Editorial for the Special Issue on Natural Medicine

As the world continues to search for innovative therapeutic solutions,the field of natural medicines has emerged as a vibrant area of research.The potential of natural products to treat a wide range of diseases,coupled with the relatively low sideeffects of such products,has captured the attention of scientists,clinicians,and the general public alike.This Special Issue on Natural Medicine aims to present the latest advancements in this exciting field,highlighting both fundamental research and clinical applications.The collection of articles in this Special Issue covers a broad spectrum of topics,ranging from medicinal chemistry to biological mechanisms,and from the study of single botanic compounds to complex plant formulas.We are particularly pleased to include a comprehensive review by Yi Wang et al.on the bioactivities,mechanisms,production,and potential application of bile acids in preventing and treating infectious diseases.This review not only summarizes the current landscape of bile acids research but also highlights several promising compounds for future investigations,such as the recent interest in ursodeoxycholic acid.In a related topic,Shishan Yu’s team has developed artificial bear bile using synthetic chemistry and enzyme engineering,providing a sustainable substitute for natural bear bile.This innovation meets medical needs while addressing animal welfare issues,representing a notable progression in the field.

Neg-Entropy Mechanism as a Target for Natural Medicines

Current strategies for drug discovery research mainly focus on molecular targets,in which structure biology plays a central role,such as the detailed mechanism of a drug-target interaction.The principle of this approach is the presumed molecular mechanism or genetic background of the disease being treated.Although this approach has brought progress in understanding the mode of action for some drugs,most prevalent illnesses-especially chronic diseases-are multifactorial and present with a group of symptoms,as is often the case in cardiovascular diseases,metabolic disorders,cancers,and so forth.The newly emerging term“multi-morbidity”(i.e.,multiple co-occurring diseases)describes a grand challenge for this strategy,and successful drug intervention for multimorbidity should be multifaceted[1].So,our research team has shifted its attention to a new direction that views the disease as a whole instead of a single-molecule abnormality,and focusing on drugs with multiple targets.

Hepatitis C: From inflammatory pathogenesis to antiinflammatory/hepatoprotective therapy

Hepatitis C virus(HCV) infection commonly causes progressive liver diseases that deteriorate from chronic inflammation to fibrosis, cirrhosis and even to hepatocellular carcinoma. A long-term, persistent and uncontrolled inflammatory response is a hallmark of these diseases and further leads to hepatic injury and more severe disease progression. The levels of inflammatory cytokines and chemokines change with the states of infection and treatment, and therefore, they may serve as candidate biomarkers for disease progression and therapeutic effects. The mechanisms of HCV-induced inflammation involve classic pathogen pattern recognition, inflammasome activation, intrahepatic inflammatory cascade response, and oxidative and endoplasmic reticulum stress. Direct-acting antivirals(DAAs) are the first-choice therapy for effectively eliminating HCV, but DAAs alone are not sufficient to block the uncontrolled inflammation and severe liver injury in HCV-infected individuals. Some patients who achieve a sustained virologic response after DAA therapy are still at a long-term risk for progression to liver cirrhosis and hepatocellular carcinoma. Therefore, coupling with antiinflammatory/hepatoprotective agents with anti-HCV effects is a promising therapeutic regimen for these patients during or after treatment with DAAs. In this review, we discuss the relationship between inflammatory mediators and HCV infection, summarize the mechanismsof HCV-induced inflammation, and describe the potential roles of anti-inflammatory/hepatoprotective drugs with anti-HCV activity in the treatment of advanced HCV infection.

MicroRNA-mediated interactions between host andhepatitis C virus

Micro RNAs(mi RNAs) are small noncoding RNAs. More than 2500 mature mi RNAs are detected in plants, animals and several types of viruses. Hepatitis C virus(HCV), which is a positive-sense, singlestranded RNA virus, does not encode viral mi RNA. However, HCV infection alters the expression of host mi RNAs, either in cell culture or in patients with liver disease progression, such as liver fibrosis, cirrhosis, and hepatocellular carcinoma. In turn, host mi RNAs regulate HCV life cycle through directly binding to HCV RNAs or indirectly targeting cellular m RNAs. Increasing evidence demonstrates that mi RNAs are one of the centered factors in the interaction network between virus and host. The competitive viral and host RNA hypothesis proposes a latent cross-regulation pattern between host m RNAs and HCV RNAs. High loads of HCV RNA sequester and de-repress host mi RNAs from their normal host targets and thus disturb host gene expression, indicating a means of adaptation for HCV to establish a persistent infection. Some special mi RNAs are closely correlated with liver-specific disease progression and the changed levels of mi RNAs are even higher sensitivity and specificity than those of traditional proteins. Therefore, some of them can serve as novel diagnostic/prognostic biomarkers in HCVinfected patients with liver diseases. They are also attractive therapeutic targets for development of new anti-HCV agents.

Transformation of berberine to its demethylated metabolites by the CYP51 enzyme in the gut microbiota

Berberine(BBR)is an isoquinoline alkaloid extracted from Coptis chinensis that improves diabetes,hyperlipidemia and inflammation.Due to the low oral bioavailability of BBR,its mechanism of action is closely related to the gut microbiota.This study focused on the CYP51 enzyme of intestinal bacteria to elucidate a new mechanism of BBR transformation by demethylation in the gut microbiota through multiple analytical techniques.First,the docking of BBR and CYP51 was performed;then,the pharmacokinetics of BBR was determined in ICR mice in vivo,and the metabolism of BBR in the liver,kidney,gut microbiota and single bacterial strains was examined in vitro.Moreover,16S rRNA analysis of ICR mouse feces indicated the relationship between BBR and the gut microbiota.Finally,recombinant E.coli containing cyp51 gene was constructed and the CYP51 enzyme lysate was induced to express.The metabolic characteristics of BBR were analyzed in the CYP51 enzyme lysate system.The results showed that CYP51 in the gut microbiota could bind stably with BBR,and the addition of voriconazole(a specific inhibitor of CYP51)slowed down the metabolism of BBR,which prevented the production of the demethylated metabolites thalifendine and berberrubine.This study demonstrated that CYP51 promoted the demethylation of BBR and enhanced its intestinal absorption,providing a new method for studying the metabolic transformation mechanism of isoquinoline alkaloids in vivo.

Multi-Omics Analysis Provides Insight into the Possible Molecular Mechanism of Hay Fever Based on Gut Microbiota

Due to the worldwide epidemic of allergic disease and a cure nowhere in sight,there is a crucial need to explore its pathophysiological mechanisms.As allergic disease has been associated with gut dysbiosis,we searched for a possible mechanism from the perspective of the molecular interface between host and microbiota with concurrent metabolomics and microbiome composition analysis.Sprague-Dawley rats were injected with Artemisia pollen extract to stimulate a hyper reaction to pollen.This hyper reaction decreased the circulation of valine,isoleucine,aspartate,glutamate,glutamine,indole-propionate(IPA),and myo-inositol,and reduced short-chain fatty acids(SCFAs)in feces.Several beneficial genera belonging to Ruminococcaceae,Lachnospiraceae,and Clostridiales declined in the model group,whereas Helicobacter and Akkermansia were only expressed in the model group.Furthermore,the expression of intestinal claudin-3 and liver fatty acid binding protein was downregulated in the model group and associated with metabolic changes and bacteria.Our results suggest that alterations in amino acids as well as their derivatives(especially valine,and IPA which is the reductive product of tryptophan),SCFAs,and the gut microbiome(specifically Akkermansia and Helicobacter)may disrupt the intestinal barrier function by inhibiting the expression of claudin proteins and affecting the mucus layer,which further results in hay fever.

Multi-Omics-Guided Discovery of Omicsynins Produced by Streptomyces sp.1647:Pseudo-Tetrapeptides Active Against Influenza A Viruses and Coronavirus HCoV-229E

Many microorganisms have mechanisms that protect cells against attack from viruses.The fermentation components of Streptomyces sp.1647 exhibit potent anti-influenza A virus(IAV)activity.This strain was isolated from soil in southern China in the 1970s,but the chemical nature of its antiviral substance(s)has remained unknown until now.We used an integrated multi-omics strategy to identify the antiviral agents from this streptomycete.The antibiotics and Secondary Metabolite Analysis Shell(antiSMASH)analysis of its genome sequence revealed 38 biosynthetic gene clusters(BGCs)for secondary metabolites,and the target BGCs possibly responsible for the production of antiviral components were narrowed down to three BGCs by bioactivity-guided comparative transcriptomics analysis.Through bioinformatics analysis and genetic manipulation of the regulators and a biosynthetic gene,cluster 36 was identified as the BGC responsible for the biosynthesis of the antiviral compounds.Bioactivity-based molecular networking analysis of mass spectrometric data from different recombinant strains illustrated that the antiviral compounds were a class of structural analogues.Finally,18 pseudo-tetrapeptides with an internal ureido linkage,omicsynins A1–A6,B1–B6,and C1–C6,were identified and/or isolated from fermentation broth.Among them,11 compounds(omicsynins A1,A2,A6,B1–B3,B5,B6,C1,C2,and C6)are new compounds.Omicsynins B1–B4 exhibited potent antiviral activity against IAV with the 50%inhibitory concentration(IC_(50))of approximately 1μmol·L^(-1)and a selectivity index(SI)ranging from 100 to 300.Omicsynins B1–B4 also showed significant antiviral activity against human coronavirus HCoV-229E.By integrating multi-omics data,we discovered a number of novel antiviral pseudo-tetrapeptides produced by Streptomyces sp.1647,indicating that the secondary metabolites of microorganisms are a valuable source of novel antivirals.

Treating Chronic Diseases by Regulating the Gut Microbiota

Chronic diseases comprise a wide range of abnormal conditions and illnesses that impair patients’physical and/or mental functioning,and last for a long time.Largely a contemporary plague,chronic diseases are responsible for the observed morbidity and mortality in developed countries as well as in some developing countries [1,2].

Forge ahead and improve the core competitiveness of Animal Models and Experimental Medicine(AMEM)

After 5 years of accumulation, Animal Models and Experimental Medicine(AMEM) has received 396 manuscripts from 46 countries and regions, including Chinese mainland, Iran, the United States, India, Israel, Nigeria, Brazil, Bangladesh, Sri Lanka, the Netherlands, Denmark, Australia, Japan, and Spain. It has become an important international exchange and display platform for innovative research results in the field of laboratory animal science and basic medicine.

Our endeavor to write a new chapter in the development of laboratory animal sciences

Since the beginning of the 21st century,with the wide application of molecular biology and genetic engineering technology,the more holistic discipline of laboratory animal sciences has also developed rapidly and many excellent innovations based on laboratory animals,animal models and experimental medicine have continued to emerge.Animal Models and Experimental Medicine(AMEM)was launched in 2018,which was timely and attracted the attention of the industry.Four years have passed and AMEM has achieved fruitful results.

Carrimycin inhibits coronavirus replication by decreasing the efficiency of programmed–1 ribosomal frameshifting through directly binding to the RNA pseudoknot of viral frameshift-stimulatory element

The pandemic of SARS-CoV-2 worldwide with successive emerging variants urgently calls for small-molecule oral drugs with broad-spectrum antiviral activity.Here,we show that carrimycin,a new macrolide antibiotic in the clinic and an antiviral candidate for SARS-CoV-2 in phase III trials,decreases the efficiency of programmed–1 ribosomal frameshifting of coronaviruses and thus impedes viral replication in a broad-spectrum fashion.Carrimycin binds directly to the coronaviral frameshift-stimulatory element(FSE)RNA pseudoknot,interrupting the viral protein translation switch from ORF1a to ORF1b and thereby reducing the level of the core components of the viral replication and transcription complexes.Combined carrimycin with known viral replicase inhibitors yielded a synergistic inhibitory effect on coronaviruses.Because the FSE mechanism is essential in all coronaviruses,carrimycin could be a new broad-spectrum antiviral drug for human coronaviruses by directly targeting the conserved coronaviral FSE RNA.This finding may open a new direction in antiviral drug discovery for coronavirus variants.

Target fishing and mechanistic insights of the natural anticancer drug candidate chlorogenic acid

Chlorogenic acid(CGA)is a natural product that effectively inhibits tumor growth,demonstrated in many preclinical models,and phase II clinical trials for patients with glioma.However,its direct proteomic targets and anticancer molecular mechanisms remain unknown.Herein,we developed a novel bi-functional photo-affinity probe PAL/CGA and discovered mitochondrial acetyl-CoA acetyltransferase 1(ACAT1)was one of the main target proteins of CGA by using affinity-based protein profiling(AfBPP)chemical proteomic approach.We performed in-depth studies on ACAT1/CGA interactions via multiple assays including SPR,ITC,and cryo-EM.Importantly,we demonstrated that CGA impaired cancer cell proliferation by inhibiting the phosphorylation of tetrameric ACAT1 on Y407 residue through a novel mode of action in vitro and in vivo.Our study highlights the use of AfBPP platforms in uncovering unique druggable modalities accessed by natural products.And identifying the molecular target of CGA sheds light on the future clinical application of CGA for cancer therapy.

Morinda officinalis oligosaccharides increase serotonin in the brain and ameliorate depression via promoting 5-hydroxytryptophan production in the gut microbiota

Morinda officinalis oligosaccharides(MOO) are an oral drug approved in China for the treatment of depression in China. However, MOO is hardly absorbed so that their anti-depressant mechanism has not been elucidated. Here, we show that oral MOO acted on tryptophan → 5-hydroxytryptophan(5-HTP) → serotonin(5-HT) metabolic pathway in the gut microbiota. MOO could increase tryptophan hydroxylase levels in the gut microbiota which accelerated 5-HTP production from tryptophan;meanwhile, MOO inhibited 5-hydroxytryptophan decarboxylase activity, thus reduced 5-HT generation,and accumulated 5-HTP. The raised 5-HTP from the gut microbiota was absorbed to the blood, and then passed across the blood-brain barrier to improve 5-HT levels in the brain. Additionally, pentasaccharide,as one of the main components in MOO, exerted the significant anti-depressant effect through a mechanism identical to that of MOO. This study reveals for the first time that MOO can alleviate depression via increasing 5-HTP in the gut microbiota.

Berberine treats atherosclerosis via a vitamine-like effect downregulating Choline-TMA-TMAO production pathway in gut microbiota

Trimethylamine-N-oxide(TMAO)derived from the gut microbiota is an atherogenic metabolite.This study investigates whether or not berberine(BBR)could reduce TMAO production in the gut microbiota and treat atherosclerosis.Effects of BBR on TMAO production in the gut microbiota,as well as on plaque development in atherosclerosis were investigated in the culture of animal intestinal bacterial,HFD-fed animals and atherosclerotic patients,respectively.We found that oral BBR in animals lowers TMAO biosynthesis in intestine through interacting with the enzyme/co-enzyme of choline-trimethylamine lyase(CutC)and flavincontaining monooxygenase(FMO)in the gut microbiota.This action was performed by BBR’s metabolite dihydroberberine(a reductive BBR by nitroreductase in the gut microbiota),via a vitamine-like effect down-regulating Choline-TMA-TMAO production pathway.Oral BBR decreased TMAO production in animal intestine,lowered blood TMAO and interrupted plaque formation in blood vessels in the HFD-fed hamsters.Moreover,21 patients with atherosclerosis exhibited the average decrease of plaque score by 3.2%after oral BBR(0.5 g,bid)for 4 months(^(*)P<0.05,n=21);whereas the plaque score in patients treated with rosuvastatin plus aspirin,or clopidogrel sulfate or ticagrelor(4 months,n=12)increased by 1.9%.TMA and TMAO in patients decreased by 38 and 29%in faeces(^(*)P<0.05;^(*)P<0.05),and 37 and 35%in plasma(^(***)P<0.001;^(*)P<0.05),after 4 months on BBR.BBR might treat atherosclerotic plaque at least partially through decreasing TMAO in a mode of action similar to that of vitamins.

Oral berberine improves brain dopa/dopamine levels to ameliorate Parkinson’s disease by regulating gut microbiota

The phenylalanine-tyrosine-dopa-dopamine pathway provides dopamine to the brain.Iin this process,tyrosine hydroxylase(TH)isthe rate-limiting enzyme that hydroxylates tyrosine and generates levodopa(L-dopa)with tetranydrobiopterin(BH_(4))as a coenzyme.Here,we show that oral berberine(BBR)might supply H^(·) through dihydroberberine(reduced BBR produced by bacterial nitroreductase)and promote the production of BHl from dihydrobiopterin;the increased BH,enhances TH activity,which accelerates the production of L-dopa by the gut bacteria.Oral BBR acts in a way similar to vitamins.The L-dopa produced by theintestinal bacteria enters the brain through the circulation and is transformed to dopamine.To verify the gut-brain dialog activatedby BBR's effect,Enterococcus foecalis or Enterococcus faecium was transplanted into Parkinson's disease(PD)mice.The bacteriasignificantly increased brain dopamine and ameliorated PD manifestation in mice;additionally,combination of BBR with bacteriashowed better therapeutic effect than that with bacteria alone.Moreover,2,4,6-trimethy-pyranylium tetrafluoroborate(TMP-TFB)-derivatized matrix-assisted laser desorption mass spectrometry(MALDI-MS)imaging of dopamine identihed elevated striataldopamine levels in mouse brains with oral Enterococcus,and BBR strengthened the imaging intensity of brain dopamine.Theseresults demonstrated that BBR was an agonist of TH in Enterococcus and could lead to the production of L-dopa in the gut.Furthermore,a study of 28 patients with hyperlipidemia conhrmed that oral BBR increased bloodfecal L-dopa by the intestinalbacteria.Hence,BBR might improve the brain function by upregulating the biosynthesis of-dopa in the gut microbiota through avitamin-like effect.

Phenolic constituents from the roots of Alangium chinense

Three new phenolics（1–3） and twenty-eight known compounds（4–31） were isolated from an ethanolic extract of roots of Alangium chinense. Compound 11 exhibited antiviral activity against Coxsackie virus B3 with IC50 values of 16.89 mmol/L. Compounds 1, 10–17, 19–21, and 23 showed strong antioxidant activity against Fe^2＋-cysteine-induced rat liver microsomal lipid peroxidation, with IC50 values of 0.14–8.18 mmol/L.

Azvudine is a thymus-homing anti-SARS-CoV-2 drug effective in treating COVID-19 patients

Azvudine(FNC)is a nucleoside analog that inhibits HIV-1 RNA-dependent RNA polymerase(RdRp).Recently,we discovered FNC an agent against SARS-CoV-2,and have taken it into Phase III trial for COVID-19 patients.FNC monophosphate analog inhibited SARS-CoV-2 and HCoV-OC43 coronavirus with an EC_(50) between 1.2 and 4.3 μM,depending on viruses or cells,and selective index(SI)in 15-83 range.Oral administration of FNC in rats revealed a substantial thymus-homing feature,with FNC triphosphate(the active form)concentrated in the thymus and peripheral blood mononuclear cells(PBMC).Treating SARS-CoV-2 infected rhesus macaques with FNC(0.07 mg/kg, qd,orally)reduced viral load,recuperated the thymus,improved lymphocyte profiles,alleviated in flammation and orga n damage,and lessened grou nd・glass opacities in chest X-ray.Sin gle-cell seque ncing suggested the promotion of thymus function by FNC.A randomized,single-arm clinical trial of FNC on compassionate use(n=31)showed that oral FNC(5 mg,qd)cured all COVID-19 patients,with 100%viral ribonucleic acid negative conversion in 3.29±2.22 days(range:1-9 days)and 100%hospital discharge rate in 9.00±4.93 days(range:2-25 days).The side-effect of FNC is minor and transient dizziness and nausea in 16.12%(5/31)patients.Thus,FNC might cure COVID-19 through its anti-SARS-CoV-2 activity concentrated in the thymus,followed by promoted immunity.

Antiviral stereoisomers of 3,5-bis(2-hydroxybut-3-en-1-yl)-1,2,4-thiadiazole from the roots of Isatis indigotica

Four stereoisomers of 3,5-bis（2-hydroxybut-3-en-1-yl）-l,2,4-thiadiazole, named insatindigothiadia- zoles A-D （1a-1d）, were isolated from the roots oflsatis indigotica. Their structures were determined by spectroscopic analysis; specifically, the absolute configurations were assigned by using the MPA determination rule based on △δrs values of MPA esters, and supported by electronic CD （ECD） calculations. Proposed biosynthetic pathways and preliminary investigations of the biological activities of la-1d against influenza virus A （H3N2）, Coxsackie virus B3, and/or HSV-1 are also discussed.

Recent advances in the anti-HCV mechanisms of interferon

Interferon(IFN)in combination with ribavirin has been the standard of care(SOC)for chronic hepatitis C for the past few decades.Although the current SOC lacks the desired efficacy,and 4 new direct-acting antiviral agents have been recently approved,interferons are still likely to remain the cornerstone of therapy for some time.Moreover,as an important cytokine system of innate immunity,host interferon signaling provides a powerful antiviral response.Nevertheless,the mechanisms by which HCV infection controls interferon production,and how interferons,in turn,trigger anti-HCV activities as well as control the outcome of HCV infection remain to be clarified.In this report,we review current progress in understanding the mechanisms of IFN against HCV,and also summarize the knowledge of induction of interferon signaling by HCV infection.