Rational ab initio Design of a Humanized Nanobody against KRAS using the PIA Method

The KRAS oncoprotein remains a therapeutic challenge due to the limitations of current covalent inhibitors. This work presents the rational design of PIAKRASv2- Nb, a 100 Molecular dynamics simulations, extended up to 10 ns, confirm the persistence of the binding pose and reveal a three-phase mechanism: rapid anchoring, interface maturation, and convergence to a stable equilibrium state with ~30 residue-residue contacts. These dynamic metrics are consistent with those observed in successful therapeutic nanobodies like Caplacizumab or VHH72, consolidating the profile of PIA-KRASv2-Nb (seed 72) as a pan-mutant therapeutic candidate against KRAS. This study demonstrates that the PIA method can generate therapeutically optimal nanobodies ab initio , combining high affinity, intrinsic humanization, and conformational reproducibility, with direct implications for tackling targets traditionally considered "undruggable."