Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents

Figures & data

Table 1. PBP1b inhibitory activity and antimicrobial effect (MIC) of boronic acid derivatives.

Compound	Structure	RA [%] @500 µM or IC50 [µM]^a	MIC E. coli [µM]	MIC S. aureus [µM]
1		127.1 ± 14.4 µM	>250	>250
2		206.5 ± 21.7 µM	>250	125
3		86.3 ± 8.4%	–	–
4		60.9 ± 7.6%	–	–
5		85.7 ± 9.5%	–	–
6		81.1 ± 1.6%	–	–
7		90.3 ± 3.4%^b	–	–
8		212.8 ± 15.2 µM	>250	>250
9		28.2 ± 7.4 µM	>250	>250

^aAztreonam IC₅₀ found to be below the concentration of the enzyme in the assay (0.8 µM).

^bMeasured at 1 mM concentration.

Scheme 1. The synthesis of boroproline derivatives.

Scheme 2. (A) Complex formation of penicillins with penicillin-binding protein. Bulky groups near the covalent enzyme-ligand bond are encircled. (B) Complex formation of branched boronic acids with penicillin-binding proteins.

Scheme 3. The synthesis of branched boronic acid derivatives.

Scheme 4. The synthesis of branched boronic acid derivatives.

Table 2. PBP1b inhibitory activity and antimicrobial effect (MIC) of branched boronic acids.

Compound	Structure	RA [%]	MIC E. coli [µM]	MIC S. aureus [µM]
15		105.1 ± 0.1 @1mM	–	–
16		68.6 ± 3.3 @1mM	–	–
17		48.1 ± 2.0 @500 µM	–	–
18		66.3 ± 7.0 @500 µM	–	–
19		68.9 ± 8.2 @500 µM	>250	62.5

Scheme 5. The synthesis of branched boronic acid derivatives.

Scheme 6. Serine activation and attack on the boronic acid. Electron movements are shown by curly arrows. Interatomic distances used for defining reaction coordinates are shown with straight arrows.

Table 3. Experimental activities, and computed barrier and reaction free energies for selected boronic acids towards PBP1b.

Compound	Structure	RA [%] or IC50 [µM]	Barrier^a [kcal/mol]	Reaction energy^b [kcal/mol]
9		28.2 ± 7.4 µM	+6	−7
7		90.3 ± 3.4% @1 mM	+12	−4
19		68.9 ± 8.2% @500 µM	+12	−2

^aΔG_tm in Figure S1.

^bΔG_mc in Figure S1.

Scheme 7. Reaction scheme of investigated carbonyl derivatives of boronic acid with lysine.

Table 4. PBP1b inhibitory activity and antimicrobial effect (MIC) of potential lysine labelling boronic acid derivatives.

Compound	Structure	RA [%] or IC50 [µM]	MIC E. coli [µM]	MIC S. aureus [µM]
29		119.4 ± 6.0 µM	>250	>250
30		199.7 ± 15.3 µM	>250	>250
31		96.7 ± 0.1% @500 µM 97.4 ± 1.0% @1 mM	–	–
32		96.6 ± 0.6% @500 µM 105.2 ± 6.8% @1 mM	–	–
33		56.9 ± 0.8% @500 µM 47.1 ± 0.6% @1 mM	–	–

Scheme 8. The synthesis of the diazaborine-forming warhead-containing compounds.

Scheme 9. Reaction mechanism investigated by QM/MM simulations for Lys463 labelling by compound 29.