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Jul 2024
Saiki MasatoshiCorresponding author
Amyloid fibrils, which are caused by abnormal conformation and the mis-assembly of proteins, are responsible for several conformational diseases, including prion diseases. To develop methods to prevent amyloid formation, blocking peptides with hydrophilic substitutions covering the stem forming regions of barnase 1-24 were prepared and examined for their ability to block amyloid-forming fragments—prion, Amyloid β, Pmel 17—. When these fragments were mixed with the synthetic blocking peptides, the result was a decline in the intensity of fluorescence, suggesting that amyloid formation was inhibited. Therefore, amyloidogenesis appears to be specifically inhibited by disrupting the hydrophobic interactions between core amyloid regions.
Oct 2024 DOI 10.14302/issn.2688-5328.ijp-24-5319
Puri NivritiCorresponding author
Chronic pain affects over 30% of the global population, and reliance on external drugs for treatment has led to major issues, including the present opioid epidemic. A healthier option is necessary, which is why music therapy’s analgesic effects have been extensively studied within the last 20 years. Not only is music relatively harmless but given that chronic pain patients require repeated treatment, musical intervention is far more accessible and economical. While the mechanisms underlying music-induced analgesia are relatively unclear, the production of endogenous opioids while listening to music through both the descending pain modulatory circuit and the limbic system, is postulated to play this role. This review describes the brain regions and pathways by which music may trigger the release of endogenous opioids such as enkephalins, endorphins, and dynorphins. More importantly, it discusses the cellular mechanisms through which these neuropeptides are thought to mediate pleasure-induced analgesia in chronic pain patients.
Apr 2024
Ma YongCorresponding author
A procedure has been developed for synthesizing peptides in an aqueous solution with a reusable solid phase. Specifically designed linker molecule is employed to attach peptides to hydrophilic solid phases, enabling Solid Phase Peptide Synthesis (SPPS) in aqueous solutions. The linker molecule is utilized to connect peptides to an anionic exchange resin during peptide synthesis in an aqueous solution. The general structure of the linker molecule is Fmoc-AA-CH2-Ph-Rx-SO3-, the Fmoc (9-fluorenylmethoxycarbonyl) group serves as a protecting group for amino acids. Amino acids (AA) are linked to the solid phase through a structure of Methoxyphenylcarbonyl group, which is cleavable under strong acidic conditions. The sulfate group is present for forming an ionic bond with the solid resin in an aqueous solution. In this procedure, Fmoc-AA are utilized as building blocks for sequentially adding amino acids in peptide synthesis. Due to Fmoc-AA poor solubility in aqueous solutions, a procedure was developed to enhance the solubility of hydrophobic compounds, with a specific emphasis on dissolving Fmoc-protected Amino Acids (Fmoc-AA) in an aqueous solution. This enhancement facilitates SPPS in aqueous conditions with Fmoc-AA as building blocks. Cationic exchange resin, which is reusable, serves as the solid phase. Our research objective is to shift from the use of organic solvents to an aqueous system while maintaining the existing SPPS practices in organic solvents as closely as possible. This transition involves minimal alterations, maintaining consistency with the organic solvent system, except for the utilization of novel peptide linker molecule to hydrophilic solid resins that are commercially available. This approach is designed to facilitate a more readily acceptable transition for the peptide synthesis industry from using organic solvents to aqueous solution, contributing to greener and more sustainable synthetic methodologies.
Feb 2022
Ahmed Kamal SamiaCorresponding author
Professor Dr. Virology department, Animal Health Research Institute, Egypt
Cancer cells need strong drug to be eliminated. Cancer lesions cure could achieve by topical application of crude bee venom. Bee venom medication used to prevent malignancies in groups most at risk (predisposing factors). Bee venom crosses the blood brain barriers because its components are very small. However, Bee venom contraindicated administered by intravenous injection because it’s hemolytic substance, mellitin which is powerful anticoagulant. However, the cationic peptides mellitin govern the mode of action of bee venom as anticancer and antiviral in vivo; 1 there is a negative charge on cancer cells, viral infected cells, diseased cells, and generally any cells that contain toxins or damage, and viruses are carrying negative charge even when it is outside the living body. 2Bee venom component (melittin) carries a positive charge, it destruct negatively charged cancer cells. 3 The role that the herpes virus is likely to play in increasing the severity of cancerous diseases, worsen the conditions: herpes viruses are opportunistic viruses that strike the body whose immunity is weakened for any reason. Therefore, the role of herpes virus must be neutralized when you planning to treat a cancer patient. Fortunately, bee venom is a powerful antiviral, and thus we hit three birds with one stone, that is, we kill cancer cells, kill opportunistic viruses, and improve tissue immunity to participate in the fight against cancer and get rid of toxic exudates more efficiently.
Apr 2019 DOI 10.14302/issn.2641-9181.ijnr-19-2771
Ozcelik FatihCorresponding author
University of Health Sciences, Faculty of Medicine, Department of Medical Biochemistry, Istanbul, Turkey
In literature, it has been reported that adrenomedullin, which is generally thought to have vasodilator, natriuretic and diuretic effects, is synthesized in almost all body, especially CNS, vascular muscles and endothelium, heart, liver, lung, kidney, gastric mocosa, intestinal endothelium and various blood cells. It has been found that the possible effects of adrenomedullin can be demonstrated directly or indirectly by means of active mediators, neuropeptides, enzymes and hormones. It is also suggested that it regulates the endocrine system by affecting the hypothalamic-pituitary axis. It increases in heart failure, acute coronary syndromes, hypertensive conditions, cerebrovascular accessory, chronic renal failure and periodontitis and decreases in peptic ulcer and intestinal diseases. However, it is still not clear whether increase/decrease in adrenomedullin level is a cause of a disease or is a result of damage due to an illness. This peptide, which could be thought to multifunctional, should be considered as a molecule with genetic coding that may have different effects on different tissues and conditions. For all these reasons, we aimed to review the multifonctional behavior of adrenemedullin in the light of the current literature to pioneer new hypotheses and discuss possible mechanisms.
Jan 2019 DOI 10.14302/issn.2643-0282.imsj-18-2448
Santiago Freitas e Silva KleberCorresponding author
Biological Sciences Institute, Federal University of Goiás, Brazil
Fungal infections increased substantially in the last years, becoming a relevant public health problem. Many of these infections account for high rates of morbidity and mortality. The emergence of resistant fungal clinical isolates have also motivate studies to find new antifungal therapies. Candida albicans is an oportunistic pathogen and affects a great number of immunocompromised patients worldwide. The marine ecosystem has been considered a rich source of bioactive metabolites due to the complexity and originality of its structures. Proteins and peptides from marine organisms have been shown to have antiviral, anti-inflammatory, antimalarial, anticancer, antimicrobial and antifungal properties. Arenicins are antimicrobial peptides isolated from the marine lugworm Arenicola marina with 21 amino acid residues in a β-hairpin structure. Dihydrofolate reductase, exo-b-(1,3)-glucanase and sterol 14α-demethylase are essential C. albincas enzymes that take part in DNA, cell wall and membrane metabolism, respectively. The present study evaluates the interaction of arenicin with important enzymes of C. albicans related to cell wall, ergosterol and DNA metabolism in order to elucidate possible molecular targets. We showed through an in silico approach, that a single compound from a marine worm (A. marina), can bind to three C. albicans essential proteins. The interaction occurs in regions inside the active site or at least near, with amino acid residues evaluated as hot spots. Arenicin is a new promising antifugal drug. The next step is to investigate protein-protein interactions performed by DHFR, EBG and CYP51 and assess whether arenicin is able to disrupt essential interaction or not.
Aug 2018
Paranina AlinaCorresponding author
Department of physical geography and environmental management, Herzen State Pedagogical University of Russia, Russia
Journal of Biosemiotic Research is a new periodical devoted to a young, actively developing science. A review of recent scientific publications shows that in the broad scientific space of biosemiotics contemporary questions and "eternal themes" interact, not finding an answer in the private sciences - anthropology, semiotics of culture and philosophy1,2. To solve them, the fundamental foundations of science and new achievements, the opportunities of the latest technologies and scientific communications are attracted. Like all young sciences, biosemiotics has many definitions. We give here the most famous ones. "Biosemiotics: (bios, life + semion = sign) is an interdisciplinary field of theoretical and empirical research, analyzing communication and signification in living systems. Signed processes, ranging from molecular to ecological and evolutionary, have been studied throughout the history of biology; however, very often descriptions of information and communication aspects of living systems were considered only metaphorical, believing that the essence of them can be understood with the help of physical and chemical descriptions. In biosemiotics, on the other hand, information sign processes are considered as the primordial, basic system of phenomena of life, requiring a new understanding..."3. "Biosemiotics explores sign systems of various levels: molecular biological (genetic code), intracellular (signal peptides), intercellular (mediators, immune interactions), intraorganism (hormones, conditioned reflex reactions) and interorganism (telergons, pheromones, attractants) ... In addition, biosemiotics covers all the problems associated with the problem of the existence of language and thinking in animals." However, today we can go further and add to the analysis the next stage of evolution, standing between animals and modern human (Homo sapiens sapiens).
Apr 2018 DOI 10.14302/issn.2326-0793.jpgr-18-2004
Anwar PervezCorresponding author
Department of Biochemistry and molecular Biology, University of Gujrat Sialkot subcampus, Pakistan
Human proteome project was revolutionized about 40 years ago with purpose of summarizing whole proteomic data at one place. It was launched after human genome project to map and observe all proteins. The goal related proteomic study is to draft the entire human proteome in disease diagnosis by using bioinformatics tools. Pillars of human proteome project provide different databases related to proteins at transcriptional and translational level. Human proteome organization(HUPO) published biology disease HUPO whose aim is to measure protein and proteome by life and processes related to human diseases. Different human organ like plasma, liver, brain and diabetic base project are used to characterize human disease and health. Major data resources accumulated in databases like peptides Atlas, GPMDB and neXtProt for proteins. Matrices of human proteome project identify and characterize the protein products as Post translational modification (PTM), splice various isoforms from 20,300 proteins. Matrices related to different years make proteomes counterpart by magnify the research biomedical community with high output of instruments and specimen pre-analytical protocols. CALIPHO multidisciplinary group provides information about protein complexities, interactions, function and structure complexities after Uniport and Swissprot. Different bioinformatics tools are used for structural and functional annotations of protein, disease diagnosis and mutations due to protein. Extensive study of human proteome project has been proved helpful in disease treatment at translational and post- translational levels. In future, human proteome project along with bioinformatics will include protein profiling, biomarkers, Mass spectrophotometer technique and cross analysis of different proteome projects.
Mar 2018
Liu XiaopingCorresponding author
School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China
An important use of proteomics data from Mass Spectrometry (MS) is the classification of tumor types with respect to peptides in specific cancer types. It is highly critical to find an optimal set of markers among specific cancer peptides whose expression can be clinically utilized to build assays for the diagnosis or to track the progression of specific cancer types. A number of feature selection algorithms have been proposed to obtain the classification of MS data. In this article, we proposed an improved feature selection algorithm based on feature weighting. Relief algorithm can calculate the weight of different features according to the correlation between their characteristics and categories. F-score is a simple filter-based feature selection method by evaluating how two sets of real numbers discriminate from each other. The main goal of this paper is to introduce a new feature weighting selection algorithm combining score from f-value and weight from relief, which is more accurate when classifying high-resolution MALDI-TOF (matrix-assisted laser desorption and ionization time-of-flight) MS data. We have developed a four-step strategy for data processing based on: (1) Align the study sets by binning of raw MS data, (2) local maximum search(LMS) peak detection, (3) a new combination feature weighting selection algorithm and (4) support vector machines achieve a satisfactory performance of identifying cancer and the healthy. The best parameter set for LMS were achieved with control variable method, which achieve an average accuracy of 97.4167% (sd = 0.0146) and the best accuracy of 98.6111% in 1000 independent 10 -fold cross validations.
Jul 2017 DOI 10.14302/issn.2326-0793.JPGR-17-1571
C. P. Figueiredo HenriqueCorresponding author
AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Belo Horizonte, Brazil
Perkinsus marinus is an intracellular parasitic protozoan that is responsible for serious disease epizootics in marine bivalve mollusks worldwide. Despite all available information on P. marinus genomics, more baseline data is required at the proteomic level. Our aim was to study the proteome profile of in vitro cultured P. marinus isolated from oysters Crassostrea spp. using a label-free shotgun UDMSE approach. A total of 4073 non-redundant proteins were identified across three biological replicates with stringent identification. Proteins specifically related to adaptive survival, cell recognition, antioxidants, regulation of apoptosis and others were detected. Important virulence factors of P. marinus were identified including serine protease and iron-dependent superoxide dismutase. Other proteins with involvement in several pathogens invasion strategies were rhoptries, serine-threonine kinases, and protein phosphatases. Interestingly, peptides corresponding to retroviruses polyproteins were identified in all replicates. The interactomic analysis of P. marinus proteins demonstrated extensive clusters network related to biological processes. In conclusion, we provide the first comprehensive proteomic profile of P. marinus that can be useful for further investigations on Perkinsus biology and virulence mechanisms.
Jul 2013 DOI 10.14302/issn.2326-0793.jpgr-13-252
I. Chen EmilyCorresponding author
Stony Brook University, Proteomics Center, School Of Medicine, NY
In biomedical research the use of mammalian tissues is crucial to increase our understanding of complex human diseases. Mass spectrometry-based proteomic approach has become the most powerful tool of studying large-scale protein expression profiles in mammalian tissues. To perform global proteome analysis quantification of mammalian tissues, we generated 15N SILAC mice to obtain tissue-matched labeled peptide libraries for mass spectrometry-based quantitative proteomic analysis. We developed a new labeling protocol to circumvent adverse effects of introducing 15N labeled diet to mice, and showed that the new labeling scheme has no significant effect on the fertility and reproduction of C57/BL6 mice. Using labeled tissues from these mice, we compared the reproducibility of mass spectrometry-based quantification with or without 15N labeled internal standards among biological replicates of young and old brains. We found that labeled-based quantification is less susceptible to variations from instrument conditions and produces more consistent quantifications among biological replicates than label-free quantification. Lastly, we showed that over 60% of peptides from the human brain are quantifiable with internal standards from 15N labeled mouse brain and therefore present a promising alternative of quantifying human tissues that do not have existing cell lines available for SILAC labeling.
Jan 2013 DOI 10.14302/issn.2328-0182.japst-12-145
Parhi RabinarayanCorresponding author
GITAM Institute of Pharmacy, GITAM University, Gandhi Nagar Campus, Rushikonda, Visakhapatnam-530045, Andhra Pradesh, India
The challenges ever faced by pharmaceutical industry is mainly due to discovery of new drugs and development of new technologies. Supercritical fluid (SCF) technology is one such technique, which has become an important tool in the production of different particulate systems along with extraction and drying of protein and peptides during last couple of decade because of its specific properties such as flexibility in use, reduced environmental concern and its simplicity. In this review, we briefly describe the operating principles and parameters influencing each one of SCF processes along with their merits and perspectives. The application of SCF technology in pharmaceutical industry, including particle and crystal engineering, composite particles’ preparation, coating of solid dosage form, liposome preparation, extraction and protein and peptide drying are discussed.