We started from a known potent Nipah-neutralizing antibody, 8XC4, a ~450-residue IgG fragment with two chains and four domains. In the 8XC4 structure, a buried CDRH3 loop penetrates a central cavity on the Nipah G (NiV-G) domain, and we treat this loop as a modular binding element. To exploit this binding mode, we tested three scaffolding strategies: (1) grafting the loop onto the canonical binding loop of the human Kunitz (APPI) domain, (2) grafting it onto the variable loop of the Adhiron (Affimer) scaffold, and (3) truncating 8XC4 to its VH and VL domains and connecting them with a flexible Gly-Ser linker to create an scFv. We then used AlphaFold2-multimer (ipTM/iPAE) and SolMPNN for some basic quality checks but decided to make no further changes.
id: wild-yak-marble

Nipah Virus Glycoprotein G
0.38
81.23
--
26.6 kDa
250
id: rough-raven-cedar

Nipah Virus Glycoprotein G
0.33
71.06
--
6.6 kDa
61
id: steady-ant-dust

Nipah Virus Glycoprotein G
0.00
79.26
--
9.9 kDa
84