Frontiers in Protein and Peptide Sciences

Epitopes are parts of an antigen that are recognized by the immune system. Identification of epitopic regions on an immunogenic protein is important for several clinical and biotechnological applications. Various bioinformatics tools are currently available which can be used for the prediction of epitopic regions, and the immune response generated against selected epitopic regions can be monitored through a variety of immunological techniques. In this chapter, we provide an overview of widely used in silico tools for the prediction of epitopic regions, followed by biophysical methods used for their characterization. Furthermore, a brief description of important immunological approaches for measuring immune responses elicited by epitopes is also given. It is anticipated that the information provided in this chapter will help researchers in selecting appropriate tools for the prediction and validation of epitopes on a protein target for vaccine development and diagnostics.

Immunoinformatics is currently an emerging field that has accelerated immunological research to a great extent. It is playing a significant role in antigen identification, immunodiagnostic development, and vaccine design. The arrival of genome sequencing with recent advancements in immunoinformatics has provided a lot of data that can be annotated using databases and tools to reduce the cost required for antibody and vaccine development, ultimately saving time, cost, and resources. The selection and identification of immunogenic regions from the pathogen genomes by computational methods play an important role in devising new hypotheses by a comprehensive examination of immunologic data composite, which is otherwise impossible to achieve by using traditional methods alone. Presently, many epitopebased vaccines, especially multi-epitope vaccines designed employing immunoinformatics approaches, are successfully trailed and being developed against pathogens. In this chapter, we provide an outline of the recent progress in the field of vaccinology and immunoinformatics, enlisted recent tools and databases available for epitopes prediction, validation, and vaccine design, and give a brief description of the role of immunoinformatics in vaccine design against recent COVID-19.

Thermostable proteins have many applications. They have utility in food and beverages, paper and pulp industries, animal feed production, laundry and detergent, and molecular biology and diagnostics. Many factors contribute to protein thermostability. These include covalent and non-covalent interactions, protein folding and conformation, and other thermodynamic factors. Although the available protein structures have been increasing over time, the increase in available protein sequences is overwhelmingly enormous. Also, structure determination can be a challenging job and many proteins are difficult to crystallize. This has resulted in a sequence-structure gap. The use of computer-assisted structure prediction has helped in filling this gap. There are many in silico strategies and methods available to predict and analyze protein structure and properties. These can be used to determine protein stability and are quite useful for in silico protein analysis to improve function and thermostability.

Proteomics is rapidly expanding with the advent of high throughput technologies and offers a greater understanding of the complexity of life and the process of evolution. Protein profile comparison between genetically heterogeneous individuals may provide important insights into physiological diversity and function. A new term, pan-proteomics, has also been introduced that permits the qualitative and quantitative comparison of proteomes of genetically heterogeneous organisms. Here in this chapter, various aspects of pan-proteomics along with its basic methodology and applications have been discussed.

Bioinformatics tools have produced enormous data in different repositories over the past decade, which is of great interest today for in-silico analysis. Proteins contain one or more peptides that are essential molecules having biological and biomedical functions. Instead of working with sequences, proteomics, and peptidomics, researchers now concentrate more on molecules' processes and metabolic interactions in which proteins or peptides are involved. As a preliminary assessment of possible biological roles, bioinformatics methods are an essential step and greatly reduce experimental verification time and cost. This chapter offers a brief overview of computational methods for predicting the biological features of peptides and proteins. Algorithms using structural, evolutionary, or statistical patterns and strategies based on molecular docking are considered based on machine learning techniques, which are the most common today. The protein and bioactive peptide databases are reported, providing the knowledge required to develop new algorithms. The biological functions for forecasting, the features of proteins, and peptides should be considered, based on the possibility of concluding their natural role. The report includes a list of online resources that researchers can use to evaluate possible protein function and peptides.

Plants are tamed to function as production factories of pharmaceuticals. Recently, several pharmaceuticals, including therapeutics, drugs, vaccines, vitamins, antibiotics, nutraceuticals, and diagnostic molecules, have been produced through these green factories. Compared with conventional systems, for example, bacterial, yeast, fungal, and mammalian cell cultures, plants are accepted as a cost-effective source of pharmaceuticals products. Considering plants as a versatile, cost-effective, and robust production platform, the system could be exploited in different ways like plant cell culture, transient expression and harvesting, and stable transgenics. This chapter highlights the importance and potential of molecular pharming with special emphasis on methodological aspects, proving the suitability of plants as the most appropriate biopharmaceutical production platform with recent interventions.

Transgenic plants have been developed since the early 1980s, when researchers were able to transform a piece of foreign DNA into a plant genome. Since then, the technology has expanded enormously, giving rise to many private and public ventures in the field of plant-based recombinant technology. The technology has helped in crop improvement against various biotic and abiotic stresses such as insect resistance and herbicide tolerance, as well as improving their nutritional values, for example, Golden rice. In addition to crop improvement, the technology has enabled plants to be used as green factories for the production of recombinant proteins. Several platforms are available for the heterologous expression of foreign proteins, each of which represents its own set of advantages and limitations. Plants offer many advantages for inexpensive yet large-scale production of high-value targets, making them extremely attractive for commercial applications. In this chapter, we briefly discuss the need for using plants as solar-powered cellular factories to produce recombinant proteins. We provide a snapshot of different expression systems and argue that the plant-based expression system is highly commercially feasible not only for the production of highvalue targets but also to help address global challenges like Covid-19.

Many strides have been made in the development of antibody-based detection systems for rapid and sensitive analysis of Fusarium pathogens and their toxins. Antibody cross-reactivity, specificity, and binding affinity with antigenic molecules affect the efficacy in which these molecules serve their own functions. Researchers are, therefore, directed in investigating the principles that govern crossreactivity, specificity, and the relationship between them, using various tools such as optimised ELISA. This is important because the ability of Fusarium spp. to infect and produce mycotoxins in agronomic crops passes these toxins to animals and humans after contact or ingestion. Antibodies that recognise and bind particular antigens with great affinity and specificity, especially for the effective relief of unwanted Fusarium pathogenic materials in humans and animals, are thus required. Furthermore, the demand for fungal contaminants free agriculture, emerging antifungal drug resistance, and the fatal health effects of fungal infections in immunocompromised humans and animals drive the need for the development of a rapid, sensitive, reliable, and accurate relief system for these pathogens. Therefore, this chapter provides a succinct review on the role of antibody cross-reactivity and specificity, with reference to basic principles, challenges, and detection for rapid and reliable assessment in Fusarium pathogens.

Infectious diseases pose an increasing threat to global health. The world has experienced many outbreaks due to Emerging Infectious Diseases (EIDs) in the 21st century. Vaccination proves to be the most successful public health intervention to counter such outbreaks. Vaccines against many diseases are available. Most of these vaccines either consist of live or attenuated strains, thus posing health risks. There is a need for new and safe vaccines to prevent and mitigate the impact of outbreaks due to emerging and endemic infectious diseases. The requisition of plant-based medicine is increasing day by day because of their non-toxic nature with no to very few side effects and readily available at a reasonable cost. In the present chapter, we will discuss the importance of plant molecular pharming (PMP) with its perspective on human diseases. Several advantages of PMP in relation to the United Nations’ sustainable development goals (SDGs) will also be deliberated.

Plant molecular farming (PMF) aims to develop plants that express and accumulate proteins of our interest in considerable quantities. Transgenic plants produce edible vaccines, antibodies, therapeutic proteins for human and animal health, and other recombinant proteins required for industrial purposes. Plant systems (PS) to produce pharmaceutical products are preferred over microbial and mammalian systems as they require less input to grow and produce higher biomass. Hence, a variety of proteins are synthesized by plants that are completely free from human pathogens and mammalian toxins. Additionally, they have immunity against infectious and other lifethreatening diseases such as cancer. In this review, plant-inferred therapeutic and nontherapeutic protein items that are in the position of clinical progression or commercialization are summarized. Available plant production platforms are also compared along with associated biosafety and regulatory issues. Further, plant transformation techniques are also analyzed for the development of genetically modified organisms in vaccine production. The use of PMF on a commercial scale is still a long way to go before it is achievable. New methods and techniques are needed to be developed to solve the problems of low yield, scalability, stability, and efficacy of the recombinant proteins, as well as biosafety and regulatory issues. Hence, this strategy will be the ultimate proposed solution to protect humans and animals from health threats in the future.

With the increase in the prevalence of cardiovascular diseases internationally, particularly cardiac failure (CF) and atherosclerosis, the investigation for new biological markers remains one of the main priorities. In contrast to complicated diagnostic methods that might not be appropriate to be employed on a larger population, biological markers are effective for the screening of the population. Owing to their non-invasive detection with typically high accuracy and sensitivity, circulating biomarkers have become increasingly significant for routine medical practice. Cardiac troponins and natriuretic peptides (NPs), specifically brain NP (BNP), mid-regional pro arterial NP, and N-terminal (NT) pro BNP, are validated blood biological markers in the diagnosis of CF and prediction of CF-associated outcomes. Inflammatory proteins like C-reactive protein can also have increased importance in anti-inflammatory treatment guidance. Moreover, next-generation biological markers like galectin-3, growth/differentiation factor 15, diverse miRNAs, and soluble suppression of tumorigenicity-2 might have additional value in the analysis of ventricular remodeling and differentiation of CF subtypes. In this chapter, we will first discuss the biological markers as per the major categories of cardiovascular disease, i.e., myocardial stress, inflammation, plaque instability, myocardial injury, systemic stress, calcium homeostasis, and platelet activation. Lastly, we will describe the multimarker methods, including various combinations of novel and established biomarkers that may improve the risk prediction of CF at the population level.

Animals have been utilized extensively as part and parcel of pharmaceutical and vaccine development. Many studies from animal models for human diseases have re-affirmed inventions in the field of medicine. Animal nutraceuticals of biological origin have marked exceptional promise by enhancing the production and performance of commercial animals. Transgenic animals have helped transform laboratory-scale developments into clinical applications. The nutraceutical potential of animal products is a fascinating area of research with considerable anti-microbial, anti-cancer, antiinflammatory, anti-diabetic and neuroprotective functions. Vaccines in veterinary sciences have been revolutionized based on the efficacy demonstrated by animal models. Vaccines are being routinely used against bacteria, viruses and some parasites at commercial levels. Third-generation vaccines that were thought to be very expensive in the last century are now being commercially produced and marketed worldwide for animal health. Most recently, many avenues have opened that encourage the use of biologically derived pharmaceuticals and vaccine products. This chapter deals with a very comprehensive contrast of history and recent trends in veterinary pharmaceuticals and vaccines. It concludes that more research focus is required to come up with more efficient treatment and prophylactic approaches amidst mutating pathogens of concern.

Plants are exploited as bioreactors for the cost-effective production of pharmaceuticals, predominantly for the expression and accumulation of antigenic proteins, to be used as vaccines for livestock and poultry. Due to the high body mass of large animals and large population of poultry and other birds, a larger quantity of vaccines is needed continuously. It increases the production costs of vaccines for these animals. Under high biomass production ability, plants represent promising biofactory with added advantages of pathogen-free production of desired proteins in bulk quantities. Hence, plant-based transient, as well as stable expression systems, have been exceedingly applied to express immunogenic proteins. We have been using various plants like soybean and Trifolium to produce edible vaccines for poultry and livestock, respectively. Here we have reviewed various types of vaccines with a special focus on their plant-based expression with examples of Infectious Bursal Disease (IBD), New Castle Disease (ND), and Foot and Mouth Disease (FMD).