Current status of antivirals and druggable targets of SARS CoV-2 and other human pathogenic coronaviruses

Abstract

Coronaviridae is a peculiar viral family, with a very large RNA genome and characteristic appearance, endowed with remarkable tendency to transfer from animals to humans. Since the beginning of the 21st century, three highly transmissible and pathogenic coronaviruses have crossed the species barrier and caused deadly pneumonia, inflicting severe outbreaks and causing human health emergencies of inconceivable magnitude. Indeed, in the past two decades, two human coronaviruses emerged causing serious respiratory illness: severe acute respiratory syndrome coronavirus (SARS-CoV-1) and Middle Eastern respiratory syndrome coronavirus (MERS-CoV), causing more than 10,000 cumulative cases, with mortality rates of 10 % for SARS-CoV-1 and 34.4 % for MERS-CoV. More recently, the severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) has emerged in China and has been identified as the etiological agent of the recent COVID-19 pandemic outbreak. It has rapidly spread throughout the world, causing nearly 22 million cases and ∼ 770,000 deaths worldwide, with an estimated mortality rate of ∼3.6 %, hence posing serious challenges for adequate and effective prevention and treatment. Currently, with the exception of the nucleotide analogue prodrug remdesivir, and despite several efforts, there is no known specific, proven, pharmacological treatment capable of efficiently and rapidly inducing viral containment and clearance of SARS-CoV-2 infection as well as no broad-spectrum drug for other human pathogenic coronaviruses. Another confounding factor is the paucity of molecular information regarding the tendency of coronaviruses to acquire drug resistance, a gap that should be filled in order to optimize the efficacy of antiviral drugs. In this light, the present review provides a systematic update on the current knowledge of the marked global efforts towards the development of antiviral strategies aimed at coping with the infection sustained by SARS-CoV-2 and other human pathogenic coronaviruses, displaying drug resistance profiles. The attention has been focused on antiviral drugs mainly targeting viral protease, RNA polymerase and spike glycoprotein, that have been tested in vitro and/or in clinical trials as well as on promising compounds proven to be active against coronaviruses by an in silico drug repurposing approach. In this respect, novel insights on compounds, identified by structure-based virtual screening on the DrugBank database endowed by multi-targeting profile, are also reported. We specifically identified 14 promising compounds characterized by a good in silico binding affinity towards, at least, two of the four studied targets (viral and host proteins). Among which, ceftolozane and NADH showed the best multi-targeting profile, thus potentially reducing the emergence of resistant virus strains. We also focused on potentially novel pharmacological targets for the development of compounds with anti-pan coronavirus activity. Through the analysis of a large set of viral genomic sequences, the current review provides a comprehensive and specific map of conserved regions across human coronavirus proteins which are essential for virus replication and thus with no or very limited tendency to mutate. Hence, these represent key druggable targets for novel compounds against this virus family. In this respect, the identification of highly effective and innovative pharmacological strategies is of paramount importance for the treatment and/or prophylaxis of the current pandemic but potentially also for future and unavoidable outbreaks of human pathogenic coronaviruses.

Keywords: Antiviral agents; Antiviral resistance; Conservation; Coronavirus; Entry inhibitors; Nucleoside analogs; Outbreaks; Protease; Protease inhibitors; RNA polymerase; SARS-CoV-2; Spike.

Fig. 1

Amino acid sequence alignment of 3CL-PR across SARS-CoV-2, SARS-CoV-1, HCoV-NL63, HCoV-229E, HCoV-HKU-1, HCoV-OC43 and MERS-CoV. Conserved amino acids shared across human coronaviruses are indicated by dots and highlighted in cyan. Amino acid residues of the catalytic dyad are highlighted in dark red, residues involved in dimerization interface are in light blue according to Goyal and Goyal (2020), Zhang et al. (2020), while residues composing the substrate-binding cleft are in dark blue according to Muramatsu et al. (2016), Hsu et al. (2005), Zhang et al. (2020), Goyal and Goyal (2020). The domains of 3CL-PR are reported according to Zhang et al. (2020). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Amino acid sequence alignment of RdRp across SARS-CoV-2, SARS-CoV-1, HCoV-NL63, HCoV-229E, HCoV-HKU-1, HCoV-OC43 and HCoV-MERS. The right hand RdRp domain (residues 366-920) is reported. Conserved amino acids across human coronaviruses are indicated by dots and highlighted in cyan. Residues encompassing motifs A–E are highlighted in light blue. The catalytic residues S759, D760 and D761 and the classic divalent-cation–binding residue D618 are highlighted in dark red. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.) The start and end of each RdRp functional domains (fingers, palm and thumb) are also indicated. The numbering of RdRp domains and motifs is according to Gao et al., Science 2020.

Fig. 3

Amino acid sequence alignment of the Spike subunit S2 across SARS-CoV-2, SARS-CoV-1, HCoV-NL63, HCoV-229E, HCoV-HKU-1, HCoV-OC43 and MERS-CoV. Conserved amino acids across human coronaviruses are indicated by dots and highlighted in cyan. The figures report only the functional domain of the spike subunit S2 according to Xia et al., 2020. FP, fusion peptide; HR, heptad repeats; TMD, transmembrane domain; Cyt-D, cytoplasmic domain.

Fig. 4

Receptor binding domain (RBD) sequence alignment of the spike subunit S1 within different groups of human coronaviruses. Amino acid sequences of SARS-CoV-2 and SARS-CoV-1 (group 2b), HCoV-HKU-1 and HCoV-OC43 (group 2a), HCoV-NL63, and HCoV-229E (group 1b), and MERS-CoV are shown. Conserved amino acids within each group are denoted as dots and highlighted in cyan.

Fig. 5

Surface 3D representation of the conserved regions of SARS-CoV-2. In panels A) 3CL-PR, B) RdRp and C) spike subunit S2, optimized structures are shown. Amino acid residues that are conserved in all coronaviruses, those conserved in SARS-CoV-2, SARS-CoV-1 and MERS-CoV, those conserved in SARS-CoV-2 and SARS-CoV-1, those conserved in SARS-CoV-2 and at least another CoV and those that are present only in SARS-CoV-2 are indicated, respectively, in blue, light blue, pale cyan, salmon and red. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 6

3D representation of the lowest energy pose of ceftolozane. Ceftolozane is docked into A) 3CL-PR, B) RdRp, C) ACE2/spike interface and D) ACE2 proteins. The ligand is depicted in green carbon sticks, whereas the targets are shown, respectively, as salmon, slate, yellow and orange cartoon and the zinc cations are represented as light magenta spheres. Salt bridges, HBs and π-cation interactions are reported as magenta, yellow and dark green dashed lines, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 7

3D representation of the lowest energy pose of NADH. NADH is docked into: A) 3CL-PR, B) RdRp, C) ACE2/spike interface and D) ACE2 proteins. The ligand is depicted as green carbon sticks, the targets are shown, respectively, as salmon, slate, yellow and orange cartoon and the zinc cations are represented as light magenta spheres. Salt bridges, HBs and π-cation interactions are reported as magenta, yellow and darkgreen dashed lines, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)