Toward target 2035: EUbOPEN - a public–private partnership to enable & unlock biology in the open

Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public–private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents. The substantial outputs of this programme include a chemogenomic compound library covering one third of the druggable proteome, as well as 100 chemical probes, both profiled in patient derived assays, as well as hundreds of data sets deposited in existing public data repositories and a project-specific data resource for exploring EUbOPEN outputs

Toward target 2035:EUbOPEN - a public-private partnership to enable & unlock biology in the open

Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public-private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents. The substantial outputs of this programme include a chemogenomic compound library covering one third of the druggable proteome, as well as 100 chemical probes, both profiled in patient derived assays, as well as hundreds of data sets deposited in existing public data repositories and a project-specific data resource for exploring EUbOPEN outputs.</p

Target 2035-update on the quest for a probe for every protein

Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome

Structural Analysis of Ginsenosides and Sugars: An Electrospray and Tandem Mass Spectrometry Study

Carbohydrates are an abundant class of biological molecules. This thesis presents methodologies for structure characterization of a class of triterpene glycosides, the ginsenosides, sugars and polyols. The sugars included simple monosaccharides, as well as complex saccharides such as the carrageenans, a family of sulfated polysaccharides. The methodologies employed positive and negative ion electrospray ionization (ESI) mass spectrometry and tandem mass spectrometry (MS/MS). Positive ion electrospray mass spectrometry (ESMS) of solutions containing a ginsenoside and any alkali metal ion produced the [M+metal]+ ion. By contrast, when the transition metal ions, Ni++, Co++ and Zn++, are used, the [M+Metal-H]+ ion was observed. Collision-induced dissociation (CID) of the metal attachment ions accommodated their structure characterization. The relative intensity ratio of the product ions provided information on the point of attachment of the sugars to the core, as well as whether they are monosaccharides or disaccharides. Negative ion ESMS of basic solutions of ginsenosides showed a peak corresponding to the [M-H]- ion whose CID spectrum provided the identity of the core, the sugars comprised in the ginsenoside and their order of attachment to the ginsenoside. Both positive and negative ion CID experiments provided information that can be used to propose a structure for ginsenosides. In line with this, these methodologies were used to develop a liquid chromatography mass spectrometry (LC/MS) and LC/MS/MS method for separation and structural characterization of new ginsenosides from root extracts. The structure proposals for ten new ginsenosides are provided. The carrageenans are a family of partially sulfated polysaccharides of which there are three major types, kappa (k), iota (i) and lamda (l). These types are different because each has a disaccharide subunit containing a specific number of sulfate groups with Na+ counterions. Both matrix-assisted laser/desorption ionization time-of-flight mass spectrometry and negative ion ESMS proved to be useful structure probes for these compounds. Dilute solutions of carrageenans undergo H+ exchange and subsequent expulsion of SO3 thus generating a carrageenan with lower sulfate content. Ginsenosides differing only in the presence of geometric isomeric sugars are not differentiated by CID experiments. This observation raised the question of differentiating geometric and (stereo) isomeric polyols using ESMS and MS/MS experiments. Two approaches were investigated to address this question; the first employing negative ion, and the other positive ion mode. The structures of polyols and sugars were analyzed as their boric acid complexes by negative ion infusion ESMS and MS/MS experiments. The positive ion approach employed complexation to oxovanadium(IV), VO++. In both systems, ethylene glycol the simplest polyol was employed as the internal standard. Full scan ESMS experiments provided information on the ease of complexation of the analyte relative to ethylene glycol by comparing the intensity ratio of ions corresponding to their complexes with boric acid and VO++. CID experiments probed the structures of these complexes. Both methodologies were valuable for differentiating geometric and stereoisomeric diols, and isomeric methyl glycosides. Both ESI and MALDI involve solution- and gas-phase processes. A small chemical ionization mass spectrometry project involving alkylation reactions of N-ethyl- and N-methylaniline, and o-, m- and p-ethyl- and o-, m- and p-methylaniline with iodomethane and iodoethane was undertaken. It was observed that the N-site is the primary site for alkylation.Doctor of Philosophy (PhD

Identifying mono methyl arginines with PTMScan® Mono-Methyl Arginine Motif [mme-RG] Kit from CST

The protocol described useful tips for using PTMScan® Mono-Methyl Arginine Motif [mme-RG] Kit from CST.</p

Mapping of phosphorylation modifications of insect cell derived huntingtin (2017/10/05)

Huntingtin structure-function open lab notebook project</p

Mapping of phosphorylation modifications of insect cell derived huntingtin (2017/10/04)

Huntingtin structure-function open lab notebook project</p