key: cord-0830283-ju81kiyw authors: Balmeh, Negar; Mahmoudi, Samira; Mohammadi, Niloofar; Karabedianhajiabadi, Anasik title: Predicted therapeutic targets for COVID-19 disease by inhibiting SARS-CoV-2 and its related receptors date: 2020-08-07 journal: Inform Med Unlocked DOI: 10.1016/j.imu.2020.100407 sha: 7957d654d295d290ba1492c76ec7e31f4a862e02 doc_id: 830283 cord_uid: ju81kiyw The SARS-CoV-2 causes severe pulmonary infectious disease with an exponential spread-ability. In the present research, we have tried to look into the molecular cause of disease, dealing with the development and spread of the coronavirus disease 2019 (COVID-19). Therefore, different approaches have investigated against disease development and infection in this research; First, We identified hsa-miR-1307-3p out of 1872 pooled microRNAs, as the best miRNA, with the highest affinity to SARS-CoV-2 genome and its related cell signaling pathways. Second, the findings presented that this miRNA had a considerable role in PI3K/Act, endocytosis, and type 2 diabetes, moreover, it may play a critical role in the prevention of GRP78 production and the virus entering, proliferation and development. Third, nearly 1033 medicinal herbal compounds were collected and docked with ACE2, TMPRSS2, GRP78, and AT1R receptors, which were the most noticeable receptors in causing the COVID-19. Among them, there were three common compounds including berbamine, hypericin, and hesperidin, which were more effective and appropriate to prevent the COVID-19 infection. Also, it was revealed some of these chemical compounds which had a greater affinity for AT1R receptor inhibitors can be suitable therapeutic targets for inhibiting AT1R and preventing the adverse side effects of this receptor. According to the result, clinical assessment of these three herbal compounds and hsa-miR-1307-3p may have significant outcomes for the prevention, control, and treatment of COVID-19 infection. The SARS-CoV-2 induces severe respiratory syndrome in humans (1) . The viral major proteins include spike (S) protein, matrix protein (M), small envelope protein (E) protein, and nucleocapsid protein (N) (2) . The location of viral attachment to the host cell resides within the S protein (3) . SARS-CoV-2 is able to bind to angiotensin-converting enzyme 2 (ACE2) (4), transmembrane protease serine 2 (TMPRSS2) (5) , glucose regulating protein 78 (GRP78) (6) . There are several strategies to tackle the SARS-CoV-2, including inhibiting virus multiplication, inhibiting virus entry through receptors (blocking receptors), and blocking viral proteins. The first approach is using miRNAs' to attach to the 3'UTR of the SARS-CoV-2 genome, so that viral translation will be inhibited (7, 8) . Blocking the aforementioned three receptors is the second approach to prevent SARS-CoV-2. It has suggested that decreasing the levels of ACE2 on the cell surface or inhibiting its function, helps in preventing SARS-CoV-2 infection (9) . By binding the spike protein to the ACE2, the angiotensin 2 is produced in large quantities by the ACE and then binds to the AT1R receptor. This process leads to fibrosis and damage lung tissues. A possible way of combating the infection could be the injection of soluble ACE2 into the bloodstream which will have the two-fold effect; preventing the attachment of the virus to noninfected cells and replenishing ACE2 in infected cells (3) . Secondly, it is assumed that SARS-CoV-2 uses the serine protease TMPRSS2 for S protein priming (10, 11) . So, the inhibition of TMPRSS2 protease is required for a robust blockade of viral entry. Thirdly, given the fact that diabetic individuals are more likely to get infected by the SARS-CoV-2 virus as its receptor is highly expressed on the lung and intestine and liver cells of individuals with type 2 diabetes. To J o u r n a l P r e -p r o o f our knowledge the role of GRP78 is facilitating the entrance of virus to the host cells (12) . Finally, the AT1R receptor is one of the important receptors in modulating of blood pressure. High blood pressure is directly linked to the SARS-CoV-2 virus, by inhibition of this receptor, presumably we would be able to prohibit lung injury. Researches have shown that some of the AT1R-blockers such as Azilsartan and Olmesartan can overexpress the ACE2 and it could be a risky situation for SARA-CoV-2 entry (13) . The third approach could be to target the respective enzyme to prevent the virus from progressing and surviving in the host cell. In this study, we have surveyed these approaches to address alternative therapeutic methods against viral infection. For this purpose, thirty medicinal herbs that have the most impact on the pathways associated with each receptor were selected to analyze their affinity to bind the ACE2, TMPRSS2, GRP78, and AT1R receptors. Besides, to control the virus genome, a comprehensive investigation was performed on the SARS-CoV-2 genome inhibitors. Information about the virus (structure, reproduction, and genome) was obtained from the Viral Zone database (www.viralzone.expasy.org) (14) . The nucleotide sequences of all 1872 miRNAs were downloaded from the miRBase database (http://mirbase.org) (15) and their expression levels were determined in normal lung squamous cells and lung tissue through TCGA-Assembler 2 package by R software, version 4.0.0 (16); non-expressed microRNAs were deleted. Then, the 3'UTR sequence of the SARS-COV-2 RNA was obtained from NCBI database entry MTO49951.1 (www.ncbi.nlm.nih.gov) (17) . The J o u r n a l P r e -p r o o f affinity between each miRNA and 3'UTR of the viral genome was computed by the RNAhybrid database (https://bio.tools/rnahybrid) (18) . By using the miRWalk database (http://mirwalk.umm.uni-heidelberg.de/) (19) and the TransmiR database (http://www.cuilab.cn/) (20) the targetome and transcription factors of the best miRNA were achieved. Then, those which had expression in lung tissue were checked and selected by the TCGA-Assembler 2 package of R software. Finally, the signaling pathways of the selected miRNAs, targetome, and transcription factors were separately obtained from the KEGG database (www.kegg.jp) (21) . The schematic figure of the signaling pathways related to both targetome and transcription factors of the best miRNAs were drowned by the Biorender software. The targetome schematic figure was produced by Cytoscape software, version 3.8.0 (22) . First, the sequence of ACE2, GRP78, TMPRSS2, and AT1R receptors were acquired from the NCBI database and modeled using SWISS-MODEL modeling tools (https://swissmodel.expasy.org/) (23). The SARS-CoV-2 structure was downloaded from the RCSB PDB database (https://www.rcsb.org/) (24) and the binding site of each receptor related to SARS-CoV-2 obtained from articles. After determining thirty medicinal herbs ( The 3-D structure of receptor blockers (Table2) and herbal compounds were prepared for docking by removing all water and H-bond optimization, then, Gasteiger charges were added. After that, molecular docking analysis was performed for each herbal compound and receptor blockers using AutoDock vina. Figures were made by Chimera software version 1.14 (26). The activity, daily dose carcinogenicity, blood-brain barrier penetration, and antiviral features caught from way 2 drug (27) (www.pharmaexpert.ru/passonline/predict.php), lazar (lazar.insilico.ch/predict) (28) and AVCpred (http://crdd.osdd.net/servers/avcpred) (29), respectively. According to affinity examination between 3'UTR of SARS-CoV-2 and all 1872 miRNAs, 42 miRNAs with the highest score were identified (Table 3) . Among them, hsa-miR-1307 3p had the highest score among miRNAs with -37.6 kCal/mol, and high expression level in lung and squamous tissues ( Figure 1 ). Approximately 377 predicted and valid targets of hsa-miR-1307 which were predicted The best herbal compounds for ACE2, TMPRSS2, GRP78, and AT1R receptors were identified based on their binding energy. Thirty-five common medicinal herbal compounds and blocker drugs were investigated between ACE2, TMPRSS2, GRP78, and AT1R; with a score of -7 kCal/mol or higher. Among them, Berbamine had the highest binding energy for all four receptors (Supplementary Table 1 ). Berbamine, Hesperidin, and Hypericin were the best common compounds for interaction with The results of molecular docking also showed a high tendency of compounds to receptors. The molecular docking results of the ACE2, TMPRSS2, GRP78, and AT1R receptors with medicinal herbal compounds are presented in Supplementary Table 2 . The results of molecular docking to compare the binding energy between the available blocking drugs and the herbal compounds investigated from the present study presented that the affinity of herbal compounds to bind to the ACE2, TMPRSS2, GRP78, and ACE2 receptors were higher. ( Table 4 ) The lazar database had no result for Hestridine, but characteristics of other top three common compounds include antitussive, respiratory analeptic, hepatoprotection, antivirus, RNA synthesis J o u r n a l P r e -p r o o f inhibitor. Furthermore, features such as blood-brain barrier penetration, carcinogenicity, maximum recommended daily dose, and antiviral ability of each three common herbal compounds were surveyed and presented in Table 4 . The high mortality rate around the world due to COVID-19 has led to the recognition and treatment of the SARS-CoV-2. There has been a lot of research on this disease over the past few months, but there is still a need for a comprehensive study that considers all aspects of the disease (30) . In this bioinformatics study, it was tried to attend different approaches related to the SARS-CoV-2 before and after the infection. The most important receptors for SARS-Cov-2 are ACE2 (31) TMPRSS2 (32) , and GRP78 (6), which by blocking these receptors can protect the body against the virus. In the process of infecting by SARS-CoV-2, binding the virus to ACE2 prevents the attachment of angiotensin 1 If the lung cell is infected with the SARS-CoV-2, preventing the virus from replicating is another treatment option (38) . Many studies have shown that miRNAs play an important role in inhibiting viruses' replication by preventing the translation of the viral genome (7) . In this study, among 1872 miRNAs, has-miR-1307-3p was selected as the best miRNA because of its high J o u r n a l P r e -p r o o f affinity to SARS-CoV-2 genome 3'UTR and high expression in lung tissue (39) . Increased expression of hsa-miR-1307-3p may lead to a reduction in SARS-CoV-2 replication through binding to the 3'UTR site of the virus genome. miRNAs can be synthesized for therapeutic purposes and inserted into the target area, but their delivery is a complicated and meticulous process. Therefore, the use of TFs to induce the expression of the desired miRNA by lung cells may be a better choice. After obtaining all the signaling pathways related to the hsa-miR-1307-3p transcription factors, the receptors responsible for activating the TFs were also examined. As a result, using the ligand of each of these receptors can lead to the expression of the TFs genes; eventually triggers the induction of the hsa-miR-1307-3p production. Of important, hsa-miR-1307-3p can affect receptors that are responsible for survival and proliferation. The hsa-miR-1307-3p also affects anti-apoptotic proteins like BCL2 and inhibits them to induce apoptosis, leading to the prohibition of the proliferation. Investigations have proven that the PI3K signaling pathway is so critical for virus survival and spread (40) . The hsa-miR-1307-3p inhibits the PI3K pathway by suppressing the activators of PI3K, and eventually, the cell cycle proliferation is prevented. On the other hand, hsa-miR-1307-3p can ban clathrindependent endocytosis by inhibiting AP-2, PIP5K, and might suppress exocytosis by inhibiting of actin. It has been confirmed that endocytosis and exocytosis are associated with virus entry and spread, therefore, controlling these pathways by hsa-miR-1307-3p could be an effective strategy for SARS-CoV-2 infection. The WHO has stated that obesity and Diabetes mellitus are other risk factors for developing COVID-19. In obesity that leads to type 2 diabetes, hyperglycemia leads to inhibition of the immune system (41) as well as the activation of PKC, as a result of its activity, inhibits IRS2, and leads to indirect inhibition of ACT, which in turn leads to glycogenesis and glucose uptake. On the other hand, hyperglycemia increases the expression of GRP78 on the cell surface, which can activate the ACT pathway to reduce blood sugar (42) . Activating the tyrosine kinase receptor activates the ERK protein, and this protein inhibits IRS1 that also indirectly prevents the ACT and its downstream pathway. Studies have implicated that GRP78, which is increased in response to hyperglycemia in diabetes, is a receptor for COVID-19. The hsa-miR-1307-3p can induce glycogenesis and glucose uptaking by inhibiting PKC and ERK, which are inhibitors of RS1 and RS2. Thus, this miRNA indirectly reduces GRP78 production by lowering blood sugar. On the other hand, hsa-miR-1307-3p inhibits insulin expression by inhibiting PDX1 and VDCC, which activates insulin, increasing insulin-dependent proliferative pathways in type 2 diabetes. MicroRNA 1307 also inhibits insulin expression by inhibiting insulin-activated PDX1 and VDCC, resulting in insulin-dependent proliferative pathways in type 2 diabetes, thus controlling insulin-dependent proliferative pathways in type 2 diabetes. Studies have shown (40) that in COVID-19, with increased cytokine storms, lung tissue damage increases. For example, one of the treatment strategies for receptor inhibition is cytokines such as interleukin 6 receptor. Therefore, hsa-miR-1307-3p can be a therapeutic solution to inhibit tissue damage by inhibiting cytokine receptors. The results of this study have indicated the inhibiting effect of Berbamine, Hypericin, and Hesperidin on ACE2, TMPRSS2, GRP78, and AT1R receptors. Also, enrichment analysis of hsa-mir-1307-3p revealed the suppressing role of this miRNA on proliferative, endocytosis, exocytosis, and diabetes signaling pathways. Additionally, hsa-miR-1307-3p targets genes in type 2 diabetes indirectly by repressing the GRP78 receptor expression. Overall, further clinical J o u r n a l P r e -p r o o f assessment of these herbal compounds and hsa-miR-1307-3p is required to validate the treating ability of these compounds over COVID-19 infection. The authors declare that there are no conflicts of interest. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. VDCC, Voltage-dependent calcium channels; WHO, World Health Organization. Recent advances and perspectives of nucleic acid detection for coronavirus Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response COVID-19 Spike-host cell receptor GRP78 binding site prediction RNAi and cellular miRNAs in infections by mammalian viruses Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2. Science (80-) Efficient activation of the severe acute respiratory syndrome coronavirus spike protein by the transmembrane protease TMPRSS2 A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry Middle East respiratory syndrome coronavirus and bat coronavirus HKU9 both can utilize GRP78 for attachment onto host cells Angiotensin receptor blockers as tentative SARS-CoV-2 therapeutics ViralZone: a knowledge resource to understand virus diversity annotating high confidence microRNAs using deep sequencing data TCGA-assembler: open-source software for retrieving and processing TCGA data Database resources of the national center for biotechnology information Tools and data services registry miRWalk: An online resource for prediction of microRNA binding sites TransmiR v2. 0: an updated transcription factor-microRNA regulation database KEGG: new perspectives on genomes, pathways, diseases and drugs Cytoscape: a software environment for integrated models of biomolecular interaction networks SWISS-MODEL: homology modelling of protein structures and complexes Hm berman, j. westbrook, z. feng, g. gilliland, tn bhat, h. weissig, in shindyalov, pe bourne PubChem substance and compound databases UCSF Chimera-a visualization system for exploratory research and analysis Computer-aided prediction of biological activity spectra for chemical compounds: opportunities and limitations Lazar: a modular predictive toxicology framework AVC pred: an integrated web server for prediction and design of antiviral compounds Screening and druggability analysis of some plant metabolites against SARS-CoV-2: An integrative computational approach Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor Inhibitors of RAS might be a good choice for the therapy of COVID-19 pneumonia. Zhonghua jie he he hu xi za zhi= Zhonghua jiehe he huxi zazhi= Repurposing therapeutics for COVID-19: supercomputer-based docking to the SARS-CoV-2 viral spike protein and viral spike protein-human ACE2 interface Review of Evidence Available on Hesperidin-Rich Products as Potential Tools against COVID-19 and Hydrodynamic Cavitation-Based Extraction as a Method of Increasing Their Production Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods Berbamine inhibits the infection of SARS-CoV-2 and aviviruses by compromising TPRMLs-mediated endolysosomal tra cking of viral receptors Structure-based drug designing towards the identification of potential anti-viral for COVID-19 by targeting endoribonuclease NSP15 Identification and classification of differentially expressed genes reveals potential molecular signatures associated with SARS-CoV-2 infection in lung adenocarcinoma cells Antiviral potential of ERK/MAPK and PI3K/AKT/mTOR signaling modulation for Middle East respiratory syndrome coronavirus infection as identified by temporal kinome analysis Diabetes in COVID-19: Prevalence, pathophysiology, prognosis and practical considerations Cell surface expression of 78-kDa glucoseregulated protein (GRP78) mediates diabetic nephropathy