The goal of many metabolomic studies is to identify the molecular structure of endogenous molecules that are differentially expressed among sampled or treatment groups. The identified compounds can ...then be used to gain an understanding of disease mechanisms. Unfortunately, despite recent advances in a variety of analytical techniques, small molecule (<1000 Da) identification remains difficult. Rarely can a chemical structure be determined from experimental “features” such as retention time, exact mass, and collision induced dissociation spectra. Thus, without knowing structure, biological significance remains obscure. In this study we explore an identification method in which the measured exact mass of an unknown is used to query available chemical databases to compile a list of candidate compounds. Predictions are made for the candidates using models of experimental features that have been measured for the unknown. The predicted values are used to filter the candidate list by eliminating compounds with predicted values substantially different from the unknown. The intent is to reduce the list of candidates to a reasonable number that can be obtained and measured for confirmation. To facilitate this exploration, we measured data and created models for two experimental features; MS Ecom
50
(the energy in eV required to fragment 50% of a selected precursor ion) and HPLC retention index. Using a dataset of 52 compounds, Ecom
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models were developed based on both Molconn and CODESSA structural descriptors. These models gave r
2
values of 0.89 to 0.94 depending on the number of inputs, the modeling algorithm chosen, and whether neutral or protonated structures were used. The retention index model was developed with 400 compounds using a back propagation artificial neural network and 33 Molconn structure descriptors. External validation gave a v
2
= 0.86 and standard error of 38 retention index units. As a test of the validity of the filtering approach, the Ecom
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and retention index models, along with exact mass and collision induced dissociation spectra matching, were used to identify 1,3-dicyclohexylurea in human plasma. This compound was not previously known to exist in human biofluids and its elemental formula was identical to 315 other candidate compounds downloaded from PubChem. These results suggest that the use of Ecom
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and retention index predictive models can improve non-targeted metabolite structure identification using HPLC/MS derived structural features.
Transporters are proteins which span the plasma membrane and regulate the traffic of small molecules in and out of the cell. Transporters play a particularly important role in chemical signalling ...between neurons in the CNS, where they act to control the concentration of neurotransmitters in the synapse. The majority of transporters which are actively being pursued as targets for drug discovery are CNS located and this reflects the history of the field which began with the tricyclic antidepressants (TCAs) over half a century ago. The use of transporter inhibition to regulate the synaptic concentrations of key neurotransmitters is an established approach in the discovery of psychiatric medications. This volume reviews advances in the field of transporters as targets for drug discovery in the last 10 years. The volume will be of interest to scientists engaged in drug research in the pharmaceutical industry, biotech and academia. Following an overview chapter, seven chapters written by leading experts in their area reflect a range of topics pertinent to the transporter field. General topics include recent advances in the structural biology of transporters and its impact on potential structure based drug design and the design of ligands for Positron Emission Tomography and the importance of molecular imaging in understanding early clinical data. Medicinal chemistry approaches are described outlining the discovery of selective serotonin, noradrenaline and dopamine reuptake inhibitors, current efforts towards the discovery of mixed re-uptake inhibitors with varied ‘flavours’ of monoamine inhibition, advances in the development of inhibitors for the glycine transporter and the discovery of subtype selective EAAT inhibitors. In addition to being an interesting read, the reader will receive a critical overview of progress made in this rapidly developing field.
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