Table 3.
List of interacting amino acids between RBDs and bromelain-derived peptide. The position of the interacting residues in pocket and mutation sites are indicated in italics, while the key amino acid residues that play a role in binding RBD to hACE2 are marked in bold.
| Variants | H-Bonds | Non-Bonded Contacts | ||
|---|---|---|---|---|
| RBD | Bromelain-Derived Peptide | RBD | Bromelain-Derived Peptide | |
| WT | Arg452 (2) | Glu7, Val5 | Arg403 | Tyr2 |
| Tyr453 (2) | Tyr2 (2) | Tyr449 (6) | Gly3 (2); Ala4 (2) Val5 (2); | |
| Glu484, Gln493 | Asn6 (2) | Arg452 (9) | Val5 (4); Glu7 (5) | |
| Ser494 (2) | Val5 (2) | Tyr453 (4) | Tyr2 (4) | |
| Gln498 | Tyr2 | Glu484 (5) | Asn6 (5) | |
| Thr500 | Asp1 | Phe490 | Asn6 | |
| Gln493 (4) | Ala4 (2); Asn6 (2) | |||
| Ser494 (8) | Gly3; Ala4 (2); Val5 (5) | |||
| Gly496 (5) | Tyr2; Gly3 (4) | |||
| Gln498 (9) | Asp1 (4); Tyr2 (5); | |||
| Thr500 (7) | Asp1 (7) | |||
| Asn501 (10) | Asp1 (10) | |||
| Gly502 | Asp1 | |||
| Tyr505 (4) | Asp1 (3); Tyr2 | |||
| BR | Gly482 | Lys2 | Tyr449 (3) | Asn6 (3) |
| Ser494 | Asn6 | Leu452 (4) | Val8 (4) | |
| Thr500 | Tyr2 | Ile472 (2); Gly482 | Lys9 (3) | |
| Tyr505 | Asp1 | Lys484 (5) | Glu7 (5) | |
| Phe490 (4) | Val8 (3); Lys9 | |||
| Leu492 (3) | Glu7 (2); Val8 | |||
| Gln493 (7) | Val5; Asn6 (5); Glu7 | |||
| Ser494 (5) | Ala4; Asn6 (4) | |||
| Gly496 (2) | Ala4 (2) | |||
| Thr500 (2) | Tyr2 (2) | |||
| Tyr501 (12) | Tyr2 (11); Ala4 | |||
| Gly502 | Tyr2 (2) | |||
| Tyr505 (8) | Asp1 (5); Tyr2 (3) | |||
| SA | Gly482 | Lys9 | Tyr449 (4) | Asn6 (4) |
| Lys484 | Glu7 | Leu452 | Val8 | |
| Ser494 | Asn6 | Tyr453 | Val5 | |
| Gly502 | Asp1 | Thr470; Ile472 (2); Gly482 | Lys9 (4) | |
| Lys484 (4) | Glu7 (4) | |||
| Phe490 (6) | Val8 (3); Lys9 (3) | |||
| Leu492 | Glu7 | |||
| Gln493 (9) | Val5 (2); Asn6 (4); Glu7 (3) | |||
| Ser494 (7) | Val5 (2); Asn6 (5) | |||
| Gly496 (2) | Ala4 (2) | |||
| Thr500 (4) | Tyr2 (4) | |||
| Tyr501 (20) | Asp1 (2); Tyr2 (9); Gly3 (6); Ala4 (3) | |||
| Gly502 (6) | Asp1 (6) | |||
| Tyr505 (8) | Asp1 (6); Tyr2 (2) | |||
| UK | Asn487; Tyr489 | Glu7 (2) | Arg403 (3); Glu406 (4); Lys417 (5); Ile418 (2); Tyr453 (9) | Tyr2 (23) |
| Gly496; Tyr501 | Asp1 (2) | Tyr453 | Gly3 | |
| Leu455 (3) | Gly3; Ala4 (2) | |||
| Phe456 (6) | Val5 (3); Asn6 (3) | |||
| Ala475 (2) | Glu7; Val8 | |||
| Gly485 | Glu7 | |||
| Phe486 (6) | Glu7 (3); Lys9 (3) | |||
| Asn487 (14) | Glu7 (10); Val8 (4) | |||
| Tyr489 (8) | Glu7 (8) | |||
| Gln493 | Gly3 | |||
| Tyr495 (3) | Asp1; Tyr2 (2) | |||
| Gly496 (4); Tyr501 (5); Tyr505 (4) | Asp1 (13) | |||
| CA (USA) | Arg452; Gln493 | Asn6 (2) | Tyr449 (8) | Gly3 (2); Ala4 (2); Val5 (4) |
| Ser494 | Val5 | Arg452 (2) | Asn6 (2) | |
| Thr500 | Asp1 | Tyr453 (3) | Tyr2 (2) | |
| Ile472; Glu484 (7) | Val8 (8) | |||
| Phe490 (9) | Asn6 (6); Val8 (3) | |||
| Leu492 (3) | Asn6 (3) | |||
| Gln493 (8) | Ala4; Val5 (3); Asn6 (4) | |||
| Ser494 | Ala4; Val5 (3) | |||
| Tyr495 (2) | Tyr2 (2) | |||
| Gly496 (9) | Tyr2 (4); Gly3 (5) | |||
| Gln498 (4) | Asp1 (2); Gly3 (2) | |||
| Thr500 (8) | Asp1 (8) | |||
| Asn501 (13) | Asp1 (12); Tyr2 | |||
| Tyr505 (4) | Asp1 (3); Tyr2 | |||
| SG (NY1) | Arg403 | Asp1 | Arg403 (4) | Asp1 (4) |
| Tyr453 | Tyr2 | Tyr449 (8) | Tyr2 (8) | |
| Glu484 | Asn6 | Tyr453 | Tyr2 | |
| Glu484 (6) | Asn6 (5); Val8 | |||
| Gly485 (7) | Asn6 (2); Glu7 (3); Val8 (2) | |||
| Phe486 (13) | Glu7 (3); Val8 (7); Lys9 (3) | |||
| Asn487; Cys488 | Asn6 (2) | |||
| Tyr489 (7) | Val5 (4); Asn6 (3) | |||
| Gln493 (12) | Tyr2 (3); Gly3 (5); Ala4 (4) | |||
| Ser494 (4) | Tyr2 (4) | |||
| Gly496 (4) | Asp1 (2); Tyr2 (2) | |||
| Asn501; Tyr505 (4) | Asp1 (5) | |||
| SN(NY2) | Lys417 (3) | Asp1 (2); Tyr2 | Arg403 (10) | Asp1 (8); Tyr2 (2) |
| Gln493 | Ala4 | Lys417 (7) | Asp1 (6); Tyr2 | |
| Gly496 | Tyr2 | Tyr453 (8) | Tyr2 (6); Gly3 (2) | |
| Tyr505 | Asp1 | Leu455 (4) | Tyr2; Gly3; Ala4 (2) | |
| Phe456 | Val5 | |||
| Glu484 (8) | Asn6 (2); Glu7 (2); Val8 (4) | |||
| Gly485 (12) | Glu7 (10); Val8 (2) | |||
| Phe486 (2) | Glu7 (2) | |||
| Tyr489 (7) | Val5 (3); Asn6 (4) | |||
| Gln493 (4) | Ala4 (4) | |||
| Ser494 | Tyr2 | |||
| Tyr495 (5) | Tyr2 (5) | |||
| Gly496 (3) | Tyr2 (3) | |||
| Tyr505 (2) | Asp1 (2) | |||
| SC | Arg403 | Asp1 | Arg403 (5) | Asp1 (5) |
| Tyr449 | Tyr2 | Tyr449 (9), Tyr453 | Tyr2 (10) | |
| Glu484 | Asn6 | Glu484 (5) | Asn6 (5) | |
| Asn487 | Glu7 | Gly485 (8) | Asn6; Glu7 (4); Val8 (3) | |
| Gln493 | Ala4 | Phe486 (12) | Glu7 (4); Val8 (5); Lys9 (3) | |
| Asn487 (2) | Glu7 (2) | |||
| Cys488 | Asn6 | |||
| Tyr489 (5) | Val5 (3); Asn6 | |||
| Asn493 (14) | Tyr2 (6); Gly3 (5); Ala4 (3) | |||
| Ser494 | Tyr2 | |||
| Gly496 (9) | Asp1 (5); Tyr2 (4) | |||
| Asn501; Tyr505 (3) | Asp1 (4) | |||
| IN | Gln409; Lys417 | Asp1 (2) | Arg403 (10) | Asp1 (2); Tyr2 (4) |
| Asn487 | Glu7 | Glu406 (4) | Asp1 (2); Tyr2 (2) | |
| Gly496 | Tyr2 | Gln409 | Asp1 (2) | |
| Gly416 (2) | Asp1 (2) | |||
| Lys417 (10) | Asp1 (8); Tyr2 (2) | |||
| Tyr453 (15) | Tyr2 (13); Gly3 (2) | |||
| Leu455 (4) | Tyr2; Gly3; Ala4 (2) | |||
| Gly485 (6) | Glu7 (2); Val8 (4) | |||
| Phe486 (6) | Glu7 (3); Val8 (3) | |||
| Asn487 (3) | Glu7 (3) | |||
| Tyr489 (7) | Asn6 (3); Glu7 (4) | |||
| Gly496 (2) | Tyr2 (2) | |||
| NG | Gly482 | Lys9 | Tyr449 (4) | Ala4 (2); Asn6 (2) |
| Lys484; Gln493 | Glu7 (2) | Leu452 (3) | Val8 (3) | |
| Ser494 (2) | Asn6 (2) | Gly482 (3) | Lys9 (3) | |
| Gly496 | Ala4 | Lys484 (5) | Glu7 (5) | |
| Gly502 | Asp1 | Phe490 (11) | Glu7; Val8 (3); Lys9 (7) | |
| Leu492 (2) | Glu7 (2) | |||
| Gln493 (8) | Val5; Asn6 (3); Glu7 (3) | |||
| Ser494 (7) | Ala4; Val5; Asn6 (5) | |||
| Gly496 (7) | Gly3; Ala4 (6) | |||
| Gln498 (8) | Tyr2 (5); Gly3 (3) | |||
| Asn501 (13) | Asp1; Tyr2 (9); Gly3 (3) | |||
| Gly502 (2) | Asp1 | |||
| Tyr505 (14) | Asp1 (12); Tyr2 (2) | |||