The Nipah virus (NiV) attachment glycoprotein G mediates host-cell entry by binding to ephrin-B2 and ephrin-B3 receptors. To design compact antiviral binders, we used the BindCraft generative-design pipeline to create mini-protein (65–120 aa) candidates against functionally validated regions of the G ectodomain (Chain A): (1) residues 201–300, critical for single-domain antibody n425. Bthis region was prepared in Maestro (Schrödinger) and energy-minimized with the OPLS4 force field before design. BindCraft backbone generation, ProteinMPNN sequence optimization, AlphaFold2-multimer prediction, and Rosetta refinement produced compact binders predicted to form stable interfaces. We applied BindCraft, combined with ProteinMPNN, AlphaFold2, and Rosetta, to design de novo binders against experimentally supported G regions (450–603), using PDB 2VSM as structural references. Structural Rationale and Target Selection Region 1: Residues 200–300 (Chain A positions 217, 231, 257–259, 264–270) • This region sits on the β-propeller head of G and forms part of tn45 binding site (8XPY). • These positions exhibit structural roles in shaping the local docking surface and appear to influence loop flexibility—characteristics favorable for small peptide or loop-oriented mini-protein engagement. Target Preparation Before binder design, each target region was refined in Maestro (Schrödinger 2024-4): 1. Imported Chain A coordinates from 2VSM 2. Assigned protonation states at pH 7.0 and optimized H-bonding networks via Protein Preparation Wizard. 3. Performed energy minimization with the OPLS4 force field until convergence (RMSD < 0.3 Å). 4. Verified absence of steric clashes and ensured solvent accessibility of all hotspot residues.
id: solid-dove-fern

Nipah Virus Glycoprotein G
0.74
67.79
--
10.9 kDa
90
id: noble-lion-moss

Nipah Virus Glycoprotein G
0.42
69.40
--
11.5 kDa
96
id: lunar-goat-clay

Nipah Virus Glycoprotein G
0.58
80.67
--
10.3 kDa
88
id: violet-ant-wave

Nipah Virus Glycoprotein G
0.77
80.61
--
10.7 kDa
90
id: frozen-cat-thorn

Nipah Virus Glycoprotein G
0.46
71.29
--
11.5 kDa
96
id: quiet-crane-quartz

Nipah Virus Glycoprotein G
0.73
79.34
--
9.6 kDa
78
id: small-jaguar-plume

Nipah Virus Glycoprotein G
0.66
84.01
--
10.4 kDa
88
id: shy-jaguar-moss

Nipah Virus Glycoprotein G
0.14
80.79
--
9.7 kDa
78
id: scarlet-vole-cedar

Nipah Virus Glycoprotein G
0.47
74.02
--
9.1 kDa
75
id: green-cat-onyx

Nipah Virus Glycoprotein G
0.63
71.24
--
10.1 kDa
86