Scaffold Hopping of α-Rubromycin Enables Direct Access to FDA-Approved Cromoglicic Acid as a SARS-CoV-2 MPro Inhibitor

The COVID-19 pandemic is still active around the globe despite the newly introduced vaccines. Hence, finding effective medications or repurposing available ones could offer great help during this serious situation. During our anti-COVID-19 investigation of microbial natural products (MNPs), we came across α-rubromycin, an antibiotic derived from Streptomyces collinus ATCC19743, which was able to suppress the catalytic activity (IC50 = 5.4 µM and Ki = 3.22 µM) of one of the viral key enzymes (i.e., MPro). However, it showed high cytotoxicity toward normal human fibroblasts (CC50 = 16.7 µM). To reduce the cytotoxicity of this microbial metabolite, we utilized a number of in silico tools (ensemble docking, molecular dynamics simulation, binding free energy calculation) to propose a novel scaffold having the main pharmacophoric features to inhibit MPro with better drug-like properties and reduced/minimal toxicity. Nevertheless, reaching this novel scaffold synthetically is a time-consuming process, particularly at this critical time. Instead, this scaffold was used as a template to explore similar molecules among the FDA-approved medications that share its main pharmacophoric features with the aid of pharmacophore-based virtual screening software. As a result, cromoglicic acid (aka cromolyn) was found to be the best hit, which, upon in vitro MPro testing, was 4.5 times more potent (IC50 = 1.1 µM and Ki = 0.68 µM) than α-rubromycin, with minimal cytotoxicity toward normal human fibroblasts (CC50 > 100 µM). This report highlights the potential of MNPs in providing unprecedented scaffolds with a wide range of therapeutic efficacy. It also revealed the importance of cheminformatics tools in speeding up the drug discovery process, which is extremely important in such a critical situation.

(Diptera: Culicidae)

The bio-efficacy of crude ethyl acetate extract, fractions and a compound phenyl acetic acid from the ethyl acetate extract of Streptomyces collinus was evaluated on Culex quinquefasciatus Say and Aedes aegypti L. mosquitoes (Diptera: Culicidae). The larvae were exposed to concentrations of 2.5, 5.0, 7.5 and 10.0 ppm for fractions and 0.5, 1.0, 1.5 and 2.0 ppm for compound. After 24 h, the larval mortality was assessed and the LC₅₀ and LC₉₀ values were calculated. Similarly, per cent ovicidal activity was calculated for eggs after 120 h post treatment for phenyl acetic acid. Among the eleven fractions screened, fraction 7 from the ethyl acetate extract of Streptomyces collinus exhibited good larvicidal activity against both mosquito species. The LC₅₀ and LC₉₀ values of fraction 7 were 4.42, 6.23 ppm against Cx. quinquefasciatus larvae and 5.13, 14.51 ppm against Ae. aegypti larvae, respectively. Further, the isolated compound, phenyl acetic acid from fraction 7 recorded 100% larvicidal activity at 2 ppm concentration with LC₅₀ and LC₉₀ values of 2.07, 4.87 ppm on Cx. quinquefasciatus larvae and 3.81, 9.87 ppm on Ae. aegypti larvae, respectively. Phenyl acetic acid presented 50.3% and 42.0% ovicidal activity against Cx. quinquefasciatus and Ae. aegypti eggs at 2 ppm concentration after 120 h post treatment. The compound, phenyl acetic acid could be used in mosquito control programme.