ChemGPS-NP:  Tuned for Navigation in Biologically Relevant Chemical Space

Larsson, Josefin; Gottfries, Johan; Mureşan, Sorel; Backlund, Anders

doi:10.1021/np070002y

Cited by 196 publications

(167 citation statements)

References 36 publications

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“…As outlined by Larsson et al [61], this map of the natural products chemical space differs from previously published versions of the so-called "drug-like space" [59]. Most notably, the major dimensions of the map are arranged in a different order, interpretable as reflecting differences in strategies between medicinal chemists and evolutionarily affected biosynthesis.…”

Section: Strategies For Selectionmentioning

confidence: 90%

“…Not only are all predicted molecules well described within the model, in contrast to the original ChemGPS, but also, strong clustering patterns are discernable from the plots [61].…”

Section: Strategies For Selectionmentioning

confidence: 92%

“…Studies have, however, demonstrated the inadequacy of this model for handling the diversity of natural products chemistry [60]. This observation triggered the development of a device tuned for explorations of the biologically relevant regions of chemical space [61].…”

Section: Strategies For Selectionmentioning

confidence: 99%

“…This tool, a map of the natural products chemical space, known as "ChemGPS-NP" [61], was developed using the same principles as applied to the original ChemGPS, but with a significantly larger scope. Initially based on SMILES representations (compact one-line alphanumerical strings) of more than 120 000 structural formulae, a model was constructed based on more than 900 physical-chemical descriptors.…”

Section: Strategies For Selectionmentioning

confidence: 99%

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Modern pharmacognosy: Connecting biology and chemistry

Bohlin

Göransson

Backlund

2007

Pure and Applied Chemistry

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In many countries today, the number of students selecting chemistry for higher studies is decreasing. At the same time, interest in the environmental aspects of chemistry, green chemistry, and sustainable use of natural products is increasing among the young generation of students. By modernizing and renewing a venerable proven science, pharmacognosy would have a strategic position to connect biology and chemistry. This multidisciplinary subject is important for discovery of novel and unique molecules with drug potential, and for revealing unknown targets, by studying evolutionary structure-activity optimization in nature. In this paper, the overall aim and strategies of our research are presented and exemplified by three different research projects.Natural products are involved in scientific issues important for a sustainable society, and a multidisciplinary subject such as pharmacognosy can, therefore, be useful in increasing future interest in both chemistry and biology.Keywords: pharmacognosy; prediction of selection; cyclotides; cytoxicity; marine sponges; antifouling.The decrease in the number of students pursuing higher studies in chemistry is an international trend. In a recent editorial in Science, education in chemistry and other science subjects was discussed, with emphasis on the situation in the United States [1]. It was noted that the educational methods were oldfashioned and also, that the number of students in each class was very high. As a result, many students did not pursue their studies in subjects like chemistry. At the same time, the importance of the environment, green chemistry, and the sustainable use of natural products is evident in the younger generation of students.It is obvious that something must be done to increase interest in the scientific disciplines, to enable us to handle the complexity and number of science-based problems in the future. In the university setting, educational programs need to be developed in many different ways. One way would be to blend different disciplines and teach about complex questions in society in a multidisciplinary way and in this way revitalize scientific education. By using such a holistic approach, the science teaching would probably be more exciting for students. In fact, this is a proven concept: During the 18 th century, the famous Swedish scientist Linnaeus used a holistic approach in his scientific work and teaching. Linnaeus even wrote numerous theses for dissertations in different disciplines, including interdisciplinary works such as Medicamenta graveolentia (Drugs with a strong smell), Sapor medicamentorum (The taste of drugs),

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Section: Strategies For Selectionmentioning

confidence: 90%

“…Not only are all predicted molecules well described within the model, in contrast to the original ChemGPS, but also, strong clustering patterns are discernable from the plots [61].…”

Section: Strategies For Selectionmentioning

confidence: 92%

Section: Strategies For Selectionmentioning

confidence: 99%

Section: Strategies For Selectionmentioning

confidence: 99%

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Modern pharmacognosy: Connecting biology and chemistry

Bohlin

Göransson

Backlund

2007

Pure and Applied Chemistry

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“…In an effort to rationalize the description of compounds, including chemotherapeutic agents, we recently established Chemical Global Positioning System including Natural Products (ChemGPS-NP) [8]. This is a chemography-based [9] model tuned for the characterization of and navigation in biologically relevant chemical space [8], which was recently made freely available through http://chemgps.bmc.uu.se/ [10].…”

Section: Introductionmentioning

confidence: 99%

ChemGPS‐NP Mapping of Chemical Compounds for Prediction of Anticancer Mode of Action

et al. 2009

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A combined graph describing the growth inhibition values from a number of human cancer cell lines represents an activity profile for a compound. The fact that compounds with similar activity profiles often show similar Mode of Action (MOA) has frequently been used in prediction of MOA. Obtaining the profiles is demanding with respect to both time and resources. Therefore, as a work and time efficient alternative, we explore the central premise of medicinal chemistry that structurally similar molecules often have similar biological activity. In this study we investigate correlations between chemical structure and MOA, and subsequently use this as a complementing basis for prediction. The correlations between MOA and activity profile on one hand and between MOA and chemical structure on the other were analyzed for anticancer agents, classified with regard to MOA, using Principal Component Analysis (PCA), chemographic mapping with ChemGPS-NP, and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). The compounds clustered according to MOA both based on chemical structures and activity profiles. The subsequent validation with external test sets showed that initial PCA scores prediction or chemographic mapping followed by OPLS-DA could be used for the prediction of MOA as well as identification of novel MOAs in a highly accurate way. An efficient and straight forward procedure for the prediction of MOA of anticancer agents is suggested. With todays resistance problems in cancer therapy, there is a need for new anticancer agents and mechanisms. We believe that the fast initial virtual guidance this procedure implies, especially the novel step using ChemGPS-NP, could be of general use in early stages of cancer research.

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Cheminformatics

Villar

2010

Kirk-Othmer Encyclopedia of Chemical Technology

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This article provides an introductory overview of some salient aspects of a field that is becoming mission critical to chemical research. As the volume of data generated by all chemistry projects continues to expand, management, analysis, visualization and dissemination of the data has to be automated. Cheminformatics deals with the complex issues that result from this data explosion and the applications that have been generated.

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ChemGPS-NP: Tuned for Navigation in Biologically Relevant Chemical Space

Cited by 196 publications

References 36 publications

Modern pharmacognosy: Connecting biology and chemistry

Modern pharmacognosy: Connecting biology and chemistry

ChemGPS‐NP Mapping of Chemical Compounds for Prediction of Anticancer Mode of Action

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