Structure-Based Reverse Vaccinology Failed in the Case of HIV Because It Disregarded Accepted Immunological Theory

Regenmortel, M.H.V. Van

doi:10.1007/978-3-030-32459-9_21

Cited by 4 publications

(5 citation statements)

References 191 publications

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“…Similarly, the structural vaccinology approach focuses on the conformational features of the viral epitope that makes them good candidate antigens. 17 This involves the analysis of the vaccine candidate to ascertain the conformational structures and a property that may elicit the best immunological response from monoclonal antibodies since reports of van Regenmortel 33 suggest monoclonal antibodies recognize conformational rather than linear epitopes.…”

Section: Applications Of Bioinformatics In Vaccine Design For Covid-1mentioning

confidence: 99%

The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment

Chukwudozie

Duru

Ndiribe

et al. 2021

Bioinform Biol Insights

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The application of bioinformatics to vaccine research and drug discovery has never been so essential in the fight against infectious diseases. The greatest combat of the 21st century against a debilitating disease agent SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus discovered in Wuhan, China, December 2019, has piqued an unprecedented usage of bioinformatics tools in deciphering the molecular characterizations of infectious pathogens. With the viral genome data of SARS-COV-2 been made available barely weeks after the reported outbreak, bioinformatics platforms have become an all-time critical tool to gain time in the fight against the disease pandemic. Before the outbreak, different platforms have been developed to explore antigenic epitopes, predict peptide-protein docking and antibody structures, and simulate antigen-antibody reactions and lots more. However, the advent of the pandemic witnessed an upsurge in the application of these pipelines with the development of newer ones such as the Coronavirus Explorer in the development of efficacious vaccines, drug repurposing, and/or discovery. In this review, we have explored the various pipelines available for use, their relevance, and limitations in the timely development of useful therapeutic candidates from genomic data knowledge to clinical therapy.

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Section: Applications Of Bioinformatics In Vaccine Design For Covid-1mentioning

confidence: 99%

The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment

Chukwudozie

Duru

Ndiribe

et al. 2021

Bioinform Biol Insights

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“…An effective vaccine will contribute to elimination of HIV infection worldwide, however, candidate vaccines evaluated to date have failed to demonstrate efficacy [ 43 ]. A vaccine is an invention that certainly involves an empirical trial-and-error step that inherently differs from a rational design approach; in the case of HIV vaccines, the so-called rational design approach failed because the immunogenicity and antigenicity were confused [ 44 ]. The major barriers for HIV vaccine development are the failure to produce adequate vaccine immunogens and the inability of conventional delivery approaches to produce the needed immune response [ 45 ].…”

Section: Nanotechnology Approaches For Prevention Of Hiv Infectionmentioning

confidence: 99%

Nanosystems Applied to HIV Infection: Prevention and Treatments

Macchione

Bedoya

Figueroa

et al. 2020

IJMS

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Sexually-transmitted infections (STIs) are a global health concern worldwide as they cause acute diseases, infertility, and significant mortality. Among the bacterial, viral, and parasitic pathogens that can be sexually transmitted, human immunodeficiency virus (HIV) has caused one of the most important pandemic diseases, which is acquired immune deficiency syndrome (AIDS). 32.7 million people have died from AIDS-related illnesses since the start of the epidemic. Moreover, in 2019, 38 million people were living with HIV worldwide. The need to deal with this viral infection becomes more obvious, because it represents not only a problem for public health, but also a substantial economic problem. In this context, it is necessary to focus efforts on developing methods for prevention, detection and treatment of HIV infections that significantly reduce the number of newly infected people and provide a better quality of life for patients. For several decades, biomedical research has been developed allowing quick solutions through the contribution of effective tools. One of them is the use of polymers as vehicles, drug carrier agents, or as macromolecular prodrugs. Moreover, nanosystems (NSs) play an especially important role in the diagnosis, prevention, and therapy against HIV infection. The purpose of this work is to review recent research into diverse NSs as potential candidates for prevention and treatment of HIV infection. Firstly, this review highlights the advantages of using nanosized structures for these medical applications. Furthermore, we provide an overview of different types of NSs used for preventing or combating HIV infection. Then, we briefly evaluate the most recent developments associated with prevention and treatment alternatives. Additionally, the implications of using different NSs are also addressed.

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“…Thus, non-reductionist data structures help discover preexisting functions ( propositional knowledge). To validate such propositions, new tools or methods ( prescriptive knowledge) may be required to conduct operations previously unfeasible ( 27 , 62 , 63 ).…”

Section: Visualization Of Reductionist and Non-reductionist Paradigmsmentioning

confidence: 99%

Nature and Consequences of Biological Reductionism for the Immunological Study of Infectious Diseases

Rivas

Leitner²,

Jankowski

et al. 2017

Front. Immunol.

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Evolution has conserved “economic” systems that perform many functions, faster or better, with less. For example, three to five leukocyte types protect from thousands of pathogens. To achieve so much with so little, biological systems combine their limited elements, creating complex structures. Yet, the prevalent research paradigm is reductionist. Focusing on infectious diseases, reductionist and non-reductionist views are here described. The literature indicates that reductionism is associated with information loss and errors, while non-reductionist operations can extract more information from the same data. When designed to capture one-to-many/many-to-one interactions—including the use of arrows that connect pairs of consecutive observations—non-reductionist (spatial–temporal) constructs eliminate data variability from all dimensions, except along one line, while arrows describe the directionality of temporal changes that occur along the line. To validate the patterns detected by non-reductionist operations, reductionist procedures are needed. Integrated (non-reductionist and reductionist) methods can (i) distinguish data subsets that differ immunologically and statistically; (ii) differentiate false-negative from -positive errors; (iii) discriminate disease stages; (iv) capture in vivo, multilevel interactions that consider the patient, the microbe, and antibiotic-mediated responses; and (v) assess dynamics. Integrated methods provide repeatable and biologically interpretable information.

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Structure-Based Reverse Vaccinology Failed in the Case of HIV Because It Disregarded Accepted Immunological Theory

Cited by 4 publications

References 191 publications

The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment

The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment

Nanosystems Applied to HIV Infection: Prevention and Treatments

Nature and Consequences of Biological Reductionism for the Immunological Study of Infectious Diseases

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