key: cord-0916144-205apm4k
authors: Khalifa, Ibrahim; Nawaz, Asad; Sobhy, Remah; Althawb, Sami A.; Barakat, Hassan
title: Polyacylated anthocyanins constructively network with catalytic dyad residues of 3CL(pro) of 2019-nCoV than monomeric anthocyanins: A structural-relationship activity study with 10 anthocyanins using in-silico approaches
date: 2020-07-24
journal: J Mol Graph Model
DOI: 10.1016/j.jmgm.2020.107690
sha: 5f2fc937b6c68dde6ad2aae3530c308509547e20
doc_id: 916144
cord_uid: 205apm4k

Coronavirus epidemic 2019 (COVID-19), caused by novel coronavirus (2019-nCoV), is newly increasing worldwide and elevating global health concerns. Similar to SARS-CoV and MERS-CoV, the viral key 3-chymotrypsin-like cysteine protease enzyme (3CL(Pro)), which controls 2019-nCoV duplications and manages its life cycle, could be pointed as a drug discovery target. Herein, we theoretically studied the binding ability of 10 structurally different anthocyanins with the catalytic dyad residues of 3CL(pro) of 2019-nCoV using molecular docking modelling. The results revealed that the polyacylated anthocyanins, including phacelianin, gentiodelphin, cyanodelphin, and tecophilin, were found to authentically bind with the receptor binding site and catalytic dyad (Cys145 and His41) of 2019-nCoV-3CL(pro). Our analyses revealed that the top four hits might serve as potential anti-2019-nCoV leading molecules for further optimization and drug development process to combat COVID-19. This study unleashed that anthocyanins with specific structure could be used as effective anti-COVID-19 natural components.

Nowadays, novel coronavirus (2019-nCoV) was reported in late 2019 and emerged as a hot 43 research topic. The 2019-nCoV gained the immense attention of scientists all over the world. 44

The discovery of its whole-genome sequence has helped researchers to quickly identify the virus 45 in patients and try to control its symptoms [1, 2] . The 2019-nCoV belongs to the ß-coronavirus 46 group, sharing ancestry with bat coronavirus HKU9-1, similar to SARS-coronaviruses that 47 despite of sequence diversity its spike protein interacts with the human ACE 2 -receptor [3]. By 48

July 1, 2020, the global death toll reached 509,112 with 10,449,151 confirmed cases in 213 49 countries (https://www.worldometers.info/coronavirus). 50

Recent findings revealed that 2019-nCoV genes share >80.0% nucleotide identity, and 89.1% 51 nucleotide similarity with SARS-CoV genes [4, 5] . Generally, on the transcription of gene, ~800 52 kDa of polypeptide obtains from ß-coronaviruses, which is proteolytically breakdown into 53 numerous proteins. In addition, it was found that papain-like protease (3CL Pro ) controls the virus 54 replication through leading the proteolytic processing. The 3CL Pro cleaves the polyprotein at 11 55 different sites to produce numerous non-structural proteins [6] . Consequently, 3CL Pro plays a key 56 role in the virus duplication and unlike structural/accessory protein-encoding genes located at the 57 3' end which shows great variability [7] . Hence, it may be a potential target for the inhibitor of 58 anti-COVID-19. 59

Studies based on the structural analysis have identified the potential inhibitors of MERS-CoV 60 3CL pro and SARS-CoV [8] . Bioactive substances, especially anthocyanins, have drawn 61 considerable attention owing to their potential for drug development against various diseases 62 without exerting any side effects [9] [10] [11] [12] . Anthocyanins belong to the widespread category of 63 phenolic compounds, collectively known as flavonoids, and are mainly soluble in water with 64 4 multifunction and health-promoting effects [13] [14] [15] Keeping in mind the literature review and to the best of our knowledge, few studies are available 76 on the screening of various anthocyanins using computational approach against different viruses 77

[19] but no report is available against COVID-19. Most importantly, it was hypothesized that the 78 biological activities, including antiviral effects, of anthocyanins are structural-dependent. For 79 example, it was found that hydroxyl (-OH) or methoxyl (-OCH 3 ) substitutions on the flavan 80 nucleus, the number of -OH moieties in the molecule, the degree of methylation of -OH-moieties, 81 the nature and/or the number of sugar moiety attached to aglycone molecule, and the specific 82 position of these attachments are the main factors affecting the biological activity of 83 anthocyanins [20] [21] [22] . Therefore, we selected 10 different anthocyanins in order to represent the 84 different glycosylation and acylation patterns with various flavan and sugar moieties of 85 anthocyanins. Therefore, this study was conducted to gain structural insights regarding the 86 potential anti-COVID-19 effects of 10 structurally different anthocyanins that can target the 87 3CL Pro of 2019-nCoV using in silico approaches (molecular docking and drug scan). The 88 consequences of this research will help the researcher to improve the natural therapeutics against 89 COVID-19. The 3D structure of 3CL pro of 2019-nCoV (PDB: 6y84) was obtained from the Protein Data 111 Bank (http://www.rcsb.org) with a resolution of 2.16 Å. The water molecules and already bound 112 ligands were removed from the structure to refine the structure of 3CL pro . Energy minimization 113 and 3D protonation were conducted using MOE, and the minimized structure was then used in 114 the subsequent steps [23]. 115

The 10 anthocyanins with different structures and remdesivir were docked with the allosteric 117 ligands of 3CL pro -2019-nCoV using MOE docking tool. Identification of potent binding sites was 118 done using MOE site finder tool and subsequently taken by docking process. Ten suitable 119 docked poses were produced by applying a scoring function London dG. Force field algorithm 120 was then applied to refine the docking process and to keep the receptor rigid. From these, the 121 most suitable molecules and interacting ligands were scrutinized based on RMSD (Root-Mean-122

Square Deviation) which is generally measured in terms of docking score, Angstrom (Å), and co-123 crystallized ligand. The LigX tool of MOE was used to analyze the ligand receptor binding, 124 which revealed the potential residues interacting with ligands graphically. It also produces 2D-125 images signifying the forces stabilizing ligand molecules within the receptor's binding pockets 126 [24] . For the analysis of drug likeness of 10 anthocyanins, all anthocyanins were filtered based 127 on bearing appropriate molecular attributes to be anti-COVID-19 drug candidates. The predicted 128 pharmacophore of phacelianin was also created [25]. 129

To verify the results of the current study and to assess the binding performance and stability of other ligands (Fig. 2) . Recently, it was found that the sequence of SARS-CoV-2 3CL pro clustered 145 with bat SARS-like coronaviruses and sharing 99.02% sequence identity [3]. Furthermore, it was 146 found that SARS-CoV-2 is more comparable to SARS-CoV than MERS-CoV, and shares a 147 mutual forebear with bat coronaviruses [26, 27] . The results also discovered that SARS-CoV-2 148 has a Cys-His catalytic dyad (Cys145 and His41), reliable with SARS 3CL pro (Cys145 and 149 His41), TGEV 3CL pro (Cys144 and His41), and HCoV 3CL pro (Cys144 and His41) [28] . It was 150 disclosed that the SARS-CoV-2 3CL pro receptor-binding pocket conformation resembles with the 151 binding pocket of SARS-CoV 3CL pro and increases the possibility that inhibitors intended for 152 SARS-CoV 3CL pro may also inhibit the activity of SARS-CoV-2 3CL pro . 153

To manage with the constant need of a novel and effective small molecule as anti-COVID-19 154 therapeutics with negligible side effects, research is now directing more on computational drug 155 discovery [29] . To fasten the drug approval procedure and to discover more efficacious inhibitors 156 8 with a novel structure that can improve the antiviral therapeutics status, computational drug 157 discovery approaches are highly reliable. From the ground-breaking detail of structural diversity 158 among anthocyanins, virtual screening was done to discover novel allosteric compounds as anti-159 COVID-19. The allosteric regulation has been reported as an effective strategy to attain 160 irreversible inhibition. The spatial orientation and dock score of current reported four top-ranked 161 leads to the efficient binding of functional residues with maximum binding affinity. These 162 anthocyanins meet the drug likelihood criteria are tabulated in Table 1 average RMSD values of 1.6± 0.01 Å (Fig. S2A) . It was also suggested that the normal behavior 225 for phacelianin-SARS-CoV-2 3CL pro complex; where it was remained compact and stable 226 throughout the 50 ns of MD simulations (Fig. S2B) . Likewise, H-bonds, which are the key 227 stabilizing forces in proteins, suggested that the phacelianin-SARS-CoV-2 3CL pro complex 228 remains stable throughout the simulation, with no obvious fluctuations (Fig. S2C) . It can be 229 concluded from this study that each of phacelianin, gentiodelphin, cyanodelphin, and tecophilin 230

and their sources such as pomegranates may serve as possible anti-SARS-CoV-2 drug sources. 231

Phacelianin is a form of anthocyanins flavonoid. Hydroxy groups (-OH), ketone groups (=O) and 232 O + groups in phacelianin are predicted to play a key role in the interaction with the amino acid 233 residue at the active site of SARS-CoV-2 3CL pro (Fig. 4) . 234 235

In conclusion, our study revealed that some medicinal plants rich in anthocyanins, especially 237 phacelianin, gentiodelphin, cyanodelphin, and tecophilin, could be theoretically used to treat the 238 outbreak of COVID-19. We screened the structural relationship activity of 10 anthocyanins as 239 potential antiviral components. We found that the polyacylated anthocyanins are better than both 240 of diacylated and monomeric anthocyanins that may inhibit SARS-CoV-2 3CL pro and then the 241 virus replication. Further, in vitro and in vivo studies are needed to transmute these potential 242 anthocyanins inhibitors into clinical drugs. We predict that the understandings obtained in the 243 current study may evidence valued for discovering and unindustrialized novel natural anti-244 COVID-19 therapeutic agents in the near future. 

Medicinal 337 plants and cancer chemoprevention

Anti influenza 339 virus activity of a red-fleshed potato anthocyanin

Binding of 341 a natural anthocyanin inhibitor to influenza neuraminidase by mass spectrometry

The signaling pathways, 344 and therapeutic targets of antiviral agents: Focusing on the antiviral approaches and clinical 345 perspectives of anthocyanins in the management of viral diseases

Stabilizing and modulating color by copigmentation: Insights from theory and experiment. 348 Chemical reviews

Zhou, R, Binding mechanism of remdesivir to SARS-CoV-2 RNA dependent 350 RNA polymerase

Remdesivir for severe acute respiratory syndrome 352

coronavirus 2 causing COVID-19: An evaluation of the evidence

Structures required of polyphenols for inhibiting advanced glycation end 355 products formation

Position and orientation of gallated proanthocyanidins 357 in lipid bilayer membranes: influence of polymerization degree and linkage type

[22] Khalifa, I., Xia, D., Dutta, K., Peng, J., Jia, Y., Li, C, Mulberry anthocyanins exert anti-315AGEs effects by selectively trapping glyoxal and structural-dependently blocking the lysyl 316 residues of β-lactoglobulins. Bioorg. Chem. 96 (2020) 103615. 317