Small‐Molecule Library Synthesis on Silicon‐Functionalized SynPhase Lanterns

Jeremy R. Duvall1, Anita Vrcic1, Lisa A. Marcaurelle1

1 Chemical Biology Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
Publication Name:  Current Protocols in Chemical Biology
Unit Number:   
DOI:  10.1002/9780470559277.ch100038
Online Posting Date:  July, 2010
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Abstract

Silicon-functionalized SynPhase Lanterns are useful for the combinatorial synthesis of small-molecule libraries. Lanterns bearing an alkyl-tethered diisopropylarylsilane are first activated with triflic acid to afford the corresponding diisopropylsilyl triflate, which is then reacted with a library scaffold bearing a free alcohol. Once the scaffold has been loaded onto the solid phase, a variety of transformations can be run, including amine cappings, cross-coupling reactions, and amide bond formation. These reactions can yield a variety of products when run sequentially using split-pool synthesis strategies. Upon completion of the solid-phase transformations, the small molecules are released from the Lanterns using HF/pyridine. Using the techniques described here, libraries can be made ranging from a few compounds to >10,000 members in a highly efficient manner. Curr. Protoc. Chem. Biol. 2:135-151 © 2010 by John Wiley & Sons, Inc.

Keywords: solid-phase; combinatorial; synthesis; diversity; Lanterns; silicon

     
 
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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Loading of a Library Scaffold onto a Silicon-Functionalized Lantern
  • Basic Protocol 2: Solid-Phase Transformations of Small-Molecule Libraries on Lanterns
  • Basic Protocol 3: Cleavage of Functionalized Scaffold from Solid Support
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Loading of a Library Scaffold onto a Silicon-Functionalized Lantern

 Materials
  • L-series alkyl tethered diisopropylarylsilane Lanterns (Mimotopes, cat. no. MIL10431000;http://www.mimotopes.com; also see Ryba et al., 2009)
  • Transtems (stems with enclosed RF transponder, Mimotopes, cat. no. MIT10260010)
  • Standard color tagging kit (colored cogs and spindles, Mimotopes, cat. no. MIT10430001)
  • 3% trifluoromethanesulfonic acid solution in dichloromethane (TfOH in DCM; see recipe)
  • Dichloromethane (DCM, anhydrous for reactions; HPLC grade for washings)
  • Nitrogen source
  • 2,6-lutidine (anhydrous; Aldrich, cat. no. 336106)
  • Library scaffold containing primary or secondary alcohol (coevaporated from benzene or toluene)
  • N,N-dimethylformamide (DMF, HPLC grade)
  • Tetrahydrofuran (THF, containing BHT as inhibitor)
  • Isopropanol
  • Oven-dried reaction vessel with screw top: e.g., ChemGlass, cat. no. CG-1880-42; (http://www.chemglass.com/) or Mimotopes, cat. no. MIA10140006 (http://www.mimotopes.com)
  • Incubator shaker (New Brunswick Scientific, model M1353-0004 or similar for large libraries)
  • Rubber septa (Sigma-Aldrich, cat. no. Z512222 or similar)
  • Washing apparatus (ceramic Buchner funnel and waste container)
  • Lyophilizer or high-vacuum manifold
  • SynPhase work station (cleavage tray, Lantern tray, stem ejector, SynPhase press and stem tray; Mimotopes, cat. no. MIA10910001)
  • Transort RF reader and software (Mimotopes, cat. no. MIT10520001)

CAUTION: TfOH is highly corrosive and personal contact can result in injury. Extreme caution should be exercised.

NOTE: Transtems can be attached to Lanterns using the SynPhase press (see SynPhase workstation) to enable RF sorting with the Transort reader and software.

Basic Protocol 2: Solid-Phase Transformations of Small-Molecule Libraries on Lanterns

 Materials
  • Lanterns, loaded (see Basic Protocol 1)
  • Tetrahydrofuran (THF), anhydrous, containing BHT inhibitor
  • Tetrakis(triphenylphosphine)palladium(0) (Pd(PPh3)4; Aldrich, cat. no. 216666)
  • 1,3-dimethylbarbituric acid (DMBA)
  • N,N-dimethylformamide (DMF, HPLC grade)
  • 0.1 M sodium cyanide in a 1:1 THF/H2O solution (prepare fresh)
  • Isopropanol
  • Dichloromethane (DCM, anhydrous for reactions; HPLC grade for washings)
  • 20% (v/v) piperidine in DMF (store up to 1 month at 25°C)
  • Thiophenol
  • Potassium carbonate
  • Methanol (MeOH)
  • Potassium trimethylsilanolate (KOTMS; Aldrich, cat. no. 324868)
  • Tributylphosphine (PBu3)
  • 2,6-lutidine (anhydrous)
  • Sulfonyl chlorides
  • Isocyanates
  • Triethylamine (EtN3, anhydrous)
  • Carboxylic acids
  • (Benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate (PyBOP; Aldrich, cat. no. 377848)
  • Sodium triacetoxyborohydride [Na(OAc)3BH]
  • 2% (v/v) acetic acid in DMF
  • Aldehydes
  • Ethanol (EtOH)
  • Boronic acids
  • Bis(triphenylphosphine)palladium(II) dichloride (Pd(PPh3)2Cl2; Aldrich, cat. no. 412720)
  • Nitrogen source
  • Alkynes
  • N,N-diisopropylethylamine (DIEA)
  • Copper (I) iodide (CuI)
  • Amines
  • Oven-dried reaction vessel with screw top (e.g., ChemGlass, cat. no. CG-1880-42, Mimotopes, cat. no. MIA10140006)
  • Ceramic Büchner funnel
  • Incubator shaker (New Brunswick Scientific, model M1353-0004 or similar for large libraries)
  • Additional reagents and equipment for quality control analysis (Basic Protocol 3)

CAUTION: Some washes require the use of a solution of NaCN to remove residual metals (e.g., Pd, Cu). Exercise great caution when performing these washes as NaCN is highly toxic.

Basic Protocol 3: Cleavage of Functionalized Scaffold from Solid Support

 Materials
  • Lanterns, loaded, subjected to desired solid-phase transformations (see Basic Protocol 2)
  • Cleavage solution (see recipe)
  • Methoxytrimethylsilane (TMSOMe; 99%, Aldrich, cat. no. 253006-250g)
  • Methanol (MeOH)
  • Dichloroethane (DCE)
  • Dimethylsulfoxide (DMSO)
  • Labeled deep 96-well plate (Seahorse Biosciences, cat. no. XPO128; http://www.seahorsebio.com/)
  • Other 96-well plates to use as covers
  • Spreadsheet software
  • Multichannel pipettors and polypropylene reservoir
  • Labeled tube rack with preweighed 2-D barcoded glass mini-tubes (Tradewinds, 1.2-ml hi-recovery mini-tube, cat. no. 063227-0301, http://www.twdtradewinds.com/, or similar)
  • Centrifugal evaporator (e.g., Genevac HT12 or HT24, SP Industries)
  • Automated weighing station (e.g., FlexiWeigh, Mettler Toledo)
  • 2-D barcode reader (e.g., VisionMatePlus, Thermo Fisher Scientific)
  • Additional reagents and equipment for liquid chromatography/mass spectrometry (LC-MS)

CAUTION: Use proper personal protection equipment when handling HF/pyridine (safety glasses, nitrile gloves, and lab coat). Labware that comes into contact with HF/pyridine should be quenched with methoxy- or ethoxytrimethylsilane. Prepare a solution of 25% methoxytrimethylsilane in THF and keep it nearby at all times.

NOTE: Remove any identifiers (Transtems or colored spindles) prior to cleavage. For removing Transtems, the use of a Stem Recycler Module (SynPhase stem recycler module for L- and D-series Lanterns; Mimotopes, cat. no. MIA10880001) is required.
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Figures

  •  FigureFigure 1. (A) Composition of SynPhase Lanterns: an unreactive base polymer and an outer polymer graft consisting of polystyrene or polyamide. (B) Lanterns are available in three sizes to accommodate different loading needs. A-series: 75 µmol/Lantern (5 mm × 5 mm). D-series: 35 µmol/Lantern (12.5 mm × 5 mm). L-series: 15 µmol/Lantern (17 mm × 6 mm). Figure reproduced with permission from Mimotopes.
    View Image
  •  FigureFigure 2. Use of silicon-functionalized Lanterns for library synthesis: activation, loading, split-pool synthesis, and cleavage.
    View Image
  •  FigureFigure 3. Representative solid-phase transformations useful for split-pool library synthesis on silicon-functionalized Lanterns.
    View Image
  •  FigureFigure 4. L-Series SynPhase Lanterns equipped with (A) radio frequency (RF) tags and (B) color-coded spindles and cogs. (C) Work station for RF-directed sorting.
    View Image

Videos

Literature Cited

Literature Cited
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 Internet Resources
    http://www.mimotopes.com/knowledgeBase.asp?cid=26,34

An introduction to SynPhase Lanterns is provided on the Mimotopes Web site, as well as a variety of protocols for Lanterns with alternate linkers.

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