Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S

Abstract

We synthesized and evaluated new zwitterionic inhibitors against glycoside hydrolase-like phosphorylase Streptomyces coeticotor (Sco) GlgEI-V279S which plays a role in α-glucan biosynthesis. Sco GlgEI-V279S serves as a model enzyme for validated anti-tuberculosis (TB) target Mycobacterium tuberculosis (Mtb) GlgE. Pyrrolidine inhibitors 5 and 6 were designed based on transition state considerations and incorporate a phosphonate on the pyrrolidine moiety to expand the interaction network between the inhibitor and the enzyme active site. Compounds 5 and 6 inhibited Sco GlgEI-V279S with Ki = 45 ± 4 μM and 95 ± 16 μM, respectively, and crystal structures of Sco GlgE-V279S-5 and Sco GlgE-V279S-6 were obtained at a 3.2 Å and 2.5 Å resolution, respectively.

Stereoselective Synthesis of a 4-⍺-Glucoside of Valienamine, Inhibition, and X-Ray Structural Studies Involving a Bacterial Glycoside Hydrolase-Like Enzyme of The GH13 Family

“…In both enzyme-compound structures, the interactions of the glucose moiety bound within the -2 subsite are the same as that observed in previously published Sco GlgE1-V279S/inhibitor complex structures. [50][51][52][53] However, interactions between the carbocycle moieties and the amino acid residues forming the -1 subsite differ signi cantly from each other. In the Sco GlgE1-V279S/7 complex, the interactions are similar to those observed in the substrate-bound (M1P and maltose) and substrate-mimic (MCP) complexes because the saturated carbocycle in 7 maintains the expected chair conformation.…”

“…Indeed, all previously published structures of GlgE with any hexose analog have a hydroxyl at this position that interacts directly with the enzyme nucleophile. 50,52 Although speculative, such a bidentate interaction could be envisioned to stabilize a 3 H 4 or B 2,5 -TSs in the enzyme catalyzed reaction. We note some studies have suggested that reactions catalyzed by this enzyme class proceed through a 4 C 1 → 4 H 3 -TS → 1 S 3 conformational itinerary leading to a 4 C 1 enzyme-bound intermediate.…”

“…Out of those zwitterionic pyrrolidine-phosphonates, the methyl phosphonate pyrrolidine (MPP) is the most potent inhibitor against Sco GlgE1-V279S exhibiting an equilibrium dissociation constant (K i ) of 45 ± 4 μM. 52 The comparison of the active sites ( Figure 10) of Sco GlgE1-V279S/8 and Sco GlgE1-V279S/MPP (PDB:5VT4) clearly indicates interactions between GlgE residues forming the -2 subsite and the glucose moiety bound within that site are conserved in all the previously published GlgE structures. When comparing the -1 subsite of both structures, the pyrrolidine ring of Sco GlgE1-V279S/MPP complex and the attened carbocycle moiety of Sco GlgE1-V279S/8 complex mimic some aspects of the enzyme substrate conformations adopted during the formation of the rst TS.…”

“…The reactions were initiated by addition of 50 nM Sco GlgE1-V279S to the reaction mixture consisting of 20 mM Tris pH 7.5, 150 mM NaCl, 500 nM MESG, 0.25 U PNP, 0.5 mM glycogen (as maltose acceptor) and 250 µM M1P. 27,52 In the various reactions, the compound 8 concentration was varied from 0 to 1000 µM, except in the positive control that lacked inhibitor, and the negative control that lacked enzyme. All of the reactions were performed in triplicate using a Synergy H4 plate reader (Bio Tek) to measure the absorbance at 360 nm.…”

Promising Recent Strategies with Potential Clinical Translational Value to Combat Antibacterial Resistant Surge

“…In recent years there have been sustained efforts to make a breakthrough in anti-tuberculosis drug development utilizing this key strategic information. Sucheck and co-workers developed a series of considerably effective trehalose and other glyco-conjugate-based Mtb GlgE inhibitors [217,218,219,220]. Another important chemical moiety from the classical medicinal chemistry viewpoint are the pyrazolo[1,5-a]pyrimidine and its derivatives.…”