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      Screening Ultra-Large Encoded Compound Libraries Leads to Novel Protein–Ligand Interactions and High Selectivity

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          Abstract

          The DNA-encoded library (DEL) discovery platform has emerged as a powerful technology for hit identification in recent years. It has become one of the major parallel workstreams for small molecule drug discovery along with other strategies such as HTS and data mining. For many researchers working in the DEL field, it has become increasingly evident that many hits and leads discovered via DEL screening bind to target proteins with unique and unprecedented binding modes. This Perspective is our attempt to analyze reports of DEL screening with the purpose of providing a rigorous and useful account of the binding modes observed for DEL-derived ligands with a focus on binding mode novelty.

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          Most cited references153

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          New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays.

          This report describes a number of substructural features which can help to identify compounds that appear as frequent hitters (promiscuous compounds) in many biochemical high throughput screens. The compounds identified by such substructural features are not recognized by filters commonly used to identify reactive compounds. Even though these substructural features were identified using only one assay detection technology, such compounds have been reported to be active from many different assays. In fact, these compounds are increasingly prevalent in the literature as potential starting points for further exploration, whereas they may not be.
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            Ubiquitin signalling in the NF-kappaB pathway.

            The transcription factor NF-kappaB (nuclear factor kappa enhancer binding protein) controls many processes, including immunity, inflammation and apoptosis. Ubiquitination regulates at least three steps in the NF-kappaB pathway: degradation of IkappaB (inhibitor of NF-kappaB), processing of NF-kappaB precursors, and activation of the IkappaB kinase (IKK). Recent studies have revealed several enzymes involved in the ubiquitination and deubiquitination of signalling proteins that mediate IKK activation through a degradation-independent mechanism.
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              Kinase drug discovery 20 years after imatinib: progress and future directions

              Protein kinases regulate nearly all aspects of cell life, and alterations in their expression, or mutations in their genes, cause cancer and other diseases. Here, we review the remarkable progress made over the past 20 years in improving the potency and specificity of small-molecule inhibitors of protein and lipid kinases, resulting in the approval of more than 70 new drugs since imatinib was approved in 2001. These compounds have had a significant impact on the way in which we now treat cancers and non-cancerous conditions. We discuss how the challenge of drug resistance to kinase inhibitors is being met and the future of kinase drug discovery. Twenty years have passed since the first small-molecule protein kinase inhibitor, imatinib, gained FDA approval. Here, Cohen et al. review advances in improving the potency and specificity of small-molecule protein kinase inhibitors and assess approaches to overcome the challenge of drug resistance. Applications of these compounds in cancers and other disorders, as well as future directions in the field, are discussed.
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                Author and article information

                Journal
                J Med Chem
                J Med Chem
                jm
                jmcmar
                Journal of Medicinal Chemistry
                American Chemical Society
                0022-2623
                1520-4804
                10 January 2024
                25 January 2024
                : 67
                : 2
                : 864-884
                Affiliations
                []AstraZeneca , Cambridge CB2 0AA, U.K.
                []X-Chem, Inc. , Waltham, Massachusetts 02453, United States
                Author notes
                Author information
                https://orcid.org/0000-0002-0406-922X
                Article
                10.1021/acs.jmedchem.3c01861
                10823476
                38197367
                f26fd19a-6a6d-4b9a-840a-4d93c11ba0f3
                © 2024 The Authors. Published by American Chemical Society

                Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works ( https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 04 October 2023
                : 04 December 2023
                : 17 November 2023
                Categories
                Perspective
                Custom metadata
                jm3c01861
                jm3c01861

                Pharmaceutical chemistry
                Pharmaceutical chemistry

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