1
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Fitzgerald P, Dixit A, Zhang C, Mobley DL, Paegel BM. Building Block-Centric Approach to DNA-Encoded Library Design. J Chem Inf Model 2024; 64:4661-4672. [PMID: 38860710 PMCID: PMC11200258 DOI: 10.1021/acs.jcim.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Anjali Dixit
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Chris Zhang
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - David L. Mobley
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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2
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Anderson MJ, Carton TP, Salvini CLA, Crawford JJ, Pairaudeau G, Waring MJ. Micelle-Promoted Reductive Amination of DNA-Conjugated Amines for DNA-Encoded Library Synthesis. Chemistry 2024; 30:e202400239. [PMID: 38251309 DOI: 10.1002/chem.202400239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/23/2024]
Abstract
DNA-encoded libraries (DELs) have become a leading technology for hit identification in drug discovery projects as large, diverse libraries can be generated. DELs are commonly synthesised via split-and-pool methodology; thus, chemical transformations utilised must be highly efficient, proceeding with high conversions. Reactions performed in DEL synthesis also require a broad substrate scope to produce diverse, drug-like libraries. Many pharmaceutical compounds incorporate multiple C-N bonds, over a quarter of which are synthesised via reductive aminations. However, few on-DNA reductive amination procedures have been developed. Herein is reported the application of the micelle-forming surfactant, TPGS-750-M, to the on-DNA reductive amination of DNA-conjugated amines, yielding highly efficient conversions with a broad range of aldehydes, including medicinally relevant heterocyclic and aliphatic substrates. The procedure is compatible with DNA amplification and sequencing, demonstrating its applicability to DEL synthesis.
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Affiliation(s)
- Matthew J Anderson
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Thomas P Carton
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | | | | | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
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3
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Walvekar P, Lulinski P, Kumar P, Aminabhavi TM, Choonara YE. A review of hyaluronic acid-based therapeutics for the treatment and management of arthritis. Int J Biol Macromol 2024; 264:130645. [PMID: 38460633 DOI: 10.1016/j.ijbiomac.2024.130645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
Hyaluronic acid (HA), a biodegradable, biocompatible and non-immunogenic therapeutic polymer is a key component of the cartilage extracellular matrix (ECM) and has been widely used to manage two major types of arthritis, osteoarthritis (OA) and rheumatoid arthritis (RA). OA joints are characterized by lower concentrations of depolymerized (low molecular weight) HA, resulting in reduced physiological viscoelasticity, while in RA, the associated immune cells are over-expressed with various cell surface receptors such as CD44. Due to HA's inherent viscoelastic property and its ability to target CD44, there has been a surge of interest in developing HA-based systems to deliver various bioactives (drugs and biologics) and manage arthritis. Considering therapeutic benefits of HA in arthritis management and potential advantages of novel delivery systems, bioactive delivery through HA-based systems is beginning to display improved outcomes over bioactive only treatment. The benefits include enhanced bioactive uptake due to receptor-mediated targeting, prolonged retention of bioactives in the synovium, reduced expressions of proinflammatory mediators, enhanced cartilage regeneration, reduced drug toxicity due to sustained release, and improved and cost-effective treatment. This review provides an underlying rationale to prepare and use HA-based bioactive delivery systems for arthritis applications. With special emphasis given to preclinical/clinical results, this article reviews various bioactive-loaded HA-based particulate carriers (organic and inorganic), gels, scaffolds and polymer-drug conjugates that have been reported to treat and manage OA and RA. Furthermore, the review identifies several key challenges and provides valuable suggestions to address them. Various developments, strategies and suggestions described in this review may guide the formulation scientists to optimize HA-based bioactive delivery systems as an effective approach to manage and treat arthritis effectively.
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Affiliation(s)
- Pavan Walvekar
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa; Department of Pharmaceutics, SET's College of Pharmacy, Dharwad 580 002, Karnataka, India
| | - Piotr Lulinski
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Pradeep Kumar
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa
| | - Tejraj M Aminabhavi
- School of Advanced Sciences, KLE Technological University, Hubballi 580031, Karnataka, India.
| | - Yahya E Choonara
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa.
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4
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Minibaeva G, Ivanova A, Polishchuk P. EasyDock: customizable and scalable docking tool. J Cheminform 2023; 15:102. [PMID: 37915072 PMCID: PMC10619229 DOI: 10.1186/s13321-023-00772-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023] Open
Abstract
Docking of large compound collections becomes an important procedure to discover new chemical entities. Screening of large sets of compounds may also occur in de novo design projects guided by molecular docking. To facilitate these processes, there is a need for automated tools capable of efficiently docking a large number of molecules using multiple computational nodes within a reasonable timeframe. These tools should also allow for easy integration of new docking programs and provide a user-friendly program interface to support the development of further approaches utilizing docking as a foundation. Currently available tools have certain limitations, such as lacking a convenient program interface or lacking support for distributed computations. In response to these limitations, we have developed a module called EasyDock. It can be deployed over a network of computational nodes using the Dask library, without requiring a specific cluster scheduler. Furthermore, we have proposed and implemented a simple model that predicts the runtime of docking experiments and applied it to minimize overall docking time. The current version of EasyDock supports popular docking programs, namely Autodock Vina, gnina, and smina. Additionally, we implemented a supplementary feature to enable docking of boron-containing compounds, which are not inherently supported by Vina and smina, and demonstrated its applicability on a set of 55 PDB protein-ligand complexes.
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Affiliation(s)
- Guzel Minibaeva
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic
| | - Aleksandra Ivanova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic
| | - Pavel Polishchuk
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic.
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5
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Seydimemet M, Yang Y, Lv Y, Liu J, Yan Z, Zhao Y, Wang X, Lu X. Design, Construction, and Screening of Diversified Pyrimidine-Focused DNA-Encoded Libraries. ACS Med Chem Lett 2023; 14:1073-1078. [PMID: 37583819 PMCID: PMC10424316 DOI: 10.1021/acsmedchemlett.3c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Pyrimidine is a ubiquitous component in natural products and approved drugs, providing an ideal modular scaffold for generating libraries with drug-like properties. DNA-encoded library technology introduces a novel library modality where each small molecule is covalently linked to a unique oligo tag. This technology offers the advantages of rapidly generating and interrogating large-scale libraries containing billions of members, substantially reducing the entry barrier to their use in both academia and the pharmaceutical industry. In this Letter, we describe the synthesis of three DNA-encoded libraries based on different functionalized pyrimidine cores featuring diversified chemoselectivity and regioselectivity. Preliminary screening of these DNA-encoded libraries against BRD4 identified compounds with nanomolar inhibition activities.
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Affiliation(s)
- Mengnisa Seydimemet
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yixuan Yang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yuhan Lv
- School
of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong P.R. China
| | - Jiaxiang Liu
- Alphama
Biotechnology Suzhou Co., Ltd., 108 Yuxin Road, Suzhou City, Jiangsu Province 215123, China
| | - Ziqin Yan
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yujun Zhao
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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6
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Chai J, Arico-Muendel CC, Ding Y, Pollastri MP, Scott S, Mantell MA, Yao G. Synthesis of a DNA-Encoded Macrocyclic Library Utilizing Intramolecular Benzimidazole Formation. Bioconjug Chem 2023. [PMID: 37216465 DOI: 10.1021/acs.bioconjchem.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Macrocycles occupy chemical space "beyond the rule of five". They bridge traditional bioactive small molecule drugs and macromolecules and have the potential to modulate challenging targets such as PPI or proteases. Here we report an on-DNA macrocyclization reaction utilizing intramolecular benzimidazole formation. A 129-million-member macrocyclic library composed of a privileged benzimidazole core, a dipeptide sequence (natural or non-natural), and linkers of varying length and flexibility was designed and synthesized.
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Affiliation(s)
- Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Christopher C Arico-Muendel
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Michael P Pollastri
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sarah Scott
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Mark A Mantell
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Gang Yao
- Encoded Library Technologies/NCE Molecular Discovery, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
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7
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Lin J, Jia S, Zhang W, Nian M, Liu P, Yang L, Zuo J, Li W, Zeng H, Zhang X. Recent Advances in Small Molecule Inhibitors for the Treatment of Osteoarthritis. J Clin Med 2023; 12:jcm12051986. [PMID: 36902773 PMCID: PMC10004353 DOI: 10.3390/jcm12051986] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Osteoarthritis refers to a degenerative disease with joint pain as the main symptom, and it is caused by various factors, including fibrosis, chapping, ulcers, and loss of articular cartilage. Traditional treatments can only delay the progression of osteoarthritis, and patients may need joint replacement eventually. As a class of organic compound molecules weighing less than 1000 daltons, small molecule inhibitors can target proteins as the main components of most drugs clinically. Small molecule inhibitors for osteoarthritis are under constant research. In this regard, by reviewing relevant manuscripts, small molecule inhibitors targeting MMPs, ADAMTS, IL-1, TNF, WNT, NF-κB, and other proteins were reviewed. We summarized these small molecule inhibitors with different targets and discussed disease-modifying osteoarthritis drugs based on them. These small molecule inhibitors have good inhibitory effects on osteoarthritis, and this review will provide a reference for the treatment of osteoarthritis.
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Affiliation(s)
- Jianjing Lin
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Shicheng Jia
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Shantou University Medical College, Shantou 515041, China
| | - Weifei Zhang
- Department of Bone and Joint, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Mengyuan Nian
- Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Peng Liu
- Department of Bone and Joint, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Li Yang
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Jianwei Zuo
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Wei Li
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Correspondence: (W.L.); (H.Z.); (X.Z.)
| | - Hui Zeng
- Department of Bone and Joint, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Correspondence: (W.L.); (H.Z.); (X.Z.)
| | - Xintao Zhang
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Correspondence: (W.L.); (H.Z.); (X.Z.)
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8
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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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9
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Ashruf OS, Ansari MY. Natural Compounds: Potential Therapeutics for the Inhibition of Cartilage Matrix Degradation in Osteoarthritis. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010102. [PMID: 36676051 PMCID: PMC9866583 DOI: 10.3390/life13010102] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/24/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease characterized by enzymatic degradation of the cartilage extracellular matrix (ECM) causing joint pain and disability. There is no disease-modifying drug available for the treatment of OA. An ideal drug is expected to stop cartilage ECM degradation and restore the degenerated ECM. The ECM primarily contains type II collagen and aggrecan but also has minor quantities of other collagen fibers and proteoglycans. In OA joints, the components of the cartilage ECM are degraded by matrix-degrading proteases and hydrolases which are produced by chondrocytes and synoviocytes. Matrix metalloproteinase-13 (MMP-13) and a disintegrin and metalloproteinase with thrombospondin motifs 4 and 5 (ADAMTS5) are the major collagenase and aggrecanase, respectively, which are highly expressed in OA cartilage and promote cartilage ECM degradation. Current studies using various in vitro and in vivo approaches show that natural compounds inhibit the expression and activity of MMP-13, ADAMTS4, and ADAMTS5 and increase the expression of ECM components. In this review, we have summarized recent advancements in OA research with a focus on natural compounds as potential therapeutics for the treatment of OA with emphasis on the prevention of cartilage ECM degradation and improvement of joint health.
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Affiliation(s)
- Omer S. Ashruf
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209, State Route 44, Rootstown, OH 44272, USA
- College of Medicine, Northeast Ohio Medical University, 4209, State Route 44, Rootstown, OH 44272, USA
| | - Mohammad Yunus Ansari
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209, State Route 44, Rootstown, OH 44272, USA
- Musculoskeletal Research Focus Area, Northeast Ohio Medical University, 4209, State Route 44, Rootstown, OH 44272, USA
- Correspondence:
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10
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Cuffaro D, Ciccone L, Rossello A, Nuti E, Santamaria S. Targeting Aggrecanases for Osteoarthritis Therapy: From Zinc Chelation to Exosite Inhibition. J Med Chem 2022; 65:13505-13532. [PMID: 36250680 PMCID: PMC9620172 DOI: 10.1021/acs.jmedchem.2c01177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Indexed: 11/30/2022]
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease. In 1999, two members of the A Disintegrin and Metalloproteinase with Thrombospondin Motifs (ADAMTS) family of metalloproteinases, ADAMTS4 and ADAMTS5, or aggrecanases, were identified as the enzymes responsible for aggrecan degradation in cartilage. The first aggrecanase inhibitors targeted the active site by chelation of the catalytic zinc ion. Due to the generally disappointing performance of zinc-chelating inhibitors in preclinical and clinical studies, inhibition strategies tried to move away from the active-site zinc in order to improve selectivity. Exosite inhibitors bind to proteoglycan-binding residues present on the aggrecanase ancillary domains (called exosites). While exosite inhibitors are generally more selective than zinc-chelating inhibitors, they are still far from fulfilling their potential, partly due to a lack of structural and functional data on aggrecanase exosites. Filling this gap will inform the design of novel potent, selective aggrecanase inhibitors.
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Affiliation(s)
- Doretta Cuffaro
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Lidia Ciccone
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Elisa Nuti
- Department
of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Salvatore Santamaria
- Department
of Immunology and Inflammation, Imperial
College London, Du Cane Road, London W12
0NN, U.K.
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11
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Furka Á. Forty years of combinatorial technology. Drug Discov Today 2022; 27:103308. [PMID: 35760283 DOI: 10.1016/j.drudis.2022.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Combinatorial technology has been facilitating the synthesis and screening of large molecular libraries containing millions of organic compounds ever since its introduction 40 years ago. It has changed the paradigms of pharmaceutical research from focusing on single compounds to focusing on immense collections of compounds. It inspired the development of dynamic combinatorial libraries, fragment-based drug discovery and virtual library screening. Combinatorial technology was revitalized by the development of DNA encoding. Amplification of DNA oligomers plus next-generation sequencing has made it possible to successfully screen billions of compounds in a single process.
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Affiliation(s)
- Árpád Furka
- Eötvös Loránd University Budapest Hungary, 1077 Rozsa u. 23-25, Budapest, Hungary.
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12
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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13
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Zhao P, Liu D, Song C, Li D, Zhang X, Horecny I, Zhang F, Yan Y, Zhuang L, Li J, Liu S, Mao Y, Feng J, Liu J, Tao W. Discovery of Isoindoline Amide Derivatives as Potent and Orally Bioavailable ADAMTS-4/5 Inhibitors for the Treatment of Osteoarthritis. ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE 2022; 5:458-467. [DOI: 10.1021/acsptsci.2c00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Peng Zhao
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Dong Liu
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Chunying Song
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Di Li
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Xinzhu Zhang
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Ivana Horecny
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Fengqi Zhang
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Yuna Yan
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Linghang Zhuang
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Jing Li
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Suxing Liu
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Yuchang Mao
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Jun Feng
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
| | - Jian Liu
- Eternity Bioscience Inc., 6 Cedarbrook Drive, Cranbury, New Jersey 08512, United States
| | - Weikang Tao
- Shanghai Hengrui Pharmaceutical Co. Ltd., 279 Wenjing Road, Shanghai 200245, China
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14
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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] [MESH Headings] [Grants] [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
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Seino A. K. Jongkees
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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15
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Siripuram VK, Sunkari YK, Nguyen TL, Flajolet M. DNA-Compatible Suzuki-Miyaura Cross-Coupling Reaction of Aryl Iodides With (Hetero)Aryl Boronic Acids for DNA-Encoded Libraries. Front Chem 2022; 10:894603. [PMID: 35774858 PMCID: PMC9237475 DOI: 10.3389/fchem.2022.894603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
An efficient method for the C-C bond formation via water soluble Na2PdCl4/sSPhos mediated Suzuki-Miyaura cross-coupling reaction of DNA-conjugated aryl iodide with (het)aryl boronic acids has been developed. This reaction proceeds at 37°C in water and acetonitrile (4:1) system. We also demonstrated that numerous aromatic and heteroaromatic boronic acids of different electronic natures, and harboring various functional groups, were highly compatible providing the desired coupling products in good to excellent yields. This DNA-compatible Suzuki-Miyaura cross-coupling reaction has strong potential to construct DNA-Encoded Libraries (DELs) in the context of drug discovery.
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Affiliation(s)
| | | | | | - Marc Flajolet
- *Correspondence: Vijay Kumar Siripuram, ; Marc Flajolet,
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16
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Yu Y, Liu M, Choi VNT, Cheung YW, Tanner JA. Selection and characterization of DNA aptamers inhibiting a druggable target of osteoarthritis, ADAMTS-5. Biochimie 2022; 201:168-176. [PMID: 35700850 DOI: 10.1016/j.biochi.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/15/2023]
Abstract
There is a critical need for the development of more potent inhibitors for osteoarthritis (OA) therapy given the poor life quality of arthritis patients. Aggrecanase ADAMTS-5 (a disintegrin and metalloproteinase with thrombospondin motifs 5) is an established drug target identified for osteoarthritis. In this study, we evolved and characterized two new DNA aptamer inhibitors of ADAMTS-5, namely apt21 and apt25. The aptamers exhibited nanomolar binding affinity and high specificity against ADAMTS-5. KD values of apt21 and apt25 were determined by the Enzyme-linked Oligonucleotide Assay (ELONA) at 1.54 ± 0.16 nM and 1.79 ± 0.08 nM, respectively. Circular Dichroism (CD) analysis demonstrated that both aptamers formed monovalent cation dependent G-quadruplex structures. Calcium ions did not affect the binding of the aptamers to ADAMTS-5. The inhibitory effects of apt21 and apt25 on ADAMTS-5 were evaluated by the Förster Resonance Energy Transfer (FRET) assay, in which IC50 values of apt21 and apt25 were estimated at 52.76 ± 6.70 μM and 61.14 ± 9.67 μM, respectively. These two aptamers are the first DNA G-quadruplex aptamers demonstrated to inhibit ADAMTS-5 and could have value for OA therapy.
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Affiliation(s)
- Yuanyuan Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, PR China
| | - Mengping Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Vanessa N T Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, PR China.
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17
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Castan IFSF, Madin A, Pairaudeau G, Waring MJ. Scope of on-DNA nucleophilic aromatic substitution on weakly-activated heterocyclic substrates for the synthesis of DNA-encoded libraries. Bioorg Med Chem 2022; 63:116688. [PMID: 35430536 DOI: 10.1016/j.bmc.2022.116688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022]
Abstract
DNA-Encoded Libraries (DEL) represent a promising hit finding strategy for drug discovery. Nonetheless, the available DNA-compatible chemistry remains of limited scope. Nucleophilic aromatic substitution (SNAr) has been extensively used in DEL synthesis but has generally been restricted to highly activated (hetero)arenes. Herein, we report an optimised procedure for SNAr reactions through the use of factorial experimental design (FED) on-DNA using 15% THF as a co-solvent. This method gave conversions of >95% for pyridine and pyrazine scaffolds for 36 secondary cyclic amines. This analysis provides a new DNA-compatible SNAr reaction to produce high yielding libraries. The scope of this reaction on other amines is described. This work identifies challenges for the further development for DNA-compatible SNAr reactions. 2009 Elsevier Ltd. All rights reserved.
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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
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, 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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18
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Adamik R, Buchholcz B, Darvas F, Sipos G, Novák Z. The Potential of Micellar Media in the Synthesis of DNA-Encoded Libraries. Chemistry 2022; 28:e202103967. [PMID: 35019168 PMCID: PMC9305553 DOI: 10.1002/chem.202103967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/17/2022]
Abstract
DNA‐encoded library (DEL) technology has become widely used in drug discovery research. The construction of DELs requires robust organic transformations that proceed in aqueous media under mild conditions. Unfortunately, the application of water as reaction medium for organic synthesis is not evident due to the generally limited solubility of organic reagents. However, the use of surfactants can offer a solution to this issue. Oil‐in‐water microemulsions formed by surfactant micelles are able to localize hydrophobic reagents inside them, resulting in high local concentrations of the organic substances in an otherwise poorly solvated environment. This review provides a conceptual and critical summary of micellar synthesis possibilities that are well suited to DEL synthesis. Existing examples of micellar DEL approaches, together with a selection of micellar organic transformations fundamentally suitable for DEL are discussed.
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Affiliation(s)
- Réka Adamik
- ELTE "Lendület" Catalysis and Organic Synthesis Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117, Budapest, Hungary
| | | | - Ferenc Darvas
- Innostudio Inc., Záhony u. 7, 1031, Budapest, Hungary
| | | | - Zoltán Novák
- ELTE "Lendület" Catalysis and Organic Synthesis Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117, Budapest, Hungary
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19
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Gui Y, Wong CS, Zhao G, Xie C, Hou R, Li Y, Li G, Li X. Converting Double-Stranded DNA-Encoded Libraries (DELs) to Single-Stranded Libraries for More Versatile Selections. ACS OMEGA 2022; 7:11491-11500. [PMID: 35415338 PMCID: PMC8992267 DOI: 10.1021/acsomega.2c01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 06/06/2023]
Abstract
DNA-encoded library (DEL) is an efficient high-throughput screening technology platform in drug discovery and is also gaining momentum in academic research. Today, the majority of DELs are assembled and encoded with double-stranded DNA tags (dsDELs) and has been selected against numerous biological targets; however, dsDELs are not amendable to some of the recently developed selection methods, such as the cross-linking-based selection against immobilized targets and live-cell-based selections, which require DELs encoded with single-stranded DNAs (ssDELs). Herein, we present a simple method to convert dsDELs to ssDELs using exonuclease digestion without library redesign and resynthesis. We show that dsDELs could be efficiently converted to ssDELs and used for affinity-based selections either with purified proteins or on live cells.
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Affiliation(s)
- Yuhan Gui
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Clara Shania Wong
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Chao Xie
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
| | - Rui Hou
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK,
Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology
Parks, New Territories, Hong Kong SAR , China
| | - Yizhou Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences; Key Laboratory of Biorheological Science
and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 401331, China
| | - Gang Li
- Institute
of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Xiaoyu Li
- Department
of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China
- Laboratory
for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK,
Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology
Parks, New Territories, Hong Kong SAR , China
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20
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Clement-Lacroix P, Little CB, Smith MM, Cottereaux C, Merciris D, Meurisse S, Mollat P, Touitou R, Brebion F, Gosmini R, De Ceuninck F, Botez I, Lepescheux L, van der Aar E, Christophe T, Vandervoort N, Blanqué R, Comas D, Deprez P, Amantini D. Pharmacological characterization of GLPG1972/S201086, a potent and selective small-molecule inhibitor of ADAMTS5. Osteoarthritis Cartilage 2022; 30:291-301. [PMID: 34626798 DOI: 10.1016/j.joca.2021.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/29/2021] [Accepted: 08/09/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE A disintegrin and metalloproteinase with thrombospondin motifs 5 (ADAMTS5) is a key enzyme in degradation of cartilage in osteoarthritis (OA). We report the pharmacological characterization of GLPG1972/S201086, a new, potent and selective small-molecule ADAMTS5 inhibitor. METHODS Potency and selectivity of GLPG1972/S201086 for ADAMTS5 were determined using fluorescently labeled peptide substrates. Inhibitory effects of GLPG1972/S201086 on interleukin-1α-stimulated glycosaminoglycan release in mouse femoral head cartilage explants and on interleukin-1β-stimulated release of an ADAMTS5-derived aggrecan neoepitope (quantified with ELISA) in human articular cartilage explants were determined. In the destabilization of the medial meniscus (DMM) mouse and menisectomized (MNX) rat models, effects of oral GLPG1972/S201086 on relevant OA histological and histomorphometric parameters were evaluated. RESULTS GLPG1972/S201086 inhibited human and rat ADAMTS5 (IC50 ± SD: 19 ± 2 nM and <23 ± 1 nM, respectively), with 8-fold selectivity over ADAMTS4, and 60->5,000-fold selectivity over other related proteases in humans. GLPG1972/S201086 dose-dependently inhibited cytokine-stimulated aggrenolysis in mouse and human cartilage explants (100% at 20 μM and 10 μM, respectively). In DMM mice, GLPG1972/S201086 (30-120 mg/kg b.i.d) vs vehicle reduced femorotibial cartilage proteoglycan loss (23-37%), cartilage structural damage (23-39%) and subchondral bone sclerosis (21-36%). In MNX rats, GLPG1972/S201086 (10-50 mg/kg b.i.d) vs vehicle reduced cartilage damage (OARSI score reduction, 6-23%), and decreased proteoglycan loss (∼27%) and subchondral bone sclerosis (77-110%). CONCLUSIONS GLPG1972/S201086 is a potent, selective and orally available ADAMTS5 inhibitor, demonstrating significant protective efficacy on both cartilage and subchondral bone in two relevant in vivo preclinical OA models.
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Affiliation(s)
| | - C B Little
- Raymond Purves Bone and Joint Research Laboratories, University of Sydney, Kolling Institute, Northern Sydney Local Health District, Royal North Shore Hospital, St Leonards, NSW, Australia.
| | - M M Smith
- Raymond Purves Bone and Joint Research Laboratories, University of Sydney, Kolling Institute, Northern Sydney Local Health District, Royal North Shore Hospital, St Leonards, NSW, Australia.
| | | | | | | | - P Mollat
- Galapagos SASU, Romainville, France.
| | - R Touitou
- Galapagos SASU, Romainville, France.
| | - F Brebion
- Galapagos SASU, Romainville, France.
| | - R Gosmini
- Galapagos SASU, Romainville, France.
| | | | - I Botez
- Institut de Recherches Servier, France.
| | | | | | | | | | - R Blanqué
- Galapagos SASU, Romainville, France.
| | - D Comas
- Galapagos SASU, Romainville, France.
| | - P Deprez
- Galapagos SASU, Romainville, France.
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21
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Billings KJ, Grenier-Davies MC. Library Synthesis: Building Block Selection, Handling, and Tracking. Methods Mol Biol 2022; 2541:1-11. [PMID: 36083536 DOI: 10.1007/978-1-0716-2545-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Careful selection and manipulation of small molecule building blocks is crucial to the success of a DNA-encoded library. Building block selection impacts the quality of the hits arising out of a selection assay, while proper sample handling and tracking ensure follow-up synthetic work is done with the appropriate synthetic map in mind. In this chapter, possible strategies for building block selection are outlined, as well as best practices for handling and tracking samples to be used for validation and library synthesis.
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Affiliation(s)
| | - Melissa C Grenier-Davies
- Encoded Library Technologies/NCE Molecular Discovery, R & D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA
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22
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Hou R, He Y, Yan G, Hou S, Xie Z, Liao C. Zinc enzymes in medicinal chemistry. Eur J Med Chem 2021; 226:113877. [PMID: 34624823 DOI: 10.1016/j.ejmech.2021.113877] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/27/2021] [Accepted: 09/17/2021] [Indexed: 12/31/2022]
Abstract
In humans, more than three hundred diverse enzymes that require zinc as an essential cofactor have been identified. These zinc enzymes have demonstrated different and important physiological functions and some of them have been considered as valuable therapeutic targets for drug discovery. Indeed, many drugs targeting a few zinc enzymes have been marketed to treat a variety of diseases. This review discusses drug discovery and drug development based on a dozen of zinc enzymes, including their biological functions and pathogenic roles, their best in class inhibitors (and clinical trial data when available), coordination and binding modes of representative inhibitors, and their implications for further drug design. The opportunities and challenges in developing zinc enzyme inhibitors for the treatment of human disorders are highlighted, too.
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Affiliation(s)
- Rui Hou
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yan He
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Guangwei Yan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Shuzeng Hou
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
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23
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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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24
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Furka Á. Combinatorial technology revitalized by DNA-encoding. MedComm (Beijing) 2021; 2:481-489. [PMID: 34766157 PMCID: PMC8554669 DOI: 10.1002/mco2.84] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/12/2023] Open
Abstract
Combinatorial chemistry invented nearly 40 years ago was welcomed with enthusiasm in the drug research community. The method offered access to a practically unlimited number of new compounds. The new compounds however are mixtures, and methods had to be developed for the identification of the bioactive components. This was one of the reasons why the method could not providethe expected cornucopia of new drugs. Among the different screening methods, two approaches seem to offer the best results. One of them is based on the intrinsic property of the combinatorial split and pool solid-phase synthesis: One compound forms on each bead of the solid support. Different methods have been developed to encode the beads and identify the structure of compounds formed on them. The most important method applies DNA oligomers for encoding. As a second approach in screening, DNA-encoded combinatorial libraries are synthesized omitting the solid support and the mixtures are screened in solution using affinity binding methods. Libraries containing billions and even trillions of components are synthesized and successfully tested, which led to the identification of a significant number of new leads.
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Affiliation(s)
- Árpád Furka
- Department of Organic ChemistryEötvös Loránd UniversityBudapestHungary
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25
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Jiang L, Lin J, Zhao S, Wu J, Jin Y, Yu L, Wu N, Wu Z, Wang Y, Lin M. ADAMTS5 in Osteoarthritis: Biological Functions, Regulatory Network, and Potential Targeting Therapies. Front Mol Biosci 2021; 8:703110. [PMID: 34434966 PMCID: PMC8381022 DOI: 10.3389/fmolb.2021.703110] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/05/2021] [Indexed: 01/16/2023] Open
Abstract
ADAMTS5 is involved in the pathogenesis of OA. As the major aggrecanase-degrading articular cartilage matrix, ADAMTS5, has been regarded as a potential target for OA treatment. We here provide an updated insight on the regulation of ADAMTS5 and newly discovered therapeutic strategies for OA. Pathophysiological and molecular mechanisms underlying articular inflammation and mechanotransduction, as well as chondrocyte hypertrophy were discussed, and the role of ADAMTS5 in each biological process was reviewed, respectively. Senescence, inheritance, inflammation, and mechanical stress are involved in the overactivation of ADAMTS5, contributing to the pathogenesis of OA. Multiple molecular signaling pathways were observed to modulate ADAMTS5 expression, namely, Runx2, Fgf2, Notch, Wnt, NF-κB, YAP/TAZ, and the other inflammatory signaling pathways. Based on the fundamental understanding of ADAMTS5 in OA pathogenesis, monoclonal antibodies and small molecule inhibitors against ADAMTS5 were developed and proved to be beneficial pre-clinically both in vitro and in vivo. Recent novel RNA therapies demonstrated potentials in OA animal models. To sum up, ADAMTS5 inhibition and its signaling pathway–based modulations showed great potential in future therapeutic strategies for OA.
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Affiliation(s)
- Lejian Jiang
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Spine Lab, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiachen Lin
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sen Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jiaqian Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongming Jin
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Yu
- Department of Operating Room, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nan Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Yue Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Spine Lab, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mao Lin
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Spine Lab, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
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26
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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: 14] [Impact Index Per Article: 4.7] [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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27
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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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28
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Brebion F, Gosmini R, Deprez P, Varin M, Peixoto C, Alvey L, Jary H, Bienvenu N, Triballeau N, Blanque R, Cottereaux C, Christophe T, Vandervoort N, Mollat P, Touitou R, Leonard P, De Ceuninck F, Botez I, Monjardet A, van der Aar E, Amantini D. Discovery of GLPG1972/S201086, a Potent, Selective, and Orally Bioavailable ADAMTS-5 Inhibitor for the Treatment of Osteoarthritis. J Med Chem 2021; 64:2937-2952. [PMID: 33719441 DOI: 10.1021/acs.jmedchem.0c02008] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There are currently no approved disease-modifying osteoarthritis (OA) drugs (DMOADs). The aggrecanase ADAMTS-5 is key in the degradation of human aggrecan (AGC), a component of cartilage. Therefore, ADAMTS-5 is a promising target for the identification of DMOADs. We describe the discovery of GLPG1972/S201086, a potent and selective ADAMTS-5 inhibitor obtained by optimization of a promising hydantoin series following an HTS. Biochemical activity against rat and human ADAMTS-5 was assessed via a fluorescence-based assay. ADAMTS-5 inhibitory activity was confirmed with human aggrecan using an AGC ELISA. The most promising compounds were selected based on reduction of glycosaminoglycan release after interleukin-1 stimulation in mouse cartilage explants and led to the discovery of GLPG1972/S201086. The anticatabolic activity was confirmed in mouse cartilage explants (IC50 < 1.5 μM). The cocrystal structure of GLPG1972/S201086 with human recombinant ADAMTS-5 is discussed. GLPG1972/S201086 has been investigated in a phase 2 clinical study in patients with knee OA (NCT03595618).
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Affiliation(s)
- Franck Brebion
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Romain Gosmini
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Pierre Deprez
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Marie Varin
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - Luke Alvey
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Hélène Jary
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Natacha Bienvenu
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - Roland Blanque
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Céline Cottereaux
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - Nele Vandervoort
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Patrick Mollat
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Robert Touitou
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Philip Leonard
- Structural Biology, Charles River, Chesterford Research Park, CB10 1XL Saffron Walden, United Kingdom
| | - Frédéric De Ceuninck
- Institut de Recherches Servier, Center for Therapeutic Innovation, Immuno-inflammatory Disease, 78290 Croissy sur Seine, France
| | - Iuliana Botez
- Institut de Recherches Servier, Chemistry Center of Excellence, 78290 Croissy sur Seine, France
| | - Alain Monjardet
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - David Amantini
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230 Romainville, France
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29
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Sun CP, Zhang XY, Morisseau C, Hwang SH, Zhang ZJ, Hammock BD, Ma XC. Discovery of Soluble Epoxide Hydrolase Inhibitors from Chemical Synthesis and Natural Products. J Med Chem 2020; 64:184-215. [PMID: 33369424 DOI: 10.1021/acs.jmedchem.0c01507] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Soluble epoxide hydrolase (sEH) is an α/β hydrolase fold protein and widely distributed in numerous organs including the liver, kidney, and brain. The inhibition of sEH can effectively maintain endogenous epoxyeicosatrienoic acids (EETs) levels and reduce dihydroxyeicosatrienoic acids (DHETs) levels, resulting in therapeutic potentials for cardiovascular, central nervous system, and metabolic diseases. Therefore, since the beginning of this century, the development of sEH inhibitors is a hot research topic. A variety of potent sEH inhibitors have been developed by chemical synthesis or isolated from natural sources. In this review, we mainly summarized the interconnected aspects of sEH with cardiovascular, central nervous system, and metabolic diseases and then focus on representative inhibitors, which would provide some useful guidance for the future development of potential sEH inhibitors.
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Affiliation(s)
- Cheng-Peng Sun
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College (Institute) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Xin-Yue Zhang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College (Institute) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China
| | - Christophe Morisseau
- Department of Entomology and Nematology, UC Davis Comprehensive Cancer Center, University of California, Davis, California 95616, United States
| | - Sung Hee Hwang
- Department of Entomology and Nematology, UC Davis Comprehensive Cancer Center, University of California, Davis, California 95616, United States
| | - Zhan-Jun Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Bruce D Hammock
- Department of Entomology and Nematology, UC Davis Comprehensive Cancer Center, University of California, Davis, California 95616, United States
| | - Xiao-Chi Ma
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College (Institute) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian 116044, People's Republic of China.,College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou 311121, People's Republic of China
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30
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Li K, Qu Y, An Y, Breinlinger E, Webster MP, Wen H, Ding D, Zhao M, Shi X, Wang J, Su W, Cui W, Satz AL, Yang H, Kuai L, Little A, Peng X. DNA-Compatible Copper-Catalyzed Oxidative Amidation of Aldehydes with Non-Nucleophilic Arylamines. Bioconjug Chem 2020; 31:2092-2097. [DOI: 10.1021/acs.bioconjchem.0c00392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ke Li
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Yi Qu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Eric Breinlinger
- AbbVie Bioresearch Center, 381 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Matthew P. Webster
- Research and Development, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Huanan Wen
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Duanchen Ding
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Meng Zhao
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xiaodong Shi
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Jiangong Wang
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Alexander L. Satz
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Hongfang Yang
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Andrew Little
- AbbVie Bioresearch Center, 381 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Xuanjia Peng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
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31
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Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library. Proc Natl Acad Sci U S A 2020; 117:16782-16789. [PMID: 32641511 PMCID: PMC7382296 DOI: 10.1073/pnas.2005447117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To rapidly identify small-molecule lead compounds to target healthcare-associated proteases, we constructed a unique 9.8-million-membered protease-focused DNA-encoded chemical library. Affinity selection of this library with a healthcare-relevant protease (i.e., thrombin, a key protein necessary for blood coagulation) revealed potent inhibitors in the first screening attempt. Our results emphasize the utility of a structurally focused DNA-encoded chemical library approach to rapidly uncover hits for healthcare targets (e.g., proteases) where no drug exists (e.g., male contraception) and for emerging diseases (e.g., coronavirus disease 2019). DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a class of protein targets. Herein, a protease-focused DNA-encoded chemical library was designed that utilizes chemotypes known to engage conserved catalytic protease residues. The three-cycle library features functional moieties such as guanidine, which interacts strongly with aspartate of the protease catalytic triad, as well as mild electrophiles such as sulfonamide, urea, and carbamate. We developed a DNA-compatible method for guanidinylation of amines and reduction of nitriles. Employing these optimized reactions, we constructed a 9.8-million-membered DNA-encoded chemical library. Affinity selection of the library with thrombin, a common protease, revealed a number of enriched features which ultimately led to the discovery of a 1 nM inhibitor of thrombin. Thus, structurally focused DNA-encoded chemical libraries have tremendous potential to find clinically useful high-affinity hits for the rapid discovery of drugs for targets (e.g., proteases) with essential functions in infectious diseases (e.g., severe acute respiratory syndrome coronavirus 2) and relevant healthcare conditions (e.g., male contraception).
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32
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Coley CW, Eyke NS, Jensen KF. Autonomous Discovery in the Chemical Sciences Part I: Progress. Angew Chem Int Ed Engl 2020; 59:22858-22893. [DOI: 10.1002/anie.201909987] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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33
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Coley CW, Eyke NS, Jensen KF. Autonome Entdeckung in den chemischen Wissenschaften, Teil I: Fortschritt. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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34
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An YL, Li K, Shen Y, Hong Z, Chen L, Hu Y, Zhou L, Wang D, Shi X, Liu S, Su W, Cui W, Kuai L, Yang H, Peng X. DNA Compatible Intermolecular Wittig Olefination for the Construction of α, β-Unsaturated Carbonyl Compounds. Org Lett 2020; 22:3931-3935. [DOI: 10.1021/acs.orglett.0c01215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xuanjia Peng
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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35
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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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36
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Design and Construction of a Focused DNA-Encoded Library for Multivalent Chromatin Reader Proteins. Molecules 2020; 25:molecules25040979. [PMID: 32098353 PMCID: PMC7070942 DOI: 10.3390/molecules25040979] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022] Open
Abstract
Chromatin structure and function, and consequently cellular phenotype, is regulated in part by a network of chromatin-modifying enzymes that place post-translational modifications (PTMs) on histone tails. These marks serve as recruitment sites for other chromatin regulatory complexes that ‘read’ these PTMs. High-quality chemical probes that can block reader functions of proteins involved in chromatin regulation are important tools to improve our understanding of pathways involved in chromatin dynamics. Insight into the intricate system of chromatin PTMs and their context within the epigenome is also therapeutically important as misregulation of this complex system is implicated in numerous human diseases. Using computational methods, along with structure-based knowledge, we have designed and constructed a focused DNA-Encoded Library (DEL) containing approximately 60,000 compounds targeting bi-valent methyl-lysine (Kme) reader domains. Additionally, we have constructed DNA-barcoded control compounds to allow optimization of selection conditions using a model Kme reader domain. We anticipate that this target-class focused approach will serve as a new method for rapid discovery of inhibitors for multivalent chromatin reader domains.
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37
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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: 99] [Impact Index Per Article: 24.8] [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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38
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Chen Q, Cheng X, Zhang L, Li X, Chen P, Liu J, Zhang L, Wei H, Li Z, Dou D. Exploring the Lower Limit of Individual DNA-Encoded Library Molecules in Selection. SLAS DISCOVERY 2019; 25:523-529. [DOI: 10.1177/2472555219893949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA-encoded library (DEL) technology has been used as an ultra-high-throughput screening approach for hit identification of drug targets. This process is an affinity-based selection and requires incubation of DEL molecules with the target. Currently, in most reported cases, the input (i.e., the copy number) of individual DEL molecules varies from 105 to 107. With the ever-increasing DEL size and screening cost, lowering the input of DEL molecules while maintaining an appropriate signal-to-noise ratio in a selection is of paramount importance. In this article, we varied the input of DEL ranging from 103 to 105 in selections with two different protein targets to explore the lower limit of DEL molecule input. The results could facilitate the optimization of the DEL selection process and reduce costs related to library consumption.
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Affiliation(s)
- Qiuxia Chen
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuemin Cheng
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Lifang Zhang
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Xianyang Li
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Purui Chen
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Jian Liu
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Lanjun Zhang
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Hong Wei
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
| | - Zhonghan Li
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Dengfeng Dou
- Lead Generation Unit, HitGen Inc., Shuangliu District, Chengdu, China
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39
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Liu W, Deng W, Sun S, Yu C, Su X, Wu A, Yuan Y, Ma Z, Li K, Yang H, Peng X, Dietrich J. A Strategy for the Synthesis of Sulfonamides on DNA. Org Lett 2019; 21:9909-9913. [DOI: 10.1021/acs.orglett.9b03843] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wei Liu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Wei Deng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Saisai Sun
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Chunyan Yu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xubo Su
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Aliang Wu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Youlang Yuan
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Zhonglin Ma
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Ke Li
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Hongfang Yang
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xuanjia Peng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Justin Dietrich
- Research and Development, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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40
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Poondla N, Chandrasekaran AP, Kim KS, Ramakrishna S. Deubiquitinating enzymes as cancer biomarkers: new therapeutic opportunities? BMB Rep 2019. [PMID: 30760385 PMCID: PMC6476481 DOI: 10.5483/bmbrep.2019.52.3.048] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer remains a life-threatening disease and accounts for the major mortality rates worldwide. The practice of using biomarkers for early detection, staging, and customized therapy may increase cancer patients’ survival. Deubiquitinating enzymes (DUBs) are a family of proteases that remove ubiquitin tags from proteins of interest undergoing proteasomal degradation. DUBs play several functional roles other than deubiquitination. One of the important roles of DUBs is regulation of tumor progression. Several reports have suggested that the DUB family members were highly-elevated in various cancer cells and tissues in different stages of cancer. These findings suggest that the DUBs could be used as drug targets in cancer therapeutics. In this review, we recapitulate the role of the DUB family members, including ubiquitin-specific protease, otubain protease, and important candidates from other family members. Our aim was to better understand the connection between DUB expression profiles and cancers to allow researchers to design inhibitors or gene therapies to improve diagnosis and prognosis of cancers.
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Affiliation(s)
- Naresh Poondla
- Graduate School of Biomedical Science and Engineering, Department of Biomedical Science, Hanyang University, Seoul 04763, Korea
| | - Arun Pandian Chandrasekaran
- Graduate School of Biomedical Science and Engineering, Department of Biomedical Science, Hanyang University, Seoul 04763, Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Department of Biomedical Science, Hanyang University, Seoul 04763; College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Department of Biomedical Science, Hanyang University, Seoul 04763; College of Medicine, Hanyang University, Seoul 04763, Korea
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41
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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: 67] [Impact Index Per Article: 13.4] [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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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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Phelan JP, Lang SB, Sim J, Berritt S, Peat AJ, Billings K, Fan L, Molander GA. Open-Air Alkylation Reactions in Photoredox-Catalyzed DNA-Encoded Library Synthesis. J Am Chem Soc 2019; 141:3723-3732. [PMID: 30753065 DOI: 10.1021/jacs.9b00669] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA-encoded library (DEL) technology is a powerful tool commonly used by the pharmaceutical industry for the identification of compounds with affinity to biomolecular targets. Success in this endeavor lies in sampling diverse chemical libraries. However, current DELs tend to be deficient in C(sp3) carbon counts. We report unique solutions to the challenge of increasing both the chemical diversity of these libraries and their C(sp3) carbon counts by merging Ni/photoredox dual catalytic C(sp2)-C(sp3) cross-coupling as well as photoredox-catalyzed radical/polar crossover alkylation protocols with DELs. The successful integration of multiple classes of radical sources enables the rapid incorporation of a diverse set of alkyl fragments.
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Affiliation(s)
- James P Phelan
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Simon B Lang
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Jaehoon Sim
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Simon Berritt
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Andrew J Peat
- GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Katelyn Billings
- GlaxoSmithKline , 200 Cambridge Park Drive , Cambridge , Massachusetts 02140 , United States
| | - Lijun Fan
- GlaxoSmithKline , 200 Cambridge Park Drive , Cambridge , Massachusetts 02140 , United States
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
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Garcia JP, Stein J, Cai Y, Riemers F, Wexselblatt E, Wengel J, Tryfonidou M, Yayon A, Howard KA, Creemers LB. Fibrin-hyaluronic acid hydrogel-based delivery of antisense oligonucleotides for ADAMTS5 inhibition in co-delivered and resident joint cells in osteoarthritis. J Control Release 2018; 294:247-258. [PMID: 30572032 DOI: 10.1016/j.jconrel.2018.12.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 02/06/2023]
Abstract
To date no disease-modifying drugs for osteoarthritis (OA) are available, with treatment limited to the use of pain killers and prosthetic replacement. The ADAMTS (A Disintegrin and Metallo Proteinase with Thrombospondin Motifs) enzyme family is thought to be instrumental in the loss of proteoglycans during cartilage degeneration in OA, and their inhibition was shown to reverse osteoarthritic cartilage degeneration. Locked Nucleic Acid (LNA)-modified antisense oligonucleotides (gapmers) released from biomaterial scaffolds for specific and prolonged ADAMTS inhibition in co-delivered and resident chondrocytes, is an attractive therapeutic strategy. Here, a gapmer sequence identified from a gapmer screen showed 90% ADAMTS5 silencing in a monolayer culture of human OA chondrocytes. Incorporation of the gapmer in a fibrin-hyaluronic acid hydrogel exhibited a sustained release profile up to 14 days. Gapmers loaded in hydrogels were able to transfect both co-embedded chondrocytes and chondrocytes in a neighboring gapmer-free hydrogel, as demonstrated by flow cytometry and confocal microscopy. Efficient knockdown of ADAMTS5 was shown up to 14 days in both cell populations, i.e. the gapmer-loaded and gapmer-free hydrogel. This work demonstrates the use applicability of a hydrogel as a platform for combined local delivery of chondrocytes and an ADAMTS-targeting gapmer for catabolic gene modulation in OA.
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Affiliation(s)
- João Pedro Garcia
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Jeroen Stein
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Yunpeng Cai
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Frank Riemers
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Jesper Wengel
- Nucleic Acid Center, University of Southern Denmark, Denmark
| | - Marianna Tryfonidou
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Laura B Creemers
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands.
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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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Ruff Y, Berst F. Efficient copper-catalyzed amination of DNA-conjugated aryl iodides under mild aqueous conditions. MEDCHEMCOMM 2018; 9:1188-1193. [PMID: 30109007 PMCID: PMC6072498 DOI: 10.1039/c8md00185e] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022]
Abstract
Herein, we describe the development of copper-catalyzed cross-coupling of DNA-conjugated aryl iodides with aliphatic amines. This protocol leverages a novel ligand, 2-((2,6-dimethoxyphenyl)amino)-2-oxoacetic acid, to effect the transformation in aqueous DMSO, under mild conditions and in air, making it an ideal candidate for the synthesis of DNA-encoded libraries.
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Affiliation(s)
- Yves Ruff
- Novartis Institutes for BioMedical Research , Novartis Pharma AG , Novartis Campus , 4002 Basel , Switzerland .
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research , Novartis Pharma AG , Novartis Campus , 4002 Basel , Switzerland .
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Li X, He P, Li Z, Wang H, Liu M, Xiao Y, Xu D, Kang Y, Wang H. Interleukin‑1β‑mediated suppression of microRNA‑27a‑3p activity in human cartilage via MAPK and NF‑κB pathways: A potential mechanism of osteoarthritis pathogenesis. Mol Med Rep 2018; 18:541-549. [PMID: 29749508 DOI: 10.3892/mmr.2018.8970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/29/2018] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to investigate the role of microRNA (miR)‑27a‑3p in osteoarthritis (OA). Reverse transcription‑quantitative polymerase chain reaction and western blotting were performed to determine the expression of miR‑27a‑3p and aggrecanase‑2 (ADAMTS5) in cartilage tissues from patients with OA and healthy controls, and also in interleukin (IL)‑1β‑treated primary human chondrocytes. Primary human chondrocytes were transfected with miR‑27a‑3p. A luciferase reporter assay was used to validate the direct contact between miR‑27a‑3p and its putative binding site in the 3'‑untranslated region ADAMTS5 mRNA. Furthermore, the effects of IL‑1β‑induced activation of mitogen‑activated protein kinase (MAPK) and nuclear factor (NF)‑κB on miR‑27a‑3p were evaluated using specific inhibitors. The results revealed that the level of miR‑27a‑3p was reduced in OA cartilage tissues compared with those of normal controls. In addition, decreased miR‑27a‑3p and increased ADAMTS5 expression was observed in a time‑ and dose‑dependent manner in chondrocytes treated with IL‑1β. Furthermore, overexpression of miR‑27a‑3p suppressed the expression of ADAMTS5 in human chondrocytes induced by IL‑1β. miR‑27a‑3p overexpression also decreased the luciferase activity of the wild‑type ADAMTS5 reporter plasmid. Mutation of the miR‑27a‑3p binding site in the 3'‑untranslated region of ADAMTS5 mRNA abolished the miR‑27a‑3p‑mediated repression of reporter activity. Furthermore, the use of specific inhibitors demonstrated that IL‑1β may regulate miR‑27a‑3p expression via NF‑κB and MAPK signaling pathways in chondrocytes. The present study concluded that miR‑27a‑3p was downregulated in human OA and was suppressed by IL‑1β, and functions as a crucial regulator of ADAMTS5 in OA chondrocytes. In addition, IL‑1β‑mediated suppression of miR‑27a‑3p activity may occur via the MAPK and NF‑κB pathways. The present study may provide a novel strategy for clinical treatment of OA caused by upregulation of miR‑27a‑3p.
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Affiliation(s)
- Xing Li
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Peiheng He
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Ziqing Li
- Department of Anatomy and Cell Biology, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104‑6030, USA
| | - Haixing Wang
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Minghao Liu
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yinbo Xiao
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Dongliang Xu
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yan Kang
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Hua Wang
- Department of Orthopedics, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
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Li Y, De Luca R, Cazzamalli S, Pretto F, Bajic D, Scheuermann J, Neri D. Versatile protein recognition by the encoded display of multiple chemical elements on a constant macrocyclic scaffold. Nat Chem 2018; 10:441-448. [PMID: 29556050 PMCID: PMC6044424 DOI: 10.1038/s41557-018-0017-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 01/04/2018] [Indexed: 11/09/2022]
Abstract
In nature, specific antibodies can be generated as a result of an adaptive selection and expansion of lymphocytes with suitable protein binding properties. We attempted to mimic antibody-antigen recognition by displaying multiple chemical diversity elements on a defined macrocyclic scaffold. Encoding of the displayed combinations was achieved using distinctive DNA tags, resulting in a library size of 35,393,112. Specific binders could be isolated against a variety of proteins, including carbonic anhydrase IX, horseradish peroxidase, tankyrase 1, human serum albumin, alpha-1 acid glycoprotein, calmodulin, prostate-specific antigen and tumour necrosis factor. Similar to antibodies, the encoded display of multiple chemical elements on a constant scaffold enabled practical applications, such as fluorescence microscopy procedures or the selective in vivo delivery of payloads to tumours. Furthermore, the versatile structure of the scaffold facilitated the generation of protein-specific chemical probes, as illustrated by photo-crosslinking.
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Affiliation(s)
- Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Shapingba, Chongqing, China
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Roberto De Luca
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Samuele Cazzamalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | | | - Davor Bajic
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.
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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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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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