Deconvoluting the responses of polymer-scaffolded dynamic combinatorial libraries to biomacromolecular templates

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1 Supporting Information Deconvoluting the responses of polymer-scaffolded dynamic combinatorial libraries to biomacromolecular templates Antonio J. Ruiz-Sanchez, a Patrick L. Higgs, a Daniel T. Peters, b Andrew T. Turley, a Matthew A. Dobson, a Adam J. North a and David A. Fulton* a a Chemical Nanoscience Laboratory, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK. Fax: +44 (0) ; Tel: +44(0) ; b Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom General Experimental All chemicals, including Girard s reagent T (R2) were purchased from Sigma-Aldrich or Alfa Aesar and were used as received without further purification. N, N-dimethylacrylamide was purified by vacuum distillation at 60 C. 1 H and 13 C NMR spectra of synthesised compounds were recorded on a Bruker Avance 300 spectrometer at 300 and 75 MHz respectively, or on a Bruker Avance III HD spectrometer at 700 MHz and 125 MHz, with the residual solvent signal as an internal standard. High-resolution mass spectrometry was performed on a Waters LCT Premier mass spectrometer (Waters Inc.). Gel permeation chromatography (GPC) was conducted on a Varian ProStar instrument (Varian Inc.) equipped with a Varian 325 UV-Vis dual wavelength detector (254 nm), a Dawn Heleos II multi-angle laser light scattering detector (Wyatt Technology Corp.), a Viscotek 3580 differential RI detector, and a pair of PL gel 5 µm Mixed D mm columns with guard column (Polymer Laboratories Inc.) in series. Near monodisperse methyl methacrylate standards (Agilent Technologies) were used for calibration. Data collection was performed with Galaxie software (Varian Inc.) and chromatograms analyzed with the Cirrus software (Varian Inc.) and Astra software (Wyatt Technology Corp.). Synthetic Procedures Copolymer scaffold (P1) Aldehyde-functionalized random copolymer P1 was prepared by RAFT polymerization according to literature. i The composition of P1 was determined by comparing the integration of the aldehyde protons with the integration of the N(CH 3 ) 2 protons of dimethylacrylamide. The monomer composition was determined to be 5:1 DMA:aldehyde monomer (monomer composition was not identical to the feed ratio of 4:1 DMA: aldehyde monomer as a consequence of the difference in reactivity of the two monomers).the PDI was found to be 1.19 and the M n to be 19 kda.

2 2-(2-Hydroxyethoxy)acetohydrazide (R1) Synthesis of 2-(2-Hydroxyethoxy)acethohydrazide (R1): (i) Na, RT to 100 C, 3 h. (ii) 2- bromoacetic acid, 100 C, 48 h. (iii) MeOH, H 2 SO 4, Reflux, 12 h. (iv) NH 2 NH 2 H 2 O, MeOH, reflux, 4 h. Residue R1 was prepared following the above scheme using a modification of the existing literature procedure. i To a stirred solution of ethylene glycol (100 ml, 1.8 mol) at room temperature under an atmosphere of nitrogen was added sodium (9.2 g, 400 mmol) in small pieces and the reaction stirred until a homogenous liquid was obtained. The resulting yellow-coloured reaction was heated to 100 C for 3 h followed by the addition of bromoacetic acid (27.8 g, 200 mmol) to yield immediately a dark orange-coloured mixture. The reaction was heated at 100 C for a further 48 h followed by removal of excess ethylene glycol by vacuum distillation. The remaining residue was taken up in HCl (37%, 120 ml) then filtered and the filtrate dried under reduced pressure to leave a viscous brown oil. The oil was dissolved in MeOH (100 ml) and then H 2 SO 4 (5 ml) was added and the resulting solution was heated at reflux for 12 h then cooled to room temperature and neutralised by the dropwise addition of saturated NaHCO 3 solution until effervescence ceased. The solution was concentrated to a volume of 50 ml under reduced pressure, diluted by the addition of CH 2 Cl 2 (200 ml) then extracted with brine (100 ml). The brine was backwashed with CH 2 Cl 2 (3 x 80 ml) and the combined organic extracts were dried under reduced pressure to afford around 12.5 g of crude product as a brown oil. A portion of the crude product (2.0 g) was dissolved in MeOH and hydrazine monohydrate (1 ml) was added and the mixture heated at reflux for 4 h then dried under reduced pressure to afford a crystalline white solid. The solid was suspended in CH 2 Cl 2 (50 ml), sonicated for 20 min then filtered. This process was repeated twice at which point the solid was judged pure by TLC analysis to yield R1 as a crystalline white solid (1.12 g) whose spectroscopic analysis was identical to that published previously. Sulfoacetylhydrazide (R3) Residue R3 was prepared as described in the literature ii with the only modification being the use of sodium sulphite instead of potassium sulphite.

3 ((3-sulfopropyl)dimethylammonio)acetohydrazide (R4) Synthesis of ((3-sulfopropyl)dimethylammonio)acetohydrazide (R4): (i) 1,3-propanesultone, CAN, RT, 12 h. (ii) NH 2 NH 2 H 2 O, H 2 O, RT, 18 h. Residue R4 was prepared following the above scheme. N,N-Dimethylglycine ethyl ester (6.05 g, 45.4 mmol) and 1,3-propanesultone (1.85 g, mmol) were dissolved in 5 ml of MeCN and the resulting solution left to stand at room temperature for 12 h. A white solid precipitate was formed which was filtration and washed 3 times with MeCN to obtain a white solid (3.55 g) which was used without further purification. A portion of the white precipitate (1.1 g ) was dissolved in H 2 O (10 ml ) and hydrazine monohydrate (3.5 ml ) was added and the reaction mixture left at room temperature for 18 h, then evaporated to dryness to afford a pale yellow oil. The oil was cooled in an ice-bath and MeOH was added dropwise to yield a white precipitate which was isolated by filtration (0.73 g, 70%). 1 H-NMR (300 MHZ, D 2 O, ppm): 2.23 (m, 2 H, CH 2 CH 2 SO 3 ), 2.95 (t, 2 H, J = 7.2 Hz, CH 2 CH 2 SO 3 ), 3.29 (s, 6 H, CH 3 ), 3.67 (m, 2 H, CH 2 CH 2 CH 2 SO 3 ), 4.05 (s, 2 H, COCH 2 N). 13 C-NMR (75 MHz, ppm): 18.3, 47.1, 51.8, 61.8, 64.09, Preparation of PS-DCLs PS-DCLs were prepared in 100 mm NH 4 OAc-AcOH/D 2 O buffer, pd 4.5 so that they contained 5.77 mg/ml aldehyde polymer P1 (total concentration of aldehyde = 3.8 mm). The total concentration of acylhydrazides R1-R4 was 11.6 mm, or 3.0 equivalents of residue (total) for every aldehyde group. After 24 h incubation at room temperature the samples were analysed by 1 H NMR spectroscopy to determine the starting composition. Templates were then added to the samples to afford a final concentration of 2.88 mg/ml of protein (BSA & HSA) and 1.00 mg/ml of DNA. The samples were left to re-equilibriate for 24 h and then analysed again by 1 H NMR Spectroscopy. To confirm that the re-equilibriation process was complete the samples were reanalysed after 48 h no further change was observed relative to the 1 H NMR spectra obtained after 24 h. 1 H NMR spectra of PS- DCLs were measured using a Bruker Avance III HD spectrometer ( 1 H at 700 MHz) and were analysed using MestreNova software.

4 Discussion of 1 H NMR spectroscopic analysis of compositional changes in PS-DCLs upon templation and the experimentally determined Limits of Quantification We have demonstrated previously i,ii that the PS-DCL residue compositional changes upon template addition can be monitored indirectly through 1 H NMR spectroscopy. Integral analysis of the α-methylene resonances of R1-R4 was used to determine the mole fractions (X n ) of the unconjugated residues in solution (a) before and (b) after the addition of template. Changes in the PS-DCL composition were expressed as a change in mole fraction ( X n ) for each residue, calculated from the equation: = Limits of Quantification: The S/N ratio of all signals integrated was found to be >400. To determine the lower limit of compositional change which can be ascertained with confidence by 1 H NMR spectroscopic integral analysis we experimentally determined the limits of quantification (LOQ) for all four residues. The LOQ is the limit at which the difference between two distinct values can be reasonably discerned, and changes in mole fraction which fall below these limits were considered as being too small to quantify with confidence. To determine LOQ we measured the integrals of mixtures of residues R1/R2 and R3/R4 prepared at known concentrations chosen to cover the range of concentration changes typically observed when PS-DCLs undergo compositional re-equlibriation in the presence of templates (Fig S1-2). Fig.S1: Mole fraction plot of R1/R2 titration. St. Dev. = , LOQ = Mole Fraction, X n (NMR) y = x R² = y = x R² = Titration Point

5 Fig. S2: Mole fraction plot of R3/R4 titration. St. Dev. = , LOQ = y = x R² = Mole Fraction, X n (NMR) y = x R² = Titration Point Assuming error in NMR integrations is normally distributed, the LOQ was calculated from the equation: LOQ = 6 σ /b where σ = the standard deviation of each line as determined by linear regression analysis and b is the slope of each line. By choosing 6 standard deviations in the LOQ we have > 99% confidence that observed changes in molecule fraction are as a consequence of compositional changes.

6 Protein Comparison Fig. S3: Structural comparison of porcine Pepsin, BSA and HSA. HSA (Blue, PDB code: 4K2C) was superposed onto BSA (Gold, PDB code: 4F5S) using the GESAMT superpose routine of the CCP4MG software package. The structures are highly similar with an RMSD of 1.8 Å over 561 Cα atoms. Porcine Pepsin (Orange, PDB code: 4PEP) was then superposed onto HSA in the same way, with an RMSD of 4.7 Å over 134 Cα atoms. Protein structures are depicted in ribbon format. Fig. S4: Electrostatic surface comparison of HSA, BSA and porcine Pepsin. Two separate views are shown of electrostatic surface representations of HSA (left), BSA (middle), and Pepsin (right), with positive electrostatic potential coloured blue and negative electrostatic potential in red. Electrostatic surface representations were generated using CCP4MG. HSA BSA Pepsin

7 References i Mahon, C. S.; Jackson, A. W.; Murray, B. S.; Fulton, D. A. "Templating a polymer-scaffolded dynamic combinatorial library" Chem. Commun. 2011, 47, ii Mahon, C. S.; Jackson, A. W.; Murray, B. S.; Fulton, D. A. "Investigating Templating Within Polymer-Scaffolded Dynamic Combinatorial Libraries" Polym. Chem. 2013, 4, iii Guide to NMR Method Development and Validation-Part 1: Identification and Quantification Technical Report No. 01/2014 Eurolal aisbl 2014).

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