key: cord-1046363-l1b4mw9d authors: Prashantha, C.N.; Gouthami, K.; Lavanya, L.; Bhavanam, Sivaramireddy; Jain, Ajay; Shakthiraju, R.G.; Suraj, V.; Sahana, K.V.; Sujana, H.S.; Guruprasad, N.M.; Ramachandra, R. title: Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of Coronavirus date: 2020-10-13 journal: J Mol Graph Model DOI: 10.1016/j.jmgm.2020.107769 sha: 83f77af03b430094480695163e0ee042d842e836 doc_id: 1046363 cord_uid: l1b4mw9d The Target spike protein docking with antimalarial, antimicrobial, anti-inflammatory and HIV-Protease inhibitors. The docking processed using AutoDock Vina and the binding affinity score is noted based on kcal/mol and estimated inhibitory constant (KI). [Figure: see text] by Coronavirus (CoV) it belongs to the family of Coronaviridae [1, 2] . Initially most of the infected people reported in China, Wuhan city in 2019 with a large extent of seafood and animal meat market [3, 4] . Many researchers have reported that the disease is distributed among humans, mammals and birds with the large implications on respiratory, gastrointestinal and neurological infections [5] . In the beginning of January 2020, the disease is increasing in China and distributed throughout world with quantifiable speed [6] . [7] [8] [9] . In April 12, 2020, the disease infected patients 1,896,156; deaths 117,671 and recovered 438,205 cases were reported globally [10] . The most common symptoms observed with the patients are fever, runny nose, sore throat, diarrhea, tiredness, dry cough and some patients have observed aches and pains in the body [11] . Some people become infected but have not develop any symptoms; about 80% of population was recovered from the disease without needing special treatment [12] . Till date, there are no approved drugs and therapeutic protocols recommended to prevent the disease. It is the greatest challenge of both pharmaceutical companies and research organizations to develop novel anticorona viral drug. Understanding the molecular structure of the virus is important to researchers to develop targeted therapies to the disease. Based on the taxonomy of corona virus, SARS-CoV2 is causing disease in 2020 [13] . SARS-CoV2 belongs to the group of single stranded RNA (++ssRNA) virus associated with nucleoprotein within the capsid comprised of matrix protein. The virus has spherical or pleomorphic enveloped proteins surrounded by a fatty outer layer covered with a thin layer of crown like structure (spike protein) made of glycoprotein projections. It also associated with membrane glycoprotein, hemagglutinin-acetylesterase glycoprotein, and small envelope glycoprotein [14] [15] [16] . The target spike glycoprotein has two importance functions (1) receptor binding domain (RBD), (2) cleavage site. The RBD grapping hook that grip onto host receptor such as zinc peptidase angiotensin-converting enzyme 2 (ACE2) [17] [18] , J o u r n a l P r e -p r o o f aminopeptidase N (APN) [19] [20] , and dipeptidyl peptidase 4 (DPP4) [21] [22] and the cleave site that can opens host receptor that allows the virus to enter host cells. The envelop (E) is small, integral membrane structural protein involved in virus' life cycle and pathogenesis, but still the complete structural and functional information remains unknown [23] . The membrane (M) protein is most abundant structural protein involved in viral envelop and integrate in pathogenesis. The integration of S with M proteins in necessary for viral envelope and cause pathogenesis [24] [25] . The nucleocapsid protein relating to viral genome involved in CoV replication cycle and the host cellular response to viral infection [26] . Although, the interaction between viral and human proteins is suggested as potential targets for identification of therapeutic protocols. The solidarity trails of World Health Organization (WHO) and Indian Council of Medical research (ICMR) proposed the FDA approved drugs, trails with the combination of antimalarial drugs chloroquine and Hydroxychloroquine can helps to prevent the disease. Chloroquine prevents the viral attachment itself to the ACE2 receptors but it causes several side effects in this regard the current trail made with the less toxic derivative Hydroxychloroquine [27] [28] [29] . The effect of these two drugs is still being studied to understand the inhibition of SARS-CoV2. Another set of trails include antiHIV drug combination such as Lipinovir-Ritonavir regulates inflammation in the body that can split HIV proteins [30] , these combinations also recommended to inhibit SARS-CoV2. The another trailed drug remdesivir is a nucleotide analog originally created to inhibit Ebola virus, but this drug also recommended to inhibit the novel Coronavirus by targeting the action of a key enzyme that facilitates its replication [31] . Some studies are looking at the investigation of viral protein structure and its behavior as a potential target for future drugs. In recent study suggested that the recommended drugs might help patients with mild cased of COVID19, but that study has limitations. Researchers also evaluating the results of the disease in severe condition go into overdrive with inflammation that can damage the lungs and other organs, but so far there is no proof that it has that effect. Based on these limitations, the current research is designed to evaluate the drugs with target proteins. The major objective is to design the target proteins of both structural and non-structural proteins. Second objective is to J o u r n a l P r e -p r o o f study the modeling and evaluating the target proteins to predict active site amino acids. Third objective is focused o screening of recommended drugs based on pharmacophore and pharmacokinetic analysis. Fourth objective is to predict the protein-ligand interaction and virtual screening to understand how strong the drug can interact with target proteins to predict the potential effect against SARS-CoV2. The insilico analyses were performed using HP Z440 workstation with Next-generation HP Intel Xeon E5-1630v4 3.70 Hz processor. The antimalarial, antibiotic, anti-inflammatory and HIV-protease inhibitor drugs were retrieved from Drug Bank database [32] and the conformational structures were observed in Chemsketch v12.0 [33] . Pharmacophore properties are analyzed using Molinspiration [34] . Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties of chemical structure were analyzed using admetSAR tool [35] . Further, the docking studies were carried out using AutoDock 4.2 [36] and Virtual screening using AutoDock Vina [37] . The intermolecular interactions were analyzed using Pymol [38] and BIOVIA Discovery Studio (DS) 2017 R2 [39] . Based on data mining approaches and clinical practicing antimalarial drugs such as Chloroquine The experimental spike protein sequence was retrieved from GenBank database translated as a large polypeptide that is subsequently cleaved to S1 and S2 domains [40] [41] . Using C-ITASSER pipeline to create three dimensional protein models based on deep convolutional neural-network guide to the I-TASSER (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) fragment assembly simulations [42] . The 3D protein structure is evaluated using Structure analysis and verification server (SAVES v5.0)36 (https://servicesn.mbi.ucla.edu/SAVES/) and RAMAPAGE37. SAVES is used to understand the complexity of protein structure based on atom-to-atom interaction of Ψ versus Φ conformational angels of 3D macromolecule measures the torsion angels of Cα (ideal) -N-Cβ (obs) and the results were represented in Ramachandran Plot. Active site amino acids were predicted using the CastP calculation server based on the delineating measures of surface regions such as surface area and surface volume of 3D protein structure. Molecular docking studies used to find the binding affinity of the ligand molecule with target protein. The homology modeled protein structure docked with selected chemical structures using AutoDock 4.2 and virtual screening by AutoDock Vina. The protein structure is selected to add Gasteiger chargers and hydrogen atoms to the polar group of amino acids the macromolecule, whereas ligand structure by adding torsion counts of amide bonds rotatable and all active bonds non-rotatable and generated the PDBQT file for both protein and ligand structures. Grid space was set in Autogrid by selecting important residues with the grid box size x=54Å, y=54Å and z=54Å and grid spacing of 0.886Å that provides search space, the grid centre was selected at dimensions x=−22.885, y=-10.008, z=514.693 used to calculate grid parameters that help to understand the grid energy with equilibrated energy distribution. AutoDock was used to dock protein and ligand structures by adding Lamarckian genetic algorithm (LGA) with default parameters. The best docking conformation of protein-ligand interactions is predicted with the energy value in kcal/mol and followed by the analysis of hydrogen bonding interaction and the hydrophobic interaction. The best docking complex of protein-ligand was screened based on clustering analysis and visualized using Pymol and BIOVIA Discovery Studio (2017V). Pharmacophore analysis is performed to understand the drug-like character of the chemicals based on Lipinski and Veber's Rule with selected parameters such as logP, TPSA, J o u r n a l P r e -p r o o f molecular weight, hydrogen bond donor, hydrogen bond acceptor, volume, number of rotatable bonds and total number of atoms, bioactive properties such as GPCR, ion channel, kinase inhibitor, nuclear receptor, protease inhibitor and enzyme inhibitor properties are predicted using molinspiration. ADMET analysis is performed to the selected compounds using admetSAR tool to screen the compounds based on absorption, distribution, metabolism, excretion and toxicity prediction. The most important parameters such as blood-brain barrier, acute toxicity, carcinogenicity, LD 50 , maximum recommended daily dose and Mutagenicity are predicted by lazar toxicity predictions server. Prediction of protein structure is important in molecular docking, using I-TASSER to build three dimensional protein structure and used for homology modeling using SwissPDBViewer (SPDBV) software. Ramachandran plot were predicted to understand the complexity of amino acids within allowed region, energy is minimized to the protein structure with e-value=-39051.781. Using SAVES to predict the ERRAT value of 89.2% and Verify3D of 81.6%. CastP is used to predict ligand binding sites with Fmoc-amino acids Lys353, Arg355, Arg403, Lys417, Ile418, Asp424, Pro426, Asp427, Phe429, Tyr453, Leu455, Asn460, Leu461, Lys462, Pro463, Phe464, Ser469, Gln493, Tyr495, Gly496, Phe515, Leu517 amino acids ( Fig. 1 ). Spike protein structure predicted using I-TASSER, the red label represents (1) Spike receptor binding domain (330-583) which corresponds to immunogenic ACE2 receptor binding domain. (2) Coronavirus S2 glycoprotein (662-1270) is translated as a large polypeptide that is subsequently cleaved to S1 and S2 domains from Molecular docking plays vital role in computer-aided drug discovery to predict best active molecules to the target protein. Using AutoDock 4.2 and AutoDock Vina to predict the best drug binding sites towards the affinity of active site amino acids are screened based on binding energy and number of hydrogen bonds formed to the target amino acids. The antimalarial drugs such as Chloroquine, Hydroxychloroquine, Artemisinin, Gly416 amino acids ( Fig.3 ; Table 2 ). J o u r n a l P r e -p r o o f (Fig. 4, Table 3 ). The antibiotic drugs is also docked with target receptors by forming 3-6 hydrogen bonds and the interaction energy ranges from -6.0 to -9.0kcal/mol. The Azithromycin is strong interaction with target receptor by forming 2 hydrogen bonds within active site amino acids and Leu492 amino acids ( Fig. 5; Table 4 ). Table: 1). The outbreak of research is to finding multiple treatment plans for Coronavirus infection Perspectives for repurposing drugs for the coronavirus disease 2019 Chapter 31 -Coronaviruses, Fenner and White's Medical Virology A Novel Coronavirus from Patients with Pneumonia in China WHO Statement Regarding Cluster of Pneumonia Cases in Wuhan First case of 2019 novel coronavirus in the United States A Novel Coronavirus Emerging in China -Key Questions for Impact Assessment Clinical features of patients infected with 2019 novel coronavirus in Wuhan Novel Wuhan (2019-nCoV) Coronavirus Korean Society of Epidemiology 2019-nCoV Task Force Team. An interim review of the epidemiological characteristics of 2019 novel coronavirus Host Factors in Coronavirus Replication Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China Report 2: Estimating the potential total number of novel Coronavirus cases in Wuhan City Structure, Function, and Evolution of Coronavirus Spike Proteins SARS-Associated Coronavirus Understanding the coronavirus Novel Coronavirus disease 2019 (COVID-19): The importance of recognising possible early ocular manifestation and using protective eyewear Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Human coronavirus NL63 employs the severe acute respiratory syndrome Coronavirus receptor for cellular entry Aminopeptidase-N is a major receptor for the enteropathogenic coronavirus TGEV Further characterization of aminopeptidase-N as a receptor for coronaviruses Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC Receptor usage and cell entry of bat coronavirus HKU4 provide insight into bat-to-human transmission of MERS coronavirus Coronavirus envelope protein: current knowledge Coronavirus envelope (E) protein remains at the site of assembly A structural analysis of M protein in coronavirus assembly and morphology Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Chloroquine and hydroxychloroquine in the treatment of COVID-19 with or without diabetes: A systematic search and a narrative review with a special reference to India and other developing countries Chloroquine and hydroxychloroquine as available weapons to fight COVID-19 Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19 Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency DrugBank: a comprehensive resource for in silico drug discovery and exploration ACD/ChemSketch 1.0 (freeware) ACD/ChemSketch 2.0 and its Tautomers, Dictionary, and 3D Plug-ins Application of pharmaceutical profiling assays for optimization of drug-like properties ADMET in silico modelling: towards prediction paradise? Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading The PyMOL-Molecular Graphics System Discovery Studio Modeling Environment The structure of a rigorously conserved RNA element within the SARS virus genome Cloning and Sequencing of the Gene Encoding the Spike Protein of the Coronavirus IBV Protein structure and sequence re-analysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1 • Corona virus infection is a pandemic disease caused from Coronaviridae. • The Spike protein is the major target to attached to the host-receptor ACE2 • Computational Approaches to build the 3D structure of protein • Drug selection for preclinical trials to study the efficacy and disease treatment • Molecular docking approaches to screen the compounds based on binding energy We thank Dr.C.N.Prashantha, Assistant Professor, Department of Biotechnology, School of Applied Sciences, REVA University for providing overall guidance towards the docking studies. The authors declare no conflict of interest. The authors declare no conflict of interest.