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Comparative Evaluation of Reproducibility of Phage-Displayed Peptide Selections and NGS Data, through High-Fidelity Mapping of Massive Peptide Repertoires. Int J Mol Sci 2023; 24:ijms24021594. [PMID: 36675109 PMCID: PMC9862337 DOI: 10.3390/ijms24021594] [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: 11/15/2022] [Revised: 01/08/2023] [Accepted: 01/08/2023] [Indexed: 01/14/2023] Open
Abstract
Phage-displayed peptide selections generate complex repertoires of several hundred thousand peptides as revealed by next-generation sequencing (NGS). In repeated peptide selections, however, even in identical experimental in vitro conditions, only a very small number of common peptides are found. The repertoire complexities are evidence of the difficulty of distinguishing between effective selections of specific peptide binders to exposed targets and the potential high background noise. Such investigation is even more relevant when considering the plethora of in vivo expressed targets on cells, in organs or in the entire organism to define targeting peptide agents. In the present study, we compare the published NGS data of three peptide repertoires that were obtained by phage display under identical experimental in vitro conditions. By applying the recently developed tool PepSimili we evaluate the calculated similarities of the individual peptides from each of these three repertoires and perform their mappings on the human proteome. The peptide-to-peptide mappings reveal high similarities among the three repertoires, confirming the desired reproducibility of phage-displayed peptide selections.
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Hong D, Zhang C, Wu W, Lu X, Zhang L. Modulation of the gut-brain axis via the gut microbiota: a new era in treatment of amyotrophic lateral sclerosis. Front Neurol 2023; 14:1133546. [PMID: 37153665 PMCID: PMC10157060 DOI: 10.3389/fneur.2023.1133546] [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: 12/29/2022] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
There are trillions of different microorganisms in the human digestive system. These gut microbes are involved in the digestion of food and its conversion into the nutrients required by the body. In addition, the gut microbiota communicates with other parts of the body to maintain overall health. The connection between the gut microbiota and the brain is known as the gut-brain axis (GBA), and involves connections via the central nervous system (CNS), the enteric nervous system (ENS), and endocrine and immune pathways. The gut microbiota regulates the central nervous system bottom-up through the GBA, which has prompted researchers to pay considerable attention to the potential pathways by which the gut microbiota might play a role in the prevention and treatment of amyotrophic lateral sclerosis (ALS). Studies with animal models of ALS have shown that dysregulation of the gut ecology leads to dysregulation of brain-gut signaling. This, in turn, induces changes in the intestinal barrier, endotoxemia, and systemic inflammation, which contribute to the development of ALS. Through the use of antibiotics, probiotic supplementation, phage therapy, and other methods of inducing changes in the intestinal microbiota that can inhibit inflammation and delay neuronal degeneration, the clinical symptoms of ALS can be alleviated, and the progression of the disease can be delayed. Therefore, the gut microbiota may be a key target for effective management and treatment of ALS.
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Affiliation(s)
- Du Hong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Chi Zhang
- Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Wenshuo Wu
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaohui Lu
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Liping Zhang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Liping Zhang
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3
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Jan Z, Mollazadeh S, Abnous K, Taghdisi SM, Danesh A, Ramezani M, Alibolandi M. Targeted Delivery Platforms for the Treatment of Multiple Sclerosis. Mol Pharm 2022; 19:1952-1976. [PMID: 35501974 DOI: 10.1021/acs.molpharmaceut.1c00892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multiple sclerosis (MS) is a neurodegenerative condition of the central nervous system (CNS) that presents with varying levels of disability in patients, displaying the significance of timely and effective management of this complication. Though several treatments have been developed to protect nerves, comprehensive improvement of MS is still considered an essential bottleneck. Therefore, the development of innovative treatment methods for MS is one of the core research areas. In this regard, nanoscale platforms can offer practical and ideal approaches to the diagnosis and treatment of various diseases, especially immunological disorders such as MS, to improve the effectiveness of conventional therapies. It should be noted that there is significant progress in the development of neuroprotective strategies through the implementation of various nanoparticles, monoclonal antibodies, peptides, and aptamers. In this study, we summarize different particle systems as well as targeted therapies, such as antibodies, peptides, nucleic acids, and engineered cells for the treatment of MS, and discuss their potential in the treatment of MS in the preclinical and clinical stages. Future advances in targeted delivery of medical supplies may offer new strategies for complete recovery as well as practical treatment of progressive forms of MS.
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Affiliation(s)
- Zeinab Jan
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Science, 7GJP+VPQ Mashhad, Iran
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, F82C+G8V Bojnurd, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, 7GJP+VPQ Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, 7GJP+VPQ Mashhad, Iran
| | - Abolghasem Danesh
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Science, 7GJP+VPQ Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, 7GJP+VPQ Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, 7GJP+VPQ Mashhad, Iran
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Cui H, Huang Y, Wu Y, Ma J, Cao X, Xie J, Zhang Y. The expression of diacylglycerol kinase isoforms α and ζ correlates with the progression of experimental autoimmune encephalomyelitis in rats. Histochem Cell Biol 2021; 156:437-448. [PMID: 34312706 DOI: 10.1007/s00418-021-02011-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2021] [Indexed: 12/26/2022]
Abstract
Multiple sclerosis (MS) is characterized by neuroinflammation and neurodegeneration, whose precise processes are not fully understood. Diacylglycerol kinase (DGK) isozymes of α, β, γ and ζ expressed abundantly in the brain and/or the immune system, may be regulatory targets for MS. In this study, we analyzed the four DGK isozymes along the induction, peak and recovery phases in an experimental autoimmune encephalomyelitis (EAE) rat model of MS. The expression of these DGK isozymes and the diacylglycerol (DAG) pathway in the EAE rat brainstems were analyzed by qRT-PCR, immunohistochemistry, immunofluorescence double staining, western blotting and ELISA. Our results showed that the mRNA content of the four DGK isozymes decreased significantly, and their immunoreactivity in myelin sheathes (DGKα, β) and neurons (DGKγ, ζ) became weaker at the beginning of the induction phase. With the progressive increase in clinical signs, DGKα, DGKγ and DGKζ mRNA increased and DGKβ mRNA decreased, and microglia were involved in the formation of perivascular cuffing. In the peak phase, both DGKα and DGKζ were expressed in neurons and inflammatory cells, and DGKζ was also positive in microglia. During the recovery phase, the mRNA content and immunoreactivity of these DGK isozymes generally reached normal levels. Moreover, our results revealed that changes in DAG accumulation and PKCδ phosphorylation were almost the same as those of DGKα and DGKζ mRNA. In summary, the four DGK isozymes are involved in the EAE process. The predominant and broad presence of DGKα and DGKζ suggests that they may regulate the pathological process by attenuating DAG/PKCδ pathway signaling during EAE evolution.
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Affiliation(s)
- Huilin Cui
- Department of Histology and Embryology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Yige Huang
- Department of Histology and Embryology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Ying Wu
- Department of Histology and Embryology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jinfeng Ma
- Department of General Surgery, Shanxi Cancer Hospital, Taiyuan, 030013, Shanxi, China
| | - Ximei Cao
- Department of Histology and Embryology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jianshan Xie
- Department of Histology and Embryology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Yu Zhang
- Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, and the Department of Physiology, Shanxi Medical University, No.56 Xinjiannan Road, Taiyuan, 030001, Shanxi, China.
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Vargas-Sanchez K, Losada-Barragán M, Mogilevskaya M, Novoa-Herrán S, Medina Y, Buendía-Atencio C, Lorett-Velásquez V, Martínez-Bernal J, Gonzalez-Reyes RE, Ramírez D, Petry KG. Screening for Interacting Proteins with Peptide Biomarker of Blood-Brain Barrier Alteration under Inflammatory Conditions. Int J Mol Sci 2021; 22:ijms22094725. [PMID: 33946948 PMCID: PMC8124558 DOI: 10.3390/ijms22094725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases are characterized by increased permeability of the blood-brain barrier (BBB) due to alterations in cellular and structural components of the neurovascular unit, particularly in association with neuroinflammation. A previous screening study of peptide ligands to identify molecular alterations of the BBB in neuroinflammation by phage-display, revealed that phage clone 88 presented specific binding affinity to endothelial cells under inflammatory conditions in vivo and in vitro. Here, we aimed to identify the possible target receptor of the peptide ligand 88 expressed under inflammatory conditions. A cross-link test between phage-peptide-88 with IL-1β-stimulated human hCMEC cells, followed by mass spectrometry analysis, was used to identify the target of peptide-88. We modeled the epitope-receptor molecular interaction between peptide-88 and its target by using docking simulations. Three proteins were selected as potential target candidates and tested in enzyme-linked immunosorbent assays with peptide-88: fibronectin, laminin subunit α5 and laminin subunit β-1. Among them, only laminin subunit β-1 presented measurable interaction with peptide-88. Peptide-88 showed specific interaction with laminin subunit β-1, highlighting its importance as a potential biomarker of the laminin changes that may occur at the BBB endothelial cells under pathological inflammation conditions.
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Affiliation(s)
- Karina Vargas-Sanchez
- Grupo de Neurociencia Translacional, Facultad de Medicina, Universidad de los Andes, Bogotá 111711, Colombia
- Correspondence: ; Tel.: +57-13102405706
| | - Monica Losada-Barragán
- Grupo de Biología Celular y Funcional e Ingeniería de Moléculas, Departamento de Biología, Universidad Antonio Nariño, Bogotá 110231, Colombia; (M.L.-B.); (Y.M.)
| | - Maria Mogilevskaya
- Grupo de Investigación GINIC-HUS, Universidad ECCI, Bogotá 111311, Colombia;
| | - Susana Novoa-Herrán
- Grupo de Investigación en Hormonas (Hormone Research Laboratory), Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia; or
- Grupo de Fisiología Molecular, Subdirección de Investigación Científica y Tecnológica, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Yehidi Medina
- Grupo de Biología Celular y Funcional e Ingeniería de Moléculas, Departamento de Biología, Universidad Antonio Nariño, Bogotá 110231, Colombia; (M.L.-B.); (Y.M.)
| | - Cristian Buendía-Atencio
- Grupo de Investigación en Modelado y Computación Científica, Departamento de Química, Universidad Antonio Nariño, Bogotá 110231, Colombia;
| | - Vaneza Lorett-Velásquez
- Facultad de Medicina y Ciencias de la Salud, Universidad Militar Nueva Granada, Bogotá 110231, Colombia; (V.L.-V.); (J.M.-B.)
| | - Jessica Martínez-Bernal
- Facultad de Medicina y Ciencias de la Salud, Universidad Militar Nueva Granada, Bogotá 110231, Colombia; (V.L.-V.); (J.M.-B.)
| | - Rodrigo E. Gonzalez-Reyes
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencia Neurovitae-UR, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá 111711, Colombia;
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, El llano Subercaseaux 2801, Santiago 8900000, Chile;
| | - Klaus G. Petry
- INSERM U1049 and U1029 Neuroinflammation and Angiogenesis Group, Bordeaux University, F33000 Bordeaux, France;
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Rayatpour A, Javan M. Targeting the brain lesions using peptides: A review focused on the possibility of targeted drug delivery to multiple sclerosis lesions. Pharmacol Res 2021; 167:105441. [PMID: 33503478 DOI: 10.1016/j.phrs.2021.105441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/05/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
As described by Jean Martin Charcot in 1868, multiple sclerosis (MS) is an inflammatory, demyelinating and neurodegenerative disease of the central nervous system (CNS) which leads to permanent disability in patients. Following CNS insults, astrocytes and microglial cells undergo changes, which lead to scar formation in the site of injury. Owning to the pathophysiology of MS lesions, changes in both cellular and extracellular matrix (ECM) components occur over the progression of disease. In spite of advances in therapeutic approaches, drug delivery to MS lesions appears of great interest with big challenges and limitations. Targeting with peptides is a novel promising approach in the field of drug delivery. Recently peptides have been used for active targeting of different pathological disorders in which specific peptides make targeted accumulation of cargos to enhance local drug concentration at the pathological area, lead to increased therapeutic efficacy and decreased side effects. However, specific approaches for targeting the lesion in MS are still lacking. In this review, we discuss the changes of the ECM components as well as the cellular characteristics of demyelinated lesions and emphasis on opportunities for peptide based targeted drug delivery to highlight the possibility of such approaches for neurodegenerative disease with specific focus on MS.
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Affiliation(s)
- Atefeh Rayatpour
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Javan
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran; Institute for Brain and Cognition, Tarbiat Modares University, Tehran, Iran; Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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7
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Acharya B, Meka RR, Venkatesha SH, Lees JR, Teesalu T, Moudgil KD. A novel CNS-homing peptide for targeting neuroinflammatory lesions in experimental autoimmune encephalomyelitis. Mol Cell Probes 2020; 51:101530. [PMID: 32035108 DOI: 10.1016/j.mcp.2020.101530] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/26/2020] [Accepted: 02/04/2020] [Indexed: 12/14/2022]
Abstract
Using phage peptide library screening, we identified peptide-encoding phages that selectively home to the inflamed central nervous system (CNS) of mice with experimental autoimmune encephalomyelitis (EAE), a model of human multiple sclerosis (MS). A phage peptide display library encoding cyclic 9-amino-acid random peptides was first screened ex-vivo for binding to the CNS tissue of EAE mice, followed by in vivo screening in the diseased mice. Phage insert sequences that were present at a higher frequency in the CNS of EAE mice than in the normal (control) mice were identified by DNA sequencing. One of the phages selected in this manner, denoted as MS-1, was shown to selectively recognize CNS tissue in EAE mice. Individually cloned phages with this insert preferentially homed to EAE CNS after an intravenous injection. Similarly, systemically-administered fluorescence-labeled synthetic MS-1 peptide showed selective accumulation in the spinal cord of EAE mice. We suggest that peptide MS-1 might be useful for targeted drug delivery to CNS in EAE/MS.
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Affiliation(s)
- Bodhraj Acharya
- University of Maryland School of Medicine, Baltimore, MD, USA; Baltimore VA Medical Center, Baltimore, MD, USA
| | - Rakeshchandra R Meka
- University of Maryland School of Medicine, Baltimore, MD, USA; Baltimore VA Medical Center, Baltimore, MD, USA
| | - Shivaprasad H Venkatesha
- University of Maryland School of Medicine, Baltimore, MD, USA; Baltimore VA Medical Center, Baltimore, MD, USA
| | - Jason R Lees
- Uniformed Services University of Health Sciences (USUHS), Bethesda, MD, USA
| | - Tambet Teesalu
- Institute of Biomedicine and Translational Medicine, University of Tartu (UT), Estonia; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Kamal D Moudgil
- University of Maryland School of Medicine, Baltimore, MD, USA; Baltimore VA Medical Center, Baltimore, MD, USA. https://webmail.umaryland.edu/src/compose.php?send_to=kmoud001%40umaryland.edu
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8
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Jafari B, Pourseif MM, Barar J, Rafi MA, Omidi Y. Peptide-mediated drug delivery across the blood-brain barrier for targeting brain tumors. Expert Opin Drug Deliv 2019; 16:583-605. [DOI: 10.1080/17425247.2019.1614911] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Behzad Jafari
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz,
Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Urmia University of Medical Sciences, Urmia,
Iran
| | - Mohammad M. Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz,
Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz,
Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz,
Iran
| | - Mohammad A. Rafi
- Department of Neurology, College of Medicine, Thomas Jefferson University, Philadelphia,
PA, USA
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz,
Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz,
Iran
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