Femtomolar inhibition by a virtually designed molecule: Pseudoeriocitrin as a potent inhibitor

Abstract

Pseudoeriocitrin is a virtually designed molecule created in silico by assuming the formation of oxygen radicals in eriocitrin, resulting in a different geometry. It achieves femtomolar-level inhibition in in silico docking studies, demonstrating higher inhibitory efficacy than eriocitrin. This study investigated the mechanisms underlying the extraordinary inhibitory activity of pseudoeriocitrin through a 3D analysis of potential interactions using an in silico protein-ligand docking method. Although it is difficult to reach a definitive conclusion, the absence of hydrogen donors renders the pseudoeriocitrin structure highly toxic. The high binding affinity of pseudoeriocitrin, which inhibits various proteins at the femtomolar level, with the lowest inhibition constant value of 3.45 fM, is presumably due to its planar structure and the abundance of oxygen radicals, which facilitate the formation of hydrogen bonds with atoms in the active site of the proteins. This study is the first to demonstrate the structure-activity relationship of pseudoeriocitrin through in silico docking method. The results indicate that the large core structure, abundance of oxygen atoms, planar geometry, and femtomolar-level inhibition are interrelated. The chemical properties resulting from these unique biological properties should be examined from multiple perspectives. In addition, further research is required to explore the synthesis of non-radical pseudoeriocitrin.

Keywords

Eriocitrin / Femtomolar inhibition / Molecular docking / Pseudoeriocitrin

Funding

None.

Conflict of interest

The authors declare that they have no competing interests.

References

[1] Kamb M, Roy S. Helminths, Soil-Transmitted. Travel- Associated Infections & Diseases. CDC Yellow Book. United Kingdom: Oxford University Press; 2024. Available from: https://wwwnc.cdc.gov/travel/yellowbook/2024/infections-diseases/helminths-soil-transmitted [Last accessed on 2023 May 01].

[2] Giray H, Keskinoğlu P. Ilkokul öğrencilerinde Enterobius vermicularis varliği ve etkileyen etmenler [The prevalence of Enterobius vermicularis in schoolchildren and affecting factors]. Turk Parazitol Derg. 2006;30(2):99-102.

[3] Strelkauska A, Edwards A, Fahnert B, Pryor G, Strelkauskas J. Microbiology: A Clinical Approach. NY, USA: Garland Science; 2015. doi: 10.1201/9780429258701

[4] Karaman D. Prediction on the Anthelmintic Effects of Some Herbal Ligands and Their Derivatives with In Silico Molecular Modelling Method Doctoral Thesis. Bursa, Türkiye: Bursa Uludag University; 2022.

[5] Yelekçi K, Büyüktürk B, Kayrak N. In silico identification of novel and selective monoamine oxidase B inhibitors. J Neural Transm (Vienna). 2013;120(6):853-858. doi: 10.1007/s00702-012-0954-0

[6] Inoue T, Sugimoto Y, Masuda H, Kamei C. Antiallergic effect of flavonoid glycosides obtained from Mentha piperita L. Biol Pharm Bull. 2002; 25(2):256-259. doi: 10.1248/bpb.25.256

[7] Diab KA, Shafik RE, Yasuda S. In vitro Antioxidant and antiproliferative activities of novel orange peel extract and it’s fractions in leukemia HL-60 cells. Asian Pac J Cancer Prev. 2015; 16(16):7053-7060. doi: 10.7314/apjcp.2015.16.16.7053

[8] Guo G, Shi W, Shi F, et al. Anti-inflammatory effects of eriocitrin against the dextran sulfate sodium-induced experimental colitis in murine model. J Biochem Mol Toxicol. 2019; 33(11):e22400. doi: 10.1002/jbt.22400

[9] Miyake Y, Yamamoto K, Osawa T. Isolation of eriocitrin (eriodictyol 7-rutinoside) from lemon fruit (Citrus limon BURM. F.) and its antioxidative activity. Food Sci Technol Int Tokyo. 1997; 3(1):84-89. doi: 10.3136/fsti9596t9798.3.84

[10] Ferreira PS, Manthey JA, Nery MS, Cesar TB. Pharmacokinetics and biodistribution of eriocitrin in rats. J Agric Food Chem. 2012; 69(6):1796-1805. doi: 10.1021/acs.jafc.0c04553

[11] Huey R, Morris GM, Olson AJ, Goodsell DS. Semiempirical free energy force field with charge-based desolvation. J Comput Chem. 2007; 28(6):1145-1152. doi: 10.1002/jcc.20634

[12] Morris GM, Huey R, Lindstrom W, et al. Autodock4 and Autodocktools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785-2791. doi: 10.1002/jcc.21256

[13] Dassault Systèmes BIOVIA. Discovery Studio Modeling Environment Release. San Diego: BIOVIA; 2020.

[14] Taylor CM, Wang Q, Rosa BA, et al. Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways. PLoS Pathog. 2013; 9(8):e1003505. doi: 10.1371/journal.ppat.1003505

[15] Inaoka DK, Shiba T, Sato D, et al. Structural insights into the molecular design of flutolanil derivatives targeted for fumarate respiration of parasite mitochondria. Int J Mol Sci. 2015; 16(7):15287-15308. doi: 10.3390/ijms160715287

[16] Sharma P, Maklashina E, Cecchini G, Iverson TM. The roles of SDHAF2 and dicarboxylate in covalent flavinylation of SDHA, the human complex II flavoprotein. PNAS. 2020; 117:23548-23556. doi: 10.1073/pnas.2007391117

[17] Ti SC, Alushin GM, Kapoor TM. Human β-tubulin isotypes can regulate microtubule protofilament number and stability. Dev Cell. 2018; 47(2):175-190. doi: 10.1016/j.devcel.2018.08.014

[18] Robinson MW, McFerran N, Trudgett A, Houy L, Fairweather IA. Possible model of benzimidazole binding to beta-tubulin disclosed by invoking an inter-domain movement. J Mol Graph Model. 2004; 23(3): 275-284. doi: 10.1016/j.jmgm.2004.08.001

[19] Hsiao YS, Jogl G, Esser V, Tong L. Crystal structure of rat carnitine palmitoyltransferase II (CPT-II). Biochem Biophys Res Commun. 2006; 346(3):974-980. doi: 10.1016/j.bbrc.2006.06.006

[20] Rufer AC, Thoma R, Benz J, et al. The crystal structure of carnitine palmitoyltransferase 2 and implications for diabetes treatment. Structure. 2006; 14(4):713-723. doi: 10.1016/j.str.2006.01.008

[21] Waterhouse A, Bertoni M, Bienert S, et al. SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Res. 2018 ;46(W1):W296-W303. doi: 10.1093/nar/gky427

[22] Roy A, Kucukural A, Zhang Y. I-TASSER: A unified platform for automated protein structure and function prediction. Nat Protoc. 2010; 5(4):725-738. doi: 10.1038/nprot.2010.5

[23] Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER suite: Protein structure and function prediction. Nat Methods. 2015; 12(1):7-8. doi: 10.1038/nmeth.3213

[24] Yang J, Zhang Y. I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Res. 2015; 43:W174-W181. doi: 10.1093/nar/gkv342

[25] Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem. 1998; 19(14):1639-1662. doi: 10.1002/(SICI)1096-987X(19981115)19:14<1639:AID-JCC10>3.0.CO;2-B

[26] Daina A, Michielin O, Zoete V. SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017; 7:42717. doi:10.1038/srep42717

[27] Ritchie TJ, Ertl P, Lewis R. The graphical representation of ADME-related molecule properties for medicinal chemists. Drug Discov Today. 2011; 16:65-72. doi: 10.1016/j.drudis.2010.11.002

[28] Amić A, Marković Z, Dimitrić Marković JM, Stepanić V, Lučić B, Amić D. Towards an improved prediction of the free radical scavenging potency of flavonoids: The significance of double PCET mechanisms. Food Chem. 2014;152:578-585. doi: 10.1016/j.foodchem.2013.12.025

[29] Brown MJ, Mensah LM, Doyle ML, et al. Rational design of femtomolar inhibitors of isoleucyl tRNA synthetase from a binding model for pseudomonic acid-A. Biochemistry. 2000; 39(20):6003-6011. doi: 10.1021/bi000148v.

[30] Ramalingam A, Kuppusamy M, Sambandam S, et al. Synthesis, spectroscopic, topological, hirshfeld surface analysis, and anti-covid-19 molecular docking investigation of isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl- 1,2,5,6-tetrahydropyridine-3-carboxylate. Heliyon. 2022;8(10):e10831. doi: 10.1016/j.heliyon.2022.e10831

[31] Gatfaoui S, Issaoui N, Brandan SA, et al. Deciphering non-covalent interactions of 1,3-benzenedimethanaminium bis(trioxonitrate): Synthesis, empirical and computational study. J Mol Struc. 2022; 1250:131720. doi: 10.1016/j.molstruc.2021.131720.

[32] Akman F, Demirpolat A, Kazachenko| AS, Kazachenko AS, Issaoui N, Al-Dossary O. Molecular structure, electronic properties, reactivity (ELF, LOL, and Fukui), and NCI-RDG studies of the binary mixture of water and essential oil of Phlomis bruguieri. Molecules. 2023; 28(6):2684. doi: 10.3390/molecules28062684

[33] Karaman D, Girişgin AO, Girişgin O. Molecular dockings of secondary metabolites to evaluate anthelmintic potential. Sigma J Eng Nat Sci. 2026;3(44).

[34] Medimagh M, Issaoui N, Gatfaoui S, et al. Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and molecular docking study. Heliyon. 2021; 7:e08204. doi: 10.1016/j.heliyon.2021.e08204

[35] Gatfaoui S, Issaoui N, Roisnel T, Marouani HA. Proton transfer compound template phenylethylamine: Synthesis, a collective experimental and theoretical investigations. J Mol Struc. 2019; 1191:183-196. doi: 10.1016/j.molstruc.2019.04.093