Immunophysics

We study the physical basis of immune system function and regulation. We explore the structure and dynamics of immune system proteins and how proteins interact with each other, with their environment, and with small ligands. We address fundamental questions such as: what is the mechanism of immune system function at molecular and cellular level? What is the mechanism of immune system regulation and how the immune system discriminates between "self" and "nonself"? How does autoimmune disease relate to failure of immune system regulation at molecular and cellular level?

Immunoengineering

We use immunophysics knowledge to design immune system regulators or inhibitors with tailored structural and physicochemical properties and with desired biological activities. Our efforts focus on the design of native and viral regulators of the complement system, by introducing knowledge-based perturbations in structure, dynamics, interactions, and eventually function. We also work on the design of other proteins outside the immune system.

Drug Design and Discovery

We use structure-dynamics-interactions-function relations to design low-molecular mass peptide-based inhibitors of immune system proteins. We use structure-based pharmacophore modeling, virtual screening, and conformational selection-based protein-ligand docking to discover small molecules (< 500 Da) that bind on complement proteins. Many of our targets involve proteins, regulators, and receptors of the complement system and their interactions. Our drug candidates are peptides, peptidomimetics, and small organic molecules. Our aim is to develop drugs against autoimmune/inflammatory diseases and other pathological conditions involving inappropriate activation/regulation of the complement system, such as age-related macular degeneration (AMD), atypical hemolytic uremic syndrome (aHUS), paroxysmal nocturnal hemoglobinuria (PNH) and C3 glomerulopathy (C3G), and other complement-mediated diseases.

Biomarker Discovery and Design

We use structure/dynamics-based pharmacophore modeling, virtual screening of large chemical databases (of millions of chemical compounds and billions of conformations), and conformational selection-based protein-ligand docking to discover small molecules that have affinity for binding on complement proteins or protein fragments and also have fluorescence properties. These molecules have the potential to become diagnostic biomarkers for early detection and spatiotemporal monitoring of AMD, and for other complement-mediated diseases. Some of these molecules also have the potential to become theranostics or carriers of therapeutics.

Systems Immunology Modeling

We construct comprehensive diagrams of protein-protein interactions of the complement system activation pathways, and we use experimental knowledge on protein concentrations and kinetic parameters to develop mathematical models for quantitative analysis of protein dynamics. The models are based on the solution of systems of ordinary differential equations (ODEs). We have developed a quantitative stand-alone model of the alternative pathway and a unified model of the alternative, classical, and lectin pathways of complement system activation.

Our Methods

Computational

We use computational methods such as structural and physicochemical analysis of proteins and protein complexes, molecular dynamics simulations, electrostatic calculations, free energy calculations, similarity analysis, Brownian dynamics simulations, homology modeling, structure and dynamics based pharmacophore modeling, virtual screening, conformational selection based protein-ligand docking, network analysis of allosteric pathways, and modeling of dynamics of protein-protein interaction pathways using systems of ordinary differential equations.

Experimental

Wet lab. We use binding methods for protein-protein and protein-ligand interactions, such as microscale thermophoresis (MST) and surface plasmon resonance (SPR). We use biochemical and functional/immunological assays, such as enzyme-linked immunosorbent assay (ELISA) and cell hemolysis assays for quantification of complement activation and inhibition.

Dry lab. We use nuclear magnetic resonance (NMR) spectroscopy for structure determination and study of dynamics of peptides and proteins, and we have expertise with optical spectroscopy methods, such as Raman scattering, Fourier transform infrared (FTIR) spectroscopy, circular dichroism (CD), UV-visible absorption spectroscopy, and fluorescence spectroscopy. 

Tool Development

Structural bioinformatics. We have developed the computational protocol AESOP (Analysis of Electrostatic Structures Of Proteins) for the calculation of electrostatic similarity indices and free energies, based on Poisson-Boltzmann electrostatics, and for clustering analyses of families of homologous proteins and alanine scans.

Translational bioinformatics. (1) We have developed a mathematical model that describes the dynamics of the complement system activation pathways. This tool has the potential for a clinical application in personalized treatment of patients with genetic predisposition for complement-mediated diseases. It can be used to identify the target(s) of inhibition and calculate the effects of drug inhibitors on the activity of complement system, as well as susceptibility to infection. (2) We have developed a probabilistic, probit, tool for the identification of co-receptor selectivity of HIV-1 entry into human cells. This tools has potential in clinical translation for the determination of patient-specific drug treatment, using combinations of co-receptor specific cell entry drugs.

Our Research Systems

Immunophysics. Some of our active research projects in immunophysics include protein-protein interactions within the complement system, involving C3 and its fragments C3b, iC3b, C3c and C3d, proteins C4 and C5, receptors CR1 and CR2, and regulators Factor H, Factor H related proteins, DAF, MCP, and properdin. In addition, we study the catalytic mechanism of complement serine proteases, such as Factor D, Factor B, C1s, C1r, and C2. We also work on the structural modeling and dynamics of GPCRs, such as C3aR, C5aR1, CXCR1, CXCR4, CCR5, CCR7, and non-GPCR C5aR2, and on docking studies with interacting proteins.

Immunoengineering. Our efforts in immunoengineering involve complement control proteins, including native receptors and regulators, viral inhibitor proteins of the pox family, and S. aureus bacterial proteins. We also work on the anti-bacterial proteins known as human defensins, SUMO proteins, and plant proteins, among others.

Drug design/discovery. Our efforts on drug design involve peptide-based inhibitors of the complement system. These are peptides and peptidomimetics of the compstatin family which target C3, and peptides derived from pro-inflammatory proteins C3a and C5a which target C3aR and C5aR1/R2, respectively. Our goal is to design potent and efficacious compstatin analogs and C3aR and C5aR1/R2 agonists and antagonists. We also perform similar studies for the discovery of non-peptidic complement inhibitors. In addition, we study the effect of known non-peptidic inhibitors in the structure of serine proteases of the complement system. The eventual goal of this study is design inhibitors that will be specific to complement serine proteases, without affecting the function of broad-range serine proteases. We also work with peptides derived from the V3-loop of the HIV-1 glycoprotein gp120 and their interactions with co-receptors CXCR4 and CCR5. The goal of this study is to design entry inhibitors against HIV.

Biomarker discovery/design. Our efforts on biomarker design involve the discovery of low-molecular mass chemical compounds that have fluorescence properties and are ligands of complement proteins. Such chemical compounds have the potential to become diagnostic imaging agents for the detection of complement-mediated diseases.