Multifunctional Analysis of Chia Seed (Salvia hispanica L.) Bioactive Peptides Using Peptidomics and Molecular Dynamics Simulations Approaches
Abstract
:1. Introduction
2. Results and Discussion
3. Materials and Methods
3.1. Materials
3.2. Preparation of Chia Seed Peptides
3.3. Peptidomics Analysis of Low Molecular Weight Peptides by Liquid Chromatography-Mass Spectrometry
3.4. In Silico Analysis of Identified Peptides for their Potential Bioactivities
3.5. Construction of Human Molecular Targets and Identified Peptides
3.6. Molecular Dynamics and Ensemble Docking Calculations
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No. | Peptide Sequence | Peptide Ranker Score | PreAIP | AntiAngio-Pred | AHTpin | |||
---|---|---|---|---|---|---|---|---|
Score | Prediction | Score | Prediction | Score | Prediction | |||
Database peptides | ||||||||
1 | FNLVFFLL | 0.951 | 0.416 | AIP | −0.21 | Non-AAP | −0.58 | Non-AHT |
2 | EGDVFWIPRF | 0.940 | 0.418 | AIP | −0.5 | Non-AAP | −0.12 | Non-AHT |
3 | DHFPFIY | 0.933 | 0.518 | AIP | 0.04 | AAP | 0.47 | AHT |
4 | EGGIWPF | 0.929 | 0.344 | AIP | 0.48 | AAP | −0.1 | Non-AHT |
5 | GFEWITF | 0.922 | 0.57 | AIP | 0.47 | AAP | −0.89 | Non-AHT |
6 | GLDFPELPLGM | 0.919 | 0.481 | AIP | −0.61 | Non-AAP | 1.31 | AHT |
7 | GQTPLFPRIF | 0.912 | 0.412 | AIP | 0.41 | AAP | 0.65 | AHT |
8 | GDAHYDPLFPF | 0.909 | 0.323 | Non-AIP | −1.23 | Non-AAP | 0.95 | AHT |
9 | NNVFYPF | 0.903 | 0.344 | AIP | −0.34 | Non-AAP | 0.22 | AHT |
10 | EYPPLGRF | 0.901 | 0.395 | AIP | 1.01 | AAP | 1.04 | AHT |
11 | KPLPFELF | 0.898 | 0.409 | AIP | 0.6 | AAP | 0.55 | AHT |
12 | DVWDPFQDFPL | 0.895 | 0.461 | AIP | 0.11 | AAP | 0.41 | AHT |
13 | SDKNGYFF | 0.883 | 0.418 | AIP | −0.82 | Non-AAP | −1.16 | Non-AHT |
14 | VPIPVPLPF | 0.883 | 0.318 | Non-AIP | −0.24 | Non-AAP | 2.29 | AHT |
15 | SNVFDPF | 0.876 | 0.338 | Non-AIP | −0.87 | Non-AAP | −0.06 | Non-AHT |
16 | TPLFPRIF | 0.876 | 0.393 | AIP | 1.03 | AAP | 0.58 | AHT |
17 | DQNPRSFFL | 0.873 | 0.444 | AIP | 1 | AAP | −0.67 | Non-AHT |
18 | QLQRWFR | 0.871 | 0.519 | AIP | 2.22 | AAP | −0.62 | Non-AHT |
19 | GFEWVAF | 0.868 | 0.59 | AIP | −0.94 | Non-AAP | 0.3 | AHT |
20 | SFNLPIL | 0.867 | 0.408 | AIP | −0.4 | Non-AAP | −0.15 | Non-AHT |
21 | QEGGIWPF | 0.863 | 0.37 | AIP | 0.39 | AAP | −0.52 | Non-AHT |
22 | GSRFDWTR | 0.858 | 0.488 | AIP | 2.17 | AAP | −1.36 | Non-AHT |
23 | ADFYNPR | 0.853 | 0.303 | Non-AIP | 0.92 | AAP | 0.44 | AHT |
24 | APSKDAPMF | 0.851 | 0.452 | AIP | −0.16 | Non-AAP | −0.24 | Non-AHT |
25 | GFEWITFK | 0.847 | 0.578 | AIP | 0.28 | AAP | −0.66 | Non-AHT |
26 | NGFEWITF | 0.842 | 0.549 | AIP | 0.4 | AAP | −1.03 | Non-AHT |
27 | VNEGDVFWIPRF | 0.841 | 0.414 | AIP | −1.1 | Non-AAP | −0.52 | Non-AHT |
28 | SSNVFDPF | 0.841 | 0.304 | Non-AIP | −0.93 | Non-AAP | −0.17 | Non-AHT |
29 | FNIVFPG | 0.839 | 0.385 | AIP | −1.68 | Non-AAP | 0.76 | AHT |
30 | VPVFPPPLN | 0.837 | 0.435 | Non-AIP | −0.26 | Non-AAP | 2 | AHT |
31 | GIDIPPPR | 0.835 | 0.316 | Non-AIP | 0.55 | AAP | 0.47 | AHT |
32 | APAEKGFAGF | 0.832 | 0.402 | AIP | −1.39 | Non-AAP | 0.23 | AHT |
33 | DQNPRSFF | 0.830 | 0.433 | AIP | 1.05 | AAP | −0.92 | Non-AHT |
34 | SRPWPIDY | 0.827 | 0.486 | AIP | 2.26 | AAP | −0.04 | Non-AHT |
35 | QNGFEWITF | 0.825 | 0.573 | AIP | 0.46 | AAP | −1.47 | Non-AHT |
36 | RPGDVFVFPR | 0.825 | 0.383 | AIP | −0.98 | Non-AAP | 0.22 | AHT |
37 | DNGIIYPW | 0.823 | 0.32 | Non-AIP | −0.36 | Non-AAP | 0.15 | AHT |
38 | NPQAGRF | 0.822 | 0.376 | AIP | −0.43 | Non-AAP | 0.03 | AHT |
39 | APVGSPVGSTGGNFGVF | 0.817 | 0.476 | AIP | −1.1 | Non-AAP | 0.39 | AHT |
40 | APPPVLAL | 0.816 | 0.396 | AIP | 0.61 | AAP | 0.07 | AHT |
41 | FPLLNYL | 0.813 | 0.554 | AIP | −0.18 | Non-AAP | 1.31 | AHT |
42 | RNNVFYPF | 0.811 | 0.378 | AIP | 0.61 | AAP | 0.49 | AHT |
43 | GNIFRGL | 0.811 | 0.452 | AIP | −0.34 | Non-AAP | −0.6 | Non-AHT |
44 | FPGLADRM | 0.810 | 0.333 | Non-AIP | −1.01 | Non-AAP | 0.67 | AHT |
45 | SNEWDPSFR | 0.806 | 0.393 | AIP | 0.81 | AAP | −1.34 | Non-AHT |
46 | SMLSPHW | 0.806 | 0.42 | AIP | 0.22 | AAP | −0.24 | Non-AHT |
47 | SLDVWDPFQDFPL | 0.804 | 0.464 | AIP | 0.44 | AAP | 0.59 | AHT |
48 | SPDLIRRM | 0.803 | 0.399 | AIP | 1.12 | AAP | −0.74 | Non-AHT |
49 | FGNVFKGM | 0.803 | 0.32 | Non-AIP | −1.68 | Non-AAP | −0.8 | Non-AHT |
De novo peptides | ||||||||
1 | QFRF | 0.980 | 0.361 | AIP | ND | - | −0.05 | Non-AHT |
2 | FDRF | 0.978 | 0.301 | Non-AIP | ND | - | −0.79 | Non-AHT |
3 | GRPW | 0.971 | 0.266 | Non-AIP | ND | - | 0.84 | AHT |
4 | FWDR | 0.964 | 0.347 | AIP | ND | - | −0.74 | Non-AHT |
5 | FRSF | 0.962 | 0.339 | Non-AIP | ND | - | −0.76 | Non-AHT |
6 | GPHW | 0.958 | 0.354 | AIP | ND | - | 1 | AHT |
7 | KPPF | 0.955 | 0.294 | Non-AIP | ND | - | 2.09 | AHT |
8 | WLPR | 0.943 | 0.306 | Non-AIP | ND | - | 1.13 | AHT |
9 | FWDH | 0.938 | 0.318 | Non-AIP | ND | - | −0.61 | Non-AHT |
10 | FDKF | 0.937 | 0.32 | Non-AIP | ND | - | −0.87 | Non-AHT |
11 | FRGL | 0.937 | 0.318 | Non-AIP | ND | - | −0.38 | Non-AHT |
12 | DFKF | 0.932 | 0.336 | Non-AIP | ND | - | −0.87 | Non-AHT |
13 | KDFLFP | 0.929 | 0.352 | AIP | −0.03 | Non-AAP | −0.79 | Non-AHT |
14 | EFRF | 0.922 | 0.289 | Non-AIP | ND | - | 0.99 | AHT |
15 | APHW | 0.918 | 0.389 | AIP | ND | - | 0.03 | AHT |
16 | RPAF | 0.909 | 0.28 | Non-AIP | ND | - | 0.89 | AHT |
17 | ARGW | 0.908 | 0.317 | Non-AIP | ND | - | −0.76 | Non-AHT |
18 | FKAF | 0.907 | 0.31 | Non-AIP | ND | - | −0.67 | Non-AHT |
19 | WEFLTF | 0.907 | 0.329 | Non-AIP | 0.43 | AAP | −0.89 | Non-AHT |
20 | HVFF | 0.878 | 0.349 | AIP | ND | - | −0.21 | Non-AHT |
21 | WAPH | 0.873 | 0.313 | Non-AIP | ND | - | 0.99 | AHT |
22 | RPSF | 0.872 | 0.334 | Non-AIP | ND | - | 0.7 | AHT |
23 | HPAYW | 0.871 | 0.392 | AIP | 0.1 | AAP | 1.81 | AHT |
24 | DLRF | 0.863 | 0.319 | Non-AIP | ND | - | −0.56 | Non-AHT |
25 | QLRF | 0.863 | 0.344 | AIP | ND | - | 0.21 | AHT |
26 | GKFL | 0.850 | 0.316 | Non-AIP | ND | - | −0.48 | Non-AHT |
27 | QRYF | 0.848 | 0.327 | Non-AIP | ND | - | 0.89 | AHT |
28 | FWDNH | 0.834 | 0.345 | AIP | −0.63 | Non-AAP | 0.05 | AHT |
29 | FPLK | 0.834 | 0.336 | Non-AIP | ND | - | 1.07 | AHT |
30 | RAFL | 0.831 | 0.349 | AIP | ND | - | −0.42 | Non-AHT |
31 | FPLLN | 0.820 | 0.483 | AIP | −0.1 | Non-AAP | 0.22 | AHT |
32 | WDPSYR | 0.816 | 0.325 | Non-AIP | 2.67 | AAP | 0.11 | AHT |
33 | GLKF | 0.810 | 0.348 | AIP | ND | - | −0.48 | Non-AHT |
34 | HPNPRL | 0.808 | 0.358 | AIP | 0.51 | AAP | 0.98 | AHT |
No. | Peptide Sequence | Intestinal Stability | Hydrophobicity | Hydropathicity | Hydrophilicity | Charge | Molecular Weight |
---|---|---|---|---|---|---|---|
Database peptides | |||||||
1 | FNLVFFLL | 0.73 | 0.42 | 2.56 | −1.78 | 0 | 1012.35 |
2 | EGDVFWIPRF | 2.391 | −0.02 | −0.01 | −0.27 | −1 | 1265.57 |
3 | DHFPFIY | 1.094 | 0.11 | 0.07 | −0.94 | −1 | 938.13 |
4 | EGGIWPF | 0.945 | 0.19 | 0.07 | −0.67 | −1 | 805 |
5 | GFEWITF | 2.512 | 0.24 | 0.66 | −1.09 | −1 | 899.11 |
6 | GLDFPELPLGM | 2.79 | 0.12 | 0.46 | −0.29 | −2 | 1188.54 |
7 | GQTPLFPRIF | 1.079 | −0.01 | 0.16 | −0.58 | 1 | 1175.52 |
8 | GDAHYDPLFPF | 2.144 | 0.02 | −0.35 | −0.37 | −2 | 1278.52 |
9 | NNVFYPF | 0.798 | 0.06 | −0.01 | −1.2 | 0 | 900.09 |
10 | EYPPLGRF | 0.392 | −0.15 | −0.79 | −0.07 | 0 | 978.21 |
11 | KPLPFELF | 1.859 | 0.05 | 0.32 | −0.33 | 0 | 990.3 |
12 | DVWDPFQDFPL | 1.608 | −0.03 | −0.41 | −0.23 | −3 | 1378.65 |
13 | SDKNGYFF | 1.183 | −0.17 | −0.98 | −0.1 | 0 | 977.14 |
14 | VPIPVPLPF | 2.283 | 0.3 | 1.46 | −1.01 | 0 | 978.35 |
15 | SNVFDPF | 0.585 | 0.01 | 0.06 | −0.43 | −1 | 824.97 |
16 | TPLFPRIF | 1.143 | 0.05 | 0.69 | −0.75 | 1 | 990.3 |
17 | DQNPRSFFL | 1.023 | −0.27 | −0.89 | −0.01 | 0 | 1123.34 |
18 | QLQRWFR | 1.066 | −0.48 | −1.47 | −0.19 | 2 | 1033.3 |
19 | GFEWVAF | 2.466 | 0.27 | 0.97 | −1.06 | −1 | 855.06 |
20 | SFNLPIL | 2.342 | 0.2 | 1.29 | −1.06 | 0 | 803.04 |
21 | QEGGIWPF | 1.213 | 0.08 | −0.38 | −0.56 | −1 | 933.15 |
22 | GSRFDWTR | 0.667 | −0.44 | −1.56 | 0.38 | 1 | 1024.21 |
23 | ADFYNPR | 1.132 | −0.33 | −1.4 | 0.13 | 0 | 882.02 |
24 | APSKDAPMF | 1.538 | −0.09 | −0.34 | 0.17 | 0 | 963.22 |
25 | GFEWITFK | 2.682 | 0.07 | 0.09 | −0.58 | 0 | 1027.3 |
26 | NGFEWITF | 2.499 | 0.13 | 0.14 | −0.93 | −1 | 1013.23 |
27 | VNEGDVFWIPRF | 2.24 | −0.02 | 0.05 | −0.33 | −1 | 1478.84 |
28 | SSNVFDPF | 0.2 | −0.02 | −0.05 | −0.34 | −1 | 912.06 |
29 | FNIVFPG | 2.136 | 0.28 | 1.26 | −1.16 | 0 | 793.02 |
30 | VPVFPPPLN | 1.974 | 0.14 | 0.57 | −0.79 | 0 | 979.3 |
31 | GIDIPPPR | 0.964 | −0.13 | −0.53 | 0.3 | 0 | 864.1 |
32 | APAEKGFAGF | 3.43 | 0.05 | 0.12 | −0.05 | 0 | 994.24 |
33 | DQNPRSFF | 1.044 | −0.36 | −1.48 | 0.21 | 0 | 1010.17 |
34 | SRPWPIDY | 1.413 | −0.22 | −1.21 | −0.15 | 0 | 1033.25 |
35 | QNGFEWITF | 2.539 | 0.04 | −0.27 | −0.8 | −1 | 1141.38 |
36 | RPGDVFVFPR | 3.379 | −0.19 | −0.21 | 0.1 | 1 | 1189.51 |
37 | DNGIIYPW | 0.959 | 0.07 | −0.28 | −0.76 | −1 | 977.19 |
38 | NPQAGRF | 0.929 | −0.31 | −1.27 | 0.06 | 1 | 788.95 |
39 | APVGSPVGSTGGNFGVF | 2.935 | 0.14 | 0.53 | −0.56 | 0 | 1549.95 |
40 | APPPVLAL | 1.457 | 0.24 | 1.32 | −0.76 | 0 | 777.06 |
41 | FPLLNYL | 1.841 | 0.22 | 1.11 | −1.43 | 0 | 879.14 |
42 | RNNVFYPF | 0.769 | −0.17 | −0.58 | −0.67 | 1 | 1056.29 |
43 | GNIFRGL | 1.294 | −0.03 | 0.33 | −0.41 | 1 | 775.99 |
44 | FPGLADRM | 2.43 | −0.09 | 0.04 | −0.01 | 0 | 906.16 |
45 | SNEWDPSFR | 0.992 | −0.37 | −1.81 | 0.43 | −1 | 1137.29 |
46 | SMLSPHW | 1.339 | 0.02 | −0.23 | −0.91 | 0 | 857.09 |
47 | SLDVWDPFQDFPL | 1.558 | 0 | −0.12 | −0.31 | −3 | 1578.91 |
48 | SPDLIRRM | 1.23 | −0.38 | −0.59 | 0.55 | 1 | 987.27 |
49 | FGNVFKGM | 1.854 | 0.07 | 0.44 | −0.57 | 1 | 899.19 |
De novo peptides | |||||||
1 | QFRF | ND | −0.31 | −0.6 | −0.45 | 1 | 596.73 |
2 | FDRF | ND | −0.32 | −0.6 | 0.25 | 0 | 583.68 |
3 | GRPW | ND | −0.33 | −1.85 | −0.1 | 1 | 514.64 |
4 | FWDR | ND | −0.38 | −1.52 | 0.02 | 0 | 622.73 |
5 | FRSF | ND | −0.2 | 0.07 | −0.42 | 1 | 555.67 |
6 | GPHW | ND | 0.01 | −1.53 | −0.97 | 0 | 495.6 |
7 | KPPF | ND | −0.16 | −1.07 | 0.12 | 1 | 487.64 |
8 | WLPR | ND | −0.23 | −0.8 | −0.55 | 1 | 570.74 |
9 | FWDH | ND | −0.04 | −1.2 | −0.85 | −1 | 603.69 |
10 | FDKF | ND | −0.15 | −0.45 | 0.25 | 0 | 555.67 |
11 | FRGL | ND | −0.11 | 0.42 | −0.33 | 1 | 491.63 |
12 | DFKF | ND | −0.15 | −0.45 | 0.25 | 0 | 555.67 |
13 | KDFLFP | 1.208 | −0.29 | −0.6 | 0.25 | 0 | 597.71 |
14 | EFRF | ND | 0.04 | −0.97 | −1.1 | 0 | 509.62 |
15 | APHW | ND | −0.02 | 0.07 | −0.13 | 0 | 765.97 |
16 | RPAF | ND | −0.24 | −0.38 | 0 | 1 | 489.61 |
17 | ARGW | ND | −0.25 | −1 | −0.22 | 1 | 488.6 |
18 | FKAF | ND | 0.09 | 0.88 | −0.62 | 1 | 511.66 |
19 | WEFLTF | 1.16 | 0.22 | 0.72 | −1.27 | −1 | 842.04 |
20 | HVFF | ND | 0.34 | 1.65 | −1.75 | 0 | 548.69 |
21 | WAPH | ND | 0.04 | −0.98 | −1.1 | 0 | 509.62 |
22 | RPSF | ND | −0.37 | −1.02 | 0.2 | 1 | 505.61 |
23 | HPAYW | 1.398 | 0.03 | −1.04 | −1.34 | 0 | 672.81 |
24 | DLRF | ND | −0.33 | −0.35 | 0.43 | 0 | 549.66 |
25 | QLRF | ND | −0.33 | −0.35 | −0.28 | 1 | 562.71 |
26 | GKFL | ND | 0.05 | 0.57 | −0.33 | 1 | 463.62 |
27 | QRYF | ND | −0.46 | −1.63 | −0.4 | 1 | 612.73 |
28 | FWDNH | 1.425 | −0.16 | −1.66 | −0.64 | −1 | 717.81 |
29 | FPLK | ND | −0.01 | 0.28 | −0.32 | 1 | 503.68 |
30 | RAFL | ND | −0.09 | 0.97 | −0.45 | 1 | 505.65 |
31 | FPLLN | 1.991 | 0.19 | 1.06 | −1.18 | 0 | 602.78 |
32 | WDPSYR | 1.486 | −0.4 | −2.1 | 0.1 | 0 | 822.95 |
33 | GLKF | ND | 0.05 | 0.57 | −0.33 | 1 | 463.62 |
34 | HPNPRL | 1.534 | −0.4 | −1.77 | 0.15 | 1 | 732.91 |
Parameters | NNVFYPF | FNIVFPG | SRPWPIDY | QLQRWFR | GSRFDWTR | DFKF | DLRF | FKAF | FRSF | QFRF |
---|---|---|---|---|---|---|---|---|---|---|
MW (g/mol) | 899.9 | 792.93 | 899.07 | 10.33.19 | 1024.1 | 555.63 | 549.62 | 511.62 | 555.63 | 596.68 |
H-bond donors | 8 | 6 | 8.5 | 17.5 | 14.5 | 5.75 | 7.75 | 5.75 | 7.75 | 9.75 |
H-bond acceptors | 19.25 | 17 | 19 | 22.5 | 22.4 | 10.25 | 11.25 | 9.25 | 10.95 | 12.75 |
logP o/w a | −3.56 | −1.83 | −2.79 | −5.68 | −4.64 | −1.06 | −1.83 | −1.43 | −1.28 | −3.14 |
logS wat b | −1.87 | −3.77 | −0.49 | −1.18 | −0.24 | −0.68 | −0.64 | −0.79 | −2.72 | −0.96 |
NlogK has Serum Protein Binding c | −2.39 | −1.88 | −2.53 | −3.35 | −3.18 | −1.23 | −1.54 | −1.02 | −1.26 | -1.75 |
Apparent Caco-2 Permeability (nm/s) d | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Apparent MDCK Permeability (nm/s) e | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
logKp for skin permeability f | −9.04 | −6.92 | −8.53 | −14.29 | −13.53 | −8.69 | −9.95 | −8.26 | −8.62 | −10.60 |
Qualitative Model for Human Oral Absorption | Low | Low | Low | Low | Low | Low | Low | Low | Low | Low |
Most similar pharmaceutical drugs | Troxerutin, Voglibose, Monoxerutin | Lymecycline, Troxerutin, Proglumetacin | Razoxane, Hexoprenaline, Dihydralazine | Everolimus, Amiodarone, Fenethylline | Everolimus, Droxidopa, Polaprezinc | Hexoprenaline, Lisinopril, Lymecycline | Hexoprenaline, Voglibose, Lymecycline | Hexoprenaline, Lisinopril, Lymecycline | Aminopterin, Lymecycline, Hexobendine | Hexobendine, Hexoprenaline, Lymecycline |
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Aguilar-Toalá, J.E.; Vidal-Limon, A.; Liceaga, A.M. Multifunctional Analysis of Chia Seed (Salvia hispanica L.) Bioactive Peptides Using Peptidomics and Molecular Dynamics Simulations Approaches. Int. J. Mol. Sci. 2022, 23, 7288. https://doi.org/10.3390/ijms23137288
Aguilar-Toalá JE, Vidal-Limon A, Liceaga AM. Multifunctional Analysis of Chia Seed (Salvia hispanica L.) Bioactive Peptides Using Peptidomics and Molecular Dynamics Simulations Approaches. International Journal of Molecular Sciences. 2022; 23(13):7288. https://doi.org/10.3390/ijms23137288
Chicago/Turabian StyleAguilar-Toalá, José E., Abraham Vidal-Limon, and Andrea M. Liceaga. 2022. "Multifunctional Analysis of Chia Seed (Salvia hispanica L.) Bioactive Peptides Using Peptidomics and Molecular Dynamics Simulations Approaches" International Journal of Molecular Sciences 23, no. 13: 7288. https://doi.org/10.3390/ijms23137288