Peptide and Protein Design, Antigenic and Immunogenic Determinants, Peptide & Protein Folding

Pravin T. P. Kaumaya

Pravin T. P. Kaumaya

Ph.D., 1981, Portsmouth School of Pharmacy, England

Peptide and Protein Design, Antigenic and Immunogenic Determinants, Peptide & Protein Folding.

Research efforts in my laboratory are primarily based on exploiting the immune system’s exquisite specificity which offers one of the simplest and most effective ways to prevent and control disease. To achieve our goals a multidisciplinary research approach is being pursued which is at the interface of chemistry and biology with special emphasis on modulation of the immune response. We have and are continuing to develop innovative approaches to antigen specific vaccination as well as developing immunotherapies for cancer and autoimmune diseases. Therefore, we are actively pursuing an interdisciplinary approach to testing a novel multi-epitope cancer vaccine that bridges the synthetic, preclinical, and clinical elements of vaccine development. Several long term objectives include: 1) developing a widely applicable vaccine targeting the HER-2 oncoprotein (breast/ovarian/tumor/cancer vaccine and to gain understanding of immune response to self peptides in normal and pathologic conditions, 2) developing a widely applicable blockade strategy targeting costimulatory molecules (CD28:B7, CD40:CD40L) and also to elucidate the underlining mechanisms in downregulating immune responses as well as to gain understanding the biological active conformation of these peptide mimics and how they interact with the costimulatory molecules, 3) developing a B cell and T-cell vaccine for the retrovirus – HTLV-I (the causative agent of Adult T-cell Leukemia).

For peptide vaccines to become a practical reality, rationally designed, highly engineered synthetic constructs must incorporate enough antigenic determinants to elicit all three arms of the immune system. Novel vaccines designed to stimulate both antibody and T cell responses against human tumors are urgently required. It is critical to identify general rules for the definition of immunogenicity so that vaccine optimization is rational rather than empirical. Identification of the biologically relevant epitopes, devising strategies to engineer conformationally dependent sequences¸ adopting ways to increase the immunogenicity in an outbred population, delivering the immunogen in a safe and efficacious vehicle, developing animal models are at the basis of our approaches to developing new anticancer and retroviral vaccines. With these factors in mind, we have developed strategies for the design of PEPTIDE VACCINES that can provide optimal B cell, T helper cell and cytotoxic T cell responses. Our approach for the design of peptide vaccines with improved binding affinities, titers, and enhanced immunity a priori relies on the engineering of structured peptides which mimic antibody recognition sites and approaches to bypass MHC “restriction” of the T cell response. The immune responses (B-cell and T cell) to these peptides are then extensively studied to correlate biological or immunological reactivity with structure. This process of design, synthesis, structural characterization and immunological testing may point to a general strategy for tailoring peptide vaccines with more useful antigenic and immunogenic characteristics. Empirical and computational approaches are applied to the engineering and synthesis of complex peptide sequences designed to adopt well defined -secondary and three dimensional structures. A variety of biophysical techniques (CD, FTIR, SAXS, NMR, MS and X-Ray crystallography) are used to extensively characterize the chemical and structural properties of the synthetic peptides.

On the other spectrum of our research goals, overwhelming experimental evidence has emerged in recent years concerning the impact of costimulatory signals for complete T cell activation and has allowed investigators to develop new strategies for immune intervention, both for suppression of the immune system and for stimulation of the immune system. Attempts to block T cell costimulation as a therapeutic strategy in autoimmunity and transplantation have gained tremendous momentum. We are developing novel immunotherapeutic strategies that take advantage of normal mechanisms of tolerance to self antigen for immune intervention both for suppression of the immune system (autoimmune diseases (Multiple Sclerosis) and transplantation) and for stimulation of the immune system (vaccines). Our focus has been directed towards developing novel peptide mimics of ligand-binding regions of several costimulatory molecules (CD28:B7 and CD40:CD40L) in an attempt to block T cell costimulation pathways by use of retro-inverso (RI) modification of peptides that preserves the parent peptide overall topology and provides at the same time stability to proteolysis, leading to derivatives with prolonged half-life in vitro and in vivo. Blocking T cell costimulation as a therapeutic strategy in autoimmunity and transplantation is a major thrust in our laboratories.

Recent Publications

Kaumaya, P.T.P., Berndt, K., Heindorn, D., Trewhella, J., Kezdy, F.J. and Goldberg, E. (1990) Synthesis and Biophysical Characterization of Topographic Immunogenic Determinants with aa Topologies. Biochemistry, 29,13-23.

Kaumaya, P.T.P., VanBuskirk, A., Goldberg, E. and Pierce, S.K. (1992) Design and Immunological Properties of Topographic Immunogenic Determinants of a Protein Antigen (LDH-C4) as Vaccines. J. Biol. Chem., 267, 6338-6346.

Kaumaya, P.T.P., Seo, Y.H., Kobs, S., Ngua, l., Sheridan, J. and Stevens, V. (1993) Peptide vaccines incorporating a “promiscuous” T cell epitope bypass certain haplotype restricted immune responses and provide broad spectrum immunogenicity. J. Molec. Recog. 6, 81-94.

Kobs-Conrad, S., Lee, H., DiGeorge, A.M. and Kaumaya, P.T.P. (1993) Engineered Topographic Determinants with ab, bab, and baba Topologies show High Affinity Binding to Native Protein Antigen LDH-C4. J. Biol. Chem., 268, 25285-25295.

Lairmore, M.D., DiGeorge, A.M., Conrad, S.F., Trevino, A. and Kaumaya, P.T.P. (1995) HTLV-I Peptides Constructs incorporating Promiscuous T cell epitopes overcome genetic restriction, elicit neutralizing antibodies and T cell help. J. Virol.,69 (10),6077-6089

Kaumaya, P.T.P. (1996) Synthetic Peptide Vaccines: Dream or Reality. In Peptides in Immunology (Schneider, C.H., Ed.) Wiley and Sons, Ltd., pp. 117-148

Bakaletz, L. O., Leake, E. R., Billy, J. M., and Kaumaya, P. T. P. (1997) Relative Immunogenicity and Efficacy of Two Synthetic Chimeric Peptides of Fimbrin as Vaccinogens against Nasopharyngeal Colonization by Nontypeable Haemophilus Influenzae in the Chinchilla. Vaccine 15 (9), 955-961.

Dakappagari, N.K., Douglas, D.B., Triozzi, P.L., Stevens, V.C., and Kaumaya, P.T.P. (2000) Prevention of Mammary Tumors with a Chimeric HER-2 B-cell Epitope Peptide Vaccine. Cancer Research 60, 3782-3789

Frangione, M., Albretch, B., Dakappagari, N., Rose, T., Brooks, C.L., Schwendeman, S.P., Lairmore, M.D., and Kaumaya, P.T.P. (2001) Enhanced Immunogenicity of a Conformational Epitope of Human T-Lymphotropic Virus Type 1 using a Novel Chimeric Peptide. Vaccine 19, 1068-1081

Frangione-Beebe, M., Rose, T., Kaumaya, P.T.P., and Schwendeman, S.P. (2001) Microencapsulation of a Synthetic Peptide for HTLV-1 in Biodegradable Poly(D,L-lactise-co-glycolide) Microspheres using a Novel Encapsulation Technique. J. of Microencapsulation 18 (5), 663-677

Srinivasan, M., Wardrop, R.M., Whitacre, C., and Kaumaya, P.T.P. (2001) A Retro-Inverso Peptide Mimic of CD28 Encompassing the MYPPPY Motif Adopts a Polyproline Type II Helix and Inhibits Encaphalitogenic T cell in Vitro. J. Immunol 167:578-585

Roshni Sundaram, Christopher M Walker, and Pravin T.P. Kaumaya. (2001) Evaluation of HTLV-1 Cytotoxic T-cell Epitopes in HLA-A2.1 Transgenic Mice. In Peptides: The Wave of the Future (Eds Houghten R.A and Lebl, M) Kluwer Academic Publisher, Dordrecht, Netherlands. In Press

Pravin T.P. Kaumaya, John Pyles and Naveen Dakappagari. (2001) A combination of HER-2 peptide epitope vaccines mediate superior biological effects. In Peptides: The Wave of the Future (Eds Houghten R.A and Lebl, M) Kluwer Academic Publisher, Dordrecht, Netherlands. In Press

Sundaram, R., Dakappagari., and Pravin T.P. Kaumaya. (2002) Synthetic Peptides as Cancer Vaccine. Bioplolymers 66 (3),200-216

Sundaram, R, Yiping Sun, C.Walker, F.A.Lemonnier, S.Jacobson, and Pravin T.P. Kaumaya. (2003) A Novel HTLV-1 Epitope CTL Peptide Construct Elicits Robust Cellular Immune Responses in HLA-A*0201 Transgenic ß2 M, Db Double Knockout Mice. Vaccine 21, 2767-2781

Dakappagari, N., Parihar,R., J.Pyles, W.E. Carson, and Pravin T.P. Kaumaya. (2003) A Chimeric Multi HER-2 B cell epitope Peptide Vaccine mediates Superior Anti-tumor Responses. J. Immunol. 170:4242-4253

Utano Tomaru, Yoshihisa Yamano, Masahiro Nagai, Dragan Maric, Pravin T.P. Kaumaya, William Biddison, and Steven Jacobson. (2003) Acquisition of Peptide/HLA-GFP Complexes by Virus-Specific T Cells Differentiate Stages of T Cell Maturation Associated with The Outcome of Chronic Viral Infections. Nature Medicine 9(4), 469-475.

Sundaram, R., Beebe, M., and Kaumaya, P.T.P. (2004) Structural and Immunogenicity analysis of chimeric B-cell epitope constructs derived from gp46 and gp21 subunits of the env glycoproteins of HTLV-1. J. Peptide Res., 63, 132-140

Roshni Sundaram, Marcus P. Lynch , Sharad V. Rawale, Yiping Sun, Merdud Kazanji and Pravin T.P. Kaumaya. (2004) Denovo Design of Peptide Immunogens that Mimic the Coiled Coil Region of Human T-cell Leukemia Virus Type-1 gp21 Transmembrane Subunit for Induction of Native Protein Reactive Neutralizing Antibodies. J. Biol Chem., April 1, Epub ahead of Print); 279 (23) 24141-24151

Roshni Sundaram, Sharad Rawale , Naveen Dakappagari, Donn Young, Christopher M Walker, Francois Lemonnier, Steven Jacobson and Pravin T.P. Kaumaya. (2004) Protective Efiicacy of Multiepitope HLA-A*0201 restricted CTL Peptide construct against challenge with HTLV-1 TAX recombinant vaccinia virus. J. Acquir. Immune Defic. Syndr. 37 (3), 1329-1339

Roshni Sundaram, Melanie Beebe and Pravin T.P. Kaumaya (2004) Structural and Immunogenicity analysis of Chimeric B-cell epitope constructs derived from the gp46 and gp21 subunits of the env proteins of HTLV-1. J. Peptide Res. 63, 1-9

Naveen K. Dakappagari, Kenneth D. Lute, Sharad Rawale, Joan T. Steele, Stephanie D. Allen, Gary Phillips, R. Todd Reilly, and Pravin T.P. Kaumaya (2005) Conformational HER-2/neu B-Cell Epitope Peptide Vaccine Designed to Incorporate Two Native Disulfide Bonds Enhances Tumor Cell Binding and Antitumor Activities. J.Biol Chem (manuscript in press)

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