Honors & Awards

  • Macular Degeneration Research Postdoctoral Fellow, BrightFocus Foundation (2021-2023)
  • Dean's Postdoctoral Fellowship Finalist, Stanford School of Medicine (Jul. 2021)
  • SUMS Seed Grant Program, Role: Co-PI (PI: Dr. Mahajan), Stanford Dean of Research (Jul. 2019)

Professional Education

  • Doctor of Philosophy, University of Iowa, Biochemistry (2019)
  • Bachelor of Science, Yonsei University, Systems Biology (2013)

Lab Affiliations

All Publications

  • Peptidomimetics Therapeutics for Retinal Disease. Biomolecules Parsons, D. E., Lee, S. H., Sun, Y. J., Velez, G., Bassuk, A. G., Smith, M., Mahajan, V. B. 2021; 11 (3)


    Ocular disorders originating in the retina can result in a partial or total loss of vision, making drug delivery to the retina of vital importance. However, effectively delivering drugs to the retina remains a challenge for ophthalmologists due to various anatomical and physicochemical barriers in the eye. This review introduces diverse administration routes and the accordant pharmacokinetic profiles of ocular drugs to aid in the development of safe and efficient drug delivery systems to the retina with a focus on peptidomimetics as a growing class of retinal drugs, which have great therapeutic potential and a high degree of specificity. We also discuss the pharmacokinetic profiles of small molecule drugs due to their structural similarity to small peptidomimetics. Lastly, various formulation strategies are suggested to overcome pharmacokinetic hurdles such as solubility, retention time, enzymatic degradation, tissue targeting, and membrane permeability. This knowledge can be used to help design ocular delivery platforms for peptidomimetics, not only for the treatment of various retinal diseases, but also for the selection of potential peptidomimetic drug targets.

    View details for DOI 10.3390/biom11030339

    View details for PubMedID 33668179

  • Structure-based phylogeny identifies Avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice. The Journal of clinical investigation Sun, Y. J., Velez, G. n., Parsons, D. E., Li, K. n., Ortiz, M. E., Sharma, S. n., McCray, P. B., Bassuk, A. G., Mahajan, V. B. 2021


    Drugs targeting host proteins can act prophylactically to reduce viral burden early in disease and limit morbidity, even with antivirals and vaccination. Transmembrane serine protease 2 (TMPRSS2) is a human protease required for SARS-CoV-2 viral entry and may represent such a target. We hypothesized that drugs selected from proteins related by their tertiary structure, rather than their primary structure, were likely to interact with TMPRSS2. We created a structure-based phylogenetic computational tool named 3DPhyloFold to systematically identify structurally similar serine proteases with known therapeutic inhibitors and demonstrated effective inhibition of SARS-CoV-2 infection in vitro and in vivo. Several candidate compounds, Avoralstat, PCI-27483, Antipain, and Soybean-Trypsin-Inhibitor, inhibited TMPRSS2 in biochemical and cell infection assays. Avoralstat, a clinically tested Kallikrein-related B1 inhibitor, inhibited SARS-CoV-2 entry and replication in human airway epithelial cells. In an in vivo proof of principle, Avoralstat significantly reduced lung tissue titers and mitigated weight-loss when administered prophylactically to SARS-CoV-2 susceptible mice indicating its potential to be repositioned for COVID-19 prophylaxis in humans.

    View details for DOI 10.1172/JCI147973

    View details for PubMedID 33844653

  • A Fluorescence-Based Assay to Determine PDZ-Ligand Binding Thermodynamics. Methods in molecular biology (Clifton, N.J.) Sun, Y. J., Fuentes, E. J. 2021; 2256: 137-148


    Postsynaptic density-95, disks-large, and zonula occludens-1 (PDZ) domain interactions with cognate linear binding motifs (i.e., PDZ-binding motifs or PBMs) are important for many biological processes and can be pathological when disrupted. There are hundreds of PDZ-PBM interactions reported but few have been quantitatively determined. Moreover, PDZ-PBM interactions have been identified as potential therapeutic targets. To thoroughly understand PDZ-PBM binding energetics and their specificity, we have developed a sensitive and quantitative equilibrium binding assay. Here, we describe a protocol for determining PDZ-PBM binding energetics using fluorescence anisotropy-based methodology.

    View details for DOI 10.1007/978-1-0716-1166-1_8

    View details for PubMedID 34014520

  • Novel PRPF31 gene loss of function for retinitis pigmentosa 11 Chemudupati, T., Sun, Y., Yang, J., Ng, B., Mahajan, V. B. ASSOC RESEARCH VISION OPHTHALMOLOGY INC. 2020
  • Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. Cell reports Velez, G., Sun, Y. J., Khan, S., Yang, J., Herrmann, J., Chemudupati, T., MacLaren, R. E., Gakhar, L., Wakatsuki, S., Bassuk, A. G., Mahajan, V. B. 2020; 30 (3): 881


    Increased calpain activity is linked to neuroinflammation including a heritable retinal disease caused by hyper-activating mutations in the calcium-activated calpain-5 (CAPN5) protease. Although structures for classical calpains are known, the structure of CAPN5, a non-classical calpain, remains undetermined. Here we report the 2.8A crystal structure of the human CAPN5 protease core (CAPN5-PC). Compared to classical calpains, CAPN5-PC requires high calcium concentrations for maximal activity. Structure-based phylogenetic analysis and multiple sequence alignment reveal that CAPN5-PC contains three elongated flexible loops compared to its classical counterparts. The presence of a disease-causing mutation (c.799G>A, p.Gly267Ser) on the unique PC2L2 loop reveals a function in this region for regulating enzymatic activity. This mechanism could be transferred to distant calpains, using synthetic calpain hybrids, suggesting an evolutionary mechanism for fine-tuning calpain function by modifying flexible loops. Further, the open (inactive) conformation of CAPN5-PC provides structural insight into CAPN5-specific residues that can guide inhibitor design.

    View details for DOI 10.1016/j.celrep.2019.12.077

    View details for PubMedID 31968260

  • A physics-based energy function allows the computational redesign of a PDZ domain. Scientific reports Opuu, V. n., Sun, Y. J., Hou, T. n., Panel, N. n., Fuentes, E. J., Simonson, T. n. 2020; 10 (1): 11150


    Computational protein design (CPD) can address the inverse folding problem, exploring a large space of sequences and selecting ones predicted to fold. CPD was used previously to redesign several proteins, employing a knowledge-based energy function for both the folded and unfolded states. We show that a PDZ domain can be entirely redesigned using a "physics-based" energy for the folded state and a knowledge-based energy for the unfolded state. Thousands of sequences were generated by Monte Carlo simulation. Three were chosen for experimental testing, based on their low energies and several empirical criteria. All three could be overexpressed and had native-like circular dichroism spectra and 1D-NMR spectra typical of folded structures. Two had upshifted thermal denaturation curves when a peptide ligand was present, indicating binding and suggesting folding to a correct, PDZ structure. Evidently, the physical principles that govern folded proteins, with a dash of empirical post-filtering, can allow successful whole-protein redesign.

    View details for DOI 10.1038/s41598-020-67972-w

    View details for PubMedID 32636412

    View details for PubMedCentralID PMC7341745

  • SGEF forms a complex with Scribble and Dlg1 and regulates epithelial junctions and contractility JOURNAL OF CELL BIOLOGY Awadia, S., Hug, F., Arnold, T. H., Goicoechea, S. M., Sun, Y., Hou, T., Kreider-Letterman, G., Massimi, P., Banks, L., Fuentes, E. J., Miller, A. L., Garcia-Mata, R. 2019; 218 (8): 2699–2725


    The canonical Scribble polarity complex is implicated in regulation of epithelial junctions and apical polarity. Here, we show that SGEF, a RhoG-specific GEF, forms a ternary complex with Scribble and Dlg1, two members of the Scribble complex. SGEF targets to apical junctions in a Scribble-dependent fashion and functions in the regulation of actomyosin-based contractility and barrier function at tight junctions as well as E-cadherin-mediated formation of adherens junctions. Surprisingly, SGEF does not control the establishment of polarity. However, in 3D cysts, SGEF regulates the formation of a single open lumen. Interestingly, SGEF's nucleotide exchange activity regulates the formation and maintenance of adherens junctions, and in cysts the number of lumens formed, whereas SGEF's scaffolding activity is critical for regulation of actomyosin contractility and lumen opening. We propose that SGEF plays a key role in coordinating junctional assembly and actomyosin contractility by bringing together Scribble and Dlg1 and targeting RhoG activation to cell-cell junctions.

    View details for DOI 10.1083/jcb.201811114

    View details for Web of Science ID 000478788200019

    View details for PubMedID 31248911

    View details for PubMedCentralID PMC6683736

  • Biochemical and Structural Characterization of De Novo Designed PDZ Domains Fuentes, E. J., Sun, Y., Sternke, M., Opuu, V., Panel, N., Barrick, D., Simonson, T. CELL PRESS. 2019: 320A
  • Novel mutations in the 3-box motif of the BACK domain of KLHL7 associated with nonsyndromic autosomal dominant retinitis pigmentosa. Orphanet journal of rare diseases Oh, J. K., Lima de Carvalho, J. R., Sun, Y. J., Ragi, S. n., Yang, J. n., Levi, S. R., Ryu, J. n., Bassuk, A. G., Mahajan, V. B., Tsang, S. H. 2019; 14 (1): 295


    Mutations in the Kelch-like protein 7 (KLHL7) represent a recently described and, to date, poorly characterized etiology of inherited retinal dystrophy. Dominant mutations in KLHL7 are a cause of isolated, non-syndromic retinitis pigmentosa (RP). In contrast, recessive loss-of-function mutations are known to cause Crisponi or Bohring-Opitz like cold induced sweating syndrome-3 (BOS-3). In this study, the phenotype and progression of five unrelated patients with KLHL7 mediated autosomal dominant RP (adRP) are characterized. Clinical evaluation of these patients involved a complete ophthalmic exam, full-field electroretinography (ffERG), and imaging, including fundus photography, spectral domain optical coherence tomography (SD-OCT), short wavelength fundus autofluorescence (SW-AF), and near-infrared fundus autofluorescence (NIR-AF). Molecular diagnoses were performed using whole-exome sequencing or gene panel testing. Disease progression was monitored in three patients with available data for a mean follow up time of 4.5 ± 2.9 years. Protein modeling was performed for all variants found in this study in addition to those documented in the literature for recessive loss-of-function alleles causing Crisponi or Bohring-Opitz like cold-induced sweating syndrome.Genetic testing in three patients identified two novel variants within the 3-box motif of the BACK domain: c.472 T > C:p.(Cys158Arg) and c.433A > T:p.(Asn145Tyr). Clinical imaging demonstrated hyperautofluorescent ring formation on both SW-AF and NIR-AF in three patients, with diffuse peripheral and peripapillary atrophy seen in all but one case. SD-OCT demonstrated a phenotypic spectrum, from parafoveal atrophy of the outer retina with foveal sparing to widespread retinal thinning and loss of photoreceptors. Incidence of cystoid macular edema was high with four of five patients affected. Protein modeling of dominant alleles versus recessive loss-of-function alleles showed dominant alleles localized to the BTB and BACK domains while recessive alleles were found in the Kelch domain.We report the phenotype in five patients with KLHL7 mediated adRP, two novel coding variants, and imaging biomarkers using SW-AF and NIR-AF. These findings may influence future gene-based therapies for adRP and pave the way for mechanistic studies that elucidate the pathogenesis of KLHL7-mediated RP.

    View details for DOI 10.1186/s13023-019-1275-2

    View details for PubMedID 31856884

  • A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Frontiers in molecular biosciences Panel, N. n., Sun, Y. J., Fuentes, E. J., Simonson, T. n. 2017; 4: 65


    PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or "PB/LIE" free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo. The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

    View details for DOI 10.3389/fmolb.2017.00065

    View details for PubMedID 29018806

    View details for PubMedCentralID PMC5623046

  • Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Structure (London, England : 1993) Liu, X. n., Speckhard, D. C., Shepherd, T. R., Sun, Y. J., Hengel, S. R., Yu, L. n., Fowler, C. A., Gakhar, L. n., Fuentes, E. J. 2016; 24 (12): 2053–66


    Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.

    View details for DOI 10.1016/j.str.2016.08.019

    View details for PubMedID 27998539

    View details for PubMedCentralID PMC5488749