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Chen B, Moriarty T, Steenackers H, Vles G, Onsea J, Vackier T, Spriet I, Lavigne R, Richards RG, Metsemakers WJ. Exploring the potential of naturally occurring antimicrobials for managing orthopedic-device-related infections. J Bone Jt Infect 2024; 9:249-260. [PMID: 39539734 PMCID: PMC11555427 DOI: 10.5194/jbji-9-249-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/29/2024] [Indexed: 11/16/2024] Open
Abstract
Orthopedic-device-related infections (ODRIs) are challenging clinical complications that are often exacerbated by antibiotic resistance and biofilm formation. This review explores the efficacy of naturally occurring antimicrobials - including agents sourced from bacteria, fungi, viruses, animals, plants and minerals - against pathogens common in ODRIs. The limitations of traditional antibiotic agents are presented, and innovative naturally occurring antimicrobials, such as bacteriophage therapy and antimicrobial peptides, are evaluated with respect to their interaction with conventional antibiotics and antibiofilm efficacy. The integration of these natural agents into clinical practice could revolutionize ODRI treatment strategies, offering effective alternatives to conventional antibiotics and mitigating resistance development. However, the translation of these compounds from research into the clinic may require the substantial investment of intellectual and financial resources.
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Affiliation(s)
- Baixing Chen
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | | | - Hans Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
| | - Georges F. Vles
- Department of Orthopaedic Surgery, University Hospitals Leuven, Leuven, Belgium
- Institute for Orthopaedic Research and Training (IORT), KU Leuven, Leuven, Belgium
| | - Jolien Onsea
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Thijs Vackier
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
| | - Isabel Spriet
- Pharmacy Department, University Hospitals Leuven, Leuven, Belgium
- Pharmacotherapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | | | - Willem-Jan Metsemakers
- Department of Trauma Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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2
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Zhydzetski A, Głowacka-Grzyb Z, Bukowski M, Żądło T, Bonar E, Władyka B. Agents Targeting the Bacterial Cell Wall as Tools to Combat Gram-Positive Pathogens. Molecules 2024; 29:4065. [PMID: 39274911 PMCID: PMC11396672 DOI: 10.3390/molecules29174065] [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: 07/28/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/16/2024] Open
Abstract
The cell wall is an indispensable element of bacterial cells and a long-known target of many antibiotics. Penicillin, the first discovered beta-lactam antibiotic inhibiting the synthesis of cell walls, was successfully used to cure many bacterial infections. Unfortunately, pathogens eventually developed resistance to it. This started an arms race, and while novel beta-lactams, either natural or (semi)synthetic, were discovered, soon upon their application, bacteria were developing resistance. Currently, we are facing the threat of losing the race since more and more multidrug-resistant (MDR) pathogens are emerging. Therefore, there is an urgent need for developing novel approaches to combat MDR bacteria. The cell wall is a reasonable candidate for a target as it differentiates not only bacterial and human cells but also has a specific composition unique to various groups of bacteria. This ensures the safety and specificity of novel antibacterial agents that target this structure. Due to the shortage of low-molecular-weight candidates for novel antibiotics, attention was focused on peptides and proteins that possess antibacterial activity. Here, we describe proteinaceous agents of various origins that target bacterial cell wall, including bacteriocins and phage and bacterial lysins, as alternatives to classic antibiotic candidates for antimicrobial drugs. Moreover, advancements in protein chemistry and engineering currently allow for the production of stable, specific, and effective drugs. Finally, we introduce the concept of selective targeting of dangerous pathogens, exemplified by staphylococci, by agents specifically disrupting their cell walls.
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Affiliation(s)
- Aliaksandr Zhydzetski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Zuzanna Głowacka-Grzyb
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Tomasz Żądło
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Benedykt Władyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
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3
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Zhang Y, Li R, Zou G, Guo Y, Wu R, Zhou Y, Chen H, Zhou R, Lavigne R, Bergen PJ, Li J, Li J. Discovery of Antimicrobial Lysins from the "Dark Matter" of Uncharacterized Phages Using Artificial Intelligence. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404049. [PMID: 38899839 PMCID: PMC11348152 DOI: 10.1002/advs.202404049] [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: 04/17/2024] [Revised: 05/29/2024] [Indexed: 06/21/2024]
Abstract
The rapid rise of antibiotic resistance and slow discovery of new antibiotics have threatened global health. While novel phage lysins have emerged as potential antibacterial agents, experimental screening methods for novel lysins pose significant challenges due to the enormous workload. Here, the first unified software package, namely DeepLysin, is developed to employ artificial intelligence for mining the vast genome reservoirs ("dark matter") for novel antibacterial phage lysins. Putative lysins are computationally screened from uncharacterized Staphylococcus aureus phages and 17 novel lysins are randomly selected for experimental validation. Seven candidates exhibit excellent in vitro antibacterial activity, with LLysSA9 exceeding that of the best-in-class alternative. The efficacy of LLysSA9 is further demonstrated in mouse bloodstream and wound infection models. Therefore, this study demonstrates the potential of integrating computational and experimental approaches to expedite the discovery of new antibacterial proteins for combating increasing antimicrobial resistance.
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Affiliation(s)
- Yue Zhang
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- Hubei Hongshan LaboratoryCollege of Food Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Runze Li
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- Hubei Hongshan LaboratoryCollege of Food Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Geng Zou
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- Hubei Hongshan LaboratoryCollege of Food Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Yating Guo
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- College of Veterinary MedicineHuazhong Agricultural UniversityWuhan430070China
| | - Renwei Wu
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- College of Veterinary MedicineHuazhong Agricultural UniversityWuhan430070China
| | - Yang Zhou
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
| | - Huanchun Chen
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- College of Veterinary MedicineHuazhong Agricultural UniversityWuhan430070China
| | - Rui Zhou
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- College of Veterinary MedicineHuazhong Agricultural UniversityWuhan430070China
| | - Rob Lavigne
- Department of BiosystemsLaboratory of Gene TechnologyKU LeuvenLeuven3001Belgium
| | - Phillip J. Bergen
- Monash Biomedicine Discovery InstituteDepartment of MicrobiologyFaculty of MedicineNursing and Health SciencesMonash UniversityMelbourne3800Australia
| | - Jian Li
- Monash Biomedicine Discovery InstituteDepartment of MicrobiologyFaculty of MedicineNursing and Health SciencesMonash UniversityMelbourne3800Australia
| | - Jinquan Li
- National Key Laboratory of Agricultural MicrobiologyKey Laboratory of Environment Correlative DietologyCollege of Biomedicine and HealthShenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhan430070China
- Hubei Hongshan LaboratoryCollege of Food Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- College of Veterinary MedicineHuazhong Agricultural UniversityWuhan430070China
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518000China
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Notin P, Rollins N, Gal Y, Sander C, Marks D. Machine learning for functional protein design. Nat Biotechnol 2024; 42:216-228. [PMID: 38361074 DOI: 10.1038/s41587-024-02127-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelerating the generation of proteins for applications in biotechnology and medicine. To make sense of the exploding diversity of machine learning approaches, we introduce a unifying framework that classifies models on the basis of their use of three core data modalities: sequences, structures and functional labels. We discuss the new capabilities and outstanding challenges for the practical design of enzymes, antibodies, vaccines, nanomachines and more. We then highlight trends shaping the future of this field, from large-scale assays to more robust benchmarks, multimodal foundation models, enhanced sampling strategies and laboratory automation.
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Affiliation(s)
- Pascal Notin
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Computer Science, University of Oxford, Oxford, UK.
| | | | - Yarin Gal
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Debora Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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5
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Goormaghtigh F, Van Bambeke F. Understanding Staphylococcus aureus internalisation and induction of antimicrobial tolerance. Expert Rev Anti Infect Ther 2024; 22:87-101. [PMID: 38180805 DOI: 10.1080/14787210.2024.2303018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024]
Abstract
INTRODUCTION Staphylococcus aureus, a human commensal, is also one of the most common and serious pathogens for humans. In recent years, its capacity to survive and replicate in phagocytic and non-phagocytic cells has been largely demonstrated. In these intracellular niches, bacteria are shielded from the immune response and antibiotics, turning host cells into long-term infectious reservoirs. Moreover, neutrophils carry intracellular bacteria in the bloodstream, leading to systemic spreading of the disease. Despite the serious threat posed by intracellular S. aureus to human health, the molecular mechanisms behind its intracellular survival and subsequent antibiotic treatment failure remain elusive. AREA COVERED We give an overview of the killing mechanisms of phagocytes and of the impressive arsenal of virulence factors, toxins and stress responses deployed by S. aureus as a response. We then discuss the different barriers to antibiotic activity in this intracellular niche and finally describe innovative strategies to target intracellular persisting reservoirs. EXPERT OPINION Intracellular niches represent a challenge in terms of diagnostic and treatment. Further research using ad-hoc in-vivo models and single cell approaches are needed to better understand the molecular mechanisms underlying intracellular survival and tolerance to antibiotics in order to identify strategies to eliminate these persistent bacteria.
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Affiliation(s)
- Frédéric Goormaghtigh
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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6
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Razew A, Laguri C, Vallet A, Bougault C, Kaus-Drobek M, Sabala I, Simorre JP. Staphylococcus aureus sacculus mediates activities of M23 hydrolases. Nat Commun 2023; 14:6706. [PMID: 37872144 PMCID: PMC10593780 DOI: 10.1038/s41467-023-42506-w] [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: 04/13/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
Peptidoglycan, a gigadalton polymer, functions as the scaffold for bacterial cell walls and provides cell integrity. Peptidoglycan is remodelled by a large and diverse group of peptidoglycan hydrolases, which control bacterial cell growth and division. Over the years, many studies have focused on these enzymes, but knowledge on their action within peptidoglycan mesh from a molecular basis is scarce. Here, we provide structural insights into the interaction between short peptidoglycan fragments and the entire sacculus with two evolutionarily related peptidases of the M23 family, lysostaphin and LytM. Through nuclear magnetic resonance, mass spectrometry, information-driven modelling, site-directed mutagenesis and biochemical approaches, we propose a model in which peptidoglycan cross-linking affects the activity, selectivity and specificity of these two structurally related enzymes differently.
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Affiliation(s)
- Alicja Razew
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
- International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106, Warsaw, Poland
| | - Cedric Laguri
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
| | - Alicia Vallet
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
| | - Catherine Bougault
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
| | - Magdalena Kaus-Drobek
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106, Warsaw, Poland
| | - Izabela Sabala
- International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland.
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106, Warsaw, Poland.
| | - Jean-Pierre Simorre
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France.
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7
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Harhala MA, Gembara K, Rybicka I, Kaźmierczak ZM, Miernikiewicz P, Majewska JM, Budziar W, Nasulewicz-Goldeman A, Nelson DC, Owczarek B, Dąbrowska K. Immunogenic epitope scanning in bacteriolytic enzymes Pal and Cpl-1 and engineering Pal to escape antibody responses. Front Immunol 2023; 14:1075774. [PMID: 37781366 PMCID: PMC10540205 DOI: 10.3389/fimmu.2023.1075774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/16/2023] [Indexed: 10/03/2023] Open
Abstract
Bacteriolytic enzymes are promising antibacterial agents, but they can cause a typical immune response in vivo. In this study, we used a targeted modification method for two antibacterial endolysins, Pal and Cpl-1. We identified the key immunogenic amino acids, and designed and tested new, bacteriolytic variants with altered immunogenicity. One new variant of Pal (257-259 MKS → TFG) demonstrated decreased immunogenicity while a similar mutant (257-259 MKS → TFK) demonstrated increased immunogenicity. A third variant (280-282 DKP → GGA) demonstrated significantly increased antibacterial activity and it was not cross-neutralized by antibodies induced by the wild-type enzyme. We propose this variant as a new engineered endolysin with increased antibacterial activity that is capable of escaping cross-neutralization by antibodies induced by wild-type Pal. We show that efficient antibacterial enzymes that avoid cross-neutralization by IgG can be developed by epitope scanning, in silico design, and substitutions of identified key amino acids with a high rate of success. Importantly, this universal approach can be applied to many proteins beyond endolysins and has the potential for design of numerous biological drugs.
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Affiliation(s)
- Marek Adam Harhala
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Katarzyna Gembara
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Izabela Rybicka
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Zuzanna Maria Kaźmierczak
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Paulina Miernikiewicz
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Joanna Marta Majewska
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Wiktoria Budziar
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
| | - Anna Nasulewicz-Goldeman
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Daniel C. Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
| | - Barbara Owczarek
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Krystyna Dąbrowska
- Laboratory of Phage Molecular Biology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
- Research and Development Centre, Regional Specialist Hospital, Wroclaw, Poland
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8
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Nicholas-Haizelden K, Murphy B, Hoptroff M, Horsburgh MJ. Bioprospecting the Skin Microbiome: Advances in Therapeutics and Personal Care Products. Microorganisms 2023; 11:1899. [PMID: 37630459 PMCID: PMC10456854 DOI: 10.3390/microorganisms11081899] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Bioprospecting is the discovery and exploration of biological diversity found within organisms, genetic elements or produced compounds with prospective commercial or therapeutic applications. The human skin is an ecological niche which harbours a rich and compositional diversity microbiome stemming from the multifactorial interactions between the host and microbiota facilitated by exploitable effector compounds. Advances in the understanding of microbial colonisation mechanisms alongside species and strain interactions have revealed a novel chemical and biological understanding which displays applicative potential. Studies elucidating the organismal interfaces and concomitant understanding of the central processes of skin biology have begun to unravel a potential wealth of molecules which can exploited for their proposed functions. A variety of skin-microbiome-derived compounds display prospective therapeutic applications, ranging from antioncogenic agents relevant in skin cancer therapy to treatment strategies for antimicrobial-resistant bacterial and fungal infections. Considerable opportunities have emerged for the translation to personal care products, such as topical agents to mitigate various skin conditions such as acne and eczema. Adjacent compound developments have focused on cosmetic applications such as reducing skin ageing and its associated changes to skin properties and the microbiome. The skin microbiome contains a wealth of prospective compounds with therapeutic and commercial applications; however, considerable work is required for the translation of in vitro findings to relevant in vivo models to ensure translatability.
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Affiliation(s)
- Keir Nicholas-Haizelden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
| | - Barry Murphy
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Malcolm J. Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
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9
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Zhu X, Guo J, Yang Y, Liu J. Macrophage Polarization Induced by Bacteria-Responsive Antibiotic-Loaded Nanozymes for Multidrug Resistance-Bacterial Infections Management. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204928. [PMID: 36587984 DOI: 10.1002/smll.202204928] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Inherited bacterial resistance and biofilm-induced local immune inactivation are important factors in the failure of antibiotics to fight against bacterial infections. Herein, antibiotic-loaded mesoporous nanozymes (HA@MRuO2 -Cip/GOx) are fabricated for overcoming bacterial resistance, and activating the local immunosuppression in biofilm microenvironment (BME). HA@MRuO2 -Cip/GOx are prepared by physical adsorption between ciprofloxacin (Cip) or glucose oxidase (GOx) and MRuO2 NPs, and modified with hyaluronic acid (HA). In vitro, HA@MRuO2 -Cip/GOx cleaves extracellular DNA (eDNA) to disrupt biofilm, thereby enhancing Cip kill planktonic bacteria. Furthermore, HA@MRuO2 -Cip/GOx can induce polarization and enhance phagocytosis of a macrophage-derived cell line. More importantly, in vivo therapeutic performance confirms that HA@MRuO2 -Cip/GOx can trigger macrophage-related immunity, and effectively alleviate MRSA-bacterial lung infections. Accordingly, nanocatalytic therapy combined with targeted delivery of antibiotics could enhance the treatment of bacterial infections.
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Affiliation(s)
- Xufeng Zhu
- Department of Chemistry, College of Chemistry and Materials, Jinan University, Guangzhou, 511436, China
| | - Jiaqi Guo
- Department of Chemistry, College of Chemistry and Materials, Jinan University, Guangzhou, 511436, China
| | - Yonglan Yang
- Department of Chemistry, College of Chemistry and Materials, Jinan University, Guangzhou, 511436, China
| | - Jie Liu
- Department of Chemistry, College of Chemistry and Materials, Jinan University, Guangzhou, 511436, China
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10
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Liu F, Chen S, Zou Y, Jiao Y, Tang Y. A simple and efficient fluorescent labeling method in Staphylococcus aureus for real-time tracking of invasive bacteria. Front Microbiol 2023; 14:1128638. [PMID: 36846783 PMCID: PMC9950555 DOI: 10.3389/fmicb.2023.1128638] [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: 12/21/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Bacterial fluorescent labeling is a powerful tool for the diagnosis and treatment of bacterial infections. Here, we present a simple and efficient labeling strategy for Staphylococcus aureus. Intracellular labeling of bacteria was achieved by heat shock using Cyanine 5.5 (Cy5.5) near-infrared-I dyes in S. aureus (Cy5.5@S. aureus). Several key factors, such as Cy5.5 concentration and labeling time, were systematically evaluated. Further, the cytotoxicity of Cy5.5 and the stability of Cy5.5@S. aureus was evaluated by flow cytometry, inverted fluorescence microscopy, and transmission electron microscopy. In addition, Cy5.5@S. aureus were used to explore the phagocytic behavior of RAW264.7 macrophages. These results proved that Cy5.5@S. aureus had a uniform fluorescence intensity and high luminance; additionally, our method had no significant adverse effects on S. aureus compared to unlabeled S. aureus infections. Our method provides researchers with a useful option for analyzing the behavior of S. aureus as an infectious agent. This technique can be broadly applied to study host cell-bacteria interactions at the molecular level, and to in vivo tracing of bacterial infections.
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Affiliation(s)
- Fei Liu
- Naval Medical Center, Naval Medical University, Shanghai, China
| | - Sijie Chen
- Department of Nursing, The 940th Hospital of Joint Logistic Support Force of People’s Liberation Army (PLA), Lanzhou, China
| | - Yingxin Zou
- Naval Medical Center, Naval Medical University, Shanghai, China
| | - Yong Jiao
- Naval Medical Center, Naval Medical University, Shanghai, China
| | - Ying Tang
- Naval Medical Center, Naval Medical University, Shanghai, China,*Correspondence: Ying Tang,
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11
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Fang Y, Chang AY, Verma D, Miyashita SI, Eszterhas S, Lee PG, Shen Y, Davis LR, Dong M, Bailey-Kellogg C, Griswold KE. Functional Deimmunization of Botulinum Neurotoxin Protease Domain via Computationally Driven Library Design and Ultrahigh-Throughput Screening. ACS Synth Biol 2023; 12:153-163. [PMID: 36623275 PMCID: PMC9872818 DOI: 10.1021/acssynbio.2c00426] [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: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) is a widely used cosmetic agent that also has diverse therapeutic applications; however, adverse antidrug immune responses and associated loss of efficacy have been reported in clinical uses. Here, we describe computational design and ultrahigh-throughput screening of a massive BoNT/A light-chain (BoNT/A-LC) library optimized for reduced T cell epitope content and thereby dampened immunogenicity. We developed a functional assay based on bacterial co-expression of BoNT/A-LC library members with a Förster resonance energy transfer (FRET) sensor for BoNT/A-LC enzymatic activity, and we employed high-speed fluorescence-activated cell sorting (FACS) to identify numerous computationally designed variants having wild-type-like enzyme kinetics. Many of these variants exhibited decreased immunogenicity in humanized HLA transgenic mice and manifested in vivo paralytic activity when incorporated into full-length toxin. One variant achieved near-wild-type paralytic potency and a 300% reduction in antidrug antibody response in vivo. Thus, we have achieved a striking level of BoNT/A-LC functional deimmunization by combining computational library design and ultrahigh-throughput screening. This strategy holds promise for deimmunizing other biologics with complex superstructures and mechanisms of action.
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Affiliation(s)
- Yongliang Fang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Andrew Y. Chang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Deeptak Verma
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shin-Ichiro Miyashita
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Food, Aroma and Cosmetic Chemistry, Tokyo
University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Susan Eszterhas
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Pyung-Gang Lee
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yi Shen
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lydia R. Davis
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Min Dong
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chris Bailey-Kellogg
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Karl E. Griswold
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
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12
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Razew A, Schwarz JN, Mitkowski P, Sabala I, Kaus-Drobek M. One fold, many functions-M23 family of peptidoglycan hydrolases. Front Microbiol 2022; 13:1036964. [PMID: 36386627 PMCID: PMC9662197 DOI: 10.3389/fmicb.2022.1036964] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2023] Open
Abstract
Bacterial cell walls are the guards of cell integrity. They are composed of peptidoglycan that provides rigidity to sustain internal turgor and ensures isolation from the external environment. In addition, they harbor the enzymatic machinery to secure cell wall modulations needed throughout the bacterial lifespan. The main players in this process are peptidoglycan hydrolases, a large group of enzymes with diverse specificities and different mechanisms of action. They are commonly, but not exclusively, found in prokaryotes. Although in most cases, these enzymes share the same molecular function, namely peptidoglycan hydrolysis, they are leveraged to perform a variety of physiological roles. A well-investigated family of peptidoglycan hydrolases is M23 peptidases, which display a very conserved fold, but their spectrum of lytic action is broad and includes both Gram- positive and Gram- negative bacteria. In this review, we summarize the structural, biochemical, and functional studies concerning the M23 family of peptidases based on literature and complement this knowledge by performing large-scale analyses of available protein sequences. This review has led us to gain new insight into the role of surface charge in the activity of this group of enzymes. We present relevant conclusions drawn from the analysis of available structures and indicate the main structural features that play a crucial role in specificity determination and mechanisms of latency. Our work systematizes the knowledge of the M23 family enzymes in the context of their unique antimicrobial potential against drug-resistant pathogens and presents possibilities to modulate and engineer their features to develop perfect antibacterial weapons.
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Affiliation(s)
| | | | | | - Izabela Sabala
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Kaus-Drobek
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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13
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Li Y, Champion JA. Self-assembling nanocarriers from engineered proteins: Design, functionalization, and application for drug delivery. Adv Drug Deliv Rev 2022; 189:114462. [PMID: 35934126 DOI: 10.1016/j.addr.2022.114462] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 01/24/2023]
Abstract
Self-assembling proteins are valuable building blocks for constructing drug nanocarriers due to their self-assembly behavior, monodispersity, biocompatibility, and biodegradability. Genetic and chemical modifications allow for modular design of protein nanocarriers with effective drug encapsulation, targetability, stimuli responsiveness, and in vivo half-life. Protein nanocarriers have been developed to deliver various therapeutic molecules including small molecules, proteins, and nucleic acids with proven in vitro and in vivo efficacy. This article reviews recent advances in protein nanocarriers that are not derived from natural protein nanostructures, such as protein cages or virus like particles. The protein nanocarriers described here are self-assembled from rationally or de novo designed recombinant proteins, as well as recombinant proteins complexed with other biomolecules, presenting properties that are unique from those of natural protein carriers. Design, functionalization, and therapeutic application of protein nanocarriers will be discussed.
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Affiliation(s)
- Yirui Li
- BioEngineering Program, Georgia Institute of Technology, United States
| | - Julie A Champion
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive NW, Atlanta, GA 30332, United States; BioEngineering Program, Georgia Institute of Technology, United States.
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14
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Zha J, Li J, Su Z, Akimbekov N, Wu X. Lysostaphin: Engineering and Potentiation toward Better Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11441-11457. [PMID: 36082619 DOI: 10.1021/acs.jafc.2c03459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lysostaphin is a potent bacteriolytic enzyme with endopeptidase activity against the common pathogen Staphylococcus aureus. By digesting the pentaglycine crossbridge in the cell wall peptidoglycan of S. aureus including the methicillin-resistant strains, lysostaphin initiates rapid lysis of planktonic and sessile cells (biofilms) and has great potential for use in agriculture, food industries, and pharmaceutical industries. In the past few decades, there have been tremendous efforts in potentiating lysostaphin for better applications in these fields, including engineering of the enzyme for higher potency and lower immunogenicity with longer-lasting effects, formulation and immobilization of the enzyme for higher stability and better durability, and recombinant expression for low-cost industrial production and in situ biocontrol. These achievements are extensively reviewed in this article focusing on applications in disease control, food preservation, surface decontamination, and pathogen detection. In addition, some basic properties of lysostaphin that have been controversial and only elucidated recently are summarized, including the substrate-binding properties, the number of zinc-binding sites, the substrate range, and the cleavage site in the pentaglycine crossbridge. Resistance to lysostaphin is also highlighted with a focus on various mechanisms. This article is concluded with a discussion on the limitations and future perspectives for the actual applications of lysostaphin.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jingyuan Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zheng Su
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Nuraly Akimbekov
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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15
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Mptx2 defends against peritoneal infection by methicillin-resistant staphylococcus aureus. Int Immunopharmacol 2022; 108:108856. [DOI: 10.1016/j.intimp.2022.108856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 11/15/2022]
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16
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Ramírez-Rendon D, Passari AK, Ruiz-Villafán B, Rodríguez-Sanoja R, Sánchez S, Demain AL. Impact of novel microbial secondary metabolites on the pharma industry. Appl Microbiol Biotechnol 2022; 106:1855-1878. [PMID: 35188588 PMCID: PMC8860141 DOI: 10.1007/s00253-022-11821-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 12/18/2022]
Abstract
Microorganisms are remarkable producers of a wide diversity of natural products that significantly improve human health and well-being. Currently, these natural products comprise half of all the pharmaceuticals on the market. After the discovery of penicillin by Alexander Fleming 85 years ago, the search for and study of antibiotics began to gain relevance as drugs. Since then, antibiotics have played a valuable role in treating infectious diseases and have saved many human lives. New molecules with anticancer, hypocholesterolemic, and immunosuppressive activity have now been introduced to treat other relevant diseases. Smaller biotechnology companies and academic laboratories generate novel antibiotics and other secondary metabolites that big pharmaceutical companies no longer develop. The purpose of this review is to illustrate some of the recent developments and to show the potential that some modern technologies like metagenomics and genome mining offer for the discovery and development of new molecules, with different functions like therapeutic alternatives needed to overcome current severe problems, such as the SARS-CoV-2 pandemic, antibiotic resistance, and other emerging diseases. KEY POINTS: • Novel alternatives for the treatment of infections caused by bacteria, fungi, and viruses. • Second wave of efforts of microbial origin against SARS-CoV-2 and related variants. • Microbial drugs used in clinical practice as hypocholesterolemic agents, immunosuppressants, and anticancer therapy.
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Affiliation(s)
- Dulce Ramírez-Rendon
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, Mexico
| | - Ajit Kumar Passari
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, Mexico
| | - Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, Mexico.
| | - Arnold L Demain
- Charles A. Dana Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ, 07940, USA
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17
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Hennigan JN, Lynch MD. The past, present, and future of enzyme-based therapies. Drug Discov Today 2022; 27:117-133. [PMID: 34537332 PMCID: PMC8714691 DOI: 10.1016/j.drudis.2021.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/15/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
Enzyme-based therapeutics (EBTs) have the potential to tap into an almost unmeasurable amount of enzyme biodiversity and treat myriad conditions. Although EBTs were some of the first biologics used clinically, the rate of development of newer EBTs has lagged behind that of other biologics. Here, we review the history of EBTs, and discuss the state of each class of EBT, their potential clinical advantages, and the unique challenges to their development. Additionally, we discuss key remaining technical barriers that, if addressed, could increase the diversity and rate of the development of EBTs.
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Affiliation(s)
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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18
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Cox JR, Blazeck J. Protein engineering: a driving force toward synthetic immunology. Trends Biotechnol 2021; 40:509-521. [PMID: 34627648 DOI: 10.1016/j.tibtech.2021.09.005] [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: 07/09/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
The full application of the diverse toolkit of protein engineering has made it easier to control the immune system. In particular, synthetic cytokine variants and engineered immune receptor platforms have shown promise for the treatment of various indications with dysregulated immune function, particularly cancer. Here, we review recent advances in the control of immune cell signaling and therapeutic potency that have employed protein engineering strategies. We further discuss how safety concerns are driving the design of immunotherapeutics toward 'user-defined' control or requiring multiple distinct inputs before a functional response, highlighting emergent control strategies employed for chimeric antigen receptor (CAR) engineering.
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Affiliation(s)
- John R Cox
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, GA 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, GA 30332, USA.
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19
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Furlon JM, Mitchell SJ, Bailey-Kellogg C, Griswold KE. Bioinformatics-driven discovery of novel Clostridioides difficile lysins and experimental comparison with highly active benchmarks. Biotechnol Bioeng 2021; 118:2482-2492. [PMID: 33748952 PMCID: PMC10049856 DOI: 10.1002/bit.27759] [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: 12/31/2020] [Revised: 03/07/2021] [Accepted: 03/13/2021] [Indexed: 11/11/2022]
Abstract
Clostridioides difficile is the single most deadly bacterial pathogen in the United States, and its global prevalence and outsized health impacts underscore the need for more effective therapeutic options. Towards this goal, a novel group of modified peptidoglycan hydrolases with significant in vitro bactericidal activity have emerged as potential candidates for treating C. difficile infections (CDI). To date, discovery and development efforts directed at these CDI-specific lysins have been limited, and in particular there has been no systematic comparison of known or newly discovered lysin candidates. Here, we detail bioinformatics-driven discovery of six new anti-C. difficile lysins belonging to the amidase-3 family of enzymes, and we describe experimental comparison of their respective catalytic domains (CATs) with highly active CATs from the literature. Our quantitative analyses include metrics for expression level, inherent antibacterial activity, breadth of strain selectivity, killing of germinating spores, and structural and functional measures of thermal stability. Importantly, prior studies have not examined stability as a performance metric, and our results show that the panel of eight enzymes possess widely variable thermal denaturation temperatures and resistance to heat inactivation, including some enzymes that exhibit marginal stability at body temperature. Ultimately, no single enzyme dominated with respect to all performance measures, suggesting the need for a balanced assessment of lysin properties during efforts to find, engineer, and develop candidates with true clinical potential.
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Affiliation(s)
- Jacob M Furlon
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, USA
| | | | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, USA.,Lyticon LLC, Lebanon, New Hampshire, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, USA.,Lyticon LLC, Lebanon, New Hampshire, USA
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20
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Yachnin BJ, Mulligan VK, Khare SD, Bailey-Kellogg C. MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform. J Chem Inf Model 2021; 61:2368-2382. [PMID: 33900750 PMCID: PMC8225355 DOI: 10.1021/acs.jcim.1c00056] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As non-"self" macromolecules, biotherapeutics can trigger an immune response that can reduce drug efficacy, require patients to be taken off therapy, or even cause life-threatening reactions. To enable the flexible and facile design of protein biotherapeutics while reducing the prevalence of T-cell epitopes that drive immune recognition, we have integrated into the Rosetta protein design suite a new scoring term that allows design protocols to account for predicted or experimentally identified epitopes in the optimized objective function. This flexible scoring term can be used in any Rosetta design trajectory, can be targeted to specific regions of a protein, and can be readily extended to work with a variety of epitope predictors. By performing extensive design runs with varied design parameter choices for three case study proteins as well as a larger diverse benchmark, we show that the incorporation of this scoring term enables the effective exploration of an alternative, deimmunized sequence space to discover diverse proteins that are potentially highly deimmunized while retaining physical and chemical qualities similar to those yielded by equivalent nondeimmunizing sequence design protocols.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry and Chemical Biology and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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21
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Sharma N, Chhillar AK, Dahiya S, Punia A, Choudhary P, Gulia P, Behl A, Dangi M. Chemotherapeutic Strategies for Combating Staphylococcus aureus Infections. Mini Rev Med Chem 2021; 22:26-42. [PMID: 33797362 DOI: 10.2174/1389557521666210402150325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 11/22/2022]
Abstract
Staphylococcus aureus is a prominent human pathogen that causes nosocomial and community acquired infections. The accelerating emergence and prevalence of staphylococcal infections have grotesque health consequences which are mostly due to its anomalous capability to acquire drug resistance and scarcity of novel classes of antibacterials. Many combating therapies are centered on primary targets of S. aureus which are cell envelope, ribosomes and nucleic acids. This review describes various chemotherapeutic strategies for combating S. aureus infections which includes monotherapy, combination drug therapy, phage endolysin therapy, lysostaphins and antibacterial drones. Monotherapy has dwindled in due course of time but combination therapy, endolysin therapy, lysostaphin and antibacterial drones are emerging alternatives which efficiently conquer the shortcomings of monotherapy. Combinations of more than one antibiotic agents or combination of adjuvant with antibiotics provide a synergistic approach to combat infections causing pathogenic strains. Phage endolysin therapy and lysostaphin are also presents as possible alternatives to conventional antibiotic therapies. Antibacterial Drones goes a step further by specifically targeting the virulence genes in bacteria giving them a certain advantage over existing antibacterial strategies. But the challenge remains on the better understanding of these strategies for executing and implementing them in health sector. In this day and age, most of the S. aureus strains are resistant to ample number of antibiotics, so there is an urgent need to overcome such multidrug resistant strains for the welfare of our community.
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Affiliation(s)
| | | | | | - Aruna Punia
- Centre for Biotechnology, MDU, Rohtak 124001. India
| | | | - Prity Gulia
- Centre for Biotechnology, MDU, Rohtak 124001. India
| | | | - Mehak Dangi
- Centre for Bioinformatics, MDU, Rohtak 124001. India
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22
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Mitchell SJ, Verma D, Griswold KE, Bailey-Kellogg C. Building blocks and blueprints for bacterial autolysins. PLoS Comput Biol 2021; 17:e1008889. [PMID: 33793553 PMCID: PMC8051824 DOI: 10.1371/journal.pcbi.1008889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/16/2021] [Accepted: 03/17/2021] [Indexed: 01/31/2023] Open
Abstract
Bacteria utilize a wide variety of endogenous cell wall hydrolases, or autolysins, to remodel their cell walls during processes including cell division, biofilm formation, and programmed death. We here systematically investigate the composition of these enzymes in order to gain insights into their associated biological processes, potential ways to disrupt them via chemotherapeutics, and strategies by which they might be leveraged as recombinant antibacterial biotherapies. To do so, we developed LEDGOs (lytic enzyme domains grouped by organism), a pipeline to create and analyze databases of autolytic enzyme sequences, constituent domain annotations, and architectural patterns of multi-domain enzymes that integrate peptidoglycan binding and degrading functions. We applied LEDGOs to eight pathogenic bacteria, gram negatives Acinetobacter baumannii, Klebsiella pneumoniae, Neisseria gonorrhoeae, and Pseudomonas aeruginosa; and gram positives Clostridioides difficile, Enterococcus faecium, Staphylococcus aureus, and Streptococcus pneumoniae. Our analysis of the autolytic enzyme repertoires of these pathogens reveals commonalities and differences in their key domain building blocks and architectures, including correlations and preferred orders among domains in multi-domain enzymes, repetitions of homologous binding domains with potentially complementarity recognition modalities, and sequence similarity patterns indicative of potential divergence of functional specificity among related domains. We have further identified a variety of unannotated sequence regions within the lytic enzymes that may themselves contain new domains with important functions.
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Affiliation(s)
- Spencer J. Mitchell
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
| | - Deeptak Verma
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America
- Lyticon LLC, Lebanon, New Hampshire, United States of America
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
- Lyticon LLC, Lebanon, New Hampshire, United States of America
- * E-mail:
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23
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Electrostatic-Mediated Affinity Tuning of Lysostaphin Accelerates Bacterial Lysis Kinetics and Enhances In Vivo Efficacy. Antimicrob Agents Chemother 2021; 65:AAC.02199-20. [PMID: 33468459 DOI: 10.1128/aac.02199-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022] Open
Abstract
Drug-resistant bacterial pathogens are a serious threat to global health, and antibacterial lysins are at the forefront of innovative treatments for these life-threatening infections. While lysins' general mechanism of action is well understood, the design principles that might enable engineering of performance-enhanced variants are still being formulated. Here, we report a detailed analysis of molecular determinants underlying the in vivo efficacy of lysostaphin, a canonical anti-MRSA (methicillin-resistant Staphylococcus aureus) lysin. Systematic analysis of bacterial binding, growth inhibition, lysis kinetics, and in vivo therapeutic efficacy revealed that binding affinity, and not inherent catalytic firepower, is the dominant driver of lysostaphin efficacy. This insight enabled electrostatic affinity tuning of lysostaphin to produce a single point mutant that manifested dramatically enhanced processivity and lysis kinetics and trended toward improved in vivo efficacy. More generally, these studies provide important insights into the complex relationships between lysin electrostatics, bacterial targeting, cell lysis efficiency, and in vivo efficacy. The lessons learned may enable engineering of other high-performance antibacterial biocatalysts.
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24
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Deimmunized Lysostaphin Synergizes with Small-Molecule Chemotherapies and Resensitizes Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics. Antimicrob Agents Chemother 2021; 65:AAC.01707-20. [PMID: 33318001 DOI: 10.1128/aac.01707-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/06/2020] [Indexed: 12/25/2022] Open
Abstract
There is an urgent need for novel agents to treat drug-resistant bacterial infections, such as multidrug-resistant Staphylococcus aureus (MRSA). Desirable properties for new antibiotics include high potency, narrow species selectivity, low propensity to elicit new resistance phenotypes, and synergy with standard-of-care (SOC) chemotherapies. Here, we describe analysis of the antibacterial potential exhibited by F12, an innovative anti-MRSA lysin that has been genetically engineered to evade detrimental antidrug immune responses in human patients. F12 possesses high potency and rapid onset of action, it has narrow selectivity against pathogenic staphylococci, and it manifests synergy with numerous SOC antibiotics. Additionally, resistance to F12 and β-lactam antibiotics appears mutually exclusive, and, importantly, we provide evidence that F12 resensitizes normally resistant MRSA strains to β-lactams both in vitro and in vivo These results suggest that combinations of F12 and SOC antibiotics are a promising new approach to treating refractory S. aureus infections.
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25
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Jayakumar J, Kumar VA, Biswas L, Biswas R. Therapeutic applications of lysostaphin against Staphylococcus aureus. J Appl Microbiol 2021; 131:1072-1082. [PMID: 33382154 DOI: 10.1111/jam.14985] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/11/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Staphylococcus aureus, an opportunistic pathogen, causes diverse community and nosocomial-acquired human infections, including folliculitis, impetigo, sepsis, septic arthritis, endocarditis, osteomyelitis, implant-associated biofilm infections and contagious mastitis in cattle. In recent days, both methicillin-sensitive and methicillin-resistant S. aureus infections have increased. Highly effective anti-staphylococcal agents are urgently required. Lysostaphin is a 27 kDa zinc metallo antimicrobial lytic enzyme that is produced by Staphylococcus simulans biovar staphylolyticus and was first discovered in the 1960s. Lysostaphin is highly active against S. aureus strains irrespective of their drug-resistant patterns with a minimum inhibitory concentration of ranges between 0·001 and 0·064 μg ml-1 . Lysostaphin has activity against both dividing and non-dividing S. aureus cells; and can seep through the extracellular matrix to kill the biofilm embedded S. aureus. In spite of having excellent anti-staphylococcal activity, its clinical application is hindered because of its immunogenicity and reduced bio-availability. Extensive research with lysostaphin lead to the development of several engineered lysostaphin derivatives with reduced immunogenicity and increased serum half-life. Therapeutic efficacy of both native and engineered lysostaphin derivatives was studied by several research groups. This review provides an overview of the therapeutic applications of native and engineered lysostaphin derivatives developed to eradicate S. aureus infections.
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Affiliation(s)
- J Jayakumar
- Center for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - V A Kumar
- Department of Microbiology, Amrita Institute of Medical Sciences and Research Center, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - L Biswas
- Center for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - R Biswas
- Center for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
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