Arnold J. Mandell - US grants

The development of a prototype software package, the Gen-Pep Algorithm, an entirely new, receptor sequence, hydrophobic free energy eigenfunction-based proprietary system for short peptide design, will be completed. Its feasibility with respect to a yield of new peptides which elicit target receptor-mediated biological activation in receptor cDNA transfected cell lines will be tested using Cytosensor Microphysiometry. Gen-Pep exploits a sequence of linear transformations of the hydrophobic free energies of the amino acid sequences of peptide and their receptors and includes eigenvalue decomposition and complex pole spectral and wavelet transformation and a constructive step using the leading eigenvectors. Given a peptide receptor sequence, this system generates a family of candidate peptides to interact with it. As exemplars, short peptide analogues of neurotensin and cholecystokinin will be designed and tested for their recently demonstrated direct action on the D2 dopamine receptor and the dopamine transporter proteins respectively. New short peptide analogues of (longer peptide) epidemoid growth factor, transforming growth factor and fibrobast growth factor will be designed and tested similarly. Licensing and support of Gen-Pep including a superfamily hydrophobic free energy eigenfunction library, contract new peptide development for biotechnology, companies and new peptide-drug development constitute the three commercial goals of the enterprise. PROPOSED COMMERCIAL APPLICATION 1) Licensing Gen-Pep software, support and eigenfunction library for an annual fee to biotechnology and pharmaceutical research concerns. 2) Contracting with similar entities for Cielo Institute, Inc. to generate and preliminarily test promising candidate, short peptides designed for specific purposes. 3) Developing and testing new peptide ligands for patenting by Cielo Institute, Inc.

DESCRIPTION (provided by applicant): One mechanism of emergent anticancer multidrug resistance is the induction of an ATP-dependent, membrane transport system, P-glycoprotein, P-gp, a pump which effluxes anticancer agents. We offer a peptide ligand design scheme as an agent source alternative to currently prominent empirically discovered small molecule inhibitors of substrate and/or nucleotide binding which often fail because they themselves are subject to and/or induce the P-gp pump in tumor cells. Our new scheme for computational hierarchical hydrophobic mode analysis and membrane protein mode matched peptide design target membrane protein extracellular loops and induce conformational transitions manifested by either positive or negative allosteric changes in their responses to their natural ligands and with approximately 30-50% hit rates. The cooperative conformational motions of P-gp?s nearly symmetric halves required for normal function make this approach different from and perhaps more promising than the more common binding-site targeted, small molecule inhibitors. Work since the previous submission suggest that these receptor hydrophobic mode matched algorithmic peptides, reversed in sequence and expressed in D amino acids, retro-inverso forms, less likely to be subject to the action and induction of the P-gp pump as well as the actions of peptidases (thus more easily deliverable, even orally), have similar effects in magnitude and direction as their ortho congeners. Hydrophobic mode-matched, algorithmically designed, conformationally active allosteric ortho and retro-inverso peptide agents will be tested against cancer drug transport and ATP utilization in spheroblasts, right sided vesicles and whole cell prokaryote systems expressing human P-gp. Ligand mode specificity will be addressed using 50 peptides generated from randomized eigenvector templates. The non-multidrug ATP-dependent transporter MDR3 will serve as a control for target specificity. Evidence that the anticipated 30% (75) or more of the 250 normal vector generated candidate algorithmic peptides will down regulate, impair or abrogate transport by this Phase I study using this in vitro simple cell system will encourage a Phase I submission for expanded peptide design and testing in P-gp expressing in vitro and in vivo mammalian cells systems as well as drug resistant human tumor cell lines.