1
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Tsai CT, Lin CW, Ye GL, Wu SC, Yao P, Lin CT, Wan L, Tsai HHG. Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models. ACS OMEGA 2024; 9:9357-9374. [PMID: 38434814 PMCID: PMC10905719 DOI: 10.1021/acsomega.3c08676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024]
Abstract
The escalating menace of multidrug-resistant (MDR) pathogens necessitates a paradigm shift from conventional antibiotics to innovative alternatives. Antimicrobial peptides (AMPs) emerge as a compelling contender in this arena. Employing in silico methodologies, we can usher in a new era of AMP discovery, streamlining the identification process from vast candidate sequences, thereby optimizing laboratory screening expenditures. Here, we unveil cutting-edge machine learning (ML) models that are both predictive and interpretable, tailored for the identification of potent AMPs targeting World Health Organization's (WHO) high-priority pathogens. Furthermore, we have developed ML models that consider the hemolysis of human erythrocytes, emphasizing their therapeutic potential. Anchored in the nuanced physical-chemical attributes gleaned from the three-dimensional (3D) helical conformations of AMPs, our optimized models have demonstrated commendable performance-boasting an accuracy exceeding 75% when evaluated against both low-sequence-identified peptides and recently unveiled AMPs. As a testament to their efficacy, we deployed these models to prioritize peptide sequences stemming from PEM-2 and subsequently probed the bioactivity of our algorithm-predicted peptides vis-à-vis WHO's priority pathogens. Intriguingly, several of these new AMPs outperformed the native PEM-2 in their antimicrobial prowess, thereby underscoring the robustness of our modeling approach. To elucidate ML model outcomes, we probe via Shapley Additive exPlanations (SHAP) values, uncovering intricate mechanisms guiding diverse actions against bacteria. Our state-of-the-art predictive models expedite the design of new AMPs, offering a robust countermeasure to antibiotic resistance. Our prediction tool is available to the public at https://ai-meta.chem.ncu.edu.tw/amp-meta.
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Affiliation(s)
- Cheng-Ting Tsai
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Chia-Wei Lin
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Gen-Lin Ye
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Shao-Chi Wu
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Philip Yao
- Aurora
High School, 109 W Pioneer Trail, Aurora, Ohio 44202, United States
| | - Ching-Ting Lin
- School
of Chinese Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Lei Wan
- School
of Chinese Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Hui-Hsu Gavin Tsai
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
- Research
Center of New Generation Light Driven Photovoltaic Modules, National Central University, Taoyuan 32001, Taiwan
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2
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He S, Yang Z, Li X, Wu H, Zhang L, Shan A, Wang J. Boosting stability and therapeutic potential of proteolysis-resistant antimicrobial peptides by end-tagging β-naphthylalanine. Acta Biomater 2023; 164:175-194. [PMID: 37100185 DOI: 10.1016/j.actbio.2023.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/16/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Recently, much emphasis has been placed on solving the intrinsic defects of antimicrobial peptides (AMPs), especially their susceptibility to protease digestion for the systemic application of antibacterial biomaterials. Although many strategies have increased the protease stability of AMPs, antimicrobial activity was severely compromised, thereby substantially weakening their therapeutic effect. To address this issue, we introduced hydrophobic group modifications at the N-terminus of proteolysis-resistant AMPs D1 (AArIIlrWrFR) through end-tagging with stretches of natural amino acids (W and I), unnatural amino acid (Nal) and fatty acids. Of these peptides, N1 tagged with a Nal at N-terminus showed the highest selectivity index (GMSI = 19.59), with a 6.73-fold improvement over D1. In addition to potent broad-spectrum antimicrobial activity, N1 also exhibited high antimicrobial stability toward salts, serum and proteases in vitro and ideal biocompatibility and therapeutic efficacy in vivo. Furthermore, N1 killed bacteria through multiple mechanisms, involving disruption of bacterial membranes and inhibition of bacterial energy metabolism. Indeed, appropriate terminal hydrophobicity modification opens up new avenues for developing and applying high-stability peptide-based antibacterial biomaterials. STATEMENT OF SIGNIFICANCE: To improve the potency and stability of proteolysis-resistant antimicrobial peptides (AMPs) without increasing toxicity, we constructed a convenient and tunable platform based on different compositions and lengths of hydrophobic end modifications. By tagging an Nal at the N-terminal, the obtained target compound N1 exhibited strong antimicrobial activity and desirable stability under multifarious environments in vitro (protease, salts and serum), and also showed favorable biocompatibility and therapeutic efficacy in vivo. Notably, N1exerted its bactericidal effect by damaging bacterial cell membranes and inhibiting bacterial energy metabolism in a dual mode. The findings provide a potential method for designing or optimizing proteolysis-resistant AMPs thus promoting the development and application of peptide-based antibacterial biomaterial.
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Affiliation(s)
- Shiqi He
- Animal Science and Technology College, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Zhanyi Yang
- Animal Science and Technology College, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Xuefeng Li
- Animal Science and Technology College, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Hua Wu
- Animal Science and Technology College, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Licong Zhang
- Animal Science and Technology College, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Anshan Shan
- Animal Science and Technology College, Northeast Agricultural University, Harbin 150030, P. R. China.
| | - Jiajun Wang
- Animal Science and Technology College, Northeast Agricultural University, Harbin 150030, P. R. China.
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3
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Lomonte B. Lys49 myotoxins, secreted phospholipase A 2-like proteins of viperid venoms: A comprehensive review. Toxicon 2023; 224:107024. [PMID: 36632869 DOI: 10.1016/j.toxicon.2023.107024] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Abstract
Muscle necrosis is a potential clinical complication of snakebite envenomings, which in severe cases can lead to functional or physical sequelae such as disability or amputation. Snake venom proteins with the ability to directly damage skeletal muscle fibers are collectively referred to as myotoxins, and include three main types: cytolysins of the "three-finger toxin" protein family expressed in many elapid venoms, the so-called "small" myotoxins found in a number of rattlesnake venoms, and the widespread secreted phospholipase A2 (sPLA2) molecules. Among the latter, protein variants that conserve the sPLA2 structure, but lack such enzymatic activity, have been increasingly found in the venoms of many viperid species. Intriguingly, these sPLA2-like proteins are able to induce muscle necrosis by a mechanism independent of phospholipid hydrolysis. They are commonly referred to as "Lys49 myotoxins" since they most often present, among other substitutions, the replacement of the otherwise invariant residue Asp49 of sPLA2s by Lys. This work comprehensively reviews the historical developments and current knowledge towards deciphering the mechanism of action of Lys49 sPLA2-like myotoxins, and points out main gaps to be filled for a better understanding of these multifaceted snake venom proteins, to hopefully lead to improved treatments for snakebites.
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Affiliation(s)
- Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, 11501, Costa Rica.
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4
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Zhang F, Yang P, Mao W, Zhong C, Zhang J, Chang L, Wu X, Liu H, Zhang Y, Gou S, Ni J. Short, mirror-symmetric antimicrobial peptides centered on "RRR" have broad-spectrum antibacterial activity with low drug resistance and toxicity. Acta Biomater 2022; 154:145-167. [PMID: 36241015 DOI: 10.1016/j.actbio.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/31/2022] [Accepted: 10/03/2022] [Indexed: 12/14/2022]
Abstract
The increasingly severe bacterial resistance worldwide pushes people to discover and design potential antibacterial drugs unavoidably. In this work, a series of short, mirror-symmetric peptides were designed and successfully synthesized, centered on "RRR" and labeled with hydrophobic amino acids at both ends. Based on the structure-activity relationship analysis, LWWR (LWWRRRWWL-NH2) was screened as a desirable mirror-symmetric peptide for further study. As expected, LWWR displayed broad-spectrum antibacterial activity against the standard bacteria and antibiotic-resistant strains. Undoubtedly, the high stability of LWWR in a complex physiological environment was an essential guarantee to maximizing its antibacterial activity. Indeed, LWWR also exhibited a rapid bactericidal speed and a low tendency to develop bacterial resistance, based on the multiple actions of non-receptor-mediated membrane actions and intra-cellular mechanisms. Surprisingly, although LWWR showed similar in vivo antibacterial activity compared with Polymyxin B and Melittin, the in vivo safety of LWWR was far higher than that of them, so LWWR had better therapeutic potential. In summary, the desirable mirror-symmetric peptide LWWR was promised as a potential antibacterial agent to confront the antibiotics resistance crisis. STATEMENT OF SIGNIFICANCE: Witnessing the growing problem of antibiotic resistance, a series of short, mirror-symmetric peptides based on the symmetric center "RRR" and hydrophobic terminals were designed and synthesized in this study. Among, LWWR (LWWRRRWWL-NH2) presented broad-spectrum antibacterial activity both in vitro and in vivo due to its multiple mechanisms and good stability. Meanwhile, the low drug resistance and toxicity of LWWR also suggested its potential for clinical application. The findings of this study will provide some inspiration for the design and development of potential antibacterial agents, and contribute to the elimination of bacterial infections worldwide as soon as possible.
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Affiliation(s)
- Fangyan Zhang
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Ping Yang
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Wenbo Mao
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Chao Zhong
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Jingying Zhang
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Linlin Chang
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xiaoyan Wu
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hui Liu
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yun Zhang
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Sanhu Gou
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Jingman Ni
- Institute of Materia Medica and Research Unit of Peptide Science, 2019RU066, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1 Xian Nong Tan Street, Beijing 100050, P. R. China; Institute of Pharmaceutics, School of Pharmacy and Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China.
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5
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Antimicrobial characterization of a titanium coating derived from mussel-glue and Bothrops asper snake venom for the prevention of implant-associated infections caused by Staphylococcus. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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6
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Wu CL, Peng KL, Yip BS, Chih YH, Cheng JW. Boosting Synergistic Effects of Short Antimicrobial Peptides With Conventional Antibiotics Against Resistant Bacteria. Front Microbiol 2021; 12:747760. [PMID: 34733262 PMCID: PMC8558513 DOI: 10.3389/fmicb.2021.747760] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023] Open
Abstract
The global spread of antibiotic-resistant infections has meant that there is an urgent need to develop new antimicrobial alternatives. In this study, we developed a strategy to boost and/or synergize the activity of conventional antibiotics by combination with antimicrobial peptides tagged with the bulky non-natural amino acid β-naphthylalanine (Nal) to their N- or C-terminus. A checkerboard method was used to evaluate synergistic effects of the parent peptide and the Nal-tagged peptides. Moreover, boron-dipyrro-methene labeled vancomycin was used to characterize the synergistic mechanism of action between the peptides and vancomycin on the bacterial strains. These Nal-tagged antimicrobial peptides also reduced the antibiotic-induced release of lipopolysaccharide from Gram-negative bacteria by more than 99.95%. Our results demonstrate that Nal-tagged peptides could help in developing antimicrobial peptides that not only have enhanced antibacterial activities but also increase the synergistic effects with conventional antibiotics against antibiotic-resistant bacteria.
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Affiliation(s)
- Chih-Lung Wu
- Department of Medical Science, Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Kuang-Li Peng
- Department of Medical Science, Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Bak-Sau Yip
- Department of Medical Science, Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Neurology, National Taiwan University Hospital Hsinchu Branch, Hsinchu, Taiwan
| | - Ya-Han Chih
- Department of Medical Science, Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jya-Wei Cheng
- Department of Medical Science, Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
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7
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Zhong C, Zhang F, Yao J, Zhu Y, Zhu N, Zhang J, Ouyang X, Zhang T, Li B, Xie J, Ni J. New Antimicrobial Peptides with Repeating Unit against Multidrug-Resistant Bacteria. ACS Infect Dis 2021; 7:1619-1637. [PMID: 33829758 DOI: 10.1021/acsinfecdis.0c00797] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the aim of tackling the increasingly serious antimicrobial resistance and improving the clinical potential of AMPs, a facile de novo strategy was adopted in this study, and a series of new peptides comprising repeating unit (WRX)n (X represents I, L, F, W, and K; n = 2, 3, 4, or 5) and amidation at C-terminus were designed. Most of the newly designed peptides exhibited a broad range of excellent antimicrobial activities against various bacteria, especially difficult-to-kill multidrug-resistant bacteria clinical isolates. Among (WRK)4 and (WRK)5, with n = 4 and n = 5 of repeating unit WRK, the highest selectivity for anionic bacterial membranes over a zwitterionic mammalian cell membrane is presented with strong antimicrobial potential and low toxicity. Additionally, both (WRK)4 and (WRK)5 emerged with fast killing speed and low tendency of resistance in sharp contrast to the conventional antibiotics ciprofloxacin, gentamicin, and imipenem, as well as having antimicrobial activity through multiple mechanisms including a membrane-disruptive mechanism and an intramolecular mechanism (nucleic acid leakage, DNA binding and ROS generation) characterized by a series of assays. Furthermore, (WRK)4 exerted impressive therapeutic effects in vivo similarly to polymyxin B but displayed much lower toxicity in vivo than polymyxin B. Taken together, the newly designed peptides (WRK)4 and (WRK)5 presented tremendous potential as novel antimicrobial candidates in response to the growing antimicrobial resistance.
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Affiliation(s)
- Chao Zhong
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Fangyan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jia Yao
- The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Yuewen Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Ningyi Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jingying Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xu Ouyang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Tianyue Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Beibei Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Junqiu Xie
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jingman Ni
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao 999078, China
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8
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Zhong C, Zhang F, Yao J, Zhu Y, Zhu N, Zhang Y, Liu H, Gou S, Ni J. Antimicrobial peptides with symmetric structures against multidrug-resistant bacteria while alleviating antimicrobial resistance. Biochem Pharmacol 2021; 186:114470. [PMID: 33610592 DOI: 10.1016/j.bcp.2021.114470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/26/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022]
Abstract
In response to the dramatically increasing antimicrobial resistance, a series of new symmetric peptides were designed and synthesized in this study by a "WWW" motif as the symmetric center, arginine as the positive charge amino acid and the terminus symmetrically tagged with hydrophobic amino acids. Amongst the new symmetric peptide FRRW (FRRWWWRRF-NH2) presented the highest cell selectivity for bacteria over mammalian cell and exerted excellent antimicrobial potential against a broad of bacteria, especially difficult-to-kill multidrug-resistant strains clinical isolates. FRRW also displayed perfect stability in physiological salt ions and rapid killing speed as well as acted on multiple mechanisms including non-receptor mediated membrane and intra-molecular mechanisms. Importantly, FRRW emerged a low tendency of resistance in contrast to traditional antibiotics ciprofloxacin and gentamicin. What's more, FRRW could resist or alleviate or even reverse the ciprofloxacin- and gentamicin-resistance by changing the permeability of bacterial membrane and inhibiting the efflux pumps of bacteria. Furthermore, FRRW exhibited remarkable effectiveness and higher safety in vivo than polymyxin B. In summary, the new symmetric peptide FRRW was promised to be as a new antimicrobial candidate for overcoming the increasing bacterial resistance.
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Affiliation(s)
- Chao Zhong
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Fangyan Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jia Yao
- The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Yuewen Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Ningyi Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yun Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Hui Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Sanhu Gou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jingman Ni
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China; School of Pharmacy, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao 999078, China.
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9
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He S, Yang Z, Yu W, Li J, Li Z, Wang J, Shan A. Systematically Studying the Optimal Amino Acid Distribution Patterns of the Amphiphilic Structure by Using the Ultrashort Amphiphiles. Front Microbiol 2020; 11:569118. [PMID: 33324358 PMCID: PMC7725003 DOI: 10.3389/fmicb.2020.569118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/19/2020] [Indexed: 02/01/2023] Open
Abstract
Amphipathicity has traditionally been considered to be essential for the de novo design or systematic optimization of antimicrobial peptides (AMPs). However, the current research methods to study the relationship between amphiphilicity and antimicrobial activity are inappropriate, because the key parameters (hydrophobicity, positive charge, etc.) and secondary structure of AMPs are changed. To systematically and accurately study the effects of amphiphilicity on antimicrobial properties of AMPs, we designed parallel series of AMPs with a different order of amino acids in a sequence composed only of Arg and either Trp (WR series) or Leu (LR series), under conditions in which other vital parameters were fixed. Furthermore, based on the WR and LR peptides that can form stable amphiphilic β-sheet structures in the anionic membrane-mimetic environment, we found that high β-sheet amphipathic was accompanied by strong antimicrobial activity. Of such peptides, W5 ([RW]4W) and L5 ([RL]4L) with a nicely amphipathic β-sheet structure possessed the optimal therapeutic index. W5 and L5 also exhibited high stability in vitro and a potent membrane-disruptive mechanism. These results suggest that the alternate arrangement of hydrophobic and hydrophilic residues to form a stable amphipathic β-sheet structure is an essential factor that significantly affects the antimicrobial properties.
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Affiliation(s)
- Shiqi He
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Zhanyi Yang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Weikang Yu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Zhongyu Li
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Jiajun Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
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10
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Antimicrobial Peptides with Enhanced Salt Resistance and Antiendotoxin Properties. Int J Mol Sci 2020; 21:ijms21186810. [PMID: 32948086 PMCID: PMC7554977 DOI: 10.3390/ijms21186810] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/08/2020] [Accepted: 09/12/2020] [Indexed: 12/14/2022] Open
Abstract
A strategy was described to design antimicrobial peptides (AMPs) with enhanced salt resistance and antiendotoxin activities by linking two helical AMPs with the Ala-Gly-Pro (AGP) hinge. Among the designed peptides, KR12AGPWR6 demonstrated the best antimicrobial activities even in high salt conditions (NaCl ~300 mM) and possessed the strongest antiendotoxin activities. These activities may be related to hydrophobicity, membrane-permeability, and α-helical content of the peptide. Amino acids of the C-terminal helices were found to affect the peptide-induced permeabilization of LUVs, the α-helicity of the designed peptides under various LUVs, and the LPS aggregation and size alternation. A possible model was proposed to explain the mechanism of LPS neutralization by the designed peptides. These findings could provide a new approach for designing AMPs with enhanced salt resistance and antiendotoxin activities for potential therapeutic applications.
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11
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Chou S, Li Q, Nina Z, Shang L, Li J, Li J, Wang Z, Shan A. Peptides With Triplet-Tryptophan-Pivot Promoted Pathogenic Bacteria Membrane Defects. Front Microbiol 2020; 11:537. [PMID: 32328042 PMCID: PMC7160233 DOI: 10.3389/fmicb.2020.00537] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/12/2020] [Indexed: 02/05/2023] Open
Abstract
Development of probiotic-ineffective antimicrobial peptides (AMPs)-based coatings that can kill pathogenic bacteria at low concentrations but are essentially harmless (even high concentrations) to probiotic organisms is a relatively new trend for therapy against GI tract infections. In this study, a series of triplet-tryptophan-pivot peptides with various hydrophilic amino acids was constructed. One AMP in particular, S7, showed bactericidal activity against Staphylococcus epidermidis, Pseudomonas aeruginosa, Escherichia coli and antibiotic-resistant Staphylococcus aureus, yet was shown to be harmless to Lactobacillus rhamnosus, a key GI tract commensal. Furthermore, antibacterial mechanism assays, drug resistance assays, and mouse model tests suggested that S7 was useful in a clinical setting as it proved to significantly reduce bacterial load and cytokines (TNF-α, IL-6; P < 0.05) with a low probability of resistance via bacterial membrane physical destruction and formation of intracellular ROS. Combined, the results show that a triplet-tryptophan-pivot peptide containing a pair of serine residues was an excellent pathogen-selective candidate for medical devices and was potentially useful in food preservation, crop protection, and human health.
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Affiliation(s)
- Shuli Chou
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Qiuke Li
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Zaitseva Nina
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Lu Shang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Jinze Li
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Zhihua Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
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12
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Yang Z, He S, Wang J, Yang Y, Zhang L, Li Y, Shan A. Rational Design of Short Peptide Variants by Using Kunitzin-RE, an Amphibian-Derived Bioactivity Peptide, for Acquired Potent Broad-Spectrum Antimicrobial and Improved Therapeutic Potential of Commensalism Coinfection of Pathogens. J Med Chem 2019; 62:4586-4605. [PMID: 30958004 DOI: 10.1021/acs.jmedchem.9b00149] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Commensalism coinfection of pathogens has seriously jeopardized human health. Currently, Kunitzin-RE, as an amphibian-derived bioactivity peptide, is regarded as a potential antimicrobial candidate. However, its antimicrobial properties were unsatisfactory. In this study, a set of shortened variants of Kunitzin-RE was developed by the interception of a peptide fragment and single-site mutation to investigate the effect of chain length, positive charge, hydrophobicity, amphipathicity, and secondary structure on antimicrobial properties. Among them, W8 (AARIILRWRFR) significantly broadened the antimicrobial spectrum and showed the highest antimicrobial activity (GMall = 2.48 μM) against all the fungi and bacteria tested. Additionally, W8 showed high cell selectivity and salt tolerance in vitro, whereas it showed high effectiveness against mice keratitis cause by infection by C. albicans 2.2086. Additionally, it also had obviously lipopolysaccharide-binding ability and a potent membrane-disruptive mechanism. Overall, these findings contributed to the design of short antimicrobial peptides and to combat the serious threat of commensalism coinfection of pathogens.
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Affiliation(s)
- Zhanyi Yang
- Institute of Animal Nutrition , Northeast Agricultural University , Harbin 150030 , P. R. China
| | - Shiqi He
- Institute of Animal Nutrition , Northeast Agricultural University , Harbin 150030 , P. R. China
| | - Jiajun Wang
- Institute of Animal Nutrition , Northeast Agricultural University , Harbin 150030 , P. R. China
| | - Yi Yang
- Institute of Animal Nutrition , Northeast Agricultural University , Harbin 150030 , P. R. China
| | - Licong Zhang
- Institute of Animal Nutrition , Northeast Agricultural University , Harbin 150030 , P. R. China
| | - Yanbing Li
- College of Animal Science and Veterinary Medicine , Bayi Agricultural University , Daqing 163000 , P. R. China
| | - Anshan Shan
- Institute of Animal Nutrition , Northeast Agricultural University , Harbin 150030 , P. R. China
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13
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Wang J, Dou X, Song J, Lyu Y, Zhu X, Xu L, Li W, Shan A. Antimicrobial peptides: Promising alternatives in the post feeding antibiotic era. Med Res Rev 2018; 39:831-859. [PMID: 30353555 DOI: 10.1002/med.21542] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]
Abstract
Antimicrobial peptides (AMPs), critical components of the innate immune system, are widely distributed throughout the animal and plant kingdoms. They can protect against a broad array of infection-causing agents, such as bacteria, fungi, parasites, viruses, and tumor cells, and also exhibit immunomodulatory activity. AMPs exert antimicrobial activities primarily through mechanisms involving membrane disruption, so they have a lower likelihood of inducing drug resistance. Extensive studies on the structure-activity relationship have revealed that net charge, hydrophobicity, and amphipathicity are the most important physicochemical and structural determinants endowing AMPs with antimicrobial potency and cell selectivity. This review summarizes the recent advances in AMPs development with respect to characteristics, structure-activity relationships, functions, antimicrobial mechanisms, expression regulation, and applications in food, medicine, and animals.
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Affiliation(s)
- Jiajun Wang
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Xiujing Dou
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Jing Song
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Yinfeng Lyu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Xin Zhu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Lin Xu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Weizhong Li
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Anshan Shan
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
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14
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Pérez Y, Gómara MJ, Yuste E, Gómez-Gutierrez P, Pérez JJ, Haro I. Structural Study of a New HIV-1 Entry Inhibitor and Interaction with the HIV-1 Fusion Peptide in Dodecylphosphocholine Micelles. Chemistry 2017; 23:11703-11713. [DOI: 10.1002/chem.201702531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Yolanda Pérez
- Nuclear Magnetic Resonance Facility; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
| | - Maria José Gómara
- Unit of Synthesis and Biomedical Applications of Peptides; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
| | - Eloísa Yuste
- Department of Chemical Engineering (ETSEIB); Universitat Politecnica de Catalunya; 08034 Barcelona Spain
- Present address: AIDS Immunopathology Unit; Centro Nacional Microbiología; Instituto de Salud Carlos III; 28029 Madrid Spain
| | | | | | - Isabel Haro
- Unit of Synthesis and Biomedical Applications of Peptides; IQAC-CSIC; Jordi Girona, 18-26 08034 Barcelona Spain
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15
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Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study. Biophys J 2017; 111:2676-2688. [PMID: 28002744 DOI: 10.1016/j.bpj.2016.10.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/14/2016] [Accepted: 10/27/2016] [Indexed: 01/02/2023] Open
Abstract
A large number of antimicrobial peptides (AMPs) acts with high selectivity and specificity through interactions with membrane lipid components. These peptides undergo complex conformational changes in solution; upon binding to an interface, one major conformation is stabilized. Here we describe a study of the interaction between tritrpticin (TRP3), a cathelicidin AMP, and micelles of different chemical composition. The peptide's structure and dynamics were examined using one-dimensional and two-dimensional NMR. Our data showed that the interaction occurred by conformational selection and the peptide acquired similar structures in all systems studied, despite differences in detergent headgroup charge or dipole orientation. Fluorescence and paramagnetic relaxation enhancement experiments showed that the peptide is located in the interface region and is slightly more deeply inserted in 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-1'-rac-glycerol (LMPG, anionic) than in 1-lauroyl-2-hydroxy-sn-glycero-3-phosphocholine (LLPC, zwitterionic) micelles. Moreover, the tilt angle of an assumed helical portion of the peptide is similar in both systems. In previous work we proposed that TRP3 acts by a toroidal pore mechanism. In view of the high hydrophobic core exposure, hydration, and curvature presented by micelles, the conformation of TRP3 in these systems could be related to the peptide's conformation in the toroidal pore.
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16
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Yu HY, Chen YA, Yip BS, Wang SY, Wei HJ, Chih YH, Chen KH, Cheng JW. Role of β-naphthylalanine end-tags in the enhancement of antiendotoxin activities: Solution structure of the antimicrobial peptide S1-Nal-Nal in complex with lipopolysaccharide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1114-1123. [PMID: 28288781 DOI: 10.1016/j.bbamem.2017.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/08/2017] [Accepted: 03/09/2017] [Indexed: 12/18/2022]
Abstract
Lipopolysaccharide (LPS, endotoxin) is the major component of Gram-negative bacterial outer surface membrane. LPS released from bacteria into bloodstream during infection may cause serious unwanted stimulation of host's immune system and lead to septic shock of the patient. Recently, we have developed a strategy to increase salt resistance and LPS neutralization of short antimicrobial peptides by adding β-naphthylalanine end-tags to their termini. Herein, correlations between membrane immersion depth, orientation, and antiendotoxin activities of the antimicrobial peptides S1 and S1-Nal-Nal have been investigated via solution structure, paramagnetic resonance enhancement, and saturation transfer difference NMR studies. Unlike the parent peptide S1, S1-Nal-Nal rotated its two terminal β-naphthylalanine residues into the hydrophobic lipid A motif of LPS micelles. The LPS-induced inflammation may then be prohibited by the blocked lipid A motif.
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Affiliation(s)
- Hui-Yuan Yu
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yi-An Chen
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Bak-Sau Yip
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan; Department of Neurology, National Taiwan University Hospital Hsinchu Branch, Hsinchu 300, Taiwan
| | - Siou-Ying Wang
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Hsiu-Ju Wei
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Ya-Han Chih
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Kuan-Hao Chen
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Jya-Wei Cheng
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu 300, Taiwan.
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17
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Chen J, Zhu Y, Song Y, Wang L, Zhan J, He J, Zheng J, Zhong C, Shi X, Liu S, Ren L, Wang Y. Preparation of an antimicrobial surface by direct assembly of antimicrobial peptide with its surface binding activity. J Mater Chem B 2017; 5:2407-2415. [DOI: 10.1039/c6tb03337g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The designed antimicrobial peptide has surface binding activity onto titanium, gold, polymethyl methacrylate and hydroxyapatite substrates.
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Affiliation(s)
- Junjian Chen
- School of Materials Science and Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Yuchen Zhu
- National Engineering Research Centre for Tissue Restoration & Reconstruction
- Guangzhou 510006
- China
| | - Yancheng Song
- The Third Affiliated Hospital of Southern Medical University
- Guangzhou 510630
- China
| | - Lin Wang
- Guangdong Province Key Laboratory of Biomedical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Jiezhao Zhan
- National Engineering Research Centre for Tissue Restoration & Reconstruction
- Guangzhou 510006
- China
| | - Jingcai He
- Guangdong Province Key Laboratory of Biomedical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Jian Zheng
- National Engineering Research Centre for Tissue Restoration & Reconstruction
- Guangzhou 510006
- China
| | - Chunting Zhong
- Guangdong Province Key Laboratory of Biomedical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Xuetao Shi
- School of Materials Science and Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Sa Liu
- National Engineering Research Centre for Tissue Restoration & Reconstruction
- Guangzhou 510006
- China
| | - Li Ren
- National Engineering Research Centre for Tissue Restoration & Reconstruction
- Guangzhou 510006
- China
| | - Yingjun Wang
- School of Materials Science and Engineering
- South China University of Technology
- Guangzhou 510641
- China
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18
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Chu HL, Yip BS, Chen KH, Yu HY, Chih YH, Cheng HT, Chou YT, Cheng JW. Novel antimicrobial peptides with high anticancer activity and selectivity. PLoS One 2015; 10:e0126390. [PMID: 25970292 PMCID: PMC4430538 DOI: 10.1371/journal.pone.0126390] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/01/2015] [Indexed: 01/08/2023] Open
Abstract
We describe a strategy to boost anticancer activity and reduce normal cell toxicity of short antimicrobial peptides by adding positive charge amino acids and non-nature bulky amino acid β-naphthylalanine residues to their termini. Among the designed peptides, K4R2-Nal2-S1 displayed better salt resistance and less toxicity to hRBCs and human fibroblast than Nal2-S1 and K6-Nal2-S1. Fluorescence microscopic studies indicated that the FITC-labeled K4R2-Nal2-S1 preferentially binds cancer cells and causes apoptotic cell death. Moreover, a significant inhibition in human lung tumor growth was observed in the xenograft mice treated with K4R2-Nal2-S1. Our strategy provides new opportunities in the development of highly effective and selective antimicrobial and anticancer peptide-based therapeutics.
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Affiliation(s)
- Hung-Lun Chu
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Bak-Sau Yip
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
- Department of Neurology, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan
| | - Kuan-Hao Chen
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Hui-Yuan Yu
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ya-Han Chih
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Hsi-Tsung Cheng
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yu-Ting Chou
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
- * E-mail: (JWC); (YTC)
| | - Jya-Wei Cheng
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, Hsinchu, 300, Taiwan
- * E-mail: (JWC); (YTC)
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