Multiple-targets Directed Screening of Flavonoid Compounds from Citrus Species to find out Antimalarial Lead with Predicted Mode of Action: An In Silico and Whole Cell-based In vitro Approach

Neelutpal       Gogoi; Dipak      Chetia; Bhaskarjyoti       Gogoi; Aparoop       Das

doi:10.2174/1573409916666191226103000

Abstract

Background: Development of resistance by the malaria parasite Plasmodium falciparum has created challenges in the eradication of this deadly infectious disease. Hence newer strategies are adopted to combat this disease and simultaneously, new lead/hit identification is going on worldwide to develop new chemotherapeutic agents against malaria.

Objective: In this study, 44 flavonoids found mainly in the fruit juice of Citrus species having traditional use in malaria-associated fever were selected for in silico multiple-target directed screening against three vital targets of the parasite namely dihydroorotate dehydrogenase (PfDHODH), dihydrofolate reductase thymidine synthase (PfDHFR-TS) and plasma membrane P-type cation translocating ATPase (PfATP4) to find out new lead molecule(s).

Methods: The in silico screening was carried out using different protocols of the Biovia Discovery Studio 2018 software and Network analyzer plugin of Cytoscape 3.6.0 followed by in vitro screening of the best lead.

Results: After screening, CF8 or luteolin was found to have good binding affinity against PfDHODH and PfATP4 with –CDocker energy 42.2719 and 33.1447 with respect to their cocrystal ligands. These findings were also supported by structure-based pharmacophore, DFT (Density Functional Theory) study and finally by in vitro screening of the lead with IC50 values of 8.23 μm and 12.41 μm against 3D7 (chloroquine-sensitive) and RKL-9 (chloroquine-resistant) strain of P. falciparum, respectively.

Conclusion: Our study found a moderately active lead molecule with the predicted mode of action which can be utilized to design some new derivatives with more safety and efficacy by targeting the two enzymes.

Keywords: Malaria, Plasmodium falciparum, Citrus species, in silico study, multiple-targets screening, antimalarial lead.

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[1] 
World Malaria Report, 2017. (Available from:. https://www.who.int/malaria/publications/world-malaria-report-2017/en/
[2] 
Warrell, D.A.; Hemingway, J.; Marsh, K.; Sinden, R.E.; Butcher, G.A.; Snow, R.W. Malaria; Oxford Textbook of Medicine, 2010. 
[3] 
Prugnolle, F.; Durand, P.; Ollomo, B.; Duval, L.; Ariey, F.; Arnathau, C.; Gonzalez, J.P.; Leroy, E.; Renaud, F. A fresh look at the origin of Plasmodium falciparum, the most malignant malaria agent. PLoS Pathog.,  2011, 7(2)e1001283
[http://dx.doi.org/10.1371/journal.ppat.1001283] [PMID:  21383971] 
[4] 
Shah, N.K.; Valecha, N. Antimalarial drug resistance. Recent Adv. in Malaria,  2016, 113(8), 383-407.
[http://dx.doi.org/10.1002/9781118493816.ch14] 
[5] 
Amato, R.; Pearson, R.D.; Almagro-Garcia, J.; Amaratunga, C.; Lim, P.; Suon, S.; Sreng, S.; Drury, E.; Stalker, J.; Miotto, O.; Fairhurst, R.M.; Kwiatkowski, D.P. Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study. Lancet Infect. Dis.,  2018, 18(3), 337-345.
[http://dx.doi.org/10.1016/S1473-3099(18)30068-9] [PMID:  29398391] 
[6] 
Phyo, A.P.; Nosten, F. The artemisinin resistance in southeast asia: an imminent global threat to malaria elimination; Towards Malaria Elimination - A Leap Forward, 2018. 
[http://dx.doi.org/10.5772/intechopen.76519] 
[7] 
Flannery, E.L.; Chatterjee, A.K.; Winzeler, E.A. Antimalarial drug discovery - approaches and progress towards new medicines. Nat. Rev. Microbiol.,  2013, 11(12), 849-862.
[http://dx.doi.org/10.1038/nrmicro3138] [PMID:  24217412] 
[8] 
Odugbemi, T.O.; Akinsulire, O.R.; Aibinu, I.E.; Fabeku, P.O. Medicinal plants useful for malaria therapy in Okeigbo, Ondo State, Southwest Nigeria. Afr. J. Tradit. Complement. Altern. Med.,  2006, 4(2), 191-198.
[PMID:  20162091] 
[9] 
Pierre, S.; Toua, V. Tchobsala; Fohouo, F.N.T.; Nloga, a M.N.; Messi, J. Medicinal plants used in traditional treatment of malaria in cameroon. J. Ecol. Nat. Environ.,  2011, 3(3), 104-117.
[10] 
Ruiz, L.; Ruiz, L.; Mac, O.M.; Cobos, M.; Gutierrez-Choquevilca, A.L.; Roumy, V. Plants used by native amazonian groups from the nanay river (peru) for the treatment of malaria. J. Ethnopharmacol.,  2011, 133(2), 917-921.
[http://dx.doi.org/10.1016/j.jep.2010.10.039] [PMID:  21040768] 
[11] 
Montanari, A.; Chen, J.; Widmer, W. Citrus flavonoids: a review of past biological activity against disease. Discovery of new flavonoids from Dancy tangerine cold pressed peel oil solids and leaves. Adv. Exp. Med. Biol.,  1998, 439, 103-116.
[http://dx.doi.org/10.1007/978-1-4615-5335-9_8] 
[12] 
Nogata, Y.; Sakamoto, K.; Shiratsuchi, H.; Ishii, T.; Yano, M.; Ohta, H. Flavonoid composition of fruit tissues of citrus species. Biosci. Biotechnol. Biochem.,  2006, 70(1), 178-192.
[http://dx.doi.org/10.1271/bbb.70.178] [PMID:  16428836] 
[13] 
Kaur, K.; Jain, M.; Kaur, T.; Jain, R. Antimalarials from nature. Bioorg. Med. Chem.,  2009, 17(9), 3229-3256.
[http://dx.doi.org/10.1016/j.bmc.2009.02.050] [PMID:  19299148] 
[14] 
Gattuso, G.; Barreca, D.; Gargiulli, C.; Leuzzi, U.; Caristi, C. Flavonoid composition of citrus juices. Molecules,  2007, 12(8), 1641-1673.
[http://dx.doi.org/10.3390/12081641] [PMID:  17960080] 
[15] 
Li, K.; Schurig-Briccio, L.A.; Feng, X.; Upadhyay, A.; Pujari, V.; Lechartier, B.; Fontes, F.L.; Yang, H.; Rao, G.; Zhu, W.; Gulati, A.; No, J.H.; Cintra, G.; Bogue, S.; Liu, Y.L.; Molohon, K.; Orlean, P.; Mitchell, D.A.; Freitas-Junior, L.; Ren, F.; Sun, H.; Jiang, T.; Li, Y.; Guo, R.T.; Cole, S.T.; Gennis, R.B.; Crick, D.C.; Oldfield, E. Multitarget drug discovery for tuberculosis and other infectious diseases. J. Med. Chem.,  2014, 57(7), 3126-3139.
[http://dx.doi.org/10.1021/jm500131s] [PMID:  24568559] 
[16] 
Talevi, A. Multi-target pharmacology: possibilities and limitations of the “skeleton key approach” from a medicinal chemist perspective. Front. Pharmacol.,  2015, 6(SEP), 205.
[http://dx.doi.org/10.3389/fphar.2015.00205] [PMID:  26441661] 
[17] 
Raphemot, R.; Lafuente-Monasterio, M.J.; Gamo-Benito, F.J.; Clardy, J.; Derbyshire, E.R. Discovery of dual-stage malaria inhibitors with new targets. Antimicrob. Agents Chemother.,  2015, 60(3), 1430-1437.
[http://dx.doi.org/10.1128/AAC.02110-15] [PMID:  26666931] 
[18] 
Ma, X.H.; Shi, Z.; Tan, C.; Jiang, Y.; Go, M.L.; Low, B.C.; Chen, Y.Z. In-silico approaches to multi-target drug discovery: computer aided multi-target drug design, multi-target virtual screening. Pharm. Res.,  2010, 27(5), 739-749.
[http://dx.doi.org/10.1007/s11095-010-0065-2] [PMID:  20221898] 
[19] 
Chaparro, M.J.; Calderón, F.; Castañeda, P.; Fernández-Alvaro, E.; Gabarró, R.; Gamo, F.J.; Gómez-Lorenzo, M.G.; Martín, J.; Fernández, E. Efforts aimed to reduce attrition in antimalarial drug discovery: a systematic evaluation of the current antimalarial targets portfolio. ACS Infect. Dis.,  2018, 4(4), 568-576.
[http://dx.doi.org/10.1021/acsinfecdis.7b00211] [PMID:  29320160] 
[20] 
Yuthavong, Y.; Tarnchompoo, B.; Vilaivan, T.; Chitnumsub, P.; Kamchonwongpaisan, S.; Charman, S.A.; McLennan, D.N.; White, K.L.; Vivas, L.; Bongard, E.; Thongphanchang, C.; Taweechai, S.; Vanichtanankul, J.; Rattanajak, R.; Arwon, U.; Fantauzzi, P.; Yuvaniyama, J.; Charman, W.N.; Matthews, D. Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target. Proc. Natl. Acad. Sci. USA,  2012, 109(42), 16823-16828.
[http://dx.doi.org/10.1073/pnas.1204556109] [PMID:  23035243] 
[21] 
Phillips, M.A.; Rathod, P.K. Plasmodium dihydroorotate dehydrogenase: a promising target for novel anti-malarial chemotherapy. Infect. Disord. Drug Targets,  2010, 10(3), 226-239.
[http://dx.doi.org/10.2174/187152610791163336] [PMID:  20334617] 
[22] 
Spillman, N.J.; Kirk, K. The malaria parasite cation ATPase PfATP4 and its role in the mechanism of action of a new arsenal of antimalarial drugs. Int. J. Parasitol. Drugs Drug Resist.,  2015, 5(3), 149-162.
[http://dx.doi.org/10.1016/j.ijpddr.2015.07.001] [PMID:  26401486] 
[23] 
Flannery, E.L.; McNamara, C.W.; Kim, S.W.; Kato, T.S.; Li, F.; Teng, C.H.; Gagaring, K.; Manary, M.J.; Barboa, R.; Meister, S.; Kuhen, K.; Vinetz, J.M.; Chatterjee, A.K.; Winzeler, E.A.; Spillman, N.J.; Kirk, K. Mutations in the P-type cation-transporter ATPase 4, PfATP4, mediate resistance to both aminopyrazole and spiroindolone antimalarials. ACS Chem. Biol.,  2015, 10(2), 413-420.
[http://dx.doi.org/10.1021/cb500616x] [PMID:  25322084] 
[24] 
Phillips, M.A.; White, K.L.; Kokkonda, S.; Deng, X.; White, J.; El Mazouni, F.; Marsh, K.; Tomchick, D.R.; Manjalanagara, K.; Rudra, K.R.; Wirjanata, G.; Noviyanti, R.; Price, R.N.; Marfurt, J.; Shackleford, D.M.; Chiu, F.C.K.; Campbell, M.; Jimenez-Diaz, M.B.; Bazaga, S.F.; Angulo-Barturen, I.; Martinez, M.S.; Lafuente-Monasterio, M.; Kaminsky, W.; Silue, K.; Zeeman, A.M.; Kocken, C.; Leroy, D.; Blasco, B.; Rossignol, E.; Rueckle, T.; Matthews, D.; Burrows, J.N.; Waterson, D.; Palmer, M.J.; Rathod, P.K.; Charman, S.A. A Triazolopyrimidine-based dihydroorotate dehydrogenase inhibitor with improved drug-like properties for treatment and prevention of malaria. ACS Infect. Dis.,  2016, 2(12), 945-957.
[http://dx.doi.org/10.1021/acsinfecdis.6b00144] [PMID:  27641613] 
[25] 
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic Acids Res.,  2000, 28(1), 235-242.
[http://dx.doi.org/10.1093/nar/28.1.235] [PMID:  10592235] 
[26] 
Jiménez-Díaz, M.B.; Ebert, D.; Salinas, Y.; Pradhan, A.; Lehane, A.M.; Myrand-Lapierre, M.E.; O’Loughlin, K.G.; Shackleford, D.M.; De Almeida, M.J.; Carrillo, A.K.; Clark, J.A.; Dennis, A.S.M.; Diep, J.; Deng, X.; Duffy, S.; Endsley, A.N.; Fedewa, G.; Guiguemde, W.A.; Gómez, M.G.; Holbrook, G.; Horst, J.; Kim, C.C.; Liu, J.; Lee, M.C.S.; Matheny, A. SantosMartínez, M.; Miller, G.; Rodríguez-Alejandre, A.; Sanz, L.; Sigal, M.; Spillman, N.J.; Stein, P.D.; Wang, Z.; Zhu, F.; Waterson, D.; Knapp, S.; Shelat, A.; Avery, V.M.; Fidock, D.A.; Gamo, F-J.; Charman, S.A.; Mirsalis, J.C.; Ma, H.; Ferrer, S.; Kirk, K.; Angulo-Barturen, I.; Kyle, D.E.; De Risi, J.L.; Floyd, D.M.; Guy, R.K. (+)-SJ733, a clinical candidate for malaria that acts through atp4 to induce rapid host-mediated clearance of plasmodium. Proc. Natl. Acad. Sci. USA,  2015, 112(42)E5764
[PMID:  26430239] 
[27] 
Jain, A.N. Bias, reporting, and sharing: computational evaluations of docking methods. J. Comput. Aided Mol. Des.,  2008, 22(3-4), 201-212.
[http://dx.doi.org/10.1007/s10822-007-9151-x] [PMID:  18075713] 
[28] 
Rao, S.N.; Head, M.S.; Kulkarni, A.; LaLonde, J.M. Validation studies of the site-directed docking program LibDock. J. Chem. Inf. Model.,  2007, 47(6), 2159-2171.
[http://dx.doi.org/10.1021/ci6004299] [PMID:  17985863] 
[29] 
Ramsay, R.R.; Popovic-Nikolic, M.R.; Nikolic, K.; Uliassi, E.; Bolognesi, M.L. A perspective on multi-target drug discovery and design for complex diseases. Clin. Transl. Med.,  2018, 7(1), 3.
[http://dx.doi.org/10.1186/s40169-017-0181-2] [PMID:  29340951] 
[30] 
Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res.,  2003, 13(11), 2498-2504.
[http://dx.doi.org/10.1101/gr.1239303] [PMID:  14597658] 
[31] 
Gogoi, B.; Gogoi, D.; Silla, Y.; Kakoti, B.B.; Bhau, B.S. Network pharmacology-based virtual screening of natural products from Clerodendrum species for identification of novel anti-cancer therapeutics. Mol. Biosyst.,  2017, 13(2), 406-416.
[http://dx.doi.org/10.1039/C6MB00807K] [PMID:  28070575] 
[32] 
Ponnan, P.; Gupta, S.; Chopra, M.; Tandon, R.; Baghel, A.S.; Gupta, G.; Prasad, A.K.; Rastogi, R.C.; Bose, M.; Raj, H.G. 2D-QSAR, docking studies, and in silico admet prediction of polyphenolic acetates as substrates for protein acetyltransferase function of glutamine synthetase of Mycobacterium tuberculosis. ISRN Struct. Biol.,  2013, 2013, 1-12.
[http://dx.doi.org/10.1155/2013/373516] 
[33] 
Dearden, J.C. In silico prediction of drug toxicity. J. Comput. Aided Mol. Des.,  2003, 17(2-4), 119-127.
[http://dx.doi.org/10.1023/A:1025361621494] [PMID:  13677480] 
[34] 
Wu, G.; Robertson, D.H.; Brooks, C.L., III; Vieth, M. Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J. Comput. Chem.,  2003, 24(13), 1549-1562.
[http://dx.doi.org/10.1002/jcc.10306] [PMID:  12925999] 
[35] 
Lin, C.H.; Chang, T.T.; Sun, M.F.; Chen, H.Y.; Tsai, F.J.; Chang, K.L.; Fisher, M.; Chen, C.Y.C. Potent inhibitor design against H1N1 swine influenza: structure-based and molecular dynamics analysis for M2 inhibitors from traditional Chinese medicine database. J. Biomol. Struct. Dyn.,  2011, 28(4), 471-482.
[http://dx.doi.org/10.1080/07391102.2011.10508589] [PMID:  21142218] 
[36] 
Rella, M.; Rushworth, C.A.; Guy, J.L.; Turner, A.J.; Langer, T.; Jackson, R.M. Structure-based pharmacophore design and virtual screening for novel angiotensin converting enzyme 2 inhibitors. J. Chem. Inf. Model.,  2006, 46(2), 708-716.
[http://dx.doi.org/10.1021/ci0503614] [PMID:  16563001] 
[37] 
Liao, H.S.; Liu, H.L.; Chen, W.H.; Ho, Y. Structure-Based pharmacophore modeling and virtual screening to identify novel inhibitors for anthrax lethal factor. Med. Chem. Res.,  2014, 23(8), 3725-3732.
[http://dx.doi.org/10.1007/s00044-014-0947-7] 
[38] 
Kaushik, P.; Khokra, S.L.; Rana, A.C.; Kaushik, D. 2014 Pharmacophore modeling and molecular docking studies on pinus roxburghii as a target for diabetes mellitus.Adv. Bioinformatics.,; 
[http://dx.doi.org/10.1155/2014/903246] 
[39] 
Greenwood, J.R.; Calkins, D.; Sullivan, A.P.; Shelley, J.C. Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. J. Comput. Aided Mol. Des.,  2010, 24(6-7), 591-604.
[http://dx.doi.org/10.1007/s10822-010-9349-1] [PMID:  20354892] 
[40] 
Tirado-Rives, J.; Jorgensen, W.L. Performance of B3LYP density functional methods for a large set of organic molecules. J. Chem. Theory Comput.,  2008, 4(2), 297-306.
[http://dx.doi.org/10.1021/ct700248k] [PMID:  26620661] 
[41] 
Zheng, Y.; Zheng, M.; Ling, X.; Liu, Y.; Xue, Y.; An, L.; Gu, N.; Ji, M. Design, synthesis, quantum chemical studies and biological activity evaluation of pyrazole-benzimidazole derivatives as potent Aurora A/B kinase inhibitors. Bioorg. Med. Chem. Lett.,  2013, 23(12), 3523-3530.
[http://dx.doi.org/10.1016/j.bmcl.2013.04.039] [PMID:  23664099] 
[42] 
Trager, W.; Jensen, J.B. Human malaria parasites in continuous culture. Science,  1976, 193(4254), 673-675.
[http://dx.doi.org/10.1126/science.781840] [PMID:  781840] 
[43] 
Kumawat, M.K.; Chetia, D. Synthesis, antimalarial activity evaluation and molecular docking studies of some novel dispiro-1,2,4,5-tetraoxanes. Bangladesh J. Pharmacol.,  2015, 10(4), 917-923.
[http://dx.doi.org/10.3329/bjp.v10i4.24532] 
[44] 
Lambros, C.; Vanderberg, J.P. Synchronization of Plasmodium falciparum erythrocytic stages in culture. J. Parasitol.,  1979, 65(3), 418-420.
[http://dx.doi.org/10.2307/3280287] [PMID:  383936] 
[45] 
Pandey, A.K.; Sharma, S.; Pandey, M.; Alam, M.M.; Shaquiquzzaman, M.; Akhter, M. 4, 5-Dihydrooxazole-pyrazoline hybrids: Synthesis and their evaluation as potential antimalarial agents. Eur. J. Med. Chem.,  2016, 123, 476-486.
[http://dx.doi.org/10.1016/j.ejmech.2016.07.055] [PMID:  27494165] 
[46] 
Teke, G.N.; Kuete, V. Acute and subacute toxicities of african
 medicinal plants. Toxicol. Sur. African Med. Plants, 2014, 63-98.. 
[http://dx.doi.org/10.1016/B978-0-12-800018-2.00005-4] 
[47] 
Lehane, A.M.; Saliba, K.J. Common dietary flavonoids inhibit the growth of the intraerythrocytic malaria parasite. BMC Res. Notes,  2008, 1, 26.
[http://dx.doi.org/10.1186/1756-0500-1-26] [PMID:  18710482] 

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DOI https://dx.doi.org/10.2174/1573409916666191226103000	Print ISSN 1573-4099
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Multiple-targets Directed Screening of Flavonoid Compounds from Citrus Species to find out Antimalarial Lead with Predicted Mode of Action: An In Silico and Whole Cell-based In vitro Approach

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