Recent Advances in System Based Study for Anti-Malarial Drug Development Process

Author(s): Brijesh S. Yadav*, Navaneet Chaturvedi, Ninoslav Marina.

Journal Name: Current Pharmaceutical Design

Volume 25 , Issue 31 , 2019

Abstract:

Background: Presently, malaria is one of the most prevalent and deadly infectious disease across Africa, Asia, and America that has now started to spread in Europe. Despite large research being carried out in the field, still, there is a lack of efficient anti-malarial therapeutics. In this paper, we highlight the increasing efforts that are urgently needed towards the development and discovery of potential antimalarial drugs, which must be safe and affordable. The new drugs thus mentioned are also able to counter the spread of malaria parasites that have been resistant to the existing agents.

Objective: The main objective of the review is to highlight the recent development in the use of system biologybased approaches towards the design and discovery of novel anti-malarial inhibitors.

Method: A huge literature survey was performed to gain advance knowledge about the global persistence of malaria, its available treatment and shortcomings of the available inhibitors. Literature search and depth analysis were also done to gain insight into the use of system biology in drug discovery and how this approach could be utilized towards the development of the novel anti-malarial drug.

Results: The system-based analysis has made easy to understand large scale sequencing data, find candidate genes expression during malaria disease progression further design of drug molecules those are complementary of the target proteins in term of shape and configuration.

Conclusion: The review article focused on the recent computational advances in new generation sequencing, molecular modeling, and docking related to malaria disease and utilization of the modern system and network biology approach to antimalarial potential drug discovery and development.

Keywords: Antimalarial, plasmodium species, system biology, NGS (New Generation Sequencing), molecular docking, networking, drug discovery.

[1]
World Malaria Report 2018.. https://www.who.int/malaria/publications/world-malaria-report-2018/en/ Accessed 27 Nov 2018
[2]
Tse EG, Korsik M, Todd MH. The past, present and future of anti-malarial medicines. Malar J 2019; 18(1): 93.
[http://dx.doi.org/10.1186/s12936-019-2724-z] [PMID: 30902052]
[3]
Yadav BS, Tripathi V. Recent advances in the system biology-based target identification and drug discovery. Curr Top Med Chem 2018; 18(20): 1737-44.
[http://dx.doi.org/10.2174/1568026618666181025112344]
[4]
Shanks GD, Edstein MD, Jacobus D. Evolution from double to triple-antimalarial drug combinations. Trans R Soc Trop Med Hyg 2015; 109(3): 182-8.
[http://dx.doi.org/10.1093/trstmh/tru199] [PMID: 25549631]
[5]
Mishra M, Mishra VK, Kashaw V, Iyer AK, Kashaw SK. Comprehensive review on various strategies for antimalarial drug discovery. Eur J Med Chem 2017; 125: 1300-20.
[http://dx.doi.org/10.1016/j.ejmech.2016.11.025] [PMID: 27886547]
[6]
Phillips MA, Burrows JN, Manyando C, van Huijsduijnen RH, Van Voorhis WC, Wells TNC. Malaria. Nat Rev Dis Primers 2017; 3: 17050.
[http://dx.doi.org/10.1038/nrdp.2017.50] [PMID: 28770814]
[7]
Okombo J, Chibale K. Recent updates in the discovery and development of novel antimalarial drug candidates. MedChemComm 2018; 9(3): 437-53.
[http://dx.doi.org/10.1039/C7MD00637C] [PMID: 30108934]
[8]
Ashley EA, Phyo AP. Drugs in development for malaria. Drugs 2018; 78(9): 861-79.
[http://dx.doi.org/10.1007/s40265-018-0911-9] [PMID: 29802605]
[9]
Cortopassi WA, Celmar Costa Franca T, Krettli AU. A systems biology approach to antimalarial drug discovery. Expert Opin Drug Discov 2018; 13(7): 617-26.
[http://dx.doi.org/10.1080/17460441.2018.1471056] [PMID: 29737894]
[10]
Mace KE, Arguin PM, Tan KR. Malaria surveillance - United States, 2015. MMWR Surveill Summ 2018; 67(7): 1-28.
[http://dx.doi.org/10.15585/mmwr.ss6707a1] [PMID: 29723168]
[11]
Gerstenlauer C. Recognition and management of malaria. Nurs Clin North Am 2019; 54(2): 245-60.
[http://dx.doi.org/10.1016/j.cnur.2019.02.010]
[12]
WHO World malaria report. Geneva: World Health Organization 2018.
[13]
Gardner MJ, Hall N, Fung E, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002; 419(6906): 498-511.
[http://dx.doi.org/10.1038/nature01097] [PMID: 12368864]
[14]
Nair S, Nkhoma SC, Serre D, et al. Single-cell genomics for dissection of complex malaria infections. Genome Res 2014; 24(6): 1028-38.
[http://dx.doi.org/10.1101/gr.168286.113] [PMID: 24812326]
[15]
Pizzi E, Frontali C. Low-complexity regions in Plasmodium falciparum proteins. Genome Res 2001; 11(2): 218-29.
[16]
Bailey JA, Mvalo T, Aragam N, et al. Use of massively parallel pyrosequencing to evaluate the diversity of and selection on Plasmodium falciparum csp T-cell epitopes in Lilongwe, Malawi. J Infect Dis 2012; 206(4): 580-7.
[http://dx.doi.org/10.1093/infdis/jis329] [PMID: 22551816]
[17]
Mideo N, Kennedy DA, Carlton JM, Bailey JA, Juliano JJ, Read AF. Ahead of the curve: next generation estimators of drug resistance in malaria infections. Trends Parasitol 2013; 29(7): 321-8.
[http://dx.doi.org/10.1016/j.pt.2013.05.004] [PMID: 23746748]
[18]
Lin JT, Hathaway NJ, Saunders DL, et al. Using amplicon deep sequencing to detect genetic signatures of Plasmodium vivax relapse. J Infect Dis 2015; 212(6): 999-1008.
[http://dx.doi.org/10.1093/infdis/jiv142] [PMID: 25748326]
[19]
Rao PN, Uplekar S, Kayal S, et al. A method for amplicon deep sequencing of drug resistance genes in Plasmodium falciparum clinical isolates from India. J Clin Microbiol 2016; 54(6): 1500-11.
[http://dx.doi.org/10.1128/JCM.00235-16] [PMID: 27008882]
[20]
Flannery EL, Wang T, Akbari A, et al. Next-generation sequencing of Plasmodium vivax patient samples shows evidence of direct evolution in drug-resistance genes. ACS Infect Dis 2015; 1(8): 367-79.
[http://dx.doi.org/10.1021/acsinfecdis.5b00049] [PMID: 26719854]
[21]
Auer PL, Johnsen JM, Johnson AD, et al. Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. Am J Hum Genet 2012; 91(5): 794-808.
[http://dx.doi.org/10.1016/j.ajhg.2012.08.031] [PMID: 23103231]
[22]
Van Tyne D, Tan Y, Daily JP, et al. Plasmodium falciparum gene expression measured directly from tissue during human infection. Genome Med 2014; 6(11): 110.
[23]
Oyola SO, Ariani CV, Hamilton WL, et al. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malar J 2016; 15(1): 597.
[http://dx.doi.org/10.1186/s12936-016-1641-7] [PMID: 27998271]
[24]
Nag S, Kofoed PE, Ursing J, et al. Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots. Malar J 2018; 17(1): 91.
[http://dx.doi.org/10.1186/s12936-018-2232-6] [PMID: 29471822]
[25]
von Wülfingen BB. Biology and the systems view. Is there a move towards systems approaches in the life sciences? EMBO Rep 2009; 10(Suppl. 1): S37-41.
[http://dx.doi.org/10.1038/embor.2009.124] [PMID: 19636302]
[26]
Bardini R, Politano G, Benso A, Di Carlo S. Multi-level and hybrid modelling approaches for systems biology. Comput Struct Biotechnol J 2017; 15(15): 396-402.
[http://dx.doi.org/10.1016/j.csbj.2017.07.005] [PMID: 28855977]
[27]
Azmi AS, Wang Z, Philip PA, Mohammad RM, Sarkar FH. Proof of concept: network and systems biology approaches aid in the discovery of potent anticancer drug combinations. Mol Cancer Ther 2010; 9(12): 3137-44.
[http://dx.doi.org/10.1158/1535-7163.MCT-10-0642] [PMID: 21041384]
[28]
Altaf-Ul-Amin M, Afendi FM, Kiboi SK, Kanaya S. Systems biology in the context of big data and networks. BioMed Res Int 2014; 2014 428570
[http://dx.doi.org/10.1155/2014/428570] [PMID: 24982882]
[29]
Barabási AL, Oltvai ZN. Network biology: understanding the cell’s functional organization. Nat Rev Genet 2004; 5(2): 101-13.
[http://dx.doi.org/10.1038/nrg1272] [PMID: 14735121]
[30]
Menche J, Sharma A, Kitsak M, et al. Disease networks. Uncovering disease-disease relationships through the incomplete interactome. Science 2015; 347(6224) 1257601
[http://dx.doi.org/10.1126/science.1257601] [PMID: 25700523]
[31]
Cheng F, Kovács IA, Barabási AL. Publisher Correction: Network-based prediction of drug combinations. Nat Commun 1806; 10(1): 1806.
[32]
Noble D. Computational models of the heart and their use in assessing the actions of drugs. J Pharmacol Sci 2008; 107(2): 107-17.
[http://dx.doi.org/10.1254/jphs.CR0070042] [PMID: 18566519]
[33]
Schoeberl B, Kudla A, Masson K, et al. Systems biology driving drug development: from design to the clinical testing of the anti-ErbB3 antibody seribantumab (MM-121). NPJ Syst Biol Appl 2017; 3: 16034.
[http://dx.doi.org/10.1038/npjsba.2016.34] [PMID: 28725482]
[34]
Jamal S, Periwal V, Scaria V. Open Source Drug Discovery Consortium. Predictive modeling of anti-malarial molecules inhibiting apicoplast formation. BMC Bioinformatics 2013; 14(1): 55.
[http://dx.doi.org/10.1186/1471-2105-14-55] [PMID: 23419172]
[35]
Pradhan A, Siwo GH, Singh N, et al. Chemogenomic profiling of Plasmodium falciparum as a tool to aid antimalarial drug discovery. Sci Rep 2015; 6: 15930.
[36]
Kazmin D, Nakaya HI, Lee EK, et al. Systems analysis of protective immune responses to RTSS malaria vaccination in humans. Proc Natl Acad Sci USA 2017; 114(9): 2425-30.
[http://dx.doi.org/10.1073/pnas.1621489114] [PMID: 28193898]
[37]
LaMonte GM, Almaliti J, Bibo-Verdugo B, et al. Development of a potent inhibitor of the Plasmodium proteasome with reduced mammalian toxicity. J Med Chem 2017; 60(15): 6721-32.
[http://dx.doi.org/10.1021/acs.jmedchem.7b00671] [PMID: 28696697]
[38]
Klonis N, Crespo-Ortiz MP, Bottova I, et al. Artemisinin activity against Plasmodium falciparum requires hemoglobin uptake and digestion. Proc Natl Acad Sci USA 2011; 108(28): 11405-10.
[39]
Goodman CD, Su V, McFadden GI. The effects of anti-bacterials on the malaria parasite Plasmodium falciparum. Mol Biochem Parasitol 2007; 152(2): 181-91.
[http://dx.doi.org/10.1016/j.molbiopara.2007.01.005] [PMID: 17289168]
[40]
Wilson DW, Goodman CD, Sleebs BE, et al. Macrolides rapidly inhibit red blood cell invasion by the human malaria parasite, Plasmodium falciparum. BMC Biol 2015; 13(1): 52.
[http://dx.doi.org/10.1186/s12915-015-0162-0] [PMID: 26187647]
[41]
Sanasam BD, Kumar S. PRE-binding protein of Plasmodium falciparum is a potential candidate for vaccine design and development: An in silico evaluation of the hypothesis. Med Hypotheses 2019; 125(125): 119-23.
[http://dx.doi.org/10.1016/j.mehy.2019.01.006] [PMID: 30902138]
[42]
Kumari M, Chandra S, Tiwari N, Subbarao N. 3D QSAR, pharmacophore and molecular docking studies of known inhibitors and designing of novel inhibitors for M18 aspartyl aminopeptidase of Plasmodium falciparum. BMC Struct Biol 2016; 16(1): 12.
[http://dx.doi.org/10.1186/s12900-016-0063-7] [PMID: 27534744]
[43]
WHO World Malaria Report. Geneva: World Health Organization 2017.
[44]
Sullivan DJ, Liu Y, Mott BT, Kaludov N, Martinov MN. Discovery of novel liver-stage antimalarials through quantum similarity. PLoS One 2015; 10(5) e0125593
[http://dx.doi.org/10.1371/journal.pone.0125593] [PMID: 25951139]
[45]
Oyelade J, Isewon I. Uwoghiren EAromolaran O, Oladipupo O. In silico knockout screening of Plasmodium falciparum reactions and prediction of novel essential reactions by analysing the metabolic network. BioMed Res Int 2018; 2018 8985718
[46]
Rout S, Mahapatra RK. In silico study of M18 aspartyl amino peptidase (M18AAP) of Plasmodium vivax as an antimalarial drug target. Bioorg Med Chem 2019; 27(12): 2553-71.
[47]
Bass C, Jones CM. Mosquitoes boost body armor to resist insecticide attack. Proc Natl Acad Sci USA 2016; 113(33): 9145-7.
[http://dx.doi.org/10.1073/pnas.1610992113] [PMID: 27496323]
[48]
Alout H, Yameogo B, Djogbénou LS, et al. Interplay between Plasmodium infection and resistance to insecticides in vector mosquitoes. J Infect Dis 2014; 210(9): 1464-70.
[http://dx.doi.org/10.1093/infdis/jiu276] [PMID: 24829465]
[49]
Tun KM, Imwong M, Lwin KM, et al. Spread of artemisinin-resistant Plasmodium falciparum in Myanmar: a cross-sectional survey of the K13 molecular marker. Lancet Infect Dis 2015; 15(4): 415-21.
[http://dx.doi.org/10.1016/S1473-3099(15)70032-0] [PMID: 25704894]
[50]
Musyoka TM, Njuguna JN, Tastan Bishop Ö. Comparing sequence and structure of falcipains and human homologs at prodomain and catalytic active site for malarial peptide based inhibitor design. Malar J 2019; 18(1): 159.
[http://dx.doi.org/10.1186/s12936-019-2790-2] [PMID: 31053072]
[51]
Kalani K, Agarwal J, Alam S, Khan F, Pal A, Srivastava SK. In silico and in vivo anti-malarial studies of 18β glycyrrhetinic acid from Glycyrrhiza glabra. PLoS One 2013; 8(9) e74761
[http://dx.doi.org/10.1371/journal.pone.0074761] [PMID: 24086367]
[52]
Corey VC, Lukens AK, Istvan ES, et al. A broad analysis of resistance development in the malaria parasite. Nat Commun 2016; 15: 11901.
[http://dx.doi.org/10.1038/ncomms11901]
[53]
Sinha S, Singh A, Medhi B, Sehgal R. Systematic review: insight into antimalarial peptide. Int J Pept Res Ther 2016; 22(3): 325-40.
[http://dx.doi.org/10.1007/s10989-016-9512-1]
[54]
Lau JL, Dunn MK. Therapeutic peptides: Historical perspectives, current development trends, and future directions. Bioorg Med Chem 2018; 26(10): 2700-7.
[55]
Haney EF, Straus SK, Hancock RE. Reassessing the host defense peptide landscape. Front Chem 2019; 7.
[56]
Di L. Strategic approaches to optimizing peptide ADME properties. AAPS J 2015; 17(1): 134-43.
[http://dx.doi.org/10.1208/s12248-014-9687-3]
[57]
Hansch C, Kurup A, Garg R, Gao H. Chem-bioinformatics and QSAR: a review of QSAR lacking positive hydrophobic terms. Chem Rev 2001; 101(3): 619-72.
[http://dx.doi.org/10.1021/cr0000067] [PMID: 11712499]
[58]
Parihar N, Nandi S. In-silico combinatorial design and pharmacophore modeling of potent antimalarial 4-anilinoquinolines utilizing QSAR and computed descriptors. Springerplus 2015; 4(1): 819.
[http://dx.doi.org/10.1186/s40064-015-1593-3] [PMID: 29021931]
[59]
Masand VH, Toropov AA, Toropova AP, Mahajan DT. QSAR models for anti-malarial activity of 4-aminoquinolines. Curr Comput Aided Drug Des 2014; 10(1): 75-82.
[http://dx.doi.org/10.2174/1573409910666140303114621] [PMID: 24801104]
[60]
Sahu NK, Sharma MC, Mourya V, Kohli DV. QSAR studies of some side chain modified 7-chloro-4-aminoquinolines as antimalarial agents. Arab J Chem 2014; 7(5): 701-7.
[http://dx.doi.org/10.1016/j.arabjc.2010.12.005]
[61]
Hadni H, Mazigh M, Charif EM, Bouayad A, Elhallaoui M. Molecular modeling of antimalarial agents by 3D-QSAR study and molecular docking of two hybrids 4-aminoquinoline-1, 3, 5-triazine and 4-aminoquinoline-oxalamide derivatives with the receptor protein in its both wild and mutant types. Biochem Res Int 2018; 2018 8639173
[62]
Lima MNN, Melo-Filho CC, Cassiano GC, et al. QSAR-driven design and discovery of novel compounds with antiplasmodial and transmission blocking activities. Front Pharmacol 2018; 9: 146.
[http://dx.doi.org/10.3389/fphar.2018.00146] [PMID: 29559909]
[63]
Salawu EO. In silico study reveals how E64 approaches, binds to, and inhibits falcipain-2 of Plasmodium falciparum that causes malaria in humans. Sci Rep 2018; 8(1): 16380.
[http://dx.doi.org/10.1038/s41598-018-34622-1] [PMID: 30401806]
[64]
Penna-Coutinho J, Cortopassi WA, Oliveira AA, França TC, Krettli AU. Antimalarial activity of potential inhibitors of Plasmodium falciparum lactate dehydrogenase enzyme selected by docking studies. PLoS One 2011; 6(7) e21237
[http://dx.doi.org/10.1371/journal.pone.0021237] [PMID: 21779323]
[65]
Roy KK, Bhunia SS, Saxena AK. CoMFA, CoMSIA, and docking studies on thiolactone-class of potent anti-malarials: identification of essential structural features modulating anti-malarial activity. Chem Biol Drug Des 2011; 78(3): 483-93.
[http://dx.doi.org/10.1111/j.1747-0285.2011.01158.x] [PMID: 21672165]
[66]
Qidwai T, Yadav DK, Khan F, Dhawan S, Bhakuni RS. QSAR, docking and ADMET studies of artemisinin derivatives for antimalarial activity targeting plasmepsin II, a hemoglobin-degrading enzyme from P. falciparum. Curr Pharm Des 2012; 18(37): 6133-54.
[http://dx.doi.org/10.2174/138161212803582397] [PMID: 22670592]
[67]
Burrows JN, Duparc S, Gutteridge WE, et al. New developments in anti-malarial target candidate and product profiles. Malar J 2017; 16(1): 26.
[http://dx.doi.org/10.1186/s12936-016-1675-x] [PMID: 28086874]
[68]
Burns AL, Dans MG, Balbin JM, et al. Targeting malaria parasite invasion of red blood cells as an antimalarial strategy. FEMS Microbiol Rev 2019; 43(3): 223-38.
[http://dx.doi.org/10.1093/femsre/fuz005] [PMID: 30753425]
[69]
Baragaña B, Hallyburton I, Lee MCS, et al. A novel multiple-stage antimalarial agent that inhibits protein synthesis. Nature 2015; 522(7556): 315-20.
[http://dx.doi.org/10.1038/nature14451] [PMID: 26085270]
[70]
Baragaña B, Norcross NR, Wilson C, et al. Discovery of a quinoline-4-carboxamide derivative with a novel mechanism of action, multistage antimalarial activity, and potent in vivo efficacy. J Med Chem 2016; 59(21): 9672-85.
[http://dx.doi.org/10.1021/acs.jmedchem.6b00723] [PMID: 27631715]
[71]
Burrows JN, van Huijsduijnen RH, Möhrle JJ, Oeuvray C, Wells TN. Designing the next generation of medicines for malaria control and eradication. Malar J 2013; 12: 187.
[http://dx.doi.org/10.1186/1475-2875-12-187] [PMID: 23742293]
[72]
Hameed PS, Solapure S, Patil V, et al. Triaminopyrimidine is a fast-killing and long-acting antimalarial clinical candidate. Nat Commun 2015; 6: 6715.
[http://dx.doi.org/10.1038/ncomms7715] [PMID: 25823686]
[73]
MMV and Zydus join forces to develop new antimalarial 2017.. https://www.mmv.org/newsroom/press-releases/mmv-and-zydus-join-forces-develop-new Accessed 2018
[74]
Le Manach C, Nchinda AT, Paquet T, et al. Identification of a potential antimalarial drug candidate from a series of 2-aminopyrazines by optimization of aqueous solubility and potency across the parasite life cycle. J Med Chem 2016; 59(21): 9890-905.
[http://dx.doi.org/10.1021/acs.jmedchem.6b01265] [PMID: 27748596]
[75]
Younis Y, Douelle F, Feng TS, et al. 3,5-Diaryl-2-aminopyridines as a novel class of orally active antimalarials demonstrating single dose cure in mice and clinical candidate potential. J Med Chem 2012; 55(7): 3479-87.
[http://dx.doi.org/10.1021/jm3001373] [PMID: 22390538]
[76]
Luth MR, Gupta P, Ottilie S, Winzeler EA. Using in vitro evolution and whole genome analysis to discover next generation targets for antimalarial drug discovery. ACS Infect Dis 2018; 4(3): 301-14.
[http://dx.doi.org/10.1021/acsinfecdis.7b00276] [PMID: 29451780]
[77]
IUPHAR/MMV Guide to Malaria Pharmacology Project.. pharmacology.org/ Accessed 14 Jan 2019


Rights & PermissionsPrintExport Cite as


Article Details

VOLUME: 25
ISSUE: 31
Year: 2019
Page: [3367 - 3377]
Pages: 11
DOI: 10.2174/1381612825666190902162105
Price: $65

Article Metrics

PDF: 16
HTML: 3