The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects

Evaluation of in vitro SARS-CoV-2 inactivation by a new quaternary ammonium compound: Bromiphen bromide

The pneumonia (COVID-19) outbreak caused by the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which unpredictably exploded in late December of 2019 has stressed the importance of being able to control potential pathogens with the aim of limiting their spread. Although vaccines are well known as a powerful tool for ensuring public health and controlling the pandemic, disinfection and hygiene habits remain crucial to prevent infection from spreading and maintain the barrier, especially when the microorganism can persist and survive on textiles, surfaces, and medical devices. During the coronavirus disease pandemic, around half of the disinfectants authorized by the US Environmental Protection Agency contained quaternary ammonium compounds (QACs); their effectiveness had not been proven. Herein, the in vitro SARS-CoV-2 inactivation by p-bromodomiphen bromide, namely bromiphen (BRO), a new, potent, and fast-acting QAC is reported. This study demonstrates that BRO, with a dose as low as 0.02%, can completely inhibit SARS-CoV-2 replication in just 30 s. Its virucidal activity was 10- and 100-fold more robust compared to other commercially available QACs, namely domiphen bromide and benzalkonium chloride. The critical micellar concentration and the molecular lipophilicity potential surface area support the relevance of the lipophilic nature of these molecules for their activity.

Molecular Docking Studies of Boron‐Containing Compounds as Dual Inhibitors of SARS‐Cov‐2 Spike Receptor Binding Domain/ACE2 Complex and Main Protease and ADMET Investigations

The severe acute respiratory syndrome SARS‐CoV‐2 is the causative agent of COVID‐19. Preventing binding of SARS‐CoV‐2 Spike glycoprotein to human ACE2 enzyme and inhibition of MPRO enzyme are still attractive drug targets for treatment of COVID‐19 infection. Boron atom‐containing compounds show anticancer, antibacterial, antiviral, antifungal, antiparasitic, anti‐inflammatory, antituberculosis, anti‐dermatophytic and anti‐fertility activities. In the current study, the ADMET properties of ligands were calculated by the aim of SwissADME and pkCSM pharmacokinetics web tools. The results revealed that the ligands meet drug‐likeness properties. Furthermore, we have performed molecular docking study of boron containing dioxaborepine and oxadiazaborole derivatives to investigate binding properties of ligands against SARS‐CoV‐2 Spike glycoprotein/ACE2 complex and inhibition of MPRO enzyme. Through the ligands a derivative of dioxaborepine showed best binding score against SARS‐CoV‐2 Spike glycoprotein/ACE2 complex with a binding score of −8.93 kcal/mol and a oxadiazaborole derivative exhibited a binding score value of −8.36 kcal which is the best binding ligand to the MPRO enzyme binding site. The analysis of binding poses of ligands and ligand‐residue interactions of the systems revealed that dioxaborepines and oxadiazaboroles could have block binding of Spike glycoprotein to human ACE2 enzyme and could have inhibition effects on MPRO enzyme.

Potential RNA-dependent RNA polymerase (RdRp) inhibitors as prospective drug candidates for SARS-CoV-2

The SARS-CoV-2 pandemic is considered as one of the most disastrous pandemics for human health and the world economy. RNA-dependent RNA polymerase (RdRp) is one of the key enzymes that control viral replication. RdRp is an attractive and promising therapeutic target for the treatment of SARS-CoV-2 disease. It has attracted much interest of medicinal chemists, especially after the approval of Remdesivir. This study highlights the most promising SARS-CoV-2 RdRp repurposed drugs in addition to natural and synthetic agents. Although many in silico predicted agents have been developed, the lack of in vitro and in vivo experimental data has hindered their application in drug discovery programs.

Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3–d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro

In this paper, an environmentally benign, convenient, and efficient one-pot three-component reaction has been developed for the regioselective synthesis of novel 5-aroyl(or heteroaroyl)-6-(alkylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-diones (4a‒n) through the sequential condensation of aryl(or heteroaryl)glyoxal monohydrates (1a‒g), 1,3-dimethylbarbituric acid (2), and alkyl(viz. cyclohexyl or tert-butyl)isocyanides (3a or 3b) catalyzed by ultra-low loading ZrOCl₂•8H₂O (just 2 mol%) in water at 50 ˚C. After synthesis and characterization of the mentioned furo[2,3-d]pyrimidines (4a‒n), their multi-targeting inhibitory properties were investigated against the active site and putative allosteric hotspots of both SARS-CoV-2 main protease (M^Pro) and papain-like protease (PL^Pro) based on molecular docking studies and compare the attained results with various medicinal compounds which approximately in three past years were used, introduced, and or repurposed to fight against COVID-19. Furthermore, drug-likeness properties of the mentioned small heterocyclic frameworks (4a‒n) have been explored using in silico ADMET analyses. Interestingly, the molecular docking studies and ADMET-related data revealed that the novel series of furo[2,3-d]pyrimidines (4a‒n), especially 5-(3,4-methylendioxybenzoyl)-6-(cyclohexylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-dione (4g) as hit one is potential COVID-19 drug candidate, can subject to further in vitro and in vivo studies. It is worthwhile to note that the protein-ligand-type molecular docking studies on the human body temperature-dependent M^Pro protein that surprisingly contains zinc^II (Zn^II) ion between His41/Cys145 catalytic dyad in the active site, which undoubtedly can make new plans for designing novel SARS-CoV-2 M^Pro inhibitors, is performed for the first time in this paper, to the best of our knowledge.

Development of a database of RNA helicase inhibitors (VHIMDB) of pathogenic viruses and in silico screening for the potential drug molecules

The pathogenic RNA virus that infects human beings contains the RNA helicase enzyme, responsible for the replication of the viral genome. The enzyme is used as a suitable target against which the drug molecule acts. Therefore, the identification and proposal the novel compounds that can be targeted toward the helicase enzymes to stop the functioning of the enzyme is desirable. Although many viral helicase inhibitor molecules have been identified, still yet no unique database is available for these compounds. This research work envisages developing a curated database of RNA helicase inhibitors. The database contains in total of 353 entries that are computationally predicted and experimentally verified RNA helicase inhibitors. The database contains information like compound name, chemical properties, chemical format, and name of the target virus to which it acts against it with a user-friendly menu-driven search engine. Presently, the database is freely available at: https://vhimdb.rsatpathy.in/. Further, in silico screening of the whole database by drug-likeness and toxicity resulted in 14 potential drug molecules. The selected molecules were analyzed for their effectiveness in binding by using molecular docking score and interaction with the helicase enzymes of three categories of pathogenic viruses (SARS-CoV-2, SARS-CoV, and MERS-CoV).