Chen Laboratory

Principal Investigator: Beibei “Bill” Chen, PhD

Associate Professor of Medicine,
Division of Pulmonary, Allergy and Critical Care Medicine

Director, Small Molecule Therapeutic Center

Co-Director, Acute Lung Injury Center of Excellence

Email: chenb@upmc.edu

Phone: 412-692-2210

Research

Figure 1. Protein ubiquitination pathway

Table 1. Summary of previously identified E3 ligase/substrate pathways in from my lab.

My lab focuses on identifying and studying molecular pathways that modulate the inflammatory cascade (1), mitochondria function/mitophagy (2), and DAMPs/inflammasome/necroptosis (3) in order to develop novel therapeutics for various inflammatory diseases. We seek to identify therapeutic targets that regulate these processes within the context of a unifying control mechanism which could provide new opportunities for translation of basic observations to pre-clinical models, and ultimately therapeutics for human diseases. Specifically, we have been studying the role of protein ubiquitination for many years, and have made several important discoveries that connect E3 ligases to their target proteins and biological activities (Table 1). Protein ubiquitination is the major protein processing pathways in cells by which ubiquitin (Ub) flags a targeted protein for degradation through the 26s proteasome or lysosome (Figure 1). Protein ubiquitination has been implicated in many diseases, and there has been an increasing interest in investigating the role of protein ubiquitination in inflammatory conditions. There are now several FDA approved compounds, including proteasome inhibitors that target the downstream components of this pathway. However, majority of the >800 upstream E3 ligases remains poorly characterized. Thus we investigate how and which protein ubiquitination processes impact the above three areas.

Inflammatory cascade (1): Here, the innate immune system is activated to secrete large amounts of pro-inflammatory cytokines (i.e. cytokine storm) after bacterial infection, which activates receptors on immune effector cells (e.g. T-cells, macrophages, etc.). In this area, we will investigate the new protein pathways that are involved in immune regulation, cytokine signaling and inflammation resolution.

Mitochondria function/Mitophagy/Autophagy (2): In many inflammatory conditions, the bacterial component, host inflammation, and cellular stress can all damage mitochondria. However, mitophagy is critical in keeping the cell healthy as it prevents the accumulation of dysfunctional mitochondria, whose persistence can lead to cellular degeneration. We have several ongoing studies showing that expression of E3 ligases leading to the depletion of several key mitophagy proteins, thus disrupting the clearance of damaged mitochondria. Consequently, it is important to continue investigating the protein ubiquitination pathways in mitophagy.

DAMPs/Inflammasome/necroptosis (3): When the mitophagy pathway is impaired, damaged mitochondria will release many molecules, such as cardiolipin, mitochondrial DNA, formyl peptide cytochrome c, etc, known as DAMPs. DAMPs can initiate and perpetuate a noninfectious inflammatory response, which often leads to unresolved inflammation through inflammasome and necroptosis pathways. We have shown that the ubiquitin pathway directly regulates several inflammasome components such as NALP3 and NALP7. Currently, we are continuing investigate other protein ubiquitination pathways in inflammasome and necroptosis.

Figure 3. Drug discovery strategy

Based on the new molecular mechanisms revealed from the basic science, we aim to develop small molecules therapeutics and prove their efficacy in proof-of-concept preclinical models. We have developed specialized approaches to small molecule drug discovery in the academic environment. For the last few years, we have screened, designed, tested, and developed inhibitors of PDE4, Fbxo3, HECTD2, FIEL1, StamBP, Fbxo7, and Fbxo48, and showed their efficacy in various in vivo models. There are two major approaches we use to develop small molecule therapeutics in my lab (Figure 3). A target-based approach requires reliable structural information on the protein target. However, we often use a structural biology approach to predict the target structure based on homology modeling. In the scenario in which there is little to no structural data on the protein target, or the lack of a well-defined E3 ligase/Substrate pathway, we will employ a ligand-based approach using HTS. We have assembled two HTS systems in my lab (Figure 4). We also have several compound libraries (e.g. FDA-approved compound library, ChemDiv 100K diversity compound library, etc) that we routinely use. We deploy various phenotypic screens to identify compounds that break E3 ligase/substrate interactions.

In both approaches, once the “hit” molecules have been identified and tested, we will start the “hit to lead” campaign. We have developed a sophisticated testing algorithm to fully evaluate these compounds focusing on their target engaging and in vitro efficacy, off-targeting, ADME and toxicity. We have significant experience in designing, synthesizing, modifying novel compounds. One of the successful examples is the first-in-class small molecule FBXO3 inhibitors. Investigation new drug (IND) application for one of my lead compounds, BC-1261, has been cleared by the US Food and Drug Administration to begin a Phase 1 clinical trial for the treatment of inflammatory bowel disease (IBD).

Figure 4. Target-based drug discovery using computer based in silico screen and ligand-based approach using HTS and HCS.

Publications

Evankovich J, Lear T, Mckelvey A, Dunn S, Londino J, Liu Y, *Chen BB, *Mallampalli RK. Receptor for advanced glycation end products is targeted by Fbxo10 for ubiquitination and degradation. FASEB J. 2017 Sep;31(9):3894-3903. doi: 10.1096/fj.201700031R. PMID: 28515150 *co-senior authors.

Bednash JS, Weathington NM, Londino James, Rojas M, Gulick DL, Fort R, Han S, McKelvey AC, Chen BB, Rama K. Mallampalli. Therapeutic targeting of the deubiquitinase STAMBP reduces inflammation by destabilizing the NALP7 inflammasome. Nature Communication 8:15203 | DOI: 10.1038/ncomms15203

McKelvey AC, Lear T, Dunn SR, Evankovich J, Landino JD, Bednash JS, Zhang Y, McVerry BJ, Liu Y, *Chen BB. RING Finger E3 Ligase PPP1R11 Regulates TLR2 Signaling and Innate Immunity. eLife 2016 Nov 2;5. pii: e18496. doi: 10.7554/eLife.18496. PMID: 27805901, PMCID: PMC5092053. *corresponding author.

Lear T, McKelvey AC, Rajbhandari S, Coon TA, Connelly W, Zhao J, Dunn SR, Liu Y, Zhang Y, *Chen BB. Ubiquitin E3 Ligase FIEL1 Regulates Fibrotic Lung Injury through SUMO-E3 Ligase PIAS4. JEM 2016 May 30;213(6):1029-46. PMID: 27162319, PMCID: PMC4886359. *corresponding author.

Coon TA, McKelvey AC, Lear T, Rajbhandari S, Dunn RS, Connelly W, Zhao J, Han S, Liu Y, McVerry BJ, Zhang Y, *Chen BB. The proinflammatory role of HECTD2 in innate immunity and experimental lung injury. Sci Trans Med. 2015 Jul 8;7(295):295ra109. PMID: 26157031, PMCID – in process, NIHMS743551. *corresponding author.

Zou C, Li J, Xiong S, Chen Y, Wu Q, Weathington NM, Han SY, Snavely C, Chen BB and Mallampalli RK. Mortality factor 4 like 1 (Morf4l1) protein mediates epithelial cell death in experimental pneumonia. Sci Trans Med. 2015 Oct 28;7(311):311ra171. PMID: 26511508, PMCID: PMC4758684, NIHMS743552.

Coon TA, McKelvey AC, Weathington NM, Birru RL, Lear T, Leikauf GD, *Chen BB. Novel PDE4 Inhibitors Derived From Chinese Medicine Forsythia. PLOS ONE. 2014 Dec 30;9(12):e115937. PMID: 25549252; PMCID: PMC4280171. *corresponding author.

Mallampalli RK, Coon TA, Glasser JR, Wang C, Dunn SR, Weathington, NM, Zhao J, Zou C, Zhao Y, *Chen BB. Targeting F box protein Fbxo3 to control cytokine-driven inflammation. J Immunol. 2013 Nov 15;191(10):5247-55. doi: 10.4049/jmmunol.1300456. [Epub 2013 Oct 11.] *corresponding author. PMCID: PMC3845358.

*Chen BB, Coon TA, Glasser JR, McVerry BJ, Zhao J, Zhao Y, Zou C, Ellis BM, Sciurba FC, Zhang Y, *Mallampalli RK. A combinatorial F box protein directed pathway controls TRAF stability to regulate inflammation. Nat Immunol. 2013 Mar 31. doi: 10.1038/ni.2565. [Epub ahead of print] *corresponding author. PMCID: PMC3631463. Highlighted in Nat Rev Immunol and Nat Rev Drug Design.

Coon TA, Glasser JR, Mallampalli RK, *Chen BB. Novel E3 ligase component FBXL7 ubiquitinates and degrades Aurora A, causing mitotic arrest. Cell Cycle. 2012 Feb 15;11(4):721-9. doi: 10.4161/cc.11.4.19171. [Epub 2012 Feb 15.] *corresponding author, cover story. PMID: 22306998; PMCID: PMC3318106