University Directory

Zhiyu Li, PhD

Professor: Pharmaceutical Sciences
Vice-Chair, Department of Pharmaceutical Sciences: Pharmaceutical Sciences

Zhiyu Li PhD

Department

Office

McNeil Graduate Study and Research Center 209

Phone

215-596-8943
Contact

Dr. Li's current research efforts focus on utilizing computational and bioinformatics methods to gain insight into protein sequence, structure and function relationships and to explore their application in molecular modeling, drug design and protein engineering.

There are several research areas that Li is interested in. First is the development of computational tools to aid in the structural prediction of transmembrane proteins such as G-protein coupled receptors. Transmembrane proteins are essential to many important cellular activities such as signal and energy transduction, mediation of the senses and immune recognition. These proteins are important therapeutic targets. The G-protein coupled receptor (GPCR) superfamily alone represents the targets of ~27% of drugs currently available in the market. Despite their biological importance, high-resolution TM protein structures remain scarce compared with soluble proteins. As a result, computational modeling has played a key role in the studies of membrane proteins.

A second research area of interest is to apply structural modeling tools to the construction of protein and protein-complex models designed to help elucidate biological mechanisms. An active project currently ongoing in this area is to model three-dimensional structures of chemoreceptor-CheR complexes through collaboration with experimentalists. Another project is to construct the structure models of tumor endothelial marker-antibody complex.

The third area of interest is to apply the knowledge gained through the analysis of protein structures to biomedical problems such as computer-aided molecular design and protein engineering. Li is especially interested in the emerging field of network medicine. For instance, works are under-way to design selective protein kinase inhibitors for the treatment of cancer.

    • BS, Tsinghua University
    • MS, Tsinghua University
    • PhD, Vanderbilt University
    • Malik F. and Li Z. "Non-Peptide Agonists and Positive Allosteric Modulators of Glucagon-Like Peptide-1 Receptor: Alternative Approaches for Treatment of Type 2 Diabetes." British J. Pharmacology. (2022) 179: 511-525.
    • Regan K., Saghafi A., Li Z. "Splice Junction Identification Using Long Short-Term Memory Neural Networks." Current Genomics. (2021) 22(5): 384-390.
    • Dang Z., Zhu L., Xie L., Lee K.-H., Malik F., Li Z., Huang L., Chen C-H. "Design and Synthesis of Quinolizidine Derivatives as Influenza Virus and HIV-1 Inhibitors." Current Med. Chem. (2021) 28(24): 4995-5003.
    • Redij T., Ma J., Li Z., Hua X., Li Z. "Discovery of a Potential Positive Allosteric Modulator of Glucagon-like Peptide 1 Receptor Through Virtual Screening and Experimental Study." J. Computer-Aided Mol. Des. (2019) 33: 973-981.
    • Gunderwala A., Nimbvikar A., Cope N., Li Z., Wang Z. "Development of Allosteric Braf Peptide Inhibitors Targeting the Dimer Interface of BRAF." ACS Chemical Biology (2019) 14: 1481-1489.
    • Redij T., Chaudhari R., Li, Z., Hua X., Li Z. "Structural Modeling and In SilicoScreening of Potential Small Molecule Allosteric Agonists of Glucagon-Like Peptide 1 Receptor." ACS Omega (2019) 4: 961-970.
    • Mao B., Gao M., Chen C., Li Z., Zhang H.-Y., Zhang Q. Design, Synthesis and Biological Evaluation of Novel N-nitrophenyl Derivatives Based on the Structure of Acetohydroxyacid Synthase. Pesticide Biochemistry and Physiology. (2018) 145: 100-107.
    • Dang Z., Xie H., Zhu L., Zhang Q., Li Z., Huang, L., Chen C.-H. "Structure Optimization of Aloperine Derivatives as HIV-1 Entry Inhibitors." ACS Medicinal Chemistry Letters. (2017) 8: 1199-1203.
    • Yuan X., Yang M., Chen X., Zhang X., Sukhadia S., Musolino N., Bao H., Chen T., Xu C., Wang Q., Santoro S., Ricklin D., Hu J., Lin R., Yang W., Li Z., Qin W., and Zhao A. "Characterization of the First Fully Human Anti-TEM1 ScFv in Models of Solid Tumor Imaging and Immunotoxin-based Therapy." Cancer Immunol Immunother. [2017] 66(3): 367-378. Note: The figure from this publication showing the binding of scFv78 to human and murine TEM1, was featured on the cover of this issue of the Journal.
    • Dong D., Xia G., Li Z., Li Z. "Human Serum Albumin and Her2-binding Affibody Fusion Proteins for Targeted Delivery of Fatty Acid-modified Molecules and Therapy." Mol. Pharmacology [2016] 13(10): 3370-3380.
    • Chaudhari R. and Li Z. "PyMine: a PyMOL Plugin to Integrate and Visualize Data for Drug Discovery." BMC Research Notes [2015] 8: 517 DOI: 10.1186/s13104-015-1483-3.
    • Chaudhari R., Heim A. J., and Li Z. "Improving Homology Modeling of G-protein Coupled Receptors Through Multiple-template Derived Conserved Inter-residue Interactions" J. Computer-Aided Molecular Design (2015] 29: 413-420.
    • Rogers B., Dong D., Li Z., and Li Z. "Recombinant Human Serum Albumin Fusion Proteins and Novel Applications in Drug Delivery and Therapy." Curr Pharm Des. [2015] 21: 1899-1907.
    • Menezes M.J., Guo Y., Zhang J., Riley L.G., Cooper S.T., Thorburn D.R., Li J., Dong D., Li Z., Glessner J., Davis R.L., Sue C.M., Alexander S.I., Arbuckle S., Kirwan P., Keating B.J., Xu X., Hakonarson H., Christodoulou J. "Mutation in Mitochondrial Ribosomal Protein S7 (MRPS7) Causes Congenital Sensorineural Deafness, Progressive Hepatic and Renal Failure, and Lactic Acidemia."Hum. Mol. Genet. (2015] 24:2297-2307.
    • I. Kufareva, V. Katritch, participants of GPCR Dock 2013 (Box 1), R. C. Stevens, and R. Abagyan. "Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges." Structure (2014) 22: 1120-1139.
    • S. Chaudhuri, S. Pratap, V. Paromov, Z. Li, and H. Xie. "Identification of a Diguanylate Cyclase and its Role in porphyromonas gingivalis Virulence." Infection and Immunity (2014) 82(7): 2728-2735.
    • A. J. Heim and Z. Li. "Developing a High-quality Scoring Function for Membrane Protein Structures Based on Specific Inter-residue Interactions." J. Computer-Aided Molecular Design (2012) 26: 301-309.
    • J. Gao, Z. Li, T. Russelld, and Z. Li. "Antibody Affinity Purification Using Metallic Nickel Particles." J. Chromatography B, (2012) 895–896: 89–93.
    • V. Pabuwal and Z. Li. "Comparison Analysis of Primary Ligand Binding Sites in Seven-helix Membrane Proteins." Biopolymers (2011) 95: 31-38.
    • J. Gao and Z. Li. "Uncover the Conserved Property Underlying Sequence-distant and Structure-similar Proteins." Biopolymers (2010) 93: 340-347.
    • J. Gao and Z. Li. "Conserved Network Properties of Helical Membrane Protein Structures and Its Implication for Improving Membrane Protein Homology Modeling at the Twilight Zone." J. Computer-Aided Mol. Des. (2009) 23: 755-763.
    • U. K. Muppirala, S. Desensi, T. P. Lybrand, G. L. Hazelbauer and Z. Li. "Molecular Modeling of Flexible Arm-mediated Interactions Between a Bacterial Chemoreceptor and Its Modification Enzyme." Protein Sci. (2009) 18: 1702-1714.
    • J. Gao and Z. Li. "Comparing Four Different Approaches for the Determination of Inter-residue Interactions Provides Insight for the Structure Prediction of Helical Membrane Proteins." Biopolymers (2009) 91: 547-556.
    • V. Pabuwal and Z. Li. "Comparative Analysis of the Packing Topology of Structurally Important Residues in Helical Membrane and Soluble Proteins." Protein Eng. Des. Sel. (2009) 22: 67-73.
    • J. Gao and Z. Li. "Inter-residue Interactions in Protein Structures Exhibit Power-law Behavior." Biopolymers (2008) 89: 1174-1178.
    • J. F. Galan, J. Gao, V. Pabuwal, P. J. Meek and Z. Li. "Application of Network Theory in Understanding and Predicting Protein Structure and Function." Current Proteomics (2008) 5(3): 181-190.
    • W. Lai, L. Huang, P. Ho, Z. Li, D. Montefiori and C.-H. Chen. "Small Molecules Target HIV-1 V3 Loop with Broad Anti-HIV-1 Entry Activity." Antimicrob. Agents Chemother. (2008) 52: 128-136.
    • V. Pabuwal and Z. Li. "Network Pattern of Residue Packing in Helical Membrane Proteins and Its Application in Membrane Protein Structure Prediction." Protein Eng. Des. Sel. (2008) 21: 55-64.
    • U. K. Muppirala and Z. Li. "A Simple Approach for Protein Structure Discrimination Based on the Network Pattern of Conserved Hydrophobic Residues." Protein Eng. Des. Sel. (2006) 19: 265-275.
    • M. Dong, Z. Li, D. I. Pinon, T. P. Lybrand, and L. J. Miller. "Spatial Approximation Between the Amino Terminus of a Peptide Agonist and the Top of the Sixth Transmembrane Segment of the Secretin Receptor." J. Bio. Chem. (2004) 279: 2894-2903.
    • M. Dong*, Z. Li*, M. Zang, D. I. Pinon, T. P. Lybrand and L. J. Miller. "Spatial Approximation Between Two Residues in the Mid-region of Secretin and the Amino Terminus of Its Receptor. Incorporation of Seven Sets of Such Constraints Into a Three-dimensional Model of the Agonist-bound Secretin Receptor." J. Bio. Chem. (2003) 278: 48300-48312. *Contributed equally
    • M. Zang, M. Dong, D. I. Pinon, X.-Q. Ding, E. M. Hadac, Z. Li, T. P. Lybrand, and L. J. Miller, . "Spatial Approximation Between a Photolabile Residue in Position 13 of Secretin and the Amino- Terminus of the Secretin Receptor." Mol. Pharmacology (2003) 63: 993-1001.
    • M. Dong, M. Zang, D. I. Pinon, Z. Li, T. P. Lybrand, and L. J. Miller. "Interaction Among Four Residues Distributed Through the Secretin Pharmacophore and a Focused Region of the Secretin Receptor Amino Terminus." Mol. Endocrinology (2002) 16: 2490-2501.
    • Z. Li, L. Huang, P. Dande, B. Gold, and M. P. Stone. "Structure of a Tethered Cationic 3-aminopropyl Chain Incorporated Into an Oligodeoxynucleotide: Evidence for 3 '-orientation in the Major Groove Accompanied by DNA Bending." J. Am. Chem. Soc. (2002) 124: 8553-8560.
    • Z. Li, P. J. Tamura, A. S. Wilkinson, C. M. Harris, T. M. Harris, and M. P. Stone. "Intercalation of the (1R,2S,3R,4S)-N-6-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2 '-deoxyadenosyl Adduct in the N-ras Codon 61 Sequence: DNA Sequence Effects." Biochemistry (2001) 40: 6743-6755.
    • Z. Li, H.-Y. Kim, P. J. Tamura, C. M. Harris, T. M. Harris, and M. P. Stone. "Intercalation of the (1S,2R,3S,4R)-N-6[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[alpha]anthracenyl)]-2 '-deoxyadenosyl Adduct in an Oligodeoxynucleotide Containing the Human N-ras Codon 61 Sequence." Biochemistry (1999) 38: 16045-16057.
    • Z. Li, H.-Y. Kim, P. J. Tamura, C. M. Harris, T. M. Harris, and M. P. Stone. "Role of a Polycyclic Aromatic Hydrocarbon Bay Region Ring in Modulating DNA Adduct Structure: The Non-bay Region (8S,9R,10S,11R)-N-6-[11-(8,9,10,11-tetrahydro-8,9,10-trihydroxybenz[a] Anthracenyl)]-2 '-deoxyadenosyl Adduct in Codon 61 of the Human N-ras Protooncogene." Biochemistry (1999) 38: 14820-14832.
    • Z. Li, H. Mao, H.-Y. Kim, P. J. Tamura, C. M. Harris, T. M. Harris, and M. P. Stone. "Intercalation Of the (-)-(1R,2S,3R,4S)-N-6-[1-benz[a]anthracenyl]-2 '-deoxyadenosyl Adduct in An Oligodeoxynucleotide Containing the Human N-ras Codon 61 Sequence." Biochemistry (1999) 38: 2969-2981.
    • S. Xu and Z. Li. "Alignment Mechanism of Liquid Crystal Molecules on the Fluorated Polyimide Surface." Tsinghua Science and Technology (1997) 2: 798-800.
    • (Chinese) S. Xu and Z. Li. "Study of Alignment Process Technologies of Liquid Crystal Molecules on Surface of Fluorated Polyimide." Journal of Tsinghua University (Science and Technology) (1997) 37: 17-20.
    • Using computational and bioinformatic methods to generate and analyze three-dimensional structures of protein molecules
    • Gain insight into protein sequence, structure, and function relationships