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Chemical Biology and Therapeutics Science

The Use of Informer Sets in Screening: Perspectives on an Efficient Strategy to Identify New Probes.
Clemons PA, Bittker JA, Wagner FF, et al. The Use of Informer Sets in Screening: Perspectives on an Efficient Strategy to Identify New Probes. SLAS Discov. 2021;26(7):855-861. doi:10.1177/24725552211019410.
Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.
Usanov DL, Chan AI, Maianti JPablo, Liu DR. Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules. Nat Chem. 2018;10(7):704-714. doi:10.1038/s41557-018-0033-8.
Targeting a Therapy-Resistant Cancer Cell State Using Masked Electrophiles as GPX4 Inhibitors
Eaton JK, Furst L, Ruberto RA, et al. Targeting a Therapy-Resistant Cancer Cell State Using Masked Electrophiles as GPX4 Inhibitors. bioRxiv. 2018. doi:10.1101/376764.
A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells.
Chaikind B, Bessen JL, Thompson DB, Hu JH, Liu DR. A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells. Nucleic Acids Res. 2016;44(20):9758-9770. doi:10.1093/nar/gkw707.
Diversity-oriented synthesis yields novel multistage antimalarial inhibitors.
Kato N, Comer E, Sakata-Kato T, et al. Diversity-oriented synthesis yields novel multistage antimalarial inhibitors. Nature. 2016;538(7625):344-349. doi:10.1038/nature19804.
Inhibition of DYRK1A Stimulates Human β-Cell Proliferation.
Dirice E, Walpita D, Vetere A, et al. Inhibition of DYRK1A Stimulates Human β-Cell Proliferation. Diabetes. 2016;65(6):1660-71. doi:10.2337/db15-1127.
Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage.
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420-4. doi:10.1038/nature17946.
Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance.
Badran AH, Guzov VM, Huai Q, et al. Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance. Nature. 2016;533(7601):58-63. doi:10.1038/nature17938.
Correlating chemical sensitivity and basal gene expression reveals mechanism of action.
Rees MG, Seashore-Ludlow B, Cheah JH, et al. Correlating chemical sensitivity and basal gene expression reveals mechanism of action. Nat Chem Biol. 2016;12(2):109-16. doi:10.1038/nchembio.1986.
Discovery and characterization of a peptide that enhances endosomal escape of delivered proteins in vitro and in vivo.
Li M, Tao Y, Shu Y, et al. Discovery and characterization of a peptide that enhances endosomal escape of delivered proteins in vitro and in vivo. J Am Chem Soc. 2015;137(44):14084-93. doi:10.1021/jacs.5b05694.
Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset.
Seashore-Ludlow B, Rees MG, Cheah JH, et al. Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset. Cancer Discov. 2015;5(11):1210-23. doi:10.1158/2159-8290.CD-15-0235.
Development of potent in vivo mutagenesis plasmids with broad mutational spectra.
Badran AH, Liu DR. Development of potent in vivo mutagenesis plasmids with broad mutational spectra. Nat Commun. 2015;6:8425. doi:10.1038/ncomms9425.
Continuous directed evolution of DNA-binding proteins to improve TALEN specificity.
Hubbard BP, Badran AH, Zuris JA, et al. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. Nat Methods. 2015;12(10):939-42. doi:10.1038/nmeth.3515.
KRAS Genomic Status Predicts the Sensitivity of Ovarian Cancer Cells to Decitabine.
Stewart ML, Tamayo P, Wilson AJ, et al. KRAS Genomic Status Predicts the Sensitivity of Ovarian Cancer Cells to Decitabine. Cancer Res. 2015;75(14):2897-906. doi:10.1158/0008-5472.CAN-14-2860.
Small molecule-triggered Cas9 protein with improved genome-editing specificity.
Davis KM, Pattanayak V, Thompson DB, Zuris JA, Liu DR. Small molecule-triggered Cas9 protein with improved genome-editing specificity. Nat Chem Biol. 2015;11(5):316-8. doi:10.1038/nchembio.1793.
Niche-Based Screening in Multiple Myeloma Identifies a Kinesin-5 Inhibitor with Improved Selectivity over Hematopoietic Progenitors.
Chattopadhyay S, Stewart AL, Mukherjee S, et al. Niche-Based Screening in Multiple Myeloma Identifies a Kinesin-5 Inhibitor with Improved Selectivity over Hematopoietic Progenitors. Cell Rep. 2015;10(5):755-770. doi:10.1016/j.celrep.2015.01.017.
Synthesis of oxazocenones via gold(I)-catalyzed 8-endo-dig hydroalkoxylation of alkynamides.
Scully SS, Zheng S-L, Wagner BK, Schreiber SL. Synthesis of oxazocenones via gold(I)-catalyzed 8-endo-dig hydroalkoxylation of alkynamides. Org Lett. 2015;17(3):418-21. doi:10.1021/ol503273v.
Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo.
Zuris JA, Thompson DB, Shu Y, et al. Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. Nat Biotechnol. 2015;33(1):73-80. doi:10.1038/nbt.3081.
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types.
Howe EA, De Souza A, Lahr DL, et al. BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. Nucleic Acids Res. 2015;43(Database issue):D1163-70. doi:10.1093/nar/gku1244.
Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling.
McDonald RI, Guilinger JP, Mukherji S, Curtis EA, Lee WI, Liu DR. Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling. Nat Chem Biol. 2014;10(12):1049-54. doi:10.1038/nchembio.1655.
A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations.
Dickinson BC, Packer MS, Badran AH, Liu DR. A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations. Nat Commun. 2014;5:5352. doi:10.1038/ncomms6352.
Diversity-oriented synthesis-facilitated medicinal chemistry: toward the development of novel antimalarial agents.
Comer E, Beaudoin JA, Kato N, et al. Diversity-oriented synthesis-facilitated medicinal chemistry: toward the development of novel antimalarial agents. J Med Chem. 2014;57(20):8496-502. doi:10.1021/jm500994n.
NAMPT is the cellular target of STF-31-like small-molecule probes.
Adams DJ, Ito D, Rees MG, et al. NAMPT is the cellular target of STF-31-like small-molecule probes. ACS Chem Biol. 2014;9(10):2247-54. doi:10.1021/cb500347p.
Reprogramming the specificity of sortase enzymes.
Dorr BM, Ham HOk, An C, Chaikof EL, Liu DR. Reprogramming the specificity of sortase enzymes. Proc Natl Acad Sci U S A. 2014;111(37):13343-8. doi:10.1073/pnas.1411179111.
Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling.
Wawer MJ, Li K, Gustafsdottir SM, et al. Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. Proc Natl Acad Sci U S A. 2014;111(30):10911-6. doi:10.1073/pnas.1410933111.
Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones.
Maianti JPablo, McFedries A, Foda ZH, et al. Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones. Nature. 2014;511(7507):94-8. doi:10.1038/nature13297.
Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.
Wawer MJ, Jaramillo DE, Dančík V, et al. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles. J Biomol Screen. 2014;19(5):738-48. doi:10.1177/1087057114530783.
Connecting Small Molecules with Similar Assay Performance Profiles Leads to New Biological Hypotheses.
Dančík V, Carrel H, Bodycombe NE, et al. Connecting Small Molecules with Similar Assay Performance Profiles Leads to New Biological Hypotheses. J Biomol Screen. 2014;19(5):771-81. doi:10.1177/1087057113520226.
Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification.
Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol. 2014;32(6):577-82. doi:10.1038/nbt.2909.
Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity.
Guilinger JP, Pattanayak V, Reyon D, et al. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat Methods. 2014;11(4):429-35. doi:10.1038/nmeth.2845.
Negative selection and stringency modulation in phage-assisted continuous evolution.
Carlson JC, Badran AH, Guggiana-Nilo DA, Liu DR. Negative selection and stringency modulation in phage-assisted continuous evolution. Nat Chem Biol. 2014;10(3):216-22. doi:10.1038/nchembio.1453.
Identification of ligand-target pairs from combined libraries of small molecules and unpurified protein targets in cell lysates.
McGregor LM, Jain T, Liu DR. Identification of ligand-target pairs from combined libraries of small molecules and unpurified protein targets in cell lysates. J Am Chem Soc. 2014;136(8):3264-70. doi:10.1021/ja412934t.
Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming.
Choudhary A, He KHu, Mertins P, et al. Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming. PLoS One. 2014;9(4):e95194. doi:10.1371/journal.pone.0095194.
A small-molecule inducer of PDX1 expression identified by high-throughput screening.
Yuan Y, Hartland K, Boskovic Z, et al. A small-molecule inducer of PDX1 expression identified by high-throughput screening. Chem Biol. 2013;20(12):1513-22. doi:10.1016/j.chembiol.2013.10.013.
Synthesis of piperlogs and analysis of their effects on cells.
Bošković ŽV, Hussain MM, Adams DJ, Dai M, Schreiber SL. Synthesis of piperlogs and analysis of their effects on cells. Tetrahedron. 2013;69(36). doi:10.1016/j.tet.2013.05.080.
An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules.
Basu A, Bodycombe NE, Cheah JH, et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell. 2013;154(5):1151-1161. doi:10.1016/j.cell.2013.08.003.
Gossypol and an HMT G9a inhibitor act in synergy to induce cell death in pancreatic cancer cells.
Yuan Y, Tang AJ, Castoreno AB, et al. Gossypol and an HMT G9a inhibitor act in synergy to induce cell death in pancreatic cancer cells. Cell Death Dis. 2013;4:e690. doi:10.1038/cddis.2013.191.
Small-molecule inhibitors of cytokine-mediated STAT1 signal transduction in β-cells with improved aqueous solubility.
Scully SS, Tang AJ, Lundh M, Mosher CM, Perkins KM, Wagner BK. Small-molecule inhibitors of cytokine-mediated STAT1 signal transduction in β-cells with improved aqueous solubility. J Med Chem. 2013;56(10):4125-9. doi:10.1021/jm400397x.
Discovery of small-molecule enhancers of reactive oxygen species that are nontoxic or cause genotype-selective cell death.
Adams DJ, Bošković ŽV, Theriault JR, et al. Discovery of small-molecule enhancers of reactive oxygen species that are nontoxic or cause genotype-selective cell death. ACS Chem Biol. 2013;8(5):923-9. doi:10.1021/cb300653v.
Macrocyclic Hedgehog Pathway Inhibitors: Optimization of Cellular Activity and Mode of Action Studies.
Dockendorff C, Nagiec MM, Weïwer M, et al. Macrocyclic Hedgehog Pathway Inhibitors: Optimization of Cellular Activity and Mode of Action Studies. ACS Med Chem Lett. 2012;3(10):808-813. doi:10.1021/ml300172p.
Synthesis, cellular evaluation, and mechanism of action of piperlongumine analogs.
Adams DJ, Dai M, Pellegrino G, et al. Synthesis, cellular evaluation, and mechanism of action of piperlongumine analogs. Proc Natl Acad Sci U S A. 2012;109(38):15115-20. doi:10.1073/pnas.1212802109.
A small-molecule probe of the histone methyltransferase G9a induces cellular senescence in pancreatic adenocarcinoma.
Yuan Y, Wang Q, Paulk J, et al. A small-molecule probe of the histone methyltransferase G9a induces cellular senescence in pancreatic adenocarcinoma. ACS Chem Biol. 2012;7(7):1152-7. doi:10.1021/cb300139y.
Inhibition of histone deacetylase 3 protects beta cells from cytokine-induced apoptosis.
Chou DHung-Chieh, Holson EB, Wagner FF, et al. Inhibition of histone deacetylase 3 protects beta cells from cytokine-induced apoptosis. Chem Biol. 2012;19(6):669-73. doi:10.1016/j.chembiol.2012.05.010.
A human islet cell culture system for high-throughput screening.
Walpita D, Hasaka T, Spoonamore J, et al. A human islet cell culture system for high-throughput screening. J Biomol Screen. 2012;17(4):509-18. doi:10.1177/1087057111430253.
Unbiased binding assays for discovering small-molecule probes and drugs.
Kemp MM, Weïwer M, Koehler AN. Unbiased binding assays for discovering small-molecule probes and drugs. Bioorg Med Chem. 2012;20(6):1979-89. doi:10.1016/j.bmc.2011.11.071.
GW8510 increases insulin expression in pancreatic alpha cells through activation of p53 transcriptional activity.
Fomina-Yadlin D, Kubicek S, Vetere A, et al. GW8510 increases insulin expression in pancreatic alpha cells through activation of p53 transcriptional activity. PLoS One. 2012;7(1):e28808. doi:10.1371/journal.pone.0028808.
Roscovitine inhibits EBNA1 serine 393 phosphorylation, nuclear localization, transcription, and episome maintenance.
Kang M-S, Lee EKyung, Soni V, et al. Roscovitine inhibits EBNA1 serine 393 phosphorylation, nuclear localization, transcription, and episome maintenance. J Virol. 2011;85(6):2859-68. doi:10.1128/JVI.01628-10.
Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's Aβ peptide and reduce its cytotoxicity.
Chen J, Armstrong AH, Koehler AN, Hecht MH. Small molecule microarrays enable the discovery of compounds that bind the Alzheimer's Aβ peptide and reduce its cytotoxicity. J Am Chem Soc. 2010;132(47):17015-22. doi:10.1021/ja107552s.
Distinct biological network properties between the targets of natural products and disease genes.
Dančík V, Seiler KPetri, Young DW, Schreiber SL, Clemons PA. Distinct biological network properties between the targets of natural products and disease genes. J Am Chem Soc. 2010;132(27):9259-61. doi:10.1021/ja102798t.
A complex task? Direct modulation of transcription factors with small molecules.
Koehler AN. A complex task? Direct modulation of transcription factors with small molecules. Curr Opin Chem Biol. 2010;14(3):331-40. doi:10.1016/j.cbpa.2010.03.022.
Detecting protein-small molecule interactions using fluorous small-molecule microarrays.
Vegas AJ, Koehler AN. Detecting protein-small molecule interactions using fluorous small-molecule microarrays. Methods Mol Biol. 2010;669:43-55. doi:10.1007/978-1-60761-845-4_4.
Binding affinity and kinetic analysis of targeted small molecule-modified nanoparticles.
Tassa C, Duffner JL, Lewis TA, et al. Binding affinity and kinetic analysis of targeted small molecule-modified nanoparticles. Bioconjug Chem. 2010;21(1):14-9. doi:10.1021/bc900438a.
A small molecule that binds Hedgehog and blocks its signaling in human cells.
Stanton BZ, Peng LF, Maloof N, et al. A small molecule that binds Hedgehog and blocks its signaling in human cells. Nat Chem Biol. 2009;5(3):154-6. doi:10.1038/nchembio.142.
Small-molecule microarrays as tools in ligand discovery.
Vegas AJ, Fuller JH, Koehler AN. Small-molecule microarrays as tools in ligand discovery. Chem Soc Rev. 2008;37(7):1385-94. doi:10.1039/b703568n.
Identification of the molecular target of small molecule inhibitors of HDL receptor SR-BI activity.
Nieland TJF, Shaw JT, Jaipuri FA, et al. Identification of the molecular target of small molecule inhibitors of HDL receptor SR-BI activity. Biochemistry. 2008;47(1):460-72. doi:10.1021/bi701277x.
Detecting binding interactions using microarrays of natural product extracts.
Schmitz K, Haggarty SJ, McPherson OM, Clardy J, Koehler AN. Detecting binding interactions using microarrays of natural product extracts. J Am Chem Soc. 2007;129(37):11346-7. doi:10.1021/ja073965s.
Influence of HDL-cholesterol-elevating drugs on the in vitro activity of the HDL receptor SR-BI.
Nieland TJF, Shaw JT, Jaipuri FA, et al. Influence of HDL-cholesterol-elevating drugs on the in vitro activity of the HDL receptor SR-BI. J Lipid Res. 2007;48(8):1832-45. doi:10.1194/jlr.M700209-JLR200.
A pipeline for ligand discovery using small-molecule microarrays.
Duffner JL, Clemons PA, Koehler AN. A pipeline for ligand discovery using small-molecule microarrays. Curr Opin Chem Biol. 2007;11(1):74-82. doi:10.1016/j.cbpa.2006.11.031.
Fluorous-based small-molecule microarrays for the discovery of histone deacetylase inhibitors.
Vegas AJ, Bradner JE, Tang W, et al. Fluorous-based small-molecule microarrays for the discovery of histone deacetylase inhibitors. Angew Chem Int Ed Engl. 2007;46(42):7960-4. doi:10.1002/anie.200703198.
Ring-opening and ring-closing reactions of a shikimic acid-derived substrate leading to diverse small molecules.
Miao H, Tallarico JA, Hayakawa H, et al. Ring-opening and ring-closing reactions of a shikimic acid-derived substrate leading to diverse small molecules. J Comb Chem. 2007;9(2):245-53. doi:10.1021/cc060135m.
Small molecules, big players: the National Cancer Institute's Initiative for Chemical Genetics.
Tolliday N, Clemons PA, Ferraiolo P, et al. Small molecules, big players: the National Cancer Institute's Initiative for Chemical Genetics. Cancer Res. 2006;66(18):8935-42. doi:10.1158/0008-5472.CAN-06-2552.
A robust small-molecule microarray platform for screening cell lysates.
Bradner JE, McPherson OM, Mazitschek R, et al. A robust small-molecule microarray platform for screening cell lysates. Chem Biol. 2006;13(5):493-504. doi:10.1016/j.chembiol.2006.03.004.
A method for the covalent capture and screening of diverse small molecules in a microarray format.
Bradner JE, McPherson OM, Koehler AN. A method for the covalent capture and screening of diverse small molecules in a microarray format. Nat Protoc. 2006;1(5):2344-52. doi:10.1038/nprot.2006.282.
The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions.
Glasfeld A, Koehler AN, Schumacher MA, Brennan RG. The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. J Mol Biol. 1999;291(2):347-61. doi:10.1006/jmbi.1999.2946.