Disulfide-rich architectures are valuable pharmacological tools or therapeutics. Besides, a ligand-induced conjugate strategy offers potential advantages in potency, selectivity, and duration of action for novel covalent drugs. Combining the plentiful disulfide-rich architecture library and ligand-induced conjugate via thiol-disulfide interchange would supply great benefits for developing site specific covalent inhibitors. Cysteine-cysteine (Cys-Cys) disulfide bonds are intrinsically unstable in endogenous reductive environment, while cysteine-penicillamine (Cys-Pen) disulfide bonds show satisfactory stability. We envisioned the Cys-Pen disulfide as a potential ligand-induced covalent bonding warhead, and this disulfide could reconstruct with the protein cysteine in the vicinity of the peptide binding site to form a new disulfide. To evaluate our design, protein PLCγ1-c src homology 2 domain and RGS3-PDZ domain were tested as models. Both proteins were successfully modified by Cys-Pen disulfide and formed new disulfides between proteins and peptides. The new disulfide was then analyzed to confirm it was a newly formed disulfide bond between Pen of the ligand and a protein Cys near the ligand binding site. HDAC4 was then chosen as a model by utilizing its "CXXC" domain near its catalytic pocket. The designed Cys-Pen cyclic peptide inhibitor of HDAC4 showed satisfactory selectivity and inhibitory effect.