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Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs

Olga V. Kalinina, Oliver Wichmann, Gordana Apic, Robert B. Russell, Roland L. Dunbrack
2011 PLoS Computational Biology  
For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein  ...  The growth rate of confident predictions is twice that of experimental complexes, meaning that a complete structural drug-protein repertoire will be available at least ten years earlier than by Xray and  ...  Acknowledgments We thank Anne-Claude Gavin and Peer Bork (both at EMBL, Heidelberg) for a critical reading of the manuscript.  ... 
doi:10.1371/journal.pcbi.1002043 pmid:21573205 pmcid:PMC3088657 fatcat:xdqsxlfp5jdtzgev7b33hqgkfy

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

Murat Iskar, Georg Zeller, Xing-Ming Zhao, Vera van Noort, Peer Bork
2012 Current Opinion in Biotechnology  
Moreover, such integrative approaches may not only provide systemic insights into mechanisms of drugs and diseases, but also reveal new biological aspects of the 'system' human.  ...  We discuss here how computational data integration enables systemic views on a drug's action and allows to tackle complex problems such as the large-scale prediction of drug targets, drug repurposing,  ...  Acknowledgements We thank the members of the Bork group for helpful discussions.  ... 
doi:10.1016/j.copbio.2011.11.010 pmid:22153034 fatcat:pkugebecubb5fjbtrzynmratpm

Inorganic chemical biology: from small metal complexes in biological systems to metalloproteins

Sheila S David, Eric Meggers
2008 Current Opinion in Chemical Biology  
Proteins are gaining importance as nontraditional targets for metal complexes either by using the metal as a structural scaffold or by exploiting the reactivity of coordination compounds towards protein  ...  DNA remains the most important target for metal-based anticancer drugs.  ...  of inorganic complexes will not be forgotten.  ... 
doi:10.1016/j.cbpa.2008.03.008 pmid:18374664 pmcid:PMC2744206 fatcat:ulr4lovnmzhpfhmtecghf4g7g4

Emerging Trends in Cancer Drug Discovery—From Drugging the "Undruggable" to Overcoming Resistance

Joachim Rudolph, Jeff Settleman, Shiva Malek
2021 Cancer Discovery  
Treatment resistance is a major impediment to the goal of durable efficacy and cure, but the confluence of new biological insights, novel drug modalities, and drug combinations is predicted to enable transformative  ...  targeting of RNA.  ...  Scott Rosenberg for generating the structure figures for the manuscript and Dr. Kevan Shokat for helpful discussions. Published first April 2, 2021.  ... 
doi:10.1158/ pmid:33811118 fatcat:5kcqdysv75e4xdda534g5trifa

Computational methods for drug design and discovery: focus on China

Mingyue Zheng, Xian Liu, Yuan Xu, Honglin Li, Cheng Luo, Hualiang Jiang
2013 TIPS - Trends in Pharmacological Sciences  
Application of these methods spans a wide range, from drug target identification to hit discovery and lead optimization.  ...  For each selected method, a short background precedes an assessment of the method with respect to the needs of drug discovery, and, in particular, work from China is highlighted.  ...  Chen et al. established such an approach to build a target-focused library for finding hits towards studied targets by combining the scores of structural diversity, binding affinity, and drug-likeness  ... 
doi:10.1016/ pmid:24035675 pmcid:PMC7126378 fatcat:beegy5gxh5ex5nv2kablrzzqb4

Docking and chemoinformatic screens for new ligands and targets

Peter Kolb, Rafaela S Ferreira, John J Irwin, Brian K Shoichet
2009 Current Opinion in Biotechnology  
Computer-based docking screens are now widely used to discover new ligands for targets of known structure; in the last two years alone, the discovery of ligands for more than 20 proteins has been reported  ...  This method, which returns to an older, pharmacology logic, has been surprisingly successful in predicting new 'offtargets' for established drugs.  ...  In collaboration with Roth's group, we have tried to predict and test new off-target effects of established drugs.  ... 
doi:10.1016/j.copbio.2009.08.003 pmid:19733475 pmcid:PMC2766606 fatcat:eabfhmlafbezvglpxwf5u6u57y

Network Pharmacology Bridges Traditional Application and Modern Development of Traditional Chinese Medicine

Chang-xiao Liu, Rui Liu, Hui-rong Fan, Xue-feng Xiao, Xiao-peng Chen, Hai-yu Xu, Yan-ping Lin
2015 Chinese Herbal Medicines  
It focused on the theoretical system and potential prospect of TCM network applied in TCM research and development including predicting new drug targets, action mechanism, new drug discovery; evaluating  ...  pharmacodynamics, pharmacokinetics, safety, toxicology, quality control, and bioinformatics of drugs.  ...  Network pharmacology has become one of the new strategies for new drug discovery based on single-target drug research in recent years.  ... 
doi:10.1016/s1674-6384(15)60014-4 fatcat:ercr2myhsjhtfgow5ddpqzxjri

Systematic synergy modeling: understanding drug synergy from a systems biology perspective

Di Chen, Xi Liu, Yiping Yang, Hongjun Yang, Peng Lu
2015 BMC Systems Biology  
Owing to drug synergy effects, drug combinations have become a new trend in combating complex diseases like cancer, HIV and cardiovascular diseases.  ...  With a comprehensive and deep insight into the mechanism of drug synergy, systems biology opens a novel avenue for rational design of effective drug combinations.  ...  Acknowledgments The writing of the review was supported by the National Natural Science  ... 
doi:10.1186/s12918-015-0202-y pmid:26377814 pmcid:PMC4574089 fatcat:5vzb3djkl5ak3lorogp5qorkj4

Navigating Traditional Chinese Medicine Network Pharmacology and Computational Tools

Ming Yang, Jia-Lei Chen, Li-Wen Xu, Guang Ji
2013 Evidence-Based Complementary and Alternative Medicine  
The concept of "network target" has ushered in a new era in the field of traditional Chinese medicine (TCM).  ...  , including the principles of herb combination, biological foundations of herb or herbal formulae action, and molecular basis of TCM syndromes.  ...  Acknowledgments The authors are grateful to the anonymous reviewers and the editors for their helpful comments and suggestions, which substantially improved the quality of this paper.  ... 
doi:10.1155/2013/731969 pmid:23983798 pmcid:PMC3747450 fatcat:566jdvzpsfd2zljqooveu6qdyu

Applications of NMR to structure-based drug design in structural genomics

Robert Powers
2002 Journal of Structural and Functional Genomics  
A variety of NMR methodologies that cover a range of inherent resolution are described in the context of structure-based drug design in the era of structural genomics.  ...  Structural genomics is poised to have a tremendous impact on traditional structure-based drug design programs.  ...  The design of drugs using structural information is an iterative procedure where each pass of the design cycle requires obtaining a new structure for the lead compound(s) complexed with the protein of  ... 
pmid:12836668 fatcat:mjj63iknf5aklp24sfwmnwgoq4

Advanced Systems Biology Methods in Drug Discovery and Translational Biomedicine

Jun Zou, Ming-Wu Zheng, Gen Li, Zhi-Guang Su
2013 BioMed Research International  
of drug adverse effects, drug repositioning, and drug combination prediction.  ...  In addition, important advances in drug discovery, to which systems biology makes significant contributions, are discussed, including drug-target networks, prediction of drug-target interactions, investigation  ...  Likewise, many proteins are targeted by more than one drug containing distinct chemical structures.  ... 
doi:10.1155/2013/742835 pmid:24171171 pmcid:PMC3792523 fatcat:nhsv3ig7vzgspjhnzkaj3pwypm

Network Pharmacology-based on the Active Components and Molecular Mechanisms of Andrographis paniculata (Burm. f.) Wall. ex Nees in Treating Inflammation

Wen-ping Xiao, Wan-ju Zhang, Xu-jie Xiong, Lan-ying Xu
2021 Indian Journal of Pharmaceutical Education and Research  
Materials and Methods: The chemical components of AP. were screened by TCMSP database, in combination with literature.  ...  The functions of target genes and related pathways were analyzed and screened by database, the Component-Target-Pathways network of anti-inflammation effect of AP was established by using Cytoscape software  ...  ACKNOWLEDGEMENT Authors are thankful to Huanggang Normal University, College of Chemistry and Chemical Engineering for financial assistance.  ... 
doi:10.5530/ijper.55.3.149 fatcat:3t7ayuttsffrba6t5vmemibvri

Mycobacterial drug discovery

Katherine A. Abrahams, Gurdyal S. Besra
2020 RSC Medicinal Chemistry  
Innovations in mycobacterial drug discovery to accelerate the identification of new drug candidates with confirmed targets and whole cell activity.  ...  Innovations in combining these two opposing directives are anticipated to drive the rapid discovery and validation of new targets with the concurrent delivery of vast diverse chemical scaffolds for progression  ...  Another exciting chemical-genetics tool has been developed for concomitant discovery of inhibitors and their target.  ... 
doi:10.1039/d0md00261e pmid:34085044 pmcid:PMC8126887 fatcat:iojtvrp34rcozfxrcljuw5d5wi

A Review on Applications of Computational Methods in Drug Screening and Design

Xiaoqian Lin, Xiu Li, Xubo Lin
2020 Molecules  
In this review, we firstly discussed roles of multiscale biomolecular simulations in identifying drug binding sites on the target macromolecule and elucidating drug action mechanisms.  ...  Also, several application examples of combining various methods was discussed.  ...  In general, bioinformatics can help reveal the key genes from a massive amount of genomic data [1, 2] and thus provide possible target proteins for drug screening and design.  ... 
doi:10.3390/molecules25061375 pmid:32197324 fatcat:n4p3cpcgtjdyhdjitu2kcngxae

From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns

Sebastian Salentin, Melissa F. Adasme, Jörg C. Heinrich, V. Joachim Haupt, Simone Daminelli, Yixin Zhang, Michael Schroeder
2017 Scientific Reports  
Drug repositioning identifies new indications for known drugs. Here we report repositioning of the malaria drug amodiaquine as a potential anti-cancer agent.  ...  This work proves that PLIP interaction patterns are viable tools for computational repositioning and can provide search query information from a given drug and its target to identify structurally unrelated  ...  Acknowledgements We thank Alex Mestiashvili for technical support and Petra Lennig for help with the chemical classification of hit compounds and fruitful discussions.  ... 
doi:10.1038/s41598-017-11924-4 pmid:28900272 pmcid:PMC5595859 fatcat:2enk2daezbgurlzlhhzle75zuq
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