Solution Structure And Constrained Molecular Dynamics Study Of Vitamin B12 Conjugates Of The Anorectic Peptide PYY(3-36)

#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).

2016oct5_fig_4_b12_pyy_front_v2

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.

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).

Losing weight is not always about anticipating swimsuit season or squeezing into skinny jeans—for the clinically obese, losing weight is about fighting serious illness and reclaiming health. But the primal part of the brain that regulates appetite will not place a moratorium on hunger just because someone and their doctor acknowledge the need to lose weight. Researchers at Syracuse University are working toward a unique solution: a stick of chewing gum that suppresses appetite.

A slightly-larger version of the image on the site is reproduced above (with the image credit most welcome on the site). For a bit more information about the general properties of B12 and its potential applications for other diet-related issues, a few articles described here @swv link to more complete discussions…

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

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

* B12-Insulin Bioconjugate/Transcobalamin(II)/Insulin Receptor Cover Image For The April Issue Of Clinical Chemistry

* New B12-Insulin-TCII-Insulin Receptor Cover Image For This Month’s ChemMedChem (March 2009)

* Exploring the Implications of Vitamin B12 Conjugation to Insulin on Insulin Receptor Binding and Cellular Uptake

The Inelastic Neutron Scattering Spectrum Of Nicotinic Acid And Its Assignment By Solid-State Density Functional Theory

Accepted in Chemical Physics Letters.  What began as a reasonably straightforward inelastic neutron scattering (INS) assignment was expanded upon reviewer request to include an analysis of the potential for in-cell nicotinic acid (or niacin, depending on who you ask.   Not to be confused with this Niacin, which would be another post altogether) prototropic tautomerization (technically, one might consider this just proton migration along the chain of the nicotinic acid molecules in the solid-state, which might just be more supported as, providing the punch line early, proton migration does not seem to occur in this system), a point that was mentioned in the paper as a possibility within the crystal cell but not originally examined as part of the spectral assignment.   In the crystal cell picture shown below, tautomerization would result in proton H5 migrating to N’, yielding a chain (if it propagated down the entire one-dimensional chain of nicotinic acid molecules in the solid-state) of zwitterions (molecules with both positive and negative charges on the covalent framework).   Anyone with experience in the solid-state study of amino acids knows that zwitterions are not only stable species in the solid-state, but they can also the dominant species in the solid-state, as ionic interactions and the dipole alignment that results from the alignment of, in this case, zwitterions, can yield greater stability than the neutral species, where only hydrogen bonding and dispersions forces occur in the crystal packing arrangement.

The inelastic neutron scattering assignment by solid-state density functional theory (DFT) strongly supports that, at the 25 K temperature of the neutron experiment, the crystal cell is of the neutral, non-zwitterionic form (as shown below, which labels the possible arrangements of hydrogens in the Z=4 crystal cell).  Furthermore, despite the existence of several potentially stable proton arrangements in the crystal cell (the three additional forms shown below), the nicotinic acid crystal cell seems to prefer the neutral form even through room temperature.  Fortunately, previous studies using other spectroscopic methods seem to agree.  As has been the case for the vast majority of all of the previous INS studies, the solid-state DFT calculations were performed with DMol3 and the INS simulated spectra generated with Dr. A. J. Ramirez-Cuesta’s most excellent aClimax program.

As is often the case when a competent reviewer serves you a critical analysis of your submitted work, the final result is all the better for it.

Matthew R. Hudson, Damian G. Allis, and Bruce S. Hudson

Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, NY 13244-4100, USA

Keywords: nicotinic acid, niacin, vitamin B3, inelastic neutron scattering spectroscopy, solid-state density functional theory

Abstract: The 25 K inelastic neutron scattering (INS) spectrum of nicotinic acid has been measured and assigned by solid-state density functional theory (DFT). Vibrational mode energies involving the carboxylic acid proton are found to be significantly altered due to intermolecular hydrogen-bonding. There is good overall agreement between experiment and simulation in all regions of the spectrum, with identified deviations considered in detail by spectral region: phonon (25 – 300 cm-1), molecular (300 – 1600 cm-1), and high-frequency (>2000 cm-1). The relative energies, geometries, and vibrational spectra associated with hypothesized tautomerization in the solid-state have also been investigated.

www.elsevier.com/locate/cplett
en.wikipedia.org/wiki/Inelastic_neutron_scattering
en.wikipedia.org/wiki/Nicotinic_acid
en.wikipedia.org/wiki/Niacin
www.niacinb3.com
en.wikipedia.org/wiki/Tautomerization
en.wikipedia.org/wiki/Zwitterion
en.wikipedia.org/wiki/Amino_acids
en.wikipedia.org/wiki/Density_functional_theory
chemistry.syr.edu
www.syr.edu
www.isis.rl.ac.uk/MolecularSpectroscopy/aclimax/
accelrys.com/products/materials-studio/modules/dmol3.html