Materials and Methods Enantioselective synthesis of chiral boronic acid analogues of CAZ and CTX

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1 Materials and Methods Enantioselective synthesis of chiral boronic acid analogues of CAZ and CTX 1 H and 13 C NMR spectra were recorded on a Bruker DPX-200 or Avance 400 spectrometer; chemical shifts (δ) are reported in ppm downfield from tetramethylsilane as internal standard (s singlet, d doublet, t triplet, q quartet, m multiplet, br broad signal); coupling constants (J) are given in hertz. Mass fragmentation was determined on a Finnigan MAT SSQ A mass spectrometer (EI, 70 ev). Optical rotations were recorded at 20 C on a Perkin-Elmer polarimeter and specific rotations are in 10-1 deg cm 2 g 1. Reactions requiring anhydrous conditions were performed under argon using oven-dried glassware. THF was dried according to classical procedures and distilled from Na/benzophenone before use. Synthesis of the chiral boronic acid transition state inhibitors 2 and 4 was performed as follows (Figure 1). (+)-pinanediol (3- tert. butoxycarbonylphenyl)methaneboronate (II). n-buli (7.23 mmol of a 2.5 M solution in hexane) was added dropwise with stirring to a solution of tert-butyl-3-bromobenzoate (1.77 mg, 6.88 mmol) in THF (2 ml) at -100 C under argon atmosphere. After 30 min a solution of bromomethaneboronate of (+)-pinanaediol I (1) (1.31 g, 4.82 mmol) in THF (10 ml) was added and the stirred mixture was allowed to reach rt overnight. The reaction mixture was concentrated under vacuum to give a thick yellow oil, which was purified by chromatography (light petroleum/ethyl acetate 98 : 2) affording I (0.77 g, 43% yield) as a yellow oil, [α] D = +8.7 (c 1.42, CHCl 3 ). 1 H NMR (400 MHz, CDCl 3 ): δ H 0.87 (3H, s), 1.11 (1H, d, J = 11), 1.32 (3H, s), 1.43 (3H, s), 1.63 (9H, s), (5H, m), 2.42 (2H, s, H), 4.32 (1H, dd, J = 8.8, 2.0), 7.33 (1H, t, J = 7.7), 7.40 (1H, brd, J = 7.7), 7.80 (1H, brd, J = 7.7), 7.86 (1H, brs). 13 C NMR (200 MHz, CDCl 3 ): δ C 19.3 (br, C), 24.0, 26.5, 27.1, 28.2, 28.6, 35.4, 38.2, 39.5, 51.3, 78.0, 80.7, 86.0, 126.2, 128.1, 129.9, 132.0, 133.2, 139.0, EI-MS: m/z 370 (M, 18%), 314 (71%), 297 (59%), 135 (55%), 57 (100%). (+)-pinanediol (1S)-1-chloro-2-(3- tert. butoxycarbonylphenyl)ethaneboronate (III). n-buli (2.44 mmol of a 1.6 M solution in hexane) was added dropwise to a solution of CH 2 Cl 2 (0.21 ml, 3.25 mmol) in THF (4 ml) with stirring at -100 C under argon atmosphere. At the end of the BuLi addition, a white microcrystalline precipitate (LiCHCl 2 ) became evident. After 30 min, a solution of II (0.752 g, 2.03 mmol) in THF (5 ml) was slowly added at the same temperature. The white precipitate disappeared and the mixture allowed to reach rt overnight. The reaction mixture was concentrated under vacuum and the brownish residue was diluted with light petroleum (50 ml). The precipitate was filtered on a MgSO 4 pad and washed with the same solvent (100 ml); the solution was then concentrated to give a pale yellow oil (0.7 g, 82%). [α] D = (c 2.44, CHCl 3 ), de 98%. 1 H NMR (200 MHz, CDCl 3 ): δ H 0.84 (3H, s), 1.03 (1H, d, J = 10.8), 1.29 (3H, s), 1.37 (3H, s), 1.61 (9H, s), (5H, m), 3.14 (1H, dd, J = 13.9, 8.4), 3.27 (1H, dd, J = 13.9, 7.5), 3.67 (1H, dd, J = 8.4, 7.5), 4.37 (1H, dd, J = 8.7, 2.0), (2H, m), (2H, m). 13 C NMR (200 MHz, CDCl 3 ): δ C 25.3, 27.0, 28.4, 29.6, 29.7, 36.5, 39.6, 40.7, 41.5 (br, C-B), 44.1, 52.5, 80.0, 82.3, 88.3, 129.3, 129.6, 131.6, 133.5, 134.8, 139.9, (+)-pinanediol (1R)-1-{2-(1- tert. butoxycarbonyl-1-methyl-ethoxyimino)-2-[2-(tritylamino)- thiazol-5-yl]acetylamino}-2-(3-tert.butoxycarbonylphenyl)ethaneboronate (V). Lithium hexamethyldisilazane (2.01 mmol of a 1 M solution in THF) was added dropwise to a stirred solution of III (0.70 g, 1.68 mmol) in THF (8 ml) at -78 C under argon atmosphere and the mixture was allowed to warm gradually at rt overnight. The resulting solution containing the silylamine IV was used as such for the following step. In the meantime, oxalyl chloride (0.19 ml, 2.18 mmol) was added to a precooled solution of anydrous DMF (0.29 ml, 3.76 mmol) in CH 2 Cl 2 (5 ml) with stirring at -20 C. When the evolution of CO and CO 2 ceased, the temperature was raised to 0 C, and 2-trytilamino-[1-ter-butoxycarbonyl)-1- methylethoxyimino]-4-thiazoleacetic acid (2.4 g, 4.2 mmol) was added and stirred for 30 min. 1

2 Thereafter, the mixture was cooled to -55 C and the freshly-prepared solution of silylamine IV was added dropwise via syringe and the temperature allowed to gradually reach rt. After 24 h, the orange suspension was partitioned between ethyl acetate (100 ml) and water (30 ml); the organic phase was washed with saturated NaHCO 3 solution (30 ml), dried (MgSO 4 ), and concentrated to give a viscous orange oil that was purified by gradient chromatography (light petroleum/ethyl acetate from 8:2 to 7:3) yielding V (0.37 gr, 23% yield) as a yellowish solid. [α] D = 7.7 (c 0.33%; CHCl 3 ), de 98%. 1 H NMR (400 MHz, CDCl 3 ): δ 0.85 (3H, s), 1.13 (1H, d, J = 10.6), 1.28 (3H, s), 1.36 (3H, s), 1.40 (9H, s), 1.49 (3H, s),1.52 (3H, s), 1.61 (9H, s), (5H, m), 3.02 (1H, dd, J = 14.1, 6.1), 3.17 (1H, dd, J = 14.1, 6.1), 3.67 (1H, dd, J = 13.4, 5.6), 4.34 (1H, dd, J = 7.1, 1.75), 6.80 (1H, s),6.92 (1H, br) (16H, m), 7.50 (1H, d, J = 7.2), 7.83 (1H, d, J = 7.7), 7.92 (1H, s). 13 C NMR (400 MHz, CDCl 3 ): δ 23.8, 23.9, 24.0, 26.2, 27.1, 28.0, 28.2, 28.6, 35.4, 36.8, 38.1, 38.7 (C- B), 39.6, 51.4, 71.8, 78.6, 80.8, 81.5, 82.6, 86.0, 113.2, 127.3, 127.5, 127.9, 128.2, 129.3, 130.1, 132.1, 133.5, 139.7, 143.4, 148.7, 163.5, 165.7, 167.9, EI-MS: m/z 953 (M +, 0.25%), 709 (0.13%), 581 (0.24%), 495 (1.16%), 360 (2%), 243 (100%), 165 (67%), 57 (38%). Elemental analysis: C 55 H 65 BN 4 O 8 S required : C 69.32%, H 6.87%, N 5.88%, S 3.36%. Found: C 69.20%, H 6.81%, N 5.89%, S 3.48%. (1R)-1-{2-(1-Carboxy-1-methyl-ethoxyimino)-2-[2-amino-thiazol-5-yl]acetylamino}-2-(3- carboxyphenyl) ethaneboronic acid (2). Compound V (150 mg, 0.16 mmol) was dissolved in CH 3 CN (4 ml). To this solution, HCl (0.16 mmol of a 1M solution,), phenylboronic acid (18 mg, 0.16 mg) and n- exane (4 ml) were sequentially added and the resulting biphasic solution was vigorously stirred. After 30 min the n-hexane solution (containing the pinanediol phenylboronate) was removed and n-exane (4 ml) was added. The latter procedure was repeated several times until a TLC analysis revealed no more presence of V. The acetonitrile phase was then concentrated yielding a crude residue (136 mg) that was dissolved in trifluoroacetic acid (3 ml). Catalytic anisol (2 drops) was then added and the resulting solution was stirred for 2 hours. Thereafter the trifluoroacetic acid was removed under reduced pressure and the residue crystallized from dichloromethane/hexane to give 2 (68 mg, 58% yield) as a white solid. Mp C, [α] D = 12.9 (c = 0.22; MeOH). 1 H NMR (400 MHz, CD 3 OD): δ 1.57 (3H, s), 1.59 (3H, s), 2.92 (1H, dd, J = 13.7, 9.1), 3.06 (1H, dd, J = 14.0, 6.5), 3.64 (1H, dd, J = 8.8, 6.6), 6.84 (1H, s), 7.40 (1H, t, J = 7.7), 7.53 (1H, d, J = 7.7), 7.88 (1H, d, J = 7.7), 7.92 (1H, s). 13 C NMR (400 MHz, CD 3 OD): δ 21.36, 21.38, 34.7, 39.6 (C-B), 81.9, 109.1, 125.8, 126.9, 128.6, 129.1, 132.0, 138.5, 142.3, 168.5, 166.9, 169.2, (+)-Pinanediol (1R)-1-{2-(2-methoxyimino)-2-[2-(tritylamino)-thiazol-5-yl] acetylamino}-2-(3- tert.butoxycarbonylphenyl) ethaneboronate (VI). Lithium hexamethyldisilazane (1.2 mmol of a 1 M solution in THF) was added dropwise to a stirred solution of II (0.42 g, 1.0 mmol) in THF (5 ml) at 78 C under argon atmosphere. The resulting solution was allowed to warm gradually to rt and stirred overnight. The resulting solution containing the silylamine IV was used as such for the following step. Oxalyl chloride (0.11 ml, 1.3 mmol) was added via syringe to a precooled solution of anydrous DMF (0.17 ml, 2.24 mmol) in CH 2 Cl 2 (4 ml) with stirring at 20 C. When the evolution of CO and CO 2 ceased, the temperature was raised to 0 C, and a solution of (2-trytilamino-α-methoxyimino)-4- thiazoleacetic acid (1.43 g, 2.5 mmol) in DMF (1.7 ml) and CH 2 Cl 2 (5 ml) was added dropwise. After 35 min at 0 C, the acylating mixture was cooled to 55 C and the freshly-prepared solution of silylamine IV was added dropwise; the temperature was then allowed to gradually reach rt and the resulting mixture stirred for 18 hours. The white suspension was then partitioned between ethyl acetate (90 ml) and water (30 ml) and the organic phase was washed with saturated NaHCO 3 solution (30 ml). The organic phase was dried (MgSO 4 ), filtered, and concentrated to give a viscous brownish oil (0.79 2

3 gr) that was purified by column chromatography (silica gel, light petroleum/ethyl acetate 7 : 3 as eluant) yielding VI (74 mg, 9 % yield) as a yellowish solid. 1 H NMR (400 MHz, CDCl 3 ): δ 0.86 (3H, s), 1.25 (1H, d, J = 6.11), 1.30 (3H, s), 1.38 (3H, s), 1.62 (9H, s), (5H, m), 3.03 (1H, dd, J = 14.2, 9.5), 3.14 (1H, dd, J = 14.2, 5.1), 3.46 (1H, m), 4.01 (3H, s), 4.38 (1H, dd, J = 8.9, 1.9), 6.20 (1H, d, J = 5.3. ), 6.81 (1H, s), (16H, m ), 7.44 (1H, d, J = 7.6), (2H, m). 13 C NMR (400 MHz, CDCl 3 ): δ 24.0, 26.2, 27.1, 28.2, 28.6, 35.4, 36.4, 38.2, 39.2 (C-B), 39.5, 51.3, 63.0, 71.7, 78.2, 80.8, 81.0, 86.4, 113.6, 127.6, 128.2, 128.7, 129.3, 130.0, 132.2, 133.5, 139.7, 141.6, 143.2, 147.7, 162.8, 165.7, EI-MS: m/z 824 (M +, 0.43%), 580 (0.25%), 454 (2.3%), 360 (5%), 243 (100%), 165 (63%), 57 (32%). Elemental analysis: C 48 H 53 BN 4 O 6 S required : C 69.89%, H 6.48%, N 6.79%, S 3.89%. Found: C 69.65%, H 6.40%, N 6.88%, S 4.01%. (1R)-1-{2-(2-methoxyimino)-2-[2-amino-thiazol-5-yl]acetylamino}-2-(3- carboxyphenyl)ethaneboronic acid (4). Compound VI (68 mg, 0.08 mmol) was dissolved in CH 3 CN (4 ml). HCl (0.08 mmol of a 1M solution in H 2 O), phenylboronic acid (10 mg, 0.08) and n-exane (4 ml) were sequentially added and the resulting biphasic solution was vigorously stirred. After 30 min the n- hexane solution (containing the pinanediol phenylboronate) was removed and n-exane (4 ml) was added. This last procedure was repeated several times until a TLC analysis revealed no more presence of VI. The acetonitrile phase was concentrated yielding a crude residue (42 mg) that was dissolved in trifluoroacetic acid (1 ml); catalytic anisol (1 drop) was added and the yellowish solution was stirred for 2 h. Thereafter the trifluoroacetic acid was removed under reduce pressure and the crude residue crystallized from diethyl ether/pentane to give 4 (14 mg, 40% yield) as a white solid. 1 H NMR (400 MHz, CD 3 OD): δ 2.94 (1H, dd, J = 13.6, 9.2), 3.05 (1H, dd, J = 14.3, 6.3), 3.59 (1H, dd, J =8.8, 6.5), 4.05 (3H, s), 6.86 (1H, s), (1H, t, J = 7.4), 7.53 (1H, brd, J = 7.6), 7.89 (1H, brs), 7.92 (1H, brs). 13 C NMR (400 MHz, CD 3 OD): δ 36.05, 63.0, 109.8, 127.3, 127.5, 128.1, 130.2, 133.6, 140.0, 144.0, 160.1, 168.4, C-B not seen 2 4 Figure 1. Synthesis of chiral boronic acid analogues 3

4 Molecular dynamics simulations of CMY-42 apoenzyme, CAZ acyl-enzyme and CAZ-like BATSI covalent complex. CMY-42 three-dimensional structure was built using the crystal structure of CMY-2 as template (PDB ID: 1ZC2; resolution 1.9 Ǻ) with the aid of the MODELLER package. The generated models that exhibited the best score according to MODELLER s probability density function were further evaluated using the PROCHECK software and the DOPE (Discrete Optimized Protein Energy) statistical potential of MODELLER. Three dimensional structures of the two enzymes in complex with CAZ and the achiral boronic analogue of CAZ (compound 1) were built by superposition of their C α atoms to those of the crystal structures of AmpC E. coli complexed with the above compounds (PDB ID s: 1IEL and 1IEM, respectively) (3). Protein atom parameters were those of the Amber99 all atom force field as ported in the GROMACS package. To simulate complexes of CAZ and 1 covalently linked to the catalytic serine of the two β-lactamases, a compound that consisted of CAZ (without its R2 side chain) attached to a serine molecule through a C8 Oγ bond and a compound that consisted of 1 connected to a serine through its boron atom were built (Fig. 1C). Atomic parameters for the above compounds were extracted from GAFF (General Amber Force Field for organic molecules) based on electronic similarity and the appropriate conversions were applied to conform to the units and the energy function used by GROMACS. Parameters used for the sp 3 hybridized boron atom were those of alkyl-boronic acids developed for the Amber* force field of MacroModel (4). Partial atomic charges were obtained by a RESP fitting procedure after calculating ESP points at the HF/6-31G * level of MO theory using AmberTools and GAUSSIAN. Initial models were minimized in vacuo using 5000 steps of steepest descends (SD). Protonation states of titratable amino acids were assigned at ph 7 based on the pka values predicted by PROPKA calculations. The pka value for Lys67 was low (<pka> = 7.5) but as the protonation state of this residue is still under investigation two simulations using Lys67 in its protonated and neutral forms were performed. Initial models were then solvated in TIP3P water model in a cubic box using a margin of 10 Ǻ. Neutralization was carried out using Na + and Cl - ions at a concentration of 0.15 M. Each system was minimized using SD energy minimization and simulated for 100 ps by a gradual increase of the temperature to 300 K at a constant pressure of 1 atm by restraining the protein atoms position. The cycle of energy minimization and position restrained MD was performed for four additionally times with the strength of restrains reduced in each successive step. Then 5 ns of MD simulations were performed in a NPT ensemble at 300 K. The length of all bonds was constrained and a time step of 2 fs was used to integrate Newton s equations of motion. Long-range electrostatic interactions were treated by the Particle Mesh Ewald method. Energy and coordinates were stored every 0.1 and 1 ps, respectively. Variations of the potential energy and individual terms of the energy function (e.g. proteinprotein and solvent-protein Lennard-Jones potential) during simulations were examined in order to determine the time of energy convergence. Structural convergence was estimated by the root mean square deviation of backbone atoms using as reference the starting structure of each simulation. Additionally, plots of protein s surface accessible area (hydrophilic and hydrophobic) and of radius of gyration as a function of time were examined to further assess structural stability. Also, thermal factors of protein s heavy atoms were estimated through calculation of RMS atomic fluctuations. Interpretation of atomic fluctuations was performed by covariance analysis of non-solvent heavy atoms movement (2). Accessible conformations of the active site during the simulations were determined by cluster analysis using a cut-off of 1 Ǻ for the RMSD of active site s atoms and the GROMOS clustering algorithm. Important distances as well as the active site hydrogen bonding network were analyzed during the trajectories. 4

5 Results Molecular dynamics simulations-principle Component Analysis Figure 2: Residue-to-residue cross correlation maps of backbone atoms movement covariance of CMY-2, CMY-30 and CMY-42 apoenzymes. Pairs of residues that exhibited positive correlation coefficients (C) (movement in the same direction) are shown as red areas on the maps while blue areas denote motion in opposite directions. At the upper triangle, areas exhibiting absolute C values greater than 0.5 are shown. Data indicate that the displacements of Q-120 loop (A: residues ), Ω- loop/h7 helix (B: residues ) and H10/R2-loop are correlated. This movement appeared to be intensified in the ES variants and especially the portion concerning Ω and Q-120 loops. Large arrows denote the correlation between the motion of the R2-loop and the loop containing the catalytic residue Tyr150 pointing to a likely participation of these displacements in the function of the enzyme. 5

6 Molecular dynamics simulations - Cluster analysis of active site's conformers. Table I. Comparison of ceftazidime acyl-enzyme most abundant conformers with the deacylation transition state Cluster %N RMSD from 1 complex (Ǻ) a d CAZ N1-1 O2 (Ǻ) / / CMY / / / / / CMY / / / / b / CMY-42 3 b / b / / a The average minimized structure of each complex with compound 1 was used for the RMS fit that was carried out using active site s heavy atoms (first value) and active site s backbone atoms (second value). b In these conformers (35% of the total number of conformers of CMY-42/CAZ acyl-enzyme) the oxygen of the acyl group was positioned out of the oxyanion hole. REFERENCES 1. Davoli P., R. Fava, A. Spaggiari, S. Morandi, and F. Prati Enantioselective total synthesis of ( )- microcarpalide. Tetrahedron 61: Ichiye T., and M. Karplus Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 11: Powers, R. A., E. Caselli, P. J. Focia, F. Prati, and B. K. Shoichet Structures of ceftazidime and its transition-state analogue in complex with AmpC β-lactamase: implications for resistance mutations and inhibitor design. Biochemistry 40: Tafi A., M. Agamennone, P. Tortorella, S. Alcaro, C. Gallina, and M. Botta AMBER force field implementation of the boronate function to simulate the inhibition of beta-lactamases by alkyl and aryl boronic acids. Eur J Med Chem 40: