Researchers are exploring drug repurposing candidates that target nucleotide binding pockets of multiple SARS-CoV-2 proteins

Researchers are exploring drug repurposing candidates that target nucleotide binding pockets of multiple SARS-CoV-2 proteins

In a recent study published in virology Researchers pursued direct-acting drugs against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that compete for nucleotide binding pockets (NBPs) of SARS-CoV-2 proteins.

Studie: Direkt wirkende antivirale SARS-CoV-2-Medikamente mit mehreren Zielen gegen die Nukleotidbindungstaschen virusspezifischer Proteine. Bildnachweis: PHOTOCREO Michal Bednarek/Shutterstock

background

SARS-CoV-2 belongs to the subgroup of beta coronaviruses (β-CoV) of the family Coronaviridae in the order Nidovirales. It infects several mammalian species, including humans, and causes acute respiratory infections. It is an enveloped, single-stranded, positive-sense ribonucleic acid (RNA) virus with a 13-kilobase genome containing 14 open reading frames (ORFs). The 5ˈ end of the SARS-CoV-2 genome has ORFs 1a and 1b, which encode polyproteins pp1a and pp1ab, which are translated into nonstructural proteins (NSPs) 1 to 16. The remaining 3ˈ third genome encodes structural proteins, including tip (S), membrane (M), envelope (E), and nucleocapsid (N).

SARS-CoV-2 has evolved into more than 40,000 genomic variants since its emergence in 2019. The pandemic caused by SARS-CoV-2 continues to claim lives worldwide. Therefore, there is an urgent need for antiviral drugs that could combat the re-emergence and emergence of new variants of concern (VOCs). Biologists have quickly developed 3D structures of almost all SARS-CoV-2 proteins, which are now all available in the Protein Data Bank (PDB) and could help in structure-based drug development.

Previously, researchers have formulated nucleotide derivatives that compete with the physiological nucleotides for binding to the NBPs of viral proteins as antiviral drugs. For example, the US Food and Drug Administration (FDA) has approved azidothymidine (AZT) as a drug against the human immunodeficiency virus (HIV) that targets its reverse transcriptase (RT) protein.

About the study

In the present study, researchers attempted to reuse pharmacologically active compounds that bind to the NBPs of six SARS-CoV-2 proteins. They specifically targeted the C-terminal domain (CTD) and N-terminal domain (NTD) of nsp12, nsp13, nsp14, nsp15, nsp16 and the N protein. They identified these NBPs based on the atomic structures available in the PDB. Likewise, they performed structure-assisted virtual in silico screening of three libraries to quickly identify multi-target antivirals against SARS-CoV-2.

The Single Molecular Multi-Target (SMMT) approach helped researchers obtain several potential small anti-SARS-CoV-2 molecules with multi-target properties. They used isothermal calorimetry (ITC) to measure binding parameters such as affinity and kinetics of the identified antiviral compounds. Finally, the team used cell-based SARS-CoV-2 assays to confirm the antiviral activity of a subset of these compounds.

The team performed molecular docking of multiple nucleotide mono- and triphosphates (NMPs/NTPs). [(e.g., adenosine mono- and tri-phosphate (AMP and ATP)] and remdesivir. The latter, a nucleotide prodrug of an adenosine analog, served as a positive control. The researchers flagged each molecule as a potential drug candidate if it had a favorable molecular toxicity range and pharmacokinetic (PK) properties had. They used the online tool SwissADME for in silico drug-likeness analysis, which characterized the selected molecules based on their absorption, distribution, metabolism and excretion (ADME) properties.

In addition, the team used the BOILED-Egg (Brain Or IntestinaL EstimateD Permeation) model to predict the gastrointestinal (GI) absorption or blood-brain barrier (BBB) ​​permeation of a compound, as well as substrate/non-substrate analysis of P-glycoprotein (Pgp).

Study results

Since nucleosides/nucleotides are the building blocks of RNA, i.e. the viral genome, molecules that target the nucleoside skeleton could be promising antiviral molecules. Although it is difficult to assess the in vivo behavior of these molecules, in silico methods have proven to be very useful in providing clear evidence of the interaction of a drug molecule with the target protein and its bioavailability in the host organism.

First, the researchers selected the top 30 compounds whose binding energy was equal to or greater than the positive control in the selected set of SARS-CoV-2 proteins. The team predicted the drug-likeness of the top ten of these 30 compounds. They obtained the final binding energy after molecular docking of the compounds. Although these ten compounds exhibited high binding energies for the viral targets, their physicochemical parameters did not show acceptable properties for drug-likeness.

Furthermore, the team evaluated these compounds using thermodynamic criteria, revealing only three top compounds with anti-SARS-CoV-2 potential. These were olaparib, INCB28060 and VX-809. Interestingly, three promising compounds from each library also had similarly interacting amino acids. Furthermore, three out of nine potential compounds (INCB28060, darglitazone sodium, and columbianadine) demonstrated significant antiviral activity in various in vitro tests. The most potent compound was darglitazone sodium, whose half-maximal effective concentration (EC50) was less than 10 µM.

All three drug candidates also showed inhibitory properties, but INCB28060 and darglitazone sodium had the greatest anti-SARS-CoV-2 activity. Interestingly, Columbianadine has been shown to have analgesic, anti-inflammatory and antitumor properties and is also an inhibitor of voltage-gated calcium (Ca2+) channels. The antiviral effect of columbianadine against SARS-CoV-2 via modulation of ion channel activity requires further experimental investigation.

Diploma

The current study highlighted the utility of structure-based methods in discovering a potential drug molecule that could target multiple proteins of SARS-CoV-2. According to the authors, these drug molecules are in clinical testing and could soon be used for antiviral therapy against SARS-CoV-2.

Reference:

• Ruchi Rani, Siwen Long, Akshay Pareek, Preeti Dhaka, Ankur Singh, Pravindra Kumar, Gerald McInerney, Shailly Tomar. (2022). Direkt wirkende antivirale SARS-CoV-2-Medikamente mit mehreren Zielen gegen die Nukleotidbindungstaschen virusspezifischer Proteine. Virologie. doi: https://doi.org/10.1016/j.virol.2022.08.008 https://www.sciencedirect.com/science/article/pii/S0042682222001386