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Figure S1. Chemical structures of FDA-approved inhibitors.

Figure S2. Chemical structures of P1/P1’ analogues of BEA268.

Figure S3. Chemical structures of P2/P2’ and central hydroxyl analogues of BEA268.

Figure S4. Chemical structures of cyclic urea inhibitors.

Figure S5. Chemical structures of cyclic sulfamide inhibitors.

Figure S6. Other inhibitors used in this study, namely HOE/BAY 793, MVT-101, JG-365, KNI272 and QF34.

Figure S7. Illustration of modelling the structure of HIV-1 PR-AHA008 complex. (a) The chemical structures of potential inhibitors of AHA001, DMP323 and AHA008. (b) The structure of AHA008 was constructed by substituting the side chain R2 of inhibitor AHA001 by those of inhibitor DMP323. The initial structure of protease was retrieved from the PR structure of PDB code: 1AJX.

Table S1. Parameters of the bonded potentials for inhibitors in the coarse-grained MD models

Table S2. The sequences of substrates as HIV-1 PR inhibitors.

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