Next Article in Journal
The Role of Efflux Pumps in the Transition from Low-Level to Clinical Antibiotic Resistance
Next Article in Special Issue
Fragments of a Wheat Hevein-Like Antimicrobial Peptide Augment the Inhibitory Effect of a Triazole Fungicide on Spore Germination of Fusarium oxysporum and Alternaria solani
Previous Article in Journal
Silver Antibacterial Synergism Activities with Eight Other Metal(loid)-Based Antimicrobials against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus
Previous Article in Special Issue
Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database
Review

Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches

1
Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia
2
Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia
3
Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia
4
Chemical Engineering Program, Universidad de Cartagena, Cartagena 130015, Colombia
5
Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota DC 111711, Colombia
6
School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide 5005, Australia
*
Authors to whom correspondence should be addressed.
Received: 5 November 2020 / Revised: 20 November 2020 / Accepted: 23 November 2020 / Published: 30 November 2020
(This article belongs to the Special Issue Synthesis and Utility of Antimicrobial Peptides)
One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications. View Full-Text
Keywords: antimicrobial peptides; antibiotic resistance; deep learning; molecular dynamics; microfluidics; library screening; rational; non-rational antimicrobial peptides; antibiotic resistance; deep learning; molecular dynamics; microfluidics; library screening; rational; non-rational
Show Figures

Figure 1

MDPI and ACS Style

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.; Cruz, J.C. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics 2020, 9, 854. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics9120854

AMA Style

Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, Cruz JC. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics. 2020; 9(12):854. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics9120854

Chicago/Turabian Style

Puentes, Paola R., 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 Juan C. Cruz 2020. "Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches" Antibiotics 9, no. 12: 854. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics9120854

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop