Virtual Screening of TIPO Natural Compound Database on

HCV NS5B RNA Polymerase 虛擬篩選在智慧局天然小分子資料庫上進行C型肝炎RNA聚合酶NS5B抑制劑之篩選結果

Material and method

Crystal Structures of HCV NS5B with its inhibitor (1Z4U, 1YVF,

2FVC) were being used as the research protein. We first draw the

structure then do energy minimization in Sybyl® . Then we used

the generated compounds to go on docking by using GOLD® . We

used Catalyst® CoMFA, and CoMSIA to do hypothesis analysis.

For the database screening part, we used the same parameter

which we established and ran it with GOLD® , later we estimate the

inhibition ability of each potent molecule.

Virtual Screening is one methodology of CADD (computer-assisted drug design), it can not only increase the hit rate of screening result library, but

also decrease the manpower of laborious experiment, and hence it has become a powerful tool used by giant pharmaceutical companies. We have

established the 3D model of HCV NS5B RNA polymerase, validated by known inhibitors, run the virtual screening process on TIPO Natural Compound

Database consisted of around 40K molecules. Our result shows that on the top 200 hits, there are some compounds can be found on Taiwan native

species or common TCMs, including Agrimonia pilosa, Mallotus japonicus, Magnolia officinalis etc. Our future work is to establish the molecular level

assay system for NS5B and to collect those related plants to test the reliability of our model.

Result

1. Result & Model

2. Database Screening Results

Figure 8. (Left) CoMFA test set cross validation result. Training set non-cross

validation 0.993. Leave-one-out validation 0.755. Cross-validation validation

0.653.(data not shown). Test set cross validation qcv2=0.6826.(Right) CoMSIA

test se cross validation result. Training set non-cross validation 0.991. Leave-

one-out validation 0.775. Cross-validation validation 0.663.(data not shown).

Test set cross validation qcv2=0.6917. Both component are 6, and group is 10.

Figure 9. Catalyst® contour map. Light blue contour indicating

hydrophobic interaction, white color contour indicating aromatic

planar, green color contour indicating hydrogen bond acceptor.

Table 1. Among the top 25 potential hits, 6 hits exist in Taiwan

native plants by reports, the following table shows the ID,

score, Name, MW and Formula. These Natural Compounds’

structure and the natural resources are also shown here.

Conclusion 1. In pharmacophore study, we defined several regions to have hydrogen bond

acceptor, and several region to have hydrophobic effect and steric effect. We

can refine structure in the future by CoMFA, CoMSIA model.

2.The CoMFA, CoMSIA, and Catalyst® models we generated here can aid us in

the estimation of unknown docked molecule, narrowing down the possible hits.

3.The possible natural compound hits selected by this methodology can help us

to accelerate our drug discovery progress, these hits need to be verified by

NS5B enzyme activity assay in the future.

Wei Lien1,2 、Thy-Hou Lin2 and Ting-Shou Chen1 (連偉、林志侯、陳廷碩)

Pharmaceutical Analysis Department, Pharmaceutical Technology Division, Biomedical Engineering Research Laboratories, ITRI1

Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University2

生醫所醫藥組藥物分析研究部1、清華大學生命科學學院分子醫學研究所2

Figure 1. Comparing the crystal ligand with the ligand generated from

GOLD method, 1Z4U(left) and 2FVC(right). The green ligand is from

the crystal structure, and the yellow ligand is generated by Gold

docking. We found that the RMSD values between the both ligands

are 0.357(left) and 0.576(right).

Figure 4. CoMFA contour map. Background protein

indicating lipophilicity. (Color Margin) Green: Steric favor.

Yellow: steric disfavor. Blue: Negative charge favor. Red:

Positive charge favor.

Figure 5. CoMSIA contour map. Background protein

indicating lipophilicity. Cyan color indicating

hydrophobic favor, white color indicating hydrophobic

disfavor.

Figure 7. CoMSIA contour map.

Background protein indicating hydrogen

donor favor. Purple color indicating

hydrogen bond acceptor favor.

Figure 2. Contour map of CoMFA generated by 2FVC

ligands docked into 1Z4U receptor. (Color Margin) Green:

Steric favor. Yellow: steric disfavor. Blue: Negative charge

favor. Red: Positive charge favor.

Figure 3. Contour map generated by 1Z4U+1YVF ligands

docked into 1Z4U receptor. (Color Margin) Green: Steric favor.

Yellow: steric disfavor. Blue: Negative charge favor. Red:

Positive charge favor.

Figure 6. CoMSIA contour map.

Background protein indicating cavity depth.

Green color indicating steric favor, yellow

color indicating steric disfavor.

qcv2

Actual IC50

Predicted IC50

qcv2

Actual IC50

Predicted IC50

124898027

Mallotus japonicus

121737157

Agrimonia pilosa

55620649

Agrimonia pilosa

55620627

Agrimonia pilosa

55829581

Agrimonia pilosa 138635110

Magnolia officinalis