In Silico Characterization of Gelsemium Compounds as Glycine Receptor Ligands
Abstract
1. Introduction
2. Materials and Methods
2.1. Library Preparation
2.2. ADMET and Toxicologic Profiling Gelsemium Compounds
2.3. Protein Selection and Preparation
2.4. Protein-Ligand Docking
2.5. Molecular Dynamics Simulations
3. Results
3.1. Pharmacokinetic and Toxicological Profile of Gelsemium Compounds
3.2. Glycine Receptors Binding Predictions for Gelsemium Compounds
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ADMET | Absorption, Distribution, Metabolism, Excretion, and Toxicity |
AMES | Ames test for mutagenicity |
BBB | Blood–Brain Barrier |
CL | Clearence |
CNS | Central Nervous System |
DILI | Drug-Induced Liver Injury |
PHOA | Predicted Human Oral Absorption |
HERG I | Human Ether-à-go-go-Related Gene inhibition (Kv11.1 potassium channel) |
MM-GBSA | Molecular Mechanics Generalized Born Surface Area |
RMSD | Root Mean Square Deviation |
RMSF | Root Mean Square Fluctuation |
MD | Molecular Dynamics |
ΔGbind | Binding Free Energy |
Pgp | P-glycoprotein |
LIP | Lipinski’s Rule of Five violations |
VEB | Veber’s Rule violations |
OA | Oral Absorption |
QPlogBB | Predicted log of Brain/Blood Partition Coefficient |
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Group | Number | Molecules |
---|---|---|
Indolic compounds | ||
Gelsedine (GS) | 33 | 11-Methoxygelsecrotonidine, 11,14-Dihydroxygelsenicine, 14-Acetoxy-15-hydroxygelsenicine, 14-Acetoxygelselegine, 14α-Hydroxygelsamydine, 14α-Hydroxyelegansamine, 14-Dehydroxygelsefuranidine, 14-Hydroxygelsecrotonidine, 14-Hydroxygelsedilam, 14-Hydroxygelsenicine, 14,15-Dihydroxygelsenicine, 15-Hydroxy-Nb-methylgelsedilam, 19α-Hydroxygelsamydine, 19-Oxogelsenicine, 4,20-Dehydrogelsemicine, Gelegamine C, Gelegamine E, Gelsecrotonidine, Gelsedilam, Gelsedine, Gelsefuranidine, Gelseganine D, Gelseiridone, Gelselenidine, Gelsemicine, Gelseziridine, Gs-1, Gs-3, Gelsemolenine A, Gelsemolenine B, Gelsemoxonine, Gelsenicine, Gelseoxazolidinine |
Gelsemine (GM) | 9 | 19R-Hydroxydihydrogelsemine, 19-(R)-Hydroxydihydrogelsevirine, 21-Oxogelsemine, 21-Oxogelsevirine, Gelsebanine, Gelsemine, Gelsevirine, Gelsevirine N-oxide, Nb-Demethylgelsevirine |
Humantenine (HT) | 24 | 19(E)-Humantenine, (4R)-Humantenine N4-oxide, 4,5-Dehydrorankinidine, 6-Hydroxyhumantenine, 11-Hydroxyhumantenine, 11-Hydroxyrankinidine, 11-Methoxygelsemamide, 11-Methoxyhumantenine, 14-Hydroxyrankinidine, 15-Hydroxyhumantenine, 15-Hydroxyrankinidine, 20-Hydroxydihydrorankinidine, Gelegamine A, Gelegamine B, Gelseganine A, Gelsemamide, Humantenine, Humanteniridine, Humantenirine, Humantenoxenine, N-Desmethoxyhumantenine, N-Desmethoxyrankinidine, Rankinidine, Rankiniridine |
Koumine (KO) | 10 | 21-(2-oxopropyl)-koumine, 21-Oxokoumine, 19-(R)-Hydroxydihydrokoumine, 19-(S)-Hydroxydihydrokoumine, Dihydrokoumine, Furanokoumine, Gelseganine C, Koumine, Kounaminal, Koumine N-oxide |
Sarpagine (SA) | 12 | 19E:16-epi-Voacarpine, 19-(Z)-Akuammidine, 3-Hydroxykoumidine, Anhydrovobasindiol, Dehydrokoumidine, Gelsempervine A, Gelsempervine B, Gelsempervine C, Gelsempervine D, Koumidine, N-Methoxyanhydrovobasinediol, Koumicine N-oxide |
Yohimbane (YO) | 3 | Sempervilam, Sempervirine, Ourouparine |
Non-indolic compounds | ||
Iridoids (IR) | 25 | 7-Deoxygelsemide, 9-Deoxygelsemide, 9-Hydroxysemperoside, Brasoside, GEIR-1, GEIR-2, GEIR-3, Geleganoid A, Geleganoid B, Geleganoid C, Geleganoid D, Geleganoid E, Geleganoid F, Geleganosides A, Geleganosides B, Gelemide-7-glucoside, Gelsemide, Gelsemiol, Gelsemiol-1-glucoside, Gelsemiol-3-glucoside, Gouwenoside A, GRIR-1, GSIR-1, Semperoside, Sweroside |
Megastigmane Glycosides (MG) | 6 | (3R, 5S, 6S, 7E, 9R)-Megastigman-7-ene-3,5,6,9-tetrol-9-O-β-D-glucopyranoside, (6R, 7E, 9R)-9-Hydroxy-4,7-megastigmadien-3-one-9-O-[α-L-arabinopyranosyl-(1->6)-β-D-glucopyranoside], (6S, 7E, 9R)-6,9-Dihydroxy-4,7-megastigmadien-3-one-9-O-[α-L-arabinopyranosyl-(1->6)-β-D-glucopyranoside], Eleganosides A, Eleganosides B, Foliasalacioside B1 |
Steroides (ST) | 7 | 12β-Hydroxy-5α-pregn-16-ene-3,20dione, 12β-Hydroxy-pregna-1,16-diene-3,20-dione, 21-Hydroxy-5α-pregn-16-ene-3,20-dione, 3-Oxoandrosta-16-ene-17-carboxylic acid, 3-Oxoandrosta-4,16-diene-17-carboxylic acid, Stigmasterol, β-Sitosterol |
Lignin- Phenolic acids-Flavonoids (LPF) | 16 | 3,4-Dihydroxyphenylaldehyde, 7-O-β-D-Glucopyranosylscopoletin, (+)-8-Hydroxypinoresinol, caffeic acid, 4-O-Caffeoylquinic acid, Ferulic acid, Gallic acid, Protocatechuic acid, 1-O-Caffeoylquinic acid, Cleomiscosin A, Cleomiscosin C, Ferulic acid ethyl ester, Gelsemiunoside A, Gelsemiunoside B, Tamarixetin 3-O-β-D-galactopyranoside, Tamarixin |
Coumarin—Terpenoids—Fructose and its derivative (CTF) | 9 | 7-O-β-D-Apiofuranosyl-(1->6)-β-D-glucopyranosylscopoletin, 3-Hydroxy-27-p-(E)-coumaroyloxy ursan-12-en-28-oic acid, Scoparone, Scopoletin, Scopolin, Ethyl-α-D-Fructofuranoside, Ethyl-β-D-Fructopyranoside, Fabiatrin, n-Butyl-α-D-Fructofuranoside |
Other type (OT) | 8 | Bis(2-ethylhexyl) phthalate, Gelebolines A, Gelebolines B, Gelebolines C, Gelsebamine, Gelsenine, 2-(4-hydroxyphenyl)ethyl heptadecanoate, Uridine |
Docking Score (kcal/mol) | ΔGbind (kcal/mol) | BBB Permeability | CNS Activity Score | ||||
---|---|---|---|---|---|---|---|
Name | Type | Open | Closed | Open | Closed | ||
Indolic compounds | |||||||
Gelegamine C | GS | −2.814 | −10.993 | −8.94 | −54.71 | No | 1 |
19-(Z)-Akuammidine | SA | −2.262 | −10.299 | −30.78 | −38.14 | Yes | 1 |
14-Acetoxygelselegine | GS | −0.105 | −10.176 | −13.8 | −62.25 | No | 1 |
Koumidine | SA | −3.471 | −10.095 | −8.28 | −40.92 | Yes | 1 |
14-Hydroxyrankinidine | HT | −3.708 | −9.837 | −23.37 | −49.7 | No | 1 |
3-Hydroxykoumidine | SA | −2.537 | −9.331 | −29.9 | −57.66 | Yes | 0 |
Gelsempervine C | SA | −3.661 | −9.185 | −13.74 | −48.23 | No | 1 |
Koumicine N-oxide | SA | −2.773 | −9.099 | −12.85 | −43.19 | Yes | 1 |
Gelsevirine | GM | −2.989 | −9.065 | −27.9 | −36.3 | Yes | 2 |
Gelseganine A | HT | −1.482 | −9.055 | −19.32 | −40.4 | No | 1 |
Non indolic compounds | |||||||
7-O-β-D-Apiofuranosyl-(1-6)-β-D-glucopyranosylscopoletin | CTF | −8.03 | −11.65 | −35.97 | −67.2 | No | −2 |
Fabiatrin | CTF | −4.27 | −11.21 | −25.85 | −63.89 | No | −2 |
(6S,7E,9R)-6,9-Dihydroxy-4,7-Megastigmadien-3-one-9-O-[α-L-Arabinopyranosyl-(1-6)-β-D-Glucopyranoside] | MG | −10.94 | −7.263 | −0.34 | −57.19 | No | −2 |
Tamarixin | LPF | −4.83 | −10.69 | −21.38 | −55.83 | No | −2 |
Tamarixetin 3-O-β-D-galactopyranoside | LPF | −6.38 | −10.65 | −27.55 | −49.81 | No | −2 |
Foliasalacioside B1 | MG | −6.23 | −10.33 | −36.47 | −43.82 | No | −2 |
Scopolin | CTF | −6.87 | −10.25 | −31.2 | −48.22 | No | −2 |
1-O-Caffeoylquinic Acid | LPF | −2.085 | −9.506 | −36.88 | −46.49 | No | −2 |
Gelebolines C | OT | −3.20 | −9.72 | −26.26 | −59.38 | Yes | 0 |
(+)-8-Hydroxypinoresinol | LPF | −4.03 | −9.33 | −33.8 | −45.1 | No | −1 |
Docking Score (kcal/mol) | ΔGbind (kcal/mol) | BBB Permeability | CNS Activity Score | ||||
---|---|---|---|---|---|---|---|
Name | Type | Open | Closed | Open | Closed | ||
Indolic compounds | |||||||
Koumine | KO | −3.022 | −10.138 | −0.33 | −48.87 | Yes | 2 |
Sempervirine | YO | −2.768 | −9.13 | −27.75 | −47.47 | Yes | 1 |
Koumicine N-oxide | SA | −3.314 | −9.017 | −15.38 | −18.06 | Yes | 1 |
6-Hydroxyhumantenine | HT | −3.294 | −9.016 | −30.73 | −40.41 | No | 1 |
19-(Z)-Akuammidine | SA | −3.474 | −8.977 | −23.3 | −39.57 | Yes | 1 |
Gelsedine | GS | −3.079 | −8.897 | −30.41 | −45.51 | Yes | 1 |
Dihydrokoumine | KO | −4.179 | −8.673 | −7.67 | −43.39 | Yes | 2 |
Gelseganine D | GS | −3.307 | −8.643 | −27.39 | −66.54 | No | −2 |
11-Hydroxyhumantenine | HT | −3.155 | −8.549 | −28.96 | −40.07 | Yes | 1 |
14-Hydroxygelsecrotonidine | GS | −3.401 | −8.504 | −32.91 | −49.21 | No | −2 |
Non indolic compounds | |||||||
Foliasalacioside B1 | MG | −5.696 | −10.668 | −25.09 | −48.78 | No | −2 |
Fabiatrin | CTF | −8.354 | −10.346 | −42.64 | −57.76 | No | −2 |
(6R, 7E, 9R)-9-Hydroxy-4,7-megastigmadien-3-one-9-O-[α-L-arabinopyranosyl-(1->6)-β-D-glucopyranoside] | MG | −7.095 | −10.282 | −43.07 | −41.8 | No | −2 |
Eleganosides A | MG | −8.102 | −10.24 | −34.09 | −54.36 | No | −2 |
7-O-β-D-Apiofuranosyl-(1-6)-β-D-glucopyranosylscopoletin | CTF | −9.195 | −9.492 | −39.48 | −55.38 | No | −2 |
Tamarixin | LPF | −7.656 | −9.381 | −38.49 | −47.62 | No | −2 |
Gelsenine | OT | −3.137 | −9.217 | −33.53 | −59.92 | No | 1 |
Gelsemiol-1-glucoside | IR | −6.507 | −9.103 | −22.81 | −48.87 | No | −2 |
Cryptochlorogenic Acid | LPF | −5.007 | −9.031 | −12.87 | −30.95 | No | −2 |
Scopolin | CTF | −7.884 | −8.982 | −26.75 | −48.56 | No | −2 |
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Millar-Obreque, C.; González-Muñoz, V.; Marileo, A.M.; Salgado-Martínez, B.; Gaete-Riquelme, K.; Ramírez-Molina, O.; Godoy, P.A.; Fuentealba, J.; Yévenes, G.E.; Burgos, C.F. In Silico Characterization of Gelsemium Compounds as Glycine Receptor Ligands. Compounds 2025, 5, 40. https://doi.org/10.3390/compounds5040040
Millar-Obreque C, González-Muñoz V, Marileo AM, Salgado-Martínez B, Gaete-Riquelme K, Ramírez-Molina O, Godoy PA, Fuentealba J, Yévenes GE, Burgos CF. In Silico Characterization of Gelsemium Compounds as Glycine Receptor Ligands. Compounds. 2025; 5(4):40. https://doi.org/10.3390/compounds5040040
Chicago/Turabian StyleMillar-Obreque, Camila, Vicente González-Muñoz, Ana M. Marileo, Bernardita Salgado-Martínez, Krishna Gaete-Riquelme, Oscar Ramírez-Molina, Pamela A. Godoy, Jorge Fuentealba, Gonzalo E. Yévenes, and Carlos F. Burgos. 2025. "In Silico Characterization of Gelsemium Compounds as Glycine Receptor Ligands" Compounds 5, no. 4: 40. https://doi.org/10.3390/compounds5040040
APA StyleMillar-Obreque, C., González-Muñoz, V., Marileo, A. M., Salgado-Martínez, B., Gaete-Riquelme, K., Ramírez-Molina, O., Godoy, P. A., Fuentealba, J., Yévenes, G. E., & Burgos, C. F. (2025). In Silico Characterization of Gelsemium Compounds as Glycine Receptor Ligands. Compounds, 5(4), 40. https://doi.org/10.3390/compounds5040040