Current Protein and Peptide Science - Volume 18, Issue 9, 2017

Background: In the search of bioactive molecules, nature has always been an important source and most of the drugs in clinic are either natural products or derived from natural products. The ocean has played significant role as thousands of molecules and their metabolites with different types of biological activity such as antimicrobial, anti-inflammatory, anti-malarial, antioxidant, anti HIV and anticancer activity have been isolated from marine organisms. In particular, marine peptides have attracted much attention due to their high specificity against cancer cell lines that may be attributed to the various unusual amino acid residues and their sequences in the peptide chain. This review aims to identify the various anticancer agents isolated from the marine system and their anticancer potential. Method: We did literature search for the anticancer peptides isolated from the different types of microorganism found in the marine system. Total one eighty eight papers were reviewed concisely and most of the important information from these papers were extracted and kept in the present manuscript. Results: This review gives details about the isolation, anticancer potential and mechanism of action of the anticancer peptides of the marine origin. Many of these molecules such as aplidine, dolastatin 10, didemnin B, kahalalide F, elisidepsin (PM02734) are in clinical trials for the treatment of various cancers. Conclusion: With the interdisciplinary and collaborative research and technical advancements we can search more promising and affordable anticancer drugs in future.

Background: Recent advances in proteomics methodologies allow for high throughput profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights in the underlying macromolecular recognition events, as determinants of biomolecular specificity identified by proteomics approaches may be compared to structure-based analysis of corresponding protein-protein interfaces. Method: Here, we present an overview of experimental and computational methodologies and tools applied in the area and provide an outlook beyond the protein class of proteases. Results and Conclusion: We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.

Background: In the past few decades, with the upsurge of various deadly diseases, development of accurate diagnostic methods is inevitable for maintaining good health. There is an urgent requirement of specific and sensitive biomarkers in order to improve diagnosis, guide molecular targeted therapy, and predict and examine therapeutic response across a wide spectrum of disease. Method: We undertook a structured search of bibliographic databases for peer-reviewed research literature to evaluate the significance of peptides as valuable tools for diagnostic applications as well as the techniques used for discovery of peptide biomarkers. Result: On the basis of extensive literature survey, peptide biomarkers are classified according to their diagnosis approach. In addition, we summarize a few techniques used in peptide biomarker discovery such as peptidomics and peptide microarray. Conclusion: Small size, stability, easy and inexpensive production, capability to migrate throughout the body, fast clearance from body and low immunogenicity, as well as the remarkable quality of peptides to mirror the change in protease expression or activation associated with a pathological process, have established them as a promising biomarker.

Background: Amyloid fibrils, which are implicated in several diseases, are highly ordered structures formed by aggregation of proteins. Intriguingly, several short peptides, some of which are unrelated to the disease-causing proteins, also aggregate to form amyloid fibrils in vitro. The aggregation behavior of these short peptides can be modulated so that they form nanostructures that are not in any way related to amyloid fibrils. These observations have led to extensive research aimed at getting insights into how peptides aggregate to form amyloids as well as non-amyloidogenic structures. Methods: This review examines the aggregation behavior of peptides that form highly polymorphic structures including fibrils, nanotubes, nanospheres and hydrogels. The review also describes how short peptides composed of only two and three hydrophobic and aromatic amino acids can selfassemble to form nanotubes and nanospheres. Results: Peptides with widely varying amino acid composition and lengths aggregate to form indistinguishable fibrils and nanostructures. The potential application of these aggregated structures in the design of novel biomaterials is reviewed and highlighted. Conclusion: It is evident that highly polymorphic aggregated structures of peptides can be obtained by varying conditions such as solvent of dissolution, temperatures, pH and even surfaces of deposition.

Background: Accurate and swift detection of viruses causing diseases in humans represent continuous challenges to diagnostic and epidemiological research. Efficient and rapid diagnosis is crucial for effective implication of disease management strategies. Multitude approaches attempted to identify individual viruses, includes serological assays and molecular methods. Detection assays based on peptides have become increasingly substantial and indispensable for its advantages over conventional methods. Methods: We have primarily outlined the progress made in peptide based diagnostic systems for the commonly found viral infections in India - Influenza virus, Chikungunya virus, Dengue virus, Rotavirus, Japanese encephalitis virus (JEV), Epstein-Barr virus (EBV), Human Immunodeficiency virus (HIV) and Hepatitis C virus (HCV). Further, we have documented the recent advancements that could impact the upcoming developments of peptide based diagnostic assays. Results: In this review we identified that very few studies in development of peptide based assays for viral infections has been reported. In a country specific scenario like India and its burdened health care system, sensitive and rapid diagnostic kits based on peptides could be considered as a better alternative to the conventional serological tests including whole antigenic proteins. Conclusion: The finding of this review uncovers the importance of a peptide based diagnostic system for rapid detection of viral infections. Even though, in recent times, peptide based assays have intrigued researchers, further work in this domain is entailed.

Background: Chemical crosslinking refers to intermolecular or intramolecular joining of two or more molecules by a covalent bond. The reagents that are used for the purpose are referred to as ‘crosslinking reagents’ or ‘crosslinkers’. Based on factors like reactivity and spacer length these are classified into different types, each having its own specific function and application. In recent times, chemical crosslinking has emerged as an efficient tool for the study of biomolecules like proteins. It finds its application in various studies including the attachment of proteins to a solid support for the study of membrane receptors, protein-protein complexes, protein-DNA complexes, and others. When coupled with techniques like mass spectroscopy, it has been used not only for the determination of three dimensional structures of proteins but also for the study of protein-protein interactions and determination of interesting sites. This combination of mass spectrometry techniques and bioinformatics, added yet another dimension to our present day understanding of protein chemistry. Thus, chemical crosslinking has multitude uses that it can be put to. Methods: We undertook a systematic search of bibliographic databases and search engine such as Google Scholar, Scifinder, Scopus, Mendeley etc for review of research literature. We excluded research paper which only reported synthesis of crosslinker molecules and did not involve any mass spectrometry studies. Results: Sixty-four papers were included in the review. The majority of references were taken from last ten years as there has been an immense progress in this area in the recent years. Eleven classical papers in this field were included which talk about basic of this methodology. Thirty-two papers discussed about various types of organic groups used for designing chemical cross-linkers and various methodologies which were used to enhance the crosslinking efficiency. These papers also highlight various strategies used to enhance detection of cross-linked proteins and various computer software used to detect cross-linking sites from mass data. Twenty-one papers showed the proof concept application of this methodology to detect protein crosslinking in-vivo and in-vitro. Conclusion: The findings of this review confirm the importance chemical crosslinking combined with mass spectroscopy as a low cost alternative to understand protein-protein interaction. The information generated by this methodology can help in better understating of various diseases and for the development of better drugs for them.

The structure and function of proteins involved in plant-microbe interactions is investigated through large-scale proteomics technology in a complex biological sample. Since the whole genome sequences are now available for several plant species and microbes, proteomics study has become easier, accurate and huge amount of data can be generated and analyzed during plant-microbe interactions. Proteomics approaches are highly important and relevant in many studies and showed that only genomics approaches are not sufficient enough as much significant information are lost as the proteins and not the genes coding them are final product that is responsible for the observed phenotype. Novel approaches in proteomics are developing continuously enabling the study of the various aspects in arrangements and configuration of proteins and its functions. Its application is becoming more common and frequently used in plant-microbe interactions with the advancement in new technologies. They are more used for the portrayal of cell and extracellular destructiveness and pathogenicity variables delivered by pathogens. This distinguishes the protein level adjustments in host plants when infected with pathogens and advantageous partners. This review provides a brief overview of different proteomics technology which is currently available followed by their exploitation to study the plant-microbe interaction.

Inulinase has attracted attention due to their number of applications in various industries viz. pharmaceuticals, food and bioethanol. Enzymes due to their unique properties and enormous power of catalysis at very wide range of temperature are always in demand in industries. There are certain techniques which are employed to improve the productivity of enzymes as well as enhancing their catalytic activity. Modeling of structure of inulinase will provide an overview of the catalytic domain and help in improvising catalytic potential. In the present review we have discussed on the topics of different substrate specificity and statistical optimization methods for the improvement of inulinase production. Recovery of enzyme is a cost effective approach and crucial step in the industrial application of enzyme and can be achieved by different immobilizing techniques. Immobilized inulinases have been widely studied and applied in different bioreactor systems. Kluyveromyces, Aspergillus, Staphylococcus, Xanthomonas, and Pseudomonas are few high level of inulinase producing microorganisms and are commercially employed for production of certain important product. Since inulins are used as prebiotic, it has also great impact in the nutritional biology field. Inulinase in food industries and inulin as probiotic are also discussed.