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https://www.readbyqxmd.com/read/27935197/ring-expansion-approach-to-medium-sized-lactams-and-analysis-of-their-medicinal-lead-like-properties
#1
Laetitia G Baud, Morgan Ann Manning, Helen L Arkless, Thomas C Stephens, William Paul Unsworth
Medium-sized rings are widely considered to be under-represented in biological screening libraries for lead identification in medicinal chemistry. To help address this, a library of medium-sized lactams has been generated using a simple, scalable and versatile ring expansion protocol. Analysis of the library using open access computational tool LLAMA suggests that these lactams and their derivatives have highly promising physicochemical and 3D spatial properties and thus have much potential in drug discovery...
December 9, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27933468/conditional-screening-for-ultra-high-dimensional-covariates-with-survival-outcomes
#2
Hyokyoung G Hong, Jian Kang, Yi Li
Identifying important biomarkers that are predictive for cancer patients' prognosis is key in gaining better insights into the biological influences on the disease and has become a critical component of precision medicine. The emergence of large-scale biomedical survival studies, which typically involve excessive number of biomarkers, has brought high demand in designing efficient screening tools for selecting predictive biomarkers. The vast amount of biomarkers defies any existing variable selection methods via regularization...
December 8, 2016: Lifetime Data Analysis
https://www.readbyqxmd.com/read/27924064/toward-the-use-of-precision-medicine-for-the-treatment-of-head-and-neck-squamous-cell-carcinoma
#3
REVIEW
Wang Gong, Yandi Xiao, Zihao Wei, Yao Yuan, Min Qiu, Chongkui Sun, Xin Zeng, Xinhua Liang, Mingye Feng, Qianming Chen
Precision medicine is a new strategy that aims at preventing and treating human diseases by focusing on individual variations in people's genes, environment and lifestyle. Precision medicine has been used for cancer diagnosis and treatment and shows evident clinical efficacy. Rapid developments in molecular biology, genetics and sequencing technologies, as well as computational technology, has enabled the establishment of "big data", such as the Human Genome Project, which provides a basis for precision medicine...
December 4, 2016: Oncotarget
https://www.readbyqxmd.com/read/27921034/crowdsourcing-precision-cerebrovascular-health-imaging-and-cloud-seeding-a-million-brains-initiative%C3%A2
#4
David S Liebeskind
Crowdsourcing, an unorthodox approach in medicine, creates an unusual paradigm to study precision cerebrovascular health, eliminating the relative isolation and non-standardized nature of current imaging data infrastructure, while shifting emphasis to the astounding capacity of big data in the cloud. This perspective envisions the use of imaging data of the brain and vessels to orient and seed A Million Brains Initiative™ that may leapfrog incremental advances in stroke and rapidly provide useful data to the sizable population around the globe prone to the devastating effects of stroke and vascular substrates of dementia...
2016: Frontiers in Medicine
https://www.readbyqxmd.com/read/27914918/epigenetic-game-theory-how-to-compute-the-epigenetic-control-of-maternal-to-zygotic-transition
#5
REVIEW
Qian Wang, Kirk Gosik, Sujuan Xing, Libo Jiang, Lidan Sun, Vernon M Chinchilli, Rongling Wu
Epigenetic reprogramming is thought to play a critical role in maintaining the normal development of embryos. How the methylation state of paternal and maternal genomes regulates embryogenesis depends on the interaction and coordination of the gametes of two sexes. While there is abundant research in exploring the epigenetic interactions of sperms and oocytes, a knowledge gap exists in the mechanistic quantitation of these interactions and their impact on embryo development. This review aims at formulating a modeling framework to address this gap through the integration and synthesis of evolutionary game theory and the latest discoveries of the epigenetic control of embryo development by next-generation sequencing...
November 9, 2016: Physics of Life Reviews
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#6
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913993/antifreeze-glycopeptides-from-structure-and-activity-studies-to-current-approaches-in-chemical-synthesis
#7
REVIEW
Małgorzata Urbańczyk, Jerzy Góra, Rafał Latajka, Norbert Sewald
Antifreeze glycopeptides (AFGPs) are a class of biological antifreeze agents found predominantly in Arctic and Antarctic species of fish. They possess the ability to regulate ice nucleation and ice crystal growth, thus creating viable life conditions at temperatures below the freezing point of body fluids. AFGPs usually consist of 4-55 repetitions of the tripeptide unit Ala-Ala-Thr that is O-glycosylated at the threonine side chains with β-D-galactosyl-(1 → 3)-α-N-acetyl-D-galactosamine. Due to their interesting properties and high antifreeze activity, they have many potential applications, e...
December 2, 2016: Amino Acids
https://www.readbyqxmd.com/read/27900742/-precision-nursing-individual-based-knowledge-translation
#8
Li-Chi Chiang, Mei-Ling Yeh, Sui-Lung Su
U.S. President Obama announced a new era of precision medicine in the Precision Medicine Initiative (PMI). This initiative aims to accelerate the progress of personalized medicine in light of individual requirements for prevention and treatment in order to improve the state of individual and public health. The recent and dramatic development of large-scale biologic databases (such as the human genome sequence), powerful methods for characterizing patients (such as genomics, microbiome, diverse biomarkers, and even pharmacogenomics), and computational tools for analyzing big data are maximizing the potential benefits of precision medicine...
December 2016: Hu Li za Zhi the Journal of Nursing
https://www.readbyqxmd.com/read/27896745/molecular-similarity-concepts-for-informatics-applications
#9
Jürgen Bajorath
The assessment of small molecule similarity is a central task in chemoinformatics and medicinal chemistry. A variety of molecular representations and metrics are applied to computationally evaluate and quantify molecular similarity. A critically important aspect of molecular similarity analysis in chemoinformatics and pharmaceutical research is that one is typically not interested in quantifying the degree of structural or chemical similarity between compounds per se, but rather in extrapolating from molecular similarity to property similarity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27894336/curcumin-and-long-chain-omega-3-polyunsaturated-fatty-acids-for-prevention-of-type-2-diabetes-cop-d-study-protocol-for-a-randomised-controlled-trial
#10
Rohith N Thota, Shamasunder H Acharya, Kylie A Abbott, Manohar L Garg
BACKGROUND: Lifestyle interventions, including increase in physical activity and dietary counselling, have shown the ability to prevent type 2 diabetes (T2D) in high-risk state individuals, but the prevalence is still skyrocketing in Australia, in line with global prevalence. Currently, no medicines are approved by the Therapeutic Goods Administration in Australia for the management of prediabetes. Therefore, there is a need of developing a safer, biologically efficacious and cost-effective alternative for delaying the transition of individual health state from prediabetes into T2D...
November 29, 2016: Trials
https://www.readbyqxmd.com/read/27885191/-modeling-and-simulation-of-trabecular-pattern-formation-in-a-cancellous-bone-defect-under-mechanical-forces
#11
Taiji Adachi
Understanding regeneration of the trabecular structure in cancellous bone defects is an important issue in bone tissue engineering and regenerative medicine. Biochemical and biomechanical viewpoints are indispensable for understanding the fundamental mechanism that underlies the regeneration of the trabecular structure. In vitro observations of the Turing pattern-like bone differentiation into osteoblasts from human mesenchymal stem cells suggest that mathematical modeling and simulation based on a reaction-diffusion system model would help us to understand the mechanism of trabecular pattern formation during cancellous bone regeneration...
2016: Clinical Calcium
https://www.readbyqxmd.com/read/27875945/3d-printing-articular-cartilage-recapitulating-the-complexity-of-native-tissue
#12
Ting Guo, Josephine Lembong, Lijie Grace Zhang, John P Fisher
In the past few decades, the field of tissue engineering combined with rapid prototyping (RP) techniques has been successful in creating biological substitutes that mimic tissues. Its applications in regenerative medicine have drawn efforts in research from various scientific fields, diagnostics, and clinical translation to therapies. While some areas of therapeutics are well developed, such as skin replacement, many others such as cartilage repair can still greatly benefit from tissue engineering and RP due to the low success and / or inefficiency of current existing, often surgical treatments...
November 22, 2016: Tissue Engineering. Part B, Reviews
https://www.readbyqxmd.com/read/27874291/zwitterionic-structures-from-physicochemical-properties-toward-computer-aided-drug-designs
#13
Zhiwei Yang, Qinyi Li, Gang Yang
Zwitterions, used widely in chemical, biological and medicinal fields, show distinct physicochemical properties relative to ordinary ampholytes, which largely decide their bioavailability and biological activities. In the present manuscript, these properties are discussed in order to facilitate our understanding of zwitterionic structures, followed by various examples of zwitterionic drugs and the critical role these properties play. We specifically focus our discussions on neuraminidase inhibitors (NAIs), which are used in the treatment and prevention of influenza, covering their computer-assisted design, transformation to zwitterionic isomers and interaction mechanisms of NAIs with proteins...
December 2016: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/27863564/designing-and-developing-pet-based-precision-model-in-thyroid-carcinoma-the-potential-avenues-for-a-personalized-clinical-care
#14
REVIEW
Sandip Basu, Rahul Vithalrao Parghane
This communication enumerates the current uses and potential areas where PET could be clinically utilized for developing "precision medicine" type model in thyroid carcinoma. (1) In routine clinics, PET imaging (with fluorodeoxyglucose [FDG]) is utilized to investigate patients of differentiated thyroid carcinoma (DTC) with high thyroglobulin and negative iodine scintigraphy (TENIS) and in medullary carcinoma thyroid (MCT) when the tumor markers (eg, calcitonin and carcino embryonic antigen [CEA]) are raised postoperatively (PET with FDG, (68)Ga-DOTA-NOC/TATE, FDOPA)...
January 2017: PET Clinics
https://www.readbyqxmd.com/read/27863562/molecular-imaging-and-precision-medicine-pet-computed-tomography-and-therapy-response-assessment-in-oncology
#15
REVIEW
Sara Sheikhbahaei, Esther Mena, Puskar Pattanayak, Mehdi Taghipour, Lilja B Solnes, Rathan M Subramaniam
A variety of methods have been developed to assess tumor response to therapy. Standardized qualitative criteria based on 18F-fluoro-deoxyglucose PET/computed tomography have been proposed to evaluate the treatment effectiveness in specific cancers and these allow more accurate therapy response assessment and survival prognostication. Multiple studies have addressed the utility of the volumetric PET biomarkers as prognostic indicators but there is no consensus about the preferred segmentation methodology for these metrics...
January 2017: PET Clinics
https://www.readbyqxmd.com/read/27862046/the-role-of-different-sampling-methods-in-improving-biological-activity-prediction-using-deep-belief-network
#16
Fahimeh Ghasemi, Afshin Fassihi, Horacio Pérez-Sánchez, Alireza Mehri Dehnavi
Thousands of molecules and descriptors are available for a medicinal chemist thanks to the technological advancements in different branches of chemistry. This fact as well as the correlation between them has raised new problems in quantitative structure activity relationship studies. Proper parameter initialization in statistical modeling has merged as another challenge in recent years. Random selection of parameters leads to poor performance of deep neural network (DNN). In this research, deep belief network (DBN) was applied to initialize DNNs...
November 14, 2016: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27818233/systems-biology-dissection-of-mechanisms-and-chemical-basis-of-herbal-formula-in-treating-chronic-myocardial-ischemia
#17
Shuzhen Guo, Peng Li, Bangze Fu, Wenjing Chuo, Kuo Gao, Wuxia Zhang, Junyao Wang, Jianxin Chen, Wei Wang
Herbal medicine is a mixture of multiple compounds, and is intended to exhibit therapeutic effects by attacking multiple disease-causing modules simultaneously. However, it is still a challenge for scientists to untangle the complex biological mechanisms and underlying material basis of herbal medicine. Here, this study was designed to build a systems-biology platform for exploring the molecular mechanisms and corresponding active compounds, with a typical example applied to an herbal formula Qishenkel (QSKL) in the treatment of chronic myocardial ischemia...
November 3, 2016: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/27809954/biologically-active-secondary-metabolites-from-the-fungi
#18
Gerald F Bills, James B Gloer
Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals...
November 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/27807743/exploring-human-diseases-and-biological-mechanisms-by-protein-structure-prediction-and-modeling
#19
Juexin Wang, Joseph Luttrell, Ning Zhang, Saad Khan, NianQing Shi, Michael X Wang, Jing-Qiong Kang, Zheng Wang, Dong Xu
Protein structure prediction and modeling provide a tool for understanding protein functions by computationally constructing protein structures from amino acid sequences and analyzing them. With help from protein prediction tools and web servers, users can obtain the three-dimensional protein structure models and gain knowledge of functions from the proteins. In this chapter, we will provide several examples of such studies. As an example, structure modeling methods were used to investigate the relation between mutation-caused misfolding of protein and human diseases including epilepsy and leukemia...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27807271/top-down-models-in-biology-explanation-and-control-of-complex-living-systems-above-the-molecular-level
#20
REVIEW
Giovanni Pezzulo, Michael Levin
It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience...
November 2016: Journal of the Royal Society, Interface
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