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Parvez AK, Jubyda FT, Karmakar J, Jahan A, Akter NE, Ayaz M, Kabir T, Akter S, Huq MA. Antimicrobial potential of biopolymers against foodborne pathogens: An updated review. Microb Pathog 2025; 204:107583. [PMID: 40228749 DOI: 10.1016/j.micpath.2025.107583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 03/26/2025] [Accepted: 04/11/2025] [Indexed: 04/16/2025]
Abstract
Biopolymers are natural polymers produced by the cells of living organisms such as plants, animals, microbes, etc. As these natural molecules possess antimicrobial activities against pathogens, they can be a suitable candidate for antimicrobials combating drug-resistant microorganisms including food-borne pathogens. Plant-derived biopolymers such as cellulose, starch, pullulans; microbes-derived chitosan, poly-L-lysine; animal-derived collagen, gelatin, spongin, etc. are proven to possess antimicrobial properties. They exert their antimicrobial activity against food-borne pathogens namely Salmonella typhi, Vibrio cholerae, Bacillus cereus, Clostridium perfringens, E. coli, Campylobacter jejuni, Staphylococcus aureus, etc. As antimicrobial resistance becomes a global phenomenon and threatens the effective prevention and treatment of infections caused by pathogens, biopolymers could be a promising candidate/substitute for conventional antimicrobials available in markets. Biopolymers can have detrimental effects on microbial cells such as disruption of the cell walls and cell membranes; damage to the DNA caused by strand breakage, unwinding, or cross-linking resulting in impeded DNA transcription and replication; lowering the amount of energy required for metabolic processes by compromising the proton motive force. Biopolymers also interfere with the quorum sensing mechanism and biofilm formation of microbes and modulate the host immune system by downregulating mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-κB) signaling pathways resulting in the decreased production of pro-inflammatory cytokines. Furthermore, conjugating these biopolymers with other antimicrobial agents could be a promising approach to control multidrug-resistant foodborne pathogens. This review provides an overview of the various sources of biopolymers with special reference to their antimicrobial applications, especially against foodborne pathogens, and highlights their antimicrobial mechanisms.
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Affiliation(s)
| | - Fatema Tuz Jubyda
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Joyoshrie Karmakar
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Airen Jahan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nayeem-E Akter
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Mohammed Ayaz
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Tabassum Kabir
- M Abdur Rahim Medical College Hospital, Dinajpur, Bangladesh
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 13120, Republic of Korea
| | - Md Amdadul Huq
- Department of Life Sciences, College of BioNano Technology, Gachon University, Seongnam, 13120, Republic of Korea.
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Li K, Wu Y, Li Y, Guo Y, Kong Y, Wang Y, Liang Y, Fan Y, Huang L, Zhang R, Zhou F. AMPCliff: Quantitative definition and benchmarking of activity cliffs in antimicrobial peptides. J Adv Res 2025:S2090-1232(25)00292-9. [PMID: 40318764 DOI: 10.1016/j.jare.2025.04.046] [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: 01/31/2025] [Revised: 04/09/2025] [Accepted: 04/29/2025] [Indexed: 05/07/2025] Open
Abstract
INTRODUCTION Activity cliff (AC) is a phenomenon that a pair of similar molecules differ by a small structural alternation but exhibit a large difference in their biochemical activities. This phenomenon affects various tasks ranging from virtual screening to lead optimization in drug development. The AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in pharmaceutical peptides with canonical amino acids. OBJECTIVES This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids. METHODS This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models. RESULTS A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the metric minimum inhibitory concentration (MIC), and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the -log(MIC) values on the benchmark dataset. CONCLUSION Our findings highlight limitations in current deep learning-based representation models. To more accurately capture the properties of antimicrobial peptides (AMPs), it is essential to integrate atomic-level dynamic information that reflects their underlying mechanisms of action.
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Affiliation(s)
- Kewei Li
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yuqian Wu
- School of Software, Jilin University, Changchun 130012 Jilin, China
| | - Yinheng Li
- Department of Computer Science, Columbia University, 116th and Broadway, New York City, NY 10027, United States
| | - Yutong Guo
- School of Life Sciences, Jilin University, Changchun 130012 Jilin, China
| | - Yanwen Kong
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yan Wang
- School of Computer Engineering, Changchun University of Engineering, Changchun 130103 Jilin, China
| | - Yiyang Liang
- Changchun Wenli High School, Changchun 130062 Jilin, China
| | - Yusi Fan
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Ruochi Zhang
- School of Artificial Intelligence, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012 Jilin, China.
| | - Fengfeng Zhou
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China; School of Biology and Engineering, Guizhou Medical University, Guiyang 550025 Guizhou, China.
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Efficacy of natural antimicrobial peptides versus peptidomimetic analogues: a systematic review. Future Med Chem 2022; 14:1899-1921. [PMID: 36421051 DOI: 10.4155/fmc-2022-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Aims: This systematic review was carried out to determine whether synthetic peptidomimetics exhibit significant advantages over antimicrobial peptides in terms of in vitro potency. Structural features - molecular weight, charge and length - were examined for correlations with activity. Methods: Original research articles reporting minimum inhibitory concentration values against Escherichia coli, indexed until 31 December 2020, were searched in PubMed/ScienceDirect/Google Scholar and evaluated using mixed-effects models. Results: In vitro antimicrobial activity of peptidomimetics resembled that of antimicrobial peptides. Net charge significantly affected minimum inhibitory concentration values (p < 0.001) with a trend of 4.6% decrease for increments in charge by +1. Conclusion: AMPs and antibacterial peptidomimetics exhibit similar potencies, providing an opportunity to exploit the advantageous stability and bioavailability typically associated with peptidomimetics.
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Wang Y, Haqmal MA, Liang YD, Muhammad I, Zhao XO, Elken EM, Gao YH, Jia Y, He CG, Wang YM, Kong LC, Ma HX. Antibacterial activity and cytotoxicity of a novel bacteriocin isolated from Pseudomonas sp. strain 166. Microb Biotechnol 2022; 15:2337-2350. [PMID: 35849816 PMCID: PMC9437881 DOI: 10.1111/1751-7915.14096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Pseudomonas sp. strain 166 was isolated from soil samples from Changbai Mountains. A novel bacteriocin PA166 from Pseudomonas sp. 166 was purified using ammonium sulfate, dextran gel chromatography column and Q-Sepharose column chromatography successively. The molecular mass of bacteriocin PA166 was found to be 49.38 kDa by SDS-PAGE and liquid chromatography-mass spectrometry (MS)/MS. Bacteriocin PA166 showed stability at a wide range of pH (2-10), and thermal stability (40, 60, 80 and 100°C). The bacteriocin PA166 antimicrobial activity was slightly inhibited by Ca2+ , K+ and Mg2+ . The minimum bactericidal concentrations of bacteriocin PA166 against five Pasteurella multocida strains ranged from 2 to 8 μg ml-1 . Bacteriocin PA166 showed low cytotoxicity and a higher treatment index (TI = 82.51). Fluorescence spectroscopy indicated that bacteriocin PA166 destroyed the cell membrane to exert antimicrobial activity. In summary, bacteriocin PA166 had strong antibacterial activity, high TI and low toxicity, and hence could serve as a potential clinical therapeutic drug.
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Affiliation(s)
- Yu Wang
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - M Aman Haqmal
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Yue-Dong Liang
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Inam Muhammad
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China.,Department of Animal Sciences, Shaheed Benazir Bhutto University Sheringal Dir Upper-Pakistan, Sheringal, Pakistan
| | - Xiao-Ou Zhao
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Emad Mohammed Elken
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China.,Animal Production Department, Faculty of Agriculture, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Yun-Hang Gao
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Yu Jia
- Jilin Agricultural University, College of Life Science, Changchun, China
| | - Cheng-Guang He
- Jilin Agricultural University, College of Life Science, Changchun, China
| | - Yi-Ming Wang
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China
| | - Ling-Cong Kong
- College of Veterinary Medicine, Jilin Agricultural University, 130118, Changchun, Jilin, China.,The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun, 130118, China
| | - Hong-Xia Ma
- Jilin Agricultural University, College of Life Science, Changchun, China.,The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun, 130118, China.,The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Changchun, China
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Lin Q, Fu Q, Chen D, Yu B, Luo Y, Huang Z, Zheng P, Mao X, Yu J, Luo J, Yan H, He J. Functional Characterization of Porcine NK-Lysin: A Novel Immunomodulator That Regulates Intestinal Inflammatory Response. Molecules 2021; 26:molecules26144242. [PMID: 34299517 PMCID: PMC8307250 DOI: 10.3390/molecules26144242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
Porcine NK-Lysine (PNKL) is a new antimicrobial peptide (AMP) identified in the small intestine. In this study, PNKL protein was obtained through heterologous expression in Escherichia coli and was estimated by SDS-PAGE at 33 kDa. The antibacterial activities of PNKL were determined using various bacterial strains and showed broad-spectrum antimicrobial activity against Gram-negative and Gram-positive bacteria. Furthermore, E. coli K88-challenged IPEC-J2 cells were used to determine PNKL influences on inflammatory responses. Hemolytic assays showed that PNKL had no detrimental impact on cell viability. Interestingly, PNKL elevated the viability of IPEC-J2 cells exposure to E. coli K88. PNKL significantly decreased the cell apoptosis rate, and improved the distribution and abundance of tight junction protein ZO-1 in IPEC-J2 cells upon E. coli K88-challenge. Importantly, PNKL not only down regulated the expressions of inflammatory cytokines such as the IL-6 and TNF-α, but also down regulated the expressions of NF-κB, Caspase3, and Caspase9 in the E. coli K88-challenged cells. These results suggest a novel function of natural killer (NK)-lysin, and the anti-bacterial and anti-inflammatory properties of PNKL may allow it a potential substitute for conventionally used antibiotics or drugs.
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Affiliation(s)
- Qian Lin
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Qingqing Fu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Bing Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Yuheng Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Ping Zheng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Xiangbing Mao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Jie Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Junqiu Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Hui Yan
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Q.F.); (D.C.); (B.Y.); (Y.L.); (Z.H.); (P.Z.); (X.M.); (J.Y.); (J.L.); (H.Y.)
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
- Correspondence: ; Tel.: +86-28-8629-1781; Fax: +86-28-8629-0922
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High Cell Selectivity and Bactericidal Mechanism of Symmetric Peptides Centered on d-Pro-Gly Pairs. Int J Mol Sci 2020; 21:ijms21031140. [PMID: 32046328 PMCID: PMC7037546 DOI: 10.3390/ijms21031140] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) have a unique action mechanism that can help to solve global problems in antibiotic resistance. However, their low therapeutic index and poor stability seriously hamper their development as therapeutic agents. In order to overcome these problems, we designed peptides based on the sequence template XXRXXRRzzRRXXRXX-NH2, where X represents a hydrophobic amino acid like Phe (F), Ile (I), and Leu (L), while zz represents Gly-Gly (GG) or d-Pro-Gly (pG). Showing effective antimicrobial activity against Gram-negative bacteria and low toxicity, designed peptides had a tendency to form an α-helical structure in membrane-mimetic environments. Among them, peptide LRpG (X: L, zz: pG) showed the highest geometric mean average treatment index (GMTI = 73.1), better salt, temperature and pH stability, and an additive effect with conventional antibiotics. Peptide LRpG played the role of anti-Gram-negative bacteria through destroying the cell membrane. In addition, peptide LRpG also exhibited an anti-inflammatory activity by effectively neutralizing endotoxin. Briefly, peptide LRpG has the potential to serve as a therapeutic agent to reduce antibiotic resistance owing to its high therapeutic index and great stability.
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