An Odyssey in antiviral drug development—50 years at the Rega Institute:1964–2014

I.How it started I entered the Rega Institute for Medical Research in August 1964,as a medical student,to start working under the guidance of Prof.Piet De Somer,then professor of microbiology at the Leuven School of Medicine.When I graduated

人肿瘤坏死因子β(hTNFβ)在变铅青链霉菌中的表达研究(英文)

以变铅青链霉菌为宿主研究了人TNFβ(hTNFβ)的异源表达。应用链霉菌S .venezuelaeCBS76 2 70分泌产生的枯草杆菌蛋白酶抑制剂vsi基因的启动子、表达调控序列和分泌信号肽序列 ,分别对hTNFβ进行了直接分泌表达、分泌融合表达和胞内表达。将hTNFβ的cDNA分别直接融合于vsi信号肽序列下游 2个氨基酸处、vsi全长基因之后以及vsi起始密码子ATG的下游 ,获得的表达盒分别克隆至链霉菌高拷贝质粒pIJ486 ,转化StreptomyceslividansTK2 4,获得了重组菌株S .lividans(pIJ486 hTNFβ)、S .lividans(pIJ486 vsi hTNFβ)和S .lividans(pIVPA hTNFβ)。分别对不同的重组菌株进行摇瓶培养 ,对其培养的上清液和细胞裂解液进行SDS PAGE和Western杂交 ,结果表明 :hTNFβ在重组菌株中均获得了表达 ,且直接分泌产物和胞内表达产物均具有生物学活性。hTNFβ直接分泌表达产物的分子量约为 16kDa,NB培养基中培养 48h时表达水平约为 0 7mg L。胞内表达产物分子量与对照重组hTNFβ一致(18 7kDa) ,但随培养时间的延长逐步降解为 16kDa ,NB培养基中培养 48h时的表达水平 (2 5 1mg L)远高于其直接分泌表达水平。

小鼠胸腺上皮细胞系MTEC1产生30kD的MCP-1类趋化因子

髓质型小鼠胸腺上皮细胞系MTEC1自发分泌趋化因子(Chemokines),细胞培养上清先经CPG珠(Controlled-pore glass beads)初步浓缩纯化,再依次经肝素-Sepharose柱亲和层析、阳离子交换FPLC及RP-HPLC分离纯化,得到了一个30kD的蛋白质分子,对淋巴细胞和单核巨噬细胞均有趋化活性。此蛋白分子N端封闭,因而先经甲酸水解得到蛋白片段,分析了其中24个氨基酸的序列,发现其与小鼠MCP-1/JE(Monocyte Chemoattractant Pro-tein-1)完全相同。以上结果说明,MTEC1产生的是mMCP-1/JE类趋化因子。

Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase

Recently emerged SARS-CoV-2 caused a major outbreak of coronavirus disease 2019(COVID-19)and instigated a widespread fear,threatening global health safety.To date,no licensed antiviral drugs or vaccines are available against COVID-19 although several clinical trials are under way to test possible therapies.During this urgent situation,computational drug discovery methods provide an alternative to tiresome high-throughput screening,particularly in the hit-to-lead-optimization stage.Identification of small molecules that specifically target viral replication apparatus has indicated the highest potential towards antiviral drug discovery.In this work,we present potential compounds that specifically target SARS-CoV-2 vital proteins,including the main protease,Nsp12 RNA polymerase and Nsp13 helicase.An integrative virtual screening and molecular dynamics simulations approach has facilitated the identification of potential binding modes and favourable molecular interaction profile of corresponding compounds.Moreover,the identification of structurally important binding site residues in conserved motifs located inside the active site highlights relative importance of ligand binding based on residual energy decomposition analysis.Although the current study lacks experimental validation,the structural information obtained from this computational study has paved way for the design of targeted inhibitors to combat COVID-19 outbreak.

Interactive Study between Two Types of 1-[2-(Hydroxyethoxy)methyl] -6-naphthylmethylthymines and HIV-1 Reverse Transcriptase

Two different types of 1-[2-(hydroxyethoxy)methyl]-6-naphthylmethylthymines have been designed, synthesized and evaluated for their anti-HIV-1 activities in different cells lines. The binding free energy (DG) including steric and electrostatic between the two different ligands and reverse transcriptase Non-Nucleoside Binding Pocket (NNBP) have been docked and calculated to evaluate their accommodation circumstance on a SGI work station. The DG and anti-HIV-1 activity has been correlated in order to guide further drug design, which showed that the steric binding effect dominated in the whole binding action between the compounds and reverse transcriptase (RT). The results showed that more negative DG led to higher activity of compounds.

Molecular identification of hepatitis B virus genotypes/subgenotypes:Revised classification hurdles and updated resolutions

The clinical course of infections with the hepatitis B virus(HBV)substantially varies between individuals,as a consequence of a complex interplay between viral,host,environmental and other factors.Due to the high genetic variability of HBV,the virus can be categorized into different HBV genotypes and subgenotypes,which considerably differ with respect to geographical distribution,transmission routes,disease progression,responses to antiviral therapy or vaccination,and clinical outcome measures such as cirrhosis or hepatocellular carcinoma.However,HBV(sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods.Thus,an accurate,holistic and dynamic classification system is essential.In this review article,we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification.Analyzing fulllength genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system.Careful attention must be paid to all aspects of phylogenetic analysis,such as bootstrapping values and meeting the necessary thresholds for(sub)genotyping.Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel.As many of these strains were misclassified due to genetic differences resulting from recombination,we propose the term"recombino-subgenotype".Moreover,immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV(sub)genotypes.We therefore suggest the term"immigro-subgenotype"to distinguish exotic(sub)genotypes from native ones.We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis,diagnosis and treatment.

Gelatin degradation assay reveals MMP-9 inhibitors and function of O-glycosylated domain

AIM: To establish a novel, sensitive and high-throughput gelatinolytic assay to define new inhibitors and compare domain deletion mutants of gelatinase B/matrix metalloproteinase (MMP)-9. METHODS: Fluorogenic Dye-quenched (DQ)TM-gelatin was used as a substrate and biochemical parameters (substrate and enzyme concentrations, DMSO solvent concentrations) were optimized to establish a highthroughput assay system. Various small-sized libraries (ChemDiv, InterBioScreen and ChemBridge) of hetero-cyclic, drug-like substances were tested and compared with prototypic inhibitors. RESULTS: First, we designed a test system with gelatin as a natural substrate. Second, the assay was validated by selecting a novel pyrimidine-2,4,6-trione (barbitu- rate) inhibitor. Third, and in line with present structural data on collagenolysis, it was found that deletion of the O-glycosylated region significantly decreased gelatinolytic activity (kcat/kM ± 40% less than full-length MMP-9). CONCLUSION: The DQTM-gelatin assay is useful in high-throughput drug screening and exosite targeting. We demonstrate that flexibility between the catalytic and hemopexin domain is functionally critical for gelatinolysis.

Anti-hepatitis C virus potency of a new autophagy inhibitor using human liver slices model

AIM: To evaluate the antiviral potency of a new antihepatitis C virus(HCV) antiviral agent targeting the cellular autophagy machinery. METHODS: Non-infected liver slices, obtained from human liver resection and cut in 350 μm-thick slices(2.7 × 106 cells per slice) were infected with cell culture-grown HCV Con1b/C3 supernatant(multiplicity of infection = 0.1) cultivated for up to ten days. HCV infected slices were treated at day 4 post-infection with GNS-396 for 6 d at different concentrations. HCV replication was evaluated by strand-specific real-time quantitative reverse transcription- polymerase chain reaction. The infectivity titers of supernatants were evaluated by foci formation upon inoculation into naive Huh-7.5.1 cells. The cytotoxic effect of the drugs was evaluated by lactate dehydrogenase leakage assays. RESULTS: The antiviral efficacy of a new antiviral drug, GNS-396, an autophagy inhibitor, on HCV infection of adult human liver slices was evidenced in a dosedependent manner. At day 6 post-treatment, GNS-396 EC50 was 158 nmol/L without cytotoxic effect(compared to hydroxychloroquine EC50 = 1.17 μmol/L).CONCLUSION: Our results demonstrated that our ex vivo model is efficient for evaluation the potency of autophagy inhibitors, in particular a new quinoline derivative GNS-396 as antiviral could inhibit HCV infection in a dosedependent manner without cytotoxic effect.

Early prediction of major depression in chronic hepatitis C patients during peg-interferon α-2b treatment by assessment of vegetative-depressive symptoms after four weeks

AIM: To study the predictive value of the vegetative- depressive symptoms of the Zung Depression Rating Scale for the occurrence of depression during treatment with peg-interferon α-2b of chronic hepatitis C (CHC) patients. METHODS: The predictive value of vegetative- depressive symptoms at 4 wk of treatment for the occurrence of a subsequent diagnosis of major depressive disorder (MDD) was studied in CHC patients infected after substance use in a prospective, multi- center treatment trial in Belgium. The presence of vegetative-depressive symptoms was assessed using the Zung Scale before and 4 wk after the start of antiviral treatment. RESULTS: Out of 49 eligible patients, 19 (39%) developed MDD. The area under the ROC curve of the vegetative Zung subscale was 0.73, P = 0.004. The sensitivity at a cut-point of > 15/35 was 95% (95% CI: 74-100). The positive predictive value equalled 44% (95% CI: 29-60). CONCLUSION: In this group of Belgian CHC patients infected after substance use, antiviral treatment caused a considerable risk of depression. Seven vegetativedepressive symptoms of the Zung scale at wk 4 of treatment predicted 95% of all emerging depressions, at a price of 56% false positive test results.

An extremely rare case of delusional parasitosis in a chronic hepatitis C patient during pegylated interferon alpha-2b and ribavirin treatment

During treatment of chronic hepatitis C patients with interferon and ribavirin, a lot of side effects are described. Twenty-three percent to 44% of patients develop depression. A minority of patients evolve to psychosis. To the best of our knowledge, no cases of psychogenic parasitosis occurring during interferon therapy have been described in the literature. We present a 49-year-old woman who developed a delusional parasitosis during treatment with pegylated interferon alpha-2b weekly and ribavirin. She complained of seeing parasites and the larvae of fleas in her stools. This could not be confirmed by any technical examination. All the complaints disappeared after stopping pegylated interferon alpha-2b and reappeared after restarting it. She had a complete sustained viral response.

Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches

The papain-like protease(PLpro)is vital for the replication of coronaviruses(Co Vs),as well as for escaping innate-immune responses of the host.Hence,it has emerged as an attractive antiviral drug-target.In this study,computational approaches were employed,mainly the structure-based virtual screening coupled with all-atom molecular dynamics(MD)simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)PLpro,which can be further developed as potential pan-PLprobased broad-spectrum antiviral drugs.The sequence,structure,and functional conserveness of most deadly human Co Vs PLprowere explored,and it was revealed that functionally important catalytic triad residues are well conserved among SARS-Co V,SARS-Co V-2,and middle east respiratory syndrome coronavirus(MERS-Co V).The subsequent screening of a focused protease inhibitors database composed of^7,000 compounds resulted in the identification of three candidate compounds,ADM13083841,LMG15521745,and SYN15517940.These three compounds established conserved interactions which were further explored through MD simulations,free energy calculations,and residual energy contribution estimated by MM-PB(GB)SA method.All these compounds showed stable conformation and interacted well with the active residues of SARS-Co V-2 PLpro,and showed consistent interaction profile with SARS-Co V PLproand MERS-Co V PLproas well.Conclusively,the reported SARS-Co V-2 PLprospecific compounds could serve as seeds for developing potent pan-PLprobased broad-spectrum antiviral drugs against deadly human coronaviruses.Moreover,the presented information related to binding site residual energy contribution could lead to further optimization of these compounds.

Structure-based design and optimization lead to the identification of novel dihydrothiopyrano[3,2-d]pyrimidine derivatives as potent HIV-1 inhibitors against drug-resistant variants

With our continuous endeavors in seeking potent anti-HIV-1 agents,we reported here the discovery,biological characterization,and druggability evaluation of a class of nonnucleoside reverse transcriptase inhibitors.To fully explore the chemical space of the NNRTI-binding pocket,novel series of dihydrothiopyrano[3,2-d]pyrimidines were developed by employing the structure-based design strategy.Most of the derivatives were endowed with prominent antiviral activities against HIV-1 wild-type and resistant strains at nanomolar levels.Among them,compound 23h featuring the aminopiperidine moiety was identified as the most potent inhibitor,with EC50values ranging from 3.43 to 21.4 nmol/L.Especially,for the challenging double-mutants F227L+V106A and K103N+Y181C,23h exhibited 2.3-to 14.5-fold more potent activity than the first-line drugs efavirenz and etravirine.Besides,the resistance profiles of 23h achieved remarkable improvement compared to efavirenz and etravirine.The binding target of 23h was further confirmed to be HIV-1 reverse transcriptase.Molecular modeling studies were also performed to elucidate the biological evaluation results and give guidance for the optimization campaign.Furthermore,no apparent inhibition of the major CYP450 enzymes and hERG channel was observed for 23h.Most importantly,23h was characterized by good pharmacokinetic properties and excellent safety in vivo.Collectively,23h holds great promise as a potential candidate for its effective antiviral efficacy and favorable drug-like profiles.

Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 Mpro inhibitors

The main protease(M^(pro))of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle.The covalent M^(pro)inhibitor nirmatrelvir(in combination with ritonavir,a pharmacokinetic enhancer)and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use.Effective antiviral drugs are needed to fight the pandemic,while non-covalent M^(pro)inhibitors could be promising alternatives due to their high selectivity and favorable druggability.Numerous non-covalent M^(pro)inhibitors with desirable properties have been developed based on available crystal structures of M^(pro).In this article,we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent M^(pro)inhibitors,followed by a general overview and critical analysis of the available information.Prospective viewpoints and insights into current strategies for the development of non-covalent M^(pro)inhibitors are also discussed.

The chemokines CXCL8 and CXCL12:molecular and functional properties,role in disease and efforts towards pharmacological intervention

Chemokines are an indispensable component of our immune system through the regulation of directional migration and activation of leukocytes.CxCL8 is the most potent human neutrophil-attracting chemokine and plays crucial roles in the response to infection and tissue injury.CXCL8 activity inherently depends on interaction with the human CXC chemokine receptors CXCR1 and CXCR2,the atypical chemokine receptor ACKR1,and glycosaminoglycans.Furthermore,(hetero)dimerization and tight regulation of transcription and translation,as well as post-translational modifications further fine-tune the spatial and temporal activity of CXCL8 in the context of inflammatory diseases and cancer.The CxCL8 interaction with receptors and glycosaminoglycans is therefore a promising target for therapy,as illustrated by multiple ongoing clinical trials.CXCL8-mediated neutrophil mobilization to blood is directly opposed by CXCL12,which retains leukocytes in bone marrow.CXCL12 is primarily a homeostatic chemokine that induces migration and activation of hematopoietic progenitor cells,endothelial cells,and several leukocytes through interaction with CXCR4,ACKR1,and ACKR3.Thereby,it is an essential player in the regulation of embryogenesis,hematopoiesis,and angiogenesis.However,CXCL12 can also exert inflammatory functions,as illustrated by its pivotal role in a growing list of pathologies and its synergy with CXCL8 and other chemokines to induce leukocyte chemotaxis.Here,we review the plethora of information on the CXCL8 structure,interaction with receptors and glycosaminoglycans,different levels of activity regulation,role in homeostasis and disease,and therapeutic prospects.Finally,we discuss recent research on CXCL12 biochemistry and biology and its role in pathology and pharmacology.

Picomolar inhibitor of reverse transcriptase featuring significantly improved metabolic stability

Considering the undesirable metabolic stability of our recently identified NNRTI 5(t1/2=96 min)in human liver microsomes,we directed our efforts to improve its metabolic stability by introducing a new favorable hydroxymethyl side chain to the C-5 position of pyrimidine.This strategy provided a series of novel methylol-biphenyl-diarylpyrimidines with excellent anti-HIV-1 activity.The best compound 9g was endowed with remarkably improved metabolic stability in human liver microsomes(t1/2=2754 min),which was about 29-fold longer than that of 5(t1/2=96 min).This compound conferred picomolar inhibition of WT HIV-1(EC50=0.9 nmol/L)and low nanomolar activity against five clinically drug-resistant mutant strains.It maintained particularly low cytotoxicity(CC50=264μmol/L)and good selectivity(SI=256,438).Molecular docking studies revealed that compound 9g exhibited a more stable conformation than 5 due to the newly constructed hydrogen bond of the hydroxymethyl group with E138.Also,compound 9g was characterized by good safety profiles.It displayed no apparent inhibition of CYP enzymes and h ERG.The acute toxicity assay did not cause death and pathological damage in mice at a single dose of 2 g/kg.These findings paved the way for the discovery and development of new-generation anti-HIV-1 drugs.

Development of fluorine-substituted NH_(2)-biphenyl-diarylpyrimidines as highly potent non-nucleoside reverse transcriptase inhibitors:Boosting the safety and metabolic stability

Our recent studies for nonnucleoside reverse transcriptase inhibitors identified a highly potent compound JK-4b against WT HIV-1(EC_(50)=1.0 nmol/L),but the poor metabolic stability in human liver microsomes(t_(1/2)=14.6 min)and insufficient selectivity(SI=2059)with high cytotoxicity(CC_(50)=2.08μmol/L)remained major issues associated with JK-4b.The present efforts were devoted to the introduction of fluorine into the biphenyl ring of JK-4b,leading to the discovery of a novel series of fluorine-substituted NH_(2)-biphenyl-diarylpyrimidines with noticeable inhibitory activity toward WT HIV-1 strain(EC_(50)=1.8–349 nmol/L).The best compound 5t in this collection(EC_(50)=1.8 nmol/L,CC_(50)=117μmol/L)was 32-fold in selectivity(SI=66,443)compared to JK-4b and showed remarkable potency toward clinically multiple mutant strains,such as L100I,K103N,E138K,and Y181C.The metabolic stability of 5t was also significantly improved(t_(1/2)=74.52 min),approximately 5-fold higher than JK-4b in human liver microsomes(t_(1/2)=14.6 min).Also,5t possessed good stability in both human and monkey plasma.No significant in vitro inhibition effect toward CYP enzyme and hERG was observed.The single-dose acute toxicity test did not induce mice death or obvious pathological damage.These findings pave the way for further development of 5t as a drug candidate.

新型2,2'-缩水-L-苏糖嘧啶膦酸核苷的合成

首先通过九步反应合成了一系列L-苏糖嘧啶核苷膦酸酯. 用二乙胺基三氟化硫(DAST)处理L-苏糖嘧啶核苷膦酸酯, 分别以中高收率得到相应的2,2'-缩水-1-(L-苏糖)尿嘧啶核苷膦酸酯类似物. 对所得到的L-苏糖嘧啶核苷膦酸酯和2,2'-缩水-L-苏糖嘧啶膦酸核苷进行了初步的生物学评价, 未发现任何活性.

Structure-directed expansion of biphenyl-pyridone derivatives as potent non-nucleoside reverse transcriptase inhibitors with significantly improved potency and safety

Following our previous work on human immunodeficiency virus-1(HIV-1)non-nucleoside reverse transcriptase inhibitors(NNRTIs),a series of novel biphenyl-pyridone derivatives were synthesized and evaluated for their anti-HiV-1 activity to expand their structure-activity relationship.Some of them exhibited low nanomolar activity toward wild-type HiV-1 and clinically relevant single/double mutant strains.The most active compound B1 was 231-fold more potent(EC_(50)=17nmol/L)than the lead compound 2(EC_(50)=3.93μmol/L)against wild-type(WT)HIV-1.This compound was approximately 3.5-fold less cytotoxic(CC_(50)=100.58μmol/L)than compound 2(CC_(50)=28.24μmol/L),presenting a higher selectivity index(SI)value of 5923.Compared with 2,the antiviral potency of B1 was significantly increased against five single mutant strains(L1001,K103N,E138K,Y181C and Y188L)and two double mutant strains(F227L+V106A and K103N+Y181C).Especially,K103N,Y181C and K103N+Y181C were more sensitive to B1 than both 2 and doravirine.Besides,the enzymatic inhibitory activity of B1 against wild-type HIV-1 reverse transcriptase was approximately 32-fold higher(IC_(50)=100nmol/L)than 2(IC_(50)=3.21μmol/L).Molecular docking studies and dynamic simulations were conducted to explain their potent activity.Taken together,this research represents an important step toward the discovery of novel biphenylpyridone drug candidates for HIV therapy.

Author correction to ‘Approved HIV reverse transcriptase inhibitors in the past decade’ [Acta Pharmaceutica Sinica B 12 (2022) 1567e1590]

The authors regret that the trade name“Acriptega”should be replaced by“Kocitaf”in this article,because the“Acriptega”represents the antiviral regimen of TDFþFTCþDTG,and the“Kocitaf”represents the TAFþFTCþDTG regimen.Although it does not affect the conclusion,it is an obvious error.The authors apologize for any inconvenience caused to the journal and readers.

Linker optimization of HEPT derivatives as potent non-nucleoside HIV-1 reverse transcriptase inhibitors: From S=O to CHOR

A novel series of CHOR-HEPT non-nucleoside HIV-1 reverse transcriptase inhibitors were developed by means of structure-based design strategy based on compound 6 reported previously by our group. Most of these compounds showed moderate to good activity toward wild-type HIV-1 strain with EC50values in the range of 0.18–51.88 μmol/L and SI values in the range of 4–907. The compound 14aj with a CHOH linker and compound 13i with a CHOTMS linker in this series exhibited improved anti-HIV-1 activity(EC50= 0.18 μmol/L, and 0.20 μmol/L) with higher selectivity(SI = 907, and 665) as comparison with the lead compound 6(EC50= 0.59 μmol/L, SI = 9). These two compounds 14aj and 13i were more sensitive than 6 toward clinically relevant mutant L100I, K103N and E138K viruses, which were further evaluated for their activity against wild-type reverse transcriptase and displayed a good correlation with the cell-based activity. Preliminary molecular modeling investigations provided insight for further structural optimization of HEPT.