12 research outputs found
Evaluation of Different Methods for Identification of Structural Alerts Using Chemical Ames Mutagenicity Data Set as a Benchmark
Identification of structural alerts
for toxicity is useful in drug
discovery and other fields such as environmental protection. With
structural alerts, researchers can quickly identify potential toxic
compounds and learn how to modify them. Hence, it is important to
determine structural alerts from a large number of compounds quickly
and accurately. There are already many methods reported for identification
of structural alerts. However, how to evaluate those methods is a
problem. In this paper, we tried to evaluate four of the methods for
monosubstructure identification with three indices including accuracy
rate, coverage rate, and information gain to compare their advantages
and disadvantages. The Kazius’ Ames mutagenicity data set was
used as the benchmark, and the four methods were MoSS (graph-based),
SARpy (fragment-based), and two fingerprint-based methods including
Bioalerts and the fingerprint (FP) method we previously used. The
results showed that Bioalerts and FP could detect key substructures
with high accuracy and coverage rates because they allowed unclosed
rings and wildcard atom or bond types. However, they also resulted
in redundancy so that their predictive performance was not as good
as that of SARpy. SARpy was competitive in predictive performance
in both training set and external validation set. These results might
be helpful for users to select appropriate methods and further development
of methods for identification of structural alerts
Quantitative and Systems Pharmacology. 1. <i>In Silico</i> Prediction of Drug–Target Interactions of Natural Products Enables New Targeted Cancer Therapy
Natural
products with diverse chemical scaffolds have been recognized
as an invaluable source of compounds in drug discovery and development.
However, systematic identification of drug targets for natural products
at the human proteome level via various experimental assays is highly
expensive and time-consuming. In this study, we proposed a systems
pharmacology infrastructure to predict new drug targets and anticancer
indications of natural products. Specifically, we reconstructed a
global drug–target network with 7,314 interactions connecting
751 targets and 2,388 natural products and built predictive network
models via a balanced substructure–drug–target network-based
inference approach. A high area under receiver operating characteristic
curve of 0.96 was yielded for predicting new targets of natural products
during cross-validation. The newly predicted targets of natural products
(e.g., resveratrol, genistein, and kaempferol) with high scores were
validated by various literature studies. We further built the statistical
network models for identification of new anticancer indications of
natural products through integration of both experimentally validated
and computationally predicted drug–target interactions of natural
products with known cancer proteins. We showed that the significantly
predicted anticancer indications of multiple natural products (e.g.,
naringenin, disulfiram, and metformin) with new mechanism-of-action
were validated by various published experimental evidence. In summary,
this study offers powerful computational systems pharmacology approaches
and tools for the development of novel targeted cancer therapies by
exploiting the polypharmacology of natural products
Evaluation of Different Methods for Identification of Structural Alerts Using Chemical Ames Mutagenicity Data Set as a Benchmark
Identification of structural alerts
for toxicity is useful in drug
discovery and other fields such as environmental protection. With
structural alerts, researchers can quickly identify potential toxic
compounds and learn how to modify them. Hence, it is important to
determine structural alerts from a large number of compounds quickly
and accurately. There are already many methods reported for identification
of structural alerts. However, how to evaluate those methods is a
problem. In this paper, we tried to evaluate four of the methods for
monosubstructure identification with three indices including accuracy
rate, coverage rate, and information gain to compare their advantages
and disadvantages. The Kazius’ Ames mutagenicity data set was
used as the benchmark, and the four methods were MoSS (graph-based),
SARpy (fragment-based), and two fingerprint-based methods including
Bioalerts and the fingerprint (FP) method we previously used. The
results showed that Bioalerts and FP could detect key substructures
with high accuracy and coverage rates because they allowed unclosed
rings and wildcard atom or bond types. However, they also resulted
in redundancy so that their predictive performance was not as good
as that of SARpy. SARpy was competitive in predictive performance
in both training set and external validation set. These results might
be helpful for users to select appropriate methods and further development
of methods for identification of structural alerts
Table_1_A Computational Systems Pharmacology Approach to Investigate Molecular Mechanisms of Herbal Formula Tian-Ma-Gou-Teng-Yin for Treatment of Alzheimer’s Disease.XLSX
<p>Traditional Chinese medicine (TCM) is typically prescribed as formula to treat certain symptoms. A TCM formula contains hundreds of chemical components, which makes it complicated to elucidate the molecular mechanisms of TCM. Here, we proposed a computational systems pharmacology approach consisting of network link prediction, statistical analysis, and bioinformatics tools to investigate the molecular mechanisms of TCM formulae. Taking formula Tian-Ma-Gou-Teng-Yin as an example, which shows pharmacological effects on Alzheimer’s disease (AD) and its mechanism is unclear, we first identified 494 formula components together with corresponding 178 known targets, and then predicted 364 potential targets for these components with our balanced substructure-drug–target network-based inference method. With Fisher’s exact test and statistical analysis we identified 12 compounds to be most significantly related to AD. The target genes of these compounds were further enriched onto pathways involved in AD, such as neuroactive ligand–receptor interaction, serotonergic synapse, inflammatory mediator regulation of transient receptor potential channel and calcium signaling pathway. By regulating key target genes, such as ACHE, HTR2A, NOS2, and TRPA1, the formula could have neuroprotective and anti-neuroinflammatory effects against the progression of AD. Our approach provided a holistic perspective to study the relevance between TCM formulae and diseases, and implied possible pharmacological effects of TCM components.</p
Presentation_1_A Computational Systems Pharmacology Approach to Investigate Molecular Mechanisms of Herbal Formula Tian-Ma-Gou-Teng-Yin for Treatment of Alzheimer’s Disease.PDF
<p>Traditional Chinese medicine (TCM) is typically prescribed as formula to treat certain symptoms. A TCM formula contains hundreds of chemical components, which makes it complicated to elucidate the molecular mechanisms of TCM. Here, we proposed a computational systems pharmacology approach consisting of network link prediction, statistical analysis, and bioinformatics tools to investigate the molecular mechanisms of TCM formulae. Taking formula Tian-Ma-Gou-Teng-Yin as an example, which shows pharmacological effects on Alzheimer’s disease (AD) and its mechanism is unclear, we first identified 494 formula components together with corresponding 178 known targets, and then predicted 364 potential targets for these components with our balanced substructure-drug–target network-based inference method. With Fisher’s exact test and statistical analysis we identified 12 compounds to be most significantly related to AD. The target genes of these compounds were further enriched onto pathways involved in AD, such as neuroactive ligand–receptor interaction, serotonergic synapse, inflammatory mediator regulation of transient receptor potential channel and calcium signaling pathway. By regulating key target genes, such as ACHE, HTR2A, NOS2, and TRPA1, the formula could have neuroprotective and anti-neuroinflammatory effects against the progression of AD. Our approach provided a holistic perspective to study the relevance between TCM formulae and diseases, and implied possible pharmacological effects of TCM components.</p
Development of In Silico Models for Predicting Potential Time-Dependent Inhibitors of Cytochrome P450 3A4
Cytochrome P450 3A4 (CYP3A4) is one of the major drug
metabolizing
enzymes in the human body and metabolizes ∼30–50% of
clinically used drugs. Inhibition of CYP3A4 must always be considered
in the development of new drugs. Time-dependent inhibition (TDI) is
an important P450 inhibition type that could cause undesired drug–drug
interactions. Therefore, identification of CYP3A4 TDI by a rapid convenient
way is of great importance to any new drug discovery effort. Here,
we report the development of in silico classification models for prediction
of potential CYP3A4 time-dependent inhibitors. On the basis of the
CYP3A4 TDI data set that we manually collected from literature and
databases, both conventional machine learning and deep learning models
were constructed. The comparisons of different sampling strategies,
molecular representations, and machine-learning algorithms showed
the benefits of a balanced data set and the deep-learning model featured
by GraphConv. The generalization ability of the best model was tested
by screening an external data set, and the prediction results were
validated by biological experiments. In addition, several structural
alerts that are relevant to CYP3A4 time-dependent inhibitors were
identified via information gain and frequency analysis. We anticipate
that our effort would be useful for identification of potential CYP3A4
time-dependent inhibitors in drug discovery and design
Presentation_2_A Computational Systems Pharmacology Approach to Investigate Molecular Mechanisms of Herbal Formula Tian-Ma-Gou-Teng-Yin for Treatment of Alzheimer’s Disease.ZIP
<p>Traditional Chinese medicine (TCM) is typically prescribed as formula to treat certain symptoms. A TCM formula contains hundreds of chemical components, which makes it complicated to elucidate the molecular mechanisms of TCM. Here, we proposed a computational systems pharmacology approach consisting of network link prediction, statistical analysis, and bioinformatics tools to investigate the molecular mechanisms of TCM formulae. Taking formula Tian-Ma-Gou-Teng-Yin as an example, which shows pharmacological effects on Alzheimer’s disease (AD) and its mechanism is unclear, we first identified 494 formula components together with corresponding 178 known targets, and then predicted 364 potential targets for these components with our balanced substructure-drug–target network-based inference method. With Fisher’s exact test and statistical analysis we identified 12 compounds to be most significantly related to AD. The target genes of these compounds were further enriched onto pathways involved in AD, such as neuroactive ligand–receptor interaction, serotonergic synapse, inflammatory mediator regulation of transient receptor potential channel and calcium signaling pathway. By regulating key target genes, such as ACHE, HTR2A, NOS2, and TRPA1, the formula could have neuroprotective and anti-neuroinflammatory effects against the progression of AD. Our approach provided a holistic perspective to study the relevance between TCM formulae and diseases, and implied possible pharmacological effects of TCM components.</p
Development of In Silico Models for Predicting Potential Time-Dependent Inhibitors of Cytochrome P450 3A4
Cytochrome P450 3A4 (CYP3A4) is one of the major drug
metabolizing
enzymes in the human body and metabolizes ∼30–50% of
clinically used drugs. Inhibition of CYP3A4 must always be considered
in the development of new drugs. Time-dependent inhibition (TDI) is
an important P450 inhibition type that could cause undesired drug–drug
interactions. Therefore, identification of CYP3A4 TDI by a rapid convenient
way is of great importance to any new drug discovery effort. Here,
we report the development of in silico classification models for prediction
of potential CYP3A4 time-dependent inhibitors. On the basis of the
CYP3A4 TDI data set that we manually collected from literature and
databases, both conventional machine learning and deep learning models
were constructed. The comparisons of different sampling strategies,
molecular representations, and machine-learning algorithms showed
the benefits of a balanced data set and the deep-learning model featured
by GraphConv. The generalization ability of the best model was tested
by screening an external data set, and the prediction results were
validated by biological experiments. In addition, several structural
alerts that are relevant to CYP3A4 time-dependent inhibitors were
identified via information gain and frequency analysis. We anticipate
that our effort would be useful for identification of potential CYP3A4
time-dependent inhibitors in drug discovery and design
Adverse Drug Events: Database Construction and in Silico Prediction
Adverse
drug events (ADEs) are the harms associated with uses of given medications
at normal dosages, which are crucial for a drug to be approved in
clinical use or continue to stay on the market. Many ADEs are not
identified in trials until the drug is approved for clinical use,
which results in adverse morbidity and mortality. To date, millions
of ADEs have been reported around the world. Methods to avoid or reduce
ADEs are an important issue for drug discovery and development. Here,
we reported a comprehensive database of adverse drug events (namely
MetaADEDB), which included more than 520 000 drug–ADE
associations among 3059 unique compounds (including 1330 drugs) and
13 200 ADE items by data integration and text mining. All compounds
and ADEs were annotated with the most commonly used concepts defined
in Medical Subject Headings (MeSH). Meanwhile, a computational method,
namely the phenotypic network inference model (PNIM), was developed
for prediction of potential ADEs based on the database. The area under
the receive operating characteristic curve (AUC) is more than 0.9
by 10-fold cross validation, while the AUC value was 0.912 for an
external validation set extracted from the US-FDA Adverse Events Reporting
System, which indicated that the prediction capability of the method
was reliable. MetaADEDB is accessible free of charge at http://www.lmmd.org/online_services/metaadedb/. The database and the method provide us a useful tool to search
for known side effects or predict potential side effects for a given
drug or compound
Adverse Drug Events: Database Construction and in Silico Prediction
Adverse
drug events (ADEs) are the harms associated with uses of given medications
at normal dosages, which are crucial for a drug to be approved in
clinical use or continue to stay on the market. Many ADEs are not
identified in trials until the drug is approved for clinical use,
which results in adverse morbidity and mortality. To date, millions
of ADEs have been reported around the world. Methods to avoid or reduce
ADEs are an important issue for drug discovery and development. Here,
we reported a comprehensive database of adverse drug events (namely
MetaADEDB), which included more than 520 000 drug–ADE
associations among 3059 unique compounds (including 1330 drugs) and
13 200 ADE items by data integration and text mining. All compounds
and ADEs were annotated with the most commonly used concepts defined
in Medical Subject Headings (MeSH). Meanwhile, a computational method,
namely the phenotypic network inference model (PNIM), was developed
for prediction of potential ADEs based on the database. The area under
the receive operating characteristic curve (AUC) is more than 0.9
by 10-fold cross validation, while the AUC value was 0.912 for an
external validation set extracted from the US-FDA Adverse Events Reporting
System, which indicated that the prediction capability of the method
was reliable. MetaADEDB is accessible free of charge at http://www.lmmd.org/online_services/metaadedb/. The database and the method provide us a useful tool to search
for known side effects or predict potential side effects for a given
drug or compound