1
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Schwedler JL, Stefan MA, Thatcher CE, McIlroy PR, Sinha A, Phillips AM, Sumner CA, Courtney CM, Kim CY, Weilhammer DR, Harmon B. Therapeutic efficacy of a potent anti-Venezuelan equine encephalitis virus antibody is contingent on Fc effector function. MAbs 2024; 16:2297451. [PMID: 38170638 PMCID: PMC10766394 DOI: 10.1080/19420862.2023.2297451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
The development of specific, safe, and potent monoclonal antibodies (Abs) has led to novel therapeutic options for infectious disease. In addition to preventing viral infection through neutralization, Abs can clear infected cells and induce immunomodulatory functions through engagement of their crystallizable fragment (Fc) with complement proteins and Fc receptors on immune cells. Little is known about the role of Fc effector functions of neutralizing Abs in the context of encephalitic alphavirus infection. To determine the role of Fc effector function in therapeutic efficacy against Venezuelan equine encephalitis virus (VEEV), we compared the potently neutralizing anti-VEEV human IgG F5 (hF5) Ab with intact Fc function (hF5-WT) or containing the loss of function Fc mutations L234A and L235A (hF5-LALA) in the context of VEEV infection. We observed significantly reduced binding to complement and Fc receptors, as well as differential in vitro kinetics of Fc-mediated cytotoxicity for hF5-LALA compared to hF5-WT. The in vivo efficacy of hF5-LALA was comparable to hF5-WT at -24 and + 24 h post infection, with both Abs providing high levels of protection. However, when hF5-WT and hF5-LALA were administered + 48 h post infection, there was a significant decrease in the therapeutic efficacy of hF5-LALA. Together these results demonstrate that optimal therapeutic Ab treatment of VEEV, and possibly other encephalitic alphaviruses, requires neutralization paired with engagement of immune effectors via the Fc region.
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Affiliation(s)
- Jennifer L. Schwedler
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Maxwell A. Stefan
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Christine E. Thatcher
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Peter R. McIlroy
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Anupama Sinha
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Ashlee M. Phillips
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christopher A. Sumner
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Colleen M. Courtney
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Christina Y. Kim
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Dina R. Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Brooke Harmon
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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2
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McCollum C, Courtney CM, O’Connor NJ, Aunins TR, Jordan TX, Rogers KL, Brindley S, Brown JM, Nagpal P, Chatterjee A. Safety and Biodistribution of Nanoligomers Targeting the SARS-CoV-2 Genome for the Treatment of COVID-19. ACS Biomater Sci Eng 2023; 9:1656-1671. [PMID: 36853144 PMCID: PMC10000012 DOI: 10.1021/acsbiomaterials.2c00669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023]
Abstract
As the world braces to enter its fourth year of the coronavirus disease 2019 (COVID-19) pandemic, the need for accessible and effective antiviral therapeutics continues to be felt globally. The recent surge of Omicron variant cases has demonstrated that vaccination and prevention alone cannot quell the spread of highly transmissible variants. A safe and nontoxic therapeutic with an adaptable design to respond to the emergence of new variants is critical for transitioning to the treatment of COVID-19 as an endemic disease. Here, we present a novel compound, called SBCoV202, that specifically and tightly binds the translation initiation site of RNA-dependent RNA polymerase within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome, inhibiting viral replication. SBCoV202 is a Nanoligomer, a molecule that includes peptide nucleic acid sequences capable of binding viral RNA with single-base-pair specificity to accurately target the viral genome. The compound has been shown to be safe and nontoxic in mice, with favorable biodistribution, and has shown efficacy against SARS-CoV-2 in vitro. Safety and biodistribution were assessed using three separate administration methods, namely, intranasal, intravenous, and intraperitoneal. Safety studies showed the Nanoligomer caused no outward distress, immunogenicity, or organ tissue damage, measured through observation of behavior and body weight, serum levels of cytokines, and histopathology of fixed tissue, respectively. SBCoV202 was evenly biodistributed throughout the body, with most tissues measuring Nanoligomer concentrations well above the compound KD of 3.37 nM. In addition to favorable availability to organs such as the lungs, lymph nodes, liver, and spleen, the compound circulated through the blood and was rapidly cleared through the renal and urinary systems. The favorable biodistribution and lack of immunogenicity and toxicity set Nanoligomers apart from other antisense therapies, while the adaptability of the nucleic acid sequence of Nanoligomers provides a defense against future emergence of drug resistance, making these molecules an attractive potential treatment for COVID-19.
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Affiliation(s)
- Colleen
R. McCollum
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Colleen M. Courtney
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Sachi Bio, Colorado Technology Center, Louisville, Colorado 80027, United States
| | - Nolan J. O’Connor
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Thomas R. Aunins
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Tristan X. Jordan
- Department
of Microbiology, New York University Langone, New York, New York 10016, United States
| | - Keegan L. Rogers
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Stephen Brindley
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Jared M. Brown
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Prashant Nagpal
- Sachi Bio, Colorado Technology Center, Louisville, Colorado 80027, United States
- Antimicrobial
Regeneration Consortium Labs, Louisville, Colorado 80027, United States
| | - Anushree Chatterjee
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Sachi Bio, Colorado Technology Center, Louisville, Colorado 80027, United States
- Antimicrobial
Regeneration Consortium Labs, Louisville, Colorado 80027, United States
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3
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Courtney CM, Sharma S, Fallgren C, Weil MM, Chatterjee A, Nagpal P. Reversing radiation-induced immunosuppression using a new therapeutic modality. Life Sci Space Res (Amst) 2022; 35:127-139. [PMID: 36336358 DOI: 10.1016/j.lssr.2022.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/05/2022] [Accepted: 05/09/2022] [Indexed: 06/16/2023]
Abstract
Radiation-induced immune suppression poses significant health challenges for millions of patients undergoing cancer chemotherapy and radiotherapy treatment, and astronauts and space tourists travelling to outer space. While a limited number of recombinant protein therapies, such a Sargramostim, are approved for accelerating hematologic recovery, the pronounced role of granulocyte-macrophage colony-stimulating factor (GM-CSF or CSF2) as a proinflammatory cytokine poses additional challenges in creating immune dysfunction towards pathogenic autoimmune diseases. Here we present an approach to high-throughput drug-discovery, target validation, and lead molecule identification using nucleic acid-based molecules. These Nanoligomer™ molecules are rationally designed using a bioinformatics and an artificial intelligence (AI)-based ranking method and synthesized as a single-modality combining 6-different design elements to up- or downregulate gene expression of target gene, resulting in elevated or diminished protein expression of intended target. This method additionally alters related gene network targets ultimately resulting in pathway modulation. This approach was used to perturb and identify the most effective upstream regulators and canonical pathways for therapeutic intervention to reverse radiation-induced immunosuppression. The lead Nanoligomer™ identified in a screen of human donor derived peripheral blood mononuclear cells (PBMCs) upregulated Erythropoietin (EPO) and showed the greatest reversal of radiation induced cytokine changes. It was further tested in vivo in a mouse radiation-model with low-dose (3 mg/kg) intraperitoneal administration and was shown to regulate gene expression of epo in lung tissue as well as counter immune suppression. These results point to the broader applicability of our approach towards drug-discovery, and potential for further investigation of our lead molecule as reversible gene therapy to treat adverse health outcomes induced by radiation exposure.
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Affiliation(s)
- Colleen M Courtney
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States
| | - Sadhana Sharma
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States
| | - Christina Fallgren
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Michael M Weil
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Anushree Chatterjee
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States
| | - Prashant Nagpal
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States.
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4
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McCollum CR, Courtney CM, O’Connor NJ, Aunins TR, Ding Y, Jordan TX, Rogers KL, Brindley S, Brown JM, Nagpal P, Chatterjee A. Nanoligomers Targeting Human miRNA for the Treatment of Severe COVID-19 Are Safe and Nontoxic in Mice. ACS Biomater Sci Eng 2022; 8:3087-3106. [PMID: 35729709 PMCID: PMC9236218 DOI: 10.1021/acsbiomaterials.2c00510] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/07/2022] [Indexed: 12/27/2022]
Abstract
The devastating effects of the coronavirus disease 2019 (COVID-19) pandemic have made clear a global necessity for antiviral strategies. Most fatalities associated with infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) result at least partially from uncontrolled host immune response. Here, we use an antisense compound targeting a previously identified microRNA (miRNA) linked to severe cases of COVID-19. The compound binds specifically to the miRNA in question, miR-2392, which is produced by human cells in several disease states. The safety and biodistribution of this compound were tested in a mouse model via intranasal, intraperitoneal, and intravenous administration. The compound did not cause any toxic responses in mice based on measured parameters, including body weight, serum biomarkers for inflammation, and organ histopathology. No immunogenicity from the compound was observed with any administration route. Intranasal administration resulted in excellent and rapid biodistribution to the lungs, the main site of infection for SARS-CoV-2. Pharmacokinetic and biodistribution studies reveal delivery to different organs, including lungs, liver, kidneys, and spleen. The compound was largely cleared through the kidneys and excreted via the urine, with no accumulation observed in first-pass organs. The compound is concluded to be a safe potential antiviral treatment for COVID-19.
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Affiliation(s)
- Colleen R. McCollum
- Department of Chemical and Biological Engineering,
University of Colorado Boulder, 3415 Colorado Avenue,
Boulder, Colorado 80303, United States
| | - Colleen M. Courtney
- Department of Chemical and Biological Engineering,
University of Colorado Boulder, 3415 Colorado Avenue,
Boulder, Colorado 80303, United States
- Sachi Bioworks, Inc., 685 S
Arthur Ave Unit 5, Colorado Technology Center, Louisville, Colorado 80027, United
States
| | - Nolan J. O’Connor
- Department of Chemical and Biological Engineering,
University of Colorado Boulder, 3415 Colorado Avenue,
Boulder, Colorado 80303, United States
| | - Thomas R. Aunins
- Department of Chemical and Biological Engineering,
University of Colorado Boulder, 3415 Colorado Avenue,
Boulder, Colorado 80303, United States
| | - Yuchen Ding
- Department of Chemical and Biological Engineering,
University of Colorado Boulder, 3415 Colorado Avenue,
Boulder, Colorado 80303, United States
| | - Tristan X. Jordan
- Department of Microbiology, New York
University Langone, New York, New York 10016, United
States
| | - Keegan L. Rogers
- Department of Pharmaceutical Sciences,
University of Colorado Anschutz Medical Campus, Aurora,
Colorado 80045, United States
| | - Stephen Brindley
- Department of Pharmaceutical Sciences,
University of Colorado Anschutz Medical Campus, Aurora,
Colorado 80045, United States
| | - Jared M. Brown
- Department of Pharmaceutical Sciences,
University of Colorado Anschutz Medical Campus, Aurora,
Colorado 80045, United States
| | - Prashant Nagpal
- Sachi Bioworks, Inc., 685 S
Arthur Ave Unit 5, Colorado Technology Center, Louisville, Colorado 80027, United
States
- Antimicrobial Regeneration
Consortium, Boulder, Colorado 80301, United
States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering,
University of Colorado Boulder, 3415 Colorado Avenue,
Boulder, Colorado 80303, United States
- Sachi Bioworks, Inc., 685 S
Arthur Ave Unit 5, Colorado Technology Center, Louisville, Colorado 80027, United
States
- Antimicrobial Regeneration
Consortium, Boulder, Colorado 80301, United
States
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5
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Stefan MA, Light YK, Schwedler JL, McIlroy PR, Courtney CM, Saada EA, Thatcher CE, Phillips AM, Bourguet FA, Mageeney CM, McCloy SA, Collette NM, Negrete OA, Schoeniger JS, Weilhammer DR, Harmon B. Development of potent and effective synthetic SARS-CoV-2 neutralizing nanobodies. MAbs 2021; 13:1958663. [PMID: 34348076 PMCID: PMC8344751 DOI: 10.1080/19420862.2021.1958663] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
The respiratory virus responsible for coronavirus disease 2019 (COVID-19), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected nearly every aspect of life worldwide, claiming the lives of over 3.9 million people globally, at the time of this publication. Neutralizing humanized nanobody (VHH)-based antibodies (VHH-huFc) represent a promising therapeutic intervention strategy to address the current SARS-CoV-2 pandemic and provide a powerful toolkit to address future virus outbreaks. Using a synthetic, high-diversity VHH bacteriophage library, several potent neutralizing VHH-huFc antibodies were identified and evaluated for their capacity to tightly bind to the SARS-CoV-2 receptor-binding domain, to prevent binding of SARS-CoV-2 spike (S) to the cellular receptor angiotensin-converting enzyme 2, and to neutralize viral infection. Preliminary preclinical evaluation of multiple VHH-huFc antibody candidates demonstrate that they are prophylactically and therapeutically effective in vivo against wildtype SARS-CoV-2. The identified and characterized VHH-huFc antibodies described herein represent viable candidates for further preclinical evaluation and another tool to add to our therapeutic arsenal to address the COVID-19 pandemic.
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Affiliation(s)
- Maxwell A. Stefan
- Systems Biology Department, Sandia National Laboratories, Livermore, USA
| | - Yooli K. Light
- Systems Biology Department, Sandia National Laboratories, Livermore, USA
| | - Jennifer L. Schwedler
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, USA
| | - Peter R. McIlroy
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, USA
| | - Colleen M. Courtney
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, USA
| | - Edwin A. Saada
- Systems Biology Department, Sandia National Laboratories, Livermore, USA
| | - Christine E. Thatcher
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, USA
| | - Ashlee M. Phillips
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, USA
| | - Feliza A. Bourguet
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, USA
| | | | - Summer A. McCloy
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, USA
| | - Nicole M. Collette
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, USA
| | - Oscar A. Negrete
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, USA
| | | | - Dina R. Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, USA
| | - Brooke Harmon
- Systems Biology Department, Sandia National Laboratories, Livermore, USA
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6
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Aunins TR, Eller KA, Courtney CM, Levy M, Goodman SM, Nagpal P, Chatterjee A. Isolating the Escherichia coli Transcriptomic Response to Superoxide Generation from Cadmium Chalcogenide Quantum Dots. ACS Biomater Sci Eng 2019; 5:4206-4218. [PMID: 33417778 DOI: 10.1021/acsbiomaterials.9b01087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanomaterials have been extensively used in the biomedical field and have recently garnered attention as potential antimicrobial agents. Cadmium telluride quantum dots (QDs) with a bandgap of 2.4 eV (CdTe-2.4) were previously shown to inhibit multidrug-resistant clinical isolates of bacterial pathogens via light-activated superoxide generation. Here we investigate the transcriptomic response of Escherichia coli to phototherapeutic CdTe-2.4 QDs both with and without illumination, as well as in comparison with the non-superoxide-generating cadmium selenide QDs (CdSe-2.4) as a negative control. Our analysis sought to separate the transcriptomic response of E. coli to the generation of superoxide by the CdTe-2.4 QDs from the presence of cadmium chalcogenide nanoparticles alone. We used comparisons between illuminated CdTe-2.4 conditions and all others to establish the superoxide generation response and used comparisons between all QD conditions and the no treatment condition to establish the cadmium chalcogenide QD response. In our analysis of the gene expression experiments, we found eight genes to be consistently differentially expressed as a response to superoxide generation, and these genes demonstrate a consistent association with the DNA damage response and deactivation of iron-sulfur clusters. Each of these responses is characteristic of a bacterial superoxide response. We found 18 genes associated with the presence of cadmium chalcogenide QDs but not the generation of superoxide by CdTe-2.4, including several that implicated metabolism of amino acids in the E. coli response. To explore each of these gene sets further, we performed both gene knockout and amino acid supplementation experiments. We identified the importance of leucyl-tRNA downregulation as a cadmium chalcogenide QD response and reinforced the relationship between CdTe-2.4 stress and iron-sulfur clusters through examination of the gene tusA. This study demonstrates the transcriptomic response of E. coli to CdTe-2.4 and CdSe-2.4 QDs and parses the different effects of superoxide versus material effects on the bacteria. Our findings may provide useful information toward the development of QD-based antibacterial therapy in the future.
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7
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Collins LT, Otoupal PB, Campos JK, Courtney CM, Chatterjee A. Design of a De Novo Aggregating Antimicrobial Peptide and a Bacterial Conjugation-Based Delivery System. Biochemistry 2018; 58:1521-1526. [DOI: 10.1021/acs.biochem.8b00888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Logan T. Collins
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Peter B. Otoupal
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Jocelyn K. Campos
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Colleen M. Courtney
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
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8
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Levy M, Courtney CM, Chowdhury PP, Ding Y, Grey EL, Goodman SM, Chatterjee A, Nagpal P. Assessing Different Reactive Oxygen Species as Potential Antibiotics: Selectivity of Intracellular Superoxide Generation Using Quantum Dots. ACS Appl Bio Mater 2018; 1:529-537. [DOI: 10.1021/acsabm.8b00292] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Max Levy
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Colleen M. Courtney
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Partha P. Chowdhury
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Yuchen Ding
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Emerson L. Grey
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Samuel M. Goodman
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Prashant Nagpal
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
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9
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Goodman SM, Levy M, Li FF, Ding Y, Courtney CM, Chowdhury PP, Erbse A, Chatterjee A, Nagpal P. Designing Superoxide-Generating Quantum Dots for Selective Light-Activated Nanotherapy. Front Chem 2018; 6:46. [PMID: 29594097 PMCID: PMC5861142 DOI: 10.3389/fchem.2018.00046] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/19/2018] [Indexed: 12/25/2022] Open
Abstract
The rapid emergence of superbugs, or multi-drug resistant (MDR) organisms, has prompted a search for novel antibiotics, beyond traditional small-molecule therapies. Nanotherapeutics are being investigated as alternatives, and recently superoxide-generating quantum dots (QDs) have been shown as important candidates for selective light-activated therapy, while also potentiating existing antibiotics against MDR superbugs. Their therapeutic action is selective, can be tailored by simply changing their quantum-confined conduction-valence band (CB-VB) positions and alignment with different redox half-reactions-and hence their ability to generate specific radical species in biological media. Here, we show the design of superoxide-generating QDs using optimal QD material and size well-matched to superoxide redox potential, charged ligands to modulate their uptake in cells and selective redox interventions, and core/shell structures to improve their stability for therapeutic action. We show that cadmium telluride (CdTe) QDs with conduction band (CB) position at -0.5 V with respect to Normal Hydrogen Electron (NHE) and visible 2.4 eV bandgap generate a large flux of selective superoxide radicals, thereby demonstrating the effective light-activated therapy. Although the positively charged QDs demonstrate large cellular uptake, they bind indiscriminately to cell surfaces and cause non-selective cell death, while negatively charged and zwitterionic QD ligands reduce the uptake and allow selective therapeutic action via interaction with redox species. The stability of designed QDs in biologically-relevant media increases with the formation of core-shell QD structures, but an appropriate design of core-shell structures is needed to minimize any reduction in charge injection efficiency to adsorbed oxygen molecules (to form superoxide) and maintain similar quantitative generation of tailored redox species, as measured using electron paramagnetic resonance (EPR) spectroscopy and electrochemical impedance spectroscopy (EIS). Using these findings, we demonstrate the rational design of QDs as selective therapeutic to kill more than 99% of a priority class I pathogen, thus providing an effective therapy against MDR superbugs.
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Affiliation(s)
- Samuel M Goodman
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States.,Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Max Levy
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States.,Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Fei-Fei Li
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States.,Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Yuchen Ding
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States.,Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, United States
| | - Colleen M Courtney
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Partha P Chowdhury
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States.,Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Annette Erbse
- Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO, United States
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Prashant Nagpal
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States.,Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States.,Materials Science and Engineering, University of Colorado Boulder, Boulder, CO, United States
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10
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Courtney CM, Goodman SM, Nagy TA, Levy M, Bhusal P, Madinger NE, Detweiler CS, Nagpal P, Chatterjee A. Potentiating antibiotics in drug-resistant clinical isolates via stimuli-activated superoxide generation. Sci Adv 2017; 3:e1701776. [PMID: 28983513 PMCID: PMC5627983 DOI: 10.1126/sciadv.1701776] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/13/2017] [Indexed: 05/25/2023]
Abstract
The rise of multidrug-resistant (MDR) bacteria is a growing concern to global health and is exacerbated by the lack of new antibiotics. To treat already pervasive MDR infections, new classes of antibiotics or antibiotic adjuvants are needed. Reactive oxygen species (ROS) have been shown to play a role during antibacterial action; however, it is not yet understood whether ROS contribute directly to or are an outcome of bacterial lethality caused by antibiotics. We show that a light-activated nanoparticle, designed to produce tunable flux of specific ROS, superoxide, potentiates the activity of antibiotics in clinical MDR isolates of Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae. Despite the high degree of antibiotic resistance in these isolates, we observed a synergistic interaction between both bactericidal and bacteriostatic antibiotics with varied mechanisms of action and our superoxide-producing nanoparticles in more than 75% of combinations. As a result of this potentiation, the effective antibiotic concentration of the clinical isolates was reduced up to 1000-fold below their respective sensitive/resistant breakpoint. Further, superoxide-generating nanoparticles in combination with ciprofloxacin reduced bacterial load in epithelial cells infected with S. enterica serovar Typhimurium and increased Caenorhabditis elegans survival upon infection with S. enterica serovar Enteriditis, compared to antibiotic alone. This demonstration highlights the ability to engineer superoxide generation to potentiate antibiotic activity and combat highly drug-resistant bacterial pathogens.
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Affiliation(s)
- Colleen M. Courtney
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Samuel M. Goodman
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Toni A. Nagy
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Max Levy
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Pallavi Bhusal
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Nancy E. Madinger
- Division of Infectious Diseases, University of Colorado Denver, Aurora, CO 80045, USA
| | - Corrella S. Detweiler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Prashant Nagpal
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Materials Science and Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
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11
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Reynolds TS, Courtney CM, Erickson KE, Wolfe LM, Chatterjee A, Nagpal P, Gill RT. ROS mediated selection for increased NADPH availability in Escherichia coli. Biotechnol Bioeng 2017; 114:2685-2689. [PMID: 28710857 DOI: 10.1002/bit.26385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/21/2017] [Accepted: 07/12/2017] [Indexed: 11/10/2022]
Abstract
The economical production of chemicals and fuels by microbial processes remains an intense area of interest in biotechnology. A key limitation in such efforts concerns the availability of key co-factors, in this case NADPH, required for target pathways. Many of the strategies pursued for increasing NADPH availability in Escherichia coli involve manipulations to the central metabolism, which can create redox imbalances and overall growth defects. In this study we used a reactive oxygen species based selection to search for novel methods of increasing NADPH availability. We report a loss of function mutation in the gene hdfR appears to increase NADPH availability in E. coli. Additionally, we show this excess NADPH can be used to improve the production of 3HP in E. coli.
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Affiliation(s)
- Thomas S Reynolds
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Colleen M Courtney
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Keesha E Erickson
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Lisa M Wolfe
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Prashant Nagpal
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado.,Materials Science and Engineering, University of Colorado, Boulder, Boulder, Colorado
| | - Ryan T Gill
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado
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12
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Bordoy AE, Varanasi US, Courtney CM, Chatterjee A. Transcriptional Interference in Convergent Promoters as a Means for Tunable Gene Expression. ACS Synth Biol 2016; 5:1331-1341. [PMID: 27346626 DOI: 10.1021/acssynbio.5b00223] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An important goal of synthetic biology involves the extension and standardization of novel biological elements for applications in medicine and biotechnology. Transcriptional interference, occurring in sets of convergent promoters, offers a promising mechanism for building elements for the design of tunable gene regulation. Here, we investigate the transcriptional interference mechanisms of antisense roadblock and RNA polymerase traffic in a set of convergent promoters as novel modules for synthetic biology. We show examples of elements, including antisense roadblock, relative promoter strengths, interpromoter distance, and sequence content that can be tuned to give rise to repressive as well as cooperative behaviors, therefore resulting in distinct gene expression patterns. Our approach will be useful toward engineering new biological devices and will bring new insights to naturally occurring cis-antisense systems. Therefore, we are reporting a new biological tool that can be used for synthetic biology.
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Affiliation(s)
- Antoni E. Bordoy
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
| | - Usha S. Varanasi
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
| | - Colleen M. Courtney
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
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13
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Courtney CM, Goodman SM, McDaniel JA, Madinger NE, Chatterjee A, Nagpal P. Photoexcited quantum dots for killing multidrug-resistant bacteria. Nat Mater 2016; 15:529-34. [PMID: 26779882 DOI: 10.1038/nmat4542] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/14/2015] [Indexed: 05/22/2023]
Abstract
Multidrug-resistant bacterial infections are an ever-growing threat because of the shrinking arsenal of efficacious antibiotics. Metal nanoparticles can induce cell death, yet the toxicity effect is typically nonspecific. Here, we show that photoexcited quantum dots (QDs) can kill a wide range of multidrug-resistant bacterial clinical isolates, including methicillin-resistant Staphylococcus aureus, carbapenem-resistant Escherichia coli, and extended-spectrum β-lactamase-producing Klebsiella pneumoniae and Salmonella typhimurium. The killing effect is independent of material and controlled by the redox potentials of the photogenerated charge carriers, which selectively alter the cellular redox state. We also show that the QDs can be tailored to kill 92% of bacterial cells in a monoculture, and in a co-culture of E. coli and HEK 293T cells, while leaving the mammalian cells intact, or to increase bacterial proliferation. Photoexcited QDs could be used in the study of the effect of redox states on living systems, and lead to clinical phototherapy for the treatment of infections.
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Affiliation(s)
- Colleen M Courtney
- Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80303, USA
| | - Samuel M Goodman
- Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80303, USA
| | - Jessica A McDaniel
- Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80303, USA
| | - Nancy E Madinger
- Division of Infectious Diseases, University of Colorado, Denver, Aurora, Colorado 80045, USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Prashant Nagpal
- Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Materials Science and Engineering, University of Colorado, Boulder, Boulder, Colorado 80303, USA
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14
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Courtney CM, Chatterjee A. Sequence-Specific Peptide Nucleic Acid-Based Antisense Inhibitors of TEM-1 β-Lactamase and Mechanism of Adaptive Resistance. ACS Infect Dis 2015; 1:253-63. [PMID: 27622741 DOI: 10.1021/acsinfecdis.5b00042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent surge of drug-resistant superbugs and shrinking antibiotic pipeline are serious challenges to global health. In particular, the emergence of β-lactamases has caused extensive resistance against the most frequently prescribed class of β-lactam antibiotics. Here, we develop novel synthetic peptide nucleic acid-based antisense inhibitors that target the start codon and ribosomal binding site of the TEM-1 β-lactamase transcript and act via translation inhibition mechanism. We show that these antisense inhibitors are capable of resensitizing drug-resistant Escherichia coli to β-lactam antibiotics exhibiting 10-fold reduction in the minimum inhibitory concentration (MIC). To study the mechanism of resistance, we adapted E. coli at MIC levels of the β-lactam/antisense inhibitor combination and observed a nonmutational, bet-hedging based adaptive antibiotic resistance response as evidenced by phenotypic heterogeneity as well as heterogeneous expression of key stress response genes. Our data show that both the development of new antimicrobials and an understanding of cellular response during the development of tolerance could aid in mitigating the impending antibiotic crisis.
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Affiliation(s)
- Colleen M. Courtney
- Department of Chemical and Biological Engineering and ‡BioFrontiers
Institute, 596 UCB, University of Colorado, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering and ‡BioFrontiers
Institute, 596 UCB, University of Colorado, Boulder, Colorado 80303, United States
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