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https://www.readbyqxmd.com/read/28809952/computational-and-experimental-analysis-of-short-peptide-motifs-for-enzyme-inhibition
#1
Jinglin Fu, Luca Larini, Anthony J Cooper, John W Whittaker, Azka Ahmed, Junhao Dong, Minyoung Lee, Ting Zhang
The metabolism of living systems involves many enzymes that play key roles as catalysts and are essential to biological function. Searching ligands with the ability to modulate enzyme activities is central to diagnosis and therapeutics. Peptides represent a promising class of potential enzyme modulators due to the large chemical diversity, and well-established methods for library synthesis. Peptides and their derivatives are found to play critical roles in modulating enzymes and mediating cellular uptakes, which are increasingly valuable in therapeutics...
2017: PloS One
https://www.readbyqxmd.com/read/28809010/bioinformatics-resources-for-interpreting-proteomics-mass-spectrometry-data
#2
Iulia M Lazar
Developments in mass spectrometry (MS) instrumentation have supported the advance of a variety of proteomic technologies that have enabled scientists to assess differences between healthy and diseased states. In particular, the ability to identify altered biological processes in a cell has led to the identification of novel drug targets, the development of more effective therapeutic drugs, and the growth of new diagnostic approaches and tools for personalized medicine applications. Nevertheless, large-scale proteomic data generated by modern mass spectrometers are extremely complex and necessitate equally complex bioinformatics tools and computational algorithms for their interpretation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28806184/noninfectious-aortitis-what-the-cardiologist-needs-to-know
#3
Ingolf Töpel
PURPOSE OF REVIEW: To sum up a group of noninfectious inflammatory diseases of the aorta and its branches relevant to a cardiologist's daily routine. To describe pathogenetic and clinical advances as well as modern diagnostic tools. To overview most recent treatment options and patient-tailored therapies. To provide an insight in future directions of research. RECENT FINDINGS: Pathophysiology of large vessel vasculitides (LVV) are still poorly defined. At least a certain number of patients with idiopathic periaortitis seem to part of the group of IgG4-related diseases which has implications for therapy...
August 12, 2017: Current Opinion in Cardiology
https://www.readbyqxmd.com/read/28799716/rational-design-of-membrane-pore-forming-peptides
#4
Max Pillong, Jan A Hiss, Petra Schneider, Yen-Chu Lin, Gernot Posselt, Bernhard Pfeiffer, Markus Blatter, Alex T Müller, Simon Bachler, Claudia S Neuhaus, Petra S Dittrich, Karl-Heinz Altmann, Silja Wessler, Gisbert Schneider
Specific interactions of peptides with lipid membranes are essential for cellular communication and constitute a central aspect of the innate host defense against pathogens. A computational method for generating innovative membrane-pore-forming peptides inspired by natural templates is presented. Peptide representation in terms of sequence- and topology-dependent hydrophobic moments is introduced. This design concept proves to be appropriate for the de novo generation of first-in-class membrane-active peptides with the anticipated mode of action...
August 11, 2017: Small
https://www.readbyqxmd.com/read/28757583/chalcone-derivatives-promising-starting-points-for-drug-design
#5
REVIEW
Marcelo N Gomes, Eugene N Muratov, Maristela Pereira, Josana C Peixoto, Lucimar P Rosseto, Pedro V L Cravo, Carolina H Andrade, Bruno J Neves
Medicinal chemists continue to be fascinated by chalcone derivatives because of their simple chemistry, ease of hydrogen atom manipulation, straightforward synthesis, and a variety of promising biological activities. However, chalcones have still not garnered deserved attention, especially considering their high potential as chemical sources for designing and developing new effective drugs. In this review, we summarize current methodological developments towards the design and synthesis of new chalcone derivatives and state-of-the-art medicinal chemistry strategies (bioisosterism, molecular hybridization, and pro-drug design)...
July 25, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28756658/polymers-for-3d-printing-and-customized-additive-manufacturing
#6
Samuel Clark Ligon, Robert Liska, Jürgen Stampfl, Matthias Gurr, Rolf Mülhaupt
Additive manufacturing (AM) alias 3D printing translates computer-aided design (CAD) virtual 3D models into physical objects. By digital slicing of CAD, 3D scan, or tomography data, AM builds objects layer by layer without the need for molds or machining. AM enables decentralized fabrication of customized objects on demand by exploiting digital information storage and retrieval via the Internet. The ongoing transition from rapid prototyping to rapid manufacturing prompts new challenges for mechanical engineers and materials scientists alike...
August 9, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28750804/ligand-assisted-protein-structure-laps-an-experimental-paradigm-for-characterizing-cannabinoid-receptor-ligand-binding-domains
#7
David R Janero, Anisha Korde, Alexandros Makriyannis
Detailed characterization of the ligand-binding motifs and structure-function correlates of the principal GPCRs of the endocannabinoid-signaling system, the cannabinoid 1 (CB1R) and cannabinoid 2 (CB2R) receptors, is essential to inform the rational design of drugs that modulate CB1R- and CB2R-dependent biosignaling for therapeutic gain. We discuss herein an experimental paradigm termed "ligand-assisted protein structure" (LAPS) that affords a means of characterizing, at the amino acid level, CB1R and CB2R structural features key to ligand engagement and receptor-dependent information transmission...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28748934/synergy-of-synthesis-computation-and-nmr-reveals-correct-baulamycin-structures
#8
Jingjing Wu, Paula Lorenzo, Siying Zhong, Muhammad Ali, Craig P Butts, Eddie L Myers, Varinder K Aggarwal
Small-molecule, biologically active natural products continue to be our most rewarding source of, and inspiration for, new medicines. Sometimes we happen upon such molecules in minute quantities in unique, difficult-to-reach, and often fleeting environments, perhaps never to be discovered again. In these cases, determining the structure of a molecule-including assigning its relative and absolute configurations-is paramount, enabling one to understand its biological activity. Molecules that comprise stereochemically complex acyclic and conformationally flexible carbon chains make such a task extremely challenging...
July 26, 2017: Nature
https://www.readbyqxmd.com/read/28744848/systems-and-precision-medicine-approaches-to-diabetes-heterogeneity-a-big-data-perspective
#9
Enrico Capobianco
Big Data, and in particular Electronic Health Records, provide the medical community with a great opportunity to analyze multiple pathological conditions at an unprecedented depth for many complex diseases, including diabetes. How can we infer on diabetes from large heterogeneous datasets? A possible solution is provided by invoking next-generation computational methods and data analytics tools within systems medicine approaches. By deciphering the multi-faceted complexity of biological systems, the potential of emerging diagnostic tools and therapeutic functions can be ultimately revealed...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28735540/the-n%C3%A2-%C3%AF-interaction
#10
Robert W Newberry, Ronald T Raines
The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group...
July 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28735000/application-of-pharmacometrics-and-quantitative-systems-pharmacology-to-cancer-therapy-the-example-of-luminal-a-breast-cancer
#11
REVIEW
Brett Fleisher, Ashley N Brown, Sihem Ait-Oudhia
Breast cancer (BC) is the most common cancer in women, and the second most frequent cause of cancer-related deaths in women worldwide. It is a heterogeneous disease composed of multiple subtypes with distinct morphologies and clinical implications. Quantitative systems pharmacology (QSP) is an emerging discipline bridging systems biology with pharmacokinetics (PK) and pharmacodynamics (PD) leveraging the systematic understanding of drugs' efficacy and toxicity. Despite numerous challenges in applying computational methodologies for QSP and mechanism-based PK/PD models to biological, physiological, and pharmacological data, bridging these disciplines has the potential to enhance our understanding of complex disease systems such as BC...
July 19, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28726912/3d-material-cytometry-3dmac-a-very-high-replicate-high-throughput-analytical-method-using-microfabricated-shape-specific-cell-material-niches
#12
Kirsten Parratt, Jenny Jeong, Peng Qiu, Krishnendu Roy
Studying cell behavior within 3D material niches is key to understanding cell biology in health and diseases, and developing biomaterials for regenerative medicine applications. Current approaches to studying these cell-material niches have low throughput and can only analyze a few replicates per experiment resulting in reduced measurement assurance and analytical power. Here, we report 3D material cytometry (3DMaC), a novel high-throughput method based on microfabricated, shape-specific 3D cell-material niches and imaging cytometry...
August 8, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28720284/modeling-of-plasmas-for-biomedicine
#13
REVIEW
Natalia Yu Babaeva, George V Naidis
Studies in plasma medicine, which are currently actively expanding, are of multidisciplinary character, involving physical, chemical and biological processes. Rapid progress has been achieved in this field due to synergy between experimental and theoretical/computational methods. Joint use of diagnostic tools and computations gives a better understanding of mechanisms of interaction of plasma with bio-objects. This review focuses on recent achievements in modeling of plasma for biomedical applications. Various computational approaches used in these studies are described...
July 15, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28714509/a-comparative-review-of-computational-methods-for-pathway-perturbation-analysis-dynamical-and-topological-perspectives
#14
REVIEW
Q Vanhaelen, A M Aliper, A Zhavoronkov
Stem cells offer great promise within the field of regenerative medicine but despite encouraging results, the large scale use of stem cells for therapeutic applications still faces challenges when it comes to controlling signaling pathway responses with respect to environmental perturbations. This step is critical for the elaboration of stable and reproducible differentiation protocols, and computational modeling can be helpful to overcome these difficulties. This article is a comparative review of the mechanism-based methods used for hypothesis-driven approaches and data-driven methods which are two types of computational approaches commonly used for analysing the dynamics of pathways involved in stem cell regulation...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28713546/2017-iscb-overton-prize-christoph-bock
#15
EDITORIAL
Christiana N Fogg, Diane E Kovats, Bonnie Berger
The International Society for Computational Biology (ISCB) each year recognizes the achievements of an early to mid-career scientist with the Overton Prize. This prize honors the untimely death of Dr. G. Christian Overton, an admired computational biologist and founding ISCB Board member. Winners of the Overton Prize are independent investigators who are in the early to middle phases of their careers and are selected because of their significant contributions to computational biology through research, teaching, and service...
2017: F1000Research
https://www.readbyqxmd.com/read/28690664/chinese-herbal-medicine-meets-biological-networks-of-complex-diseases-a-computational-perspective
#16
REVIEW
Shuo Gu, Jianfeng Pei
With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28672838/recent-advances-in-conotoxin-classification-by-using-machine-learning-methods
#17
REVIEW
Fu-Ying Dao, Hui Yang, Zhen-Dong Su, Wuritu Yang, Yun Wu, Ding Hui, Wei Chen, Hua Tang, Hao Lin
Conotoxins are disulfide-rich small peptides, which are invaluable peptides that target ion channel and neuronal receptors. Conotoxins have been demonstrated as potent pharmaceuticals in the treatment of a series of diseases, such as Alzheimer's disease, Parkinson's disease, and epilepsy. In addition, conotoxins are also ideal molecular templates for the development of new drug lead compounds and play important roles in neurobiological research as well. Thus, the accurate identification of conotoxin types will provide key clues for the biological research and clinical medicine...
June 25, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28649444/reverse-engineering-highlights-potential-principles-of-large-gene-regulatory-network-design-and-learning
#18
Clément Carré, André Mas, Gabriel Krouk
Inferring transcriptional gene regulatory networks from transcriptomic datasets is a key challenge of systems biology, with potential impacts ranging from medicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. These techniques are usually used to validate algorithm predictions...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28643930/moving-towards-precision-orthodontics-an-evolving-paradigm-shift-in-the-planning-and-delivery-of-customized-orthodontic-therapy
#19
REVIEW
A H Jheon, S Oberoi, R C Solem, S Kapila
Advances in precision medicine portend similar progress in orthodontics and will be increasingly harnessed to achieve customized treatment approaches and enhance treatment efficiencies. Our goal is to provide a background on emerging advances in computer technologies and biomedicine and highlight their current and likely future applications to precision orthodontics. A review of orthodontically relevant technologies and advances in pertinent biological research was undertaken. Innovations in computer hardware and software, and 3D imaging technologies offer the ability for customized treatment and biomechanical planning that will be more fully realized within the next few decades...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643003/recent-developments-in-solution-nuclear-magnetic-resonance-nmr-based-molecular-biology
#20
REVIEW
Joshua J Ziarek, Diego Baptista, Gerhard Wagner
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors...
June 23, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
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