1
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Fitzgerald PR, Dixit A, Zhang C, Mobley DL, Paegel BM. Building Block-Centric Approach to DNA-Encoded Library Design. J Chem Inf Model 2024; 64:4661-4672. [PMID: 38860710 DOI: 10.1021/acs.jcim.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.
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Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Anjali Dixit
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Chris Zhang
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Brian M Paegel
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
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2
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Keller M, Petrov D, Gloger A, Dietschi B, Jobin K, Gradinger T, Martinelli A, Plais L, Onda Y, Neri D, Scheuermann J. Highly pure DNA-encoded chemical libraries by dual-linker solid-phase synthesis. Science 2024; 384:1259-1265. [PMID: 38870307 DOI: 10.1126/science.adn3412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
The first drugs discovered using DNA-encoded chemical library (DEL) screens have entered late-stage clinical development. However, DEL technology as a whole still suffers from poor chemical purity resulting in suboptimal performance. In this work, we report a technique to overcome this issue through self-purifying release of the DEL after magnetic bead-based synthesis. Both the first and last building blocks of each assembled library member were linked to the beads by tethers that could be cleaved by mutually orthogonal chemistry. Sequential cleavage of the first and last tether, with washing in between, ensured that the final library comprises only the fully complete compounds. The outstanding purity attained by this approach enables a direct correlation of chemical display and encoding, allows for an increased chemical reaction scope, and facilitates the use of more diversity elements while achieving greatly improved signal-to-noise ratios in selections.
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Affiliation(s)
- Michelle Keller
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Dimitar Petrov
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Gloger
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Bastien Dietschi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Kilian Jobin
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Timon Gradinger
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Louise Plais
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Yuichi Onda
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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3
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Douchez A, Poupart J, Yang G, Vaillancourt L, Marinier A. Squaramide Formation for DNA-Encoded Library Synthesis. Bioconjug Chem 2024. [PMID: 38874002 DOI: 10.1021/acs.bioconjchem.4c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
DNA-encoded libraries (DELs) can be considered as one of the most powerful tools for the discovery of small molecules of biological interest. However, the ability to access large DELs is contingent upon having chemical transformations that work in aqueous phase and generate minimal DNA alterations and the availability of building blocks compatible with on-DNA chemistry. In addition, accessing scaffolds of interest to medicinal chemists can be challenging in a DEL setting because of inherent limitations of DNA-supported chemistry. In this context, a squaramide formation reaction was developed by using a two-step process. The mild and high-yielding reaction tolerates a wide array of functional groups and was shown to be safe for DNA, thereby making this methodology ideal for DELs.
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Affiliation(s)
- Antoine Douchez
- Drug Discovery Unit, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Julien Poupart
- Drug Discovery Unit, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Gaoqiang Yang
- Drug Discovery Unit, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Louis Vaillancourt
- Drug Discovery Unit, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Anne Marinier
- Drug Discovery Unit, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
- Département de chimie, Faculté des Arts et Sciences, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
- Département de pharmacologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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4
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Liang J, Lambrecht MJ, Arenzana TL, Aubert-Nicol S, Bao L, Broccatelli F, Cai J, Eidenschenk C, Everett C, Garner T, Gruber F, Haghshenas P, Huestis MP, Hsu PL, Kou P, Jakalian A, Larouche-Gauthier R, Leclerc JP, Leung DH, Martin A, Murray J, Prangley M, Rutz S, Kakiuchi-Kiyota S, Satz AL, Skelton NJ, Steffek M, Stoffler D, Sudhamsu J, Tan S, Wang J, Wang S, Wang Q, Wendorff TJ, Wichert M, Yadav A, Yu C, Wang X. Optimization of a Novel DEL Hit That Binds in the Cbl-b SH2 Domain and Blocks Substrate Binding. ACS Med Chem Lett 2024; 15:864-872. [PMID: 38894924 PMCID: PMC11181488 DOI: 10.1021/acsmedchemlett.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
We were attracted to the therapeutic potential of inhibiting Casitas B-lineage lymphoma proto-oncogene-b (Cbl-b), a RING E3 ligase that plays a critical role in regulating the activation of T cells. However, given that only protein-protein interactions were involved, it was unclear whether inhibition by a small molecule would be a viable approach. After screening an ∼6 billion member DNA-encoded library (DEL) using activated Cbl-b, we identified compound 1 as a hit for which the cis-isomer (2) was confirmed by biochemical and surface plasmon resonance (SPR) assays. Our hit optimization effort was greatly accelerated when we obtained a cocrystal structure of 2 with Cbl-b, which demonstrated induced binding at the substrate binding site, namely, the Src homology-2 (SH2) domain. This was quite noteworthy given that there are few reports of small molecule inhibitors that bind to SH2 domains and block protein-protein interactions. Structure- and property-guided optimization led to compound 27, which demonstrated measurable cell activity, albeit only at high concentrations.
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Affiliation(s)
- Jun Liang
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael J. Lambrecht
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Teresita L. Arenzana
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Linda Bao
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Fabio Broccatelli
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianping Cai
- Roche
Pharma Research and Early Development (pRED), Roche Innovation Center
Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Celine Eidenschenk
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christine Everett
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Thomas Garner
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Felix Gruber
- Roche
Pharma Research and Early Development (pRED), Roche Innovation Center
Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Pouyan Haghshenas
- Paraza
Pharma, 2525 Avenue Marie-Curie, Montreal, Quebec H4S 2E1, Canada
| | - Malcolm P. Huestis
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter L. Hsu
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ponien Kou
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Araz Jakalian
- Paraza
Pharma, 2525 Avenue Marie-Curie, Montreal, Quebec H4S 2E1, Canada
| | | | | | - Dennis H. Leung
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Aaron Martin
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeremy Murray
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Madeleine Prangley
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sascha Rutz
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Alexander Lee Satz
- Roche
Pharma Research and Early Development (pRED), Roche Innovation Center
Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Nicholas J. Skelton
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Micah Steffek
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Stoffler
- Roche
Pharma Research and Early Development (pRED), Roche Innovation Center
Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jawahar Sudhamsu
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sophia Tan
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Wang
- WuXi
AppTec Co., Ltd. 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, P. R. China
| | - Shouliang Wang
- WuXi
AppTec Co., Ltd. 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, P. R. China
| | - Qiuyue Wang
- WuXi
AppTec Co., Ltd. 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, P. R. China
| | - Timothy J. Wendorff
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Moreno Wichert
- Roche
Pharma Research and Early Development (pRED), Roche Innovation Center
Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Arun Yadav
- Paraza
Pharma, 2525 Avenue Marie-Curie, Montreal, Quebec H4S 2E1, Canada
| | - Christine Yu
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xiaojing Wang
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
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5
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Krieger IV, Yalamanchili S, Dickson P, Engelhart CA, Zimmerman MD, Wood J, Clary E, Nguyen J, Thornton N, Centrella PA, Chan B, Cuozzo JW, Gengenbacher M, Guié MA, Guilinger JP, Bienstock C, Hartl H, Hupp CD, Jetson R, Satoh T, Yeoman JTS, Zhang Y, Dartois V, Schnappinger D, Keefe AD, Sacchettini JC. Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. ACS Infect Dis 2024; 10:1561-1575. [PMID: 38577994 PMCID: PMC11091879 DOI: 10.1021/acsinfecdis.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.
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Affiliation(s)
- Inna V. Krieger
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | | | - Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Matthew D Zimmerman
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Jeremy Wood
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Ethan Clary
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Jasmine Nguyen
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Natalie Thornton
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Paolo A. Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Auron
Therapeutics, 55 Chapel
Street, Newton, Massachusetts 02458, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Relay
Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Martin Gengenbacher
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Corey Bienstock
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Hajnalka Hartl
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Orogen
Therapeutics, 12 Gill
Street, Woburn, Massachusetts 01801, United States
| | - Christopher D. Hupp
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Ipsen Bioscience
Inc., 1 Main Street, Cambridge, Massachusetts 02142, United States
| | - Rachael Jetson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Valo
Health, 75 Hayden Avenue, Lexington, Massachusetts 02141, United States
| | - Takashi Satoh
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- EXO
Therapeutics, 150 Cambridgepark
Drive, suite 300, Cambridge, Massachusetts 02140, United States
| | - John T. S. Yeoman
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Recludix
Pharmaceuticals, 222
Third Street, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Veronique Dartois
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
- Hackensack
Meridian School of Medicine, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Anthony D. Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - James C. Sacchettini
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
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6
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Neri D. Designing drugs with reversible activity. Nat Biotechnol 2024:10.1038/s41587-024-02242-y. [PMID: 38689026 DOI: 10.1038/s41587-024-02242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Affiliation(s)
- Dario Neri
- Philogen SpA, Siena, Italy.
- ETH Zürich, Zurich, Switzerland.
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7
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Shields JD, Howells R, Lamont G, Leilei Y, Madin A, Reimann CE, Rezaei H, Reuillon T, Smith B, Thomson C, Zheng Y, Ziegler RE. AiZynth impact on medicinal chemistry practice at AstraZeneca. RSC Med Chem 2024; 15:1085-1095. [PMID: 38665822 PMCID: PMC11042116 DOI: 10.1039/d3md00651d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/15/2024] [Indexed: 04/28/2024] Open
Abstract
AstraZeneca chemists have been using the AI retrosynthesis tool AiZynth for three years. In this article, we present seven examples of how medicinal chemists using AiZynth positively impacted their drug discovery programmes. These programmes run the gamut from early-stage hit confirmation to late-stage route optimisation efforts. We also discuss the different use cases for which AI retrosynthesis tools are best suited.
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Affiliation(s)
- Jason D Shields
- Early Oncology R&D, AstraZeneca 35 Gatehouse Drive Waltham MA 02451 USA
| | - Rachel Howells
- Early Oncology R&D, AstraZeneca 1 Francis Crick Avenue Cambridge CB2 0AA UK
| | - Gillian Lamont
- Early Oncology R&D, AstraZeneca 1 Francis Crick Avenue Cambridge CB2 0AA UK
| | - Yin Leilei
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA Beijing 100176 P.R. China
| | - Andrew Madin
- Discovery Sciences, AstraZeneca 1 Francis Crick Avenue Cambridge CB2 0AA UK
| | | | - Hadi Rezaei
- Early Oncology R&D, AstraZeneca 35 Gatehouse Drive Waltham MA 02451 USA
| | - Tristan Reuillon
- Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Mölndal Sweden
| | - Bryony Smith
- Early Oncology R&D, AstraZeneca 1 Francis Crick Avenue Cambridge CB2 0AA UK
| | - Clare Thomson
- Early Oncology R&D, AstraZeneca 1 Francis Crick Avenue Cambridge CB2 0AA UK
| | - Yuting Zheng
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA Beijing 100176 P.R. China
| | - Robert E Ziegler
- Early Oncology R&D, AstraZeneca 35 Gatehouse Drive Waltham MA 02451 USA
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8
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Dickson P. DNA-Encoded Library Technology─A Catalyst for Covalent Ligand Discovery. ACS Chem Biol 2024; 19:802-808. [PMID: 38527941 DOI: 10.1021/acschembio.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The identification of novel covalent ligands for therapeutic purposes has long depended on serendipity, with dedicated hit finding techniques emerging only in the early 2000s. Advances in chemoproteomics have enabled robust characterization of putative drugs to derisk the unique liabilities associated with covalent hit molecules, leading to a renewed interest in this targeting modality. DNA-encoded library (DEL) technology has similarly emerged over the past two decades as a highly efficient method to identify new chemical equity toward protein targets of interest. A number of commercial and academic groups have reported methods in covalent DEL synthesis and hit identification; however, it is evident that there is still much to be done to fully realize the power of this technology for covalent ligand discovery. This perspective will explore the current approaches in covalent DEL technology and reflect on the next steps to advance this field.
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Affiliation(s)
- Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
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9
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Wang X, Zhu Y, Zhao Q, Lu W, Xu Y, Hu H, Lu X. Chemical Space Profiling of SARS-CoV-2 PL pro Using DNA-Encoded Focused Libraries. ACS Med Chem Lett 2024; 15:555-564. [PMID: 38628804 PMCID: PMC11017295 DOI: 10.1021/acsmedchemlett.4c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-encoded library (DEL) technology is gaining attention for its rapid construction and deconvolution capabilities. Our study explored a novel strategy using rational DELs tailored for the SARS-CoV-2 papain-like protease, which revealed new fragments. Structural changes post-DEL screening mimic traditional medicinal chemistry lead optimization. We unveiled unique aromatic structures offering an alternative optimization path. Notably, we identified superior binding fragments targeting the BL2 groove. Derivative 16 emerged as the most promising by exhibiting IC50 values of 0.25 μM. Derivative 6, which features an aromatic fragment capped with a naphthalene moiety, showed IC50 values of 2.91 μM. Molecular modeling revealed hydrogen bond interactions with Lys157 residue and potential covalent interactions with nearby amino acid residues. This research underscored DEL's potential for fragment-based drug discovery against SARS-CoV-2 protease.
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Affiliation(s)
- Xudong Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ying Zhu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Qingyi Zhao
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Weiwei Lu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Yechun Xu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Hangchen Hu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced
Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Xiaojie Lu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
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10
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Anderson MJ, Carton TP, Salvini CLA, Crawford JJ, Pairaudeau G, Waring MJ. Micelle-Promoted Reductive Amination of DNA-Conjugated Amines for DNA-Encoded Library Synthesis. Chemistry 2024; 30:e202400239. [PMID: 38251309 DOI: 10.1002/chem.202400239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/23/2024]
Abstract
DNA-encoded libraries (DELs) have become a leading technology for hit identification in drug discovery projects as large, diverse libraries can be generated. DELs are commonly synthesised via split-and-pool methodology; thus, chemical transformations utilised must be highly efficient, proceeding with high conversions. Reactions performed in DEL synthesis also require a broad substrate scope to produce diverse, drug-like libraries. Many pharmaceutical compounds incorporate multiple C-N bonds, over a quarter of which are synthesised via reductive aminations. However, few on-DNA reductive amination procedures have been developed. Herein is reported the application of the micelle-forming surfactant, TPGS-750-M, to the on-DNA reductive amination of DNA-conjugated amines, yielding highly efficient conversions with a broad range of aldehydes, including medicinally relevant heterocyclic and aliphatic substrates. The procedure is compatible with DNA amplification and sequencing, demonstrating its applicability to DEL synthesis.
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Affiliation(s)
- Matthew J Anderson
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Thomas P Carton
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | | | | | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
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11
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Matsukiyo Y, Yamanaka C, Yamanishi Y. De Novo Generation of Chemical Structures of Inhibitor and Activator Candidates for Therapeutic Target Proteins by a Transformer-Based Variational Autoencoder and Bayesian Optimization. J Chem Inf Model 2024; 64:2345-2355. [PMID: 37768595 DOI: 10.1021/acs.jcim.3c00824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Deep generative models for molecular generation have been gaining much attention as structure generators to accelerate drug discovery. However, most previously developed methods are chemistry-centric approaches, and comprehensive biological responses in the cell have not been taken into account. In this study, we propose a novel computational method, TRIOMPHE-BOA (transcriptome-based inference and generation of molecules with desired phenotypes using the Bayesian optimization algorithm), to generate new chemical structures of inhibitor or activator candidates for therapeutic target proteins by integrating chemically and genetically perturbed transcriptome profiles. In the algorithm, the substructures of multiple molecules that were selected based on the transcriptome analysis are fused in the design of new chemical structures by exploring the latent space of a Transformer-based variational autoencoder using Bayesian optimization. Our results demonstrate the usefulness of the proposed method in terms of having high reproducibility of existing ligands for 10 therapeutic target proteins when compared with previous methods. Moreover, this method can be applied to proteins without detailed 3D structures or known ligands and is expected to become a powerful tool for more efficient hit identification.
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Affiliation(s)
- Yuki Matsukiyo
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Chikashige Yamanaka
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
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12
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Siripuram V, Sunkari YK, Ma F, Nguyen TL, Flajolet M. Reversible and Fully Controllable Generation of Organo-Soluble DNA (osDNA). ACS OMEGA 2024; 9:14771-14780. [PMID: 38585059 PMCID: PMC10993399 DOI: 10.1021/acsomega.3c06755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 04/09/2024]
Abstract
The present work describes a complete and reversible transformation of DNA's properties allowing solubilization in organic solvents and subsequent chemical modifications that are otherwise not possible in an aqueous medium. Organo-soluble DNA (osDNA) moieties are generated by covalently linking a dsDNA fragment to a polyether moiety with a built-in mechanism, rendering the process perfectly reversible and fully controllable. The precise removal of the polyether moiety frees up the initial DNA fragment, unaltered, both in sequence and nature. The solubility of osDNA was confirmed in six organic solvents of decreasing polarity and six types of osDNAs. As a proof of concept, in the context of DNA-encoded library (DEL) technology, an amidation reaction was successfully performed on osDNA in 100% DMSO. The development of osDNA opens up entirely new avenues for any DNA applications that could benefit from working in nonaqueous solutions, including chemical transformations.
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Affiliation(s)
- Vijay
Kumar Siripuram
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Yashoda Krishna Sunkari
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Fei Ma
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Thu-Lan Nguyen
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Marc Flajolet
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
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13
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Zhou Y, Shen W, Gao Y, Peng J, Li Q, Wei X, Liu S, Lam FS, Mayol-Llinàs J, Zhao G, Li G, Li Y, Sun H, Cao Y, Li X. Protein-templated ligand discovery via the selection of DNA-encoded dynamic libraries. Nat Chem 2024; 16:543-555. [PMID: 38326646 DOI: 10.1038/s41557-024-01442-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.
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Grants
- AoE/P-705/16, 17301118, 17111319, 17303220, 17300321, 17318322, C7005-20G, C7016-22G, and 2122-7S04 Research Grants Council, University Grants Committee (RGC, UGC)
- 21877093, 22222702, and 91953119 National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)
- Health@InnoHK Innovation and Technology Commission (ITF)
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Affiliation(s)
- Yu Zhou
- 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 Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Gao
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qingrong Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xueying Wei
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shihao Liu
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Joan Mayol-Llinàs
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, 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, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 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, China
| | - Hongzhe Sun
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China.
| | - Yan Cao
- School of Pharmacy, Naval Medical University, Shanghai, 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 Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
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14
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Willems S, Detta E, Baldini L, Tietz D, Trabocchi A, Brunschweiger A. Diversifying DNA-Tagged Amines by Isocyanide Multicomponent Reactions for DNA-Encoded Library Synthesis. ACS OMEGA 2024; 9:7719-7724. [PMID: 38405463 PMCID: PMC10882610 DOI: 10.1021/acsomega.3c07136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 02/27/2024]
Abstract
In DNA-encoded library synthesis, amine-substituted building blocks are prevalent. We explored isocyanide multicomponent reactions to diversify DNA-tagged amines and reported the Ugi-azide reaction with high yields and a good substrate scope. In addition, the Ugi-aza-Wittig reaction and the Ugi-4-center-3-component reaction, which used bifunctional carboxylic acids to provide lactams, were explored. Five-, six-, and seven-membered lactams were synthesized from solid support-coupled DNA-tagged amines and bifunctional building blocks, providing access to structurally diverse scaffolds.
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Affiliation(s)
- Suzanne Willems
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Elena Detta
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Lorenzo Baldini
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Deniz Tietz
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Andrea Trabocchi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Andreas Brunschweiger
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
- Institute
of Pharmacy and Food Chemistry, Julius Maximilian
University Würzburg, Am Hubland, 97074 Würzburg, Germany
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15
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Ma P, Zhang S, Huang Q, Gu Y, Zhou Z, Hou W, Yi W, Xu H. Evolution of chemistry and selection technology for DNA-encoded library. Acta Pharm Sin B 2024; 14:492-516. [PMID: 38322331 PMCID: PMC10840438 DOI: 10.1016/j.apsb.2023.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 02/08/2024] Open
Abstract
DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.
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Affiliation(s)
- Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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16
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Rama-Garda R, Martin-Ortega MD, Sánchez ADJ, Priego J, de Blas J, Torrado A, Domínguez E, Haro R, Rivera-Sagredo A, Román JP, Lorite MJ, Johansson HE, Loza MI, Amigo J, Sobrino B, Lallena MJ, Toledo MÁ. Design, synthesis and validation of a new Crimped Head-Piece for DNA-Encoded libraries generation. Bioorg Med Chem 2024; 99:117596. [PMID: 38232459 DOI: 10.1016/j.bmc.2024.117596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Codification of DNA Encoded Libraries (DELs) is critical for successful ligand identification of molecules that bind a protein of interest (POI). There are different encoding strategies that permit, for instance, the customization of a DEL for testing single or dual pharmacophores (single strand DNA) or for producing and screening large diversity libraries of small molecules (double strand DNA). Both approaches challenges, either from the synthetic and encoding point of view, or from the selection methodology to be utilized for the screening. The Head-Piece contains the DNA sequence that is attached to a chemical compound, allowing the encoding of each molecule with a unique DNA tag. Designing the Head-Piece for a DNA-encoded library involves careful consideration of several key aspects including DNA barcode identity, sequence length and attachment chemistry. Here we describe a double stranded DNA versatile Head-Piece that can be used for the generation of single or dual pharmacophore libraries, but also shows other advanced DEL functionalities, stability and enlarged encoding capacity.
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Affiliation(s)
- Ramón Rama-Garda
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain; BioFarma, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña 15782, Spain.
| | - María Dolores Martin-Ortega
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | | | - Julián Priego
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Jesús de Blas
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Alicia Torrado
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Eduardo Domínguez
- Genomic Medicine, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña, Spain
| | - Rubén Haro
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Alfonso Rivera-Sagredo
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - José Pablo Román
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - María José Lorite
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | | | - María Isabel Loza
- BioFarma, Universidad de Santiago de Compostela (USC), Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), A Coruña 15782, Spain
| | - Jorge Amigo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Servizo Galego de Saúde (SERGAS), Instituto de Investigaciones Sanitarias (IDIS), A Coruña 15706, Spain
| | - Beatriz Sobrino
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Servizo Galego de Saúde (SERGAS), Instituto de Investigaciones Sanitarias (IDIS), A Coruña 15706, Spain
| | - María José Lallena
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
| | - Miguel Ángel Toledo
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Alcobendas, Madrid 28108, Spain
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17
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Mason JW, Chow YT, Hudson L, Tutter A, Michaud G, Westphal MV, Shu W, Ma X, Tan ZY, Coley CW, Clemons PA, Bonazzi S, Berst F, Briner K, Liu S, Zécri FJ, Schreiber SL. DNA-encoded library-enabled discovery of proximity-inducing small molecules. Nat Chem Biol 2024; 20:170-179. [PMID: 37919549 PMCID: PMC10917151 DOI: 10.1038/s41589-023-01458-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/24/2023] [Indexed: 11/04/2023]
Abstract
Small molecules that induce protein-protein associations represent powerful tools to modulate cell circuitry. We sought to develop a platform for the direct discovery of compounds able to induce association of any two preselected proteins, using the E3 ligase von Hippel-Lindau (VHL) and bromodomains as test systems. Leveraging the screening power of DNA-encoded libraries (DELs), we synthesized ~1 million DNA-encoded compounds that possess a VHL-targeting ligand, a variety of connectors and a diversity element generated by split-and-pool combinatorial chemistry. By screening our DEL against bromodomains in the presence and absence of VHL, we could identify VHL-bound molecules that simultaneously bind bromodomains. For highly barcode-enriched library members, ternary complex formation leading to bromodomain degradation was confirmed in cells. Furthermore, a ternary complex crystal structure was obtained for our most enriched library member with BRD4BD1 and a VHL complex. Our work provides a foundation for adapting DEL screening to the discovery of proximity-inducing small molecules.
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Affiliation(s)
- Jeremy W Mason
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Yuen Ting Chow
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Liam Hudson
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Antonin Tutter
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Gregory Michaud
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Wei Shu
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Xiaolei Ma
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
| | - Simone Bonazzi
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Frédéric Berst
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Karin Briner
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Frédéric J Zécri
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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18
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Collie GW, Clark MA, Keefe AD, Madin A, Read JA, Rivers EL, Zhang Y. Screening Ultra-Large Encoded Compound Libraries Leads to Novel Protein-Ligand Interactions and High Selectivity. J Med Chem 2024; 67:864-884. [PMID: 38197367 PMCID: PMC10823476 DOI: 10.1021/acs.jmedchem.3c01861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
The DNA-encoded library (DEL) discovery platform has emerged as a powerful technology for hit identification in recent years. It has become one of the major parallel workstreams for small molecule drug discovery along with other strategies such as HTS and data mining. For many researchers working in the DEL field, it has become increasingly evident that many hits and leads discovered via DEL screening bind to target proteins with unique and unprecedented binding modes. This Perspective is our attempt to analyze reports of DEL screening with the purpose of providing a rigorous and useful account of the binding modes observed for DEL-derived ligands with a focus on binding mode novelty.
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Affiliation(s)
| | | | | | | | | | | | - Ying Zhang
- X-Chem,
Inc., Waltham, Massachusetts 02453, United States
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19
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Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
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Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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20
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Fuchs N, Zhang L, Calvo-Barreiro L, Kuncewicz K, Gabr M. Inhibitors of Immune Checkpoints: Small Molecule- and Peptide-Based Approaches. J Pers Med 2024; 14:68. [PMID: 38248769 PMCID: PMC10817355 DOI: 10.3390/jpm14010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
The revolutionary progress in cancer immunotherapy, particularly the advent of immune checkpoint inhibitors, marks a significant milestone in the fight against malignancies. However, the majority of clinically employed immune checkpoint inhibitors are monoclonal antibodies (mAbs) with several limitations, such as poor oral bioavailability and immune-related adverse effects (irAEs). Another major limitation is the restriction of the efficacy of mAbs to a subset of cancer patients, which triggered extensive research efforts to identify alternative approaches in targeting immune checkpoints aiming to overcome the restricted efficacy of mAbs. This comprehensive review aims to explore the cutting-edge developments in targeting immune checkpoints, focusing on both small molecule- and peptide-based approaches. By delving into drug discovery platforms, we provide insights into the diverse strategies employed to identify and optimize small molecules and peptides as inhibitors of immune checkpoints. In addition, we discuss recent advances in nanomaterials as drug carriers, providing a basis for the development of small molecule- and peptide-based platforms for cancer immunotherapy. Ongoing research focused on the discovery of small molecules and peptide-inspired agents targeting immune checkpoints paves the way for developing orally bioavailable agents as the next-generation cancer immunotherapies.
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Affiliation(s)
- Natalie Fuchs
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Longfei Zhang
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Laura Calvo-Barreiro
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Katarzyna Kuncewicz
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
- Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Moustafa Gabr
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
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21
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Sharique M, Matsuo B, Granados A, Kim S, Arshad M, Oh H, Wu VE, Huang M, Csakai A, Marcaurelle LA, Molander GA. On-DNA hydroalkylation of N-vinyl heterocycles via photoinduced EDA-complex activation. Chem Sci 2023; 14:14193-14199. [PMID: 38098729 PMCID: PMC10717525 DOI: 10.1039/d3sc03731b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/22/2023] [Indexed: 12/17/2023] Open
Abstract
The emergence of DNA-encoded library (DEL) technology has provided a considerable advantage to the pharmaceutical industry in the pursuit of discovering novel therapeutic candidates for their drug development initiatives. This combinatorial technique not only offers a more economical, spatially efficient, and time-saving alternative to the existing ligand discovery methods, but also enables the exploration of additional chemical space by utilizing novel DNA-compatible synthetic transformations to leverage multifunctional building blocks from readily available substructures. In this report, a decarboxylative-based hydroalkylation of DNA-conjugated N-vinyl heterocycles enabled by single-electron transfer (SET) and subsequent hydrogen atom transfer through electron-donor/electron-acceptor (EDA) complex activation is detailed. The simplicity and robustness of this method permits inclusion of a broad array of alkyl radical precursors and DNA-tethered nitrogenous heterocyles to generate medicinally relevant substituted heterocycles with pendant functional groups. Moreover, a successful telescoped route provides the opportunity to access a broad range of intricate structural scaffolds by employing basic carboxylic acid feedstocks.
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Affiliation(s)
- Mohammed Sharique
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Bianca Matsuo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Albert Granados
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Saegun Kim
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Mahwish Arshad
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Hyunjung Oh
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
| | - Victoria E Wu
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Minxue Huang
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Adam Csakai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Lisa A Marcaurelle
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104-6323 USA
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22
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Wang H, Zhao G, Zhang T, Li Y, Zhang G, Li Y. Comparative Study of DNA Barcode Integrity Evaluation Approaches in the Early-Stage Development of DNA-Compatible Chemical Transformation. ACS Pharmacol Transl Sci 2023; 6:1724-1733. [PMID: 37974618 PMCID: PMC10644510 DOI: 10.1021/acsptsci.3c00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Indexed: 11/19/2023]
Abstract
DNA-encoded libraries (DEL) have emerged as an important drug discovery technical platform for target-based compound library selection. The success rate of DEL depends on both the chemical diversity of combinatorial libraries and the accuracy of DNA barcoding. Therefore, it is critical that the chemistry applied to library construction should efficiently transform on a wide range of substrates while preserving the integrity of DNA tags. Although several analytical methods have been developed to measure DNA damage caused by DEL chemical reactions, efficient and cost-effective evaluation criteria for DNA damage detection are still demanding. Herein, we set standards for evaluating the DNA compatibility of chemistry development at the laboratory level. Based on four typical DNA damage models of three different DEL formats, we evaluated the detection capabilities of four analytical methods, including ultraperformance liquid chromatography (UPLC-MS), electrophoresis, quantitative polymerase chain reaction (qPCR), and Sanger sequencing. This work systematically revealed the scope and capability of different analytical methods in assessing DNA damages caused by chemical transformation. Based on the results, we recommended UPLC-MS and qPCR as efficient methods for DNA barcode integrity analysis in the early-stage development of DNA-compatible chemistry. Meanwhile, we identified that Sanger sequencing was unreliable to assess DNA damage in this application.
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Affiliation(s)
- Huicong Wang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Tianyang Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing
National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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23
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Wei H, Zhang T, Li Y, Zhang G, Li Y. Covalent Capture and Selection of DNA-Encoded Chemical Libraries via Photo-Activated Lysine-Selective Crosslinkers. Chem Asian J 2023; 18:e202300652. [PMID: 37721712 DOI: 10.1002/asia.202300652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 09/19/2023]
Abstract
Covalent crosslinking probes have arisen as efficient toolkits to capture and elucidate biomolecular interaction networks. Exploiting the potential of crosslinking in DNA-encoded chemical library (DEL) selection methods significantly boosted bioactive ligand discovery in complex physiological contexts. Herein, we incorporated o-nitrobenzyl alcohol (o-NBA) as a photo-activated lysine-selective crosslinker into divergent DEL formats and achieved covalent capture of ligand-target interactions featuring improved crosslinking efficiency and site-specificity. In addition, covalent DEL selection was realized with the modularly designed o-NBA-functionalized mock libraries.
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Affiliation(s)
- Haimei Wei
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Tianyang Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190, P. R. China
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24
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Pasieka A, Diamanti E, Uliassi E, Laura Bolognesi M. Click Chemistry and Targeted Degradation: A Winning Combination for Medicinal Chemists? ChemMedChem 2023; 18:e202300422. [PMID: 37706617 DOI: 10.1002/cmdc.202300422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/01/2023] [Indexed: 09/15/2023]
Abstract
Click chemistry is universally recognized as a powerful strategy for the fast and precise assembly of diverse building blocks. Targeted Protein Degradation (TPD) is a new therapeutic modality based on heterobifunctional small-molecule degraders that provides new opportunities to medicinal chemists dealing with undruggable targets and incurable diseases. Here, we highlight how very recently the TPD field and that of click chemistry have merged, opening up the possibility for fine-tuning the properties of a degrader, chemically assembled through a "click" synthesis. By reviewing concrete examples, we want to provide the reader with the insight that the application of click and bioorthogonal chemistry in the TDP field may be a winning combination.
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Affiliation(s)
- Anna Pasieka
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Eleonora Diamanti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Elisa Uliassi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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25
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Oehler S, Lucaroni L, Migliorini F, Elsayed A, Prati L, Puglioli S, Matasci M, Schira K, Scheuermann J, Yudin D, Jia M, Ban N, Bushnell D, Kornberg R, Cazzamalli S, Neri D, Favalli N, Bassi G. A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition. Nat Chem 2023; 15:1431-1443. [PMID: 37400597 DOI: 10.1038/s41557-023-01257-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
DNA-encoded chemical libraries (DELs) consist of large chemical compound collections individually linked to DNA barcodes, facilitating pooled construction and screening. However, screening campaigns often fail if the molecular arrangement of the building blocks is not conducive to an efficient interaction with a protein target. Here we postulated that the use of rigid, compact and stereo-defined central scaffolds for DEL synthesis may facilitate the discovery of very specific ligands capable of discriminating between closely related protein targets. We synthesized a DEL comprising 3,735,936 members, featuring the four stereoisomers of 4-aminopyrrolidine-2-carboxylic acid as central scaffolds. The library was screened in comparative selections against pharmaceutically relevant targets and their closely related protein isoforms. Hit validation results revealed a strong impact of stereochemistry, with large affinity differences between stereoisomers. We identified potent isozyme-selective ligands against multiple protein targets. Some of these hits, specific to tumour-associated antigens, demonstrated tumour-selective targeting in vitro and in vivo. Collectively, constructing DELs with stereo-defined elements contributed to high library productivity and ligand selectivity.
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Affiliation(s)
| | | | | | - Abdullah Elsayed
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Kristina Schira
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Denis Yudin
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Min Jia
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | - Roger Kornberg
- NeoTX Therapeutics LTD, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | | | - Dario Neri
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Philogen SPA, Siena, Italy
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26
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Schneider L, Sauter B, Dagher K, Gillingham D. Recording Binding Information Directly into DNA-Encoded Libraries Using Terminal Deoxynucleotidyl Transferase. J Am Chem Soc 2023; 145:20874-20882. [PMID: 37704585 PMCID: PMC10540198 DOI: 10.1021/jacs.3c05961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 09/15/2023]
Abstract
Terminal deoxynucleotidyl transferase (TdT) is an unusual DNA polymerase that adds untemplated dNTPs to 3'-ends of DNA. If a target protein is expressed as a TdT fusion and incubated with a DNA-encoded library (DEL) in the presence of dATP, the binders of the target induce proximity between TdT and the DNA, promoting the synthesis of a poly-adenine (polyA) tail. The polyA tail length is proportional to the binding affinity, effectively serving as a stable molecular record of binding events. The polyA tail is also a convenient handle to enrich binders with magnetic poly(dT)25 beads before sequencing. In a benchmarking system, we show that ligands spanning nanomolar to double-digit micromolar binding can be cleanly identified by TdT extension, whereas only the tightest binding ligands are identified by classical affinity selection. The method is simple to implement and can function on any DEL that bears a free 3'-end.
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Affiliation(s)
| | - Basilius Sauter
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
| | - Koder Dagher
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
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27
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Sunkari YK, Nguyen TL, Siripuram VK, Flajolet M. Impact of organic chemistry conditions on DNA durability in the context of DNA-encoded library technology. iScience 2023; 26:107573. [PMID: 37664608 PMCID: PMC10470182 DOI: 10.1016/j.isci.2023.107573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
High-power screening (HPS) technologies, such as DNA-encoded library (DEL) technology, could exponentially increase the dimensions of the chemical space accessible for drug discovery. The intrinsic fragile nature of DNA is associated with cumbersome limitations and DNA durability (e.g., depurination, loss of phosphate groups, adduct formation) is compromised in numerous organic chemistry conditions that require empirical testing. An atlas of reaction conditions (temperature, pH, solvent/buffer, ligands, oxidizing reagents, catalysts, scavengers in function of time) that have been systematically tested in multiple combinations, indicates precisely limits useful for DEL construction. More importantly, this approach could be used broadly to effectively evaluate DNA-compatibility of any novel on-DNA chemical reaction, and it is compatible with different molecular methodologies. This atlas and the general approach presented, by allowing novel reaction conditions to be performed in presence of DNA, should greatly help in expanding the DEL chemical space as well as any field involving DNA durability.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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28
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Fitzgerald P, Cochrane WG, Paegel BM. Dose-Response Activity-Based DNA-Encoded Library Screening. ACS Med Chem Lett 2023; 14:1295-1303. [PMID: 37736190 PMCID: PMC10510511 DOI: 10.1021/acsmedchemlett.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/04/2023] [Indexed: 09/23/2023] Open
Abstract
Dose-response, or "conforming" behavior, increases confidence in a screening hit's authenticity. Here, we demonstrate dose-response solid-phase DNA-encoded library (DEL) screening. Compound dose in microfluidic droplets is modulated via the UV intensity of photocleavage from DEL beads. A 55,296-member DEL was screened at different UV intensities against model enzyme drug targets factor Xa (FXa) and autotaxin (ATX). Both screens yielded photochemical dose-dependent hit rates (FXa hit rates of 0.08/0.05% at 100/30% UV exposure; ATX hit rates of 0.24/0.08% at 100/20% UV exposure). FXa hits contained structures reflective of FXa inhibitors and four hits inhibited FXa (IC50 = 4.2 ± 0.1, 7.4 ± 0.3, 9.0 ± 0.3, and 19 ± 2 μM.) The top ATX hits (two dihydrobenzamidazolones and a tetrahydroisoquinoline) were validated as inhibitors (IC50 = 7 ± 2, 13 ± 2, and 1 ± 0.3 μM). Photochemical dose-response DEL screening data prioritized hits for synthesis, the rate-limiting step in DEL lead identification.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Wesley G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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29
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Peterson AA, Liu DR. Small-molecule discovery through DNA-encoded libraries. Nat Rev Drug Discov 2023; 22:699-722. [PMID: 37328653 PMCID: PMC10924799 DOI: 10.1038/s41573-023-00713-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 06/18/2023]
Abstract
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
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Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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30
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Zhang C, Pitman M, Dixit A, Leelananda S, Palacci H, Lawler M, Belyanskaya S, Grady L, Franklin J, Tilmans N, Mobley DL. Building Block-Based Binding Predictions for DNA-Encoded Libraries. J Chem Inf Model 2023; 63:5120-5132. [PMID: 37578123 PMCID: PMC10466377 DOI: 10.1021/acs.jcim.3c00588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 08/15/2023]
Abstract
DNA-encoded libraries (DELs) provide the means to make and screen millions of diverse compounds against a target of interest in a single experiment. However, despite producing large volumes of binding data at a relatively low cost, the DEL selection process is susceptible to noise, necessitating computational follow-up to increase signal-to-noise ratios. In this work, we present a set of informatics tools to employ data from prior DEL screen(s) to gain information about which building blocks are most likely to be productive when designing new DELs for the same target. We demonstrate that similar building blocks have similar probabilities of forming compounds that bind. We then build a model from the inference that the combined behavior of individual building blocks is predictive of whether an overall compound binds. We illustrate our approach on a set of three-cycle OpenDEL libraries screened against soluble epoxide hydrolase (sEH) and report performance of more than an order of magnitude greater than random guessing on a holdout set, demonstrating that our model can serve as a baseline for comparison against other machine learning models on DEL data. Lastly, we provide a discussion on how we believe this informatics workflow could be applied to benefit researchers in their specific DEL campaigns.
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Affiliation(s)
- Chris Zhang
- Department
of Chemistry, University of California,
Irvine, 1120 Natural Sciences II, Irvine, California 92697, United States
| | - Mary Pitman
- Department
of Pharmaceutical Sciences, University of
California, Irvine, 856
Health Sciences Road, Irvine, California 92697, United States
| | - Anjali Dixit
- Department
of Pharmaceutical Sciences, University of
California, Irvine, 856
Health Sciences Road, Irvine, California 92697, United States
| | - Sumudu Leelananda
- Anagenex, 20 Maguire Road Suite 302, Lexington, Massachusetts 02421, United States
| | - Henri Palacci
- Anagenex, 20 Maguire Road Suite 302, Lexington, Massachusetts 02421, United States
| | - Meghan Lawler
- Anagenex, 20 Maguire Road Suite 302, Lexington, Massachusetts 02421, United States
| | - Svetlana Belyanskaya
- Anagenex, 20 Maguire Road Suite 302, Lexington, Massachusetts 02421, United States
| | - LaShadric Grady
- Anagenex, 20 Maguire Road Suite 302, Lexington, Massachusetts 02421, United States
| | - Joe Franklin
- Anagenex, 20 Maguire Road Suite 302, Lexington, Massachusetts 02421, United States
| | - Nicolas Tilmans
- Anagenex, 20 Maguire Road Suite 302, Lexington, Massachusetts 02421, United States
| | - David L. Mobley
- Department
of Chemistry, University of California,
Irvine, 1120 Natural Sciences II, Irvine, California 92697, United States
- Department
of Pharmaceutical Sciences, University of
California, Irvine, 856
Health Sciences Road, Irvine, California 92697, United States
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31
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Cavett V, Chan AI, Cunningham CN, Paegel BM. Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening. ACS CENTRAL SCIENCE 2023; 9:1603-1610. [PMID: 37637732 PMCID: PMC10451030 DOI: 10.1021/acscentsci.3c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Indexed: 08/29/2023]
Abstract
Encoded combinatorial library technologies have dramatically expanded the chemical space for screening but are usually only analyzed by affinity selection binding. It would be highly advantageous to reformat selection outputs to "one-bead-one-compound" solid-phase libraries, unlocking activity-based and cellular screening capabilities. Here, we describe hydrogel-encapsulated magnetic beads that enable such a transformation. Bulk emulsion polymerization of polyacrylamide hydrogel shells around magnetic microbeads yielded uniform particles (7 ± 2 μm diameter) that are compatible with diverse in-gel functionalization (amine, alkyne, oligonucleotides) and transformations associated with DNA-encoded library synthesis (acylation, enzymatic DNA ligation). In a case study of reformatting mRNA display libraries, transcription from DNA-templated magnetic beads encapsulated in gel particles colocalized both RNA synthesis via hybridization with copolymerized complementary DNA and translation via puromycin labeling. Two control epitope templates (V5, HA) were successfully enriched (50- and 99-fold, respectively) from an NNK5 library bead screen via FACS. Proximity-driven library synthesis in concert with magnetic sample manipulation provides a plausible means for reformatting encoded combinatorial libraries at scale.
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Affiliation(s)
- Valerie Cavett
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Alix I Chan
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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32
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Hudson L, Mason JW, Westphal MV, Richter MJR, Thielman JR, Hua BK, Gerry CJ, Xia G, Osswald HL, Knapp JM, Tan ZY, Kokkonda P, Tresco BIC, Liu S, Reidenbach AG, Lim KS, Poirier J, Capece J, Bonazzi S, Gampe CM, Smith NJ, Bradner JE, Coley CW, Clemons PA, Melillo B, Hon CSY, Ottl J, Dumelin CE, Schaefer JV, Faust AME, Berst F, Schreiber SL, Zécri FJ, Briner K. Diversity-oriented synthesis encoded by deoxyoligonucleotides. Nat Commun 2023; 14:4930. [PMID: 37582753 PMCID: PMC10427684 DOI: 10.1038/s41467-023-40575-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Diversity-oriented synthesis (DOS) is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors and derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We also show screening results for three diverse protein targets. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.
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Affiliation(s)
- Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthieu J R Richter
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher J Gerry
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Guoqin Xia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Heather L Osswald
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John M Knapp
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ben I C Tresco
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Katherine S Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jennifer Poirier
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - John Capece
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Simone Bonazzi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christian M Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Nichola J Smith
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - James E Bradner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, 02139, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - C Suk-Yee Hon
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Christoph E Dumelin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jonas V Schaefer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Ann Marie E Faust
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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33
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Abstract
DNA-encoded libraries (DELs) are widely used in the discovery of drug candidates, and understanding their design principles is critical for accessing better libraries. Most DELs are combinatorial in nature and are synthesized by assembling sets of building blocks in specific topologies. In this study, different aspects of library topology were explored and their effect on DEL properties and chemical diversity was analyzed. We introduce a descriptor for DEL topological assignment (DELTA) and use it to examine the landscape of possible DEL topologies and their coverage in the literature. A generative topographic mapping analysis revealed that the impact of library topology on chemical space coverage is secondary to building block selection. Furthermore, it became apparent that the descriptor used to analyze chemical space dictates how structures cluster, with the effects of topology being apparent when using three-dimensional descriptors but not with common two-dimensional descriptors. This outcome points to potential challenges of attempts to predict DEL productivity based on chemical space analyses alone. While topology is rather inconsequential for defining the chemical space of encoded compounds, it greatly affects possible interactions with target proteins as illustrated in docking studies using NAD/NADP binding proteins as model receptors.
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Affiliation(s)
- William K Weigel
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, Utah 84112, United States
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34
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Seydimemet M, Yang Y, Lv Y, Liu J, Yan Z, Zhao Y, Wang X, Lu X. Design, Construction, and Screening of Diversified Pyrimidine-Focused DNA-Encoded Libraries. ACS Med Chem Lett 2023; 14:1073-1078. [PMID: 37583819 PMCID: PMC10424316 DOI: 10.1021/acsmedchemlett.3c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Pyrimidine is a ubiquitous component in natural products and approved drugs, providing an ideal modular scaffold for generating libraries with drug-like properties. DNA-encoded library technology introduces a novel library modality where each small molecule is covalently linked to a unique oligo tag. This technology offers the advantages of rapidly generating and interrogating large-scale libraries containing billions of members, substantially reducing the entry barrier to their use in both academia and the pharmaceutical industry. In this Letter, we describe the synthesis of three DNA-encoded libraries based on different functionalized pyrimidine cores featuring diversified chemoselectivity and regioselectivity. Preliminary screening of these DNA-encoded libraries against BRD4 identified compounds with nanomolar inhibition activities.
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Affiliation(s)
- Mengnisa Seydimemet
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yixuan Yang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yuhan Lv
- School
of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong P.R. China
| | - Jiaxiang Liu
- Alphama
Biotechnology Suzhou Co., Ltd., 108 Yuxin Road, Suzhou City, Jiangsu Province 215123, China
| | - Ziqin Yan
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yujun Zhao
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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35
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Salvini CLA, Darlot B, Davison J, Martin MP, Tudhope SJ, Turberville S, Kawamura A, Noble MEM, Wedge SR, Crawford JJ, Waring MJ. Fragment expansion with NUDELs - poised DNA-encoded libraries. Chem Sci 2023; 14:8288-8294. [PMID: 37564419 PMCID: PMC10411621 DOI: 10.1039/d3sc01171b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Optimisation of the affinity of lead compounds is a critical challenge in the identification of drug candidates and chemical probes and is a process that takes many years. Fragment-based drug discovery has become established as one of the methods of choice for drug discovery starting with small, low affinity compounds. Due to their low affinity, the evolution of fragments to desirable levels of affinity is often a key challenge. The accepted best method for increasing the potency of fragments is by iterative fragment growing, which can be very time consuming and complex. Here, we introduce a paradigm for fragment hit optimisation using poised DNA-encoded chemical libraries (DELs). The synthesis of a poised DEL, a partially constructed library that retains a reactive handle, allows the coupling of any active fragment for a specific target protein, allowing rapid discovery of potent ligands. This is illustrated for bromodomain-containing protein 4 (BRD4), in which a weakly binding fragment was coupled to a 42-member poised DEL via Suzuki-Miyaura cross coupling resulting in the identification of an inhibitor with 51 nM affinity in a single step, representing an increase in potency of several orders of magnitude from an original fragment. The potency of the compound was shown to arise from the synergistic combination of substructures, which would have been very difficult to discover by any other method and was rationalised by X-ray crystallography. The compound showed attractive lead-like properties suitable for further optimisation and demonstrated BRD4-dependent cellular pharmacology. This work demonstrates the power of poised DELs to rapidly optimise fragments, representing an attractive generic approach to drug discovery.
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Affiliation(s)
- Catherine L A Salvini
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Benoit Darlot
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Jack Davison
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Susan J Tudhope
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Shannon Turberville
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Akane Kawamura
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Stephen R Wedge
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - James J Crawford
- Genentech Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Michael J Waring
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
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36
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An Y, Lee J, Seo H, Bae S, Kang J, Lee J, Kim J, Nam MH, Song M, Hwang GT. Groebke-Blackburn-Bienaymé Reaction for DNA-Encoded Library Technology. Org Lett 2023; 25:4445-4450. [PMID: 37310879 DOI: 10.1021/acs.orglett.3c01366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study presents a DNA-compatible synthesis of diverse 5-arylimidazo[1,2-a]pyridin-3-amine derivatives using the Suzuki-Miyaura reaction, followed by a Groebke-Blackburn-Bienaymé (GBB) reaction. The GBB reaction demonstrates a wide substrate scope, mild one-pot reaction conditions, and compatibility with subsequent enzymatic ligation, highlighting its potential in DNA-encoded library technology.
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Affiliation(s)
- Yujin An
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Juyeon Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyewon Seo
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Seri Bae
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jihee Kang
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jieon Lee
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jinwoo Kim
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Myung Hee Nam
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
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37
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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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38
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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39
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Cui M, Nguyen D, Gaillez MP, Heiden S, Lin W, Thompson M, Reddavide FV, Chen Q, Zhang Y. Trio-pharmacophore DNA-encoded chemical library for simultaneous selection of fragments and linkers. Nat Commun 2023; 14:1481. [PMID: 36932079 PMCID: PMC10023787 DOI: 10.1038/s41467-023-37071-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The split-and-pool method has been widely used to synthesize chemical libraries of a large size for early drug discovery, albeit without the possibility of meaningful quality control. In contrast, a self-assembled DNA-encoded chemical library (DEL) allows us to construct an m x n-member library by mixing an m-member and an n-member pre-purified sub-library. Herein, we report a trio-pharmacophore DEL (T-DEL) of m x l x n members through assembling three pre-purified and validated sub-libraries. The middle sub-library is synthesized using DNA-templated synthesis with different reaction mechanisms and designed as a linkage connecting the fragments displayed on the flanking two sub-libraries. Despite assembling three fragments, the resulting compounds do not exceed the up-to-date standard of molecular weight regarding drug-likeness. We demonstrate the utility of T-DEL in linker optimization for known binding fragments against trypsin and carbonic anhydrase II and by de novo selections against matrix metalloprotease-2 and -9.
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Affiliation(s)
- Meiying Cui
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Michelle Patino Gaillez
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Weilin Lin
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | | | - Qinchang Chen
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, China.
- School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Yixin Zhang
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
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40
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Stanway-Gordon H, Odger JA, Waring MJ. Development of a Micellar-Promoted Heck Reaction for the Synthesis of DNA-Encoded Libraries. Bioconjug Chem 2023; 34. [PMID: 36883323 PMCID: PMC10119937 DOI: 10.1021/acs.bioconjchem.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/22/2023] [Indexed: 03/09/2023]
Abstract
The capability of DNA encoded libraries (DELs) as a method of small molecule hit identification is becoming widely established in drug discovery. While their selection method offers advantages over more traditional means, DELs are limited by the chemistry that can be utilized to construct them. Significant advances in DNA compatible chemistry have been made over the past five years; however such procedures are still often burdened by substrate specificity and/or incomplete conversions, reducing the fidelity of the resulting libraries. One such reaction is the Heck coupling, for which current DNA-compatible protocols are somewhat unreliable. Utilizing micellar technology, we have developed a highly efficient DNA-compatible Heck reaction that proceeds on average to 95% conversion to product across a broad variety of structurally significant building blocks and multiple DNA conjugates. This work continues the application of micellar catalysis to the development of widely applicable, effective DNA-compatible reactions for use in DELs.
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Affiliation(s)
- Harriet
A. Stanway-Gordon
- Cancer Research Horizons
Therapeutic Innovation, Chemistry, School of Natural and Environmental
Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1
7RU, United Kingdom
| | - Jake A. Odger
- Cancer Research Horizons
Therapeutic Innovation, Chemistry, School of Natural and Environmental
Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1
7RU, United Kingdom
| | - Michael J. Waring
- Cancer Research Horizons
Therapeutic Innovation, Chemistry, School of Natural and Environmental
Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1
7RU, United Kingdom
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41
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Abstract
The Human Genome Project ultimately aimed to translate DNA sequence into drugs. With the draft in hand, the Molecular Libraries Program set out to prosecute all genome-encoded proteins for drug discovery with automated high-throughput screening (HTS). This ambitious vision remains unfulfilled, even while innovations in sequencing technology have fully democratized access to genome-scale sequencing. Why? While the central dogma of biology allows us to chart the entirety of cellular metabolism through sequencing, there is no direct coding for chemistry. The rules of base pairing that relate DNA gene to RNA transcript and amino acid sequence do not exist for relating small-molecule structure with macromolecular binding partners and subsequently cellular function. Obtaining such relationships genome-wide is unapproachable via state-of-the-art HTS, akin to attempting genome-wide association studies using turn-of-the-millennium Sanger DNA sequencing.Our laboratory has been engaged in a multipronged technology development campaign to revolutionize molecular screening through miniaturization in pursuit of genome-scale drug discovery capabilities. The compound library was ripe for miniaturization: it clearly needed to become a consumable. We employed DNA-encoded library (DEL) synthesis principles in the development of solid-phase DELs prepared on microscopic beads, each harboring 100 fmol of a single library member and a DNA tag whose sequence describes the structure of the library member. Loading these DEL beads into 100 pL microfluidic droplets followed by online photocleavage, incubation, fluorescence-activated droplet sorting, and DNA sequencing of the sorted DEL beads reveals the chemical structures of bioactive compounds. This scalable library synthesis and screening platform has proven useful in several proof-of-concept projects involving current clinical targets.Moving forward, we face the problem of druggability and proteome-scale assay development. Developing biochemical or cellular assays for all genome-encoded targets is not scalable and likely impossible as most proteins have ill-defined or unknown activity and may not function outside of their native contexts. These are the dark undruggable expanses, and charting them will require advanced synthesis and analytical technologies that can generalize probe discovery, irrespective of mature protein function, to fulfill the Genome Project's vision of proteome-wide control of cellular pharmacology.
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Krishna Sunkari Y, Kumar Siripuram V, Flajolet M. Diversity-Oriented Synthesis (DOS) of On-DNA Peptidomimetics from Acid-Derived Phosphonium Ylides. Chemistry 2023; 29:e202203037. [PMID: 36653313 DOI: 10.1002/chem.202203037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 01/20/2023]
Abstract
The DNA-encoded library (DEL) technology represents a revolutionary drug-discovery tool with unprecedented screening power originating from the association of combinatorial chemistry and DNA barcoding. The chemical diversity of DELs and its chemical space will be further expanded as new DNA-compatible reactions are introduced. This work introduces the use of DOS in the context of on-DNA peptidomimetics. Wittig olefination of aspartic acid-derived on-DNA Wittig ylide, combined with a broad substrate scope of aldehydes, led to formation of on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated ketones. The synthesis of on-DNA multi-peptidyl-ylides was performed by incorporating sequential amino acids onto a monomeric ylide. Di-, tri- and tetrameric peptidyl-ylides were validated for Wittig olefination and led to on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated-based peptidomimetics, an important class of intermediates. One on-DNA aryl Wittig ylide was also developed and applied to Wittig olefination for synthesis of on-DNA chalcone-based molecules. Furthermore, DOS was used successfully with electron-deficient peptidomimetics and led to the development of different heterocyclic cores containing on-DNA peptidomimetics.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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43
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Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
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Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
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44
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Wen X, Wu X, Jin R, Lu X. Privileged heterocycles for DNA-encoded library design and hit-to-lead optimization. Eur J Med Chem 2023; 248:115079. [PMID: 36669370 DOI: 10.1016/j.ejmech.2022.115079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023]
Abstract
It is well known that heterocyclic compounds play a key role in improving drug activity, target selectivity, physicochemical properties as well as reducing toxicity. In this review, we summarized the representative heterocyclic structures involved in hit compounds which were obtained from DNA-encoded library from 2013 to 2021. In some examples, the state of the art in heterocycle-based DEL synthesis and hit-to-lead optimization are highlighted. We hope that more and more novel heterocycle-based DEL toolboxes and in-depth pharmaceutical research on these lead compounds can be developed to accelerate the discovery of new drugs.
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Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Rui Jin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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45
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Steffek M, Helgason E, Popovych N, Rougé L, Bruning JM, Li KS, Burdick DJ, Cai J, Crawford T, Xue J, Decurtins W, Fang C, Grubers F, Holliday MJ, Langley A, Petersen A, Satz AL, Song A, Stoffler D, Strebel Q, Tom JYK, Skelton N, Staben ST, Wichert M, Mulvihill MM, Dueber EC. A Multifaceted Hit-Finding Approach Reveals Novel LC3 Family Ligands. Biochemistry 2023; 62:633-644. [PMID: 34985287 DOI: 10.1021/acs.biochem.1c00682] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autophagy-related proteins (Atgs) drive the lysosome-mediated degradation pathway, autophagy, to enable the clearance of dysfunctional cellular components and maintain homeostasis. In humans, this process is driven by the mammalian Atg8 (mAtg8) family of proteins comprising the LC3 and GABARAP subfamilies. The mAtg8 proteins play essential roles in the formation and maturation of autophagosomes and the capture of specific cargo through binding to the conserved LC3-interacting region (LIR) sequence within target proteins. Modulation of interactions of mAtg8 with its target proteins via small-molecule ligands would enable further interrogation of their function. Here we describe unbiased fragment and DNA-encoded library (DEL) screening approaches for discovering LC3 small-molecule ligands. Both strategies resulted in compounds that bind to LC3, with the fragment hits favoring a conserved hydrophobic pocket in mATG8 proteins, as detailed by LC3A-fragment complex crystal structures. Our findings demonstrate that the malleable LIR-binding surface can be readily targeted by fragments; however, rational design of additional interactions to drive increased affinity proved challenging. DEL libraries, which combine small, fragment-like building blocks into larger scaffolds, yielded higher-affinity binders and revealed an unexpected potential for reversible, covalent ligands. Moreover, DEL hits identified possible vectors for synthesizing fluorescent probes or bivalent molecules for engineering autophagic degradation of specific targets.
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Affiliation(s)
- Micah Steffek
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Elizabeth Helgason
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lionel Rougé
- Structure Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - John M Bruning
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ke Sherry Li
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianping Cai
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Terry Crawford
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Xue
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Willy Decurtins
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Chunlin Fang
- WuXi AppTec (Wuhan) Company, Ltd., No. 666 GaoXin Road, WuHan East Lake High-tech Development Zone, Hubei 430075, China
| | - Felix Grubers
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michael J Holliday
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Allyson Langley
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ann Petersen
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Alexander Lee Satz
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Aimin Song
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Stoffler
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Quentin Strebel
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jeffrey Y K Tom
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Skelton
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven T Staben
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Moreno Wichert
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melinda M Mulvihill
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Erin C Dueber
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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Sharma K, Sharma KK, Sharma A, Jain R. Peptide-based drug discovery: Current status and recent advances. Drug Discov Today 2023; 28:103464. [PMID: 36481586 DOI: 10.1016/j.drudis.2022.103464] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.
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Affiliation(s)
- Komal Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anku Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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Abstract
Cancer immunotherapy with immune-checkpoint blockade has improved the outcomes of patients with various malignancies, yet a majority do not benefit or develop resistance. To address this unmet need, efforts across the field are targeting additional coinhibitory receptors, costimulatory proteins, and intracellular mediators that could prevent or bypass anti-PD1 resistance mechanisms. The CD28 costimulatory pathway is necessary for antigen-specific T cell activation, though prior CD28 agonists did not translate successfully to clinic due to toxicity. Casitas B lymphoma-b (Cbl-b) is a downstream, master regulator of both CD28 and CTLA-4 signaling. This E3 ubiquitin ligase regulates both innate and adaptive immune cells, ultimately promoting an immunosuppressive tumor microenvironment (TME) in the absence of CD28 costimulation. Recent advances in pharmaceutical screening and computational biology have enabled the development of novel platforms to target this once 'undruggable' protein. These platforms include DNA encoded library screening, allosteric drug targeting, small-interfering RNA inhibition, CRISPR genome editing, and adoptive cell therapy. Both genetic knock-out models and Cbl-b inhibitors have been shown to reverse immunosuppression in the TME, stimulate cytotoxic T cell activity, and promote tumor regression, findings augmented with PD1 blockade in experimental models. In translating Cbl-b inhibitors to clinic, we propose specific gene expression profiles that may identify patient populations most likely to benefit. Overall, novel Cbl-b inhibitors provide antigen-specific immune stimulation and are a promising therapeutic tool in the field of immuno-oncology.
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Affiliation(s)
- Ryan C Augustin
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Riyue Bao
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason J Luke
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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48
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Morishita EC. Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies. Expert Opin Drug Discov 2023; 18:207-226. [PMID: 36322542 DOI: 10.1080/17460441.2022.2134852] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The field of RNA-targeted small molecules is rapidly evolving, owing to the advances in experimental and computational technologies. With the identification of several bioactive small molecules that target RNA, including the FDA-approved risdiplam, the biopharmaceutical industry is gaining confidence in the field. This review, based on the literature obtained from PubMed, aims to disseminate information about the various technologies developed for targeting RNA with small molecules and propose areas for improvement to develop drugs more efficiently, particularly those linked to diseases with unmet medical needs. AREAS COVERED The technologies for the identification of RNA targets, screening of chemical libraries against RNA, assessing the bioactivity and target engagement of the hit compounds, structure determination, and hit-to-lead optimization are reviewed. Along with the description of the technologies, their strengths, limitations, and examples of how they can impact drug discovery are provided. EXPERT OPINION Many existing technologies employed for protein targets have been repurposed for use in the discovery of RNA-targeted small molecules. In addition, technologies tailored for RNA targets have been developed. Nevertheless, more improvements are necessary, such as artificial intelligence to dissect important RNA structures and RNA-small-molecule interactions and more powerful chemical probing and structure prediction techniques.
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49
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Scarpellini C, Valembois S, Goossens K, Vadi M, Lanthier C, Klejborowska G, Van Der Veken P, De Winter H, Bertrand MJM, Augustyns K. From PERK to RIPK1: Design, synthesis and evaluation of novel potent and selective necroptosis inhibitors. Front Chem 2023; 11:1160164. [PMID: 37090247 PMCID: PMC10119423 DOI: 10.3389/fchem.2023.1160164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Receptor-Interacting serine/threonine-Protein Kinase 1 (RIPK1) emerged as an important driver of inflammation and, consequently, inflammatory pathologies. The enzymatic activity of RIPK1 is known to indirectly promote inflammation by triggering cell death, in the form of apoptosis, necroptosis and pyroptosis. Small molecule Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors have therefore recently entered clinical trials for the treatment of a subset of inflammatory pathologies. We previously identified GSK2656157 (GSK'157), a supposedly specific inhibitor of protein kinase R (PKR)-like ER kinase (PERK), as a much more potent type II Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitor. We now performed further structural optimisation on the GSK'157 scaffold in order to develop a novel class of more selective Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors. Based on a structure-activity relationship (SAR) reported in the literature, we anticipated that introducing a substituent on the para-position of the pyridinyl ring would decrease the interaction with PERK. Herein, we report a series of novel GSK'157 analogues with different para-substituents with increased selectivity for Receptor-Interacting serine/threonine-Protein Kinase 1. The optimisation led to UAMC-3861 as the best compound of this series in terms of activity and selectivity for Receptor-Interacting serine/threonine-Protein Kinase 1 over PERK. The most selective compounds were screened in vitro for their ability to inhibit RIPK1-dependent apoptosis and necroptosis. With this work, we successfully synthesised a novel series of potent and selective type II Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors based on the GSK'157 scaffold.
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Affiliation(s)
- Camilla Scarpellini
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Sophie Valembois
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Kenneth Goossens
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Mike Vadi
- Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research, Ghent, Belgium
- Laboratory Cell Death and Inflammation, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Caroline Lanthier
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Greta Klejborowska
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Mathieu J. M. Bertrand
- Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research, Ghent, Belgium
- Laboratory Cell Death and Inflammation, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- *Correspondence: Koen Augustyns,
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50
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Gibaut QMR, Akahori Y, Bush JA, Taghavi A, Tanaka T, Aikawa H, Ryan LS, Paegel BM, Disney MD. Study of an RNA-Focused DNA-Encoded Library Informs Design of a Degrader of a r(CUG) Repeat Expansion. J Am Chem Soc 2022; 144:21972-21979. [PMID: 36399603 PMCID: PMC9878440 DOI: 10.1021/jacs.2c08883] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A solid-phase DNA-encoded library (DEL) was studied for binding the RNA repeat expansion r(CUG)exp, the causative agent of the most common form of adult-onset muscular dystrophy, myotonic dystrophy type 1 (DM1). A variety of uncharged and novel RNA binders were identified to selectively bind r(CUG)exp by using a two-color flow cytometry screen. The cellular activity of one binder was augmented by attaching it with a module that directly cleaves r(CUG)exp. In DM1 patient-derived muscle cells, the compound specifically bound r(CUG)exp and allele-specifically eliminated r(CUG)exp, improving disease-associated defects. The approaches herein can be used to identify and optimize ligands and bind RNA that can be further augmented for functionality including degradation.
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Affiliation(s)
- Quentin M. R. Gibaut
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yoshihiro Akahori
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Toru Tanaka
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Haruo Aikawa
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Lucas S. Ryan
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States; Department of Chemistry and Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
| | - Matthew D. Disney
- Department of Chemistry, UF Scripps Biomedical Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
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