Synthetic antimicrobial peptides: From choice of the best sequences to action mechanisms

Tomasz, 1994, Multiple-antibiotic-resistant pathogenic bacteria -- A report on the rockefeller university workshop, N. Engl. J. Med., 330, 1247, 10.1056/NEJM199404283301725 Holmes, 2016, Understanding the mechanisms and drivers of antimicrobial resistance, Lancet, 387, 176, 10.1016/S0140-6736(15)00473-0 Pfaller, 2007, Epidemiology of invasive candidiasis: a persistent public health problem, Clin. Microbiol. Rev., 20, 133, 10.1128/CMR.00029-06 Biswaro, 2018, Antimicrobial peptides and nanotechnology, recent advances and challenges, Front. Microbiol., 9, 855, 10.3389/fmicb.2018.00855 Pfalzgraff, 2018, Antimicrobial peptides and their therapeutic potential for bacterial skin infections and wounds, Front. Pharmacol., 9, 281, 10.3389/fphar.2018.00281 Oliveira, 2019, Mo-CBP3-PepI, Mo-CBP3-PepII, and Mo-CBP3-PepIII are synthetic antimicrobial peptides active against human pathogens by stimulating ROS generation and increasing plasma membrane permeability, Biochimie, 157, 10, 10.1016/j.biochi.2018.10.016 Lopes, 2019, Peptide from thaumatin plant protein exhibits selective anticandidal activity by inducing apoptosis via membrane receptor, Phytochemistry, 159, 46, 10.1016/j.phytochem.2018.12.006 Dias, 2019, RcAlb-PepII, a synthetic small peptide bioinspired in the 2S albumin from the seed cake of Ricinus communis, is a potent antimicrobial agent against Klebsiella pneumoniae and Candida parapsilosis, Biochim. Biophys. Acta Biomembr., 183092 Gautam, 2015, 59 Sharma, 2016, dPABBs: a novel in silico approach for predicting and designing anti-biofilm peptides, Sci. Rep., 6, 21839, 10.1038/srep21839 Huang, 2010, Alpha-helical cationic antimicrobial peptides: relationships of structure and function, Protein Cell, 1, 143, 10.1007/s13238-010-0004-3 Boman, 2003, buibui, J. Intern. Med., 254, 197, 10.1046/j.1365-2796.2003.01228.x Lata, 2007 Lata, 2010, AntiBP2: improved version of antibacterial peptide prediction, BMC Bioinf., 11, S19, 10.1186/1471-2105-11-S1-S19 Lin, 1999, Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana, Nature, 402, 761, 10.1038/45471 Wang, 2009, APD2: the updated antimicrobial peptide database and its application in peptide design, Nucleic Acids Res., 37, 10.1093/nar/gkn823 Gasteiger, 2005, Protein identification and analysis tools on the ExPASy server, 571 Wang, 2016, APD3: the antimicrobial peptide database as a tool for research and education, Nucleic Acids Res., 44, D1087, 10.1093/nar/gkv1278 Sharma, 2014, Designing of peptides with desired half-life in intestine-like environment, BMC Bioinf., 15, 282, 10.1186/1471-2105-15-282 Meher, 2016, Prediction of donor splice sites using random forest with a new sequence encoding approach, BioData Min., 9, 4, 10.1186/s13040-016-0086-4 Molero-Abraham, 2015, EPIPOX: immunoinformatic characterization of the shared T-cell epitome between Variola virus and related pathogenic orthopoxviruses, J. Immunol. Res., 2015, 1, 10.1155/2015/738020 Chaudhary, 2016, A web server and mobile app for computing hemolytic potency of peptides, Sci. Rep., 6, 22843, 10.1038/srep22843 Gautam, 2013, In silico approach for predicting toxicity of peptides and proteins, PLoS One, 8 Thévenet, 2012, PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides, Nucleic Acids Res., 40, W288, 10.1093/nar/gks419 DeLano, 2005 Lovell, 2003, Structure validation by Cα geometry: ϕ,ψ and Cβ deviation, Proteins Struct. Funct. Genet., 50, 437, 10.1002/prot.10286 Lopes, 2020, A purified chitin-binding protein from Moringa oleifera seeds, is a potent antidermatophytic protein: in vitro mechanisms of action, in vivo effect against infection, and clinical application as a hydrogel for skin infection, Int. J. Biol. Macromol., 149, 432, 10.1016/j.ijbiomac.2020.01.257 2008 Kelly, 2005, How to study proteins by circular dichroism, Biochim. Biophys. Acta Protein Proteonomics, 1751, 119, 10.1016/j.bbapap.2005.06.005 Miles, 2018, CDtoolX, a downloadable software package for processing and analyses of circular dichroism spectroscopic data, Protein Sci., 27, 1717, 10.1002/pro.3474 Freitas, 2019, Study of milk coagulation induced by chymosin using atomic force microscopy, Food Biosci, 29, 81, 10.1016/j.fbio.2019.04.003 Lima, 2020, Anticandidal activity of synthetic peptides: mechanism of action revealed by scanning electron and fluorescence microscopies and synergism effect with nystatin, J. Pept. Sci., 1 Collier, 2011, Evolving the use of peptides as components of biomaterials, Biomaterials, 32, 4198, 10.1016/j.biomaterials.2011.02.030 Lyu, 2016, Antimicrobial activity, improved cell selectivity and mode of action of short PMAP-36-derived peptides against bacteria and Candida, Sci. Rep., 6, 27258, 10.1038/srep27258 Kim, 2018, Mechanisms driving the antibacterial and antibiofilm properties of Hp1404 and its analogue peptides against multidrug-resistant Pseudomonas aeruginosa, Sci. Rep., 8 Jiang, 2008, Effects of net charge and the number of positively charged residues on the biological activity of amphipathic α-helical cationic antimicrobial peptides, Biopolym. - Pept. Sci. Sect., 90, 369, 10.1002/bip.20911 Chen, 2007, Role of peptide hydrophobicity in the mechanism of action of alpha-helical antimicrobial peptides, Antimicrob. Agents Chemother., 51, 1398, 10.1128/AAC.00925-06 Chen, 2002, Determination of stereochemistry stability coefficients of amino acid side-chains in an amphipathic alpha-helix, J. Pept. Res., 59, 18, 10.1046/j.1397-002x.2001.10994.x Whitmore, 2007 Luo, 1997, Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water, Biochemistry, 36, 8413, 10.1021/bi9707133 Su, 2010, Membrane-bound dynamic structure of an arginine-rich cell-penetrating peptide, the protein transduction domain of HIV tat, from solid-state NMR, Biochemistry, 49, 6009, 10.1021/bi100642n Zasloff, 2002, Antimicrobial peptides of multicellular organisms, Nature, 415, 389, 10.1038/415389a Stanaway, 2019, The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017, Lancet Infect. Dis., 19, 369, 10.1016/S1473-3099(18)30685-6 Tsai, 2016, Novel antimicrobial peptides with promising activity against multidrug resistant Salmonella enterica serovar Choleraesuis and its stress response mechanism, J. Appl. Microbiol., 121, 952, 10.1111/jam.13203 Freitas, 2020, Identification, characterization, and antifungal activity of cysteine peptidases from Calotropis procera latex, Phytochemistry, 169 Weitzman, 1995, The dermatophytes, Clin. Microbiol. Rev., 8, 240, 10.1128/CMR.8.2.240 Lopes, 2013, Antifungal activity of phlorotannins against dermatophytes and yeasts: approaches to the mechanism of action and influence on Candida albicans virulence factor, PLoS One, 8, 10.1371/journal.pone.0072203 Rahman, 2014, Antifungal potential of essential oil and ethanol extracts of Lonicera japonica Thunb. against dermatophytes, EXCLI J, 13, 427 Martinez-Rossi, 2018, Dermatophyte resistance to antifungal drugs: mechanisms and prospectus, Front. Microbiol., 9, 10.3389/fmicb.2018.01108 Rogozhin, 2015, A novel antifungal peptide from leaves of the weed Stellaria media L, Biochimie, 116, 125, 10.1016/j.biochi.2015.07.014 Hristova, 2011, A look at arginine in membranes, J. Membr. Biol., 239, 49, 10.1007/s00232-010-9323-9 Rice, 2017, Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association, Biochim. Biophys. Acta Biomembr., 1859, 1941, 10.1016/j.bbamem.2017.06.002 Nguyen, 2011, Investigating the cationic side chains of the antimicrobial peptide tritrpticin: hydrogen bonding properties govern its membrane-disruptive activities, Biochim. Biophys. Acta Biomembr., 1808, 2297, 10.1016/j.bbamem.2011.05.015 Bonucci, 2014, Human neutrophil peptide 1 variants bearing arginine modified cationic side chains: effects on membrane partitioning, Biophys. Chem., 190–191, 32, 10.1016/j.bpc.2014.04.003 Mishra, 2013, Structural location determines functional roles of the basic amino acids of KR-12, the smallest antimicrobial peptide from human cathelicidin LL-37, RSC Adv., 10.1039/c3ra42599a Armas, 2019, Design, antimicrobial activity and mechanism of action of Arg-rich ultra-short cationic lipopeptides, PLoS One, 14, 10.1371/journal.pone.0212447 De La Fuente-Núñez, 2016, Synthetic antibiofilm peptides, Biochim. Biophys. Acta Biomembr., 1858, 1061, 10.1016/j.bbamem.2015.12.015 McEwen, 2018, Antimicrobial resistance: a one health perspective, Microbiol. Spectr., 6, 10.1128/microbiolspec.ARBA-0009-2017 De Zoysa, 2015, Antimicrobial peptides with potential for biofilm eradication: synthesis and structure activity relationship studies of battacin peptides, J. Med. Chem., 58, 625, 10.1021/jm501084q Lum, 2015, Activity of novel synthetic peptides against Candida albicans, Sci. Rep., 5, 10.1038/srep09657 Roscetto, 2018, Antifungal and anti-biofilm activity of the first cryptic antimicrobial peptide from an archaeal protein against Candida spp. clinical isolates, Sci. Rep., 8, 10.1038/s41598-018-35530-0 Paulone, 2017, The synthetic killer peptide KP impairs Candida albicans biofilm in vitro, PLoS One, 12, 10.1371/journal.pone.0181278 Lim, 2003, Ciprofloxacin-induced acute interstitial nephritis and autoimmune hemolytic anemia, Ren. Fail., 25, 647, 10.1081/JDI-120022557 Knopik-Skrocka, 2002, The mechanism of the hemolytic activity of polyene antibiotics, Cell. Mol. Biol. Lett., 7, 31 Jindal, 2015