Sains Malaysiana 45(7)(2016): 1113–1120
Inhibitors of Leishmania
mexicana Phosphoglycerate Mutase Identified
by Virtual
Screening and Verified by Inhibition
Studies
(Pengenalpastian
Perencat Fosfogliserat
Mutase daripada Leishmania
mexicana melalui
Saringan Maya dan Pengesahannya menerusi Kajian Perencatan)
FAZIA
ADYANI
AHMAD
FUAD1*,
DOUGLAS
R.
HOUSTON2,
PAUL
A.M.
MICHELS2,
LINDA A.
FOTHERGILL-GILMORE2
& MALCOLM D. WALKINSHAW2
1Department of Biotechnology Engineering,
Faculty of Engineering, International Islamic University Malaysia,
50728 Gombak, Kuala Lumpur, Malaysia
2Centre for Transitional and Chemical
Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology,
The University of Edinburgh, The King’s Buildings, Edinburgh EH9
3BF, United Kingdom
Diserahkan: 10 September 2015/Diterima: 11 Februari 2016
ABSTRACT
Cofactor-independent phosphoglycerate
mutase has been proposed as a therapeutic target for the treatment
of trypanosomatid diseases. In this paper,
we report the identification of compounds that could potentially
be developed as selective inhibitors of cofactor-independent phosphoglycerate
mutase from Leishmania mexicana (LmiPGAM). Virtual screening was used
in this search, as well as compounds identified by high-throughput
screening. A ligand-based virtual screen programme,
ultra fast shape recognition with atom types (UFSRAT),
was used to screen for compounds resembling the substrate/product,
before a structure-based approach was applied using AutoDock
4 and AutoDock Vina
in a consensus docking scheme. In this way eight selected compounds
were identified. In addition, three compounds from the Library of
Pharmacologically Active Compounds (LOPAC) were selected from the published results of high-throughput
screening of this library. The inhibitory effects of these compounds
were tested at a fixed concentration of 1 mM.
The results showed that seven compounds inhibited LmiPGAM activity
and of these, two compounds (one each from high-throughput and virtual
screening) showed substantial inhibition (i.e. 14% and 49% remaining
activity, respectively). Taken together, the findings from this
study indicate that these compounds have potential as novel inhibitors
that specifically target LmiPGAM.
Keywords: Cofactor-independent
phosphoglycerate mutase; glycolysis; Leishmania mexicana;
virtual screening analyses
ABSTRAK
Fosfogliserat mutase bebas-kofaktor telah dicadangkan sebagai sasaran terapeutik bagi penyakit yang disebabkan oleh tripanosomatida. Di sini kami melaporkan
pengenalpastian sebatian
yang berpotensi untuk
dibangunkan sebagai perencat kepada fosfogliserat mutase bebas-kofaktor
daripada Leishmania mexicana (LmiPGAM).
Saringan
secara maya telah
diaplikasikan dalam
kajian ini, selain
daripada beberapa
jenis sebatian yang dikenalpasti melalui saringan berprosesan tinggi. Program saringan
maya berasaskan ligan, Ultra Fast Shape Recognition
with Atom Types (UFSRAT), telah
digunakan untuk
menyaring sebatian yang menyerupai substrat/produk, sebelum pendekatan berasaskan struktur digunakan menerusi program AutoDock 4 dan AutoDock Vina
di dalam skim simulasi
pengikatan ligan kepada reseptor (docking) yang konsensus. Melalui kaedah ini, lapan sebatian terpilih telah dikenal pasti. Selain daripada itu, tiga
sebatian daripada
Library of Pharmacologically Active Compounds (LOPAC) yang dikenal
pasti melalui
kaedah saringan berprosesan tinggi terhadap perpustakaan ini yang telah diterbitkan turut dipilih untuk analisis
lanjutan. Kesan perencatan
kesemua sebatian
ini telah diuji
pada kepekatan
yang ditetapkan pada 1 mM. Hasil analisis ini
telah menunjukkan bahawa tujuh sebatian
merencat aktiviti
LmiPGAM, dengan
dua sebatian
(masing-masing daripada saringan berprosesan tinggi dan maya)
menunjukkan perencatan
yang ketara (14% dan
49% baki aktiviti). Secara keseluruhannya, hasil daripada kajian ini menunjukkan bahawa sebatian ini berpotensi sebagai perencat novel yang spesifik kepada LmiPGAM.
Kata kunci: Analisis
saringan maya;
fosfogliserat mutase bebas-kofaktor;
glikolisis; Leishmania Mexicana
RUJUKAN
Blackburn,
E.A., Fuad, F.A.A., Morgan, H.P., Nowicki,
M.W., Wear, M.A., Michels, P.A.M., Fothergill-Gilmore,
L.A. & Walkinshaw, M.D. 2014. Trypanosomatid
phosphoglycerate mutases have multiple conformational and oligomeric
states. Biochem.
Biophys.
Res. Commun. 450: 936-941.
Chevalier,
N., Rigden, D.J., van Roy, J., Opperdoes,
F.R. & Michels, P.A.M. 2000. Trypanosoma
brucei contains a 2,3-bisphosphoglycerate
independent phosphoglycerate mutase. Eur. J. Biochem.
267: 1464-1472.
Cosconati,
S., Forli, S., Perryman, A.L., Harris, R., Goddsell,
D.S. & Olson, A.J. 2010. Virtual screening with AutoDock: Theory and practice. Expert
Opin. Drug Discov. 5: 597-607.
Crowther, G.J.,
Booker, M.L., He, M., Li, T., Raverdy,
S., Novelli, J.F., He, P., Dale, N.R.G., Fife, A.M., Barker, R.H.,
Kramer, M.L., van Voorhis, W.C., Carlow, C.K.S. & Wang, M.W. 2014. Cofactor-independent
phosphoglycerate mutase from nematodes has limited druggability,
as revealed by two high-throughput screens. PLoS
Negl. Trop. Dis. 8: e2628.
de Winter, H. 2014.
Silicos-it Chemoinformatics Services and Software
http://silicos-it.be.s3-website-eu.west-1. amazonaws.com/.
Dolinsky,
T.J., Czodrowski, P., Li, H., Nielsen,
J.E., Jensen, J.H., Klebe, G. & Baker,
N.A. 2007. PDB2PQR: Expanding
and upgrading automated preparation of biomolecular structures for
molecular simulations. Nucleic Acids Res. 35(Web Server issue):
522-525.
Fothergill-Gilmore,
L.A. & Michels, P.A.M. 1993. Evolution of Glycolysis. Progr. Biophys.
Mol. Biol. 59: 105-236.
Fuad, F.A.A. 2012.
Effects of metal ions on the structural and biochemical properties
of trypanosomatid phosphoglycerate mutase.
PhD thesis. Institute of Structural and Molecular Biology,
School of Biological Sciences. The University of Edinburgh, Edinburgh
(Unpublished).
Fuad,
F.A.A., Fothergill-Gilmore, L.A., Nowicki,
M.W., Eades, L.J., Morgan, H.P., McNae,
I.W., Michels, P.A.M. & Walkinshaw,
M.D. 2011. Phosphoglycerate
mutase from Trypanosoma brucei is
hyperactivated by cobalt in vitro,
but not in vivo. Metallomics
3: 1310-1317.
Gohlke,
H., Hendlich, M. & Klebe,
G. 2000.
Knowledge-based scoring function to predict protein-ligand
interactions. J. Mol. Biol. 295: 337-356.
Golgher,
D., Vianna, C.H. & Moura, A.C. 2011. Drugs against
leishmaniasis: Overview of market needs and pipeline. Drug
Dev. Res. 72: 463-470.
Hann, M.M. & Oprea, T.I. 2004. Pursuing the leadlikeness concept in pharmaceutical
research. Curr. Opin. Chem. Biol. 8: 255-263.
Hawkins,
P.C.D., Skillman, A.G. & Nicholls, A. 2007. Comparison of shape-matching and docking as virtual screening tools.
J. Med. Chem. 50: 74-82.
Houston,
D.R. & Walkinshaw, M.D. 2013. Consensus docking: Improving the reliability
of docking in a virtual screening context. J. Chem. Inf. Model.
53: 384-390.
Hsin, K.Y., Morgan,
H.P., Shave, S.R., Hinton, A.C., Taylor, P. & Walkinshaw, M.D. 2011. EDULISS: A small-molecule database with data mining
and pharmacophore searching capabilities. Nucleic Acids Res.
39(Database issue): 1042- 1048.
Huey,
R., Morris, G.M., Olson, A.J. & Goodsell,
D.S. 2007.
A semi-empirical free energy force field with
charge-based desolvation. J. Comput.
Chem. 28: 1145-1152.
Jedrzejas,
M.J., Chander, M., Setlow,
P. & Krishnasamy, G. 2000. Structure and mechanism of action of a novel phosphoglycerate mutase
from Bacillus stearothermophilus.
EMBO J. 19: 1419-1431.
Li,
H., Robertson, A.D. & Jensen, J.H. 2005. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61: 704-721.
Lipinski,
C.A., Lombardo, F., Dominy, B.W. &
Feeney, P.J. 1997.
Experimental and computational approaches to estimate
solubility and permeability in drug discovery and development settings.
Adv. Drug Del. Rev. 23: 3-25.
Mercaldi,
G., Pereira, H., Cordeiro, A., Michels,
P.A.M. & Thiemann, O. 2012. Phosphoglycerate mutase from Trypanosoma
brucei: Structure and catalytic mechanism
FEBS J. 279: 2012-2021.
Messaoudi, B., Belguith, H. & Ben Hamida, J.
2013. Homology modelling and virtual screening approaches to identify
potent inhibitors of VEB-1 β-lactamase. Theor. Biol. Med. Modelling 10: 22. doi: 10.1186/1742-4682-10-22.
Naderer,
T., Ellis, M.A., Sernee, M.F., De Souza,
D.P., Curtis, J., Handman, E. & McConville,
M.J. 2006.
Virulence of Leishmania major
in macrophages and mice requires the gluconeogenic
enzyme fructose-1,6-bisphosphatase. Proc.
Natl. Acad. Sci. U.S.A. 103: 5502-5507.
Nowicki,
M.W., Kuaprasert, B., McNae,
I.W., Morgan, H.P., Harding, M.M., Michels,
P.A.M., Fothergill-Gilmore, L.A. & Walkinshaw, M.D. 2009. Crystal structures
of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism
and a new enzyme subclass. J. Mol. Biol. 394: 535-543.
Nukui,
M., Mello, L.V., Littlejohn, J.E., Setlow,
B., Setlow, P., Kim, K., Leighton, T. & Jedrzejas,
M.J. 2007.
Structure and molecular mechanism of Bacillus anthracis cofactor-independent
phosphoglycerate mutase: A crucial enzyme for spores and growing
cells of Bacillus species. Biophys. J.
92: 977-988.
O’Boyle,
N.M., Banck, M., James, C.A., Morley,
C., Vandermeersch, T. & Hutchison, G.R. 2011. Open Babel: An
open chemical toolbox. J. Cheminform.
3: 33.
Roychowdhury, A., Kundu, A., Rose, M., Gujar, A., Mukherjee, S. & Das, A.K.
2015. Complete catalytic cycle of cofactor-independent phosphoglycerate
mutase involves a spring-loaded mechanism. FEBS J. 282: 1097-1110.
Sauton,
N., Lagorce, D., Villoutreix,
B.O. & Miteva, M.A. 2008. MS-DOCK: Accurate
multiple conformation generator and rigid docking protocol for multi-step
virual ligand screening. BMC Bioinformatics 9: 184-196.
Shave, S., Blackburn, E.A., Adie,
J., Houston, D.R., Auer, M., Webster, S.P., Taylor, P. & Walkinshaw,
M.D. 2015. UFSRAT: Ultra-fast shape recognitions with atom types
– the discovery of novel bioactive small molecular scaffolds for
FKBP12 and 11bHSD1. PLoS ONE 10(2): e0116570.
Taylor, P., Blackburn, E., Sheng,
Y.G., Harding, S., Hsin, K-Y., Kan,
D., Shave, S. & Walkinshaw, M.D. 2008.
Ligand discovery and virtual screening using the program LIDAEUS.
British J. Pharm. 153: S55-S67.
Trott, O. & Olson,
A.J. 2010.
AutoDock Vina:
Improving the speed and accuracy of docking with a new scoring function,
efficient optimization, and multithreading. J. Comput.
Chem. 31: 455-461.
Verlinde, C.L.M.J., Hannaert, V., Blonski, C., Willson, M., Périé, J.J., Fothergill-Gilmore,
L.A., Opperdoes, F.R., Gelb, M.H., Hol,
W.G.J. & Michels, P.A.M. 2001.
Glycolysis as a target for the design of new anti-trypanosome drugs.
Drug Resist. Updat. 4: 50-65.
Wang, R., Lai, L. & Wang, S.
2002. Further development and validation of empirical
scoring functions for structure-based binding affinity prediction.
J. Comput. Aided Mol. Des. 16: 11-26.
Wang, R. & Wang, S. 2001. How
does consensus scoring work for virtual library screening? An
idealized computer experiment. J. Chem. Inf. Comput.
Sci. 41: 1422-1426.
WHO-NTD report. 2015. http://www.who.int/neglected_
diseases/9789241564861/en/.
*Pengarang
untuk surat-menyurat;
email: fazia_adyani@iium.edu.my
|