Screening of large and diverse libraries is the 'bread and butter' in the first phase of the discovery of novel drugs. However, maintenance and periodic renewal of high-quality large compound collections pose considerable logistic, environmental and monetary problems. Here, we exercise an alternative, the 'on-the-fly' synthesis of large and diverse libraries on a nanoscale in a highly automated fashion. For the first time, we show the feasibility of the synthesis of a large library based on 16 different chemistries in parallel on several 384-well plates using the acoustic dispensing ejection (ADE) technology platform. In contrast to combinatorial chemistry, we produced 16 scaffolds at the same time and in a sparse matrix fashion, and each compound was produced by a random combination of diverse large building blocks. The synthesis, analytics, resynthesis of selected compounds, and chemoinformatic analysis of the library are described. The advantages of the herein described automated nanoscale synthesis approach include great library diversity, absence of library storage logistics, superior economics, speed of synthesis by automation, increased safety, and hence sustainable chemistry.

CATRIN Department of Innovative Chemistry Palacký University Olomouc Olomouc Czech Republic

Department of Drug Design University of Groningen Groningen The Netherlands

Erratum v

Green Chem. 2023 May 3;25(10):4138. doi: 10.1039/d3gc90037a. PubMed

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Dandapani S. Rosse G. Southall N. Salvino J. M. Thomas C. J. Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening. Curr. Protoc. Chem. Biol. 2012;4:177–191. doi: 10.1002/9780470559277.ch110252. PubMed DOI PMC

Abou-Gharbia M. Childers W. E. Discovery of Innovative Therapeutics: Today's Realities and Tomorrow's Vision. 2. Pharma's Challenges and Their Commitment to Innovation. J. Med. Chem. 2014;57:5525–5553. doi: 10.1021/jm401564r. PubMed DOI

Follmann M. Briem H. Steinmeyer A. Hillisch A. Schmitt M. H. Haning H. Meier H. An approach towards enhancement of a screening library: The Next Generation Library Initiative (NGLI) at Bayer—against all odds? Drug Discovery Today. 2019;24:668–672. doi: 10.1016/j.drudis.2018.12.003. PubMed DOI

Belyanskaya S. L. Ding Y. Callahan J. F. Lazaar A. L. Israel D. I. Discovering Drugs with DNA-Encoded Library Technology: From Concept to Clinic with an Inhibitor of Soluble Epoxide Hydrolase. ChemBioChem. 2017;18:837–842. doi: 10.1002/cbic.201700014. PubMed DOI

Osborne J. Panova S. Rapti M. Urushima T. Jhoti H. Fragments: where are we now? Biochem. Soc. Trans. 2020;48:271–280. doi: 10.1042/BST20190694. PubMed DOI

Anderson A. C. The process of structure-based drug design. Chem. Biol. 2003;10:787–797. doi: 10.1016/j.chembiol.2003.09.002. PubMed DOI

Schreiber S. L. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science. 2000;287:1964–1969. doi: 10.1126/science.287.5460.1964. PubMed DOI

Shoichet B. K. Virtual screening of chemical libraries. Nature. 2004;432:862–865. doi: 10.1038/nature03197. PubMed DOI PMC

Liu R. Li X. Lam K. S. Combinatorial chemistry in drug discovery. Curr. Opin. Chem. Biol. 2017;38:117–126. doi: 10.1016/j.cbpa.2017.03.017. PubMed DOI PMC

Yu H. S. Modugula K. Ichihara O. Kramschuster K. Keng S. Abel R. Wang L. General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes. J. Chem. Theory Comput. 2021;17:450–462. doi: 10.1021/acs.jctc.0c01004. PubMed DOI

Lyu J. Wang S. Balius T. E. Singh I. Levit A. Moroz Y. S. O'Meara M. J. Che T. Algaa E. Tolmachova K. Tolmachev A. A. Shoichet B. K. Roth B. L. Irwin J. J. Ultra-large library docking for discovering new chemotypes. Nature. 2019;566:224–229. doi: 10.1038/s41586-019-0917-9. PubMed DOI PMC

Ying Y. Kun Y. Matthew P. R. Karl L. Robert A. Brian S. Steven J. Efficient Exploration of Chemical Space with Docking and Deep-Learning. Chem. Theory Comput. 2021;17:7106–7119. doi: 10.1021/acs.jctc.1c00810. PubMed DOI

Pearce N. M. Krojer T. Bradley A. R. Collins P. Nowak R. P. Talon R. Marsden B. D. Kelm S. Shi J. Deane C. M. von Delft F. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat. Commun. 2017;8:15123. doi: 10.1038/ncomms15123. PubMed DOI PMC

Nichols C. Ng J. Keshu A. Kelly G. Conte M. R. Marber M. S. Fraternali F. De Nicola G. F. Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein–Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α–TAB1 Complexes. J. Med. Chem. 2020;63:7559–7568. doi: 10.1021/acs.jmedchem.0c00403. PubMed DOI

Sutanto F. Shaabani S. Oerlemans R. Eris D. Patil P. Hadian M. Wang M. Sharpe M. E. Groves M. R. Dömling A. Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification. Angew. Chem., Int. Ed. 2021:18231–18239. doi: 10.1002/anie.202105584. PubMed DOI PMC

Neochoritis C. G. Zhao T. Dömling A. Tetrazoles via Multicomponent Reactions. Chem. Rev. 2019;119:1970–2042. doi: 10.1021/acs.chemrev.8b00564. PubMed DOI PMC

Dömling A. Wang W. Wang K. Chemistry and Biology Of Multicomponent Reactions. Chem. Rev. 2012;112:3083–3135. doi: 10.1021/cr100233r. PubMed DOI PMC

Dömling A. Recent Developments in Isocyanide Based Multicomponent Reactions in Applied Chemistry. Chem. Rev. 2006;106:17–89. doi: 10.1021/cr0505728. PubMed DOI

Hadimioglu B. Stearns R. Ellson R. Moving Liquids with Sound: The Physics of Acoustic Droplet Ejection for Robust Laboratory Automation in Life Sciences. J. Lab. Autom. 2016;21:4–18. doi: 10.1177/2211068215615096. PubMed DOI

Cao H. Liu H. Dömling A. Efficient multicomponent reaction synthesis of the schistosomiasis drug praziquantel. Chem. – Eur. J. 2010;16:12296–12298. doi: 10.1002/chem.201002046. PubMed DOI

Osipyan A. Shaabani S. Warmerdam R. Shishkina S. V. Boltz H. Dömling A. Automated, Accelerated Nanoscale Synthesis of Iminopyrrolidines. Angew. Chem., Int. Ed. 2020;59:12423–12427. doi: 10.1002/anie.202000887. PubMed DOI PMC

McKeown M. R. Shaw D. L. Fu H. Liu S. Xu X. Marineau J. J. Huang Y. Zhang X. Buckley D. L. Kadam A. Zhang Z. Blacklow S. C. Qi J. Zhang W. Bradner J. E. Biased multicomponent reactions to develop novel bromodomain inhibitors. J. Med. Chem. 2014;57:9019–9027. doi: 10.1021/jm501120z. PubMed DOI PMC

Desroy N. Housseman C. Bock X. Joncour A. Bienvenu N. Cherel L. Labeguere V. Rondet E. Peixoto C. Grassot J. M. Picolet O. Annoot D. Triballeau N. Monjardet A. Wakselman E. Roncoroni V. Le Tallec S. Blanque R. Cottereaux C. Vandervoort N. Christophe T. Mollat P. Lamers M. Auberval M. Hrvacic B. Ralic J. Oste L. van der Aar E. Brys R. Heckmann B. Discovery of 2-[[2-Ethyl-6-[4-[2-(3-hydroxyazetidin-1-yl)-2-oxoethyl]piperazin-1-yl]-8-methylimidazo[1,2-a]pyridin-3-yl]methylamino]-4-(4-fluorophenyl)thiazole-5-carbonitrile (GLPG1690), a First-in-Class Autotaxin Inhibitor Undergoing Clinical Evaluation for the Treatment of Idiopathic Pulmonary Fibrosis. J. Med. Chem. 2017;60:3580–3590. doi: 10.1021/acs.jmedchem.7b00032. PubMed DOI

Boltjes A. Dömling A. The Groebke-Blackburn-Bienaymé Reaction. Eur. J. Org. Chem. 2019:7007–7049. doi: 10.1002/ejoc.201901124. PubMed DOI PMC

Aouali M. Mhalla D. Allouche F. El Kaim L. Tounsi S. Trigui M. Chabchoub F. Synthesis, antimicrobial and antioxidant activities of imidazotriazoles and new multicomponent reaction toward 5-amino-1-phenyl[1,2,4]triazole derivatives. Med. Chem. Res. 2015;24:2732–2741. doi: 10.1007/s00044-015-1322-z. DOI

Khoury K. Sinha M. K. Nagashima T. Herdtweck E. Dömling A. J. A. C. Efficient assembly of iminodicarboxamides by a “truly” four–component reaction. Angew. Chem. 2012;124:10426–10429. doi: 10.1002/ange.201205366. PubMed DOI PMC

Malawska B. Kulig K. Gajda J. Szczeblewski D. Musiał A. Wieckowski K. Maciag D. Stables J. P. Design, synthesis and pharmacological evaluation of alpha-substituted N-benzylamides of gamma-hydroxybutyric acid with potential GABA-ergic activity. Part 6. Search for new anticonvulsant compounds. Acta Pol. Pharm. 2007;64:127–137. PubMed

Beck B. Srivastava S. Khoury K. Herdtweck E. Dömling A. One-pot multicomponent synthesis of two novel thiolactone scaffolds. Mol. Divers. 2010;14:479–491. doi: 10.1007/s11030-010-9249-2. PubMed DOI

Kim Y. B. Park S. J. Geum G. C. Jang M. S. Kang S. B. Lee D. H. Kim Y. S. An Efficient Synthesis of α-Amino-δ-valerolactones by the Ugi Five-Center Three-Component Reaction. Bull. Korean Chem. Soc. 2002;23:1277–1320. doi: 10.5012/bkcs.2002.23.9.1277. DOI

Demharter A. Hörl W. Herdtweck E. Ugi I. Synthesis of Chiral 1,1′-Iminodicarboxylic Acid Derivatives from α-Amino Acids, Aldehydes, Isocyanides, and Alcohols by the Diastereoselective Five-Center–Four-Component Reaction. Angew. Chem., Int. Ed. Engl. 1996;35:173–175. doi: 10.1002/anie.199601731. DOI

Ugi I. Demharter A. Hörl W. Schmid T. Ugi reactions with trifunctional α-amino acids, aldehydes, isocyanides and alcohols. Tetrahedron. 1996;52:11657–11664. doi: 10.1016/0040-4020(96)00647-3. DOI

Beck B. Srivastava S. Domling A. New end-on thiolactone scaffold by an isocyanide-based multicomponent reaction. Heterocycles. 2008;73:177.

Cho S. Keum G. Kang S. B. Han S. Y. Kim Y. An efficient synthesis of 2,5-diketopiperazine derivatives by the Ugi four-center three-component reaction. Mol. Diversity. 2003;6:283–286. doi: 10.1023/B:MODI.0000006812.16141.b5. PubMed DOI

Bon R. S. van Vliet B. Sprenkels N. E. Schmitz R. F. de Kanter F. J. Stevens C. V. Swart M. Bickelhaupt F. M. Groen M. B. Orru R. V. Multicomponent synthesis of 2-imidazolines. Mol. Divers. 2005;70:3542–3553. PubMed

Gunawan S. Hulme C. Bifunctional building blocks in the Ugi-azide condensation reaction: a general strategy toward exploration of new molecular diversity. Org. Biomol. Chem. 2013;11:6036–6046. doi: 10.1039/C3OB40900G. PubMed DOI PMC

Nixey T. Kelly M. Hulme C. The one-pot solution phase preparation of fused tetrazole-ketopiperazines. Tetrahedron Lett. 2000;41:8729–8733. doi: 10.1016/S0040-4039(00)01563-X. DOI

Vazquez M. L. Kaila N. Strohbach J. W. Trzupek J. D. Brown M. F. Flanagan M. E. Mitton-Fry M. J. Johnson T. A. TenBrink R. E. Arnold E. P. Basak A. Heasley S. E. Kwon S. Langille J. Parikh M. D. Griffin S. H. Casavant J. M. Duclos B. A. Fenwick A. E. Harris T. M. Han S. Caspers N. Dowty M. E. Yang X. Banker M. E. Hegen M. Symanowicz P. T. Li L. Wang L. Lin T. H. Jussif J. Clark J. D. Telliez J.-B. Robinson R. P. Unwalla R. Identification of N-{cis-3-[Methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide (PF-04965842): A Selective JAK1 Clinical Candidate for the Treatment of Autoimmune Diseases. J. Med. Chem. 2018;61:1130–1152. doi: 10.1021/acs.jmedchem.7b01598. PubMed DOI

Sander T. Freyss J. von Korff M. Rufener C. DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis. J. Chem. Inf. Model. 2015;55:460–473. doi: 10.1021/ci500588j. PubMed DOI

Wishart D. S. Knox C. Guo A. C. Shrivastava S. Hassanali M. Stothard P. Chang Z. Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006;34:668–672. doi: 10.1093/nar/gkj067. PubMed DOI PMC

Ghose A. K. Viswanadhan V. N. Wendoloski J. J. A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J. Comb. Chem. 1999;1:55–68. doi: 10.1021/cc9800071. PubMed DOI

Muegge I. Heald S. L. Brittelli D. Simple Selection Criteria for Drug-like Chemical Matter. J. Med. Chem. 2001;44:1841–1846. doi: 10.1021/jm015507e. PubMed DOI

Wager T. T. Hou X. Verhoest P. R. Villalobos A. Central Nervous System Multiparameter Optimization Desirability: Application in Drug Discovery. ACS Chem. Neurosci. 2016;7:767–775. doi: 10.1021/acschemneuro.6b00029. PubMed DOI

Rankovic Z. CNS Drug Design: Balancing Physicochemical Properties for Optimal Brain Exposure. J. Med. Chem. 2015;58:2584–2608. doi: 10.1021/jm501535r. PubMed DOI

Sauer W. H. B. Schwarz M. K. Molecular Shape Diversity of Combinatorial Libraries: A Prerequisite for Broad Bioactivity. J. Chem. Inf. Comput. Sci. 2003;43:987–1003. doi: 10.1021/ci025599w. PubMed DOI

Schaller D. Šribar D. Noonan T. Deng L. Nguyen T. N. Pach S. Machalz D. Bermudez M. Wolber G. Next generation 3D pharmacophore modeling. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2020;10:e1468.

Boss C. Hazemann J. Kimmerlin T. von Korff M. Lüthi U. Peter O. Sander T. Siegrist R. The screening compound collection: a key asset for drug discovery. Chimia. 2017;71:667–677. doi: 10.2533/chimia.2017.667. PubMed DOI

Wang Y. Shaabani S. Ahmadianmoghaddam M. Gao L. Xu R. Kurpiewska K. Kalinowska-Tluscik J. Olechno J. Ellson R. Kossenjans M. Acoustic droplet ejection enabled automated reaction scouting. ACS Cent. Sci. 2019;5:451–457. doi: 10.1021/acscentsci.8b00782. PubMed DOI PMC

Hadian M. Shaabani S. Patil P. Shishkina S. V. Böltz H. Dömling A. J. G. C. Sustainability by design: automated nanoscale 2,3,4-trisubstituted quinazoline diversity. Green Chem. 2020;22:2459–2467. doi: 10.1039/D0GC00363H. DOI

Neochoritis C. G. Shaabani S. Ahmadianmoghaddam M. Zarganes-Tzitzikas T. Gao L. Novotná M. Mitríková T. Romero A. R. Irianti M. I. Xu R. Rapid approach to complex boronic acids. Sci. Adv. 2019;5:eaaw4607. doi: 10.1126/sciadv.aaw4607. PubMed DOI PMC

Shaabani S. Xu R. Ahmadianmoghaddam M. Gao L. Stahorsky M. Olechno J. Ellson R. Kossenjans M. Helan V. Dömling A. J. G. C. Automated and accelerated synthesis of indole derivatives on a nano-scale. Green Chem. 2019;21:225–232. doi: 10.1039/C8GC03039A. PubMed DOI PMC

Sutanto F. Shaabani S. Neochoritis C. G. Zarganes-Tzitzikas T. Patil P. Ghonchepour E. Dömling A. Multicomponent reaction–derived covalent inhibitor space. Sci. Adv. 2021;7:eabd9307. doi: 10.1126/sciadv.abd9307. PubMed DOI PMC

Gao K. Shaabani S. Xu R. Zarganes-Tzitzikas T. Gao L. Ahmadianmoghaddam M. Groves M. R. Dömling A. Nanoscale, automated, high throughput synthesis and screening for the accelerated discovery of protein modifiers. RSC Med. Chem. 2021;12:809–818. doi: 10.1039/D1MD00087J. PubMed DOI PMC

Lin S. Dikler S. Blincoe W. D. Ferguson R. D. Sheridan R. P. Peng Z. Conway D. V. Zawatzky K. Wang H. Cernak T. J. S. Mapping the dark space of chemical reactions with extended nanomole synthesis and MALDI-TOF MS. Science. 2018;361:eaar6236. doi: 10.1126/science.aar6236. PubMed DOI

Gesmundo N. J. Sauvagnat B. Curran P. J. Richards M. P. Andrews C. L. Dandliker P. J. Cernak T. J. N. Nanoscale synthesis and affinity ranking. Nature. 2018;557:228–232. doi: 10.1038/s41586-018-0056-8. PubMed DOI

Shevlin M. Practical high-throughput experimentation for chemists. ACS Med. Chem. Lett. 2017;8:601–607. doi: 10.1021/acsmedchemlett.7b00165. PubMed DOI PMC

Barhate C. Donnell A. F. Davies M. Li L. Zhang Y. Yang F. Black R. Zipp G. Zhang Y. Cavallaro C. Microscale purification in support of high-throughput medicinal chemistry. Chem. Commun. 2021;57:11037–11040. doi: 10.1039/D1CC03791A. PubMed DOI

Plowright A. T. Johnstone C. Kihlberg J. Pettersson J. Robb G. Thompson R. A. Hypothesis driven drug design: improving quality and effectiveness of the design-make-test-analyse cycle. Drug Discovery Today. 2012;17:56–62. doi: 10.1016/j.drudis.2011.09.012. PubMed DOI

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