Exploration of potential inhibitors for autophagy-related protein 8 as antileishmanial agents.
Leishmania donovani
Apoptosis
atg8
urolithin A
Journal
Chemical biology & drug design
ISSN: 1747-0285
Titre abrégé: Chem Biol Drug Des
Pays: England
ID NLM: 101262549
Informations de publication
Date de publication:
06 2022
06 2022
Historique:
revised:
25
12
2021
received:
14
09
2021
accepted:
29
01
2022
pubmed:
12
2
2022
medline:
18
5
2022
entrez:
11
2
2022
Statut:
ppublish
Résumé
Leishmaniasis is considered a tropical neglected disease, which is caused by an intramacrophagic parasite, Leishmania. It is endemic in 89 different countries. Autophagy-related protein 8 (Ldatg8) is responsible for the transformation of parasites from promastigote to amastigote differentiation. Ldatg8 is one of the key drug targets of Leishmania donovani (L. donovani) responsible for the defense of parasites during stress conditions. Virtual screening of natural ligand library had been performed against Ldatg8 to identify novel and potent inhibitors. Molecular docking and molecular dynamics simulation studies showed that urolithin A stably blocked Ldatg8. Urolithins are combinations of coumarin and isocoumarin. Further, we evaluated the antileishmanial effects of urolithin A by antileishmanial assays. Urolithin A inhibited the growth and proliferation of L. donovani promastigotes with an IC
Substances chimiques
Antiprotozoal Agents
0
Autophagy-Related Protein 8 Family
0
Coumarins
0
Reactive Oxygen Species
0
3,8-dihydroxy-6H-dibenzo(b,d)pyran-6-one
1143-70-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
816-827Informations de copyright
© 2022 John Wiley & Sons Ltd.
Références
Ahmad, V. (2020). A molecular docking study against COVID-19 protease with a pomegranate phyto-constituents’ urolithin’ and other repurposing drugs: From a supplement to ailment. Journal of Pharmaceutical Research International, 32(11), 51-62. https://doi.org/10.9734/jpri/2020/v32i1130545
Arish, M., Husein, A., Ali, R., Tabrez, S., Naz, F., Ahmad, M. Z., & Rub, A. (2018). Sphingosine-1-phosphate signaling in Leishmania donovani infection in macrophages. PLoS Neglected Tropical Diseases, 12(8), e0006647. https://doi.org/10.1371/journal.pntd.0006647
Bor, T., Aljaloud, S. O., Gyawali, R., & Ibrahim, S. A. (2016). Antimicrobials from herbs, spices, and plants. Fruits, vegetables, and herbs (pp. 551-578). Elsevier.
Burza, S., Croft, S. L., & Boelaert, M. (2018). Leishmaniasis. Lancet, 392(10151), 951-970. https://doi.org/10.1016/s0140-6736(18)31204-2
Cerdá, B., Periago, P., Espín, J. C., & Tomás-Barberán, F. A. (2005). Identification of urolithin a as a metabolite produced by human colon microflora from ellagic acid and related compounds. Journal of Agriculture and Food Chemistry, 53(14), 5571-5576. https://doi.org/10.1021/jf050384i
Cheng, T., Li, Q., Zhou, Z., Wang, Y., & Bryant, S. H. (2012). Structure-based virtual screening for drug discovery: A problem-centric review. American Association of Pharmaceutical Scientists Journal, 14(1), 133-141. https://doi.org/10.1208/s12248-012-9322-0
Cowan, M. M. (1999). Plant products as antimicrobial agents. Clinical Microbiology Reviews, 12(4), 564-582. https://doi.org/10.1128/cmr.12.4.564
Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology, 1263, 243-250. https://doi.org/10.1007/978-1-4939-2269-7_19
Darden, T., Perera, L., Li, L., & Pedersen, L. (1999). New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure, 7(3), R55-60. https://doi.org/10.1016/s0969-2126(99)80033-1
de Andrade Monteiro, C., & Ribeiro Alves dos Santos, J. (2019). Phytochemicals and their antifungal potential against pathogenic yeasts. Phytochemicals in human health (pp. 1-31).
Dell'Agli, M., Galli, G. V., Bulgari, M., Basilico, N., Romeo, S., Bhattacharya, D., Taramelli, D., & Bosisio, E. (2010). Ellagitannins of the fruit rind of pomegranate (Punica granatum) antagonize in vitro the host inflammatory response mechanisms involved in the onset of malaria. Malaria Journal, 9, 208. https://doi.org/10.1186/1475-2875-9-208
Giménez-Bastida, J. A., Truchado, P., Larrosa, M., Espín, J. C., Tomás-Barberán, F. A., Allende, A., & García-Conesa, M. T. (2012). Urolithins, ellagitannin metabolites produced by colon microbiota, inhibit Quorum Sensing in Yersinia enterocolitica: Phenotypic response and associated molecular changes. Food Chemistry, 132(3), 1465-1474. https://doi.org/10.1016/j.foodchem.2011.12.003
Giri, S., & Shaha, C. (2019). Leishmania donovani parasite requires Atg8 protein for infectivity and survival under stress. Cell Death & Disease, 10(11), 808. https://doi.org/10.1038/s41419-019-2038-7
Goto, H., & Lauletta Lindoso, J. A. (2012). Cutaneous and mucocutaneous leishmaniasis. Infectious Disease Clinics of North America, 26(2), 293-307. https://doi.org/10.1016/j.idc.2012.03.001
Herwaldt, B. L. (1999). Leishmaniasis. Lancet, 354(9185), 1191-1199. https://doi.org/10.1016/s0140-6736(98)10178-2
Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463-1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463:AID-JCC4>3.0.CO;2-H
Kashif, M., Tabrez, S., Husein, A., Arish, M., Kalaiarasan, P., Manna, P. P., Subbarao, N., Akhter, Y., & Rub, A. (2018). Identification of novel inhibitors against UDP-galactopyranose mutase to combat leishmaniasis. Journal of Cellular Biochemistry, 119(3), 2653-2665. https://doi.org/10.1002/jcb.26433
Kim, S. (2016). Getting the most out of PubChem for virtual screening. Expert Opinion on Drug Discovery, 11(9), 843-855. https://doi.org/10.1080/17460441.2016.1216967
Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Reviews Drug Discovery, 3(11), 935-949. https://doi.org/10.1038/nrd1549
Kujawska, M., & Jodynis-Liebert, J. (2020). Potential of the ellagic acid-derived gut microbiota metabolite - Urolithin A in gastrointestinal protection. World Journal of Gastroenterology, 26(23), 3170-3181. https://doi.org/10.3748/wjg.v26.i23.3170
Kutzner, C., Apostolov, R., Hess, B., & Grubmüller, H. (2014). Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. Parallel computing: Accelerating computational science and engineering (CSE) (pp. 722-730): IOS Press.
Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4), 477-486. https://doi.org/10.1007/bf00228148
Lengauer, T., & Rarey, M. (1996). Computational methods for biomolecular docking. Current Opinion in Structural Biology, 6(3), 402-406. https://doi.org/10.1016/s0959-440x(96)80061-3
Maretti-Mira, A. C., de Pinho Rodrigues, K. M., de Oliveira-Neto, M. P., Pirmez, C., & Craft, N. (2011). MMP-9 activity is induced by Leishmania braziliensis infection and correlates with mucosal leishmaniasis. Acta Tropica, 119(2-3), 160-164. https://doi.org/10.1016/j.actatropica.2011.05.009
Mehreen, A., Waheed, M., Liaqat, I., & Arshad, N. (2016). Phytochemical, antimicrobial, and toxicological evaluation of traditional herbs used to treat sore throat. BioMed Research International, 2016, 8503426. https://doi.org/10.1155/2016/8503426
Mukherjee, D., Singh, C. B., Dey, S., Mandal, S., Ghosh, J., Mallick, S., Hussain, A., Swapana, N., Ross, S. A., & Pal, C. (2016). Induction of apoptosis by zerumbone isolated from Zingiber zerumbet (L.) Smith in protozoan parasite Leishmania donovani due to oxidative stress. The Brazilian Journal of Infectious Diseases, 20(1), 48-55. https://doi.org/10.1016/j.bjid.2015.10.002
Mukherjee, D., Yousuf, M., Dey, S., Chakraborty, S., Chaudhuri, A., Kumar, V., & Pal, C. (2020). Targeting the trypanothione reductase of tissue-residing Leishmania in Hosts’ reticuloendothelial system: A flexible water-soluble ferrocenylquinoline-based preclinical drug candidate. Journal of Medicinal Chemistry, 63(24), 15621-15638. https://doi.org/10.1021/acs.jmedchem.0c00690
Murray, H. W., Berman, J. D., Davies, C. R., & Saravia, N. G. (2005). Advances in leishmaniasis. Lancet, 366(9496), 1561-1577. https://doi.org/10.1016/s0140-6736(05)67629-5
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. https://doi.org/10.1186/1758-2946-3-33
Piscopo, T. V., & Mallia Azzopardi, C. (2007). Leishmaniasis. Postgraduate Medical Journal, 83(976), 649-657. https://doi.org/10.1136/pgmj.2006.047340corr1
Rahman, F., Tabrez, S., Ali, R., Akand, S. K., Zahid, M., Alaidarous, M. A., & Rub, A. (2021). Virtual screening of natural compounds for potential inhibitors of Sterol C-24 methyltransferase of Leishmania donovani to overcome leishmaniasis. Journal of Cellular Biochemistry, 122(9), 1216-1228. https://doi.org/10.1002/jcb.29944
Rahman, F., Tabrez, S., Ali, R., Alqahtani, A. S., Ahmed, M. Z., & Rub, A. (2021). Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins. Journal of Traditional and Complementary Medicine, 11(2), 173-179. https://doi.org/10.1016/j.jtcme.2021.01.006
Rappé, A. K., Casewit, C. J., Colwell, K., Goddard, W. A. III, & Skiff, W. M. (1992). UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. Journal of the American Chemical Society, 114(25), 10024-10035. https://doi.org/10.1021/ja00051a040
Rollinger, J. M., Stuppner, H., & Langer, T. (2008). Virtual screening for the discovery of bioactive natural products. Progress in Drug Research, 65(211), 213-249. https://doi.org/10.1007/978-3-7643-8117-2_6
Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355-1363. https://doi.org/10.1107/s0907444904011679
Sultana, S. S., Ghosh, J., Chakraborty, S., Mukherjee, D., Dey, S., Mallick, S., Dutta, A., Paloi, S., Khatua, S., Dutta, T., Bhattacharya, S., Acharya, K., Ghorai, N., & Pal, C. (2018). Selective in vitro inhibition of Leishmania donovani by a semi-purified fraction of wild mushroom Grifola frondosa. Experimental Parasitology, 192, 73-84. https://doi.org/10.1016/j.exppara.2018.07.006
Tabrez, S., Rahman, F., Ali, R., Alouffi, A. S., Akand, S. K., Alshehri, B. M., & Rub, A. (2020). Cynaroside inhibits Leishmania donovani UDP-galactopyranose mutase and induces reactive oxygen species to exert antileishmanial response. Bioscience Reports, 41(1), 1-26. https://doi.org/10.1042/bsr20203857
Thompson, A. M., O’Connor, P. D., Marshall, A. J., Yardley, V., Maes, L., Gupta, S., & Denny, W. A. (2021). Heteroaryl ether analogues of an antileishmanial 7-substituted 2-nitroimidazooxazine lead afford attenuated hERG risk: In vitro and in vivo appraisal. European Journal of Medicinal Chemistry, 209, 112914. https://doi.org/10.1016/j.ejmech.2020.112914
Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363-w367. https://doi.org/10.1093/nar/gky473
Tomás-Barberan, F. A., Espín, J. C., & García-Conesa, M. T. (2009). Bioavailability and metabolism of ellagic acid and ellagitannins. Chemistry and biology of ellagitannins: An underestimated class of Bioactive plant polyphenols (pp. 273-297). World Scientific.
Torres-Guerrero, E., Quintanilla-Cedillo, M. R., Ruiz-Esmenjaud, J., & Arenas, R. (2017). Leishmaniasis: A review. F1000Res, 6, 750. https://doi.org/10.12688/f1000research.11120.1
Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701-1718. https://doi.org/10.1002/jcc.20291
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12(1), 7-8. https://doi.org/10.1038/nmeth.3213
Yousuf, M. D., Mukherjee, D., Dey, S., Chatterjee, S., Pal, A., Sarkar, B., Pal, C., & Adhikari, S. (2018). Synthesis and biological evaluation of polyhydroxylated oxindole derivatives as potential antileishmanial agent. Bioorganic & Medicinal Chemistry Letters, 28(6), 1056-1062. https://doi.org/10.1016/j.bmcl.2018.02.023
Zulfiqar, B., Shelper, T. B., & Avery, V. M. (2017). Leishmaniasis drug discovery: Recent progress and challenges in assay development. Drug Discovery Today, 22(10), 1516-1531. https://doi.org/10.1016/j.drudis.2017.06.004