1
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Castro RBD, Badaró de Moraes JV, de Souza ACA, Favarato ES, Voorwald FA, Dos Santos FM, Bressan GC, Vasconcellos RDS, Fietto JLR. High-resolution mapping of linear epitopes from LiNTPDase2: Advancing leishmaniasis detection using optimized protein and peptide antigens. Diagn Microbiol Infect Dis 2024; 110:116448. [PMID: 39029390 DOI: 10.1016/j.diagmicrobio.2024.116448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Visceral Leishmaniasis, caused by Leishmania infantum, is a tropical neglected disease and the most dangerous form of Leishmaniasis. It occurs zoonotically, with domestic transmission posing risks to humans as dogs have high susceptibility and are natural reservoirs of the parasite. Given their epidemiological role, improvements are needed in diagnosing Canine Visceral Leishmaniasis (CVL). Thus, we mapped linear epitopes from the rLiNTPDase2 antigen through peptide microarray and identified six positive epitopes. Validation through peptide ELISA revealed three promising peptides with accuracies of 78.6%, 85.92%, and 79.59%. Their combination yielded 97.58% accuracy. Negative epitopes were also found, which interacted with CVL-negative and Chagas Disease positive samples. Their removal from the rLiNTPDase2 sequence resulted in the rNT2.neg, which obtained enhanced specificity over rLiNTPDase2. The rNT2.neg validation achieved 87.50% sensitivity, 90.55% specificity, and 93.5% accuracy within 127 CVL-positive and 96 CVL-negative samples. Therefore, three peptides and rNT2.neg show significant promise for CVL diagnosis.
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Affiliation(s)
- Raissa Barbosa de Castro
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil.
| | - João Victor Badaró de Moraes
- Department of General Biology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil
| | - Anna Cláudia Alves de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil
| | - Evandro Silva Favarato
- Department of Veterinary, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil
| | - Fabiana Azevedo Voorwald
- Department of Veterinary, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil
| | - Fabiane Matos Dos Santos
- Departament of Pharmacy and Nutrition, Universidade Federal do Espírito Santo, Alto Universitário S/N, 29500-000, Alegre, ES, Brazil
| | - Gustavo Costa Bressan
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil
| | - Raphael de Souza Vasconcellos
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil
| | - Juliana Lopes Rangel Fietto
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil; Instituto de Biotecnologia Aplicada à Agropecuária (Bioagro), Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, 36570-000, Viçosa, MG, Brazil
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2
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Pritam M, Dutta S, Medicherla KM, Kumar R, Singh SP. Computational analysis of spike protein of SARS-CoV-2 (Omicron variant) for development of peptide-based therapeutics and diagnostics. J Biomol Struct Dyn 2024; 42:7321-7339. [PMID: 37498146 DOI: 10.1080/07391102.2023.2239932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
In the last few years, the worldwide population has suffered from the SARS-CoV-2 pandemic. The WHO dashboard indicated that around 504,079,039 people were infected and 6,204,155 died from COVID-19 caused by different variants of SARS-CoV-2. Recently, a new variant of SARS-CoV-2 (B.1.1.529) was reported by South Africa known as Omicron. The high transmissibility rate and resistance towards available anti-SARS-CoV-2 drugs/vaccines/monoclonal antibodies, make Omicron a variant of concern. Because of various mutations in spike protein, available diagnostic and therapeutic treatments are not reliable. Therefore, the present study explored the development of some therapeutic peptides that can inhibit the SARS-CoV-2 virus interaction with host ACE2 receptors and can also be used for diagnostic purposes. The screened linear B cell epitopes derived from receptor-binding domain of spike protein of Omicron variant were evaluated as peptide inhibitor/vaccine candidates through different bioinformatics tools including molecular docking and simulation to analyze the interaction between Omicron peptide and human ACE2 receptor. Overall, in-silico studies revealed that Omicron peptides OP1-P12, OP14, OP20, OP23, OP24, OP25, OP26, OP27, OP28, OP29, and OP30 have the potential to inhibit Omicron interaction with ACE2 receptor. Moreover, Omicron peptides OP20, OP22, OP23, OP24, OP25, OP26, OP27, and OP30 have shown potential antigenic and immunogenic properties that can be used in design and development vaccines against Omicron. Although the in-silico validation was performed by comparative analysis with the control peptide inhibitor, further validation through wet lab experimentation is required before its use as therapeutic peptides.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manisha Pritam
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Somenath Dutta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Department of Bioinformatics, Pondicherry Central University, Puducherry, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
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3
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Song L, Jiang S, Yang Q, Huang W, Qiu Y, Chen Z, Sun X, Wang T, Wu S, Chen Y, Zeng H, Wang Z, Kang L. Development of a Novel Peptide-Based PET Tracer [ 68Ga]Ga-DOTA-BP1 for BCMA Detection in Multiple Myeloma. J Med Chem 2024. [PMID: 39167092 DOI: 10.1021/acs.jmedchem.4c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
B-cell maturation antigen (BCMA) has emerged as a promising tumor marker for the diagnosis and treatment of multiple myeloma. The noninvasive and rapid detection of BCMA expression in vivo provides significant value in screening and evaluating multiple myeloma patients receiving BCMA-targeted therapy. We identified the BCMA-targeting peptide BP1 from a one-bead-one-compound (OBOC) peptide library using a high-throughput microarray strategy. The BCMA-targeting specificity and affinity of BP1 were assessed by surface plasmon resonance imaging (SPRi), flow cytometry, and confocal imaging. BCMA-positive (H929) and BCMA-negative (K562) subcutaneous tumor models were established and labeled with 68Ga for BP1, followed by PET imaging and biodistribution studies. PET imaging demonstrated that 68Ga-labeled BP1 has significant specific uptake in multiple myeloma, enabling rapid identification of BCMA expression and precise delineation of the disease. Thus, BP1 represents an ideal candidate for multiple myeloma imaging.
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Affiliation(s)
- Lele Song
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Sujun Jiang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Qi Yang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Wenpeng Huang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Yongkang Qiu
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Zhao Chen
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Xinyao Sun
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Tianyao Wang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Sitong Wu
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Yongshou Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Huajie Zeng
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
| | - Zihua Wang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350122, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
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4
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Pike S, Wuest M, Lopez-Campistrous A, Hu MY, Derda R, Wuest F, McMullen T. First-Generation Radiolabeled Cyclic Peptides for Molecular Imaging of Platelet-Derived Growth Factor Receptor α. Mol Pharm 2024. [PMID: 39152916 DOI: 10.1021/acs.molpharmaceut.4c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Abstract
Occult nodal spread and metastatic disease require longstanding imaging and biochemical assessments for thyroid cancer, a disease that has a propensity for diffuse, small-volume disease. We have developed a 64Cu-labeled platelet-derived growth factor receptor α (PDGFRA) antibody for immuno-PET of PDGFRA in metastatic papillary thyroid cancer (PTC). The present work describes the discovery of small cyclic PDGFRA-targeting peptides, their binding features, and radiolabeling with positron emitter gallium-68 (68Ga) for in vitro and in vivo characterization in thyroid cancer models. Phage-display technology with two separate libraries and seven different cell lines was used through three rounds of biopanning as well as flow cytometry and comparative analysis with recombinant protein to select specific peptide sequences. Phenotypic binding analysis was completed by using phosphorylation and cell migration assays. In vitro protein binding was analyzed with thermophoresis and flow cytometry using the fluorescent-labeled PDGFRA peptide. Peptide candidates were modified with the NOTA chelator for radiolabeling with 68Ga. In vitro cell uptake was studied in various thyroid cancer cell lines. In vivo studies of 68Ga-labeled peptides included metabolic stability and PET imaging. From the original library (1013 compounds), five different peptide groups were identified based on biopanning experiments with and without the α subunit of PDGFR, leading to ∼50 peptides. Subsequent phenotypic screening revealed two core peptide sequences (CP16 and CP18) that demonstrated significant changes in the level of PDGFRA phosphorylation and cell migration. Alanine scan sublibraries were created from these two lead peptide sequences, and peptides were radiolabeled using 68Ga-GaCl3 at pH 4.5, resulting in RCP > 95% within 34-40 min, including SPE purification. Cyclic peptide CP18.5 showed the strongest effects on cell migration, flow cytometry, and binding by visual interference color assay. 68Ga-labeled PDGFRA-targeting peptides showed elevated cell and tumor uptake in models of thyroid cancer, with 68Ga-NOTA-CP18.5 being the lead candidate. However, metabolic stability in vivo was compromised for 68Ga-NOTA-CP18.5 vs 68Ga-NOTA-CP18 but without impacting tumor uptake or clearance profiles. First-generation radiolabeled cyclic peptides have been developed as novel radiotracers, particularly 68Ga-NOTA-CP18.5, for the molecular imaging of PDGFRA in thyroid cancer.
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Affiliation(s)
- Susan Pike
- Department of Oncology, University of Alberta, Edmonton, Canada T6G 1Z2
| | - Melinda Wuest
- Department of Oncology, University of Alberta, Edmonton, Canada T6G 1Z2
| | | | - Mi Yao Hu
- Department of Oncology, University of Alberta, Edmonton, Canada T6G 1Z2
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Canada T6G 2N4
| | - Frank Wuest
- Department of Oncology, University of Alberta, Edmonton, Canada T6G 1Z2
| | - Todd McMullen
- Department of Surgery, University of Alberta, Edmonton, Canada T6G 2B7
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5
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Cimmino L, Diaferia C, Rosa M, Morelli G, Rosa E, Accardo A. Hybrid peptide-PNA monomers as building blocks for the fabrication of supramolecular aggregates. J Pept Sci 2024; 30:e3573. [PMID: 38471735 DOI: 10.1002/psc.3573] [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: 01/17/2024] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/14/2024]
Abstract
Advantages like biocompatibility, biodegradability and tunability allowed the exploitation of peptides and peptidomimetics as versatile therapeutic or diagnostic agents. Because of their selectivity towards transmembrane receptors or cell membranes, peptides have also been identified as suitable molecules able to deliver in vivo macromolecules, proteins or nucleic acids. However, after the identification of the homodimer diphenylalanine (FF) as an aggregative motif inside the Aβ1-42 polypeptide, short and ultrashort peptides have been studied as building blocks for the fabrication of supramolecular, ordered nanostructures for applications in biotechnological, biomedical and industrial fields. In this perspective, many hybrid molecules that combine FF with other chemical entities have been synthesized and characterized. Two novel hybrid derivatives (tFaF and cFgF), in which the FF homodimer is alternated with the peptide-nucleic acid (PNA) heterodimer "g-c" (guanine-cytosine) or "a-t" (adenine-thymine) and their dimeric forms (tFaF)2 and (cFgF)2 were synthesized. The structural characterization performed by circular dichroism (CD), Fourier transform infrared (FTIR) and fluorescence spectroscopies highlighted the capability of all the FF-PNA derivatives to self-assemble into β-sheet structures. As a consequence of this supramolecular organization, the resulting aggregates also exhibit optoelectronic properties already reported for other similar nanostructures. This photoemissive behavior is promising for their potential applications in bioimaging.
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Affiliation(s)
| | - Carlo Diaferia
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Mariangela Rosa
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Elisabetta Rosa
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
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6
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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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7
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Scalzitti N, Miralavy I, Korenchan DE, Farrar CT, Gilad AA, Banzhaf W. Computational peptide discovery with a genetic programming approach. J Comput Aided Mol Des 2024; 38:17. [PMID: 38570405 DOI: 10.1007/s10822-024-00558-0] [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: 12/08/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
The development of peptides for therapeutic targets or biomarkers for disease diagnosis is a challenging task in protein engineering. Current approaches are tedious, often time-consuming and require complex laboratory data due to the vast search spaces that need to be considered. In silico methods can accelerate research and substantially reduce costs. Evolutionary algorithms are a promising approach for exploring large search spaces and can facilitate the discovery of new peptides. This study presents the development and use of a new variant of the genetic-programming-based POET algorithm, called POETRegex , where individuals are represented by a list of regular expressions. This algorithm was trained on a small curated dataset and employed to generate new peptides improving the sensitivity of peptides in magnetic resonance imaging with chemical exchange saturation transfer (CEST). The resulting model achieves a performance gain of 20% over the initial POET models and is able to predict a candidate peptide with a 58% performance increase compared to the gold-standard peptide. By combining the power of genetic programming with the flexibility of regular expressions, new peptide targets were identified that improve the sensitivity of detection by CEST. This approach provides a promising research direction for the efficient identification of peptides with therapeutic or diagnostic potential.
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Affiliation(s)
- Nicolas Scalzitti
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Iliya Miralavy
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - David E Korenchan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christian T Farrar
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Assaf A Gilad
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA.
- Department of Chemical Engineering, Michigan State University, East Lansing, MI, USA.
- Department of Radiology, Michigan State University, East Lansing, MI, USA.
| | - Wolfgang Banzhaf
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA.
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
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8
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Rockett T, Almahyawi M, Ghimire ML, Jonnalagadda A, Tagliaferro V, Seashols-Williams SJ, Bertino MF, Caputo GA, Reiner JE. Cluster-Enhanced Nanopore Sensing of Ovarian Cancer Marker Peptides in Urine. ACS Sens 2024; 9:860-869. [PMID: 38286995 PMCID: PMC10897939 DOI: 10.1021/acssensors.3c02207] [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: 10/19/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024]
Abstract
The development of novel methodologies that can detect biomarkers from cancer or other diseases is both a challenge and a need for clinical applications. This partly motivates efforts related to nanopore-based peptide sensing. Recent work has focused on the use of gold nanoparticles for selective detection of cysteine-containing peptides. Specifically, tiopronin-capped gold nanoparticles, trapped in the cis-side of a wild-type α-hemolysin nanopore, provide a suitable anchor for the attachment of cysteine-containing peptides. It was recently shown that the attachment of these peptides onto a nanoparticle yields unique current signatures that can be used to identify the peptide. In this article, we apply this technique to the detection of ovarian cancer marker peptides ranging in length from 8 to 23 amino acid residues. It is found that sequence variability complicates the detection of low-molecular-weight peptides (<10 amino acid residues), but higher-molecular-weight peptides yield complex, high-frequency current fluctuations. These fluctuations are characterized with chi-squared and autocorrelation analyses that yield significantly improved selectivity when compared to traditional open-pore analysis. We demonstrate that the technique is capable of detecting the only two cysteine-containing peptides from LRG-1, an emerging protein biomarker, that are uniquely present in the urine of ovarian cancer patients. We further demonstrate the detection of one of these LRG-1 peptides spiked into a sample of human female urine.
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Affiliation(s)
- Thomas
W. Rockett
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mohammed Almahyawi
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- King
Fahd Medical Research Center, King Abdulaziz
University, Jeddah 21589, Saudi Arabia
| | - Madhav L. Ghimire
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Aashna Jonnalagadda
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Victoria Tagliaferro
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Sarah J. Seashols-Williams
- Department
of Forensic Sciences, Virginia Commonwealth
University, Richmond, Virginia 23284, United States
| | - Massimo F. Bertino
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gregory A. Caputo
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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9
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Okasha H. Fundamental Uses of Peptides as a New Model in Both Treatment and Diagnosis. Recent Pat Biotechnol 2024; 18:110-127. [PMID: 38282442 DOI: 10.2174/1872208317666230512143508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/16/2023] [Accepted: 04/04/2023] [Indexed: 01/30/2024]
Abstract
An amino acid short chain is known as a peptide. Peptide bonds are the connections that hold the amino acids of a peptide together in a particular order. Characteristically, the shorter length of peptides helps to identify them from proteins. Different ways are used to classify peptides, including chain length, source of peptides, or their biological functions. The fact that peptides serve several purposes suggests that there is a foundation for improvement in peptide production and structure to enhance action. In addition, many patents on peptides for therapeutic and diagnostic approaches have been obtained. This review aims to give an overview of peptides used recently in treatment and diagnosis.
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Affiliation(s)
- Hend Okasha
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Giza, 12411, Egypt
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10
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Grakh K, Mittal D, Prakash A, Kumar R, Jindal N. uspA gene-based phylogenetic analysis and antigenic epitope prediction for Escherichia coli strains of avian origin. Front Vet Sci 2023; 10:1183048. [PMID: 38188721 PMCID: PMC10767999 DOI: 10.3389/fvets.2023.1183048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Pathogenic Escherichia coli (E. coli) is responsible for various local and systemic infections in animal and human populations. Conventional methods for the detection and identification of E. coli are time-consuming and less reliable for atypical strains. The uspA gene has been widely used as a target for the detection of E. coli. The present study was aimed at phylogenetic analysis of the uspA gene sequences to determine the evolutionary relationships between the strains and other members of the Enterobacteriaceae family. In addition, the unique differences in the sequences of the current study with Salmonella and Shigella species were tested using Tajima's molecular clock test. Antigenic epitope prediction was performed to locate the B-cell epitope region of the UspA protein. Two E. coli isolates of avian origin and strains from the National Center for Biotechnology Information (NCBI) database were used for prediction. The Immune Epitope Database (IEDB) server, Bepitope, ABCpred, SVMTrip, and ElliPro server were used to identify B-cell epitopes. The 3D structure was predicted using SWISS-MODEL. Phylogenetic analysis of the isolates from the current study revealed that both OM837340 and OM837341 sequences from the current study had maximum nucleotide homology (nt) of 99.87%-100% with E. coli isolates and minimum nt homology of 84.08% with Salmonella enteritidis and S. Hissar. The isolates in the current study had a homology of 98.87%, while the homology with Shigella species was 99.25%. Seven silent mutations were observed in the coding region of the UspA protein of ECO9LTBW (current study). Modeling of the UspA protein revealed a maximum homology of 67.86% with the Protein Data Bank in Europe (PDBe), also validated by the Ramachandran plot. No significant differences were found in the coding regions of uspA of Salmonella, Shigella, and E. coli with Tajima's test. For the E. coli isolates, a total of 24 linear B-cell and seven discontinuous epitopes were predicted using in-silico analysis. When the results of the predicted peptides were compared, two peptides, namely ARPYNA and YSDLYTGLIDVNLGDMQKRISEE, were found suitable candidates. In conclusion, the uspA gene appears to be conserved among E. coli isolates and can be used for molecular detection.
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Affiliation(s)
| | - Dinesh Mittal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
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11
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Giorgio A, Del Gatto A, Pennacchio S, Saviano M, Zaccaro L. Peptoids: Smart and Emerging Candidates for the Diagnosis of Cancer, Neurological and Autoimmune Disorders. Int J Mol Sci 2023; 24:16333. [PMID: 38003529 PMCID: PMC10671428 DOI: 10.3390/ijms242216333] [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: 10/18/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Early detection of fatal and disabling diseases such as cancer, neurological and autoimmune dysfunctions is still desirable yet challenging to improve quality of life and longevity. Peptoids (N-substituted glycine oligomers) are a relatively new class of peptidomimetics, being highly versatile and capable of mimicking the architectures and the activities of the peptides but with a marked resistance to proteases and a propensity to cross the cellular membranes over the peptides themselves. For these properties, they have gained an ever greater interest in applications in bioengineering and biomedical fields. In particular, the present manuscript is to our knowledge the only review focused on peptoids for diagnostic applications and covers the last decade's literature regarding peptoids as tools for early diagnosis of pathologies with a great impact on human health and social behavior. The review indeed provides insights into the peptoid employment in targeted cancer imaging and blood-based screening of neurological and autoimmune diseases, and it aims to attract the scientific community's attention to continuing and sustaining the investigation of these peptidomimetics in the diagnosis field considering their promising peculiarities.
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Affiliation(s)
- Anna Giorgio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy;
| | - Annarita Del Gatto
- Institute of Biostructure and Bioimaging (IBB), CNR, 80131 Naples, Italy;
- Interuniversity Research Centre on Bioactive Peptides (CIRPeB) “Carlo Pedone”, University of Naples “Federico II”, 80131 Naples, Italy
| | - Simone Pennacchio
- Institute of Condensed Matter Chemistry and Technologies for Energy (ICMATE), CNR, 35127 Padova, Italy;
| | | | - Laura Zaccaro
- Institute of Biostructure and Bioimaging (IBB), CNR, 80131 Naples, Italy;
- Interuniversity Research Centre on Bioactive Peptides (CIRPeB) “Carlo Pedone”, University of Naples “Federico II”, 80131 Naples, Italy
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12
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Ferreira R, Amado F, Vitorino R. Empowering peptidomics: utilizing computational tools and approaches. Bioanalysis 2023; 15:1315-1325. [PMID: 37737150 DOI: 10.4155/bio-2023-0102] [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] [Indexed: 09/23/2023] Open
Abstract
Bioinformatics plays a critical role in the advancement of peptidomics by providing powerful tools for data analysis, interpretation and integration. Peptidomics is concerned with the study of peptides, short chains of amino acids with diverse biological functions. This area includes peptide identification and characterization, database construction, de novo sequencing, functional annotation, omics data integration and systems biology. Artificial intelligence techniques, such as machine learning and natural language processing, aid in the interpretation of peptide sequence data and the generation of biological insights. By using bioinformatics approaches, peptidomics researchers can accelerate peptide discovery, understand their functions and gain insights into complex molecular interactions.
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Affiliation(s)
- Rita Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Francisco Amado
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Universidade do Porto, Porto, Portugal
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
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13
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Mishra PKK, Jena A, Sarkhel SP, Behera SK, Das A, Sabarinath T, Jena D, Mandal KD, Sahu A, Kumar A, Kumar V, Kadam RG, Sathapathy S, Rao TP. Prediction, Synthesis and Evaluation of a Synthetic Peptide as an Enzyme-Linked Immunosorbent Assay (ELISA) Candidate for Screening of Bovine Antibodies against Theileria annulata. Microorganisms 2023; 11:2663. [PMID: 38004674 PMCID: PMC10673593 DOI: 10.3390/microorganisms11112663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Tick-borne diseases (TBDs) of livestock are endemic across various parts of tropical countries. Theileriosis is one such economically important TBD, caused by the Theileriidae family of organisms, which is transmitted by ticks. Theileria annulata, the causative agent of tropical theileriosis, contributes a significant loss to the dairy sector by causing anorexia, high fever, anemia, inflammatory changes in vital organs and icterus, thus, a loss in milk yield. Though vaccines are available, their protective efficacy is not absolute, and treatment is limited to early diagnosis of the causative agent. Routinely, microscopic identification of piroplasms in the erythrocytes (Giemsa-stained) of infected animals or schizonts in lymph node biopsies are practiced for diagnosis. PCR-based techniques (multiplex, uniplex, nested and real-time) have been reported to perform well in diagnosing active infection. Several attempts have been made using serological assays like Dot blot, ELISA and ICT, but the results were of variable sensitivity and specificity. Recombinant proteins like the Theileria annulata merozoite surface antigen (Tams1) and Theileria annulata surface protein (TaSP) have been explored as antigenic candidates for these assays. In the present study, we predicted an immunogenic peptide, i.e., TaSP-34, from the TaSP using various computational tools. The predicted peptide was custom synthesized. The diagnostic potential of the peptide was assessed by indirect plate ELISA to detect the bovine-IgM against Theileria annulata. Alongside, a recombinant truncated TaSP (rTaSP(tr)) was expressed and purified, which was used to compare the performance of the peptide as a diagnostic candidate. The IgM-based peptide ELISA was 100% sensitive and 92.77% specific as compared to PCR (Tams1 targeting), while 98.04% sensitivity and 97.44% specificity were observed in comparison with rTaSP(tr) ELISA. Almost perfect agreement between peptide ELISA and Tams1 PCR was observed with a Cohen's kappa coefficient (κ-value) of 0.901 and agreement of 95.31%. Further, the κ-value between the peptide ELISA and rTaSP(tr) ELISA was found to be 0.95, and the agreement was 97.65%, which shows a good correlation between the two tests. The findings suggest that the TaSP-34 peptide can be an efficient and new-generation diagnostic candidate for the diagnosis of T. annulata. Furthermore, the peptide can be synthesized commercially at a larger scale and can be a cost-effective alternative for the protein-based diagnostic candidates for T. annulata.
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Affiliation(s)
- Prasanta Kumar Koustasa Mishra
- Unit of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, RGSC, Banaras Hindu University, Mirzapur 231001, Uttar Pradesh, India; (D.J.); (K.D.M.); (V.K.); (R.G.K.)
| | - Anupama Jena
- Fisheries and Animal Resource Development Department, Bhubaneswar 751001, Odisha, India; (A.J.); (A.D.)
| | - Souti Prasad Sarkhel
- Department of Veterinary Parasitology, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, RGSC, Banaras Hindu University, Mirzapur 231001, Uttar Pradesh, India;
| | - Sujit Kumar Behera
- Department of Epidemiology & Public Health, Central University of Tamil Nadu, Tiruvarur 610001, Tamil Nadu, India;
| | - Annada Das
- Fisheries and Animal Resource Development Department, Bhubaneswar 751001, Odisha, India; (A.J.); (A.D.)
| | - Thankappan Sabarinath
- Clinical Bacteriological Laboratory, Indian Council of Agricultural Research—Indian Veterinary Research Institute, Nainital 263138, Uttarakhand, India;
| | - Dayanidhi Jena
- Unit of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, RGSC, Banaras Hindu University, Mirzapur 231001, Uttar Pradesh, India; (D.J.); (K.D.M.); (V.K.); (R.G.K.)
| | - Kruti Debnath Mandal
- Unit of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, RGSC, Banaras Hindu University, Mirzapur 231001, Uttar Pradesh, India; (D.J.); (K.D.M.); (V.K.); (R.G.K.)
| | - Adhikari Sahu
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar 751003, Odisha, India;
| | - Anshuman Kumar
- Department of Animal Genetics and Breeding, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, RGSC, Banaras Hindu University, Mirzapur 231001, Uttar Pradesh, India;
| | - Vinod Kumar
- Unit of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, RGSC, Banaras Hindu University, Mirzapur 231001, Uttar Pradesh, India; (D.J.); (K.D.M.); (V.K.); (R.G.K.)
| | - Rahul Ganpatrao Kadam
- Unit of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, RGSC, Banaras Hindu University, Mirzapur 231001, Uttar Pradesh, India; (D.J.); (K.D.M.); (V.K.); (R.G.K.)
| | - Srinivas Sathapathy
- Department of Veterinary Anatomy and Histology, College of Veterinary Science and Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar 751003, Odisha, India;
| | - Thavitiki Prasada Rao
- Department of Veterinary Physiology and Biochemistry, Sri Venkateswara Veterinary University, College of Veterinary Science, Garividi 535101, Andhra Pradesh, India;
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14
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Buonocore M, Grimaldi M, Santoro A, Covelli V, Marino C, Napolitano E, Novi S, Tecce MF, Ciaglia E, Montella F, Lopardo V, Perugini V, Santin M, D’Ursi AM. Exploiting the Features of Short Peptides to Recognize Specific Cell Surface Markers. Int J Mol Sci 2023; 24:15610. [PMID: 37958593 PMCID: PMC10650159 DOI: 10.3390/ijms242115610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Antibodies are the macromolecules of choice to ensure specific recognition of biomarkers in biological assays. However, they present a range of shortfalls including a relatively high production cost and limited tissue penetration. Peptides are relatively small molecules able to reproduce sequences of highly specific paratopes and, although they have less biospecificity than antibodies, they offer advantages like ease of synthesis, modifications of their amino acid sequences and tagging with fluorophores and other molecules required for detection. This work presents a strategy to design peptide sequences able to recognize the CD44 hyaluronic acid receptor present in the plasmalemma of a range of cells including human bone marrow stromal mesenchymal cells. The protocol of identification of the optimal amino acid sequence was based on the combination of rational design and in silico methodologies. This protocol led to the identification of two peptide sequences which were synthesized and tested on human bone marrow mesenchymal stromal cells (hBM-MSCs) for their ability to ensure specific binding to the CD44 receptor. Of the two peptides, one binds CD44 with sensitivity and selectivity, thus proving its potential to be used as a suitable alternative to this antibody in conventional immunostaining. In the context of regenerative medicine, the availability of this peptide could be harnessed to functionalize tissue engineering scaffolds to anchor stem cells as well as to be integrated into systems such as cell sorters to efficiently isolate MSCs from biological samples including various cell subpopulations. The data here reported can represent a model for developing peptide sequences able to recognize hBM-MSCs and other types of cells and for their integration in a range of biomedical applications.
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Affiliation(s)
- Michela Buonocore
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Department of Chemical Sciences, University of Naples Federico II, 80138 Naples, Italy
| | - Manuela Grimaldi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
| | - Angelo Santoro
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Scuola di Specializzazione in Farmacia Ospedaliera, University of Salerno, 84084 Fisciano, Italy
| | - Verdiana Covelli
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80138 Naples, Italy
| | - Carmen Marino
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Enza Napolitano
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Sara Novi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Mario Felice Tecce
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Francesco Montella
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Valentina Lopardo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Valeria Perugini
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton BN2 4AT, UK; (V.P.); (M.S.)
| | - Matteo Santin
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton BN2 4AT, UK; (V.P.); (M.S.)
| | - Anna Maria D’Ursi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
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15
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Aquino VH, Fumagalli MJ, Silva A, de Moura Negrini BV, Rojas A, Guillen Y, Bernal C, Figueiredo LTM. Linear epitope mapping in the E and NS1 proteins of dengue and Zika viruses: Prospection of peptides for vaccines and diagnostics. PLoS One 2023; 18:e0292451. [PMID: 37788262 PMCID: PMC10547212 DOI: 10.1371/journal.pone.0292451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
The arrival of the Zika virus (ZIKV) in dengue virus (DENV)-endemic areas has posed challenges for both differential diagnosis and vaccine development. Peptides have shown promise in addressing these issues. The aim of this study was to identify the linear epitope profile recognized by serum samples from dengue and Zika patients in the E and NS1 proteins of DENV and ZIKV. This cross-sectional study included individuals of all ages with laboratory-confirmed DENV and ZIKV infections, who were selected through convenience sampling. The serum samples from dengue and Zika patients detected epitopes evenly distributed across the viral proteins in a peptide microarray platform. However, several epitopes were located within "epitope hotspots", characterized by clusters of peptides recognized in more than 30% of the sub-arrays analyzed using individual or pooled serum samples. The serum samples from dengue and Zika patients showed a high level of cross-reactivity with peptides in the DENV and ZIKV proteins. Analysis using an additional peptide microarray platform, which contained peptides selected based on the results of the initial screening, revealed that two DENV and one ZIKV peptide, highly specific to their related viruses, were located within the epitope hotspots; however, they presented low detection rates (32.5, 35.0, and 28.6%, respectively). In addition, two DENV peptides detected at similarly high rates by both dengue and Zika patients were also found within the epitope hotspots. These hotspots contain several immunodominant epitopes that are recognized by a larger number of individuals when compared to 15-amino acid (aa) sequence peptides. Thus, epitope hotspots may have greater potential to serve as antigens in diagnostic tests and vaccine development than peptides composed of only 15 amino acids.
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Affiliation(s)
- Victor Hugo Aquino
- Immunology Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marcilio J. Fumagalli
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Angélica Silva
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | - Alejandra Rojas
- Production Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Yvalena Guillen
- Production Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Cynthia Bernal
- Production Department, Research Institute for Health Sciences, National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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16
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Martucci LF, Eichler RA, Silva RN, Costa TJ, Tostes RC, Busatto GF, Seelaender MC, Duarte AJ, Souza HP, Ferro ES. Intracellular peptides in SARS-CoV-2-infected patients. iScience 2023; 26:107542. [PMID: 37636076 PMCID: PMC10448160 DOI: 10.1016/j.isci.2023.107542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/29/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Intracellular peptides (InPeps) generated by the orchestrated action of the proteasome and intracellular peptidases have biological and pharmacological significance. Here, human plasma relative concentration of specific InPeps was compared between 175 patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and 45 SARS-CoV-2 non-infected patients; 2,466 unique peptides were identified, of which 67% were InPeps. The results revealed differences of a specific group of peptides in human plasma comparing non-infected individuals to patients infected by SARS-CoV-2, following the results of the semi-quantitative analyses by isotope-labeled electrospray mass spectrometry. The protein-protein interactions networks enriched pathways, drawn by genes encoding the proteins from which the peptides originated, revealed the presence of the coronavirus disease/COVID-19 network solely in the group of patients fatally infected by SARS-CoV-2. Thus, modulation of the relative plasma levels of specific InPeps could be employed as a predictive tool for disease outcome.
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Affiliation(s)
- Luiz Felipe Martucci
- Department of Pharmacology, Biomedical Sciences Institute, São Paulo 05508-000, Brazil
| | | | - Renée N.O. Silva
- Department of Pharmacology, Biomedical Sciences Institute, São Paulo 05508-000, Brazil
| | - Tiago J. Costa
- Department of Pharmacology, Ribeirao Preto Medical School, Ribeirão Preto 14049-900, Brazil
| | - Rita C. Tostes
- Department of Pharmacology, Ribeirao Preto Medical School, Ribeirão Preto 14049-900, Brazil
| | - Geraldo F. Busatto
- Department of Psichiatry, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Marilia C.L. Seelaender
- Department of Surgery, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Alberto J.S. Duarte
- Department of Patology, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Heraldo P. Souza
- Department of Internal Medicine, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Sciences Institute, São Paulo 05508-000, Brazil
- Department of Patology, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
- Department of Internal Medicine, Medical School and Hospital das Clínicas, University of São Paulo, 01246-903 SP, Brazil
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17
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Scalzitti N, Miralavy I, Korenchan DE, Farrar CT, Gilad AA, Banzhaf W. Computational Peptide Discovery with a Genetic Programming Approach. RESEARCH SQUARE 2023:rs.3.rs-3307450. [PMID: 37693481 PMCID: PMC10491332 DOI: 10.21203/rs.3.rs-3307450/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background The development of peptides for therapeutic targets or biomarkers for disease diagnosis is a challenging task in protein engineering. Current approaches are tedious, often time-consuming and require complex laboratory data due to the vast search space. In silico methods can accelerate research and substantially reduce costs. Evolutionary algorithms are a promising approach for exploring large search spaces and facilitating the discovery of new peptides. Results This study presents the development and use of a variant of the initial POET algorithm, called P O E T R e g e x , which is based on genetic programming, where individuals are represented by a list of regular expressions. The program was trained on a small curated dataset and employed to predict new peptides that can improve the problem of sensitivity in detecting peptides through magnetic resonance imaging using chemical exchange saturation transfer (CEST). The resulting model achieves a performance gain of 20% over the initial POET variant and is able to predict a candidate peptide with a 58% performance increase compared to the gold-standard peptide. Conclusions By combining the power of genetic programming with the flexibility of regular expressions, new potential peptide targets were identified to improve the sensitivity of detection by CEST. This approach provides a promising research direction for the efficient identification of peptides with therapeutic or diagnostic potential.
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Affiliation(s)
- Nicolas Scalzitti
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Iliya Miralavy
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - David E. Korenchan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christian T. Farrar
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Assaf A. Gilad
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Chemical Engineering, Michigan State University, East Lansing, MI, USA
- Department of Radiology, Michigan State University, East Lansing, MI, USA
| | - Wolfgang Banzhaf
- BEACON Center of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
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18
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Braz BA, Hospinal-Santiani M, Martins G, Beirão BCB, Bergamini MF, Marcolino-Junior LH, Soccol CR, Thomaz-Soccol V. Disposable electrochemical platform based on solid-binding peptides and carbon nanomaterials: an alternative device for leishmaniasis detection. Mikrochim Acta 2023; 190:321. [PMID: 37491620 DOI: 10.1007/s00604-023-05891-z] [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: 04/22/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
Neglected tropical diseases are those caused by infectious agents or parasites and are considered endemic in low-income populations. These diseases also have unacceptable indicators and low investment in research, drug production, and control. Tropical diseases such as leishmaniasis are some of the main causes of morbidity and mortality around the globe. Electrochemical immunosensors are promising tools for diagnostics against these diseases. One such benefit is the possibility of assisting diagnosis in isolated regions, where laboratory infrastructure is lacking. In this work, different peptides were investigated to detect antibodies against Leishmania in human and canine serum samples. The peptides evaluated (395-KKG and 395-G) have the same recognition site but differ on their solid-binding domains, which ensure affinity to spontaneously bind to either graphene oxide (GO) or graphene quantum dots (GQD). Cyclic voltammetry and differential pulse voltammetry were employed to investigate the electrochemical behavior of each assembly step and the role of each solid-binding domain coupled to its anchoring material. The graphene affinity peptide (395-G) showed better reproducibility and selectivity when coupled to GQD. Under the optimized set of experimental conditions, negative and positive human serum samples responses were distinguished based on a cut-off value of 82.5% at a 95% confidence level. The immunosensor showed selective behavior to antibodies against Mycobacterium leprae and Mycobacterium tuberculosis, which are similar antibodies and potentially sources of false positive tests. Therefore, the use of the graphene affinity peptide as a recognition site achieved outstanding performance for the detection of Leishmania antibodies.
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Affiliation(s)
- Beatriz A Braz
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Manuel Hospinal-Santiani
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Gustavo Martins
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil
| | - Breno C B Beirão
- Graduate Program in Microbiology, Parasitology, and Pathology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Márcio F Bergamini
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil.
| | - Luiz H Marcolino-Junior
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), CEP, CP 19032, Curitiba, PR, 81531-980, Brazil.
| | - Carlos R Soccol
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
| | - Vanete Thomaz-Soccol
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), CEP, Curitiba, PR, 81531-980, Brazil
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Santana PA, Álvarez CA, Valenzuela S, Manchego A, Guzmán F, Tirapegui C, Ahumada M. Stability of ACE2 Peptide Mimetics and Their Implications on the Application for SARS-CoV2 Detection. BIOSENSORS 2023; 13:bios13040473. [PMID: 37185548 PMCID: PMC10136198 DOI: 10.3390/bios13040473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023]
Abstract
The SARS-CoV-2 worldwide outbreak prompted the development of several tools to detect and treat the disease. Among the new detection proposals, the use of peptides mimetics has surged as an alternative to avoid the use of antibodies, of which there has been a shortage during the COVID-19 pandemic. However, the use of peptides in detection systems still presents some questions to be answered, mainly referring to their stability under different environmental conditions. In this work, we synthesized an ACE2 peptide mimic and evaluated its stability in different pH, salinity, polarity, and temperature conditions. Further, the same conditions were assessed when using the ability of the peptide mimic to detect the recombinant SARS-CoV-2 spike protein in a biotin-streptavidin-enzyme-linked assay. Finally, we also tested the capacity of the peptide to detect SARS-CoV-2 from patients' samples. The results indicate that the peptide is structurally sensitive to the medium conditions, with relevance to the pH, where basic pH favored its performance when used as a SARS-CoV-2 detector. Further, the proposed peptide mimic was able to detect SARS-CoV-2 comparably to RT-qPCR results. Therefore, the present study promotes knowledge advancement, particularly in terms of stability considerations, in the application of peptide mimics as a replacement for antibodies in detection systems.
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Affiliation(s)
- Paula A Santana
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Claudio A Álvarez
- Laboratorio de Fisiología y Genética Marina, Centro de Estudios Avanzados en Zonas Áridas, Larrondo 1281, Coquimbo 1780000, Chile
- Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile
| | - Santiago Valenzuela
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Alberto Manchego
- Laboratorio de Microbiología, Facultad de Medicina Veterinaria y Parasitología Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 3673, Peru
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Cristian Tirapegui
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Manuel Ahumada
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago 8910272, Chile
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago 8910272, Chile
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20
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Pagniez J, Petitdidier E, Parra-Zuleta O, Pissarra J, Bras-Gonçalves R. A systematic review of peptide-based serological tests for the diagnosis of leishmaniasis. Parasite 2023; 30:10. [PMID: 37010451 PMCID: PMC10069404 DOI: 10.1051/parasite/2023011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/06/2023] [Indexed: 04/04/2023] Open
Abstract
Serological methods should meet the needs of leishmaniasis diagnosis due to their high sensitivity and specificity, economical and adaptable rapid diagnostic test format, and ease of use. Currently, the performances of serological diagnostic tests, despite improvements with recombinant proteins, vary greatly depending on the clinical form of leishmaniasis and the endemic area. Peptide-based serological tests are promising as they could compensate for antigenic variability and improve performance, independently of Leishmania species and subspecies circulating in the endemic areas. The objective of this systematic review was to inventory all studies published from 2002 to 2022 that evaluate synthetic peptides for serological diagnosis of human leishmaniases and also to highlight the performance (e.g., sensitivity and specificity) of each peptide reported in these studies. All clinical forms of leishmaniasis, visceral and tegumentary, and all Leishmania species responsible for these diseases were considered. Following PRISMA statement recommendations, 1,405 studies were identified but only 22 articles met the selection criteria and were included in this systematic review. These original research articles described 77 different peptides, of which several have promising performance for visceral or tegumentary leishmaniasis diagnosis. This review highlights the importance of and growing interest in synthetic peptides used for serological diagnosis of leishmaniases, and their performances compared to some widely used tests with recombinant proteins.
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Affiliation(s)
- Julie Pagniez
- UMR177 INTERTRYP 911 avenue Agropolis B.P. 64501 34394 Montpellier France
| | - Elodie Petitdidier
- UMR177 INTERTRYP 911 avenue Agropolis B.P. 64501 34394 Montpellier France
| | | | - Joana Pissarra
- UMR177 INTERTRYP 911 avenue Agropolis B.P. 64501 34394 Montpellier France
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21
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Costa RODA, Passos TS, Silva EMDS, dos Santos NCS, Morais AHDA. Encapsulated Peptides and Proteins with an Effect on Satiety. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1166. [PMID: 37049259 PMCID: PMC10097199 DOI: 10.3390/nano13071166] [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: 02/26/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
The world scenario has undergone a nutritional transition in which some countries have left the reality of malnutrition and now face an epidemic of excess body weight. Researchers have been looking for strategies to reverse this situation. Peptides and proteins stand out as promising molecules with anti-obesity action. However, oral administration and passage through the gastrointestinal tract face numerous physiological barriers that impair their bioactive function. Encapsulation aims to protect the active substance and modify the action, one possibility of potentiating anti-obesity activity. Research with encapsulated peptides and proteins has demonstrated improved stability, delivery, controlled release, and increased bioactivity. However, it is necessary to explore how proteins and peptides affect weight loss and satiety, can impact the nutritional status of obesity, and how encapsulation can enhance the bioactive effects of these molecules. This integrative review aimed to discuss how the encapsulation of protein molecules impacts the nutritional status of obesity. From the studies selected following pre-established criteria, it was possible to infer that the encapsulation of proteins and peptides can contribute to greater efficiency in reducing weight gain, changes in adipose tissue function, and lower hormone levels that modulate appetite and body weight in animals with obesity.
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Affiliation(s)
- Rafael O. de A. Costa
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Thaís S. Passos
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Eloyse Mikaelly de S. Silva
- Nutrition Course, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | | | - Ana Heloneida de A. Morais
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
- Nutrition Course, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
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22
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Wack JS, Brahm K, Babel P, Dalton JAR, Schmitz K. Effect of macrocyclization and tetramethylrhodamine labeling on chemokine binding peptides. J Pept Sci 2023:e3486. [PMID: 36843216 DOI: 10.1002/psc.3486] [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: 12/08/2022] [Revised: 02/05/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023]
Abstract
Receptor-derived peptides have played an important role in elucidating chemokine-receptor interactions. For the inflammatory chemokine CXC-class chemokine ligand 8 (CXCL8), a site II-mimetic peptide has been derived from parts of extracellular loops 2 and 3 and adjacent transmembrane helices of its receptor CXC-class chemokine receptor 1 (Helmer et al., RSC Adv., 2015, 5, 25657). The peptide sequence with a C-terminal glutamine did not bind to CXCL8, whereas one with a C-terminal glutamate did but with low micromolar affinity. We sought to improve the affinity and protease stability of the latter peptide through cyclization while also cyclizing the former for control purposes. To identify a cyclization strategy that permits a receptor-like interaction, we conducted a molecular dynamics simulation of CXCL8 in complex with full-length CXC-class chemokine receptor 1. We introduced a linker to provide an appropriate spacing between the termini and used an on-resin side-chain-to-tail cyclization strategy. Upon chemokine binding, the fluorescence intensity of the tetramethylrhodamine (TAMRA)-labeled cyclic peptides increased whereas the fluorescence anisotropy decreased. Additional molecular dynamics simulations indicated that the fluorophore interacts with the peptide macrocycle so that chemokine binding leads to its displacement and observed changes in fluorescence. Macrocyclization of both 18-amino acid-long peptides led to the same low micromolar affinity for CXCL8. Likewise, both TAMRA-labeled linear peptides interacted with CXCL8 with similar affinities. Interestingly, the linear TAMRA-labeled peptides were more resistant to tryptic digestion than the unlabeled counterparts, whereas the cyclized peptides were not degraded at all. We conclude that the TAMRA fluorophore tends to interact with peptides altering their protease stability and behavior in fluorescence-based assays.
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Affiliation(s)
- Julia S Wack
- Biological Chemistry, Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Kevin Brahm
- Biological Chemistry, Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Philipp Babel
- Computational Biology and Simulation, Technical University of Darmstadt, Darmstadt, Germany
| | - James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Ronin Institute, Montclair, New Jersey, USA
| | - Katja Schmitz
- Biological Chemistry, Clemens-Schöpf-Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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23
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Li SY, Yoshida Y, Kubota M, Zhang BS, Matsutani T, Ito M, Yajima S, Yoshida K, Mine S, Machida T, Hayashi A, Takemoto M, Yokote K, Ohno M, Nishi E, Kitamura K, Kamitsukasa I, Takizawa H, Sata M, Yamagishi K, Iso H, Sawada N, Tsugane S, Iwase K, Shimada H, Iwadate Y, Hiwasa T. Utility of atherosclerosis-associated serum antibodies against colony-stimulating factor 2 in predicting the onset of acute ischemic stroke and prognosis of colorectal cancer. Front Cardiovasc Med 2023; 10:1042272. [PMID: 36844744 PMCID: PMC9954151 DOI: 10.3389/fcvm.2023.1042272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/11/2023] [Indexed: 02/12/2023] Open
Abstract
Introduction Autoantibodies against inflammatory cytokines may be used for the prevention of atherosclerosis. Preclinical studies consider colony-stimulating factor 2 (CSF2) as an essential cytokine with a causal relationship to atherosclerosis and cancer. We examined the serum anti-CSF2 antibody levels in patients with atherosclerosis or solid cancer. Methods We measured the serum anti-CSF2 antibody levels via amplified luminescent proximity homogeneous assay-linked immunosorbent assay based on the recognition of recombinant glutathione S-transferase-fused CSF2 protein or a CSF2-derived peptide as the antigen. Results The serum anti-CSF2 antibody (s-CSF2-Ab) levels were significantly higher in patients with acute ischemic stroke (AIS), acute myocardial infarction (AMI), diabetes mellitus (DM), and chronic kidney disease (CKD) compared with healthy donors (HDs). In addition, the s-CSF2-Ab levels were associated with intima-media thickness and hypertension. The analyzes of samples obtained from a Japan Public Health Center-based prospective study suggested the utility of s-CSF2-Ab as a risk factor for AIS. Furthermore, the s-CSF2-Ab levels were higher in patients with esophageal, colorectal, gastric, and lung cancer than in HDs but not in those with mammary cancer. In addition, the s-CSF2-Ab levels were associated with unfavorable postoperative prognosis in colorectal cancer (CRC). In CRC, the s-CSF2-Ab levels were more closely associated with poor prognosis in patients with p53-Ab-negative CRC despite the lack of significant association of the anti-p53 antibody (p53-Ab) levels with the overall survival. Conclusion S-CSF2-Ab was useful for the diagnosis of atherosclerosis-related AIS, AMI, DM, and CKD and could discriminate poor prognosis, especially in p53-Ab-negative CRC.
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Affiliation(s)
- Shu-Yang Li
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoichi Yoshida
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Comprehensive Stroke Center, Chiba University Hospital, Chiba, Japan
| | - Masaaki Kubota
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bo-Shi Zhang
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoo Matsutani
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaaki Ito
- Department of Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Yajima
- Department of Gastroenterological Surgery, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Kimihiko Yoshida
- Department of Gastroenterological Surgery, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Seiichiro Mine
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Neurological Surgery, Chiba Prefectural Sawara Hospital, Chiba, Japan
- Department of Neurological Surgery, Chiba Cerebral and Cardiovascular Center, Chiba, Japan
| | - Toshio Machida
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Neurological Surgery, Chiba Cerebral and Cardiovascular Center, Chiba, Japan
- Department of Neurosurgery, Eastern Chiba Medical Center, Chiba, Japan
| | - Aiko Hayashi
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Minoru Takemoto
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Diabetes, Metabolism and Endocrinology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mikiko Ohno
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Pharmacology, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Eiichiro Nishi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Pharmacology, Shiga University of Medical Science, Otsu, Shiga, Japan
| | | | | | - Hirotaka Takizawa
- Port Square Kashiwado Clinic, Kashiwado Memorial Foundation, Chiba, Japan
| | - Mizuki Sata
- Department of Public Health Medicine, Faculty of Medicine, and Health Services Research and Development Center, University of Tsukuba, Tsukuba, Japan
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Kazumasa Yamagishi
- Department of Public Health Medicine, Faculty of Medicine, and Health Services Research and Development Center, University of Tsukuba, Tsukuba, Japan
| | - Hiroyasu Iso
- Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Norie Sawada
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Shoichiro Tsugane
- Division of Cohort Research, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Katsuro Iwase
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hideaki Shimada
- Department of Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, Japan
- Department of Gastroenterological Surgery, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Yasuo Iwadate
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Comprehensive Stroke Center, Chiba University Hospital, Chiba, Japan
| | - Takaki Hiwasa
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
- Comprehensive Stroke Center, Chiba University Hospital, Chiba, Japan
- Department of Clinical Oncology, Toho University Graduate School of Medicine, Tokyo, Japan
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24
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Zhang B, Xu W, Yin C, Tang Y. Characterization of low-level D-amino acid isomeric impurities of Semaglutide using liquid chromatography-high resolution tandem mass spectrometry. J Pharm Biomed Anal 2023; 224:115164. [PMID: 36462248 DOI: 10.1016/j.jpba.2022.115164] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/26/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022]
Abstract
Under the guideline issued by Food and Drug Administration (FDA), ANDAs for Certain Highly Purified Synthetic Peptide Drug Products That Refer to Listed Drugs of rDNA Origin Guidance for Industry, a synthetic Semaglutide that is intended to be a "generic" of the approved rDNA origin Semaglutide is under exploring. Thus, each peptide-related impurity that is 0.10% of the drug substance or greater need to be identified for Semaglutide covered by this guidance. Among others, characterization of the low-level D-amino acid (D form) isomeric impurities are always the most challenging ones. Reverse-phase high-performance liquid chromatography (RP-UPLC) was used to separate the impurities, followed by high resolution mass spectrometry (HRMS) to determine the molecular weight of the impurities that existed in both formulations. Following the targeted D form isomers off-line collection, the samples went through lyophilization, deuterated hydrochloric acid (D-HCl) hydrolyzation with low level D/L form shifting suppression substrates, chiral derivatization and RP-UPLC tandem mass spectrometry analysis of different amino acids by comparing with standards. Herein, we reported an accurate, straightforward characterization method with low limit of detection for the low-level D-Ser8, D-His1 and D-Asp9 Semaglutide impurities in Semaglutide formulations. The developed UPLC tandem HRMS method entails a valuable step forward in the detection of trace levels of the D-isomers of Semaglutide and other peptide products.
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Affiliation(s)
- Baole Zhang
- Centre for Research & Development, Hybio Pharmaceutical Co., Hybio Innovation Industry Building, No. 7, Guansheng 4th RD, Guanlan High-tech Park, Longhua District, Shenzhen, Guangdong 518110, P.R. China
| | - Wanglong Xu
- Centre for Research & Development, Hybio Pharmaceutical Co., Hybio Innovation Industry Building, No. 7, Guansheng 4th RD, Guanlan High-tech Park, Longhua District, Shenzhen, Guangdong 518110, P.R. China
| | - Chuanlong Yin
- Centre for Research & Development, Hybio Pharmaceutical Co., Hybio Innovation Industry Building, No. 7, Guansheng 4th RD, Guanlan High-tech Park, Longhua District, Shenzhen, Guangdong 518110, P.R. China
| | - Yangming Tang
- Centre for Research & Development, Hybio Pharmaceutical Co., Hybio Innovation Industry Building, No. 7, Guansheng 4th RD, Guanlan High-tech Park, Longhua District, Shenzhen, Guangdong 518110, P.R. China.
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25
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Sharma K, Sharma KK, Sharma A, Jain R. Peptide-based drug discovery: Current status and recent advances. Drug Discov Today 2023; 28:103464. [PMID: 36481586 DOI: 10.1016/j.drudis.2022.103464] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.
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Affiliation(s)
- Komal Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anku Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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Inflammageing and Cardiovascular System: Focus on Cardiokines and Cardiac-Specific Biomarkers. Int J Mol Sci 2023; 24:ijms24010844. [PMID: 36614282 PMCID: PMC9820990 DOI: 10.3390/ijms24010844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
The term "inflammageing" was introduced in 2000, with the aim of describing the chronic inflammatory state typical of elderly individuals, which is characterized by a combination of elevated levels of inflammatory biomarkers, a high burden of comorbidities, an elevated risk of disability, frailty, and premature death. Inflammageing is a hallmark of various cardiovascular diseases, including atherosclerosis, hypertension, and rapid progression to heart failure. The great experimental and clinical evidence accumulated in recent years has clearly demonstrated that early detection and counteraction of inflammageing is a promising strategy not only to prevent cardiovascular disease, but also to slow down the progressive decline of health that occurs with ageing. It is conceivable that beneficial effects of counteracting inflammageing should be most effective if implemented in the early stages, when the compensatory capacity of the organism is not completely exhausted. Early interventions and treatments require early diagnosis using reliable and cost-effective biomarkers. Indeed, recent clinical studies have demonstrated that cardiac-specific biomarkers (i.e., cardiac natriuretic peptides and cardiac troponins) are able to identify, even in the general population, the individuals at highest risk of progression to heart failure. However, further clinical studies are needed to better understand the usefulness and cost/benefit ratio of cardiac-specific biomarkers as potential targets in preventive and therapeutic strategies for early detection and counteraction of inflammageing mechanisms and in this way slowing the progressive decline of health that occurs with ageing.
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27
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Chen Y, Han J, Zhao Y, Zhao X, Zhao M, Zhang J, Wang J. 18F-labeled FGFR1 peptide: a new PET probe for subtype FGFR1 receptor imaging. Front Oncol 2023; 13:1047080. [PMID: 37182162 PMCID: PMC10174317 DOI: 10.3389/fonc.2023.1047080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction The fibroblast growth factor receptor (FGFR) family is highly expressed in a variety of tumor types and represents a new target for cancer therapy. Different FGFR subtype aberrations have been found to exhibit highly variable sensitivity and efficacy to FGFR inhibitors. Methods The present study is the first to suggest an imaging method for assessing FGFR1 expression. The FGFR1-targeting peptide NOTA-PEG2-KAEWKSLGEEAWHSK was synthesized by manual solid-phase peptide synthesis and high-pressure liquid chromatography (HPLC) purification and then labeled with fluorine-18 using NOTA as a chelator. In vitro and in vivo experiments were conducted to evaluate the stability, affinity and specificity of the probe. Tumor targeting efficacy and biodistribution were evaluated by micro-PET/CT imaging in RT-112, A549, SNU-16 and Calu-3 xenografts. Results The radiochemical purity of [18F]F-FGFR1 was 98.66% ± 0.30% (n = 3) with excellent stability. The cellular uptake rate of [18F]F-FGFR1 in the RT-112 cell line (FGFR1 overexpression) was higher than that in the other cell lines and could be blocked by the presence of excess unlabeled FGFR1 peptide. Micro-PET/CT imaging revealed a significant concentration of [18F]F-FGFR1 in RT-112 xenografts with no or very low uptake in nontargeted organs and tissues, which demonstrated that [18F]F-FGFR1 was selectively taken up by FGFR1-positive tumors. Conclusion [18F]F-FGFR1 showed high stability, affinity, specificity and good imaging capacity for FGFR1-overexpressing tumors in vivo, which provides new application potential in the visualization of FGFR1 expression in solid tumors.
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Affiliation(s)
- Yang Chen
- Department of Nuclear Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jingya Han
- Department of Nuclear Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yan Zhao
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xinming Zhao
- Department of Nuclear Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Hebei Provincial Key Laboratory of Tumor Microenvironment and Drug Resistance, Shijiazhuang, China
- *Correspondence: Xinming Zhao,
| | - Mengmeng Zhao
- Department of Nuclear Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jingmian Zhang
- Department of Nuclear Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jianfang Wang
- Department of Nuclear Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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28
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Synthesis and evaluation of a para-carboxylated benzyl-DOTA for labeling peptides and polypeptides. Nucl Med Biol 2022; 114-115:18-28. [PMID: 36088873 DOI: 10.1016/j.nucmedbio.2022.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Radiolabeled peptides and low-molecular-weight (LMW) polypeptides show high and persistent radioactivity levels in the kidney. To develop a DOTA-based bifunctional chelating agent that provides a radiometabolite with a rapid elimination rate from the kidney, a para-carboxyl Bn-DOTA (p-COOH-Bn-DOTA) was designed, synthesized, and evaluated. METHODS A precursor compound, p-COOH-Bn-DOTA(tBu)4, was synthesized in 9 steps using N-Boc-p-iodo-L-phenylalanine as the starting material. A synthetic somatostatin analog (TOC) was used as a representative peptide metabolized in the renal lysosomes. p-COOH-Bn-DOTA-conjugated TOC (DOTA-Bn-TOC) was synthesized by the conventional solid-phase peptide synthesis using p-COOH-Bn-DOTA(tBu)4. DOTA-tris(tBu ester) was also conjugated with TOC to prepare DOTATOC. 111In-labeling of the peptides was conducted under similar conditions. The radiochemical conversions, stability against apo-transferrin (apoTf), and in vivo behaviors were compared. RESULTS [111In]In-DOTA-Bn-TOC was obtained with higher radiochemical conversions than [111In]In-DOTATOC. Both 111In-labeled TOC derivatives remained stable against apoTf. In biodistribution studies, [111In]In-DOTA-Bn-TOC exhibited higher initial uptake in the kidney, followed by a faster elimination rate of radioactivity into the urine than [111In]In-DOTATOC. The metabolic studies showed that the shorter residence time of the radiometabolite from [111In]In-DOTA-Bn-TOC was responsible for the renal radioactivity decline. CONCLUSION p-COOH-Bn-DOTA provides stable 111In-labeled peptides in high yields at low peptide concentrations. p-COOH-Bn-DOTA also provides a radiometabolite with a short residence time in the kidney. Such characteristics would render p-COOH-Bn-DOTA useful to the future application to radiolabeled LMW polypeptides with low renal radioactivity levels.
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Aguilar-Montes de Oca S, Montes-de-Oca-Jiménez R, Carlos Vázquez-Chagoyán J, Barbabosa-Pliego A, Eliana Rivadeneira-Barreiro P, C. Zambrano-Rodríguez P. The Use of Peptides in Veterinary Serodiagnosis of Infectious Diseases: A Review. Vet Sci 2022; 9:vetsci9100561. [PMID: 36288174 PMCID: PMC9610506 DOI: 10.3390/vetsci9100561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 12/04/2022] Open
Abstract
Peptides constitute an alternative and interesting option to develop treatments, vaccines, and diagnostic tools as they demonstrate their scope in several health aspects; as proof of this, commercial peptides for humans and animals are available on the market and used daily. This review aimed to know the role of peptides in the field of veterinary diagnosis, and include peptide-based enzyme-linked immunosorbent assay (pELISA), lateral flow devices, and peptide latex agglutination tests that have been developed to detect several pathogens including viruses and bacteria of health and production relevance in domestic animals. Studies in cattle, small ruminants, dogs, cats, poultry, horses, and even aquatic organisms were reviewed. Different studies showed good levels of sensitivity and specificity against their target, moreover, comparisons with commercial kits and official tests were performed which allowed appraising their performance. Chemical synthesis, recombinant DNA technology, and enzymatic synthesis were reviewed as well as their advantages and drawbacks. In addition, we discussed the intrinsic limitations such as the small size or affinity to polystyrene membrane and mention several strategies to overcome these problems. The use of peptides will increase in the coming years and their utility for diagnostic purposes in animals must be evaluated.
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Affiliation(s)
- Saúl Aguilar-Montes de Oca
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca 50200, CP, Mexico
| | - Roberto Montes-de-Oca-Jiménez
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca 50200, CP, Mexico
- Correspondence:
| | - Juan Carlos Vázquez-Chagoyán
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca 50200, CP, Mexico
| | - Alberto Barbabosa-Pliego
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca 50200, CP, Mexico
| | | | - Pablo C. Zambrano-Rodríguez
- Departamento de Veterinaria, Facultad de Ciencias Veterinarias, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador
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30
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iPSCs in Neurodegenerative Disorders: A Unique Platform for Clinical Research and Personalized Medicine. J Pers Med 2022; 12:jpm12091485. [PMID: 36143270 PMCID: PMC9500601 DOI: 10.3390/jpm12091485] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
In the past, several animal disease models were developed to study the molecular mechanism of neurological diseases and discover new therapies, but the lack of equivalent animal models has minimized the success rate. A number of critical issues remain unresolved, such as high costs for developing animal models, ethical issues, and lack of resemblance with human disease. Due to poor initial screening and assessment of the molecules, more than 90% of drugs fail during the final step of the human clinical trial. To overcome these limitations, a new approach has been developed based on induced pluripotent stem cells (iPSCs). The discovery of iPSCs has provided a new roadmap for clinical translation research and regeneration therapy. In this article, we discuss the potential role of patient-derived iPSCs in neurological diseases and their contribution to scientific and clinical research for developing disease models and for developing a roadmap for future medicine. The contribution of humaniPSCs in the most common neurodegenerative diseases (e.g., Parkinson’s disease and Alzheimer’s disease, diabetic neuropathy, stroke, and spinal cord injury) were examined and ranked as per their published literature on PUBMED. We have observed that Parkinson’s disease scored highest, followed by Alzheimer’s disease. Furthermore, we also explored recent advancements in the field of personalized medicine, such as the patient-on-a-chip concept, where iPSCs can be grown on 3D matrices inside microfluidic devices to create an in vitro disease model for personalized medicine.
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Takahashi K, Chida S, Suwatthanarak T, Iida M, Zhang M, Fukuyama M, Maeki M, Ishida A, Tani H, Yasui T, Baba Y, Hibara A, Okochi M, Tokeshi M. Non-competitive fluorescence polarization immunosensing for CD9 detection using a peptide as a tracer. LAB ON A CHIP 2022; 22:2971-2977. [PMID: 35713150 DOI: 10.1039/d2lc00224h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This paper is the first report of a non-competitive fluorescence polarization immunoassay (NC-FPIA) using a peptide as a tracer. The NC-FPIA can easily and quickly quantify the target after simply mixing them together. This feature is desirable for point-of-need applications such as clinical diagnostics, infectious disease screening, on-site analysis for food safety, etc. In this study, the NC-FPIA was applied to detect CD9, which is one of the exosome markers. We succeeded in detecting not only CD9 but also CD9 expressing exosomes derived from HeLa cells. This method can be applied to various targets if a tracer for the target can be prepared, and expectations are high for its future uses.
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Affiliation(s)
- Kazuki Takahashi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Shunsuke Chida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Thanawat Suwatthanarak
- Department of Chemical Science & Engineering, Tokyo Institute of Technology, 2-12-2 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Mikiko Iida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Min Zhang
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Mao Fukuyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Masatoshi Maeki
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Akihiko Ishida
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
| | - Hirofumi Tani
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
- Institute of Nano-Life Systems, Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Nano-Life Systems, Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba 263-0024, Japan
| | - Akihide Hibara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Mina Okochi
- Department of Chemical Science & Engineering, Tokyo Institute of Technology, 2-12-2 O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Manabu Tokeshi
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
- Institute of Nano-Life Systems, Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), 4-9-1, Anagawa, Inage-ku, Chiba 263-0024, Japan
- Innovative Research Center for Preventive Medical Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Nandhini KP, Albericio F, de la Torre BG. 2-Methoxy-4-methylsulfinylbenzyl Alcohol as a Safety-Catch Linker for the Fmoc/ tBu Solid-Phase Peptide Synthesis Strategy. J Org Chem 2022; 87:9433-9442. [PMID: 35801570 DOI: 10.1021/acs.joc.2c01057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fmoc and Boc group are the two main groups used to protect the α-amino function in Solid-Phase Peptide Synthesis (SPPS). In this regard, the use of the Mmsb linker allows the combination of these two groups. Peptide-O-Mmsb-Resin is stable to the piperidine and trifluoroacetic acid (TFA) treatment used to remove Fmoc and Boc, respectively. The peptide is detached in a two-step protocol, namely reduction of the sulfoxide to the sulfide with Me3SiCl and Ph3P, and then treatment with TFA. The advantage of this strategy has been demonstrated by the following: preparation of peptide with no diketopiperazine formation in sequences prone to this side reaction; on-resin cyclization without the concourse of common organic reagents such as Pd(0) but of difficult use in a biological laboratory; and on-resin disulfide formation in a total side-chain unprotected peptide. The use of Mmsb linker together with Msib (4-(methylsulfinyl)benzyl) and Msbh (4,4'-bis(methylsulfinyl)benzhydryl) described in the accompanying manuscript add a fourth dimension to the SPPS protecting group scheme.
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Affiliation(s)
- K P Nandhini
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa.,Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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Mahajan R, Suriyanarayanan S, Olsson GD, Wiklander JG, Aastrup T, Sellergren B, Nicholls IA. Oxytocin-Selective Nanogel Antibody Mimics. Int J Mol Sci 2022; 23:2534. [PMID: 35269677 PMCID: PMC8909970 DOI: 10.3390/ijms23052534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022] Open
Abstract
Oxytocin imprinted polymer nanoparticles were synthesized by glass bead supported solid phase synthesis, with NMR and molecular dynamics studies used to investigate monomer-template interactions. The nanoparticles were characterized by dynamic light scattering, scanning- and transmission electron microscopy and X-ray photoelectron spectroscopy. Investigation of nanoparticle-template recognition using quartz crystal microbalance-based studies revealed sub-nanomolar affinity, kd ≈ 0.3 ± 0.02 nM (standard error of the mean), comparable to that of commercial polyclonal antibodies, kd ≈ 0.02-0.2 nM.
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Affiliation(s)
- Rashmi Mahajan
- Bioorganic and Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden; (R.M.); (G.D.O.); (J.G.W.)
| | - Subramanian Suriyanarayanan
- Bioorganic and Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden; (R.M.); (G.D.O.); (J.G.W.)
| | - Gustaf D. Olsson
- Bioorganic and Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden; (R.M.); (G.D.O.); (J.G.W.)
| | - Jesper G. Wiklander
- Bioorganic and Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden; (R.M.); (G.D.O.); (J.G.W.)
| | - Teodor Aastrup
- Attana AB, Greta Arwidssons Väg 21, 11419 Stockholm, Sweden;
| | - Börje Sellergren
- Biofilms Research Center for Biointerfaces, Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden;
| | - Ian A. Nicholls
- Bioorganic and Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden; (R.M.); (G.D.O.); (J.G.W.)
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34
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Yang F, Liu L, Neuenschwander PF, Idell S, Vankayalapati R, Jain KG, Du K, Ji H, Yi G. Phage Display-Derived Peptide for the Specific Binding of SARS-CoV-2. ACS OMEGA 2022; 7:3203-3211. [PMID: 35128233 PMCID: PMC8751651 DOI: 10.1021/acsomega.1c04873] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/06/2021] [Indexed: 05/10/2023]
Abstract
Beginning from the end of 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic swept all over the world and is still afflicting the whole global population. Given that the vaccine-manufacturing ability is limited and the virus can evolve quickly, vaccination alone may not be able to end the pandemic, thus developing fast and accurate diagnoses and effective therapeutics will always be unmet needs. Phage display peptide library has been used in screening antigen-specific peptides for the invention of novel mimic receptors/ligands. Here, we report that a 12-mer phage display peptide library has been screened against the SARS-CoV-2 receptor-binding domain (RBD), and five of the screened peptides show binding ability with the RBD protein by the enzyme-linked immune sorbent assay. The surface plasmon resonance assay further demonstrates that peptide no. 1 can specifically bind to SARS-CoV-2 RBD with a binding affinity constant (K d) of 5.8 μM. Transmission electron microscopy coupled with a magnetic bead assay further confirms that the screened peptide can specifically bind the inactivated SARS-CoV-2 virus. This SARS-CoV-2-specific peptide holds great promise as a new bioreceptor/ligand for the rapid and accurate detection of SARS-CoV-2.
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Affiliation(s)
- Fan Yang
- Department
of Pulmonary Immunology, The University
of Texas Health Science Center at Tyler, Tyler, Texas 75708-3154, United States
| | - Li Liu
- Department
of Microsystems Engineering, Rochester Institute
of Technology, Rochester, New York 14623-5603, United States
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623-5603, United States
| | - Pierre Fernand Neuenschwander
- Department
of Cellular and Molecular Biology, The University
of Texas Health Science Center at Tyler, Tyler, Texas 75708-3154, United States
| | - Steven Idell
- Department
of Cellular and Molecular Biology, The University
of Texas Health Science Center at Tyler, Tyler, Texas 75708-3154, United States
| | - Ramakrishna Vankayalapati
- Department
of Pulmonary Immunology, The University
of Texas Health Science Center at Tyler, Tyler, Texas 75708-3154, United States
| | - Krishan Gopal Jain
- Department
of Cellular and Molecular Biology, The University
of Texas Health Science Center at Tyler, Tyler, Texas 75708-3154, United States
| | - Ke Du
- Department
of Microsystems Engineering, Rochester Institute
of Technology, Rochester, New York 14623-5603, United States
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623-5603, United States
| | - Honglong Ji
- Department
of Cellular and Molecular Biology, The University
of Texas Health Science Center at Tyler, Tyler, Texas 75708-3154, United States
| | - Guohua Yi
- Department
of Pulmonary Immunology, The University
of Texas Health Science Center at Tyler, Tyler, Texas 75708-3154, United States
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35
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Tsurusawa N, Chang J, Namba M, Makioka D, Yamura S, Iha K, Kyosei Y, Watabe S, Yoshimura T, Ito E. Modified ELISA for Ultrasensitive Diagnosis. J Clin Med 2021; 10:5197. [PMID: 34768717 PMCID: PMC8585087 DOI: 10.3390/jcm10215197] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
An enzyme-linked immunosorbent assay (ELISA) can be used for quantitative measurement of proteins, and improving the detection sensitivity to the ultrasensitive level would facilitate the diagnosis of various diseases. In the present review article, we first define the term 'ultrasensitive'. We follow this with a survey and discussion of the current literature regarding modified ELISA methods with ultrasensitive detection and their application for diagnosis. Finally, we introduce our own newly devised system for ultrasensitive ELISA combined with thionicotinamide adenine dinucleotide cycling and its application for the diagnosis of infectious diseases and lifestyle-related diseases. The aim of the present article is to expand the application of ultrasensitive ELISAs in the medical and biological fields.
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Affiliation(s)
- Naoko Tsurusawa
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Jyunhao Chang
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Mayuri Namba
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Daiki Makioka
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Sou Yamura
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Kanako Iha
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Yuta Kyosei
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Satoshi Watabe
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan;
| | - Teruki Yoshimura
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu 061-0293, Hokkaido, Japan;
| | - Etsuro Ito
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan;
- Graduate Institute of Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
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