Applying computer simulations in battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic

Abstract

Coronavirus disease 2019 (COVID-19) has made many concerns for healthcare services especially, in finding useful therapeutic(s). Despite the scientists’ struggle to find and/or creating possible drugs, so far there is no treatment with high efficiency for the disease. During the pandemic, researchers have performed some molecular analyses to find potential therapeutics out of both the natural and synthetic available medicines. Computer simulations and related data have shown a significant role in drug discovery and development before. In this field, antiviral drugs, phytochemicals, anti-inflammatory agents, etc. were essential groups of compounds tested against COVID-19, using molecular modeling, molecular dynamics (MD), and docking tools. The results indicate promising effects of such compounds to be used in further experimental and clinical trials; Chloroquine, Chloroquine-OH, and Umifenovir as viral entry inhibitors, Remdesivir, Ribavirin, Lopinavir, Ritonavir, and Darunavir as viral replication inhibitors, and Sirolimus are the examples, which were tested clinically on patients after comprehensive assessments of the available data on molecular simulation. This review summarizes the outcomes of various computer simulations data in the battle against COVID-19.

A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds

“…The antiviral activities of natural products and herbs are been extensively studied and are proven to show the remarkable activity against coronavirus [ [18] , [19] , [20] , [21] ]. Hence, keeping in mind the current situation we have focussed on various classes of the compound such as antiviral drugs ( abacavir, acyclovir, quinoline, hydroxyquinoline ), antimicrobial drugs ( levofloxacin, amoxicillin, cloxacillin, ofloxacin ), natural compounds ( lycorine, saikosaponin, myricetin, amentoflavone ), herbal compounds ( silymarin, palmatine, curcumin, eugenin ) available in Indian Ayurveda .…”

Flavonoids as Promising Antiviral Agents against SARS-CoV-2 Infection: A Mechanistic Review

“…Previous in silico studies and molecular analysis of different CoVs showed the potential antiviral effects of phytochemicals at different stages of viral biogenesis, including binding to ACE2, surface gangliosides, RdRp, viral spike protein, and viral protease in host cells and paved the way for more clinical and experimental studies [ 9 , 117 , 118 , 119 , 120 , 121 , 122 , 123 ]. Nevertheless, it should be considered that an acceptable antiviral activity in virtual screenings does not necessarily guarantee in vivo antiviral activity, and that is why an overview of flavonoids with antiviral properties in experimental studies is a further step toward the selection of natural antiviral agents.…”

“…SARS, MERS, and SARS-CoV-2 are all RNA βCoVs. SARS-CoV-2 genome is 88% identical to bat-derived severe acute respiratory syndromes (SARS)-like CoVs, 79% similar to SARS-CoV, and 50% similar to MERS-CoV [ 8 , 9 ]. SARS-CoV-2 proteins are 90%–100% homologous to SARS-CoV; though, orf10 and orf8 are different between SARS-CoV-2 and SARS-CoV.…”

Spike protein of SARS-COV-2 as a potential target for phytochemical constituents: A literature review

“…20,21 Similarly, a study conducted on thirteen compounds of plants in the TCM system pharmacology (TCMSP) database, discovered a compound Dihydrotanshinone I to possess high binding affinity with the viral spike protein. 22 Plants belonging to the Glycyrrhiza spp. exert various pharmacological actions and are extensively utilized in the TCM system.…”