Article(id=1195687995278934923, tenantId=1146029695717560320, journalId=1190317699101192196, issueId=1195707415279747621, articleNumber=1001-2494(2024)03-0249-07, orderNo=null, doi=10.11669/cpj.2024.03.008, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1689782400000, receivedDateStr=2023-07-20, revisedDate=null, revisedDateStr=null, acceptedDate=null, acceptedDateStr=null, onlineDate=1763003832883, onlineDateStr=2025-11-13, pubDate=1707321600000, pubDateStr=2024-02-08, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1763008464047, onlineIssueDateStr=2025-11-13, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=1763003832883, onlineFirstDateStr=2025-11-13, sourceXml=null, magXml=null, createTime=1763003832883, creator=13701087609, updateTime=1763003832883, updator=13701087609, issue=Issue{id=1195707415279747621, tenantId=1146029695717560320, journalId=1190317699101192196, year='2024', volume='59', issue='3', pageStart='193', pageEnd='284', issueExtLink='null', onlineDate='null', pubDate='1707321600000', pubDateStr='2024-02-08', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1763008462972, creator='13701087609', updateTime=1763009150406, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1195710298666611616, tenantId=1146029695717560320, journalId=1190317699101192196, issueId=1195707415279747621, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1195710298670805921, tenantId=1146029695717560320, journalId=1190317699101192196, issueId=1195707415279747621, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=249, endPage=255, ext={EN=ArticleExt(id=1195687995471872911, articleId=1195687995278934923, tenantId=1146029695717560320, journalId=1190317699101192196, language=EN, title=Text-Convolutional Neural Network-based Discovery of Antibacterial Agents, columnId=null, journalTitle=Chinese Pharmaceutical Journal, columnName=null, runingTitle=null, highlight=null, articleAbstract=

OBJECTIVE To build a text-convolutional neural network(Text-CNN)-based prediction model for anti-Staphylococcus aureus(S.aureus) activity and identify anti-S.aureus hits by virtual screening. OBJECTIVE A dataset containing 26327 compounds annotated with S.aureus activity data was collected and curated from the ChEMBL database. Ten pairs of training and test sets were generated by random partition for 10 times and then 10 models were built using the Text-CNN algorithm. The best-performing model was determined by model evaluation and further studied by Y-randomization test and applicability domain analysis. Following that, the best-performing model was used to virtually screen the in-house chemical library, by which the potential antibacterial agents were determined. The micro-broth dilution method was used to test anti-S.aureus activity of the potential hits. RESULTS The machine-learning model(named Text-CNN3) performed well in classification. Evaluated on the test set, its Mathews correlation coefficient was 0.573 and the area under the ROC curve was 0.881. With this model for virtual screening as well as antibacterial screening, compounds Y5 and Y7 were identified as antibacterial compounds, with minimum inhibitory concentrations(MIC) of 8 and 4 μg·mL-1, respectively. CONCLUSION The Text-CNN3 model in this study is effective to identify anti-S.aureus compounds, while the antibacterial hits Y5 and Y7 are worthy of further study.

, authors=null, authorsList=YAO Mingli, GAO Dingjia, ZHANG Jie, LI Shan, WU Song, SI Xinxin, XIA Jie, authorCompany=null, correspAuthors=SI Xinxin, XIA Jie, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1195688630502080822, articleId=1195687995278934923, tenantId=1146029695717560320, journalId=1190317699101192196, language=CN, title=基于文本卷积神经网络模型的抗菌药物发现, columnId=1190352405612040510, journalTitle=中国药学杂志, columnName=论著, runingTitle=null, highlight=null, articleAbstract=

目的 基于文本卷积神经网络(Text-Convolutional Neural Network, Text-CNN)算法,构建抗金黄色葡萄球菌(Staphylococcus aureus)活性的预测模型,通过虚拟筛选发现具有抑制S. aureus活性的苗头化合物。方法 从ChEMBL 数据库中收集并整理了 26327个标注有S.aureus活性数据的化合物,通过随机采样建立10 组训练集和测试集,采用 Text-CNN算法建立10个模型,通过模型评估选择性能最佳的模型,对该模型进行Y-随机化检验和应用域分析。使用该模型虚拟筛选内部化合物库,确定潜在的抗菌化合物,并采用微量肉汤稀释法测定化合物的抗S.aureus活性。结果 名为Text-CNN3的机器学习模型具有良好的分类性能,该模型对于测试集的马修斯相关系数为 0.573,ROC 曲线下面积为 0.881。基于该模型的虚拟筛选和抗菌活性测试,发现了两个抗菌活性化合物 Y5 和 Y7,其对S.aureus的最低抑菌浓度(minimal inhibitory concentration,MIC)分别为8和 4 μg·mL-1结论 本研究建立的Text-CNN3模型可有效发现抗S.aureus化合物,所发现的苗头化合物Y5 和 Y7有进一步研究的意义和价值。

, authors=

姚明丽,女,硕士研究生 研究方向:分子信息学与药物设计

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*司鑫鑫,女,博士,副教授 研究方向:分子药理学;
夏杰,男,博士,副研究员 研究方向:分子信息学与药物设计
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姚明丽,女,硕士研究生 研究方向:分子信息学与药物设计

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姚明丽,女,硕士研究生 研究方向:分子信息学与药物设计

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A-distribution of pairwise structural similarity(Tanimoto coefficient, Tc) based on the Morgan2 fingerprints; B-the Matthews correlation coefficient(MCC) and the area under the receiver operating characteristic curve(ROC AUC) of 10 text-CNN models evaluated on test sets.

, figureFileSmall=X3V3cfOxZPTSQ5eSXsyt/A==, figureFileBig=scUVnobUrrhcvfqY/+F/2w==, tableContent=null), ArticleFig(id=1197101867525255828, tenantId=1146029695717560320, journalId=1190317699101192196, articleId=1195687995278934923, language=CN, label=图3, caption=金黄色葡萄球菌建模数据集及模型的分类性能

A-基于Morgan2指纹的两两结构相似度(Tanimoto系数,Tc)分布;B-10个Text-CNN模型在测试集上的评估分类性能:马修斯相关系数(MCC)和受试者工作特征曲线下面积(ROC AUC)。

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The hyperparameters of each model and classification performance on the test set

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Models Hyperparameters SE SP MCC AUC
Batch
size
Dropout
rate
Learning
rate
Text-CNN0 64 0.1 0.000 1 0.849 0.732 0.564 0.878
Text-CNN1 64 0.1 0.000 1 0.953 0.439 0.485 0.863
Text-CNN2 64 0.1 0.000 1 0.889 0.640 0.545 0.867
Text-CNN3 32 0.1 0.000 1 0.900 0.652 0.573 0.881
Text-CNN4 32 0.1 0.000 1 0.833 0.751 0.561 0.879
Text-CNN5 128 0.1 0.001 0.835 0.742 0.559 0.865
Text-CNN6 64 0.1 0.000 1 0.903 0.635 0.564 0.871
Text-CNN7 32 0.1 0.000 1 0.881 0.694 0.582 0.878
Text-CNN8 32 0.1 0.000 1 0.905 0.616 0.551 0.868
Text-CNN9 32 0.1 0.000 1 0.879 0.673 0.557 0.876
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每个模型的超参数和在测试集上的性能指标

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Models Hyperparameters SE SP MCC AUC
Batch
size
Dropout
rate
Learning
rate
Text-CNN0 64 0.1 0.000 1 0.849 0.732 0.564 0.878
Text-CNN1 64 0.1 0.000 1 0.953 0.439 0.485 0.863
Text-CNN2 64 0.1 0.000 1 0.889 0.640 0.545 0.867
Text-CNN3 32 0.1 0.000 1 0.900 0.652 0.573 0.881
Text-CNN4 32 0.1 0.000 1 0.833 0.751 0.561 0.879
Text-CNN5 128 0.1 0.001 0.835 0.742 0.559 0.865
Text-CNN6 64 0.1 0.000 1 0.903 0.635 0.564 0.871
Text-CNN7 32 0.1 0.000 1 0.881 0.694 0.582 0.878
Text-CNN8 32 0.1 0.000 1 0.905 0.616 0.551 0.868
Text-CNN9 32 0.1 0.000 1 0.879 0.673 0.557 0.876
), ArticleFig(id=1197101868158595739, tenantId=1146029695717560320, journalId=1190317699101192196, articleId=1195687995278934923, language=EN, label=Tab.2, caption=

Performance and hyperparameters of three models trained in Y-randomization tests

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Models Hyperparameters SE SP MCC AUC
batch
size
dropout
rate
learning
rate
M1 64 0.3 0.001 1.000 0.000 -0.009 0.509
M2 32 0.1 0.001 0.999 0.000 -0.016 0.478
M3 64 0.2 0.01 1.000 0.000 0.000 0.506
), ArticleFig(id=1197101868208927388, tenantId=1146029695717560320, journalId=1190317699101192196, articleId=1195687995278934923, language=CN, label=表2, caption=

Y-随机化检验中建立的模型的性能和超参数

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Models Hyperparameters SE SP MCC AUC
batch
size
dropout
rate
learning
rate
M1 64 0.3 0.001 1.000 0.000 -0.009 0.509
M2 32 0.1 0.001 0.999 0.000 -0.016 0.478
M3 64 0.2 0.01 1.000 0.000 0.000 0.506
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The structures of potential hit compounds and in vitro anti-S. aureus(ATCC29213) activity

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ID Chemical
structure
MIC
/μg·mL-1
Y1 >32
Y2 >32
Y3 >32
Y4 >32
Y5 8
Y6 >32
Y7 4
Y8 >32
Y9 >32
Levofloxacin 0.015
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潜在的苗头化合物的结构及体外抗S.aureus(ATCC29213) 活性

, figureFileSmall=null, figureFileBig=null, tableContent=
ID Chemical
structure
MIC
/μg·mL-1
Y1 >32
Y2 >32
Y3 >32
Y4 >32
Y5 8
Y6 >32
Y7 4
Y8 >32
Y9 >32
Levofloxacin 0.015
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基于文本卷积神经网络模型的抗菌药物发现
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姚明丽 1 , 高丁佳 2 , 张洁 3 , 李珊 2 , 吴松 3 , 司鑫鑫 1, * , 夏杰 3, *
中国药学杂志 | 论著 2024,59(3): 249-255
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中国药学杂志 |论著 2024 , 59 (3) : 249 -255
基于文本卷积神经网络模型的抗菌药物发现
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姚明丽1, 高丁佳2, 张洁3, 李珊2, 吴松3, 司鑫鑫1, *, 夏杰3, *
作者信息
  • 1 江苏海洋大学药学院, 江苏 连云港 222005
  • 2 南京航空航天大学经济与管理学院, 南京 210016
  • 3 中国医学科学院北京协和医学院药物研究所, 北京 100050
通讯作者:
*司鑫鑫,女,博士,副教授 研究方向:分子药理学;
夏杰,男,博士,副研究员 研究方向:分子信息学与药物设计
Text-Convolutional Neural Network-based Discovery of Antibacterial Agents
YAO Mingli1, GAO Dingjia2, ZHANG Jie3, LI Shan2, WU Song3, SI Xinxin1, *, XIA Jie3, *
Affiliations
  • 1 School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
  • 2 School of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
  • 3 Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China
出版时间: 2024-02-08 doi: 10.11669/cpj.2024.03.008
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目的 基于文本卷积神经网络(Text-Convolutional Neural Network, Text-CNN)算法,构建抗金黄色葡萄球菌(Staphylococcus aureus)活性的预测模型,通过虚拟筛选发现具有抑制S. aureus活性的苗头化合物。方法 从ChEMBL 数据库中收集并整理了 26327个标注有S.aureus活性数据的化合物,通过随机采样建立10 组训练集和测试集,采用 Text-CNN算法建立10个模型,通过模型评估选择性能最佳的模型,对该模型进行Y-随机化检验和应用域分析。使用该模型虚拟筛选内部化合物库,确定潜在的抗菌化合物,并采用微量肉汤稀释法测定化合物的抗S.aureus活性。结果 名为Text-CNN3的机器学习模型具有良好的分类性能,该模型对于测试集的马修斯相关系数为 0.573,ROC 曲线下面积为 0.881。基于该模型的虚拟筛选和抗菌活性测试,发现了两个抗菌活性化合物 Y5 和 Y7,其对S.aureus的最低抑菌浓度(minimal inhibitory concentration,MIC)分别为8和 4 μg·mL-1结论 本研究建立的Text-CNN3模型可有效发现抗S.aureus化合物,所发现的苗头化合物Y5 和 Y7有进一步研究的意义和价值。

金黄色葡萄球菌  /  文本卷积神经网络  /  活性预测  /  最低抑菌浓度

OBJECTIVE To build a text-convolutional neural network(Text-CNN)-based prediction model for anti-Staphylococcus aureus(S.aureus) activity and identify anti-S.aureus hits by virtual screening. OBJECTIVE A dataset containing 26327 compounds annotated with S.aureus activity data was collected and curated from the ChEMBL database. Ten pairs of training and test sets were generated by random partition for 10 times and then 10 models were built using the Text-CNN algorithm. The best-performing model was determined by model evaluation and further studied by Y-randomization test and applicability domain analysis. Following that, the best-performing model was used to virtually screen the in-house chemical library, by which the potential antibacterial agents were determined. The micro-broth dilution method was used to test anti-S.aureus activity of the potential hits. RESULTS The machine-learning model(named Text-CNN3) performed well in classification. Evaluated on the test set, its Mathews correlation coefficient was 0.573 and the area under the ROC curve was 0.881. With this model for virtual screening as well as antibacterial screening, compounds Y5 and Y7 were identified as antibacterial compounds, with minimum inhibitory concentrations(MIC) of 8 and 4 μg·mL-1, respectively. CONCLUSION The Text-CNN3 model in this study is effective to identify anti-S.aureus compounds, while the antibacterial hits Y5 and Y7 are worthy of further study.

Staphylococcus aureus  /  Text-CNN  /  activity prediction  /  minimum inhibitory concentration
姚明丽, 高丁佳, 张洁, 李珊, 吴松, 司鑫鑫, 夏杰. 基于文本卷积神经网络模型的抗菌药物发现. 中国药学杂志, 2024 , 59 (3) : 249 -255 . DOI: 10.11669/cpj.2024.03.008
YAO Mingli, GAO Dingjia, ZHANG Jie, LI Shan, WU Song, SI Xinxin, XIA Jie. Text-Convolutional Neural Network-based Discovery of Antibacterial Agents[J]. Chinese Pharmaceutical Journal, 2024 , 59 (3) : 249 -255 . DOI: 10.11669/cpj.2024.03.008
抗生素耐药性(antibiotic resistance)给人类健康带来巨大威胁,WHO 已经将其列为全球公共卫生的严重威胁之一。当前,抗生素耐药性逐步演变成了抗生素危机,全球每年有70万人死于该危机[1-2]。据推测,如果在抗生素研发方面没有显著进展,预计到2050年每年将有1 000万人死亡[3]。为应对抗生素耐药性,新药研发至关重要。众所周知,抗菌药物的研发是一个周期长、耗资高且成功率低的过程[4]。近 20 年来,全球范围内获批上市的抗菌药物品种仅有三种新结构类型,即恶唑烷酮类(如利奈唑胺)、脂肽类(如达托霉素)、截短侧耳素类(如瑞他莫林)。其余上市的抗菌药物(如非达霉素、康替唑胺、苹果酸奈诺沙星)和正处于临床开发阶段的抗菌药物中,大部分药物属于以上类型或者临床使用的抗菌药物的衍生物[5]。相同类型的抗生素易产生交叉耐药,无法从根本上克服抗生素耐药性,因此亟需发现新结构类型的抗菌药物。
虚拟筛选技术是快速发现新结构类型的抗菌药物先导结构的有效手段。近年来,随着人工智能技术的快速发展,越来越多的研究人员开始采用该技术方法建立抗菌活性预测模型并开展虚拟筛选研究[6-9],发现了多个抗菌化合物(图1)。比如,Wang等[6]使用朴素贝叶斯、支持向量机、递归拆分和k-最近邻法,基于理化性质描述符和分子指纹构建了近千个机器学习模型,并将性能最佳的模型应用于抗金黄色葡萄球菌(Staphylococcus aureus)化合物的虚拟筛选,并发现化合物C1和C2对S.aureus表现出较好的抗菌活性,其最低抑菌浓度(minimal inhibitory concentration,MIC)范围4~16 μg·mL-1。Stokes等[7]采用有向消息传递深度神经网络(directed message passing nerural network, D-MPNN)建立了抗菌活性预测模型,并对ZINC15化合物库进行预测和筛选,发现了具有抗S.aureus活性的化合物C3和C4,其MIC分别为 2和 0.25 μg·mL-1
2014年,Kim等[10]首次提出文本卷积神经网络(text-convolutional neural network,Text-CNN)算法并将其运用到文本分类任务中,取得了较好的应用效果。Text-CNN算法的出现,使得将药物分子的简化分子线性输入规范(simplified molecular input line entry system,SMILES)表示作为输入建立活性预测模型成为可能。文献检索结果表明,目前还没有采用Text-CNN模型进行虚拟筛选并发现抗菌化合物的报道。基于此,本研究通过收集标注有S.aureus活性数据的化合物,对数据进行预处理后,采用Text-CNN算法构建了10个Text-CNN模型,随后通过模型评价确定性能最佳模型用于虚拟筛选,并进行体外抗菌活性测试,发现了具有抗S.aureus活性的苗头化合物。
从ChEMBL 29数据库(https://www.ebi.ac.uk/chembl/)下载标注有S.aureus最低抑菌浓度的化学生物学数据102,891条。使用RDKit(2019.09.3版)和MolVS(0.1.1版)去盐、中和、SMILES标准化[11]。仅保留具有确切MIC值的化合物,同一个化合物若存在多条MIC数据则取其平均值。根据类药性( drug-likeness) 原则,仅保留相对分子质量不大于600且可旋转键不多于20的化合物。根据MIC值是否小于32 μg·mL-1,将化合物标记为活性化合物和非活性化合物。随机抽取 80% 数据作为训练集,另外 20%数据作为测试集。该随机拆分过程重复10次,获得 10 对训练集和测试集。
化合物结构采用SMILES表示,随后对SMILES进行原子级分词(atom-level tokenization)提取词元(token)。具体操作包括:①将多字符元素符号(例如“Cl”及“Br”)视为单独的词元;②将用方括号表示的特殊符号(例如[O-]、[nH]等)也视为词元;③将剩余单个字符的原子视为词元。
首先,对ChEMBL数据集内的小分子化合物进行原子级分词,共得到256个词元并构成分词词典。同样地,将S.aureus数据集内的小分子化合物的SMILES进行分词得到词元,根据分词词典用词元的ID进行编码。经统计,本研究中的S.aureus数据集内小分子化合物SMILES的词元的数量最多为91。为保持所有小分子化合物SMILES的编码长度一致,使用keras(https://keras.io/)的pad_sequences函数将SMILES编码后填充至91个词元长度,用作Text-CNN模型的输入。即对于长度不足的在末尾补0,而对于长度超过91的则进行截断。
本研究采用的卷积神经网络架构如图2所示[12]。input为输入层,用于接受经编码后的SMILES张量;embedding为词嵌入层,将input层传递的输入转换到预定义的向量空间;conv_0、conv_1、conv_2都是一维卷积层,每一层设置若干个卷积核,通过卷积操作进行特征提取;随后,经过batch_normalization、batch_normalization_1、batch_normalization_2进行批规范化,避免梯度消失;然后,分别经过maxpool_0、maxpool_1、maxpool_2池化层进行最大池化,即对特征求最大值;concatenate层则对前面经卷积、批规范化、池化后得到的特征进行合并连接;dropout层通过设置dropout率,冻结部分权重,防止过拟合;最后,dense层通过接收特征向量作为输入,并采用合适的激活函数进行分类。本研究使用TensorFlow中集成的Keras API建立Text-CNN模型。
如上所述,所有化合物的SMILES的词元长度被固定为91,因此此处设置输入大小为91。词嵌入层输出维度设置为50,即SMILES输入模型后,词嵌入层实现将维数为词典大小(256维)的输入映射到维数为50的实值向量。
图2所示,本模型共设置3种一维卷积层,卷积核大小分别设置为2、3、4,步长均设置为1,激活函数为ReLU,且每种卷积核的个数设置为256个。在经过一维卷积层进行特征提取、批规范化和最大池化操作后,对特征进行合并连接,然后使用 SoftMax 函数进行二分类,输出两种可能状态,即有抗菌活性或无活性。模型损失函数采用sparse_categorical_crossentropy,优化器采用Adam算法,模型训练的迭代次数设置为40。
除此以外的超参数是采用10折交叉验证以及网格搜索来确定的。具体而言,无效神经元的比例(dropout rate)的搜索范围:0.1、0.2、0.3,批大小(batch size)的搜索范围为32、64、128,学习率(learning rate)的搜索范围为0.000 1、0.001、0.01。对于每一组超参数的组合,计算10次训练所得到的准确度的平均值。通过比较不同超参数组合各自在10折交叉验证中的准确度确定最佳超参数。
本研究通过灵敏度(sensitivity,SE)、特异性(specificity,SP)[13]、马修斯相关系数(Matthews correlation coefficient,MCC)[14]以及受试者工作特征曲线(receiver operating characteristic,ROC)曲线下面积(area under the curve,AUC)[15]这四个指标对模型的性能进行评估。其中,SE又称真阳性率,是指实际为阳性的样本判断为阳性的百分比。SP又称为真阴性率,是实际为阴性的样本判断为阴性的比例。真阳性(true positive,TP)代表活性化合物数量,假阳性(false positive,FP)表示将非活性化合物预测为活性化合物的数量,真阴性(true negative,TN)代表非活性化合物的数量,假阴性(false negative,FN)表示将活性化合物预测为非活性化合物的数量,MCC则是以上4个方面的综合指标。AUC 代表阳性样本排在阴性样本前的概率,其值越高,说明模型对于阳性样本的排序效果越好,具体定义见公式1~3:
$ \mathrm{SE}=\frac{T P}{T P+F N}$
$ \mathrm{SE}=\frac{T N}{T N+F P}$
$ \mathrm{MCC}=\frac{T P \times T N-F P \times F N}{\sqrt{(T P+F P)(T P+F N)(T N+F P)(T N+F N)}}$
Y-随机化检验(Y-randomization test)用于验证模型的鲁棒性[16]。在本研究中,Y随机化检验共进行 3 次。在每次检验中,保持训练集中的特征数据不改变,将训练集中活性和非活性标签进行随机打乱,从而生成一个新的训练集。然后,通过10折交叉验证以及网格搜索确定最优超参数后重新训练模型。在模型性能评估中,使用和原模型相同的测试集。如果重新训练得到的模型性能远不如原模型的性能,那么原模型的预测性能就不具有偶然性。
基于 MACCS 指纹计算测试集中每个化合物与训练集中任意化合物的谷本系数(tanimoto coefficient,Tc)。通过设置Tc阈值(从1到0.5,逐步降低0.05),逐步剔除测试集中与训练集化合物相似度超过阈值的化合物,使用模型预测排除相似结构后的测试集内化合物的活性,计算AUC值,由此研究模型性能随着多样性增加的变化趋势。
选取性能最好的抗菌活性预测模型虚拟筛选课题组内部的化合物库(含435个化合物),保留预测为有抗菌活性的化合物。通过计算每个预测有抗菌活性的化合物与上文所述的S.aureus数据集内活性化合物的相似度(即基于MACCS的Tc值)[17],若与已知活性化合物两两之间高度相似(Tc不小于0.75的分子被认为是已知活性化合物的类似物[18-20]),则从列表中删除该化合物。使用Discovery Studio软件(v16.1.0)中的“Cluster Ligands”模块根据FCFP_6指纹[21]将分子聚成10簇。最终,考虑化合物的可合成性等因素,挑选一定数量的化合物进行体外抗菌活性测试。
采用微量肉汤稀释法[22]对化合物的体外抗菌活性进行评价,采用的代表性S.aureus为标准菌株 ATCC29213,活性指标为MIC。
将96孔培养板灭菌后,第1列中加入200 μL的供试菌液,剩余11列都加100 μL菌液。然后将待测样品用DMSO溶解配制浓度至1.6 mg·mL-1,取4 μL溶液加入至含有200 μL菌液的孔里,采用2倍梯度稀释,将第1孔中含有化合物的菌液逐个加入到其余各孔(含100 μL菌液)中,各孔中的化合物终浓度分别为32、16、8、4、2、1、0.50、0.25、0.125、0.062 5、0.031 25、0.015 625 μg·mL-1。将96孔板转移至37 ℃培养箱内培养16~20 h。培养结束后,将96孔板置于超净台内,观察每个孔内细菌的生长情况,从第1个孔至最后一个孔,未见细菌生长的首个孔所对应的化合物浓度即为该化合物的MIC。实验采用3复孔,设置空白对照组和阳性对照组(左氧氟沙星)。
为了保持数据集内活性与非活性化合物的平衡,本研究设置32 μg·mL-1作为阈值。为此,抗菌活性化合物和非抗菌活性化合物的数量分别为18 489和7 838。图3A显示了基于Morgan2指纹所计算的化合物两两间的结构相似度值Tc的分布。由该图可见,由于大多数化合物之间的Tc值小于0.25,该S.aureus建模数据集具有高度的化学结构多样性。
如方法所述,本研究通过随机采样获得了10 组训练集和测试集,随后针对每一组训练-测试集的数据,采用 Text-CNN 算法建立抗S.aureus活性预测模型。表1图3B 展示了所建立的10个模型的超参数和在测试集上的性能指标。所有模型的MCC 范围为 0.485~0.582,AUC值范围为 0.863~0.881,表明各模型的分类性能相差不大。其中,基于第4对训练-测试集所建立的名为Text-CNN3的分类模型性能最好,其AUC值为0.881。建立该模型所采用的超参数为:批量大小为 32,无效神经元的比例为 0.1,学习率为 0.001。
表2 展示了Y-随机化检验过程中所建立的3个Text-CNN 模型的分类性能。其AUC 值分别为0.509、0.478和0.506,MCC值分别为-0.009、-0.016和0.000。MCC和AUC两个指标显著低于Text-CNN3模型(AUC:0.881; MCC:0.573),证明基于Y-随机化后的数据集训练得到的模型无法准确预测抗菌活性。因此,模型 Text-CNN3 的预测性能具有鲁棒性。
本研究还对Text-CNN3模型的适用域进行了研究。结果显示(图4),AUC 值随着测试子集内化合物间相似度值Tc阈值的减小而减小。说明测试集内化合物越多样,模型性能越差。为使得AUC 值大于 0.70(即较好的分类性能),化合物库内的分子与训练集内分子的相似度建议在0.80以上。
采用 Text-CNN3 模型对药物所内部化合物库(435个)进行预测(图5),保留预测为有活性的化合物137个。为保证结构新颖性,保留其与已知抗S.aureus化合物的相似度值Tc小于0.75的化合物36 个。最后,基于FCFP_6指纹将其聚成10簇,根据结构多样性和合成可行性选取9个化合物(表3)。经过PubChem查询,结果显示上述化合物的抗菌活性未见报道。购买上述化合物并进行体外抗菌活性评价,发现化合物Y5(7S)-4-氨基-7-甲基-5,6,7,8-四氢-[1]苯甲硫醇[3-d][1,3]噻嗪-2-硫酮和Y7(5Z)-3-[(4-乙基苯胺基)甲基]-5-[(4-碘苯基)亚甲基]-1,3-噻唑烷-2,4-二酮对S.aureus(ATCC29213)有较好的抑制活性,MIC分别为8和4 μg·mL-1
本研究通过收集和处理标注有S.aureus活性数据的化合物,建立了可用于机器学习建模的数据集,含26 327个S.aureus相关化合物。随后通过随机采样建立了 10 对训练集和测试集。本文首次采用基于化合物的SMILES表示及原子级分词方法,以Text-CNN算法训练了10 个抗S.aureus活性预测模型。经模型性能评估,Text-CNN3模型性能最好,且该模型通过了Y随机化测试和适用域分析,可以用于虚拟筛选。在此基础上,本研究开展了基于Text-CNN3模型的虚拟筛选,经过结构相似度比对和聚类分析,选定9个结构多样的化合物进行体外抗S.aureus活性评价,发现化合物Y5和Y7可以有效抑制S.aureus(MIC: 4~8 μg·mL-1),是新结构类型的抗菌药物苗头化合物。
本研究通过理论研究和药物发现实践,验证了Text-CNN算法用于抗菌药物发现的价值。但本研究尚存在一定的局限性:一方面,化合物Y5Y7的抗菌活性与左氧氟沙星等上市药物还有较大差距,需进一步通过化学结构改造提高其抗菌活性。另一方面,Text-CNN3的性能指标还有提升空间,后续应注重发展更为新颖的方法提升其预测性能。
  • 中国医学科学院医学与健康科技创新工程重大协同创新项目资助(2021-I2M-1-069)
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doi: 10.11669/cpj.2024.03.008
  • 接收时间:2023-07-20
  • 首发时间:2025-11-13
  • 出版时间:2024-02-08
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  • 收稿日期:2023-07-20
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中国医学科学院医学与健康科技创新工程重大协同创新项目资助(2021-I2M-1-069)
作者信息
    1 江苏海洋大学药学院, 江苏 连云港 222005
    2 南京航空航天大学经济与管理学院, 南京 210016
    3 中国医学科学院北京协和医学院药物研究所, 北京 100050

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*司鑫鑫,女,博士,副教授 研究方向:分子药理学;
夏杰,男,博士,副研究员 研究方向:分子信息学与药物设计
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2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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