| # Reference protocol and permeability yardsticks |
|
|
| The MD pipeline in this folder is a deliberate copy of one published protocol, |
| with the numbers it should be read against collected here. |
|
|
| ## Sources |
|
|
| - **"Linker-Dependent Folding Rationalizes PROTAC Cell Permeability," |
| *J. Med. Chem.* 2022 (PMC9574858).** The MD paper, and the template for |
| `protac_md.py` and `analyze_conformations.py`. Three CRBN/BRD4 PROTACs with |
| different linkers, PEG-like against alkyl. |
| - **Atilaw et al., "Solution Conformations Shed Light on PROTAC Cell |
| Permeability," *ACS Med. Chem. Lett.* 2021, 12, 107-114.** NMR plus Monte |
| Carlo conformational search and NAMFIS, not MD, on one VHL PROTAC (ERK5). It |
| is the source of the folded-versus-extended framing and of the Rg cutoff |
| below, nothing else. |
|
|
| ## Protocol |
|
|
| | Setting | Reference choice | Here | |
| |---|---|---| |
| | Engine / ligand force field | Amber 18, GAFF, geometry pre-optimized in Gaussian | OpenMM 8, OpenFF Sage 2.2 with AM1-BCC charges | |
| | Solvent | explicit chloroform, ~3000 molecules, truncated octahedron | explicit chloroform via packmol, plus water as a polar reference | |
| | Production | 100 ns after equilibration | 50-100 ns, `--prod-ns` | |
| | Replicas | 3 | 3, independent velocity seeds | |
| | Ensemble | 300 K, PBC, ~10,000 snapshots per trajectory | 300 K / 1 bar NPT, 10 ps per frame | |
| | Convergence | RMSD, converged within 5-10 ns | RMSD to the first frame plus replica-mean spread | |
| | Analyses | Rg (cpptraj), 3D PSA (PyMOL), intramolecular H-bonds, PMI shape, PCA and K-means into 5 clusters | Rg, 3D PSA (mdtraj SASA over N, O and polar H), H-bonds, PCA and K-means | |
|
|
| Chloroform stands in for the membrane interior: its dielectric constant of 4.8 |
| is close to what a molecule sees while crossing a bilayer. |
|
|
| ## Yardsticks |
|
|
| - **Rg below 7 A** marks the folded, passively permeable regime. This cutoff is |
| from the 2021 NMR paper, on a single VHL PROTAC, and it does not separate the |
| compounds in the 2022 MD paper. |
| - **Mean Rg alone does not discriminate.** In the 2022 MD paper: |
|
|
| | compound | P_passive (nm/s) | dominant Rg | compact local minimum | |
| |---|---|---|---| |
| | PROTAC 1, most permeable | 30 ± 1.5 | just over 8 A | 5.6 A | |
| | PROTAC 2 | 11 ± 1.7 | just over 7 A | 5.5 A | |
| | PROTAC 3, least permeable | 6 ± 1.4 | 7-9.5 A, extended | none | |
| |
| Their most permeable compound sits mainly just above 8 A, overlapping their |
| worst. What separates the two is whether a compact minimum near 5.5 A is |
| accessible at all: PROTACs 1 and 2 have one, PROTAC 3 does not. Report the Rg |
| distribution and the compact-state population, which is what `rg_basins.py` |
| computes, rather than the mean. Absolute Rg is also not strictly transferable |
| across chemical series; theirs is CRBN/BRD4, the runs here are VHL/EGFR. |
| - **3D PSA** rises as permeability falls: 190-265 A^2 for the two more permeable |
| compounds against 290-330 A^2 for the poorly permeable one. The rough cutoff |
| for low-to-moderate permeability is 200-210 A^2, from the 2021 paper. Absolute |
| values depend on the polar-atom selection; `validate_psa.py` and |
| `psa_method_probe.py` pin down where this convention sits relative to theirs. |
| - Permeability correlates inversely with 3D PSA and with intramolecular H-bond |
| count. |
|
|
