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Groover KE, Randall JR, Davies BW. Development of a Selective and Stable Antimicrobial Peptide. ACS Infect Dis 2024; 10:2151-2160. [PMID: 38712889 PMCID: PMC11185160 DOI: 10.1021/acsinfecdis.4c00142] [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: 02/23/2024] [Revised: 04/17/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024]
Abstract
Antimicrobial peptides (AMPs) are presented as potential scaffolds for antibiotic development due to their desirable qualities including broad-spectrum activity, rapid action, and general lack of susceptibility to current resistance mechanisms. However, they often lose antibacterial activity under physiological conditions and/or display mammalian cell toxicity, which limits their potential use. Identification of AMPs that overcome these barriers will help develop rules for how this antibacterial class can be developed to treat infection. Here we describe the development of our novel synthetic AMP, from discovery through in vivo application. Our evolved AMP, DTr18-dab, has broad-spectrum antibacterial activity and is nonhemolytic. It is active against planktonic bacteria and biofilm, is unaffected by colistin resistance, and importantly is active in both human serum and a Galleria mellonella infection model. Several modifications, including the incorporation of noncanonical amino acids, were used to arrive at this robust sequence. We observed that the impact on antibacterial activity with noncanonical amino acids was dependent on assay conditions and therefore not entirely predictable. Overall, our results demonstrate how a relatively weak lead can be developed into a robust AMP with qualities important for potential therapeutic translation.
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Affiliation(s)
- Kyra E. Groover
- Department
of Molecular Biosciences, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Justin R. Randall
- Department
of Molecular Biosciences, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Bryan W. Davies
- Department
of Molecular Biosciences, The University
of Texas at Austin, Austin, Texas 78712, United States
- John
Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas 78712, United States
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MacNair CR, Rutherford ST, Tan MW. Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 2024; 22:262-275. [PMID: 38082064 DOI: 10.1038/s41579-023-00993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 04/19/2024]
Abstract
Resistance threatens to render antibiotics - which are essential for modern medicine - ineffective, thus posing a threat to human health. The discovery of novel classes of antibiotics able to overcome resistance has been stalled for decades, with the developmental pipeline relying almost entirely on variations of existing chemical scaffolds. Unfortunately, this approach has been unable to keep pace with resistance evolution, necessitating new therapeutic strategies. In this Review, we highlight recent efforts to discover non-traditional antimicrobials, specifically describing the advantages and limitations of antimicrobial peptides and macrocycles, antibodies, bacteriophages and antisense oligonucleotides. These approaches have the potential to stem the tide of resistance by expanding the physicochemical property space and target spectrum occupied by currently approved antibiotics.
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Affiliation(s)
- Craig R MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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Randall JR, Groover KE, O'Donnell AC, Garza JM, Cole TJ, Davies BW. Adapting antibacterial display to identify serum-active macrocyclic peptide antibiotics. PNAS NEXUS 2023; 2:pgad270. [PMID: 37637199 PMCID: PMC10449418 DOI: 10.1093/pnasnexus/pgad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023]
Abstract
The lack of available treatments for many antimicrobial-resistant infections highlights the critical need for antibiotic discovery innovation. Peptides are an underappreciated antibiotic scaffold because they often suffer from proteolytic instability and toxicity toward human cells, making in vivo use challenging. To investigate sequence factors related to serum activity, we adapt an antibacterial display technology to screen a library of peptide macrocycles for antibacterial potential directly in human serum. We identify dozens of new macrocyclic peptide antibiotic sequences and find that serum activity within our library is influenced by peptide length, cationic charge, and the number of disulfide bonds present. Interestingly, an optimized version of our most active lead peptide permeates the outer membrane of Gram-negative bacteria without strong inner-membrane disruption and kills bacteria slowly while causing cell elongation. This contrasts with traditional cationic antimicrobial peptides, which kill rapidly via lysis of both bacterial membranes. Notably, this optimized variant is not toxic to mammalian cells and retains its function in vivo, suggesting therapeutic promise. Our results support the use of more physiologically relevant conditions when screening peptides for antimicrobial activity which retain in vivo functionality.
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Affiliation(s)
- Justin R Randall
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kyra E Groover
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Angela C O'Donnell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Joseph M Garza
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - T Jeffrey Cole
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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4
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Randall JR, Groover KE, O’Donnell AC, Garza JM, Cole TJ, Davies BW. Adapting antibacterial display to identify serum active macrocyclic peptide antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550711. [PMID: 37546850 PMCID: PMC10402130 DOI: 10.1101/2023.07.28.550711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The lack of available treatments for many antimicrobial resistant infections highlights the critical need for antibiotic discovery innovation. Peptides are an underappreciated antibiotic scaffold because they often suffer from proteolytic instability and toxicity towards human cells, making in vivo use challenging. To investigate sequence factors related to serum activity, we adapt an antibacterial display technology to screen a library of peptide macrocycles for antibacterial potential directly in human serum. We identify dozens of new macrocyclic peptide antibiotic sequences and find that serum activity within our library is influenced by peptide length, cationic charge, and the number of disulfide bonds present. Interestingly, an optimized version of our most active lead peptide permeates the outer membrane of gram-negative bacteria without strong inner membrane disruption and kills bacteria slowly while causing cell elongation. This contrasts with traditional cationic antimicrobial peptides, which kill rapidly via lysis of both bacterial membranes. Notably, this optimized variant is not toxic to mammalian cells and retains its function in vivo , suggesting therapeutic promise. Our results support the use of more physiologically relevant conditions when screening peptides for antimicrobial activity which retain in vivo functionality. Significance Traditional methods of natural antibiotic discovery are low throughput and cannot keep pace with the development of antimicrobial resistance. Synthetic peptide display technologies offer a high-throughput means of screening drug candidates, but rarely consider functionality beyond simple target binding and do not consider retention of function in vivo . Here, we adapt a function-based, antibacterial display technology to screen a large library of peptide macrocycles directly for bacterial growth inhibition in human serum. This screen identifies an optimized non-toxic macrocyclic peptide antibiotic retaining in vivo function, suggesting this advancement could increase clinical antibiotic discovery efficiency.
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Affiliation(s)
- Justin R. Randall
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
| | - Kyra E. Groover
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
| | - Angela C. O’Donnell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
| | - Joseph M. Garza
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
| | - T. Jeffrey Cole
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
| | - Bryan W. Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
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Randall JR, Wang X, Groover KE, O'Donnell AC, Davies BW. Using display technologies to identify macrocyclic peptide antibiotics. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119473. [PMID: 37011732 PMCID: PMC10198949 DOI: 10.1016/j.bbamcr.2023.119473] [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: 03/31/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 04/03/2023]
Abstract
Antibiotic resistant bacterial infections are now a leading cause of global mortality. While drug resistance continues to spread, the clinical antibiotic pipeline has become bare. This discord has focused attention on developing new strategies for antimicrobial discovery. Natural macrocyclic peptide-based products have provided novel antibiotics and antibiotic scaffolds targeting several essential bacterial cell envelope processes, but discovery of such natural products remains a slow and inefficient process. Synthetic strategies employing peptide display technologies can quickly screen large libraries of macrocyclic sequences for specific target binding and general antibacterial potential providing alternative approaches for new antibiotic discovery. Here we review cell envelope processes that can be targeted with macrocyclic peptide therapeutics, outline important macrocyclic peptide display technologies, and discuss future strategies for both library design and screening.
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Affiliation(s)
- Justin R Randall
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
| | - Xun Wang
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Kyra E Groover
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Angela C O'Donnell
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA
| | - Bryan W Davies
- University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, USA.
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Randall JR, DuPai CD, Cole TJ, Davidson G, Groover KE, Slater SL, Mavridou DA, Wilke CO, Davies BW. Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. SCIENCE ADVANCES 2023; 9:eade0008. [PMID: 36630516 PMCID: PMC9833666 DOI: 10.1126/sciadv.ade0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Peptide macrocycles are a rapidly emerging class of therapeutic, yet the design of their structure and activity remains challenging. This is especially true for those with β-hairpin structure due to weak folding properties and a propensity for aggregation. Here, we use proteomic analysis and common antimicrobial features to design a large peptide library with macrocyclic β-hairpin structure. Using an activity-driven high-throughput screen, we identify dozens of peptides killing bacteria through selective membrane disruption and analyze their biochemical features via machine learning. Active peptides contain a unique constrained structure and are highly enriched for cationic charge with arginine in their turn region. Our results provide a synthetic strategy for structured macrocyclic peptide design and discovery while also elucidating characteristics important for β-hairpin antimicrobial peptide activity.
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Affiliation(s)
- Justin R. Randall
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Cory D. DuPai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - T. Jeffrey Cole
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Gillian Davidson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Kyra E. Groover
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Sabrina L. Slater
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Claus O. Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Bryan W. Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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7
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da Costa de Souza G, Roque-Borda CA, Pavan FR. Beta-lactam resistance and the effectiveness of antimicrobial peptides against KPC-producing bacteria. Drug Dev Res 2022; 83:1534-1554. [PMID: 36042694 DOI: 10.1002/ddr.21990] [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: 05/02/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 11/12/2022]
Abstract
Bacterial resistance is a problem that is giving serious cause for concern because bacterial strains such as Acinetobacter baumannii and Pseudomonas aeruginosa are difficult to treat and highly opportunistic. These bacteria easily acquire resistance genes even from other species, which confers greater persistence and tolerance towards conventional antibiotics. These bacteria have the highest death rate in hospitalized intensive care patients, so strong measures must be taken. In this review, we focus on the use of antimicrobial peptides (AMPs) as an alternative to traditional drugs, due to their rapid action and lower risk of generating resistance by microorganisms. We also present an overview of beta-lactams and explicitly explain the activity of AMPs against carbapenemase-producing bacteria as potential alternative agents for infection control.
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Affiliation(s)
- Guilherme da Costa de Souza
- School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, São Paulo State University, São Paulo, Brazil
| | - Cesar Augusto Roque-Borda
- School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, São Paulo State University, São Paulo, Brazil
| | - Fernando R Pavan
- School of Pharmaceutical Sciences, Tuberculosis Research Laboratory, São Paulo State University, São Paulo, Brazil
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