1
|
Benyamini P. Phylogenetic Tracing of Evolutionarily Conserved Zonula Occludens Toxin Reveals a "High Value" Vaccine Candidate Specific for Treating Multi-Strain Pseudomonas aeruginosa Infections. Toxins (Basel) 2024; 16:271. [PMID: 38922165 PMCID: PMC11209546 DOI: 10.3390/toxins16060271] [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: 05/03/2024] [Revised: 06/09/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Extensively drug-resistant Pseudomonas aeruginosa infections are emerging as a significant threat associated with adverse patient outcomes. Due to this organism's inherent properties of developing antibiotic resistance, we sought to investigate alternative strategies such as identifying "high value" antigens for immunotherapy-based purposes. Through extensive database mining, we discovered that numerous Gram-negative bacterial (GNB) genomes, many of which are known multidrug-resistant (MDR) pathogens, including P. aeruginosa, horizontally acquired the evolutionarily conserved gene encoding Zonula occludens toxin (Zot) with a substantial degree of homology. The toxin's genomic footprint among so many different GNB stresses its evolutionary importance. By employing in silico techniques such as proteomic-based phylogenetic tracing, in conjunction with comparative structural modeling, we discovered a highly conserved intermembrane associated stretch of 70 amino acids shared among all the GNB strains analyzed. The characterization of our newly identified antigen reveals it to be a "high value" vaccine candidate specific for P. aeruginosa. This newly identified antigen harbors multiple non-overlapping B- and T-cell epitopes exhibiting very high binding affinities and can adopt identical tertiary structures among the least genetically homologous P. aeruginosa strains. Taken together, using proteomic-driven reverse vaccinology techniques, we identified multiple "high value" vaccine candidates capable of eliciting a polarized immune response against all the P. aeruginosa genetic variants tested.
Collapse
Affiliation(s)
- Payam Benyamini
- Department of Health Sciences at Extension, University of California Los Angeles, 1145 Gayley Ave., Los Angeles, CA 90024, USA
| |
Collapse
|
2
|
Preda M, Manolescu LSC, Chivu RD. Advances in Alpha Herpes Viruses Vaccines for Human. Vaccines (Basel) 2023; 11:1094. [PMID: 37376483 DOI: 10.3390/vaccines11061094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Alpha herpes simplex viruses are an important public health problem affecting all age groups. It can produce from common cold sores and chicken pox to severe conditions like encephalitis or newborn mortality. Although all three subtypes of alpha herpes viruses have a similar structure, the produced pathology differs, and at the same time, the available prevention measures, such as vaccination. While there is an available and efficient vaccine for the varicella-zoster virus, for herpes simplex virus 1 and 2, after multiple approaches from trivalent subunit vaccine to next-generation live-attenuated virus vaccines and bioinformatic studies, there is still no vaccine available. Although there are multiple failed approaches in present studies, there are also a few promising attempts; for example, the trivalent vaccine containing herpes simplex virus type 2 (HSV-2) glycoproteins C, D, and E (gC2, gD2, gE2) produced in baculovirus was able to protect guinea pigs against vaginal infection and proved to cross-protect against HSV-1. Another promising vaccine is the multivalent DNA vaccine, SL-V20, tested in a mouse model, which lowered the clinical signs of infection and produced efficient viral eradication against vaginal HSV-2. Promising approaches have emerged after the COVID-19 pandemic, and a possible nucleoside-modified mRNA vaccine could be the next step. All the approaches until now have not led to a successful vaccine that could be easy to administer and, at the same time, offer antibodies for a long period.
Collapse
Affiliation(s)
- Madalina Preda
- Department of Microbiology, Parasitology and Virology, Faculty of Midwives and Nursing, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Research Department, Marius Nasta Institute of Pneumology, 050159 Bucharest, Romania
| | - Loredana Sabina Cornelia Manolescu
- Department of Microbiology, Parasitology and Virology, Faculty of Midwives and Nursing, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Department of Virology, Institute of Virology "Stefan S. Nicolau", 030304 Bucharest, Romania
| | - Razvan Daniel Chivu
- Department of Public Health and Health Management, Faculty of Midwifery and Nursing, "Carol Davila" University of Medicine and Pharmacy, 050474 Bucharest, Romania
| |
Collapse
|
3
|
Behl A, Nair A, Mohagaonkar S, Yadav P, Gambhir K, Tyagi N, Sharma RK, Butola BS, Sharma N. Threat, challenges, and preparedness for future pandemics: A descriptive review of phylogenetic analysis based predictions. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105217. [PMID: 35065303 DOI: 10.1016/j.meegid.2022.105217] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 12/01/2021] [Accepted: 01/14/2022] [Indexed: 11/27/2022]
Abstract
For centuries the world has been confronted with many infectious diseases, with a potential to turn into a pandemic posing a constant threat to human lives. Some of these pandemics occurred due to the emergence of new disease or re-emergence of previously known diseases with a few mutations. In such scenarios their optimal prevention and control options were not adequately developed. Most of these diseases are highly contagious and for their timely control, knowledge about the pathogens and disease progression is the basic necessity. In this review, we have presented a documented chronology of the earlier pandemics, evolutionary analysis of the infectious disease with pandemic potential, the role of RNA, difficulties in controlling pandemics, and the likely pathogens that could trigger future pandemics. In this study, the evolutionary history of the pathogens was identified by carrying out phylogenetic analysis. The percentage similarity between different infectious diseases is critically analysed for the identification of their correlation using online sequence matcher tools. The Baltimore classification system was used for finding the genomic nature of the viruses. It was observed that most of the infectious pathogens rise from their animal hosts with some mutations in their genome composition. The phylogenetic tree shows that the single-stranded RNA diseases have a common origin and many of them are having high similarity percentage. The outcomes of this study will help in the identification of potential pathogens that can cause future pandemics. This information will be helpful in the development of early detection techniques, devising preventive mechanism to limit their spread, prophylactic measures, Infection control and therapeutic options, thereby, strengthening our approach towards global preparedness against future pandemics.
Collapse
Affiliation(s)
- Amanpreet Behl
- Department of Molecular Medicine, Jamia Hamdard Univeristy, Hamdard Nagar, New Delhi, Delhi 110062, India
| | - Ashrit Nair
- Department of Textile and Fibre Engineering, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
| | - Sanika Mohagaonkar
- Department of Metabolism, Digestion and Reproduction, Imperial College, London, United Kingdom
| | - Pooja Yadav
- Department of Medical Elementology and Toxicology, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Kirtida Gambhir
- Stem cell and Gene Therapy Research Group, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organisation, Delhi 110054, India
| | - Nishant Tyagi
- Stem cell and Gene Therapy Research Group, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organisation, Delhi 110054, India
| | - Rakesh Kumar Sharma
- Saveetha Institute of Medical and Technical Sciences, 162, Poonamallee High Road, Chennai 600077, Tamil Nadu, India
| | - Bhupendra Singh Butola
- Department of Textile and Fibre Engineering, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India
| | - Navneet Sharma
- Department of Textile and Fibre Engineering, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
| |
Collapse
|
4
|
Farnudian-Habibi A, Mirjani M, Montazer V, Aliebrahimi S, Katouzian I, Abdolhosseini S, Rahmani A, Keyvani H, Ostad SN, Rad-Malekshahi M. Review on Approved and Inprogress COVID-19 Vaccines. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH 2022; 21:e124228. [PMID: 36060923 PMCID: PMC9420219 DOI: 10.5812/ijpr.124228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 11/24/2022]
Abstract
The last generation of Coronavirus named COVID-19 is responsible for the recent worldwide outbreak. Concerning the widespread and quick predominance, there is a critical requirement for designing appropriate vaccines to surmount this grave problem. Correspondingly, in this revision, COVID-19 vaccines (which are being developed until March 29th, 2021) are classified into specific and non-specific categories. Specific vaccines comprise genetic-based vaccines (mRNA, DNA), vector-based, protein/recombinant protein vaccines, inactivated viruses, live-attenuated vaccines, and novel strategies including microneedle arrays (MNAs), and nanoparticles vaccines. Moreover, specific vaccines such as BCG, MRR, and a few other vaccines are considered Non-specific. What is more, according to the significance of Bioinformatic sciences in the cutting-edge vaccine design and rapid outbreak of COVID-19, herein, Bioinformatic principles including reverse vaccinology, epitopes prediction/selection and, their further applications in the design of vaccines are discussed. Last but not least, safety, challenges, advantages, and future prospects of COVID-19 vaccines are highlighted.
Collapse
Affiliation(s)
- Amir Farnudian-Habibi
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mobina Mirjani
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahideh Montazer
- Department of Clinical Pharmacy, Virtual University of Medical Sciences, Tehran, Iran
| | - Shima Aliebrahimi
- Department of Medical Education, Virtual University of Medical Sciences, Tehran, Iran
| | - Iman Katouzian
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), 8054 Monash University LPO, Clayton, 3168, Victoria, Australia
| | - Saeed Abdolhosseini
- School of Electrical and Computer Engineering, College of Engineering, University of Tehran, 14395-515 Tehran, Iran
| | - Ali Rahmani
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Nasser Ostad
- Toxicology and Poisoning Research Centre, Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding Author: Toxicology and Poisoning Research Centre, Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mazda Rad-Malekshahi
- Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding Author: Department of Pharmaceutical Biomaterials, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
5
|
Wijesinghe VN, Farouk IA, Zabidi NZ, Puniyamurti A, Choo WS, Lal SK. Current vaccine approaches and emerging strategies against herpes simplex virus (HSV). Expert Rev Vaccines 2021; 20:1077-1096. [PMID: 34296960 DOI: 10.1080/14760584.2021.1960162] [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] [Indexed: 12/17/2022]
Abstract
Introduction: Vaccine development for the disease caused by the herpes simplex virus (HSV) has been challenging over the years and is always in dire need of novel approaches for prevention and cure. To date, the HSV disease remains incurable and challenging to prevent. The disease is extremely widespread due to its high infection rate, resulting in millions of infection cases worldwide.Areas covered: This review first explains the diverse forms of HSV-related disease presentations and reports past vaccine history for the disease. Next, this review examines current and novel HSV vaccine approaches being studied and tested for efficacy and safety as well as vaccines in clinical trial phases I to III. Modern approaches to vaccine design using bioinformatics are described. Finally, we discuss measures to enhance new vaccine development pipelines for HSV.Expert opinion: Modernized approaches using in silico analysis and bioinformatics are emerging methods that exhibit potential for producing vaccines with enhanced targets and formulations. Although not yet fully established for HSV disease, we describe current studies using these approaches for HSV vaccine design to shed light on these methods. In addition, we provide up-to-date requirements of immunogenicity, adjuvant selection, and routes of administration.
Collapse
Affiliation(s)
| | - Isra Ahmad Farouk
- School of Science, Monash University, Bandar Sunway, Selangor, Malaysia
| | | | | | - Wee Sim Choo
- School of Science, Monash University, Bandar Sunway, Selangor, Malaysia
| | - Sunil Kumar Lal
- School of Science, Monash University, Bandar Sunway, Selangor, Malaysia.,Tropical Medicine & Biology Platform, Monash University, Bandar Sunway, Selangor, Malaysia
| |
Collapse
|
6
|
Kulikowski CA. Pandemics: Historically Slow "Learning Curve" Leading to Biomedical Informatics and Vaccine Breakthroughs. Yearb Med Inform 2021; 30:290-301. [PMID: 33882592 PMCID: PMC8416199 DOI: 10.1055/s-0041-1726482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The worldwide tragedy of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic vividly demonstrates just how inadequate mitigation and control of the spread of infectious diseases can be when faced with a new microorganism with unknown pathogenic effects. Responses by governments in charge of public health, and all other involved organizations, have proved largely wanting. Data infrastructure and the information and communication systems needed to deal with the pandemic have likewise not been up to the task. Nevertheless, after a year of the worldwide outbreak, hope arises from this being the first major pandemic event in history where genomic and related biosciences - relying on biomedical informatics - have been essential in decoding the viral sequence data and producing the mRNA and other biotechnologies that unexpectedly rapidly have led to investigation, design, development, and testing of useful vaccines. Medical informatics may also help support public health actions and clinical interventions - but scalability and impact will depend on overcoming ingrained human shortcomings to deal with complex socio-economic, political, and technological disruptions together with the many ethical challenges presented by pandemics. OBJECTIVES The principal goal is to review the history of biomedical information and healthcare practices related to past pandemics in order to illustrate just how exceptional and dependent on biomedical informatics are the recent scientific insights into human immune responses to viral infection, which are enabling rapid antiviral vaccine development and clinical management of severe cases - despite the many societal challenges ahead. METHODS This paper briefly reviews some of the key historical antecedents leading up to modern insights into epidemic and pandemic processes with their biomedical and healthcare information intended to guide practitioners, agencies, and the lay public in today's ongoing pandemic events. CONCLUSIONS Poor scientific understanding and excessively slow learning about infectious disease processes and mitigating behaviors have stymied effective treatment until the present time. Advances in insights about immune systems, genomes, proteomes, and all the other -omes, became a reality thanks to the key sequencing technologies and biomedical informatics that enabled the Human Genome Project, and only now, 20 years later, are having an impact in ameliorating devastating zoonotic infectious pandemics, including the present SARS-CoV-2 event through unprecedently rapid vaccine development. In the future these advances will hopefully also enable more targeted prevention and treatment of disease. However, past and present shortcomings of most of the COVID-19 pandemic responses illustrate just how difficult it is to persuade enough people - and especially political leaders - to adopt societally beneficial risk-avoidance behaviors and policies, even as these become better understood.
Collapse
|