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Profile

Andrey Ivanov

  • Department of Pharmacology & Chemical Biology
    Assistant Professor
  • andrey.ivanov@emory.edu
  • Ivanov Lab Website
  • Pubmed publications
  • Emory University School of Medicine
    Pharmacology
    615 Michael St., Whitehead Building #405-J
Head shot of Andrey Ivanov

Overview

Research Area: Molecular biology and computational systems pharmacology to identify disease targets and chemical probes.
Research Interests: Dr. Ivanov combines experimental molecular biology with state-of-the-art bioinformatics and computational chemistry to study and regulate the molecular connectivity between the biological pathways. He develops and apply methods of computational molecular modeling, cheminformatics, and virtual screening to facilitate drug discovery and therapeutic development.

Research

Publications

  • Uncovering the rewired IAP-JAK regulatory axis as an immune-dependent vulnerability of LKB1-mutant lung cancer.
    Nat Commun Volume: 16 Page(s): 2324
    03/08/2025 Authors: Shu C; Li J; Rui J; Fan D; Niu Q; Bai R; Cicka D; Doyle S; Wahafu A; Zheng X
  • Decoding the functional impact of the cancer genome through protein-protein interactions.
    Nat Rev Cancer Volume: 25 Page(s): 189 - 208
    03/01/2025 Authors: Fu H; Mo X; Ivanov AA
  • Polo-like Kinase 1 Inhibitors Demonstrate In Vitro and In Vivo Efficacy in Preclinical Models of Small Cell Lung Cancer.
    Cancers (Basel) Volume: 17
    01/28/2025 Authors: Zhang G; Pannucci A; Ivanov AA; Switchenko J; Sun S-Y; Sica GL; Liu Z; Huang Y; Schmitz JC; Owonikoko TK
  • Protocol to discover actionable cancer vulnerabilities enabled by neomorph protein-protein interactions with the AVERON Notebook.
    STAR Protoc Volume: 5 Page(s): 103441
    12/20/2024 Authors: Chen H; Revennaugh B; Fu H; Ivanov AA
  • Best practices to evaluate the impact of biomedical research software-metric collection beyond citations.
    Bioinformatics Volume: 40
    08/02/2024 Authors: Afiaz A; Ivanov AA; Chamberlin J; Hanauer D; Savonen CL; Goldman MJ; Morgan M; Reich M; Getka A; Holmes A
  • AVERON notebook to discover actionable cancer vulnerabilities enabled by neomorph protein-protein interactions.
    iScience Volume: 27 Page(s): 110035
    06/21/2024 Authors: Chen H; Revennaugh B; Fu H; Ivanov AA
  • Pharmacological suppression of the OTUD4/CD73 proteolytic axis revives antitumor immunity against immune-suppressive breast cancers.
    J Clin Invest Volume: 134
    03/26/2024 Authors: Zhu Y; Banerjee A; Xie P; Ivanov AA; Uddin A; Jiao Q; Chi JJ; Zeng L; Lee JY; Xue Y
  • Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer's disease.
    J Biol Chem Volume: 299 Page(s): 105382
    12/01/2023 Authors: Du Y; Bradshaw WJ; Leisner TM; Annor-Gyamfi JK; Qian K; Bashore FM; Sikdar A; Nwogbo FO; Ivanov AA; Frye SV
  • TMPRSS2 and SARS-CoV-2 SPIKE interaction assay for uHTS.
    J Mol Cell Biol Volume: 15
    08/03/2023 Authors: Cicka D; Niu Q; Qui M; Qian K; Miller E; Fan D; Mo X; Ivanov AA; Sarafianos SG; Du Y
  • Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?
    ArXiv
    06/05/2023 Authors: Afiaz A; Ivanov AA; Chamberlin J; Hanauer D; Savonen CL; Goldman MJ; Morgan M; Reich M; Getka A; Holmes A
  • Development of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic strategy for Alzheimer's disease.
    bioRxiv
    05/22/2023 Authors: Du Y; Bradshaw WJ; Leisner TM; Annor-Gyamfi JK; Qian K; Bashore FM; Sikdar A; Nwogbo FO; Ivanov AA; Frye SV
  • Targeting PLK1 effectively suppresses growth of small cell lung cancer
    Volume: 83
    04/01/2023 Authors: Schmitz JC; Zhang G; Ivanov AA; Pannucci A; Ridinger M; Owonikoko TK
  • Acquisition of taxane resistance by p53 inactivation in ovarian cancer cells.
    Acta Pharmacol Sin Volume: 43 Page(s): 2419 - 2428
    09/01/2022 Authors: Shu C; Zheng X; Wuhafu A; Cicka D; Doyle S; Niu Q; Fan D; Qian K; Ivanov AA; Du Y
  • Systematic discovery of mutation-directed neo-protein-protein interactions in cancer.
    Cell Volume: 185 Page(s): 1974 - 1985.e12
    05/26/2022 Authors: Mo X; Niu Q; Ivanov AA; Tsang YH; Tang C; Shu C; Li Q; Qian K; Wahafu A; Doyle SP
  • Discovery of the first chemical tools to regulate MKK3-mediated MYC activation in cancer.
    Bioorg Med Chem Volume: 45 Page(s): 116324
    09/01/2021 Authors: Yang X; Fan D; Troha AH; Ahn HM; Qian K; Liang B; Du Y; Fu H; Ivanov AA
  • Hypomorph mutation-directed small-molecule protein-protein interaction inducers to restore mutant SMAD4-suppressed TGF- signaling.
    Cell Chem Biol Volume: 28 Page(s): 636 - 647.e5
    05/20/2021 Authors: Tang C; Mo X; Niu Q; Wahafu A; Yang X; Qui M; Ivanov AA; Du Y; Fu H
  • YAP1 Expression in SCLC Defines a Distinct Subtype With T-cell-Inflamed Phenotype.
    J Thorac Oncol Volume: 16 Page(s): 464 - 476
    03/01/2021 Authors: Owonikoko TK; Dwivedi B; Chen Z; Zhang C; Barwick B; Ernani V; Zhang G; Gilbert-Ross M; Carlisle J; Khuri FR
  • High expression of MKK3 is associated with worse clinical outcomes in African American breast cancer patients.
    J Transl Med Volume: 18 Page(s): 334
    09/01/2020 Authors: Yang X; Amgad M; Cooper LAD; Du Y; Fu H; Ivanov AA
  • NSD3S stabilizes MYC through hindering its interaction with FBXW7.
    J Mol Cell Biol Volume: 12 Page(s): 438 - 447
    07/03/2020 Authors: Gonzalez-Pecchi V; Kwan AK; Doyle S; Ivanov AA; Du Y; Fu H
  • Online informatics resources to facilitate cancer target and chemical probe discovery.
    RSC Med Chem Volume: 11 Page(s): 611 - 624
    06/01/2020 Authors: Yang X; Fu H; Ivanov AA
  • Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal.
    Methods Mol Biol Volume: 2074 Page(s): 145 - 164
    01/01/2020 Authors: Ivanov AA
  • Discovery and targeting MKK3-MYC protein-protein interaction for therapeutic interrogation in cancer
    Volume: 79
    07/01/2019 Authors: Yang X; Du Y; Fu H; Ivanov AA
  • In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer.
    Nat Commun Volume: 9 Page(s): 2732
    07/16/2018 Authors: Grzeskowiak CL; Kundu ST; Mo X; Ivanov AA; Zagorodna O; Lu H; Chapple RH; Tsang YH; Moreno D; Mosqueda M
  • The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery.
    Bioinformatics Volume: 34 Page(s): 1183 - 1191
    04/01/2018 Authors: Ivanov AA; Revennaugh B; Rusnak L; Gonzalez-Pecchi V; Mo X; Johns MA; Du Y; Cooper LAD; Moreno CS; Khuri FR
  • Development of a Time-Resolved Fluorescence Resonance Energy Transfer Ultrahigh-Throughput Screening Assay for Targeting the NSD3 and MYC Interaction.
    Assay Drug Dev Technol Volume: 16 Page(s): 96 - 106
    01/01/2018 Authors: Xiong J; Pecchi VG; Qui M; Ivanov AA; Mo X; Niu Q; Chen X; Fu H; Du Y
  • OncoPPi-informed discovery of mitogen-activated protein kinase kinase 3 as a novel binding partner of c-Myc.
    Oncogene Volume: 36 Page(s): 5852 - 5860
    10/19/2017 Authors: Ivanov AA; Gonzalez-Pecchi V; Khuri LF; Niu Q; Wang Y; Xu Y; Bai Y; Mo X; Prochownik EV; Johns MA
  • Corrigendum: The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies.
    Nat Commun Volume: 8 Page(s): 15350
    04/18/2017 Authors: Li Z; Ivanov AA; Su R; Gonzalez-Pecchi V; Qi Q; Liu S; Webber P; McMillan E; Rusnak L; Pham C
  • AKT1, LKB1, and YAP1 Revealed as MYC Interactors with NanoLuc-Based Protein-Fragment Complementation Assay.
    Mol Pharmacol Volume: 91 Page(s): 339 - 347
    04/01/2017 Authors: Mo X; Qi Q; Ivanov AA; Niu Q; Luo Y; Havel J; Goetze R; Bell S; Moreno CS; Cooper LAD
  • The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies.
    Nat Commun Volume: 8 Page(s): 14356
    02/16/2017 Authors: Li Z; Ivanov AA; Su R; Gonzalez-Pecchi V; Qi Q; Liu S; Webber P; McMillan E; Rusnak L; Pham C
  • MEDICI: Mining Essentiality Data to Identify Critical Interactions for Cancer Drug Target Discovery and Development.
    PLoS One Volume: 12 Page(s): e0170339
    01/01/2017 Authors: Harati S; Cooper LAD; Moran JD; Giuste FO; Du Y; Ivanov AA; Johns MA; Khuri FR; Fu H; Moreno CS
  • Transforming Big Data into Cancer-Relevant Insight: An Initial, Multi-Tier Approach to Assess Reproducibility and Relevance.
    Mol Cancer Res Volume: 14 Page(s): 675 - 682
    08/01/2016 Authors: Cancer Target Discovery and Development Network
  • Enabling systematic interrogation of protein-protein interactions in live cells with a versatile ultra-high-throughput biosensor platform.
    J Mol Cell Biol Volume: 8 Page(s): 271 - 281
    06/01/2016 Authors: Mo X-L; Luo Y; Ivanov AA; Su R; Havel JJ; Li Z; Khuri FR; Du Y; Fu H
  • Predicting the essentialities of protein-protein interactions in cancer
    CANCER RESEARCH Volume: 75
    11/15/2015 Authors: Cooper LAD; Moran JD; Li Z; Du Y; Harati S; Ivanov AA; Webber P; Havel JJ; Johns MA; Fu H
  • Targeting protein-protein interactions as an anticancer strategy.
    Trends Pharmacol Sci Volume: 34 Page(s): 393 - 400
    07/01/2013 Authors: Ivanov AA; Khuri FR; Fu H
  • Computational modeling reveals druggable cavities at the MKK3 and p38 protein interaction interface
    Volume: 73
    04/15/2013 Authors: Ivanov AA; Nim S; Du Y; Fu H
  • Saccharomyces cerevisiae Apn1 mutation affecting stable protein expression mimics catalytic activity impairment: implications for assessing DNA repair capacity in humans.
    DNA Repair (Amst) Volume: 11 Page(s): 753 - 765
    09/01/2012 Authors: Morris LP; Degtyareva N; Sheppard C; Heyburn L; Ivanov AA; Kow YW; Doetsch PW
  • The adenosine deaminases of Plasmodium vivax and Plasmodium falciparum exhibit surprising differences in ligand specificity.
    J Mol Graph Model Volume: 35 Page(s): 43 - 48
    05/01/2012 Authors: Ivanov A; Matsumura I
  • Application of the bridgehead fragments for the design of conformationally restricted melatonin analogues.
    Bioorg Chem Volume: 39 Page(s): 67 - 72
    04/01/2011 Authors: Zefirova ON; Baranova TY; Ivanova AA; Ivanov AA; Zefirov NS
  • Functionalized congeners of A3 adenosine receptor-selective nucleosides containing a bicyclo[3.1.0]hexane ring system.
    J Med Chem Volume: 52 Page(s): 7580 - 7592
    12/10/2009 Authors: Tosh DK; Chinn M; Ivanov AA; Klutz AM; Gao Z-G; Jacobson KA
  • Enhanced potency of nucleotide-dendrimer conjugates as agonists of the P2Y14 receptor: multivalent effect in G protein-coupled receptor recognition.
    Bioconjug Chem Volume: 20 Page(s): 1650 - 1659
    08/19/2009 Authors: Das A; Zhou Y; Ivanov AA; Carter RL; Harden TK; Jacobson KA
  • Molecular recognition in the P2Y(14) receptor: Probing the structurally permissive terminal sugar moiety of uridine-5'-diphosphoglucose.
    Bioorg Med Chem Volume: 17 Page(s): 5298 - 5311
    07/15/2009 Authors: Ko H; Das A; Carter RL; Fricks IP; Zhou Y; Ivanov AA; Melman A; Joshi BV; Kovc P; Hajduch J
  • Evaluation of homology modeling of G-protein-coupled receptors in light of the A(2A) adenosine receptor crystallographic structure.
    J Med Chem Volume: 52 Page(s): 3284 - 3292
    05/28/2009 Authors: Ivanov AA; Barak D; Jacobson KA
  • Design, synthesis, and bioactivity of putative tubulin ligands with adamantane core.
    Bioorg Med Chem Lett Volume: 18 Page(s): 5091 - 5094
    09/15/2008 Authors: Zefirova ON; Nurieva EV; Lemcke H; Ivanov AA; Shishov DV; Weiss DG; Kuznetsov SA; Zefirov NS
  • Molecular modeling of a PAMAM-CGS21680 dendrimer bound to an A2A adenosine receptor homodimer.
    Bioorg Med Chem Lett Volume: 18 Page(s): 4312 - 4315
    08/01/2008 Authors: Ivanov AA; Jacobson KA
  • Probing distal regions of the A2B adenosine receptor by quantitative structure-activity relationship modeling of known and novel agonists.
    J Med Chem Volume: 51 Page(s): 2088 - 2099
    04/10/2008 Authors: Ivanov AA; Wang B; Klutz AM; Chen VL; Gao Z-G; Jacobson KA
  • Probing the binding site of the A1 adenosine receptor reengineered for orthogonal recognition by tailored nucleosides.
    Biochemistry Volume: 46 Page(s): 7437 - 7448
    06/26/2007 Authors: Palaniappan KK; Gao Z-G; Ivanov AA; Greaves R; Adachi H; Besada P; Kim HO; Kim AY; Choe SA; Jeong LS
  • Structure-activity relationship of uridine 5'-diphosphoglucose analogues as agonists of the human P2Y14 receptor.
    J Med Chem Volume: 50 Page(s): 2030 - 2039
    05/03/2007 Authors: Ko H; Fricks I; Ivanov AA; Harden TK; Jacobson KA
  • Structure-activity relationships of 2,N(6),5'-substituted adenosine derivatives with potent activity at the A2B adenosine receptor.
    J Med Chem Volume: 50 Page(s): 1810 - 1827
    04/19/2007 Authors: Adachi H; Palaniappan KK; Ivanov AA; Bergman N; Gao Z-G; Jacobson KA
  • Molecular modeling of the human P2Y2 receptor and design of a selective agonist, 2'-amino-2'-deoxy-2-thiouridine 5'-triphosphate.
    J Med Chem Volume: 50 Page(s): 1166 - 1176
    03/22/2007 Authors: Ivanov AA; Ko H; Cosyn L; Maddileti S; Besada P; Fricks I; Costanzi S; Harden TK; Calenbergh SV; Jacobson KA
  • Molecular dynamics simulation of the P2Y14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety.
    Bioorg Med Chem Lett Volume: 17 Page(s): 761 - 766
    02/01/2007 Authors: Ivanov AA; Fricks I; Kendall Harden T; Jacobson KA
  • Computer aided comparative analysis of the binding modes of the adenosine receptor agonists for all known subtypes of adenosine receptors.
    J Mol Graph Model Volume: 25 Page(s): 740 - 754
    01/01/2007 Authors: Ivanov AA; Palyulin VA; Zefirov NS
  • Structure activity and molecular modeling analyses of ribose- and base-modified uridine 5'-triphosphate analogues at the human P2Y2 and P2Y4 receptors.
    Biochem Pharmacol Volume: 71 Page(s): 540 - 549
    02/14/2006 Authors: Jacobson KA; Costanzi S; Ivanov AA; Tchilibon S; Besada P; Gao Z-G; Maddileti S; Harden TK
  • Agonists and antagonists for P2 receptors.
    Novartis Found Symp Volume: 276 Page(s): 58 - 68
    01/01/2006 Authors: Jacobson KA; Costanzi S; Joshi BV; Besada P; Shin DH; Ko H; Ivanov AA; Mamedova L
  • Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling.
    J Comput Aided Mol Des Volume: 20 Page(s): 417 - 426
    01/01/2006 Authors: Ivanov AA; Costanzi S; Jacobson KA
  • Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists.
    J Med Chem Volume: 48 Page(s): 6813 - 6820
    11/03/2005 Authors: Ivanov AA; Baskin II; Palyulin VA; Piccagli L; Baraldi PG; Zefirov NS
  • Highly diverse, massive organic data as explored by a composite QSPR strategy: an advanced study of boiling point.
    SAR QSAR Environ Res Volume: 16 Page(s): 231 - 246
    06/01/2005 Authors: Ivanova AA; Ivanov AA; Oliferenko AA; Palyulin VA; Zefirov NS
  • Molecular modeling study of the mechanism of ligand binding to human melatonin receptors.
    Dokl Biochem Biophys Volume: 403 Page(s): 284 - 288
    01/01/2005 Authors: Voronkov AE; Ivanov AA; Baskin II; Palyulin VA; Zefirov NS
  • The study of the mechanism of binding of human ML1A melatonin receptor ligands using molecular modeling.
    Dokl Biochem Biophys Volume: 394 Page(s): 49 - 52
    01/01/2004 Authors: Ivanov AA; Voronkov AE; Baskin II; Palyulin VA; Zefirov NS
  • Molecular modeling of the human A2a adenosine receptor.
    Dokl Biochem Biophys Volume: 389 Page(s): 94 - 97
    01/01/2003 Authors: Ivanov AA; Baskin II; Palyulin VA; Zefirov NS
  • Molecular modeling the human A1 adenosine receptor and study of the mechanisms of its selective ligand binding.
    Dokl Biochem Biophys Volume: 386 Page(s): 271 - 274
    01/01/2002 Authors: Ivanov AA; Baskin II; Palyulin VA; Zefirov NS
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