#50, published in ChemMedChem (11 (2016), 9, 1015-1020), DOI:cmdc.201600073.
The key to molecular dynamics simulations is recycling – specifically, going into a first project with enough organization to know how to use everything in the next study. While that first successful connectivity table, parameter assignment, and RESP charge generation for something as Frankenstein-esque as vitamin B12 is the north face of Everest, that next simulation is simply a matter of having atom codes in your PDB file standardized.
And, speaking of PDBs, article #50 has the added bonus of having its own entry in the Protein Databank as 2NA5 – quite a treat (to me, anyway).
And furthermore, this is the first of my publications to benefit from the Research Computing infrastructure on the Syracuse University campus – the throughput of calculations for future work is completely unprecedented in my history of resource access anywhere (the drop in storage prices is very real to some of us).
Authors: Henry K.E., Kerwood D.J., Allis D.G., Workinger J.L., Bonaccorso R.L., Holz G.G., Roth C.L., Zubieta J., and Doyle R.P.
Abstract: Vitamin B12–peptide conjugates have considerable therapeutic potential through improved pharmacokinetic and/or pharmacodynamic properties imparted on the peptide upon covalent attachment to vitamin B12 (B12). There remains a lack of structural studies investigating the effects of B12 conjugation on peptide secondary structure. Determining the solution structure of a B12–peptide conjugate or conjugates and measuring functions of the conjugate(s) at the target peptide receptor may offer considerable insight concerning the future design of fully optimized conjugates. This methodology is especially useful in tandem with constrained molecular dynamics (MD) studies, such that predictions may be made about conjugates not yet synthesized. Focusing on two B12 conjugates of the anorectic peptide PYY(3–36), one of which was previously demonstrated to have improved food intake reduction compared with PYY(3–36), we performed NMR structural analyses and used the information to conduct MD simulations. The study provides rare structural insight into vitamin B12 conjugates and validates the fact that B12 can be conjugated to a peptide without markedly affecting peptide secondary structure.
The back cover picture shows two views at 150 degree rotation of vitamin B12 conjugated to the potent anti- hyperglycemia peptide glucagon-like peptide-1 (GLP-1). The conjugate displays similar receptor binding and agonism to unconjugated GLP-1, including insulin potentiation from human transplant pancreatic islet cells, which bodes well for oral delivery of GLP-1 through the B12 dietary pathway. For more details, see the Communication by Robert P. Doyle et al. on p. 582 ff.
From the free press department… The cover for the April, 2013 issue of ChemMEDChem (just the cover art this time, no theoretical content in the associated article. All the theory’s figured out!). I’m still awaiting the journal’s posting of the article content but wanted to get something up in March. For related content, see the discussion on the “MedChemComm September 2012 Front Cover Image For The ‘Examining The Effects Of Vitamin B12 Conjugation…’ Paper” post or any of the B12-related posts on this site (www.somewhereville.com/index.php?s=b12). This work is similar in scope to the B12-insulin bioconjugate work in the previous studies, but now includes a different peptide (glucagon-like peptide-1) with similar properties.
A brief post about some free research press (and the new addition to the Cover Gallery). Having already been featured on the cover of the ChemMedChem March 2009 issue (see the New B12-Insulin-TCII-Insulin Receptor Cover Image For This Month’s ChemMedChem (March 2009) post) , the side-on view of the B12-Insulin/TCII/Insulin Receptor structure was chosen for this month’s cover of Clinical Chemistry. While the originating article itself is not included in the issue (I should have recommended citing the ChemMedChem article in the image caption), several diabetes-related articles are featured in this month’s issue.
ON THE COVER: Scientists are investigating ways to develop effective oral insulin therapies. One such model is a vitamin B12–insulin conjugate bound to transcobalamin II and is shown here docked in the insulin receptor. The discovery of easier ways to deliver insulin into the blood stream would improve the lives of the millions of individuals living with diabetes. This month’s issue of Clinical Chemistry contains 4 articles related to diabetes. The first 2 articles provide readers with a point/counterpoint discussion of the value of reporting estimated glucose along with Hb A1c. Next is an article on the association of apolipoprotein B with incident type 2 diabetes. Lastly, the development of the first radioimmunoassay for insulin led to a Nobel Prize and is chronicled in this month’s Citation Classic feature. (See pages 545, 547, 666, and 671.) Image reproduced with permission from Damian G. Allis and Robert P. Doyle, Department of Chemistry, Syracuse University.
As a brief explanation of the image, this “scene” is meant to show (without proper molecular dynamics simulations to show how well it would work) that the Transcobalamin(II) transport/protection protein for cobalamin/cyanocobalamin (vitamin B12) and the B12-insulin bioconjugate discussed in the ChemMedChem article is small enough to fit within the Insulin Receptor protein such that insulin may still be able to bind to its receptor. This is the final piece of the puzzle in the proposed mechanism (and experimentally demonstrated event) by which the B12-insulin bioconjugate retains all of the benefits of free B12 (transport from the digestive system to the bloodstream) and insulin (proper receptor binding and the subsequent induction of cellular glucose uptake).
The figure caption and April 2010 Table of Contents can be found in PDF format at the Clinical Chemistry website (with a local copy of the PDF also available HERE.