About

Irina Kufareva, Ph.D, is a professor at the Skaggs School of Pharmacy and Pharmaceutical Sciences with a research focus on structural, molecular, and architectural principles of tumor and immune cell responses to stimuli and drugs through computational approaches. Her work primarily centers on GPCRs and G proteins, key classes of cell signaling molecules, where she develops methods for accurate computational prediction of transient interactions of proteins and chemicals with conformationally variable protein interfaces. Her research includes elucidating the structural basis of ligand binding and signaling in chemokine GPCRs such as CXCR4, ACKR3, CCR5, and CCR2, which are involved in cancer progression, metastasis, HIV infection, inflammation, and autoimmunity. Additionally, she has contributed to understanding non-receptor activation of heterotrimeric G proteins and has solved the first structure of a G protein complexed with a non-receptor activator. Her recent work involves network-based modeling and reverse-engineering of cell signaling to decode principles of biological information transfer, aiming to inform therapeutic strategies in cancer and inflammatory diseases. Dr. Kufareva holds a background in mathematics and computer science from Tomsk State University and completed postdoctoral training in Computational Structural Biology at The Scripps Research Institute. She has served as Associate Founding Director of the UC San Diego Center for Network Medicine and has contributed to the development of computational tools such as chemical field docking and the Pocketome encyclopedia of binding sites.

Research topics

• Biology
• Cell biology
• Pharmacology
• Neuroscience
• Internal medicine
• Chemistry
• Medicine
• Biochemistry
• Computational biology
• Immunology

Selected publications

• Monocyte Migration Emerges from a Divergent Chemokine Signaling Network

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-04

  articleOpen access

  Migration of leukocytes in the context of immune homeostasis or inflammatory diseases is regulated by activation of chemokine receptors by chemokine ligands. To elucidate how these interactions give rise to cell migration, we mapped the chemokine-stimulated signal transduction network in monocytic THP-1 cells. Global phosphoproteomics revealed 630 time-resolved changes in phosphorylated proteins downstream of the chemokine receptor CCR2. We used the "PHONEMeS" network modeling algorithm to generate the most parsimonious signal transduction network consistent with the observed protein phosphorylation data. The CCR2 signaling network is highly divergent, acting via multiple branches to regulate proteins required for cell migration. We validated this model using kinase inhibitors targeting different branches of the network and successfully blocked chemokine-stimulated cell migration. Thus, chemotaxis is an emergent property resulting from an integrated cellular response to divergent signaling pathways. This paradigm suggests that physiological regulation or pharmacological blockade of chemokine-driven inflammation could potentially be achieved by inhibiting any of the divergent pathways within the network.

  PublisherDOI

• Supplemental Data for 'Signaling bias of the protease-activated receptor-1 is dictated by distinct GRK5 and β-arrestin-2 determinants'

  Open MIND · 2026-02-28

  dataset1st authorCorresponding

  The dataset contains 7 ensembles of structural models of unactivated, thrombin-activated, and APC-activated PAR1 with and without intracellular effectors. To gain insight into the conformational preferences of unactivated PAR1, thrombin-activated PAR1, and APC-activated PAR1, we built an ensemble of 100 structural models of each of these molecular species using AlphaFold 3 (AF3). To investigate the structural basis of favorable core-mediated coupling between βarr2 and APC-activated but not Th-activated PAR1, we constructed 100 models of βarr2 complexes with Th-activated PAR1 with distal C-terminus phosphorylated, and APC-activated PAR1 with both distal and proximal C-terminus phosphorylated. Our results are consistent with Th-activated but not APC-activated PAR1 forming multimeric complexes that simultaneously include a core-engaged heterotrimeric G protein and a tail-hanging βarr2. To reveal the structural basis for such complexes, we generated 100 models of either thrombin- or APC-activated PAR1 with different phospho-sites in complex with both Gq and βarr2 using AF3.

  DOI

• BPS2026 – The C-terminal PDZ-binding motif of Cx40 is regulated by phosphorylation and required for the formation of functional intercellular channels

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• Elevated conformational dynamics makes ACKR3 activation-prone and G protein-incompetent

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-20

  articleOpen accessSenior authorCorresponding

  Abstract The atypical receptor ACKR3 works together with the canonical chemokine receptor CXCR4 to drive cell migration along gradients of their shared agonist CXCL12. CXCR4 promotes chemotaxis by activating canonical G protein pathways and recruiting β-arrestins. ACKR3 indirectly regulates CXCR4-mediated chemotaxis by scavenging CXCL12. Unlike canonical chemokine receptors, ACKR3 does not couple to G proteins and instead is 100% biased towards β-arrestins. CXCR4 activation by CXCL12 is exquisitely sensitive to subtle changes in both receptor and ligand. By contrast, ACKR3 is activation-prone: it recruits β-arrestins in response to many ligands and is much less sensitive to mutations, suggesting distinct activation mechanisms compared to CXCR4. To explore the basis of these differences, we compared the dynamics of ACKR3 and CXCR4 complexes with chemokines using molecular dynamic (MD) simulations. Ten-microsecond atomistic MD simulations revealed that CXCR4 adopts a stable active state when bound to WT CXCL12 but transitions to an inactive state when in complex with the antagonist variant, [P2G]CXCL12. By comparison, ACKR3 exhibits a variable transmembrane (TM) 6 state distribution and persistently “active” TM7 when complexed with either WT CXCL12 or [P2G]CXCL12, the latter retaining substantial agonistic activity at ACKR3. We further identified ligand-mediated residue interaction networks in the TM core that regulate TM6 and TM7 activation in CXCR4 but are absent or disrupted in ACKR3, resulting in less constrained receptor dynamics. These findings were validated by BRET-based assays with CXCL12 and ACKR3 mutants. Together, the data suggests that the unique conformational dynamics of ACKR3 govern its activation propensity, its ligand promiscuity, and its atypical effector coupling.

  PublisherOA PDFDOI

• Signaling bias of the protease-activated receptor-1 is dictated by distinct GRK5 and β-arrestin-2 determinants

  Cell Reports · 2026-03-01 · 1 citations

  articleOpen access

  G protein-coupled receptors (GPCRs) exhibit signaling bias or preferential activation of heterotrimeric G proteins versus GPCR kinase (GRK)-mediated β-arrestin signaling. The protease-activated receptor-1 (PAR1) activates both G protein and β-arrestin in response to thrombin but only β-arrestin in response to activated protein C (APC). Thrombin-activated PAR1-G protein signaling is desensitized by β-arrestin-1, whereas APC-activated PAR1 signaling is propagated by β-arrestin-2. The mechanisms underlying PAR1 biased signaling are not known. Here, using computational modeling combined with cellular and biochemical studies, we reveal the molecular basis of signaling by thrombin- and APC-activated PAR1. Although both thrombin- and APC-induced PAR1 signaling are regulated by the same GRK, GRK5, the two types of signaling are differentially dependent on GRK5 membrane anchoring, PAR1 C-terminal phosphorylation sites, and the binding mode of β-arrestin-2. These differences translate into distinct β-arrestin-2 conformations and define the APC cytoprotective signaling signature, which contrasts with thrombin inflammatory signaling.

  PublisherDOI

• A NOD2-Encoded Toggle Switch Resolves the Host–Microbe Battle Over Cyclic AMP Control

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-31

  articleOpen access

  SUMMARY Pathogens hijack macrophages by triggering pathological cAMP surges that block phagolysosomal killing—a defect mirrored in phagocytes from refractory colitis. We identify a host-encoded, pathogen-specific surge-protector comprised of a three-protein toggle: The innate sensor NOD2 binds and masks an evolutionarily conserved motif in GIV that activates trimeric-GTPase Gαi , enforcing a biphasic surge-to-plunge cAMP-program : early, NOD2•GIV assembly permits a brief, tolerogenic cAMP rise, whereas subsequent GIV•Gαi engagement collapses cAMP to drive phagolysosomal fusion and microbial clearance. Structural, biochemical, and ultrastructural analyses reveal how molecular toggling imposes precise spatial and temporal control. Pharmacogenomic perturbations pinpoint cAMP–PKA hyperactivation as the defining lesion in GIV-deficient macrophages. Functional studies in primary macrophages and human gut organoid co-cultures show that toggling the NOD2•GIV•Gαi-axis is necessary and sufficient to convert tolerant macrophages into microbicidal machines that preserve mucosal barrier integrity. These findings uncover a druggable cAMP-control pathway with therapeutic promise in colitis. GRAPHIC ABSTRACT eTOC Blurb Pathogens hijack macrophages by inducing cAMP surges that help them evade clearance. Anandachar et al. identify a host “toggle switch” in which NOD2 and G proteins compete for GIV, driving a rapid and robust surge-to-plunge transition in cAMP. This temporal switch limits tolerogenic signaling, restores microbial clearance and barrier integrity, and unveils a targetable host pathway in infection and IBD. Highlights Pathogens exploit cAMP surges in macrophages to block phagolysosomal killing of microbes GIV acts as a molecular “toggle” linking NOD2 sensing to Gαi-mediated cAMP control Structural and mutagenesis studies reveal mutually exclusive binding of NOD2 and Gαi to GIV Pharmacogenomic perturbations pinpoint PKA, not EPAC, as the critical downstream effector Organoid co-cultures show NOD2-GIV-PKA crosstalk safeguards microbial clearance and gut barrier integrity

  PublisherOA PDFDOI

• Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-06

  articleOpen accessSenior authorCorresponding

  Abstract Understanding protein proximities in the theoretical ligand space is essential for developing therapeutics with desirable polypharmacology, predicting off-targets, and discovering surrogate ligands for poorly characterized proteins. This is especially important for G protein-coupled receptors (GPCRs) - a major class of drug targets, many of which still lack known ligands. Circumventing this limitation, we present GPCR-CoINPocket v2, a contact-informed metric for detecting GPCR pharmacological similarities from amino-acid sequences alone. We first establish a “gold standard” of pharmacological relatedness using ChEMBL-derived ligand sets. We then replace traditional evolutionary amino acid similarity matrices with a chemically-informed matrix derived from protein:ligand interaction patterns across 3,306 structures, significantly improving early detection of shared pharmacology between distantly homologous receptors. An additional unconstrained, contact-informed matrix further enhances predictive performance. Pilot application of the method revealed previously unrecognized similarities between the β 2 adrenoceptor and three Class A peptide GPCRs, which we confirmed experimentally by demonstrating the binding of select ligands of these receptors to the β 2 . Dimensionality reduction of similarity scores recapitulates known receptor relationships and predicts neighbors of orphan GPCRs later confirmed experimentally. Overall, GPCR-CoINPocket v2 provides a powerful sequence-based framework to prioritize ligand space, predict polypharmacology, and accelerate GPCR drug discovery and deorphanization.

  PublisherDOI

• BPS2026 – Comparative proximity biotinylation mapping reveals the role of endolysosomal retrofusion in intracellular trafficking of monocytic GPCRs

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• Supplemental Data for 'Signaling bias of the protease-activated receptor-1 is dictated by distinct GRK5 and β-arrestin-2 determinants'

  Zenodo (CERN European Organization for Nuclear Research) · 2026-02-28

  datasetOpen access1st authorCorresponding

  The dataset contains 7 ensembles of structural models of unactivated, thrombin-activated, and APC-activated PAR1 with and without intracellular effectors. To gain insight into the conformational preferences of unactivated PAR1, thrombin-activated PAR1, and APC-activated PAR1, we built an ensemble of 100 structural models of each of these molecular species using AlphaFold 3 (AF3). To investigate the structural basis of favorable core-mediated coupling between βarr2 and APC-activated but not Th-activated PAR1, we constructed 100 models of βarr2 complexes with Th-activated PAR1 with distal C-terminus phosphorylated, and APC-activated PAR1 with both distal and proximal C-terminus phosphorylated. Our results are consistent with Th-activated but not APC-activated PAR1 forming multimeric complexes that simultaneously include a core-engaged heterotrimeric G protein and a tail-hanging βarr2. To reveal the structural basis for such complexes, we generated 100 models of either thrombin- or APC-activated PAR1 with different phospho-sites in complex with both Gq and βarr2 using AF3.

  PublisherDOI

• Rules of engagement: Determinants of chemokine receptor activation and selectivity by CCL27 and CCL28

  Journal of Biological Chemistry · 2025-09-19 · 1 citations

  articleOpen access

  The distinct functional roles of chemokines CCL27 and CCL28 in epithelial immunity of skin and mucosal tissues, respectively, are coordinated by their shared receptor, CCR10, and the CCL28-specific receptor, CCR3. To identify determinants of receptor activation, internalization and binding specificity, we conducted structure-function studies focused on the N termini of these two chemokines. Deletion of two N-terminal residues of CCL27 resulted in a CCR10 antagonist, highlighting the critical roles of these residues in driving receptor pharmacology. Extension with a Phe produced a CCR10 superagonist by occupying a unique subpocket in the receptor. Swapping the CCL28 N terminus onto the CCL27 globular domain (NT28-CCL27) also resulted in a superagonist of CCR10, but the opposite swap (NT27-CCL28) showed equivalent or reduced activity compared to WT CCL28, indicating that the CCL28 N terminus is a stronger driver of CCR10 signaling. The effects of these mutations were rationalized by AlphaFold models of the CCR10 complexes. Modeling also revealed that the reduced size of the binding pocket, and more basic nature of the N terminus and extracellular loops of CCR3 compared to CCR10, contribute to its specificity for CCL28 while CCR10 accommodates both ligands. The basic nature of CCL28 also contributes to its high affinity for glycosaminoglycans and is likely important for its retention in mucosal tissues. These data illustrate how the modular nature of these chemokines enables their overlapping but nonredundant functions, and how this modularity can be exploited to produce engineered chemokines for probing or targeting CCR10 in disease.

  PublisherDOI

Recent grants

• NIH Grant R01GM117424

  NIH · $2.2M · 2020

• Computationally informed discovery of scavenging-sparing inhibitors of CC chemokine receptor 2

  NIH · $434k · 2020–2024

• NIH Grant R01AI118985

  NIH · $2.7M · 2021

Frequent coauthors

• Ruben Abagyan

  University of Montana

  155 shared

• Tracy M. Handel

  University of California, San Diego

  74 shared

• Pradipta Ghosh

  University of California, San Diego

  33 shared

• Tony Ngo

  Học viện Tư pháp

  26 shared

• Anne B. Young

  Defence Research and Development Canada

  25 shared

• Mel Β. Feany

  Brigham and Women's Hospital

  25 shared

• Tiago F. Outeiro

  25 shared

• Allison Amore

  Massachusetts General Hospital

  25 shared

Awards & honors

• Invited lectures at the ASCEPT-MPGPCR Joint Scientific Meeti…
• 5th Hawaiian GPCR workshop, Kona, Hawaii (2017)
• 256th ACS National Meeting, Boston, MA (2018)
• Gordon Research Conference on Molecular Pharmacology, Ventur…
• Mail-in reviewer for the NIH NCF study section (2017)