Inhibition of SARS-CoV-2 main protease 3CL^pro by means of α-ketoamide and pyridone-containing pharmaceuticals using in silico molecular docking

Highlights

• •α-ketoamide and pyridone-containing drugs (KPCD) are 3-chymotrypsin-like protease (3CL^pro) inhibitors.
• •KPCD exhibited significant binding affinity to the catalytic residues of the 3CL^pro.
• •The repurposing possibility of six of these approved drugs for COVID-19 treatment.

Abstract

The coronavirus disease infections (COVID-19) caused by a new type of coronavirus (SARS-CoV-2) have been emerging in the entire world. Therefore, it is necessary to find out potential therapeutic pharmaceuticals for this disease. This study investigates the inhibitory effect of the 3-chymotrypsin-like protease of SARS-CoV-2 (3CL^pro) using pharmaceuticals containing α-ketoamide group and pyridone ring based on molecular docking. Of these, eight pharmaceuticals approved by US-Food and Drug Administration have shown good contact with the catalytic residues of 3CL^pro. They are telaprevir, temsirolimus, pimecrolimus, aminoglutethimide, apixaban, buspirone, lenalidomide, and pomalidomide. Their binding affinity score ranged from -5.6 to -7.4 kcal/mol. Hydrogen bonds were observed and reported. To the knowledge, this study report for the first time a compound that could be binding to ALA²⁸⁵, the new residue resulting from genetic modification of 3CL^pro of SARS-CoV-2 that has increased its catalytic activity 3.6-fold compared with its predecessor 3CL^pro of SARS-CoV. It is recommended that telaprevir, and pyridone-containing pharmaceuticals including aminoglutethimide, apixaban, buspirone, lenalidomide, and pomalidomide be repurposed for COVID-19 treatment after suitable validation and clinical trials.

1. Introduction

In December 2019, a novel coronavirus named SARS-CoV-2 was reported, after an outbreak-pandemic of the pulmonary disease in Wuhan city in China called coronavirus disease-19 (COVID-19). The causes of the first infections were attributed to foods made from bat and bat-like animals. Then COVID-19 were melodramatically spread by human-to-human transmission through all the world. As of April 25, 2000, confirmed cases worldwide were 2,803,571, and mortality was 195,997 according to the Asian news network [1], [2], [3], [4]. The most important symptoms of COVID-19 are high fever, dyspnea, nonproductive cough, headache, fatigue, difficulty breathing, and frost-glass-like symptoms in the lungs [5], [6], [7].

Coronaviruses have the largest RNA genomes (27 to 31 KB) compared to other viruses. SARS-CoV-2 are positive-stranded RNA viruses and belongs to class b of the genus Betacoronavirus. recent studies have shown that the RNA genomes of SARS-CoV-2 are identical to about 82% of that of SARS-CoV [8], [9], [10], [11]. The 229E gene encodes two polyproteins involved in releasing of functional polypeptides, that are essential for viral replication and transcription. The extensive proteolytic processing responsible from the production of the polypeptides is achieved by the 3-chymotrypsin-like protease of SARS-CoV-2 (M^pro, or 3CL^pro), as it cleaves at least 11 sites on the polyproteins translated from the viral RNA. Thus, drugs that inhibit this enzyme can be an effective therapeutic agent for COVID-19 [12], [13].

Recently several studies have been conducted on some pharmaceuticals, synthetic and natural products to study their ability to inhibit 3CL^pro using the molecular docking approach. Of these tested drugs are darunavir, favipiravir isoflavone, myricitrin, chloroquine phosphate, remdesivir, indinavir, valrubicin, lopinavir, carfilzomib, eravacycline, elbasvir, and methyl rosmarinate [14], [15], [16], [17], [18], [19], [20]. Zhang el. have reported α-ketoamide and pyridone containing-synthetic compounds with a good inhibitory effect against 3CL^pro [21]. However, more research is still needed in this regard, the aim of this research study was to investigate the inhibitory effect of 3CL^pro using approved drugs that contain α-ketoamide group and pyridone ring.

2. Materials and methods

2.1. Pharmaceuticals containing α-ketoamide group and pyridone ring

The DrugBank database search engine has used to find α-ketoamide and pyridone-containing drugs. Based on these criteria, twelve drugs approved by the U.S. Food and Drug Administration were found. Six of them have α-ketoamide functional group are telaprevir, temsirolimus, pimecrolimus, everolimus, sirolimus, and tacrolimus. While pyridone-containing-pharmaceuticals are aminoglutethimide, apixaban, buspirone, lenalidomide, pomalidomide, and ubrogepant.

2.2. Buildup and energy minimization of the molecular structures

The three-dimensional structures generated and minimized via UCSF Chimera software (v 1.10.2.), using the smile string code offered by the PubChem database. The crystal structure of 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2 was obtained from the Protein Data Bank database (PDB ID: 6Y2E).

2.3. Molecular docking

Molecular docking experiments performed utilizing AutoDock Vina tool implemented in UCSF Chimera software v 1.10.2., adopting the default values for the parameters, and a grid box (-16.302 × -26.086 × 17.551) Å centered at (29.176, 58.386, 75.078) Å. Water was added as a solvent with a total solvent accessible surface area of 14358.5. The predicted score values (binding affinity) were explored using View Dock tool. The verify of docking results, binding sites, and image processing were conducted using UCSF Chimera [22], [23], [24].

3. Results and discussion

The α-ketoamide and pyridone-containing synthetic compound used as a reference in this study docked with 3CL^pro containing water residues as a solvent to represents the real environment. It was showed a good inhibitory effect with binding affinity ranged between -5.0 to -6.0 kcal/mole. The chemical structure of the reference compound was monitored in Scheme 1 , α-ketoamide functional group and pyridone ring were indicated by blue and red circles, respectively [21]. The search on the DrugBank database revealed that there is no pharmaceutical containing both of the functional groups. Of the α-ketoamide set, everolimus, eirolimus, and tacrolimus have excluded because those drugs were approved as immunosuppressive agents. Whereas, ubrogepant belongs to pyridone containing-drugs was showed no binding affinity to the active residues of CL^pro. The binding affinity score of the remaining pharmaceuticals with CL^pro were ranged from -5.6 to -7.4 kcal/mol (Tables 1 and 2 ).

Scheme 1.

Chemical structure of reference compound.

Table 1.

The binding affinity of the α-ketoamide-containing pharmaceuticals with 3-chymotrypsin-like protease (CL^pro).

Pharmaceutical name	Structure	Score (kcal/mol)	RMSD	Hydrogen bond	Van der Waals (distance)
Telaprevir		-5.9	25.88 - 30.63	Glu166	His41 (3.185 Å/ 3.334 Å/ 3.574 Å/ 3.796 Å). Cys145 (3.553Å/ 3.826 Å). Glu166 (17 side contacts, distance range: 3.201Å to 3.920 Å)
Temsirolimus		-7.1	2.41 - 7.91	-	Ala285 (3.436 Å)
Pimecrolimus		-6.7	31.63 - 34.72	-	Glu166 (13 side contacts, distance range: 2.817Å to 4.113 Å)

Table 2.

The binding affinity of the pyridone-containing pharmaceuticals with 3-chymotrypsin-like protease (CLpro).

Pharmaceutical name	Structure	Score (kcal/mol)	RMSD	Hydrogen bond (distance)	Van der Waals (distance)
Aminoglutethimide		-5.6	1.85 - 2.35	Glu166 (2.480Å/ 2.647Å)	Cys145 (4.027Å). His41 (distance: 3.331Å/ 3.599 Å/ 3.889Å). Glu166 (14 side contacts, distance range: 2.480Å to 4.034Å).
Apixaban		-7.4	23.15 - 25.97	-	Ala285 (3.302Å/ 3.546 Å). His41 (distance: 2.720 Å/ 2.875 Å/ 2.948 Å/ 3.131Å/ 3.635Å). Glu166 (6 side contacts, distance range: 3.423Å to 4.076Å)
Buspirone		-6.9	2.02 -7.79	Cys145 Glu166	His41 (3.531 Å/ 3.708 Å/ 3.762 Å/ 3.951 Å). Cys145 (distance: 3.831Å). Glu166 (12 side contacts, distance range: 3.107 Å to 4.142 Å).
Lenalidomide		-6.5	27.28 - 29.07	Cys145 Glu166	His41 (distance: 3.324 Å). Cys145 (distance: 3.814 Å). Glu166 (9 side contacts, distance range: 3.137 Å to 3.919 Å).
Pomalidomide		-6.6	1.69 -3.04	Cys145 Glu166	His41 (distance: 3.377 Å). Cys145 (distance: 3.616 Å/ 3.823 Å). Glu166 (13 side contacts, distance range: 2.310 Å to 3.948 Å).

The inhibitory effect of CL^pro was investigated based on hydrogen-bonds and Van der Waals interactions between the selected drugs and the catalytic residues of CL^pro (Cys¹⁴⁵ and His⁴¹), the important residues for keeping the enzyme on the correct conformation (Ser¹ and Glu¹⁶⁶), and the residue resulting from the genetic mutation that led to a 3.6-fold increase in the reproductive effectiveness of the virus (Ala²⁸⁵) [3], [21]. Telaprevir, the anti-hepatitis B virus has the most potent activity among the α-ketoamide-containing drugs. Maybe its activity could be increased by combination use with temsirolimus that used for the treatment of renal cell carcinoma. Figs. 1 -3 show the interactions between these drugs and CL^pro, Hydrogen bonds in blue stripes, and Van der Waals yellow stripes.

Fig. 2.

Temsirolimus docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of temsirolimuscyan, nitrogen atoms are blue, oxygens red. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 1.

Telaprevir docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of telapreviris cyan, nitrogen atoms are blue, oxygens red. Below, a magnified images of contact sites of telapreviris with HIS⁴¹, CYS¹⁴⁵ and GLU¹⁶⁶. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 3.

Pimecrolimus docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of pimecrolimus, nitrogen atoms are blue, oxygens red. Below, a magnified images of contact sites of pimecrolimus with GLU¹⁶⁶. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

The pyridone-containing pharmaceuticals have shown a tendency to interacts with His⁴¹ and other active residues as shown in Figs. 4 -8 . Of these, aminoglutethimide is used in the treatment of seizures, breast cancer, and prostate cancer [25], [26]. Aminoglutethimide has shown the latest binding affinity, however, is interacts with Cys¹⁴⁵ also and has an ability to make hydrogen bonds with Glu¹⁶⁶. Buspirone, lenalidomide, and pomalidomide are approved in 1986, 2005, and 2013, respectively. They are used to treat anxiety disorders, multiple myeloma, and anemia [27], [28], [29]. These three medications may be the best inhibitors for CL^pro as they have shown a significant tendency to make hydrogen bonds with Cys¹⁴⁵, however, apixaban may be an exception. Apixaban is approved in 2012 for the prevention and treatment of thromboembolic diseases, its advantage has an ability to bind with the Ala²⁸⁵. In this group, the pyridone ring played a key role in inhibiting the CL^pro, by making hydrogen bonds with the catalytic residues. The thing that opens the door is wide for many researches into developing new simple inhibitors of this enzyme, as in fact, the pyridone-containing pharmaceuticals are very simple and easy to produce in large commercial quantities commensurate with the spread of this pandemic.

Fig. 5.

Apixaban docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of apixaban is cyan, nitrogen atoms are blue, oxygens red. Below, different side of view of magnified images of contact sites of apixaban with ALA²⁸⁵, HIS⁴¹, and GLU¹⁶⁶. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 6.

Buspirone docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of buspirone is cyan, nitrogen atoms are blue, oxygens red. Below, different side of view of a magnified images of contact sites of Buspirone with HIS⁴¹, CYS¹⁴⁵ and GLU¹⁶⁶. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 7.

Lenalidomide docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of lenalidomide is cyan, nitrogen atoms are blue, oxygens red. Below, different side of view of a magnified images of contact sites of lenalidomide with HIS⁴¹, CYS¹⁴⁵ and GLU¹⁶⁶. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 4.

Aminoglutethimide docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of Aminoglutethimide is cyan, nitrogen atoms are blue, oxygens red. Below, a magnified images of contact sites of Aminoglutethimide with HIS⁴¹, CYS¹⁴⁵ and GLU¹⁶⁶. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 8.

Pomalidomide docked with 3-chymotrypsin-like protease (3CL^pro) of SARS-CoV-2. Hydrocarbon skeleton of pomalidomide is cyan, nitrogen atoms are blue, oxygens red. Below, different side of view of a magnified images of contact sites of pomalidomide with HIS⁴¹, CYS¹⁴⁵ and GLU¹⁶⁶. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

To sum, telaprevir, aminoglutethimide, apixaban, buspirone, lenalidomide, and pomalidomide have shown a good binding affinity to the catalytic sites of CL^pro. This study suggests the repurposing of these drugs for COVID-19 treatment after a suitable in vitro and in vivo validation as well as clinical trials. To the knowledge, this study report for the first time a 3CL^pro inhibitor regarding their contacts with ALA²⁸⁵.

Data availability

The data will be available upon request.

CRediT authorship contribution statement

Amin O. Elzupir: Conceptualization, Investigation, Methodology, Software, Writing - review & editing.

Declaration of Competing Interest

The author declares that he has no conflict of interest.