Selection and redesign for high selectivity of membrane-active antimicrobial peptides from a dedicated sequence/function database

Rončević, Tomislav; Vukičević, Damir; Krce, Lucija; Benincasa, Monica; Aviani, Ivica; Maravić, Ana; Tossi, Alessandro

doi:10.1016/j.bbamem.2019.01.017

Cited by 26 publications

(15 citation statements)

References 39 publications

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“…An increase in AMP selective index has also been achieved by QSAR methods, including a computational tool called Mutator ( Table 1). It suggests residue variations by improving peptide selectivity through appropriate mutations, limited to one or two amino-acid substitutions based on QSAR criteria ( Table 2) (Rončević et al, 2019). Interestingly, QSAR has also been used to identify motifs in coiled-coil peptides aiming at facilitating the production of silver nanoparticles forming peptides with antibacterial potential ( Table 2) (Bozic Abram et al, 2016).…”

Section: Antibp2mentioning

confidence: 99%

“…Therefore, diverse computational approaches for designing AMPs consider the helical content as a crucial determinant for generating improved AMPs. Based upon the data summarized here, QSAR-designed AMPs, including dadapin peptides (Rončević et al, 2019), undergo a coil-tohelix transition (Table 2) from hydrophilic to hydrophobic or membrane-like conditions [e.g., 2,2,2-trifluoroethanol (TFE), sodium dodecyl sulfate (SDS), and dodecylphosphocholine (DPC) micelles, as well as liposomes]. Moreover, the de novo design of peptides with greater helicity has resulted in broadspectrum antibacterial activities compared with AMPs with low helical content (Table 2) (Faccone et al, 2014).…”

Section: Structure Profile In Computer-made Ampsmentioning

confidence: 99%

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Computer-Aided Design of Antimicrobial Peptides: Are We Generating Effective Drug Candidates?

et al. 2020

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Computer-Aided Design of Antimicrobial Peptides http://crdd.osdd.net/raghava/antibp2/ ClassAMP Uses RF and SVM to predict the propensity of a protein sequence to have antibacterial, antifungal, or antiviral activity http://www.bicnirrh.res.in/classamp/ AMPA Web tool for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs http://tcoffee.crg.cat/apps/ampa/do DBAASP Provides users with information on detailed structure (chemical, 3D) and activity for those peptides, for which antimicrobial activity against particular target species have been evaluated experimentally https://dbaasp.org/home Joker An algorithm to design antimicrobial peptides using their language https://github.com/williamfp7/Joker

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Section: Antibp2mentioning

confidence: 99%

Section: Structure Profile In Computer-made Ampsmentioning

confidence: 99%

Computer-Aided Design of Antimicrobial Peptides: Are We Generating Effective Drug Candidates?

et al. 2020

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“…A balance between the hydrophobic and hydrophilic character of the peptide facilitates antibacterial activity and selectivity of AMPs, emphasizing a clearly amphipathic structure in an α‐helical conformation (Zhong et al, 2020). This is supported by Rončević et al (2019) in their study based on quantitative structure–activity relationship (QSAR) criteria for the evaluation of an algorithm that implements variations on peptides. The sequences were designed to position amino acids in a configuration where hydrophobic and polar residues did not disrupt amphipathicity, as it is known to correlate with potent membrane‐directed activity.…”

Section: Determinant Features Controlling Antimicrobial Activity Of Pmentioning

confidence: 85%

Review of antimicrobial peptides as promoters of food safety: Limitations and possibilities within the food industry

Madrazo

Campos

2020

Journal of Food Safety

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Antimicrobial peptides (AMPs) are a group of molecules that has gained interest in research due to their important role in the inhibition of bacterial agents. Their structure shows heterogeneity among the different types of AMPs. However, most of them stand out for their cationic nature and amphipathic character that allows them to interact with membrane components of bacterial cells. Some features such as high selectivity and thermostability have attracted the interest of the food industry toward the application of AMPs in food preservation due to their ability to inhibit foodborne pathogens and spoilage microorganisms. Despite this, there is a limited number of AMPs used as food preservatives nowadays. Therefore, this review aims to offer an overview of AMPs, challenges, and potential applications in the food industry.

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“…In this case, we select for activity against Gram-positive bacteria, which is followed by optimization using the Mutator. They were shown to have high selectivity indices and comparable activities against Gram-positive and Gram-negative strains [210].…”

Section: Strategies For Identifying or Designing New Ampsmentioning

confidence: 99%

Antimicrobial Peptides as Anti-Infective Agents in Pre-Post-Antibiotic Era?

Rončević

Puizina

Tossi

2019

IJMS

Self Cite

106

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Resistance to antibiotics is one of the main current threats to human health and every year multi-drug resistant bacteria are infecting millions of people worldwide, with many dying as a result. Ever since their discovery, some 40 years ago, the antimicrobial peptides (AMPs) of innate defense have been hailed as a potential alternative to conventional antibiotics due to their relatively low potential to elicit resistance. Despite continued effort by both academia and start-ups, currently there are still no antibiotics based on AMPs in use. In this study, we discuss what we know and what we do not know about these agents, and what we need to know to successfully translate discovery to application. Understanding the complex mechanics of action of these peptides is the main prerequisite for identifying and/or designing or redesigning novel molecules with potent biological activity. However, other aspects also need to be well elucidated, i.e., the (bio)synthetic processes, physiological and pathological contexts of their activity, and a quantitative understanding of how physico-chemical properties affect activity. Research groups worldwide are using biological, biophysical, and algorithmic techniques to develop models aimed at designing molecules with the necessary blend of antimicrobial potency and low toxicity. Shedding light on some open questions may contribute toward improving this process.

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Selection and redesign for high selectivity of membrane-active antimicrobial peptides from a dedicated sequence/function database

Cited by 26 publications

References 39 publications

Computer-Aided Design of Antimicrobial Peptides: Are We Generating Effective Drug Candidates?

Computer-Aided Design of Antimicrobial Peptides: Are We Generating Effective Drug Candidates?

Review of antimicrobial peptides as promoters of food safety: Limitations and possibilities within the food industry

Antimicrobial Peptides as Anti-Infective Agents in Pre-Post-Antibiotic Era?

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