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Novel progressive deep learning algorithm for uncovering multiple single nucleotide polymorphism interactions to predict paclitaxel clearance in patients with nonsmall cell lung cancer

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Cancer Innovation 2024年第4期3卷 13-25页

作者： Wei Chen Haiyan Zhou Mingyu Zhang Yafei Shi Taifeng Li Di Qian Jun Yang Feng Yu Guohui Li school of Basic Medicine and Clinical pharmacy China Pharmaceutical UniversityNanjingChina pharmacy Department National Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina

Background:The rate at which the anticancer drug paclitaxel is cleared from the body markedly impacts its dosage and chemotherapy ***,paclitaxel clearance varies among individuals,primarily because of genetic *** metabolic variability arises from a nonlinear process that is influenced by multiple single nucleotide polymorphisms(SNPs).Conventional bioinformatics methods struggle to accurately analyze this complex process and,currently,there is no established efficient algorithm for investigating SNP ***:We developed a novel machine‐learning approach called GEP‐CSIs data mining *** algorithm,an advanced version of GEP,uses linear algebra computations to handle discrete *** GEP‐CSI algorithm calculates a fitness function score based on paclitaxel clearance data and genetic polymorphisms in patients with nonsmall cell lung *** data were divided into a primary set and a validation set for the ***:We identified and validated 1184 three‐SNP combinations that had the highest fitness function ***,SERPINA1,ATF3 and EGF were found to indirectly influence paclitaxel clearance by coordinating the activity of genes previously reported to be significant in paclitaxel *** intriguing was the discovery of a combination of three SNPs in genes FLT1,EGF and *** SNPs‐related proteins were confirmed to interact with each other in the protein–protein interaction network,which formed the basis for further exploration of their functional roles and ***:We successfully developed an effective deep‐learning algorithm tailored for the nuanced mining of SNP interactions,leveraging data on paclitaxel clearance and individual genetic polymorphisms.

关键词： deep learning algorithm paclitaxel single nucleotide polymorphisms

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Computer-aided molecular design and optimization of potent inhibitors disrupting APC-Asef interaction

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Acta Pharmaceutica Sinica B 2024年第6期14卷 2631-2645页

作者： Xuefei Wang Zeqian Du Yuegui Guo Jie Zhong Kun Song Junyuan Wang Jianqiang Yu Xiuyan Yang Chen-Ying Liu Ting Shi Jian Zhang Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationShanghai Jiao Tong UniversitySchool of MedicineShanghai 200025China Key Laboratory of Protection Development and Utilization of Medicinal Resources in Liupanshan AreaMinistry of EducationPeptide&Protein Drug Research CenterSchool of PharmacyNingxia Medical UniversityYinchuan 750004China State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Department of Colorectal and Anal Surgery Xinhua HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China Basic Science Research center Base(pharmaceutical Science) Yantai UniversityYantai 264005China Medicinal Chemistry and bioinformatics center Shanghai Jiao Tong UniversitySchool of MedicineShanghai 200025China State Key Laboratory of pharmaceutical Biotechnology Nanjing UniversityNanjing 210023China

Colorectal cancer(CRC)is the second leading cause of cancer mortality *** initial diagnosis,approximately 20%of patients are diagnosed with metastatic CRC(mCRC).Although the APC-Asef interaction is a well-established target for mCRC therapy,the discovery and development of effective and safe drugs for mCRC patients remains an urgent and challenging *** this study,we identified a novel structural scaffold based on MAI inhibitors,the first-in-class APC-Asef inhibitors we reported *** model-driven optimizations of the N-terminal cap and experimental evaluations of inhibitory activity were performed,and 24-fold greater potency was obtained with the best inhibitor compared to the parental *** addition,the cocrystal structure validated that the two-layerπ-πstacking interactions were essential for inhibitor stabilization in the bound ***,in vitro and in vivo studies have demonstrated that novel inhibitors suppressed lung metastasis in CRC by disrupting the APC-Asef *** results provide an intrinsic structural basis to further explore drug-like molecules for APC-Asef-mediated CRC therapy.

关键词： APC-Asef Peptidomimetic Computer-aided molecular design ONIOM model π-πstacking Metastatic colorectal cancer

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Glycodiversification of gentamicins through in vivo glycosyltransferase swapping enabled the creation of novel hybrid aminoglycoside antibiotics with potent activity and low ototoxicity

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Acta Pharmaceutica Sinica B 2024年第9期14卷 4149-4163页

作者： Xinyun Jian Cheng Wang Shijuan Wu Guo Sun Chuan Huang Chengbing Qiu Yuanzheng Liu Peter FLeadlay Dong Liu Zixin Deng Fuling Zhou Yuhui Sun Department of Hematology Zhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan 430071China Key Laboratory of Combinatorial Biosynthesis and Drug Discovery(Ministry of Education) Wuhan UniversityWuhan 430071China school of pharmacy Huazhong University of Science and TechnologyWuhan 430030China school of life sciences Co-Innovation Center of NeuroregenerationNantong Laboratory of Development and DiseasesNantong UniversityNantong 226019China Department of Biochemistry University of CambridgeCambridge CB21GAUK Department of Biochemistry and Molecular Biology Biomedicine Discovery InstituteMonash UniversityClayton VIC 3800Australia ARC Centre of excellence for Innovations in Protein and Peptide Science Monash UniversityClayton VIC 3800Australia

Aminoglycosides(AGs)are a class of antibiotics with a broad spectrum of ***,their use is limited by safety concerns associated with nephrotoxicity and ototoxicity,as well as drug *** address these issues,semi-synthetic approaches for modifying natural AGs have generated new generations of AGs,however,with limited types of modification due to significant challenges in *** study explores a novel approach that harness the bacterial biosynthetic machinery of gentamicins and kanamycins to create hybrid *** was achieved by glycodiversification of gentamicins via swapping the glycosyltransferase(GT)in their producer with the GT from kanamycins biosynthetic pathway and resulted in the creation of a series of novel AGs,therefore referred to as genkamicins(GKs).The manipulation of the hybrid biosynthetic pathway enabled the targeted accumulation of different GK species and the isolation and characterization of six GK *** compounds display retained antimicrobial activity against a panel of World Health Organization(WHO)critical priority pathogens,and GK-C2a,in particular,demonstrates low ototoxicity compared to clinical drugs in zebrafish *** study provides a new strategy for diversifying the structure of AGs and a potential avenue for developing less toxic AG drugs to combat infectious diseases.

关键词： Antibiotic Aminoglycoside biosynthesis Biosynthetic engineering Ototoxicity

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Hydrogen sulfide responsive nanoplatforms: Novel gas responsive drug delivery carriers for biomedical applications

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Asian Journal of pharmaceutical sciences 2024年第1期19卷 1-17页

作者： Jiafeng Zou Zeting Yuan Xiaojie Chen You Chen Min Yao Yang Chen Xiang Li Yi Chen Wenxing Ding Chuanhe Xia Yuzheng Zhao Feng Gao Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism School of PharmacyEast China University of Science and TechnologyShanghai 200237China Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province School of Pharmaceutical SciencesZhejiang Chinese Medical UniversityHangzhou 310053China Shanghai Key Laboratory of Functional Materials Chemistry East China University of Science and TechnologyShanghai 200237China Shanghai Key Laboratory of New Drug Design School of PharmacyEast China University of Science and TechnologyShanghai 200237China Optogenetics and Synthetic Biology Interdisciplinary Research center State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghai 200237China CAS center for excellence in Brain Science Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China Research Unit of New Techniques for Live-cell Metabolic Imaging Chinese Academy of Medical SciencesBeijing 100050China

Hydrogen sulfide(H_(2)S)is a toxic,essential gas used in various biological and physical processes and has been the subject of many targeted studies on its role as a new gas *** studies have mainly focused on the production and pharmacological side effects caused by H_(2)***,effective strategies to remove H_(2)S has become a key research ***,the development of novel nanoplatforms has provided new tools for the targeted removal of H_(2)*** paper was performed to review the association between H_(2)S anddisease,relatedH_(2)S inhibitory drugs,aswell as H_(2)S responsive nanoplatforms(HRNs).This review first analyzed the role of H_(2)S in multiple tissues and ***,common drugs used to eliminate H_(2)S,as well as their potential for combination with anticancer agents,were *** only the existing studies on HRNs,but also the inhibition H_(2)S combined with different therapeutic methods were both sorted out in this ***,this review provided in-depth analysis of the potential of HRNs about treatment or detection in ***,potential challenges of HRNs were *** study demonstrates the excellent potential of HRNs for biomedical applications.

关键词： Hydrogen sulfide Disease mechanisms Removal of hydrogen sulfide Responsive nanoplatforms Challenges Biomedical applications

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Gene-knockout by iSTOP enables rapid reproductive disease modeling and phenotyping in germ cells of the founder generation

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Science China(life sciences) 2024年第5期67卷 1035-1050页

作者： Yaling Wang Jingwen Chen Xueying Huang Bangguo Wu Peng Dai Feng Zhang Jinsong Li Lingbo Wang State Key Laboratory of Genetic Engineering Shanghai Key Laboratory of Metabolic Remodeling and HealthInstitute of Metabolism and Integrative BiologyFudan UniversityShanghai 200438China Institute of Reproduction and Development Obstetrics and Gynecology HospitalFudan UniversityShanghai 200011China NHC Key Lab of Reproduction Regulation(Shanghai Institute for Biomedical and pharmaceutical Technologies) School of PharmacyFudan UniversityShanghai 200433China Shanghai Key Laboratoryof Maternal and Fetal Medicine Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalFrontier Science Center for Stem Cell ResearchSchoolof Life Sciences and TechnologyTongji UniversityShanghai 200092China State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai 200031China

Cytosine base editing achieves C·G-to-T·A substitutions and can convert four codons(CAA/CAG/CGA/TGG)into STOP-codons(induction of STOP-codons,iSTOP)to knock out genes with reduced *** enables direct phenotyping in founders’somatic cells,but it remains unknown whether this works in founders’germ cells so as to rapidly reveal novel genes for ***,we initially establish that iSTOP in mouse zygotes enables functional characterization of known genes in founders’germ cells:Cfap43-iSTOP male founders manifest expected sperm features resembling human“multiple morphological abnormalities of the flagella”syndrome(i.e.,MMAF-like features),while oocytes of Zp3-iSTOP female founders have no zona *** further illustrate iSTOP’s utility for dissecting the functions of unknown genes with Ccdc183,observing MMAF-like features and male infertility in Ccdc183-iSTOP founders,phenotypes concordant with those of Ccdc183-KO *** ultimately establish that CCDC183 is essential for sperm morphogenesis through regulating the assembly of outer dynein arms and participating in the intra-flagellar *** study demonstrates iSTOP as an efficient tool for direct reproductive disease modeling and phenotyping in germ cells of the founder generation,and rapidly reveals the essentiality of Ccdc183 in fertility,thus providing a time-saving approach for validating genetic defects(like nonsense mutations)for human infertility.

关键词： disease modeling infertility multiple morphological abnormalities of the flagella(MMAF) induction of STOP-codons(iSTOP CRISPR-STOP) sperm motility

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The chromosome-scale assembly of the Notopterygium incisum genome provides insight into the structural diversity of coumarins

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Acta Pharmaceutica Sinica B 2024年第8期14卷 3760-3773页

作者： Qien Li Yiqun Dai Xin-Cheng Huang Lanlan Sun Kaixuan Wang Xiao Guo Dingqiao Xu Digao Wan Latai An Zixuan Wang Huanying Tang Qi Qi Huihui Zeng Minjian Qin Jia-Yu Xue Yucheng Zhao Tibetan Medicine Research center of Qinghai University Tibetan Medical CollegeQinghai UniversityXining 810016China school of pharmacy Bengbu Medical UniversityBengbu 233030China Department of Resources Science of Traditional Chinese Medicines School of Traditional Chinese PharmacyChina Pharmaceutical UniversityNanjing 210009China College of Horticulture Bioinformatics CenterAcademy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility Shaanxi University of Chinese MedicineXi’an 712046China

Coumarins,derived from the phenylpropanoid pathway,represent one of the primary metabolites found in *** alignment of the tetrahydropyran(THP)and tetrahydrofuran(THF)rings with the lactone structure results in the formation of at least four types of complex ***,the mechanisms underlying the structural diversity of coumarin remain poorly ***,we report the chromosome-level genome assembly of Notopterygium incisum,spanning 1.64 Gb,with a contig N50 value of 22.7 Mb and 60,021 annotated protein-coding ***,we identified the key enzymes responsible for shaping the structural diversity of coumarins,including two p-coumaroyl CoA 2′-hydroxylases crucial for simple coumarins basic skeleton architecture,two UbiA prenyltransferases responsible for angular or linear coumarins biosynthesis,and five CYP736 cyclases involved in THP and THF ring ***,two bifunctional enzymes capable of catalyzing both demethylsuberosin and osthenol were identified for the first *** analysis implies that tandem and ectopic duplications of the CYP736 subfamily,specifically arising in the Apiaceae,contributed to the structural diversity of coumarins in ***,this study proposes a parallel evolution scenario for the complex coumarin biosynthetic pathway among different angiosperms and provides essential synthetic biology elements for the heterologous industrial production of coumarins.

关键词： Notopterygium incisum Parallel evolution Biosynthesis Pyranocoumarins Furanocoumarins

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Exosomes derived from tumor adjacent fibroblasts efficiently target pancreatic tumors

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Acta Pharmaceutica Sinica B 2024年第7期14卷 3009-3026页

作者： Saini Setua Shabia Shabir Poornima Shaji Ana Martinez Bulnes Anupam Dhasmana Swathi Holla Nivesh K.Mittal Nirakar Sahoo Tripti Saini Francesco Giorgianni Mohammad Sikander Andrew E.Massey Bilal B.Hafeez Manish K.Tripathi Vincent P.Diego Meena Jaggi Junming Yue Nadeem Zafar Murali M.Yallapu Stephen W.Behrman Sheema Khan Subhash C.Chauhan Department of pharmaceutical sciences College of Pharmacyand College of MedicineUniversity of Tennessee Health Science Center(UTHSC)MemphisTN 36163USA Department of Computer Science Islamic University of Science and TechnologyAwantiporaJ&K 192122India Department of Immunology and Microbiology School of MedicineUniversity of Texas Rio Grande ValleyMcAllenTX 78504USA South Texas center of excellence in Cancer Research School of Medicinethe University of Texas Rio Grande ValleyMcAllenTX 78504USA Himalayan school of Biosciences and Cancer Research Institute Himalayan Institute of Medical SciencesSwami Rama Himalayan UniversityDehradun 248016India Plough center for Sterile Drug Delivery Solutions UTHSCMemphisTN 38104USA Department of Biology College of SciencesUTRGVMcAllenTX 78539USA National Institute of Biomedical Imaging and Bioengineering(NIBIB) National Institutes of HealthBethesdaMD 20892USA South Texas Diabetes and Obesity Institute UTRGVMcAllenTX 78504USA Dept.of Laboratory Medicine&Pathology University of WashingtonSeattleWA 98195USA Department of Surgery Baptist Memorial Medical EducationBaptist Memorial HospitalMemphisTN 38120USA Baptist Health sciences University MemphisTN 38104USA

The application of extracellular vesicles,particularly exosomes(EXs),is rapidly expanding in the field of medicine,owing to their remarkable properties as natural carriers of biological *** study investigates utilization of exosomes derived from stromal cells of tumor adjacent normal tissues(NAF-EXs)for personalized medicine,which can be derived at the time of diagnosis by endoscopic ***,we show that exosomes(EXs)derived from NAFs demonstrate differential bio-physical characteristics,efficient cellular internalization,drug loading efficiency,pancreatic tumor targeting and delivery of ***-derived EXs(NAF-EXs)were used for loading ormeloxifene(ORM),a potent anti-cancer and desmoplasia inhibitor as a model *** found that ORM maintains normal fibroblast cell phenotype and renders them incompatible to be triggered for a CAF-like phenotype,which may be due to regulation of Ca^(2+) influx in fibroblast ***-EXs-ORM effectively blocked oncogenic signaling pathways involved in desmoplasia and epithelial mesenchymal transition(EMT)and repressed tumor growth in xenograft mouse *** conclusion,our data suggests preferential tropism of NAF-EXs for PDAC tumors,thus imply feasibility of developing a novel personalized medicine for PDAC patients using autologous NAF-EXs for improved therapeutic outcome of anti-cancer ***,it provides the opportunity of utilizing this biological scaffold for effective therapeutics in combination with standard therapeutic regimen.

关键词： Pancreatic cancer Tumor adjacent normal tissue fibroblasts(NAF) Desmoplasia Extracellular vesicles Exosomes Tumor targeting Ormeloxifene Personalized medicine

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Integrated approach of network pharmacology and chemometrics for quality control of Chinese patent medicine:A case study on Huo-Luo-San

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Journal of Chinese pharmaceutical sciences 2024年第9期33卷 819-836页

作者： Meiling Zhu Jirong Zhang Qiurong Zhang Yu Lin Xiaoyan Li Wen Xu Wei Xu College of pharmacy Fujian University of Traditional Chinese MedicineFuzhou 350122FujianChina center for excellence in Molecular Cell Science Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai 200031China Innovation and Transformation center of Science and Technology Fujian University of Traditional Chinese MedicineFuzhou 350122FujianChina

Traditional Chinese medicine(TCM)has garnered significant global interest owing to its multi-component and multi-target theoretical framework and extensive therapeutic ***,the identification of quality markers(Q-markers)remains a formidable challenge in ***,this study aimed to integrate network pharmacology and chemometrics to identify Q-markers in Chinese patent medicine,with a focus on Huo-Luo-San(HLS)as a case ***,a widely used powdered Chinese patent medicine in China,comprises a complex formula of 10 herbs,initially formulated during the Qing dynasty for treating ***,13 components,chlorogenic acid,typhaneoside,isorhamnetin-3-O-neohesperidoside,cynaroside,notoginsenoside R_1,ginsenoside Rg_1,baicalin,berberine hydrochloride,ginsenoside Rb_1,dehydrocostus lactone,dioscin,imperatorin,and costunolide,were selected as phytochemical markers for each herb based on the Chinese Pharmacopoeia(2020 version),forming the“Herbs-Compounds-targets”network of HLS using network ***,employing network pharmacology,the 13 HLS components were quantified using *** conditions were optimized on a Waters Cortecs C_(18)column(2.1 mm×100 mm,1.6μm)with a gradient elution comprising 0.1%formic acid in water and *** detection was performed in the multiple-reaction monitoring mode,and the method underwent validation for linearity,detection limit,precision,repeatability,stability,and *** validated method was then utilized to analyze the 13 components in 15 batches of HLS *** techniques,including hierarchical cluster analysis,principal component analysis,orthogonal partial least squares projection discriminant analysis,and box map analyses,were subsequently employed to identify the ***,six components,baicalin,notoginsenoside R_1,berberine hydrochloride,dioscin,imperatorin,and chlorogenic acid,were selected as Q-markers for *** integration of netwo

关键词： Traditional Chinese medicine Quality markers Huo-Luo-San Network pharmacology Chemometrics

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Integrated proteomic profiling identifies amino acids selectively cytotoxic to pancreatic cancer cells

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The Innovation 2024年第3期5卷 138-145页

作者： Alfred Akinlalu Zachariah Flaten Komila Rasuleva Md Saimon Mia Aaron Bauer Santhalingam Elamurugan Nega Ejjigu Sudipa Maity Amara Arshad Min Wu Wenjie Xia Jia Fan Ang Guo Sijo Mathew Dali Sun Department of Electrical and Computer Engineering University of Denver2155 E Wesley AvenueDenverCO 80210USA Biomedical Engineering Program North Dakota State University1401 Centennial BoulevardEngineering AdministrationRoom 203FargoND 58102USA Department of pharmaceutical sciences School of PharmacyNorth Dakota State University1001 S.1401 Albrecht Boulevard Sudro HallFargoND 58102USA Materials and Nanotechnology Program North Dakota State University1410 North 14th AvenueCIE 201FargoND 58102USA Wenzhou Institute University of Chinese Academy of SciencesWenzhouZhejiang 325000China Department of Aerospace Engineering Iowa State UniversityAmesIA 50011USA center for Cellular and Molecular Diagnostics Tulane University School of Medicine1430 Tulane AvenueNew OrleansLA 70112USA Department of Biochemistry and Molecular Biology Tulane University School of Medicine1430 Tulane AvenueNew OrleansLA 70112USA Knoebel Institute for Healthy Aging University of Denver2155 E Wesley AvenueDenverCO 80210USA

Pancreatic adenocarcinoma(PDAC)is one of the most deadly cancers,characterized by extremely limited therapeutic options and a poor prognosis,as it is often diagnosed during late disease *** and selective treatments are urgently needed,since current therapies have limited efficacy and significant side *** proteomics analysis of extracellular vesicles,we discovered an imbalanced distribution of amino acids secreted by PDAC tumor *** findings revealed that PDAC cells preferentially excrete proteins with certain preferential amino acids,including isoleucine and histidine,via extracellular *** amino acids are associated with disease progression and can be targeted to elicit selective toxicity to PDAC tumor *** in vitro and in vivo experiments demonstrated that supplementation with these specific amino acids effectively eradicated PDAC ***,we also identified XRN1 as a potential target for these amino *** high selectivity of this treatment method allows for specific targeting of tumor metabolism with very low toxicity to normal ***,we found this treatment approach is easy-to-administer and with sustained tumor-killing ***,our findings reveal that exocytosed amino acids may serve as therapeutic targets for designing treatments of intractable PDAC and potentially offer alternative treatments for other types of cancers.

关键词： finding identif selectivity

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Identification of microRNA-like RNAs in Ophiocordyceps sinensis

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Science China(life sciences) 2019年第3期62卷 349-356页

作者： Wen Zhang Xiaona Li Lina Ma Uzair Urrehman Xilinqiqige Bao Yujing Zhang Chen-Yu Zhang Dongxia Hou Zhen Zhou State Key Laboratory of pharmaceutical Biotechnology Jiangsu Engineering Research Center for microRNA Biology and Biotechnology NJU Advanced Institute for Life Sciences (NAILS) School of Life Sciences Nanjing University The Drug Laboratory of Mongolian Medicine and Pharmacy Institute Inner Mongolia International Mongolian Hospital

Ophiocordyceps sinensis is well known as a traditional Chinese medicine and has widely been used for over 2,000 years to stimulate immune system, decrease blood pressure and to inhibit tumor growth. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less studied until the discovery of microRNA-like RNA(milRNA). High-throughput sequencing and bioinformatics approaches were used to identify conserved and novel milRNAs in O. sinensis. 40 conserved milRNAs were identified, while 23 pre-miRNA candidates encoding 31 novel milRNAs were predicted. Furthermore, the potential target genes of milRNAs in human were predicted and gene ontology analysis was applied to these genes. Enrichment analysis of GO-represented biological process showed that target genes of both conserved and novel milRNAs are involved in development, metabolic and immune processes, indicating the potential roles of milRNAs of O. sinensis in pharmacological effects as health food and traditional Chinese medicine. This study is the first report on genome-wide analysis of milRNAs in O. sinensis and it provides a useful resource to further study the potential roles of milRNAs as active components of O. sinensis in health food or traditional Chinese medicine.

关键词： Ophiocordyceps sinensis O.sinensis miRNA milRNA high-throughput sequencing

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