Kufareva group

Research overview

The long-standing goal of our work is to elucidate the structural, molecular, and architectural principles of cell signaling, including cellular responses to stimuli and drugs. We approach this challenge at multiple levels, from atomic-resolution molecular interactions to the level of cellular systems, using methods and tools of trans-scale computational biology.

At the atomic resolution level, we develop methods for accurate computational prediction of transient interactions of proteins and chemicals with conformationally variable protein interfaces, and apply these approaches to important cellular targets. This is complemented by experimental work aimed at identification of bioactive molecules, target characterization and assay development.

At the systems level, we work towards understanding the unifying engineering and architectural principles that govern intracellular signaling networks. Inspired by the philosophy of "understanding-by-building", we seek to contribute to the construction of a predictive in silico cell. This challenging task relies on synergistic efforts of experimental, computational, systems, structural, and network biologists - the team and collaborators of the UCSD Center for Network Medicine.

Contact information

Irina Kufareva, Ph.D.

Associate Adjunct Professor

Associate Director, Center for Network Medicine

Skaggs School of Pharmacy and Pharmaceutical Sciences

University of California at San Diego

Pharmaceutical Sciences Building

  • Office: Rm. 3270
  • Postdoc office: Rm. 3115
  • Lab: Rm. 3141-3151

9500 Gilman Drive, MC 0756

La Jolla, CA 92093-0756, USA

Phone: 1-858-822-4163

Email: ikufareva@ucsd.edu

News

July 14, 2020

The paper by Bryan Stephens, about the functional anatomy of the CXCR4-CXCL12 complex, has been published in Science Signaling. Furthermore, together with Tony's PLOS Biology study, it was featured in the UC San Diego Health Sciences blog post. This is another collaborative study with the Handel lab. Beautiful work, we are all so proud of you Bryan and Tony!

April 9, 2020

Tony Ngo's paper about a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity is published in PLOS Biology This is the result of a long-standing collaboration with the Handel lab. Congrats Tony, Bryan, and all!

April 2, 2020

Kirti Chahal has been awarded the CCMI training fellowship studying the oncogenic Hedgehog signaling pathway. Way to go Kirti!

September 20, 2019

The long-awaited paper by Kirti Chahal, on an unexpected activity of the approved drug Nilotinib against SMO and the Hh pathway, is now published online in PLoS ONE. Congratulations Kirti, nice work!

July 30, 2019

Our paper on GPCR-independent activation of heterotrimeric Gi proteins is published in PNAS! Congratulations to Nick Kalogriopoulos (Ghosh lab), Steve Reese (Chang lab), and Tony Ngo (Kufareva lab), who were in charge of biochemistry, structure determination, and computational analyses, respectively. Go team!

June 5, 2019

Please welcome Alexis Lona, the new summer intern from the Mater Dei Catholic High School. Alexis will stay with us till mid-August developing ways of analyzing the quantitative mass-spectrometry data on G protein coupled receptors, using custom code that he is writing in Python.

May 28, 2019

Weijun's new baby Anthony is here! Congratulations Weijun and family, and wishing you all lots of fun!

May 20, 2019

Margaret Misyutina, a rising second year Comp Sci major from UC Berkeley, joins our lab for the summer to try her programming skills in application to biological networks. Welcome Margaret!

April 24, 2019

Watch Adrian's stellar AP Capstone presentation about the research that he has done in our lab during the summer of 2018 and in 2019.

March 19, 2019

Congratulations to Adrian who just got accepted to MIT!

March 1, 2019

Kirti Chahal has been awarded the CCMI training fellowship for studying the oncogenic Hedgehog signaling pathway. Congratulations!

Jan 22, 2019

Kirti has been selected to participate in the ASPET Mentoring Network: Coaching for Career Development program for 2019-2020, and to receive a Mentoring Network travel award. Great work, way to go Kirti!

Nov 1, 2018

Tony's work was selected for a short talk presentation at the BPS-MPGPCR meeting in Melbourne, and awarded a travel scholarship. Congrats Tony!

Oct 8, 2018

Weijun Xu joined the group. He will be developing a novel network-based representation of GPCR signaling. Welcome Weijun!

July 2, 2018

Suchismita (Suchi) Roy joined the group as a postdoc. Welcome! Suchi will focus on biophysical studies of G protein interactions with non-receptor modulators like GIV.

January 1, 2018

Tony Ngo was awarded an NHMRC CJ Martin Early Career Fellowship. Congratulations, Tony!

June 20, 2017

Our (Immunity, 2017) publication on the structure of CCR5 with a chemokine was featured in the UC San Diego Health Sciences News (Crystallizing HIV’s Entry Point)

January 18, 2017

Our (Nature Communications, 2017) publication on the atypical chemokine receptor ACKR3 was featured in Case Western Reserve University news release “Structure of atypical cancer protein paves approach for drug development” (Jan 18, 2017, Marc Kaplan).

See also: Health Medicine Innovation, New Medical, EurekAlert, Medical Express, and others.

May 15, 2017

Tony Ngo joined the group as a postdoc. Welcome!

February 2, 2017

Our (Nature Chemical biology, 2017) publication about GPCR COIN-Pocket and orphan receptor ligand discovery was featured in:

  • Nature Reviews Drug Discovery Research Highlight “Picking the pocketome for orphan receptor ligands” (Katie Kingwell, Nature Reviews Drug Discovery 16, 86 (2017) doi:10.1038/nrd.2017.6)
  • Biocentury Innovation article “Pickpocketed orphans. How a new GPCR matching technique could identify ligands for orphan receptors” (Published January 26, 2017)

December 7, 2016

Our (Nature, 2016) publication on the structure of double-antagonist-bound CCR2 was reviewed in Nature News & Views article “Pharmacology: Inside-out receptor inhibition” (Dec 7, 2016, Thomas P. Sakmar and Thomas Huber), as well as the UC San Diego HS Newsroom article “Researchers Reveal 3D Structure of Cell’s Inflammation Sensor and its Inhibitors” (December 07, 2016, Heather Buschman, PhD).

See also: Genetic Engineering and Biotechnology News, Science Newsline, Phys.org, Science Daily

January 2016

According to 2015 Journal Citation Reports® Science Edition (Thomson Reuters, 2016), our (Immunology & Cell Biology, 2015) review on chemokine and chemokine receptor structure and interactions was the most cited article in 2016

March 6, 2015

Our CXCR4:vMIP-II structure publication (Science, 2015) was featured in:

Science Perspective article “Viral chemokine mimicry” (Jörg Standfuss, Science 2015, 347 (6226), pp. 1071-1072)

The UC San Diego HS Newsroom article “Pictured Together for the First Time: a Chemokine and its Receptor” January 22, 2015, Heather Buschman, Ph.D.).

See also: Science Daily

December 23, 2014

Our PNAS publication on stoichiometry and geometry of CXCR4:CXCL12 interaction (PNAS 2014) was featured as a Research Highlight in Dec 2014 issue of Biopolymers

January 2012

Our Pocketome article (Nucleic Acids Research, 2012) has been highlighted as a featured article of the issue.