Researchers has tested more than 10000 compounds and identify six drug candidates to treat COVID-19


An international team of researchers has tested more than 10,000 compounds to identify six drug candidates that may help treat COVID-19.

The research, involving University of Queensland scientist Professor Luke Guddat, tested the efficacy of approved drugs, drug candidates in clinical trials and other compounds.

“Currently there are no targeted therapeutics or effective treatment options for COVID-19,” Professor Guddat said.

“In order to rapidly discover lead compounds for clinical use, we initiated a program of high-throughput drug screening, both in laboratories and also using the latest computer software to predict how different drugs bind to the virus.

Professor Guddat said the project targeted the main COVID-19 virus enzyme, known as the main protease or Mpro, which plays a pivotal role in mediating viral replication.

“This makes it an attractive drug target for this virus, and as people don’t naturally have this enzyme, compounds that target it are likely to have low toxicity.

“We add the drugs directly to the enzyme or to cell cultures growing the virus and assess how much of each compound is required to stop the enzyme from working or to kill the virus.

“If the amount is small, then we have a promising compound for further studies.”

After assaying thousands of drugs, researchers found of the six that appear to be effective in inhibiting the enzyme, one is of particular interest.

“We’re particularly looking at several leads that have been subjected to clinical trials including for the prevention and treatment of various disorders such as cardiovascular diseases, arthritis, stroke, atherosclerosis and cancer,” Professor Guddat said.

“Compounds that are already along the pipeline to drug discovery are preferred, as they can be further tested as antivirals at an accelerated rate compared to new drug leads that would have to go through this process from scratch.”

After the enzyme’s structure was made public, the team received more than 300 requests for more information, even before the paper was published.

“To provide an analogy, we’ve provided scientists with a fishing pole, the line and the exact bait, and have in only one month caught some fish,” Professor Guddat said.

“Now it’s up to us and the other fisherman – our fellow scientists globally – to take full advantage of this breakthrough.”

“With continued and up-scaled efforts we are optimistic that new candidates can enter the COVID-19 drug discovery pipeline in the near future.”

The research has been published in Nature.

Experimental Section


COVID-19 3clpro/Mpro (PDB ID: 6LU7) [13] and 3clpro/Mpro (PDB ID: 2GTB) [6] structures were obtained from PDB (, in .pdb format. PDB is an archive for the crystal structures of biological macromolecules, worldwide [14].

The 6LU7 protein contains two chains, A and B, which form a homodimer. Chain A was used for macromolecule preparation. The native ligand for 6LU7 is n-[(5-methylisoxazol-3- yl)carbonyl]alanyl-l-valyl-n~1~-((1r,2z)-4-(benzyloxy)-4-oxo-1-{[(3r)-2-oxopyrrolidin-3- yl]methyl}but-2-enyl)-l-leucinamide.

Ligand and Drug Scan

The 3-dimensional (3D) structures were obtained from PubChem (, in .sdf format. PubChem is a chemical substance and biological activities repository consisting of three databases, including substance, compound, and bioassay databases [15]. Several ligands for which the active compound can be found in herbal medicine were

downloaded from Dr. Duke’s Phytochemical and Ethnobotanical Databases ( The compounds used in the present study were nelfinavir (CID_64143), lopinavir (CID_92727), luteolin-7-glucoside (CID_5280637), demethoxycurcumin (CID_5469424), apigenin-7-glucoside (CID_5280704), oleuropein (CID_56842347), curcumin (CID_969516), epicatechin-gallate (CID_107905), zingerol (CID_3016110), gingerol (CID_442793), catechin (CID_9064), and allicin (CID_65036), quercetin (CID_5280343), kaempferol (CID_5280863) and naringenin (CID_439246).

Drug-like properties were calculated using Lipinski’s rule of five, which proposes that molecules with poor permeation and oral absorption have molecular weights > 500, C logP > 5, more than 5 hydrogen-bond donors, and more than 10 acceptor groups [16, 17] Adherence with Lipinski’s rule of five as calculated using SWISSADME prediction (

Determination of Active Sites

The amino acids in the active site of a protein were determined using the Computed Atlas for Surface Topography of Proteins (CASTp) ( and Biovia Discovery Studio 4.5. The determination of the amino acids in the active site was used to analyse the Grid box and docking evaluation results. Discovery Studio is an offline life sciences software that provides tools for protein, ligand, and pharmacophore modelling [18].

Molecular Docking

Ligand optimisation was performed by Avogadro version 1.2, with Force Field type MMFF94, and saved in .mol2 format. Autodock version 4.2 used for protein optimisation, by removing water and other atoms, and then adding a polar hydrogen group. Autodock 4.2 was supported by Autodock tools, MGL tools, and Rasmol. Autogrid then determined the native ligand position on the binding site by arranging the grid coordinates (X, Y, and Z). Ligand tethering of the protein was performed by regulating the genetic algorithm (GA) parameters, using 10 runs of the GA criteria. The docking analyses were performed by both Autodock 4.2, Pymol version Edu and Biovia Discovery Studio 4.5.


Table 1 shows the structures and amino acids found in the active site pockets of 6LU7 and 2GTB. 6LU7 is the main protease (Mpro) found in COVID-19, which been structured and repositioned in PDB and can be accessed by the public, as of early February 2020.

2GTB is the main protease found in the CoV associated with the severe acute respiratory syndrome (SARS), which can be accessed in PDB and was suggested to be a potential drug target for 2019-nCov [6]. Xu et al. (2020) mentioned that the main protease in 2019-nCov shares 96% similarity with that in SARS.

Table 1. Protein target structures and active site amino acids (Biovia Discovery Studio 4.5, 2019) and the native ligand structure

Ligands and several drug candidate compounds have been previously selected, based on adherence to Lipinski’s rule of five. The selected ligands that did not incur more than 2 violations of Lipinski’s rule could be used in molecular docking experiments with the target protein. The drug scanning results (Table 2) show that all tested compounds in this study were accepted by Lipinski’s rule of five.


Coronaviruses (CoVs) belong to a group of viruses that can infect humans and vertebrate animals. CoV infections affect the respiratory, digestive, liver, and central nervous systems of humans and animals [19]. The present study focused on the main proteases in CoVs (3CLpro/Mpro), especially PDB ID 6LU7, as potential target proteins for COVID-19 treatment. 6LU7 is the Mpro in COVID-19

that has been structured and repositioned in PDB and has been accessible by the public since early February 2020. The Mpro of 2019-nCov shares 96% similarity with the Mpro of the SARS-CoV [6, 20]. The Mpro in CoV is essential for the proteolytic maturation of the virus and has been examined as a potential target protein to prevent the spread of infection by inhibiting the cleavage of the viral polyprotein [13]. The discovery of the Mpro protease structure in COVID-19 provides a great opportunity to identify potential drug candidates for treatment.

Proteases represent potential targets for the inhibition of CoV replication, and the protein sequences of the SARS-CoV Mpro and the 2019-nCoV Mpro are 96% identical, and the active sites in both proteins remain free from mutations. The Mpro amino acids Thr24, Thr26, and Asn119 are predicted to play roles in drug interactions [21].

The disruption of protease activity can lead to various diseases; thus, commonly, host proteases can be used as potential therapeutic targets. In many viruses, proteases play essential roles in viral replication; therefore, proteases are often used as protein targets during the development of antiviral therapeutics [22].

Nelfinavir and lopinavir are protease inhibitors with high cytotoxic values against cells infected with HIV. Lopinavir and ritonavir are protease inhibitors recommended for the treatment of SARS and MERS, which have similar mechanisms of action as HIV [23]. The antiviral effects of nelfinavir against CoV have been studied in vitro, in Vero cells infected with SARS-CoV [24]. The IC50 value for nelfinavir in SARS-CoV is 0.048 µM [25]. In the present study, we used nelfinavir and lopinavir as drug standards for comparison.

Several compounds, such as flavonoids, from medicinal plants, have been reported to show antiviral bioactivities [10–12]. We investigated kaempferol, quercetin, luteolin-7-glucoside, demethoxycurcumin, naringenin, apigenin-7-glucoside, oleuropein, curcumin, catechin, epicatechin- gallate, zingerol, gingerol, and allicin as potential inhibitors of the COVID-19 Mpro. An in silico analysis study showed that the compounds share a similar pharmacophore as nelfinavir. Several studies have investigated the presence of high numbers of these phenolic compounds belonging several medicinal plant which abundant in nature (see Table 4).

The binding energies obtained from docking 6LU7 with the native ligand, nelfinavir, lopinavir, kaempferol, quercetin, luteolin-7-glucoside, demethoxycurcumin, naringenin, apigenine-7-glucoside, oleuropein, curcumin, catechin, epicatechin-gallate, zingerol, gingerol, and allicin were -8.37, -10.72,

-9.41, -8.58, -8.47,-8.17, -7.99, -7.89, -7.83, -7.31, -7.05, -7.24, -6.67, -5.40, -5.38, -5.40, and -4.03 kcal/mol,

respectively (see Table 3 and Figure 1).

Table 4. Source of several compounds belong to medicinal plants

CompoundsSources Species nameReference
KaempferolSpinach Spinacia oleracea[26]
 Cabbage Brassica oleracea[26]
 Dill Anethum graveolens[26]
 Chinese cabbage Brassica rapa[26]
 Katuk Sauropus androgynus[27]
QuercetinDill Anethum graveolens[26]
 Fennel leaves Foeniculum vulgare[26]
 Onion Allium cepa[26]
 Oregano Oregano vulgare[26]
 Chili pepper Capsicum annum[26]
Luteolin-7-glucosideOlive Olea Europaea L[28–30]
 Star fruit Averrhoa belimbi[31]
 Chili pepper Capsicum annum[31]
 Welsh     onion/Allium fistulosum[31]
DemethoxycurcumineTurmericCurcuma longa[32, 33]
 CurcumaCurcuma xanthorriza[32, 33]
NaringeninCitrus fruitCitrus sinensis[34]
Apigenine-7-glucosideStar fruitAverrhoa belimbi[31]
 Goji berriesLycium chinense[31]
 CeleryApium graveolens[31]
 OliveOlea Europaea L[28, 29]
OleuropeinOliveOlea Europaea L[28–30]
CatechinGreen teaCamellia sinesis[35–37]
CurcuminTurmeric CurcumaCurcuma longa Curcuma xanthorriza[38–41] [32], [33]
Epicatechin gallateGreen teaCamellia sinesis[35–37]
ZingerolGingerZingiber officiale[42–44]
GingerolGingerZingiber officiale[42–44]
AllicinGarlicAllium sativum[45–47]

The results of docking analysis (Table 2 and Figure 2) showed that nelfinavir forms H-bonds with the 6LU7 amino acids Glu166, Gln189, and Gln192 (Figure 2A). Lopinavir forms H-bonds with the 6LU7 amino acids Glu166, Arg188, and Gln189 (Figure 2B). Luteolin-7-glucoside and forms H- bonds with the 6LU7 amino acid Phe140, Cys145, His163, His164, and Thr190 (Figure 2C). Demethoxycurcumin forms H-bonds with the 6LU7 amino acids Phe140, Leu141, Gly143, Ser144, Cys145, His163, Glu166, and Arg188 (Figure 2D). Apigenin-7-glucoside forms H-bonds with the 6LU7 amino acids Phe140, Cys145, Glu166, Thr190, and Gln192 (Figure 2E). Oleuropein forms H- bonds with the 6LU7 amino acids Tyr54, Leu141, His163, and Glu166 (Figure 2F). Curcumin forms H-bonds with the 6LU7 amino acids Leu141, Gly143, Ser144, Cys145, and Thr190 (Figure 2G). Catechin forms H-bonds with the 6LU7 amino acids His164, Glu166, Asp187, Thr190, and Gln192 (Figure 2H). Epicatechin-gallat forms H-bonds with the 6LU7 amino acids Asn142, His164, Glu166, and Thr190 (Figure 2I). Quercetin forms H-bonds with the 6LU7 amino acid His164, Glu166, Asp187, Gln192, Thr190 (Figure 2J). Kaempferol forms H-bonds with the 6LU7 amino acid Tyr54, His164, Glu166, Apr187, Thr190 (Figure 2J). Naringenin forms H-bonds with the 6LU7 amino acid His164, Glu166, Asp187, Thr190 (Figure 2J). Docking analysis results, including the H-bonds that interact with 6LU7 amino acids, can be observed in Table 1. All of the H-bonds interacted with amino acids in the COVID-19 Mpro active site. The binding energy results are related to the number of H-bonds formed with the active site pocket of COVID-19 Mpro.

Kaempferol and quercetin are a flavonol compounds, while luteolin-7-glucoside is a flavone within the class of flavonoid compounds [49]. Secondary metabolite compounds are commonly found in medicinal plants. Luteolin-7-glucoside and kaempferol shown in Figure 3, is a form of aglycone of flavonoid. Hydroxy groups (-OH), ketone groups (=O) and ether groups (-O-) in luteolin and kaempferol compounds are predicted to play roles amino acid residue interactions at the active site of COVID-19 Mpro [50].

The high affinity of drug compounds depends on the type and amount of bonding that occurs with the active site of the protein. In Table 2, nelfinavir forms many chemical bonds with 6LU7, including hydrogen bonds and hydrophobic bonds. Kaempferol, quercetin and luteolin-7-glucoside also forms many chemical bonds, similar to nelfinavir. Therefore, the affinity of kaempferol bonds is higher compared with other compounds.

The docking analysis in the present study showed the inhibition potential of several compounds, ranked by affinity (ΔG); nelfinavir > lopinavir > kaempferol > quercetin > luteolin-7-glucoside > demethoxycurcumin > naringenin > apigenine-7-glucoside > oleuropein > curcumin > catechin > epigallocatechin > zingerol > gingerol > allicin.

Kaempferol, quercetin, luteolin-7-glucoside, apigenin-7-glucoside, naringenin, oleuropein, demethoxycurcumin, curcumin, catechin, and epigallocatechin were the most recommended compounds found in medicinal plants as potential inhibitors of COVID-19 Mpro, which should be explored in future research.

More information: Zhenming Jin et al, Structure of Mpro from COVID-19 virus and discovery of its inhibitors, Nature (2020). DOI: 10.1038/s41586-020-2223-y

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