1
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Gruber F, McDonagh AW, Rose V, Hunter J, Guasch L, Martin RE, Geigle SN, Britton R. sp 3 -Rich Heterocycle Synthesis on DNA: Application to DNA-Encoded Library Production. Angew Chem Int Ed Engl 2024; 63:e202319836. [PMID: 38330151 DOI: 10.1002/anie.202319836] [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: 12/21/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
DNA encoded library (DEL) synthesis represents a convenient means to produce, annotate and store large collections of compounds in a small volume. While DELs are well suited for drug discovery campaigns, the chemistry used in their production must be compatible with the DNA tag, which can limit compound class accessibility. As a result, most DELs are heavily populated with peptidomimetic and sp2 -rich molecules. Herein, we show that sp3 -rich mono- and bicyclic heterocycles can be made on DNA from ketochlorohydrin aldol products through a reductive amination and cyclization process. The resulting hydroxypyrrolidines possess structural features that are desirable for DELs and target a distinct region of pharmaceutically relevant chemical space.
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Affiliation(s)
- Felix Gruber
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Anthony W McDonagh
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Victoria Rose
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - James Hunter
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Laura Guasch
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Stefanie N Geigle
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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2
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Zhou Q, Liu X, Neri D, Li W, Favalli N, Bassi G, Yang S, Yang D, Vogt PK, Wang MW. Structural insights into the interaction of three Y-shaped ligands with PI3Kα. Proc Natl Acad Sci U S A 2023; 120:e2304071120. [PMID: 37585458 PMCID: PMC10450665 DOI: 10.1073/pnas.2304071120] [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: 03/10/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023] Open
Abstract
Class IA phosphoinositide 3-kinase alpha (PI3Kα) is an important drug target because it is one of the most frequently mutated proteins in human cancers. However, small molecule inhibitors currently on the market or under development have safety concerns due to a lack of selectivity. Therefore, other chemical scaffolds or unique mechanisms of catalytic kinase inhibition are needed. Here, we report the cryo-electron microscopy structures of wild-type PI3Kα, the dimer of p110α and p85α, in complex with three Y-shaped ligands [cpd16 (compound 16), cpd17 (compound 17), and cpd18 (compound 18)] of different affinities and no inhibitory effect on the kinase activity. Unlike ATP-competitive inhibitors, cpd17 adopts a Y-shaped conformation with one arm inserted into a binding pocket formed by R770 and W780 and the other arm lodged in the ATP-binding pocket at an angle that is different from that of the ATP phosphate tail. Such a special interaction induces a conformation of PI3Kα resembling that of the unliganded protein. These observations were confirmed with two isomers (cpd16 and cpd18). Further analysis of these Y-shaped ligands revealed the structural basis of differential binding affinities caused by stereo- or regiochemical modifications. Our results may offer a different direction toward the design of therapeutic agents against PI3Kα.
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Affiliation(s)
- Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Xiao Liu
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich8093, Switzerland
| | - Wenxin Li
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich8093, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich8093, Switzerland
| | - Su Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Peter K. Vogt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Ming-Wei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Research Center for Deepsea Bioresources, Sanya572025, China
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo113-0033, Japan
- School of Pharmacy, Hainan Medical College, Haikou570228, China
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3
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Teske KA, Su W, Corona CR, Wen J, Deng J, Ping Y, Zhang Z, Zhang Q, Wilkinson J, Beck MT, Nealey KR, Vasta JD, Cong M, Meisenheimer PL, Kuai L, Robers MB. DELs enable the development of BRET probes for target engagement studies in cells. Cell Chem Biol 2023; 30:987-998.e24. [PMID: 37490918 DOI: 10.1016/j.chembiol.2023.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023]
Abstract
DNA-encoded libraries (DELs) provide unmatched chemical diversity and starting points for novel drug modalities. Here, we describe a workflow that exploits the bifunctional attributes of DEL ligands as a platform to generate BRET probes for live cell target engagement studies. To establish proof of concept, we performed a DEL screen using aurora kinase A and successfully converted aurora DEL ligands as cell-active BRET probes. Aurora BRET probes enabled the validation and stratification of the chemical series identified from primary selection data. Furthermore, we have evaluated the effective repurposing of pre-existing DEL screen data to find suitable leads for BRET probe development. Our findings support the use of DEL workflows as an engine to create cell-active BRET probes independent of structure or compound SAR. The combination of DEL and BRET technology accelerates hit-to-lead studies in a live cell setting.
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Affiliation(s)
- Kelly A Teske
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Wenji Su
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Cesear R Corona
- Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, CA 93401, USA
| | - Jing Wen
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Jason Deng
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Yan Ping
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Zaihong Zhang
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | | | - Michael T Beck
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Kendra R Nealey
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - James D Vasta
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Mei Cong
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | | | - Letian Kuai
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China.
| | - Matthew B Robers
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA.
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4
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Vasuki A, Christy HJ, Renugadevi K, Dammalli M. Structure-based pharmacophore modeling and DFT studies of Indian Ocean-derived red algal compounds as PI3Kα inhibitors. Mol Divers 2023:10.1007/s11030-023-10695-7. [PMID: 37466805 DOI: 10.1007/s11030-023-10695-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/30/2023] [Indexed: 07/20/2023]
Abstract
Phosphoinositide kinases (PIKs) are a type of lipid kinase that acts as an upstream activator of oncogenic signaling. Presently accessible therapeutic compounds have downsides, such as toxicity and dubious efficacy, as well as lengthy treatment durations, which have bred resistance. Here we attempt to screen the Indian Ocean-derived red algal compounds to be used as a promising lead for PI3Kα inhibitor development. Experimental structure of the PI3K alpha Isoform-Specific Inhibitor alpelisib complex-based pharmacophore model was constructed and used as key to mark off the suitable lead compounds from the pool of marine-derived red algal compounds of Indian Ocean. Besides, the study encompasses pharmacophore scaffold screening as well as physicochemical and pharmacokinetic parameter assessment. We employed molecular docking and molecular dynamics simulation to assess the binding type and stability of 21 red algal derivatives. Twelve compounds demonstrated a sustained binding mode within the PI3Kα binding pocket with an optimal protein backbone root-mean-square deviation, also prompted hydrogen bonding throughout the simulations, and also implies that these MNPs have firmly mediated the interaction with prime hinge region residues in the PI3Kα ATP binding pocket. DFT studies revealed that proposed compounds had the greatest occupied molecular orbital electrophilicity index, basicity, and dipole moment, all of which attributed their stability as well as binding affinity at the PI3Kα active site. Our study's findings revealed that CMNPD31054, CMNPD4798, CMNPD27861, CMNPD4799, CMNPD27860, CMNPD9533, CMNPD3732, CMNPD4221, CMNPD31058, CMNPD31052, CMNPD29281, and CMNPD31055 can be used as lead compounds for PI3KΑ isoform inhibitors design.
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Affiliation(s)
- Archana Vasuki
- Department of Bioinformatics, Sathyabama Institute of Science and Technology, Chennai, India
| | - H Jemmy Christy
- Department of Bioinformatics, Sathyabama Institute of Science and Technology, Chennai, India.
| | - K Renugadevi
- Department of Biotechnology, Sathyabama Institute of Science and Technology, Chennai, India
| | - Manjunath Dammalli
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka, India
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5
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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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6
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.
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Affiliation(s)
- Paddy R A Melsen
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Ryoji Yoshisada
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Seino A K Jongkees
- Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, de Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
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7
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Sunkari YK, Siripuram VK, Nguyen TL, Flajolet M. High-power screening (HPS) empowered by DNA-encoded libraries. Trends Pharmacol Sci 2021; 43:4-15. [PMID: 34782164 DOI: 10.1016/j.tips.2021.10.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/29/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023]
Abstract
The world is totally dependent on medications. As science progresses, new, better, and cheaper drugs are needed more than ever. The pharmaceutical industry has been predominantly dependent on high-throughput screening (HTS) for the past three decades. Considering that the discovery rate has been relatively constant, can one hope for a much-needed sudden trend uptick? DNA-encoded libraries (DELs) and similar technologies, that have several orders of magnitude more screening power than HTS, and that we propose to group together under the umbrella term of high-power screening (HPS), are very well positioned to do exactly that. HPS also offers novel screening options such as parallel screening, ex vivo and in vivo screening, as well as a new path to druggable alternatives such as proteolysis targeting chimeras (PROTACs). Altogether, HPS unlocks novel powerful drug discovery avenues.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA.
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8
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Vanhaesebroeck B, Perry MWD, Brown JR, André F, Okkenhaug K. PI3K inhibitors are finally coming of age. Nat Rev Drug Discov 2021; 20:741-769. [PMID: 34127844 PMCID: PMC9297732 DOI: 10.1038/s41573-021-00209-1] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 01/08/2023]
Abstract
Overactive phosphoinositide 3-kinase (PI3K) in cancer and immune dysregulation has spurred extensive efforts to develop therapeutic PI3K inhibitors. Although progress has been hampered by issues such as poor drug tolerance and drug resistance, several PI3K inhibitors have now received regulatory approval - the PI3Kα isoform-selective inhibitor alpelisib for the treatment of breast cancer and inhibitors mainly aimed at the leukocyte-enriched PI3Kδ in B cell malignancies. In addition to targeting cancer cell-intrinsic PI3K activity, emerging evidence highlights the potential of PI3K inhibitors in cancer immunotherapy. This Review summarizes key discoveries that aid the clinical translation of PI3Kα and PI3Kδ inhibitors, highlighting lessons learnt and future opportunities.
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Affiliation(s)
| | - Matthew W D Perry
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jennifer R Brown
- CLL Center, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Fabrice André
- Institut Gustave Roussy, INSERM U981, Université Paris Saclay, Paris, France
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge, UK
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9
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Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Waring MJ. On the design of lead-like DNA-encoded chemical libraries. Bioorg Med Chem 2021; 43:116273. [PMID: 34147943 DOI: 10.1016/j.bmc.2021.116273] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/11/2023]
Abstract
DNA-encoded libraries (DELs) are becoming an established technology for finding ligands for protein targets. We have abstracted and analysed libraries from the literature to assess the synthesis strategy, selections of reactions and monomers and their propensity to reveal hits. DELs have led to hit compounds across a range of diverse protein classes. The range of reactions and monomers utilised has been relatively limited and the hits are often higher in molecular weight than might be considered ideal. Considerations for future library designs with reference to chemical diversity and lead-like properties are discussed.
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Affiliation(s)
- Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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10
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Potowski M, Lüttig R, Vakalopoulos A, Brunschweiger A. Copper(I/II)-Promoted Diverse Imidazo[1,2-α]pyridine Synthesis on Solid-Phase Bound DNA Oligonucleotides for Encoded Library Design. Org Lett 2021; 23:5480-5484. [PMID: 34181416 DOI: 10.1021/acs.orglett.1c01834] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-encoded libraries designed around heterocyclic scaffolds have proven highly productive in target-based screening. Here, we show the synthesis of imidazopyridines on a controlled pore glass-coupled DNA oligonucleotide for solid phase-initiated encoded library synthesis. The target compounds were synthesized by a variant of the A3 coupling reaction from aminopyridines, alkynes, and aldehydes promoted by copper(I/II) and furnished diverse substituted scaffolds with functionalities for library design. Although proceeding under forcing conditions, it produced minimal DNA damage.
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Affiliation(s)
- Marco Potowski
- Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Ricarda Lüttig
- Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | | | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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11
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Xia B, Franklin GJ, Lu X, Bedard KL, Grady LC, Summerfield JD, Shi EX, King BW, Lind KE, Chiu C, Watts E, Bodmer V, Bai X, Marcaurelle LA. DNA-Encoded Library Hit Confirmation: Bridging the Gap Between On-DNA and Off-DNA Chemistry. ACS Med Chem Lett 2021; 12:1166-1172. [PMID: 34267887 PMCID: PMC8274064 DOI: 10.1021/acsmedchemlett.1c00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/20/2021] [Indexed: 11/29/2022] Open
Abstract
DNA-encoded library (DEL) technology is a powerful platform for hit identification in academia and the pharmaceutical industry. When conducting off-DNA resynthesis hit confirmation after affinity selection, PCR/sequencing, and data analysis, one typically assumes a "one-to-one" relationship between the DNA tag and the chemical structure of the attached small-molecule it encodes. Because library synthesis often yields a mixture, this approximation increases the risk of overlooking positive discoveries and valuable information. To address this issue, we apply a library synthesis "recipe" strategy for on-DNA resynthesis using a cleavable linker, followed by direct affinity selection mass spectrometry (AS-MS) evaluation and identification of binder(s) from the released small-molecule mixture. We validate and showcase this approach employing the receptor-interacting-protein kinase 2 (RIP2) DEL campaign. We also designed and developed two cleavable linkers to enable this method, a photocleavable linker (nitrophenyl-based) and acid-labile linker (tetrahydropyranyl ether). The strategy provides an effective means of hit identification and rapid determination of key active component(s) of the mixture.
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Affiliation(s)
- Bing Xia
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - G. Joseph Franklin
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Xiaojie Lu
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Katie L. Bedard
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - LaShadric C. Grady
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Jennifer D. Summerfield
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Eric X. Shi
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Bryan W. King
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Kenneth E. Lind
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Cynthia Chiu
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Eleanor Watts
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Vera Bodmer
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Xiaopeng Bai
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Lisa A. Marcaurelle
- Encoded
Library Technologies/NCE Molecular Discovery, R&D Medicinal Science
and Technology, GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
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12
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Abstract
Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.
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Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Departments of Pharmaceutical Sciences, Chemistry, & Biomedical Engineering, University of California, Irvine, 101 Theory Suite 100, Irvine, California 92617, United States
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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13
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Favalli N, Bassi G, Pellegrino C, Millul J, De Luca R, Cazzamalli S, Yang S, Trenner A, Mozaffari NL, Myburgh R, Moroglu M, Conway SJ, Sartori AA, Manz MG, Lerner RA, Vogt PK, Scheuermann J, Neri D. Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications. Nat Chem 2021; 13:540-548. [PMID: 33833446 PMCID: PMC8405038 DOI: 10.1038/s41557-021-00660-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 02/10/2021] [Indexed: 02/01/2023]
Abstract
The encoding of chemical compounds with amplifiable DNA tags facilitates the discovery of small-molecule ligands for proteins. To investigate the impact of stereo- and regiochemistry on ligand discovery, we synthesized a DNA-encoded library of 670,752 derivatives based on 2-azido-3-iodophenylpropionic acids. The library was selected against multiple proteins and yielded specific ligands. The selection fingerprints obtained for a set of protein targets of pharmaceutical relevance clearly showed the preferential enrichment of ortho-, meta- or para-regioisomers, which was experimentally verified by affinity measurements in the absence of DNA. The discovered ligands included novel selective enzyme inhibitors and binders to tumour-associated antigens, which enabled conditional chimeric antigen receptor T-cell activation and tumour targeting.
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Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Christian Pellegrino
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Su Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Renier Myburgh
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, USA
| | - Peter K Vogt
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
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14
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Price AK, Paegel BM. Considerations for Achieving Maximized DNA Recovery in Solid-Phase DNA-Encoded Library Synthesis. ACS COMBINATORIAL SCIENCE 2020; 22:649-655. [PMID: 32786319 DOI: 10.1021/acscombsci.0c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded library (DEL) technology enables rapid, economical synthesis, and exploration of novel chemical space. Reaction development for DEL synthesis has recently accelerated in pace with a specific emphasis on ensuring that the reaction does not compromise the integrity of the encoding DNA. However, the factors that contribute to a reaction's "DNA compatibility" remain relatively unknown. We investigated several solid-phase reactions and encoding conditions and determined their impact on DNA compatibility. Conditions that minimized the accessibility of reactive groups on the DNA encoding tag (switching solvent, low temperature, double-stranded encoding tag) significantly improved compatibility. We showcased this approach in the multistep synthesis of an acyldepsipeptide (ADEP1) fragment, which preserved 73% of DNA for a >100-fold improvement over canonical conditions. These results are particularly encouraging in the context of multistep reaction sequences to access natural product-like scaffolds and more broadly underscore the importance of reconciling the biophysical properties and reactivity of DNA with chemistry development to yield high-quality libraries of those scaffolds.
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Affiliation(s)
- Alexander K. Price
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
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15
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Kómár P, Kalinić M. Denoising DNA Encoded Library Screens with Sparse Learning. ACS COMBINATORIAL SCIENCE 2020; 22:410-421. [PMID: 32531158 DOI: 10.1021/acscombsci.0c00007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded libraries (DELs) are large, pooled collections of compounds in which every library member is attached to a stretch of DNA encoding its complete synthetic history. DEL-based hit discovery involves affinity selection of the library against a protein of interest, whereby compounds retained by the target are subsequently identified by next-generation sequencing of the corresponding DNA tags. When analyzing the resulting data, one typically assumes that sequencing output (i.e., read counts) is proportional to the binding affinity of a given compound, thus enabling hit prioritization and elucidation of any underlying structure-activity relationships (SAR). This assumption, though, tends to be severely confounded by a number of factors, including variable reaction yields, presence of incomplete products masquerading as their intended counterparts, and sequencing noise. In practice, these confounders are often ignored, potentially contributing to low hit validation rates, and universally leading to loss of valuable information. To address this issue, we have developed a method for comprehensively denoising DEL selection outputs. Our method, dubbed "deldenoiser", is based on sparse learning and leverages inputs that are commonly available within a DEL generation and screening workflow. Using simulated and publicly available DEL affinity selection data, we show that "deldenoiser" is not only able to recover and rank true binders much more robustly than read count-based approaches but also that it yields scores, which accurately capture the underlying SAR. The proposed method can, thus, be of significant utility in hit prioritization following DEL screens.
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Affiliation(s)
- Péter Kómár
- Totient, Inc., 1 Alewife Center, Cambridge Massachusetts 02140 United States
| | - Marko Kalinić
- Totient, Inc., Sinđelićeva 9, 11000 Belgrade, Serbia
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16
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Li J, Li Y, Lu F, Liu L, Ji Q, Song K, Yin Q, Lerner RA, Yang G, Xu H, Ma P. A DNA-encoded library for the identification of natural product binders that modulate poly (ADP-ribose) polymerase 1, a validated anti-cancer target. Biochem Biophys Res Commun 2020; 533:241-248. [PMID: 32381359 DOI: 10.1016/j.bbrc.2020.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 01/01/2023]
Abstract
Natural products have been an invaluable source of drug discovery, but their targets remain largely unknown. Natural products enriched DNA-encoded chemical libraries (nDELs) empower the researchers to rapidly and economically screen numerous natural products against various protein targets, and therefore promote the elucidation of the molecular mechanisms. In this work, we used poly (ADP-ribose) polymerase 1 (PARP1), as an example to explore the usage of nDEL for the functional natural products selection. We used late-stage modification approach to label three positive binders with unique DNA barcodes, whose dissociation constants range from sub-micromolar to micromolar. The selection criterion was set up according to the enrichment of these controls. Five natural products selected by this criterion directly bind to PARP1 in SPR, among which luteolin exhibits the highest inhibitory activity against PARP1. Moreover, luteolin selectively induces accumulation of DNA double-strand breaks and G2/M phase arrest in BRCA-deficient cells. All the findings from these investigations on luteolin support that PARP1 inhibition is one of the mechanisms for its anti-cancer activity.
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Affiliation(s)
- Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Ke Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Qianqian Yin
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.
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17
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Xu H, Gu Y, Zhang S, Xiong H, Ma F, Lu F, Ji Q, Liu L, Ma P, Hou W, Yang G, Lerner RA. A Chemistry for Incorporation of Selenium into DNA‐Encoded Libraries. Angew Chem Int Ed Engl 2020; 59:13273-13280. [DOI: 10.1002/anie.202003595] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Wei Hou
- College of Pharmaceutical Science Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Richard A. Lerner
- Department of Chemistry Scripps Research Institute La Jolla CA 92037 USA
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18
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Xu H, Gu Y, Zhang S, Xiong H, Ma F, Lu F, Ji Q, Liu L, Ma P, Hou W, Yang G, Lerner RA. A Chemistry for Incorporation of Selenium into DNA‐Encoded Libraries. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Wei Hou
- College of Pharmaceutical Science Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Richard A. Lerner
- Department of Chemistry Scripps Research Institute La Jolla CA 92037 USA
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19
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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20
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Kim OH, Lee JH, Mah S, Park SY, Hong S, Hong SS. HS‑146, a novel phosphoinositide 3‑kinase α inhibitor, induces the apoptosis and inhibits the metastatic ability of human breast cancer cells. Int J Oncol 2020; 56:1509-1520. [PMID: 32236634 DOI: 10.3892/ijo.2020.5018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/21/2020] [Indexed: 11/06/2022] Open
Abstract
The phosphoinositide 3‑kinase (PI3K) signaling pathway plays an important role in human cancer as it regulates critical cellular functions, such as survival, proliferation and metabolism. In the present study, a novel PI3Kα inhibitor (HS‑146) was synthesized and its anticancer effects on MCF‑7, MDA‑MB‑231, SKBR3 and BT‑474 human breast cancer cell lines were confirmed. HS‑146 was found to be most effective in inhibiting the proliferation of MCF‑7 cells and in inducing cell cycle arrest in the G0/G1 phase by downregulating cyclin D1, cyclin E, cyclin‑dependent kinase (Cdk)2 and Cdk4, and upregulating p21Waf1/Cip1 protein levels in this cell line. The induction of apoptosis by HS‑146 was confirmed by DAPI staining and western blot analysis. Cell shrinkage and nuclear condensation, which are typical morphological markers of apoptosis, were increased by HS‑146 in the MCF‑7 cells in a concentration‑dependent manner, and HS‑146 also increased the protein expression levels of cleaved poly(ADP‑ribose) polymerase (PARP) and decreased the protein expression levels of Mcl‑1 and caspase‑7. In addition, HS‑146 effectively decreased the phosphorylation levels of downstream PI3K effectors, such as Akt, mammalian target of rapamycin (mTOR), glycogen synthase kinase 3β (GSK3β), p70S6K1 and eukaryotic translation initiation factor 4E‑binding protein 1 (4E‑BP1). Hypoxia‑inducible factor (HIF)‑1α and vascular endothelial growth factor (VEGF) expression were also suppressed by HS‑146 under hypoxic conditions, and HS‑146 inhibited the migration and invasion of MCF‑7 cells in a concentration‑dependent manner. On the whole, the findings of the present study suggest that HS‑146, a novel PI3Kα inhibitor, may be an effective novel therapeutic candidate that suppresses breast cancer proliferation and metastasis by inhibiting the PI3K/Akt/mTOR pathway.
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Affiliation(s)
- Ok Hyeon Kim
- College of Korean Medicine, Dongguk University, Goyang, Gyeonggi 10326, Republic of Korea
| | - Ju-Hee Lee
- College of Korean Medicine, Dongguk University, Goyang, Gyeonggi 10326, Republic of Korea
| | - Shinmee Mah
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Sung Yun Park
- College of Korean Medicine, Dongguk University, Goyang, Gyeonggi 10326, Republic of Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Soon-Sun Hong
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon 22332, Republic of Korea
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21
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Song M, Hwang GT. DNA-Encoded Library Screening as Core Platform Technology in Drug Discovery: Its Synthetic Method Development and Applications in DEL Synthesis. J Med Chem 2020; 63:6578-6599. [PMID: 32039601 DOI: 10.1021/acs.jmedchem.9b01782] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library technology (DELT) was introduced to our medicinal chemistry society more than 20 years ago. The application of DELT in the development of clinical candidates has been actively reported in the literature recently. A few representative examples include RIP1K inhibitors for inflammatory diseases and sEH inhibitors for endothelial dysfunction or abnormal tissue repair, among many others. Here, the authors would like to recall the recent developments in on-DNA synthetic methodologies for DEL construction and to analyze recent examples in the literature of DELT-based drug development efforts pursued in both the academic and industrial sectors. With this perspective, we hope to provide a useful summary of recent DELT-based drug discovery research and to discuss the future scope of DELT in medicinal chemistry.
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Affiliation(s)
- Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
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22
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Tian J, Teuscher KB, Aho ER, Alvarado JR, Mills JJ, Meyers KM, Gogliotti RD, Han C, Macdonald JD, Sai J, Shaw JG, Sensintaffar JL, Zhao B, Rietz TA, Thomas LR, Payne WG, Moore WJ, Stott GM, Kondo J, Inoue M, Coffey RJ, Tansey WP, Stauffer SR, Lee T, Fesik SW. Discovery and Structure-Based Optimization of Potent and Selective WD Repeat Domain 5 (WDR5) Inhibitors Containing a Dihydroisoquinolinone Bicyclic Core. J Med Chem 2020; 63:656-675. [PMID: 31858797 PMCID: PMC6986559 DOI: 10.1021/acs.jmedchem.9b01608] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple chromatin-centric processes. Overexpression of WDR5 correlates with a poor clinical outcome in many human cancers, and WDR5 itself has emerged as an attractive target for therapy. Most drug-discovery efforts center on the WIN site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. Here, we describe discovery of a novel WDR5 WIN site antagonists containing a dihydroisoquinolinone bicyclic core using a structure-based design. These compounds exhibit picomolar binding affinity and selective concentration-dependent antiproliferative activities in sensitive MLL-fusion cell lines. Furthermore, these WDR5 WIN site binders inhibit proliferation in MYC-driven cancer cells and reduce MYC recruitment to chromatin at MYC/WDR5 co-bound genes. Thus, these molecules are useful probes to study the implication of WDR5 inhibition in cancers and serve as a potential starting point toward the discovery of anti-WDR5 therapeutics.
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Affiliation(s)
- Jianhua Tian
- Chemical Synthesis Core, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Kevin B. Teuscher
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Erin R. Aho
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Joseph R. Alvarado
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jonathan J. Mills
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Kenneth M. Meyers
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Rocco D. Gogliotti
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Changho Han
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jonathan D. Macdonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - J. Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - John L. Sensintaffar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Tyson A. Rietz
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Lance R. Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - William G. Payne
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - William J. Moore
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Gordon M. Stott
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jumpei Kondo
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
- Department of Biochemistry, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Masahiro Inoue
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
- Department of Biochemistry, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Robert J. Coffey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - William P. Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Shaun R. Stauffer
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, USA
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23
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Xu H, Ma F, Wang N, Hou W, Xiong H, Lu F, Li J, Wang S, Ma P, Yang G, Lerner RA. DNA-Encoded Libraries: Aryl Fluorosulfonates as Versatile Electrophiles Enabling Facile On-DNA Suzuki, Sonogashira, and Buchwald Reactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1901551. [PMID: 31832315 PMCID: PMC6891896 DOI: 10.1002/advs.201901551] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/04/2019] [Indexed: 05/07/2023]
Abstract
Using (hetero)aryl fluorosulfonates as versatile electrophiles, facile on-DNA cross-coupling reactions of Suzuki, Sonogashira, and Buchwald are reported here. Notably, all of these reactions show excellent functional group tolerance, mild reaction conditions (relative low temperature and open to air), rich heterocyclic coupling partners, and more importantly, DNA-compatibility. Thus, these new reactions based on efficient formation of C(sp2)-C(sp2), C(sp2)-C(sp), and C(sp2)-N bonds are highly amenable to synthesis of DNA-encoded libraries with great molecular diversity.
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Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Nan Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Wei Hou
- College of Pharmaceutical Scienceand Institute of Drug Development & Chemical Biology (IDD & CB)Zhejiang University of TechnologyHangzhou310014China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
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24
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Lu Y, Qin S, Zhang B, Dai A, Cai X, Ma M, Gao ZG, Yang D, Stevens RC, Jacobson KA, Wang MW, Shui W. Accelerating the Throughput of Affinity Mass Spectrometry-Based Ligand Screening toward a G Protein-Coupled Receptor. Anal Chem 2019; 91:8162-8169. [PMID: 31094506 PMCID: PMC6669887 DOI: 10.1021/acs.analchem.9b00477] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Affinity mass spectrometry (MS) enables rapid screening of compound mixtures for ligands bound to a specific protein target, yet its current throughput is limited to individually assay pools of 400-2000 compounds. Typical affinity MS screens implemented in pharmaceutical industry laboratories identify putative ligands based on qualitative analysis of compound binding to the target whereas no quantitative information is acquired to discriminate high- and low-affinity ligands in the screening phase. Furthermore, these screens require purification of a stabilized form of the protein target, which poses a great challenge for membrane receptor targets. Here, we describe a new, potentially general affinity MS strategy that allows screening of 20,000 compounds in one pool for highly efficient ligand discovery toward a G protein-coupled receptor (GPCR) target. Quantitative measurement of compound binding to the receptor enables high-affinity ligand selection using both the purified receptor and receptor-embedded cell membranes. This high-throughput, label-free and quantitative affinity MS screen resulted in discovery of three new antagonists of the A2A adenosine receptor.
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Affiliation(s)
- Yan Lu
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Bingjie Zhang
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Antao Dai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Xiaoqing Cai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Mengna Ma
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhan-Guo Gao
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Dehua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Raymond C. Stevens
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Kenneth A. Jacobson
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Ming-Wei Wang
- University of Chinese Academy of Sciences, 100049 Beijing, China
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- School of Pharmacy, Fudan University, 201203 Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
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25
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Gerry CJ, Wawer MJ, Clemons PA, Schreiber SL. DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules. J Am Chem Soc 2019; 141:10225-10235. [PMID: 31184885 DOI: 10.1021/jacs.9b01203] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is challenging to incorporate stereochemical diversity and topographic complexity into DNA-encoded libraries (DELs) because DEL syntheses cannot fully exploit the capabilities of modern synthetic organic chemistry. Here, we describe the design, construction, and validation of DOS-DEL-1, a library of 107 616 DNA-barcoded chiral 2,3-disubsituted azetidines and pyrrolidines. We used stereospecific C-H arylation chemistry to furnish complex scaffolds primed for DEL synthesis, and we developed an improved on-DNA Suzuki reaction to maximize library quality. We then studied both the structural diversity of the library and the physicochemical properties of individual compounds using Tanimoto multifusion similarity analysis, among other techniques. These analyses revealed not only that most DOS-DEL-1 members have "drug-like" properties, but also that the library more closely resembles compound collections derived from diversity synthesis than those from other sources (e.g., commercial vendors). Finally, we performed validation screens against horseradish peroxidase and carbonic anhydrase IX, and we developed a novel, Poisson-based statistical framework to analyze the results. A set of assay positives were successfully translated into potent carbonic anhydrase inhibitors (IC50 = 20.1-68.7 nM), which confirmed the success of the synthesis and screening procedures. These results establish a strategy to synthesize DELs with scaffold-based stereochemical diversity and complexity that does not require the development of novel DNA-compatible chemistry.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Mathias J Wawer
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
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26
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Ma P, Xu H, Li J, Lu F, Ma F, Wang S, Xiong H, Wang W, Buratto D, Zonta F, Wang N, Liu K, Hua T, Liu Z, Yang G, Lerner RA. Functionality‐Independent DNA Encoding of Complex Natural Products. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901485] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Nan Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Kaiwen Liu
- School of Life Science and TechnologyShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences 200031 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- iHuman InstituteShanghaiTech University 201210 Shanghai China
| | - Tian Hua
- iHuman InstituteShanghaiTech University 201210 Shanghai China
| | - Zhi‐Jie Liu
- iHuman InstituteShanghaiTech University 201210 Shanghai China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech University 201210 Shanghai China
| | - Richard A. Lerner
- Department of ChemistryScripps Research Institute La Jolla CA 92037 USA
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27
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Ma P, Xu H, Li J, Lu F, Ma F, Wang S, Xiong H, Wang W, Buratto D, Zonta F, Wang N, Liu K, Hua T, Liu ZJ, Yang G, Lerner RA. Functionality-Independent DNA Encoding of Complex Natural Products. Angew Chem Int Ed Engl 2019; 58:9254-9261. [PMID: 31020752 DOI: 10.1002/anie.201901485] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Indexed: 01/06/2023]
Abstract
DNA encoded chemical libraries (DELs) link the powers of genetics and chemical synthesis via combinatorial optimization. Through combinatorial chemistry, DELs can grow to the unprecedented size of billions to trillions. To take full advantage of the DEL approach, linking the power of genetics directly to chemical structures would offer even greater diversity in a finite chemical world. Natural products have evolved an incredible structural diversity along with their biological evolution. Herein, we used traditional Chinese medicines (TCMs) as examples in a late-stage modification toolbox approach to annotate these complex organic compounds with amplifiable DNA barcodes, which could be easily incorporated into a DEL. The method of end-products labeling also generates a cluster of isomers with a single DNA tag at different sites. These isomers provide an additional spatial diversity for multiple accessible pockets of targeted proteins. Notably, a novel PARP1 inhibitor from TCM has been identified from the natural products enriched DEL (nDEL).
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Affiliation(s)
- Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Nan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Kaiwen Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, 92037, USA
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28
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Kunig V, Potowski M, Gohla A, Brunschweiger A. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem 2019; 399:691-710. [PMID: 29894294 DOI: 10.1515/hsz-2018-0119] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
Abstract
DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.
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Affiliation(s)
- Verena Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Marco Potowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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29
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Yuen LH, Dana S, Liu Y, Bloom SI, Thorsell AG, Neri D, Donato AJ, Kireev D, Schüler H, Franzini RM. A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes. J Am Chem Soc 2019; 141:5169-5181. [DOI: 10.1021/jacs.8b08039] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Srikanta Dana
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Yu Liu
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Samuel I. Bloom
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Dario Neri
- Department of Pharmaceutical Sciences, ETH Zürich, Vladimir Prelog Weg 3, 8093 Zürich, Switzerland
| | - Anthony J. Donato
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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30
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Miller MS, Thompson PE, Gabelli SB. Structural Determinants of Isoform Selectivity in PI3K Inhibitors. Biomolecules 2019; 9:biom9030082. [PMID: 30813656 PMCID: PMC6468644 DOI: 10.3390/biom9030082] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) are important therapeutic targets for the treatment of cancer, thrombosis, and inflammatory and immune diseases. The four highly homologous Class I isoforms, PI3K, PI3K, PI3K and PI3K have unique, non-redundant physiological roles and as such, isoform selectivity has been a key consideration driving inhibitor design and development. In this review, we discuss the structural biology of PI3Ks and how our growing knowledge of structure has influenced the medicinal chemistry of PI3K inhibitors. We present an analysis of the available structure-selectivity-activity relationship data to highlight key insights into how the various regions of the PI3K binding site influence isoform selectivity. The picture that emerges is one that is far from simple and emphasizes the complex nature of protein-inhibitor binding, involving protein flexibility, energetics, water networks and interactions with non-conserved residues.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia.
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Departments of Medicine, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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31
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Sannino A, Gabriele E, Bigatti M, Mulatto S, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries. Chembiochem 2019; 20:955-962. [DOI: 10.1002/cbic.201800766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Elena Gabriele
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | | | - Sara Mulatto
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jacopo Piazzi
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Florent Samain
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
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32
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Gerry CJ, Yang Z, Stasi M, Schreiber SL. DNA-Compatible [3 + 2] Nitrone-Olefin Cycloaddition Suitable for DEL Syntheses. Org Lett 2019; 21:1325-1330. [PMID: 30762372 DOI: 10.1021/acs.orglett.9b00017] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The limited scope of DNA-compatible chemistry restricts the types of chemical features that can be incorporated into DNA-encoded libraries (DELs). Here, a method to synthesize DNA-conjugated polycyclic isoxazolidines via a [3 + 2] nitrone-olefin cycloaddition is described. The reaction is compatible with many olefin-containing substrates and diverse N-alkylhydroxylamines. The ability to perform subsequent DNA ligation and PCR amplification was also confirmed. This methodology facilitates the synthesis of DELs containing topographically complex compounds with underexplored chemical features.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Zhenhua Yang
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Michele Stasi
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
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33
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Leontiadou H, Galdadas I, Athanasiou C, Cournia Z. Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations. Sci Rep 2018; 8:15544. [PMID: 30341384 PMCID: PMC6195558 DOI: 10.1038/s41598-018-27044-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 05/04/2018] [Indexed: 12/19/2022] Open
Abstract
Phosphoinositide 3-kinase alpha (PI3Kα) is involved in fundamental cellular processes including cell proliferation and differentiation and is frequently mutated in human malignancies. One of the most common mutations is E545K, which results in an amino acid substitution of opposite charge. It has been recently proposed that in this oncogenic charge-reversal mutation, the interactions between the protein catalytic and regulatory subunits are abrogated, resulting in loss of regulation and constitutive PI3Kα activity, which can lead to oncogenesis. To assess the mechanism of the PI3Kα E545K activating mutation, extensive Molecular Dynamics simulations were performed to examine conformational changes differing between the wild type (WT) and mutant proteins as they occur in microsecond simulations. In the E545K mutant PI3Kα, we observe a spontaneous detachment of the nSH2 PI3Kα domain (regulatory subunit, p85α) from the helical domain (catalytic subunit, p110α) causing significant loss of communication between the regulatory and catalytic subunits. We examine the allosteric network of the two proteins and show that a cluster of residues around the mutation is important for delivering communication signals between the catalytic and regulatory subunits. Our results demonstrate the dynamical and structural effects induced by the p110α E545K mutation in atomic level detail and indicate a possible mechanism for the loss of regulation that E545K confers on PI3Kα.
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Affiliation(s)
- Hari Leontiadou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Ioannis Galdadas
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Christina Athanasiou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece.
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34
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Wang X, Sun H, Liu J, Dai D, Zhang M, Zhou H, Zhong W, Lu X. Ruthenium-Promoted C–H Activation Reactions between DNA-Conjugated Acrylamide and Aromatic Acids. Org Lett 2018; 20:4764-4768. [DOI: 10.1021/acs.orglett.8b01837] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- 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, P. R. China
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. China
| | - Hui Sun
- 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, P. R. China
| | - Jiaxiang Liu
- 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, P. R. China
| | - Dongcheng Dai
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. China
| | - Mingqiang Zhang
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. China
| | - Hu Zhou
- 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, P. R. China
| | - Wenge Zhong
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd., 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P. R. 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, P. R. China
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35
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Neri D, Lerner RA. DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information. Annu Rev Biochem 2018; 87:479-502. [PMID: 29328784 PMCID: PMC6080696 DOI: 10.1146/annurev-biochem-062917-012550] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.
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Affiliation(s)
- Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), 8093 Zürich, Switzerland;
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA;
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36
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Leveridge M, Chung CW, Gross JW, Phelps CB, Green D. Integration of Lead Discovery Tactics and the Evolution of the Lead Discovery Toolbox. SLAS DISCOVERY 2018; 23:881-897. [PMID: 29874524 DOI: 10.1177/2472555218778503] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There has been much debate around the success rates of various screening strategies to identify starting points for drug discovery. Although high-throughput target-based and phenotypic screening has been the focus of this debate, techniques such as fragment screening, virtual screening, and DNA-encoded library screening are also increasingly reported as a source of new chemical equity. Here, we provide examples in which integration of more than one screening approach has improved the campaign outcome and discuss how strengths and weaknesses of various methods can be used to build a complementary toolbox of approaches, giving researchers the greatest probability of successfully identifying leads. Among others, we highlight case studies for receptor-interacting serine/threonine-protein kinase 1 and the bromo- and extra-terminal domain family of bromodomains. In each example, the unique insight or chemistries individual approaches provided are described, emphasizing the synergy of information obtained from the various tactics employed and the particular question each tactic was employed to answer. We conclude with a short prospective discussing how screening strategies are evolving, what this screening toolbox might look like in the future, how to maximize success through integration of multiple tactics, and scenarios that drive selection of one combination of tactics over another.
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Affiliation(s)
- Melanie Leveridge
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
| | - Chun-Wa Chung
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
| | - Jeffrey W Gross
- 2 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Collegeville, PA, USA
| | - Christopher B Phelps
- 3 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Cambridge, MA, USA
| | - Darren Green
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
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37
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Wei L, Chintala S, Ciamporcero E, Ramakrishnan S, Elbanna M, Wang J, Hu Q, Glenn ST, Murakami M, Liu L, Gomez EC, Sun Y, Conroy J, Miles KM, Malathi K, Ramaiah S, Anbarasu A, Woloszynska-Read A, Johnson CS, Conroy J, Liu S, Morrison CD, Pili R. Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts. Oncotarget 2018; 7:76374-76389. [PMID: 27823983 PMCID: PMC5363516 DOI: 10.18632/oncotarget.13062] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 10/22/2016] [Indexed: 11/25/2022] Open
Abstract
Purpose Effective systemic therapeutic options are limited for bladder cancer. In this preclinical study we tested whether bladder cancer gene alterations may be predictive of treatment response. Experimental design We performed genomic profiling of two bladder cancer patient derived tumor xenografts (PDX). We optimized the exome sequence analysis method to overcome the mouse genome interference. Results We identified a number of somatic mutations, mostly shared by the primary tumors and PDX. In particular, BLCAb001, which is less responsive to cisplatin than BLCAb002, carried non-sense mutations in several genes associated with cisplatin resistance, including MLH1, BRCA2, and CASP8. Furthermore, RNA-Seq analysis revealed the overexpression of cisplatin resistance associated genes such as SLC7A11, TLE4, and IL1A in BLCAb001. Two different PIK3CA mutations, E542K and E545K, were identified in BLCAb001 and BLCAb002, respectively. Thus, we tested whether the genomic profiling was predictive of response to a dual PI3K/mTOR targeting agent, LY3023414. Despite harboring similar PIK3CA mutations, BLCAb001 and BLCAb002 exhibited differential response, both in vitro and in vivo. Sustained target modulation was observed in the sensitive model BLCAb002 but not in BLCAb001, as well as decreased autophagy. Interestingly, computational modelling of mutant structures and affinity binding to PI3K revealed that E542K mutation was associated with weaker drug binding than E545K. Conclusions Our results suggest that the presence of activating PIK3CA mutations may not necessarily predict in vivo treatment response to PI3K targeted therapies, while specific gene alterations may be predictive for cisplatin response in bladder cancer models and, potentially, in patients as well.
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Affiliation(s)
- Lei Wei
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Sreenivasulu Chintala
- Genitourinary Program, Roswell Park Cancer Institute, Buffalo, NY, USA.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA.,Genitourinary Program, Indiana University-Simon Cancer Center, Indianapolis, IN, USA
| | - Eric Ciamporcero
- Genitourinary Program, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Swathi Ramakrishnan
- Genitourinary Program, Roswell Park Cancer Institute, Buffalo, NY, USA.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - May Elbanna
- Genitourinary Program, Roswell Park Cancer Institute, Buffalo, NY, USA.,Genitourinary Program, Indiana University-Simon Cancer Center, Indianapolis, IN, USA
| | - Jianmin Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qiang Hu
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Sean T Glenn
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Mitsuko Murakami
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Lu Liu
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Eduardo Cortes Gomez
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Yuchen Sun
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jacob Conroy
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kiersten Marie Miles
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Anna Woloszynska-Read
- Genitourinary Program, Roswell Park Cancer Institute, Buffalo, NY, USA.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Candace S Johnson
- Genitourinary Program, Roswell Park Cancer Institute, Buffalo, NY, USA.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jeffrey Conroy
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Carl D Morrison
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Roberto Pili
- Genitourinary Program, Roswell Park Cancer Institute, Buffalo, NY, USA.,Genitourinary Program, Indiana University-Simon Cancer Center, Indianapolis, IN, USA
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38
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Kuai L, O’Keeffe T, Arico-Muendel C. Randomness in DNA Encoded Library Selection Data Can Be Modeled for More Reliable Enrichment Calculation. SLAS DISCOVERY 2018; 23:405-416. [DOI: 10.1177/2472555218757718] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA Encoded Libraries (DELs) use unique DNA sequences to tag each chemical warhead within a library mixture to enable deconvolution following affinity selection against a target protein. With next-generation sequencing, millions to billions of sequences can be read and counted to report binding events. This unprecedented capability has enabled researchers to synthesize and analyze numerically large chemical libraries. Despite the common perception that each library member undergoes a miniaturized affinity assay, selections with higher complexity libraries often produce results that are difficult to rank order. In this study, we aimed to understand the robustness of DEL selection by examining the sequencing readouts of warheads and chemotype families among a large number of experimentally repeated selections. The results revealed that (1) the output of DEL selection is intrinsically noisy but can be reliably modeled by the Poisson distribution, and (2) Poisson noise is the dominating noise at low copy counts and can be estimated even from a single experiment. We also discuss the shortcomings of data analyses based on directly using copy counts and their linear transformations, and propose a framework that incorporates proper normalization and confidence interval calculation to help researchers better understand DEL data.
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39
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Brown DG, Brown GA, Centrella P, Certel K, Cooke RM, Cuozzo JW, Dekker N, Dumelin CE, Ferguson A, Fiez-Vandal C, Geschwindner S, Guié MA, Habeshian S, Keefe AD, Schlenker O, Sigel EA, Snijder A, Soutter HT, Sundström L, Troast DM, Wiggin G, Zhang J, Zhang Y, Clark MA. Agonists and Antagonists of Protease-Activated Receptor 2 Discovered within a DNA-Encoded Chemical Library Using Mutational Stabilization of the Target. SLAS DISCOVERY 2018; 23:429-436. [DOI: 10.1177/2472555217749847] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The discovery of ligands via affinity-mediated selection of DNA-encoded chemical libraries is driven by the quality and concentration of the protein target. G-protein-coupled receptors (GPCRs) and other membrane-bound targets can be difficult to isolate in their functional state and at high concentrations, and therefore have been challenging for affinity-mediated selection. Here, we report a successful selection campaign against protease-activated receptor 2 (PAR2). Using a thermo-stabilized mutant of PAR2, we conducted affinity selection using our >100-billion-compound DNA-encoded library. We observed a number of putative ligands enriched upon selection, and subsequent cellular profiling revealed these ligands to comprise both agonists and antagonists. The agonist series shared structural similarity with known agonists. The antagonists were shown to bind in a novel allosteric binding site on the PAR2 protein. This report serves to demonstrate that cell-free affinity selection against GPCRs can be achieved with mutant stabilized protein targets.
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Affiliation(s)
- Dean G. Brown
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Waltham, MA, USA
| | - Giles A. Brown
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | | | - Kaan Certel
- X-Chem Pharmaceuticals, Waltham, MA, USA
- Novartis Institute for BioMedical Research, Cambridge, MA, USA
| | - Robert M. Cooke
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | | | - Niek Dekker
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | - Christoph E. Dumelin
- X-Chem Pharmaceuticals, Waltham, MA, USA
- Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Andrew Ferguson
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Waltham, MA, USA
- X-Chem, Inc., Waltham, MA, USA
| | | | - Stefan Geschwindner
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | | | - Sevan Habeshian
- X-Chem Pharmaceuticals, Waltham, MA, USA
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Oliver Schlenker
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | | | - Arjan Snijder
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | | | - Linda Sundström
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | - Dawn M. Troast
- X-Chem Pharmaceuticals, Waltham, MA, USA
- Morphic Therapeutic, Waltham, MA
| | - Giselle Wiggin
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | - Jing Zhang
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Waltham, MA, USA
- Entasis Therapeutics, Waltham, MA
| | - Ying Zhang
- X-Chem Pharmaceuticals, Waltham, MA, USA
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40
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Pirali T, Ciraolo E, Aprile S, Massarotti A, Berndt A, Griglio A, Serafini M, Mercalli V, Landoni C, Campa CC, Margaria JP, Silva RL, Grosa G, Sorba G, Williams R, Hirsch E, Tron GC. Identification of a Potent Phosphoinositide 3-Kinase Pan Inhibitor Displaying a Strategic Carboxylic Acid Group and Development of Its Prodrugs. ChemMedChem 2017; 12:1542-1554. [PMID: 28857471 PMCID: PMC5697638 DOI: 10.1002/cmdc.201700340] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/25/2017] [Indexed: 02/03/2023]
Abstract
Activation of the phosphoinositide 3-kinase (PI3K) pathway is a key signaling event in cancer, inflammation, and other proliferative diseases. PI3K inhibitors are already approved for some specific clinical indications, but their systemic on-target toxicity limits their larger use. In particular, whereas toxicity is tolerable in acute treatment of life-threatening diseases, this is less acceptable in chronic conditions. In the past, the strategy to overcome this drawback was to block selected isoforms mainly expressed in leukocytes, but redundancy within the PI3K family members challenges the effectiveness of this approach. On the other hand, decreasing exposure to selected target cells represents a so-far unexplored alternative to circumvent systemic toxicity. In this manuscript, we describe the generation of a library of triazolylquinolones and the development of the first prodrug pan-PI3K inhibitor.
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Affiliation(s)
- Tracey Pirali
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Elisa Ciraolo
- Department of Molecular Biotechnology and Health SciencesUniversity of TorinoVia Nizza 5210126TorinoItaly
| | - Silvio Aprile
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Alberto Massarotti
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Alex Berndt
- MRC Laboratory of Molecular BiologyMedical Research CouncilCambridgeCB2 0QHUK
| | - Alessia Griglio
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Marta Serafini
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Valentina Mercalli
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Clarissa Landoni
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Carlo Cosimo Campa
- Department of Molecular Biotechnology and Health SciencesUniversity of TorinoVia Nizza 5210126TorinoItaly
| | - Jean Piero Margaria
- Department of Molecular Biotechnology and Health SciencesUniversity of TorinoVia Nizza 5210126TorinoItaly
| | - Rangel L. Silva
- Department of Pharmacology, Ribeirão Preto Medical SchoolUniversity of São PauloAvenida Bandeirantes 390014049-900Ribeirão PretoBrazil
| | - Giorgio Grosa
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Giovanni Sorba
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
| | - Roger Williams
- MRC Laboratory of Molecular BiologyMedical Research CouncilCambridgeCB2 0QHUK
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health SciencesUniversity of TorinoVia Nizza 5210126TorinoItaly
- Kither Biotech S.r.l.Molecular Biotechnology CenterVia Nizza 5210126TorinoItaly
| | - Gian Cesare Tron
- Dipartimento di Scienze del FarmacoUniversità degli Studi del Piemonte Orientale “A. Avogadro”Largo Donegani 228100NovaraItaly
- Kither Biotech S.r.l.Molecular Biotechnology CenterVia Nizza 5210126TorinoItaly
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41
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Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening. Nat Commun 2017; 8:16081. [PMID: 28714473 PMCID: PMC5520047 DOI: 10.1038/ncomms16081] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 05/24/2017] [Indexed: 12/18/2022] Open
Abstract
The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery. Encoded Library Technology (ELT) has streamlined the identification of chemical ligands for protein targets in drug discovery. Here, the authors optimize the ELT approach to screen multiple proteins in parallel and identify promising targets and antibacterial compounds for S. aureus, A. baumannii and M. tuberculosis.
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42
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Cuozzo JW, Centrella PA, Gikunju D, Habeshian S, Hupp CD, Keefe AD, Sigel EA, Soutter HH, Thomson HA, Zhang Y, Clark MA. Discovery of a Potent BTK Inhibitor with a Novel Binding Mode by Using Parallel Selections with a DNA-Encoded Chemical Library. Chembiochem 2017; 18:864-871. [PMID: 28056160 DOI: 10.1002/cbic.201600573] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Indexed: 12/21/2022]
Abstract
We have identified and characterized novel potent inhibitors of Bruton's tyrosine kinase (BTK) from a single DNA-encoded library of over 110 million compounds by using multiple parallel selection conditions, including variation in target concentration and addition of known binders to provide competition information. Distinct binding profiles were observed by comparing enrichments of library building block combinations under these conditions; one enriched only at high concentrations of BTK and was competitive with ATP, and another enriched at both high and low concentrations of BTK and was not competitive with ATP. A compound representing the latter profile showed low nanomolar potency in biochemical and cellular BTK assays. Results from kinetic mechanism of action studies were consistent with the selection profiles. Analysis of the co-crystal structure of the most potent compound demonstrated a novel binding mode that revealed a new pocket in BTK. Our results demonstrate that profile-based selection strategies using DNA-encoded libraries form the basis of a new methodology to rapidly identify small molecule inhibitors with novel binding modes to clinically relevant targets.
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Affiliation(s)
- John W Cuozzo
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
| | | | - Diana Gikunju
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
| | - Sevan Habeshian
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
| | | | - Anthony D Keefe
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
| | - Eric A Sigel
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
| | - Holly H Soutter
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
| | | | - Ying Zhang
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
| | - Matthew A Clark
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA, 02453, USA
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43
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Yuen LH, Franzini RM. Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View. Chembiochem 2017; 18:829-836. [DOI: 10.1002/cbic.201600567] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| | - Raphael M. Franzini
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
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44
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Mendes KR, Malone ML, Ndungu JM, Suponitsky-Kroyter I, Cavett VJ, McEnaney PJ, MacConnell AB, Doran TM, Ronacher K, Stanley K, Utset O, Walzl G, Paegel BM, Kodadek T. High-throughput Identification of DNA-Encoded IgG Ligands that Distinguish Active and Latent Mycobacterium tuberculosis Infections. ACS Chem Biol 2017; 12:234-243. [PMID: 27957856 DOI: 10.1021/acschembio.6b00855] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The circulating antibody repertoire encodes a patient's health status and pathogen exposure history, but identifying antibodies with diagnostic potential usually requires knowledge of the antigen(s). We previously circumvented this problem by screening libraries of bead-displayed small molecules against case and control serum samples to discover "epitope surrogates" (ligands of IgGs enriched in the case sample). Here, we describe an improved version of this technology that employs DNA-encoded libraries and high-throughput FACS-based screening to discover epitope surrogates that differentiate noninfectious/latent (LTB) patients from infectious/active TB (ATB) patients, which is imperative for proper treatment selection and antibiotic stewardship. Normal control/LTB (10 patients each, NCL) and ATB (10 patients) serum pools were screened against a library (5 × 106 beads, 448 000 unique compounds) using fluorescent antihuman IgG to label hit compound beads for FACS. Deep sequencing decoded all hit structures and each hit's occurrence frequencies. ATB hits were pruned of NCL hits and prioritized for resynthesis based on occurrence and homology. Several structurally homologous families were identified and 16/21 resynthesized representative hits validated as selective ligands of ATB serum IgGs (p < 0.005). The native secreted TB protein Ag85B (though not the E. coli recombinant form) competed with one of the validated ligands for binding to antibodies, suggesting that it mimics a native Ag85B epitope. The use of DNA-encoded libraries and FACS-based screening in epitope surrogate discovery reveals thousands of potential hit structures. Distilling this list down to several consensus chemical structures yielded a diagnostic panel for ATB composed of thermally stable and economically produced small molecule ligands in place of protein antigens.
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Affiliation(s)
- Kimberly R. Mendes
- Opko Health, Inc., 5353 Parkside
Drive Jupiter, Florida 33458, United States
| | | | - John Maina Ndungu
- Opko Health, Inc., 5353 Parkside
Drive Jupiter, Florida 33458, United States
| | | | | | | | | | | | - Katharina Ronacher
- Department
of Science and Technology/National Research Foundation Centre of Excellence
for Biomedical TB Research/Medical Research Council Centre for Molecular
and Cellular Biology, Division of Molecular Biology and Human Genetics,
Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Kim Stanley
- Department
of Science and Technology/National Research Foundation Centre of Excellence
for Biomedical TB Research/Medical Research Council Centre for Molecular
and Cellular Biology, Division of Molecular Biology and Human Genetics,
Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ofelia Utset
- Opko Health, Inc., 5353 Parkside
Drive Jupiter, Florida 33458, United States
| | - Gerhard Walzl
- Department
of Science and Technology/National Research Foundation Centre of Excellence
for Biomedical TB Research/Medical Research Council Centre for Molecular
and Cellular Biology, Division of Molecular Biology and Human Genetics,
Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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45
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Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska K, Nocek BP, Taipale M, Savchenko A, Ensminger AW. Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila. Mol Syst Biol 2016; 12:893. [PMID: 27986836 PMCID: PMC5199130 DOI: 10.15252/msb.20167381] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pathogens deliver complex arsenals of translocated effector proteins to host cells during infection, but the extent to which these proteins are regulated once inside the eukaryotic cell remains poorly defined. Among all bacterial pathogens, Legionella pneumophila maintains the largest known set of translocated substrates, delivering over 300 proteins to the host cell via its Type IVB, Icm/Dot translocation system. Backed by a few notable examples of effector–effector regulation in L. pneumophila, we sought to define the extent of this phenomenon through a systematic analysis of effector–effector functional interaction. We used Saccharomyces cerevisiae, an established proxy for the eukaryotic host, to query > 108,000 pairwise genetic interactions between two compatible expression libraries of ~330 L. pneumophila‐translocated substrates. While capturing all known examples of effector–effector suppression, we identify fourteen novel translocated substrates that suppress the activity of other bacterial effectors and one pair with synergistic activities. In at least nine instances, this regulation is direct—a hallmark of an emerging class of proteins called metaeffectors, or “effectors of effectors”. Through detailed structural and functional analysis, we show that metaeffector activity derives from a diverse range of mechanisms, shapes evolution, and can be used to reveal important aspects of each cognate effector's function. Metaeffectors, along with other, indirect, forms of effector–effector modulation, may be a common feature of many intracellular pathogens—with unrealized potential to inform our understanding of how pathogens regulate their interactions with the host cell.
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Affiliation(s)
- Malene L Urbanus
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Andrew T Quaile
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Mariya Morar
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Chitong Rao
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Mandy Lam
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Christina Oatway
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marianne E Cuff
- Biosciences Division, Argonne National Laboratory, Structural Biology Center, Lemont, IL, USA.,Midwest Center for Structural Genomics, Lemont IL, USA
| | - Jerzy Osipiuk
- Biosciences Division, Argonne National Laboratory, Structural Biology Center, Lemont, IL, USA.,Midwest Center for Structural Genomics, Lemont IL, USA
| | - Karolina Michalska
- Biosciences Division, Argonne National Laboratory, Structural Biology Center, Lemont, IL, USA.,Midwest Center for Structural Genomics, Lemont IL, USA
| | - Boguslaw P Nocek
- Biosciences Division, Argonne National Laboratory, Structural Biology Center, Lemont, IL, USA.,Midwest Center for Structural Genomics, Lemont IL, USA
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada .,Midwest Center for Structural Genomics, Lemont IL, USA
| | - Alexander W Ensminger
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Public Health Ontario, Toronto, ON, Canada
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46
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Abstract
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces. This Review provides an overview of the development and applications of DNA-encoded chemistry, highlighting the challenges and future directions for the use of this technology.
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47
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Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
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48
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Discovery of cofactor-specific, bactericidal Mycobacterium tuberculosis InhA inhibitors using DNA-encoded library technology. Proc Natl Acad Sci U S A 2016; 113:E7880-E7889. [PMID: 27864515 DOI: 10.1073/pnas.1610978113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Millions of individuals are infected with and die from tuberculosis (TB) each year, and multidrug-resistant (MDR) strains of TB are increasingly prevalent. As such, there is an urgent need to identify novel drugs to treat TB infections. Current frontline therapies include the drug isoniazid, which inhibits the essential NADH-dependent enoyl-acyl-carrier protein (ACP) reductase, InhA. To inhibit InhA, isoniazid must be activated by the catalase-peroxidase KatG. Isoniazid resistance is linked primarily to mutations in the katG gene. Discovery of InhA inhibitors that do not require KatG activation is crucial to combat MDR TB. Multiple discovery efforts have been made against InhA in recent years. Until recently, despite achieving high potency against the enzyme, these efforts have been thwarted by lack of cellular activity. We describe here the use of DNA-encoded X-Chem (DEX) screening, combined with selection of appropriate physical properties, to identify multiple classes of InhA inhibitors with cell-based activity. The utilization of DEX screening allowed the interrogation of very large compound libraries (1011 unique small molecules) against multiple forms of the InhA enzyme in a multiplexed format. Comparison of the enriched library members across various screening conditions allowed the identification of cofactor-specific inhibitors of InhA that do not require activation by KatG, many of which had bactericidal activity in cell-based assays.
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Ding Y, Franklin GJ, DeLorey JL, Centrella PA, Mataruse S, Clark MA, Skinner SR, Belyanskaya S. Design and Synthesis of Biaryl DNA-Encoded Libraries. ACS COMBINATORIAL SCIENCE 2016; 18:625-629. [PMID: 27571034 DOI: 10.1021/acscombsci.6b00078] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA-encoded library technology (ELT) is a powerful tool for the discovery of new small-molecule ligands to various protein targets. Here we report the design and synthesis of biaryl DNA-encoded libraries based on the scaffold of 5-formyl 3-iodobenzoic acid. Three reactions on DNA template, acylation, Suzuki-Miyaura coupling and reductive amination, were applied in the library synthesis. The three cycle library of 3.5 million diversity has delivered potent hits for phosphoinositide 3-kinase α (PI3Kα).
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Affiliation(s)
- Yun Ding
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - G. Joseph Franklin
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer L. DeLorey
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Paolo A. Centrella
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Sibongile Mataruse
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Matthew A. Clark
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Steven R. Skinner
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Svetlana Belyanskaya
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
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Concha N, Huang J, Bai X, Benowitz A, Brady P, Grady LC, Kryn LH, Holmes D, Ingraham K, Jin Q, Pothier Kaushansky L, McCloskey L, Messer JA, O’Keefe H, Patel A, Satz AL, Sinnamon RH, Schneck J, Skinner SR, Summerfield J, Taylor A, Taylor JD, Evindar G, Stavenger RA. Discovery and Characterization of a Class of Pyrazole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase. J Med Chem 2016; 59:7299-304. [DOI: 10.1021/acs.jmedchem.6b00746] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Nestor Concha
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jianzhong Huang
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Xiaopeng Bai
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Andrew Benowitz
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Pat Brady
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - LaShadric C. Grady
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Luz Helena Kryn
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27009, United States
| | - David Holmes
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Karen Ingraham
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Qi Jin
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | | | - Lynn McCloskey
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jeffrey A. Messer
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Heather O’Keefe
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Amish Patel
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Alexander L. Satz
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Robert H. Sinnamon
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jessica Schneck
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Steve R. Skinner
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | | | - Amy Taylor
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - J. David Taylor
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Ghotas Evindar
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Robert A. Stavenger
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
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