| Literature DB >> 35637779 |
Amany Belal1, Mohamed A Elanany2, Reem I Alsantali1, Munira M Alrooqi3, Abdalla R Mohamed4, Sherifa Hasabelnaby5.
Abstract
Rhinitis is an allergic disease that causes troubles and restlessness for patients. In this research work we will focus on finding promising organic molecules with potential ability to target histamine receptor with no sedative side effect. Phalazines and their isosteres, pyrimidines and pyridines have been reported to target H1 receptors, for this reason we have searched for library of these basic scaffolds, this library which has 184 organic molecules will be subjected for further explorations through computer aided drug design techniques. Swiss ADMET will be used to gather these compounds in clusters. Cluster with low potential to penetrate BBB is selected for virtual screening through pharmacophore model. Then molecular docking that revealed the stability of the complex formed between the investigated molecules and H1 receptor. ADMET profile showed three compounds (XVIII), (XX), and (XXI) with no toxicity on liver and no effect on CYP2D6, these three compounds were subjected to molecular dynamic simulations and compound (XVIII) showed the most stable complex with the target protein (H1). Finally, we can say this work helped us to find new compounds with promising potential to target H1 without ability to penetrate BBB, so they can be used as useful candidates in treatment of rhinitis and deserve to be subjected for preclinical and clinical investigations. Supplementary Information: The online version contains supplementary material available at 10.1134/S1068162022330019. © Pleiades Publishing, Ltd. 2022, ISSN 1068-1620, Russian Journal of Bioorganic Chemistry, 2022, Vol. 48, No. 2, pp. 438–456. © Pleiades Publishing, Ltd., 2022.Entities:
Keywords: histamine H1; molecular docking; molecular dynamics; pharmacophores; phthalazine; pyridines; pyrimidines; rhinitis; virtual screening
Year: 2022 PMID: 35637779 PMCID: PMC9134989 DOI: 10.1134/S1068162022330019
Source DB: PubMed Journal: Russ J Bioorg Chem ISSN: 1068-1620 Impact factor: 1.254
Fig. 2. Various heterocyclic derivatives with antihistaminic potential.
Fig. 4. Cluster 1 (part 1) 2D chemical structures.
Fig. 8. H1 generated e-pharmacophore.
Fig. 9. Validation results of 7DFL. Green: co-crystallized pose, pink: re-docked pose.
Fig. 10. 2D Binding interactions of azelastine.
Cluster 1 binding scores and interactions against histamine H1 receptor (PDBID: 7DFL)
| Compound | Score | Interactions | |
|---|---|---|---|
| H-bond | Hydrophobic interactions | ||
| ( | –7.51 | PRO161, HIS167, THR194, ASN198 | LEU154, LEU157, TRP158, PHE168, PHE190, MET193, ILE197 |
| ( | –9.81 | ASP107, ASP178, LYS179, HIS450 | TRP103, LEU104, ASP107, TYR108, LYS179, CYS180, TYR431, HIS450, MET451, ILE454 |
| ( | –8.81 | ASN84, TYR108, THR182 | TYR87, ASP107, TYR108, SER111, ILE115, LYS179, CYS180, TYR431, PHE432, MET451, ILE454 |
| ( | –7.66 | ASP107, TYR108, TYR431, GLU447 | LEU104, ASP107, TYR108, LYS179, TYR431, HIS450, ILE454 |
| ( | –8.38 | ASP107, TYR108 | TRP103, LEU104, TYR108, LYS179, TYR431, HIS450, MET451, ILE454 |
| ( | –8.30 | —————————- | TYR87, TRP103, ASP107, TYR108, LYS179, TYR431, HIS450, MET451 |
| ( | –5.79 | TRP158 | PRO161, HIS167, TRP189, PHE190, MET193 |
| ( | –8.62 | ASP107, THR112, LYS191, ASN198 | LEU104, TYR108, LYS179, PHE435, HIS450, MET451, ILE454 |
| ( | –8.22 | ASP107, THR112, LYS179, TYR431 | LEU104, TYR108, LYS179, TYR431, MET451, ILE454, TYR458 |
| ( | –7.99 | ASP107, THR112, LYS191, ASN198, TYR431 | LEU104, TYR108, SER111, LYS179, TYR431, MET451, ILE454 |
| ( | –7.97 | ASP107, TYR108, ASN198 | ASP107, TYR108, LYS179, PHE184, TYR185, TRP428, TYR431, PHE432, ILE438, HIS450, ILE454 |
| ( | –5.84 | SER155, TRP158 | LEU157, ILE160, PRO161, ILE197 |
| ( | –5.82 | SER155, TRP158 | PHE116, LEU157, TRP158, ILE160, PRO161, PHE190, ILE197 |
| ( | –5.29 | LEU157, THR194 | ILE160, PRO161 |
| ( | –5.99 | SER155, TRP158 | LEU154, LEU157, TRP158, ILE160, PRO161, PHE190, ILE197 |
| ( | –7.75 | LEU154, TRP158, PRO161 | LEU157, TRP158, ILE160, HIS167, PHE168, ILE197 |
| ( | –7.48 | —————————- | LEU154, LEU157, ILE160, PRO161, HIS167, PHE168, TRP189, PHE190, ILE197 |
| ( | –9.62 | ASN84, ASP107, GLU447, TYR458 | ASP107, TYR108, LYS179, ILE434, HIS450, MET451 |
| ( | –7.11 | LEU157, PRO161 | LEU157, HIS167, PHE190, MET193 |
| ( | –6.26 | LEU154, TRP158, THR194 | PHE116, LEU154, LEU157, TRP158, PRO161, MET193, ILE197 |
| ( | –6.35 | LEU154 | TRP158, ILE160, PRO161, PHE190, MET193, ILE197 |
| ( | –6.39 | ASN198 | LEU154, ILE197 |
| ( | –5.81 | SER155, TRP158, THR194 | PHE116, LEU157, TRP158, PRO161, ILE197, |
| ( | –6.19 | TRP158, THR194 | PHE116, LEU154, LEU157, TRP158, PRO161, PHE190, ILE197 |
| ( | –6.12 | PRO161 | PRO161 |
| ( | –8.52 | TYR87, CYS180, TYR431 | ASP107, LYS179, HIS450, MET451, ILE454 |
| ( | –5.94 | TRP158, THR194 | LEU157, ILE160, PRO161, PHE190, ILE197 |
| ( | –8.04 | TYR87, CYS180, HIS450 | LEU104, TYR108, LYS179, TYR431, ILE438, HIS450, MET451, ILE454, TYR458 |
| ( | –7.40 | ASN84, ASP107, HIS450, TYR458 | ASP107, TYR108, LYS179, TYR431, PHE435, ILE438, HIS450, MET451, ILE454 |
| ( | –8.17 | TYR87, SER111, TYR431 | ASP107, TYR108, LYS179, PHE184, TYR431, ILE438, HIS450, MET451, ILE454 |
| ( | –6.31 | TRP158 | LEU154, TRP158, PRO161, PHE190, MET193, ILE197 |
| ( | –6.93 | SER111, TYR431, TYR458 | LEU104, TRP158, LYS179, TYR185, TYR431, PHE432, PHE435, ILE438, HIS450, ILE454 |
| ( | –6.57 | TYR87, LYS179, CYS180, LYS191, TYR431 | ASP107, TYR108, LYS191, TYR431, HIS450, MET451, ILE454 |
| ( | –6.64 | TRP158, THR194, ASN198 | LEU154, SER155, LEU157, ILE160, PRO161, HIS167, PHE168, PHE190, ILE197 |
| ( | –6.64 | TRP158, THR194, ASN198 | LEU157, TRP158, ILE160, PRO161, HIS167, PHE168, PHE190, ILE197 |
| ( | –8.29 | TYR87, ASP107, CYS180, TYR458 | ASP107, LYS179, TYR431, ILE438, HIS450, MET451, ILE454 |
| ( | –8.48 | TYR87, ASP107, CYS180, HIS450 | TRP103, TYR108, LYS179, TYR431, ILE438, HIS450, MET451, ILE454 |
| ( | –8.54 | TYR87, CYS180, TYR431 | ASP107, LYS179, ILE438, HIS450, MET451, ILE454 |
| ( | –6.35 | LEU154, THR194, ASN198 | TRP158, ILE160, PRO161, HIS167, PHE168, PHE190 |
| ( | –5.86 | LEU154 | LEU154, LEU157, ILE160, PRO161, HIS167, PHE190, ILE197 |
| ( | –8.42 | ASN84, SER111, TYR431 | ASP107, LYS179, PHE435, HIS450, MET451, ILE454 |
| ( | –8.35 | ASN84, SER111, TYR431, HIS450 | TYR87, TRP103, LEU104, ASP107, TYR108, ILE115, LYS179, TRP428, PHE432, HIS450, MET451, ILE454 |
| ( | –7.17 | ASN84, ASN198, HIS450, ILE454 | TYR87, TRP103, LEU104, ASP107, TYR108, TYR431, PHE432, HIS450, MET451, ILE454, TYR458 |
| ( | –7.61 | ASN84, TYR108, SER111, THR112, TYR431, HIS450 | ASN84, TRP103, LEU104, ASP107, TYR108, TRP428, TYR431, HIS450, MET451, ILE454 |
| ( | –8.43 | TYR108, SER111, ASN198, PHE435 | TRP103, ASP107, TYR108, ILE115, LYS179, TRP428, TYR431, PHE432, ILE438, HIS450, ILE454 |
| ( | –8.03 | ASN84, TYR108, ASN198, HIS450, ILE454 | TYR87, TRP103, ASP107, TYR108, LYS179, TYR431, PHE432, HIS450, MET451, TYR458 |
| ( | –8.30 | ASN84, TYR108, ASN198, HIS450 | TYR87, TRP103, LEU104, ASP107, TYR108, TRP158, LYS179, TYR431, PHE432, PHE435, HIS450, MET451, ILE454, |
| ( | –8.07 | SER111 | TRP103, ASP107, TYR108, LYS179, TYR431, PHE432, HIS430, ILE454, TYR458 |
| ( | –8.52 | TYR108, SER111 | TRP103, ASP107, TYR108, TRP158, LYS179, TRP428, TYR431, PHE432, ILE438, HIS450, ILE454, TYR458 |
| ( | –7.05 | ASN198, HIS450, ILE454 | TYR87, TRP103, LEU104, ASP107, TYR108, TYR431, PHE432, HIS450, MET451, ILE454, TYR458 |
| ( | –6.86 | ASP107, THR112, ASN198 | TRP103, LEU104, ASP107, TYR108, LYS179, CYS180, TYR431, PHE432, HIS450, ILE454, TYR458 |
| ( | –9.40 | ASP107, ASP178. ASN198 | TYR87, ASP107, TYR108, LYS179, TYR431, PHE432, HIS450, MET451, ILE454 |
| ( | –8.97 | ASN84, SER111, ASN198, TYR431 | TYR87, TRP103, LEU104, TYR108, TRP158, LYS179, TYR431, PHE432, HIS450, MET451, ILE454 |
| ( | –8.57 | TYR108, LYS179, TYR431, ASN446, HIS450 | TRP103, ASP107, TYR108, LYS179, PHE432, ILE438, ASN446, HIS450, ILE454, TYR458 |
| ( | –9.07 | ASP107, TYR431 | LEU104, ASP107, TYR108, TRP158, LYS179, TYR431, PHE432, HIS450, ILE454 |
| ( | –9.12 | ASP107, TYR108. LYS179, GLU447 | LEU104, ASP107, TYR108, TRP158, LYS179, TYR431, PHE432, HIS450, ILE454, TYR458 |
| ( | –9.27 | ASP107, TYR108, ASN198, TYR431 | TRP103, ASP107, TYR108, LYS179, TYR431, HIS450, MET451, ILE454 |
| ( | –9.52 | ASP107, TYR108, GLU447 | TYR87, TRP103, LEU104, ASP107, TYR108, TRP158, LYS179, TYR431, PHE432, HIS450, ILE454 |
| ( | —— | —————————– | —————————– |
| ( | –7.82 | ASP107, LYS179, GLU447, HIS450 | TYR87, LEU104, TYR108, ASP178, LYS179, TYR431, HIS450, MET451, ILE454 |
| ( | –8.88 | SER111, THR112, ASN198, TYR458 | LEU104, ASP107, TYR108, TRP158, LYS179, TYR431, PHE432, HIS450, MET451, ILE454 |
| ( | —— | —————————– | —————————– |
| ( | –7.81 | ASP107, TYR108, LYS191, TYR431 | TYR108, LYS179, TYR431, HIS450, MET451, ILE454 |
| ( | –4.50 | ASP107, TYR108, TYR431 | TRP103, LEU104, ASP107, TYR108, TRP158, HIS450, MET451, ILE454, TYR458 |
| ( | –6.73 | HIS450 | TRP103, LEU104, ASP107, TYR108, TYR431, HIS450, ILE454 |
| ( | –7.48 | —————————– | LEU104, ASP107, TYR108, ILE115, LYS179, CYS180, TYR431, PHE432, ILE454, TYR458 |
| ( | –8.23 | TYR108, TYR458 | TRP103, ASP107, TYR108, LYS179, TYR431, PHE432, ILE438, HIS450, ILE454 |
| Azelastine | –7.33 | ASP107, TYR108, TYR431 | TYR87, TYR108, LYS179, TYR431, MET451, ILE454 |
Fig. 11. Cluster 1 interactions frequency diagram.
Fig. 12. 2D And 3D interactions of compound (II) (top) and (XVIII) (bottom).
Fig. 14. RMSD (in Angstrom) values of molecular dynamics of protein alone, and in addition of compounds (XVIII, XX and XXI), respectively.
Fig. 15. RMSF analysis (in Angstrom) values of molecular dynamics of protein alone, and in addition of compounds (XVIII, XX and XXI), respectively. Ligand contacts are highlighted in green.
Fig. 16. 2D ligand-protein interactions diagram.
Molecular mechanics-generalized born surface area (MM-GBSA) calculations
| Compound | dG binding | dG binding Coulomb | dG binding (NS) | dG binding (NS) Coulomb |
|---|---|---|---|---|
| ( | –64.28 | –6.65 | –83.66 | –4.79 |
| ( | –36.76 | –15.87 | –47.17 | –15.26 |
| ( | –37.76 | –8.64 | –44.01 | –18.59 |
ADMET results for cluster 1
| Compound | Solubility | HIA | BBB | CYP2D6 | Hepatotoxicity | Log p_98 | PSA_98 |
|---|---|---|---|---|---|---|---|
| ( | 1 | 1 | 4 | False | True | 5.211 | 85.634 |
| ( | 1 | 1 | 4 | False | True | 5.211 | 85.634 |
| ( | 1 | 1 | 4 | False | True | 5.211 | 85.634 |
| ( | 1 | 1 | 4 | False | True | 5.093 | 83.311 |
| ( | 2 | 0 | 1 | False | True | 4.828 | 78.604 |
| ( | 2 | 0 | 2 | False | True | 4.189 | 84.238 |
| ( | 1 | 1 | 4 | True | True | 6.02 | 63.423 |
| ( | 1 | 1 | 4 | True | True | 6.02 | 63.423 |
| ( | 1 | 1 | 4 | False | True | 4.956 | 86.358 |
| ( | 1 | 1 | 4 | False | True | 4.956 | 86.358 |
| ( | 2 | 0 | 2 | False | True | 3.594 | 88.515 |
| ( | 3 | 0 | 3 | False | True | 2.226 | 80.253 |
| ( | 3 | 0 | 2 | False | True | 2.557 | 67.699 |
| ( | 3 | 0 | 3 | False | True | 0.835 | 67.665 |
| ( | 2 | 0 | 2 | False | True | 3.124 | 79.023 |
| ( | 2 | 0 | 4 | False | True | 3.192 | 102.359 |
| ( | 2 | 0 | 2 | False | True | 3.522 | 89.805 |
| ( | 2 | 0 | 3 | False | False | 3.374 | 89.805 |
| ( | 2 | 0 | 4 | False | True | 4.089 | 101.128 |
| ( | 3 | 0 | 3 | False | False | 1.799 | 106.578 |
| ( | 2 | 0 | 4 | False | False | 2.496 | 106.578 |
| ( | 3 | 0 | 3 | False | True | 0.461 | 109.931 |
| ( | 4 | 0 | 3 | False | True | 0.188 | 103.226 |
| ( | 3 | 0 | 3 | False | False | 0.886 | 103.226 |
| ( | 3 | 0 | 3 | False | True | 2.051 | 103.226 |
| ( | 3 | 0 | 3 | False | True | 1.771 | 101.213 |
| ( | 3 | 0 | 3 | False | True | 1.213 | 71.102 |
| ( | 3 | 0 | 3 | False | True | 1.636 | 82.363 |
| ( | 2 | 0 | 3 | False | True | 2.469 | 88.403 |
| ( | 2 | 0 | 2 | True | True | 3.411 | 88.403 |
| ( | 2 | 0 | 3 | False | True | 2.452 | 97.333 |
| ( | 2 | 0 | 3 | False | True | 2.452 | 97.333 |
| ( | 2 | 0 | 4 | False | True | 2.691 | 113.926 |
| ( | 2 | 0 | 2 | False | True | 3.207 | 71.102 |
| ( | 2 | 0 | 2 | False | True | 3.207 | 71.102 |
| ( | 2 | 0 | 3 | False | True | 2.78 | 80.032 |
| ( | 2 | 0 | 3 | False | True | 2.78 | 80.032 |
| ( | 3 | 0 | 3 | False | True | 1.771 | 101.213 |
| ( | 3 | 0 | 3 | False | True | 1.646 | 82.363 |
| ( | 3 | 0 | 3 | False | True | 1.646 | 82.363 |
| ( | 2 | 0 | 3 | False | True | 2.322 | 105.704 |
| ( | 0 | 1 | 4 | False | True | 6.049 | 59.147 |
| ( | 1 | 0 | 2 | False | True | 3.337 | 85.159 |
| ( | 2 | 0 | 3 | False | True | 3.204 | 88.73 |
| ( | 1 | 0 | 2 | False | True | 3.912 | 83.153 |
| ( | 1 | 0 | 1 | False | True | 4.561 | 71.43 |
| ( | 1 | 0 | 1 | False | True | 4.797 | 71.43 |
| ( | 1 | 0 | 1 | False | True | 4.2 | 71.957 |
| ( | 1 | 0 | 1 | False | True | 4.724 | 71.957 |
| ( | 1 | 0 | 2 | False | True | 3.327 | 87.66 |
| ( | 1 | 0 | 2 | False | True | 3.85 | 72.605 |
| ( | 2 | 0 | 2 | False | True | 2.997 | 77.725 |
| ( | 1 | 0 | 1 | False | True | 4.73 | 61.563 |
| ( | 1 | 0 | 1 | False | True | 4.73 | 61.563 |
| ( | 2 | 0 | 2 | False | True | 3.823 | 84.328 |
| ( | 2 | 0 | 4 | False | True | 3.526 | 101.629 |
| ( | 2 | 0 | 2 | False | True | 4.451 | 78.604 |
| ( | 2 | 0 | 2 | False | True | 3.911 | 82.119 |
| ( | 2 | 0 | 4 | False | True | 4.579 | 86.358 |
| ( | 1 | 1 | 1 | True | True | 5.642 | 63.423 |
| ( | 2 | 0 | 4 | False | True | 4.555 | 89.653 |
| ( | 2 | 1 | 4 | False | True | 4.33 | 101.539 |
| ( | 2 | 0 | 4 | True | True | 4.784 | 86.358 |
| ( | 2 | 0 | 4 | True | True | 4.784 | 86.358 |
| ( | 3 | 0 | 3 | False | True | 1.007 | 80.56 |
| ( | 2 | 0 | 3 | False | True | 2.773 | 80.032 |
| ( | 2 | 0 | 1 | False | True | 4.19 | 71.102 |
Solubility: 0 (extremely low), 1 (very low), 2 (low), 3 (good), 4 (optimal).
Absorption: 0 (good), 1 (moderate), 2 (poor), 3 (very poor).
BBB permeability: 0 (very high), 1 (high), 2 (medium), 3 (low), 4 (undefined).