Virtual Screening, Molecular Modelling and Biochemical Studies to Exploit PF14_0660 as a Target to Identify Novel Anti-malarials

Author(s): Vimee Raturi, Kumar Abhishek, Subhashis Jana, Subhendu Sekhar Bag, Vishal Trivedi*.

Journal Name: Letters in Drug Design & Discovery

Volume 16 , Issue 4 , 2019

Submit Manuscript
Submit Proposal

Graphical Abstract:


Abstract:

Background: Malaria Parasite relies heavily on signal transduction pathways to control growth, the progression of the life cycle and sustaining stress for its survival. Unlike kinases, Plasmodium's phosphatome is one of the smallest and least explored for identifying drug target for clinical intervention. PF14_0660 is a putative protein present on the chromosome 14 of Plasmodium falciparum genome.

Methods: Multiple sequence alignment of PF14_0660 with other known protein phosphatase indicate the presence of phosphatase motif with specific residues essential for metal binding, catalysis and providing structural stability. PF14_0660 is a mixed α/β type of protein with several β -sheet and α-helix arranged to form βαβαβα sub-structure. The surface properties of PF14_0660 is conserved with another phosphate of this family, but it profoundly diverges from the host protein tyrosine phosphatase. PF14_0660 was cloned, over-expressed and protein is exhibiting phosphatase activity in a dose-dependent manner. Docking of Heterocyclic compounds from chemical libraries into the PF14_0660 active site found nice fitting of several candidate molecules.

Results: Compound PPinh6, PPinh 7 and PPinh 5 are exhibiting antimalarial activity with an IC50 of 1.4 ± 0.2µM, 3.8 ± 0.3 µM and 9.4 ± 0.6µM respectively. Compound PPinh 6 and PPinh 7 are inhibiting intracellular PF14_0660 phosphatase activity and killing parasite through the generation of reactive oxygen species.

Conclusion: Hence, a combination of molecular modelling, virtual screening and biochemical study allowed us to explore the potentials of PF14_0660 as a drug target to design anti-malarials.

Keywords: Plasmodium falciparum, phosphatase activity, molecular modelling, virtual screening, anti-malarials, tyrosine phosphatase.

[1]
Organization, W.H. World malaria report 2015.2016;
[2]
Parija, S.; Praharaj, I. Drug resistance in malaria. Indian J. Med. Microbiol., 2011, 29(3), 243.
[3]
Mukherjee, A.; Sadhukhan, G.C. Anti-malarial Drug Design by Targeting Apicoplasts: New Perspectives. J. Pharm. , 2016, 19(1), 7.
[4]
Imwong, M. Novel point mutations in the dihydrofolate reductase gene of Plasmodium vivax: Evidence for sequential selection by drug pressure. Antimicrob. Agents Chemother., 2003, 47(5), 1514-1521.
[5]
Alam, A. Novel antimalarial drug targets: hope for new antimalarial drugs. Expert Rev. Clin. Pharmacol., 2009, 2(5), 469-489.
[6]
Dua, V.K.; Dev, V.; Phookan, S.; Gupta, N.C.; Sharma, V.P.; Subbarao, S.K. Multi-drug resistant Plasmodium falciparum malaria in Assam, India: Timing of recurrence and anti-malarial drug concentrations in whole blood. Am. J. Trop. Med. Hyg., 2003, 69(5), 555-557.
[7]
Nosten, F.; White, N.J. Artemisinin-based combination treatment of falciparum malaria. Am. J. Tropic. Med. Hygiene., 2007, 77(6_Suppl), 181-192.
[8]
Hayton, K.; Su, X-Z. Drug resistance and genetic mapping in Plasmodium falciparum. Curr. Genet., 2008, 54(5), 223-239.
[9]
Botté, C.Y. Atypical lipid composition in the purified relict plastid (apicoplast) of malaria parasites. Proc. Natl. Acad. Sci. USA, 2013, 110(18), 7506-7511.
[10]
MacRae, J.; Maréchal, E.; Biot, C.; Botté, C.Y. The apicoplast: a key target to cure malaria. Curr. Pharm. Des., 2012, 18(24), 3490-3504.
[11]
Collins, C.R.; Hackett, F.; Strath, M.; Penzo, M.; Withers-Martinez, C.; Baker, D.A.; Blackman, M.J. Malaria parasite cGMP-dependent protein kinase regulates blood stage merozoite secretory organelle discharge and egress. PLoS Pathog., 2013, 9(5), e1003344.
[12]
Wilkes, J.M.; Doerig, C. The protein-phosphatome of the human malaria parasite Plasmodium falciparum. BMC Genomics, 2008, 9(1), 412.
[13]
Pandey, R. Genome wide in silico analysis of Plasmodium falciparum phosphatome. BMC Genomics, 2014, 15(1), 1024.
[14]
Bajsa, J.; Duke, S.O.; Tekwani, B.L. Plasmodium falciparum serine/threonine phoshoprotein phosphatases (PPP): From housekeeper to the ‘holy grail’. Curr. Drug Targets, 2008, 9(11), 997-1012.
[15]
Moorhead, G.B.; Trinkle-Mulcahy, L.; Ulke-Lemée, A. Emerging roles of nuclear protein phosphatases. Nat. Rev. Mol. Cell Biol., 2007, 8(3), 234-244.
[16]
Andreeva, A.V. Kutuzov, M.A. PPP family of protein Ser/Thr phosphatases: two distinct branches? Mol. Biol. Evol., 2001, 18(3), 448-452.
[17]
Shi, Y. Serine/threonine phosphatases: Mechanism through structure. Cell, 2009, 139(3), 468-484.
[18]
Patzewitz, E-M.; Guttery, D.S.; Poulin, B.; Ramakrishnan, C.; Ferguson, D.J.; Wall, R.J.; Brady, D.; Holder, A.A.; Szöőr, B.; Tewari, R. An ancient protein phosphatase, SHLP1, is critical to microneme development in Plasmodium ookinetes and parasite transmission. Cell Reports, 2013, 3(3), 622-629.
[19]
Tsuruta, H.; Mikami, B.; Aizono, Y. Crystal structure of cold-active protein-tyrosine phosphatase from a psychrophile. Shewanella sp. J. Biochem., 2005, 137(1), 69-77.
[20]
Kuntal, B.K.; Aparoy, P.; Reddanna, P. EasyModeller: A graphical interface to MODELLER. BMC Res. Notes, 2010, 3, 226.
[21]
Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol., 1963, 7, 95-99.
[22]
Zhang, Z.; Li, Y.; Lin, B.; Schroeder, M.; Huang, B. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics, 2011, 27(15), 2083-2088.
[23]
Morris, G.M. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem., 2009, 30(16), 2785-2791.
[24]
Bag, S.S.; Jana, S.; Pradhan, M.K. Synthesis, photophysical properties of triazolyl-donor/acceptor chromophores decorated unnatural amino acids: Incorporation of a pair into Leu-enkephalin peptide and application of triazolylperylene amino acid in sensing BSA. Bioorg. Med. Chem., 2016, 24(16), 3579-3595.
[25]
Trivedi, V. Purification and biochemical characterization of a heme containing peroxidase from the human parasite. P. falciparum. Protein Expr. Purif., 2005, 41(1), 154-161.
[26]
Trivedi, V.; Chand, P.; Srivastava, K.; Puri, S.K.; Maulik, P.R.; Bandyopadhyay, U. Clotrimazole inhibits hemoperoxidase of Plasmodium falciparum and induces oxidative stress. Proposed antimalarial mechanism of clotrimazole. J. Biol. Chem., 2005, 280(50), 41129-41136.
[27]
Johnson, J.D.; Richard, A.D.; Lucia, G.; Miriam, L-S.; Norma, E.R.; Norman, C.W. Assessment and continued validation of the malaria SYBR green I-based fluorescence assay for use in malaria drug screening. Antimicrob. Agents Chemother., 2007, 51(6), 1926-1933.
[28]
Voegtli, W.C.; White, D.J.; Reiter, N.J.; Rusnak, F.; Rosenzweig, A.C. Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes. Biochemistry, 2000, 39(50), 15365-15374.
[29]
Rusnak, F.; Mertz, P. Calcineurin: Form and function. Physiol. Rev., 2000, 80(4), 1483-1521.
[30]
Rusnak, F. Manganese-activated phosphatases. Met. Ions Biol. Syst., 2000, 37, 305-343.
[31]
Klabunde, T. Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures. J. Mol. Biol., 1996, 259(4), 737-748.
[32]
Gibbons, J.A.; Weiser, D.C.; Shenolikar, S. Importance of a surface hydrophobic pocket on protein phosphatase-1 catalytic subunit in recognizing cellular regulators. J. Biol. Chem., 2005, 280(16), 15903-15911.
[33]
Gunjan, S.; Singh, S.K.; Sharma, T.; Dwivedi, H.; Chauhan, B.S.; Imran, S.M.; Tripathi, R. Mefloquine induces ROS mediated programmed cell death in malaria parasite: Plasmodium. Apoptosis, 2016, 21(9), 955-964.
[34]
Becker, K.; Tilley, L.; Vennerstrom, J.L.; Roberts, D.; Rogerson, S.; Ginsburg, H. Oxidative stress in malaria parasite-infected erythrocytes: host-parasite interactions. Int. J. Parasitol., 2004, 34(2), 163-189.
[35]
Wallace, A.C.; Laskowski, R.A.; Thornton, J.M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. Des. Sel., 1995, 8(2), 127-134.


Rights & PermissionsPrintExport Cite as


Article Details

VOLUME: 16
ISSUE: 4
Year: 2019
Page: [417 - 426]
Pages: 10
DOI: 10.2174/1570180815666180727121200
Price: $58

Article Metrics

PDF: 19
HTML: 1