1. Drug Discovery and Zika Virus
Sandra Porter, PhD
President, Digital World Biology LLC
Shoreline Community College,
Austin Community College
co-PI Bio-Link, Bio-Link.org
AC2 Bio-Link Regional Center ©

2. Bioinformatics for instructors
On-line course - through Austin Community College
Jan 16- mid May
$500
Sign up on list and I will send info about registration ©

3. What is Zika virus?
Zika virus is an emerging health concern in the western hemisphere.
The virus is transmitted by Aedes aegyptii mosquitoes and by sex
And it's spreading
Zika virus is transmitted by the Aedes aegypti mosquito & sex ©

4. What is Zika virus? The spread of Zika virus is quite alarming because
The virus infects and kills developing brain cells & other cells in the nervous system
As a result > infections with Zika have been linked to an increase in birth defects, in particular microcephaly, vision problems, and other neurological defects.
In adults, infections can cause a form of paralysis, known as Guillian Barre syndrome ©

5. Why study Zika virus? Good topic to engage students
many are of child-bearing age
many live in areas that will be impacted by Zika
Working on Zika virus is empowering - Show students that the tools we're learning about in class can be used to study serious, and immediate real world problems
So, what can students do?
We don't have a wet lab, we don't have cultures of Zika virus or cells
We can use bioinformatics to search for drugs
Look at drugs that work on other viruses - are they likely to work on Zika ©

6. Protein Related Protein Drug Drug General approach©

7. General approach
1. Use BLAST to find a structure of a drug bound to a protein from a related virus
2. Use molecular modeling to identify key residues that are bound to the drug
3. Examine aligned sequences – are the amino acids that bind the drug present in Zika proteins? ©

8. NCBI Zika Virus Resource
Google : NCBI zika
NCBI Zika virus resource
Start with Health Map ©

9. Is Zika virus in your neighborhood?
Where is Zika Virus?
Is Zika virus in your neighborhood?
5 minutes - asking the room ©

10. Where is Zika Virus? Spend a couple of minutes -
Want you to do - zoom in -look at your state -
see if Zika virus has been reported & when
11: 10
5,264 cases of Zika virus in the United States (224 local via mosquitoes, 77 sex)
36,575 cases of Zika virus in US Territories - as of April 26, 2017, CDC.gov ©

11. NCBI Zika Virus Resource
Google : NCBI zika
NCBI Zika virus resource
Start with Health Map ©

12. Expasy ViralZone
picture
scroll down ©

13. Expasy ViralZone Map of the genome
Take a couple of minutes and look at this
What is the Zika genome made of?
How big is the genome?
How big is the polyprotein?
Which proteins are the polymerase (NS5)? and the protease (NS3)?
What do they do? ©

14. Zika virus life cycle Map of the genome
Take a couple of minutes and look at this
What is the Zika genome made of?
How big is the genome?
How big is the polyprotein?
Which proteins are the polymerase (NS5)? and the protease (NS3)?
What do they do? ©

15. NCBI Zika Virus Resource
Google : NCBI zika
NCBI Zika virus resource
Start with Health Map ©

16. Zika Virus Reference Genome
Not very helpful ©

17. Zika Virus Reference Genome
GenBank record -
Students need to find links to the
protease
and the polymerase
And note where they stop and start ©

18. Zika Virus Reference Genome©

19. Find structures of related proteins & drugs
Choose a protein:
- NS3 protease or
- NS5 RNA polymerase
Pick which one to look
Protease or Polymerase
Click the link ©

20. Zika Protein BLAST search
Run BLAST ©

21. Zika Virus Reference Genome©

22. How does BLAST work?
Run BLAST ©

23. Use BLAST to search for similar structures
Exclude Zika
Change the database ©

24. NS3 Protease Results - Protein annotations aren't perfect©

25. NS5 RNA polymerase search©

26. Find structures of related proteins & drugs
Pick a structure to study:
- Must contain right protein
- Must contain drug / inhibitor
Need to look at our results - and find something that has a drug or inhibitor
*might need more than 100 structures (default) ©

27. Find structures of related proteins & drugs
A little tricky
Involves reading & scanning for information
Sometimes information can be grouped ©

28. Find structures of related proteins & drugs
Here's an example ©

29. 1. Use BLAST to find a structure of a drug bound to a related virus √
General approach
1. Use BLAST to find a structure of a drug bound to a related virus √
2. Use molecular modeling to identify key residues that are bound to the drug
3. Examine aligned sequences – are the amino acids that bind the drug present in Zika proteins? ©

30. Example: HCV & Sovaldi® (Sofusbuvir)
Sofusbuvir inhibits Hepatitis C virus RNA polymerase
4WTG - contains Sofusbuvir bound to Hep C RNA pol.
Identify residues that bind to the drug
1. Download 4WTG, open in Molecule World
2. Open sequence viewer, select the drug (6GS)
3. Open selection menu > select nearby
4. Open Show/Hide menu > Show all residues
5. Color by residue
Limited time - we're going to look at an example that I found ©

31. Example: HCV & Sovaldi® (Sofusbuvir)©

32. 1. Use BLAST to find a structure of a drug bound to a related virus √
General approach
1. Use BLAST to find a structure of a drug bound to a related virus √
2. Use molecular modeling to identify key residues that are bound to the drug
3. Examine aligned sequences – are the amino acids that bind the drug present in Zika proteins? ©

33. Zika NS5 polymerase aligned to HCV RNA pol
11:30 ©

34. Student results
5K5M – T68 – inhibits RNA dependent RNA polymerase in Dengue virus ©

35. Student results
3E90 A protease inhibitor, Naph-Kkr-H, complexed with West Nile Virus protease ©

36. Student results
5IQ6 Dengue Virus Serotype 3 RNA Dependent RNA Polymerase bound to an inhibitor ©