Structure-based drug design, which relies on precise
understanding
of the target protein and its interaction with the drug candidate,
is dramatically expedited by advances in computational methods for
candidate prediction. Yet, the accuracy needs to be improved with
more structural data from high throughput experiments, which are challenging
to generate, especially for dynamic and weak associations. Herein,
we applied native mass spectrometry (native MS) to rapidly characterize
ligand binding of an allosteric heterodimeric complex of SARS-CoV-2
nonstructural proteins (nsp) nsp10 and nsp16 (nsp10/16), a complex
essential for virus survival in the host and thus a desirable drug
target. Native MS showed that the dimer is in equilibrium with monomeric
states in solution. Consistent with the literature, well characterized
small cosubstrate, RNA substrate, and product bind with high specificity
and affinity to the dimer but not the free monomers. Unsuccessfully
designed ligands bind indiscriminately to all forms. Using neutral
gas collision, the nsp16 monomer with bound cosubstrate can be released
from the holo dimer complex, confirming the binding to nsp16 as revealed
by the crystal structure. However, we observed an unusual migration
of the endogenous zinc ions bound to nsp10 to nsp16 after collisional
dissociation. The metal migration can be suppressed by using surface
collision with reduced precursor charge states, which presumably resulted
in minimal gas-phase structural rearrangement and highlighted the
importance of complementary techniques. With minimal sample input
(∼μg), native MS can rapidly detect ligand binding affinities
and locations in dynamic multisubunit protein complexes, demonstrating
the potential of an “all-in-one” native MS assay for
rapid structural profiling of protein-to-AI-based compound systems
to expedite drug discovery.