OpenLB
Open Library of Bioscience
Advanced Search
Interface focus
Dec 06, 2017;7 (6): 20160153.

What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?

Ernest Y Lee, Michelle W Lee, Benjamin M Fulan, Andrew L Ferguson, Gerard C L Wong
Author Information
  1. Ernest Y Lee: Department of Bioengineering, University of California, Los Angeles, CA 90095, USA. ORCID
  2. Michelle W Lee: Department of Bioengineering, University of California, Los Angeles, CA 90095, USA. ORCID
  3. Benjamin M Fulan: Department of Mathematics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  4. Andrew L Ferguson: Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ORCID
  5. Gerard C L Wong: Department of Bioengineering, University of California, Los Angeles, CA 90095, USA.
PMID: 29147555 DOI: 10.1098/rsfs.2016.0153

Abstract

Antimicrobial peptides (AMPs) are a diverse class of well-studied membrane-permeating peptides with important functions in innate host defense. In this short review, we provide a historical overview of AMPs, summarize previous applications of machine learning to AMPs, and discuss the results of our studies in the context of the latest AMP literature. Much work has been recently done in leveraging computational tools to design new AMP candidates with high therapeutic efficacies for drug-resistant infections. We show that machine learning on AMPs can be used to identify essential physico-chemical determinants of AMP functionality, and identify and design peptide sequences to generate membrane curvature. In a broader scope, we discuss the implications of our findings for the discovery of membrane-active peptides in general, and uncovering membrane activity in new and existing peptide taxonomies.

Keywords

amphiphilic peptides antimicrobial peptides machine learning membrane curvature

References

  1. Biochim Biophys Acta. 1999 Dec 15;1462(1-2):157-83 [PMID: 10590307]
  2. Nat Rev Mol Cell Biol. 2006 Jan;7(1):9-19 [PMID: 16365634]
  3. Annu Rev Biochem. 2011;80:101-23 [PMID: 21438688]
  4. Annu Rev Phys Chem. 2011;62:483-506 [PMID: 21219150]
  5. Biophys J. 2003 Jun;84(6):3751-8 [PMID: 12770881]
  6. Biochim Biophys Acta. 1999 Dec 15;1462(1-2):55-70 [PMID: 10590302]
  7. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W32-7 [PMID: 16845018]
  8. Nature. 2016 Jan 28;529(7587):484-9 [PMID: 26819042]
  9. Methods Mol Biol. 2008;494:127-59 [PMID: 18726572]
  10. Trends Biotechnol. 1998 Feb;16(2):82-8 [PMID: 9487736]
  11. J Am Chem Soc. 2009 Oct 28;131(42):15102-3 [PMID: 19807082]
  12. Biochem Biophys Res Commun. 1998 Mar 6;244(1):253-7 [PMID: 9514864]
  13. FEBS Lett. 1997 Nov 3;417(1):135-40 [PMID: 9395091]
  14. Nat Cell Biol. 2012 Sep;14(9):944-9 [PMID: 22902598]
  15. Wiley Interdiscip Rev Comput Mol Sci. 2014 Sep 1;4(5):468-481 [PMID: 25285160]
  16. Biophys J. 2003 May;84(5):3052-60 [PMID: 12719236]
  17. Biophys J. 2004 Jul;87(1):396-407 [PMID: 15240474]
  18. PLoS One. 2012;7(12):e51444 [PMID: 23240023]
  19. J Am Chem Soc. 2011 May 4;133(17):6720-7 [PMID: 21473577]
  20. J Chem Phys. 2009 Aug 21;131(7):074104 [PMID: 19708729]
  21. Nucleic Acids Res. 2016 Jan 4;44(D1):D1087-93 [PMID: 26602694]
  22. Proc Natl Acad Sci U S A. 1987 Aug;84(15):5449-53 [PMID: 3299384]
  23. Biochemistry. 1992 Dec 15;31(49):12416-23 [PMID: 1463728]
  24. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13588-13593 [PMID: 27849600]
  25. Biochim Biophys Acta. 2014 Sep;1838(9):2269-79 [PMID: 24743021]
  26. Biochemistry. 1996 Sep 3;35(35):11361-8 [PMID: 8784191]
  27. Biophys J. 2000 Oct;79(4):2002-9 [PMID: 11023904]
  28. J Biol Chem. 1993 Oct 15;268(29):22112-8 [PMID: 8408070]
  29. Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13155-60 [PMID: 26460016]
  30. Q Rev Biophys. 1977 Feb;10(1):1-34 [PMID: 327501]
  31. J Biol Chem. 1982 Jun 10;257(11):6010-5 [PMID: 7076661]
  32. FEBS Lett. 2010 May 3;584(9):1840-7 [PMID: 19837069]
  33. Biochim Biophys Acta. 2001 Oct 1;1514(2):253-60 [PMID: 11557025]
  34. J Phys Chem B. 2008 Jun 12;112(23):6988-96 [PMID: 18479112]
  35. Biochemistry. 1996 Oct 29;35(43):13723-8 [PMID: 8901513]
  36. ACS Chem Biol. 2009 Jan 16;4(1):65-74 [PMID: 19055425]
  37. Bioinformatics. 2013 Apr 1;29(7):960-2 [PMID: 23426256]
  38. Biophys J. 1996 Jun;70(6):2659-66 [PMID: 8744303]
  39. Eur J Biochem. 1991 Dec 18;202(3):849-54 [PMID: 1765098]
  40. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20595-600 [PMID: 19106303]
  41. Biochim Biophys Acta. 2007 Oct;1768(10):2500-9 [PMID: 17599802]
  42. IEEE Trans Pattern Anal Mach Intell. 2009 May;31(5):855-68 [PMID: 19299860]
  43. Biopolymers. 1998;47(6):451-63 [PMID: 10333737]
  44. J Phys Chem B. 2013 Oct 10;117(40):12145-56 [PMID: 24024591]
  45. PLoS One. 2011 Apr 13;6(4):e18476 [PMID: 21533231]
  46. Mol Inform. 2017 Jan;36(1-2): [PMID: 28124834]
  47. Nature. 2002 Jan 24;415(6870):389-95 [PMID: 11807545]
  48. J Mol Biol. 2010 Sep 10;402(1):139-53 [PMID: 20655315]
  49. Curr Opin Solid State Mater Sci. 2013 Aug;17(4):151-163 [PMID: 24778573]
  50. FEMS Microbiol Lett. 1998 Mar 1;160(1):91-6 [PMID: 9495018]
  51. FEBS Lett. 2010 May 3;584(9):1806-13 [PMID: 19925791]
  52. Nat Rev Immunol. 2003 Sep;3(9):710-20 [PMID: 12949495]
  53. Phys Rev Lett. 2004 May 14;92(19):198304 [PMID: 15169456]
  54. Biophys J. 2001 Oct;81(4):2203-14 [PMID: 11566791]
  55. Antimicrob Agents Chemother. 2001 Oct;45(10):2838-44 [PMID: 11557478]
  56. Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7781-6 [PMID: 20385839]
  57. Biochem J. 1993 Aug 15;294 ( Pt 1):1-14 [PMID: 8363559]
  58. FEMS Microbiol Lett. 2002 Jan 10;206(2):143-9 [PMID: 11814654]
  59. J Pept Sci. 2011 May;17(5):298-305 [PMID: 21480436]
  60. Angew Chem Int Ed Engl. 2008;47(16):2986-9 [PMID: 18338358]
  61. Nucleic Acids Res. 2009 Jan;37(Database issue):D933-7 [PMID: 18957441]
  62. J Am Chem Soc. 2013 Sep 18;135(37):13710-9 [PMID: 23962302]
  63. J Biomol NMR. 1991 Jul;1(2):167-73 [PMID: 1726781]
  64. J Biol Chem. 1992 Mar 5;267(7):4292-5 [PMID: 1537821]
  65. Nat Rev Mol Cell Biol. 2008 Feb;9(2):112-24 [PMID: 18216768]
  66. Chem Phys Lipids. 2015 Jan;185:11-45 [PMID: 24835737]
  67. Proteins. 2008 Nov 1;73(2):420-30 [PMID: 18442133]
  68. Biochemistry. 1996 Sep 24;35(38):12612-22 [PMID: 8823199]
  69. FEBS Lett. 1997 Feb 17;403(2):208-12 [PMID: 9042968]
  70. Biochim Biophys Acta. 1999 Dec 15;1462(1-2):71-87 [PMID: 10590303]
  71. Antimicrob Agents Chemother. 1998 Jan;42(1):154-60 [PMID: 9449277]
  72. J Am Chem Soc. 2012 Feb 8;134(5):2613-20 [PMID: 22211521]
  73. Nature. 2007 Oct 4;449(7162):564-9 [PMID: 17873860]
  74. Biochemistry. 2002 Aug 6;41(31):9852-62 [PMID: 12146951]
  75. PLoS One. 2011 Feb 09;6(2):e16968 [PMID: 21347392]
  76. Phys Rev Lett. 1988 May 9;60(19):1966-1969 [PMID: 10038189]
  77. Antimicrob Agents Chemother. 2001 Nov;45(11):3256-61 [PMID: 11600395]
  78. Biophys J. 2004 Jul;87(1):366-74 [PMID: 15240471]
  79. BMC Bioinformatics. 2007 Jul 23;8:263 [PMID: 17645800]
  80. Macromolecules. 2013;46(5):1908-1915 [PMID: 23750051]
  81. Biopolymers. 1995;37(5):319-38 [PMID: 7632881]
  82. J Am Chem Soc. 2012 Nov 21;134(46):19207-16 [PMID: 23061419]
  83. Biochim Biophys Acta. 2014 Sep;1838(9):2250-9 [PMID: 24853655]
  84. Science. 2012 Jun 1;336(6085):1157-60 [PMID: 22539553]
  85. Biophys J. 2001 Sep;81(3):1475-85 [PMID: 11509361]
  86. J Biol Chem. 2012 Jun 22;287(26):21866-72 [PMID: 22566697]
  87. Anal Biochem. 2013 May 15;436(2):168-77 [PMID: 23395824]
  88. Nucleic Acids Res. 2013 Jan;41(Database issue):D524-9 [PMID: 23203988]
  89. PLoS Comput Biol. 2013;9(9):e1003212 [PMID: 24039565]
  90. J Biol Chem. 2008 Nov 21;283(47):32637-43 [PMID: 18818205]
  91. FEBS Lett. 1999 Apr 1;448(1):62-6 [PMID: 10217411]
  92. J Biomol NMR. 1997 Feb;9(2):127-35 [PMID: 9090128]
  93. Nat Biotechnol. 2006 Dec;24(12):1551-7 [PMID: 17160061]
  94. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D590-2 [PMID: 14681488]
  95. Clin Infect Dis. 2005 May 1;40(9):1333-41 [PMID: 15825037]
  96. Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10926-31 [PMID: 26283363]
  97. Bacteriol Rev. 1957 Dec;21(4):273-94 [PMID: 13488885]
  98. J Am Chem Soc. 2010 Jan 13;132(1):195-201 [PMID: 20000420]
  99. Antimicrob Agents Chemother. 2002 Mar;46(3):605-14 [PMID: 11850238]
  100. Proc Natl Acad Sci U S A. 2005 Aug 9;102(32):11167-72 [PMID: 16055561]
  101. Biochemistry. 1997 Oct 21;36(42):12869-80 [PMID: 9335545]
  102. Biochemistry. 2004 Mar 30;43(12):3590-9 [PMID: 15035629]
  103. Science. 1998 Jul 3;281(5373):78-81 [PMID: 9651248]
  104. Proc Natl Acad Sci U S A. 2003 May 27;100(11):6302-7 [PMID: 12738879]
  105. Pharmacol Rev. 2003 Mar;55(1):27-55 [PMID: 12615953]
  106. Biochemistry. 1997 May 20;36(20):6124-32 [PMID: 9166783]
  107. Science. 1974 Sep 6;185(4154):862-4 [PMID: 4843792]
  108. Bioorg Med Chem. 2017 Jul 8;:null [PMID: 28728899]
  109. Proteins. 1990;8(2):103-17 [PMID: 2235991]
  110. Curr Biol. 2016 Jan 11;26(1):R14-9 [PMID: 26766224]
  111. J Med Chem. 2009 Apr 9;52(7):2006-15 [PMID: 19296598]
  112. Nat Rev Microbiol. 2005 Mar;3(3):238-50 [PMID: 15703760]
  113. J Biol Chem. 1995 Jan 20;270(3):1048-56 [PMID: 7836358]
  114. PLoS Comput Biol. 2015 Apr 07;11(4):e1004074 [PMID: 25849257]
  115. J Am Chem Soc. 2007 Oct 10;129(40):12141-7 [PMID: 17880067]

Grants

  1. T32 GM008185/NIGMS NIH HHS
Journal Article Review
Article has an altmetric score of 1

Word Cloud

Created with Highcharts 10.0.0peptidesmachineAMPslearningAMPcanmembraneantimicrobialdiscussdesignnewidentifypeptidecurvatureAntimicrobialdiverseclasswell-studiedmembrane-permeatingimportantfunctionsinnatehostdefenseshortreviewprovidehistoricaloverviewsummarizepreviousapplicationsresultsstudiescontextlatestliteratureMuchworkrecentlydoneleveragingcomputationaltoolscandidateshightherapeuticefficaciesdrug-resistantinfectionsshowusedessentialphysico-chemicaldeterminantsfunctionalitysequencesgeneratebroaderscopeimplicationsfindingsdiscoverymembrane-activegeneraluncoveringactivityexistingtaxonomieslearning?amphiphilic

Similar Articles

Cited By