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Letters in Drug Design & Discovery

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ISSN (Print): 1570-1808
ISSN (Online): 1875-628X

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Research Article

Identification of Putative “Multifunctional Drug” Against Anthrax Toxins via Integrative Computational Approach

Author(s): Nousheen Bibi*, Sehraiz Razzaq, Faisal Nouroz, Farhat Amin, Ambreen Shahnaz and Mohammad Amjad Kamal

Volume 17, Issue 12, 2020

Page: [1516 - 1530] Pages: 15

DOI: 10.2174/1570180817999200818175544

Price: $65

Abstract

Background: The intentional dissemination of the “anthrax letter” led the researchers to increase their efforts towards the development of medical countermeasures against anthrax bioterrorism. A virulent strain of Bacillus anthracis secretes deadly three protein exotoxin (protective antigen, lethal factor and edema factor) that is the causative agent of anthrax and considered as serious biological weapons.

Objective: Due to limited existing therapeutics options, there is still an insecure situation to combat anthrax. This prompted us to design a multifunctional inhibitor instead of a traditional one that competes simultaneously with the Protective Antigen (PA), Lethal Factor (LF) and Edema Factor (EF) for their binding sites.

Methods: We integrated a pharmacophore modeling approach with the virtual screening and molecular docking analysis in the context of unique structural characteristics of deadly anthrax toxins.

Results: Initially, we screened 56,000 natural compounds against designed pharmacophore consensus that returned 351 hits. Out of these initial screening hits, only 100 compounds passed out through Lipinski filter that comprised of 12 chemically relevant clusters. By exclusion of duplicate and based on their fit score in each cluster, 15 unique compounds were selected for detailed study. Putative multifunctional compounds subjected to deep structural analysis in the milieu of anthrax toxins binding pockets to gauge critical structural crunch.

Conclusion: Our integrative approach provides a novel therapeutic window to develop a small molecular inhibitor that simultaneously targets three components of anthrax deadly toxin at the molecular level to elicit the desired biological process.

Keywords: Anthrax, multifunctional inhibitors, pharmacophore, virtual screening, molecular docking, protective antigen.

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[1]
Dixon, TC Meselson, M; Guillemin, J; Hanna, PC Engl. J. Med., 1999, (341), 815-826.
[2]
Leppla, S.H. Anthrax toxins. Bacterial toxins and virulence factors in diseases. Handbook of Natural Toxins; ; , 1995, pp. (8)543-572.
[3]
Collier, R.J.; Young, J.A.T. Anthrax toxin. Annu. Rev. Cell Dev. Biol., 2003, 19(19), 45-70.
[http://dx.doi.org/10.1146/annurev.cellbio.19.111301.140655] [PMID: 14570563]
[4]
Mourez, M.; Kane, R.S.; Mogridge, J.; Metallo, S.; Deschatelets, P.; Sellman, B.R.; Whitesides, G.M.; Collier, R.J. Designing a polyvalent inhibitor of anthrax toxin. Nat. Biotechnol., 2001, 19(10), 958-961.
[http://dx.doi.org/10.1038/nbt1001-958] [PMID: 11581662]
[5]
Petosa, C.; Collier, R.J.; Klimpel, K.R.; Leppla, S.H.; Liddington, R.C. Crystal structure of the anthrax toxin protective antigen. Nature, 1997, 385(6619), 833-838.
[http://dx.doi.org/10.1038/385833a0] [PMID: 9039918]
[6]
Lacy, D.B.; Wigelsworth, D.J.; Melnyk, R.A.; Harrison, S.C.; Collier, R.J. Structure of heptameric protective antigen bound to an anthrax toxin receptor: A role for receptor in pH-dependent pore formation. Proc. Natl. Acad. Sci. USA, 2004, 101(36), 13147-13151.
[http://dx.doi.org/10.1073/pnas.0405405101] [PMID: 15326297]
[7]
Abboud, N.; Casadevall, A. Immunogenicity of Bacillus anthracis protective antigen domains and efficacy of elicited antibody responses depend on host genetic background. Clin. Vaccine Immunol., 2008, 15(7), 1115-1123.
[http://dx.doi.org/10.1128/CVI.00015-08] [PMID: 18480236]
[8]
Mogridge, J.; Mourez, M.; Collier, R.J. Involvement of domain 3 in oligomerization by the protective antigen moiety of anthrax toxin. J. Bacteriol., 2001, 183(6), 2111-2116.
[http://dx.doi.org/10.1128/JB.183.6.2111-2116.2001] [PMID: 11222612]
[9]
Little, S.F.; Lowe, J.R. Location of receptor-binding region of protective antigen from Bacillus anthracis. Biochem. Biophys. Res. Commun., 1991, 180(2), 531-537.
[http://dx.doi.org/10.1016/S0006-291X(05)81097-6] [PMID: 1953724]
[10]
Rosovitz, M.J.; Schuck, P.; Varughese, M.; Chopra, A.P.; Mehra, V.; Singh, Y.; McGinnis, L.M.; Leppla, S.H. Alanine-scanning mutations in domain 4 of anthrax toxin protective antigen reveal residues important for binding to the cellular receptor and to a neutralizing monoclonal antibody. J. Biol. Chem., 2003, 278(33), 30936-30944.
[http://dx.doi.org/10.1074/jbc.M301154200] [PMID: 12771151]
[11]
Leppla, S.H.; Arora, N.; Varughese, M. Anthrax toxin fusion proteins for intracellular delivery of macromolecules. J. Appl. Microbiol., 1999, 87(2), 284.
[http://dx.doi.org/10.1046/j.1365-2672.1999.00890.x] [PMID: 10475968]
[12]
Quinn, C.P.; Singh, Y.; Klimpel, K.R.; Leppla, S.H. Functional mapping of anthrax toxin lethal factor by in-frame insertion mutagenesis. J. Biol. Chem., 1991, 266(30), 20124-20130.
[PMID: 1939073]
[13]
Pannifer, A.D.; Wong, T.Y.; Schwarzenbacher, R.; Renatus, M.; Petosa, C.; Bienkowska, J.; Lacy, D.B.; Collier, R.J.; Park, S.; Leppla, S.H.; Hanna, P.; Liddington, R.C. Crystal structure of the anthrax lethal factor. Nature, 2001, 414(6860), 229-233.
[http://dx.doi.org/10.1038/n35101998] [PMID: 11700563]
[14]
Leppla, S.H. Anthrax toxin edema factor: A bacterial adenylate cyclase that increases cyclic AMP concentrations of eukaryotic cells. Proc. Natl. Acad. Sci. USA, 1982, 79(10), 3162-3166.
[http://dx.doi.org/10.1073/pnas.79.10.3162] [PMID: 6285339]
[15]
Makiya, M.; Dolan, M.; Agulto, L.; Purcell, R.; Chen, Z. Structural basis of anthrax edema factor neutralization by a neutralizing antibody. Biochem. Biophys. Res. Commun., 2012, 417(1), 324-329.
[http://dx.doi.org/10.1016/j.bbrc.2011.11.108] [PMID: 22155239]
[16]
Bradley, K.A.; Mogridge, J.; Mourez, M.; Collier, R.J.; Young, J.A. Identification of the cellular receptor for anthrax toxin. Nature, 2001, 414(6860), 225-229.
[http://dx.doi.org/10.1038/n35101999] [PMID: 11700562]
[17]
Bonuccelli, G.; Sotgia, F.; Frank, P.G.; Williams, T.M.; de Almeida, C.J.; Tanowitz, H.B.; Scherer, P.E.; Hotchkiss, K.A.; Terman, B.I.; Rollman, B.; Alileche, A.; Brojatsch, J.; Lisanti, M.P. ATR/TEM8 is highly expressed in epithelial cells lining Bacillus anthracis’ three sites of entry: Implications for the pathogenesis of anthrax infection. Am. J. Physiol. Cell Physiol., 2005, 288(6), C1402-C1410.
[http://dx.doi.org/10.1152/ajpcell.00582.2004] [PMID: 15689409]
[18]
Scobie, H.M.; Rainey, G.J.; Bradley, K.A.; Young, J.A. Human capillary morphogenesis protein 2 functions as an anthrax toxin receptor. Proc. Natl. Acad. Sci. USA, 2003, 100(9), 5170-5174.
[http://dx.doi.org/10.1073/pnas.0431098100] [PMID: 12700348]
[19]
Bann, J.G. Anthrax toxin protective antigen--insights into molecular switching from prepore to pore. Protein Sci., 2012, 21(1), 1-12.
[http://dx.doi.org/10.1002/pro.752] [PMID: 22095644]
[20]
Kintzer, A.F.; Thoren, K.L.; Sterling, H.J.; Dong, K.C.; Feld, G.K.; Tang, I.I.; Zhang, T.T.; Williams, E.R.; Berger, J.M.; Krantz, B.A. The protective antigen component of anthrax toxin forms functional octameric complexes. J. Mol. Biol., 2009, 392(3), 614-629.
[http://dx.doi.org/10.1016/j.jmb.2009.07.037] [PMID: 19627991]
[21]
Mogridge, J.; Cunningham, K.; Collier, R.J. Stoichiometry of anthrax toxin complexes. Biochemistry, 2002, 41(3), 1079-1082.
[http://dx.doi.org/10.1021/bi015860m] [PMID: 11790132]
[22]
Pilpa, R.M.; Bayrhuber, M.; Marlett, J.M.; Riek, R.; Young, J.A.T. A receptor-based switch that regulates anthrax toxin pore formation. PLoS Pathog., 2011, 7(12)e1002354
[http://dx.doi.org/10.1371/journal.ppat.1002354] [PMID: 22174672]
[23]
Zhang, S.; Udho, E.; Wu, Z.; Collier, R.J.; Finkelstein, A. Protein translocation through anthrax toxin channels formed in planar lipid bilayers. Biophys. J., 2004, 87(6), 3842-3849.
[http://dx.doi.org/10.1529/biophysj.104.050864] [PMID: 15377524]
[24]
Basilio, D.; Kienker, P.K.; Briggs, S.W.; Finkelstein, A. A kinetic analysis of protein transport through the anthrax toxin channel. J. Gen. Physiol., 2011, 137(6), 521-531.
[http://dx.doi.org/10.1085/jgp.201110627] [PMID: 21624946]
[25]
Duesbery, N.S.; Webb, C.P.; Leppla, S.H.; Gordon, V.M.; Klimpel, K.R.; Copeland, T.D.; Ahn, N.G.; Oskarsson, M.K.; Fukasawa, K.; Paull, K.D.; Vande Woude, G.F. Proteolytic inactivation of MAP-kinase-kinase by anthrax lethal factor. Science, 1998, 280(5364), 734-737.
[http://dx.doi.org/10.1126/science.280.5364.734] [PMID: 9563949]
[26]
Vitale, G.; Bernardi, L.; Napolitani, G.; Mock, M.; Montecucco, C. Susceptibility of mitogen-activated protein kinase kinase family members to proteolysis by anthrax lethal factor. Biochem. J., 2000, 352(Pt 3), 739-745.
[http://dx.doi.org/10.1042/bj3520739] [PMID: 11104681]
[27]
Tang, WJ; Guo, Q. The adenylyl cyclase activity of anthrax edema factor. Mol. Aspects Med., 2009, 30,6, 423-30.
[http://dx.doi.org/10.1016/j.mam.2009.06.001]
[28]
Ahuja, N.; Kumar, P.; Bhatnagar, R. The adenylate cyclase toxins. Crit. Rev. Microbiol., 2004, 30(3), 187-196.
[http://dx.doi.org/10.1080/10408410490468795] [PMID: 15490970]
[29]
Beharry, Z.; Chen, H.; Gadhachanda, V.R.; Buynak, J.D.; Palzkill, T. Evaluation of penicillin-based inhibitors of the class A and B beta-lactamases from Bacillus anthracis. Biochem. Biophys. Res. Commun., 2004, 313(3), 541-545.
[http://dx.doi.org/10.1016/j.bbrc.2003.11.158] [PMID: 14697223]
[30]
Shoop, W.L.; Xiong, Y.; Wiltsie, J.; Woods, A.; Guo, J.; Pivnichny, J.V.; Felcetto, T.; Michael, B.F.; Bansal, A.; Cummings, R.T.; Cunningham, B.R.; Friedlander, A.M.; Douglas, C.M.; Patel, S.B.; Wisniewski, D.; Scapin, G.; Salowe, S.P.; Zaller, D.M.; Chapman, K.T.; Scolnick, E.M.; Schmatz, D.M.; Bartizal, K.; MacCoss, M.; Hermes, J.D. Anthrax lethal factor inhibition. Proc. Natl. Acad. Sci. USA, 2005, 102(22), 7958-7963.
[http://dx.doi.org/10.1073/pnas.0502159102] [PMID: 15911756]
[31]
Drum, C.L.; Yan, S-Z.; Bard, J.; Shen, Y-Q.; Lu, D.; Soelaiman, S.; Grabarek, Z.; Bohm, A.; Tang, W-J. Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin. Nature, 2002, 415(6870), 396-402.
[http://dx.doi.org/10.1038/415396a] [PMID: 11807546]
[32]
Santelli, E.; Bankston, L.A.; Leppla, S.H.; Liddington, R.C. Crystal structure of a complex between anthrax toxin and its host cell receptor. Nature 430, 2004, 905-908.
[http://dx.doi.org/10.1038/nature02763]
[33]
Duke’s, J. Phytochemical and ethnobotanical database., 2008.
[34]
Irwin, J.J.; Sterling, T.; Mysinger, M.M.; Bolstad, E.S.; Coleman, R.G. ZINC: a free tool to discover chemistry for biology. J. Chem. Inf. Model., 2012, 52(7), 1757-1768.
[http://dx.doi.org/10.1021/ci3001277] [PMID: 22587354]
[35]
Cheng, F.; Li, W. Zhou, Shen YJ, Wu Z, Liu G, Lee PW, Tang Y. Admet SAR: A comprehensive source and free tool for assessment of chemical ADMET properties. J. Chem. Inf. Model., 2012, (52), 3099-30105.
[http://dx.doi.org/10.1021/ci300367a] [PMID: 23092397]
[36]
Drwal, MN; Banerjee, P.; Dunkel, M.; Wettig, MR; Preissner, R. ProTox: A web server for the in silico prediction of rodent oral toxicity J. Nucleic Acids Res., 2014, (42), 53-58.
[37]
Wolber, G.; Langer, T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model., 2005, 45(1), 160-169.
[http://dx.doi.org/10.1021/ci049885e] [PMID: 15667141]
[38]
Wolber, G; Dronhoter, A.A; Langer, T. Computer aided molecular design., 2006, (20), 773-778.
[39]
Detector Performance Analysis Using, ROC Curves-MATLAB & Simulink Example, www.mathworks.com
[40]
Irwin, J.J.; Shoichet, B.K. ZINC--a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model., 2005, 45(1), 177-182.
[http://dx.doi.org/10.1021/ci049714+] [PMID: 15667143]
[41]
Pilot, Pipeline Accelrys Software Inc 2010.
[42]
SciFinder; American Chemical Society, 2013.
[43]
Morris, G.M.; Huey, R.; Lindstrom, W.; Sanner, M.F.; Belew, R.K.; Goodsell, D.S.; Olson, A.J. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem., 2009, 30(16), 2785-2791.
[http://dx.doi.org/10.1002/jcc.21256] [PMID: 19399780]
[44]
Duhovny, D.; Nussinov, R.; Wolfson, H.J. Efficient unbound docking of rigid molecules. Proceedings of the Fourth International Workshop on Algorithms in Bioinformatics, 2002, pp. 185-200.
[http://dx.doi.org/0.1007/3-540-45784-4_14]
[45]
Pierce, B.G.; Wiehe, K.; Hwang, H.; Kim, B.H.; Vreven, T.; Weng, Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics, 2014, 30(12), 1771-1773.
[http://dx.doi.org/10.1093/bioinformatics/btu097] [PMID: 24532726]
[46]
Wallace, A.C.; Laskowski, R.A.; Thornton, J.M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 1995, 8(2), 127-134.
[http://dx.doi.org/10.1093/protein/8.2.127] [PMID: 7630882]
[47]
Qamar, T.U.; Mumtaz, A.; Ashfaq, U.A.; Azhar, S.; Fatima, T.; Hassan, M.; Hussain, S.S.; Akram, W.; Idrees, S. Computer aided screening of phytochemicals from Garcinia against the Dengue NS2B/NS3 Protease. Bioinformation, 2014, 10(3), 115-118.
[http://dx.doi.org/10.6026/97320630010115] [PMID: 24748749]
[48]
Zhu, P.J.; Hobson, J.P.; Southall, N.; Qiu, C.; Thomas, C.J.; Lu, J.; Inglese, J.; Zheng, W.; Leppla, S.H.; Bugge, T.H.; Austin, C.P.; Liu, S. Quantitative high-throughput screening identifies inhibitors of anthrax-induced cell death. Bioorg. Med. Chem., 2009, 17(14), 5139-5145.
[http://dx.doi.org/10.1016/j.bmc.2009.05.054] [PMID: 19540764]
[49]
Tonello, F.; Seveso, M.; Marin, O.; Mock, M.; Montecucco, C. Screening inhibitors of anthrax lethal factor. Nature, 2002, 418(6896), 386.
[http://dx.doi.org/10.1038/418386a] [PMID: 12140548]
[50]
Nestorovich, E.M.; Karginov, V.A.; Berezhkovskii, A.M.; Bezrukov, S.M. Blockage of anthrax PA63 pore by a multicharged high-affinity toxin inhibitor. Biophys. J., 2010, 99(1), 134-143.
[http://dx.doi.org/10.1016/j.bpj.2010.03.070] [PMID: 20655841]
[51]
Moayeri, M.; Leppla, S.H. Cellular and systemic effects of anthrax lethal toxin and edema toxin. Mol. Aspects Med., 2009, 30(6), 439-455.
[http://dx.doi.org/10.1016/j.mam.2009.07.003] [PMID: 19638283]
[52]
Young, J.A.; Collier, R.J. Anthrax toxin: Receptor binding, internalization, pore formation, and translocation. Annu. Rev. Biochem., 2007, 76(76), 243-265.
[http://dx.doi.org/10.1146/annurev.biochem.75.103004.142728] [PMID: 17335404]
[53]
Fox, J.L. Anthrax drug first antibacterial mAb to win approval. Nat. Biotechnol., 2013, 31(1), 8.
[http://dx.doi.org/10.1038/nbt0113-8] [PMID: 23302914]
[54]
Cryan, L.M.; Habeshian, K.A.; Caldwell, T.P.; Morris, M.T.; Ackroyd, P.C.; Christensen, K.A.; Rogers, M.S. Identification of small molecules that inhibit the interaction of TEM8 with anthrax protective antigen using a FRET assay. J. Biomol. Screen., 2013, 18(6), 714-725.
[http://dx.doi.org/10.1177/1087057113478655] [PMID: 23479355]

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