Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches
Abstract
:1. Introduction
2. Antimicrobial Peptides
2.1. Antibacterial
2.2. Antivirals
2.3. Antifungal
2.4. Antiparasitic
3. Peptide Library Design
3.1. Rational
Deep Learning
3.2. Non-Rational
3.2.1. Phage Display
3.2.2. Bacterial Display
3.2.3. Yeast Surface Display
3.2.4. Library Screening
4. Molecular Dynamics (MD)
4.1. Configuration of the System
4.2. Molecular Dynamics (MD) Simulations Method
4.3. Information Provided by the MD Simulations
5. Microfluidic Approaches
5.1. Droplet-Based Screening
5.2. Membrane-Based Screening
5.3. Combinatorial Microarray Screening
6. Concluding Remarks
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Peptide | Amino Acid Sequence | Biological Activity | Method |
---|---|---|---|
CAMEL0 [243] | KWKLFKKIGAVLKVL | Antimicrobial | MD |
CAMEL17 [243] | KWNLNGNINAVLKVL | Antimicrobial | MD |
LL-37 [175] | LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES | Antimicrobial | MD |
AcrAP1 [244] | FLFSLIPHAISGLISAFK | Antimicrobial | MD |
Chrys-3 [177] | FIGLLISAGKAIHDLIRRRH | Antimicrobial | MD |
Pin2 [245] | FWGALAKGALKLIPSLFSSFSKKD | Antimicrobial | MD |
Melittin [246] | GIGAVLKVLTTGLPALISWIKRKRQQ | Antimicrobial | MD |
Putative Bacteriocin 3 [247] | IKKIGKKAAKKVIVKAIQAI | Antimicrobial | DL |
Putative Bacteriocin 4 [247] | KKIGKKAAKKVIVKAIQAIV | Antimicrobial | DL |
RaCa-1 [116] | GLLDIIKTTGKDFAVKILDNLKCKLAGGCPP | Antimicrobial | DL |
RaCa-2 [116] | FFPIIARLAAKVIPSLVCAVTKKC | Antimicrobial | DL |
RaCa-3 [116] | GLWETIKTTGKSIALNLLDKIKCKIAGGCPP | Antimicrobial | DL |
RaCa-7 [116] | FFPRVLPLANKFLPTIYCALPKSVGN | Antimicrobial | DL |
Cecropin A [248] | KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK-NH2 | Translocating/Antimicrobial | MF |
Cecropin B [228] | KWKVFKKIEKMGRNIRNGIVKAGPAIAVLGEAKAL-NH2 | Antimicrobial | MF |
Smp43 [249] | GVWDWIKKTAGKIWNSEPVKALKSQALNAAKNFVAEKIGATPS | Antimicrobial | MF |
Cinnamycin [250] | CRQSCSFGPFTFVCDGNTK | Antimicrobial | MF |
RWRWR [218] | Ac-RWVRVpGO(FAM)WIRQ-NH2 | Traslocating | MF |
OWRWR [218] | Ac-OWVRVpGO(FAM)WIRQ-NH2 | Traslocating | MF |
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Puentes, P.R.; Henao, M.C.; Torres, C.E.; Gómez, S.C.; Gómez, L.A.; Burgos, J.C.; Arbeláez, P.; Osma, J.F.; Muñoz-Camargo, C.; Reyes, L.H.; et al. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics 2020, 9, 854. https://doi.org/10.3390/antibiotics9120854
Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, et al. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics. 2020; 9(12):854. https://doi.org/10.3390/antibiotics9120854
Chicago/Turabian StylePuentes, Paola Ruiz, María C. Henao, Carlos E. Torres, Saúl C. Gómez, Laura A. Gómez, Juan C. Burgos, Pablo Arbeláez, Johann F. Osma, Carolina Muñoz-Camargo, Luis H. Reyes, and et al. 2020. "Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches" Antibiotics 9, no. 12: 854. https://doi.org/10.3390/antibiotics9120854
APA StylePuentes, P. R., Henao, M. C., Torres, C. E., Gómez, S. C., Gómez, L. A., Burgos, J. C., Arbeláez, P., Osma, J. F., Muñoz-Camargo, C., Reyes, L. H., & Cruz, J. C. (2020). Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics, 9(12), 854. https://doi.org/10.3390/antibiotics9120854