Archive for the ‘Themed Issues’ Category

MedChemComm call for papers: Epigenetics themed issue

MedChemComm themed issue: Epigenetics

Guest Editors: Dr Mark Bunnage (Pfizer) and Prof. James E. Bradner (Harvard Medical School)

Submission Deadline: 16th June 2014

Submissions are now open for a high-profile themed issue on Epigenetics. The scope of the issue covers all areas of epigenetics within medicinal chemistry.

New research in MedChemComm is published as Concise Articles: flexible articles that have no strict page limits or formatting requirements. Manuscripts can be submitted in any reasonable format using our submission system. Template is not required. Please indicate that it is for the Epigenetics themed issue in the comments to the editor field. The level of quality of this issue will be high, and all manuscripts will undergo the journal’s normal peer review process.

The deadline for submissions to the themed issue is 16th June 2014, although submissions before this date are of course welcomed.

If you would like to contribute to this issue please contact the Editorial Office.

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A Focus On Computer-Aided Drug Discovery

A recent workshop on the role of computer aided drug discovery was jointly held by the Royal Society of Chemistry and the Biochemical Society with the aim of aiding collaborations between biological scientists and computational chemists.

Following this workshop we have brought together a collection of articles and books that highlight recent research on computer-aided drug discovery and related areas. Below is a slection from across the Royal Society of Chemistry and you can also find a collection of articles from the Biochemical Society HERE…

All of the Communications, Papers and Reviews below are free to access until 7 February 2014.

Books
(PDFs of the front matter, table of contents and first chapter are free to view.)

Drug Design Strategies: Quantitative ApproachesPhysico-Chemical and Computational Approaches to Drug Discovery
Editors: Javier Luque, Xavier Barril

Drug Design Strategies
Editors: David J Livingstone, Andrew M Davis

Innovations in Biomolecular Modeling and Simulations: Volume 2:

Chapter 11 – Structure-based Design Technology CONTOUR and its Application to Drug Discovery
Zhijie Liu, Peter Lindblom, David A. Claremon and Suresh B. Singh

Chapter 12 – Molecular Simulation in Computer-aided Drug Design: Algorithms and Applications
Robert V. Swift and Rommie E. Amaro

Chapter 13– Computer-aided Drug Discovery: Two Antiviral Drugs for HIV/AIDS
J. Andrew McCammon

G Protein-Coupled Receptors: From Structure to Function:

Chapter 18 – Structure-based Virtual Screening for Ligands of G Protein-coupled Receptors
Stefano Costanzi

Reviews

Informatic strategies for the discovery of polyketides and nonribosomal peptides
Chad Johnston, Ashraf Ibrahim and Nathan Magarvey
Med. Chem. Commun., 2012, DOI: 10.1039/C2MD20120H, Review Article

Molecular docking for virtual screening of natural product databases
Dik-Lung Ma, Daniel Shiu-Hin Chan and Chung-Hang Leung
Chem. Sci., 2011, DOI: 10.1039/C1SC00152C, Minireview

Approaches to discover non-ATP site kinase inhibitors
Lori Krim Gavrin and Eddine Saiah
Med. Chem. Commun., 2013, DOI: 10.1039/C2MD20180A, Review Article

Drug repositioning by structure-based virtual screening
Dik-Lung Ma, Daniel Shiu-Hin Chan and Chung-Hang Leung
Chem. Soc. Rev., 2013, DOI: 10.1039/C2CS35357A, Review Article

Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification
Susana M. Tomasio, Heather P. Harding, David Ron, Benedict C. S. Cross and Peter J. Bond
Mol. BioSyst., 2013, DOI: 10.1039/C3MB70234K, Review Article

Network-based drug repositioning
Zikai Wu, Yong Wang and Luonan Chen
Mol. BioSyst., 2013, DOI: 10.1039/C3MB25382A, Review Article


Communications and Papers

Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein–protein interactions
Philipp Thiel, Lars Röglin, Nicole Meissner, Sven Hennig, Oliver Kohlbacher and Christian Ottmann
Chem. Commun., 2013, DOI: 10.1039/C3CC44612C, Communication

Plugging the explicit σ-holes in molecular docking
Michal Kolář, Pavel Hobza and Agnieszka K. Bronowska
Chem. Commun., 2013, DOI: 10.1039/C2CC37584B, Communication

Fragments to link. A multiple docking strategy for second site binders
Márton Vass and György M. Keserű
Med. Chem. Commun., 2013, DOI: 10.1039/C2MD20267K, Concise Article

A rapid identification of hit molecules for target proteins via physico-chemical descriptors
Goutam Mukherjee and B. Jayaram
Phys. Chem. Chem. Phys., 2013, DOI: 10.1039/C3CP44697B, Paper

Discovery of novel inhibitors for human farnesyltransferase (hFTase) via structure-based virtual screening
Xiaojuan Yu, Xue Zhao, Lili Zhu, Chuanxin Zou, Xiaofeng Liu, Zhenjiang Zhao, Jin Huang and Honglin Li
Med. Chem. Commun., 2013,DOI: 10.1039/C3MD00058C, Concise Article

Prediction of chemical–protein interactions: multitarget-QSAR versus computational chemogenomic methods
Feixiong Cheng, Yadi Zhou, Jie Li, Weihua Li, Guixia Liu and Yun Tang
Mol. BioSyst., 2012, DOI: 10.1039/C2MB25110H, Paper

Identification of novel inhibitors of p53–MDM2 interaction facilitated by pharmacophore-based virtual screening combining molecular docking strategy
Weisi Wang, Xiaolei Zhu, Xueqin Hong, Lin Zheng, Hong Zhu and Yongzhou Hu
Med. Chem. Commun., 2013, DOI: 10.1039/C2MD20208E, Concise Article

Predicting cancer drug mechanisms of action using molecular network signatures
Justin R. Pritchard, Peter M. Bruno, Michael T. Hemann and Douglas A. Lauffenburger
Mol. BioSyst., 2013, DOI: 10.1039/C2MB25459J, Paper

Prospective use of molecular field points in ligand-based virtual screening: efficient identification of new reversible Cdc25 inhibitors
James C. Collins, Alan Armstrong, Kathryn L. Chapman, Hayley C. Cordingley, Albert A. Jaxa-Chamiec, Katie E. Judd, David J. Mann, Katherine A. Scott, Catherine J. Tralau-Stewart and Caroline M. R. Low
Med. Chem. Commun., 2013, DOI: 10.1039/C3MD00047H, Concise Article

Discovery of Rho-kinase inhibitors by docking-based virtual screening
Mingyun Shen, Huidong Yu, Youyong Li, Pixu Li, Peichen Pan, Shunye Zhou, Liling Zhang, Shang Li, Simon Ming-Yuen Lee and Tingjun Hou
Mol. BioSyst., 2013, DOI: 10.1039/C3MB00016H, Paper

Prediction of adverse drug reactions by a network based external link prediction method
Jiao Lin, Qifan Kuang, Yizhou Li, Yongqing Zhang, Jing Sun, Zhanling Ding and Menglong Li
Anal. Methods, 2013, DOI: 10.1039/C3AY41290C, Paper

Targeting the inactive conformation of protein kinases: computational screening based on ligand conformation
Pascal Bonnet, Daniel Mucs and Richard A. Bryce
Med. Chem. Commun., 2012, DOI: 10.1039/C1MD00256B, Concise Article

Structure-oriented bioinformatic approach exploring histidine-rich clusters in proteins
Shujian Cun, Yau-Tsz Lai, Yuen-Yan Chang and Hongzhe Sun
Metallomics, 2013, DOI: 10.1039/C3MT00026E, Concise Article

Rational design of small modified peptides as ACE inhibitors
Daniel G. Silva, Matheus P. Freitas, Elaine F. F. da Cunha, Teodorico C. Ramalho and Cleiton A. Nunes
Med. Chem. Commun., 2012, DOI: 10.1039/C2MD20214J, Concise Article

Development of a novel class of B-RafV600E-selective inhibitors through virtual screening and hierarchical hit optimization
Xiangqian Kong, Jie Qin, Zeng Li, Adina Vultur, Linjiang Tong, Enguang Feng, Geena Rajan, Shien Liu, Junyan Lu, Zhongjie Liang, Mingyue Zheng, Weiliang Zhu, Hualiang Jiang, Meenhard Herlyn, Hong Liu, Ronen Marmorstein and Cheng Luo
Org. Biomol. Chem., 2012, DOI: 10.1039/C2OB26081F, Paper

Computational design of a thermostable mutant of cocaine esterase via molecular dynamics simulations
Xiaoqin Huang, Daquan Gao and Chang-Guo Zhan
Org. Biomol. Chem., 2011, DOI: 10.1039/C0OB00972E, Paper

Structure determinants of indolin-2-on-3-spirothiazolidinones as MptpB inhibitors: An in silico study
Yinfeng Yang, Jinghui Wang, Yan Li, Wei Xiao, Zhenzhong Wang, Jingxiao Zhang, Weimin Gao, Shuwei Zhang and Ling Yang
Soft Matter, 2013, DOI: 10.1039/C3SM51995C, Paper

Synthesis of novel PPARα/γ dual agonists as potential drugs for the treatment of the metabolic syndrome and diabetes type II designed using a new de novo design program PROTOBUILD
Yushma Bhurruth-Alcor, Therese Røst, Michael R. Jorgensen, Christos Kontogiorgis, Jon Skorve, Robert G. Cooper, Joseph M. Sheridan, William D. O. Hamilton, Jonathan R. Heal, Rolf K. Berge and Andrew D. Miller
Org. Biomol. Chem., 2011, DOI: 10.1039/C0OB00146E, Paper

Anticancer loading and controlled release of novel water-compatible magnetic nanomaterials as drug delivery agents, coupled to a computational modeling approach
Pierre Dramou, Pengli Zuo, Hua He, Lien Ai Pham-Huy, Wenyue Zou, Deli Xiao, Chuong Pham-Huy and Theophilus Ndorbor
J. Mater. Chem. B, 2013, DOI: 10.1039/C3TB20502A, Paper

An NMR crystallography DFT-D approach to analyse the role of intermolecular hydrogen bonding and π–π interactions in driving cocrystallisation of indomethacin and nicotinamide
Dmytro V. Dudenko, Jonathan R. Yates, Kenneth D. M. Harris and Steven P. Brown
CrystEngComm, 2013, DOI: 10.1039/C3CE41240G, Paper

Modelling the possible bioactivity of ellagitannin-derived metabolites. In silico tools to evaluate their potential xenoestrogenic behavior
Luca Dellafiora, Pedro Mena, Pietro Cozzini, Furio Brighenti and Daniele Del Rio
Food Funct., 2013,4, DOI: 10.1039/C3FO60117J, Paper

Towards ab initio screening of co-crystal formation through lattice energy calculations and crystal structure prediction of nicotinamide, isonicotinamide, picolinamide and paracetamol multi-component crystals
H. C. Stephen Chan, John Kendrick, Marcus A. Neumann and Frank J. J. Leusen
CrystEngComm, 2013, DOI: 10.1039/C3CE40107C, Paper

You may also be interested in the upcoming Faraday Discussion on Molecular Simulations and Visualization in 2014 – Find out more here…

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MedChemComm call for papers: Carbohydrate themed issue

MedChemComm themed issue: Carbohydrates

Guest Editors: Sylvie Garneau-Tsodikova (University of Kentucky, USA) and Timor Baasov (Technion-Israel Institute of Technology, Israel)

Submission Deadline: 28th February 2014

Submissions are now open for a high-profile themed issue on Carbohydrates, due for publication in MedChemComm in summer 2014. The scope of the issue covers all areas of carbohydrate chemistry and biology which are relevant to drug discovery.

New research in MedChemComm is published as Concise Articles: flexible articles that have no strict page limits or formatting requirements. Manuscripts can be submitted in any reasonable format using our submission system. Template is not required. Please indicate that it is for the Carbohydrates themed issue in the comments to the editor field. The level of quality of this issue will be high, and all manuscripts will undergo the journal’s normal peer review process.

The deadline for submissions to the themed issue is 28th February 2014, although submissions before this date are of course welcomed.

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MedChemComm papers in 2013 Cancer Nanotechnology collection

We are pleased to present a web collection of articles from publications across the RSC journal portfolio demonstrating the use of (nano)technology in the diagnosis, imaging and treatment of cancer.

Here are some Med Chem Comm articles in this special cancer nanotechnology collection:

Towards biocompatible nanovalves based on mesoporous silica nanoparticles
Ying-Wei Yang
Med. Chem. Commun., 2011,2, 1033-1049
DOI: 10.1039/C1MD00158B

Silver nanoparticles—the real “silver bullet” in clinical medicine?
Kenneth K. Y. Wong and Xuelai Liu
Med. Chem. Commun., 2010,1, 125-131
DOI: 10.1039/C0MD00069H

Engineering of peglayted camptothecin into core–shell nanomicelles for improving solubility, stability and combination delivery
Haiqing Dong, Chunyan Dong, Yue Feng, Tianbin Ren, Zhonghai Zhang, Lan Li and Yongyong Li  
Med. Chem. Commun., 2012,3, 1555-1561
DOI: 10.1039/C2MD20153D

Hard shell gas-filled contrast enhancement particles for colour Doppler ultrasound imaging of tumors
H. Paul Martinez, Yuko Kono, Sarah L. Blair, Sergio Sandoval, Jessica Wang-Rodriguez, Robert F. Mattrey, Andrew C. Kummel and William C. Trogler
Med. Chem. Commun., 2010,1, 266-270
DOI: 10.1039/C0MD00139B

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Call for papers: Chemical Biology for Target Identification and Validation

MedChemComm themed issue: Chemical Biology for Target Identification and Validation

Guest Editors: Nathanael Gray (Harvard University, USA) and Lyn Jones (Pfizer, Cambridge, USA)

Submission Deadline: 30th September 2013

Submissions are now open for a high-profile themed issue on Chemical Biology for Target Identification and Validation, due for publication in MedChemComm in early 2014. It will receive great exposure and significant promotion.

Scope
Part of MedChemComm’s mission is to publish high level chemistry biology research which enables drug discovery. This special issue will be broad in scope, covering advances in the discovery, development and application of chemical biology to elucidate and validate new therapeutic targets. Relevant topics include (but are not limited to):

  • the use of –omics and imaging technologies
  • immunoprecipitation and affinity chromatography to identify novel targets and therapeutic modalities
  • the creation and development of new techniques to assess target (and off-target) engagement
  • advances in areas such as chemogenomics, microarrays, yeast three hybrid, RNAi and chem/bioinformatics

New research in MedChemComm is published as Concise Articles. This article type encompasses both Communication and Full Paper styles and is generally between 3 and 7 pages in length, but there is no strict page limit.

Manuscripts can be submitted in any reasonable format using our submission system. Template is not required. Please indicate that it is for the Chemical Biology themed issue in the comments to the editor field. The level of quality of this issue will be high, and all manuscripts will undergo the journal’s normal peer review process.

The deadline for submissions to the themed issue is 30th September 2013, although submissions before this date are of course welcomed.

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Drug-target residence time: introducing a web focus

MedChemComm is delighted to present a concise web focus on drug-target residence time.

Koen Augustyns, Professor of Medicinal Chemistry at the University of Antwerp, Belgium, introduces the topic and has hand-picked 3 articles for this spotlight:

‘Analysis of drug-target residence time has begun to play a larger role in drug discovery as suggested by recent literature. For compounds with a slow off rate, long action at the target may render a perfect pharmacokinetic profile unnecessary, and selectivity vs. other targets inhibited only briefly may be more readily achieved. Specific, irreversible inhibition may be considered as the logical extreme for this approach. For other targets or therapeutic areas, other kinetic profiles may be desirable. The topic is timely as indicated by a recently launched Innovative Medicines Initiative project and the organization of several symposia exclusively focusing on this subject. However, there is a real need to build a better understanding in the medicinal chemistry and drug discovery community of the preferred profiles and screening methods for compounds with optimized drug-target residence times.’

In this MedChemComm web focus Georges Vauquelin comments on the determination of drug-target residence time by radioligand binding and functional assays and discusses their physiological relevance. Duncan C. Miller et al. investigate how molecular properties may affect the dissociation kinetics of ligand from its biological target. Finally, Juswinder Singh et al. describe the superiority of a novel EGFR targeted covalent inhibitor over its reversible analogues in overcoming drug resistance.

Interested? Why not read these three articles now:

Determination of drug–receptor residence times by radioligand binding and functional assays: experimental strategies and physiological relevance
Georges Vauquelin
Med. Chem. Commun., 2012,3, 645-651
DOI: 10.1039/C2MD20015E, Review Article

Investigation of the effect of molecular properties on the binding kinetics of a ligand to its biological target
Duncan C. Miller, Graham Lunn, Peter Jones, Yogesh Sabnis, Nichola L. Davies and Paul Driscoll
Med. Chem. Commun., 2012,3, 449-452
DOI: 10.1039/C2MD00270A, Concise Article

Superiority of a novel EGFR targeted covalent inhibitor over its reversible counterpart in overcoming drug resistance
Juswinder Singh, Erica Evans, Margit Hagel, Matthew Labinski, Alex Dubrovskiy, Mariana Nacht, Russell C. Petter, Aravind Prasad, Michael Sheets, Thia St Martin, Robert Tjin Tham Sjin, William Westlin and Zhendong Zhu
Med. Chem. Commun., 2012,3, 780-783
DOI: 10.1039/C2MD20017A, Concise Article

We hope that you find this selection interesting and stimulating to read – and why not submit your latest research in the area today!

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Themed Issue Highlighting New Talent In Medicinal Chemistry Now Published

Welcome to the first issue of MedChemComm of 2013. Join us in taking a look at our successes from the last year and in looking forward to another exciting year for the journal by reading our New Year Editorial.

Not only is this issue the first of a new year it is also our New Talent themed issue, where we showcase the strength of research being carried out by some of tomorrow’s leaders in the field with 36 high quality articles.

This stunning cover (right) highlights the work of Seung Bum Park et al. who have discovered a novel heterobiaryl pyrazolopyridine skeleton as a selective FLT3 inhibitor from phenotype-based viability profiling and hypothesis-driven deconvolution.

Discovery of a highly selective FLT3 kinase inhibitor from phenotypic cell viability profiling
Sanghee Lee, Ala Jo and Seung Bum Park
DOI: 10.1039/C2MD20169K

Stars, stars everywhere, and it’s not just the rising stars featured in this issue that we’re talking about with this cover (left) from Stephen P. Andrews and Benjamin Tehan. Andrews & Tehan review the first example of structure-based drug design with G protein-coupled receptors (GPCRs) thanks to StaR® proteins (stabilised GPCRs), and how this has enabled the identification of a preclinical candidate for the treatment of Parkinson’s disease.

Stabilised G protein-coupled receptors in structure-based drug design: a case study with adenosine A2A receptor

Stephen P. Andrews and Benjamin Tehan
DOI: 10.1039/C2MD20164J

Read it all today by visiting our journal home page.

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Drug discovery: on the origins of drug polypharmacology – a review

‘The ability of many drugs, unintended most often, to interact with multiple proteins is commonly referred to as polypharmacology. Could this be a reminiscent chemical signature of early protein evolution?’ asks Jordi Mestres.

In this review article, Xavier Jalencas and Jordi Mestres (Chemogenomics Laboratory, Hospital del Mar Research Institute, Barcelona) explore the origins of drug polypharmacology and provide clues as to why most drugs hit multiple targets. Covering both the chemical (including molecular properties and fragment composition of the drug themselves) and the biological sources of polypharmacology (describing target phylogeny and binding site similarity), the article also provides some direct key implications of polypharmacology for drug discovery, while questioning whether this multitarget ability could have come from adaptative mechanisms…

Take this fascinating journey and read the full review today!

On the origins of drug polypharmacology
Xavier Jalencas and Jordi Mestres
Med. Chem. Commun, 2013, Advance Article
DOI:10.1039/C2MD20242E

This article is part of MedChemComm’s New Talent themed issue

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Type III secretion systems inhibitors – an updated comprehensive review

Howard C. Hang (The Rockefeller University) et al.’s review article reflects the latest updates on Type III secretion systems (T3SSs) inhibitors. ‘T3SSs are central to the virulence of many human Gram-negative pathogens such as Salmonella, Shigella, Pseudomonas, enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli,(EHEC), Vibrio, Yersinia, and Chlamydia’ explains Hang, and are exciting targets for anti-bacterial development.

The article not only provides the reader with a comprehensive view of the severall classes of small molecules that inhibit the secretion and translocation of bacterial effector proteins, their mode of action and prospects for clinical development, but also brings insights into the different methods developed to allow the screening of very large libraries of molecules.

A must-read for anyone interested in bacterial virulence and small molecule inhibitors.

Small molecules aimed at type III secretion systems to inhibit bacterial virulence
Lun K. Tsou, Paul D. Dossa and Howard C. Hang
Med. Chem. Commun., 2012, DOI: 10.1039/C2MD20213A

This review is part of MedChemComm’s New Talent themed issue:

Highlighting medicinal chemistry research in its broadest sense and showcasing the strength of research being carried out by tomorrow’s leaders in the field: view the collection grow

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Themed issue: still time to submit to the Drugs in Middle Space themed issue

There’s still time to submit to the MedChemComm web themed issue on Drugs in Middle Space. Guest edited by David Rees (Astex Therapeutics, UK) and Nick Terrett (Ensemble Therapeutics, USA) this issue will feature research and review articles focussing on non-traditional drug molecules that occupy the ‘middle space’ between ‘Rule of 5′ compliant small molecules and biologicals.

 

Deadline for submission: 30th September 2012

 

Appropriate topics include the design, synthesis, optimization, modelling, analysis and profiling of peptides, peptidomimetics, macrocycles, natural products, natural product mimetics, and any other molecule in range of approximately 500 to 3000 Daltons. We will seek an emphasis on how this range of structural classes is providing novel approaches to address challenging disease targets and in particular those that might hitherto have been categorised as ‘undruggable’.

Submissions for this issue can be submitted anytime from now until 30th September 2012 using the journal’s online submission system. Please add the phrase ‘Invited article for Drugs in Middle Space’ in the comments to the editor field. All manuscripts will undergo strict peer review and will be assessed using the same criteria as for regular MedChemComm articles.

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