Unnatural amino acids: promising implications for the development of new antimicrobial peptides

References

• Agostini F, Völler J‐S, Koksch B, Acevedo‐Rocha CG, Kubyshkin V, Budisa N. 2017. Biocatalysis with unnatural amino acids: enzymology meets xenobiology. Angew Chem. 129(33):9810–9835.
   Google Scholar
• Ahn M, Gunasekaran P, Rajasekaran G, Kim EY, Lee S-J, Bang G, Cho K, Hyun J-K, Lee H-J, Jeon YH, et al. 2017. Pyrazole derived ultra-short antimicrobial peptidomimetics with potent anti-biofilm activity. Eur J Med Chem. 125:551–564.
   PubMed Web of Science ®Google Scholar
• Almaaytah A, Qaoud MT, Abualhaijaa A, Al-Balas Q, Alzoubi KH. 2018. Hybridization and antibiotic synergism as a tool for reducing the cytotoxicity of antimicrobial peptides. Infect Drug Resist. 11:835–847.
   PubMed Web of Science ®Google Scholar
• Almahboub SA, Narancic T, Devocelle M, Kenny ST, Palmer-Brown W, Murphy C, Nikodinovic-Runic J, O’Connor KE. 2018. Biosynthesis of 2-aminooctanoic acid and its use to terminally modify a lactoferricin B peptide derivative for improved antimicrobial activity. Appl Microbiol Biotechnol. 102(2):789–799.
   PubMed Web of Science ®Google Scholar
• Anderhuber N, Fladischer P, Gruber-Khadjawi M, Mairhofer J, Striedner G, Wiltschi B. 2016. High-level biosynthesis of norleucine in E. coli for the economic labeling of proteins. J Biotechnol. 235:100–111.
   PubMed Web of Science ®Google Scholar
• Arias M, Jensen KV, Nguyen LT, Storey DG, Vogel HJ. 2015. Hydroxy-tryptophan containing derivatives of tritrpticin: modification of antimicrobial activity and membrane interactions. Biochim Biophys Acta. 1848(1 Pt B):277–288.
   PubMed Web of Science ®Google Scholar
• Arias M, Piga KB, Hyndman ME, Vogel HJ. 2018. Improving the activity of Trp-rich antimicrobial peptides by Arg/Lys substitutions and changing the length of cationic residues. Biomolecules. 8(2):19.
   PubMed Web of Science ®Google Scholar
• Asfaw H, Laqua K, Walkowska AM, Cunningham F, Martinez-Martinez MS, Cuevas-Zurita JC, Ballell-Pages L, Imming P. 2017. Design, synthesis and structure-activity relationship study of wollamide B; a new potential anti TB agent. PLoS One. 12(4):e0176088.
   PubMed Web of Science ®Google Scholar
• Bagheri M, Beyermann M, Dathe M. 2009. Immobilization reduces the activity of surface-bound cationic antimicrobial peptides with no influence upon the activity spectrum. Antimicrob Agents Chemother. 53(3):1132–1141.
   PubMed Web of Science ®Google Scholar
• Bagheri M, Hancock REW. 2017. High-performance liquid chromatography and mass spectrometry-based design of proteolytically stable antimicrobial peptides. In: Hansen PR, editors. Antimicrobial peptides: methods and protocols. New York (NY): Springer New York; p. 61–71.
   Google Scholar
• Bao K, Yuan WY, Ma CB, Yu X, Wang L, Hong M, Xi XP, Zhou M, Chen TB. 2018. Modification targeting the "Rana Box" motif of a novel nigrocin peptide from Hylarana latouchii enhances and broadens its potency against multiple bacteria. Front Microbiol. 9:2846.
   PubMed Web of Science ®Google Scholar
• Bechinger B, Gorr SU. 2017. Antimicrobial peptides: mechanisms of action and resistance. J Dent Res. 96(3):254–260.
   PubMed Web of Science ®Google Scholar
• Ha Gan B, Gaynord J, Rowe SM, Deingruber T, Spring DR. 2021. The multifaceted nature of antimicrobial peptides: current synthetic chemistry approaches and future directions. Chem Soc Rev. 50(13):7820–7880.
   PubMed Web of Science ®Google Scholar
• Bhonsle JB, Clark T, Bartolotti L, Hicks RP. 2013. A brief overview of antimicrobial peptides containing unnatural amino acids and ligand-based approaches for peptide ligands. Curr Top Med Chem. 13(24):3205–3244.
   PubMed Web of Science ®Google Scholar
• Bisht GS, Rawat DS, Kumar A, Kumar R, Pasha S. 2007. Antimicrobial activity of rationally designed amino terminal modified peptides. Bioorg Med Chem Lett. 17(15):4343–4346.
   PubMed Web of Science ®Google Scholar
• Blaskovich MAT. 2016. Unusual amino acids in medicinal chemistry. J Med Chem. 59(24):10807–10836.
   PubMed Web of Science ®Google Scholar
• Braunstein A, Papo N, Shai Y. 2004. In vitro activity and potency of an intravenously injected antimicrobial peptide and its DL amino acid analog in mice infected with bacteria. Antimicrob Agents Chemother. 48(8):3127–3129.
   PubMed Web of Science ®Google Scholar
• Brogden KA. 2005. Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat Rev Microbiol. 3(3):238–250.
   PubMed Web of Science ®Google Scholar
• Buckholtz GA, Reger NA, Anderton WD, Schimoler PJ, Roudebush SL, Meng WS, Miller MC, Gawalt ES. 2016. Reducing Escherichia coli growth on a composite biomaterial by a surface immobilized antimicrobial peptide. Mater Sci Eng C Mater Biol Appl. 65:126–134.
   PubMed Web of Science ®Google Scholar
• Buer BC, Meagher JL, Stuckey JA, Marsh ENG. 2012. Structural basis for the enhanced stability of highly fluorinated proteins. Proc Natl Acad Sci USA. 109(13):4810–4815.
   PubMed Web of Science ®Google Scholar
• Cao L, Langen LV, Sheldon RA. 2003. Immobilised enzymes: carrier-bound or carrier-free? Curr Opin Biotechnol. 14(4):387–394.
   PubMed Web of Science ®Google Scholar
• Cardoso M, Cândido E, Chan L, Torres MDT, Oshiro K, Rezende S, Porto WF, Lu TK, Fuente-Nunez Cdl, Craik DJ, et al. 2018. A computationally designed peptide derived from Escherichia coli as a potential drug template for antibacterial and antibiofilm therapies. ACS Infect Dis. 4(12):1727–1736.
   PubMed Web of Science ®Google Scholar
• Cardoso MH, Meneguetti BT, Costa BO, Buccini DF, Oshiro K, Preza S, Carvalho C, Migliolo L, Franco OL. 2019. Non-Lytic antibacterial peptides that translocate through bacterial membranes to act on intracellular targets. Int J Mol Sci. 20(19):4877.
   PubMed Web of Science ®Google Scholar
• Carreira EM, Turner N, Hönig M, Sondermann P. 2017. Enantioselective chemo- and biocatalysis: partners in retrosynthesis. Angew Chem Int Ed Engl. 56(31):8942–8973.
   PubMed Web of Science ®Google Scholar
• Chen CX, Hu J, Yang C, Zhang Y, Wang F, Mu QM, Pan F, Xu H, Lu JR. 2016. Amino acid side chains affect the bioactivity of designed short peptide amphiphiles. J Mater Chem B. 4(13):2359–2368.
   PubMed Web of Science ®Google Scholar
• Chen HL, Su PY, Kuo SC, Lauderdale TLY, Shih C. 2018. Adding a C-terminal cysteine (CTC) can enhance the bactericidal activity of three different antimicrobial peptides. Front Microbiol. 9:1440.
   PubMed Web of Science ®Google Scholar
• Choi H, Hwang JS, Kim H, Lee DG. 2013. Antifungal effect of CopA3 monomer peptide via membrane-active mechanism and stability to proteolysis of enantiomeric D-CopA3. Biochem Biophys Res Commun. 440(1):94–98.
   PubMed Web of Science ®Google Scholar
• Chu-Kung AF, Nguyen R, Bozzelli KN, Tirrell M. 2010. Chain length dependence of antimicrobial peptide-fatty acid conjugate activity. J Colloid Interface Sci. 345(2):160–167.
   PubMed Web of Science ®Google Scholar
• Chu HL, Yu HY, Yip BS, Chih YH, Liang CW, Cheng HT, Cheng JW. 2013. Boosting salt resistance of short antimicrobial peptides. Antimicrob Agents Chemother. 57(8):4050–4052.
   PubMed Web of Science ®Google Scholar
• Ciumac D, Gong H, Hu X, Lu JR. 2019. Membrane targeting cationic antimicrobial peptides. J Colloid Interface Sci. 537:163–185.
   PubMed Web of Science ®Google Scholar
• Cleophas RTC, Riool M, Quarles van Ufford HC, Zaat SAJ, Kruijtzer JAW, Liskamp RMJ. 2014. Convenient preparation of bactericidal hydrogels by covalent attachment of stabilized antimicrobial peptides using thiol–ene click chemistry. ACS Macro Lett. 3(5):477–480.
   PubMed Web of Science ®Google Scholar
• Conlon JM, Al-Kharrge R, Ahmed E, Raza H, Galadari S, Condamine E. 2007. Effect of aminoisobutyric acid (Aib) substitutions on the antimicrobial and cytolytic activities of the frog skin peptide, temporin-1DRa. Peptides. 28(10):2075–2080.
   PubMed Web of Science ®Google Scholar
• Costa F, Carvalho IF, Montelaro RC, Gomes P, Martins MCL. 2011. Covalent immobilization of antimicrobial peptides (AMPs) onto biomaterial surfaces. Acta Biomater. 7(4):1431–1440.
   PubMed Web of Science ®Google Scholar
• Costa FMTA, Maia SR, Gomes PAC, Martins MCL. 2015. Dhvar5 antimicrobial peptide (AMP) chemoselective covalent immobilization results on higher antiadherence effect than simple physical adsorption. Biomaterials. 52(1):531–538.
   PubMedGoogle Scholar
• Dahiya R, Kumar S, Khokra SL, Gupta SV, Sutariya VB, Bhatia D, Sharma A, Singh S, Maharaj S. 2018. Toward the synthesis and improved biopotential of an N-methylated analog of a proline-rich cyclic tetrapeptide from marine bacteria. Mar Drugs. 16(9):305.
   PubMed Web of Science ®Google Scholar
• Dennison SR, Phoenix DA. 2011. Influence of C-terminal amidation on the efficacy of modelin-5. Biochemistry. 50(9):1514–1523.
   PubMed Web of Science ®Google Scholar
• Dewan PC, Anantharaman A, Chauhan VS, Sahal D. 2009. Antimicrobial action of prototypic amphipathic cationic decapeptides and their branched dimers. Biochemistry. 48(24):5642–5657.
   PubMed Web of Science ®Google Scholar
• Dewangan RP, Bisht GS, Singh VP, Yar MS, Pasha S. 2018. Design and synthesis of cell selective α/β-diastereomeric peptidomimetic with potent in vivo antibacterial activity against methicillin resistant S. Aureus. Bioorg Chem. 76:538–547.
   PubMed Web of Science ®Google Scholar
• Dos Santos Cabrera MP, Arcisio-Miranda M, Broggio Costa ST, Konno K, Ruggiero JR, Procopio J, Ruggiero Neto J. 2008. Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel-like activity, and the role of the amidated C-terminus. J Pept Sci. 14(6):661–669.
   PubMed Web of Science ®Google Scholar
• Ellerby HM, Arap W, Ellerby LM, Kain R, Andrusiak R, Rio GD, Krajewski S, Lombardo CR, Rao R, Ruoslahti E, et al. 1999. Anti-cancer activity of targeted pro-apoptotic peptides. Nat Med. 5(9):1032–1038.
   PubMed Web of Science ®Google Scholar
• Falciani C, Lozzi L, Pollini S, Luca V, Carnicelli V, Brunetti J, Lelli B, Bindi S, Scali S, Di Giulio A, et al. 2012. Isomerization of an antimicrobial peptide broadens antimicrobial spectrum to gram-positive bacterial pathogens. PLoS One. 7(10):e46259.
   PubMed Web of Science ®Google Scholar
• Falciani C, Lozzi L, Scali S, Brunetti J, Bracci L, Pini A. 2014. Site-specific pegylation of an antimicrobial peptide increases resistance to Pseudomonas aeruginosa elastase. Amino Acids. 46(5):1403–1407.
   PubMed Web of Science ®Google Scholar
• Fanelli R, Besserer-Offroy É, René A, Côté J, Tétreault P, Collerette-Tremblay J, Longpré J-M, Leduc R, Martinez J, Sarret P, et al. 2015. Synthesis and characterization in vitro and in vivo of (L)-(trimethylsilyl)alanine containing neurotensin analogues. J Med Chem. 58(19):7785–7795.
   PubMed Web of Science ®Google Scholar
• Fernandez-Lopez S, Kim H-S, Choi EC, Delgado M, Granja JR, Khasanov A, Kraehenbuehl K, Long G, Weinberger DA, Wilcoxen KM, et al. 2001. Antibacterial agents based on the cyclic D,L-alpha-peptide architecture. Nature. 412(6845):452–455.
   PubMed Web of Science ®Google Scholar
• Fjell CD, Hiss JA, Hancock REW, Schneider G. 2011. Designing antimicrobial peptides: form follows function. Nat Rev Drug Discov. 11(1):37–51.
   PubMed Web of Science ®Google Scholar
• Fox MA, Thwaite JE, Ulaeto DO, Atkins TP, Atkins HS. 2012. Design and characterization of novel hybrid antimicrobial peptides based on cecropin A, LL-37 and magainin II. Peptides. 33(2):197–205.
   PubMed Web of Science ®Google Scholar
• Goodwin D, Simerska P, Toth I. 2012. Peptides as therapeutics with enhanced bioactivity. Curr Med Chem. 19(26):4451–4461.
   PubMed Web of Science ®Google Scholar
• Grassi L, Maisetta G, Esin S, Batoni G. 2017. Combination strategies to enhance the efficacy of antimicrobial peptides against bacterial biofilms. Front Microbiol. 8:2409.
   PubMed Web of Science ®Google Scholar
• Grimsey E, Collis DWP, Mikut R, Hilpert K. 2020. The effect of lipidation and glycosylation on short cationic antimicrobial peptides. Biochim Biophys Acta Biomembr. 1862(8):183195.
   PubMed Web of Science ®Google Scholar
• Hancock REW, Sahl HG. 2006. Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat Biotechnol. 24(12):1551–1557.
   PubMed Web of Science ®Google Scholar
• Haney EF, Barbosa SC, Baquir B, Hancock REW. 2019. Influence of non-natural cationic amino acids on the biological activity profile of innate defense regulator peptides. J Med Chem. 62(22):10294–10304.
   PubMed Web of Science ®Google Scholar
• Hao J, Luo S, Pan L. 2021. Computer-aided intelligent design using deep multi-objective cooperative optimization algorithm. Future Gener Comp SY. 124(10):49–53.
   Google Scholar
• He YK, He XF. 2016. Molecular design and genetic optimization of antimicrobial peptides containing unnatural amino acids against antibiotic-resistant bacterial infections. Biopolymers. 106(5):746–756.
   PubMed Web of Science ®Google Scholar
• Henriksen JR, Etzerodt T, Gjetting T, Andresen TL. 2014. Side chain hydrophobicity modulates therapeutic activity and membrane selectivity of antimicrobial peptide mastoparan-X. PLoS One. 9(3):e91007.
   PubMed Web of Science ®Google Scholar
• Hernandez-Gordillo V, Geisler I, Chmielewski J. 2014. Dimeric unnatural polyproline-rich peptides with enhanced antibacterial activity. Bioorg Med Chem Lett. 24(2):556–559.
   PubMed Web of Science ®Google Scholar
• Hernandez-Montelongo J, Corrales Ureña YR, Machado D, Lancelloti M, Pinheiro MP, Rischka K, Lisboa-Filho PN, Cotta MA. 2018. Electrostatic immobilization of antimicrobial peptides on polyethylenimine and their antibacterial effect against staphylococcus epidermidis. Colloids Surf B Biointerfaces. 164:370–378.
   PubMed Web of Science ®Google Scholar
• Hicks RP, Abercrombie JJ, Wong RK, Leung KP. 2013. Antimicrobial peptides containing unnatural amino acid exhibit potent bactericidal activity against ESKAPE pathogens. Bioorg Med Chem. 21(1):205–214.
   PubMed Web of Science ®Google Scholar
• Hicks RP, Bhonsle JB, Venugopal D, Koser BW, Magill AJ. 2007. De novo design of selective antibiotic peptides by incorporation of unnatural amino acids. J Med Chem. 50(13):3026–3036.
   PubMed Web of Science ®Google Scholar
• Hilpert K, Volkmer-Engert R, Walter T, Hancock REW. 2005. High-throughput generation of small antibacterial peptides with improved activity. Nat Biotechnol. 23(8):1008–1012.
   PubMed Web of Science ®Google Scholar
• Hong SY, Oh JE, Lee KH. 1999. Effect of D-amino acid substitution on the stability, the secondary structure, and the activity of membrane-active peptide. Biochem Pharmacol. 58(11):1775–1780.
   PubMed Web of Science ®Google Scholar
• Illa O, Olivares JA, Nolis P, Ortuño RM. 2017. The relevance of the relative configuration in the folding of hybrid peptides containing β-cyclobutane amino acids and γ-amino-L-proline residues. Tetrahedron. 73(44):6286–6295.
   Web of Science ®Google Scholar
• Imanishi S, Katoh T, Yin Y, Yamada M, Kawai M, Suga H. 2021. In vitro selection of macrocyclic D/L-hybrid peptides against human EGFR. J Am Chem Soc. 143(15):5680–5684.
   PubMed Web of Science ®Google Scholar
• Jenssen H, Fjell CD, Cherkasov A, Hancock REW. 2008. QSAR modeling and computer-aided design of antimicrobial peptides. J Pept Sci. 14(1):110–114.
   PubMed Web of Science ®Google Scholar
• Jia F, Wang J, Peng J, Zhao P, Kong Z, Wang K, Yan W, Wang R. 2017. D-amino acid substitution enhances the stability of antimicrobial peptide polybia-CP. Acta Biochim Biophys Sin. 49(10):916–925.
   Google Scholar
• Juretić D, Vukičević D, Tossi A. 2017. Tools for designing amphipathic helical antimicrobial peptides. In: Hansen PR, editor. Antimicrobial peptides: methods and protocols. New York (NY): Springer New York; p. 23–34.
   Google Scholar
• Kai M, Zhang W, Xie H, Liu LW, Huang SJ, Li X, Zhang ZZ, Liu YY, Zhang BZ, Song JJ, et al. 2018. Effects of linker amino acids on the potency and selectivity of dimeric antimicrobial peptides. Chin. Chem. Lett. 29(7):1163–1166. ),
   Web of Science ®Google Scholar
• Kang W, Liu H, Ma L, Wang M, Wei S, Sun P, Jiang M, Guo M, Zhou C, Dou J. 2017. Effective antimicrobial activity of a peptide mutant Cbf-14-2 against penicillin-resistant bacteria based on its unnatural amino acids. Eur J Pharm Sci. 105:169–177.
   PubMed Web of Science ®Google Scholar
• Karabi S, Chaudhary N. 2018. Antimicrobial peptides from C-terminal amphipathic region of E. coli FtsA. Biochim Biophys Acta Biomembr. 1860(12):2506–2514.
   PubMed Web of Science ®Google Scholar
• Khara JS, Priestman M, Uhía I, Hamilton MS, Krishnan N, Wang Y, Yang YY, Langford PR, Newton SM, Robertson BD, et al. 2016. Unnatural amino acid analogues of membrane-active helical peptides with anti-mycobacterial activity and improved stability. J Antimicrob Chemother. 71(8):2181–2191.
   PubMed Web of Science ®Google Scholar
• Kimura T, Hesaka A, Isaka Y. 2020. D-Amino acids and kidney diseases. Clin Exp Nephrol. 24(5):404–410.
   PubMed Web of Science ®Google Scholar
• Kleczkowska P, Hermans E, Kosson P, Kowalczyk A, Lesniak A, Pawlik K, Bojnik E, Benyhe S, Nowicka B, Bujalska-Zadrozny M, et al. 2016. Antinociceptive effect induced by a combination of opioid and neurotensin moieties vs. their hybrid peptide [Ile(9)]PK20 in an acute pain treatment in rodents. Brain Res. 1648(Pt A):172–180.
   PubMedGoogle Scholar
• Kleczkowska P, Kosson P, Ballet S, Van den Eynde I, Tsuda Y, Tourwé D, Lipkowski AW. 2010. PK20, a new opioid-neurotensin hybrid peptide that exhibits central and peripheral antinociceptive effects. Mol Pain. 6(1):86.
   PubMedGoogle Scholar
• Klippenstein V, Mony L, Paoletti P. 2018. Probing ion channel structure and function using light-sensitive amino acids. Trends Biochem Sci. 43(6):436–451.
   PubMed Web of Science ®Google Scholar
• Knappe D, Henklein P, Hoffmann R, Hilpert K. 2010. Easy strategy to protect antimicrobial peptides from fast degradation in serum. Antimicrob Agents Chemother. 54(9):4003–4005.
   PubMed Web of Science ®Google Scholar
• Lainson JC, Daly SM, Triplett K, Johnston SA, Hall PR, Diehnelt CW. 2017. Synthetic antibacterial peptide exhibits synergy with oxacillin against MRSA. ACS Med Chem Lett. 8(8):853–857.
   PubMed Web of Science ®Google Scholar
• Lavecchia A. 2015. Machine-learning approaches in drug discovery: methods and applications. Drug Discov Today. 20(3):318–331.
   PubMed Web of Science ®Google Scholar
• Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, Vlieghe E, Hara GL, Gould IM, Goossens H, et al. 2013. Antibiotic resistance—the need for global solutions. Lancet Infect Dis. 13(12):1057–1098.,
   PubMed Web of Science ®Google Scholar
• Lee CJ, Qiu TA, Sweedler JV. 2020. D-Alanine: distribution, origin, physiological relevance, and implications in disease. Biochim Biophys Acta Proteins Proteom. 1868(11):140482.
   PubMed Web of Science ®Google Scholar
• Lee DG, Kim HN, Park Y, Kim HK, Choi BH, Choi C-H, Hahm K-S. 2002. Design of novel analogue peptides with potent antibiotic activity based on the antimicrobial peptide, HP (2–20), derived from N-terminus of Helicobacter pylori ribosomal protein L1. BBA – Proteins Proteom. 1598(1–2):185–194.
   PubMed Web of Science ®Google Scholar
• Li Y, Liu T, Liu Y, Tan Z, Ju Y, Yang Y, Dong WB. 2019. Antimicrobial activity, membrane interaction and stability of the D-amino acid substituted analogs of antimicrobial peptide W3R6. J. Photoch. Photobio. 200:111645.
   Web of Science ®Google Scholar
• Lima AN, Philot EA, Trossini GHG, Scott LPB, Maltarollo VG, Honorio KM. 2016. Use of machine learning approaches for novel drug discovery. Expert Opin Drug Discov. 11(3):225–239.
   PubMed Web of Science ®Google Scholar
• Liu TQ, Zhu NY, Zhong C, Zhu YW, Gou SH, Chang LL, Bao HX, Liu H, Zhang Y, Ni JM. 2020. Effect of N-methylated and fatty acid conjugation on analogs of antimicrobial peptide anoplin. Eur J Pharm Sci. 152:105453.
   PubMed Web of Science ®Google Scholar
• Lohan S, Cameotra SS, Bisht GS. 2014. Antibacterial evaluation of structurally amphipathic, membrane active small cationic peptidomimetics: synthesized by incorporating 3-amino benzoic acid as peptidomimetic element. Eur J Med Chem. 83:102–115.
   PubMed Web of Science ®Google Scholar
• Lozeau LD, Grosha J, Kole D, Prifti F, Dominko T, Camesano TA, Rolle MW. 2017. Collagen tethering of synthetic human antimicrobial peptides cathelicidin LL37 and its effects on antimicrobial activity and cytotoxicity. Acta Biomater. 52:9–20.
   PubMed Web of Science ®Google Scholar
• Müller AT, Gabernet G, Hiss JA, Schneider G. 2017. modlAMP: python for antimicrobial peptides. Bioinformatics. 33(17):2753–2755.
   PubMed Web of Science ®Google Scholar
• Müller AT, Hiss JA, Schneider G. 2018. Recurrent neural network model for constructive peptide design. J Chem Inf Model. 58(2):472–479.
   PubMed Web of Science ®Google Scholar
• Maccari G, Di Luca M, Nifosí R, Cardarelli F, Signore G, Boccardi C, Bifone A. 2013. Antimicrobial peptides design by evolutionary multiobjective optimization. PLoS Comput Biol. 9(9):e1003212.
   PubMed Web of Science ®Google Scholar
• Manabe T, Kawasaki K. 2017. D-form KLKLLLLLKLK-NH2 peptide exerts higher antimicrobial properties than its L-form counterpart via an association with bacterial cell wall components. Sci Rep. 7(1):43384.
   PubMedGoogle Scholar
• Mangoni ML, Papo N, Saugar JM, Barra D, Shai Y, Simmaco M, Rivas L. 2006. Effect of natural L- to D-Amino acid conversion on the organization, membrane binding, and biological function of the antimicrobial peptides bombinins H. Biochemistry. 45(13):4266–4276.
   PubMed Web of Science ®Google Scholar
• Mao C, Mohanraj G, Kandiyote NS, Kasher R, Arnusch CJ. 2018. UV mediated attachment of short arginine-tryptophan antimicrobial peptides on reverse osmosis membrane surfaces inhibit Pseudomonas aeruginosa biofilm. Desalination. 431:73–79.
   Web of Science ®Google Scholar
• Meng H, Kumar K. 2007. Antimicrobial activity and protease stability of peptides containing fluorinated amino acids. J Am Chem Soc. 129(50):15615–15622.
   PubMed Web of Science ®Google Scholar
• Mura M, Wang J, Zhou Y, Pinna M, Zvelindovsky AV, Dennison SR, Phoenix DA. 2016. The effect of amidation on the behaviour of antimicrobial peptides. Eur Biophys J. 45(3):195–207.
   PubMed Web of Science ®Google Scholar
• Nahhas AF, Chang R, Webster TJ. 2018. Introducing unnatural amino acids-containing tripeptides as antimicrobial and anticancer agents. J Biomed Nanotechnol. 14(5):987–993.
   PubMed Web of Science ®Google Scholar
• Narancic T, Almahboub SA, O’Connor KE. 2019. Unnatural amino acids: production and biotechnological potential. World J. Microbiol. Biotechnol. 35(4):67.
   PubMed Web of Science ®Google Scholar
• Neumann-Staubitz P, Neumann H. 2016. The use of unnatural amino acids to study and engineer protein function. Curr Opin Struct Biol. 38:119–128.
   PubMed Web of Science ®Google Scholar
• Niu W, Guo J. 2017. Novel fluorescence-based biosensors incorporating unnatural amino acids. Methods Enzymol. 589:191–291.
   PubMed Web of Science ®Google Scholar
• Oh D, Shin SY, Lee S, Kang JH, Kim SD, Ryu PD, Hahm K-S, Kim Y. 2000. Role of the hinge region and the tryptophan residue in the synthetic antimicrobial peptides, cecropin A(1-8)-magainin 2(1–12) and its analogues, on their antibiotic activities and structures. Biochemistry. 39(39):11855–11864.
   PubMed Web of Science ®Google Scholar
• Oh JE, Lee KH. 1999. Synthesis of novel unnatural amino acid as a building block and its incorporation into an antimicrobial peptide. Bioorgan. Med. Chem. 7(12):2985–2990.
   PubMed Web of Science ®Google Scholar
• Oliva R, Chino M, Pane K, Pistorio V, De Santis A, Pizzo E, D’Errico GA-O, Pavone V, Lombardi A, Del Vecchio P, et al. 2018. Exploring the role of unnatural amino acids in antimicrobial peptides. Sci Rep. 8(1):8888.
   PubMedGoogle Scholar
• Ong ZY, Cheng JC, Huang Y, Xu KJ, Ji ZK, Fan WM, Yang YY. 2014a. Effect of stereochemistry, chain length and sequence pattern on antimicrobial properties of short synthetic β-sheet forming peptide amphiphiles. Biomaterials. 35(4):1315–1325.
   PubMed Web of Science ®Google Scholar
• Ong ZY, Wiradharma N, Yang YY. 2014b. Strategies employed in the design and optimization of synthetic antimicrobial peptide amphiphiles with enhanced therapeutic c potentials. Adv Drug Deliv Rev. 78:28–45.
   PubMed Web of Science ®Google Scholar
• Pan M, Lu C, Zheng MC, Zhou W, Song FL, Chen WD, Yao F, Liu DJ, Cai JF. 2020. Unnatural amino-acid-based star-shaped poly(L-Ornithine)s as emerging long-term and biofilm-disrupting antimicrobial peptides to treat Pseudomonas aeruginosa-infected burn wounds. Adv Healthcare Mater. 9(19):2000647.
   Web of Science ®Google Scholar
• Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. 2018. Synthetic and therapeutic applications of ammonia-lyases and aminomutases. Chem Rev. 118(1):73–118.
   PubMed Web of Science ®Google Scholar
• Peschel A, Sahl HG. 2006. The co-evolution of host cationic antimicrobial peptides and microbial resistance. Nat Rev Microbiol. 4(7):529–536.
   PubMed Web of Science ®Google Scholar
• Pizzolato-Cezar LR, Okuda-Shinagawa NM, Machini MT. 2019. Combinatory therapy antimicrobial peptide-antibiotic to minimize the ongoing rise of resistance. Front Microbiol. 10:1703.
   PubMedGoogle Scholar
• Pollegioni L, Rosini E, Molla G. 2020. Advances in enzymatic synthesis of D-Amino acids. Int J Mol Sci. 21(9):3206.
   PubMed Web of Science ®Google Scholar
• Purwin M, Markowska A, Bruzgo I, Rusak T, Surażyński A, Jaworowska U, Midura-Nowaczek K. 2017. Peptides with 6-aminohexanoic acid: synthesis and evaluation as plasmin inhibitors. Int J Pept Res Ther. 23(2):235–245.
   PubMed Web of Science ®Google Scholar
• Raj H, Szymański W, de Villiers J, Rozeboom HJ, Veetil VP, Reis CR, de Villiers M, Dekker FJ, de Wildeman S, Quax WJ, et al. 2012. Engineering methylaspartate ammonia lyase for the asymmetric synthesis of unnatural amino acids. Nat Chem. 4(6):478–484.
   PubMed Web of Science ®Google Scholar
• Ramagopal UA, Ramakumar S, Sahal D, Chauhan VS. 2001. De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: compaction mediated by weak interactions. Proc Natl Acad Sci USA. 98(3):870–874.
   PubMed Web of Science ®Google Scholar
• Reinhardt A, Neundorf I. 2016. Design and application of antimicrobial peptide conjugates. Int J Mol Sci. 17(5):701.
   PubMed Web of Science ®Google Scholar
• Russell AL, Kennedy AM, Spuches AM, Gibson WS, Venugopal D, Klapper D, Srouji AH, Bhonsle JB, Hicks RP. 2011. Determining the effect of the incorporation of unnatural amino acids into antimicrobial peptides on the interactions with zwitterionic and anionic membrane model systems. Chem Phys Lipids. 164(8):740–758.
   PubMed Web of Science ®Google Scholar
• Russell AL, Williams BC, Spuches A, Klapper D, Srouji AH, Hicks RP. 2012. The effect of the length and flexibility of the side chain of basic amino acids on the binding of antimicrobial peptides to zwitterionic and anionic membrane model systems. Bioorgan. Med. Chem. 20(5):1723–1739.
   PubMed Web of Science ®Google Scholar
• Saikia K, Sravani YD, Ramakrishnan V, Chaudhary N. 2017. Highly potent antimicrobial peptides from N-terminal membrane-binding region of. Sci Rep. 7(1):42994.
   PubMedGoogle Scholar
• Scherpenzeel MV, Pot MVD, Arnusch CJ, Liskamp RMJ, Pieters RJ. 2007. Detection of galectin-3 by novel peptidic photoprobes. Bioorg Med Chem Lett. 17(2):376–378.
   PubMed Web of Science ®Google Scholar
• Schneider P, Müller AT, Gabernet G, Button AL, Posselt G, Wessler S, Hiss JA, Schneider G. 2017. Hybrid network model for “Deep Learning” of chemical data: application to antimicrobial peptides. Mol Inf. 36(1–2):1600011.
   Web of Science ®Google Scholar
• Shao C, Zhu Y, Lai Z, Tan P, Shan A. 2019. Antimicrobial peptides with protease stability: progress and perspective. Future Med Chem. 11(16):2047–2050.
   PubMed Web of Science ®Google Scholar
• Sharma N, Furter R, Kast P, Tirrell DA. 2000. Efficient introduction of aryl bromide functionality into proteins in vivo. FEBS Lett. 467(1):37–40.
   PubMed Web of Science ®Google Scholar
• Shin A, Lee E, Jeon D, Park Y-G, Bang JK, Park Y-S, Shin SY, Kim Y. 2015. Peptoid-substituted hybrid antimicrobial peptide derived from papiliocin and magainin 2 with enhanced bacterial selectivity and anti-inflammatory activity. Biochemistry. 54(25):3921–3931.
   PubMed Web of Science ®Google Scholar
• Sim JY, Kim S, Lee J, Lim H, Kim HH, Park Z-Y, Kim JI. 2019. A significantly enhanced antibacterial spectrum of D-enantiomeric lipopeptide bactenecin. Biochem Biophys Res Commun. 514(2):497–502.
   PubMed Web of Science ®Google Scholar
• Strömstedt AA, Pasupuleti M, Schmidtchen A, Malmsten M. 2009. Evaluation of strategies for improving proteolytic resistance of antimicrobial peptides by using variants of EFK17, an internal segment of LL-37. Antimicrob Agents Chemother. 53(2):593–602.
   PubMed Web of Science ®Google Scholar
• Tall YA, Al-Rawashdeh Ba, Abualhaijaa A, Almaaytah A, Masadeh M, Alzoubi KH. 2020. Functional characterization of a novel hybrid peptide with high potency against gram-negative bacteria. Curr Pharm Des. 26(3):376–385.
   PubMed Web of Science ®Google Scholar
• Tanishiki N, Yano Y, Matsuzaki K. 2019. Endowment of pH responsivity to anticancer peptides by introducing 2,3-diaminopropionic acid residues. Chembiochem. 20(16):2109–2117.
   PubMed Web of Science ®Google Scholar
• Tapia VE, Ay B, Volkmer R. 2009. Exploring and profiling protein function with peptide arrays. In: Cretich M., Chiari M., editors. Peptide microarrays: methods and protocols. Totowa (NJ): Humana Press; p. 3–17.
   Google Scholar
• Thery T, Shwaiki LN, O’Callaghan YC, O’Brien NM, Arendt EK. 2019. Antifungal activity of a de novo synthetic peptide and derivatives against fungal food contaminants. J Pept Sci. 25(1):e3137.
   PubMed Web of Science ®Google Scholar
• Ting DSJ, Beuerman RW, Dua HS, Lakshminarayanan R, Mohammed I. 2020. Strategies in translating the therapeutic potentials of host defense peptides. Front Immunol. 11:983.
   PubMed Web of Science ®Google Scholar
• Torres MDT, Sothiselvam S, Lu TK, Fuente-Nunez CDL. 2019. Peptide design principles for antimicrobial applications. J Mol Biol. 431(18):3547–3567.
   PubMed Web of Science ®Google Scholar
• Tripathi AK, Kumari T, Tandon A, Sayeed M, Afshan T, Kathuria M, Shukla PK, Mitra K, Ghosh JK. 2017. Selective phenylalanine to proline substitution for improved antimicrobial and anticancer activities of peptides designed on phenylalanine heptad repeat. Acta Biomater. 57:170–186.
   PubMed Web of Science ®Google Scholar
• Tsuchiya K, Numata K. 2017. Chemoenzymatic synthesis of polypeptides containing the unnatural amino acid 2-aminoisobutyric acid. Chem Commun. 53(53):7318–7321.
   PubMed Web of Science ®Google Scholar
• Veltri D, Kamath U, Shehu A. 2017. Improving recognition of antimicrobial peptides and target selectivity through machine learning and genetic programming. IEEE/ACM Trans Comput Biol Bioinform. 14(2):300–313.
   PubMed Web of Science ®Google Scholar
• Veltri D, Kamath U, Shehu A. 2018. Deep learning improves antimicrobial peptide recognition. Bioinformatics. 34(16):2740–2747.
   PubMed Web of Science ®Google Scholar
• Wade D, Boman A, Wåhlin B, Drain CM, Andreu D, Boman HG, Merrifield RB. 1990. All-D amino acid-containing channel-forming antibiotic peptides. Proc Natl Acad Sci USA. 87(12):4761–4765.
   PubMed Web of Science ®Google Scholar
• Wade HM, Darling LEO, Elmore DE. 2019. Hybrids made from antimicrobial peptides with different mechanisms of action show enhanced membrane permeabilization. Biochim Biophys Acta Biomembr. 1861(10):182980.
   PubMed Web of Science ®Google Scholar
• Wang C, Yang C, Chen YC, Ma L, Huang K. 2019. Rational design of hybrid peptides: a novel drug design approach. Curr Med Sci. 39(3):349–355.
   PubMed Web of Science ®Google Scholar
• Wang D, Haapasalo M, Gao Y, Ma JZ, Shen Y. 2018. Antibiofilm peptides against biofilms on titanium and hydroxyapatite surfaces. Bioact. Mater. 3(4):418–425.
   PubMed Web of Science ®Google Scholar
• Wang GS. 2012. Post-translational modifications of natural antimicrobial peptides and strategies for peptide engineering. Curr Biotechnol. 1(1):72–79.
   PubMedGoogle Scholar
• Wang Y, Yang YJ, Chen YN, Zhao HY, Zhang S. 2016. Computer-aided design, structural dynamics analysis, and in vitro susceptibility test of antibacterial peptides incorporating unnatural amino acids against microbial infections. Comput Meth Prog Bio. 134:215–223.
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhang JW, Gao T, Zhang NH, He J, Wu F. 2021. Covalent immobilization of DJK-5 peptide on porous titanium for enhanced antibacterial effects and restrained inflammatory osteoclastogenesis. Colloids Surf B Biointerfaces. 202:111697.
   PubMed Web of Science ®Google Scholar
• Weaver BA. 2014. How Taxol/paclitaxel kills cancer cells. Mol Biol Cell. 25(18):2677–2681.
   PubMed Web of Science ®Google Scholar
• Wei XB, Wu RJ, Si DY, Liao XD, Zhang LL, Zhang RJ. 2016. Novel hybrid peptide cecropin A (1-8)-LL37 (17-30) with potential antibacterial activity. Int J Mol Sci. 17(7):983.
   PubMed Web of Science ®Google Scholar
• Willcox MDP, Hume EBH, Aliwarga Y, Kumar N, Cole N. 2008. A novel cationic-peptide coating for the prevention of microbial colonization on contact lenses. J Appl Microbiol. 105(6):1817–1825.
   PubMed Web of Science ®Google Scholar
• Wu RJ, Wang Q, Zheng ZJ, Zhao LM, Shang YJ, Wei XB, Liao XD, Zhang RJ. 2014. Design, characterization and expression of a novel hybrid peptides melittin (1-13)-LL37 (17–30). Mol Biol Rep. 41(7):4163–4169.
   PubMed Web of Science ®Google Scholar
• Xiong M, Chen M, Zhang J. 2016. Rational evolution of antimicrobial peptides containing unnatural amino acids to combat burn wound infections. Chem Biol Drug Des. 88(3):404–410.
   PubMed Web of Science ®Google Scholar
• Xue YP, Cao CH, Zheng YG. 2018. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev. 47(4):1516–1561.
   PubMed Web of Science ®Google Scholar
• Yan H, Hancock REW. 2001. Synergistic interactions between mammalian antimicrobial defense peptides. Antimicrob Agents Chemother. 45(5):1558–1560.
   PubMed Web of Science ®Google Scholar
• Yasir M, Dutta D, Hossain KR, Chen R, Ho KKK, Kuppusamy R, Clarke RJ, Kumar N, Willcox MDP. 2020. Mechanism of action of surface immobilized antimicrobial peptides against Pseudomonas aeruginosa. Front Microbiol. 10:3053.
   PubMedGoogle Scholar
• Yeaman MR, Yount NY. 2003. Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev. 55(1):27–55.
   PubMed Web of Science ®Google Scholar
• Yousefinejad S, Bagheri M, Moosavi-Movahedi AA. 2015. Quantitative sequence-activity modeling of antimicrobial hexapeptides using a segmented principal component strategy: an approach to describe and predict activities of peptide drugs containing L/D and unnatural residues. Amino Acids. 47(1):125–134.
   PubMed Web of Science ®Google Scholar
• Zhu X, Dong N, Wang Z, Ma Z, Zhang L, Ma Q, Shan A. 2014. Design of imperfectly amphipathic α-helical antimicrobial peptides with enhanced cell selectivity. Acta Biomater. 10(1):244–257.
   PubMed Web of Science ®Google Scholar
• Zotti MD, Biondi B, Peggion C, Park Y, Hahm KS, Formaggio F, Toniolo C. 2011. Synthesis, preferred conformation, protease stability, and membrane activity of heptaibin, a medium-length peptaibiotic. J Pept Sci. 17(8):1099–1387.
   Web of Science ®Google Scholar
• Zou GZ, De Leeuw E, Li C, Pazgier M, Li Cq, Zeng Py, Lu WY, Lubkowski J, Lu Wy. 2007. Toward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs. J Biol Chem. 282(27):19653–19665.
   PubMed Web of Science ®Google Scholar