Cofactor Fingerprinting with STD NMR to Characterize Proteins of Unknown Function: Identification of a Rare cCMP Cofactor Preference

Proteomics efforts have created a need for better strategies to functionally categorize newly discovered proteins. To this end, we have employed saturation transfer difference NMR with pools of closely related cofactors, to determine cofactor preferences. This approach works well for dehydrogenases and has also been applied to cyclic nucleotide‐binding proteins. In the latter application, a protein (radial spoke protein‐2, RSP2) that plays a central role in forming the radial spoke of Chlamydomonas reinhardtii flagella was shown to bind cCMP. cCMP‐binding proteins are rare, although previous reports of their presence in sperm and flagella suggest that cCMP may have a more general role in flagellar function. 31P NMR was used to monitor the preferential hydrolysis of ATP versus GTP, suggesting that RSP2 is a kinase

A Chemical Proteomic Probe for Detecting Dehydrogenases: \u3cem\u3eCatechol Rhodanine\u3c/em\u3e

The inherent complexity of the proteome often demands that it be studied as manageable subsets, termed subproteomes. A subproteome can be defined in a number of ways, although a pragmatic approach is to define it based on common features in an active site that lead to binding of a common small molecule ligand (ex. a cofactor or a cross-reactive drug lead). The subproteome, so defined, can be purified using that common ligand tethered to a resin, with affinity chromatography. Affinity purification of a subproteome is described in the next chapter. That subproteome can then be analyzed using a common ligand probe, such as a fluorescent common ligand that can be used to stain members of the subproteome in a native gel. Here, we describe such a fluorescent probe, based on a catechol rhodanine acetic acid (CRAA) ligand that binds to dehydrogenases. The CRAA ligand is fluorescent and binds to dehydrogenases at pH \u3e 7, and hence can be used effectively to stain dehydrogenases in native gels to identify what subset of proteins in a mixture are dehydrogenases. Furthermore, if one is designing inhibitors to target one or more of these dehydrogenases, the CRAA staining can be performed in a competitive assay format, with or without inhibitor, to assess the selectivity of the inhibitor for the targeted dehydrogenase. Finally, the CRAA probe is a privileged scaffold for dehydrogenases, and hence can easily be modified to increase affinity for a given dehydrogenase

An \u3cem\u3eIn Vitro\u3c/em\u3e Spectroscopic Analysis to Determine Whether Para-Chloroaniline Is Produced from Mixing Sodium Hypochlorite and Chlorhexidine

Introduction: The purpose of this in vitro study was to determine whether para-chloroaniline (PCA) is formed through the reaction of mixing sodium hypochlorite (NaOCl) and chlorhexidine (CHX). Methods: Initially, commercially available samples of chlorhexidine acetate (CHXa) and PCA were analyzed with 1H nuclear magnetic resonance (NMR) spectroscopy. Two solutions, NaOCl and CHXa, were warmed to 37ºC, and when mixed they produced a brown precipitate. This precipitate was separated in half, and pure PCA was added to 1 of the samples for comparison before they were each analyzed with 1H NMR spectroscopy. Results: The peaks in the 1H NMR spectra of CHXa and PCA were assigned to specific protons of the molecules, and the location of the aromatic peaks in the PCA spectrum defined the PCA doublet region. Although the spectrum of the precipitate alone resulted in a complex combination of peaks, on magnification there were no peaks in the PCA doublet region that were intense enough to be quantified. In the spectrum of the precipitate to which PCA was added, 2 peaks do appear in the PCA doublet region. Comparing this spectrum with that of precipitate alone, the peaks in the PCA doublet region are not visible before the addition of PCA. Conclusions: On the basis of this in vitro study, the reaction mixture of NaOCl and CHXa does not produce PCA at any measurable quantity, and further investigation is needed to determine the chemical composition of the brown precipitate

An \u3cem\u3eIn Vitro\u3c/em\u3e Spectroscopic Analysis to Determine the Chemical Composition of the Precipitate Formed by Mixing Sodium Hypochlorite and Chlorhexidine

Introduction—The purpose of this in vitro study was to determine the chemical composition of the precipitate formed by mixing sodium hypochlorite (NaOCl) and Chlorhexidine (CHX), and relative molecular weight of the components. Methods—Using commercially available chlorhexidine gluconate (CHXg), a 2% solution was formed and mixed in a 1:1 ratio with commercially available NaOCl producing a brown precipitate. The precipitate as well as a mixture of precipitate and pure chlorhexidine diacetate (CHXa) was then analyzed using 1D and 2D NMR spectroscopy. Results—The 1D and 2D NMR spectra were fully assigned, in terms of chemical shifts of all proton and carbon atoms in intact CHX. This permitted identification of CHX breakdown products with and without the aliphatic linker present, including lower molecular weight components of CHX that contained a para-substituted benzene that was not para-chloroaniline (PCA). Conclusions—Based on this in vitro study, the precipitate formed by NaOCl and CHX is composed of at least two separate molecules, all of which are smaller in size than CHX. Along with native CHX, the precipitate contains two chemical fragments derived from CHX, neither of which are PCA

Co-Developing Drugs with Indigenous Communities: Lessons from Peruvian Law and the Ayahuasca Patent Dispute

This paper will examine the issues surrounding the codevelopment of drugs derived from traditional medicines used by indigenous peoples in Amazonia, with a focus on Peru. In particular, this paper will explore what national, regional and international legal structures are in place to protect the interests of indigenous peoples, while at the same time providing medical benefit to the world. This issue is explored in the context of Peruvian, U.S., and international treaties – especially the TRIPS agreement, the Andean Community, sui generis protections, and the US-Peru Trade Promotion Agreement

Repurposing - Finding New Uses for Old (and Patented) Drugs: Bridging the Valley of Death, to Translate Academic Research Into New Medicines

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Pre-emption against terror : just war pacifist approach

Having soberly reflected upon the tragedy of September 11, 2001, the author observed that though international law and treaties restrict pre-emptive war, they do allow for war in self-defense. Consequently, some powerful nations have used this as a justification for launching pre-emptive strikes. The threats posed by the powerful nations using self-defense as a justification for pre-emptive strikes and the inability of weaker nations to do the same, greatly account for the unprecedented explosion of global terrorism. The author thinks that confronting terrorism therefore requires a pro-pacifist ethical framework whose principles have to be applied with international law to narrow the legitimacy of self-defense wars. Hence, he proposes "Moral Consistency" as a required condition for launching pre-emptive strikes with two main aims - to reduce violent conflicts and to draw a substantial distinction between reason and justification, and between crime and criminal justice

A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment

Molecular docking is a computational technique which predicts the binding energy and the preferred binding mode of a ligand to a protein target. Virtual screening is a tool which uses docking to investigate large chemical libraries to identify ligands that bind favorably to a protein target. We have developed a novel scoring based distributed protein docking application to improve enrichment in virtual screening. The application addresses the issue of time and cost of screening in contrast to conventional systematic parallel virtual screening methods in two ways. Firstly, it automates the process of creating and launching multiple independent dockings on a high performance computing cluster. Secondly, it uses a N˙ aive Bayes scoring function to calculate binding energy of un-docked ligands to identify and preferentially dock (Autodock predicted) better binders. The application was tested on four proteins using a library of 10,573 ligands. In all the experiments, (i). 200 of the 1000 best binders are identified after docking only 14% of the chemical library, (ii). 9 or 10 best-binders are identified after docking only 19% of the chemical library, and (iii). no significant enrichment is observed after docking 70% of the chemical library. The results show significant increase in enrichment of potential drug leads in early rounds of virtual screening

Solution Structures of \u3cem\u3eMycobacterium tuberculosis\u3c/em\u3e Thioredoxin C and Models of Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

Here, we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared with the solution structure. On the basis of these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function

Conserved Amino Acids in Each Subunit of the Heteroligomeric tRNA m\u3csup\u3e1\u3c/sup\u3eA58 Mtase from \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e Contribute to tRNA Binding

In Saccharomyces cerevisiae, a two-subunit methyltransferase (Mtase) encoded by the essential genes TRM6 and TRM61 is responsible for the formation of 1-methyladenosine, a modified nucleoside found at position 58 in tRNA that is critical for the stability of . The crystal structure of the homotetrameric m1A58 tRNA Mtase from Mycobacterium tuberculosis, TrmI, has been solved and was used as a template to build a model of the yeast m1A58 tRNA Mtase heterotetramer. We altered amino acids in TRM6 and TRM61 that were predicted to be important for the stability of the heteroligomer based on this model. Yeast strains expressing trm6 and trm61 mutants exhibited growth phenotypes indicative of reduced m1A formation. In addition, recombinant mutant enzymes had reduced in vitro Mtase activity. We demonstrate that the mutations introduced do not prevent heteroligomer formation and do not disrupt binding of the cofactor S-adenosyl-l-methionine. Instead, amino acid substitutions in either Trm6p or Trm61p destroy the ability of the yeast m1A58 tRNA Mtase to bind , indicating that each subunit contributes to tRNA binding and suggesting a structural alteration of the substrate-binding pocket occurs when these mutations are present