Professional Interests

The Gavathiotis laboratory investigates mechanisms of BCL-2 family proteins and other key proteins in cell death and cell survival pathways such as apoptosis, mitochondrial dynamics, selective autophagy and oncogenic signaling. We harness mechanistic and structural insights to develop first-in-class small molecules that can be used for target identification and validation and serve as the basis for novel therapeutics. Our work in these pathways has pioneered novel mechanisms, pharmacological strategies and first-in-class small molecules targeting challenging and “undruggable” targets. In this process, we have developed innovative platforms based on computational and biophysical methods as well as chemical strategies to enable the discovery and design of small molecules.  Our studies have led to several prototype therapeutics that are undergoing development towards Investigational New Drug (IND) application for oncology and aging-associated diseases. We are an interdisciplinary group that has expertise in structural and chemical biology, medicinal chemistry, drug design, computational and experimental screening, biochemical and cell biology approaches and in vivo pharmacology.

Molecular Mechanisms of Cell Death and Cell Survival Signaling

Programmed cell death is a genetically controlled physiological process that rids the body of unwanted or malfunctioning cells to maintain the normal development and homeostasis of multicellular organisms. Deregulation of cell death and cell survival programs leads to variety of disease conditions and understanding the molecular mechanisms that govern these signaling pathways is both fundamentally important and medically relevant. While our primary focus is the protein interaction network of the BCL-2 family of proteins and its role in regulating apoptosis, we have expanded our research in understanding related pathways and mechanisms of proteins involved in mitochondrial fusion and fission, selective autophagy, MAPK signaling pathway and senescence. Using chemical and structural biology, biochemical, biophysical and cell biology studies, we aim to elucidate the mechanisms that define the very determinants that modulate life and death decisions in healthy and malignant cells. These studies advance our understanding of fundamental biological mechanisms and provide novel targets for drug development.

Here is list of key contributions of molecular mechanisms and insights from our laboratory:

1) mechanism of pro-apoptotic BAX activation and the role of the BAX trigger site in regulation of BAX conformational activation and mitochondrial translocation, oligomerization and outer membrane permeabilization in apoptosis (Nature 2008, Molecular Cell 2010, Nature Chemical Biology 2012, J. Biological Chemistry 2015, Molecular Cell 2016). 2) Structure of autoinhibited BAX dimer and mechanism of BAX autoinhibition regulating apoptosis (Molecular Cell 2016) 3) Allosteric mechanism of BRAF activation by inhibitors and structural basis of RAF inhibitors activity against oncogenic BRAF (Cancer Cell 2016) 4) Structural basis of Mitofusins conformational activation and inhibition regulating mitochondrial fusion and fission (Nature 2016). 5) Allosteric mechanism of BAX inhibition and discovery of BAX small molecule allosteric site regulating BAX conformational activation (Nature Chemical Biology 2019). 6) Allosteric mechanism of BRAF dimerization control and discovery of BRAF allosteric site (Nature Communications 2020). 7) Allosteric mechanisms of BAX inhibition through engagement of the BAX trigger site and α1-α2 loop (Molecular Cell 2016, Nature Communications 2021). 8) Mechanisms of small molecule BAX activation in cancer cells and induction of apoptosis and its regulation by anti-apoptotic proteins BCL-XL and BCL-2 (Cancer Cell 2017, Nature Communications 2022)  9) Connecting inhibition of mitochondrial fusion to fission, mitochondrial outer membrane permeabilization, cytochrome c release, caspase-3/7 activation and DNA damage (Nature Communications 2022). 10) Mechanism of selective Chaperone-mediated Autophagy (CMA) activation through stabilization of RARα/NCoR1 interaction and small-molecule allosteric site (Nature Communications 2022).

Chemical Biology and Drug Discovery of Cell Death Mechanisms

We apply high-throughput screening, structure-based drug design and medicinal chemistry to discover and develop small molecules and peptide-based probes that modulate the function of protein-protein interactions. We work towards a "chemical toolbox" of activators and inhibitors of major cell death and cell survival pathways to enable us to manipulate cell signaling and fate decision in physiological and disease conditions and provide new research tools to understand biological mechanisms and prototypes for the development of novel therapeutics. Our protein targets include but are not limited to proteins of the mitochondrial cell death pathway, chaperone-mediated autophagy, mitochondrial dynamics, oncogenic kinase signaling and are typically validated in genetic models but they are considered challenging or "undruggable".

Our laboratory has identified the following first-in-class small-molecules:

1) activators of pro-apoptotic BAX that demonstrated a new paradigm for pharmacologic induction of apoptosis in cancer (Nature Chemical Biology 2012, Cancer Cell 2017, Nature Communications 2022). 2) activators of chaperone-mediated autophagy through targeting RARa that protect cells from oxidative stress and proteotoxicity (Nature Chemical Biology 2013). 3)  activators of  mitofusins that promote mitochondrial fusion, increase mitochondrial respiration and restore mitochondrial motility in CMT2A neuropathy (Science 2018, Nature Communications 2022). 4) allosteric BAX inhibitors that inhibit apoptosis and necrosis and protect from chemotherapy-induced cardiotoxicity (Nature Chemical Biology 2019, Nature Cancer 2020). 5) allosteric BRAF inhibitors that overcome resistance to FDA-approved inhibitors in melanoma and colorectal tumors (Nature Communications 2020). 6) competitive BAX inhibitors that inhibit cell death and protect from chemotherapy-induced cytotoxicity (Nature Communications 2021). 7)  inhibitors of  mitofusins that inhibit mitochondrial fusion, promote mitochondrial fission, induce mitochondrial-outer membrane permeabilization, caspase-3/7 activation and sensitize pro-apoptotic drugs (Nature Communications 2022). 8) stabilizers of NCoR1/RARa that activate chaperone-mediated autophagy and protect from neurodegeneration in Alzheimer’s models, protect from retinal degeneration and induce rejuvenation of old hematopoietic stem cells (Nature 2021, Cell 2021, Nature Communications 2022). 9) kinase inhibitors with rationally designed kinetic selectivity and favorable pharmacological properties as lead cancer therapeutics. Our integrative methodologies  have identified novel targets and mechanism of action for two FDA-approved drugs  (ponatinib and eltrombopag) presenting novel pharmacological and clinical opportunities towards novel therapies (Nature Communications 2020, Nature Communications 2021). We continue to explore repurposing opportunities of clinical drugs for different mechanisms and targets including SARS-COV-2 anti-virals in response to the COVID-19 pandemic. 

Selected Publications

Zacharioudakis E, & Gavathiotis E. Targeting Protein Conformations with Small Molecules to Control Proteins Complexes. Trends in Biochemical Sciences 2022, Aug. 16

Gomez-Sintes R, Xin Q, Jiménez-Loygorri JJ, McCabe M, Diaz A, Garner TP, Cotto-Rios X, Wu Y, Dong S, Reynolds CA, Patel B, de la Villa P, Macian F, Boya P*, Gavathiotis E*, Cuervo AM*. Targeting NCOR-RAR interaction activates chaperone mediated autophagy and protects against retinal degeneration. Nature Communications 2022 13, 4220.

Zacharioudakis E, Agianian B, Vasanth Kumar MV, Biris N, Garner T, Rabinovich-Nikitin I, Ouchida A, Margulets V, Nordstrøm LU, Riley J, Dolgalev I, Chen Y, Wittig A, Pekson R, Mathew C, Wei P, Tsirigos A, Tait S, Kirshenbaum L, Kitsis R. Gavathiotis E. Modulating mitofusins to control mitochondrial function and signaling. Nature Communications 2022 3, 377

Lopez A, Reyna DE, Gitego N, Zhou H, Kopp F, Miranda-Roman M, Nordstrom LU, Narayanagari SR, Chi P, Vilar E, Tsirigos A, Gavathiotis E. Rational targeting of apoptotic BAX and BCL-XL broadly overcomes tumor resistance. Nature Communications. 2022 13, 1199 https://doi.org/10.1038/s41467-022-28741-7

Spitz AZ and Gavathiotis E. Physiological and Pharmacological Modulation of BAX. Trends Pharmacological Sciences. 2021

Rahmani NE, Ramachandra N, Sahu S, Gitego N, Lopez A, Pradhan K, Bhagat TD, Gordon-Mitchell S, Pena BR, Kazemi M, Rao K, Giricz O, Maqbool SB, Olea R, Zhao Y, Zhang J, Dolatshad H., Tittrea V, Tatwavedi D, Singh S, Lee J, Sun T, Steidl U, Shastri A, Inoue D, Abdel-Wahab O, Pellagatti A, Gavathiotis E^*, Boultwood J^*, Verma A^*. ASXL1 mutations are associated with distinct epigenomic alterations that lead to sensitivity to venetoclax and azacytidine. Blood Cancer J. 2021 11(9):157.

Bourdenx, M*, Gavathiotis, E*, and Cuervo, AM*. Chaperone-mediated autophagy: a gatekeepe of neuronal proteostasis. Autophagy 2021, 17: 2040-2042.

Bourdenx M*, Martín-Segura A, Scrivo A, Rodriguez-Navarro JA, Kaushik S, Tasset I, Diaz A, Storm NJ, Xin Q, Juste YR, Stevenson E, Luengo E, Clement CC, Choi SJ, Krogan NJ, Mosharov EV, Santambrogio L, Grueninger F, Collin L, Swaney DL, Sulzer D, Gavathiotis E*, Cuervo AM*. Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome. Cell. 2021, 84: 2696-2714

Spitz AZ, Zacharioudakis E, Reyna DE, Garner TP, Gavathiotis E. Eltrombopag directly inhibits BAX and prevents cell death. Nature Communications 2021 12:1134

Gadsden N, Fulcher C, Li D, Shrivastava N, Thomas C, Segall J, Prystowsky M, Schlecht N, Gavathiotis E, Ow T. Palbociclib renders human papilloma virus negative head and neck squamous cell carcinoma vulnerable to the senolytic agent navitoclax. Mol. Cancer Res.  2021, 19: 862-873.

Dong S, Wang Q,  Kao YK, Diaz A , Tasset I, Kaushik S, Thiruthuvanathan V, Zintiridou A, Nieves E, Dzieciatkowska M, Reisz JA, Gavathiotis E, D'Alessandro A, Will B, Cuervo AM. Chaperone-mediated autophagy sustains hematopoietic stem cell function. Nature 2021, 130: 2643-2649

Cotto-Rios X, Agianian B, Gitego, N, Zacharioudakis E, Giricz O, Wu Y, Yiyu, Z, Verma A, Poulikakos PI, Gavathiotis E. Inhibitors of BRAF dimers using an allosteric site. Nature Communications. (2020) 11:4370

Amgalan D, Garner TP, Pekson R, Jia XF, Yanamandala M, Paulino V, Liang FG, Corbalan JJ, Lee J, Chen Y, Karagiannis GS, Sanchez LS, Liang H, Narayanagari SR, Mitchell K, Lopez A, Margulets V, Scarlata M, Santulli G, Asnani A, Peterson RT, Hazan RB, Condeelis JS, Oktay MH, Steidl U, Kirshenbaum LA, Gavathiotis E.*, Kitsis RN* A small molecule allosteric inhibitor of BAX protects against doxorubicin-induced cardiomyopathy. Nature Cancer 2020, 1: 315-328

Ow TJ, Thomas C, Fulcher CD, Chen J, Lopez A, Reyna, DE, Prystowsky MB, Smith RV, Schiff BA, Rosenblatt G, Belbin TJ, Harris JM, Childs GC, Kawachi N, Schlecht MF, Gavathiotis E. Apoptosis Signaling Molecules as Treatment Targets in Head and Neck Squamous Cell Carcinoma. The Laryngoscope. 2019, 130: 2643-2649

Chen X, Glytsou C, Zhou H, Narang S, Reyna DE, Lopez A, Sakellaropoulos T, Gong Y, Kloetgen A, Yap YS, Wang E, Gavathiotis E, Tsirigos A, Tibes R, Aifantis I. Targeting Mitochondrial Structure Sensitizes Acute Myeloid Leukemia to Venetoclax Treatment. Cancer Discov. 2019, 9:1-20

Garner TP, Amgalan D, Reyna DE, Li S, Kitsis RN, Gavathiotis E. Small Molecule Allosteric Inhibitors of BAX. Nat. Chem. Biol. 2019, 15: 1-12

Zhang J, He J, Johnson JL, Rahman F, Gavathiotis E, Cuervo AM, Catz SD. Chaperone-mediated autophagy upregulation rescues megalin expression and localization in cystinotic proximal tubule cells. Front. Endocrinol. 2019 doi: 10.3389/fendo.2019.00021

Ow TJ, Fulcher CD, Thomas C, O’Broin P, Lopez A, Reyna, DE, Smith RV, Sarta C, Prystowsky MB, Schlecht MF, Schiff BA, Rosenblatt G, Belbin TJ, Harris JM, Childs GC, Kawachi N, Guha C, Gavathiotis E. Optimal Targeting of BCL-family Proteins in Head and Neck Squamous Cell Carcinoma Requires Inhibition of Both BCL-xL and MCL-1. Oncotarget. 2019, 10:494-510.

Gavathiotis E. BCL-2 family proteins. Methods Mol. Biol. 2018, 1877: i-xi.

Reyna DE, Gavathiotis E. Liposomal parmeabilization assay to study functional interactions of BCL-2 family proteins. Methods Mol. Biol. 2018, 1877: 111-119.

Garner TP, Gavathiotis E. BCL-2 Protein Family Interaction Analysis by Nuclear Magnetic Resonance Spectroscopy. Methods Mol. Biol. 2018, 1877: 217-231.

Giricz O, Mo Y, Dahlman KB, Cotto-Rios XM, Vardabasso C, Nguyen H, Matusow B, Bartenstein M, Polishchuk V, Johnson DB, Bhagat TD, Shellooe R, Burton E, Tsai J, Zhang C, Habets G, Greally JM, Yu Y, Kenny PA, Fields GB, Pradhan K, Stanley ER, Bernstein E, Bollag G, Gavathiotis E, West BL, Sosman JA, Verma AK. The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma. JCI Insight. 2018, 3(14).

Zhang Q, Zhang J., Gavathiotis E. ICBS2017 in Shanghai-Illuminating Life with Chemical Innovation. ACS Chem. Biol. 2018. doi: 10.1021/acschembio.8b00220. PubMed PMID: 29677443.

Rocha GA, Franco F, Krezel A, Rumsey JM, Alberti JM, Knight WC, Biris N, Zacharioudakis E, Janetka JW, Baloh BH, Kitsis RN, Mochly-Rosen D, Townsend RR, Gavathiotis E, Dorn GW. Mfn2 agonists reverse mitochondrial defects in preclinical models of Charcot Marie Tooth disease type 2A. Science 2018, 360: 336-341.

Bogos A and Gavathiotis E. Current insights of BRAF inhibitors in cancer. J. Med. Chem. 2018, 61:5775-5793

Reyna DE and Gavathiotis E. Pulling the BAX trigger for tumor cell death . Oncotarget 2018, 9: 8204-8205

Galluzzi L, Vitale I, ...Gavathiotis E, ...Kroemer G. Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018 Cell Death Diff. 2018

Antony-Debré I, Paul A, Leite J, Mitchell K, Kim HM, Carvajal LA, Todorova TI, Huang K, Kumar A, Farahat AA, Bartholdy B, Narayanagari SR, Chen J, Ambesi-Impiombato A, Ferrando AA, Mantzaris I, Gavathiotis E, Verma A, Will B, Boykin DW, Wilson WD, Poon GM, Steidl U.  Pharmacological inhibition of the transcription factor PU.1 in leukemia. J. Clin. Invest. 2017, Oct 30 doi: 10.1172/JCI92504

Reyna DE, Garner TP, Lopez A, Kopp F, Choudhary GS, Sridharan A, Narayanagari SR, Mitchell K, Dong B, Bartholdy BA, Walensky LD, Verma A, Steidl U, Gavathiotis E. Direct Activation of BAX by BTSA1 Ovecomes Apoptosis Resistance in Acute Meyloid Leukemia.  Cancer Cell 2017, 32: 490–505

Karoulia Z. Gavathiotis E. Poulikakos PI.  New perspectives for targeting RAF kinase in human cancer. Nat. Rev. Cancer 2017, Oct 6.

Garner TP, Lopez A, Reyna DE, Spitz AZ, Gavathiotis E.  Progress in targeting the BCL-2 family of proteins. Curr. Opin. Chem. Biol. 2017, 39: 133-142

Gavathiotis E* and Zhou MM*. Chemical genetics and epigenetics. Curr. Opin. Chem. Biol. 2017, 39:1-3

Zhang J, Johnson JL, He J, Napolitano G, Ramadass M, Rocca C, Kiosses WB, Bucci C, Xin Q, Gavathiotis E, Cuervo AM, Cherqui S, Catz SD. Cystinosin, the small GTPase Rab11, and the Rab7 effector RILP regulate intracellular trafficking of the chaperone-mediated autophagy receptor LAMP2A.  J. Biol. Chem. 2017, jbc.M116.764076

Franco A, Kitsis RN, Fleischer JA, Gavathiotis E, Kornfeld OS, Gong G, Biris N, Benz A, Qvit N, Donnelly SK, Chen Y, Mennerick S, Hodgson L, Mochly-Rosen D, Dorn GW 2nd. Correcting mitochondrial fusion by minipulating mitofusin conformations. Nature 2016, 540: 74-79

Johnson JL, Ramadass M, He J, Brown SJ, Zhang J, Abgaryan L, Biris N, Gavathiotis E, Rosen H, Catz SD. Identification of Nexinhibs, small-molecule inhibitors of neutrophil exocytosis and inflammation. Druggability of the small GTPase Rab27a. J. Biol. Chem. 2016, 291: 25965-25982

Reyna DE and Gavathiotis E. Self-regulation of BAX-induced cell death. Oncotarget 2016

Karoulia Z, Wu Y, Ahmed AA, Xin Q, Bollard J, Krepler C, Wu X, Zhang C, Bollag G, Herlyn M, Fagin JA, Lujambio A, Gavathiotis E*, Poulikakos P*. An Integrated Model of RAF inhibitor Action Predicts Inhibitor Activity against Oncogenic BRAF Signaling. Cancer Cell 2016, 30: 1-14.

Garner TP, Reyna DE, Priyadarshi A, Chen HC, Li S, Ganesan, YT, Malashkevich VN, Almo SS, Cheng EH, Gavathiotis E. An Autoinhibited Dimeric Form of BAX Regulates the BAX Activation Pathway. Mol. Cell 2016, 63: 485-497.

Cotto-Rios XM, Gavathiotis E. Unraveling cell death mysteries. Nat. Chem. Biol. 2016 12: 470-471

Klionsky DJ, ..., Gavathiotis E, ...Zughaier SM. Guidelines for the use and intepretation of assays for monitoring autophagy. Autophagy. 2016, 12: 1-222.

Uchime O, Dai Z, Biris N, Lee D, Sidhu SS, Li S, Lai JR, Gavathiotis E. Synthetic Antibodies Inhibit Bcl-2-associated X Protein (BAX) through Blockade of the N-terminal Activation Site. J. Biol. Chem. 2015, 291: 89-102.

Chen HC, Kanai M, Inoue-Yamauchi A, Tu HC, Huang Y, Ren D, Kim H, Takeda S, Reyna DE, Chan PM, Ganesan YT, Liao CP, Gavathiotis E, Hsieh JJ, Cheng EH. An interconnected hierarchical model of cell death regulation by the BCL-2 family. Nat Cell Biol. 2015, 17: 1270-1281.

Barclay LA, Wales TE, Garner TP, Wachter F, Lee S, Guerra R, Stewart ML, Braun CR, Bird GH, Gavathiotis E, Engen JR, Walensky LD. Inhibition of Pro-apoptotic BAX by a noncanonical interaction mechanism. Mol. Cell 2015, 57: 1-14. 

Li R, Cheng C, Balasis ME, Liu Y, Garner TP, Daniel KG, Li J, Qin Y, Gavathiotis E*, Sebti SM*. Design, synthesis and evaluation of Marinopyrrole derivatives as selective inhibitors of Mcl-1 binding to pro-apoptotic Bim and dual Mcl-1/Bcl-xL inhibitors.Eur. J. Med. Chem. 2015, 90: 315-331

Cheng C, Liu Y, Balasis ME, Garner TP, Li J, Simmons NL, Berndt N, Song H, Pan L, Qin Y, Nicolaou KC, Gavathiotis E, Sebti SM. Marinopyrrole Derivatives with Sulfide Spacers as Selective Disruptors of Mcl-1 Binding to Bim. Mar. Drugs 2014, 12: 4311-4325.

Papadopoulos E, Jenni S, Kabha E, Takrouri KJ, Yi T, Salvi N, Luna RE, Gavathiotis E, Mahalingam P, Arthanari H, Rodriguez-Mias R, Freedman RY, Aktas BA, Chorev M, Halperin JA, Wagner G. Structure of the translation initiation factor eIF4E in complex with 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G, Proc. Natl. Acad. Sci. USA 2014, 111: E3187-E3195.

Bird GH, Gavathiotis E, Labelle JL, Katz SG, Walensky LD. Distinct BimBH3 (BimSAHB) Stapled Peptides for Structural and Cellular Studies. ACS Chem. Biol. 2014, 9: 831-837.

Gavathiotis E. Structural Perspectives on BCL-2 Family of Proteins. Cell Death - Mechanism and Disease. 2013 229-251.

Edwards EL, Gavathiotis E, LaBelle J, Braun GH, Opoku-Nsiah K, Bird GH, Walensky LD. Multimodal activation of apoptosis by a hydrocarbon stapled PUMA BH3 helix. Chem. & Biol. 2013; 20: 888-902.

Anguiano J. Garner T, Mahalingam M, Das BS*, Gavathiotis E* and Cuervo AM*. Chemical modulation of chaperone-mediated autophagy by novel retinoic acid derivatives. Nat. Chem. Biol. 2013, 374-382.

Cohen NA, Stewart ML, Gavathiotis E, Tepper JL, Opferman JT, Walensky LD. A competitive stapled peptide screen identified a selective small molecule that overcomes MCL-1 dependent leukemia cell survival. Chem & Biol. 2012, 19: 1175-1186.

Gavathiotis E*, Reyna DE, Bellairs JA, Leshchiner ES, Walensky LD*. Direct and selective small-molecule activation of proapoptotic BAX. Nature Chem. Bio. 2012, 8:639-645.

LaBelle JL, Katz SK, Bird GH, Gavathiotis E, Stewart ML, Lawrence C, Fisher JK, Godes M, Pitter K, Kung AL, Walensky LD. A stapled BIM peptide overcomes apoptotic resistance in hematologic cancers. J. Clin. Invest. 2012, 122:2018-2031.

Whelan RS, Konstantinidis K, Wei AC, Chen Y, Reyna DE, Jha S, Yang Y, Calvert JW, Lindsten T, Thompson CB, Crow MT, Gavathiotis E, Dorn GW 2nd, O'Rourke B, Kitsis RN. Bax regulates primary necrosis through mitochondrial dynamics. Proc Natl Acad Sci U S A. 2012, 109:6566-6571.

Walensky LD*. and Gavathiotis E*. BAX Unleashed: The Biochemical Transformation of an Inactive Cytosolic Monomer into a Toxic Mitochondrial Pore. Trends Biochem. Sci. 2011, 36:642:652

Gavathiotis E. and Walensky LD. Tracking BAX once the Trigger is Pulled. Cell Cycle 2011, 10:868-870.

Gavathiotis E, Reyna DR, Davis ML, Bird GH, Walensky LD. BH3-Triggered Structural Re-organization Drives the Activation of Pro-apoptotic BAX Mol. Cell 2010, 40:481-492.

Braun CR, Mintseris J, Gavathiotis E, Bird G, Gygi SP, Walensky LD. Photoreactive Stapled BH3 Peptides to Dissect the BCL-2 Family Interactome. Chem. Biol. 2010, 17:1325-1333.

Gavathiotis E, Suzuki M, Davis ML, Pitter K, Bird GH, Katz SG, Tu HC, Kim H, Cheng EH, Tjandra N, Walensky LD. BAX Activation is Initiated at a Novel Interaction Site. Nature 2008, 455:1076-1081.