Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Taiwan
Welcome to our laboratory, we are interested in the following topics:
Antiviral drug Discovery (Dengue)

 

Antiviral drug Discovery (Dengue):

 

  • Kan JY, Chang YJ, Lai HC, Lin HH, Chiu SW, Hung PY, Lu CH*, Lin CW*. Darunavir inhibits dengue virus replication by targeting the hydrophobic pocket of the envelope protein. Biochemical Pharmacology (2025), 235, 116839
  • Lin YF, Lai HC, Lin CS, Hung PY, Kan JY, Chiu SW, Lu CH, Petrova SF, Baltina LA*, Lin CW*. Discovery of Potent Dengue Virus NS2B-NS3 Protease Inhibitors Among Glycyrrhizic Acid Conjugates with Amino Acids and Dipeptides Esters. Viruses (2024), 16(12)
  • Lu CH, Lin CS, Lin TH, Kiu YT, Kan JY, Chang YJ, Hung PY, Koval'skaya AV, Tsypyshev DO, Tsypysheva IP*, and Lin CW*. Inhibition of dengue viruses by N-methylcytisine thio derivatives through targeting viral envelope protein and NS2B-NS3 protease. Bioorganic & Medicinal Chemistry Letter (2024), 99, 129623
  • Lin CL, Kiu YT, Kan JY, Chang YJ, Hung PY, Lu CH, Lin WL, Hsieh YW, Kao JY, Hu NJ and Lin CW*. The Antiviral Activity of Varenicline against Dengue Virus Replication during the Post-Entry Stage. Biomedicines (2023), 11, 2754

 
 
Antiviral drug Discovery (SARS-CoV-2)

 

Antiviral drug Discovery (SARS-CoV-2):

 

  • Tai LT, Yeh CY, Chang YJ, Liu JF, Hsu KC, Cheng JC* and Lu CH*. Discovery of Novel Spike Inhibitors against SARS-CoV-2 Infection. International Journal of Molecular Science (2024), 25(11), 6105
  • Nguyen U, Chang YJ, Lu CH, Chen Y, Su WC, Chao ST, Baltina LA, Petrova SF, Li SR, Hung MC, Lai MMC, Baltina LA*, Lin CW*. Glycyrrhizic acid conjugates with amino acid methyl esters target the main protease, exhibiting antiviral activity against wild-type and nirmatrelvir-resistant SARS-CoV-2 variants. Antiviral Research (2024), 227, 105920
  • Yeh YJ, Chao TL, Chang YJ, Chang SY, Lu CH, Chao CH, Su WC, Tseng CP, Lai MC, Cheng JC. Dual Effects of 3-epi-betulin from Daphniphyllum glaucescens in Suppressing SARS-CoV-2-Induced Inflammation and Inhibiting Virus Entry. International Journal of Molecular Sciences (2023) 24, 17040
  • Chang YJ, Nguyen U, Liu JJ, Li SR, Chao ST, Lai HC, Lin YF, Hsu KC, Lu CH* and Lin CW*. Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV. Antiviral Research (2023), 216: 105653.

 
 
Anticancer drug Discovery

 

Anticancer drug Discovery:

 

  • Huang YK, Cheng WC, Kuo TT, Yang JC, Wu YC, Wu HH, Lo CC, Hsieh CY, Wong SC, Lu CH, Wu WL, Liu SJ, Li YC, Lin CC, Shen CN, Hung MC, Lin JT, Yeh CC and Sher YP. Inhibition of ADAM9 promotes the selective degradation of KRAS and sensitizes pancreatic cancers to chemotherapy. Nature Cancer (2024), 5, 400-419
  • Lu CH, Chung WM, Tsai CH, Cheng JC, Hsu KC and Tzeng HE*. In vitro characterization of a small molecule PD-1 inhibitor that targets the PD-l/PD-L1 interaction. Scientific Reports (2022), 12, Article number: 303

 
 
Cancer related single amino acid variation

 

Cancer-related single amino acid variation:

 

  • Liu JJ, Yu CS, Wu HW, Chang YJ, Lin CP and Lu CH*. The structure-based cancer-related single amino acid variation prediction. Scientific Reports (2021), 11, Article number: 13599.
  • Lin YF, Liu JJ, Chang YJ, Yu CS, Yi W, Lane HY and Lu CH*. Predicting anticancer drug resistance mediated by mutations. Pharmaceuticals (2022), 15(2), 136.

 
 
Metal ion-binding sites detection and modeling

 

Metal ion-binding sites detection and modeling:

 

  • Lu CH, Chen CC, Yu CS, Liu YY, Liu JJ, Wei ST, Lin YF*. MIB2: Metal ion-binding site prediction and modeling server. Bioinformatics (2022), btac534.
  • Chi ZX, Hong BW, Tan SW, Wu YC, Li HJ, Lu CH and Li WG*. Impact Assessment of heavy metal cations to the characteristics of photosynthetic phycocyanin. Journal of Hazardous Materials (2020), 391(5) : 122225
  • Lin YF, Cheng CW, Shih CS, Hwang JK, Yu CS and Lu CH*. MIB: Metal Ion-Binding site prediction and docking server. Journal of Chemical Information and Modeling (2016), 56 (12), pp 2287-2291
  • Sindy Escobar, Susana Velasco-Lozano, CH Lu, Lin YF, Monica Mesa, Claudia Bernal, and Fernando López-Gallego*. Understanding the functional properties of bio-inorganic nanoflowers as biocatalysts by deciphering the metalbinding sites of enzymes. Journal of Materials Chemistry B (2016), 5, 4478-4486
  • Lu CH*, Lin YF, Lin JJ, Yu CS. Prediction of Metal Ion-Binding Sites in Proteins Using the Fragment Transformation Method. PLoS One (2012), 7(6):e39252

 
 
Computer-aided drug design

 

Computer-aided drug design:

 

  • Lu CH, Chang HT, Hsu LF, Lee MH, Cheng J, Wu DC and Lin WY*. In Silico and In Vitro Screening of Serine Racemase Agonist and In Vivo Efficacy on Alzheimers Disease Drosophila melanogaster. Pharmaceuticals (2023), 16(2): 280.
  • Chang YJ, Yeh CY, Cheng JC, Huang YQ, Hsu KC, Lin YF and Lu CH*. Potent sialic acid inhibitors that target influenza A virus hemagglutinin. Scientific Reports (2021), 11, Article number: 8637.
  • Fuh MT, Tseng CC, Li SM, Tsai SE, Chuang TJ, Lu CH, Yang YC, Tsai HJ and Wong FF*. Design, synthesis and biological evaluation of glycolamide, glycinamide, and β- amino carbonyl 1,2,4-triazole derivatives as DPP-4 inhibitors. Bioorganic Chemistry (2021), 114, 105049.

 
 
Localization prediction and functional annotation

 

Localization prediction and functional annotation:

 

  • Yu CS, Cheng CW, Chang KC, Su WC, Huang SW, Hwang JK and Lu CH*. CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation. PLoS One (2014), 9(6):e99368
  • Yu CS, Chen YC, Lu CH, Hwang JK*. Prediction of protein subcellular localization. Proteins: Sturcture, Function and Bioinformatics (2006), 64: 643-51

 
 
Systems biology and machine learning

 

Systems biology and machine learning:

 

  • Lu CH, Wei ST, Liu JJ, Chang YJ, Lin YF, Yu CS and Chang LY*. Recognition of a Novel Gene Signature for Human Glioblastoma. International Journal of Molecular Sciences (2022), 23(8):4157.
  • Yu CS* and Lu CH. Identification of Antifreeze Proteins and Their Functional Residues by Support Vector Machine and Genetic Algorithms based on n-Peptide Compositions. PLoS One (2011), 6(5):e20445
  • Lu CH, Chen YC, Yu CS, Hwang JK*. Predicting disulfide connectivity patterns. Proteins: Structure, Function and Bioinformatics (2007), 67: 262-70

 
 
Protein dynamics:

 

Protein dynamics and structural Bioinformatics:

 

  • Lu CH*, Yu CS, Lin YF and Chen JY. Predicting Flavin and Nicotinamide Adenine Dinucleotide–Binding Sites in Proteins Using the Fragment Transformation Method. BioMed Research International (2015), Volume 2014, Article ID 402536
  • Lu CH, Chien YT, Yu CS and Huang SW*. EXIA2: Web Server of Accurate and Rapid Protein Catalytic Residue Prediction. BioMed Research International (2014), Volume 2014, Article ID 807839
  • Lu CH, Huang SW, Lai YL, Lin CP, Shih CH, Huang CC, Hsu WL and Hwang JK*. On the relationship between the protein structure and protein dynamics. Proteins: Structure, Function and Bioinformatics (2008), 72: 625-34
  • Lin CP, Huang SW, Lai YL, Yen SC, Shih CH, Lu CH, Huang CC and Hwang JK*. Deriving protein dynamical properties from weighted protein contact number. Proteins: Structure, Function and Bioinformatics (2008), 72: 929-35
  • Lu CH, Lin YS, Chen YC, Yu CS, Chang SY, Hwang JK*. The fragment transformation method to detect the protein structural motifs. Proteins: Structure, Function and Bioinformatics (2006), 63:636-43