A Review of Methods and Progress in Highly Efficient Screening of Antimicrobial Peptides from Natural Products
-
摘要: 面对耐药病原体的挑战，天然抗微生物肽（Antimicrobial peptide，AMP）成为了开发新一代抗菌候选药物的重要来源之一，在食品、农业等领域同样有着广泛的应用。然而，从天然产物中快速筛选获得抗微生物肽仍然存在着低效、高耗等种种困难与挑战。本文首先介绍了抗微生物肽的作用机制（包括膜作用机制与非膜作用机制）；然后重点综述了AMP的高效筛选方法，包括整体细菌吸附结合法、细胞膜色谱法、磷脂膜色谱法、毛细管电泳法、比色法、薄层色谱法、荧光筛选法、高通量测序法和数据库挖掘法等；此外，展望了高效发掘抗微生物肽的发展方向。本论文为从纷繁复杂的天然产物体系中发现抗微生物肽提供了可参考的科学依据。Abstract: Natural antimicrobial peptides (AMPs) are promising candidates for developing a generation of new antimicrobials to meet the challenge of antibiotic-resistant pathogens, and they are extensively applied in medicine, food, agriculture and other fields. However, the rapid screening of AMPs from natural products still has many difficulties and challenges, such as low efficiency and high consumption. This paper firstly introduces the action mechanism of AMPs (including membrane action mechanism and non-membrane action mechanism); then, the highly efficient screening methods of AMP are systematically reviewed, including bacterial adsorption, cell membrane chromatography, phospholipid membrane chromatography, capillary electrophoresis, colorimetry, thin layer chromatography, fluorescence screening, high-throughput sequencing, and mining databases screening. In addition, the development direction of efficient exploration of AMP is also prospected. This paper provides a scientific basis for the discovery of AMPs from complex natural product systems.
-
表 1 AMP的高效筛选方法的汇总与比较
Table 1. Summary and comparison of efficient screening methods for AMP
筛选方法 AMP来源 筛选的AMP 整体细菌吸附结合法 废耗牛奶；
大鲵的血液Arg-Val-Met-Phe-Lys-Trp-Ala和Lys-Val-Ile-Ser-Met-Ile[33]；
andricin B[34]细胞膜色谱法 麻风树粕蛋白籽粕；鳀鱼提取物 JCpep7[35]；Apep10[36] 磷脂膜色谱法 卵蛋白水解物 Opep12[37] 毛细管电泳法 12条已知序列的阳离子AMP化合物
大白蛉幼虫血淋巴提取物HAL系列和HYL系列AMP[38]；
二肽 β-丙氨酰酪氨酸（β-Ala-Tyr）[39]比色法 磷脂和聚合二乙炔脂质组成的囊泡；亚洲海洋蛤蜊 K7L-毒蜂肽和W19-毒蜂肽[40]；Perinerin[41] 薄层色谱法 自行合成的10条粗肽 CAMEL和脂肽PAL-KK-NH2、Pal-KGK-NH2[42] 荧光筛选法 群居性蜜蜂（Lasioglossum laticeps）的毒液；
β-半乳糖苷酶Lasioglossin LL-III[43]；
肽GKH175W和KNK5W[44]高通量测序法 两栖类涂鱼 血红蛋白β1和淀粉样蛋白[45] 数据库挖掘法 AMP数据库；
牛乳肽数据库；
Fish-T1K数据库DASamP1[46]、
乳源AMP[47]、
小免疫肽[48]
下载: 导出CSV
-
[1] KAHN L H. Antimicrobial resistance: A one health perspective[J]. Transactions of the Royal Society of Tropical Medicine and Hygiene,2017,111(6):255−260. doi: 10.1093/trstmh/trx050 [2] TANGCHAROENSATHIEN V, SATTAYAWUTTHIPONG W, KANJANAPIMAI S, et al. Antimicrobial resistance: From global agenda to national strategic plan, Thailand[J]. Bulletin of the World Health Organization,2017,95(8):599−603. doi: 10.2471/BLT.16.179648 [3] CHELLAT M F, RAGUZ L, RIEDL R. Targeting antibiotic resistance[J]. Angewandte Chemie-International Edition,2016,55(23):6600−6626. doi: 10.1002/anie.201506818 [4] SMITH P A, KOEHLER M F T, GIRGIS H S, et al. Optimized arylomycins are a new class of gram-negative antibiotics[J]. Nature,2018,561(7722):189−194. doi: 10.1038/s41586-018-0483-6 [5] ATHANASIOU C I, KOPSINI A. Systematic review of the use of time series data in the study of antimicrobial consumption and Pseudomonas aeruginosa resistance[J]. Journal of Global Antimicrobial Resistance,2018,15:69−73. doi: 10.1016/j.jgar.2018.06.001 [6] SABATIER J-M. Antibacterial peptides[J]. Antibiotics-Basel,2020,9(4):142. doi: 10.3390/antibiotics9040142 [7] WANG G. Human antimicrobial peptides and proteins[J]. Pharmaceuticals (Basel, Switzerland),2014,7(5):545−594. doi: 10.3390/ph7050545 [8] BOPARAI J K, SHARMA P K. Mini review on antimicrobial peptides, sources, mechanism and recent applications[J]. Protein and Peptide Letters,2020,27(1):4−16. doi: 10.2174/18755305MTAwENDE80 [9] CORTES-PENFIELD N, OLIVER N T, HUNTER A, et al. Daptomycin and combination daptomycin-ceftaroline as salvage therapy for persistent methicillin-resistant Staphylococcus aureus bacteremia[J]. Infectious Diseases,2018,50(8):643−647. doi: 10.1080/23744235.2018.1448110 [10] NG S M S, TEO S W, YONG Y E, et al. Preliminary investigations into developing all-D Omiganan for treating mupirocin-resistant MRSA skin infections[J]. Chemical Biology & Drug Design,2017,90(6):1155−1160. [11] LAMB H M, WISEMAN L R. Pexiganan acetate[J]. Drugs,1998,56(6):1047−1052. doi: 10.2165/00003495-199856060-00011 [12] CIOCIOLA T, GIOVATI L, CONTI S, et al. Natural and synthetic peptides with antifungal activity[J]. Future Medicinal Chemistry,2016,8(12):1413−1433. doi: 10.4155/fmc-2016-0035 [13] DEMIRCI H, MURPHY F, MURPHY E, et al. A structural basis for streptomycin-induced misreading of the genetic code[J]. Nature Communications,2013,4:1355−1355. doi: 10.1038/ncomms2346 [14] HULTMARK D, STEINER H, RASMUSON T, et al. Insect immunity. Purification and prosperities of three inducible bactericidal proteins from hemolymph of immunized pupae of Hyalophora cecropia[J]. European Journal of Biochemistry,1980,106:7−16. [15] PRASHANTH J R, HASABALLAH N, VETTER I. Pharmacological screening technologies for venom peptide discovery[J]. Neuropharmacology,2017,127:4−19. doi: 10.1016/j.neuropharm.2017.03.038 [16] NGUYEN L T, HANEY E F, VOGEL H J. The expanding scope of antimicrobial peptide structures and their modes of action[J]. Trends in Biotechnology,2011,29(9):464−472. doi: 10.1016/j.tibtech.2011.05.001 [17] CIUMAC D, GONG H, HU X, et al. Membrane targeting cationic antimicrobial peptides[J]. Journal of Colloid and Interface Science,2019,537:163−185. doi: 10.1016/j.jcis.2018.10.103 [18] XHINDOLI D, PACOR S, BENINCASA M, et al. The human cathelicidin LL-37A pore-forming antibacterial peptide and host-cell modulator[J]. Biochimica Et Biophysica Acta-Biomembranes,2016,1858(3):546−566. doi: 10.1016/j.bbamem.2015.11.003 [19] BERGEN G, STROET M, CARON B, et al. Curved or linear? Predicting the 3-dimensional structure of α-helical antimicrobial peptides in an amphipathic environment[J]. FEBS Letters,2020:594. [20] YANG L, HARROUN T A, WEISS T M, et al. Barrel-stave model or toroidal model? A case study on melittin pores[J]. Biophysical Journal,2001,81(3):1475−1485. doi: 10.1016/S0006-3495(01)75802-X [21] MIHAJLOVIC M, LAZARIDIS T. Antimicrobial peptides in toroidal and cylindrical pores[J]. Biophysical Journal,2010,98(3):281A−281A. [22] SENGUPTA D, LEONTIADOU H, MARK A E, et al. Toroidal pores formed by antimicrobial peptides show significant disorder[J]. Biochimica Et Biophysica Acta-Biomembranes,2008,1778(10):2308−2317. doi: 10.1016/j.bbamem.2008.06.007 [23] REDDY K V R, YEDERY R D, ARANHA C. Antimicrobial peptides: Premises and promises[J]. International Journal of Antimicrobial Agents,2004,24(6):536−547. doi: 10.1016/j.ijantimicag.2004.09.005 [24] TEIXEIRA V, FEIO M J, BASTOS M. Role of lipids in the interaction of antimicrobial peptides with membranes[J]. Progress in Lipid Research,2012,51(2):149−177. doi: 10.1016/j.plipres.2011.12.005 [25] DAVID P, JAVIER A T, GUILLEM P E, et al. Insights into the antimicrobial mechanism of action of human RNase6: Structural determinants for bacterial cell agglutination and membrane permeation[J]. International Journal of Molecular Sciences,2016,17(4):552. doi: 10.3390/ijms17040552 [26] SINHA S, ZHENG L, MU Y, et al. Structure and interactions of a host defense antimicrobial peptide thanatin in lipopolysaccharide micelles reveal mechanism of bacterial cell agglutination[J]. Scientific Reports,2017,7:17795. doi: 10.1038/s41598-017-18102-6 [27] BROGDEN K A. Antimicrobial peptides: Pore formers or metabolic inhibitors in bacteria?[J]. Nature Reviews Microbiology,2005,3(3):238−250. doi: 10.1038/nrmicro1098 [28] KRAGOL G, LOVAS S, VARADI G, et al. The antibacterial peptide pyrrhocoricin inhibits the ATPase actions of DnaK and prevents chaperone-assisted protein folding[J]. Biochemistry,2001,40(10):3016−3026. doi: 10.1021/bi002656a [29] UYTERHOEVEN E T, BUTLER C H, KO D, et al. Investigating the nucleic acid interactions and antimicrobial mechanism of buforin II[J]. Febs Letters,2008,582(12):1715−1718. doi: 10.1016/j.febslet.2008.04.036 [30] WU G, FAN X, LI L, et al. Interaction of antimicrobial peptide S-thanatin with lipopolysaccharide in vitro and in an experimental mouse model of septic shock caused by a multidrug-resistant clinical isolate of Escherichia coli[J]. International Journal of Antimicrobial Agents,2010,35(3):250−254. doi: 10.1016/j.ijantimicag.2009.11.009 [31] CHEN X, LI L. Non-membrane mechanisms of antimicrobial peptide P7 against Escherichia coli[J]. Acta Microbiologica Sinica,2016,56(11):1737−1745. [32] TUCKER A T, LEONARD S P, DUBOIS C D, et al. Discovery of next-generation antimicrobials through bacterial self-screening of surface-displayed peptide libraries[J]. Cell,2018,172(3):618. doi: 10.1016/j.cell.2017.12.009 [33] PEI J J, JIANG H, LI X S, et al. Antimicrobial peptides sourced from post-butter processing waste yak milk protein hydrolysates[J]. Amb Express,2017,7:217. doi: 10.1186/s13568-017-0497-8 [34] PEI J, FENG Z, REN T, et al. Purification, characterization and application of a novel antimicrobial peptide from Andrias davidianus blood[J]. Letters in Applied Microbiology,2018,66(1):38−43. doi: 10.1111/lam.12823 [35] XIAO J, ZHANG H, NIU L, et al. Efficient screening of a novel antimicrobial peptide from Jatropha curcas by cell membrane affinity chromatography[J]. Journal of Agricultural and Food Chemistry,2011,59(4):1145−1151. doi: 10.1021/jf103876b [36] TANG W, ZHANG H, WANG L, et al. New cationic antimicrobial peptide screened from boiled-dried anchovies by immobilized bacterial membrane liposome chromatography[J]. Journal of Agricultural and Food Chemistry,2014,62(7):1564−1571. doi: 10.1021/jf4052286 [37] TANG W T, ZHANG H, WANG L, et al. Antimicrobial peptide isolated from ovalbumin hydrolysate by immobilized liposome-binding extraction[J]. European Food Research and Technology,2013,237(4):591−600. doi: 10.1007/s00217-013-2034-6 [38] TŮMOVÁ T, MONINCOVÁ L, NEŠUTA O, et al. Determination of effective charges and ionic mobilities of polycationic antimicrobial peptides by capillary isotachophoresis and capillary zone electrophoresis[J]. Electrophoresis,2017,38(16):2018−2024. doi: 10.1002/elps.201700092 [39] ŠOLÍNOVÁ V, SÁZELOVÁ P, MÁŠOVÁ A. Application of capillary and free-flow zone electrophoresis for analysis and purification of antimicrobial β-alanyl-tyrosine from hemolymph of fleshfly Neobellieria bullata[J]. Molecules,2021,26(18):5636. doi: 10.3390/molecules26185636 [40] KOLUSHEVA S, BOYER L, JELINEK R. A colorimetric assay for rapid screening of antimicrobial peptides[J]. Nature Biotechnology,2000,18(2):225−227. doi: 10.1038/72697 [41] PAN W D, LIU X H, GE F, et al. Perinerin, a novel antimicrobial peptide purified from the clamworm Perinereis aibuhitensis Grube and its partial characterization[J]. Journal of Biochemistry,2004,135(3):297−304. doi: 10.1093/jb/mvh036 [42] JASKIEWICZ M, ORLOWSKA M, OLIZAROWICZ G, et al. Rapid screening of antimicrobial synthetic peptides[J]. International Journal of Peptide Research and Therapeutics,2016,22(2):155−161. doi: 10.1007/s10989-015-9494-4 [43] KODEDOVA M, SYCHROVA H. High-throughput fluorescence screening assay for the identification and comparison of antimicrobial peptides' activity on various yeast species[J]. Journal of Biotechnology,2016,233:26−33. doi: 10.1016/j.jbiotec.2016.06.023 [44] THIRUMALAI M K, ROY A, SANIKOMMU S, et al. A simple, robust enzymatic-based high throughput screening method for antimicrobial peptides discovery against Escherichia coli[J]. Journal of Peptide Science,2014,20(5):341−348. doi: 10.1002/psc.2619 [45] YI Y, YOU X, BIAN C, et al. High-throughput identification of antimicrobial peptides from amphibious mudskippers[J]. Marine Drugs,2017,15(11):364. doi: 10.3390/md15110364 [46] MENOUSEK J, MISHRA B, HANKE M L, et al. Database screening and in vivo efficacy of antimicrobial peptides against methicillin-resistant Staphylococcus aureus USA300[J]. International Journal of Antimicrobial Agents,2012,39(5):402−406. doi: 10.1016/j.ijantimicag.2012.02.003 [47] LIU Y, EICHLER J, PISCHETSRIEDER M. Virtual screening of a milk peptide database for the identification of food-derived antimicrobial peptides[J]. Molecular Nutrition & Food Research,2015,59(11):2243−2254. [48] YI Y, LÜ Y, YOU X, et al. High throughput screening of small immune peptides and antimicrobial peptides from the fish-T1K database[J]. Genomics,2019,111(3):215−221. doi: 10.1016/j.ygeno.2018.11.023 [49] RAMYA M S, SIVASUBRAMANIAN K, RAVICHANDRAN S, et al. Screening of antimicrobial compound from the sea slug Armina babai[J]. Bangladesh Journal of Pharmacology,2014,9(3):268−274. [50] LEE W, LEE D G. Fungicidal mechanisms of the antimicrobial peptide Bac8c[J]. Biochimica Et Biophysica Acta-Biomembranes,2015,1848(2):673−679. doi: 10.1016/j.bbamem.2014.11.024 [51] ZIETEK B M, KBM S, JASCHUSCH K, et al. Identification of antimicrobial peptides from the human gut microbiome using deep learning[J]. Nature Biotechnology,2022,40:838−839. doi: 10.1038/s41587-022-01230-4 [52] MARIJA, MLADIC, BARBARA M, et al. At-line nanofractionation with parallel mass spectrometry and bioactivity assessment for the rapid screening of thrombin and factor Xa inhibitors in snake venoms[J]. Toxicon: Official Journal of the International Society on Toxinology,2016,110:79−89. doi: 10.1016/j.toxicon.2015.12.008 [53] OTVOS R A, VAN NIEROP P, NIESSEN W M A, et al. Development of an online cell-based bioactivity screening method by coupling liquid chromatography to flow cytometry with parallel mass spectrometry[J]. Analytical Chemistry,2016,88(9):4825−4832. doi: 10.1021/acs.analchem.6b00455 [54] XIE C, ALBULESCU L, BITTENBINDER M A, et al. Neutralizing effects of small molecule inhibitors and metal chelators on coagulopathic Viperinae snake venom toxins[J]. Cold Spring Harbor Laboratory,2020(9):129643. [55] ZIETEK B M, KBM S, JASCHUSCH K, et al. Bioactivity profiling of small-volume samples by nano liquid chromatography coupled to microarray bioassaying using high-resolution fractionation[J]. Analytical Chemistry,2019,91(16):10458−10466. doi: 10.1021/acs.analchem.9b01261 [56] MLADIC M, SLAGBOOM J, KOOL J, et al. Detection and identification of antibacterial proteins in snake venoms using at-line nanofractionation coupled to LC-MS[J]. Toxicon,2018:155. -
点击查看大图
图(1) / 表(1)
计量
- 文章访问数: 75
- HTML全文浏览量: 11
- PDF下载量: 21
- 被引次数: 0
