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van Teijlingen A, Edwards DC, Hu L, Lilienkampf A, Cockroft SL, Tuttle T. An active machine learning discovery platform for membrane-disrupting and pore-forming peptides. Phys Chem Chem Phys 2024; 26:17745-17752. [PMID: 38873737 PMCID: PMC11202314 DOI: 10.1039/d4cp01404a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Membrane-disrupting and pore-forming peptides (PFPs) play a substantial role in bionanotechnology and can determine the life and death of cells. The control of chemical and ion transport through cell membranes is essential to maintaining concentration gradients. Likewise, the delivery of drugs and intracellular proteins aided by pore-forming agents is of interest in treating malfunctioning cells. Known PFPs tend to be up to 50 residues in length, which is commensurate with the thickness of a lipid bilayer. Accordingly, few short PFPs are known. Here we show that the discovery of PFPs can be accelerated via an active machine learning approach. The approach identified 71 potential PFPs from the 25.6 billion octapeptide sequence space; 13 sequences were tested experimentally, and all were found to have the predicted membrane-disrupting ability, with 1 forming highly stable pores. Experimental verification of the predicted pore-forming ability demonstrated that a range of short peptides can form pores in membranes, while the positioning and characteristics of residues that favour pore-forming behaviour were identified. This approach identified more ultrashort (8-residues, unmodified, non-cyclic) PFPs than previously known. We anticipate our findings and methodology will be useful in discovering new pore-forming and membrane-disrupting peptides for a range of applications from nanoreactors to therapeutics.
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Affiliation(s)
- Alexander van Teijlingen
- 1Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
| | - Daniel C Edwards
- EaStCHEM School of Chemistry, Joseph Black Building, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Liao Hu
- EaStCHEM School of Chemistry, Joseph Black Building, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Annamaria Lilienkampf
- EaStCHEM School of Chemistry, Joseph Black Building, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Scott L Cockroft
- EaStCHEM School of Chemistry, Joseph Black Building, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Tell Tuttle
- 1Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK.
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2
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Sun L, Hristova K, Bondar AN, Wimley WC. Structural Determinants of Peptide Nanopore Formation. ACS NANO 2024; 18:15831-15844. [PMID: 38844421 PMCID: PMC11191747 DOI: 10.1021/acsnano.4c02824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 06/19/2024]
Abstract
We have evolved the nanopore-forming macrolittin peptides from the bee venom peptide melittin using successive generations of synthetic molecular evolution. Despite their sequence similarity to the broadly membrane permeabilizing cytolytic melittin, the macrolittins have potent membrane selectivity. They form nanopores in synthetic bilayers made from 1-palmitoyl, 2-oleoyl-phosphatidylcholine (POPC) at extremely low peptide concentrations and yet have essentially no cytolytic activity against any cell membrane, even at high concentration. Here, we explore the structural determinants of macrolittin nanopore stability in POPC bilayers using atomistic molecular dynamics simulations and experiments on macrolittins and single-site variants. Simulations of macrolittin nanopores in POPC bilayers show that they are stabilized by an extensive, cooperative hydrogen bond network comprised of the many charged and polar side chains interacting with each other via bridges of water molecules and lipid headgroups. Lipid molecules with unusual conformations participate in the H-bond network and are an integral part of the nanopore structure. To explore the role of this H-bond network on membrane selectivity, we swapped three critical polar residues with the nonpolar residues found in melittin. All variants have potency, membrane selectivity, and cytotoxicity that were intermediate between a cytotoxic melittin variant called MelP5 and the macrolittins. Simulations showed that the variants had less organized H-bond networks of waters and lipids with unusual structures. The membrane-spanning, cooperative H-bond network is a critical determinant of macrolittin nanopore stability and membrane selectivity. The results described here will help guide the future design and optimization of peptide nanopore-based applications.
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Affiliation(s)
- Leisheng Sun
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Kalina Hristova
- Department
of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute
for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ana-Nicoleta Bondar
- Faculty
of Physics, University of Bucharest, Atomiştilor 405, Măgurele 077125, Romania
- Forschungszentrum
Jülich, Institute of Computational
Biomedicine, IAS-5/INM-9,
Wilhelm-Johnen Straße, 5428 Jülich, Germany
| | - William C. Wimley
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
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3
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Boone K, Tjokro N, Chu KN, Chen C, Snead ML, Tamerler C. Machine learning enabled design features of antimicrobial peptides selectively targeting peri-implant disease progression. FRONTIERS IN DENTAL MEDICINE 2024; 5:1372534. [PMID: 38846578 PMCID: PMC11155447 DOI: 10.3389/fdmed.2024.1372534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024] Open
Abstract
Peri-implantitis is a complex infectious disease that manifests as progressive loss of alveolar bone around the dental implants and hyper-inflammation associated with microbial dysbiosis. Using antibiotics in treating peri-implantitis is controversial because of antibiotic resistance threats, the non-selective suppression of pathogens and commensals within the microbial community, and potentially serious systemic sequelae. Therefore, conventional treatment for peri-implantitis comprises mechanical debridement by nonsurgical or surgical approaches with adjunct local microbicidal agents. Consequently, current treatment options may not prevent relapses, as the pathogens either remain unaffected or quickly re-emerge after treatment. Successful mitigation of disease progression in peri-implantitis requires a specific mode of treatment capable of targeting keystone pathogens and restoring bacterial community balance toward commensal species. Antimicrobial peptides (AMPs) hold promise as alternative therapeutics through their bacterial specificity and targeted inhibitory activity. However, peptide sequence space exhibits complex relationships such as sparse vector encoding of sequences, including combinatorial and discrete functions describing peptide antimicrobial activity. In this paper, we generated a transparent Machine Learning (ML) model that identifies sequence-function relationships based on rough set theory using simple summaries of the hydropathic features of AMPs. Comparing the hydropathic features of peptides according to their differential activity for different classes of bacteria empowered predictability of antimicrobial targeting. Enriching the sequence diversity by a genetic algorithm, we generated numerous candidate AMPs designed for selectively targeting pathogens and predicted their activity using classifying rough sets. Empirical growth inhibition data is iteratively fed back into our ML training to generate new peptides, resulting in increasingly more rigorous rules for which peptides match targeted inhibition levels for specific bacterial strains. The subsequent top scoring candidates were empirically tested for their inhibition against keystone and accessory peri-implantitis pathogens as well as an oral commensal bacterium. A novel peptide, VL-13, was confirmed to be selectively active against a keystone pathogen. Considering the continually increasing number of oral implants placed each year and the complexity of the disease progression, prevalence of peri-implant diseases continues to rise. Our approach offers transparent ML-enabled paths towards developing antimicrobial peptide-based therapies targeting the changes in the microbial communities that can beneficially impact disease progression.
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Affiliation(s)
- Kyle Boone
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS, United States
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS, United States
| | - Natalia Tjokro
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Kalea N. Chu
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS, United States
- Bioengineering Program, University of Kansas, Lawrence, KS, United States
| | - Casey Chen
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Malcolm L. Snead
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
- Bioengineering Program, University of Kansas, Lawrence, KS, United States
| | - Candan Tamerler
- Institute for Bioengineering Research, University of Kansas, Lawrence, KS, United States
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS, United States
- Bioengineering Program, University of Kansas, Lawrence, KS, United States
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4
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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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5
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Feijoo-Coronel ML, Mendes B, Ramírez D, Peña-Varas C, de los Monteros-Silva NQE, Proaño-Bolaños C, de Oliveira LC, Lívio DF, da Silva JA, da Silva JMSF, Pereira MGAG, Rodrigues MQRB, Teixeira MM, Granjeiro PA, Patel K, Vaiyapuri S, Almeida JR. Antibacterial and Antiviral Properties of Chenopodin-Derived Synthetic Peptides. Antibiotics (Basel) 2024; 13:78. [PMID: 38247637 PMCID: PMC10812719 DOI: 10.3390/antibiotics13010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Antimicrobial peptides have been developed based on plant-derived molecular scaffolds for the treatment of infectious diseases. Chenopodin is an abundant seed storage protein in quinoa, an Andean plant with high nutritional and therapeutic properties. Here, we used computer- and physicochemical-based strategies and designed four peptides derived from the primary structure of Chenopodin. Two peptides reproduce natural fragments of 14 amino acids from Chenopodin, named Chen1 and Chen2, and two engineered peptides of the same length were designed based on the Chen1 sequence. The two amino acids of Chen1 containing amide side chains were replaced by arginine (ChenR) or tryptophan (ChenW) to generate engineered cationic and hydrophobic peptides. The evaluation of these 14-mer peptides on Staphylococcus aureus and Escherichia coli showed that Chen1 does not have antibacterial activity up to 512 µM against these strains, while other peptides exhibited antibacterial effects at lower concentrations. The chemical substitutions of glutamine and asparagine by amino acids with cationic or aromatic side chains significantly favoured their antibacterial effects. These peptides did not show significant hemolytic activity. The fluorescence microscopy analysis highlighted the membranolytic nature of Chenopodin-derived peptides. Using molecular dynamic simulations, we found that a pore is formed when multiple peptides are assembled in the membrane. Whereas, some of them form secondary structures when interacting with the membrane, allowing water translocations during the simulations. Finally, Chen2 and ChenR significantly reduced SARS-CoV-2 infection. These findings demonstrate that Chenopodin is a highly useful template for the design, engineering, and manufacturing of non-toxic, antibacterial, and antiviral peptides.
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Affiliation(s)
- Marcia L. Feijoo-Coronel
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - Bruno Mendes
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Carlos Peña-Varas
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | | | - Carolina Proaño-Bolaños
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - Leonardo Camilo de Oliveira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Diego Fernandes Lívio
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - José Antônio da Silva
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - José Maurício S. F. da Silva
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
| | - Marília Gabriella A. G. Pereira
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
| | - Marina Q. R. B. Rodrigues
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
- Departamento de Engenharia de Biossistemas, Campus Dom Bosco, Federal University of São João Del-Rei, Praça Dom Helvécio, 74, Fábricas, São João del-Rei 36301-160, Brazil
| | - Mauro M. Teixeira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Paulo Afonso Granjeiro
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - Ketan Patel
- School of Biological Sciences, University of Reading, Reading RG6 6UB, UK
| | | | - José R. Almeida
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
- School of Pharmacy, University of Reading, Reading RG6 6UB, UK
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6
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Xu K, Zhao X, Tan Y, Wu J, Cai Y, Zhou J, Wang X. A systematical review on antimicrobial peptides and their food applications. BIOMATERIALS ADVANCES 2023; 155:213684. [PMID: 37976831 DOI: 10.1016/j.bioadv.2023.213684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/29/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Food safety issues are a major concern in food processing and packaging industries. Food spoilage is caused by microbial contamination, where antimicrobial peptides (APs) provide solutions by eliminating microorganisms. APs such as nisin have been successfully and commonly used in food processing and preservation. Here, we discuss all aspects of the functionalization of APs in food applications. We briefly review the natural sources of APs and their native functions. Recombinant expression of APs in microorganisms and their yields are described. The molecular mechanisms of AP antibacterial action are explained, and this knowledge can further benefit the design of functional APs. We highlight current utilities and challenges for the application of APs in the food industry, and address rational methods for AP design that may overcome current limitations.
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Affiliation(s)
- Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - XinYi Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Junheng Wu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yiqing Cai
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China..
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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7
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Tang Z, Jiang W, Li S, Huang X, Yang Y, Chen X, Qiu J, Xiao C, Xie Y, Zhang X, Li J, Verma CS, He Y, Yang A. Design and evaluation of tadpole-like conformational antimicrobial peptides. Commun Biol 2023; 6:1177. [PMID: 37980400 PMCID: PMC10657444 DOI: 10.1038/s42003-023-05560-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023] Open
Abstract
Antimicrobial peptides are promising alternatives to conventional antibiotics. Herein, we report a class of "tadpole-like" peptides consisting of an amphipathic α-helical head and an aromatic tail. A structure-activity relationship (SAR) study of "tadpole-like" temporin-SHf and its analogs revealed that increasing the number of aromatic residues in the tail, introducing Arg to the α-helical head and rearranging the peptide topology dramatically increased antimicrobial activity. Through progressive structural optimization, we obtained two peptides, HT2 and RI-HT2, which exhibited potent antimicrobial activity, no hemolytic activity and cytotoxicity, and no propensity to induce resistance. NMR and molecular dynamics simulations revealed that both peptides indeed adopted "tadpole-like" conformations. Fluorescence experiments and electron microscopy confirmed the membrane targeting mechanisms of the peptides. Our studies not only lead to the discovery of a series of ultrashort peptides with potent broad-spectrum antimicrobial activities, but also provide a new strategy for rational design of novel "tadpole-like" antimicrobial peptides.
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Affiliation(s)
- Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Wuqiao Jiang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shuangli Li
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Yi Yang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Chuyu Xiao
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Ying Xie
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xu Zhang
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jianguo Li
- Bioinformatics Institute, A∗STAR, 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
- Singapore Eye Research Institute, Singapore, 169856, Singapore
| | - Chandra Shekhar Verma
- Bioinformatics Institute, A∗STAR, 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
- Department of Biological Sciences, National University of, Singapore, 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Yun He
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
- BayRay Innovation Center, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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8
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Ahmad B, Achek A, Farooq M, Choi S. Accelerated NLRP3 inflammasome-inhibitory peptide design using a recurrent neural network model and molecular dynamics simulations. Comput Struct Biotechnol J 2023; 21:4825-4835. [PMID: 37854633 PMCID: PMC10579963 DOI: 10.1016/j.csbj.2023.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
Anomalous NLRP3 inflammasome responses have been linked to multiple health issues, including but not limited to atherosclerosis, diabetes, metabolic syndrome, cardiovascular disease, and neurodegenerative disease. Thus, targeting NLRP3 and modulating its associated immune response might be a promising strategy for developing new anti-inflammatory drugs. Herein, we report a computational method for de novo peptide design for targeting NLRP3 inflammasomes. The described method leverages a long-short-term memory (LSTM) network based on a recurrent neural network (RNN) to model a valuable latent space of molecules. The resulting classifiers are utilized to guide the selection of molecules generated by the model based on circular dichroism spectra and physicochemical features derived from high-throughput molecular dynamics simulations. Of the experimentally tested sequences, 60% of the peptides showed NLRP3-mediated inhibition of IL-1β and IL-18. One peptide displayed high potency against NLRP3-mediated IL-1β inhibition. However, NLRC4 and AIM2 inflammasome-mediated IL-1β secretion was uninterrupted by this peptide, demonstrating its selectivity toward the NLRP3 inflammasome. Overall, these results indicate that deep learning and molecular dynamics can accelerate the discovery of NLRP3 inhibitors with potent and selective activity.
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Affiliation(s)
- Bilal Ahmad
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea
- S&K Therapeutics, Ajou University, Campus Plaza 418, Worldcup-ro 199, Yeongtong-gu, Suwon 16502, South Korea
| | - Asma Achek
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea
- Technology Development Platform, Institut Pasteur Korea, Seongnam 13488, Soouth Korea
| | - Mariya Farooq
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea
- S&K Therapeutics, Ajou University, Campus Plaza 418, Worldcup-ro 199, Yeongtong-gu, Suwon 16502, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea
- S&K Therapeutics, Ajou University, Campus Plaza 418, Worldcup-ro 199, Yeongtong-gu, Suwon 16502, South Korea
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9
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Raileanu M, Borlan R, Campu A, Janosi L, Turcu I, Focsan M, Bacalum M. No country for old antibiotics! Antimicrobial peptides (AMPs) as next-generation treatment for skin and soft tissue infection. Int J Pharm 2023:123169. [PMID: 37356506 DOI: 10.1016/j.ijpharm.2023.123169] [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: 04/12/2023] [Revised: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
In recent years, the unprecedented rise of bacterial antibiotic resistance together with the lack of adequate therapies have made the treatment of skin infections and chronic wounds challenging, urging the scientific community to focus on the development of new and more efficient treatment strategies. In this context, there is a growing interest in the use of natural molecules with antimicrobial features, capable of supporting wound healing i.e., antimicrobial peptides (AMPs), for the treatment of skin and soft tissue infections. In this review, we give a short overview of the bacterial skin infections as well as some of the classic treatments used for topical application. We then summarize the AMPs classes, stressing the importance of the appropriate selection of the peptides based on their characteristics and physicochemical properties in order to maximize the antibacterial efficacy of the therapeutic systems against multi-drug resistant pathogens. Additionally, the present paper provides a comprehensive and rigorous assessment of the latest clinical trials investigating the efficacy of AMPs in the treatment of skin and soft tissue infections, highlighting the relevant outcomes. Seeking to obtain novel and improved compounds with synergistic activity, while also decreasing some of the known side effects of AMPs, we present two employed strategies using AMPs: (i) AMPs-conjugated nanosystems for systemic and topical drug delivery systems and (ii) antibiotics-peptide conjugates as a strategy to overcome antibiotics resistance. Finally, an important property of some of the AMPs used in wound treatment is highlighted: their ability to help in wound healing by generally promoting cell proliferation and migration, and in some cases re-epithelialization and angiogenesis among others. Thus, as the pursuit of improvement is an ongoing effort, this work presents the advances made in the treatment of skin and soft tissue infections along with their advantages and limitations, while the still remaining challenges are addressed by providing future prospects and strategies to overcome them.
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Affiliation(s)
- Mina Raileanu
- Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului 30, Măgurele 077125, Romania
| | - Raluca Borlan
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, Treboniu Laurian No. 42, 400271 Cluj-Napoca, Romania
| | - Andreea Campu
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, Treboniu Laurian No. 42, 400271 Cluj-Napoca, Romania
| | - Lorant Janosi
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath Street, 400293 Cluj-Napoca, Romania
| | - Ioan Turcu
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath Street, 400293 Cluj-Napoca, Romania
| | - Monica Focsan
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, Treboniu Laurian No. 42, 400271 Cluj-Napoca, Romania.
| | - Mihaela Bacalum
- Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului 30, Măgurele 077125, Romania.
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10
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Gong H, Hu X, Zhang L, Fa K, Liao M, Liu H, Fragneto G, Campana M, Lu JR. How do antimicrobial peptides disrupt the lipopolysaccharide membrane leaflet of Gram-negative bacteria? J Colloid Interface Sci 2023; 637:182-192. [PMID: 36701864 DOI: 10.1016/j.jcis.2023.01.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/24/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
HYPOTHESIS It is widely regarded that antimicrobial peptides (AMPs) kill bacteria by physically disrupting microbial membranes and causing cytoplasmic leakage, but it remains unclear how AMPs disrupt the outer membrane (OM) of Gram-negative bacteria (GNB) and then compromise the inner membrane. We hypothesise that different AMPs impose different structural disruptions, with direct implications to their antimicrobial efficacies. EXPERIMENTS The antimicrobial activities of three typical AMPs, including the designed short AMP, G3, and two natural AMPs, melittin and LL37, against E. coli and their haemolytic activities were studied. Lipopolysaccharide (LPS) and anionic di-palmitoyl phosphatidyl glycerol (DPPG) monolayer models were constructed to mimic the outer membrane and inner membrane leaflets of Gram-negative bacteria. The binding and penetration of AMPs to the model lipid monolayers were systematically studied by neutron reflection via multiple H/D contrast variations. FINDING G3 has relatively high antimicrobial activity, low cytotoxicity, and high proteolytic stability, whilst melittin has significant haemolysis and LL37 has weaker antimicrobial activity. G3 could rapidly lyse LPS and DPPG monolayers within 10-20 min. In contrast, melittin was highly active against the LPS membrane, but the dynamic process lasted up to 80 min, with excessive stacking in the OM. LL37 caused rather weak destruction to LPS and DPPG monolayers, leading to massive adsorption on the membrane surface without penetrating the lipid tail region. These findings demonstrate that the rationally designed AMP G3 was well optimised to impose most effective destruction to bacterial membranes, consistent with its highest bactericidal activity. These different interfacial structural features associated with AMP binding shed light on the future development of active and biocompatible AMPs for infection and wound treatments.
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Affiliation(s)
- Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK; State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xuzhi Hu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Lin Zhang
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Ke Fa
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Huayang Liu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | | | - Mario Campana
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Jian Ren Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK.
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11
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Niitsu A, Sugita Y. Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. Phys Chem Chem Phys 2023; 25:3595-3606. [PMID: 36647771 DOI: 10.1039/d2cp03972a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Computational de novo protein design involves iterative processes consisting of amino acid sequence design, structural modelling and scoring, and design validation by synthesis and experimental characterisation. Recent advances in protein structure prediction and modelling methods have enabled the highly efficient and accurate design of water-soluble proteins. However, the design of membrane proteins remains a major challenge. To advance membrane protein design, considering the higher complexity of membrane protein folding, stability, and dynamic interactions between water, ions, lipids, and proteins is an important task. For introducing explicit solvents and membranes to these design methods, all-atom molecular dynamics (MD) simulations of designed proteins provide useful information that cannot be obtained experimentally. In this review, we first describe two major approaches to designing transmembrane α-helical assemblies, consensus and de novo design. We further illustrate recent MD studies of membrane protein folding related to protein design, as well as advanced treatments in molecular models and conformational sampling techniques in the simulations. Finally, we discuss the possibility to introduce MD simulations after the existing static modelling and screening of design decoys as an additional step for refinement of the design, which considers membrane protein folding dynamics and interactions with explicit membranes.
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Affiliation(s)
- Ai Niitsu
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. .,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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12
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Lu H, Cheng Z, Hu Y, Tang LV. What Can De Novo Protein Design Bring to the Treatment of Hematological Disorders? BIOLOGY 2023; 12:biology12020166. [PMID: 36829445 PMCID: PMC9952452 DOI: 10.3390/biology12020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Protein therapeutics have been widely used to treat hematological disorders. With the advent of de novo protein design, protein therapeutics are not limited to ameliorating natural proteins but also produce novel protein sequences, folds, and functions with shapes and functions customized to bind to the therapeutic targets. De novo protein techniques have been widely used biomedically to design novel diagnostic and therapeutic drugs, novel vaccines, and novel biological materials. In addition, de novo protein design has provided new options for treating hematological disorders. Scientists have designed protein switches called Colocalization-dependent Latching Orthogonal Cage-Key pRoteins (Co-LOCKR) that perform computations on the surface of cells. De novo designed molecules exhibit a better capacity than the currently available tyrosine kinase inhibitors in chronic myeloid leukemia therapy. De novo designed protein neoleukin-2/15 enhances chimeric antigen receptor T-cell activity. This new technique has great biomedical potential, especially in exploring new treatment methods for hematological disorders. This review discusses the development of de novo protein design and its biological applications, with emphasis on the treatment of hematological disorders.
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13
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Huang J, Xu Y, Xue Y, Huang Y, Li X, Chen X, Xu Y, Zhang D, Zhang P, Zhao J, Ji J. Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences. Nat Biomed Eng 2023:10.1038/s41551-022-00991-2. [PMID: 36635418 DOI: 10.1038/s41551-022-00991-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/29/2022] [Indexed: 01/14/2023]
Abstract
Systematically identifying functional peptides is difficult owing to the vast combinatorial space of peptide sequences. Here we report a machine-learning pipeline that mines the hundreds of billions of sequences in the entire virtual library of peptides made of 6-9 amino acids to identify potent antimicrobial peptides. The pipeline consists of trainable machine-learning modules (for performing empirical selection, classification, ranking and regression tasks) assembled sequentially following a coarse-to-fine design principle to gradually narrow down the search space. The leading three antimicrobial hexapeptides identified by the pipeline showed strong activities against a wide range of clinical isolates of multidrug-resistant pathogens. In mice with bacterial pneumonia, aerosolized formulations of the identified peptides showed therapeutic efficacy comparable to penicillin, negligible toxicity and a low propensity to induce drug resistance. The machine-learning pipeline may accelerate the discovery of new functional peptides.
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Affiliation(s)
- Junjie Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yanchao Xu
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yunfan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xu Li
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaohui Chen
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Yao Xu
- R&D Department of AtaGenix Laboratories Co., Ltd. (Wuhan), Wuhan, China
| | - Dongxiang Zhang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Peng Zhang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
| | - Junbo Zhao
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China.
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
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14
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Liao M, Gong H, Quan X, Wang Z, Hu X, Chen Z, Li Z, Liu H, Zhang L, McBain AJ, Waigh TA, Zhou J, Lu JR. Intramembrane Nanoaggregates of Antimicrobial Peptides Play a Vital Role in Bacterial Killing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204428. [PMID: 36417574 DOI: 10.1002/smll.202204428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Recent developments in antimicrobial peptides (AMPs) have focused on the rational design of short sequences with less than 20 amino acids due to their relatively low synthesis costs and ease of correlation of the structure-function relationship. However, gaps remain in the understanding of how short cationic AMPs interact with the bacterial outer and inner membranes to affect their antimicrobial efficacy and dynamic killing. The membrane-lytic actions of two designed AMPs, G(IIKK)3 I-NH2 (G3 ) and G(IIKK)4 I-NH2 (G4 ), and previously-studied controls GLLDLLKLLLKAAG-NH2 (LDKA, biomimetic) and GIGAVLKVLTTGLPALISWIKRKR-NH2 (Melittin, natural) are examined. The mechanistic processes of membrane damage and the disruption strength of the four AMPs are characterized by molecular dynamics simulations and experimental measurements including neutron reflection and scattering. The results from the combined studies are characterized with distinctly different intramembrane nanoaggregates formed upon AMP-specific binding, reflecting clear influences of AMP sequence, charge and the chemistry of the inner and outer membranes. G3 and G4 display different nanoaggregation with the outer and inner membranes, and the smaller sizes and further extent of insertion of the intramembrane nanoaggregates into bacterial membranes correlate well with their greater antimicrobial efficacy and faster dynamic killing. This work demonstrates the crucial roles of intramembrane nanoaggregates in optimizing antimicrobial efficacy and dynamic killing.
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Affiliation(s)
- Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, China
| | - Ziwei Wang
- National Graphene Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Xuzhi Hu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Zheng Chen
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, China
| | - Zongyi Li
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Huayang Liu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Lin Zhang
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Andrew J McBain
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thomas A Waigh
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, China
| | - Jian Ren Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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15
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Chen X, Wu X, Wang S. An optimized antimicrobial peptide analog acts as an antibiotic adjuvant to reverse methicillin-resistant Staphylococcus aureus. NPJ Sci Food 2022; 6:57. [PMID: 36509755 PMCID: PMC9744894 DOI: 10.1038/s41538-022-00171-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
The misuse of antibiotics in animal protein production has driven the emergence of a range of drug-resistant pathogens, which threaten existing public health security. Consequently, there is an urgent need to develop novel antimicrobials and new infection treatment options to address the challenges posed by the dramatic spread of antibiotic resistance. Piscidins, a class of fish-specific antimicrobial peptides (AMPs), are regarded as promising therapies for biomedical applications. Progress towards potential analogs from the piscidin family has been hampered by unenforceable structural optimization strategies. Here, we leverage a strategy of bioinformatics analysis combined with molecular dynamics (MD) simulation to identify specific functional hotspots in piscidins and rationally design related analogues. As expected, this approach yields a potent and non-toxic PIS-A-1 that can be used as an antibiotic adjuvant to reverse methicillin-resistant Staphylococcus aureus (MRSA) pathogens. Remarkably, the structural optimization scheme and application strategy proposed here will contribute richer therapeutic options for the safe production of animal protein.
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Affiliation(s)
- Xuan Chen
- grid.411604.60000 0001 0130 6528College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian 350108 China ,grid.411604.60000 0001 0130 6528College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108 China
| | - Xiaoping Wu
- grid.411604.60000 0001 0130 6528College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian 350108 China ,grid.411604.60000 0001 0130 6528College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108 China
| | - Shaoyun Wang
- grid.411604.60000 0001 0130 6528College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108 China
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16
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Matching amino acids membrane preference profile to improve activity of antimicrobial peptides. Commun Biol 2022; 5:1199. [PMID: 36347951 PMCID: PMC9643456 DOI: 10.1038/s42003-022-04164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are cationic antibiotics that can kill multidrug-resistant bacteria via membrane insertion. However, their weak activity limits their clinical use. Ironically, the cationic charge of AMPs is essential for membrane binding, but it obstructs membrane insertion. In this study, we postulate that this problem can be overcome by locating cationic amino acids at the energetically preferred membrane surface. All amino acids have an energetically preferred or less preferred membrane position profile, and this profile is strongly related to membrane insertion. However, most AMPs do not follow this profile. One exception is protegrin-1, a powerful but neglected AMP. In the present study, we found that a potent AMP, WCopW5, strongly resembles protegrin-1 and that the match between its sequence and the preferred position profile closely correlates with its antimicrobial activity. One of its derivatives, WCopW43, has antimicrobial activity comparable to that of the most effective AMPs in clinical use.
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17
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Zou W, Zhang Y, Zhou M, Chen X, Ma C, Wang T, Jiang Y, Chen T, Shaw C, Wang L. Exploring the active core of a novel antimicrobial peptide, palustrin-2LTb, from the Kuatun frog, Hylarana latouchii, using a bioinformatics-directed approach. Comput Struct Biotechnol J 2022; 20:6192-6205. [DOI: 10.1016/j.csbj.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
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18
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Parra ALC, Freitas CDT, Souza PFN, von Aderkas P, Borchers CH, Beattie GA, Silva FDA, Thornburg RW. Ornamental tobacco floral nectar is a rich source of antimicrobial peptides. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111427. [PMID: 36007629 DOI: 10.1016/j.plantsci.2022.111427] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/29/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Although floral nectar is a rich source of nutrients, it is rarely infected by microorganisms. Defense molecules such as proteins have been identified in this fluid, but defense peptides have been largely overlooked. Thus, the aim of this study was to perform an extensive peptidomic analysis of the ornamental tobacco floral nectar to seek peptides involved in nectar defense. Using LC-MS/MS, 793 peptides were sequenced and characterized. After extensive bioinformatics analysis, six peptides were selected for further characterization, synthesis, and evaluation of their antimicrobial properties against phytopathogenic fungi and bacteria. All six peptides had antimicrobial activity to some extent. However, the activity varied by peptide concentration and microorganism tested. An analysis of the action mechanism revealed damage in the cell membrane induced by peptides. The results show that floral nectar is rich in peptides and that, together with proteins and hydrogen peroxide, they contribute to plant defense against microorganisms during pollination.
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Affiliation(s)
- Aura L C Parra
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cleverson D T Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil; Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA.
| | - Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Patrick von Aderkas
- University of Victoria - Genome BC Proteomics Center, University of Victoria, Victoria, BC V8P 5C2, Canada; Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | - Gwyn A Beattie
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Fredy D A Silva
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Robert W Thornburg
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA.
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19
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Griffith A, Mateen A, Markowitz K, Singer SR, Cugini C, Shimizu E, Wiedman GR, Kumar V. Alternative Antibiotics in Dentistry: Antimicrobial Peptides. Pharmaceutics 2022; 14:1679. [PMID: 36015305 PMCID: PMC9412702 DOI: 10.3390/pharmaceutics14081679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 01/12/2023] Open
Abstract
The rise of antibiotic resistant bacteria due to overuse and misuse of antibiotics in medicine and dentistry is a growing concern. New approaches are needed to combat antibiotic resistant (AR) bacterial infections. There are a number of methods available and in development to address AR infections. Dentists conventionally use chemicals such as chlorohexidine and calcium hydroxide to kill oral bacteria, with many groups recently developing more biocompatible antimicrobial peptides (AMPs) for use in the oral cavity. AMPs are promising candidates in the treatment of (oral) infections. Also known as host defense peptides, AMPs have been isolated from animals across all kingdoms of life and play an integral role in the innate immunity of both prokaryotic and eukaryotic organisms by responding to pathogens. Despite progress over the last four decades, there are only a few AMPs approved for clinical use. This review summarizes an Introduction to Oral Microbiome and Oral Infections, Traditional Antibiotics and Alternatives & Antimicrobial Peptides. There is a focus on cationic AMP characteristics and mechanisms of actions, and an overview of animal-derived natural and synthetic AMPs, as well as observed microbial resistance.
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Affiliation(s)
- Alexandra Griffith
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Akilah Mateen
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Kenneth Markowitz
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07103, USA
| | - Steven R. Singer
- Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ 07103, USA
| | - Carla Cugini
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07103, USA
| | - Emi Shimizu
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ 07103, USA
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ 07103, USA
| | - Gregory R. Wiedman
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Vivek Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ 07103, USA
- Department of Biology, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Department of Chemical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
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20
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Lv S, Wang J, You R, Liu S, Ding Y, Hadianamrei R, Tomeh MA, Pan F, Cai Z, Zhao X. Highly selective performance of rationally designed antimicrobial peptides based on ponericin-W1. Biomater Sci 2022; 10:4848-4865. [PMID: 35861280 DOI: 10.1039/d2bm00744d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) or host-defence peptides act by penetrating and disrupting the bacterial membranes and are therefore less prone to antimicrobial resistance (AMR) compared to conventional antibiotics. However, there are still many challenges in the clinical application of the naturally occurring AMPs which necessitates further studies to establish the relationship between the chemical structure of AMPs and their antimicrobial activity and selectivity. Herein, we report a study on the relationship between the chemical structure and the biological activity of a series of rationally designed AMPs derived from Ponericin-W1, a naturally occurring AMP from ants. The peptides were designed by modification of the hydrophobic and hydrophilic regions of the lead peptide sequence in a systematic way. Their antibacterial and hemolytic activities were determined in vitro. The antibacterial activity of a representative peptide, At5 was also tested in a mouse model of skin wound infection. Furthermore, the relationship between the physicochemical properties of the peptides and their antibacterial activity was investigated. Replacing the cationic amino acids in the hydrophobic region of the peptides with hydrophobic amino acids enhanced their antibacterial activity and increasing the number of cationic amino acids in the hydrophilic region reduced their toxicity to human red blood cells and thus improved their selectivity for bacteria. Four of the designed peptides, coded as At3, At5, At8, and At10, displayed considerable antibacterial activity and high selectivity for bacteria. At5 also accelerated the wound healing in mice indicating high in vivo efficiency of this peptide. The peptides were more effective against Gram-negative bacteria and no AMR was developed against them in the bacteria even after 25 generations. The results from this study can provide a better understanding of the structural features required for strong antibacterial activity and selectivity, and serve as a guide for the future rational design of AMPs.
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Affiliation(s)
- Songwei Lv
- School of Pharmacy, Changzhou University, Changzhou 213164, China.
| | - Jingfang Wang
- School of Pharmacy, Changzhou University, Changzhou 213164, China.
| | - Rongrong You
- School of Pharmacy, Changzhou University, Changzhou 213164, China.
| | - Suyu Liu
- School of Pharmacy, Changzhou University, Changzhou 213164, China. .,Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Yujie Ding
- School of Pharmacy, Changzhou University, Changzhou 213164, China.
| | - Roja Hadianamrei
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Mhd Anas Tomeh
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Fang Pan
- School of Pharmacy, Changzhou University, Changzhou 213164, China.
| | - Zhiqiang Cai
- School of Pharmacy, Changzhou University, Changzhou 213164, China.
| | - Xiubo Zhao
- School of Pharmacy, Changzhou University, Changzhou 213164, China. .,Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
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21
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The Multistage Antimalarial Compound Calxinin Perturbates P. falciparum Ca2+ Homeostasis by Targeting a Unique Ion Channel. Pharmaceutics 2022; 14:pharmaceutics14071371. [PMID: 35890267 PMCID: PMC9319510 DOI: 10.3390/pharmaceutics14071371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 12/22/2022] Open
Abstract
Malaria elimination urgently needs novel antimalarial therapies that transcend resistance, toxicity, and high costs. Our multicentric international collaborative team focuses on developing multistage antimalarials that exhibit novel mechanisms of action. Here, we describe the design, synthesis, and evaluation of a novel multistage antimalarial compound, ‘Calxinin’. A compound that consists of hydroxyethylamine (HEA) and trifluoromethyl-benzyl-piperazine. Calxinin exhibits potent inhibitory activity in the nanomolar range against the asexual blood stages of drug-sensitive (3D7), multidrug-resistant (Dd2), artemisinin-resistant (IPC4912), and fresh Kenyan field isolated Plasmodium falciparum strains. Calxinin treatment resulted in diminished maturation of parasite sexual precursor cells (gametocytes) accompanied by distorted parasite morphology. Further, in vitro liver-stage testing with a mouse model showed reduced parasite load at an IC50 of 79 nM. A single dose (10 mg/kg) of Calxinin resulted in a 30% reduction in parasitemia in mice infected with a chloroquine-resistant strain of the rodent parasite P. berghei. The ex vivo ookinete inhibitory concentration within mosquito gut IC50 was 150 nM. Cellular in vitro toxicity assays in the primary and immortalized human cell lines did not show cytotoxicity. A computational protein target identification pipeline identified a putative P. falciparum membrane protein (Pf3D7_1313500) involved in parasite calcium (Ca2+) homeostasis as a potential Calxinin target. This highly conserved protein is related to the family of transient receptor potential cation channels (TRP-ML). Target validation experiments showed that exposure of parasitized RBCs (pRBCs) to Calxinin induces a rapid release of intracellular Ca2+ from pRBCs; leaving de-calcinated parasites trapped in RBCs. Overall, we demonstrated that Calxinin is a promising antimalarial lead compound with a novel mechanism of action and with potential therapeutic, prophylactic, and transmission-blocking properties against parasites resistant to current antimalarials.
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22
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Chen CH, Liu Y, Eskandari A, Ghimire J, Lin LC, Fang Z, Wimley WC, Ulmschneider JP, Suntharalingam K, Hu CJ, Ulmschneider MB. Integrated Design of a Membrane-Lytic Peptide-Based Intravenous Nanotherapeutic Suppresses Triple-Negative Breast Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105506. [PMID: 35246961 PMCID: PMC9069370 DOI: 10.1002/advs.202105506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/12/2022] [Indexed: 05/30/2023]
Abstract
Membrane-lytic peptides offer broad synthetic flexibilities and design potential to the arsenal of anticancer therapeutics, which can be limited by cytotoxicity to noncancerous cells and induction of drug resistance via stress-induced mutagenesis. Despite continued research efforts on membrane-perforating peptides for antimicrobial applications, success in anticancer peptide therapeutics remains elusive given the muted distinction between cancerous and normal cell membranes and the challenge of peptide degradation and neutralization upon intravenous delivery. Using triple-negative breast cancer as a model, the authors report the development of a new class of anticancer peptides. Through function-conserving mutations, the authors achieved cancer cell selective membrane perforation, with leads exhibiting a 200-fold selectivity over non-cancerogenic cells and superior cytotoxicity over doxorubicin against breast cancer tumorspheres. Upon continuous exposure to the anticancer peptides at growth-arresting concentrations, cancer cells do not exhibit resistance phenotype, frequently observed under chemotherapeutic treatment. The authors further demonstrate efficient encapsulation of the anticancer peptides in 20 nm polymeric nanocarriers, which possess high tolerability and lead to effective tumor growth inhibition in a mouse model of MDA-MB-231 triple-negative breast cancer. This work demonstrates a multidisciplinary approach for enabling translationally relevant membrane-lytic peptides in oncology, opening up a vast chemical repertoire to the arms race against cancer.
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Affiliation(s)
- Charles H. Chen
- Department of ChemistryKing's College LondonLondonSE1 1DBUK
- Synthetic Biology GroupResearch Laboratory of ElectronicsMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Yu‐Han Liu
- Institute of Biomedical SciencesAcademia SinicaTaipei115Taiwan
| | | | - Jenisha Ghimire
- Department of Biochemistry and Molecular BiologyTulane UniversityNew OrleansLA70112USA
| | | | - Zih‐Syun Fang
- Institute of Biomedical SciencesAcademia SinicaTaipei115Taiwan
| | - William C. Wimley
- Department of Biochemistry and Molecular BiologyTulane UniversityNew OrleansLA70112USA
| | - Jakob P. Ulmschneider
- Department of PhysicsInstitute of Natural SciencesShanghai Jiao Tong UniversityShanghai200240China
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23
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Chen CH, Bepler T, Pepper K, Fu D, Lu TK. Synthetic molecular evolution of antimicrobial peptides. Curr Opin Biotechnol 2022; 75:102718. [PMID: 35395425 DOI: 10.1016/j.copbio.2022.102718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 01/18/2023]
Abstract
As we learn more about how peptide structure and activity are related, we anticipate that antimicrobial peptides will be engineered to have strong potency and distinct functions and that synthetic peptides will have new biomedical applications, such as treatments for emerging infectious diseases. As a result of the enormous number of possible amino acid sequences and the low-throughput nature of antimicrobial peptide assays, computational tools for peptide design and optimization are needed for direct experimentation toward obtaining functional sequences. Recent developments in computational tools have improved peptide design, saving labor, reagents, costs, and time. At the same time, improvements in peptide synthesis and experimental platforms continue to reduce the cost and increase the throughput of peptide-drug screening. In this review, we discuss the current methods of peptide design and engineering, including in silico methods and peptide synthesis and screening, and highlight areas of potential improvement.
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Affiliation(s)
- Charles H Chen
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Tristan Bepler
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Simons Machine Learning Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Karen Pepper
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Debbie Fu
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Timothy K Lu
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Senti Biosciences, South San Francisco, CA 94080, USA.
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24
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Prediction of Linear Cationic Antimicrobial Peptides Active against Gram-Negative and Gram-Positive Bacteria Based on Machine Learning Models. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073631] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Antimicrobial peptides (AMPs) are considered as promising alternatives to conventional antibiotics in order to overcome the growing problems of antibiotic resistance. Computational prediction approaches receive an increasing interest to identify and design the best candidate AMPs prior to the in vitro tests. In this study, we focused on the linear cationic peptides with non-hemolytic activity, which are downloaded from the Database of Antimicrobial Activity and Structure of Peptides (DBAASP). Referring to the MIC (Minimum inhibition concentration) values, we have assigned a positive label to a peptide if it shows antimicrobial activity; otherwise, the peptide is labeled as negative. Here, we focused on the peptides showing antimicrobial activity against Gram-negative and against Gram-positive bacteria separately, and we created two datasets accordingly. Ten different physico-chemical properties of the peptides are calculated and used as features in our study. Following data exploration and data preprocessing steps, a variety of classification algorithms are used with 100-fold Monte Carlo Cross-Validation to build models and to predict the antimicrobial activity of the peptides. Among the generated models, Random Forest has resulted in the best performance metrics for both Gram-negative dataset (Accuracy: 0.98, Recall: 0.99, Specificity: 0.97, Precision: 0.97, AUC: 0.99, F1: 0.98) and Gram-positive dataset (Accuracy: 0.95, Recall: 0.95, Specificity: 0.95, Precision: 0.90, AUC: 0.97, F1: 0.92) after outlier elimination is applied. This prediction approach might be useful to evaluate the antibacterial potential of a candidate peptide sequence before moving to the experimental studies.
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25
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Kumari S, Booth V. Antimicrobial Peptide Mechanisms Studied by Whole-Cell Deuterium NMR. Int J Mol Sci 2022; 23:ijms23052740. [PMID: 35269882 PMCID: PMC8910884 DOI: 10.3390/ijms23052740] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/29/2022] Open
Abstract
Much of the work probing antimicrobial peptide (AMP) mechanisms has focussed on how these molecules permeabilize lipid bilayers. However, AMPs must also traverse a variety of non-lipid cell envelope components before they reach the lipid bilayer. Additionally, there is a growing list of AMPs with non-lipid targets inside the cell. It is thus useful to extend the biophysical methods that have been traditionally applied to study AMP mechanisms in liposomes to the full bacteria, where the lipids are present along with the full complexity of the rest of the bacterium. This review focusses on what can be learned about AMP mechanisms from solid-state NMR of AMP-treated intact bacteria. It also touches on flow cytometry as a complementary method for measuring permeabilization of bacterial lipid membranes in whole bacteria.
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Affiliation(s)
- Sarika Kumari
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada;
| | - Valerie Booth
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada;
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
- Correspondence: ; Tel.: +1-709-864-4523
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26
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MacDermott-Opeskin HI, Gupta V, O’Mara ML. Lipid-mediated antimicrobial resistance: a phantom menace or a new hope? Biophys Rev 2022; 14:145-162. [PMID: 35251360 PMCID: PMC8880301 DOI: 10.1007/s12551-021-00912-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/14/2021] [Indexed: 02/06/2023] Open
Abstract
Abstract The proposition of a post-antimicrobial era is all the more realistic with the continued rise of antimicrobial resistance. The development of new antimicrobials is failing to counter the ever-increasing rates of bacterial antimicrobial resistance. This necessitates novel antimicrobials and drug targets. The bacterial cell membrane is an essential and highly conserved cellular component in bacteria and acts as the primary barrier for entry of antimicrobials into the cell. Although previously under-exploited as an antimicrobial target, the bacterial cell membrane is attractive for the development of novel antimicrobials due to its importance in pathogen viability. Bacterial cell membranes are diverse assemblies of macromolecules built around a central lipid bilayer core. This lipid bilayer governs the overall membrane biophysical properties and function of its membrane-embedded proteins. This mini-review will outline the mechanisms by which the bacterial membrane causes and controls resistance, with a focus on alterations in the membrane lipid composition, chemical modification of constituent lipids, and the efflux of antimicrobials by membrane-embedded efflux systems. Thorough insight into the interplay between membrane-active antimicrobials and lipid-mediated resistance is needed to enable the rational development of new antimicrobials. In particular, the union of computational approaches and experimental techniques for the development of innovative and efficacious membrane-active antimicrobials is explored.
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Affiliation(s)
- Hugo I. MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Vrinda Gupta
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Megan L. O’Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
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27
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Gimenez-Dejoz J, Numata K. Molecular dynamics study of the internalization of cell-penetrating peptides containing unnatural amino acids across membranes. NANOSCALE ADVANCES 2022; 4:397-407. [PMID: 36132688 PMCID: PMC9419563 DOI: 10.1039/d1na00674f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/10/2021] [Indexed: 06/16/2023]
Abstract
Peptide-based delivery systems that deliver target molecules into cells have been gaining traction. These systems need cell-penetrating peptides (CPPs), which have the remarkable ability to penetrate into biological membranes and help internalize different cargoes into cells through the cell membranes. The molecular internalization mechanism and structure-function relationships of CPPs are not clear, although the incorporation of nonproteinogenic amino acids such as α-aminoisobutyric acid (Aib) has been reported to increase their helicity, biostability and penetration efficiencies. Here, we used molecular dynamics to study two Aib-containing CPPs, poly(LysAibAla)3 (KAibA) and poly(LysAibGly)3 (KAibG), that previously showed high cell internalization efficiency. KAibA and KAibG displayed the lowest internalization energies among the studied CPPs, showing distinct internalization mechanisms depending on the lipid composition of the model membranes. The presence of Aib residues allows these CPPs to adopt amphipathic folding to efficiently penetrate through the membranes. Elucidating how Aib incorporation affects CPP-membrane binding and interactions is beneficial for the design of CPPs for efficient intracellular delivery.
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Affiliation(s)
- Joan Gimenez-Dejoz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science Saitama Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science Saitama Japan
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University Kyoto Japan
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28
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Tsai CY, Salawu EO, Li H, Lin GY, Kuo TY, Voon L, Sharma A, Hu KD, Cheng YY, Sahoo S, Stuart L, Chen CW, Chang YY, Lu YL, Ke S, Ortiz CLD, Fang BS, Wu CC, Lan CY, Fu HW, Yang LW. Helical structure motifs made searchable for functional peptide design. Nat Commun 2022; 13:102. [PMID: 35013238 PMCID: PMC8748493 DOI: 10.1038/s41467-021-27655-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 12/03/2021] [Indexed: 11/09/2022] Open
Abstract
The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/ .
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Affiliation(s)
- Cheng-Yu Tsai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, 100025, Taiwan.,Department of Otolaryngology, National Taiwan University Hospital, Taipei, 100225, Taiwan
| | - Emmanuel Oluwatobi Salawu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan.,Bioinformatics Program, Institute of Information Sciences, Academia Sinica, Taipei, 115201, Taiwan.,Machine Learning Solutions Lab, Amazon Web Services (AWS), Herndon, VA, USA
| | - Hongchun Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan.,Research Center for Computer-Aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.,College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.,Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Guan-Yu Lin
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Ting-Yu Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Liyin Voon
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Adarsh Sharma
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Kai-Di Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Yi-Yun Cheng
- Praexisio Taiwan Inc., New Taipei, 221425, Taiwan
| | - Sobha Sahoo
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Lutimba Stuart
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Chih-Wei Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan.,Praexisio Taiwan Inc., New Taipei, 221425, Taiwan
| | - Yu-Lin Lu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Simai Ke
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Christopher Llynard D Ortiz
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan.,Chemical Biology and Molecular Biophysics Program, Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Bai-Shan Fang
- College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.,The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, 361005, Xiamen, China
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, 100225, Taiwan.,Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, 302058, Taiwan
| | - Chung-Yu Lan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan. .,Department of Life Science, National Tsing Hua University, Hsinchu, 300044, Taiwan.
| | - Hua-Wen Fu
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan. .,Department of Life Science, National Tsing Hua University, Hsinchu, 300044, Taiwan.
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan. .,Bioinformatics Program, Institute of Information Sciences, Academia Sinica, Taipei, 115201, Taiwan. .,Physics Division, National Center for Theoretical Sciences, Taipei, 106319, Taiwan. .,PhD Program in Biomedical Artificial Intelligence, National Tsing Hua University, Hsinchu, 300044, Taiwan.
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29
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Chen CH, Pepper K, Ulmschneider JP, Ulmschneider MB, Lu TK. Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes. Methods Mol Biol 2022; 2405:115-136. [PMID: 35298811 DOI: 10.1007/978-1-0716-1855-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Understanding the interactions between peptides and lipid membranes could not only accelerate the development of antimicrobial peptides as treatments for infections but also be applied to finding targeted therapies for cancer and other diseases. However, designing biophysical experiments to study molecular interactions between flexible peptides and fluidic lipid membranes has been an ongoing challenge. Recently, with hardware advances, algorithm improvements, and more accurate parameterizations (i.e., force fields), all-atom molecular dynamics (MD) simulations have been used as a "computational microscope" to investigate the molecular interactions and mechanisms of membrane-active peptides in cell membranes (Chen et al., Curr Opin Struct Biol 61:160-166, 2020; Ulmschneider and Ulmschneider, Acc Chem Res 51(5):1106-1116, 2018; Dror et al., Annu Rev Biophys 41:429-452, 2012). In this chapter, we describe how to utilize MD simulations to predict and study peptide dynamics and how to validate the simulations by circular dichroism, intrinsic fluorescent probe, membrane leakage assay, electrical impedance, and isothermal titration calorimetry. Experimentally validated MD simulations open a new route towards peptide design starting from sequence and structure and leading to desirable functions.
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Affiliation(s)
- Charles H Chen
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Karen Pepper
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jakob P Ulmschneider
- Department of Physics, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | | | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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30
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dos Santos-Silva CA, Tricarico PM, Vilela LMB, Roldan-Filho RS, Amador VC, d’Adamo AP, Rêgo MDS, Benko-Iseppon AM, Crovella S. Plant Antimicrobial Peptides as Potential Tool for Topic Treatment of Hidradenitis Suppurativa. Front Microbiol 2021; 12:795217. [PMID: 34966375 PMCID: PMC8710806 DOI: 10.3389/fmicb.2021.795217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
Among chronic skin autoinflammatory diseases, Hidradenitis Suppurativa (HS) stands out for its chronicity, highly variable condition, and profound impact on the patients' quality of life. HS is characterized by suppurative skin lesions in diverse body areas, including deep-seated painful nodules, abscesses, draining sinus, and bridged scars, among others, with typical topography. To date, HS is considered a refractory disease and medical treatments aim to reduce the incidence, the infection, and the pain of the lesions. For this purpose, different classes of drugs, including anti-inflammatory molecules, antibiotics and biological drugs are being used. Antimicrobial peptides (AMPs), also called defense peptides, emerge as a new class of therapeutic compounds, with broad-spectrum antimicrobial action, in addition to reports on their anti-inflammatory, healing, and immunomodulating activity. Such peptides are present in prokaryotes and eukaryotes, as part of the innate eukaryotic immune system. It has been proposed that a deregulation in the expression of AMPs in human epithelial tissues of HS patients may be associated with the etiology of this skin disease. In this scenario, plant AMPs stand out for their richness, diversity of types, and broad antimicrobial effects, with potential application for topical systemic use in patients affected by HS.
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Affiliation(s)
| | | | | | | | - Vinícius Costa Amador
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Adamo Pio d’Adamo
- Institute for Maternal and Child Health – IRCCS Burlo Garofolo, Trieste, Italy
- Department of Medical Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Mireli de Santana Rêgo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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31
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Bobde SS, Alsaab FM, Wang G, Van Hoek ML. Ab initio Designed Antimicrobial Peptides Against Gram-Negative Bacteria. Front Microbiol 2021; 12:715246. [PMID: 34867843 PMCID: PMC8636942 DOI: 10.3389/fmicb.2021.715246] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Antimicrobial peptides (AMPs) are ubiquitous amongst living organisms and are part of the innate immune system with the ability to kill pathogens directly or indirectly by modulating the immune system. AMPs have potential as a novel therapeutic against bacteria due to their quick-acting mechanism of action that prevents bacteria from developing resistance. Additionally, there is a dire need for therapeutics with activity specifically against Gram-negative bacterial infections that are intrinsically difficult to treat, with or without acquired drug resistance. Development of new antibiotics has slowed in recent years and novel therapeutics (like AMPs) with a focus against Gram-negative bacteria are needed. We designed eight novel AMPs, termed PHNX peptides, using ab initio computational design (database filtering technology combined with the novel positional analysis on APD3 dataset of AMPs with activity against Gram-negative bacteria) and assessed their theoretical function using published machine learning algorithms, and finally, validated their activity in our laboratory. These AMPs were tested to establish their minimum inhibitory concentration (MIC) and half-maximal effective concentration (EC50) under CLSI methodology against antibiotic resistant and antibiotic susceptible Escherichia coli and Staphylococcus aureus. Laboratory-based experimental results were compared to computationally predicted activities for each of the peptides to ascertain the accuracy of the computational tools used. PHNX-1 demonstrated antibacterial activity (under high and low-salt conditions) against antibiotic resistant and susceptible strains of Gram-positive and Gram-negative bacteria and PHNX-4 to -8 demonstrated low-salt antibacterial activity only. The AMPs were then evaluated for cytotoxicity using hemolysis against human red blood cells and demonstrated some hemolysis which needs to be further evaluated. In this study, we successfully developed a design methodology to create synthetic AMPs with a narrow spectrum of activity where the PHNX AMPs demonstrated higher antibacterial activity against Gram-negative bacteria compared to Gram-positive bacteria. Thus, these peptides present novel synthetic peptides with a potential for therapeutic use. Based on our findings, we propose upfront selection of the peptide dataset for analysis, an additional step of positional analysis to add to the ab initio database filtering technology (DFT) method, and we present laboratory data on the novel, synthetically designed AMPs to validate the results of the computational approach. We aim to conduct future in vivo studies which could establish these AMPs for clinical use.
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Affiliation(s)
- Shravani S. Bobde
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Fahad M. Alsaab
- School of Systems Biology, George Mason University, Manassas, VA, United States
- College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Al Ahsa, Saudi Arabia
| | - Guangshuan Wang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Monique L. Van Hoek
- School of Systems Biology, George Mason University, Manassas, VA, United States
- *Correspondence: Monique L. Van Hoek,
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32
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Bin Hafeez A, Jiang X, Bergen PJ, Zhu Y. Antimicrobial Peptides: An Update on Classifications and Databases. Int J Mol Sci 2021; 22:11691. [PMID: 34769122 PMCID: PMC8583803 DOI: 10.3390/ijms222111691] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.
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Affiliation(s)
- Ahmer Bin Hafeez
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan;
| | - Xukai Jiang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Phillip J. Bergen
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
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33
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Ting DSJ, Li J, Verma CS, Goh ETL, Nubile M, Mastropasqua L, Said DG, Beuerman RW, Lakshminarayanan R, Mohammed I, Dua HS. Evaluation of Host Defense Peptide (CaD23)-Antibiotic Interaction and Mechanism of Action: Insights From Experimental and Molecular Dynamics Simulations Studies. Front Pharmacol 2021; 12:731499. [PMID: 34690770 PMCID: PMC8528955 DOI: 10.3389/fphar.2021.731499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background/Aim: Host defense peptides (HDPs) have the potential to provide a novel solution to antimicrobial resistance (AMR) in view of their unique and broad-spectrum antimicrobial activities. We had recently developed a novel hybrid HDP based on LL-37 and human beta-defensin-2, named CaD23, which was shown to exhibit good in vivo antimicrobial efficacy against Staphylococcus aureus in a bacterial keratitis murine model. This study aimed to examine the potential CaD23-antibiotic synergism and the secondary structure and underlying mechanism of action of CaD23. Methods: Peptide-antibiotic interaction was evaluated against S. aureus, methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa using established checkerboard and time-kill assays. Fractional inhibitory concentration index (FICI) was calculated and interpreted as synergistic (FIC<0.5), additive (FIC between 0.5-1.0), indifferent (FIC between >1.0 and ≤4), or antagonistic (FIC>4). SYTOX green uptake assay was performed to determine the membrane-permeabilising action of CaD23. Molecular dynamics (MD) simulations were performed to evaluate the interaction of CaD23 with bacterial and mammalian mimetic membranes. Circular dichroism (CD) spectroscopy was also performed to examine the secondary structures of CaD23. Results: CaD23-amikacin and CaD23-levofloxacin combination treatment exhibited a strong additive effect against S. aureus SH1000 (FICI = 0.60-0.69) and MRSA43300 (FICI = 0.56-0.60) but an indifferent effect against P. aeruginosa (FIC = 1.03-1.15). CaD23 (at 25 μg/ml; 2xMIC) completely killed S. aureus within 30 min. When used at sub-MIC concentration (3.1 μg/ml; 0.25xMIC), it was able to expedite the antimicrobial action of amikacin against S. aureus by 50%. The rapid antimicrobial action of CaD23 was attributed to the underlying membrane-permeabilising mechanism of action, evidenced by the SYTOX green uptake assay and MD simulations studies. MD simulations revealed that cationicity, alpha-helicity, amphiphilicity and hydrophobicity (related to the Trp residue at C-terminal) play important roles in the antimicrobial action of CaD23. The secondary structures of CaD23 observed in MD simulations were validated by CD spectroscopy. Conclusion: CaD23 is a novel alpha-helical, membrane-active synthetic HDP that can enhance and expedite the antimicrobial action of antibiotics against Gram-positive bacteria when used in combination. MD simulations serves as a powerful tool in revealing the peptide secondary structure, dissecting the mechanism of action, and guiding the design and optimisation of HDPs.
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Affiliation(s)
- Darren Shu Jeng Ting
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom.,Anti-Infectives Research Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Jianguo Li
- Anti-Infectives Research Group, Singapore Eye Research Institute, Singapore, Singapore.,Bioinformatics Institute (AStar), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute (AStar), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Eunice T L Goh
- Anti-Infectives Research Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Mario Nubile
- Ophthalmic Clinic, University "G d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | | | - Dalia G Said
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - Roger W Beuerman
- Anti-Infectives Research Group, Singapore Eye Research Institute, Singapore, Singapore
| | | | - Imran Mohammed
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Harminder S Dua
- Academic Ophthalmology, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
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34
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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35
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Chemical syntheses of bioinspired and biomimetic polymers toward biobased materials. Nat Rev Chem 2021; 5:753-772. [DOI: 10.1038/s41570-021-00325-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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36
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Vishweshwaraiah YL, Acharya A, Hegde V, Prakash B. Rational design of hyperstable antibacterial peptides for food preservation. NPJ Sci Food 2021; 5:26. [PMID: 34471114 PMCID: PMC8410836 DOI: 10.1038/s41538-021-00109-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
We describe the design of peptides with properties like thermostability, pH stability, and antibacterial activity against a few bacterial food pathogens. Insights obtained from classical structure-function analysis of natural peptides and their mutants through antimicrobial and enzymatic assays are used to rationally develop a set of peptides. pH and thermostability assays were performed to demonstrate robust antimicrobial activity post-treatment with high temperatures and at wide pH ranges. We have also investigated the mode of action of these hyperstable peptides using membrane permeability assays, electron microscopy, and molecular dynamics simulations. Notably, through mutational studies, we show that these peptides elicit their antibacterial action via both membrane destabilization and inhibition of intracellular trypsin-the two functions attributable to separate peptide segments. Finally, toxicity studies and food preservation assays demonstrate the safety and efficacy of the designed peptides for food preservation. Overall, the study provides a general 'blueprint' for the development of stable antimicrobial peptides (AMPs). Insights obtained from this work may also be combined with combinatorial methods in high-throughput studies for future development of antimicrobials for various applications.
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Affiliation(s)
- Yashavantha L. Vishweshwaraiah
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Abhishek Acharya
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Vinayak Hegde
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh India
| | - Balaji Prakash
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India ,grid.448607.90000 0004 1781 3606Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat India
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37
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Talandashti R, Mehrnejad F, Rostamipour K, Doustdar F, Lavasanifar A. Molecular Insights into Pore Formation Mechanism, Membrane Perturbation, and Water Permeation by the Antimicrobial Peptide Pleurocidin: A Combined All-Atom and Coarse-Grained Molecular Dynamics Simulation Study. J Phys Chem B 2021; 125:7163-7176. [PMID: 34171196 DOI: 10.1021/acs.jpcb.1c01954] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The antimicrobial peptide (AMP) pleurocidin has a broad antimicrobial activity against Gram-negative and Gram-positive bacteria by perturbation and permeabilizing their membranes; however, understanding the mechanism of action of pleurocidin, a promising AMP for replacing current antibiotic agents, has tremendous importance for future applications. Hence, we applied all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations to provide molecular-level insights into the pore-forming process. The early stages of pore formation were examined by 500 ns AA simulations. The results demonstrated that pleurocidin has the ability to create a pore with two peptides through which water molecules can flow. However, the results of the 25 μs CG simulations indicate that the final pore will be created by accumulation of more than two peptides. The results show that after 2.5 μs of simulations, peptides will aggregate and create a channel-like pore across the membrane. Pleurocidin can construct a more efficient and stable pore in the anionic membranes than in the zwitterionic membranes. Moreover, the structure amphipathicity, polarity, and basic residues play crucial roles in the pore formation and flow of water molecules across the lipid bilayers. In general, the findings revealed that based on the lipid compositions of the membranes, pleurocidin could act by forming either toroidal or disordered toroidal pores with different peptide arrangements.
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Affiliation(s)
- Reza Talandashti
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, P. O. Box: 1985717443 Tehran, Iran.,Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Kiana Rostamipour
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Farahnoosh Doustdar
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran.,Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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38
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Marzuoli I, Cruz CHB, Lorenz CD, Fraternali F. Nanocapsule designs for antimicrobial resistance. NANOSCALE 2021; 13:10342-10355. [PMID: 34137751 DOI: 10.1039/d0nr08146a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The pressing need of new antimicrobial products is growing stronger, particularly because of widespread antimicrobial resistance, endangering our ability to treat common infections. The recent coronavirus pandemic has dramatically highlighted the necessity of effective antibacterial and antiviral protection. This work explores at the molecular level the mechanism of action of antibacterial nanocapsules assembled in virus-like particles, their stability and their interaction with mammal and antimicrobial model membranes. We use Molecular Dynamics with force-fields of different granularity and protein design strategies to study the stability, self-assembly and membrane poration properties of these nanocapsules.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | - Carlos H B Cruz
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | | | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
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39
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Reis PVM, Lima VM, Souza KR, Cardoso GA, Melo-Braga MN, Santos DM, Verly RM, Pimenta AMC, Dos Santos VL, de Lima ME. Synthetic Peptides Derived From Lycosa Erythrognatha Venom: Interaction With Phospholipid Membranes and Activity Against Resistant Bacteria. Front Mol Biosci 2021; 8:680940. [PMID: 34169094 PMCID: PMC8217815 DOI: 10.3389/fmolb.2021.680940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Superbugs are a public health problem, increasing the need of new drugs and strategies to combat them. Our group has previously identified LyeTxI, an antimicrobial peptide isolated from Lycosa erythrognatha spider venom. From LyeTxI, we synthesized and characterized a derived peptide named LyeTxI-b, which has shown significant in vitro and in vivo activity. In this work, we elucidate the interaction of LyeTxI-b with artificial membranes as well as its effects on resistant strains of bacteria in planktonic conditions or biofilms. Isothermal titration calorimetry revealed that LyeTxI-b interacts more rapidly and with higher intensity with artificial vesicles, showing higher affinity to anionic vesicles, when compared to synthetic LyeTxI. In calcein experiments, LyeTxI-b caused greater levels of vesicle cleavage. Both peptides showed antibacterial activity at concentrations of μmol L−1 against 12 different clinically isolated strains, in planktonic conditions, in a concentration-dependent manner. Furthermore, both peptides elicited a dose-dependent production of reactive oxygen species in methicillin-resistant Staphylococcus aureus. In S. aureus biofilm assay, LyeTxI-b was more potent than LyeTxI. However, none of these peptides reduced Escherichia coli biofilms. Our results show LyeTxI-b as a promising drug against clinically resistant strains, being a template for developing new antibiotics.
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Affiliation(s)
- Pablo V M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vinícius M Lima
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Kelton R Souza
- Departamento de Química, FACET, Universidade Federal dos Vales do Jequitinhonha e Mucuri - Campus JK, Diamantina, Brazil
| | - Gabriele A Cardoso
- Departamento de Química, FACET, Universidade Federal dos Vales do Jequitinhonha e Mucuri - Campus JK, Diamantina, Brazil
| | - Marcella N Melo-Braga
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Daniel M Santos
- Departamento de Bioquímica e Biologia Molecular, Campos Centro Oeste. Universidade Federal de São João Del-Rei, Diamantina, Brazil
| | - Rodrigo M Verly
- Departamento de Química, FACET, Universidade Federal dos Vales do Jequitinhonha e Mucuri - Campus JK, Diamantina, Brazil
| | - Adriano M C Pimenta
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vera Lúcia Dos Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Maria Elena de Lima
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil.,Faculdade Santa Casa de Belo Horizonte, Programa de Pós-Graduação em Medicina - Biomedicina, Belo Horizonte, Brazil
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40
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Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations. Nat Biomed Eng 2021; 5:613-623. [PMID: 33707779 DOI: 10.1038/s41551-021-00689-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/16/2021] [Indexed: 01/31/2023]
Abstract
The de novo design of antimicrobial therapeutics involves the exploration of a vast chemical repertoire to find compounds with broad-spectrum potency and low toxicity. Here, we report an efficient computational method for the generation of antimicrobials with desired attributes. The method leverages guidance from classifiers trained on an informative latent space of molecules modelled using a deep generative autoencoder, and screens the generated molecules using deep-learning classifiers as well as physicochemical features derived from high-throughput molecular dynamics simulations. Within 48 days, we identified, synthesized and experimentally tested 20 candidate antimicrobial peptides, of which two displayed high potency against diverse Gram-positive and Gram-negative pathogens (including multidrug-resistant Klebsiella pneumoniae) and a low propensity to induce drug resistance in Escherichia coli. Both peptides have low toxicity, as validated in vitro and in mice. We also show using live-cell confocal imaging that the bactericidal mode of action of the peptides involves the formation of membrane pores. The combination of deep learning and molecular dynamics may accelerate the discovery of potent and selective broad-spectrum antimicrobials.
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41
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Ricardo F, Pradilla D, Cruz JC, Alvarez O. Emerging Emulsifiers: Conceptual Basis for the Identification and Rational Design of Peptides with Surface Activity. Int J Mol Sci 2021; 22:4615. [PMID: 33924804 PMCID: PMC8124350 DOI: 10.3390/ijms22094615] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 01/06/2023] Open
Abstract
Emulsifiers are gradually evolving from synthetic molecules of petrochemical origin to biomolecules mainly due to health and environmental concerns. Peptides represent a type of biomolecules whose molecular structure is composed of a sequence of amino acids that can be easily tailored to have specific properties. However, the lack of knowledge about emulsifier behavior, structure-performance relationships, and the implementation of different design routes have limited the application of these peptides. Some computational and experimental approaches have tried to close this knowledge gap, but restrictions in understanding the fundamental phenomena and the limited property data availability have made the performance prediction for emulsifier peptides an area of intensive research. This study provides the concepts necessary to understand the emulsifying behavior of peptides. Additionally, a straightforward description is given of how the molecular structure and conditions of the system directly impact the peptides' ability to stabilize emulsion droplets. Moreover, the routes to design and discover novel peptides with interfacial and emulsifying activity are also discussed, along with the strategies to address some of their major pitfalls and challenges. Finally, this contribution reviews methodologies to build and use data sets containing standard properties of emulsifying peptides by looking at successful applications in different fields.
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Affiliation(s)
- Fabian Ricardo
- Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia; (F.R.); (D.P.)
| | - Diego Pradilla
- Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia; (F.R.); (D.P.)
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia;
| | - Oscar Alvarez
- Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia; (F.R.); (D.P.)
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42
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Gong H, Hu X, Liao M, Fa K, Ciumac D, Clifton LA, Sani MA, King SM, Maestro A, Separovic F, Waigh TA, Xu H, McBain AJ, Lu JR. Structural Disruptions of the Outer Membranes of Gram-Negative Bacteria by Rationally Designed Amphiphilic Antimicrobial Peptides. ACS APPLIED MATERIALS & INTERFACES 2021; 13:16062-16074. [PMID: 33797891 DOI: 10.1021/acsami.1c01643] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gram-negative bacteria are covered by both an inner cytoplasmic membrane (IM) and an outer membrane (OM). Antimicrobial peptides (AMPs) must first permeate through the OM and cell wall before attacking the IM to cause cytoplasmic leakage and kill the bacteria. The bacterial OM is an asymmetric bilayer with the outer leaflet primarily composed of lipopolysaccharides (LPSs) and the inner leaflet composed of phospholipids (PLs). Two cationic α-helical AMPs were designed to target Gram-negative bacteria, a full peptide G(IIKK)3I-NH2 (G3), and a hydrophobic lipopeptide C8-G(IIKK)2I-NH2 (C8G2, with C8 denoting the octanoyl chain). LPS dominates OM functions as the first line of defense against antibiotics, thereby reducing drug susceptibility. This work explores how the two AMPs interact with LPS through several carefully chosen OM models that facilitated measurements from solid-state nuclear magnetic resonance (ss-NMR), small-angle neutron scattering (SANS), and neutron reflectivity (NR). The results revealed that G3 molecules bound preferably to the LPS head region and functioned as bridge molecules to reassemble the dislocated lipids into bilayer stacks. In contrast, C8G2 lipopeptides could quickly penetrate into the central region of the OM to cause direct removal of some membrane lipids. Different structural disruptions implicated different antimicrobial efficacies from these AMPs. The demonstration of the structural features underlying different susceptibilities of the OM to AMPs offers a useful route for the future development of strain-specific AMPs against antimicrobial-resistant pathogens.
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Affiliation(s)
- Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Xuzhi Hu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ke Fa
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Daniela Ciumac
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Luke A Clifton
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stephen M King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Armando Maestro
- Institute Laue Langevin, 71 Avenue des Martyrs, CS-20156, 38042 Grenoble, France
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Thomas A Waigh
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Andrew J McBain
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jian Ren Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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43
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Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes. Methods Mol Biol 2021. [PMID: 32856257 DOI: 10.1007/978-1-0716-0928-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In studying biological processes and focusing on the molecular mechanisms at the basis of these, molecular dynamics (MD) simulations have demonstrated to be a very useful tool for the past 50 years. This suite of computational methods calculates the time-dependent evolution of a molecular system using physics-based first principles. In this chapter, we give a brief introduction to the theory and practical use of molecular dynamics simulations, highlighting the different models and algorithms that have been developed to tackle specific problems, with a special focus on classical force fields. Some examples of how simulations have been used in the past will help the reader in discerning their power, limitations, and significance.
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44
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Ferrando J, Solomon LA. Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions. Life (Basel) 2021; 11:life11030225. [PMID: 33802210 PMCID: PMC7999464 DOI: 10.3390/life11030225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.
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Affiliation(s)
- Juan Ferrando
- Department of Biology, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Lee A. Solomon
- Department of Chemistry and Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Correspondence: ; Tel.: +703-993-6418
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45
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Matamoros-Recio A, Franco-Gonzalez JF, Forgione RE, Torres-Mozas A, Silipo A, Martín-Santamaría S. Understanding the Antibacterial Resistance: Computational Explorations in Bacterial Membranes. ACS OMEGA 2021; 6:6041-6054. [PMID: 33718695 PMCID: PMC7948216 DOI: 10.1021/acsomega.0c05590] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/09/2021] [Indexed: 05/05/2023]
Affiliation(s)
- Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Juan Felipe Franco-Gonzalez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Rosa Ester Forgione
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, 80126 Napoli, Italy
| | - Angel Torres-Mozas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, 80126 Napoli, Italy
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
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46
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Liu R, Zuo R, Hudalla GA. Harnessing molecular recognition for localized drug delivery. Adv Drug Deliv Rev 2021; 170:238-260. [PMID: 33484737 PMCID: PMC8274479 DOI: 10.1016/j.addr.2021.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022]
Abstract
A grand challenge in drug delivery is providing the right dose, at the right anatomic location, for the right duration of time to maximize therapeutic efficacy while minimizing off-target toxicity and other deleterious side-effects. Two general modalities are receiving broad attention for localized drug delivery. In the first, referred to as "targeted accumulation", drugs or drug carriers are engineered to have targeting moieties that promote their accumulation at a specific tissue site from circulation. In the second, referred to as "local anchoring", drugs or drug carriers are inserted directly into the tissue site of interest where they persist for a specified duration of time. This review surveys recent advances in harnessing molecular recognition between proteins, peptides, nucleic acids, lipids, and carbohydrates to mediate targeted accumulation and local anchoring of drugs and drug carriers.
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Affiliation(s)
- Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Ran Zuo
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA.
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47
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Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition. J Membr Biol 2021; 254:75-96. [PMID: 33564914 DOI: 10.1007/s00232-021-00174-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 12/16/2022]
Abstract
The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore-forming peptide into a selective pore-former for different lipid types. A library of 2916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.
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48
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Simcock PW, Bublitz M, Cipcigan F, Ryadnov MG, Crain J, Stansfeld PJ, Sansom MSP. Membrane Binding of Antimicrobial Peptides Is Modulated by Lipid Charge Modification. J Chem Theory Comput 2021; 17:1218-1228. [PMID: 33395285 DOI: 10.1021/acs.jctc.0c01025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide interactions with lipid bilayers play a key role in a range of biological processes and depend on electrostatic interactions between charged amino acids and lipid headgroups. Antimicrobial peptides (AMPs) initiate the killing of bacteria by binding to and destabilizing their membranes. The multiple peptide resistance factor (MprF) provides a defense mechanism for bacteria against a broad range of AMPs. MprF reduces the negative charge of bacterial membranes through enzymatic conversion of the anionic lipid phosphatidyl glycerol (PG) to either zwitterionic alanyl-phosphatidyl glycerol (Ala-PG) or cationic lysyl-phosphatidyl glycerol (Lys-PG). The resulting change in the membrane charge is suggested to reduce the binding of AMPs to membranes, thus impeding downstream AMP activity. Using coarse-grained molecular dynamics to investigate the effects of these modified lipids on AMP binding to model membranes, we show that AMPs have substantially reduced affinity for model membranes containing Ala-PG or Lys-PG. More than 5000 simulations in total are used to define the relationship between lipid bilayer composition, peptide sequence (using five different membrane-active peptides), and peptide binding to membranes. The degree of interaction of a peptide with a membrane correlates with the membrane surface charge density. Free energy profile (potential of mean force) calculations reveal that the lipid modifications due to MprF alter the energy barrier to peptide helix penetration of the bilayer. These results will offer a guide to the design of novel peptides, which addresses the issue of resistance via MprF-mediated membrane modification.
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Affiliation(s)
- Patrick W Simcock
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Maike Bublitz
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | | | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Jason Crain
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, U.K
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
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49
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Chakraborty A, Kobzev E, Chan J, de Zoysa GH, Sarojini V, Piggot TJ, Allison JR. Molecular Dynamics Simulation of the Interaction of Two Linear Battacin Analogs with Model Gram-Positive and Gram-Negative Bacterial Cell Membranes. ACS OMEGA 2021; 6:388-400. [PMID: 33458490 PMCID: PMC7807746 DOI: 10.1021/acsomega.0c04752] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Antimicrobial peptides (AMPs) are a potential solution to the increasing threat of antibiotic resistance, but successful design of active but nontoxic AMPs requires understanding their mechanism of action. Molecular dynamics (MD) simulations can provide atomic-level information regarding how AMPs interact with the cell membrane. Here, we have used MD simulations to study two linear analogs of battacin, a naturally occurring cyclic, lipidated, nonribosomal AMP. Like battacin, these analogs are active against Gram-negative multidrug resistant and Gram-positive bacteria, but they are less toxic than battacin. Our simulations show that this activity depends upon a combination of positively charged and hydrophobic moieties. Favorable interactions with negatively charged membrane lipid head groups drive association with the membrane and insertion of hydrophobic residues, and the N-terminal lipid anchors the peptides to the membrane surface. Both effects are required for stable membrane binding.
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Affiliation(s)
- Aparajita Chakraborty
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
| | - Elisey Kobzev
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
- School
of Computational and Natural Sciences, Massey
University Auckland, Auckland 0632, New Zealand
| | - Jonathan Chan
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Department
of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, United
Kingdom
| | | | - Vijayalekshmi Sarojini
- School of
Chemical Sciences, University of Auckland, Auckland 1010, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Thomas J. Piggot
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Chemical
Biological and Radiological Sciences, Defence
Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Jane R Allison
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
- Biomolecular
Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand
- Digital
Life Institute, University of Auckland, Auckland 1010, New Zealand
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50
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Gong H, Sani MA, Hu X, Fa K, Hart JW, Liao M, Hollowell P, Carter J, Clifton LA, Campana M, Li P, King SM, Webster JRP, Maestro A, Zhu S, Separovic F, Waigh TA, Xu H, McBain AJ, Lu JR. How do Self-Assembling Antimicrobial Lipopeptides Kill Bacteria? ACS APPLIED MATERIALS & INTERFACES 2020; 12:55675-55687. [PMID: 33259204 DOI: 10.1021/acsami.0c17222] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Antimicrobial peptides are promising alternatives to traditional antibiotics. A group of self-assembling lipopeptides was formed by attaching an acyl chain to the N-terminus of α-helix-forming peptides with the sequence Cx-G(IIKK)yI-NH2 (CxGy, x = 4-12 and y = 2). CxGy self-assemble into nanofibers above their critical aggregation concentrations (CACs). With increasing x, the CACs decrease and the hydrophobic interactions increase, promoting secondary structure transitions within the nanofibers. Antimicrobial activity, determined by the minimum inhibition concentration (MIC), also decreases with increasing x, but the MICs are significantly smaller than the CACs, suggesting effective bacterial membrane-disrupting power. Unlike conventional antibiotics, both C8G2 and C12G2 can kill Staphylococcus aureus and Escherichia coli after only minutes of exposure under the concentrations studied. C12G2 nanofibers have considerably faster killing dynamics and lower cytotoxicity than their nonaggregated monomers. Antimicrobial activity of peptide aggregates has, to date, been underexploited, and it is found to be a very promising mechanism for peptide design. Detailed evidence for the molecular mechanisms involved is provided, based on superresolution fluorescence microscopy, solid-state nuclear magnetic resonance, atomic force microscopy, neutron scattering/reflectivity, circular dichroism, and Brewster angle microscopy.
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Affiliation(s)
- Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Xuzhi Hu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Ke Fa
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jack William Hart
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Peter Hollowell
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jessica Carter
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Luke A Clifton
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Mario Campana
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Peixun Li
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Stephen M King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - John R P Webster
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Armando Maestro
- Institute Laue Langevin, 71 Avenue des Martyrs, CS-20156, Grenoble 38042, France
| | - Shiying Zhu
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Thomas A Waigh
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Andrew J McBain
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jian Ren Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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