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Natural products for infectious microbes and diseases:an overview of sources,compounds,and chemical diversities

Science China(Life Sciences) 2022年第6期65卷 1123-1145页

作者： Lu Luo Jun Yang Cheng Wang Jie Wu Yafang Li Xu Zhang Hui Li Hui Zhang Yumei Zhou Aiping Lu Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Institute of Basic Medical Sciences Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100006China Institute of Hematology&Blood Diseases Hospital Chinese Academy of Medical Sciences&Peking Union Medical CollegeTianjin 300020China weMED Health Houston 77054USA Institute of Botany Chinese Academy of SciencesBeijing 100093China Akupunktur Akademiet Aabyhoej 8230Denmark The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine Guangzhou 518033China School of Chinese Medicine Hong Kong Baptist UniversityHong Kong 999077China

As coronavirus disease 2019(COVID-19) threatens human health globally,infectious disorders have become one of the most challenging problem for the medical community.Natural products(NP) have been a prolific source of antimicrobial agents with widely divergent structures and a range of vast biological activities.A dataset comprising 618 articles,including 646 NP-based compounds from 672 species of natural sources with biological activities against 21 infectious pathogens from five categories,was assembled through manual selection of published articles.These data were used to identify 268 NP-based compounds classified into ten groups,which were used for network pharmacology analysis to capture the most promising lead-compounds such as agelasine D,dicumarol,dihydroartemisinin and pyridomycin.The distribution of maximum Tanimoto scores indicated that compounds which inhibited parasites exhibited low diversity,whereas the chemistries inhibiting bacteria,fungi,and viruses showed more structural diversity.A total of 331 species of medicinal plants with compounds exhibiting antimicrobial activities were selected to classify the family sources.The family Asteraceae possesses various compounds against C.neoformans,the family Anacardiaceae has compounds against Salmonella typhi,the family Cucurbitacea against the human immunodeficiency virus(HIV),and the family Ancistrocladaceae against Plasmodium.This review summarizes currently available data on NPbased antimicrobials against refractory infections to provide information for further discovery of drugs and synthetic strategies for anti-infectious agents.

关键词： natural product infectious pathogen Drug discovery drug development in silico analysis

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Pharmaceutical applications of framework nucleic acids

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Acta Pharmaceutica Sinica B 2022年第1期12卷 76-91页

作者： Liang Chen Jie Zhang Zhun Lin Ziyan Zhang Miao Mao Jiacheng Wu Qian Li Yuanqing Zhang Chunhai Fan School of Pharmaceutical Sciences Sun Yat-sen UniversityGuangzhou 510006China School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational MedicineShanghai Jiao Tong UniversityShanghai 200240China Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acids Chemistry and NanomedicineRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai 200127China

DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids(FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for Drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.

关键词： DNA nanotechnology Self-assembly Framework nucleic acids DNA nanostructures Drug discovery Therapeutic molecules drug delivery drug analysis

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In silico comparative structural and compositional analysis of glycoproteins of RSV to study the nature of stability and transmissibility of RSV A

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Systems Microbiology and Biomanufacturing 2023年第2期3卷 312-327页

作者： Debanjan Mitra Pradeep K.Das Mohapatra Department of Microbiology Raiganj UniversityRaiganjWBIndia

The current scenario of COVID-19 makes us to think about the devastating diseases that kill so many people every year.Analysis of viral proteins contributes many things that are utterly useful in the evolution of therapeutic drugs and vaccines.In this study,sequence and structure of fusion glycoproteins and major surface glycoproteins of respiratory syncytial virus(RSV)were analysed to reveal the stability and transmission rate.RSV A has the highest abundance of aromatic residues.The Kyte–Doolittle scale indicates the hydrophilic nature of RSV A protein which leads to the higher transmission rate of this virus.Intra-protein interactions such as carbonyl interactions,cation-pi,and salt bridges were shown to be greater in RSV A compared to RSV B,which might lead to improved stability.This study discovered the presence of a network aromatic–sulphur interaction in viral proteins.Analysis of ligand binding pocket of RSV proteins indicated that drugs are performing better on RSV B than RSV A.It was also shown that increasing the number of tunnels in RSV A proteins boosts catalytic activity.This study will be helpful in Drug discovery and vaccine development.

关键词： Respiratory syncytial virus Stability Intra-protein interactions Tunnels Drug discovery

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Artificial Intelligence in Pharmaceutical Sciences

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Engineering 2023年第8期27卷 37-69页

作者： Mingkun Lu Jiayi Yin Qi Zhu Gaole Lin Minjie Mou Fuyao Liu Ziqi Pan Nanxin You Xichen Lian Fengcheng Li Hongning Zhang Lingyan Zheng Wei Zhang Hanyu Zhang Zihao Shen Zhen Gu Honglin Li Feng Zhu College of Pharmaceutical Sciences&The Second Affiliated Hospital School of MedicineZhejiang UniversityHangzhou 310058China Shanghai Key Laboratory of New drug Design East China University of Science and TechnologyShanghai 200237China Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University Alibaba-Zhejiang University Joint Research Center of Future Digital HealthcareHangzhou 330110China Innovation Center for AI and Drug discovery East China Normal UniversityShanghai 200062China Lingang Laboratory Shanghai 200031China

Drug discovery and development affects various aspects of human health and dramatically impacts the pharmaceutical market.However,investments in a new drug often go unrewarded due to the long and complex process of drug research and development(R&D).With the advancement of experimental technology and computer hardware,artificial intelligence(AI)has recently emerged as a leading tool in analyzing abundant and high-dimensional data.Explosive growth in the size of biomedical data provides advantages in applying AI in all stages of drug R&D.Driven by big data in biomedicine,AI has led to a revolution in drug R&D,due to its ability to discover new drugs more efficiently and at lower cost.This review begins with a brief overview of common AI models in the field of Drug discovery;then,it summarizes and discusses in depth their specific applications in various stages of drug R&D,such as target discovery,Drug discovery and design,preclinical research,automated drug synthesis,and influences in the pharmaceutical market.Finally,the major limitations of AI in drug R&D are fully discussed and possible solutions are proposed.

关键词： Artificial intelligence Machine learning Deep learning Target identification Target discovery drug design Drug discovery

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人工智能加速GPCR配体的发现

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Engineering 2024年第1期32卷 18-28页

作者： Wei Chen Chi Song Liang Leng Sanyin Zhang Shilin Chen State Key Laboratory of Southwestem Chinese Medicine Resources Innovative Institute of Chinese Medicine and PharmacyChengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China

G protein-coupled receptors(GPCRs)are crucial players in various physiological processes,making them attractive candidates for Drug discovery.However,traditional approaches to GPCR ligand discovery are time-consuming and resource-intensive.The emergence of artificial intelligence(AI)methods has revo-lutionized the field of GPCR ligand discovery and has provided valuable tools for accelerating the identi-fication and optimization of GPCR ligands.In this study,we provide guidelines for effectively utilizing AI methods for GPCR ligand discovery,including data collation and representation,model selection,and specific applications.First,the online resources that are instrumental in GPCR ligand discovery were sum-marized,including databases and repositories that contain valuable GPCR-related information and ligand data.Next,GPCR and ligand representation schemes that can convert data into computer-readable for-mats were introduced.Subsequently,the key applications of Al methods in the different stages of GPCR Drug discovery were discussed,ranging from GPCR function prediction to ligand design and agonist identification.Furthermore,an Al-driven multi-omics integration strategy for GPCR ligand discovery that combines information from various omics disciplines was proposed.Finally,the challenges and future directions of the application of Al in GPCR research were deliberated.In conclusion,continued advance-ments in Al techniques coupled with interdisciplinary collaborations will offer great potential for improv-ing the efficiency of GPCR ligand discovery.

关键词： G protein-coupled receptor Ligand Artificial intelligence Multi-omics Drug discovery

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Patient-derived xenograft model in colorectal cancer basic and translational research

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Animal Models and Experimental Medicine 2023年第1期6卷 26-40页

作者： Xiaofeng Liu Zechang Xin Kun Wang Hepatopancreatobiliary Surgery Department Ⅰ Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education/Beijing)Peking University Cancer Hospital and InstituteBeijingChina

Colorectal cancer(CRC)is one of the most popular malignancies globally,with 930000 deaths in 2020.The evaluation of CRC-related pathogenesis and the discovery of po-tential therapeutic targets will be meaningful and helpful for improving CRC treat-ment.With huge efforts made in past decades,the systematic treatment regimens have been applied to improve the prognosis of CRC patients.However,the sensitivity of CRC to chemotherapy and targeted therapy is different from person to person,which is an important cause of treatment failure.The emergence of patient-derived xenograft(PDX)models shows great potential to alleviate the straits.PDX models possess similar genetic and pathological characteristics as the features of primary tu-mors.Moreover,PDX has the ability to mimic the tumor microenvironment of the original tumor.Thus,the PDX model is an important tool to screen precise drugs for individualized treatment,seek predictive biomarkers for prognosis supervision,and evaluate the unknown mechanism in basic research.This paper reviews the recent advances in constructed methods and applications of the CRC PDX model,aiming to provide new knowledge for CRC basic research and therapeutics.

关键词： colorectal cancer Drug discovery patient-derived xenograft model precision medicine tumor microenvironment

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C-Aryl Glycosylation via Interrupted Pummerer Rearrangement

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Chinese Journal of Chemistry 2023年第21期41卷 2843-2847页

作者： Jiagen Li Xuefeng Jiang State Key Laboratory of Molecular&Process Engineering School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai200062 China State Key Laboratory of Elemento-Organic Chemistry Nankai UniversityTianjin300071 China State Key Laboratory of Organometallic Chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai200032 China

C-aryl glycosides are an important kind of carbohydrate derivatives for Drug discovery,due to their distinctive attributes of resistance to hydrolysis from enzymes.Herein,C-aryl glycosylation was established for the synthesis of 2-sulfur C-aryl glycals and 1,2-dihydrobenzofuran-fused C-aryl glycosides via interrupted Pummerer process,featured with sulfonium-tethered[3,3]-sigmatropic rearrangement between sulfoxide glycals and phenols.This protocol offers a broad substrate scope with diverse glycosyl and phenols.Dapagliflozin,Empagliflozin,and Ipragliflozin analogs were straightforward achieved,respectively.

关键词： Glycal Glycosylation Interrupted pummerer Rearrangement Sulfoxide Carbohydrates C-Glycosides Drug discovery

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A multidimensional platform of patient-derived tumors identifies drug susceptibilities for clinical lenvatinib resistance

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Acta Pharmaceutica Sinica B 2024年第1期14卷 223-240页

作者： Lei Sun Arabella H.Wan Shijia Yan Ruonian Liu Jiarui Li Zhuolong Zhou Ruirui Wu Dongshi Chen Xianzhang Bu Jingxing Ou Kai Li Xiongbin Lu Guohui Wan Zunfu Ke Department of Pathology the First Affiliated HospitalSun Yat-sen UniversityGuangzhou 510080China National-Local Joint Engineering Laboratory of druggability and New drug Evaluation National Engineering Research Center for New Drug and Druggability(Cultivation)Guangdong Province Key Laboratory of New Drug Design and EvaluationSchool of Pharmaceutical SciencesSun Yat-sen UniversityGuangzhou 510006China Department of Medical and Molecular Genetics Indiana University School of MedicineIndianapolisIN 46202USA Department of Medicine Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90033USA Department of Hepatic Surgery and Liver Transplantation Center Third Affiliated HospitalOrgan Transplantation InstituteSun Yat-sen UniversityOrgan Transplantation Research Center of Guangdong ProvinceGuangdong Province Engineering Laboratory for Transplantation MedicineGuangzhou 510630China Guangdong Provincial Key Laboratory of Liver Disease Research Guangzhou 510630China Department of Ultrasound Third Affiliated HospitalSun Yat-sen UniversityGuangzhou 510630China Melvin and Bren Simon Comprehensive Cancer Center Indiana UniversityIndianapolisIN 46202USA

Lenvatinib,a second-generation multi-receptor tyrosine kinase inhibitor approved by the FDA for first-line treatment of advanced liver cancer,facing limitations due to drug resistance.Here,we applied a multidimensional,high-throughput screening platform comprising patient-derived resistant liver tumor cells(PDCs),organoids(PDOs),and xenografts(PDXs)to identify drug susceptibilities for conquering lenvatinib resistance in clinically relevant settings.Expansion and passaging of PDCs and PDOs from resistant patient liver tumors retained functional fidelity to lenvatinib treatment,expediting drug repurposing screens.Pharmacological screening identified romidepsin,YM155,apitolisib,NVP-TAE684 and dasatinib as potential antitumor agents in lenvatinib-resistant PDC and PDO models.Notably,romidepsin treatment enhanced antitumor response in syngeneic mouse models by triggering immunogenic tumor cell death and blocking the EGFR signaling pathway.A combination of romidepsin and immunotherapy achieved robust and synergistic antitumor effects against lenvatinib resistance in humanized immunocompetent PDX models.Collectively,our findings suggest that patient-derived liver cancer models effectively recapitulate lenvatinib resistance observed in clinical settings and expedite Drug discovery for advanced liver cancer,providing a feasible multidimensional platform for personalized medicine.

关键词： Lenvatinib drug resistance High-throughput screening Drug discovery Patient-derived model Romidepsin EGFR Liver cancer

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Structural insight into the dual-antagonistic mechanism of AB928 on adenosine A_(2)receptors

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Science China(Life Sciences) 2024年第5期67卷 986-995页

作者： Yuan Weng Xinyu Yang Qiansen Zhang Ying Chen Yueming Xu Chenyu Zhu Qiong Xie Yonghui Wang Huaiyu Yang Mingyao Liu Weiqiang Lu Gaojie Song Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Department of Medicinal Chemistry School of PharmacyFudan UniversityShanghai 201203China

The adenosine subfamily G protein-coupled receptors A_(2A)R and A_(2B)R have been identified as promising cancer immunotherapy candidates.One of the A_(2A)R/A_(2B)R dual antagonists,AB928,has progressed to a phaseⅡclinical trial to treat rectal cancer.However,the precise mechanism underlying its dual-antagonistic properties remains elusive.Herein,we report crystal structures of the A_(2A)R complexed with AB928 and a selective A_(2A)R antagonist 2-118.The structures revealed a common binding mode on A_(2A)R,wherein the ligands established extensive interactions with residues from the orthosteric and secondary pockets.In contrast,the cAMP assay and A_(2A)R and A_(2B)R molecular dynamics simulations indicated that the ligands adopted distinct binding modes on A_(2B)R.Detailed analysis of their chemical structures suggested that AB928 readily adapted to the A_(2B)R pocket,while 2-118 did not due to intrinsic differences.This disparity potentially accounted for the difference in inhibitory efficacy between A_(2B)R and A_(2A)R.This study serves as a valuable structural template for the future development of selective or dual inhibitors targeting A_(2A)R/A_(2B)R for cancer therapy.

关键词： adenosine receptor A2AR A2BR inhibitor dual-antagonism Drug discovery

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A Nearly 20-Year Journey to Success of Azvudine for Antiviral Therapy

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Chinese Journal of Chemistry 2023年第23期41卷 3349-3357页

作者： Bin Yu Junbiao Chang College of Chemistry & School of Pharmaceutical Sciences Zhengzhou UniversityZhengzhouHenan450001 China Pingyuan Laboratory State Key Laboratory of Antiviral DrugsHenan Normal UniversityXinxiangHenan453007 China

Modified nucleosides,particularly those with 4'-modifications,are significant nucleosides used in antiviral treatments.The Drug discovery campaign of Azvudine starts from 2′-deoxynucleoside,followed by extensive modifications,such as introducing the 4’-position substitutions,a 2’-β-fluoro atom,and changing the nucleobases.Azvudine acts potently toward various HIV-1 strains by inhibiting HIV-1 reverse transcription and preventing Vif-induced A3G degradation,representing the first-in-class dual-acting antiviral agent.In July 2021,the NMPA conditionally approved Azvudine as an adjunct therapy for adult patients with high levels of HIV-1 virus load when combined with NRTIs or NNRTIs.Azvudine is capable of inhibiting SARS-CoV-2,as well as its variants,including Alpha,Beta,Delta,and Omicron.Clinical trials have revealed its real-world effectiveness among hospitalized severely or critically ill COVID-19 patients or those with pre-existing conditions.On July 25th,2022,the NMPA granted conditional authorization approving Azvudine as China's first domestic oral anti-COVID-19 agent.Generally,Azvudine at therapeutic doses is safe and well-tolerated in clinical settings.Azvudine got approval from the National Health Commission and National Administration of Traditional Chinese Medicine on August 9th to be used in the"Diagnosis and Treatment Program for Novel Coronavirus Pneumonia(Ninth Edition)"for treating common COVID-19 adult patients.On August 12th,2022,it was also approved by the National Healthcare Security Administration to be added to the list of medical reimbursements.Of note,the achievements related to Azvudine were indexed in the China Basic Research Development Report in Thirty-Five of 2022.Azvudine was also approved on January 5th,2023,to be used in the"Diagnosis and Treatment Program for Novel Coronavirus Pneumonia(Tenth Edition)"for treating COVID-19 patients.In February 2023,the Ministry of Health of the Russian Federation approved the usage of Azvudine among individuals infected with SARS-CoV-2.What is the mo

关键词： Nucleosides Azvudine HIV COVID-19 Antiviral agents Infectious diseases Drug discovery

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