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Lopez-Martinez E, Manteca A, Ferruz N, Cortajarena AL. Statistical Analysis and Tokenization of Epitopes to Construct Artificial Neoepitope Libraries. ACS Synth Biol 2023; 12:2812-2818. [PMID: 37703075 PMCID: PMC10594869 DOI: 10.1021/acssynbio.3c00201] [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: 03/31/2023] [Indexed: 09/14/2023]
Abstract
Epitopes are specific regions on an antigen's surface that the immune system recognizes. Epitopes are usually protein regions on foreign immune-stimulating entities such as viruses and bacteria, and in some cases, endogenous proteins may act as antigens. Identifying epitopes is crucial for accelerating the development of vaccines and immunotherapies. However, mapping epitopes in pathogen proteomes is challenging using conventional methods. Screening artificial neoepitope libraries against antibodies can overcome this issue. Here, we applied conventional sequence analysis and methods inspired in natural language processing to reveal specific sequence patterns in the linear epitopes deposited in the Immune Epitope Database (www.iedb.org) that can serve as building blocks for the design of universal epitope libraries. Our results reveal that amino acid frequency in annotated linear epitopes differs from that in the human proteome. Aromatic residues are overrepresented, while the presence of cysteines is practically null in epitopes. Byte pair encoding tokenization shows high frequencies of tryptophan in tokens of 5, 6, and 7 amino acids, corroborating the findings of the conventional sequence analysis. These results can be applied to reduce the diversity of linear epitope libraries by orders of magnitude.
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Affiliation(s)
- Elena Lopez-Martinez
- Centre
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014 Spain
| | - Aitor Manteca
- Centre
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014 Spain
| | - Noelia Ferruz
- Molecular
Biology Institute of Barcelona (IBMB-CSIC), Barcelona Science Park, Baldiri Reixac, 15-21, 08028, Barcelona, Spain
| | - Aitziber L. Cortajarena
- Centre
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014 Spain
- IKERBASQUE, Basque
Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
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Palma M. Epitopes and Mimotopes Identification Using Phage Display for Vaccine Development against Infectious Pathogens. Vaccines (Basel) 2023; 11:1176. [PMID: 37514992 PMCID: PMC10384025 DOI: 10.3390/vaccines11071176] [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: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Traditional vaccines use inactivated or weakened forms of pathogens which could have side effects and inadequate immune responses. To overcome these challenges, phage display has emerged as a valuable tool for identifying specific epitopes that could be used in vaccines. This review emphasizes the direct connection between epitope identification and vaccine development, filling a crucial gap in the field. This technique allows vaccines to be engineered to effectively stimulate the immune system by presenting carefully selected epitopes. Phage display involves screening libraries of random peptides or gene/genome fragments using serum samples from infected, convalescent, or vaccinated individuals. This method has been used to identify epitopes from various pathogens including SARS-CoV-2, Mycobacterium tuberculosis, hepatitis viruses, H5N1, HIV-1, Human T-lymphotropic virus 1, Plasmodium falciparum, Trypanosoma cruzi, and Dirofilaria repens. Bacteriophages offer advantages such as being immunogenic carriers, low production costs, and customization options, making them a promising alternative to traditional vaccines. The purpose of this study has been to highlight an approach that encompasses the entire process from epitope identification to vaccine production using a single technique, without requiring additional manipulation. Unlike conventional methods, phage display demonstrates exceptional efficiency and speed, which could provide significant advantages in critical scenarios such as pandemics.
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Affiliation(s)
- Marco Palma
- Institute for Globally Distributed Open Research and Education (IGDORE), 03181 Torrevieja, Spain
- Protheragen Inc., Ronkonkoma, NY 11779, USA
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3
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State of the art in epitope mapping and opportunities in COVID-19. Future Sci OA 2023; 16:FSO832. [PMID: 36897962 PMCID: PMC9987558 DOI: 10.2144/fsoa-2022-0048] [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: 07/29/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
The understanding of any disease calls for studying specific biological structures called epitopes. One important tool recently drawing attention and proving efficiency in both diagnosis and vaccine development is epitope mapping. Several techniques have been developed with the urge to provide precise epitope mapping for use in designing sensitive diagnostic tools and developing rpitope-based vaccines (EBVs) as well as therapeutics. In this review, we will discuss the state of the art in epitope mapping with a special emphasis on accomplishments and opportunities in combating COVID-19. These comprise SARS-CoV-2 variant analysis versus the currently available immune-based diagnostic tools and vaccines, immunological profile-based patient stratification, and finally, exploring novel epitope targets for potential prophylactic, therapeutic or diagnostic agents for COVID-19.
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Antanasijevic A, Schulze AJ, Reddy VS, Ward AB. High-resolution structural analysis of enterovirus-reactive polyclonal antibodies in complex with whole virions. PNAS NEXUS 2022; 1:pgac253. [PMID: 36712368 PMCID: PMC9802058 DOI: 10.1093/pnasnexus/pgac253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others. While over 100 serotypes have been described to date, vaccine only exists for EV-A71. Efforts toward rationally designed pan-NPEV vaccines would greatly benefit from structural biology methods for rapid and comprehensive evaluation of vaccine candidates and elicited antibody responses. Toward this goal, we introduced a cryo-electron-microscopy-based approach for structural analysis of virus- or vaccine-elicited polyclonal antibodies (pAbs) in complex with whole NPEV virions. We demonstrated the feasibility using coxsackievirus A21 and reconstructed five structurally distinct pAbs bound to the virus. The pAbs targeted two immunodominant epitopes, one overlapping with the receptor binding site. These results demonstrate that our method can be applied to map broad-spectrum polyclonal immune responses against intact virions and define potentially cross-reactive epitopes.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA,International AIDS Vaccine Initiative Neutralizing Antibody Center, Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Autumn J Schulze
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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Zhang Z, Li J, Jiao S, Han G, Zhu J, Liu T. Functional and clinical characteristics of focal adhesion kinases in cancer progression. Front Cell Dev Biol 2022; 10:1040311. [PMID: 36407100 PMCID: PMC9666724 DOI: 10.3389/fcell.2022.1040311] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase and an adaptor protein that primarily regulates adhesion signaling and cell migration. FAK promotes cell survival in response to stress. Increasing evidence has shown that at the pathological level, FAK is highly expressed in multiple tumors in several systems (including lung, liver, gastric, and colorectal cancers) and correlates with tumor aggressiveness and patient prognosis. At the molecular level, FAK promotes tumor progression mainly by altering survival signals, invasive capacity, epithelial-mesenchymal transition, the tumor microenvironment, the Warburg effect, and stemness of tumor cells. Many effective drugs have been developed based on the comprehensive role of FAK in tumor cells. In addition, its potential as a tumor marker cannot be ignored. Here, we discuss the pathological and pre-clinical evidence of the role of FAK in cancer development; we hope that these findings will assist in FAK-based clinical studies.
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Affiliation(s)
- Zhaoyu Zhang
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Jinlong Li
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Simin Jiao
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Guangda Han
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Jiaming Zhu
- Department of Surgical Oncology and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianzhou Liu
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Tianzhou Liu,
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Vishweshwaraiah YL, Dokholyan NV. Toward rational vaccine engineering. Adv Drug Deliv Rev 2022; 183:114142. [PMID: 35150769 PMCID: PMC8931536 DOI: 10.1016/j.addr.2022.114142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/31/2022] [Accepted: 02/07/2022] [Indexed: 12/29/2022]
Abstract
Technological revolutions in several fields have pushed the boundaries of vaccine design and provided new avenues for vaccine development. Next-generation vaccine platforms have shown promise in targeting challenging antigens, for which traditional approaches have been ineffective. With advances in protein engineering, structural biology, computational biology and immunology, the structural vaccinology approach, which uses protein structure information to develop immunogens, holds promise for future vaccine design. In this review, we highlight various vaccine development strategies, along with their advantages and limitations. We discuss the rational vaccine design approach, which focuses on structure-based vaccine design. Finally, we discuss antigen engineering using the epitope-scaffold approach, gaps in structural vaccinology, and remaining challenges in vaccine design.
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Affiliation(s)
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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Nanoparticle-based drug delivery systems in cancer: A focus on inflammatory pathways. Semin Cancer Biol 2022; 86:860-872. [PMID: 35115226 DOI: 10.1016/j.semcancer.2022.01.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 12/16/2022]
Abstract
It has become necessary to accept the clinical reality of therapeutic agents targeting the cancer-associated immune system. In recent decades, several investigations have highlighted the role of inflammation in cancer development. It has now been recognized that inflammatory cells secrete mediators, including enzymes, chemokines, and cytokines. These secreted substances produce an inflammatory microenvironment that is critically involved in cancer growth. Inflammation may enhance genomic instability leading to DNA damage, activation of oncogenes, or compromised tumor suppressor activity, all of which may promote various phases of carcinogenesis. Conventional cancer treatment includes surgery, radiation, and chemotherapy. However, treatment failure occurs because current strategies are unable to achieve complete local control due to metastasis. Nanoparticles (NPs) are a broad spectrum of drug carriers typically below the size of 100 nm, targeting tumor sites while reducing off-target consequences. More importantly, NPs can stimulate innate and adaptive immune systems in the tumor microenvironment (TME); hence, they induce a cancer-fighting immune response. Strikingly, targeting cancer cells with NPs helps eliminate drug resistance and tumor recurrence, as well as prevents inflammation. Throughout this review, we provide recent data on the role of inflammation in cancer and explore nano-therapeutic initiatives to target significant mediators, for example, nuclear factor-kappa B (NF-κB), tumor necrosis factor-α (TNF-α), and interleukins (ILs) associated with cancer-related inflammation, to escort the immunomodulators to cancer cells and associated systemic compartments. We also highlight the necessity of better identifying inflammatory pathways in cancer pathophysiology to develop effective treatment plans.
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Huang KYA. Structural basis for neutralization of enterovirus. Curr Opin Virol 2021; 51:199-206. [PMID: 34749266 DOI: 10.1016/j.coviro.2021.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 10/10/2021] [Accepted: 10/17/2021] [Indexed: 11/29/2022]
Abstract
Outbreaks of enteroviral infections are associated with morbidity and mortality in susceptible individuals worldwide. There are still no antiviral drugs or vaccines against most circulating enteroviruses. Antibody-mediated immunity is crucial for preventing and limiting enteroviral infections. In this review, we focus on enteroviruses that continue to cause endemics in recent years, such as rhinovirus, enterovirus A71, coxsackievirus, and echovirus, and introduce a structural understanding of the mechanisms of virus neutralization. The mechanisms by which virus-specific antibodies neutralize enteroviruses have been explored not only through study of viral structures, but also through understanding virus-antibody interactions at the amino acid level. Neutralizing epitopes are predominantly mapped on the canyon northern rim, canyon inner surface, canyon southern rim, and twofold and threefold plateaus of the capsid, where surface-exposed loops are located. This review also describes recent progress in deciphering the virus-receptor complex and structural rearrangements involved in the uncoating process, providing insight into plausible virus neutralization mechanisms.
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Affiliation(s)
- Kuan-Ying A Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Genomics Research Center, Academia Sinica, Taipei, Taiwan.
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Photobiomodulation and Antiviral Photodynamic Therapy in COVID-19 Management. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:517-547. [PMID: 33973198 DOI: 10.1007/978-3-030-63761-3_30] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has shocked the world by its spread and contagiousness. There is no approved vaccine and no proven treatment for this infection. Some potential treatments that have already been associated with antiviral and anti-inflammatory effects are under investigation. Photobiomodulation therapy (PBMT) is a photon-based therapy that uses light to mediate a variety of metabolic, analgesic, anti-inflammatory, and immunomodulatory effects. Antiviral photodynamic therapy (aPDT) is a branch of photodynamic therapy based on the reaction between a photosensitizing agent and a light source in the presence of oxygen, which can produce oxidative and free radical agents to damage the viral structures such as proteins and nucleic acids. This chapter aims to discuss the potential therapeutic benefit of PBMT and aPDT in the context of the novel coronavirus. Studies indicate that PBMT and aPDT could be useful in many viral and bacterial pulmonary complications like influenza, SARS-CoV, and MERS, but we found no direct study on SARS-CoV-2. With a combination of PBMT and aPDT, we may be able to combat COVID-19 with minimal interference with pharmaceutical agents. It might improve the efficacy of PBMT and aPDT by using monoclonal antibodies and preparing new photosensitizers at the nanoscale that target the lung tissue specifically. More animal and human studies would need to take place to reach an effective protocol. This chapter would encourage other scientists to work on this new platform.
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Rismanbaf A. Potential Treatments for COVID-19; a Narrative Literature Review. ARCHIVES OF ACADEMIC EMERGENCY MEDICINE 2020; 8:e29. [PMID: 32232214 PMCID: PMC7085862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
SARS-CoV-2 is a newly emerging human infectious coronavirus that causes COVID-19, which has been recognized as a pandemic by the World Health Organization (WHO) on March 11th. There is still no vaccine or definitive treatment for this virus because its pathogenesis and proliferation pathways are still unknown. Therefore, in this article, new potential COVID-19 therapies are briefly reviewed.
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Affiliation(s)
- Ali Rismanbaf
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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