Peptides/Proteins, Peptide Prodrugs and Turn Mimics

What I'm up to now: working on an NIH-funded project on cyclic prodrugs of opioid peptides, with Ron Borchardt in KU's Department of Pharmaceutical Chemistry.

A. A. Wakankar, J. L. Liu, D. VanderVelde,Y. J. Wang, S. J. Shire,and R. T. Borchardt, “The effect of cosolutes on the isomerization of aspartic acid residues and conformational stability in a monoclonal antibody,” J Pharm Sci., 2007 Jan 19; [Epub ahead of print]

Katayama, Derrick S.; Nayar, Rajiv; Chou, Danny K.; Valente, Joseph J.; Cooper, Julianne; Henry, Charles S.;Vander Velde, David G.; Villarete, Lorelie; Liu, C. P.; Manning, Mark Cornell. "Effect of buffer species on the thermally induced aggregation of interferon-tau," Journal of Pharmaceutical Sciences (2006), 95(6), 1212-1226.

Liederer, Bianca M.; Fuchs, Tarra; Vander Velde, David; Siahaan, Teruna J.; Borchardt, Ronald T. "Effects of Amino Acid Chirality and the Chemical Linker on the Cell Permeation Characteristics of Cyclic Prodrugs of Opioid Peptides," Journal of Medicinal Chemistry (2006), 49(4), 1261-1270.

Krogmeier, Stephanie L.; Reddy, D. Srinivasa; Vander Velde, David; Lushington, Gerald H.; Siahaan, Teruna J.; Middaugh, C. Russell; Borchardt, Ronald T.; Topp, Elizabeth M. "Deamidation of model β-turn cyclic peptides in the solid state," Journal of Pharmaceutical Sciences (2005), 94(12), 2616-2631.

D. S. Katayama, R. Nayar, D. K. Chou, J. Campos, J. Cooper, D. G. Vander Velde, L. Villarete, and M. C. Manning, “Solution Behavior of a Novel Type 1 Interferon,” J. Pharm. Sci., 94, 2703-2715 (2005).

K. S. Rao, M. Albro, J. A. Zirrolli, D. Vander Velde, D. N. M. Jones, and F. E. Frerman, “Protonation of Crotonyl-CoA Dienolate by Human Glutaryl-CoA Dehydrogenase Occurs by Solvent-Derived Protons,” Biochemistry, 44, 13932-13940 (2005).

B. M. Liederer, T. Fuchs, D. Vander Velde, T. J. Siahaan, and R. T. Borchardt, “Effects of Amino Acid Chirality and the Chemical Linker on the Cell Permeation Characteristics of Cyclic Prodrugs of Opioid Peptides,” J. Med. Chem.,49, 1261-1270 (2006). S. L. Krogmeier, D. S. Reddy, D. Vander Velde, G. H. Lushington, T. J. Siahaan, C. R. Middaugh, R. T. Borchardt, and E. M. Topp, “Deamidation of Model β-Turn Cyclic Peptides in the Solid State,” J. Pharm. Sci., 94, 2616-2631 (2005).

D. S. Reddy, D. Vander Velde and J. Aubé, “Synthesis and Conformational Studies of Dipeptides Constrained by Disubstituted 3-(Aminoethoxy)propionic Acid Linkers,” J. Org. Chem., 69, 1716-1719 (2004).

C. E. Stotz, R. T. Borchardt, C. R. Middaugh, T. J. Siahaan, D. Vander Velde, and E. M. Topp, “Secondary Structure of a Dynamic Type I’ Beta Hairpin Peptide,” J. Peptide Res., 63, 384-388 (2004).

B. Li, R. T. Borchardt, E. M. Topp, D. Vander Velde, and R. L. Schowen, “Racemization of an Asparagine Residue During Peptide Deamidation,” J. Am. Chem. Soc., 125, 10152-10153 (2003).

M. Chittchang, N. Salamat-Miller, H. H. Alur, D. Vander Velde, A. K. Mitra and T. P. Johnston, “Poly(L-lysine) as a model drug macromolecule with which to investigate secondary structure and microporous membrane transport, Part II : Diffusion Studies,” J. Pharm. Pharmacol.,54, 1491-1496 (2002).

J. D. Meyer, M. C. Manning, and D. G. Vander Velde, “Characterization of the Solution Conformation of Leuprolide Acetate,” J. Peptide Res., 60, 159-168 (2002).

H. Ouyang, D.G. Vander Velde, R T. Borchardt, and T.J. Siahaan, “Synthesis and conformational analysis of a coumarinic acid-based cyclic prodrug of an opioid peptide with modified sensitivity to esterase-catalyzed bioconversion,” J. Peptide Res., 59, 183-195 (2002).

C. Ampasavate, G. A. Chandorkar, D. G. Vander Velde, J. F. Stobaugh, and K. L. Audus, “Transport and metabolism of opioid peptides across BeWocells, an in vitro model of the placental barrier,” Int. J. Pharmaceutics, 233, 85-98 (2002).

M. MacDonald, D. Vander Velde, and J. Aubé, “Effect of Progressive Benzyl Substitution on the Conformations of Aminocaproic Acid-Cyclized Dipeptides,” J. Org. Chem., 66, 2636-2642 (2001).

S. A. Rogers-Sanders, D. Vander Velde, and C. K. Larive, “Evaluation of NMR diffusion measurements for the conformational analysis of flexible peptides,” Fresenius J. Anal. Chem., 369, 308-312 (2001).

J. Gao, S. L. Winslow, D. Vander Velde, J. Aubé, and R. T. Borchardt, “Transport Characteristics of Peptides and Peptidomimetics: 2. Hydroxyethylamine Bioisostere-Containing Peptidomimetics as Substrates for the Oligopeptide Transporter and P-Glycoprotein in the Intestinal Mucosa,” J. Peptide Research, 57, 316-329 (2001).

M. Xie, J. Aube‚, R. T. Borchardt, M. Morton, E. M. Topp, D. Vander Velde, and R. L. Schowen, "Reactivity toward Deamidation of Asparagine Residues in ß-Turn Structures," J. Peptide Research, 56, 165-171 (2000).

M. Macdonald, D.G. Vander Velde, and J. Aubé, "Cyclic ß-Turn Mimics Derived from Benzyl Aminocaproic Acids," Org. Lett., 2, 1653-1655 (2000).

O. S. Gudmonsson, D. G. Vander Velde, S. D. S. Jois, A. Bak, T. J. Siahaan, and R. T. Borchardt,"The Effect of Conformation of the AcyloxyalkoxyBased Cyclic Prodrugs of Opioid Peptides on the Membrane Permeability," J. Peptide Research, 53, 403-413 (1999).

O. S. Gudmonsson, S. D. S. Jois, D. G. Vander Velde, T. J. Siahaan, B. Wang, and R. T.Borchardt,"The Effect of Conformation on the Membrane Permeation of Coumarinic Acid and Phenylproprionic AcidBased Cyclic Prodrugs of Opioid Peptides," J. Peptide Research, 53, 383-392 (1999).

G. T. Knipp, D. G. Vander Velde, T. J. Siahaan, and R. T. Borchardt, “The Effect of $-Turn Structure on the Passive Diffusion of Peptides Across Caco-2 Cell Monolayers,” Pharm. Res., 14, 1332-1340 (1997).

K. Tamura, K. A. Agrios, D. Vander Velde, J. Aubé, and R. T. Borchardt, “Effect of Stereochemistry on the Transport of Aca-Linked $-Turn Peptidomimetics Across a Human Intestinal Cell Line,” Bioorg. Med. Chem., 5, 1859-1866 (1997)

F. W. Okumu, G. M. Pauletti, D. G. Vander Velde, T. J. Siahaan, and R. T. Borchardt, “Effect of Restricted Conformational Flexibility on the Permeation of Model Hexapeptides Across CACO-2 Cell Monolayers,” Pharm. Res., 14, 169-175 (1997).

M. Xie, D. Vander Velde, M. Morton, R. T. Borchardt, and R. L. Schowen, “pH-Induced Change in the Rate-Determining Step for the Hydrolysis of the Asp/Asn-Derived Cyclic-Imide Intermediate in Protein Degradation,” J. Am. Chem. Soc., 118, 8955-8956 (1996)

S. Gangwar, S. D. S. Jois, T. J. Siahaan, D. G. Vander Velde, V. J. Stella, and R. T. Borchardt, “The Effect of Conformation on Membrane Permeability of an Acyloxyalkoxy-linked Cyclic Prodrug of a Model Hexapeptide,” Pharm. Res., 13, 1657-1661 (1996).

D. Jayawickrama, S. Zink, D. G. Vander Velde, R. I. Effiong, and C. K. Larive, "Conformational Analysis of the ß-Amyloid Peptide Fragment, ß(12-28)," J. Biomol. Str. Dyn., 13, 229-244 (1995).

O. Kitagawa, D. Vander Velde, D. Dutta, M. Morton, F. Takusagawa, and J. Aubé, "Structural Analysis of -Turn Mimics Containing a Substituted 6-Aminocaproic Acid Linker," J. Am. Chem. Soc., 117, 5169-5178 (1995).

S. S. Chu, M. B. Doughty, D. Shobe, and D. G. Vander Velde, "Conformational Properties of the Proline Region of Porcine Neuropeptide Y by Circular Dichroism and 1H-NMR Spectroscopy," Biopolymers, 35, 583-593 (1995).

R. A. Gray, D. G. Vander Velde, C. J. Burke, M. C. Manning, C. R. Middaugh, and R. T. Borchardt, "Delta Sleep Inducing Peptide: Investigation of Its Solution Structure(s) and Its Potential Relationship to Permeability," Biochemistry, 33, 1323-1331 (1994).

T.J. Siahaan, S. Chakrabarty, and D.G. Vander Velde, "Conformational Study of Cyclo(1,5)-Ac-Pen-Arg-Gly-Asp-Cys-NH2 by NMR and Molecular Dynamics," Biochem. Biophys. Res. Comm., 187, 1042-1047 (1992).

R. Krishnamoorthi, C.S. Lin, and D.G. Vander Velde, "Structural Consequences of the Natural Substitution, E9K, on Reactive-Site Hydrolyzed Squash (Cucurbita maxima) Trypsin Inhibitor (CMTI), as Studied by 2D NMR," Biochemistry, 31, 4965-4969 (1992).

R. Krishnamoorthi, Y. Gong, C.S. Lin, and D.G. Vander Velde, "Hydrogen-1 NMR Studies of Cucurbita maxima Trypsin Inhibitors: Evidence for a pH-Dependent Conformational Change and His25-Tyr27 Interaction," Biochemistry, 31, 905-910 (1992).

R. Krishnamoorthi, Y. Gong, C.S. Lin, and D.G. Vander Velde, "Two-Dimensional NMR Studies of Squash Family Inhibitors. Sequence-Specific Assignments and Secondary Structure of Reactive-Site Modified Cucurbita maxima Trypsin Inhibitor III," Biochemistry, 31, 898-904 (1992).