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In Silico Studies of Selected Xanthophylls As Potential Candidates Against SARS-Cov-2 Targeting Main Protease (Mpro) and Papain-Like Protease (Plpro)

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In Silico Studies of Selected Xanthophylls As Potential Candidates Against SARS-Cov-2 Targeting Main Protease (Mpro) and Papain-Like Protease (Plpro) International journal edited by the Institute of Natural Fibres and Medicinal Plants National Research Institute Vol. 67 No. 2 2021 Received: 2021-05-06 DOI: 10.2478/hepo-2021-0009 Accepted: 2021-05-30 Available online: 2021-06-08 EXPERIMENTAL PAPER In silico studies of selected xanthophylls as potential candidates against SARS-CoV-2 targeting main protease (Mpro) and papain-like protease (PLpro) TOMASZ M. KARPIŃSKI1,* , MAREK KWAŚNIEWSKI1 , MARCIN OŻAROWSKI2 , RAHAT ALAM3,4 1Chair and Department of Medical Microbiology Poznań University of Medical Sciences Wieniawskiego 3 61-712 Poznań, Poland 2Department of Biotechnology Institute of Natural Fibres and Medicinal Plants – National Research Institute Wojska Polskiego 71b 60-630 Poznań, Poland 3Department of Genetic Engineering and Biotechnology Faculty of Biological Science and Technology Jashore University of Science and Technology Jashore-7408, Bangladesh 4Laboratory of Computational Biology Biological Solution Centre (BioSol Centre) Dhaka, Bangladesh *corresponding author: e-mail: [email protected] Summary Introduction: The main protease (Mpro) and the papain-like protease (PLpro) are essential for the replica- tion of SARS-CoV-2. Both proteases can be targets for drugs acting against SARS-CoV-2. Objective: This paper aims to investigate the in silico activity of nine xanthophylls as inhibitors of Mpro and PLpro. Methods: The structures of Mpro (PDB-ID: 6LU7) and PLpro (PDB-ID: 6W9C) were obtained from RCSB Protein Data Bank and developed with BIOVIA Discovery Studio. Active sites of proteins were performed Herba Pol 2021; 67(2): 1-8 2 TM. Karpiński, M. Kwaśniewski, M. Ożarowski, R. Alam using CASTp. For docking the PyRx was used. Pharmacokinetic parameters of ADMET were evaluated us- ing SwissADME and pkCSM. Results: β-cryptoxanthin exhibited the highest binding energy: –7.4 kcal/mol in the active site of Mpro. In PLpro active site, the highest binding energy had canthaxanthin of –9.4 kcal/mol, astaxanthin –9.3 kcal/mol, flavoxanthin –9.2 kcal/mol and violaxanthin –9.2 kcal/mol. ADMET studies presented lower toxicity of xanthophylls in comparison to ritonavir and ivermectin. Conclusion: Our findings suggest that xanthophylls can be used as potential inhibitors against SARS-CoV-2 main protease and papain-like protease. Key words: coronavirus, COVID-19, pandemics, computer-aided drug design, antiviral Słowa kluczowe: koronawirus, COVID-19, pandemia, projektowanie leków wspomagane kom- puterowo, działanie przeciwwirusowe INTRODUCTION anti-inflammatory [13, 15] and anticancer [16] ac- tivities have been described. The latest publications The SARS-CoV-2 is classified into the Betacoronavi- indicate that xanthophylls may also have a protective ruses genus, in the Riboviria kingdom, Nidovirales effect in the course of COVID-19 [17, 18]. However, order, Coronaviridae family and the Orthocorona- their mechanism of action against SARS-CoV-2 is virinae subfamily [1]. SARS-CoV-2 is a large, envel- not known. oped virus, which contains positive single-stranded, One of methods of drug discovery is in silico non-segmented RNA. It has four structural proteins: research, namely computer-aided drug design spike protein (S), nucleocapsid protein (N), mem- (CADD). CADD is a cost-effective and fast tool, as brane glycoprotein (M), and envelope protein (E) [2]. compared to traditional methods. It allows the pre- In SARS-CoV-2 are two open reading frames: ORF1a diction of protein structure and function, identifica- and ORF1ab. ORFs encode polyproteins pp1a and tion of small molecule (ligand) interactions, active pp1ab, which form the non-structural proteins (NSP site residues and the study of protein-ligand inter- 1-16) [3]. NSPs are essential for viral replication. This actions. Designing and binding ligands to a protein process is facilitated by main protease (Mpro), also (target) is referred to as docking. Docking identifies known as 3C-like protease (3CLpro), and the papain- specific hit molecules from among multiple ligands like protease (PLpro). Both proteases can be targets [19, 20]. In silico studies also determine the safety for anti-SARS-CoV-2 drugs [4]. Recent studies show of a potential drug by prediction of the absorption, that main protease can be inhibited by ritonavir and distribution, metabolism, excretion, and toxicity papain-like protease by ivermectin [5, 6]. (ADMET) profiles [21]. The SARS-CoV-2 coronavirus is responsible This paper aims to investigate thein silico activ- for recent pandemics. The virus causes a disease ity of selected xanthophylls as inhibitors of the main known as COVID-19. As of May 5, 2021, there were protease (Mpro) and the papain-like protease (PL- 153 738 171 confirmed cases of COVID-19 world- pro) of SARS-CoV-2. wide, including 3 217 281 deaths [7]. Vaccinations against SARS-CoV-2 infection were introduced very quickly [8] research on new ones is still being MATERIALS AND METHODS performed. However, there are no treatment guide- lines for COVID-19. Various drugs are used with Preparation of ligands and receptor varying degrees of success. So far, remdesivir is the only drug approved by the Food and Drug Admin- The 3D SDF structures of nine xanthophylls (asta- istration (FDA) to treat COVID-19 [9]. xanthin, canthaxanthin, β-cryptoxanthin, flavo- Xanthophylls are a group of pigments belonging xanthin, fucoxanthin, lutein, neoxanthin, violax- to carotenoids found in plants and algae. The more anthin, and zeaxanthin) was downloaded from the common ones are fucoxanthin, astaxanthin, violax- PubChem database (fig. 1). Ritonavir and ivermec- anthin, zeaxanthin, and lutein [10]. Xanthophylls tin were used as control compounds. Using the have multi-focal activity. Among others, their anti- PyRx 0.8 [23] compounds, energy was minimized bacterial [11], antibiofilm [12], antioxidant [13, 14], and files were converted to the PDBQT format for β-cryptoxanthin No 2.333 0.517 No No flavoxanthin No 2.218 2.225 No No fucoxanthin No 2.428 1.146 No No lutein No 3.491 2.572 No No neoxanthin No 2.350 2.077 No No violaxanthin No 2.132 2.054 No No zeaxanthin No 3.496 2.603 No No ritonavir No 2.703 2.231 Yes No ivermectin No 3.013 1.883 Yes No In silico studies of selected xanthophylls as potential candidates against SARS-CoV-2 targeting main protease (Mpro)... 3 astaxanthin canthaxanthin β-cryptoxanthin flavoxanthin lutein fucoxanthin neoxanthin violaxanthin zeaxanthin zeaxanthin ivermectin ritonavir Figure 1. Figureivermectin 1. ChemicalritonavirChemical structures ofof thethe selected selected molecules molecules for for computational computational studies studies Figure 1. docking. Chemical The structures structures of theof the selected SARS-CoV-2 molecules main for computationalDocking studies protease (PDB-ID: 6LU7 at a resolution of 2.16 Å) and the papain-like protease (PDB-ID: 6W9C at Active sites of proteins were performed using the a resolution of 2.70 Å) were obtained from RCSB Computed Atlas of Surface Topography of proteins Protein Data Bank [24]. The hetero-atoms, water, (CASTp) [26]. The active site of 6LU7 was in chain and ligand groups were removed from the struc- A and the active site of 6W9C was between A, B and tures using BIOVIA Discovery Studio DS2021 [25]. C chains. Vol. 67 No. 2 2021 Figure 2. Interactions of β-cryptoxanthin docked into the main protease Figure 2. Interactions of β-cryptoxanthin docked into the main protease 4 TM. Karpiński, M. Kwaśniewski, M. Ożarowski, R. Alam For docking, the Autodock Vina tool was used tive drugs or designing vaccines [30–34]. The main compiled in the PyRx 0.8 [23]. The grid boxes had protease (Mpro) and the papain-like protease (PL- the following values: for 6LU7 dimensions x, y, pro) can be targets for anti-SARS-CoV-2 drugs. Re- z: 25.7459 Å, 29.2824 Å, 30.5270 Å, centre x, y, z: search in this direction is prevalent and concerns -11.1833 Å, 14.7388 Å, 68.9308 Å, and for 6W9C di- mainly common natural compounds or repurposing mensions x, y, z: 86.9085 Å, 88.8525 Å, 95.9205 Å, of already used drugs [35–38]. Studies presented in centre x, y, z: -36.8549 Å, 11.6758 Å, 38.9205 Å. this article are first concerning the activity of xantho- phylls against SARS-CoV-2. Results indicate that some xanthophylls exhib- In silico drug-likeness and ADMET prediction ited binding energies similar to control drugs. In the case of the main protease, the binding energy of ri- Drug-likeness properties were calculated using Li- tonavir was –7.7 kcal/mol, whereas β-cryptoxanthin pinski’s rule of five [27]. According to this rule, the was –7.4 kcal/mol. In papain-like protease, the bind- orally active substance should have no more than ing energy of ivermectin was –9.5 kcal/mol, whereas one violation of the following criteria: for canthaxanthin was –9.4 kcal/mol, for astaxan- • no more than 5 H bond donors (OH, NH, and thin –9.3 kcal/mol, and for both flavoxanthin and SH); violaxanthin was –9.2 kcal/mol (tab. 1). Amino acid • no more than 10 H bond acceptors (N, O, and S residues involved in interactions between viral pro- atoms); teases and leads with the best binding energies are • molecular weight less than 500 Da; presented in figures 2–7. • octanol-water partition coefficient (log P) lower It was found that all the tested xanthophylls violat- than 5. ed two rules of Lipinski, namely molecular weight and Pharmacokinetic parameters of absorption, dis- Log P. This means that all compounds are poorly solu- tribution, metabolism, excretion, and toxicity (AD- ble in water and have low gastrointestinal absorption. MET) were evaluated using SwissADME [29]. Therefore, it would be necessary to create, for exam- ple, nanoparticles to increase the availability of xan- Ethical approval: The conducted research is not re- thophylls. Ritonavir and ivermectin, used as controls, lated to either human or animal use.
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