Celia Schiffer, Ph.D.

Academic Role: Professor

Faculty Appointment(s) In:
   Biochemistry and Molecular Pharmacology

Other Affiliation(s):
   Center for AIDS Research
   Interdisciplinary Graduate Program

Structural basis for molecular recognition in HIV Protease

Many biological processes involve complex interdependent molecular recognition events, in which molecules recognize each other with high specificity. Such events include an enzyme acting on its substrate in catalysis, a ligand activating a receptor in regulation and a two dimensional peptide chain assembling into a specific three dimensional fold. The specificity of such molecular recognition events can only be thoroughly understood by detailed analyses of the structures, functions and flexibilities of the molecules.

Investigating molecular recognition of biological macromolecules at the atomic level has been the central objective of my research. In my group we address these questions by using detailed structural and dynamic analyses (both experimental and computational) combined with functional and biophysical assays. This comprehensive approach is essential as molecular recognition is a dynamic event; usually, at least one of the molecular surfaces needs to undergo a conformational change to recognize the other.

Disruption of the life cycle of HIV, the virus that causes AIDS, is the goal of the drugs used to treat infected pediatric patients. The most successful drugs are the protease inhibitors. As the individual virus particles assemble, a series of their necessary components are attached together. For the virus particles to mature and become infectious these necessary components must be cut apart. The protease is the "scissors" molecule which "knows" where to sever these components. Protease inhibitors block these scissors and prevent the virus from maturing. Unfortunately, the virus changes (mutates) and alters the protease so that the inhibitors no longer block the "scissors" action, and the virus is once again infectious (drug resistant). Our strategy is to examine how the protease "knows" where to cut and how this "knowledge" is changed when the protease becomes drug resistant. By understanding how the protease changes, our data will be complementary to the existing efforts of the pharmaceutical industry.

Publications

Nalam, M.N., Peeters, A., Jonckers, T.H., Dierynck, I., Schiffer, C.A..  Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease ”  J. Virol. 81(17):9512-8 (2007).   17596316

Chellappan, S., Reddy, K., Ali, A., Altman, M.D., Nalam, M., Cao, H., Kairys, V., Fernandes, M.X., Tidor, B., Rana, T.,  Schiffer, C.A., Gilson, M. “Design of Mutation-Resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis” Chem. Biol. And Drug Design 69(6):455 (2007).   17539822

Chellappan, S., Kairys, V., Fernandes, M.X., Schiffer, C.A., Gilson, M.K.  "Evaluation of the Substrate Envelope Hypothesis for Inhibitors of HIV-1 Protease ”  Proteins: Structure, Function and Bioinformatics 68(2):561-7 (2007).  17574129

Chen, W., Lam, S.S., Srinath, H. Schiffer, C.A., Royer, W.E., Lin, K. “Competition between Ski and CBP for binding to Smads in TGF-b signaling ” J. Biol. Chem 282(15):11365-76 (2007).

Foulkes-Murzycki, J.E., Scott, W.R.P.,  Schiffer, C.A. “Hydrophobic Sliding: A Possible Mechanism for Drug Resistance in Human Immunodeficiency Virus Type 1 Protease ” Structure 15(2):225-33 (2007).  

Mitsuya, Y., Winters, M.A., Fessel, J., Rhee, S.-Y., Hurley, L., Horberg, M., Schiffer, C.A., Zolopa, A.R., Shafer, R.W. “N88D Facilitates the Co-Occurrence of D30N and L90M and the Development of Multidrug Resistance in HIV-1 Protease Following Nelfinavir Treatment Failure” AIDS Research and Human Retroviruses 22(12):1300-5 (2006).   

Ali, A., Reddy, G.S.K.K., Cao, H., Anjun, S.G., Nalam, M., Schiffer, C.A., Rana, T.M. “Discovery of HIV-1 Protease Inhibitors with Picomolar Affinities Incorporating N-Aryl-Oxazolidine-5-Carboxamides as Novel P2 Ligands ” J Med Chem 49(25):7342-56 (2006).  

Forget, A.L., Kudron, M.M., McGrew, D.A., Calmann, M.A., Schiffer, C.A., Knight, K.L.,  “RecA dimmers serve as a functional unit for assembly of active nucleoprotein filaments ”  Biochemistry 45(45):13537-42 (2006).   170875707

Foulkes, JE, Prabu-Jeyabalan, M., Cooper, D., Henderson, GJ, Harris, J., Swanstrom, R., Schiffer C.A. “Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity .” J. Virology 80(14): 6906-16 (2006).

Ozer, N. Haliloglu, T., Schiffer, C.A. “Substrate Specificity in HIV-1 Protease by a Biased Sequence Search Method ” Proteins. 2006 64(2):444-56. (2006).  

Kolli, M., Lastere, S., Schiffer, C.A. “Co-evolution of Nelfinavir-Resistant HIV-1 protease and the p1-p6 substrate. ” Virology 347(2):405-9 (2006).

Prabu-Jeyabalan, M., King, N.M., Nalivaika, E.A., Cammack, N., Heilek-Snyder, G., Schiffer, C.A. “Substrate Envelope and Drug Resistance: the Crystal Structure of RO1 in complex with HIV-1 Protease .”  Antimicrobial Agents and Chemotherapy 50(4):1518-21 (2006).

Prabu-Jeyabalan, M., Romano, K., Nalivaika, E.A., Schiffer, C.A.  “A possible structural intermediate in HIV-1 protease substrate recognition ” J. Virology 80(7):3607-16 (2006).

Liu, F., Wagner, S., Campbell, R.B., Nickerson, J.A., Schiffer, C.A., Ross, A.H. “PTEN enters the nucleus by diffusion. ” J Cell Biochem. 96(2):221-34 (2005).

Surleraux, D., De Kock, H. Verschueren, W., Pille, G.M.E., Peeters, A., De Meyer, S., Azijn, H., Pauwels, R., de Bethune, M.-P., King, N.M, Prabu-Jeyabalan, M., Schiffer, C.A., Wigerinck, P. “Design of Protease Inhibitors Active of Multi-drug Resistant Virus ” J. Med. Chem. 48(6):1965-73 (2005).

Surleraux, D., Tahri, A., Verschueren, W., Pille. G.M.E., Jonckers, T.H.M., Peeters, A., De Meyer, S., Azijn, H., Pauwels, R., de Bethune, M.-P., King, N.M, Prabu-Jeyabalan, M., Schiffer, C.A., Wigerinck, P. “The Discovery and Selection of TMC114, a next generation HIV-1 protease inhibitor ” J. Med. Chem. 48(6):1813-22 (2005).

Johnston, E., Winters, M.A., Rhee, S.-Y., Merigan, T.C. Schiffer, C.A., Shafer, R.W. “A Novel HIV-1 Protease Substrate-Cleft Mutation: Association with Protease Inhibitor Therapy and In Vitro Drug Resistance ” Antimicrobial Agents and Chemotherapy 48(12)4864-4868 (2004).

Prabu-Jeyabalan, M.,  Nalivaika, E.A.,  King, N.M.,   Schiffer , C.A.  “ Structural Basis for Coevolution of a Human Immunodeficiency Virus Type 1 Nucleocapsid-p1 Cleavage Site with a V82A Drug-Resistant Mutation in Viral Protease” .  J Virol. Vol 78(22):12446-54 (2004)

King, N.M.,  Prabu-Jeyabalan, M.,  Nalivaika, E.A.,  Wigerinck, P.,  de Bethune, M.P., Schiffer , C.A.   “Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor” .   J Virol.  Vol 78(21) 12012-21 (2004)

King, N.M.,  Prabu-Jeyabalan, M.,  Nalivaika, E.A., Schiffer , C.A. “Combating Susceptibility to Drug Resistance; Lessons from HIV-1 Protease”.  Chem Biol. Vol 11(10) 1333-8 (2004)

Hoffman, N., Schiffer, C.A., Swanstrom, R. “Covariation of amino acid positions in HIV-1 Protease ” Virology 314:536-548 (2003).

Schiffer, C.A., Hermans, J. “Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling ” Methods in Enzymology 374: 412-61 (2003).

Kurt, N., Haliloglu, T., Schiffer, C.A. "Prediction of Potential Binding and Non-Binding Peptides to HIV-1 Protease".  Biophysical Journal  85:853-863 (2003).

Wu, T.D., Schiffer, C.A., Gonzales, M., Kantor, R., Chou, S., Israelski, D., Zolopa, A., Fessel, J., Shafer, R.W. "Mutation patterns and structural correlates in HIV-1 Protease following varying degrees of protease inhibitor treatment " J of Virology 77(8):4836-47 (2003).

Kurt, N., Scott, W.R.P., Schiffer, C.A., Haliloglu, T.  "Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations ."  Proteins. 51(3):409-22 (2003). (NOTE: Schiffer & Haliloglu are joint last/corresponding authors)

Prabu-Jeyabalan, M., Nalivaika, E.A., King, N.M., Schiffer, C.A.  "Viability of a drug-resistant HIV-1 protease variant: structural insights for better anti-viral therapy ."  J. Virology  77(2):1306-15 (2003).

Schonhoff, C.M., Daou, M.C., Jones, S.N., Schiffer, C.A., Ross, A.H. "Nitric Oxide-Mediated Inhibition of Hdm2-p53 Binding ." Biochemistry. 41(46):13570-13574 (2002)

Pettit, S.C., Henderson, G.J., Schiffer, C.A., Swanstrom, R.  "Replacement of the P1 amino acid of Human Immunodeficiency Virus Type-1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease " J. Virology 76(20)10226-10233 (2002).

Liu, H., Radhakrishnan, P., Magoun, L., Prabu, M., Campellone, K., Savage, P., He, F., Schiffer, C., Leong, J.M.  "Point mutants of EHEC intimin that diminish Tir recognition and acting pedestals formation highlight a putative Tir binding pocket " Molecular Microbiolog 45(6), 1557-1573 (2002).

Prabu-Jeybalan, M.M., Nalivaika, E., Schiffer, C.A. "Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes ."  Structure  10(3) 369-381(2002).

Schiffer, C. Ultsch, M., Walsh, S., Somers, W., de Vos, A.M., Kossiakoff, A.  "Structure of a phage display-derived variant of human growth hormone complexed to two copies of the extracellular domain of its receptor:  evidence for strong structural coupling between receptor binding sites" J. Mol. Biol. 316, 277-289 (2002).

King, N., Melnick, L., Prabu-Jeybalan, M. Nalivaika, E., Yang, S-S., Gao, Y., Nie, X., Zepp, C., Heefner, D. Schiffer, C.A.  "Lack of Synergy for Inhibitors Targeting a Multi-drug-resistant HIV-1 Protease ." Protein Sci 2002 Feb;11(2):418-29 (2002)

Scott, W.R.P., Schiffer, C.A. "Curling of Flap Tips in HIV-1 Protease as a Mechanism for Substrate Entry and Tolerance of Drug Resistance ." Structure Vol 8, 1259-1265 (2000).

Prabu-Jeybalan, M.M., Nalivaika, E., Schiffer, C.A. "How does a symmetric dimer recognize an asymmetric substrate? The first complex of HIV-1 protease bound to a substrate from gag-pol " J. Mol. Biol. 301(5):1207-20 (2000).

Schiffer, C.A. and van Gunsteren, W.F., "Accessibility and order of water sites in and around proteins: a crystallographic time-averaging study ." Proteins Vol. 36, 501-511 (1999).

Schiffer, C.A. , van Gunsteren, W.F.,   “Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study”.Proteins. Vol 26(1) 66-71 (1996)

Peng, J.W., Schiffer, C.A., Xu, P., van Gunsteren, W.F., Ernst, R.R. "Dynamics of Antamanide with Water in Chloroform." J. Biol. NMR Vol. 8, 453-476 (1996).

Schiffer, C.A., Dötsch, V., "The Role of Protein - Solvent Interactions in Protein Unfolding ." Curr. Opin. in Biotechnology Vol. 7, 428-432 (1996).

Van Gunsteren, W.F.,  Hunenberger P.H.,  Kovacs H.,  Mark, A.E.,  Schiffer , C.A.   “Investigation of protein unfolding and stability by computer simulation”.  Philos Trans R Soc Lond B Biol Sci.  Vol 348(1323) 49-59 (1995)

Schiffer, C.A.   “Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system”. Acta Crystallography D Biol Crystallography.  Vol 51(Pt 1) 85-92 (1995)

Schiffer, C.A., Clifton, I.J., Davisson, V.J., Santi, D.V., Stroud, R.M.  "The Crystal Structure of Human Thymidylate Synthase: A Structural Mechanism for Guiding Substrates into the Active Site ."   Biochemistry Vol. 34, 16279-16287 (1995).

Schiffer, C.A., Dötsch, V., Wüthrich, K., van Gunsteren, W.F, "Exploring the Role of the Solvent in the Denaturation of a Protein: A Molecular Dynamics Study of the DNA Binding Domain of the 434 Repressor ." Biochemistry Vol. 34, 15057-15067 (1995).

Van Gunsteren, W.F.,    Brunne, R.M.,  Gros P,  Van Schaik,  R.C.,  Schiffer, C.A., Torda, A.E,.  “Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data”.   Methods Enzymol.   239 619-54.  (1994) 

Greene, P.J.,  Yu, P.L.,  Zhao J,  Schiffer , C.A. , Santi, D.  “Expression, purification, and characterization of thymidylate synthase from Lactococcus lactis”.   Protein Sci.  Vol 3(7) 1114-6 (1994).

Schiffer, C.A., Huber,R., Wüthrich, K., van Gunsteren, W.F., "Simultaneous Refinement of the Structure of BPTI against NMR data measured in solution and X-ray data measured in single crystals ." J. Mol. Biol. Vol. 241(4), 588-599 (1994).

Schiffer , C.A. ,  Caldwel , J.W., Stroud, R.M.,  Kollman, P.A.   “Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.”     Protein Sci.  Vol 1(3) 396-400 (1992).

Schiffer, C.A. , Davisson, V.J.,   Santi D.V.,   Stroud R.M.  “Crystallization of human thymidylate synthase.” J.  Mol.  Biol.  Vol.  219(2), 161-3.  (1991).

Schiffer, C.A., Caldwell, J.W., Kollman, P.A., Stroud, R.M.  "Prediction of Homologous Protein Structures Based on Conformational Searches and Energetics ". Proteins, Vol. 8(1), 30-43 (1990).

Possible Rotation Projects

1. Site directed mutagenesis and enzyme kinetics of HIV protease to determine the role of strongly conserved residues.
2. Refinement of crystal structures of HIV protease in complex with substrates or inhibitors
3. Analysis of molecular dynamics trajectories of HIV protease. Analysis of the water, peptide and protein structure.

Academic Background

B.A., University of Chicago, 1986
Ph.D., University of California, San Francisco, 1992

Postdoctoral Fellow, ETH-Zurich, 1992-94
Postdoctoral Fellow, Genentech, 1994-97

Office: Research 923, Lab 970 L&M
Phone: 508-856-8008
E-mail: Celia.Schiffer@umassmed.edu
Keywords: Biophysics, Drug Design, Structural Biology, Infectious Disease, HIV/AIDS

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