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Innovative Medicines & Omics SARS-CoV-2 inhibition by quinolines

molecular structures and mechanisms of action of these high selectivity indexes (Table 5). We also highlight that for
4-aminoquinolines indicates that strategic modifications the Omicron variant, Q2b‑Q4b molecules presented EC
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might enhance their antiviral capabilities, highlighting the values below the lowest concentration tested (0.6 µM),
need to explore the chemical diversity within this class for regardless of whether the supernatant was collected after
potential therapeutic developments. 24 or 48 h post-infection (Table 6). These results are

This study extensively explores the efficacy of comparable to those presented by mefloquine in Calu-3
4-aminoquinoline derivatives against a spectrum of (EC = 1.9 µM) and Vero E6 cells (EC = 0.6 µM), and
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pathogens, focusing on identifying molecules that exhibit those previously observed for atazanavir (EC = 2 µM),
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67
anti-SARS-CoV-2 activity. The findings demonstrated that daclatasvir (EC = 1.1 µM), and molnupiravir
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all tested 4-aminoquinoline derivatives (Q1a – Q4a, Q1b (EC = 1.97 µM), an FDA-approved drug for emergency
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– Q4b, and Q1bS) exerted significant inhibitory effects on use against COVID-19. Furthermore, our results were
SARS-CoV-2 infectivity in both Vero E6 and Calu-3 cells, better than those already reported for chloroquine
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while maintaining cell viability. Notably, compounds Q3a, (EC > 10 µM) in human pneumocytes and lopinavir/
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Q1b, and Q3b achieved the lowest EC values in human ritonavir (EC = 8.2 µM), proposed as a treatment for
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type II pneumocytes after 24 h of treatment. Furthermore, COVID-19 during 2020. 67
compound Q4b showed a notably low EC value at later In this investigation, molecular docking was used to
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treatment stages. The high selectivity index of these estimate potential inhibitors for COVID-19 treatment
molecules underscores the safety of the in vitro assays, using interactions and affinity energies between ligands
based on cytotoxicity (CC ) and EC metrics. In addition, and proteins. For the docking of the M , we used the
pro
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the antiviral efficacy of these compounds was confirmed AutoDockVina (v1.1.2) and DockThor (v2.0) software.
against the Omicron variant of SARS-CoV-2, broadening The ligands presented the following average affinity to
their potential therapeutic applicability (Table 6). M : Q3a: -6,1863 kcal/mol; Q2b: -6,3347 kcal/mol;
pro
Our results showed that the maximum concentration Q1b: -6,3203 kcal/mol; Q3b: -6,3797 kcal/mol; and
pro
(10 µM) used in the antiviral assays was not toxic to Q4b: -6,3763 kcal/mol. The M key active site is a catalytic
either cell line, and cell viability data revealed that all dyad composed of conserved residues, H41 and C145.
compounds (Q1a – Q4a; Q1b – Q4b; Q1bS) presented Table 7 presents the distance in Å between the molecules
pro
CC values >160 µM in Calu-3 cells. On the other hand, it and the C145 sulfur atom in the active site of M , cKi (µM),
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was observed that the viability of Vero E6 cells was slightly and affinity (kcal/mol) results for all docked compounds.
reduced after treatment with compounds, reaching CC Ruiz-Moreno et al. conducted an analysis of 152
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values > 100 µM, except for Q4a, which indicated the bioactive conformations of inhibitors, examining more
higher toxicity observed (CC = 84.7 µM) in this cell line than 340 million compounds to identify regions and
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(Table 5). Importantly, Q1a – Q4a, Q1b – Q4b, and Q1bS consensus interactions among them. The pharmacophoric
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compounds exhibited CC values up to 8 times higher groups of these compounds were categorized based on
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when compared to the treatment with mefloquine in either their physicochemical characteristics into hydrophobic,
Vero E6 or Calu-3 models. 16 hydrogen bond acceptors, and hydrogen bond donors. In
After treatment for 24 h, our results indicated that all addition, the pharmacophoric consensus considered the
4-aminoquinoline derivatives inhibited more than 90% of spatial positioning of the ligands and their occurrence
SARS-CoV-2 replication in Calu-3 cells (Figure 4A and B), frequency. The comprehensive engagement of all protease
while in Vero E6 cells (Figure 4C and D), the percentage subpockets was noted to contribute to improved inhibition
of viral replication inhibition reached values above and increased stability of the compounds. 69
80%, at the highest concentration analyzed (10 µM). In Analyzing the conformational and pharmacophoric
addition, it was observed that the nine tested compounds profiles of compounds Q1b, Q2b, Q3a, Q3b, and Q4b
demonstrated to be efficient in inhibiting viral replication (Figure 7), we observed interactions with residues that
in both infected cells, with mean EC values ranging from contribute to the catalytic activity of the M protein.
pro
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<0.6 µM to 2.93 µM (Tables 5 and 6), regardless of whether The quinoline nucleus, in conjunction with the chlorine
the cells were infected with the WT or Omicron variant. moiety of the compounds, is responsible for hydrophobic
In this context, it is worth mentioning that, for both interactions with the residues of the subpockets and
isolates tested, Q3a, Q1b, and Q3b presented the lower the C145 from the catalytic site. First, compound Q1b
EC values in Calu-3 cells, with concentrations below (Figure 7C and D) exhibited polar interactions with the
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1.5 µM, before 24 h post-infection (Table 6), and Q1a and residues H41, H163, and Q189. Hydrophobic interactions
Q4b had EC values <1 µM in Vero E6 cells, which reflect were also detected with C44 and C145. In addition,
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Volume 1 Issue 1 (2024) 98 doi: 10.36922/imo.3442