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

  • L‐series alkyl tethered diisopropylarylsilane Lanterns (Mimotopes, cat. no. MIL10431000;; also see Ryba et al., )
  • 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; ( or Mimotopes, cat. no. MIA10140006 (
  • 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

  • Lanterns, loaded (see protocol 1)
  • Tetrahydrofuran (THF), anhydrous, containing BHT inhibitor
  • Tetrakis(triphenylphosphine)palladium(0) (Pd(PPh 3) 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/H 2O 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 (PBu 3)
  • 2,6‐lutidine (anhydrous)
  • Sulfonyl chlorides
  • Isocyanates
  • Triethylamine (EtN 3, 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(PPh 3) 2Cl 2; 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 ( 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

  • Lanterns, loaded, subjected to desired solid‐phase transformations (see 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;
  • 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,, 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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Internet Resources,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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