Mining And Bioinformatics Research On Prescription And Drug Use Of Traditional Chinese Medicine For The Prevention And Treatment Of COVID-19

BackgroundCoronavirus Disease 2019(COVID-19),a worldwide epidemic,is a serious threat to human life and health.Traditional Chinese medicine(TCM)played an indispensable role in the prevention and treatment of COVID-1 9 in China.Thus,we investigated the potential efficacy.mechanism,characteristics of TCM prescriptions-diseases/symptoms and the potential of Chinese medicine against Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2)in terms of epidemiology,medication rules,molecular docking,bioinformatics analysis and correspondence between TCM remedies and diseases/symptoms.Objectives1.To evaluate epidemiological correlation of COVID-1 9 curative rate and regional TCM usage.2.To explore the TCM medication rules in the prevention and treatment of COVID-19.3.To screen the direct anti-SARS-CoV-2 potentials from herbal plants and compounds via molecular docking.4.To construct the molecular mechanism about herbal plants coordinate COVID-19 in multiple dimensions.5.To explore the quantitative method of evaluating efficacy of TCM remedies in the prevention and treatment of COVID-1 9.Methods1.Epidemiological correlation of COVID-19 curative rate and regional TCM usage.The coverage rate of TCM application in COVID-19 was collected from national and provincial administrations of TCM and health committees(Feb.16,2020～Mar.12,2020).The cumulative number of cured and confirmed patients(up to Mar.1 5.2020)were obtained from Chinese epidemic network,and the curative rate was calculated.The coverage rate of TCM application and curative rate of COVID-19 was presented in the form of line chart and maps:of which the correlation was evaluated through Pearson or Spearman correlation analysis.2.Database construction and medication rules analysis for TCM on prevention and treatment of COVID-19.The TCM database on prevention and treatment of COVID-19(TDCPT)was constructed by collecting TCM remedies(hereinafter referred to as COVID-19 remedies)information from the national and provincial COVID-1 9 prevention and treatment plans,government recommended plans.hospital agreement prescriptions,self-made recipes by academicians and experts and other database.The basic prescriptions contained in COVID-19 remedies were traced,and the number of COVID-19 remedies corresponding to each basic prescription were counted.TOP10 were defined as the core basic prescriptions,and thus the network of COVID-19 remedies and basic prescriptions was built.After analyzing the application frequency of herbal plants,we defined TOP10 as the core herbs,and those with 10 or more used as common herbs.We traced the efficacy attributes of common herbs to reflect the TCM therapeutic methods.3.Screening the direct anti-SARS-CoV-2 potential from herbal plants and compounds via molecular docking.Core herbs targets were obtained from TCMSP database and standardized into gene symbols by UniProt.All targets for chi-square(ATC)were constructed by all of TCMSP targets.COVID-19 targets for chi-square(CTC),column sum of the fourfold table,were the intersection of ATC and COVID-19 targets searched from GeneCards and NCBI gene.The targets number of core herbs was row sum.The key herbs were selected via chi-square and phi coefficient(Φ).Based on molecular docking,the anti-SARS-CoV-2 potential of key herbs and their compounds were further explored-7 reported drugs(remdesivir,ritonavir,etc.)with potential for treatment of COVID-19 were used as positive control.There were two core structures of SARS-CoV-2 as docking receptors,namely,the CoV spike(S)glycoprotein with a single receptor-binding domain(PDB ID:6VSB)and COVID-19 3CL hydrolase,the main protease in SARS-CoV-2 crystal structure(PDB ID:6LU7),all the compounds of key herbs and 7 positive controls were used as the ligands.The ligands structures were obtained from PubChem database,and the 3D crystal structure of receptors from PDB database,which were imported into Schrodinger Small Molecule Drug Discovery Suite.Glide module was used for molecular docking,and docking scores were used to evaluate docking efficiency.Potential compounds with docking scores lower than positive control were screened as anti-SARS COV-2 compounds.The ligands library was expanded to natural products library,and the above methods were repeated for broadspectrum screening.4.Mechanism exploration of herbal plants coordinate COVID-19 in multiple dimensions.The target counts(TC)of key herbs were traced fr-om TCMSP database.herbs-targets-TC matrix was constructed by R version 3.6.3.and the targets of at least six herbs were remained.Targets’ direction was identified by at least 3 literatures with the same results.The heat map was drawn via Python Seaborn.Based on IPA pathway analysis system,target weight and regulatory direction were both imported as "Log2 fold change" for directional pathway enrichment analysis.The TOP10 pathways in up-regulated group and down-regulated group(P<0.05)were screened respectively,and the mechanism network was constructed through pathway Builder Tool 2.0.5.Exploration on the quantitative method of TCM remedies-diseases/symptoms in the prevention and treatment of COVID-19.Based on literature search.symptoms.syndromes and medical conditions(SSMs)related to COVID-19 were obtained.SSMs targets were obtained from GeneCards and NCBI gene.Effective TCM remedies for prevention and treatment of COVID-19 were screened,of which the targets were collected from TCMSP.ETCM and TCMID,Based on chi-square test,-Log10P was used as the significant level of coherence(SLC)to quantitatively evaluate the efficacy characteristics of TCM remedies treating SSMs.Using Python Seaborn,the SLC heat map of superior remedies and SSMs was constructed,and the scatter diagram of top SLC was drawn.Results1.The coverage rate of TCM application and the curative rate of COVID-19 in 30 provinces and cities were counted.Spearman correlation analysis showed that there was a significant positive correlation between the two.2.TDCPT was constructed,including 185 COVID-19 remedies.210 herbal plants.The core basic prescriptions were Maxingshigan decoction.Yinqiao powder.Yupingfeng powder.Maxingyigan decoction,Shenfu decoction,Xuanbaichengqi decoction,Shengmai decoction.Huopoxialing decoction,Huoxiangzhengqi powder and Dayuan decoction,which were used in corresponded stages.There were 49 commonly used herbs,of which the therapeutic methods involved clearing heat,resolving phlegm,relieving cough and asthma,relieving exterior syndrome,tonifying deficiency,resolving dampness,etc.The core herbs were Radix Glycyrrhizae(Gancao),Semen Armeniacae Amarum(Xingren).Flos Lonicerae(Jinyinhua),Fructus Forsythiae(Lianqiao).Gypsum Fibrosum(Shigao).Herba Ephedrae(Mahuang).Scutellariae Radix(Huangqin).Herba Agastaches(Huoxiang).Astragali Radix(Huangqi)and Rhizoma Phragmitis(Lugen).3.ATC= 3439,CTC=172.There was significant correlation between targets of core herbs and CTC(P<0.01).Rhizoma Phragmitis(Lugen)and Gypsum Fibrosum(Shigao)were excluded for Φ<0.1.The other 8 drugs were defined as key herbs to further screen potential compounds against SRAS-CoV-2 via molecular docking.Among the 919 compounds of the key herbs.17 showed docking potentials,which were better than the best positive control.They were deried from Flos Lonicerae(Jinyinhua),Astragali Radix(Huangqi),Herba Ephedrae(Mahuang).Radix Glvcyrrhizae(Gancao)and Fructus Forsythiae(Lianqiao).Among 2042 natural products compounds.82 potential compounds were added and 57 natural products were traced,5methoxy-picroside and other five compounds were found to have better binding efficiency with 6LU7 and 6VSB.4.① Herbs-targets-TC matrix:53 were screened out of 95 targets to form 53 X 8 matrix.414 literatures were searched to clarify the target regulation direction,and 20 targets without related research were eliminated,and 33 core targets were obtained.② Core targets directional heat map:involved in the activation of immunomodulatory factors(IL10↑),the inhibition of acute inflammatory response(IL-6 ↓,TNF ↓,COX2/1 ↓.NOS2 ↓,etc.),the enhancement of antioxidant activity(CAT ↑,SOD1↑)and the regulation of apoptosis(CASP3 ↓,CASP8 ↑).③ IPA pathway enrichment analysis:129 up-regulated pathways and 335 down-regulated pathways were analyzed(P<0.05).The former included PPAR signaling pathway,interferon signaling pathway.Th2 pathway,etc.The later involved the role of PKR in interferon induction and antiviral response.IL-17A signaling pathway,IL6 signaling pathway,etc.④ The mechanism network of key herbs for prevention and treatment of COVID-19 were constructed.5.14 SSMS:It involved typical symptoms and signs of COVID-19(fever,cough or dry cough.lymphopenia,fatigue,muscle soreness and dyspnea),other symptoms and signs(expectoration,diarrhea,nausea and vomiting,decreased oxygen saturation and cytokine storm)and diseases(COVID-19.SARS and pneumonia).② 1 8 representative TCM remedies:Prevention:a representative formulae by Dr.Liu Shangyi:symptoms onset:Huoxiangzhengqi powder.Jinhuaqinggan granule and Lianhuaqingwen capsule;confirmed and developed:Maxingyigan decoction.Maxini,shigan decoction.Qingfeipaidu decoction and Huashibaidu decoction;critical:Reduning injection.Slienfu decoction,Xuanbaichengqi Decoction and Xuebijing injection;recover:Shengmai decoction:specific basic prescriptions:Dayuan decoction(anti-plague prescription).Sijunzi decoction(qitonifying prescription).Erchen decoction(phlegm-resolving prescription),Yupingfeng powder and Yinqiao powder(bested used prescriptions).③Correlation analysis:18 TCM remedies and 14 SSMS were significantly correlated(P<0.01),SLC ranking was used to quantify the efficacy of prescriptions treating diseases/symptoms,which were consistent with clinical applications of these prescriptions,and heat map was drawn for visualization.For example,the SLC of Shengmai decoction was prominent in fatigue and low in fever and cough;Shenfu decoction showed high SLC value on fatigue.lymphopenia and cytokine storm.④ Scatter diagram of top SLC:Reduning injection ranked top 5 in all 14 SSMs.The SLC of Yinqiao powder,Jinhuaqinggan granule.Lianhuaqingwen capsule and Qingfeipaidu decoction were higher in the prescriptions with more than 1000 targets.Conclusions1.Up to Mar.15.2020,there was a significant positive correlation between the coverage rate of TCM application and curative rate of COVID-19.2.The COVID-19 remedies were mostly derived from the basic prescriptions,such as Maxingshigan decoction and Yinqiao powder,which mainly involved the treatment of clearing heat,resolving phlegm,relieving cough and asthma,relieving exterior syndrome,tonifying deficiency and resolving dampness.which attached importance to qi and yin.resolving dampness pathogen and treating both manifestation and cause of diseases.3.17 compounds with anti-SARS-CoV-2 potentials originated from Flos Lonicerae(Jinyinhua).Fructus Forsythiae(Lianqiao)and other key herbs were selected,and 82 new compounds were added after broad-spectrum screening.Many potential ingredients can be traced back to the same herbal plants.The synergistic effect of many potential ingredients against SARS-CoV-2 is the possible mechanism of compatibility-synergism.4.Traditional Chinese medicines coordinate COVID-19 in multiple dimensions,including activating IL10.CAT,SOD1,CASP8,etc.,while inhibiting IL-6,TNF,COX2/1,NOS2,CASP3,etc.;promoting PPAR signaling pathway,interferon signaling pathway.Th2 pathway,etc.,while suppressing the role of PKR in interferon induction and antiviral response.IL6 signaling pathway,etc.Regulation of virus replication,inflammation,oxidative stress,apoptosis,and other biological processes etc.were mainly involved in the course of herbal plants combating COVID-19.5.SLC could be used to evaluate the applicability of TCM prescriptions in the treatment of diseases/symptoms,which is promising to be a quantitative method for efficacy evaluation.