ABclonal Knowledge Base

The 3CLpro as a Potential Target for the Intervention of COVID-19

Written by Edward Li, Ph.D | Jan 11, 2022 5:57:34 PM

The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 has raised global health concerns. As case numbers continue to climb, there is an urgent need for an active drugs against SARS-CoV-2. The development of new drugs is time-consuming and costly, and the safety of new drugs is paramount. Therefore, the strategy of drug repurposing represents one of the fastest approaches to have an active drug to fight SARS-CoV-2 during the COVID-19 pandemic.

As a matter of fact, in silico repurposing approaches have found increasing popularity during the COVID-19 epidemic [1], especially with the great breakthrough achieved using 3CLpro as a target to screen drugs. By the end of 2021, the FDA has authorized the first oral antiviral drug Paxlovid, produced by Pfizer, to treat COVID-19. Due to that much of the scientific and clinical work on drug repurposing or drug screening against SARS-CoV-2 or COVID-19 is still ongoing, in this blog we will review the latest progress on the potential targets, including 3CLpro, for the drug discovery or intervention of COVID-19.

 

How does Paxlovid work?

SARS-CoV-2 is a positive-sense, single-stranded RNA virus with ~ 30-kb long genome. Structurally, SARS-CoV-2 contains four structural proteins, that include spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins with different functions during the viral life cycle. These proteins share high sequence similarity to the sequence of the corresponding protein of SARS-CoV, and MERS-CoV [2]. During the infection and replication of SARS-CoV-2, there are many protein-protein interactions between viral and human cellular proteins. The receptor-binding domain (RBD) in the Spike proteins of SARS-CoV-2 binds to the host cell membrane receptor, Angiotensin-Converting Enzyme-2 (ACE2) in humans, this helps in the entry of the virus into the target cells [3]. The human cell surface protease TMPRSS2 cleaves ACE2 and thus, helps in S protein activation and entry of the virus into the cell by endocytosis due to conformational changes that lead to membrane fusion. After entering the cells, SARS-CoV-2 releases its genetic material (mRNA) in the cytoplasm of the host cells which undergoes translation to form long polypeptides pp1a and pp1b. These polypeptides encoded by the 5’ ORF1a and ORF1b, are processed into 16 non-structural proteins (NSP1-16) auto-proteolytically using viral proteases like papain-like protease (PLpro) and chymotrypsin-like protease (3CLpro) to form the RNA replicase/transcriptase complex (RTC) [4-6]. The viral protease RNA-dependent RNA polymerase (RdRp) encoded by NSP12 as well as other viral proteases also help in the host RNA translation [6].

Figure 1 Source: Wikimedia Foundation. (2021, July 15). Cyclin. Wikipedia. Retrieved October 13, 2021, from https://en.wikipedia.org/wiki/Cyclin#/media/File:Cyclin_Expression.svg.

Paxlovid (nirmatrelvir [PF-07321332] tablets and ritonavir tablets) is an investigational SARS-CoV-2 protease inhibitor antiviral co-packaged with ritonavir authorized for emergency use for the treatment of high-risk patients with COVID-19 to prevent severe illness which can lead to hospitalization and death. Paxlovid belongs to a general class of drugs known as protease inhibitors. Paxlovid contains the novel antiviral nirmatrelvir (PF-07321332) which works by blocking the activity of SARS-CoV-2 main protease (Mpro), also known as SARS-CoV-2 3CL protease (3CLpro) [7]. In fact, 3CLpro is already a proven drug discovery target for SARS-CoVs and MERS-CoVs. This underlines the importance of 3CL protease in the design of potent drugs against COVID-19. 3CLpro is a first choice for repurposing campaigns due to its extensive experimental support [8], available crystallographic data, and good biological evaluation data [5, 9]. The protease is an attractive target as it plays a central role in the viral life cycle by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites and complementary reports on repurposing research are available [10].

Other Candidate Targets for Intervention of COVID-19

Several in-depth reviews have summarized the major approaches, candidate targets for intervention of COVID-19, and pointed out the future direction of treatment. The widely studied targets can be classified as several categories, including targets involved in cell entry process of SARS-CoV-2, such as S glycoprotein of SARS-CoV-2, host proteins ACE2, TMPRSS2 and DPP-4, targets involved in SARS-CoV-2 replication, transcription and suppression of host immune response, such as RNA dependent RNA polymerase (RdRp), PLpro and 3CLpro, targets for cytokine storm inhibition, such as cytokine storm related inflammatory cytokine [1, 11-13].

Looking to the Future

Although a vast number of coronavirus-based or host-based trials for drugs with in vivo or in vitro activities against SARS-CoV-2 have been carried out, only a few of these drugs can be applied in clinical practice. In the long term, the intensive studies on pathogenic mechanisms of SARS-CoV-2 will give more clues in the context of developing potent drugs and vaccines against protein targets for the development of better approaches in COVID-19 therapy.

Molecular docking and simulation, as well as a literature search, can help to find various approved or candidate drugs that can target SARS-CoV-2 viral interactions with human host proteins. Various repurposed drug candidates targeting these host proteins help to interfere with the replication of SARS-CoV-2 and disease progression post-infection. Currently, more and more potential drug targets have been identified by in silico and in vitro studies of SARS-CoV-2 virus-host interactome for new drug screening and discovery. Some emerging repurposed drugs have also been screened and applied into clinical trials in COVID-19 patients by supplementing them with other approved antiviral drugs [13].

How ABclonal can Help

ABclonal offers a variety of SARS-CoV-2 research products including antibodies, proteins ELISA kits. This collection of products that can provide support for the research of drug development and therapies for COVID-19.

Research Tools for SARS-CoV-2 Viral Proteins

Target

Antibodies (Cat.No.)

Proteins (Cat.No.)

ELISA Kits (Cat.No.)

Antibody Pairs (Cat.No.)

3CLpro

A20831

RP01270LQ

 

 

Spike

A20137

 

RK04158
RK04159
RK04156

RM17599 (capture antibody)
RM17600 (detection antibody)

Spike ECD

A20497 

 

RK04135
RK04137
RK04144
RK04194

RM17608 (capture antibody)
RM17609 (detection antibody)

Spike RBD

A20141 
A20135 
A20606 
A19215 

RP01258
RP01271
RP01278
RP01282

RK04138
RK04145
RK04154

RM17611 (capture antibody)
RM17612 (detection antibody)

Spike S1

A20022 
A20834 
A20136 
A20604

RP01259
RP01261
RP01262
RP01265

 

 

Spike S2

A20284 

 

 

 

Spike S2 ECD

A20138 

 

 

 

Nucleocapsid Protein

A20142 
A20021 
A18797 
A20607 

RP01264
RP01281

RK04136
RK04139
RK04178
RK04257

RM17574 (capture antibody)
RM17575 (detection antibody)

Envelope

 

RP01263

 

 

ORF3A

A20234 

 

 

 

ORF6

A20324 

 

 

 

ORF7a

A20307 

 

 

 

ORF9b

A20260 

 

 

 

NSP1

A20200 

 

 

 

NSP2

A20280 

 

 

 

NSP3

A20236 

 

 

 

NSP4

A20281 

 

 

 

NSP6

A20322 

 

 

 

NSP7

A20201 

 

 

 

NSP8

A20202 

 

 

 

NSP9

A20308 

 

 

 

NSP10

A20325 

 

 

 

NSP12

A20233 

 

 

 

NSP13

A20282

 

 

 

NSP14

A20283

 

 

 

NSP15

A20282 

 

 

 

NSP16

A20283 

 

 

 


Antibodies for SARS-CoV-2 or COVID-19 Drug Discovery or Repurpose Related Host Targets

Category

Target

Cat.No.

Application

Reactivity

Cell Entry of SARS-CoV-2

ACE2

A4612

WB,IHC

Human,Mouse,Rat

TMPRSS2

A9126

WB,IHC

Human,Mouse,Rat

DPP-4

A4252

WB

Human,Mouse,Rat

Viral replication

Cyclophilin

A5097

WB,IHC

Human,Mouse,Rat

Nucleotide biosynthesis

IMPDH2

A9208

WB,IF

Human,Mouse,Rat

Transcriptional regulation

BRD4

A12677

WB,IHC

Human

AP1235

WB

Human

AP1276

WB

Human, Mouse, Rat

Transcriptional regulation

HDAC2

A19626

WB,IHC,IF,IP

Human,Mouse,Rat

DNMT1

A19679

WB,IHC,IF

Human,Mouse,Rat

Nuclear export

XPO1

A19625

WB,IHC,IF

Human,Mouse,Rat

Translation control

eEF1A

A11545

WB,IF

Human,Mouse,Rat

eIF4E

A19044

WB, IP

Mouse, Rat

Protein processing

GLA

A5119

WB

Human,Mouse,Rat

Protein degradation

CUL2

A5076

WB,IHC

Human,Mouse,Rat

Receptors

F2RL1

A5103

WB,IHC

Human,Mouse,Rat

Transporters

SLC1A3

A9712

WB,IHC

Human,Mouse,Rat

MRP1/ABCC1

A2223

WB

Human

Cell devision regulation

VCP

A1402

WB,IF

Human,Mouse,Rat

Cytoskeleton dynamics

MARK2/3

A6512

WB

Human,Mouse,Rat

Multifunctional kinases

CSNK2A2

A20791

WB

Human, Mouse, Rat

Immunity and Inflammation

RIPK1

A19580

WB,IP

Human

TBK1

A3458

WB,IF,IP

Human,Mouse,Rat

AP1026

WB

Human, Mouse

Redox homeostasis

LOX

A11504

WB,IHC

Human,Mouse,Rat

Cellular metabolism

NDUFs

A4602

WB,IHC

Human,Mouse,Rat

COMT

A4435

WB

Human,Rat

 

 ELISA Kits for COVID-19 Research 

Target

Cat.No.

Sensitivity

Assay Range

TNF-α

RK00030

6.9 pg/mL

15.6-1000 pg/ml

IFN-β

RK01630

2.7 pg/mL

15.6-1000pg/ml

IFN-γ

RK00015

7.3 pg/mL

15.6-1000 pg/ml

IL-1ra

RK04182

15.1 pg/mL

31.2-2000pg/ml

IL-1α

RK00031

4 pg/ml

7.8-500 pg/ml

IL-1β

RK00001

3.9 pg/mL

6.25-400 pg/ml

IL-2

RK00002

0.39 pg/mL

0.78-50 pg/ml

IL-4

RK00003

15.2 pg/mL

31.2-2000 pg/ml

IL-5

RK00033

0.7 pg/mL

11.71-750pg/ml

IL-6

RK00004

0.7 pg/mL

1.56-100pg/ml

IL-7

RK00120

5.23 pg/mL

15.6-1000 pg/mL

IL-8

RK00011

1.7 pg/mL

3.9-250 pg/ml

IL-9

RK00121

10pg/ml

31.2-2000pg/mL

IL-10

RK04259

0.63 pg/mL

3.13-200 pg/mL

IL-12 p70

RK00014

15.1pg/mL

31.2-2000pg/ml

IL-12/IL-23 p40

RK00013

7.8 pg/ml

15.6-1000 pg/ml

IL-13

RK00034

23 pg/ml

46.9-3000 pg/ml

IL-17

RK00397

4.2 pg/mL

7.8-500 pg/ml

IL-22

RK00042

15 pg/ml

31.2-2000 pg/ml

IL-23

RK00179

7.8pg/ml

31.2-2000pg/mL

IL-27

RK00159

23.4pg/mL

46.875-3000pg/ml

IL-37

RK00117

15.6pg/mL

31.25-2000 pg/mL

IL-38

RK00116

12.32 pg/mL

62.5-4000 pg/mL

CCL3/MIP 1-α

RK04215

7.8pg/ml

15.6-1000pg/ml

CCL4/MIP 1-β

RK04222

3.9pg/mL

15.6-1000pg/mL

CCL5

RK00077

6.9 pg/mL

31.2-2000 pg/mL

CCL20

RK00207

3.4 pg/mL

7.8-500pg/ml

CXCL1

RK04197

43pg/ml

78-5000pg/mL

CXCL1/IP-10

RK00054

12.6 pg/mL

31.2-2000 pg/ml

CXCL9

RK04210

7.8pg/ml

15.6-1000pg/ml

GM-CSF

RK00045

7.8 pg/mL

7.8-500 pg/ml

MCP-1

RK00052

15.2 pg/mL

31.2-2000pg/ml

M-CSF

RK00044

7 pg/mL

15.6-1000 pg/ml

HGF

RK04211

62.5pg/ml

125-8000pg/ml

PDGF-BB

RK04112

12.3 pg/mL

31.2-2000pg/ml

VEGF

RK00023

7.8 pg/mL

31.2-2000pg/ml

Reference

1. J Pharm Anal. 2021, 11(6): 683-690.
2. Nature Reviews Microbiology. 2021, 19: 685-700.
3. Cell Biosci. 2021, 11: 136.
4. Nature 2020, 582: 289-293.
5. Nat Commun 2021, 12: 743.
6. Nature. 2020, 584(7819): 154-156.
7. Protein Cell. 2021 Oct 22;1-5.
8. Nature. 2020, 583 (7816): 459-468.
9. J.Enzyme Inhib. Med. Chem. 2021, 36 (1): 147-153.
10. ACS Pharmacol. Translational Sci. 2021, 4 (3): 1096-1110.
11. Metabol Open. 2021, 12: 100121.
12. Pharmacol Ther. 2021 , 228: 107930.
13. Eur J Pharmacol. 2021, 898: 173977.