Y.Z.); (R.L.L.); (H.L.)
| | - Haiying Liu
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- Correspondence: (Y.Z.); (R.L.L.); (H.L.)
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Huang Y, Deng Y, Zhang J, Meng L, Li X. Direct ligand screening against membrane proteins on live cells enabled by DNA-programmed affinity labelling. Chem Commun (Camb) 2021; 57:3769-3772. [DOI: 10.1039/d1cc00961c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA-programmed affinity labelling (DPAL) enables the screening of chemical compounds against membrane proteins directly on live cells.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Yuqing Deng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Jianfu Zhang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Ling Meng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
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