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Advances in Protein Chemistry and Structural Biology

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https://www.readbyqxmd.com/read/30149908/preface
#1
EDITORIAL
Tatyana G Karabencheva-Christova, Christo Z Christov
No abstract text is available yet for this article.
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/30149907/the-oecd-principles-for-q-sar-models-in-the-context-of-knowledge-discovery-in-databases-kdd
#2
Gabriela Gómez-Jiménez, Karla Gonzalez-Ponce, Durbis J Castillo-Pazos, Abraham Madariaga-Mazon, Joaquin Barroso-Flores, Fernando Cortes-Guzman, Karina Martinez-Mayorga
The steps followed in the knowledge discovery in databases (KDD) process are well documented and are widely used in different areas where exploration of data is used for decision making. In turn, while different workflows for developing quantitative structure-activity relationship (QSAR) models have been proposed, including combinatorial use of QSAR, there is now agreement on common requirements for building trustable predictive models. In this work, we analyze and confront the steps involved in KDD and QSAR and present how they comply with the OECD principles for the validation, for regulatory purposes, of QSAR models...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/30149906/computational-methods-for-epigenetic-drug-discovery-a-focus-on-activity-landscape-modeling
#3
J Jesús Naveja, C Iluhí Oviedo-Osornio, José L Medina-Franco
Epigenetic drug discovery is an emerging strategy against several chronic and complex diseases. The increased interest in epigenetics has boosted the development and maintenance of large information on structure-epigenetic activity relationships for several epigenetic targets. In turn, such large databases-many in the public domain-are a rich source of information to explore their structure-activity relationships (SARs). Herein, we conducted a large-scale analysis of the SAR of epigenetic targets using the concept of activity landscape modeling...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/30149905/computational-methods-for-efficient-sampling-of-protein-landscapes-and-disclosing-allosteric-regions
#4
Canan Atilgan
Methods developed toward computational exploration of protein landscapes have become standardized tools to assess biophysical experimental findings. They are also used on their own right to discover the workings of the protein as a molecular machine, potential sites of interest for protein functioning, allosteric regions in proteins, and communication pathways between different sites on a protein. With the development of reliable force fields that describe interactions in biomolecules, molecular dynamics (MD) simulations have become the prime tool for this purpose...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/30149904/computational-methods-to-discover-compounds-for-the-treatment-of-chagas-disease
#5
Eduardo M Cortés-Ruiz, Oscar Palomino-Hernández, Karla Daniela Rodríguez-Hernández, Bertha Espinoza, José L Medina-Franco
Infectious diseases continue to be a major public health. Among these diseases, American trypanosomiasis or Chagas disease (CD) is a major cause of morbidity and death for millions of people in Latin America. The two drugs currently available for the treatment of CD have poor efficacy and major side effects. Thus, there is a pressing need to develop safe and effective drugs against this disease. Herein we review the diversity and coverage of chemical space of compounds tested as inhibitors of Trypanosoma cruzi, a parasite causing CD...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/30149903/combined-quantum-mechanics-and-molecular-mechanics-studies-of-enzymatic-reaction-mechanisms
#6
Jon Ainsley, Alessio Lodola, Adrian J Mulholland, Christo Z Christov, Tatyana G Karabencheva-Christova
The combined quantum mechanics/molecular mechanics (QM/MM) methods have become a valuable tool in computational biochemistry and received versatile applications for studying the reaction mechanisms of enzymes. The approach combines the calculations of the electronic structure of the active site by QM, with modeling of the protein environment using MM force field, which allows the long-range electrostatics and steric effects on the enzyme reactivity to be accounted for. In this review, we review some key theoretical and computational aspects of the method and we also present some applications to particular enzymatic reactions such as tryptophan-7-halogenase, cyclooxygenase-1, and the epidermal growth factor receptor...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680245/preface
#7
EDITORIAL
Rossen Donev
No abstract text is available yet for this article.
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680244/dynamical-behavior-of-somatostatin-14-and-its-cyclic-analogues-as-analyzed-in-bulk-and-on-plasmonic-silver-nanoparticles
#8
Belén Hernández, Yves-Marie Coïc, Eduardo López-Tobar, Santiago Sanchez-Cortes, Bruno Baron, Fernando Pflüger, Sergei G Kruglik, Régis Cohen, Mahmoud Ghomi
Primarily known as the inhibitor of growth hormone release, the role of somatostatin in many other inhibiting activities upon binding to its five G-protein-coupled receptors has been elucidated. Because of the short half-life of somatostatin, a number of synthetic analogues were elaborated for this peptide hormone. Herein, after recalling the main somatostatin therapeutic interests, we present the dynamical behavior of somatostatin-14 and its two currently used synthetic cyclic analogues, octreotide and pasireotide...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680243/therapeutic-monoclonal-antibodies-delivery-for-the-glioblastoma-treatment
#9
Flávia Sousa, Rui P Moura, Elias Moreira, Cláudia Martins, Bruno Sarmento
Glioblastoma multiforme (GBM) is the most common and challenging primary malignant brain tumor, being the median overall survival between 10 and 14 months due to its invasive characteristics. GBM treatment is mainly based on the maximal surgical resection and radiotherapy associated to chemotherapy. Monoclonal antibodies (mAbs) have been used in chemotherapy protocols for GBM treatment in order to improve immunotherapy and antiangiogenic processes. High specificity and affinity of mAbs for biological targets make them highly used for brain tumor therapy...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680242/linear-analogues-of-the-lipopeptide-battacin-with-potent-in-vitro-activity-against-s-aureus
#10
Hugh D Glossop, Esperanza Pearl, Gayan H De Zoysa, Vijayalekshmi Sarojini
Eight linear analogues of the lipopeptide battacin were evaluated for their antibacterial activity against the Gram-positive Staphylococcus aureus. Of this library, the enantiomeric lipopeptide analogue 9.4 exhibited nanomolar inhibitory activity (MIC=200nmol) against S. aureus. Furthermore, this lipopeptide was resilient toward degradation conditions when exposed to rat serum proteases for up to 8h.
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680241/the-structure-function-relationship-in-antimicrobial-peptides-what-can-we-obtain-from-structural-data
#11
Marlon H Cardoso, Karen G N Oshiro, Samilla B Rezende, Elizabete S Cândido, Octávio L Franco
Antimicrobial peptides (AMPs) have been widely isolated from most organisms in nature. This class of antimicrobials may undergo changes in their sequence for improved physicochemical properties, including charge, hydrophobicity, and hydrophobic moment. It is known that such properties may be directly associated with AMPs' structural arrangements and, consequently, could interfere in their modes of action against microorganisms. In this scenario, biophysical methodologies, such as nuclear magnetic resonance spectroscopy, X-ray crystallography, and cryo-electron microscopy, allied to in silico approaches, including molecular modeling, docking, and dynamics nowadays represent an enormous first step for the structural elucidation of AMPs, leading to further structure-function annotation...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680240/peptide-derivatives-of-erythropoietin-in-the-treatment-of-neuroinflammation-and-neurodegeneration
#12
Ilkcan Ercan, Kemal Ugur Tufekci, Ezgi Karaca, Sermin Genc, Kursad Genc
During the past 35 years, recombinant DNA technology has allowed the production of a wide range of hematopoietic and neurotrophic growth factors including erythropoietin (EPO). These have emerged as promising protein drugs in various human diseases. Accumulated evidences have recently demonstrated the neuroprotective effect of EPO in preclinical models of acute and chronic degenerative disorders. Nevertheless, tissue protective effect of EPO could not be translated to the clinical trials because of common lethal thromboembolic events, erythropoiesis and hypertension...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680239/protein-and-peptides-for-elderly-health
#13
Nan Shang, Chalamaiah Meram, Nandika Bandara, Jianping Wu
The world is aging rapidly; thus, the management of elderly health at an advanced age poses a new research challenge. The elderly is vulnerable to not only malnutrition but also hypofunction of all organs and a variety of chronic diseases such as sarcopenia, osteoporosis, gastrointestinal dysfunction, and mental problems. As the major macronutrient, food protein plays an important role in elderly health and well-being. In this chapter, the function of protein and peptide in elderly health as well as their effects on preventing aging-related disease is reviewed...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680238/in-silico-tools-and-databases-for-designing-peptide-based-vaccine-and-drugs
#14
Salman Sadullah Usmani, Rajesh Kumar, Sherry Bhalla, Vinod Kumar, Gajendra P S Raghava
The prolonged conventional approaches of drug screening and vaccine designing prerequisite patience, vigorous effort, outrageous cost as well as additional manpower. Screening and experimentally validating thousands of molecules for a specific therapeutic property never proved to be an easy task. Similarly, traditional way of vaccination includes administration of either whole or attenuated pathogen, which raises toxicity and safety issues. Emergence of sequencing and recombinant DNA technology led to the epitope-based advanced vaccination concept, i...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680237/smart-cell-penetrating-peptide-based-techniques-for-intracellular-delivery-of-therapeutic-macromolecules
#15
Yang He, Feng Li, Yongzhuo Huang
Many therapeutic macromolecules must enter cells to take their action. However, their treatment outcomes are often hampered by their poor transportation into target cells. Therefore, efficient intracellular delivery of these macromolecules is critical for improving their therapeutic efficacy. Cell-penetrating peptide (CPP)-based approaches are one of the most efficient methods for intracellular delivery of macromolecular therapeutics. Nevertheless, poor specificity is a significant concern for systemic administrated CPP-based delivery systems...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680236/chimeric-small-antibody-fragments-as-strategy-to-deliver-therapeutic-payloads
#16
Sandra Aguiar, Joana Dias, Ana M Manuel, Roberto Russo, Pedro M P Gois, Frederico A da Silva, Joao Goncalves
Antibody-drug conjugates (ADCs) represent an innovative class of biopharmaceuticals, which aim at achieving a site-specific delivery of cytotoxic agents to the target cell. The use of ADCs represents a promising strategy to overcome the disadvantages of conventional pharmacotherapy of cancer or neurological diseases, based on cytotoxic or immunomodulatory agents. ADCs consist of monoclonal antibodies attached to biologically active drugs by means of cleavable chemical linkers. Advances in technologies for the coupling of antibodies to cytotoxic drugs promise to deliver greater control of drug pharmacokinetic properties and to significantly improve pharmacodelivery applications, minimizing exposure of healthy tissue...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680235/transglutaminase-and-sialyltransferase-enzymatic-approaches-for-polymer-conjugation-to-proteins
#17
Katia Maso, Antonella Grigoletto, Gianfranco Pasut
Proteins hold a central role in medicine and biology, also confirmed by the several therapeutic applications based on biologic drugs. Such therapies are of great relevance thanks to high potency and safety of proteins. Nevertheless, many proteins as therapeutics might present issues like fast kidney clearance, rapid enzymatic degradation, or immunogenicity. Such defects implicate frequent administrations or administrations at high doses of the therapeutics, thus yielding or exacerbating potential side effects...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29680234/rational-design-of-liquid-formulations-of-proteins
#18
Mark C Manning, Jun Liu, Tiansheng Li, Ryan E Holcomb
Twenty years ago, a number of eminent pharmaceutical scientists collaborated on an article describing a rational approach to developing stable lyophilized protein formulations (Carpenter, Pikal, Chang, & Randolph, 1997). Since that time, no corresponding document for rational development of liquid formulations of proteins has appeared. Certainly, many of the principles underpinning rational protein formulation have been known for some time, but no overarching scheme has ever been described in the literature...
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29459037/preface
#19
EDITORIAL
Rossen Donev
No abstract text is available yet for this article.
2018: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/29459036/targeting-intramembrane-protein-protein-interactions-novel-therapeutic-strategy-of-millions-years-old
#20
Alexander B Sigalov
Intramembrane protein-protein interactions (PPIs) are involved in transmembrane signal transduction mediated by cell surface receptors and play an important role in health and disease. Recently, receptor-specific modulatory peptides rationally designed using a general platform of transmembrane signaling, the signaling chain homooligomerization (SCHOOL) model, have been proposed to therapeutically target these interactions in a variety of serious diseases with unmet needs including cancer, sepsis, arthritis, retinopathy, and thrombosis...
2018: Advances in Protein Chemistry and Structural Biology
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