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Meet Our California Scientists Clemencia Pinilla
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Clemencia Pinilla

Clemencia PinillaTorreyPinesInstituteCA

Associate Member

858.597.3883 - phone
858.597.3804 - fax
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Dr. Pinilla has over twenty years of experience and she is recognized as a pioneer in the field of combinatorial chemistry, particularly in the use of positional scanning libraries for the identification of ligands for a wide range of targets. In particular, in immunology she has studied antibody and T cell specificity and these studies have revealed an intricate balance between polyreactivity and specificity. During the last five years, she was the Project Director of the Large Scale T Cell Epitope Discovery program at Torrey Pines lnstitute, in which she led a team of researchers in the identification of vaccinia-specific T cell epitopes from human immunized donors. She was involved in the elucidation of the specificity of T cell clones of clinical relevance in multiple sclerosis, Lyme disease and cancer using positional scanning libraries. These and other studies have involved collaborative projects with multiple investigators at Torrey Pines lnstitute and other institutions in the United States and Europe. Dr. Pinilla has authored and co-authored more than one hundred peer-reviewed publications related to the identification of ligands and characterization of molecular interactions using individual compound analogs and mixture-based libraries.


  • 1986 Ph.D. in Microbiology. HSJD, National University of Colombia, Bogotá, Colombia.
  • 1984 B.S. in Microbiology. Universidad de los Andes, Bogotá, Colombia.


  • 1998 – 2004. Chief Technical Officer, Mixture Sciences Inc, San Diego, California
  • 1997 – present. Adjunct Associate Professor, Biology Department, San Diego State University
  • 1996 – present. Associate Member, Head of Immunochemistry Department, Torrey Pines Institute for Molecular Studies, San Diego, California.
  • 1991-1996. Assistant Member, Head of Immunochemistry Department, Torrey Pines Institute for Molecular Studies, San Diego, California.
  • 1989-1991.Postdoctoral Research Fellow, Torrey Pines Institute for Molecular Studies, San Diego, California, under the direction of Dr. Richard A. Houghten.
  • 1987-1989.  Postdoctoral Training, Exchange Visitor, Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, California, under the direction of Dr. Richard A. Houghten.
  • 1985-1986.  Isolation of Coding Clones for Plasmodium falciparum proteins, Department of Genetics, Harvard University, Cambridge, Massachusetts, under the direction of Dr. Jonathan Seidman.

Selected Publications (10 of 139)

  1. Houghten, R.A., Pinilla, C., Blondelle, S.E., Appel, J.R., Dooley, C.T., Cuervo, J.H. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature. 354:84-6, 1991.
  2. Pinilla, C, Appel, J.R., Blanc, P., Houghten, R.A. Rapid identification of high affinity peptide ligands using positional scanning synthetic peptide combinatorial libraries. BioTechniques. 13:901-5, 1992.
  3. Pinilla, C., Martin, R., Gran, B., Appel, J.R., Boggiano, C., Wilson, D.B., Houghten, R.A. Exploring immunological specificity using synthetic peptide combinatorial libraries. Current Opinion in Immunology. 11:193-202, 1999.
  4. Hemmer, B., Gran, B., Zhao, Y., Marques, A., Pascal, J., Tzou, A., Kondo, T., Cortese, I., Bielekova, B., Straus, S., McFarland, H. F., Houghten, R. A., Simon, R., Pinilla, C., Martin, R. Identification of candidate T cell epitopes and molecular mimics in chronic Lyme disease. Nature Medicine. 5:1375-82, 1999.
  5. Zhao, Y., Gran, B., Pinilla, C., Markovic-Plese, S., Hemmer B., Tzou, A., Whitney, L.W., Biddison, W.E., Martin, R., Simon, R. Combinatorial Peptide Libraries and Biometric Score Matrices Permit the Quantitative Analysis of Specific and Degenerate Interactions Between Clonotypic TCR and MHC Peptide. The Journal of Immunology. 167:2130-41, 2001.
  6. Pinilla, C., Appel, J.R., Borras, E., Houghten, R.A. Advances in the use of synthetic combinatorial chemistry: Mixture-based libraries. Nat Med. 9:118-22, 2003.
  7. Sospedra, M., Zhao, Y., zur Hausen, H., Muraro, P., Hamashin, C., de Villiers, E., Pinilla, C., Martin, R. Recognition of conserved amino acid motifs of common viruses and its role in autoimmunity. PloS Pathog. 1:e41, 2005.
  8. Houghten, R.A., Pinilla, C., Giulianotti, M.A., Appel, J.R., Dooley, C.T., Nefzi, A., Ostresh, J.M., Yu, Y., Maggiora, G.M., Medina Franco, J.L., Brunner, D., Schneider, J. Strategies for the use of mixture-based synthetic combinatorial libraries: scaffold ranking, direct testing in vivo, and enhanced deconvultion by computational methods. J of Comb Chem. 10(1):3-19, 2008.
  9. Singh, N., R. Guha, M. A. Giulianotti, C. Pinilla, R. A. Houghten, and J. L. Medina-Franco. 2009. Chemoinformatic analysis of combinatorial libraries, drugs, natural products, and molecular libraries small molecule repository. J Chem Inf. Model. 49:1010.
  10. Sospedra, M., Y. Zhao, M. Giulianotti, R. Simon, C. Pinilla, and R. Martin. 2010. Combining positional scanning peptide libraries, HLA-DR transfectants and bioinformatics to dissect the epitope spectrum of HLA class II cross-restricted CD4+ T cell clones. J Immunol. Methods 353:93.

Patents (5 of 10)

  1. Houghten, R. A., Pinilla, C., Lambkin, I., O’Mahony, D., Hamashin, C., Schink, A., and Osthues-Spindler, L.  Pharmaceutical formulations and ligands for use therein; mimetics for UEA-1.  (7,166,296). 1-23-2007.
  2. Petrie, C. R., McKernan, P. A., Moore, E. E., Ostresh, J. M., Meyer, J.-P., Houghten, R. A., and Pinilla, C. Dialkyl ureas as calcitonin mimetics. (6,391,917). 5-21-2002.
  3. Houghten, R. A. and Pinilla, C. Dimeric oligopeptide mixture sets. (6,287,787). 9-11-2001.
  4. Pinilla, C., Appel, J. R., and Houghten, R. A. Scanning synthetic peptide combinatorial libraries: Oligopeptide mixture sets having one predetermined residue at a single, predetermined position, methods of making and using the same. (5,556,762). 9-17-1996.
  5. Houghten, R. A., Cuervo, J. H., Pinilla, C., Appel, J. R., and Blondelle, S. E. Equimolar multiple oligomer mixtures, especially oligopeptide mixtures. (5,504,190). 4-2-1996.