Background
Materials and methods
Retrieving protein’s structure
Cleaning of protein’s structure
Determining the physicochemical properties of Mpro
Ligand selection and preparation
Molecular docking
Visualization of docking result
Analysis of docking result
ADME and drug likeness studies
Molecular dynamics simulations
Results
Refining of protein
Physicochemical properties of protein
MW | pI* | NR* | PR* | |
---|---|---|---|---|
33,796.64 | 5.95 | 26 | 22 | |
Ext. Co 1 | Ext. Co 2 | Instability Index | Aliphatic Index | GRAVY |
33,640 | 32,890 | 27.65 | 82.12 | -0.019 |
Identification of functional domains of protein
Selection of ligands
Drug-likeliness and toxicity prediction
Toxicity prediction
S.No | Ligands | AMES Toxicity | Max. tolerated dose (human) | hERG I inhibitor | hERG II inhibitor | Oral rat acute toxicity | Oral rat chronic toxicity | Hepatotoxicity | Skin sensitization | T. pyriformis toxicity | Minnow toxicity |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | α-pinene | No | 0.48 | No | No | 1.77 | 2.262 | No | No | 0.45 | 1.159 |
2 | β-pinene | No | 0.371 | No | No | 1.673 | 2.28 | No | No | 0.628 | 1.012 |
3 | Carvone | No | 0.775 | No | No | 1.86 | 1.972 | No | Yes | 0.41 | 1.445 |
4 | Myrtenol | No | 0.439 | No | No | 1.746 | 1.8 | No | Yes | 0.262 | 1.698 |
5 | Quinic acid | No | 1.626 | No | No | 1.128 | 3.529 | No | No | 0.285 | 4.869 |
6 | Caffeic acid | No | 1.145 | No | No | 2.383 | 2.092 | No | No | 0.293 | 2.246 |
7 | Quercetin | No | 0.499 | No | No | 2.471 | 2.612 | No | No | 0.288 | 3.721 |
8 | Rutin | No | 0.452 | No | Yes | 2.491 | 3.673 | No | No | 0.285 | 7.677 |
9 | Casticin | No | 0.47 | No | No | 2.302 | 1.768 | No | No | 0.317 | 2.233 |
10 | Chrysoplenetin | No | 0.491 | No | No | 2.324 | 1.773 | No | No | 0.313 | 2.248 |
11 | Apigenin | No | 0.328 | No | No | 2.45 | 2.298 | No | No | 0.38 | 2.432 |
12 | Arteannunin b | No | 0.195 | No | No | 2.052 | 1.589 | No | No | 0.45 | 1.53 |
13 | Artemisinic acid | No | 0.403 | No | No | 1.747 | 2.251 | No | Yes | 0.541 | 0.541 |
14 | Artemisinin | Yes | 0.065 | No | No | 2.459 | 1 | No | No | 0.322 | 1.406 |
15 | Deoxyartemisinin | No | 0.174 | No | No | 2.161 | 1.506 | No | No | 0.363 | 1.538 |
16 | Dihydroartemisinin | Yes | 0.014 | No | No | 2.227 | 0.995 | No | No | 0.298 | 1.067 |
17 | Artemetin | No | 0.335 | No | No | 2.36 | 1.025 | No | No | 0.332 | 1.842 |
18 | Artemether | No | 0.074 | No | No | 2.429 | 1.043 | No | No | 0.304 | 0.587 |
19 | Artemotil | No | 0.019 | No | No | 2.32 | 0.952 | No | No | 0.347 | 1.799 |
20 | Artesunate | No | 0.256 | No | No | 3.112 | 1.549 | No | No | 0.285 | 1.499 |
21 | Scopoletin | No | 0.614 | No | No | 1.95 | 1.378 | No | No | 0.516 | 1.614 |
22 | Scoparone | No | 0.494 | No | No | 2.345 | 2.408 | No | No | 0.603 | 1.223 |
23 | Scopolin | No | 0.393 | No | No | 2.391 | 3.756 | No | No | 0.286 | 4.198 |
24 | Sitogluside | No | -0.887 | No | No | 2.571 | 3.293 | No | No | 0.285 | -0.811 |
25 | Beta-sitosterol | No | -0.621 | No | Yes | 2.552 | 0.855 | No | No | 0.43 | -1.802 |
Molecular docking
S.No | Ligands | Binding Score Kc/mol | Cavity size | HBD* | HBA* | logP | Molecular Weight g/mol | Rotatable Bonds | Grid Map |
---|---|---|---|---|---|---|---|---|---|
1 | α-pinene | -4.8 | 212 | 0 | 0 | 2.9987 | 136.23 | 0 | 53.705 |
2 | β-pinene | -4.7 | 212 | 0 | 0 | 2.9987 | 136.23 | 0 | 53.705 |
3 | Carvone | -5.1 | 212 | 0 | 1 | 2.4879 | 150.22 | 1 | 53.705 |
4 | Myrtenol | -5.2 | 212 | 1 | 1 | 1.9711 | 152.23 | 1 | 53.705 |
5 | Quinic acid | -5.4 | 258 | 5 | 5 | -2.3214 | 192.17 | 1 | 71.716 |
6 | Caffeic acid | -6 | 212 | 3 | 3 | 1.1956 | 180.16 | 2 | 53.705 |
7 | Quercetin | -7.6 | 258 | 5 | 7 | 1.988 | 302.23 | 1 | 71.716 |
8 | Rutin | -6.9 | 258 | 10 | 16 | -1.6871 | 610.5 | 6 | 71.716 |
9 | Casticin | -7.6 | 258 | 2 | 8 | 2.9056 | 374.3 | 5 | 71.716 |
10 | Chrysoplenetin | -7.7 | 258 | 2 | 8 | 2.9056 | 374.3 | 5 | 71.716 |
11 | Apigenin | -7.8 | 258 | 3 | 5 | 2.5768 | 270.24 | 1 | 71.716 |
12 | Arteannunin b | -6.6 | 212 | 0 | 3 | 2.4518 | 248.32 | 0 | 53.705 |
13 | Artemisinic acid | -7 | 212 | 1 | 1 | 3–6458 | 234.33 | 2 | 53.705 |
14 | Artemisinin | -7 | 212 | 0 | 5 | 2.3949 | 282.33 | 0 | 53.705 |
15 | Deoxyartemisinin | -7.2 | 258 | 0 | 4 | 2.4633 | 266.33 | 0 | 71.716 |
16 | Dihydroartemisinin | -7.1 | 212 | 1 | 5 | 2.1867 | 284.35 | 0 | 53.705 |
17 | Artemetin | -7.6 | 258 | 1 | 8 | 3.2086 | 388.4 | 6 | 71.716 |
18 | Artemether | -7.1 | 212 | 0 | 5 | 2.8408 | 289.37 | 1 | 53.705 |
19 | Artemotil | -7.1 | 258 | 0 | 5 | 3.2309 | 312.4 | 2 | 71.716 |
20 | Artesunate | -7.5 | 258 | 1 | 7 | 2.6024 | 384.4 | 4 | 71.716 |
21 | Scopoletin | -5.9 | 212/258 | 1 | 4 | 1.5072 | 192.17 | 1 | 53.705/71.716 |
22 | Scoparone | -6 | 212 | 0 | 4 | 1.8102 | 206.19 | 2 | 53.705 |
23 | Scopolin | -7.5 | 258 | 4 | 9 | -1.0197 | 354.31 | 4 | 71.716 |
24 | Sitogluside | -7.6 | 688/239 | 4 | 6 | 5.849 | 576.8 | 9 | 56.178/58.474 |
25 | Beta-sitosterol | -6.9 | 212 | 1 | 1 | 8.0248 | 414.7 | 6 | 53.705 |
26 | Refrence Drug (Azithromycin) | -6.8 | 156 | 5 | 14 | 4.76 | 748.98 | 7 | 53.537 |
Interaction of ligands and protein
S.No | Ligand Name | Binding Energy (Kcal/mol) | No.of Hydrogen Bonds | Hydrogen Bonding | Hydrophobic Bonding | |
---|---|---|---|---|---|---|
Amino Acids | Distance | |||||
1 | Quercetin | -7.6 | 2 | O-Thr190-O4 O-Asp187-O7 | 3.03 3.07 | Arg188 His41 His164 Met165 Glu166 Leu167 Pro168 Gln192 Gln189 |
2 | Rutin | -6.9 | 6 | N-Glu166-O2 O-Leu141-O15 NE2-His163-O15 OG-Ser144-O15 N-Gly143-O16 O-Thr26-O12 | 3.26 2.92 3.32 2.82 2.76 3.14 | Thr25 Met49 Gln189 Met165 Arg188 Asp187 His41 Cys145 Asn142 |
3 | Apigenin | -7.6 | 4 | O-Leu141-O4 OG-Ser144-O4 NE2-His163-O4 O-Asp187-O5 | 2.84 2.89 3.19 3.04 | Phe140 Cys145 Met49 Met165 His41 Arg188 Gln189 His164 Glu166 |
4 | Chrysoplenetin | -7.7 | 7 | OG-Ser46-O4 N-Gly143-O5 N-Gly143-O2 N-Ser144-O2 OG-Ser144-O6 NE2-His163-O8 N-Glu166-O7 | 3.35 2.96 2.81 3.23 3.01 3.04 2.88 | Asn142 Cys145 Thr25 Thr24 Thr26 Met49 Leu141 Phe140 Met165 |
5 | Artemetin | -7.6 | 7 | N-Glu166-O7 N-Gly143-O5 N-Cys145-O2 N-Ser144-O2 OG-Ser144-O6 NE2-His163-O6 NE2-His163-O8 | 2.91 2.80 3.13 3.02 2.94 3.24 3.10 | Phe140 Leu141 Met165 Thr25 Met49 Leu27 Thr26 Asn142 |
6 | Casticin | -7.6 | 7 | N-Gly143-O5 N-Cys145-O2 N-Ser144-O2 OG-Ser144-O6 NE2-His163-O6 NE2-His163-O8 N-Glu166-O7 | 3.04 3.13 2.99 2.99 3.29 3.15 3.05 | Asn142 Thr26 Leu27 Met49 Thr25 Thr45 Leu141 Met165 Phe140 His172 |
7 | Sitogluside | -7.6–1 | 5 | NH2-Arg131-O3 OG1-Thr199-O3 NZ-Lys137-O4 O-Asp197-O6 ND2-Asn238-O6 | 2.92 2.96 3.01 3.09 2.80 | Tyr239 Tyr237 Leu287 Gly275 Ala285 Gly278 Met276 Asp289 |
-7.6–4 | 2 | OE1-Gln107-O6 OE1-Gln107-O5 | 2.92 3.28 | Ile249 Phe294 Val297 Pro252 Pro293 Gln110 His246 Glu240 Pro108 | ||
8 | Scopolin | -7.5 | 8 | NE2-His163-O7 O-Leu141-O7 O-Leu141-O9 OG-Ser144-O7 OG-Ser144-O9 N-Ser144-O9 N-Cys145-O9 N-Gly143-O8 | 3.01 2.92 2.76 2.93 3.07 2.89 3.20 3.02 | Asn142 His41 His164 Met165 Gln189 Arg188 Glu166 Phe140 |
9 | Artesunate | -7.5 | 3 | NH2-Arg131-O6 OG1-Thr199-O6 OG1-Thr199-O8 | 3.05 2.84 2.98 | Leu272 Tyr239 Leu287 Leu286 Asp197 Thr198 Asn238 Tyr237 Asp289 |
ADME properties of ligands
Absorption
Distribution
Metabolism
S.No | Ligands | CYP2D6 substrate | CYP3A4 substrate | CYP1A2 inhibitor | CYP2C19 inhibitor | CYP2C9 inhibitor | CYP2D6 inhibitor | CYP3A4 inhibitor |
---|---|---|---|---|---|---|---|---|
1 | Quercetin | No | No | Yes | No | No | No | No |
2 | Rutin | No | No | No | No | No | No | No |
3 | Casticin | No | Yes | Yes | Yes | No | No | Yes |
4 | Chrysoplenetin | No | Yes | Yes | Yes | No | No | Yes |
5 | Apigenin | No | No | Yes | Yes | No | No | No |
6 | Artemetin | No | Yes | Yes | Yes | Yes | No | No |
7 | Artesunate | No | Yes | No | No | No | No | No |
8 | Scopolin | No | No | No | No | No | No | No |
9 | Sitogluside | No | Yes | No | No | No | No | No |
10 | Azithromycin (Standard Drug) | No | Yes | No | No | No | No | No |
Excretion
S.No | Ligands | Total Clearance | Renal OCT2 Substrate |
---|---|---|---|
1 | Quercetin | 0.407 | No |
2 | Rutin | -0.369 | No |
3 | Casticin | 0.628 | No |
4 | Chrysoplenetin | 0.627 | No |
5 | Apigenin | 0.566 | No |
6 | Artemetin | 0.706 | No |
7 | Artesunate | 0.969 | No |
8 | Scopolin | 0.716 | No |
9 | Sitogluside | 0.689 | No |
10 | Azithromycin (Standard Drug) | -0.424 | No |
Lead compound identification
Comparison of standard drug with lead compound
Lipinski’s rule comparison
ADMET properties comparison
S.No | Model Name | Azithromycin | Chrysoplenetin |
---|---|---|---|
1 | AMES Toxicity | No | No |
2 | Max. tolerated dose (human) | 1.927 | 0.491 |
3 | hERG I inhibitor | No | No |
4 | hERG II inhibitor | No | No |
5 | Oral rat acute toxicity | 2.769 | 2.324 |
6 | Oral rat chronic toxicity | 1.991 | 1.773 |
7 | Hepatoxicity | Yes | No |
8 | Skin sensitization | No | No |
9 | T. pyriformis toxicity | 0.285 | 0.313 |
10 | Minnow toxicity | 7.8 | 2.248 |
S. No | Reference drug | Azithromycin | Chrysoplenetin |
---|---|---|---|
1 | Water Solubility | -4.133 | -3.605 |
2 | CaCO2 Solubility | -0.211 | 1.393 |
3 | Intestinal Absorption (human) | 45.808 | 99.856 |
4 | Skin Permeability | -2.742 | -2.743 |
5 | P-glycoprotein substrate | Yes | Yes |
6 | P-glycoprotein I inhibitor | Yes | No |
7 | P-glycoprotein II inhibitor | No | Yes |
S. No | Reference Drug | Azithromycin | Chrysoplenetin |
---|---|---|---|
1 | CYP2D6 substrate | No | No |
2 | CYP3A4 substrate | Yes | Yes |
3 | CYP1A2 inhibitor | No | Yes |
4 | CYP2C19 inhibitor | No | Yes |
5 | CYP2C9 inhibitor | No | No |
6 | CYP2D6 inhibitor | No | No |
7 | CYP3A4 inhibitor | No | Yes |
S. No | Reference Drug | Azithromycin | Chrysoplenetin |
---|---|---|---|
1 | VDss (human) | -0.214 | -0.161 |
2 | Fraction unbound (human) | 0.512 | 0.103 |
3 | BBB Permeability | -1.857 | -1.043 |
4 | CNS Permeability | -3.777 | -3.226 |
S. No | Reference Drug | Azithromycin | Chrysoplenetin |
---|---|---|---|
1 | Total Clearance | -0.424 | 0.627 |
2 | Renal OCT2 Substrate | No | No |
Physicochemical properties comparison
S. No | Drug | Molecular Formula | H-bond donor | H-bond acceptor | Log P-value | Molecular Weight g/ mol | Rotatable Bonds |
---|---|---|---|---|---|---|---|
1 | Azithromycin | C38H72N2O12 | 5 | 14 | 1.9007 | 748.996 | 7 |
2 | Chrysoplenetin | C19H18O8 | 2 | 8 | 2.9056 | 374.3 | 5 |
Docking score comparison
S.No | Compound | Binding Score |
---|---|---|
1 | Azithromycin | -6.8 |
2 | Chrysoplenetin | -7.7 |
Docking analysis comparison
S.No | Ligand Name | Binding Energy (Kcal/mol) | No.of Hydrogen Bonds | Hydrogen Bonding | Hydrophobic Bonding | |
---|---|---|---|---|---|---|
Amino Acids | Distance | |||||
1 | (Top1) Azithromycin | -6.8 | 1 | O-Thr190-O3 | 2.90 | Cys145 Gly143 Ser144 Leu141 Phe140 Asn142 Glu166 Met165 His164 Gln189 |
2 | (Top2) Chrysoplenetin | -7.7 | 7 | OG-Ser46-O4 N-Gly143-O5 N-Gly143-O2 N-Ser144-O2 OG-Ser144-O6 NE2-His163-O8 N-Glu166-O7 | 3.35 2.96 2.81 3.23 3.01 3.04 2.88 | Asn142 Cys145 Thr25 Thr24 Thr26 Met49 Leu141 Phe140 Met165 |
Molecular dynamics simulations
SASA analysis
Hydrogen bond analysis
Binding free energies analysis
Top1-MMGBSA | |
VDWAALS | -50.56 |
EEL | -10.8859 |
ESURF | -7.1783 |
DELTA TOTAL | -45.5898 |
Top1-MMPBSA | |
VDWAALS | -50.56 |
EEL | -10.8859 |
ENPOLAR | -5.678 |
DELTA TOTAL | -42.875 |
Top2-MMGBSA | |
VDWAALS | -57.1607 |
EEL | -11.0774 |
ESURF | -8.8117 |
DELTA TOTAL | -44.2875 |
Top2-MMPBSA | |
VDWAALS | -57.1607 |
EEL | -11.0774 |
ENPOLAR | -5.6832 |
DELTA TOTAL | -43.376 |