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Thorpe MP, Smith AN, Blackwell DJ, Hopkins CR, Knollmann BC, Akers WS, Johnston JN. The backbone constitution drives passive permeability independent of side chains in depsipeptide and peptide macrocycles inspired by ent-verticilide. Chem Sci 2024; 15:d4sc02758b. [PMID: 39211739 PMCID: PMC11348715 DOI: 10.1039/d4sc02758b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
The number of peptide-like scaffolds found in late-stage drug development is increasing, but a critical unanswered question in the field is whether substituents (side chains) or the backbone drive passive permeability. The backbone is scrutinized in this study. Five series of macrocyclic peptidic compounds were prepared, and their passive permeability was determined (PAMPA, Caco-2), to delineate structure-permeability relationships. Each series was based on the cell-permeable antiarrhythmic compound ent-verticilide, a cyclic oligomeric depsipeptide (COD) containing repeating ester/N-Me amide didepsipeptide monomers. One key finding is that native lipophilic ester functionality can impart a favorable level of permeability, but ester content alone is not the final determinant - the analog with highest P app was discovered by a single ester-to-N-H amide replacement. Furthermore, the relative composition of esters and N-Me amides in a series had more nuanced permeability behavior. Overall, a systematic approach to structure-permeability correlations suggests that a combinatorial-like investigation of functionality in peptidic or peptide-like compounds could better identify leads with optimal passive permeability, perhaps prior to modification of side chains.
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Affiliation(s)
- Madelaine P Thorpe
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
| | - Abigail N Smith
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
| | - Daniel J Blackwell
- Department of Medicine, Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center Medical Research Bldg IV, Room 1265, 2215B Garland Ave Nashville TN 37232-0575 USA
| | - Corey R Hopkins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Bjorn C Knollmann
- Department of Medicine, Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Vanderbilt University Medical Center Medical Research Bldg IV, Room 1265, 2215B Garland Ave Nashville TN 37232-0575 USA
| | - Wendell S Akers
- Pharmaceutical Sciences Research Center, College of Pharmacy, Lipscomb University Nashville TN 37204 USA
| | - Jeffrey N Johnston
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Nashville TN 37235-1822 USA
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2
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Blanco MJ, Gardinier KM, Namchuk MN. Advancing New Chemical Modalities into Clinical Studies. ACS Med Chem Lett 2022; 13:1691-1698. [PMID: 36385931 PMCID: PMC9661701 DOI: 10.1021/acsmedchemlett.2c00375] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/17/2022] [Indexed: 11/29/2022] Open
Abstract
Drug discovery and development has experienced an incredible paradigm shift in the past two decades. What once was considered a predominant R&D landscape of small molecules within a prescribed properties and mechanism space now includes an innovative wave of new chemical modalities. Scientists in the pharmaceutical industry can now strategize across a variety of modalities to find the best option to modulate a given target and provide treatment for a specific disease. We have witnessed a remarkable change not only in molecular design but also in creative approaches to drug delivery that have enabled advancement of novel modalities to clinical studies. In this Microperspective, we evaluate the critical differences between traditional small molecules and beyond rule of 5 compounds, peptides, oligonucleotides, and biologics for advancing into development, particularly their pharmacokinetic profiles and drug delivery strategies.
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Affiliation(s)
- Maria-Jesus Blanco
- Chemical
Sciences, Atavistik Bio, 75 Sidney Street, Cambridge Massachusetts 02139, United States
| | - Kevin M. Gardinier
- Discovery
Research, Karuna Therapeutics, 99 High Street Boston, Massachusetts 02110, United States
| | - Mark N. Namchuk
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 25 Shattuck Street Boston, Massachusetts 02115, United States
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3
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Expanding the structure-activity relationship of cytotoxic diphenyl macrocycles. Bioorg Med Chem Lett 2022; 62:128628. [PMID: 35182774 DOI: 10.1016/j.bmcl.2022.128628] [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: 11/28/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/21/2022]
Abstract
Twenty-four biaryl tetrapeptide macrocycles were synthesized as an extension of our previous work. Two groups of compounds were constructed for establishing a structure-activity relationship: one having an aromatic substituent at α-position of one exo-peptide and the other group with a variation in the size of the lipophilic chain. Compound 13t had the best cytotoxicity from all the compounds tested (in a panel of six human cancer cell lines) and low toxicity on one healthy cell line. The study identified the lipophilic chain as the main structural moiety for improving the biological activity, being the seven-carbon chain the optimal length. On the other hand, the aromatic rings at α-position did not enhance the cytotoxicity.
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4
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Macpherson A, Birtley JR, Broadbridge RJ, Brady K, Schulze MSED, Tang Y, Joyce C, Saunders K, Bogle G, Horton J, Kelm S, Taylor RD, Franklin RJ, Selby MD, Laabei M, Wonfor T, Hold A, Stanley P, Vadysirisack D, Shi J, van den Elsen J, Lawson ADG. The Chemical Synthesis of Knob Domain Antibody Fragments. ACS Chem Biol 2021; 16:1757-1769. [PMID: 34406751 DOI: 10.1021/acschembio.1c00472] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cysteine-rich knob domains found in the ultralong complementarity determining regions of a subset of bovine antibodies are capable of functioning autonomously as 3-6 kDa peptides. While they can be expressed recombinantly in cellular systems, in this paper we show that knob domains are also readily amenable to a chemical synthesis, with a co-crystal structure of a chemically synthesized knob domain in complex with an antigen showing structural equivalence to the biological product. For drug discovery, following the immunization of cattle, knob domain peptides can be synthesized directly from antibody sequence data, combining the power and diversity of the bovine immune repertoire with the ability to rapidly incorporate nonbiological modifications. We demonstrate that, through rational design with non-natural amino acids, a paratope diversity can be massively expanded, in this case improving the efficacy of an allosteric peptide. As a potential route to further improve stability, we also performed head-to-tail cyclizations, exploiting the proximity of the N and C termini to synthesize functional, fully cyclic antibody fragments. Lastly, we highlight the stability of knob domains in plasma and, through pharmacokinetic studies, use palmitoylation as a route to extend the plasma half-life of knob domains in vivo. This study presents an antibody-derived medicinal chemistry platform, with protocols for solid-phase synthesis of knob domains, together with the characterization of their molecular structures, in vitro pharmacology, and pharmacokinetics.
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Affiliation(s)
- Alex Macpherson
- UCB Pharma, Slough SL1 3WE, U.K
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | | | | | | | | | - Yalan Tang
- UCB-Ra Pharma, Cambridge, Massachusetts 02140, United States
| | - Callum Joyce
- UCB Pharma, Slough SL1 3WE, U.K
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | | | | | - John Horton
- Peptide Protein Research, Bishops Waltham SO32 1QD, U.K
| | | | | | | | | | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | - Toska Wonfor
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
| | | | | | | | | | - Jean van den Elsen
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, U.K
- Centre for Therapeutic Innovation, University of Bath, Bath BA2 7AY, U.K
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5
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Lill JR, Mathews WR, Rose CM, Schirle M. Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade. Expert Rev Proteomics 2021; 18:503-526. [PMID: 34320887 DOI: 10.1080/14789450.2021.1962300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. AREAS COVERED Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. EXPERT OPINION Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.
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Affiliation(s)
- Jennie R Lill
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - William R Mathews
- OMNI Department, Genentech Inc. 1 DNA Way, South San Francisco, CA, USA
| | - Christopher M Rose
- Department of Microchemistry, Lipidomics and Next Generation Sequencing, Genentech Inc. DNA Way, South San Francisco, CA, USA
| | - Markus Schirle
- Chemical Biology and Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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Cruz MA, Araujo TA, Avanzi IR, Parisi JR, de Andrade ALM, Rennó ACM. Collagen from Marine Sources and Skin Wound Healing in Animal Experimental Studies: a Systematic Review. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:1-11. [PMID: 33404918 DOI: 10.1007/s10126-020-10011-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Collagen (Col) from marine organisms has been emerging as an important alternative for commercial Col and it has been considered highly attractive by the industry. Despite the positive effects of Col from marine origin, there is still limited understanding of the effects of this natural biomaterial in the process of wound healing in animal studies. In this context, the purpose of this study was to perform a systematic review of the literature to examine the effects of Col from different marine species in the process of skin tissue healing using experimental models of skin wound. The search was carried out according to the orientations of Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA), and the descriptors of the Medical Subject Headings (MeSH) were defined: "marine collagen," "spongin," "spongin," "skin," and "wound." A total of 42 articles were retrieved from the databases PubMed and Scopus. After the eligibility analyses, this review covers the different marine sources of Col reported in 10 different papers from the beginning of 2011 through the middle of 2019. The results were based mainly on histological analysis and it demonstrated that Col-based treatment resulted in a higher deposition of granulation tissue, stimulation of re-epitalization and neoangiogenesis and increased amount of Col of the wound, culminating in a more mature morphological aspect. In conclusion, this review demonstrates that marine Col from different species presented positive effects on the process of wound skin healing in experimental models used, demonstrating the huge potential of this biomaterial for tissue engineering proposals.
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Affiliation(s)
- Matheus Almeida Cruz
- Department of Biosciences, Federal University of São Paulo (UNIFESP), Lab 342, 136 Silva Jardim Street, Santos, SP, 11015020, Brazil
| | - Tiago Akira Araujo
- Department of Biosciences, Federal University of São Paulo (UNIFESP), Lab 342, 136 Silva Jardim Street, Santos, SP, 11015020, Brazil
| | - Ingrid Regina Avanzi
- Department of Biosciences, Federal University of São Paulo (UNIFESP), Lab 342, 136 Silva Jardim Street, Santos, SP, 11015020, Brazil
- São Paulo State Faculty of Technology (FATEC), 350 Senador Feijó Avenue, Santos, SP, 11015502, Brazil
| | - Julia Risso Parisi
- Department of Biosciences, Federal University of São Paulo (UNIFESP), Lab 342, 136 Silva Jardim Street, Santos, SP, 11015020, Brazil
- Department of Physical Therapy, Federal University of São Carlos (UFSCar), km 235 Washington Luís Road, São Carlos, SP, 13565905, Brazil
| | - Ana Laura Martins de Andrade
- Department of Physical Therapy, Federal University of São Carlos (UFSCar), km 235 Washington Luís Road, São Carlos, SP, 13565905, Brazil
| | - Ana Claudia Muniz Rennó
- Department of Biosciences, Federal University of São Paulo (UNIFESP), Lab 342, 136 Silva Jardim Street, Santos, SP, 11015020, Brazil.
- Department of Physical Therapy, Federal University of São Carlos (UFSCar), km 235 Washington Luís Road, São Carlos, SP, 13565905, Brazil.
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Maraswami M, Goh J, Loh TP. Macrolactam Synthesis via Ring-Closing Alkene-Alkene Cross-Coupling Reactions. Org Lett 2020; 22:9724-9728. [PMID: 33258611 DOI: 10.1021/acs.orglett.0c03801] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reported herein is a practical method for macrolactam synthesis via a Rh(III)-catalyzed ring closing alkene-alkene cross-coupling reaction. The reaction proceeded via a Rh-catalyzed alkenyl sp2 C-H activation process, which allows access to macrocyclic molecules of different ring sizes. Macrolactams containing a conjugated diene framework could be easily prepared in high chemoselectivities and Z,E stereoselectivities.
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Affiliation(s)
- Manikantha Maraswami
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Jeffrey Goh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Teck-Peng Loh
- Institute of Advanced Synthesis (IAS), School of Chemistry and Chemical Engineering, Northwestern Polytechnical University (NPU), Xi'an 710072, China.,Yangtze River Delta Research Institute of NPU, Taicang, Jiangsu 215400, China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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8
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Buskes MJ, Blanco MJ. Impact of Cross-Coupling Reactions in Drug Discovery and Development. Molecules 2020; 25:E3493. [PMID: 32751973 PMCID: PMC7436090 DOI: 10.3390/molecules25153493] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022] Open
Abstract
Cross-coupling reactions have played a critical role enabling the rapid expansion of structure-activity relationships (SAR) during the drug discovery phase to identify a clinical candidate and facilitate subsequent drug development processes. The reliability and flexibility of this methodology have attracted great interest in the pharmaceutical industry, becoming one of the most used approaches from Lead Generation to Lead Optimization. In this mini-review, we present an overview of cross-coupling reaction applications to medicinal chemistry efforts, in particular the Suzuki-Miyaura and Buchwald-Hartwig cross-coupling reactions as a remarkable resource for the generation of carbon-carbon and carbon-heteroatom bonds. To further appreciate the impact of this methodology, the authors discuss some recent examples of clinical candidates that utilize key cross-coupling reactions in their large-scale synthetic process. Looking into future opportunities, the authors highlight the versatility of the cross-coupling reactions towards new chemical modalities like DNA-encoded libraries (DELs), new generation of peptides and cyclopeptides, allosteric modulators, and proteolysis targeting chimera (PROTAC) approaches.
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Affiliation(s)
| | - Maria-Jesus Blanco
- Medicinal Chemistry. Sage Therapeutics, Inc. 215 First Street, Cambridge, MA 02142, USA;
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9
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Bajaj S, Ong ST, Chandy KG. Contributions of natural products to ion channel pharmacology. Nat Prod Rep 2020; 37:703-716. [PMID: 32065187 DOI: 10.1039/c9np00056a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: Up to 2020Ion channels are a vast super-family of membrane proteins that play critical physiological roles in excitable and non-excitable cells. Their biomedical importance makes them valuable and attractive drug targets for neurological, cardiovascular, gastrointestinal and metabolic diseases, and for cancer therapy and immune modulation. Current therapeutics target only a minor subset of ion channels, leaving a large unexploited space within the ion channel field. Natural products harnessed from the almost unlimited and diverse universe of compounds within the bioenvironment have been used to modulate channels for decades. In this review we highlight the impact made by natural products on ion channel pharmacology, specifically on K+, NaV and CaV channels, and use case studies to describe the development of ion channel-modulating drugs from natural sources for the treatment of pain, heart disease and autoimmune diseases.
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Affiliation(s)
- Saumya Bajaj
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Experimental Medicine Building, 59 Nanyang Drive, 636921, Singapore.
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10
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Keshavarzi Arshadi A, Salem M, Collins J, Yuan JS, Chakrabarti D. DeepMalaria: Artificial Intelligence Driven Discovery of Potent Antiplasmodials. Front Pharmacol 2020; 10:1526. [PMID: 32009951 PMCID: PMC6974622 DOI: 10.3389/fphar.2019.01526] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
Antimalarial drugs are becoming less effective due to the emergence of drug resistance. Resistance has been reported for all available malaria drugs, including artemisinin, thus creating a perpetual need for alternative drug candidates. The traditional drug discovery approach of high throughput screening (HTS) of large compound libraries for identification of new drug leads is time-consuming and resource intensive. While virtual in silico screening is a solution to this problem, however, the generalization of the models is not ideal. Artificial intelligence (AI), utilizing either structure-based or ligand-based approaches, has demonstrated highly accurate performances in the field of chemical property prediction. Leveraging the existing data, AI would be a suitable alternative to blind-search HTS or fingerprint-based virtual screening. The AI model would learn patterns within the data and help to search for hit compounds efficiently. In this work, we introduce DeepMalaria, a deep-learning based process capable of predicting the anti-Plasmodium falciparum inhibitory properties of compounds using their SMILES. A graph-based model is trained on 13,446 publicly available antiplasmodial hit compounds from GlaxoSmithKline (GSK) dataset that are currently being used to find novel drug candidates for malaria. We validated this model by predicting hit compounds from a macrocyclic compound library and already approved drugs that are used for repurposing. We have chosen macrocyclic compounds as these ligand-binding structures are underexplored in malaria drug discovery. The in silico pipeline for this process also consists of additional validation of an in-house independent dataset consisting mostly of natural product compounds. Transfer learning from a large dataset was leveraged to improve the performance of the deep learning model. To validate the DeepMalaria generated hits, we used a commonly used SYBR Green I fluorescence assay based phenotypic screening. DeepMalaria was able to detect all the compounds with nanomolar activity and 87.5% of the compounds with greater than 50% inhibition. Further experiments to reveal the compounds’ mechanism of action have shown that not only does one of the hit compounds, DC-9237, inhibits all asexual stages of Plasmodium falciparum, but is a fast-acting compound which makes it a strong candidate for further optimization.
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Affiliation(s)
- Arash Keshavarzi Arshadi
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States
| | - Milad Salem
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL, United States
| | - Jennifer Collins
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States
| | - Jiann Shiun Yuan
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL, United States
| | - Debopam Chakrabarti
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States
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