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In Silico Studies to Support Vaccine Development. Pharmaceutics 2023; 15:pharmaceutics15020654. [PMID: 36839975 PMCID: PMC9963741 DOI: 10.3390/pharmaceutics15020654] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
The progress that has been made in computer science positioned in silico studies as an important and well-recognized methodology in the drug discovery and development process. It has numerous advantages in terms of costs and also plays a huge impact on the way the research is conducted since it can limit the use of animal models leading to more sustainable research. Currently, human trials are already being partly replaced by in silico trials. EMA and FDA are both endorsing these studies and have been providing webinars and guidance to support them. For instance, PBPK modeling studies are being used to gather data on drug interactions with other drugs and are also being used to support clinical and regulatory requirements for the pediatric population, pregnant women, and personalized medicine. This trend evokes the need to understand the role of in silico studies in vaccines, considering the importance that these products achieved during the pandemic and their promising hope in oncology. Vaccines are safer than other current oncology treatments. There is a huge variety of strategies for developing a cancer vaccine, and some of the points that should be considered when designing the vaccine technology are the following: delivery platforms (peptides, lipid-based carriers, polymers, dendritic cells, viral vectors, etc.), adjuvants (to boost and promote inflammation at the delivery site, facilitating immune cell recruitment and activation), choice of the targeted antigen, the timing of vaccination, the manipulation of the tumor environment, and the combination with other treatments that might cause additive or even synergistic anti-tumor effects. These and many other points should be put together to outline the best vaccine design. The aim of this article is to perform a review and comprehensive analysis of the role of in silico studies to support the development of and design of vaccines in the field of oncology and infectious diseases. The authors intend to perform a literature review of all the studies that have been conducted so far in preparing in silico models and methods to support the development of vaccines. From this point, it was possible to conclude that there are few in silico studies on vaccines. Despite this, an overview of how the existing work could support the design of vaccines is described.
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Somogyi E, Kremlitzka M, Csiszovszki Z, Molnár L, Lőrincz O, Tóth J, de Waal L, Pattijn S, Reineking W, Beineke A, Tőke ER. T cell immunity ameliorates COVID-19 disease severity and provides post-exposure prophylaxis after peptide-vaccination, in Syrian hamsters. Front Immunol 2023; 14:1111629. [PMID: 36761759 PMCID: PMC9902696 DOI: 10.3389/fimmu.2023.1111629] [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: 11/29/2022] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
Background The emergence of novel SARS-CoV-2 variants that resist neutralizing antibodies drew the attention to cellular immunity and calls for the development of alternative vaccination strategies to combat the pandemic. Here, we have assessed the kinetics of T cell responses and protective efficacy against severe COVID-19 in pre- and post-exposure settings, elicited by PolyPEPI-SCoV-2, a peptide based T cell vaccine. Methods 75 Syrian hamsters were immunized subcutaneously with PolyPEPI-SCoV-2 on D0 and D14. On D42, hamsters were intranasally challenged with 102 TCID50 of the virus. To analyze immunogenicity by IFN-γ ELISPOT and antibody secretion, lymphoid tissues were collected both before (D0, D14, D28, D42) and after challenge (D44, D46, D49). To measure vaccine efficacy, lung tissue, throat swabs and nasal turbinate samples were assessed for viral load and histopathological changes. Further, body weight was monitored on D0, D28, D42 and every day after challenge. Results The vaccine induced robust activation of T cells against all SARS-CoV-2 structural proteins that were rapidly boosted after virus challenge compared to control animals (~4-fold, p<0.05). A single dose of PolyPEPI-SCoV-2 administered one day after challenge also resulted in elevated T cell response (p<0.01). The vaccination did not induce virus-specific antibodies and viral load reduction. Still, peptide vaccination significantly reduced body weight loss (p<0.001), relative lung weight (p<0.05) and lung lesions (p<0.05), in both settings. Conclusion Our study provides first proof of concept data on the contribution of T cell immunity on disease course and provide rationale for the use of T cell-based peptide vaccines against both novel SARS-CoV-2 variants and supports post-exposure prophylaxis as alternative vaccination strategy against COVID-19.
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Affiliation(s)
- Eszter Somogyi
- Treos Bio Ltd, London, United Kingdom,Treos Bio Zrt, Veszprém, Hungary,PepTC Vaccines Ltd, London, United Kingdom
| | - Mariann Kremlitzka
- Treos Bio Ltd, London, United Kingdom,Treos Bio Zrt, Veszprém, Hungary,PepTC Vaccines Ltd, London, United Kingdom
| | - Zsolt Csiszovszki
- Treos Bio Ltd, London, United Kingdom,Treos Bio Zrt, Veszprém, Hungary,PepTC Vaccines Ltd, London, United Kingdom
| | - Levente Molnár
- Treos Bio Ltd, London, United Kingdom,Treos Bio Zrt, Veszprém, Hungary,PepTC Vaccines Ltd, London, United Kingdom
| | - Orsolya Lőrincz
- Treos Bio Ltd, London, United Kingdom,Treos Bio Zrt, Veszprém, Hungary,PepTC Vaccines Ltd, London, United Kingdom
| | - József Tóth
- Treos Bio Ltd, London, United Kingdom,Treos Bio Zrt, Veszprém, Hungary,PepTC Vaccines Ltd, London, United Kingdom
| | - Leon de Waal
- Viroclinics Biosciences B.V., Viroclinics Xplore, Schaijk, Netherlands
| | - Sofie Pattijn
- ImmunXperts Société Anonyme, Q2 Solutions Company, Gosselies, Belgium
| | - Wencke Reineking
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Andreas Beineke
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Enikő R. Tőke
- Treos Bio Ltd, London, United Kingdom,Treos Bio Zrt, Veszprém, Hungary,PepTC Vaccines Ltd, London, United Kingdom,*Correspondence: Enikő R. Tőke,
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Hubbard JM, Tőke ER, Moretto R, Graham RP, Youssoufian H, Lőrincz O, Molnár L, Csiszovszki Z, Mitchell JL, Wessling J, Tóth J, Cremolini C. Safety and Activity of PolyPEPI1018 Combined with Maintenance Therapy in Metastatic Colorectal Cancer: an Open-Label, Multicenter, Phase Ib Study. Clin Cancer Res 2022; 28:2818-2829. [PMID: 35472243 PMCID: PMC9365360 DOI: 10.1158/1078-0432.ccr-22-0112] [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: 01/14/2022] [Revised: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Although chemotherapy is standard of care for metastatic colorectal cancer (mCRC), immunotherapy has no role in microsatellite stable (MSS) mCRC, a "cold" tumor. PolyPEPI1018 is an off-the-shelf, multi-peptide vaccine derived from 7 tumor-associated antigens (TAA) frequently expressed in mCRC. This study assessed PolyPEPI1018 combined with first-line maintenance therapy in patients with MSS mCRC. PATIENTS AND METHODS Eleven patients with MSS mCRC received PolyPEPI1018 and Montanide ISA51VG adjuvant subcutaneously, combined with fluoropyrimidine/biologic following first-line induction with chemotherapy and a biologic (NCT03391232). In Part A of the study, 5 patients received a single dose; in Part B, 6 patients received up to three doses of PolyPEPI1018 every 12 weeks. The primary objective was safety; secondary objectives were preliminary efficacy, immunogenicity at peripheral and tumor level, and immune correlates. RESULTS PolyPEPI1018 vaccination was safe and well tolerated. No vaccine-related serious adverse event occurred. Eighty percent of patients had CD8+ T-cell responses against ≥3 TAAs. Increased density of tumor-infiltrating lymphocytes were detected post-treatment for 3 of 4 patients' liver biopsies, combined with increased expression of immune-related gene signatures. Three patients had objective response according to RECISTv1.1, and 2 patients qualified for curative surgery. Longer median progression-free survival for patients receiving multiple doses compared with a single dose (12.5 vs. 4.6 months; P = 0.017) suggested a dose-efficacy correlation. The host HLA genotype predicted multi-antigen-specific T-cell responses (P = 0.01) indicative of clinical outcome. CONCLUSIONS PolyPEPI1018 added to maintenance chemotherapy for patients with unresectable, MSS mCRC was safe and associated with specific immune responses and antitumor activity warranting further confirmation in a randomized, controlled setting.
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Affiliation(s)
- Joleen M. Hubbard
- Mayo Clinic, Rochester, Minnesota.,Corresponding Author: Joleen M. Hubbard, Mayo Clinic, 200 First Street SW, Rochester, MN 55905. Phone: 507-266-9161; Fax 507-284-1803; E-mail:
| | - Enikő R. Tőke
- Treos Bio Ltd, London, United Kingdom.,Treos Bio Zrt, Veszprém, Hungary
| | - Roberto Moretto
- Department of Translational Research and New Technologies in Medicine and Surgery, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
| | | | | | - Orsolya Lőrincz
- Treos Bio Ltd, London, United Kingdom.,Treos Bio Zrt, Veszprém, Hungary
| | - Levente Molnár
- Treos Bio Ltd, London, United Kingdom.,Treos Bio Zrt, Veszprém, Hungary
| | - Zsolt Csiszovszki
- Treos Bio Ltd, London, United Kingdom.,Treos Bio Zrt, Veszprém, Hungary
| | | | | | - József Tóth
- Treos Bio Ltd, London, United Kingdom.,Treos Bio Zrt, Veszprém, Hungary
| | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, Azienda Ospedaliera Universitaria Pisana, Pisa, Italy
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Yurina V, Adianingsih OR. Predicting epitopes for vaccine development using bioinformatics tools. Ther Adv Vaccines Immunother 2022; 10:25151355221100218. [PMID: 35647486 PMCID: PMC9130818 DOI: 10.1177/25151355221100218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
Epitope-based DNA vaccine development is one application of bioinformatics or
in silico studies, that is, computational methods,
including mathematical, chemical, and biological approaches, which are widely
used in drug development. Many in silico studies have been
conducted to analyze the efficacy, safety, toxicity effects, and interactions of
drugs. In the vaccine design process, in silico studies are
performed to predict epitopes that could trigger T-cell and B-cell reactions
that would produce both cellular and humoral immune responses. Immunoinformatics
is the branch of bioinformatics used to study the relationship between immune
responses and predicted epitopes. Progress in immunoinformatics has been rapid
and has led to the development of a variety of tools that are used for the
prediction of epitopes recognized by B cells or T cells as well as the antigenic
responses. However, the in silico approach to vaccine design is
still relatively new; thus, this review is aimed at increasing understanding of
the importance of in silico studies in the design of vaccines
and thereby facilitating future research in this field.
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Affiliation(s)
- Valentina Yurina
- Department of Pharmacy, Medical Faculty, Universitas Brawijaya, Jalan Veteran, Malang 65145, East Java, Indonesia
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