Fig. 1: Computational design of DBSA targeting a binding pocket at the PYL dimer interface.

a An extended binding pocket was discovered in the gate-open apo-PYL1 dimer interface (PDB code: 3KAY). This binding pocket partly overlaps with the ABA-binding pocket in the gate-closed PYR1 dimer (PDB code: 3K3K). b The binding pockets differ due to conformational changes in the gate loop and latch loop. The gate loop and latch loop transitions to closed state from open state after ABA binding. c Ser112 at gate loop as well as Pro115 and His142 at latch loop of PYL1 along with their homologous residues in PYR1 (Ser85, Pro88, and His115, respectively) exhibit conformational changes during conformation transition. d Fragment screening was performed to discover chemical probes targeting PYL1 dimer interface. Structural optimization and molecular docking were performed on pyrabactin to suit gate open and latch open PYL1 (PDB code: 3KAY) and PYL2 (PDB code: 3NR4), and find a conformation towards dimer interface. NBSA exhibited the lowest binding free energy. Based on structural optimization, DBSA showed the largest improvement of binding free energy in structural optimization. e NBSA binds to the pocket at the dimer interface and forms several hydrogen bonds with the PYL1 dimer. f DBSA forms an intramolecular hydrogen bond that stabilizes its conformation and forms a series of hydrogen bonds with residues at the PYL1 dimer interface. The hydrogen bonds are shown by red dotted lines.