Research Article |
Corresponding author: Thi-Kim-Quy Ha ( htkquy@ctu.edu.vn ) Corresponding author: Nguyen-Huan Pham-Khanh ( pknhuan@ctu.edu.vn ) Academic editor: Plamen Peikov
© 2024 Thi-Kim-Quy Ha, Nguyen-Huan Pham-Khanh, Thanh-Khiet Nguyen.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Ha T-K-Q, Pham-Khanh N-H, Nguyen T-K (2024) Molecular docking screening, dynamics simulations, ADMET, and semi-synthesis prediction of flavones and flavonols from the COCONUT database as potent bifunctional neuraminidase inhibitors. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e114967
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Finding new neuraminidase (N) inhibitors to improve anti-influenza treatment is necessary because of the high mutation rates of N protein. Over 3,000 flavones/flavonols and their synthesized products from the COCONUT database were performed in silico docking screening with N1-H274Y-oseltamivir protein (PDB ID: 3CL0). Several derivatives containing nitrogen heterocyclic groups or aromatic rings showed higher anti-neuraminidase potential than that of laninamivir. Especially, the linker groups between the flavone aglycone and nitrogen heterocyclic group created the interactions with the triad of arginine residues Arg118-Arg292-Arg371, which suggested these compounds could become bifunctional inhibitors against the influenza virus strains at the sialic acid binding site and the adjacent 430-cavity position through triad of arginine residues binding. ADMET indicators and the synthesis design strategy of the most suitable compound, ethyl 4-{2-[(5-hydroxy-4-oxo-2-phenyl-4H-chromen-7-yl)oxy]acetyl}piperazine-1-carboxylate, were also successfully predicted and it could be a concerned candidate for further wet-lab synthesis, in vivo and clinical study.
In silico, bifunctional neuraminidase inhibitors, ADMET, semi-synthesis design
Influenza is one of the most terrifying widespread diseases, causing so many fatalities and hospitalizations over the world’s history. This disease is an acute respiratory infection caused by influenza viruses (
Influenza A viruses are classified into different variants based on the two antigenic proteins on their surface: hemagglutinin (H) and neuraminidase (N). H protein binds to the terminal sialic acid residues of oligosaccharide receptors on epithelial cells for the penetration of the virus into the cell cytoplasm. Neuraminidase then cleaves sialic acid to release the new virions off the cell surface (
Flavonoid drugs are a typical class of pharmacological compounds that have significantly contributed to both fundamental and medical research (
The COlleCtion of Open Natural ProdUcTs (COCONUT) database is a free and open server without login for usage. This online database regroups all known compounds from natural products, which helps researchers easily search or perform in silico screening and various computational manipulations and applications (
The current study aims to conduct in silico screening of more than 3,000 flavones and flavonols and propose the simplest procedure for the semi-synthesis of the best candidate based on absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions. The results of our research will help scientists develop strategies to semi-synthesize from natural flavonoids and increase flavonoids’ bioavailability so that we can get the full benefits of flavonoids in our treatment therapy.
More than 3,000 three-dimensional (3D) structures of flavones and flavonols were downloaded from the COCONUT database website (https://coconut.naturalproducts.net/). The 3D structures of oseltamivir and laninamivir were drawn using Chem3D version 16.0 software. After that, these ligands were minimized energy using the molecular mechanics-2 (MM2) method until the root mean square (RMS) gradient value became smaller than 0.001 kcal/mol Å (
The 3D structure of the N1-H274Y-oseltamivir complex (PDB ID: 3CL0) was retrieved from the Protein Data Bank (http://www.pdb.org) (
The binding affinity predictions between the ligands (flavones, flavonols, oseltamivir, or laninamivir) and N protein 3CL0 were carried out using AutoDock Vina parameters assisted with PyRx software (
The predicted potential compounds from the molecular docking study were then performed in the molecular dynamics simulations. Firstly, the 2D structures of these candidates were drawn using the ChemDraw version 16 software, and then the 3D structures were designed and optimized using Gaussian 06 software based on the semi-empirical MP6 method (
Most potential candidates from the second step were predicted the absorption, distribution, metabolism, excretion, and toxicity (ADMET) values using pkCSM online server (https://biosig.lab.uq.edu.au/pkcsm/prediction) and SwissADME web tool (http://www.swissadme.ch). The tested compounds were converted to canonical SMILES files and uploaded to the pkCSM and SwissADME website. The web server tools were suggested for the predicted information, and the ADMET values were chosen from these databases.
The most potential candidate was proposed for the semi-synthesis strategy using the natural source (propolis extract) and other common reagents such as ethyl piperazine-1-carboxylate, ClCH2COCl, K2CO3, K2CO3, KI, dichloromethane (DCM), and acetone that assisted by simple methods (column chromatography and reflux). The semi-synthesis strategy was drawn using the ChemDraw version 16.0 software.
To evaluate the reliability of the molecular docking screening method using AutoDock Vina parameters assisted with PyRx software, two positive controls were first carried out for the molecular docking into both the entire structure and the catalytic active site of N-resistant oseltamivir protein (PDB ID: 3CL0). The binding energy of oseltamivir for the entire and catalytic active site exhibited a value of -6.7 kcal/mol (Suppl. material
The second step of molecular docking screening was carried out for more than 700 candidates (659 flavones and 112 flavonols) with N1-H274Y-oseltamivir protein (PDB ID: 3CL0) at the catalytic active site only. After completing this screening step, only the remaining 145 flavones and 18 flavonols exhibited binding energies equal to or lower than -9.5 kcal/mol (Ki value £ 0.107 µM, which is ten times stronger than that of laninamivir) (Suppl. material
Suppl. material
Molecular docking simulations and HBs interactions between N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with four flavones, two flavonols, oseltamivir, and laninamivir.
ID code | Coconut’s ID | Compound name | Formula | MW (g/mol) | LogP | Bingding energy (kcal/mol) | Ki value (nM) | H-bond number | H-bond length (Å) |
---|---|---|---|---|---|---|---|---|---|
Flavones | |||||||||
428 | CNP0284447 | 2-[(5-hydroxy-4-oxo-2-phenyl-4H-chromen-7-yl)oxy]-N-(1H-indol-4-yl)acetamide | C25H18N2O5 | 426.43 | 4.66 | -10.4 | 23.6 | 8 | Tyr347 – 3.1 Trp178 – 3.0 Glu227 – 2.2 Arg292 – 2.3 Asp151 – 2.2; 3.1 Val149 – 1.9 Thr439 – 3.0 |
581 | CNP0410985 | N-(2H-1,3-benzodioxol-5-yl)-2-[(5-hydroxy-4-oxo-2-phenyl-4H-chromen-7-yl)oxy]acetamide | C24H17NO7 | 431.40 | 4.18 | -10.5 | 19.9 | 5 | Arg152 – 2.3 Asp151 – 2.0 Arg118 – 2.5; 2.6 Val149 – 2.6 |
864 | CNP0200043 | ethyl 4-{2-[(5-hydroxy-4-oxo-2-phenyl-4H-chromen-7-yl)oxy]acetyl}piperazine-1-carboxylate | C24H24N2O7 | 452.46 | 2.85 | -9.7 | 76.8 | 5 | Arg118 – 2.5; 2.6 Val149 – 2.4 Asp151 – 2.5 Arg292 – 2.4 |
948 | CNP0392769 | N-[2-(5-methoxy-1H-indol-3-yl)ethyl]-3-methyl-4-oxo-2-phenyl-4H-chromene-8-carboxamide | C28H24N2O4 | 452.51 | 5.23 | -10.5 | 19.9 | 5 | Glu277 – 2.6 Trp178 – 2.4 Arg371 – 1.9 Arg292 – 2.0; 2.2 |
Flavonols | |||||||||
162 | CNP0032479 | 2-(3-benzyl-4-hydroxyphenyl)-3,7-dihydroxy-5-[(3-hydroxyphenyl)methoxy]-4H-chromen-4-one | C29H22O7 | 482.49 | 5.45 | -10 | 46.3 | 7 | Arg118 – 3.2; 3.3 Arg371 – 2.8; 3.0; 3.3 Arg292 – 2.9 Glu276 – 2.3 |
218 | CNP0107174 | 8-(3-hydroxy-6,7-dimethyl-4-oxo-4H-chromen-2-yl)-2,4-dihydro-1,3-benzodioxine-6-carboxylic acid | C20H16O7 | 368.34 | 3.35 | -9.7 | 76.8 | 4 | Tyr347 – 2.9; 2.9 Arg371 – 2.8 Ser404 – 2.7 |
Control ligands | |||||||||
Oseltamivir (acid form) | C14H24N2O4 | 284.35 | 0.81 | -6.7 | 12,187.7 | 5 | Glu119 – 2.3; 2.5 Tyr406 – 2.5 Arg292 – 2.1; 2.6 | ||
Laninamivir | C13H22N4O7 | 346.34 | -2.91 | -8.1 | 1,145.7 | 10 | Asn294 – 2.7; 3.1 Tyr347 – 2.7 Arg371 – 1.9 Arg292 – 2.1; 2.4 Glu277 – 2.8 Glu227 – 2.4 Trp178 – 2.8 Arg152 – 1.9 |
Among 18 flavonols selected (Suppl. material
Based on the above molecular docking screening results, we predicted that flavonoids (162, 428, 581, 864, and 948) have better bifunctional N inhibitory activity than flavonoid aglycone only (218). Before performing the molecular dynamics simulations, these candidates were analyzed as stable at low pH or not. Previous studies suggested that the N protein was generally stable in the wide pH range of 4.0–7.0, and this protein of pandemic viruses was especially stable at low pH (4.0–5.0) (
HBs play an important role in the stabilization of N protein and ligand complexes (
Percentage of HBs occupancy between N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with three flavones 428, 581, and 864.
No. | H-bond donors | H-bond acceptors | % H-bond occupancy |
---|---|---|---|
428 | |||
1 | LIGAND-Side | GLU227-Side | 58.01% |
2 | LIGAND-Side | ASP151-Side | 54.82% |
3 | LIGAND-Side | VAL149-Main | 20.25% |
4 | ARG118-Side | LIGAND-Side | 1.80% |
5 | ARG371-Side | LIGAND-Side | 0.19% |
6 | LIGAND-Side | TRP178-Main | 0.01% |
581 | |||
1 | LIGAND-Main | ASP151-Side | 45.77% |
2 | LIGAND-Side | VAL149-Main | 8.30% |
3 | ARG118-Side | LIGAND-Side | 1.55% |
4 | TYR406-Side | LIGAND-Side | 0.03% |
5 | LYS150-Main | LIGAND-Side | 0.01% |
864 | |||
1 | LIGAND-Main | ASP151-Side | 21.96% |
2 | ARG292-Side | LIGAND-Side | 6.72% |
3 | LIGAND-Side | VAL149-Main | 3.13% |
4 | ARG118-Side | LIGAND-Side | 1.61% |
5 | TYR347-Side | LIGAND-Side | 1.37% |
6 | ARG371-Side | LIGAND-Side | 1.01% |
7 | LIGAND-Side | LYS150-Main | 0.07% |
8 | ARG152-Side | LIGAND-Side | 0.04% |
After performing the molecular docking screening, dynamics simulations, and predicting the partition coefficient (LogP) values (Table
ADMET predicted values of compound 864 using Swiss ADME and pkCSM web service.
No. | ADMET properties | Value | No. | ADMET properties | Value |
---|---|---|---|---|---|
1 | Log P | 2.85 | 11 | AMES toxicity | No |
2 | TPSA (Å2)* | 109.52 | 12 | Max tolerated dose [log mg/(kg.d)] | 0.671 |
3 | HB donor | 1 | 13 | Cytochrome P450 inhibitors | Yes |
4 | HB acceptor | 7 | 14 | hERG II inhibitor | Yes |
5 | Aqueous solubility (log mol/L) | -4.063 | 15 | Oral rat acute toxicity, LD50 (mol/kg) | 2.331 |
6 | Human intestinal absorption (%) | 83.34 | 16 | Oral rat chronic toxicity (log mg/kg_bw/day) | 1.997 |
7 | Blood-brain barrier permeability (logBB) | -1.374 | 17 | Skin sensitization | No |
8 | P-glycoprotein substrate | Yes | 18 | T. pyriformis toxicity (log µg/L) | 0.342 |
9 | Total clearance [log ml/(min.kg)] | 0.581 | 19 | Minnow toxicity (log mM) | 0.658 |
10 | Bioavailability score* | 0.55 | 20 | Lipinski’s rule violations | 0 |
ADMET predictions of chemicals have significant roles in drug design and development (
Flavones are known as an essential core structure for drug design (
This study successfully carried out an in silico docking screening between N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with over 3,000 flavones and flavonols from the COCONUT database using the Autodock Vina method. During this process, several potent N inhibitors containing linker groups (e.g., ester, ether, urethane, or amide) showed bifunctional binding with the sialic acid binding cavity and the adjacent 430-cavity positions via the interactions with arginine triad Arg118-Arg292-Arg371. These linker groups were required to connect different structural fragments in order to inhibit the N protein at two distinct locations. Furthermore, results of molecular dynamics simulations, ADMET predictions, and the semi-synthesis design strategy also demonstrated the compound 864, ethyl 4-{2-[(5-hydroxy-4-oxo-2-phenyl-4H-chromen-7-yl)oxy]acetyl}piperazine-1-carboxylate, could become the effective bifunctional N inhibitors for further drug design and development, in vivo testing, and clinical trials. The results of this study could contribute to developing new types of N inhibitors from natural products to enhance the efficacy of anti-influenza therapy due to the high mutation rates of N protein in the future.
Some simple experiments were supported by bachelor in medicinal chemistry students (Ms. Hong-Ngoc Cao, Ms. Thi-Dieu-Uyen Vu).
Supporting data
Data type: doc
Explanation note: table S1. Molecular docking simulations of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with Laninamivir and Oseltamivir. table S2. Molecular docking simulations of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with flavones (first step). table S3. Molecular docking simulations of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with flavonols (first step). table S4. Molecular docking simulations of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with flavones (second step). table S5. Molecular docking simulations of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with flavonols (second step). fig. S1. 2D interaction diagrams and 3D molecular docking of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with laninamivir and oseltamivir. fig. S2. 2D interaction diagrams and 3D molecular docking of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with flavones. fig. S3. 2D interaction diagrams and 3D molecular docking of N1-H274Y-oseltamivir protein (PDB ID: 3CL0) with flavonols. Supporting data_List flavones. Supporting data_List flavonols.