Current Protein and Peptide Science - Volume 23, Issue 1, 2022

Previously, the application of proteins was uncommon as therapeutically active molecules. Some of the first applications of proteins as drugs have been insulin and vaccines for overcoming a physiological deficiency and the prevention of diseases, respectively. Nowadays, proteins have many applications, not only as drugs but also as drug delivery systems to be administered by different routes. Due to their nature, the behavior of proteins varies while the conditions of the environment are modified. For this reason, it is necessary to study their behavior for predicting the correct manufacturing, storing, or combination with other possible molecules in a formulation or into the body. The application of techniques for predicting the behavior of proteins in different environments has led to associating this type of behavior into the body with the occurrence of diseases, such as celiac disease or Alzheimer's disease. Thus, this work shows an overview of the main types of proteins applied as active therapeutically molecules, proteins-based drug delivery systems, and techniques for predicting their stability into the primary storing container and the body.

Antimicrobial Peptides (AMPs) are small, ribosomally synthesized proteins found in nearly all forms of life. In plants, AMPs play a central role in plant defense due to their distinct physicochemical properties. Due to their broad-spectrum antimicrobial activity and rapid killing action, plant AMPs have become important candidates for the development of new drugs to control plant and animal pathogens that are resistant to multiple drugs. Further research is required to explore the potential uses of these natural compounds. Computational strategies have been increasingly used to understand key aspects of antimicrobial peptides. These strategies will help to minimize the time and cost of “wet-lab” experimentation. Researchers have developed various tools and databases to provide updated information on AMPs. However, despite the increased availability of antimicrobial peptide resources in biological databases, finding AMPs from plants can still be a difficult task. The number of plant AMP sequences in current databases is still small and yet often redundant. To facilitate further characterization of plant AMPs, we have summarized information on the location, distribution, and annotations of plant AMPs available in the most relevant databases for AMPs research. We also mapped and categorized the bioinformatics tools available in these databases. We expect that this will allow researchers to advance in the discovery and development of new plant AMPs with potent biological properties. We hope to provide insights to further expand the application of AMPs in the fields of biotechnology, pharmacy, and agriculture.

Over the past two decades, the advances in the next generation sequencing (NGS) platforms have led to the identification of numerous genes/QTLs at high-resolution for their potential use in crop improvement. The genomic resources generated through these high-throughput sequencing techniques have been efficiently used in screening of particular gene of interest particularly for numerous types of plant stresses and quality traits. Subsequently, the identified-markers linked to particular trait have been used in Marker-Assisted Backcross Breeding (MABB) activities. Besides, these markers are also being used to catalogue the food crops for detection of adulteration to improve the quality of food. With the advancement of technologies, the genomic resources are originating with new markers; however, to use these markers efficiently in crop breeding, High-Throughput Techniques (HTT) such as multiplex PCR and Capillary Electrophoresis (CE) can be exploited. Robustness, ease of operation, good reproducibility and low cost are the main advantages of multiplex PCR and CE. The CE is capable of separating and characterizing proteins with simplicity, speed and small sample requirements. Keeping in view the availability of vast data generated through NGS techniques and development of numerous markers, there is a need to use these resources efficiently in crop improvement programmes. In summary, this review describes the use of molecular markers in the screening of resistance genes in breeding programme and detection of adulterations in food crops using high-throughput techniques.

Background: COVID-19 is a global threat as a result of the incessant spread of SARS-CoV- 2, necessitating the rapid availability of effective antiviral medications to protect our society. For SARSCoV- 2, a group of peptides has already been indicated, although their effectiveness has yet to be shown. SARS-CoV-2 is an enveloped virus with hydrophobic fusion protein and spike glycoproteins. Methods: Here, we have compiled a list of amphiphilic peptides that have been published, as well as their in-silico docking studies with the SARS-CoV-2 spike glycoprotein. Results: The findings demonstrated that spike protein and amphiphilic peptides with increased binding affinity create a complex. It was also observed that PalL1 (ARLPRTMVHPKPAQP), 10AN1 (FWFTLIKTQAKQPARYRRFC), THETA defensin (RCICGRGICRLL), and mucroporin M1 (LFRLIKSLIKRLVSAFK) showed the binding free energy of more than -1000 kcal/mol. Molecular pI and hydrophobicity are also important factors of peptides to enhance the binding affinity with spike protein of SARS-CoV-2. Conclusion: In light of these findings, it is crucial to compare the in-vitro to in-vivo efficacy of amphiphilic peptides in order to produce an efficient anti-SARS-CoV-2 peptide therapy that might assist control the present pandemic scenario.

Background: An extensive study of the folding and stability of proteins and their complexes has revealed a number of problems and questions that need to be answered. One of them is the effect of chaperones on the process of fibrillation of various proteins and peptides. Methods: We studied the effect of molecular chaperones, such as GroEL and α-crystallin, on the fibrillogenesis of the Aβ(1-42) peptide using electron microscopy and surface plasmon resonance. Results: Recombinant GroEL and Aβ(1-42) were isolated and purified. It was shown that the assembly of GroEL occurs without the addition of magnesium and potassium ions, as is commonly believed. According to the electron microscopy results, GroEL insignificantly affects the fibrillogenesis of the Aβ(1-42) peptide, while α-crystallin prevents the elongation of the Aβ(1-42) peptide fibrils. We have demonstrated that GroEL interacts nonspecifically with Aβ(1-42), while α-crystallin does not interact with Aβ(1-42) at all using surface plasmon resonance. Conclusion: The data obtained will help us understand the process of amyloid formation and the effect of various components on it.

Background: The importance of aromaticity vs. hydrophobicity of the central hydrophobic core (CHC, residues 17-20) in governing fibril formation in Aβ(1-42) has been the focus of an ongoing debate in the literature. Introduction: Mutations in the CHC (especially at Phe19 and Phe20) have been used to examine the relative impact of hydrophobicity and aromaticity on the degree of aggregation of Aβ(1-42). However, the results have not been conclusive. Methods: Partial least squares (PLS) modeling of aggregation rates, using reduced properties of a series of position 19 mutants, was employed to identify the physicochemical properties that had the greatest impact on the extent of aggregation. Results: The PLS models indicate that hydrophobicity at position 19 of Aβ(1-42) appears to be the primary and dominant factor in controlling Aβ(1-42) aggregation, with aromaticity having little effect. Conclusion: This study illustrates the value of using reduced properties of amino acids in conjunction with PLS modeling to investigate mutational effects in peptides and proteins, as the reduced properties can capture in a quantitative manner the different physicochemical properties of the amino acid side chains. In this particular study, hydrophobicity at position 19 was determined to be the dominant property controlling aggregation, while size, charge, and aromaticity had little impact.