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What compound should I make next? Using Matched Molecular Series for prospective medicinal chemistry

Noel M O'Boyle, Roger Sayle, Jonas Boström
2014 Journal of Cheminformatics  
Here we greatly enhance the performance of MMPA for activity prediction by extending to Matched Molecular Series [3, 4] .  ...  It will be shown that it is possible to predict, with a known degree of accuracy, what R group should increase/ decrease the activity of interest, given an observed ordering of activities for a matched  ... 
doi:10.1186/1758-2946-6-s1-o5 pmid:24765128 pmcid:PMC3980175 fatcat:uecahvdj7vaelneyyurb6c5blu

Designing the next generation of medicines for malaria control and eradication

Jeremy N Burrows, Rob Hooft van Huijsduijnen, Jörg J Möhrle, Claude Oeuvray, Timothy NC Wells
2013 Malaria Journal  
Sustained investment over the next decade in discovery and development of new molecules is essential to enable the long-term delivery of the medicines needed to combat malaria.  ...  For the parts of the world where the current gold standard artemisinin combination therapies are active, significant improvements can still be made: for example combination medicines which allow for single  ...  On the positive side, success rates for finding new chemical series have increased with improvements in high-throughput screening using live parasites and the use of large, wide-diversity compound collections  ... 
doi:10.1186/1475-2875-12-187 pmid:23742293 pmcid:PMC3685552 fatcat:zblw6r6i6jc6tebf3q76mifzey

Deciphering next-generation pharmacogenomics: an information technology perspective

G. Potamias, K. Lakiotaki, T. Katsila, M. T. M. Lee, S. Topouzis, D. N. Cooper, G. P. Patrinos
2014 Open Biology  
Othman a,c a Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia, b Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala  ...  patients and 10 matched controls using a panel of 742 miRNAs PCRbased assay.  ...  Data of predicted structure is used to verify which promoter elements could be essential for properdin expression.  ... 
doi:10.1098/rsob.140071 pmid:25030607 pmcid:PMC4118603 fatcat:xy235o2vqbbghj6dngqtrjse3m

2015 Golden Helix Symposium - Next Generation Pharmacogenomics. March 11-13, 2015, Kuala Lumpur, Malaysia: Abstracts

2015 Public Health Genomics  
Othman a,c a Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia, b Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala  ...  of antioxidant status by GBR and what transcriptional mechanisms they regulate, using HepG2 cells.  ...  Although several molecular studies were conducted, but the precise signaling molecular pathway that attributes to this phenomenon remains elusive.  ... 
doi:10.1159/000381430 pmid:25823950 fatcat:3lluvaoguzhjvbs7oi6aqhtfna

Navigating the Rapids: The Development of Regulated Next-Generation Sequencing-Based Clinical Trial Assays and Companion Diagnostics

Saumya Pant, Russell Weiner, Matthew J. Marton
2014 Frontiers in Oncology  
standards for the same.  ...  The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.  ...  ACKNOWLEDGMENTS We thank Steven Engel, Ken Emancipator, and Mya Thomae for reading the manuscript and making helpful suggestions.  ... 
doi:10.3389/fonc.2014.00078 pmid:24860780 pmcid:PMC4029014 fatcat:2p6ne7rdnffgxnvzug7bis6atu

A Next Generation Connectivity Map: L1000 Platform And The First 1,000,000 Profiles [article]

Aravind Subramanian, Rajiv Narayan, Steven M. Corsello, David D. Peck, Ted E. Natoli, Xiaodong Lu, Joshua Gould, John F. Davis, Andrew A. Tubelli, Jacob K. Asiedu, David L. Lahr, Jodi E. Hirschman (+40 others)
2017 bioRxiv   pre-print
The 1.3 million L1000 profiles described here, as well as tools for their analysis, are available at https://clue.io.  ...  We further show that the expanded CMap can be used to discover mechanism of action of small molecules, functionally annotate genetic variants of disease genes, and inform clinical trials.  ...  In principle, multi-targeted compounds could have desirable therapeutic benefits, and the CMap could be used to guide medicinal chemistry toward such dual activities.  ... 
doi:10.1101/136168 fatcat:lm5obdt2hjaj3kraonfe6fggoq

Recent advances in i-Gene tools and analysis: microarrays, next generation sequencing and mass spectrometry

Michael J Moorhouse, Hari S Sharma
2011 Indian Journal of Biochemistry & Biophysics  
Recent advances in technology and associated methodology have made the current period one of the most exciting in molecular biology and medicine.  ...  In this review, we discuss the application of modern 'High-Throughput' molecular biological technologies such as 'Microarrays' and 'Next Generation Sequencing' to scientific and biomedical research as  ...  Prior to this, we review the 'DNA makes RNA makes Protein' paradigm and its use as a information flow model for i-Gene analysis and then data processing and analysis operations.  ... 
pmid:22053690 fatcat:mpe6wtusvjgvbcpcpumkpdi2ym

Review of third and next generation synchrotron light sources

Donald H Bilderback, Pascal Elleaume, Edgar Weckert
2005 Journal of Physics B: Atomic, Molecular and Optical Physics  
, chemistry and biology, for example.  ...  , x-ray free electron laser) can take us further into the future, to provide the unique synchrotron light that is so highly prized for today's studies in science in such fields as materials science, physics  ...  Acknowledgments We thank Professor Dr Horst Schmidt-Böcking for inviting us to contribute this paper and our numerous colleagues who have grown the SR field over the last decades into a large diverse science  ... 
doi:10.1088/0953-4075/38/9/022 fatcat:6lbueln4fzdinbn6vgzf2vzbbi

Impact of Next-Generation Technologies on Exploring Socioeconomically Important Parasites and Developing New Interventions [chapter]

Cinzia Cantacessi, Andreas Hofmann, Bronwyn E. Campbell, Robin B. Gasser
2014 Msphere  
and genomes of these parasites, (iii) provides some recent examples of applications, and (ivii) emphasizes the prospects of fundamental biological explorations of parasites using these technologies for  ...  2 Summary High-throughput molecular and computer technologies have become instrumental for systems biological explorations of pathogens, including parasites.  ...  Liu Z., Liu Q., Pesce J. et al. (2004) Requirements for the development of IL-4-producing T cells during intestinal nematode infections: what it takes to make a Th2 cell in vivo.  ... 
doi:10.1007/978-1-4939-2004-4_31 pmid:25399114 fatcat:viyzkpcf2fcn5exyx2ixq3cfw4

Self‐Healing Hydrogels: The Next Paradigm Shift in Tissue Engineering?

Sepehr Talebian, Mehdi Mehrali, Nayere Taebnia, Cristian Pablo Pennisi, Firoz Babu Kadumudi, Javad Foroughi, Masoud Hasany, Mehdi Nikkhah, Mohsen Akbari, Gorka Orive, Alireza Dolatshahi‐Pirouz
2019 Advanced Science  
Given their durability and long-term stability, self-healable hydrogels have, in the past few years, emerged as promising replacements for the many brittle hydrogels currently being used in preclinical  ...  Here, the recent progress in the development of multifunctional and self-healable hydrogels for various tissue engineering applications is discussed in detail.  ...  The prospect of such self-healable android-like robots is certainly of huge interest for governments worldwide, being potentially useful for militaries preparing for the challenges of the next century  ... 
doi:10.1002/advs.201801664 pmid:31453048 pmcid:PMC6702654 fatcat:7tslhmyhprgwdfoqtd6yue72t4

Follow-up: Prospective compound design using the 'SAR Matrix' method and matrix-derived conditional probabilities of activity

Disha Gupta-Ostermann, Yoichiro Hirose, Takenao Odagami, Hiroyuki Kouji, Jürgen Bajorath
2015 F1000Research  
Gupta-Ostermann D, Bajorath J: The 'SAR Matrix' method and its extensions for applications in medicinal chemistry and chemogenomics [v2; ref status: indexed, http://f1000r.es/3rg].  ...  Follow-up: Prospective compound design using the 'SAR Matrix' method and matrix-derived conditional probabilities of activity [version 1; referees: 3 approved, 1 approved with reservations] 2015, :75 (  ...  Preeti Iyer, and Jenny Balfer for valuable contributions to the development of the SARM approach and activity prediction methods.  ... 
doi:10.12688/f1000research.6271.1 pmid:25949808 pmcid:PMC4406192 fatcat:ownjnvh4j5bkfapdvqulxdqa5e

Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde?

Maykel Cruz-Monteagudo, José L. Medina-Franco, Yunierkis Pérez-Castillo, Orazio Nicolotti, M. Natália D.S. Cordeiro, Fernanda Borges
2014 Drug Discovery Today  
The influence of activity cliffs in medicinal chemistry applications is extensively documented.  ...  In this review, the duality of activity cliffs in medicinal chemistry and computational approaches is addressed, with emphasis on the rationale and potential solutions for handling the 'ugly face' of activity  ...  are particularly relevant for medicinal chemistry applications.  ... 
doi:10.1016/j.drudis.2014.02.003 pmid:24560935 fatcat:5dieee6zvjemzkghtlukdhrfbi

Triazole–Dithiocarbamate Based Selective Lysine Specific Demethylase 1 (LSD1) Inactivators Inhibit Gastric Cancer Cell Growth, Invasion, and Migration

Yi-Chao Zheng, Ying-Chao Duan, Jin-Lian Ma, Rui-Min Xu, Xiaolin Zi, Wen-Lei Lv, Meng-Meng Wang, Xian-Wei Ye, Shun Zhu, David Mobley, Yan-Yan Zhu, Jun-Wei Wang (+4 others)
2013 Journal of Medicinal Chemistry  
In the current study, we designed and synthesized five series of 1,2,3-triazole-dithiocarbamate hybrids and screened their inhibitory activity toward LSD1.  ...  We found that some of these compounds, especially compound 26, exhibited the most specific and robust inhibition of LSD1.  ...  , which is particularly important for the prospective use of the method.  ... 
doi:10.1021/jm401002r pmid:24131029 pmcid:PMC3881423 fatcat:xstl4fikrja2fiamubdpwav4lu

Pursuing the leadlikeness concept in pharmaceutical research

Mike M Hann, Tudor I Oprea
2004 Current Opinion in Chemical Biology  
medicinal chemistry can be found need to become cost effective.  ...  More recently, the need to go further in defining what makes a good lead has been recognised with the concept of leadlikeness.  ... 
doi:10.1016/j.cbpa.2004.04.003 pmid:15183323 fatcat:pp4knrycoje5dagzbyhbowxofu

Software and resources for computational medicinal chemistry

Chenzhong Liao, Markus Sitzmann, Angelo Pugliese, Marc C Nicklaus
2011 Future Medicinal Chemistry  
CADD provides valuable insights into experimental findings and mechanism of action, new suggestions for molecular structures to synthesize, and can help make cost-effective decisions before expensive synthesis  ...  Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds  ...  The list of compounds that matches the pharmacophore query should be evaluated for promiscuous matches, such as highly flexible, feature-rich molecules.  ... 
doi:10.4155/fmc.11.63 pmid:21707404 pmcid:PMC3413324 fatcat:csjirmoxcfhntfhgirqdm3hjae
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