In silico analysis of plants against SARS-CoV-2


As we know, the World Health Organization (WHO) has played down media reports of a drug breakthrough against the coronavirus outbreak, saying there are “no known” drug treatments against the virus.

Though, there are certain claims on Anti-Corona therapeutic activity of small molecules like chloroquine and lopinavir/ritonavir which were used in the treatment of malaria and HIV correspondingly, but mechanism of their action is not illustrated.

In that regards Atrimed has taken initiative in identifying plant based molecules to address the current outbreak with substantial investigations.

Current scenario:

•The number of coronavirus cases in India is increasing.

• There are no known effective therapeutics against SARS-CoV-2

• ACE2 inhibitors are likely to facilitate SARS-CoV-2 and host interaction

• Spike Glycoprotein (S), Envelope (E) protein and Importin α3 are major structural proteins of the SARS-CoV-2.


Potential drug targets for Anti-COVID19 drugs:

• Envelope protein (E): 

Involved in assembly, budding, envelop formation and pathogenesis.


• Spike Glycoprotein (S):
Attaching the virus to receptors on susceptible host cells through ACE2 receptor.


• Importin α3:
Responsible for the import of SARSCoV-2 Integrase in to nuclear compartment.

Our Hypothesis:

We hypothesised that, the small molecules in our anti-Covid19 product can be a potential inhibitors of above mentioned drug targets and efficacious to interfere in SARS-CoV-2 and host interaction to deliver Anti-CoV viral activity.

What have we done?

The small molecules present in the major compositions of Atrimed’s anti-Covid19 product were subjected for computer aided screening, to understand their potentiality to inhibit the function of drug targets and protect the host from infection.

Our Inventory:​

The plant small molecule library consists of 4,08,000 small molecules structures, which are classified using physicochemical parameters as major classifiers


Through our topological analysis spike glycoprotein, Envelop protein from SARS_CoV-2 and human Importin α3 were identified as drug targets. Further, the target structures were modelled and validated for structure quality. The structures ensured with considerable quality were subjected for drug binding site prediction and subjected for molecular docking studies. Conclusively, molecular docking and dynamic simulation analysis have indicated that three plant small molecules for spike glycoprotein, two plant small molecules for E protein and Importin α3 respectively as a promising small molecule to treat COVID19 drugs. Molecular modelling studies are preliminary studies and it requires in vitro and in vivo experimental validation.