Peptide Springiness By Terahertz Spectroscopy – An Upcoming Cover For Angewandte Chemie (And A POV-Ray File For Generating Springs)

image_m_anie201603825-toc-0001-m

From: onlinelibrary.wiley.com/doi/10.1002/anie.201603825/full

Image caption: An approach combining terahertz spectroscopy, X-ray diffraction, and solid-state density functional theory was utilized to accurately measure the elasticities of poly-l-proline helices by probing their spring-like vibrational motions. In their communication (DOI: 10.1002/anie.201602268), T. M. Korter and co-workers reveal that poly-l-proline is less rigid than commonly expected, and that the all-cis and all-trans helical forms exhibit significantly different Young’s moduli.

Article: onlinelibrary.wiley.com/doi/10.1002/anie.201602268/abstract

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ChemMedChem Cover For April 2013 – Treating Type II Diabetes Through B12 Conjugation

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.

MedChemComm September 2012 Front Cover Image For The “Examining The Effects Of Vitamin B12 Conjugation…” Paper

Blogging a blog post recently blogged here in a post, with a zoom-in below because no decent-sized version of the same can be found on the MedChemComm site, all pertaining to the “Examining the effects of vitamin B12 conjugation on the biological activity of insulin: a molecular dynamic and in vivo oral uptake investigation” article from Susan Clardy-James, myself, Timothy J. Fairchild and Robert P. Doyle in ChemMedComm (available at pubs.rsc.org/en/Content/ArticleLanding/2012/MD/C2MD20040F).

The MedChemComm post also provides the caption for the cover (below), which I reproduce below for context:

Oral delivery of drugs aims to open up new areas of peptide/protein therapeutics associated with the removal for a need for injections. The major problems facing oral delivery of peptides/proteins is hydrolysis/proteolysis in the gastrointestinal tract and an inefficient uptake mechanism for peptides/proteins from the tract. Robert P. Doyle et al. are interested in the use of the vitamin B12 dietary uptake pathway to address these hurdles. In this paper Doyle et al. report the synthesis, purification and characterisation of a new B12-insulin conjugate attached between the B12 ribose hydroxyl group and insulin PheB1.

Examining The Effects Of Vitamin B12 Conjugation On The Biological Activity Of Insulin: A Molecular Dynamic And In Vivo Oral Uptake Investigation

Published in MedChemComm (direct link: xlink.rsc.org/?doi=C2MD20040F). And Happy Belated New Year. After the methodological work that went into the Molecular Biosystems paper, this was a remarkably simple molecular dynamics study of the changes to vitamin B12 binding in transcobalamin II (TCII) with the B12 conjugated to the first amino acid side chain in the B-Chain of insulin. The structure of the B12-insulin conjugate is shown below in a molecular dynamics snapshot, which reveals that the binding of B12 to its TCII transport protein is negligibly affected.

And apparently the experiments went well, too. Cover hopefully to follow.

Susan Clardy-James, Damian G. Allis, Timothy J. Fairchild and Robert P. Doyle

Abstract: The practical use of the vitamin B12 uptake pathway to orally deliver peptides and proteins is much debated. To understand the full potential of the pathway however, a deeper understanding of the impact B12 conjugation has on peptides and proteins is needed. We previously reported an orally active B12 based insulin conjugate attached at LysB29 with hypoglycaemic properties in STZ diabetic rats. We are exploring an alternative attachment for B12 on insulin in an attempt to determine the effect B12 has on the protein biological activity. We describe herein the synthesis, characterization, and purification of a new B12-insulin conjugate, which is attached between the B12 ribose hydroxyl group and insulin PheB1. The hypoglycemic properties resulting from oral administration (gavage) of such a conjugate in STZ diabetic rats was similar to that noted in a conjugate covalently linked at insulin LysB2911, demonstrating the availability of both position on insulin for B12 attachment. A possible rationale for this result is put forward from MD simulations. We also conclude that there is a dose dependent response that can be observed for B12-insulin conjugates, with doses of conjugate greater than 10-9 M necessary to observe even low levels of glucose drop.

NanoHive@Home’s Published Results (Finally): Analysis Of Diamondoid Mechanosynthesis Tooltip Pathologies Generated Via A Distributed Computing Approach

Published in the Journal Of Computational And Theoretical Nanoscience. This paper has been as delayed in posting as the accepted article was long in printing, which was less time than the wait for the completion of the manuscript, which itself was massive compared to the time of the experiments themselves, which was fractional compared to how long it would have been without the NanoHive@Home crew that donated so much compute time to the project so long ago. First off…

Acknowledgements

This work would not have been possible without the enormous contribution of the NanoHive@Home participants, composed of over 6,000 worldwide volunteers and their computers.

For those that were part of the NHAH community and want to see what the final work looks like, please drop me a line [nhah@somewhereville.com] so we can properly settle up.

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Gumming Up Appetite to Treat Obesity – Vitamin B12 Bioconjugate Project (& Graphic) Mention In Scientific American

From the “free press” division of the blog, a recent post by Ferris Jabr on the scientificamerican.com site highlights yet another evolutionarily fascinating application of cyanocobalamin (herein referred to as B12) out of the Rob Doyle Lab for the non-invasive delivery of small molecules into the human-person. Here, a mechanism for the delivery of human peptide YY (hPYY) into the bloodstream via a food-free mechanism (unless you count the gum flavorings as a fruit). From the thorough and accessible article (with a decent balance of sciam and non-sciam redirecting)…

CHEMICAL COUPLE: The appetite-suppressing hormone hPYY hitches a ride with vitamin B-12 from the stomach to the bloodstream (caption credit: sciam).

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Vitamin B12 In Drug Delivery: Breaking Through The Barriers To A B12 Bioconjugate Pharmaceutical

In press in Expert Opinion On Drug Delivery (DOI:10.1517/17425247.2011.539200). The theory section (the only part I can properly speak to) builds on the discussion section of the full theory paper in Molecular Biosystems from earlier this year, providing an outlet for some of the more speculative design possibilities for trinary B12 bioconjugate design. Given that (1) there are mechanisms for cleavage at both of the proposed positions and (2) the molecular dynamics work indicates that, at least, TCII (transcobalamin II) can easily accommodate a bi-functionalized cobalamin, the A-B12-C design possibility is probably the most interesting long-term idea to come out of the computational side of the B12-insulin bioconjugate study (or so I argue).

Having “B12” and “cobalamin” in a blog post guarantees a bunch of useless moderation-necessary comments from vita-spam sites.

Susan M. Clardy, Damian G. Allis, Timothy J. Fairchild & Robert P. Doyle

Syracuse University, Syracuse, Department of Chemistry, NY 13244-4100, USA

Importance of the field: Vitamin B12 (B12) is a rare and vital micronutrient for which mammals have developed a complex and highly efficient dietary uptake system. This uptake pathway consists of a series of proteins and receptors, and has been utilized to deliver several bioactive and/or imaging molecules from 99mTc to insulin.

Areas covered in this review: The current field of B12-based drug delivery is reviewed, including recent highlights surrounding the very pathway itself.

What the reader will gain: Despite over 30 years of work, no B12-based drug delivery conjugate has reached the market-place, hampered by issues such as limited uptake capacity, gastrointestinal degradation of the conjugate or high background uptake by healthy tissues. Variability in dose response among individuals, especially across ageing populations and slow oral uptake (several hours), has also slowed development and interest.

Take home message: This review is intended to stress again the great potential, as yet not fully realized, for B12-based therapeutics, tumor imaging and oral drug delivery. This review discusses recent reports that demonstrate that the issues noted above can be overcome and need not be seen as negating the great potential of B12 in the drug delivery field.

25 November 2010 Cover Art For The Journal Of Physical Chemistry A – “Computation Of Deuterium Isotope Perturbation Of 13C NMR Chemical Shifts of Alkanes: A Local Mode Zero Point Level Approach”



A bit of a sneak preview and a chance to get a second use out of an instructive pair of potentials. This new cover for an upcoming article by Kin Yang and Bruce Hudson expands upon the previous Deuterium-for-Hydrogen substitution study summarized on the blog page (and in a publication of the same name) Vicinal Deuterium Perturbations on Hydrogen NMR Chemical Shifts in Cyclohexanes. In brief, exchanging a hydrogen for a deuterium alters 13C NMR spectra because the deuterium, being twice the mass, has a narrower nuclear probability distribution. If the C-H/D stretching potential were harmonic (symmetric on both the elongation and contraction sides), this would produce no effect. As this stretching potential is anharmonic (as shown below and the background of the above image), the actual average positions of the D and H differ slightly (but enough!), with the C-D bond being, on average, slightly shorter than C-H (something that a quantum chemical calculation will not tell you without treating the nuclei as quantum mechanical objects). Different average bond length, different affect on a bound 13C.



A bit more explanation can be found at www.somewhereville.com/?p=124.

The studies continue, limited largely by the number of simple hydrocarbons with high-quality NMR spectra (and selective deuteration).

The Binding Of Vitamin B12 To Transcobalamin(II); Structural Considerations For Bioconjugate Design – A Molecular Dynamics Study

In press, in the journal Molecular Biosystems. A first official foray into molecular dynamics-only (MD-only) computational work and I am pleased to report that the computational results not only make sense with respect to the experimental results, they also indicate a possible new way to use vitamin B12 for the oral delivery of bio-active molecules more complicated than the binary bioconjugates considered to date.

The Interesting Result

The conclusion from the previous study was that the insulin B Chain (figure below) acts as a tether to separate the structured region of insulin (the region with the largest inflexible steric bulk, see below) from the region of the transcobalamin II (TCII) that bind vitamin B12. It was then determined that the approach employed for the B12-insulin bioconjugate, simply linking one biomolecule onto another with known binding and transport properties (this is a common theme in all bioconjugate design), worked because the last 10 residues in the insulin B Chain (B22 to B30) are flexible in solution (they, in fact, cover the insulin binding region in the crystal form, then uncover this region in the biologically active form).

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Cover Art For The 7 May 2010 Issue Of The Journal Of Organic Chemistry – Notes On Presentation

The cover art for the 7 May 2010 issue of the Journal of Organic Chemistry accompanies the article by (2nd semester organic chemistry professor, co-author, and 2010 American Chemical Society James Flack Norris Award in Physical Organic Chemistry recipient) John E. Baldwin and Alexey P. Kostikov entitled “On the Stereochemical Characteristic of the Thermal Reactions of Vinylcyclobutane.”

This Perspective outlines the stereochemical and mechanistic complexities inherent in the thermal reactions converting vinylcyclobutane to cyclohexene, butadiene, and ethylene. The structural isomerization and the fragmentation processes seem, at first sight, to be obvious and simple. When considered more carefully and investigated with the aid of deuterium-labeled stereochemically well-defined vinylcyclobutane derivatives there emerges a complex kinetic situation traced by 56 structure-to-structure transformations and 12 independent kinetic parameters. Experimental determinations of stereochemical details of stereomutations and [1,3] carbon sigmatropic shifts are now being pursued and will in time contribute to gaining relevant evidence casting light on the reaction dynamics involved as flexible short-lived diradical intermediates trace the paths leading from one d2-labeled vinylcyclobutane starting material to a mixture of 16 structures.

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