Researchers from North Carolina State University have created a new online service – ChemMaps – that allows users to interactively navigate the chemical space of over 8,000 drugs and 47,000 environmental compounds in 3D and real time. ChemMaps is designed to be a central resource for students and researchers who want to easily visualize and study complicated sets of chemical structures. The first release of the free-to-use website is available at www.chemmaps.com.

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Designing the Next Generation of Hair Dyes

North Carolina State University researchers have created the largest publicly available chemical database of hair dye substances as a resource for developing a new generation of hair color products that are safer for consumers, stylists and the environment.

The online Hair Dye Substance Database contains detailed information about the structure and properties of 313 substances in current and past commercial hair dyes. Using computer-based classification – what’s known as cheminformatics – researchers grouped the dyes into clusters with similar structures and properties. The results revealed some surprises and promising new avenues for research.

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Two students in Denis Fourches’ Cheminformatics lab recently received highly competitive ACS CINF awards at the American Chemical Society ACS National Meeting in Washington,DC.

Phyo Phyo Kyaw Zin presented her most recent work on the development of the PKS enumerator, a software to generate large libraries of macrocycles with user-defined constrains (she showcased a dataset of 10 million compounds). This work is done in close collaboration with Dr. Gavin Williams (Chemistry, NCSU) and has applications for the virtual screening of new bioactive macrolides for the development of new antimicrobials and agrochemicals.

Jeremy Ash presented his work on the first study using cheminformatics for the analysis and modeling of metabolomics data. The technique allows for a better identification of individual and groups of small molecule metabolites that can discriminate cancer patients versus healthy individuals. This is relevant for the development of disease biomarkers and precision medicine.

RealityConvert: A tool for preparing 3D models of biochemical structures for augmented and virtual reality

The Fourches group has developed the RealityConvert software tool and associated website, which allow users to easily convert molecular objects to high quality 3D models directly compatible for AR and VR applications. The ultimate goal of RealityConvert is to facilitate and boost the development of AR and VR contents for bioinformatics and cheminformatics applications.

RealityConvert: A tool for preparing 3D models of biochemical structures for augmented and virtual reality

Jeremy Ash (Bioinformatics, Ph.D. student) recently received a fellowship for Fall 2017 from the Triangle Center of Evolutionary Medicine (TriCEM).   His proposed project is an extension of his recently accepted publication in the Journal of Chemical Information and Modeling on the use of molecular dynamics extracted chemical descriptors to characterize and model a series of ERK2 inhibitors.  The extension will focus on the evolution of resistance to chemotherapy drugs in mitogen activated protein kinases:

Kinase inhibitors represent the new generation of highly promising bioactive molecules for combating various types of cancer. With compounds already on the market and even more currently in clinical trials, the research community is on the path to developing a large collection of kinase-mediating drugs and chemical probes. However, drug resistance is the “Achilles heel” of kinases inhibitors. As members of signaling pathways that are critical to an array of cellular processes, kinase inhibition gives rise to strong selection pressure for drug resistance conferring mutations in patients. In this project, we focus on studying the ERK1 and ERK2 kinase, especially the dynamic interactions small molecule inhibitors undergo within the ERK binding site. To do so, we will rely on our novel modeling approach that integrates several state-of-the-art cheminformatics methods (molecular docking, molecular dynamics, and machine learning). We posit this analysis will deepen the understanding of why certain inhibitors interact differently with these two isoforms. This will help identify residues where the selection pressure driving drug resistance is different, and inform chemists of strategies to design new ERK inhibitors with greater efficacy. At last, our analysis of ERK-ligand dynamic interactions that confer specificity to ERK1, ERK2, or both will aide in the development of new chemical probes capable of more selective inhibition.

The TriCEM website: http://tricem.dreamhosters.com/

Researchers from North Carolina State University have released the first chemical “map” of dyes from the Max A. Weaver Dye Library, which contains almost 100,000 samples of unique dyes and fabrics. The information could assist researchers in developing dyes with desirable properties.

NC State analytic chemist Nelson Vinueza is working on digitizing and analyzing the library so that its contents are accessible to the public. “Each vial has the chemical structure written on it, so we must first digitize those molecular structures and then select candidates to do further characterization,” Vinueza says. “Obviously with a library of this size, the time and expense associated with characterizing each dye would be prohibitive, so we needed a faster, more efficient way to be able to analyze these dyes.”

Vinueza partnered with NC State computational chemist Denis Fourches to create a cheminformatics map of the 2,700 dyes that had their molecular structures already digitized. The computer models allowed the researchers to compare dyes with similar chemical structures and properties.

The cheminformatics analysis also enabled the identification of 150 chemically unique dyes representative of the library. In order to assist researchers in developing dyes with desirable properties, these sampled chemical structures are now publicly available in the ChemSpider database (www.chemspider.com/DatasourceDetails.aspx?id=900). “There are 58 million chemicals in the ChemSpider database, and 143 of the dyes have completely unique chemistry, which is really fantastic,” Vinueza says.

“We believe that this addition can prove invaluable to researchers who are looking for particular characteristics in these chemicals, such as antibiotic or anti-cancer properties, or for dyes that absorb light in ways that could lead to better solar-cell technology,” Vinueza continues. “This dye library could prove invaluable in creating cutting-edge solutions to problems ranging from human health to the environment.”

“The chemical maps and the other cheminformatics modeling techniques we used here provide a cheaper and faster way to screen for chemical dyes with the desired properties,” Fourches says. “Doing that same analysis by experimentally characterizing and testing all samples in a lab would take decades.

“And since these dyes were constructed sequentially over time, it is straightforward to pinpoint where structural changes led to properties of interest. We actually show that small modifications of the dyes’ chemical structures can lead to dramatic changes of their properties. This library is a real treasure trove for chemists.”

The research appears in Chemical Science, and was funded by NC State Chancellor’s Faculty Excellence program. The Max A. Weaver Dye Library was donated to the NC State College of Textiles in 2014 by the Eastman Chemical Company. Vinueza and Fourches are co-corresponding authors. Postdoctoral scholar Melaine Kuenemann in the Fourches laboratory is lead author. NC State graduate students Yufei Chen and Nadia Sultana from Vinueza’s laboratory, research assistant professor Malgorzata Szymczyk, Ciba professor of Dye Chemistry Harold Freeman, Dean David Hinks, and the Environmental Protection Agency’s Antony Williams contributed to the work.

“Weaver’s Historic Accessible Collection of Synthetic Dyes:  A Cheminformatics Analysis”

DOI: 10.1039/C7SC00567A

A proof-of-concept molecular modeling study from North Carolina State University analyzes the efficiency of amine solutions in capturing carbon dioxide. This series of new computer models is the first step toward the design of cheaper, more efficient amine chemicals for capturing carbon dioxide – and reducing harmful CO2 emissions – in industrial installations…

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