Why Bestatin Prefers Human Carnosinase 2 (CN2) to Human Carnosinase 1 (CN1)

• Published in: The journal of physical chemistry. B 2024-12, Vol.128 (48), p.11876-11884
• Main Authors: Toviwek, Borvornwat, Koonawootrittriron, Skorn, Suwanasopee, Thanathip, Jattawa, Danai, Pongprayoon, Prapasiri
• Format: Article
• Language: English
• Subjects: B: Biophysical and Biochemical Systems and Processes; Carnosine - chemistry; Carnosine - metabolism; Dipeptidases - antagonists & inhibitors; Dipeptidases - chemistry; Dipeptidases - metabolism; Humans; Leucine - analogs & derivatives; Leucine - chemistry; Leucine - metabolism; Molecular Dynamics Simulation; Substrate Specificity
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.4c05571

Human carnosinases (CNs) are Xaa-His metal-ion-activated aminopeptidases that break down bioactive carnosine and other histidine-containing dipeptides. Carnosine is a bioactive peptide found in meat and prevalently used as a supplement and in functional food formulation. Nonetheless, carnosine is digested by CNs rapidly after ingestion. CNs have two isoforms (carnosinase 1 (CN1) and carnosinase 2 (CN2)), where CN1 is the main player in carnosine digestion. CNs contain a catalytic metal ion pair (Zn2+ for CN1 and Mn2+ for CN2) and two subpockets (S1 and S1′ pockets) to accommodate a substrate. Bestatin (BES) has been reported to be active for CN2; however, its inhibition ability for CN1 has remained under debate, because the underlying mechanism remains unclear. This information is important for designing novel CN1-selective inhibitors for proliferating carnosine after ingestion. Thus, molecular dynamics (MD) simulations were performed to explore the binding mechanism of BES to both CN1 and CN2. The binding of BES-CN1 and BES-CN2 was studied in comparison. The results indicated that BES could bind both CNs with different degrees of binding affinity. BES prefers CN2 because: (1) its aryl terminus is trapped by Y197 in an S1 pocket; (ii) the BES polar backbone is firmly bound by catalytic Mn2+ ions; and (iii) the S1′ pocket can shrink to accommodate the isopropyl end of BES. In contrast, the high mobility of the aryl end and the complete loss of metal–BES interactions in CN1 cause a loose BES binding. Seemingly, polar termini were required for a good CN1 inhibitor.