WORKSHOP PEMODELAN MOLEKUL

“DATABASE SENYAWA ALAM”

DAN PENAMBATAN MOLEKUL

Muhammad Yusuf
Departemen Kimia Universitas Padjadjaran
[email protected]

Sekolah Farmasi ITB

31 Maret 2017
 PLEASE USE
YOUR ATOMIC
GLASSES
www.flickr.com www.dreamstime.com
 PROTEIN
SOLUTION
IN ATOMIC
SCALE

http://www.ccpbiosim.ac.uk/annualconfs/conf2013
CELL MEMBRANE

http://hyperphysics.phy-astr.gsu.edu/hbase/biology/celmem.html http://psc.edu/science/2011/antonhighlights/
 DRUG IN ACTION
https://www.youtube.com/watch?v=1Ntoml52-K0

https://www.youtube.com/watch?v=1Ntoml52-K0
RATIONAL DRUG DESIGN
IDENTIFIKASI TARGET OBAT
https://www.youtube.com/watch?v=YSgkoldBNkI

All Terrain Media (http://atmedia.nl)

 DALAM PEMODELAN
MOLEKUL
BACA! BACA! DAN BACA!
The Importance of Resolution
• In X-ray crystallography it is
not always possible to
4Å low flawlessly resolve the crystal
density of the protein of
interest.

3Å • This results in a lower

resolution structure.

• The lower the resolution the

2Å more likely the structure is
wrong.

• The resolution of the

high template structure also
1Å
reflects in the quality of the
homology model.
Study of Receptor Behaviors from Its PDBs

Different behavior
On holo and apo form

Q
T

Proposed a conserved binding pattern of sialic terminal with H1

 Receptor’s Behavior
Loop-534

E353

R394

H524
Complex of Fevicordin – 1G50 minimized
Complex of Estradiol – 1G50 crystal
Complex of 4OH-Tamoxifen – 3ERT crystal
http://media.npr.org/assets/img/2014/03/18/ap090429040174_wide-
9bbc47f8378b34ca28d52ec76a985ed616172519-s40-c85.jpg

DRUGS HAVE BEEN

DEVELOPED AND
OTV AS LARGEST STOCKPILE MARKETED AS
OF ANTI-INFLUENZA EFFORTS IN FIGHTING
IN THE WORLD
http://s671.photobucket.com/user/perryscave/media/General/tamiflu.jpg.htm INFLUENZA VIRUS.

http://static.guim.co.uk/sys-
images/Guardian/Pix/pictures/2014/4/9/1397068075345/Packets-of-Tamiflu-009.jpg
 Oseltamivir
(Tamiflu)
is a
Neuraminidase
inhibitor

http://www.cdc.gov/flu/images/h1n1/
3D_Influenza_transparent_key_pies lice_lrg.gif
More about Neuraminidase
 Suicide Case in Japan: Is it because of Tamiflu?

R41
M85
E39
D46
I103
I105 R21
E/Q111
Y334
A158

R304
Y189 R237
Y189
E218

“This study shed insight into the neuropsychiatric side effects of oseltamivir.
It was demonstrated that replacement of positively charged R41 with neutral N41 (in
most of Asian people) increased the sensitivity of hNEU2 to oseltamivir
and reduced the catalytic activity of hNEU2.”
(Hitaoka et. al., J. Chem. Inf. Model. 2011, 51, 2706–2716)
 INVESTIGATING
THE MUTATION EFFECTS ON
STRUCTURAL BEHAVIOR of PROTEIN

6-8 Å

(Yusuf et al., 2016)

DRUG DEVELOPMENT IN
INDONESIA?
 PROMISING STARTS
FROM GENETICS TO molecular DESIGN

1. DIAGNOSTICS
2. BIOMARKER: MEDICAL DECISIONS
3. HERBAL: “SMART” NATURAL
PRODUCTS
4. VACCINES: “SMART” VACCINES
3. herbal: “smart natural products”

INDONESIA: 2ND LARGEST BIODIVERSITY

(Sodhi et al, 2004, Trends in Ecology and Evolution)

 Prediction of
Molecular Targets
of Cancer
Preventing
Flavonoid
Compounds Using
Computational
Methods

RSK2 PlosONE, 2012

ONCE WE validate THE TARGET
https://www.youtube.com/watch?v=TTtrk0Ue-Cg
OH
F

Cl

Br

Syahrul Imran, Muhammad Taha, Nor Hadiani Ismail, Syed Muhammad Kashif, Fazal Rahim, Waqas Jamil, Maywan Hariono,
Muhammad Yusuf, Habibah Wahab
Synthesis of novel flavone hydrazones: In-vitro evaluation of α-glucosidase inhibition, QSAR analysis and docking studies

European Journal of Medicinal Chemistry, Volume 105, 2015, 156–170

THE URGENCY OF ASSAY
DEVELOPMENT
 MISSING LINK in MECHANISM of ACTION

Q: APAKAH BENAR FEV-A

BERINTERAKSI DENGAN
HUMAN ESTROGEN
RECEPTOR ALPHA???
A: TARGET-BASED ASSAY
 Resveratrol sebagai anti-aging
seringkali mekanisme
molekular obat = rumit!

• Sirtuin: Enzymes that

catalyze NAD+-dependent
deacetylation reactions
• Resveratrol, a sirtuin
activator, bind at the N-
terminus of sirtuin
• In 2014, two sirtuin
activators were shown to
extend the health span and
the lifespan of mice on a
standard diet*
*Mitchell et al. Cell Reports 2014, 6 (5), 836-843.
The pleiotropic flavonoid quercetin: from its metabolism to the
inhibition of protein kinases in chronic lymphocytic leukemia
Russo et al. 2014. Food Funct. 5: 2393
Inhibition of Kinases

(Min and Kwon, 2014)

(Lamoral-Theys et al., 2010)

We demonstrated that 3′-hydroxy-flavone but not
the chemical core structure flavone blocked TNF-
α–induced nuclear factor (NF)-κB transcriptional
activity and IP-10 expression at the level of NF-
κB/IκBα phosphorylation/degradation by
inhibiting IκB kinase activity.
(Ruiz and Haller. 2006. J. Nutr. 136: 664-71)

Specificity on
Different Kinases
Different Cancer!

(Wu et al. 2013. JOC. 78: 1910-22)

 Error in automatic Process:
Alignment correction
E E E -A-V
F-D- I V V
• Core residues  conserved
• Use multiple sequence
C
alignments P A
C
C sequence  shift gaps
• Deletions in your
R R M S
R

M G
L
P
P

Known structure FDICRLPGSAEAV

Model FNVCRMP---EAI
Model FNVCR---MPEAI  Correct alignment
 www.nadi-discovery.com

Ikram et al.,
J. Chem. Inf. Model., 2015, 55 (2),
pp 308–316
 Pharmacophore
Modeling
Literature review

Hit Virtual Lead

Identified Identified

Validated target Identified Molecular

Docking
Simulation In vitro
Assay

*
Molecular * Virtual hits
Identified
Lead
Identified
Further
Dynamics Test
Simulation
IN-SILICO SCREENING FOR INFLUENZA USING NADI
Top 6 plants clusters selected as below:
Validated target No. Comp Plants
Literature review
18 Tanaman A
15 Tanaman B
7 Tanaman C
7 Tanaman D
7 Tanaman E
6 Tanaman F

Molecular
Docking
Simulation In vitro
Assay

Virtual hits • Resulted ~ 100 top compounds with

Identified lowest free energy of binding, and
clustered into plants.
Natural-product databases that can be used for virtual screening campaigns
From
The re-emergence of natural products for drug discovery in the genomics era
Alan L. Harvey, RuAngelie Edrada-Ebel& Ronald J. Quinn
Nature Reviews Drug Discovery 14, 111–129 (2015) doi:10.1038/nrd4510
 demo online

http://bioinf-applied.charite.de/supernatural_new/index.php
-11.93 kcal/mol +29.44 kcal/mol
PELAJARI KARAKTER SISI AKTIF ENZIM.
Enzymatic Assay Cell-based Assay
Compounds IC50 value (µM)

24 hours 48 hours

NSC228137 20.7 14.5

NSC349156 14 5.8

Metronidazole
Control (NS) 6.2 5

Incubation time Mortality rate (%)

(hour) 12 24 48

NSC228137 17. 3* 37.6* 56.9*

NSC349156 29. 7* 75.7** 89.1**

Metronidazole 34.8 80.5 91.4

 KETIKA HASIL DOCKING
“TIDAK” SESUAI HARAPAN

JANGAN LANGSUNG
SALAHKAN
KOMPUTER

KASIAN!
Literatures Review on Docking of Glycans
• Gambaryan, et al. 2008.
Virology Journal, 5:85
• Gambaryan, et al. 2005.
Virus Research, 114:15–
22
 Selection of Docking Methods
• Preassumptions:
• C-DOCKER (MD-based)
• Need to shape up the glycans first to be fitted into binding site
• Autodock 3 – 4.2 (GA-based)
• Too many torsions, too many num_evals, too long simulations
• Based on experience, 100 runs with 25 millions num_evals will take more
than 24 hours on a single PC.

• Scoring function is well defined to correlate with experimental values

• Autodock Vina (ILO-based)
• Do local optimization for each perturbation.
• Multithreads-compatible already.
• Worthed to try because it is fast.
Strategies on Docking
Conformational Space

Degrees of Freedom:
Torsional
Translation
Orientation

Searching
Algorithm
On Vina:
> Exhaustiveness

> Global Search/Perturbation

Local Optimizer per each C

On GA @ AD3/4/4.2:
> runs, > num_evals
CONCLUSION
LAST BUT NOT LEAST...…
We cannot work alone!