Synthesis of highly functionalized oligobenzamide proteomimetic foldamers by late stage introduction of sensitive groups† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ob00078a Click here for additional data file.

New routes are developed to allow introduction of sensitive side-chains and synthesis of challenging proteomimetic sequences.


General Experimental Considerations
All commercial solvents and reagents were used without further purification unless stated otherwise. All non-aqueous reactions were performed under an atmosphere of nitrogen and using anhydrous solvents. Water-sensitive reactions were performed in oven-dried glassware, cooled under nitrogen before use, or flame dried and cooled, under vacuum if stated. Solvents were removed under reduced pressure using a Büchi rotary evaporator. Ether refers to diethyl ether and petrol refers to petroleum spirit (b.p. 40-60 °C). Flash column chromatography was carried out using silica (35-70 μm particles) or alumina (neutral, Brockman activity 1), with crude reaction mixtures loaded in the initial solvent system or its least polar constituent. Thin layer chromatography was carried out on commercially available silica pre-coated aluminium plates (Kieselgel 60 F254, Merck) or commercially available alumina pre-coated glass plates (neutral, Brockman activity 1). Strong cation exchange columns were carried out using SCX, 5.0 g pre-packed cartridge, Supelco.
Proton and carbon NMR spectra were recorded on a Bruker Avance 500, Avance DPX300 or DRX500 spectrophotometer with an internal deuterium lock. Carbon NMR spectra were recorded with composite pulse decoupling using the waltz 16 pulse sequence. Chemical shifts are quoted in parts per million downfield of tetramethylsilane, and coupling constants (J) are given in Hz. NMR spectra were recorded at 300 K unless otherwise stated. Infra-red spectra were recorded using a Perkin-Elmer Spectrum One FT-IR spectrophotometer. Melting points were determined using a Griffin and George melting point apparatus and are uncorrected. Nominal mass spectrometry was routinely performed on a Bruker HCT Ultra spectrometer using electrospray (+) ionization. Nominal and accurate mass spectrometry using electrospray ionisation was carried out by staff or the candidate in the School of Chemistry using a Micromass LCT-KA111, Bruker MicroTOF or Bruker MaXis Impact TOF mass spectrometer. Mass-directed HPLC purifications were run on an Agilent 1260 Infinity Preparative HPLC system equipped with a Waters XBridge™ Prep C18 19 × 100 mm column, 5 μm particle size, on an acetonitrile or methanol/water gradient (5-95% acetonitrile or methanol over 8 minutes) and an Agilent 6120 Quadrupole system equipped with a quadrupole MS detector, using electrospray ionisation (ESI).

Oligobenzamide Nomenclature
To simplify the numbering and NMR assignment of oligobenzamides, we have devised a sequential nomenclature, where each of the monomer building blocks is considered separately. The monomers are numbered from 1 to 3 starting from the N-terminal. Within each monomer, the numbering is the same: the carbons from the aminobenzoic acid are numbered using the standard system (the aromatic carbon bearing the carboxylic acid is C1, the one bearing the amine is C4). Then, the lateral chain is numbered: the carbon attached to the oxygen is the Cα, and the numbering of the aliphatic part of the side chain continues with Cβ, etc. In the case of aromatic side chains,

Standard Procedure C -Nitro reduction by hydrogenation
Palladium on charcoal (10 %) was added against a flow of nitrogen to a solution of the nitro compound in methanol (10 ml per 100 mg) under a nitrogen atmosphere, the atmosphere was then replaced with hydrogen and the reaction stirred vigorously until complete by TLC (typically 2 hours). The hydrogen atmosphere was vented and the reaction mixture filtered through a pad of Celite with methanol, concentrated in vacuo and purified by flash column chromatography.

Standard Procedure D -Coupling
Dichlorotriphenylphosphorane (4.5 equivalents) was added to a solution of nitro-acid compound (1.2 equivalents) in chloroform (5 ml per 100 mg of amine) and the reaction heated to reflux with stirring under nitrogen. After 2 hours at reflux, the amine ester compound (1 equivalent) was added as solution in chloroform (1 ml) and the reaction was heated to reflux for a further 24 hours. The reaction mixture was then concentrated in vacuo and partitioned between ethyl acetate (5 ml per 100 mg of amine) and H 2 O (5 ml per 100 mg of amine). The organic layer was separated and washed with saturated aqueous sodium bicarbonate solution (5 ml per 100 mg of amine), dried over magnesium sulphate and concentrated in vacuo. The resulting residue was purified by flash column chromatography to give the desired compound.

Standard Proceedure E -Removal of Allyl Groups
Allyl functionalised trimers were treated with palladium tetrakistriphenylphosphine (10 mol%) and sodium toluenesulfinate (1.2 eq) in THF (1ml/mg) overnight, concentrated in vacuo and purified by column chromatography eluting with Et 2 O in DCM.

Standard Procedure F -Side chain introduction by Mitsunobu reaction
De-allylated nitro ester trimers were dissolved in THF (1 ml/10 ml substrate) and PPh 3 (2 eq.), alcohol (2 eq.) and DIAD (2 eq.) added sequentially. The reaction was stirred overnight at r.t., concentrated in vacuo. Amine products were isolated by SCX column and used without further purification.

COOMe, S12
Using standard procedure C on 0.19 mmol scale to give the title compound as a colourless oil (74 mg, 56%

Trimers
The allyl bearing trimers were prepared in parallel using the methods and building blocks described previously 2-7 (Standard Procedures A, B, C and D), checking at pertinent times during the synthesis by crude NMR and LC-MS, to afford the below compounds. Compounds were either pure following final precipitation or purified by preparative HPLC.

COOH, 8e
Prepared by standard procedure F followed by standard procedures C and A and purification by mass directed HPLC (6.

Competition Assays
Competition assays and protein expression were carried out as previously reported. 2

Photo-Crosslinking Experiments
A solution containing the photo-crosslinking compound (150 μM) and p300 (100 μM) in assay buffer was prepared and analysed by LC-MS on a Bruker HCT Ultra. Separate solutions containing only compound or only protein were treated identically. The solutions were then irradiated with UV light (365 nm) for 1 hour whilst cooled in an ice bath. The LC-MS analysis was then repeated. The protein signals were examined for any increase of adduct formation.