Ernesto Freire

Henry Walters Professor

114A Biology East
410-516-7743 | Lab 410-516-7742

Lab Members

Ernesto Freire received his PhD from the University of Virginia. He is a professor in the Department of Biology and holds a joint appointment in the Department of Biophysics and Biophysical Chemistry at JHMI. 

The ultimate goal of biomedical research is to cure disease. Drug development is a key endeavor towards that goal.  Two different types of drug molecules are being developed in the pharmaceutical industry: 1) Small molecule drugs; and, 2) Biologics, i.e. proteins as drug molecules, especially monoclonal antibodies.

1) Fundamental research in this laboratory has resulted in the development of a thermodynamic platform for small molecule drug discovery and optimization. This platform is permanently improved and simultaneously applied to the discovery and optimization of novel drugs against important diseases for which no successful therapies are available. The optimization platform is aimed at achieving extremely high binding affinity and selectivity as well as appropriate pharmacokinetics.

2) Subcutaneous administration of monoclonal antibodies (mAb) requires formulating the protein at concentrations exceeding 100mg/mL. At these extremely high mAb concentrations, aggregation, conformational stability and viscosity become critical issues.  Our research has developed new experimental approaches to evaluate and predict the long term stability of biologics.  These approaches have resulted in thermodynamic algorithms to identify the most stable variants of a mAb or the best formulation for a specific mAb.

Publications 2013 - 2016


  1. Yingyun Liu, Arne Schön and Ernesto Freire (2013) Optimization of CD4/gp120 Inhibitors by Thermodynamic Guided Alanine Scanning Mutagenesis, Chemical Biology and Drug Design, 81, 72-78

  2. Kamanna, K., Aneja, R., Duffy, C., Kubinski, P., Rodrigo Moreira, D., Bailey, L. D., McFadden, K., Schӧn, A., Holmes, A., Tuzer, F., Contarino, M., Freire, E., and Chaiken, I. M. (2013) Non-natural peptide triazole antagonists of HIV-1 envelope gp120, ChemMedChem 8, 322-328.

  3. LaLonde, J. M., Le-Khac, M., Jones, D. M., Courter, J. R., Park, J., Schön, A., Princiotto, A. M., Wu, X., Mascola, J. R., Freire, E., Sodroski, J., Madani, N., Hendrickson, W. A., and Smith, A. B. (2013) Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-ray and Thermodynamic Characterization, ACS Medicinal Chemistry Letters 4, 338-343.

  4. Pillaiyar Thanigaimalai, Sho Konno, Takehito Yamamoto, Yuji Koiwai Akihiro Taguchi, Kentaro Takayama, Fumika Yakushiji, Kenichi Akaji, Yoshiaki Kiso,Yuko Kawasaki, Shen-En Chen, Aurash Naser-Tavakolian, Arne Schön, Ernesto Freire,Yoshio Hayashi (2013) Design, synthesis, and biological evaluation of novel dipeptide-type SARS-CoV 3CL protease inhibitors: Structure activity relationship study. European Journal of Medicinal Chemistry 65, 436-447

  5. Schon, A., Brown, R.K., Hutchins, B. and Freire, E. (2013) Ligand binding analysis and screening by chemical denaturation shift. Analytical Biochemistry 443 (2013) 52–57

  6. Freire, E., Schon, A., Hutchins, B. and Brown, R.K (2013) Chemical denaturation as a tool in the formulation optimization of biologics Drug Discovery Today, 18 , 1007-1013

  7. Madani, N., Princiotto, A. M., Schon, A., LaLonde, J., Feng, Y., Freire, E., Park, J., Courter, J. R., Jones, D. M., Robinson, J., Liao, H. X., Moody, M. A., Permar, S., Haynes, B., Smith, A. B., 3rd, Wyatt, R., and Sodroski, J. (2014) CD4-Mimetic Small Molecules Sensitize Human Immunodeficiency Virus to Vaccine-Elicited Antibodies, Journal of Virology 88, 6542-6555.

  8. Evans, S. L., Schon, A., Gao, Q., Han, X., Zhou, X., Freire, E., and Yu, X. F. (2014) HIV-1 Vif N-terminal Motif is required for recruitment of Cul5 to Suppress APOBEC3, Retrovirology 11, 4.

  9. Courter, J. R., Madani, N., Sodroski, J., Schon, A., Freire, E., Kwong, P. D., Hendrickson, W. A., Chaiken, I. M., LaLonde, J. M., and Smith, A. B., 3rd. (2014) Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: conversion of a viral entry agonist to an antagonist, Acc Chem Res 47, 1228-1237.

  10. Afanador, G. A., Muench, S. P., McPhillie, M., Fomovska, A., Schon, A., Zhou, Y., Cheng, G., Stec, J., Freundlich, J. S., Shieh, H. M., Anderson, J. W., Jacobus, D. P., Fidock, D. A., Kozikowski, A. P., Fishwick, C. W., Rice, D. W., Freire, E., McLeod, R., and Prigge, S. T. (2013) Discrimination of potent inhibitors of Toxoplasma gondii enoyl-acyl carrier protein reductase by a thermal shift assay, Biochemistry 52, 9155-9166.

  11. Miura, T., Hidaka, K., Azai, Y., Kashimoto, K., Kawasaki, Y., Chen, S. E., de Freitas, R. F., Freire, E., and Kiso, Y. (2014) Optimization of plasmepsin inhibitor by focusing on similar structural feature with chloroquine to avoid drug-resistant mechanism of Plasmodium falciparum, Bioorganic & medicinal chemistry letters 24, 1698-1701.

  12. Patrick Ross, Wilhelm Weihofen, Fai Siu, Amy Xie, Hetal Katakia, S Kirk Wright, Ian Hunt, Richard K Brown and Ernesto Freire (2015) Isothermal Chemical Denaturation to Determine Binding Affinity of Small Molecules to G-Protein Coupled Receptors Analytical Biochemistry, 473, 41-45.

  13. Xu, Q., Ensign, L. M., Boylan, N. J., Schon, A., Gong, X., Yang, J. C., Lamb, N. W., Cai, S., Yu, T., Freire, E., and Hanes, J. (2015) Impact of Surface Polyethylene Glycol (PEG) Density on Biodegradable Nanoparticle Transport in Mucus ex Vivo and Distribution in Vivo, ACS Nano 9, 9217-9227.

  14. Schon, A., Clarkson, B. R., Siles, R., Ross, P., Brown, R. K., and Freire, E. (2015) Denatured state aggregation parameters derived from concentration dependence of protein stability, Anal Biochem 488, 45-50.

  15. Richard, J., Veillette, M., Brassard, N., Iyer, S. S., Roger, M., Martin, L., Pazgier, M., Schon, A., Freire, E., Routy, J. P., Smith, A. B., 3rd, Park, J., Jones, D. M., Courter, J. R., Melillo, B. N., Kaufmann, D. E., Hahn, B. H., Permar, S. R., Haynes, B. F., Madani, N., Sodroski, J. G., and Finzi, A. (2015) CD4 mimetics sensitize HIV-1-infected cells to ADCC, Proc Natl Acad Sci U S A 112, E2687-2694.

  16. Georgiev, I. S., Joyce, M. G., Yang, Y., Sastry, M., Zhang, B., Baxa, U., Chen, R. E., Druz, A., Lees, C. R., Narpala, S., Schon, A., Van Galen, J., Chuang, G. Y., Gorman, J., Harned, A., Pancera, M., Stewart-Jones, G. B., Cheng, C., Freire, E., McDermott, A. B., Mascola, J. R., and Kwong, P. D. (2015) Single-Chain Soluble BG505.SOSIP gp140 Trimers as Structural and Antigenic Mimics of Mature Closed HIV-1 Env, J Virol 89, 5318-5329.

  17. Do Kwon, Y., Pancera, M., Acharya, P., Georgiev, I. S., Crooks, E. T., Gorman, J., Joyce, M. G., Guttman, M., Ma, X., Narpala, S., Soto, C., Terry, D. S., Yang, Y., Zhou, T., Ahlsen, G., Bailer, R. T., Chambers, M., Chuang, G. Y., Doria-Rose, N. A., Druz, A., Hallen, M. A., Harned, A., Kirys, T., Louder, M. K., O'Dell, S., Ofek, G., Osawa, K., Prabhakaran, M., Sastry, M., Stewart-Jones, G. B., Stuckey, J., Thomas, P. V., Tittley, T., Williams, C., Zhang, B., Zhao, H., Zhou, Z., Donald, B. R., Lee, L. K., Zolla-Pazner, S., Baxa, U., Schon, A., Freire, E., Shapiro, L., Lee, K. K., Arthos, J., Munro, J. B., Blanchard, S. C., Mothes, W., Binley, J. M., McDermott, A. B., Mascola, J. R., and Kwong, P. D. (2015) Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env, Nat Struct Mol Biol 22, 522-531.

  18. Schon, A. and Freire, E. (2016) Biochim. Biophys. Acta. Three Easy Pieces, 1860, 975-980

  19. Clarkson, B. R., Schon, A., and Freire, E. (2016) Conformational stability and self-association equilibrium in biologics, Drug Discov Today 21, 342-347
Research Scientist

Arne Schon

Graduate Student

Benjamin Clarkson

Undergraduate Student

Maru Jaime


Victoria Kholodenko