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Austin MJ, Schunk HC, Ling N, Rosales AM. Peptomer substrates for quantitative pattern-recognition sensing of proteases. Chem Commun (Camb) 2023; 59:1685-1688. [PMID: 36692178 DOI: 10.1039/d2cc06587h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The utility of active proteases as biomarkers is often limited by overlapping substrate specificity. Here, this feature is leveraged to develop a quantitative pattern-recognition sensing system driven by the degradation patterns of peptide-peptoid hybrid substrates to classify proteases and estimate their concentration by multivariate data analysis.
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Affiliation(s)
- Mariah J Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Hattie C Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA. .,Biomedical Engineering Department, University of Texas at Austin, Austin, TX, 78712, USA
| | - Natalie Ling
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
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Schunk HC, Austin MJ, Taha BZ, McClellan MS, Suggs LJ, Rosales AM. Oxidative Degradation of Sequence-Defined Peptoid Oligomers. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2023; 8:92-104. [PMID: 37123435 PMCID: PMC10147340 DOI: 10.1039/d2me00179a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Due to their N-substitution, peptoids are generally regarded as resistant to biological degradation, such as enzymatic and hydrolytic mechanisms. This stability is an especially attractive feature for therapeutic development and is a selling point of many previous biological studies. However, another key mode of degradation remains to be fully explored, namely oxidative degradation mediated by reactive oxygen and nitrogen species (ROS/RNS). ROS and RNS are biologically relevant in numerous contexts where biomaterials may be present, thus, improving understanding of peptoid oxidative susceptibility is crucial to exploit their full potential in the biomaterials field, where an oxidatively-labile but enzymatically stable molecule can offer attractive properties. Toward this end, we demonstrate a fundamental characterization of sequence-defined peptoid chains in the presence of chemically generated ROS, as compared to ROS-susceptible peptides such as proline and lysine oligomers. Lysine oligomers showed the fastest degradation rates to ROS and the enzyme trypsin. Peptoids degraded in metal catalyzed oxidation conditions at rates on par with poly(prolines), while maintaining resistance to enzymatic degradation. Furthermore, lysine-containing peptide-peptoid hybrid molecules showed tunability in both ROS-mediated and enzyme-mediated degradation, with rates intermediate to lysine and peptoid oligomers. When lysine-mimetic side-chains were incorporated into a peptoid backbone, the rate of degradation matched that of the lysine peptide oligomers, but remained resistant to enzymatic degradation. These results expand understanding of peptoid degradation to oxidative and enzymatic mechanisms, and demonstrate the potential for peptoid incorporation into materials where selectivity towards oxidative degradation is necessary, or directed enzymatic susceptibility is desired.
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Affiliation(s)
- Hattie C. Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Mariah J. Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Bradley Z. Taha
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Matthew S. McClellan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Laura J. Suggs
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Adrianne M. Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
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Austin MJ, Schunk H, Watkins C, Ling N, Chauvin J, Morton L, Rosales AM. Fluorescent Peptomer Substrates for Differential Degradation by Metalloproteases. Biomacromolecules 2022; 23:4909-4923. [PMID: 36269900 DOI: 10.1021/acs.biomac.2c01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteases, especially MMPs, are attractive biomarkers given their central role in both physiological and pathological processes. Distinguishing MMP activity with degradable substrates, however, is a difficult task due to overlapping substrate specificity profiles. Here, we developed a system of peptomers (peptide-peptoid hybrids) to probe the impact of non-natural residues on MMP specificity for an MMP peptide consensus sequence. Peptoids are non-natural, N-substituted glycines with a large side-chain diversity. Given the presence of a hallmark proline residue in the P3 position of MMP consensus sequences, we hypothesized that peptoids may offer N-substituted alternatives to generate differential interactions with MMPs. To investigate this hypothesis, peptomer substrates were exposed to five different MMPs, as well as bacterial collagenase, and monitored by fluorescence resonance energy transfer and liquid chromatography-mass spectrometry to determine the rate of cleavage and the composition of degraded fragments, respectively. We found that peptoid residues are well tolerated in the P3 and P3' substrate sites and that the identity of the peptoid in these sites displays a moderate influence on the rate of cleavage. However, peptoid residues were even better tolerated in the P1 substrate site where activity was more strongly correlated with side-chain identity than side-chain position. All MMPs explored demonstrated similar trends in specificity for the peptomers but exhibited different degrees of variability in proteolytic rate. These kinetic profiles served as "fingerprints" for the proteases and yielded separation by multivariate data analysis. To further demonstrate the practical application of this tunability in degradation kinetics, peptomer substrates were tethered into hydrogels and released over distinct timescales. Overall, this work represents a significant step toward the design of probes that maximize differential MMP behavior and presents design rules to tune degradation kinetics with peptoid substitutions, which has promising implications for diagnostic and prognostic applications using array-based sensors.
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Affiliation(s)
- Mariah J Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Hattie Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States.,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Carolyn Watkins
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Natalie Ling
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Jeremy Chauvin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Logan Morton
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
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Kim J, Yu AM, Kubelick KP, Emelianov SY. Gold nanoparticles conjugated with DNA aptamer for photoacoustic detection of human matrix metalloproteinase-9. PHOTOACOUSTICS 2022; 25:100307. [PMID: 34703762 PMCID: PMC8521288 DOI: 10.1016/j.pacs.2021.100307] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/07/2021] [Accepted: 09/24/2021] [Indexed: 05/11/2023]
Abstract
Matrix metalloproteinase-9 (MMP-9) plays major roles in extracellular matrix (ECM) remodeling and membrane protein cleavage, suggesting a high correlation with cancer cell invasion and tumor metastasis. Here, we present a contrast agent based on a DNA aptamer that can selectively target human MMP-9 in the tumor microenvironment (TME) with high affinity and sensitivity. Surface modification of plasmonic gold nanospheres with the MMP-9 aptamer and its complementary sequences allows the nanospheres to aggregate in the presence of human MMP-9 through DNA displacement and hybridization. Aggregation of gold nanospheres enhances the optical absorption in the first near-infrared window (NIR-I) due to the plasmon coupling effect, thereby allowing us to detect the aggregated gold nanospheres within the TME via ultrasound-guided photoacoustic (US/PA) imaging. Selective and sensitive detection of human MMP-9 via US/PA imaging is demonstrated in solution of nanosensors with the pre-treatment of human MMP-9, in vitro in cell culture, and in vivo in a xenograft murine model of human breast cancer.
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Affiliation(s)
- Jinhwan Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony M. Yu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
| | - Kelsey P. Kubelick
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Stanislav Y. Emelianov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Correspondence to: School of Electrical & Computer Engineering, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
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Kaur J, Mishra V, Singh SK, Gulati M, Kapoor B, Chellappan DK, Gupta G, Dureja H, Anand K, Dua K, Khatik GL, Gowthamarajan K. Harnessing amphiphilic polymeric micelles for diagnostic and therapeutic applications: Breakthroughs and bottlenecks. J Control Release 2021; 334:64-95. [PMID: 33887283 DOI: 10.1016/j.jconrel.2021.04.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022]
Abstract
Amphiphilic block copolymers are widely utilized in the design of formulations owing to their unique physicochemical properties, flexible structures and functional chemistry. Amphiphilic polymeric micelles (APMs) formed from such copolymers have gained attention of the drug delivery scientists in past few decades for enhancing the bioavailability of lipophilic drugs, molecular targeting, sustained release, stimuli-responsive properties, enhanced therapeutic efficacy and reducing drug associated toxicity. Their properties including ease of surface modification, high surface area, small size, and enhanced permeation as well as retention (EPR) effect are mainly responsible for their utilization in the diagnosis and therapy of various diseases. However, some of the challenges associated with their use are premature drug release, low drug loading capacity, scale-up issues and their poor stability that need to be addressed for their wider clinical utility and commercialization. This review describes comprehensively their physicochemical properties, various methods of preparation, limitations followed by approaches employed for the development of optimized APMs, the impact of each preparation technique on the physicochemical properties of the resulting APMs as well as various biomedical applications of APMs. Based on the current scenario of their use in treatment and diagnosis of diseases, the directions in which future studies need to be carried out to explore their full potential are also discussed.
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Affiliation(s)
- Jaskiran Kaur
- School of Pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara, Punjab, India
| | - Vijay Mishra
- School of Pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara, Punjab, India
| | - Sachin Kumar Singh
- School of Pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara, Punjab, India.
| | - Monica Gulati
- School of Pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara, Punjab, India
| | - Bhupinder Kapoor
- School of Pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara, Punjab, India
| | | | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura Mahal Road, Jaipur, India
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein, South Africa
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Gopal L Khatik
- National Institute of Pharmaceutical Education and Research, Bijnor-Sisendi road, Sarojini Nagar, Lucknow, Uttar Pradesh 226301, India
| | - Kuppusamy Gowthamarajan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India; Centre of Excellence in Nanoscience & Technology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
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Hernandez DS, Schunk HC, Shankar KM, Rosales AM, Suggs LJ. Poly-d-lysine coated nanoparticles to identify pro-inflammatory macrophages. NANOSCALE ADVANCES 2020; 2:3849-3857. [PMID: 36132778 PMCID: PMC9416964 DOI: 10.1039/d0na00373e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/12/2020] [Indexed: 05/16/2023]
Abstract
Identifying pro-inflammatory macrophages (M1) is of immense importance to diagnose, monitor, and treat various pathologies. In addition, adoptive cell therapies, where harvested cells are isolated, modified to express an M1-like phenotype, then re-implanted to the patient, are also becoming more prevalent to treat diseases such as cancer. In a step toward identifying, labeling, and monitoring macrophage phenotype for adoptive cell therapies, we developed a reactive oxygen species (ROS)-sensitive, gold nanoparticle (AuNP) that fluorescently labels M1 macrophages. AuNPs are electrostatically coated with a proteolysis resistant, fluorescein isothiocyanate-conjugated, poly-d-lysine (PDL-FITC) that is susceptible to backbone cleavage by ROS. When PDL-FITC is bound to AuNPs, fluorescence is quenched via a combination of nanoparticle surface (NSET) and Forster resonance (FRET) energy transfer mechanisms. Upon ROS-induced cleavage of PDL-FITC, up to a 7-fold change in fluorescence is demonstrated. PDL-FITC AuNPs were loaded into RAW 264.7 macrophages (RAWs) and primary bone marrow- derived macrophages (BMDMs) prior to in vitro polarization. For both cell types, detectable differences in intracellular fluorescence were observed between M1 polarized and non-stimulated (M0) control groups after 24 h using both confocal imaging and flow cytometry. PDL-FITC AuNPs can potentially be useful in identifying M1 macrophages within diverse cell populations and provide longitudinal macrophage response data to external cues.
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Affiliation(s)
- Derek S Hernandez
- Department of Biomedical Engineering, University of Texas at Austin Austin TX 78712 USA
| | - Hattie C Schunk
- Department of Biomedical Engineering, University of Texas at Austin Austin TX 78712 USA
- McKetta Department of Chemical Engineering, University of Texas at Austin Austin TX 78712 USA
| | - Karan M Shankar
- Department of Biomedical Engineering, University of Texas at Austin Austin TX 78712 USA
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin Austin TX 78712 USA
| | - Laura J Suggs
- Department of Biomedical Engineering, University of Texas at Austin Austin TX 78712 USA
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