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Journal articles on the topic 'Protein Based Molecular Diseases'

Author: Grafiati

Published: 7 September 2023

Last updated: 31 July 2025

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1

Li, Yan, Yi Jia, Xiao-Lin Wang, Hai Shang, and Yu Tian. "Protein-Targeted Degradation Agents Based on Natural Products." Pharmaceuticals 16, no. 1 (2022): 46. http://dx.doi.org/10.3390/ph16010046.

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Natural products are an important source of drug lead compounds, and natural products with significant biological activity are constantly being discovered and used in clinical practice. At present, natural products play an important role in the targeted therapy of cancer, cardiovascular and cerebrovascular diseases, nervous system diseases, and autoimmune diseases. Meanwhile, in recent years, the rise of protein-targeted degradation technologies, such as proteolysis-targeting chimeras (PROTACs) and molecular glues, has provided a new solution for drug resistance caused by clinical molecular-ta

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2

Telling, Glenn. "Protein-based PCR for prion diseases?" Nature Medicine 7, no. 7 (2001): 778–79. http://dx.doi.org/10.1038/89895.

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Yadav, Kusum, Anurag Yadav, Priyanka Vashistha, Veda P. Pandey, and Upendra N. Dwivedi. "Protein Misfolding Diseases and Therapeutic Approaches." Current Protein & Peptide Science 20, no. 12 (2019): 1226–45. http://dx.doi.org/10.2174/1389203720666190610092840.

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Protein folding is the process by which a polypeptide chain acquires its functional, native 3D structure. Protein misfolding, on the other hand, is a process in which protein fails to fold into its native functional conformation. This misfolding of proteins may lead to precipitation of a number of serious diseases such as Cystic Fibrosis (CF), Alzheimer’s Disease (AD), Parkinson’s Disease (PD), and Amyotrophic Lateral Sclerosis (ALS) etc. Protein Quality-control (PQC) systems, consisting of molecular chaperones, proteases and regulatory factors, help in protein folding and prevent its aggregat

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Teribele Venturin, Gianina, and Zhen Cheng. "Small Peptide and Protein-based Molecular Probes for Imaging Neurological Diseases." Current Protein & Peptide Science 17, no. 6 (2016): 543–58. http://dx.doi.org/10.2174/1389203717666160101123500.

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Lorenzo-Pouso, Alejandro I., Mario Pérez-Sayáns, Susana B. Bravo, et al. "Protein-Based Salivary Profiles as Novel Biomarkers for Oral Diseases." Disease Markers 2018 (November 7, 2018): 1–22. http://dx.doi.org/10.1155/2018/6141845.

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The Global Burden of Oral Diseases affects 3.5 billion people worldwide, representing the number of people affected by the burden of untreated dental caries, severe periodontal disease, and edentulism. Thus, much more efforts in terms of diagnostics and treatments must be provided in the fight of these outcomes. In this sense, recently, the study of saliva as biological matrix has been identified as a new landmark initiative in the search of novel and useful biomarkers to prevent and diagnose these conditions. Specifically, saliva is a rich reservoir of different proteins and peptides and acce

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Pang, Yihe, and Bin Liu. "DMFpred: Predicting protein disorder molecular functions based on protein cubic language model." PLOS Computational Biology 18, no. 10 (2022): e1010668. http://dx.doi.org/10.1371/journal.pcbi.1010668.

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Intrinsically disordered proteins and regions (IDP/IDRs) are widespread in living organisms and perform various essential molecular functions. These functions are summarized as six general categories, including entropic chain, assembler, scavenger, effector, display site, and chaperone. The alteration of IDP functions is responsible for many human diseases. Therefore, identifying the function of disordered proteins is helpful for the studies of drug target discovery and rational drug design. Experimental identification of the molecular functions of IDP in the wet lab is an expensive and labori

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Kovacs, Gabor G. "Molecular pathology of neurodegenerative diseases: principles and practice." Journal of Clinical Pathology 72, no. 11 (2019): 725–35. http://dx.doi.org/10.1136/jclinpath-2019-205952.

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Neurodegenerative diseases are characterised by selective dysfunction and progressive loss of synapses and neurons associated with pathologically altered proteins that deposit primarily in the human brain and spinal cord. Recent discoveries have identified a spectrum of distinct immunohistochemically and biochemically detectable proteins, which serve as a basis for protein-based disease classification. Diagnostic criteria have been updated and disease staging procedures have been proposed. These are based on novel concepts which recognise that (1) most of these proteins follow a sequential dis

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Chaudhuri, Tapan K., and Subhankar Paul. "Protein-misfolding diseases and chaperone-based therapeutic approaches." FEBS Journal 273, no. 7 (2006): 1331–49. http://dx.doi.org/10.1111/j.1742-4658.2006.05181.x.

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Mishra and Dey. "Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood." Biomolecules 9, no. 11 (2019): 740. http://dx.doi.org/10.3390/biom9110740.

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Natural products from plants, such as chemopreventive agents, attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure-based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide-based therapeutics have been developed to combat

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Gul, Irfan, Amreena Hassan, Ehtishamul Haq, et al. "An Investigation of the Antiviral Potential of Phytocompounds against Avian Infectious Bronchitis Virus through Template-Based Molecular Docking and Molecular Dynamics Simulation Analysis." Viruses 15, no. 4 (2023): 847. http://dx.doi.org/10.3390/v15040847.

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Vaccination is widely used to control Infectious Bronchitis in poultry; however, the limited cross-protection and safety issues associated with these vaccines can lead to vaccination failures. Keeping these limitations in mind, the current study explored the antiviral potential of phytocompounds against the Infectious Bronchitis virus using in silico approaches. A total of 1300 phytocompounds derived from fourteen botanicals were screened for their potential ability to inhibit the main protease, papain-like protease or RNA-dependent RNA–polymerase of the virus. The study identified Methyl Rosm

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Rajesh, Netra Unni, and Anam Qudrat. "Protein Chimera-based Ca2+ Rewiring as a Treatment Modality for Neurodegeneration." Current Psychopharmacology 8, no. 1 (2019): 27–40. http://dx.doi.org/10.2174/2211556007666181001102702.

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Calcium is a versatile signaling molecule; a key regulator of an array of diverse cellular processes ranging from transcription to motility to apoptosis. It plays a critical role in neuronal signal transmission and energy metabolism through specialized mechanisms. Dysregulation of the Ca2+ signaling pathways has been linked to major psychiatric diseases. Here, we focus on molecular psychiatry, exploring the role of calcium signaling in neurological disease development and aggravation, specifically in Alzheimer’s and Huntington’s diseases. Understanding the molecular underpinnings helps us firs

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Suratanee, Apichat, and Kitiporn Plaimas. "Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations." Bioinformatics and Biology Insights 11 (January 1, 2017): 117793221772040. http://dx.doi.org/10.1177/1177932217720405.

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The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse k-nearest neighbor (R kNN) search. The R kNN search was used to identify an impact of a protein on other proteins. Then, associations between proteins and disease

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Ohue, Masahito, Yuki Kojima, and Takatsugu Kosugi. "Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties." Molecules 28, no. 15 (2023): 5652. http://dx.doi.org/10.3390/molecules28155652.

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Protein-protein interactions (PPIs) are associated with various diseases; hence, they are important targets in drug discovery. However, the physicochemical empirical properties of PPI-targeted drugs are distinct from those of conventional small molecule oral pharmaceuticals, which adhere to the ”rule of five (RO5)”. Therefore, developing PPI-targeted drugs using conventional methods, such as molecular generation models, is challenging. In this study, we propose a molecular generation model based on deep reinforcement learning that is specialized for the production of PPI inhibitors. By introdu

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Shi, Haonan. "Molecular Glues and Molecular Glue Degraders: Mechanisms, Design, and Therapeutic Applications." Transactions on Materials, Biotechnology and Life Sciences 7 (December 24, 2024): 213–20. https://doi.org/10.62051/r1m5q711.

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Molecular glues and molecular glue degraders appear to be a fast-growing class of therapeutic agents that selectively modulate protein-protein potential interactions and can enhance the selective degradation of proteins. These small molecules are providing the possibility to target proteins that previously thought to be very challenging or inaccessible that are involved in a host of diseases. The present review focuses on describing the basic concepts of molecular glues and the rationale behind the interactions and the general concept that drives their design. Special attention is paid to thei

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Rochet, Jean-Christophe. "Novel therapeutic strategies for the treatment of protein-misfolding diseases." Expert Reviews in Molecular Medicine 9, no. 17 (2007): 1–34. http://dx.doi.org/10.1017/s1462399407000385.

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Most proteins in the cell adopt a compact, globular fold that determines their stability and function. Partial protein unfolding under conditions of cellular stress results in the exposure of hydrophobic regions normally buried in the interior of the native structure. Interactions involving the exposed hydrophobic surfaces of misfolded protein conformers lead to the formation of toxic aggregates, including oligomers, protofibrils and amyloid fibrils. A significant number of human disorders (e.g. Alzheimer disease, Parkinson disease, Huntington disease, amyotrophic lateral sclerosis and type II

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Kumari, Uma, Manaswinee Bora, and MN Akshaya. "Homology Modeling and Structure Based Drug Design for Human Gastric Cancer." International Journal for Research in Applied Science and Engineering Technology 11, no. 10 (2023): 1106–14. http://dx.doi.org/10.22214/ijraset.2023.56165.

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Abstract: This research article delves into the multifaceted world of structural biology and bioinformatics, exploring a diverse array of tools and resources employed to decipher the intricacies of proteins and their implications in health and disease. The paper navigates through various computational tools and databases used for sequence analysis, structural analysis, mutation site detection, and molecular docking, shedding light on their individual contributions in unraveling the secrets of proteins. COBALT serves as the initial compass, guiding researchers in the alignment of protein sequen

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Nguyen, Thanh-Phuong, Laura Caberlotto, Melissa J. Morine, and Corrado Priami. "Network Analysis of Neurodegenerative Disease Highlights a Role of Toll-Like Receptor Signaling." BioMed Research International 2014 (2014): 1–16. http://dx.doi.org/10.1155/2014/686505.

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Despite significant advances in the study of the molecular mechanisms altered in the development and progression of neurodegenerative diseases (NDs), the etiology is still enigmatic and the distinctions between diseases are not always entirely clear. We present an efficient computational method based on protein-protein interaction network (PPI) to model the functional network of NDs. The aim of this work is fourfold: (i) reconstruction of a PPI network relating to the NDs, (ii) construction of an association network between diseases based on proximity in the disease PPI network, (iii) quantifi

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Ramly, Balqis, Nor Afiqah-Aleng, and Zeti-Azura Mohamed-Hussein. "Protein–Protein Interaction Network Analysis Reveals Several Diseases Highly Associated with Polycystic Ovarian Syndrome." International Journal of Molecular Sciences 20, no. 12 (2019): 2959. http://dx.doi.org/10.3390/ijms20122959.

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Based on clinical observations, women with polycystic ovarian syndrome (PCOS) are prone to developing several other diseases, such as metabolic and cardiovascular diseases. However, the molecular association between PCOS and these diseases remains poorly understood. Recent studies showed that the information from protein–protein interaction (PPI) network analysis are useful in understanding the disease association in detail. This study utilized this approach to deepen the knowledge on the association between PCOS and other diseases. A PPI network for PCOS was constructed using PCOS-related pro

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19

Peng, Yunhui, Emil Alexov, and Sankar Basu. "Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases." International Journal of Molecular Sciences 20, no. 3 (2019): 548. http://dx.doi.org/10.3390/ijms20030548.

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Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations—whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context in which it occurs. Such information may positively aid drug-design. Furthermore, due to the int

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20

Bastos, Paulo, Antónia Vlahou, Adelino Leite-Moreira, Lúcio Lara-Santos, Rita Ferreira, and Rui Vitorino. "Deciphering the disease-related molecular networks using urine proteomics." Trends in Analytical Chemistry 94 (September 1, 2017): 200–209. https://doi.org/10.1016/j.trac.2017.07.018.

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Despite the large number of studies focused on the impact of diseases on urine proteome, few outputs with clinical meaning were retrieved so far. The goal of this study was to identify the biological processes modulated in urine by distinct diseases to better understand disease pathogenesis and to identify urinary proteins with potential diagnosis value. We searched PubMed and SCOPUS databases for mass spectrometry- based experimental papers and pooled differentially expressed proteins by disease and targetorganic system. A total of 2572 differentially expressed proteins or peptides were poole

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Al-Suhaimi, Ebtesam, Vijaya Ravinayagam, B. Rabindran Jermy, Tarhini Mohamad, and Abdelhamid Elaissari. "Protein/ Hormone Based Nanoparticles as Carriers for Drugs Targeting Protein-Protein Interactions." Current Topics in Medicinal Chemistry 19, no. 6 (2019): 444–56. http://dx.doi.org/10.2174/1568026619666190304152320.

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Background: In this review, protein-protein interactions (PPIs) were defined, and their behaviors in normal in disease conditions are discussed. Their status at nuclear, molecular and cellular level was underscored, as for their interference in many diseases. Finally, the use of protein nanoscale structures as possible carriers for drugs targeting PPIs was highlighted. Objective: The objective of this review is to suggest a novel approach for targeting PPIs. By using protein nanospheres and nanocapsules, a promising field of study can be emerged. Methods: To solidify this argument, PPIs and th

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22

Zhao, Jian-Hua, Hsuan-Liang Liu, Hsin-Yi Lin, et al. "Chemical Chaperone and Inhibitor Discovery: Potential Treatments for Protein Conformational Diseases." Perspectives in Medicinal Chemistry 1 (January 2007): PMC.S212. http://dx.doi.org/10.4137/pmc.s212.

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Protein misfolding and aggregation cause a large number of neurodegenerative diseases in humans due to (i) gain of function as observed in Alzheimer's disease, Huntington's disease, Parkinson's disease, and Prion's disease or (ii) loss of function as observed in cystic fibrosis and α1-antitrypsin deficiency. These misfolded proteins could either lead to the formation of harmful amyloids that become toxic for the cells or to be recognized and prematurely degraded by the protein quality control system. An increasing number of studies has indicated that some low-molecular-weight compounds named a

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23

Yang, Qiya, Xi Zhang, Dhanasekaran Solairaj, Rouling Lin, Kaili Wang, and Hongyin Zhang. "TMT-Based Proteomic Analysis of Hannaella sinensis-Induced Apple Resistance-Related Proteins." Foods 12, no. 14 (2023): 2637. http://dx.doi.org/10.3390/foods12142637.

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Studies on the molecular mechanism of antagonistic yeasts to control apple postharvest diseases are not comprehensive enough. Our preliminary investigations screened the biocontrol effect of Hannaella sinensis, an antagonistic yeast, and discovered its control efficacy on apple blue mold decay. However, the molecular mechanism of H. sinensis-induced resistance in apple has not been studied. In this study, proteins from apple treated with H. sinensis and sterile saline were analyzed using TMT proteomics technology. It was found that H. sinensis treatment induced the expressions of apple resista

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Le, Vu Anh, Cam Quyen Thi Phan, and Thuy Huong Nguyen. "Data mining in mass spectrometry-based proteomics studies." Science & Technology Development Journal - Engineering and Technology 2, no. 4 (2020): 258–76. http://dx.doi.org/10.32508/stdjet.v2i4.483.

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The post-genomic era consists of experimental and computational efforts to meet the challenge of clarifying and understanding the function of genes and their products. Proteomic studies play a key role in this endeavour by complementing other functional genomics approaches, encompasses the large-scale analysis of complex mixtures, including the identification and quantification of proteins expressed under different conditions, the determination of their properties, modifications and functions. Understanding how biological processes are regulated at the protein level is crucial to understanding

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Tang, Yi-Wei, Gary W. Procop, and David H. Persing. "Molecular diagnostics of infectious diseases." Clinical Chemistry 43, no. 11 (1997): 2021–38. http://dx.doi.org/10.1093/clinchem/43.11.2021.

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Abstract Over the past several years, the development and application of molecular diagnostic techniques has initiated a revolution in the diagnosis and monitoring of infectious diseases. Microbial phenotypic characteristics, such as protein, bacteriophage, and chromatographic profiles, as well as biotyping and susceptibility testing, are used in most routine laboratories for identification and differentiation. Nucleic acid techniques, such as plasmid profiling, various methods for generating restriction fragment length polymorphisms, and the polymerase chain reaction (PCR), are making increas

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Sitkov, N. O., T. M. Zimina, V. V. Luchinin, et al. "Hybrid-Integrated Biosensor for Express Determination of Protein Markers of Diseases based on Molecular Recognition and Direct Fluorimetric Detection." Nano- i Mikrosistemnaya Tehnika 23, no. 6 (2021): 326–32. http://dx.doi.org/10.17587/nmst.23.326-332.

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Ways of creating new generation biosensors for multiparametric express diagnostics based on molecular recognition and direct fluorimetric registration of a peptide aptamer — protein marker complex were considered. The biosensor platform comprises a microfluidic channel for delivery sample solutions, coupled with flow-through zones containing covalently attached arrays of peptide probes — aptamers. An outer glass window of the biochip assembly contains a layer of luminophore ZnS:Cu, bound on it via an acrylic lacquer and intended for the re-emitting native fluorescence of bound proteins into th

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Wang, Li, and Nanbert Zhong. "Application of the ProteomeLab™ PF2D protein fractionation system in proteomic analysis for human genetic diseases." Open Chemistry 10, no. 3 (2012): 836–43. http://dx.doi.org/10.2478/s11532-012-0033-2.

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AbstractProteomic analysis has been widely used in elucidating the mechanism of diseases. As a classical proteomic approach, two-dimensional gel electrophoresis (2DGE) has been commonly applied in finding differentially expressed proteins through a first dimension of separation by the isoelectric point (pI) of proteins and a second dimension of separation according to the molecular weight (MW) of proteins. Compared to 2DGE, a recently developed commercial system from Beckman Coulter, the two-dimensional protein fractionation (PF2D), separates proteins according to the pI of proteins in the fir

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Xiao, Hanyu, Yijin Zou, Jieqiong Wang, and Shibiao Wan. "A Review for Artificial Intelligence Based Protein Subcellular Localization." Biomolecules 14, no. 4 (2024): 409. http://dx.doi.org/10.3390/biom14040409.

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Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer’s disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencin

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Singh, Om V. "Protein-misfolding diseases and the paradigm of proteomics-based therapeutic targets." Expert Review of Proteomics 7, no. 4 (2010): 463–64. http://dx.doi.org/10.1586/epr.10.71.

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Lindquist, Susan, Sylvia Krobitsch, Liming Li, and Neal Sondheimer. "Investigating protein conformation–based inheritance and disease in yeast." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 356, no. 1406 (2001): 169–76. http://dx.doi.org/10.1098/rstb.2000.0762.

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Our work supports the hypothesis that a protein can serve as an element of genetic inheritance. This protein–only mechanism of inheritance is propagated in much the same way as hypothesized for the transmission of the protein–only infectious agent in the spongiform encephalopathies; hence these protein factors have been called yeast prions. Our work has focused on [ PSI + ], a dominant cytoplasmically inherited factor that alters translational fidelity.This change in translation is produced by a self–perpetuating change in the conformation of the translation–termination factor, Sup35. Most rec

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Nevzglyadova, O. V., E. V. Mikhailova, and T. R. Soidla. "Molecular Mechanisms Underlying Alzheimer’s and Parkinson’s Diseases and the Potential Possibility of their Neutralization." Цитология 65, no. 4 (2023): 323–38. http://dx.doi.org/10.31857/s0041377123040090.

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Different protein forms inevitably load up in the cell under the influence of external and internal factors. With aging, the activity of chaperones and other components of the cell protein quality control machinery decreases. This results in accumulation of misfolded proteins with altered conformation. The most drastic alteration is the conversion of the active soluble molecules to the insoluble and inactive amyloid. Such a conformation shift of proteins is considered to lie behind the neurodegeneration process. A number of studies are devoted to neurodegeneration, but many details of the proc

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Gadhave, Kundlik, Prateek Kumar, Shivani Kapuganti, Vladimir Uversky, and Rajanish Giri. "Unstructured Biology of Proteins from Ubiquitin-Proteasome System: Roles in Cancer and Neurodegenerative Diseases." Biomolecules 10, no. 5 (2020): 796. http://dx.doi.org/10.3390/biom10050796.

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The 26S proteasome is a large (~2.5 MDa) protein complex consisting of at least 33 different subunits and many other components, which form the ubiquitin proteasomal system (UPS), an ATP-dependent protein degradation system in the cell. UPS serves as an essential component of the cellular protein surveillance machinery, and its dysfunction leads to cancer, neurodegenerative and immunological disorders. Importantly, the functions and regulations of proteins are governed by the combination of ordered regions, intrinsically disordered protein regions (IDPRs) and molecular recognition features (Mo

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Chen, Mingzhu, Yizi Zhu, Huajun Li, Yubo Zhang, and Mei Han. "A Quantitative Proteomic Approach Explores the Possible Mechanisms by Which the Small Molecule Stemazole Promotes the Survival of Human Neural Stem Cells." Brain Sciences 12, no. 6 (2022): 690. http://dx.doi.org/10.3390/brainsci12060690.

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Neurodegenerative disorders have become a serious healthcare problem worldwide and there is no efficacious cure. However, regulating the fate of stem cells is an effective way to treat these neurological diseases. In previous work, stemazole was reported to maintain the survival of human neural stem cells in the absence of growth factors and to have therapeutic effects on neurodegenerative diseases. However, although it is a promising small molecule, the molecular mechanisms against apoptosis are ambiguous. In this study, tandem mass tag (TMT)-based proteomics were performed to obtain whole pr

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Huang, Zhaohong, Xinyue Cui, Yuhao Xia, Kailong Zhao, and Guijun Zhang. "Pathfinder: Protein folding pathway prediction based on conformational sampling." PLOS Computational Biology 19, no. 9 (2023): e1011438. http://dx.doi.org/10.1371/journal.pcbi.1011438.

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The study of protein folding mechanism is a challenge in molecular biology, which is of great significance for revealing the movement rules of biological macromolecules, understanding the pathogenic mechanism of folding diseases, and designing protein engineering materials. Based on the hypothesis that the conformational sampling trajectory contain the information of folding pathway, we propose a protein folding pathway prediction algorithm named Pathfinder. Firstly, Pathfinder performs large-scale sampling of the conformational space and clusters the decoys obtained in the sampling. The heter

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Rao, V. Srinivasa, K. Srinivas, G. N. Sujini, and G. N. Sunand Kumar. "Protein-Protein Interaction Detection: Methods and Analysis." International Journal of Proteomics 2014 (February 17, 2014): 1–12. http://dx.doi.org/10.1155/2014/147648.

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Protein-protein interaction plays key role in predicting the protein function of target protein and drug ability of molecules. The majority of genes and proteins realize resulting phenotype functions as a set of interactions. The in vitro and in vivo methods like affinity purification, Y2H (yeast 2 hybrid), TAP (tandem affinity purification), and so forth have their own limitations like cost, time, and so forth, and the resultant data sets are noisy and have more false positives to annotate the function of drug molecules. Thus, in silico methods which include sequence-based approaches, structu

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Dzieciatkowska, Monika, Guihong Qi, Jinsam You, et al. "Proteomic Characterization of Cerebrospinal Fluid from Ataxia-Telangiectasia (A-T) Patients Using a LC/MS-Based Label-Free Protein Quantification Technology." International Journal of Proteomics 2011 (June 23, 2011): 1–13. http://dx.doi.org/10.1155/2011/578903.

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Cerebrospinal fluid (CSF) has been used for biomarker discovery of neurodegenerative diseases in humans since biological changes in the brain can be seen in this biofluid. Inactivation of A-T-mutated protein (ATM), a multifunctional protein kinase, is responsible for A-T, yet biochemical studies have not succeeded in conclusively identifying the molecular mechanism(s) underlying the neurodegeneration seen in A-T patients or the proteins that can be used as biomarkers for neurologic assessment of A-T or as potential therapeutic targets. In this study, we applied a high-throughput LC/MS-based la

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Tiwari, Kunal, Rahul Saxena, and Dr Sarika Saxena. "MOLECULAR TECHNIQUES ADOPTED AGAINST SARS-COV-2 IN VACCINE DEVELOPMENT." International Journal of Engineering Applied Sciences and Technology 6, no. 6 (2021): 197–206. http://dx.doi.org/10.33564/ijeast.2021.v06i06.028.

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In this review, we attempted to highlight the uniqueness and difference among vaccines. Vaccine is a biological preparation that improves immunity to diseases and protect us from Covid 19. The term vaccine applies to all biological preparations produced by the living organisms, that enhance immunity against disease and the techniques used for the development of vaccines were reverse vaccinology, structural vaccinology, synthetic biology, and vaccine adjuvants. Besides these mRNA vaccines, we will also highlight the Protein subunit vaccines, which include separated proteins from viral or bacter

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Wojtasińska, Armanda, Joanna Kućmierz, Julita Tokarek, et al. "New Insights into Cardiovascular Diseases Treatment Based on Molecular Targets." International Journal of Molecular Sciences 24, no. 23 (2023): 16735. http://dx.doi.org/10.3390/ijms242316735.

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Cardiovascular diseases (CVDs) which consist of ischemic heart disease, stroke, heart failure, peripheral arterial disease, and several other cardiac and vascular conditions are one of the most common causes of death worldwide and often co-occur with diabetes mellitus and lipid disorders which worsens the prognosis and becomes a therapeutic challenge. Due to the increasing number of patients with CVDs, we need to search for new risk factors and pathophysiological changes to create new strategies for preventing, diagnosing, and treating not only CVDs but also comorbidities like diabetes mellitu

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Kumaran, Poojitha. "Molecular docking analysis of Indole based oxadiazoles with the H-binding protein from Treponema denticola." Bioinformation 19, no. 1 (2023): 79–84. http://dx.doi.org/10.6026/97320630019084.

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Treponema denticola is a gram-negative bacteria that is associated with periodontal diseases. Literature derived, six indole based oxadiazole derivatives are docked with the target Factor H binding protein (fHbp) protein. Results show better docking interaction compared to clinically proven drugs and all compounds obey Lipinski’s rule of five. Hence, the compounds were inferred to be potential inhibitors for factor H binding protein of Treponema denticola.

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Sharma, Maneesha, Anu Bansal, Shikha Suman, and Neeta Raj Sharma. "Potential Alphavirus Inhibitors From Phytocompounds – Molecular Docking and Dynamics Based Approach." Innovative Biosystems and Bioengineering 7, no. 3 (2023): 21–31. http://dx.doi.org/10.20535/ibb.2023.7.3.285245.

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Background. Alphaviral diseases are an economic burden all over the world due to their chronicity and distribution worldwide. The glycoproteins E1 and E2 are important for binding to the surface of the host cell by interacting with the receptors and non-structural proteins named nsP2 and nsP4 are important for the replication of virus, so can be an important drug discovery target. Objective. We are aimed to explore the in silico interaction between plant-based compounds (phytocompounds) and specific protein targets, such as nonstructural protein nsP4 and glycoprotein E2 of Sindbis virus (SINV)

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Espay, Alberto J., Joaquin A. Vizcarra, Luca Marsili, et al. "Revisiting protein aggregation as pathogenic in sporadic Parkinson and Alzheimer diseases." Neurology 92, no. 7 (2019): 329–37. http://dx.doi.org/10.1212/wnl.0000000000006926.

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The gold standard for a definitive diagnosis of Parkinson disease (PD) is the pathologic finding of aggregated α-synuclein into Lewy bodies and for Alzheimer disease (AD) aggregated amyloid into plaques and hyperphosphorylated tau into tangles. Implicit in this clinicopathologic-based nosology is the assumption that pathologic protein aggregation at autopsy reflects pathogenesis at disease onset. While these aggregates may in exceptional cases be on a causal pathway in humans (e.g., aggregated α-synuclein in SNCA gene multiplication or aggregated β-amyloid in APP mutations), their near univers

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Mazanetz, Michael P., Ian M. Withers, Charles A. Laughton та Peter M. Fischer. "Exploiting glycogen synthase kinase 3β flexibility in molecular recognition". Biochemical Society Transactions 36, № 1 (2008): 55–58. http://dx.doi.org/10.1042/bst0360055.

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GSK3β (glycogen synthase kinase 3β) is involved in the phosphorylation of various important regulatory proteins. Pharmacological inhibition of this enzyme could yield treatments for a variety of diseases including diabetes and Alzheimer's disease. The understanding of events involved in the molecular recognition of inhibitors by the active site of this enzyme is key in structure-based design strategies. The present study deals with the dynamic nature of GSK3β and highlights the importance of studying protein plasticity in structure-based drug design, exemplified by our method called ASP (activ

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Yslam, Kyyasovich Orazov. "TAU PROTEIN DETECTION BY USING DEVELOPED MICROTUBULE-KINESIN SYSTEM." International Journal of Multidisciplinary Research Transactions 5, no. 4 (2023): 158–59. https://doi.org/10.5281/zenodo.7783080.

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Lack of intraneuronal transport is a common hallmark of many neurodegenerative diseases including Alzheimer’s disease (AD) [1, 2]. This often involves dysfunction of microtubule associated proteins such as tau, which normally protect microtubule stability and regulate molecular transport along the microtubules. Tauopathies, a large group of age-related neurodegenerative diseases including AD, is characterized by abnormal accumulation of tau protein [3-5]. A reliable and sensitive in vitro assay for rapid analysis of the components and conditions affecting intraneuronal microtubule-based

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Opo, F. A. Dain Md, Saleh Alkarim, Ghadeer I. Alrefaei, et al. "Pharmacophore-Model-Based Virtual-Screening Approaches Identified Novel Natural Molecular Candidates for Treating Human Neuroblastoma." Current Issues in Molecular Biology 44, no. 10 (2022): 4838–58. http://dx.doi.org/10.3390/cimb44100329.

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The mortality of cancer patients with neuroblastoma is increasing due to the limited availability of specific treatment options. Few drug candidates for combating neuroblastoma have been developed, and identifying novel therapeutic candidates against the disease is an urgent issue. It has been found that muc-N protein is amplified in one-third of human neuroblastomas and expressed as an attractive drug target against the disease. The myc-N protein interferes with the bromodomain and extraterminal (BET) family proteins. Pharmacologically inhibition of the protein potently depletes MYCN in neuro

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Bertsch, Uwe, Konstanze F. Winklhofer, Thomas Hirschberger, et al. "Systematic Identification of Antiprion Drugs by High-Throughput Screening Based on Scanning for Intensely Fluorescent Targets." Journal of Virology 79, no. 12 (2005): 7785–91. http://dx.doi.org/10.1128/jvi.79.12.7785-7791.2005.

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ABSTRACT Conformational changes and aggregation of specific proteins are hallmarks of a number of diseases, like Alzheimer's disease, Parkinson's disease, and prion diseases. In the case of prion diseases, the prion protein (PrP), a neuronal glycoprotein, undergoes a conformational change from the normal, mainly alpha-helical conformation to a disease-associated, mainly beta-sheeted scrapie isoform (PrPSc), which forms amyloid aggregates. This conversion, which is crucial for disease progression, depends on direct PrPC/PrPSc interaction. We developed a high-throughput assay based on scanning f

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Ali, Yasir, Hina Imtiaz, Muhammad Mutaal Tahir, et al. "Fragment-Based Approaches Identified Tecovirimat-Competitive Novel Drug Candidate for Targeting the F13 Protein of the Monkeypox Virus." Viruses 15, no. 2 (2023): 570. http://dx.doi.org/10.3390/v15020570.

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Monkeypox is a serious public health issue in tropical and subtropical areas. Antivirals that target monkeypox proteins might lead to more effective and efficient therapy. The F13 protein is essential for the growth and maturation of the monkeypox virus. F13 inhibition might be a viable therapeutic target for monkeypox. The in silico fragment-based drug discovery method for developing antivirals may provide novel therapeutic options. In this study, we generated 800 compounds based on tecovirimat, an FDA-approved drug that is efficacious at nanomolar quantities against monkeypox. These compound

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Berdnikova, Daria V., Paolo Carloni, Sybille Krauß, and Giulia Rossetti. "Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding." Molecules 26, no. 11 (2021): 3384. http://dx.doi.org/10.3390/molecules26113384.

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Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic res

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Kirkegaard, Thomas. "Development of heat shock protein based therapies for lysosomal diseases." Molecular Genetics and Metabolism 117, no. 2 (2016): S68. http://dx.doi.org/10.1016/j.ymgme.2015.12.322.

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Papa, Guido, Alexander Borodavka, and Ulrich Desselberger. "Viroplasms: Assembly and Functions of Rotavirus Replication Factories." Viruses 13, no. 7 (2021): 1349. http://dx.doi.org/10.3390/v13071349.

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Viroplasms are cytoplasmic, membraneless structures assembled in rotavirus (RV)-infected cells, which are intricately involved in viral replication. Two virus-encoded, non-structural proteins, NSP2 and NSP5, are the main drivers of viroplasm formation. The structures (as far as is known) and functions of these proteins are described. Recent studies using plasmid-only-based reverse genetics have significantly contributed to elucidation of the crucial roles of these proteins in RV replication. Thus, it has been recognized that viroplasms resemble liquid-like protein–RNA condensates that may be f

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Amano, Atsuo, Takayuki Nakamura, Shigenobu Kimura, et al. "Molecular Interactions of Porphyromonas gingivalisFimbriae with Host Proteins: Kinetic Analyses Based on Surface Plasmon Resonance." Infection and Immunity 67, no. 5 (1999): 2399–405. http://dx.doi.org/10.1128/iai.67.5.2399-2405.1999.

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ABSTRACT Fimbriae of Porphyromonas gingivalis are thought to play an important role in the colonization and invasion of periodontal tissues. In this study, we analyzed the interactions of P. gingivalis fimbriae with human hemoglobin, fibrinogen, and salivary components (i.e., proline-rich protein [PRP], proline-rich glycoprotein [PRG], and statherin) based on surface plasmon resonance (SPR) spectroscopy with a biomolecular interaction analyzing system (BIAcore). The real-time observation showed that the fimbriae interacted more quickly with hemoglobin and PRG than with other proteins and more

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