Computational prediction and validation of specific EmbR binding site on PknH

Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not clear.Ethambutol(EMB),one of the well-known first-line drugs in tuberculosis treatment is,unfortunately,not free from drug resistance problems.Genomic studies have shown that some genetic mutations in Mycobacterium tuberculosis(Mtb)EmbR,and EmbC/A/B genes cause EMB resistance.EmbR-PknH pair controls embC/A/B operon,which encodes EmbC/A/B genes,and EMB interacts with EmbA/B proteins.However,the EmbR binding site on PknH was unknown.We conducted molecular simulation on the EmbR-peptides binding structures and discovered phosphorylated PknH 273-280(N′-HEALS^(P)DPD-C′)makesβstrand with the EmbR FHA domain,asβ-MoRF(MoRF;molecular recognition feature)does at its binding site.Hydrogen bond number analysis also supported the peptides’β-MoRF forming activity at the EmbR FHA domain.Also,we discovered that previously known phosphorylation residues might have their chronological order according to the phosphorylation status.The discovery validated that Mtb PknH 273-280(N′-HEALSDPD-C′)has reliable EmbR binding affinity.This approach is revolutionary in the computer-aided drug discovery field,because it is the first trial to discover the protein-protein interaction site,and find binding partner in nature from this site.