Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a respiratory syndromecaused by positive RNA virus resulting in outbreak of corona virus disease 2019 (COVID-19). TheSARS-CoV-2 genome and its association to SAR-CoV-1 vary from ca. 66% to 96% depending on the type of betacoronavirdeae family members. With several drugs, viz. chloroquine,hydroxychloroquine, ivermectin, quinidine, artemisinin, remdesivir, azithromycin considered for clinical trials, there has been an inherent need to find distinctive antiviral mechanisms of these drugs.
In this work, we show the binding potential of curcumin targeted to a host of SARS-CoV-2 proteins, viz. spike,glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), membrane,glycoprotein (PDB ID: 6M17) along with nsp10 (PDB ID: 6W4H) and RNA dependent RNA,polymerase (PDB ID: 6M71) structures. Our results indicate that curcumin has potential antiviral protein binding affinity towards SARS-CoV-2 proteins which is comparable with other repurposed drugs that are considered for clinical trials.
COVID-19 has caused unprecedented morbidity and mortality in the globe. COV-SARS-2 contains 29 proteins that include 4 structural proteins, Spike, Envelope, Membrane and Nucleocapsid and the rest non-structural and adjunct proteins. A polyprotein is acted upon by an encoded protease, giving rise to 16 of these proteins. The viral RNA genome is close to 30 Kb in size. The structural proteins are mainly involved in entry, replication, assembly and propagation of the virus into lung and other cells carrying the ACE2 receptor (Chen etal., 2020). A large number of potential therapeutic molecules that include antibiotics, antiviral and anti-malarial properties are being tested against COVID-19, which has caused global devastation (R).
In a recent study, Sampangi-Ramaiah et al.,2020, have evaluated 27 natural compounds for binding affinities to both the proteases of COVID-19.Fifteen compounds have been found to have good binding affinities ranging from –6.4 kcal/mol (for Coriandrin) to –8.0 kcal/ mol (for Glabridin) and –8.1 kcal/mol (for Glucobrassicin), comparable to the anti-HIV drug Saquinavir. In the present study, we have evaluated the binding affinities of 14 drug candidates with SARS-Cov-2 proteins: spike glycoproteins (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), membrane glycoprotein (PDB ID: 6M17) nsp10 (PDB ID: 6W4H) and RNA dependent RNA polymerase (PDB ID: 6M71) structures. We find that the natural molecule, curcumin from turmeric, has good binding affinities to nucleocapsid and nsp-10, comparable to those of ivermectin, azithromycin, remedesivir and quinidine. The food supplements and nutraceuticals may turn out to be long-term option to prevent the viral infection. Turmeric is a spice used extensively in India and is described in ancient literature for its wide medicinal use ®. Curcumin,isolated from turmeric, has strong anti-oxidative and anti-inflammatory properties and has potential therapeutic effects on chronic diseases (Yan et al., 2015). Thus, curcumin, in addition to its profound immunomodulatory effects, may also bring about changes by directly binding to crucial viral proteins. The implications of these findings are discussed in this work.
Over the last decade, there have been constant reports of curcumin showing healthy effects and specific therapeutic benefits with over 120 clinical trials under process (Gupta et al., 2013). It is believed to show immense potential even though it challenges the standard doctrine contemplated by medicinal chemists. While it has been shown to have served as an adjunct drug for malaria, as proven in animal experiments, there are reports on curcumin-arteether combination curing malaria, respiratory disorders with various formulations (Vathsala et al., 2012). Conversely, checking the bioavailability and rapid metabolism from a holistic approach, there is a need to resolve structural targets and the ligands associated with it. Hence, we attempt to understand the molecular interactions and decipher the role of curcumin with SARS-CoV-2 structural and non-structural proteins. To provide molecular details of ligand recognition and better understanding of the ligandbinding behaviour of different targets/receptors, we further determined characteristic features on ligand binding, safe dosage, Ki values, and classify key factors that direct the docking complexes of drugs. The SARS family to which SARS-CoV-2 and SARS-CoV were reported, have structure resemblance with 8 amino acids related to 14 binding residues, and were known to be conserved in SARS-CoV-2 (Walls et al., 2020). It was further shown that angiotensin
converting enzyme-2 (ACE-2) interacts with the binding residues of SARSCoV-2 (Cynthia, et al.,2020, Abdul et al., 2020). We deliberate the role of curcumin, its antiviral drug binding efficiency and calculate the dosage concentration using molecular modelling approaches targeted for therapeutics of SARS-CoV-2.
Material and methods
I. Preparation of ligands: The molecular docking studies were performed using AutoDock 4.2 software (Morris et al. 2009). For the current study, 15 ligands were considered based on their current usage in treatment of COVID-19 patients based on known potent antiviral/antimalarial drugs and their plasma concentration (supplementary table 1). The ligands with 3D structures were retrieved from PubChem as sdf files, as others were subjected to a 3D structure generation on CORINA (MNAM.com) using their SMILE nomenclature. Further, pdbqt files for the ligands were generated by OpenBabel (O'Boyle et al., 2011).
II. Preparation of proteins and grid parameters: The protein data bank (PDB) structures of differentCOVID19 proteins were retrieved from RCSB Membrane Protein (6M17), polymerase (6M71), spike(6VYB), nucleocapsid (6VY0) and nsp10 (6W4H). The protein structures were visualized on PyMOL 1.3 or 2.5 (DeLano, 2002) by demarcating the transmembrane regions if any, present in the protein.While the pdbqt files were generated for the proteins to initiate the grid parameters, we considered less than 1Å and x, y, z coordinates to establish the size of the protein for docking studies. MGL tool 1.5.6 (Morris et al., 2009) was used for generating necessary protein and ligand files along with the respective grids and dock files. The grid generation and docking were subsequently executed through AutoGrid 4.2 and AutoDock 4.2 respectively (Morris et al., 2009).To find the binding affinity of ligands with selected proteins, drug targets were screened from estimated free energy of binding and inhibition constant (Ki) at 298.15 K temperature. The docked ligand-protein complexes were visualized on Chimera 1.12 (Pettersen et al., 2004) for image construction. The binding energies and affinities for the ligands were obtained from the log files of the docks generated by AutoDock.
We propose curcumin as a therapeutic target for anti-corona virus drug development. In this work,we screened 14 ligands against SARS-CoV-2 structural and non-structural proteins and evaluate the binding affinity of curcumin to that of other known drugs that are commercially available. From the current study, it is evident that curcumin could play a major role in regulating the activity of nucleocapsid and nsp10, both of which are indirectly related to the detection and processing of viral RNA. At very high concentrations, curcumin acts on the spike and membrane proteins and hence invasion itself is difficult to achieve with the given solubility and plasma concentrations of curcumin. Further study on a combinatorial administration of drugs with curcumin would demonstrate if lesser concentrations of curcumin could be effectual at the surface proteins. We hope that our studies provide an imperative role of curcumin as a potential therapeutic agent for COVID-19 treatment.
Reference & source information: https://www.preprints.org
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