Phthalide derivatives as dihydrofolate reductase inhibitors for malaria: molecular docking and molecular dynamics studies

References

• Ahmed, A., Das, M. K., Dev, V., Saifi, M. A., Wajihullah., & Y. D., Sharma. (2006). Quadruple mutations in dihydrofolate reductase of Plasmodium falciparum isolates from Car Nicobar Island, India. Antimicrobial Agents and Chemotherapy, 50, 1546–1549. https://doi.org/10.1128/AAC.50.4.1546-1549.2006
   PubMed Web of Science ®Google Scholar
• Adane, L., Bhagat, S., Arfeen, M., Bhatia, S., Sirawaraporn, R., Sirawaraporn, W., Chakraborti, A. K., & Bharatam, P. V. (2014). Design and synthesis of guanylthiourea derivatives as potential inhibitors of Plasmodium falciparum dihydrofolate reductase enzyme. Bioorganic & Medicinal Chemistry Letters, 24(2), 613–617. https://doi.org/10.1016/j.bmcl.2013.12.009
   PubMed Web of Science ®Google Scholar
• A-Elbasit, I. E., Alifrangis, M., Khalil, I. F., Bygbjerg, I. C., Masuadi, E. M., Elbashir, M. I., & Giha, H. A. (2007). The implication of dihydrofolate reductase and dihydropteroate synthetase gene mutations in modification of Plasmodium falciparum characteristics. Malaria Journal, 6, 1–8. https://doi.org/10.1186/1475-2875-6-108.
   PubMed Web of Science ®Google Scholar
• Aguiar, A. C. C., Murce, E., Cortopassi, W. A., Pimentel, A. S., Almeida, M., Barros, D. C. S., Guedes, J. S., Meneghetti, M. R., & Krettli, A. U. (2018). Chloroquine analogs as antimalarial candidates with potent in vitro and in vivo activity. International Journal for Parasitology. Drugs and Drug Resistance, 8(3), 459–464. https://doi.org/10.1016/j.ijpddr.2018.10.002
   PubMed Web of Science ®Google Scholar
• Almeida, C., Kehraus, S., Prudêncio, M., & König, G. M. (2011). Marilones A-C, phthalides from the sponge-derived fungus Stachylidium sp. Beilstein Journal of Organic Chemistry, 7, 1636–1642. https://doi.org/10.3762/bjoc.7.192
   PubMed Web of Science ®Google Scholar
• Alzain, A. A., Ismail, A., Fadlelmola, M., Mohamed, M. A., Mahjoub, M., Makki, A. A., & Elsaman, T. (2022). De novo design of novel spike glycoprotein inhibitors using e-pharmacophore modeling, molecular hybridization, ADMET, quantum mechanics and molecular dynamics studies for COVID-19. Pakistan Journal of Pharmaceutical Sciences, 35(1(Supplementary), 313–321.
   PubMed Web of Science ®Google Scholar
• Balabadra, S., Kotni, M. K., Manga, V., Allanki, A. D., Prasad, R., & Sijwali, P. S. (2017). Synthesis and evaluation of naphthyl bearing 1,2,3-triazole analogs as antiplasmodial agents, cytotoxicity and docking studies. Bioorganic & Medicinal Chemistry, 25(1), 221–232. https://doi.org/10.1016/j.bmc.2016.10.029
   PubMed Web of Science ®Google Scholar
• Balikagala, B., Fukuda, N., Ikeda, M., Katuro, O. T., Tachibana, S.-I., Yamauchi, M., Opio, W., Emoto, S., Anywar, D. A., Kimura, E., Palacpac, N. M. Q., Odongo-Aginya, E. I., Ogwang, M., Horii, T., & Mita, T. (2021). Evidence of artemisinin-resistant malaria in Africa. New England Journal of Medicine, 385(13), 1163–1171. https://doi.org/10.1056/NEJMoa2101746
   PubMed Web of Science ®Google Scholar
• Bekhit, A. A., Saudi, M. N., Hassan, A. M. M., Fahmy, S. M., Ibrahim, T. M., Ghareeb, D., El-Seidy, A. M., Nasralla, S. N., & Bekhit, A. (2019). Synthesis, in silico experiments and biological evaluation of 1,3,4-trisubstituted pyrazole derivatives as antimalarial agents. European Journal of Medicinal Chemistry, 163, 353–366. https://doi.org/10.1016/j.ejmech.2018.11.067
   PubMed Web of Science ®Google Scholar
• Bhagat, S., Arfeen, M., Das, G., Ramkumar, M., Khan, S. I., Tekwani, B. L., & Bharatam, P. V. (2019). Design, synthesis and biological evaluation of 4-aminoquinoline-guanylthiourea derivatives as antimalarial agents. Bioorganic Chemistry, 91, 103094. https://doi.org/10.1016/j.bioorg.2019.103094
   PubMed Web of Science ®Google Scholar
• Blunt, J. W., Copp, B. R., Keyzers, R. A., Munro, M. H. G., & Prinsep, M. R. (2014). Marine natural products. Natural Product Reports, 31(2), 160–258. https://doi.org/10.1039/c3np70117d
   PubMed Web of Science ®Google Scholar
• Bommu, U. D., Konidala, K. K., Pabbaraju, N., & Yeguvapalli, S. (2017). Ligand-based virtual screening, molecular docking, QSAR and pharmacophore analysis of quercetin-associated potential novel analogs against epidermal growth factor receptor. Journal of Receptor and Signal Transduction Research, 37(6), 600–610. https://doi.org/10.1080/10799893.2017.1377237
   PubMed Web of Science ®Google Scholar
• Burrows, J. N., Duparc, S., Gutteridge, W. E., Van Huijsduijnen, R. H., Kaszubska, W., Macintyre, F., Mazzuri, S., Möhrle, J. J., & Wells, T. N. C. (2017). New developments in anti‑malarial target candidate and product profiles. Malaria Journal, 16, 1–29. https://doi.org/10.1186/s12936-016-1675-x.
   PubMed Web of Science ®Google Scholar
• Choowongkomon, K., Theppabutr, S., Songtawee, N., Day, N. P. J., White, N. J., Woodrow, C. J., & Imwong, M. (2010). Computational analysis of binding between malarial dihydrofolate reductases and anti-folates. Malaria Journal, 9, 65. https://doi.org/10.1186/1475-2875-9-65.
   PubMed Web of Science ®Google Scholar
• Chughlay, M. F., Gaaloul, M. E., Donini, C., Campo, B., Berghmans, P. J., Lucardie, A., Marx, M. W., Cherkaoui-Rbati, M. H., Langdon, G., Angulo-Barturen, I., Viera, S., Rosanas-Urgell, A., Van Geertruyden, J. P., & Chalon, S. (2021). Chemoprotective antimalarial activity of p218 against plasmodium falciparum: A randomized, placebo-controlled volunteer infection study. The American Journal of Tropical Medicine and Hygiene, 104(4), 1348–1358. https://doi.org/10.4269/ajtmh.20-1165
   PubMed Web of Science ®Google Scholar
• Chughlay, M. F., Rossignol, E., Donini, C., Gaaloul, M. E., Lorch, U., Coates, S., Langdon, G., Hammond, T., Möhrle, J., & Chalon, S. (2020). First-in-human clinical trial to assess the safety, tolerability and pharmacokinetics of P218, a novel candidate for malaria chemoprotection. British Journal of Clinical Pharmacology, 86(6), 1113–1124. https://doi.org/10.1111/bcp.14219
   PubMed Web of Science ®Google Scholar
• Coban, C. (2020). Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company’s public news and information.
   Google Scholar
• Elshemy, H. A. H., Zaki, M. A., Mohamed, E. I., Khan, S. I., & Lamie, P. F. (2020). A multicomponent reaction to design antimalarial pyridyl-indole derivatives: Synthesis, biological activities and molecular docking. Bioorganic Chemistry, 97, 103673. https://doi.org/10.1016/j.bioorg.2020.103673
   PubMed Web of Science ®Google Scholar
• Fogel, G. B., Cheung, M., Pittman, E., & Hecht, D. (2008). In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase. Journal of Molecular Graphics & Modelling, 26(7), 1145–1152. https://doi.org/10.1016/j.jmgm.2007.10.006
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Ibraheem, W., Chaar, C., Camiade, E., Hervé, V., Fouquenet, D., Roux, A.-E., Si-Tahar, M., Ahmed, E., Thibonnet, J., Thiery, E., & Petrignet, J. (2022). Synthesis, antibacterial and cytotoxic evaluation of cytosporone E and analogs. Journal of Molecular Structure, 1252, 132135. https://doi.org/10.1016/j.molstruc.2021.132135
   Web of Science ®Google Scholar
• Ibraheem, W., Wils, Q., Camiade, E., Ahmed, E., Thibonnet, J., Thiery, E., & Petrignet, J. (2021). Synthesis and antibacterial activity of racemic paecilocin A and its derivatives against methicillin-sensitive and -resistant Staphylococcus aureus. Tetrahedron Letters, 67, 152888. https://doi.org/10.1016/j.tetlet.2021.152888
   Web of Science ®Google Scholar
• Suma, K. B., Kumari, A., Shetty, D., Fernandes, E., Chethan, D. V., Jays, J., & Murahari, M. (2020). Structure based pharmacophore modelling approach for the design of azaindole derivatives as DprE1 inhibitors for tuberculosis. Journal of Molecular Graphics & Modelling, 101, 107718. https://doi.org/10.1016/j.jmgm.2020.107718
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Kumar, A., Gahlawat, S. K., & Singh, V. (2020). Comparative analysis of Plasmodium falciparum dihydrofolate-reductase gene sequences from different regions of India. Heliyon, 6(4), e03715. https://doi.org/10.1016/j.heliyon.2020.e03715
   PubMed Web of Science ®Google Scholar
• Lau, T. Y., Sylvi, M., & William, T. (2013). Mutational analysis of Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase genes in the interior division of Sabah, Malaysia. Malaria Journal, 12, 445–445. https://doi.org/10.1186/1475-2875-12-445.
   PubMed Web of Science ®Google Scholar
• Maitarad, P., Saparpakorn, P., Hannongbua, S., Kamchonwongpaisan, S., Tarnchompoo, B., & Yuthavong, Y. (2009). Particular interaction between pyrimethamine derivatives and quadruple mutant type dihydrofolate reductase of Plasmodium falciparum: CoMFA and quantum chemical calculations studies. Journal of Enzyme Inhibition and Medicinal Chemistry, 24(2), 471–479. https://doi.org/10.1080/14756360802201223
   PubMed Web of Science ®Google Scholar
• McCollum, A. M., Poe, A. C., Hamel, M., Huber, C., Zhou, Z., Shi, Y. P., Ouma, P., Vulule, J., Bloland, P., Slutsker, L., Barnwell, J. W., Udhayakumar, V., & Escalante, A. A. (2006). Antifolate resistance in Plasmodium falciparum: Multiple origins and identification of novel DHFR alleles. The Journal of Infectious Diseases, 194(2), 189–197. https://doi.org/10.1086/504687
   PubMed Web of Science ®Google Scholar
• Mharakurwa, S., Kumwenda, T., Mkulama, M. A. P., Musapa, M., Chishimba, S., Shiff, C. J., Sullivan, D. J., Thuma, P. E., Liu, K., & Agre, P. (2011). Malaria antifolate resistance with contrasting Plasmodium falciparum dihydrofolate reductase (DHFR) polymorphisms in humans and Anopheles mosquitoes. Proceedings of the National Academy of Sciences of the United States of America, 108(46), 18796–18801. https://doi.org/10.1073/pnas.1116162108
   PubMed Web of Science ®Google Scholar
• Mogire, R. M., Akala, H. M., Macharia, R. W., Juma, D. W., Cheruiyot, C., Andagalu, B., Brown, M. L., El-shemy, H. A., & Nyanjom, G. (2017). Target-similarity search using Plasmodium falciparum proteome identifies approved drugs with anti-malarial activity and their possible targets. PLoS One, 12, 1–24.
   Web of Science ®Google Scholar
• Osman, E. A., Abdalla, M. A., Abdelraheem, M. O., Ali, M. F., Osman, S. A., Tanir, Y. M., Abdelrahman, M., Ibraheem, W., & Alzain, A. A. (2021). Design of novel coumarins as potent Mcl-1 inhibitors for cancer treatment guided by 3D-QSAR, molecular docking and molecular dynamics. Informatics in Medicine Unlocked, 26, 100765. https://doi.org/10.1016/j.imu.2021.100765
   Google Scholar
• Owoloye, A., Olufemi, M., Idowu, E. T., & Oyebola, K. M. (2021). Prevalence of potential mediators of artemisinin resistance in African isolates of Plasmodium falciparum. Malaria Journal, 20, 1–12. https://doi.org/10.1186/s12936-021-03987-6.
   PubMed Web of Science ®Google Scholar
• Peyrottes, S. (2012). Choline analogues in malaria chemotherapy. Current Pharmaceutical Design, 18,3454–3466. https://doi.org/10.2174/138161212801327338.
   PubMed Web of Science ®Google Scholar
• Remcho, T. P., Guggilapu, S. D., Cruz, P., Nardone, G. A., Heffernan, G., O’Connor, R. D., Bewley, C. A., Wellems, T. E., & Lane, K. D. (2020). Regioisomerization of antimalarial drug WR99210 explains the inactivity of a commercial stock. Antimicrobial Agents and Chemotherapy, 65, 1385-20. https://doi.org/10.1128/AAC.01385-20.
   Google Scholar
• Rocamora, F., Gupta, P., Istvan, E. S., Luth, M. R., Carpenter, E. F., Kümpornsin, K., Sasaki, E., Calla, J., Mittal, N., Carolino, K., Owen, E., Llinás, M., Ottilie, S., Goldberg, D. E., Lee, M. C. S., & Winzeler, E. A. (2021). PfMFR3: A multidrug-resistant modulator in Plasmodium falciparum. ACS Infectious Diseases, 7(4), 811–825. https://doi.org/10.1021/acsinfecdis.0c00676
   PubMed Web of Science ®Google Scholar
• Roos, K., Wu, C., Damm, W., Reboul, M., Stevenson, J. M., Lu, C., Dahlgren, M. K., Mondal, S., Chen, W., Wang, L., Abel, R., Friesner, R. A., & Harder, E. D. (2019). OPLS3e: Extending force field coverage for drug-like small molecules. Journal of Chemical Theory and Computation, 15(3), 1863–1874. https://doi.org/10.1021/acs.jctc.8b01026
   PubMed Web of Science ®Google Scholar
• Salentin, S., Adasme, M. F., Heinrich, J. C., Haupt, V. J., Daminelli, S., Zhang, Y., & Schroeder, M. (2017). From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns. Scientific Reports, 7, 1–13. https://doi.org/10.1038/s41598-017-11924-4.
   PubMed Web of Science ®Google Scholar
• Shibeshi, M. A., Kifle, Z. D., & Atnafie, A. S. (2020). Antimalarial drug resistance and novel targets for antimalarial drug discovery. Infection and Drug Resistance, 13, 4047–4060.
   PubMed Web of Science ®Google Scholar
• Stefanucci, A., Marrone, A., & Agamennone, M. (2015). Investigation of the N-BP binding at FPPS by combined computational approaches. Medicinal Chemistry, 11(5), 417–431. https://doi.org/10.2174/1573406410666141226132630
   PubMed Web of Science ®Google Scholar
• Stefanucci, A., Pinnen, F., Feliciani, F., Cacciatore, I., Lucente, G., & Mollica, A. (2011). Conformationally constrained histidines in the design of peptidomimetics: Strategies for the χ-space control. International Journal of Molecular Sciences, 12(5), 2853–2890. https://doi.org/10.3390/ijms12052853
   PubMed Web of Science ®Google Scholar
• Sumam de Oliveira, D., Kronenberger, T., Palmisano, G., Wrenger, C., & de Souza, E. E. (2021). Targeting SUMOylation in Plasmodium as a potential target for malaria therapy. Frontiers in Cellular and Infection Microbiology, 11, 685866–685867. https://doi.org/10.3389/fcimb.2021.685866.
   PubMed Web of Science ®Google Scholar
• Syahri, J., Yuanita, E., Nurohmah, B. A., Armunanto, R., & Purwono, B. (2017). Chalcone analogue as potent anti-malarial compounds against Plasmodium falciparum: Synthesis, biological evaluation, and docking simulation study. Asian Pacific Journal of Tropical Biomedicine, 7(8), 675–679. https://doi.org/10.1016/j.apjtb.2017.07.004
   Web of Science ®Google Scholar
• Tian, S., Wang, J., Li, Y., Li, D., Xu, L., & Hou, T. (2015). The application of in silico drug-likeness predictions in pharmaceutical research. Advanced Drug Delivery Reviews, 86, 2–10. https://doi.org/10.1016/j.addr.2015.01.009
   PubMed Web of Science ®Google Scholar
• Vivo, M. D., Masetti, M., Bottegoni, G., & Cavalli, A. (2016). Role of molecular dynamics and related methods in drug discovery. Journal of Medicinal Chemistry, 59(9), 4035–4061. https://doi.org/10.1021/acs.jmedchem.5b01684
   PubMed Web of Science ®Google Scholar
• von Delius, M., Le, C. M., Ellinger, B., Kuzikov, M., Gul, S., & Dong, V. M. (2017). Synthesis and biological activity of octaketides from the cytosporone family. Israel Journal of Chemistry, 57(10-11), 975–981. https://doi.org/10.1002/ijch.201700023
   Web of Science ®Google Scholar
• 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. (2013). Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target. Applied biological sciences, 109(42), 16823-16828. https://doi.org/10.1073/pnas.1204556109/-/DCSupplemental.
   Google Scholar
• Yuvaniyama, J., Chitnumsub, P., Kamchonwongpaisan, S., Vanichtanankul, J., Sirawaraporn, W., Taylor, P., Walkinshaw, M. D., & Yuthavong, Y. (2003). Insights into antifolate resistance from malarial DHFR-TS structures. Nature Structural Biology, 10(5), 357–365. https://doi.org/10.1038/nsb921
   PubMedGoogle Scholar