| Literature DB >> 33424034 |
Raviteja Chemboli1, Ravikumar Kapavarapu2, K Deepti1, K R S Prasad1, Alugubelli Gopi Reddy3, A V D Nagendra Kumar4, Mandava Venkata Basaveswara Rao5, Manojit Pal2.
Abstract
In view of the recent global pandemic caused by COVID-19 intense efforts have been devoted worldwide towards the development of an effective treatment for this disease. Recently, PDE4 inhibitors have been suggested to attenuate the cytokine storm in COVID-19 especially tumour necrosis factor alpha (TNF-α). In our effort we have explored the 2-substituted pyrrolo[2,3-b]quinoxalines for this purpose because of their potential inhibitory properties of PDE-4 / TNF-α. Moreover, several of these compounds appeared to be promising in silico when assessed for their binding affinities via docking into the N-terminal RNA-binding domain (NTD) of N-protein of SARS-CoV-2. A rapid and one-pot synthesis of this class of molecules was achieved via the Cu-catalyzed coupling-cyclization-desulfinylation of 3-alkynyl-2-chloroquinoxalines with t-butyl sulfinamide as the ammonia surrogate under ultrasound irradiation. Most of these compounds showed good to significant inhibition of TNF-α in vitro establishing a SAR (Structure Activity Relationship) within the series. One compound e.g. 3i was identified as a promising hit for which the desirable ADME and acceptable toxicity profile was predicted in silico.Entities:
Keywords: COVID-19; Catalysis; In silico study; Pyrrolo[2,3-b]quinoxaline; Ultrasound
Year: 2021 PMID: 33424034 PMCID: PMC7778832 DOI: 10.1016/j.molstruc.2020.129868
Source DB: PubMed Journal: J Mol Struct ISSN: 0022-2860 Impact factor: 3.196
Fig. 1Example of drugs and agents that were explored against coronavirus.
Fig. 2Previously and currently explored quinoxaline derivatives E and F as potential ligands for N-protein of SARS-CoV-2 in silico.
The binding energies of molecules 3a-j and C with the SARS-CoV-2 N-terminal RNA binding domain residues.
| Molecules | Estimated Total Energy (kcal/mol) | ||
| GEMDOCK | DOCKTHOR | SWISSDOCK | |
| -78.86 | -7.84 | -6.40 | |
| -78.42 | -7.77 | -6.17 | |
| -86.05 | -8.12 | -6.85 | |
| -86.00 | -7.83 | -6.91 | |
| -68.90 | -7.68 | -6.37 | |
| -73.11 | -7.23 | -6.11 | |
| -72.08 | -7.94 | -6.18 | |
| -64.23 | -7.44 | -6.19 | |
| -89.37 | -7.94 | -6.33 | |
| -85.33 | -8.10 | -6.98 | |
| -81.02 | -6.90 | -6.75 | |
The interaction diagrams (ribbon representation) of molecules 3a-j and the reference compound C with the SARS-CoV-2 N-terminal RNA binding domain residues.
*The box indicates compounds with similar binding modes into the target protein. The circle indicates a different binding site for the reference compound C.
The residues of the binding site involved in the interaction with the selected molecules.
| Compounds | Binding site interacting residues |
| TYR71, LYS75, | |
| TYR71, LYS75, | |
| LYS18, TYR71, | |
| TYR71, LYS75, | |
| ASP16, TYR71, LYS75, | |
| TRP5, |
The underlined residue was involved in H-bonding interaction.
Fig. 32D and 3D interaction diagram of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain with (A) compound 3c and (B) compound 3i.
Effect of catalysts/base on the coupling-cyclization of 1a to 3c.a
| Entry | Time | %Yield | |
| 1 | 2 | 51 | |
| 2 | 2 | 46 | |
| 3 | 2 | 40 | |
| 4 | 1.5 | 67 | |
| 5 | 1.5 | 32 | |
| 6 | 2 | 68 | |
| 7 | 4 | 49 | |
| 8 | 1.5 | 30 | |
| 9 | 1.5 | 36 | |
All the reactions were carried out by using 1a (2.5 mmol), 2 (2.8 mmol), Cu(OAc)2 (0.025 mmol) and Et3N (3.77 mmol) in DMF (3 mL) under ultrasound.
Isolated yield.
DBU was used in place of Et3N.
The reaction was performed under silent conditions.
The reaction was performed using 1.4 mmol of 2d.
The reaction was performed using 0.014 mmol of Cu(OAc)2.
Ultrasound assisted synthesis of compound 3c-j.a
| Time | Product ( | %Yield | |
| 1.5 | 67 | ||
| 1.5 | 71 | ||
| 2 | 59 | ||
| 1.5 | 63 | ||
| 1.5 | 73 | ||
| 2 | 60 | ||
| 4 | 65 | ||
| 1.5 | 62 | ||
All the reactions were carried out by using 1 (2.5 mmol), 2d (2.8 mmol), Cu(OAc)2 (0.025 mmol) and Et3N (3.77 mmol) in DMF (3 mL) under ultrasound.
Isolated yield.
Fig. 4Partial representation of 1H and 13C NMR spectral data of compound 3e.
Scheme 1The proposed Cu-catalytic cycle for the ultrasound assisted coupling-cyclization of 1 with 2d.
Inhibition of TNF-α by compounds 3a-j.
| Molecules | TNF-α inhibition | |
|---|---|---|
| % inhibition @ 10 μM | IC50 (μM) | |
| 66.5 | 7.12±0.48 | |
| 67.9 | 7.02±0.72 | |
| 76.1 | 5.47±0.69 | |
| 75.6 | 5.92±0.89 | |
| 56.8 | n.d. | |
| 62.4 | 7.58±0.55 | |
| 61.7 | 7.45±0.37 | |
| 53.6 | n.d. | |
| 77.3 | 5.14±0.34 | |
| 75.4 | 5.65±0.29 | |
| Rolipram | 97.7 | 0.91 ±0.02 |
| Thalidomide | n.d. | 198.91±6.32 |
n.d. = not determined.
Fig 5SAR summary of TNF-α inhibition of compound 3.
Fig. 6Concentration dependent inhibition of TNF-α by the compound 3i.
Computational ADME prediction of 3c, 3i and 3j.
| Properties | Molecules | ||
|---|---|---|---|
| (i) Physicochemical | |||
| Molecular Weight (g/mol) | 245.28 | 259.31 | 273.33 |
| Consensus Log P | 3.23 | 3.61 | 3.89 |
| Log S (ESOL) | -4.01 (Moderately soluble) | -4.47 (Moderately soluble) | -4.58 (Moderately soluble) |
| (ii) Pharmacokinetics | |||
| GI | High | High | High |
| P-gp | yes | Yes | No |
| (iii) Druglikenss | |||
| Lipinski rule | No violation | No violation | No violation |
| Veber rule | No violation | No violation | No violation |
| Bioavailability score | 0.55 | 0.55 | 0.55 |
Log P: Lipophilicity.
Log S (ESOL): water solubility, calculated by ESOL method which is a Quantitative Structure-Property Relationship (QSPR) based model.
GI: Gastrointestinal.
P-gp: permeability glycoprotein.
Predicted toxicities of compound 3i.
| Property | Predicted Value | Unit |
|---|---|---|
| AMES toxicity | Yes | Categorical (Yes/No) |
| Max. tolerated dose (human) | 0.223 | Numeric (log mg/kg/day) |
| hERG I inhibitor | No | Categorical (Yes/No) |
| hERG II inhibitor | Yes | Categorical (Yes/No) |
| Oral Rat Acute Toxicity (LD50) | 2.525 | Numeric (mol/kg) |
| Oral Rat Chronic Toxicity (LOAEL) | 0.902 | Numeric (log mg/kg_bw/day) |
| Hepatotoxicity | No | Categorical (Yes/No) |
| Skin Sensitisation | No | Categorical (Yes/No) |
| 0.314 | Numeric (log ug/L) | |
| Minnow toxicity | -0.362 | Numeric (log mM) |