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Objective: The objective of the study was to come up with of the small molecular modulators that inhibit protein–protein interfaces or interaction site in HDAC complexes. The main focus is on the mimicking or forming of tiny molecule wherever by inhibiting the protein-protein interactions in specifically HDAC protein complexes.

Methods: By mimicking of the interface of the protein interaction site like SIN3A-SMRT complex as well as SIN3A-NcoR complexes.

Results: Totally 10 molecular structures were designed through molecular docking with HDAC2 PDB Id 3MAX and were downloaded from protein data bank.

Conclusion: The results clearly indicate that before synthesis and biochemical testing of new lead and its analogs; one can use molecular modeling based methods for qualitative assessment.