Bioactive Compound Collections: From Design to Target Identification

Summary The discovery of bioactive compounds underpins many areas of basic biomedical research and constitutes a large part of medicinal chemistry and chemical biology. Synthetic chemistry is now able to provide almost any drug-like molecule imaginable. Therefore, attention has turned to increasing the biological relevance of the compounds to be used in chemical biology and medicinal chemistry research, as well as maximizing their diversity within this large area of chemical space. In this review, we outline key concepts for the design of biologically relevant compound collections by taking inspiration from nature and natural products. We highlight efficient ways to screen the resulting libraries in order to maximize hit rates and the chance of discovering new modes of action. Finally, we discuss state-of-the-art techniques for the identification of molecular targets of hits identified through phenotypic screening approaches.

[1]  M. Mann,et al.  A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC) , 2006, Nature Protocols.

[2]  S. Danishefsky,et al.  Small molecule natural products in the discovery of therapeutic agents: the synthesis connection. , 2006, The Journal of organic chemistry.

[3]  D. Newman,et al.  Natural Products as Sources of New Drugs from 1981 to 2014. , 2016, Journal of natural products.

[4]  Ian Collins,et al.  Photoaffinity labeling in target- and binding-site identification. , 2015, Future medicinal chemistry.

[5]  Melvin J. Yu,et al.  From micrograms to grams: scale-up synthesis of eribulin mesylate. , 2013, Natural product reports.

[6]  Zhangxian,et al.  Linking phenotypes and modes of action through high-content screen fingerprints. , 2015 .

[7]  Anne E Carpenter,et al.  Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes , 2016, Nature Protocols.

[8]  David J Newman,et al.  Natural products as sources of new drugs over the 30 years from 1981 to 2010. , 2012, Journal of natural products.

[9]  Anne E Carpenter,et al.  Multiplex Cytological Profiling Assay to Measure Diverse Cellular States , 2013, PloS one.

[10]  Nathan T. Ross,et al.  Englerin A Agonizes the TRPC4/C5 Cation Channels to Inhibit Tumor Cell Line Proliferation , 2015, PloS one.

[11]  P. Hergenrother,et al.  Access to a Structurally Complex Compound Collection via Ring Distortion of the Alkaloid Sinomenine. , 2016, Organic letters.

[12]  Herbert Waldmann,et al.  Biology-oriented synthesis of a natural-product inspired oxepane collection yields a small-molecule activator of the Wnt-pathway , 2011, Proceedings of the National Academy of Sciences.

[13]  Maria F. Sassano,et al.  PRESTO-TANGO: an open-source resource for interrogation of the druggable human GPCR-ome , 2015, Nature Structural &Molecular Biology.

[14]  R. Carpenter,et al.  Targeting the Sonic Hedgehog Signaling Pathway: Review of Smoothened and GLI Inhibitors , 2016, Cancers.

[15]  D. O'Hagan Pyrrole, pyrrolidine, pyridine, piperidine and tropane alkaloids. , 2001, Natural product reports.

[16]  G. Schneider,et al.  Counting on Natural Products for Drug Design , 2016 .

[17]  D. O'Hagan Pyrrole, pyrrolidine, pyridine, piperidine and tropane alkaloids (1998 to 1999) , 2000 .

[18]  Herbert Waldmann,et al.  (-)-Englerin A is a potent and selective activator of TRPC4 and TRPC5 calcium channels. , 2015, Angewandte Chemie.

[19]  H. Waldmann,et al.  A ligand-directed divergent catalytic approach to establish structural and functional scaffold diversity , 2017, Nature Communications.

[20]  G. Grynkiewicz,et al.  Tropane alkaloids as medicinally useful natural products and their synthetic derivatives as new drugs. , 2008, Pharmacological reports : PR.

[21]  Lirong Wang,et al.  TargetHunter: An In Silico Target Identification Tool for Predicting Therapeutic Potential of Small Organic Molecules Based on Chemogenomic Database , 2013, The AAPS Journal.

[22]  Quanxing Wang,et al.  Immunosuppressive and anti-inflammatory activities of sinomenine. , 2011, International immunopharmacology.

[23]  D. Newman,et al.  Natural products as sources of new drugs over the last 25 years. , 2007, Journal of natural products.

[24]  David R Spring,et al.  Diversity-oriented synthesis as a tool for the discovery of novel biologically active small molecules. , 2010, Nature communications.

[25]  Adam Nelson,et al.  Synthesis of Natural-Product-Like Molecules with Over Eighty Distinct Scaffolds** , 2008, Angewandte Chemie.

[26]  Paul J Hergenrother,et al.  Natural products as starting points for the synthesis of complex and diverse compounds. , 2014, Natural product reports.

[27]  Herbert Waldmann,et al.  Neuritogenic militarinone-inspired 4-hydroxypyridones target the stress pathway kinase MAP4K4. , 2015, Angewandte Chemie.

[28]  H. Ke,et al.  Beclin1 Controls the Levels of p53 by Regulating the Deubiquitination Activity of USP10 and USP13 , 2011, Cell.

[29]  Lorenzo Galluzzi,et al.  Pharmacological modulation of autophagy: therapeutic potential and persisting obstacles , 2017, Nature Reviews Drug Discovery.

[30]  Herbert Waldmann,et al.  Discovery of Novel Cinchona-Alkaloid-Inspired Oxazatwistane Autophagy Inhibitors. , 2017, Angewandte Chemie.

[31]  Stephen R. Johnson,et al.  Ligand and Target Discovery by Fragment-Based Screening in Human Cells , 2017, Cell.

[32]  G. Drewes,et al.  Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry , 2015, Nature Protocols.

[33]  Jongmin Park,et al.  Label-free target identification using in-gel fluorescence difference via thermal stability shift , 2016, Chemical science.

[34]  Nick Barker,et al.  Organoids as an in vitro model of human development and disease , 2016, Nature Cell Biology.

[35]  H. Waldmann,et al.  Phenotypic Identification of a Novel Autophagy Inhibitor Chemotype Targeting Lipid Kinase VPS34. , 2017, Angewandte Chemie.

[36]  G. Superti-Furga,et al.  Human Haploid Cell Genetics Reveals Roles for Lipid Metabolism Genes in Nonapoptotic Cell Death , 2015, ACS chemical biology.

[37]  H. Osada,et al.  Integrated profiling methods for identifying the targets of bioactive compounds: MorphoBase and ChemProteoBase. , 2016, Natural product reports.

[38]  S. Nijman,et al.  Functional genomics to uncover drug mechanism of action. , 2015, Nature chemical biology.

[39]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[40]  E. Mcwhinnie,et al.  DNA sequencing and CRISPR-Cas9 gene editing for target validation in mammalian cells. , 2014, Nature chemical biology.

[41]  Makoto Kinoshita,et al.  [Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen]. , 2007, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[42]  Kieron M. G. O'Connell,et al.  A two-directional strategy for the diversity-oriented synthesis of macrocyclic scaffolds. , 2012, Organic & biomolecular chemistry.

[43]  M. Prunotto,et al.  Opportunities and challenges in phenotypic drug discovery: an industry perspective , 2017, Nature Reviews Drug Discovery.

[44]  R. Hicklin,et al.  Synthesis of complex and diverse compounds through ring distortion of abietic acid. , 2014, Angewandte Chemie.

[45]  Stefan Wetzel,et al.  Natural-product-derived fragments for fragment-based ligand discovery , 2012, Nature Chemistry.

[46]  Mathias Dunkel,et al.  SuperPred: update on drug classification and target prediction , 2014, Nucleic Acids Res..

[47]  Herbert Waldmann,et al.  Novel approaches to map small molecule-target interactions. , 2016, Bioorganic & medicinal chemistry.

[48]  H. Waldmann,et al.  Small Molecules Inspired by the Natural Product Withanolides as Potent Inhibitors of Wnt Signaling , 2017, Chembiochem : a European journal of chemical biology.

[49]  Brett M. Ibbeson,et al.  Diversity-oriented synthesis as a tool for identifying new modulators of mitosis , 2014, Nature Communications.

[50]  Herbert Waldmann,et al.  Biology-oriented synthesis: harnessing the power of evolution. , 2014, Journal of the American Chemical Society.

[51]  C. Wiesmann,et al.  The discovery of first-in-class drugs: origins and evolution , 2014, Nature Reviews Drug Discovery.

[52]  P. Clemons,et al.  Target identification and mechanism of action in chemical biology and drug discovery. , 2013, Nature chemical biology.

[53]  M. Pan,et al.  A bioactive withanolide Tubocapsanolide A inhibits proliferation of human lung cancer cells via repressing Skp2 expression , 2007, Molecular Cancer Therapeutics.

[54]  Stefan Wetzel,et al.  Interactive exploration of chemical space with Scaffold Hunter. , 2009, Nature chemical biology.

[55]  Herbert Waldmann,et al.  Natural product inspired compound collections: evolutionary principle, chemical synthesis, phenotypic screening, and target identification. , 2017, Drug discovery today. Technologies.

[56]  Tudor I. Oprea,et al.  ChemProt-3.0: a global chemical biology diseases mapping , 2016, Database J. Biol. Databases Curation.

[57]  X. García‐Mera,et al.  Pyrimidine derivatives as potent and selective A3 adenosine receptor antagonists. , 2011, Journal of medicinal chemistry.

[58]  Corey Nislow,et al.  A survey of yeast genomic assays for drug and target discovery. , 2010, Pharmacology & therapeutics.

[59]  Stuart L. Schreiber,et al.  Organic chemistry: Molecular diversity by design , 2009, Nature.

[60]  Scott P. Brown,et al.  The evolution of library design: crafting smart compound collections for phenotypic screens. , 2017, Drug discovery today. Technologies.

[61]  R. Hicklin,et al.  A ring-distortion strategy to construct stereochemically complex and structurally diverse compounds from natural products. , 2013, Nature chemistry.

[62]  Michael J. Keiser,et al.  Relating protein pharmacology by ligand chemistry , 2007, Nature Biotechnology.

[63]  Aurélien Grosdidier,et al.  SwissTargetPrediction: a web server for target prediction of bioactive small molecules , 2014, Nucleic Acids Res..

[64]  Herbert Waldmann,et al.  Biology-oriented synthesis of a withanolide-inspired compound collection reveals novel modulators of hedgehog signaling. , 2015, Angewandte Chemie.

[65]  Anne Mai Wassermann,et al.  A screening pattern recognition method finds new and divergent targets for drugs and natural products. , 2014, ACS chemical biology.

[66]  M. Heinrich,et al.  Alkaloids as drug leads – A predictive structural and biodiversity-based analysis , 2014 .

[67]  H. Schöler,et al.  Epiblastin A Induces Reprogramming of Epiblast Stem Cells Into Embryonic Stem Cells by Inhibition of Casein Kinase 1. , 2016, Cell chemical biology.

[68]  Anne E Carpenter,et al.  Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling , 2014, Proceedings of the National Academy of Sciences.

[69]  Heejun Kim,et al.  Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces. , 2014, Journal of the American Chemical Society.

[70]  H. Waldmann,et al.  Highly Enantioselective Catalytic Vinylogous Propargylation of Coumarins Yields a Class of Autophagy Inhibitors. , 2017, Angewandte Chemie.

[71]  Herbert Waldmann,et al.  Target identification for small bioactive molecules: finding the needle in the haystack. , 2013, Angewandte Chemie.

[72]  R. Amaravadi,et al.  Targeting autophagy in cancer , 2018, Cancer.

[73]  Doris Chen,et al.  The solute carrier SLC35F2 enables YM155-mediated DNA damage toxicity. , 2014, Nature chemical biology.

[74]  Markus Schürmann,et al.  Branching cascades: a concise synthetic strategy targeting diverse and complex molecular frameworks. , 2011, Angewandte Chemie.

[75]  Claude Ostermann,et al.  De novo branching cascades for structural and functional diversity in small molecules , 2015, Nature Communications.

[76]  Yong Huang,et al.  Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens , 2015, PLoS Comput. Biol..

[77]  Herbert Waldmann,et al.  Discovery of a Novel Inhibitor of the Hedgehog Signaling Pathway through Cell-based Compound Discovery and Target Prediction. , 2017, Angewandte Chemie.

[78]  C. Humblet,et al.  Escape from flatland: increasing saturation as an approach to improving clinical success. , 2009, Journal of medicinal chemistry.

[79]  Stefan Wetzel,et al.  Biology-oriented synthesis. , 2011, Angewandte Chemie.

[80]  Marcus Bantscheff,et al.  Ion coalescence of neutron encoded TMT 10-plex reporter ions. , 2014, Analytical chemistry.

[81]  Katsuko Komatsu,et al.  Withanoside IV and its active metabolite, sominone, attenuate Aβ(25–35)‐induced neurodegeneration , 2006, The European journal of neuroscience.

[82]  S. Chandrasekhar,et al.  Natural product hybrids as new leads for drug discovery. , 2003, Angewandte Chemie.

[83]  G. Drewes,et al.  Tracking cancer drugs in living cells by thermal profiling of the proteome , 2014, Science.

[84]  David J Newman,et al.  Cheminformatic comparison of approved drugs from natural product versus synthetic origins. , 2015, Bioorganic & medicinal chemistry letters.

[85]  K. Komatsu,et al.  Neuritic regeneration and synaptic reconstruction induced by withanolide A , 2005, British journal of pharmacology.

[86]  A. Schuffenhauer,et al.  Charting biologically relevant chemical space: a structural classification of natural products (SCONP). , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[87]  G. Barnea,et al.  The genetic design of signaling cascades to record receptor activation , 2008, Proceedings of the National Academy of Sciences.

[88]  Chanwoo Kim,et al.  Diversity-oriented synthetic strategy for developing a chemical modulator of protein–protein interaction , 2016, Nature Communications.

[89]  G. Schneider,et al.  Discovery of a Novel Hedgehog Signaling Pathway Inhibitor by Cell-based Compound Discovery and Target Prediction , 2017 .

[90]  Iris M. Oppel,et al.  Asymmetric synthesis of natural product inspired tricyclic benzopyrones by an organocatalyzed annulation reaction. , 2008, Angewandte Chemie.

[91]  H. Schöler,et al.  Small-molecule phenotypic screening with stem cells. , 2017, Nature chemical biology.

[92]  Peter S. Kutchukian,et al.  Rethinking molecular similarity: comparing compounds on the basis of biological activity. , 2012, ACS chemical biology.

[93]  Petra Schneider,et al.  Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus , 2014, Proceedings of the National Academy of Sciences.

[94]  D. Brunner,et al.  Highthroughtput analysis of behavior for drug discovery , 2015, European journal of pharmacology.

[95]  H. Osada,et al.  Morphobase, an encyclopedic cell morphology database, and its use for drug target identification. , 2012, Chemistry & biology.

[96]  J. T. Njardarson,et al.  Analysis of the structural diversity, substitution patterns, and frequency of nitrogen heterocycles among U.S. FDA approved pharmaceuticals. , 2014, Journal of medicinal chemistry.

[97]  N. Nakamura,et al.  Withanolide derivatives from the roots of Withania somnifera and their neurite outgrowth activities. , 2002, Chemical & pharmaceutical bulletin.

[98]  Daniela Gabriel,et al.  Linking phenotypes and modes of action through high-content screen fingerprints. , 2015, Assay and drug development technologies.

[99]  R. Kurzrock,et al.  KBM-7, a human myeloid leukemia cell line with double Philadelphia chromosomes lacking normal c-ABL and BCR transcripts. , 1995, Leukemia.

[100]  Jongmin Park,et al.  Discovery and target identification of an antiproliferative agent in live cells using fluorescence difference in two-dimensional gel electrophoresis. , 2012, Angewandte Chemie.

[101]  Lassi Paavolainen,et al.  Data-analysis strategies for image-based cell profiling , 2017, Nature Methods.

[102]  P. Clemons,et al.  Distinct Biological Network Properties between the Targets of Natural Products and Disease Genes , 2010, Journal of the American Chemical Society.

[103]  T. Loh,et al.  Pd-Catalyzed Intramolecular C—N Bond Cleavage, 1,4-Migration, sp3 C—H Activation, and Heck Reaction: Four Controllable Diverse Pathways Depending on the Judicious Choice of the Base and Ligand. , 2015 .

[104]  H. Osada,et al.  Identification of a Molecular Target of a Novel Fungal Metabolite, Pyrrolizilactone, by Phenotypic Profiling Systems , 2013, Chembiochem : a European journal of chemical biology.