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    Irina Kufareva

    TitleProject Scientist
    SchoolUniversity of California, San Diego
    DepartmentSchool of Pharmacy and Pharmaceutical Science
    Address9500 Gilman Drive #0747
    CA La Jolla 92093
    Phone858-822-4163
    vCardDownload vCard

      Collapse Research 
      Collapse Research Activities and Funding
      Chemokine interaction with CXCR4 and ACKR3: structure and activation mechanisms
      NIH/NIGMS R01GM117424Sep 15, 2016 - May 31, 2020
      Role: Principal Investigator
      The structural plasticity of chemokine and gp120 recognition by CCR5
      NIH/NIAID R01AI118985May 11, 2015 - Apr 30, 2020
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Zheng Y, Han GW, Abagyan R, Wu B, Stevens RC, Cherezov V, Kufareva I, Handel TM. Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity. 2017 Jun 20; 46(6):1005-1017.e5. PMID: 28636951.
        View in: PubMed
      2. Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys. 2017 May 22; 46:175-198. PMID: 28532213.
        View in: PubMed
      3. Ghosh P, Rangamani P, Kufareva I. The GAPs, GEFs, GDIs and…now, GEMs: New kids on the heterotrimeric G protein signaling block. Cell Cycle. 2017 Apr 03; 16(7):607-612. PMID: 28287365.
        View in: PubMed
      4. Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM. Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun. 2017 Jan 18; 8:14135. PMID: 28098154.
        View in: PubMed
      5. Ngo T, Ilatovskiy AV, Stewart AG, Coleman JL, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ. Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nat Chem Biol. 2017 Feb; 13(2):235-242. PMID: 27992882.
        View in: PubMed
      6. Zheng Y, Qin L, Zacarías NV, de Vries H, Han GW, Gustavsson M, Dabros M, Zhao C, Cherney RJ, Carter P, Stamos D, Abagyan R, Cherezov V, Stevens RC, IJzerman AP, Heitman LH, Tebben A, Kufareva I, Handel TM. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature. 2016 12 15; 540(7633):458-461. PMID: 27926736.
        View in: PubMed
      7. Aznar N, Patel A, Rohena CC, Dunkel Y, Joosen LP, Taupin V, Kufareva I, Farquhar MG, Ghosh P. AMP-activated protein kinase fortifies epithelial tight junctions during energetic stress via its effector GIV/Girdin. Elife. 2016 Nov 04; 5. PMID: 27813479.
        View in: PubMed
      8. Hua T, Vemuri K, Pu M, Qu L, Han GW, Wu Y, Zhao S, Shui W, Li S, Korde A, Laprairie RB, Stahl EL, Ho JH, Zvonok N, Zhou H, Kufareva I, Wu B, Zhao Q, Hanson MA, Bohn LM, Makriyannis A, Stevens RC, Liu ZJ. Crystal Structure of the Human Cannabinoid Receptor CB1. Cell. 2016 Oct 20; 167(3):750-762.e14. PMID: 27768894.
        View in: PubMed
      9. Wescott MP, Kufareva I, Paes C, Goodman JR, Thaker Y, Puffer BA, Berdougo E, Rucker JB, Handel TM, Doranz BJ. Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices. Proc Natl Acad Sci U S A. 2016 Aug 30; 113(35):9928-33. PMID: 27543332; PMCID: PMC5024644 [Available on 02/28/17].
      10. Kufareva I. Chemokines and their receptors: insights from molecular modeling and crystallography. Curr Opin Pharmacol. 2016 Oct; 30:27-37. PMID: 27459124.
        View in: PubMed
      11. Leach K, Gregory KJ, Kufareva I, Khajehali E, Cook AE, Abagyan R, Conigrave AD, Sexton PM, Christopoulos A. Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor. Cell Res. 2016 May; 26(5):574-92. PMID: 27002221; PMCID: PMC4856764 [Available on 05/01/17].
      12. Ngo T, Kufareva I, Coleman JLj, Graham RM, Abagyan R, Smith NJ. Identifying ligands at orphan GPCRs: current status using structure-based approaches. Br J Pharmacol. 2016 Oct; 173(20):2934-51. PMID: 26837045.
        View in: PubMed
      13. Kufareva I, Gustavsson M, Holden LG, Qin L, Zheng Y, Handel TM. Disulfide Trapping for Modeling and Structure Determination of Receptor: Chemokine Complexes. Methods Enzymol. 2016; 570:389-420. PMID: 26921956; PMCID: PMC4782801.
      14. O'Hayre M, Inoue A, Kufareva I, Wang Z, Mikelis CM, Drummond RA, Avino S, Finkel K, Kalim KW, DiPasquale G, Guo F, Aoki J, Zheng Y, Lionakis MS, Molinolo AA, Gutkind JS. Inactivating mutations in GNA13 and RHOA in Burkitt's lymphoma and diffuse large B-cell lymphoma: a tumor suppressor function for the Ga13/RhoA axis in B cells. Oncogene. 2016 Jul 21; 35(29):3771-80. PMID: 26616858; PMCID: PMC4885800.
      15. Lenoir M, Kufareva I, Abagyan R, Overduin M. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily. Membranes (Basel). 2015 Oct 23; 5(4):646-63. PMID: 26512702; PMCID: PMC4704004.
      16. Hanes MS, Salanga CL, Chowdry AB, Comerford I, McColl SR, Kufareva I, Handel TM. Dual targeting of the chemokine receptors CXCR4 and ACKR3 with novel engineered chemokines. J Biol Chem. 2015 Sep 11; 290(37):22385-97. PMID: 26216880; PMCID: PMC4566214.
      17. Husby J, Bottegoni G, Kufareva I, Abagyan R, Cavalli A. Structure-based predictions of activity cliffs. J Chem Inf Model. 2015 May 26; 55(5):1062-76. PMID: 25918827; PMCID: PMC4553268.
      18. Lo IC, Gupta V, Midde KK, Taupin V, Lopez-Sanchez I, Kufareva I, Abagyan R, Randazzo PA, Farquhar MG, Ghosh P. Activation of Gai at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling. Dev Cell. 2015 Apr 20; 33(2):189-203. PMID: 25865347; PMCID: PMC4415880.
      19. Kufareva I, Salanga CL, Handel TM. Chemokine and chemokine receptor structure and interactions: implications for therapeutic strategies. Immunol Cell Biol. 2015 Apr; 93(4):372-83. PMID: 25708536; PMCID: PMC4406842.
      20. Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, Handel TM. Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science. 2015 Mar 06; 347(6226):1117-22. PMID: 25612609; PMCID: PMC4362693.
      21. Kufareva I, Handel TM, Abagyan R. Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods Mol Biol. 2015; 1335:295-311. PMID: 26260608; PMCID: PMC4551442.
      22. Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM. Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):E5363-72. PMID: 25468967; PMCID: PMC4273337.
      23. Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E, Bissig C, Gruenberg J, Abagyan R, Overduin M. Discovery of novel membrane binding structures and functions. Biochem Cell Biol. 2014 Dec; 92(6):555-63. PMID: 25394204; PMCID: PMC4267288.
      24. Lin C, Ear J, Midde K, Lopez-Sanchez I, Aznar N, Garcia-Marcos M, Kufareva I, Abagyan R, Ghosh P. Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Mol Biol Cell. 2014 Nov 05; 25(22):3654-71. PMID: 25187647; PMCID: PMC4230624.
      25. Kufareva I, Katritch V, Stevens RC, Abagyan R. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure. 2014 Aug 05; 22(8):1120-1139. PMID: 25066135; PMCID: PMC4126895.
      26. McRobb FM, Kufareva I, Abagyan R. In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor a. Toxicol Sci. 2014 Sep; 141(1):188-97. PMID: 24928891; PMCID: PMC4271121.
      27. Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ. Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model. 2014 Mar 24; 54(3):933-43. PMID: 24521202; PMCID: PMC3982395.
      28. Kawamura T, Stephens B, Qin L, Yin X, Dores MR, Smith TH, Grimsey N, Abagyan R, Trejo J, Kufareva I, Fuster MM, Salanga CL, Handel TM. A general method for site specific fluorescent labeling of recombinant chemokines. PLoS One. 2014; 9(1):e81454. PMID: 24489642; PMCID: PMC3904831.
      29. McRobb FM, Sahagún V, Kufareva I, Abagyan R. In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ Sci Technol. 2014; 48(3):1964-72. PMID: 24392850; PMCID: PMC3951377.
      30. Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R. PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun. 2014 Mar 21; 445(4):717-23. PMID: 24406170; PMCID: PMC3975830.
      31. Lindin I, Wuxiuer Y, Kufareva I, Abagyan R, Moens U, Sylte I, Ravna AW. Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theor Biol Med Model. 2013 Sep 14; 10:56. PMID: 24034446; PMCID: PMC3848485.
      32. Tan Q, Zhu Y, Li J, Chen Z, Han GW, Kufareva I, Li T, Ma L, Fenalti G, Li J, Zhang W, Xie X, Yang H, Jiang H, Cherezov V, Liu H, Stevens RC, Zhao Q, Wu B. Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science. 2013 Sep 20; 341(6152):1387-90. PMID: 24030490; PMCID: PMC3819204.
      33. Davydov DR, Davydova NY, Sineva EV, Kufareva I, Halpert JR. Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of a-naphthoflavone. Biochem J. 2013 Jul 15; 453(2):219-30. PMID: 23651100; PMCID: PMC3893034.
      34. Ziarek JJ, Getschman AE, Butler SJ, Taleski D, Stephens B, Kufareva I, Handel TM, Payne RJ, Volkman BF. Sulfopeptide probes of the CXCR4/CXCL12 interface reveal oligomer-specific contacts and chemokine allostery. ACS Chem Biol. 2013 Sep 20; 8(9):1955-63. PMID: 23802178; PMCID: PMC3783652.
      35. Ilatovskiy AV, Abagyan R, Kufareva I. Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. Int J Quantum Chem. 2013 Jun 15; 113(12):1669-1675. PMID: 25414519.
        View in: PubMed
      36. Bissig C, Lenoir M, Velluz MC, Kufareva I, Abagyan R, Overduin M, Gruenberg J. Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell. 2013 May 28; 25(4):364-73. PMID: 23664863; PMCID: PMC4129370.
      37. O'Hayre M, Vázquez-Prado J, Kufareva I, Stawiski EW, Handel TM, Seshagiri S, Gutkind JS. The emerging mutational landscape of G proteins and G-protein-coupled receptors in cancer. Nat Rev Cancer. 2013 06; 13(6):412-24. PMID: 23640210; PMCID: PMC4068741.
      38. Shah MB, Kufareva I, Pascual J, Zhang Q, Stout CD, Halpert JR. A structural snapshot of CYP2B4 in complex with paroxetine provides insights into ligand binding and clusters of conformational states. J Pharmacol Exp Ther. 2013 Jul; 346(1):113-20. PMID: 23633618; PMCID: PMC3684837.
      39. Gabrielsen M, Wolosewicz K, Zawadzka A, Kossakowski J, Nowak G, Wolak M, Stachowicz K, Siwek A, Ravna AW, Kufareva I, Kozerski L, Bednarek E, Sitkowski J, Bocian W, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z. Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors. Chem Biol Drug Des. 2013 Jun; 81(6):695-706. PMID: 23574807; PMCID: PMC3665732.
      40. Katiyar S, Kufareva I, Behera R, Thomas SM, Ogata Y, Pollastri M, Abagyan R, Mensa-Wilmot K. Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One. 2013; 8(2):e56150. PMID: 23437089; PMCID: PMC3577790.
      41. Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM. A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer. Methods Mol Biol. 2013; 1013:93-127. PMID: 23625495; PMCID: PMC4091634.
      42. Montaner S, Kufareva I, Abagyan R, Gutkind JS. Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases. Annu Rev Pharmacol Toxicol. 2013; 53:331-54. PMID: 23092247; PMCID: PMC4074518.
      43. Sager G, Ørvoll EØ, Lysaa RA, Kufareva I, Abagyan R, Ravna AW. Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. J Med Chem. 2012 Apr 12; 55(7):3049-57. PMID: 22380603; PMCID: PMC4181661.
      44. Jaronczyk M, Wolosewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP, Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z. Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors. Eur J Med Chem. 2012 Mar; 49:200-10. PMID: 22309909; PMCID: PMC3365592.
      45. Kufareva I, Abagyan R. Methods of protein structure comparison. Methods Mol Biol. 2012; 857:231-57. PMID: 22323224; PMCID: PMC4321859.
      46. Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R. Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem. 2012; 12(17):1869-82. PMID: 23116466; PMCID: PMC4085113.
      47. Kufareva I, Ilatovskiy AV, Abagyan R. Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 2012 Jan; 40(Database issue):D535-40. PMID: 22080553; PMCID: PMC3245087.
      48. Gabrielsen M, Kurczab R, Ravna AW, Kufareva I, Abagyan R, Chilmonczyk Z, Bojarski AJ, Sylte I. Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. Eur J Med Chem. 2012 Jan; 47(1):24-37. PMID: 22071255; PMCID: PMC3357065.
      49. Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P. Tyrosine phosphorylation of the Ga-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal. 2011 Sep 27; 4(192):ra64. PMID: 21954290; PMCID: PMC4226136.
      50. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure. 2011 Aug 10; 19(8):1108-26. PMID: 21827947; PMCID: PMC3154726.
      51. Katritch V, Kufareva I, Abagyan R. Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology. 2011 Jan; 60(1):108-15. PMID: 20637786; PMCID: PMC2980563.
      52. Park SJ, Kufareva I, Abagyan R. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des. 2010 May; 24(5):459-71. PMID: 20455005; PMCID: PMC2881208.
      53. Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. Spatial chemical distance based on atomic property fields. J Comput Aided Mol Des. 2010 Mar; 24(3):173-82. PMID: 20229197; PMCID: PMC2858276.
      54. Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R. Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem. 2010 Feb 25; 53(4):1799-809. PMID: 20095623; PMCID: PMC2826142.
      55. Bottegoni G, Kufareva I, Totrov M, Abagyan R. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem. 2009 Jan 22; 52(2):397-406. PMID: 19090659; PMCID: PMC2662720.
      56. Abagyan R, Kufareva I. The flexible pocketome engine for structural chemogenomics. Methods Mol Biol. 2009; 575:249-79. PMID: 19727619; PMCID: PMC2975493.
      57. Kufareva I, Abagyan R. Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem. 2008 Dec 25; 51(24):7921-32. PMID: 19053777; PMCID: PMC2669721.
      58. Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S. Optimization of high throughput virtual screening by combining shape-matching and docking methods. J Chem Inf Model. 2008 Mar; 48(3):489-97. PMID: 18302357.
        View in: PubMed
      59. Bottegoni G, Kufareva I, Totrov M, Abagyan R. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des. 2008 May; 22(5):311-25. PMID: 18273556; PMCID: PMC2641994.
      60. Hayashi T, Mo JH, Gong X, Rossetto C, Jang A, Beck L, Elliott GI, Kufareva I, Abagyan R, Broide DH, Lee J, Raz E. 3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A. 2007 Nov 20; 104(47):18619-24. PMID: 18003900; PMCID: PMC2141826.
      61. Outeiro TF, Kontopoulos E, Altmann SM, Kufareva I, Strathearn KE, Amore AM, Volk CB, Maxwell MM, Rochet JC, McLean PJ, Young AB, Abagyan R, Feany MB, Hyman BT, Kazantsev AG. Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science. 2007 Jul 27; 317(5837):516-9. PMID: 17588900.
        View in: PubMed
      62. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. PIER: protein interface recognition for structural proteomics. Proteins. 2007 May 01; 67(2):400-17. PMID: 17299750.
        View in: PubMed
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