1
|
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: 10] [Impact Index Per Article: 5.0] [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.
Collapse
Affiliation(s)
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| |
Collapse
|
2
|
Legler PM, Little SF, Senft J, Schokman R, Carra JH, Compton JR, Chabot D, Tobery S, Fetterer DP, Siegel JB, Baker D, Friedlander AM. Treatment of experimental anthrax with pegylated circularly permuted capsule depolymerase. Sci Transl Med 2021; 13:eabh1682. [PMID: 34878819 DOI: 10.1126/scitranslmed.abh1682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Patricia M Legler
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratories, Washington, DC 20375, USA
| | - Stephen F Little
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jeffrey Senft
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Rowena Schokman
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - John H Carra
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jaimee R Compton
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratories, Washington, DC 20375, USA
| | - Donald Chabot
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Steven Tobery
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - David P Fetterer
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Justin B Siegel
- Department of Chemistry, Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95616, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Arthur M Friedlander
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.,Department of Medicine, Uniformed Services University of Health Sciences, Bethesda, MD 20814, USA
| |
Collapse
|
3
|
Loraine J, Heinz E, Soontarach R, Blackwell GA, Stabler RA, Voravuthikunchai SP, Srimanote P, Kiratisin P, Thomson NR, Taylor PW. Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand. Front Microbiol 2020; 11:548. [PMID: 32328045 PMCID: PMC7153491 DOI: 10.3389/fmicb.2020.00548] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/13/2020] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistant strains of Acinetobacter baumannii are responsible for a large and increasing burden of nosocomial infections in Thailand and other countries of Southeast Asia. New approaches to their control and treatment are urgently needed and an attractive strategy is to remove the bacterial polysaccharide capsule, and thus the protection from the host's immune system. To examine phylogenetic relationships, distribution of capsule chemotypes, acquired antibiotic resistance determinants, susceptibility to complement and other traits associated with systemic infection, we sequenced 191 isolates from three tertiary referral hospitals in Thailand and used phenotypic assays to characterize key aspects of infectivity. Several distinct lineages were circulating in three hospitals and the majority belonged to global clonal group 2 (GC2). Very high levels of resistance to carbapenems and other front-line antibiotics were found, as were a number of widespread plasmid replicons. A high diversity of capsule genotypes was encountered, with only three of these (KL6, KL10, and KL47) showing more than 10% frequency. Almost 90% of GC2 isolates belonged to the most common capsule genotypes and were fully resistant to the bactericidal action of human serum complement, most likely protected by their polysaccharide capsule, which represents a key determinant of virulence for systemic infection. Our study further highlights the importance to develop therapeutic strategies to remove the polysaccharide capsule from extensively drug-resistant A. baumanii during the course of systemic infection.
Collapse
Affiliation(s)
- Jessica Loraine
- School of Pharmacy, University College London, London, United Kingdom
| | - Eva Heinz
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Grace A Blackwell
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom.,European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, Cambridge, United Kingdom
| | - Richard A Stabler
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Potjanee Srimanote
- Faculty of Allied Health Sciences, Thammasat University, Pathumtanee, Thailand
| | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom.,London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Peter W Taylor
- School of Pharmacy, University College London, London, United Kingdom
| |
Collapse
|
4
|
Mantravadi PK, Kalesh KA, Dobson RCJ, Hudson AO, Parthasarathy A. The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies. Antibiotics (Basel) 2019; 8:E8. [PMID: 30682820 PMCID: PMC6466574 DOI: 10.3390/antibiotics8010008] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/17/2019] [Accepted: 01/20/2019] [Indexed: 12/11/2022] Open
Abstract
Pathogenic antibiotic resistant bacteria pose one of the most important health challenges of the 21st century. The overuse and abuse of antibiotics coupled with the natural evolutionary processes of bacteria has led to this crisis. Only incremental advances in antibiotic development have occurred over the last 30 years. Novel classes of molecules, such as engineered antibodies, antibiotic enhancers, siderophore conjugates, engineered phages, photo-switchable antibiotics, and genome editing facilitated by the CRISPR/Cas system, are providing new avenues to facilitate the development of antimicrobial therapies. The informatics revolution is transforming research and development efforts to discover novel antibiotics. The explosion of nanotechnology and micro-engineering is driving the invention of antimicrobial materials, enabling the cultivation of "uncultivable" microbes and creating specific and rapid diagnostic technologies. Finally, a revival in the ecological aspects of microbial disease management, the growth of prebiotics, and integrated management based on the "One Health" model, provide additional avenues to manage this health crisis. These, and future scientific and technological developments, must be coupled and aligned with sound policy and public awareness to address the risks posed by rising antibiotic resistance.
Collapse
Affiliation(s)
| | | | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800 Christchurch, New Zealand.
| | - André O Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA.
| | - Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA.
| |
Collapse
|
5
|
Liu Y, Mi Z, Mi L, Huang Y, Li P, Liu H, Yuan X, Niu W, Jiang N, Bai C, Gao Z. Identification and characterization of capsule depolymerase Dpo48 from Acinetobacter baumannii phage IME200. PeerJ 2019; 7:e6173. [PMID: 30656071 PMCID: PMC6336015 DOI: 10.7717/peerj.6173] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022] Open
Abstract
Background The emergence of multidrug- or extensively drug-resistant Acinetobacter baumannii has made it difficult to treat and control infections caused by this bacterium. It is urgently necessary to search for alternatives to conventional antibiotics for control of severe A. baumannii infections. In recent years, bacteriophages and their derivatives, such as depolymerases, showed great potential as antibacterial or antivirulence agents against bacterial infections. Nonetheless, unlike broad-spectrum bactericidal antibiotics, phage-encoded depolymerase targets only a limited number of bacterial strains. Therefore, identification of novel depolymerases and evaluation of their ability to control A. baumannii infections is important. Methods A bacteriophage was isolated from hospital sewage using an extensively drug-resistant A. baumannii strain as the host bacterium, and the phage’s plaque morphology and genomic composition were studied. A polysaccharide depolymerase (Dpo48) was expressed and identified, and the effects of pH and temperature on its activity were determined. Besides, a serum killing assay was conducted, and amino acid sequences homologous to those of putative polysaccharide depolymerases were compared. Results Phage IME200 yielded clear plaques surrounded by enlarged halos, with polysaccharide depolymerase activity against the host bacterium. A tail fiber protein with a Pectate_lyase_3 domain was identified as Dpo48 and characterized . Dpo48 was found to degrade the capsule polysaccharide of the bacterial surface, as revealed by Alcian blue staining. Dpo48 manifested stable activity over a broad range of pH (5.0–9.0) and temperatures (20–70 °C). Results from in vitro serum killing assays indicated that 50% serum was sufficient to cause a five log reduction of overnight enzyme-treated bacteria, with serum complement playing an important role in these killing assays. Moreover, Dpo48 had a spectrum of activity exactly the same as its parental phage IME200, which was active against 10 out of 41 A. baumannii strains. Amino acid sequence alignment showed that the putative tail fiber proteins had a relatively short, highly conserved domain in their N-terminal sequences, but their amino acid sequences containing pectate lyase domains, found in the C-terminal regions, were highly diverse. Conclusions Phage-encoded capsule depolymerases may become promising antivirulence agents for preventing and controlling A. baumannii infections.
Collapse
Affiliation(s)
- Yannan Liu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China.,Department of Respiratory and Critical Care Medicine, 307th Hospital of PLA, Beijing, China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Liyuan Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Puyuan Li
- Department of Respiratory and Critical Care Medicine, 307th Hospital of PLA, Beijing, China
| | - Huiying Liu
- Department of Respiratory and Critical Care Medicine, 307th Hospital of PLA, Beijing, China
| | - Xin Yuan
- Department of Respiratory and Critical Care Medicine, 307th Hospital of PLA, Beijing, China
| | - Wenkai Niu
- Department of Respiratory and Critical Care Medicine, 307th Hospital of PLA, Beijing, China
| | - Ning Jiang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Changqing Bai
- Department of Respiratory and Critical Care Medicine, 307th Hospital of PLA, Beijing, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| |
Collapse
|
6
|
Antibiotic Therapy Using Phage Depolymerases: Robustness Across a Range of Conditions. Viruses 2018; 10:v10110622. [PMID: 30424521 PMCID: PMC6266388 DOI: 10.3390/v10110622] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 12/14/2022] Open
Abstract
Phage-derived depolymerases directed against bacterial capsules are showing therapeutic promise in various animal models of infection. However, individual animal model studies are often constrained by use of highly specific protocols, such that results may not generalize to even slight modifications. Here we explore the robustness of depolymerase therapies shown to succeed in a previous study of mice. Treatment success rates were reduced by treatment delay, more so for some enzymes than others: K1- and K5 capsule-degrading enzymes retained partial efficacy on delay, while K30 depolymerase did not. Phage were superior to enzymes under delayed treatment only for K1. Route of administration (intramuscular versus intraperitoneal) mattered for success of K1E, possibly for K1F, not for K1H depolymerase. Significantly, K1 capsule-degrading enzymes proved highly successful when using immune-suppressed, leukopenic mice, even with delayed treatment. Evolution of bacteria resistant to K1-degrading enzymes did not thwart therapeutic success in leukopenic mice, likely because resistant bacteria were avirulent. In combination with previous studies these results continue to support the efficacy of depolymerases as antibacterial agents in vivo, but system-specific details are becoming evident.
Collapse
|
7
|
Novel therapeutics for bacterial infections. Emerg Top Life Sci 2017; 1:85-92. [PMID: 33525811 DOI: 10.1042/etls20160017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 01/28/2023]
Abstract
The relentless increase in antibiotic resistance among all major groups of bacterial pathogens shows no sign of abating. The situation is exacerbated by a marked decline in the number of new antibiotics entering the marketplace. It is essential that new ways to treat severe bacterial infections are investigated before the antibiotic well runs dry. This review covers many promising approaches, some novel and some based on old ideas that were not considered viable when clinicians were able to exploit a wide palette of cheap and effective antibacterial chemotherapeutics. These approaches include the use of photosensitive dyes, bacteriophage and phage-encoded proteins, and agents that compromise virulence and antibiotic-resistance machineries. I also make a case for continuing in some form with tried and trusted platforms for drug discovery that served society well in the past.
Collapse
|