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Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization.doc

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Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization

AntimicrobialPeptidesDesignbyEvolutionary MultiobjectiveOptimization GiuseppeMaccari1*,MariagraziaDiLuca2,RiccardoNifos?′2,FrancescoCardarelli1,GiovanniSignore1, ClaudiaBoccardi1,AngeloBifone1 1CenterforNanotechnologyInnovation@NEST,IstitutoItalianodiTecnologia,Pisa,Italy,2NEST,ScuolaNormaleSuperioreandIstitutoNanoscienze-CNR,Pisa,Italy Abstract Antimicrobialpeptides(AMPs)areanabundantandwideclassofmoleculesproducedbymanytissuesandcelltypesina varietyofmammals,plantandanimalspecies.Linearalpha-helicalantimicrobialpeptidesareamongthemostwidespread membrane-disruptive AMPs in nature, representing a particularly successful structural arrangement in innate defense. Recently,AMPshavereceivedincreasingattentionaspotentialtherapeuticagents,owingtotheirbroadactivityspectrum andtheirreducedtendencytoinduceresistance.Theintroductionofnon-naturalaminoacidswillbeakeyrequisiteinorder tocontrasthostresistanceandincreasecompound’slife.Inthiswork,thepossibilitytodesignnovelAMPsequenceswith non-natural amino acids was achieved through a flexible computational approach, based on chemophysical profiles of peptidesequences.Quantitativestructure-activityrelationship(QSAR)descriptorswereemployedtocodeeachpeptideand traintwostatisticalmodelsinordertoaccountforstructuralandfunctionalpropertiesofalpha-helicalamphipathicAMPs. These models were then used as fitness functions for a multi-objective evolutional algorithm, together with a set of constraintsforthedesignofaseriesofcandidateAMPs.Twoab-initionaturalpeptidesweresynthesizedandexperimentally validatedforantimicrobialactivity,togetherwithaseriesofcontrolpeptides.Furthermore,awell-knownCecropin-Mellitin alpha helical antimicrobial hybrid (CM18) was optimized by shortening its amino acid sequence while maintaining its activityandapeptidewithnon-naturalaminoacidswasdesignedandtested,demonstratingthehigheractivityachievable withartificialresidues. Citation:MaccariG,DiLucaM,Nifos?′R,CardarelliF,SignoreG,etal.(2013)AntimicrobialPeptidesDesignb