In silico Analysis of Natural Iridoids as Primary Amoebic Meningoencephalitis Inhibitors: Molecular Docking, MD Simulation, MMPBSA, and DFT Analyses

Prinsa; Supriyo Saha

doi:10.18006/2024.12(6).800.828

Authors

Prinsa Department of Pharmaceutical Chemistry, Siddhartha Institute of Pharmacy, Near IT-Park, Sahastradhara Road, Dehradun 248001, Uttarakhand, India https://orcid.org/0009-0004-7496-7465
Supriyo Saha Department of Pharmaceutical Chemistry, Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun-248001, Uttarakhand, India https://orcid.org/0000-0003-1365-4698

DOI:

https://doi.org/10.18006/2024.12(6).800.828

Keywords:

Primary Amoebic Meningoencephalitis (PAM), Iridoids, Molecular Docking, MD Simulation, MMPBSA, DFT

Abstract

Iridoids have demonstrated various activities, including anti-inflammatory, anticancer, cardioprotective, antiviral, hepatoprotective, antihyperglycemic, and antiparasitic effects. The brain-eating amoeba Naegleria fowleri is responsible for primary amoebic meningoencephalitis, a brain inflammation. In this study, 52 iridoids were selected through an extensive literature survey, and 22 of these iridoids passed the drug-likeness filter. The selected iridoids were molecularly docked against the N. fowleri CYP51 receptor, using voriconazole as a standard for comparison. The docking score for voriconazole was -7.6 kcal/mol, while the scores for 10-isovaleroyl-dihydropenstemide and Patrinalloside A were -8.9 and -8.6 kcal/mol, respectively. According to molecular dynamics (MD) simulation data, the interacting amino acid residues exhibited fluctuations within a specific range, with the Root Mean Square Deviation (RMSD) values stabilizing throughout the experiment. When interacting with the receptor linked to amoebic meningoencephalitis, 10-isovaleroyl-dihydropenstemide and Patrinalloside A showed free binding energies of -71.922 kJ/mol and -61.243 kJ/mol, respectively, based on Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations. Furthermore, Fragment Molecular Orbital (FMO) and Molecular Electrostatic Potential (MEP) analyses of 10-isovaleroyl-dihydropenstemide and Patrinalloside A revealed potential nucleophilic-electrophilic attack zones, indicating they are chemically reactive. The analysis of both compounds' ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) indicated non-toxic behaviour. These findings suggest that natural iridoids have significant potential in combating primary amoebic meningoencephalitis.

Author Biographies

Prinsa, Department of Pharmaceutical Chemistry, Siddhartha Institute of Pharmacy, Near IT-Park, Sahastradhara Road, Dehradun 248001, Uttarakhand, India

Department of Pharmaceutical Chemistry, Siddhartha Institute of Pharmacy, Near IT-Park, Sahastradhara Road, Dehradun 248001, Uttarakhand, India

Supriyo Saha, Department of Pharmaceutical Chemistry, Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun-248001, Uttarakhand, India

Department of Pharmaceutical Chemistry, Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun-248001, Uttarakhand, India

References

Ahmed, U., Manzoor, M., Qureshi, S., Mazhar, M., Fatima, A., et al. (2023). Anti-amoebic effects of synthetic acridine-9(10H)-one against brain-eating amoebae. Acta Tropica, 239, 106824. DOI: https://doi.org/10.1016/j.actatropica.2023.106824

Akter, S, Alhatlani, B.Y., Abdallah, E.M., Saha, S., Ferdous, J., Hossain, M.E., Ali, F., & Kawsar, S.M.A. (2023). Exploring Cinnamoyl-Substituted Mannopyranosides: Synthesis, Evaluation of Antimicrobial Properties, and Molecular Docking Studies Targeting H5N1 Influenza A Virus. Molecules, 28(24), 8001. DOI: https://doi.org/10.3390/molecules28248001

Alamri, M.A., Alawam, A.S., Alshahrani, M.M., Kawsar, S.M.A., Prinsa., & Saha, S. (2023). Establishing the Role of Iridoids as Potential Kirsten Rat Sarcoma Viral Oncogene Homolog G12C Inhibitors Using Molecular Docking; Molecular Docking Simulation; Molecular Mechanics Poisson-Boltzmann Surface Area; Frontier Molecular Orbital Theory; Molecular Electrostatic Potential; and Absorption, Distribution, Metabolism, Excretion, and Toxicity Analysis. Molecules, 28(13), 5050. DOI: https://doi.org/10.3390/molecules28135050

Baker, N.A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J.A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of National Academy of Science USA, 98, 10037-10041. DOI: https://doi.org/10.1073/pnas.181342398

Barca, G.M.J., Bertoni, C., Carrington, L., Datta, D., De Silva, N., et al. (2020). Recent developments in the general atomic and molecular electronic structure system. Journal of Chemical Physics, 152(15), 154102. DOI: https://doi.org/10.1063/5.0005188

Boulebd, H. (2025). A comprehensive DFT-based study of the antioxidant properties of monolignols: Mechanism, kinetics, and influence of physiological environments. International Journal of Biological Macromolecule, 284(Pt 1), 138044. DOI: https://doi.org/10.1016/j.ijbiomac.2024.138044

Calis, Z, Mogulkoc, R., & Baltaci, A.K. (2020). The Roles of Flavonols/Flavonoids in Neurodegeneration and Neuroinflammation. Mini Reviews in Medicinal Chemistry, 20(15), 1475-1488. DOI: https://doi.org/10.2174/1389557519666190617150051

Chen, X., Li, H., Tian, L., Li, Q., Luo, J., & Zhang, Y. (2020). Analysis of the Physicochemical Properties of Acaricides Based on Lipinski's Rule of Five. Journal of Computational Biology, 27(9), 1397-1406. DOI: https://doi.org/10.1089/cmb.2019.0323

Cooper, A.M., Aouthmany, S., Shah, K., & Rega, P.P. (2019). Killer amoebas: Primary amoebic meningoencephalitis in a changing climate. Journal of American Academy Physician Association, 32(6), 30-35. DOI: https://doi.org/10.1097/01.JAA.0000558238.99250.4a

Daina, A., Michielin, O., & Zoete, V. (2017). Swiss ADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. DOI: https://doi.org/10.1038/srep42717

de Souza, F.N., de Lima, H.B., de Souza, L.R., Oliveira, G.S., de Paula da Silva, C.H.T., Pereira, A.C.M., & da Silva Hage-Melim, L.I. (2022). Design of Multitarget Natural Products Analogs with Potential Anti-Alzheimer's Activity. Current Computer Aided Drug Design, 18(2), 120-149. DOI: https://doi.org/10.2174/1573409918666220328141605

Elyashberg, M., Tyagarajan, S., Mandal, M., & Buevich, A.V. (2023). Enhancing Efficiency of Natural Product Structure Revision: Leveraging CASE and DFT over Total Synthesis. Molecules, 28(9), 3796. DOI: https://doi.org/10.3390/molecules28093796

Geng, X., Wang, Y., Li, H., Song, L., Luo, C., Gu, X., Zhong, H., Chen, H., Chen, X., Wang, J., & Pan, Z. (2024). Total iridoid glycoside extract of Lamiophlomis rotata (Benth) Kudo accelerates diabetic wound healing by the NRF2/COX2 axis. Chinese Medicine, 19(1), 53. DOI: https://doi.org/10.1186/s13020-024-00921-1

Goodsell, D.S., Sanner, M.F., Olson, A.J., & Forli, S. (2021). The AutoDock suite at 30. Protein Science, 30(1), 31-43. DOI: https://doi.org/10.1002/pro.3934

Grover, P., Mehta, L., Malhotra, A., Kapoor, G., Nagarajan, K., Kumar, P., Chawla, V., & Chawla, P.A. (2023). Exploring the Multitarget Potential of Iridoids: Advances and Applications. Current Topics in Medicinal Chemistry, 23(5), 371-388. DOI: https://doi.org/10.2174/1568026623666221222142217

Güémez, A., & García, E. (2021). Primary Amoebic Meningoencephalitis by Naegleria fowleri: Pathogenesis and Treatments. Biomolecules, 11(9), 1320. DOI: https://doi.org/10.3390/biom11091320

Hanson, R.M., Prilusky, J., Renjian, Z., Nakane, T., & Sussman, J.L. (2013). JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry, 53 (3-4), 207-216. DOI: https://doi.org/10.1002/ijch.201300024

Hanwell, M.D., Curtis, D.E., Lonie, D.C., Vandermeersch, T., Zurek, E., & Hutchison, G.R. (2012). Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4, 17. DOI: https://doi.org/10.1186/1758-2946-4-17

He, F., Yan, X., Zhao, N., Jiang, X., Wei, Y., Lu, F., Li, H., Li, D., & Chen, Y. (2023). Iridoid-glycoside isolation and purification from Premna fulva leaves. Journal of Separation Science, 46(14), e2300059. DOI: https://doi.org/10.1002/jssc.202300059

Kalman, M., & Ben-Tal, N. (2010). Quality assessment of protein model-structures using evolutionary conservation. Bioinformatics, 26(10), 1299-307. DOI: https://doi.org/10.1093/bioinformatics/btq114

Kar, P., Oriola, A.O., & Oyedeji, A.O. (2024). Molecular Docking Approach for Biological Interaction of Green Synthesized Nanoparticles. Molecules, 29(11), 2428. DOI: https://doi.org/10.3390/molecules29112428

Karakiliç, E., Başçeken, S., Eskiler, G.G., Uzuner, U., & Baran, A. (2025). Bioimaging of thiazolidine-4-one-based new probes, fluorimetric detection of Cu2+ "on-off" sensor property, DFT calculation, molecular docking studies, and multiple real samples application. Food Chemistry, 463(Pt 2), 141269. DOI: https://doi.org/10.1016/j.foodchem.2024.141269

Kawsar, S.M.A., Hossain, M.A., Saha, S., Abdallah, E.M., Bhat, A.R., Ahmed, S., Jamalis, J., & Ozeki Y. (2024). Nucleoside-Based Drug Target with General Antimicrobial Screening and Specific Computational Studies against SARS-CoV-2 Main Protease. Chemistry Select, 9, e202304774. DOI: https://doi.org/10.1002/slct.202304774

Kim, S., Lee, J., Jo, S., Brooks, C.L. 3rd., Lee, H.S., & Im, W. (2017). CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. Journal of Computational Chemistry, 38(21), 1879-1886. DOI: https://doi.org/10.1002/jcc.24829

Kokubu, R., Ohno, S., Manabe, N., & Yamaguchi, Y. (2024). Molecular Dynamics Simulation and Docking of MUC1 O-Glycopeptide. Methods in Molecular Biology, 2763, 373-379. DOI: https://doi.org/10.1007/978-1-0716-3670-1_32

Kumar, P., Kumar, P, Shrivastava, A., Dar, M.A., Lokhande, K.B., Singh, N., Singh, A., Velayutham, R., and Mandal, D. (2023). Immunoinformatics-based multi-epitope containing fused polypeptide vaccine design against visceral leishmaniasis with high immunogenicity and TLR binding. International Journal of Biological Macromolecule, 253(Pt 8), 127567. DOI: https://doi.org/10.1016/j.ijbiomac.2023.127567

Kumari, R., & Kumar, R. (2014). Open Source Drug Discovery Consortium, Lynn A. g_mmpbsa-A GROMACS Tool for High-Throughput MM-PBSA Calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. DOI: https://doi.org/10.1021/ci500020m

Kushwaha, P.P., Singh, A.K., Bansal, T., Yadav, A., Prajapati, K.S., Mohd, S., & Kumar, S. (2021). Identification of Natural Inhibitors Against SARSCoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach. Frontier Cellular Infection Microbiology, 11, 730288. DOI: https://doi.org/10.3389/fcimb.2021.730288

Lemkul, J.A. (2018). From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package, v1.0. Living Journal of Computational Molecular Science, 1(1) 5068. DOI: https://doi.org/10.33011/livecoms.1.1.5068

Lokhande, K., Nawani, N.K., Venkateswara, S., & Pawar, S. (2022). Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach. Journal of Biomolecular Structure Dynamics, 40(10), 4376-4388. DOI: https://doi.org/10.1080/07391102.2020.1858165

Lv, H., Ruan, M., Wen, Y., Zhou, L., Zhao, P., & Xuan, X. (2025). Toward understanding ammonia capture in two amino-functionalized metal-organic frameworks using in-situ infrared spectroscopy and DFT calculation. Spectrochima Acta A Molecular and Biomolecular Spectroscopy, 324, 124962. DOI: https://doi.org/10.1016/j.saa.2024.124962

Madero-Ayala, P.A., Mares-Alejandre, R.E., & Ramos-Ibarra, M.A. (2022). In Silico Structural Analysis of Serine Carboxypeptidase Nf314, a Potential Drug Target in Naegleria fowleri Infections. International Journal of Molecular Sciences, 23(20), 12203. DOI: https://doi.org/10.3390/ijms232012203

Maharana, J., Hwang, S.K., Singha, D.L., Panda, D., Singh, S., Okita, T.W., & Modi, M.K. (2024). Exploring the structural assembly of rice ADP-glucose pyrophosphorylase subunits using MD simulation. Journal of Molecular Graphics & Modeling, 129, 108761. DOI: https://doi.org/10.1016/j.jmgm.2024.108761

Notarte, K.I.R., Quimque, M.T.J., Macaranas, I.T., Khan, A., Pastrana, A.M., Villaflores, O.B., et al. (2023). Attenuation of Lipopolysaccharide-induced Inflammatory Responses through Inhibition of the NF-κB Pathway and the Increased NRF2 Level by a Flavonol-enriched n-Butanol Fraction from Uvaria alba. ACS Omega, 8(6), 5377–5392. DOI: https://doi.org/10.1021/acsomega.2c06451

Paggi, J.M., Pandit, A., & Dror, R.O. (2024). The Art and Science of Molecular Docking. Annual Review of Biochemistry, 93(1), 389-410. DOI: https://doi.org/10.1146/annurev-biochem-030222-120000

Park, S.W., Lee, B.H., Song, S.H., & Kim, M.K. (2023). Revisiting the Ramachandran plot based on statistical analysis of static and dynamic characteristics of protein structures. Journal of Structural Biology, 215(1), 107939. DOI: https://doi.org/10.1016/j.jsb.2023.107939

Perri, M.J., & Weber, S.H. (2014). Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program. Journal of Chemical Education, 91(12), 2206-2208. DOI: https://doi.org/10.1021/ed5004228

Prinsa., Saha, S., Bulbul, M.Z.H., Ozeki, Y., Alamri, M.A., & Kawsar S.M.A. (2024). Flavonoids as potential KRAS inhibitors: DFT, molecular docking, molecular dynamics simulation and ADMET analyses. Journal of Asian Natural Product Research, 26(8), 955-992. DOI: https://doi.org/10.1080/10286020.2024.2343821

Riyaphan, J, Pham, D.C., Leong, M.K., & Weng, C.F. (2021). In Silico Approaches to Identify Polyphenol Compounds as α-Glucosidase and α-Amylase Inhibitors against Type-II Diabetes. Biomolecules, 11(12), 1877. DOI: https://doi.org/10.3390/biom11121877

Rojo, J.U., Rajendran, R., & Salazar, J.H. (2023). Laboratory Diagnosis of Primary Amoebic Meningoencephalitis. Laboratory Medicine, 54(5), e124-e132. DOI: https://doi.org/10.1093/labmed/lmac158

Rout, M., Dey, S., Mishra, S., Panda, S., Singh, M.K., Sinha, R., Dehury, B., & Pati, S. (2024). Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus. Journal of Biomolecular Structure & Dynamics, 42(8), 3935-3948. DOI: https://doi.org/10.1080/07391102.2023.2216290

Saji, R.S., Prasana, J.C., Muthu, S., & George, J. (2021). Experimental and theoretical spectroscopic (FT-IR, FT-Raman, UV-VIS) analysis, natural bonding orbitals and molecular docking studies on 2-bromo-6-methoxynaphthalene: A potential anticancer drug. Heliyon, 7(6), e07213. DOI: https://doi.org/10.1016/j.heliyon.2021.e07213

Sakr, M.A.S., Sherbiny, F.F., & El-Etrawy, A.S. (2022). Hydrazone-based Materials; DFT, TD-DFT, NBO Analysis, Fukui Function, MESP Analysis, and Solar Cell Applications. Journal of Fluorescence, 32(5), 1857-1871. DOI: https://doi.org/10.1007/s10895-022-03000-6

Schou, C., Kolören, Z., Sendker, J., Sarigiannis, Y., Jovanovic, A., & Karanis, P. (2024). Odontites linkii subsp. cyprius Ethanolic Extract Indicated In Vitro Anti-Acanthamoeba Effect. Microorganisms, 12(11), 2303. DOI: https://doi.org/10.3390/microorganisms12112303

Shi, D.Q., Liu, J.J., Feng, Y.M., Zhou, Y., Liao, C.C., Liu, D., Li, R.T., & Li, H.M. (2023). Iridoids and sesquiterpenoids from Valeriana officinalis and their bioactivities. Phytochemistry, 205, 113478. DOI: https://doi.org/10.1016/j.phytochem.2022.113478

Sultan, R., Ahmed, A., Wei, L., Saeed, H., Islam, M., & Ishaq M. (2023). The anticancer potential of chemical constituents of Moringa oleifera targeting CDK-2 inhibition in estrogen receptor positive breast cancer using in-silico and in vitro approches. BMC Complementary Medicine and Therapies, 23(1), 396. DOI: https://doi.org/10.1186/s12906-023-04198-z

Talimarada, D., Sharma, A., Wakhradkar, M.G., Dhuri, S.N., Gunturu, K.C., Sundaram, V.N.N., & Holla, H. (2022). Synthesis, DFT analysis and in-vitro anticancer study of novel fused bicyclic pyranoneisoxazoline derivatives of Goniodiol-diacetate-a natural product derivative. Fitoterapia, 163, 105316. DOI: https://doi.org/10.1016/j.fitote.2022.105316

Vishvakarma, V.K., Pal, S., Singh, P., & Bahadur, I. (2022a). Interactions between main protease of SARS-CoV-2 and testosterone or progesterone using computational approach. Journal of Molecular Structure, 1251, 131965. DOI: https://doi.org/10.1016/j.molstruc.2021.131965

Vishvakarma, V.K., Singh, M.B., Jain, P., Kumari, K., & Singh, P. (2022b). Hunting the main protease of SARS-CoV-2 by plitidepsin: Molecular docking and temperature-dependent molecular dynamics simulations. Amino Acids, 54, 205–213. DOI: https://doi.org/10.1007/s00726-021-03098-1

Wagoner, J.A., & Baker, N.A. (2006). Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proceedings of National Academy of Science USA, 103(22), 8331-6. DOI: https://doi.org/10.1073/pnas.0600118103

Wang, C., Gong, X., Bo, A., Zhang, L., Zhang, M., Zang, E., Zhang, C., & Li, M. (2020). Iridoids: Research Advances in Their

Phytochemistry, Biological Activities, and Pharmacokinetics. Molecules, 25(2), 287. DOI: https://doi.org/10.3390/molecules25020287

Wu, Q., Ghosal, K., Kana'an, N., Roy, S., Rashed, N., Majumder, R., Mandal, M., Gao, L., & Farah, S. (2024). On-demand imidazolidinyl urea-based tissue-like, self-healable, and antibacterial hydrogels for infectious wound care. Bioactive Materials, 44, 116-130. DOI: https://doi.org/10.1016/j.bioactmat.2024.10.003

Yasir, M., Park, J., Han, E.T., Han, J.H., Park, W.S., & Chun, W. (2024). Investigating the Inhibitory Potential of Flavonoids against Aldose Reductase: Insights from Molecular Docking, Dynamics Simulations, and gmx_MMPBSA Analysis. Current Issues in Molecular Biology, 46(10), 11503-11518 DOI: https://doi.org/10.3390/cimb46100683

Yu, D., Li, H., Liu, Y., Yang, X., Yang, W., Fu, Y., Zuo, Y.A., & Huang, X. (2024). Application of the molecular dynamics simulation GROMACS in food science. Food Research International. 190, 114653. DOI: https://doi.org/10.1016/j.foodres.2024.114653

Zhang, L., Wu, L., Liu, J., Chen, K., & Li, Y. (2023). Iridoids and derivatives from Catalpa ovata with their antioxidant activities. Fitoterapia, 169, 105599. DOI: https://doi.org/10.1016/j.fitote.2023.105599

Zhang, Q., Ran, T., Li, S., Han, L., Chen, S., Lin, G., Wu, H., Wu, H., Feng, S., Chen, J., Zhang, Q., & Zhao, X. (2024). Catalpol ameliorates liver fibrosis via inhibiting aerobic glycolysis by EphA2/FAK/Srcsignaling pathway. Phytomedicine. 135, 156047. DOI: https://doi.org/10.1016/j.phymed.2024.156047