ABSTRACT
The ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer.
Subject(s)
DNA-Binding Proteins , Peptides , RNA, Messenger , Transcription Factors , Humans , Ligands , Peptides/chemistry , Peptides/metabolism , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Transcription Factors/chemistry , RNA, Messenger/genetics , RNA, Messenger/metabolism , Protein Binding , Binding SitesABSTRACT
Natural product (NP) structures are a rich source of inspiration for the discovery of new biologically relevant chemical matter. In natural product inspired pseudo-NPs, NP-derived fragments are combined de novo in unprecedented arrangements. Described here is the design and synthesis of a 155-member pyrroquinoline pseudo-NP collection in which fragments characteristic of the tetrahydroquinoline and pyrrolidine NP classes are combined with eight different connectivities and regioisomeric arrangements. Cheminformatic analysis and biological evaluation of the compound collection by means of phenotyping in the morphological "cell painting" assay followed by principal component analysis revealed that the pseudo-NP classes are chemically diverse and that bioactivity patterns differ markedly, and are dependent on connectivity and regioisomeric arrangement of the fragments.
Subject(s)
Biological Products/chemical synthesis , Pyrrolidines/chemistry , Quinolines/chemistry , Biological Products/chemistry , Cycloaddition Reaction , Drug Design , Principal Component Analysis , StereoisomerismABSTRACT
Covering: up to 2020 Natural products (NPs) provide inspiration for the design of biologically active compounds and libraries. In this review, we cover several experimental and in silico approaches, which have been used to simplify NPs and guide NP-based library design. Earlier approaches, like the structural classification of natural products (SCONP) and biology-oriented synthesis (BIOS), focus on the identification of activity determining scaffolds and the synthesis of corresponding compound collections. More recently, NP fragments identified by means of cheminformatic analysis of the Dictionary of Natural Products (DNP) have been combined in unprecedented fashions to yield pseudo natural products (pseudo NPs), which show biological activities unrelated to the guiding NPs. Each approach was also the source of chemical innovation, in which synthetic methods were established for the rapid assembly of NP-inspired compounds and libraries.
Subject(s)
Biological Products/chemical synthesis , Evolution, Chemical , Biological Products/chemistry , Biological Products/pharmacology , Computer Simulation , Molecular StructureABSTRACT
Phosphoanhydrides (P-anhydrides) are ubiquitously occurring modifications in nature. Nucleotides and their conjugates, for example, are among the most important building blocks and signaling molecules in cell biology. To study and manipulate their biological functions, a diverse range of analogues have been developed. Phosphate-modified analogues have been successfully applied to study proteins that depend on these abundant cellular building blocks, but very often both the preparation and purification of these molecules are challenging. This study discloses a general access to P-anhydrides, including different nucleotide probes, that greatly facilitates their preparation and isolation. The convenient and scalable synthesis of, for example, (18) O labeled nucleoside triphosphates holds promise for future applications in phosphoproteomics.
Subject(s)
Anhydrides/chemical synthesis , Nucleosides/chemistry , Nucleotides/chemistry , Phosphates/chemical synthesis , Anhydrides/chemistry , Molecular Structure , Phosphates/chemistryABSTRACT
P-Amidites can be used in iterative couplings to selectively give mixed P(III) -P(V) anhydrides. These intermediates can be oxidized followed by a rapid removal of the two terminal fluorenylmethyl groups. An iterative synthesis (coupling, oxidation, deprotection) of nucleoside oligophosphates can be carried out in solution and on a solid support. The coupling rates and yields are high, the procedures convenient (non-dry reagents and solvents, ambient conditions, unprotected nucleotides), and the purification is very simple. The method works with all canonical nucleosides and holds promise for significant simplification of the usually cumbersome process of P-anhydride bond construction.
