| Literature DB >> 35982736 |
Ifeoma Felicia Chukwuma1,2, Florence Nkechi Nworah1, Victor Onukwube Apeh3, Kingsley Ozioma Omeje1, Ekene John Nweze1, Chukwudi Daniel Asogwa1, Timothy Prince Chidike Ezeorba1,2,4.
Abstract
The geometrical increase in diabetes mellitus (DM) and the undesirable side effects of synthetic drugs have intensified efforts to search for an effective and safe anti-diabetic therapy. This study aimed to identify the antioxidant and anti-diabetic agents in the ethanol extract of Leptadenia hastata (EELH). The phytochemicals, antioxidant vitamins, and minerals present in EELH were determined using standard procedures to achieve this aim. Gas chromatography coupled with mass spectroscopy and flame ionization detector (GC-MS/GC-FID) was employed to identify bioactive compounds. An e-pharmacophore model was generated from the extra precision, and energy-minimized docked position of standard inhibitor, acarbose onto human pancreatic amylase (HPA, PDB-6OCN). It was used to screen the GC-MS/GC-FID library of compounds. The top-scoring compounds were subjected to glide XP-docking and prime MM-GBSA calculation with the Schrodinger suite-v12.4. The Adsorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) prediction of the best-fit compounds was made using SwissADME and PROTOX-II webservers. Further validation of the docking results was performed with the in vitro analysis of the α-amylase and α-glucosidase inhibitory activities. EELH contains appreciable amounts of antioxidant and anti-diabetic phytoconstituents. The top-4 scoring compounds (rutin, epicatechin, kaempferol, and naringenin) from the EELH phytochemical library interacted with amino acid residues within and around the HPA active site. The ADMET prediction shows that epicatechin, kaempferol, and naringenin had favorable drug-likeness, pharmacokinetic properties, and a good safety profile. EELH demonstrated good inhibitory actions against α-amylase and α-glucosidase with 1C50 values of 14.14 and 4.22 µg/mL, respectively. Thus, L hastata phytoconstituents are promising novel candidates for developing an anti-diabetic drug.Entities:
Keywords: ADMET; Leptadenia hastata; diabetes mellitus; human pancreatic amylase; molecular docking; pharmacophore modeling
Year: 2022 PMID: 35982736 PMCID: PMC9379957 DOI: 10.1177/11779322221115436
Source DB: PubMed Journal: Bioinform Biol Insights ISSN: 1177-9322
Phytochemical screening of the EELH leaves.
| Phytochemical | Observation | Inference | Remark |
|---|---|---|---|
| Alkaloids | Reddish-brown ppt |
| Moderate |
| Flavonoid | Yellow ppt |
| High |
| Tannins | Light green |
| Low |
| Saponin | Light emulsion |
| Low |
| Cardiac glycoside | Brown color |
| Moderate |
| Terpenoids | Colorless | − | Absence |
| Steroids | Light brown |
| Low |
, ++, and +++ denote low, moderate, and high concentrations, respectively.
Figure 1.Antioxidant vitamins (A) and minerals (B) composition of EELH.
Values are presented as mean ± SD of triplicate determination. Mean values with different letters of alphabet differed from each other significantly at P < .5.
EELH indicates ethanol extract of L hastata.
Figure 2.Chromatogram of different peaks identified in EELH using (A) GC-MS and (B) GC-FID.
GC-FID indicates gas chromatography–flame ionization detector; GC-MS, gas chromatography–mass spectrophotometer.
GC-MS profiling of volatile compounds in EELH.
| S/N | Compounds | RT | Area | Mol. Weight, (g/mol) | Formulae |
|---|---|---|---|---|---|
| 1 | Cyclooctane | 1.688 | 0.05 | 112.21 | C8H16 |
| 2 | 2,4-Dinitro-1,3-dimethyl-benzene Benzoic acid | 1.798 | 0.26 | 172.58 | C7H4N2O6 |
| 3 | 2-Pyrrolidinone | 8.420 | 0.65 | 85.11 | C4H7NO |
| 4 | Triacetin | 13.529 | 0.35 | 218.21 | C9H14O6 |
| 5 | 1,2,3-Benzenetriol | 322.785 | 24.74 | 126.11 | C6H6O3 |
| 6 | 1,2-Benzenediol | 14.327 | 0.19 | 110.11 | C6H6O2 |
| 7 | Acetophenone | 14.911 | 0.52 | 120.15 | C6H5COCH3 |
| 8 | Benzoic acid | 34.481 | 4.20 | 122.12 | C6H5COOH |
| 9 | Vanillic acid | 16.580 | 0.19 | 168.14 | C8H8O4 |
| 10 | Triethyl citrate | 17.789 | 0.70 | 176.283 | C12H20O7 |
| 11 | Pyrazole-5-carboxylic acid | 38.912 | 0.94 | 162.09 | C5H4F2N2O2 |
| 12 | Propanoyl chloride | 19.159 | 0.29 | 92.52 | C3H5ClO |
| 13 | Phthalic acid | 20.269 | 12.47 | 166.14 | C8H6O4 |
| 14 | n-Hexadecanoic acid | 21.118 | 2.52 | 256.4 | C16H32O2 |
| 15 | Dibutyl phthalate | 21.275 | 1.50 | 278.34 | C16H22O4 |
| 16 | IH-Imidazole-4,5-dicarboxylic acid | 21.468 | 3.47 | 156.10 | C5H4N2O4 |
| 17 | Diisooctyl phthalate | 22.406 | 25.81 | 390.5561 | C24H38O4 |
| 18 | 5-Amino-2H-pyrazole-3-carboxamide | 22.538 | 0.43 | 169.18 | C7H11N3O2 |
| 19 | 5-Acetoxymethyl-2-furaldehyde | 22.591 | 0.39 | 168.1467 | C8H8O4 |
| 20 | IH-3a | 22.638 | 0.56 | 142.20 | C11H10 |
| 21 | Benzene | 22.695 | 0.67 | 78.11 | C6H6 |
| 22 | Trans-3-Undecene-1,5-diyne | 22.807 | 0.69 | 146.23 | C11H14 |
| 23 | 3-Isopropyl-5-(phenoxymethyl)-2-oxazolidinone | 22.919 | 0.95 | 129.1570 | C6H11NO2 |
| 24 | 1-Octyl-2-(6-(4) | 23.138 | 0.49 | 292.5 | C19H32O2 |
| 25 | 1-Docosene | 23.444 | 0.80 | 308.6 | C22H44 |
| 26 | Trans-3-Undecene-1,5-diyne | 47.326 | 0.95 | 146.23 | C11H14 |
| 27 | s-triazole-3-carboxaldehyde | 23.806 | 0.17 | 97.08 | C3H3N3O |
| 28 | 1-octyl-2-(6-[hexyl] cyclopropane | 23.841 | 0.16 | 126.24 | C9H18 |
| 29 | Methyl 4-(2,4-dinitrophenylhydrazono) valerate | 23.859 | 0.38 | 130.18 | C7H14O2 |
| 30 | 2-Heptanol | 24.318 | 7.01 | 116.201 | C7H16O |
| 31 | 1-Methyl-2-benzylimino-1,2-dihydroquinoline | 24.712 | 0.02 | 145.20 | C8H8N2O |
| 32 | Silane | 24.882 | 7.68 | 32.12 | H4Si |
Abbreviation: RT, retention time.
Non-volatile compounds identified with GC-FID in EELH.
| S/N | Compounds | RT | Area | Mol. weight, (g/mol) | Formula | Class of compounds |
|---|---|---|---|---|---|---|
| 1 | Rutin | 0.386 | 2631.04 | 610.521 | C27H30O16 | Flavonoid |
| 2 | Lunamarine | 0.873 | 4824.98 | 469.311 | C18H15NO14 | Glycoside |
| 3 | Naringin | 3.093 | 3389.30 | 580.53 | C27H32O14 | Flavonoid |
| 4 | Cardiac glycosides | 5.483 | 2954.84 | 780.9 | C14H64O13 | Steroid |
| 5 | Ephedrine | 7.873 | 2954.84 | 165.236 | C10H15NO | Alkaloid |
| 6 | Anthocyanin | 9.350 | 3057.12 | 1730.5 | C78H89O44 | Flavonoid |
| 7 | Naringenin | 10.830 | 6003.07 | 272.25 | C15H12O5 | Flavonoid |
| 8 | Sparteine | 14.036 | 3250.66 | 234.38 | C15H26N2 | Alkaloid |
| 9 | Phenol | 19.973 | 4928.68 | 94.11 | C6H5OH | Phenol |
| 10 | Flavanones | 20.616 | 3419.69 | 222.24 | C15H10O2 | Flavonoid |
| 11 | Steroids | 36.363 | 6954.48 | 358.4 | C19H28O2 | Steroid |
| 12 | Epicatechin | 25.960 | 7289.28 | 290.27 | C15H14O6 | Flavonoid |
| 13 | Kaempferol | 29.326 | 5273.28 | 286.23 | C15H10O6 | Flavonoid |
| 14 | Phytate | 31.653 | 6802.67 | 660.04 | C6H18O24P6 | Steroid |
| 15 | Cyanogenic glycoside | 34.150 | 3084.59 | 247.24 | C10H17NO6 | Glycoside |
| 16 | Sapogenin | 36.773 | 4449.93 | 1031.18 | C51H82O21 | Saponin |
| 17 | Catechin | 36.640 | 8024.05 | 290.26 | C15H14O6 | Flavonoid |
Abbreviations: GC-FID, gas chromatography–flame ionization detector; RT, retention time.
Figure 3.E-pharmacophore model of the IFD docked complex of acarbose and apo crystal structure of HPA (6OCN_A). (A) This shows the 3D representation of the docked complex and the interaction of acarbose atoms in the active site of HPA (6OCN_A). (B) The generated e-pharmacophore model is based on the stabilized and energy-minimized interaction in the complex. (C) Pharmacophore model on the interacting atoms of acarbose. (D) Pharmacophore model in the protein complex of acarbose and HPA (6OCN_A).
HPA indicates human pancreatic amylase; IFD, induced-fit docking.
Selected compounds screened from the EELH phytochemical libraries using the pharmacophore hypothesis (blue shade) and their docking score and ligand efficiencies (green shade).
| Screened compounds | Number sites matched | Matched ligand sites | Align score/ vector score | Fitness | Glide rotatable bonds | Docking score | XP GScore | Glide evdw | Glide energy |
|---|---|---|---|---|---|---|---|---|---|
| Rutin | 5/5 | A(14) D(25) D(26) D(21) D(23) | 1.51/0.154 | 0.516 | 16 | −10.517 | −10.545 | −39.294 | −56.721 |
| Epicatechin | 4/5 | A(-) D(10) D(9) D(11) D(8) | 0.96/0.65 | 1.119 | 6 | −7.398 | −7.398 | −25.501 | −41.799 |
| Kaempferol | 3/5 | A(-) D(7) D(8) D(9) D(-) | 0.977/0.727 | 1.185 | 5 | −7.031 | −7.031 | −26.454 | −36.163 |
| Cardiac glycoside | 5/5 | A(5) D(18) D(19) D(16) D(13) | 1.397/0.477 | 0.685 | 12 | −6.495 | −6.495 | −31.144 | −42.945 |
| Naringenin | 3/5 | A(-) D(-) D(8) D(6) D(7) | 0.848/0.743 | 1.179 | 4 | −6.413 | −6.413 | −27.668 | −39.632 |
| Sapogenin A | 4/5 | A(-) D(7) D(8) D(9) D(6) | 1.826/0.571 | 0.531 | 6 | −4.284 | −4.284 | −28.773 | −33.787 |
| 5-Amino-2H-pyrazole-3-carboxamide | 3/5 | A(-) D(3) D(4) D(6) D(-) | 0.887 | 0.992 | 1 | −2.97 | −2.97 | −17.543 | −19.442 |
Figure 4.3D representation of molecular docking poses of selected hit compounds from the extract of L hastata.
Figure 5.2D representation of molecular docking poses of selected hit compounds from the extract of L hastata (rutin [A], epicatechin [B], kaempferol [C], naringenin [D]).
Binding free energy calculated with MM-GBSA approach.
| Compounds | ΔGbind
| ΔGbind
| ΔGbind
| ΔGbind
| ΔGbind
| ΔGbind
|
|---|---|---|---|---|---|---|
| Rutin | −37.19 | −54.62 | −5.43 | −10.14 | −35.75 | 6.31 |
| Epicatechin | −28.49 | −41.16 | −4.5 | −9.76 | −25.39 | 3.38 |
| Kaempferol | −32.36 | −20.22 | −3.58 | −9.45 | −27.52 | 1.26 |
| Naringenin | −29.6 | −30.43 | −2.6 | −6.4 | −28.61 | 1.93 |
| Acarbose | −67.10 | −41.45 | −7.45 | −22.53 | −55.50 | 6.25 |
Abbreviation: MM-GBSA, molecular mechanics–generalized Born surface area.
ADMET prediction output of test compounds.
| Parameters | Rutin | Epicatechin | Kaempferol | Naringenin | Acarbose |
|---|---|---|---|---|---|
| Drug-likeness | |||||
| Mol. weight (g/mol) | 610.52 | 290.3 | 286.24 | 272.3 | 645.60 g/mol |
| # Rotatable bonds | 6 | 1 | 1 | 1 | 9 |
| iLog P | 2.43 | 1.47 | 1.70 | 1.75 | 0.63 |
| # H-bond acceptor | 16 | 6 | 6 | 5 | 19 |
| # H-bond donor | 10 | 5 | 4 | 3 | 14 |
| Molar reactivity | 141.38 | 74.33 | 76.01 | 71.57 | 136.69 |
| TPSA (A
| 269.43 | 110.4 | 111.13 | 86.99 | 321.17 A
|
| Lipinski violations | 3 | 0 | 0 | 0 | 3 |
| Veber violations | 1 | 0 | 0 | 0 | 1 |
| Bioavailability score | 0.17 | 0.55 | 0.55 | 0.55 | 0.17 |
| Pharmacokinetics | |||||
| GI absorption | Low | High | High | High | Low |
| BBB permeant | No | No | No | No | No |
| P-gp substrate | Yes | Yes | No | Yes | Yes |
| CYP1A2 inhibitor | No | No | Yes | Yes | No |
| CYP2C19 inhibitor | No | No | No | No | No |
| CYP2C9 inhibitor | No | No | No | No | No |
| CYP2D6 inhibitor | No | No | Yes | No | No |
| CYP3A4 inhibitor | No | No | Yes | Yes | No |
| Log Kp (cm/s) (skin permeation) | −10.26 | −7.82 | −6.70 | −6.17 | −16.29 cm/s |
| Toxicity | |||||
| Predicted LD50 (mg/kg) | 5000 | 10 000 | 3919 | 2000 | 24 000 |
| Predicted toxicity class | 5 | 6 | 5 | 4 | 6 |
| Hepatotoxicity | − | − | − | − | + |
| Carcinogenicity | − | − | − | − | − |
| Immunogenicity | + | − | − | − | + |
| Mutagenicity | − | − | − | − | − |
| Cytotoxicity | − | − | − | + | − |
Abbreviation: ADMET, Adsorption, Distribution, Metabolism, Excretion, and Toxicity; BBB, blood brain barrier; GI, gastrointestinal; LD50, lethal dose 50; TPSA, topological polar surface area; P-gp, P-glycoprotein; CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4, cytochrome P450 enzymes variants..
Figure 6.Effects of L hastata extract on α-amylase (A) and α-glucosidase (B) enzymes activities.