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1.
Circulation ; 150(4): 272-282, 2024 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-38841854

RESUMO

BACKGROUND: A hypothetical concern has been raised that sacubitril/valsartan might cause cognitive impairment because neprilysin is one of several enzymes degrading amyloid-ß peptides in the brain, some of which are neurotoxic and linked to Alzheimer-type dementia. To address this, we examined the effect of sacubitril/valsartan compared with valsartan on cognitive function in patients with heart failure with preserved ejection fraction in a prespecified substudy of PARAGON-HF (Prospective Comparison of Angiotensin Receptor Neprilysin Inhibitor With Angiotensin Receptor Blocker Global Outcomes in Heart Failure With Preserved Ejection Fraction). METHODS: In PARAGON-HF, serial assessment of cognitive function was conducted in a subset of patients with the Mini-Mental State Examination (MMSE; score range, 0-30, with lower scores reflecting worse cognitive function). The prespecified primary analysis of this substudy was the change from baseline in MMSE score at 96 weeks. Other post hoc analyses included cognitive decline (fall in MMSE score of ≥3 points), cognitive impairment (MMSE score <24), or the occurrence of dementia-related adverse events. RESULTS: Among 2895 patients included in the MMSE substudy with baseline MMSE score measured, 1453 patients were assigned to sacubitril/valsartan and 1442 to valsartan. Their mean age was 73 years, and the median follow-up was 32 months. The mean±SD MMSE score at randomization was 27.4±3.0 in the sacubitril/valsartan group, with 10% having an MMSE score <24; the corresponding numbers were nearly identical in the valsartan group. The mean change from baseline to 96 weeks in the sacubitril/valsartan group was -0.05 (SE, 0.07); the corresponding change in the valsartan group was -0.04 (0.07). The mean between-treatment difference at week 96 was -0.01 (95% CI, -0.20 to 0.19; P=0.95). Analyses of a ≥3-point decline in MMSE, decrease to a score <24, dementia-related adverse events, and combinations of these showed no difference between sacubitril/valsartan and valsartan. No difference was found in the subgroup of patients tested for apolipoprotein E ε4 allele genotype. CONCLUSIONS: Patients with heart failure with preserved ejection fraction in PARAGON-HF had relatively low baseline MMSE scores. Cognitive change, measured by MMSE, did not differ between treatment with sacubitril/valsartan and treatment with valsartan in patients with heart failure with preserved ejection fraction. REGISTRATION: URL: https://www.clinicaltrials.gov; Unique identifier: NCT01920711.


Assuntos
Aminobutiratos , Antagonistas de Receptores de Angiotensina , Compostos de Bifenilo , Cognição , Combinação de Medicamentos , Insuficiência Cardíaca , Volume Sistólico , Tetrazóis , Valsartana , Humanos , Compostos de Bifenilo/uso terapêutico , Valsartana/uso terapêutico , Valsartana/efeitos adversos , Aminobutiratos/uso terapêutico , Aminobutiratos/efeitos adversos , Masculino , Insuficiência Cardíaca/tratamento farmacológico , Insuficiência Cardíaca/fisiopatologia , Feminino , Idoso , Cognição/efeitos dos fármacos , Volume Sistólico/efeitos dos fármacos , Antagonistas de Receptores de Angiotensina/uso terapêutico , Antagonistas de Receptores de Angiotensina/efeitos adversos , Pessoa de Meia-Idade , Tetrazóis/uso terapêutico , Tetrazóis/efeitos adversos , Estudos Prospectivos , Neprilisina/antagonistas & inibidores , Resultado do Tratamento , Disfunção Cognitiva/tratamento farmacológico , Idoso de 80 Anos ou mais
2.
Brief Bioinform ; 24(1)2023 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-36418927

RESUMO

Synergistic drug combinations can improve the therapeutic effect and reduce the drug dosage to avoid toxicity. In previous years, an in vitro approach was utilized to screen synergistic drug combinations. However, the in vitro method is time-consuming and expensive. With the rapid growth of high-throughput data, computational methods are becoming efficient tools to predict potential synergistic drug combinations. Considering the limitations of the previous computational methods, we developed a new model named Siamese Network and Random Matrix Projection for AntiCancer Drug Combination prediction (SNRMPACDC). Firstly, the Siamese convolutional network and random matrix projection were used to process the features of the two drugs into drug combination features. Then, the features of the cancer cell line were processed through the convolutional network. Finally, the processed features were integrated and input into the multi-layer perceptron network to get the predicted score. Compared with the traditional method of splicing drug features into drug combination features, SNRMPACDC improved the interpretability of drug combination features to a certain extent. In addition, the introduction of convolutional networks can better extract the potential information in the features. SNRMPACDC achieved the root mean-squared error of 15.01 and the Pearson correlation coefficient of 0.75 in 5-fold cross-validation of regression prediction for response data. In addition, SNRMPACDC achieved the AUC of 0.91 ± 0.03 and the AUPR of 0.62 ± 0.05 in 5-fold cross-validation of classification prediction of synergistic or not. These results are almost better than all the previous models. SNRMPACDC would be an effective approach to infer potential anticancer synergistic drug combinations.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica , Biologia Computacional , Protocolos de Quimioterapia Combinada Antineoplásica/farmacologia , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Sinergismo Farmacológico , Biologia Computacional/métodos , Combinação de Medicamentos , Simulação por Computador
3.
Brief Bioinform ; 24(1)2023 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-36562722

RESUMO

Combination therapy is a promising strategy for confronting the complexity of cancer. However, experimental exploration of the vast space of potential drug combinations is costly and unfeasible. Therefore, computational methods for predicting drug synergy are much needed for narrowing down this space, especially when examining new cellular contexts. Here, we thus introduce CCSynergy, a flexible, context aware and integrative deep-learning framework that we have established to unleash the potential of the Chemical Checker extended drug bioactivity profiles for the purpose of drug synergy prediction. We have shown that CCSynergy enables predictions of superior accuracy, remarkable robustness and improved context generalizability as compared to the state-of-the-art methods in the field. Having established the potential of CCSynergy for generating experimentally validated predictions, we next exhaustively explored the untested drug combination space. This resulted in a compendium of potentially synergistic drug combinations on hundreds of cancer cell lines, which can guide future experimental screens.


Assuntos
Antineoplásicos , Aprendizado Profundo , Sinergismo Farmacológico , Biologia Computacional/métodos , Linhagem Celular Tumoral , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Combinação de Medicamentos
4.
Brief Bioinform ; 24(5)2023 09 20.
Artigo em Inglês | MEDLINE | ID: mdl-37544660

RESUMO

Combination therapies have brought significant advancements to the treatment of various diseases in the medical field. However, searching for effective drug combinations remains a major challenge due to the vast number of possible combinations. Biomedical knowledge graph (KG)-based methods have shown potential in predicting effective combinations for wide spectrum of diseases, but the lack of credible negative samples has limited the prediction performance of machine learning models. To address this issue, we propose a novel model-agnostic framework that leverages existing drug-drug interaction (DDI) data as a reliable negative dataset and employs supervised contrastive learning (SCL) to transform drug embedding vectors to be more suitable for drug combination prediction. We conducted extensive experiments using various network embedding algorithms, including random walk and graph neural networks, on a biomedical KG. Our framework significantly improved performance metrics compared to the baseline framework. We also provide embedding space visualizations and case studies that demonstrate the effectiveness of our approach. This work highlights the potential of using DDI data and SCL in finding tighter decision boundaries for predicting effective drug combinations.


Assuntos
Algoritmos , Reconhecimento Automatizado de Padrão , Benchmarking , Combinação de Medicamentos , Interações Medicamentosas
5.
Cell Mol Life Sci ; 81(1): 64, 2024 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-38280930

RESUMO

Silenced protein tyrosine phosphatase receptor type R (PTPRR) participates in mitogen-activated protein kinase (MAPK) signaling cascades during the genesis and development of tumors. Rat sarcoma virus (Ras) genes are frequently mutated in lung adenocarcinoma, thereby resulting in hyperactivation of downstream MAPK signaling. However, the molecular mechanism manipulating the regulation and function of PTPRR in RAS-mutant lung adenocarcinoma is not known. Patient records collected from the Cancer Genome Atlas and Gene Expression Omnibus showed that silenced PTPRR was positively correlated with the prognosis. Exogenous expression of PTPRR suppressed the proliferation and migration of lung cancer cells. PTPRR expression and Src homology 2 containing protein tyrosine phosphatase 2 (SHP2) inhibition acted synergistically to control ERK1/2 phosphorylation in RAS-driven lung cancer cells. Chromatin immunoprecipitation assay revealed that HDAC inhibition induced enriched histone acetylation in the promoter region of PTPRR and recovered PTPRR transcription. The combination of the HDAC inhibitor SAHA and SHP2 inhibitor SHP099 suppressed the progression of lung cancer markedly in vitro and in vivo. Therefore, we revealed the epigenetic silencing mechanism of PTPRR and demonstrated that combination therapy targeting HDAC and SHP2 might represent a novel strategy to treat RAS-mutant lung cancer.


Assuntos
Adenocarcinoma de Pulmão , Neoplasias Pulmonares , Humanos , Histonas/metabolismo , Acetilação , Adenocarcinoma de Pulmão/genética , Neoplasias Pulmonares/patologia , Proteína Tirosina Fosfatase não Receptora Tipo 11/genética , Proteína Tirosina Fosfatase não Receptora Tipo 11/metabolismo , Linhagem Celular Tumoral , Proteínas Tirosina Fosfatases Classe 7 Semelhantes a Receptores/genética , Proteínas Tirosina Fosfatases Classe 7 Semelhantes a Receptores/metabolismo
6.
BMC Bioinformatics ; 25(1): 250, 2024 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-39080535

RESUMO

BACKGROUND: The potential benefits of drug combination synergy in cancer medicine are significant, yet the risks must be carefully managed due to the possibility of increased toxicity. Although artificial intelligence applications have demonstrated notable success in predicting drug combination synergy, several key challenges persist: (1) Existing models often predict average synergy values across a restricted range of testing dosages, neglecting crucial dose amounts and the mechanisms of action of the drugs involved. (2) Many graph-based models rely on static protein-protein interactions, failing to adapt to dynamic and higher-order relationships. These limitations constrain the applicability of current methods. RESULTS: We introduce SAFER, a Sub-hypergraph Attention-based graph model, addressing these issues by incorporating complex relationships among biological knowledge networks and considering dosing effects on subject-specific networks. SAFER outperformed previous models on the benchmark and the independent test set. The analysis of subgraph attention weight for the lung cancer cell line highlighted JAK-STAT signaling pathway, PRDM12, ZNF781, and CDC5L that have been implicated in lung fibrosis. CONCLUSIONS: SAFER presents an interpretable framework designed to identify drug-responsive signals. Tailored for comprehending dose effects on subject-specific molecular contexts, our model uniquely captures dose-level drug combination responses. This capability unlocks previously inaccessible avenues of investigation compared to earlier models. Furthermore, the SAFER framework can be leveraged by future inquiries to investigate molecular networks that uniquely characterize individual patients and can be applied to prioritize personalized effective treatment based on safe dose combinations.


Assuntos
Redes Neurais de Computação , Humanos , Linhagem Celular Tumoral , Sinergismo Farmacológico , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/metabolismo , Relação Dose-Resposta a Droga , Transdução de Sinais/efeitos dos fármacos , Antineoplásicos/farmacologia
7.
BMC Bioinformatics ; 25(1): 327, 2024 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-39390357

RESUMO

BACKGROUND: Drug combination treatments have proven to be a realistic technique for treating challenging diseases such as cancer by enhancing efficacy and mitigating side effects. To achieve the therapeutic goals of these combinations, it is essential to employ multi-targeted drug combinations, which maximize effectiveness and synergistic effects. RESULTS: This paper proposes 'MultiComb', a multi-task deep learning (MTDL) model designed to simultaneously predict the synergy and sensitivity of drug combinations. The model utilizes a graph convolution network to represent the Simplified Molecular-Input Line-Entry (SMILES) of two drugs, generating their respective features. Also, three fully connected subnetworks extract features of the cancer cell line. These drug and cell line features are then concatenated and processed through an attention mechanism, which outputs two optimized feature representations for the target tasks. The cross-stitch model learns the relationship between these tasks. At last, each learned task feature is fed into fully connected subnetworks to predict the synergy and sensitivity scores. The proposed model is validated using the O'Neil benchmark dataset, which includes 38 unique drugs combined to form 17,901 drug combination pairs and tested across 37 unique cancer cells. The model's performance is tested using some metrics like mean square error ( MSE ), mean absolute error ( MAE ), coefficient of determination ( R 2 ), Spearman, and Pearson scores. The mean synergy scores of the proposed model are 232.37, 9.59, 0.57, 0.76, and 0.73 for the previous metrics, respectively. Also, the values for mean sensitivity scores are 15.59, 2.74, 0.90, 0.95, and 0.95, respectively. CONCLUSION: This paper proposes an MTDL model to predict synergy and sensitivity scores for drug combinations targeting specific cancer cell lines. The MTDL model demonstrates superior performance compared to existing approaches, providing better results.


Assuntos
Aprendizado Profundo , Sinergismo Farmacológico , Humanos , Linhagem Celular Tumoral , Neoplasias/tratamento farmacológico , Antineoplásicos/farmacologia
8.
BMC Bioinformatics ; 25(1): 140, 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38561679

RESUMO

Drug combination therapy is generally more effective than monotherapy in the field of cancer treatment. However, screening for effective synergistic combinations from a wide range of drug combinations is particularly important given the increase in the number of available drug classes and potential drug-drug interactions. Existing methods for predicting the synergistic effects of drug combinations primarily focus on extracting structural features of drug molecules and cell lines, but neglect the interaction mechanisms between cell lines and drug combinations. Consequently, there is a deficiency in comprehensive understanding of the synergistic effects of drug combinations. To address this issue, we propose a drug combination synergy prediction model based on multi-source feature interaction learning, named MFSynDCP, aiming to predict the synergistic effects of anti-tumor drug combinations. This model includes a graph aggregation module with an adaptive attention mechanism for learning drug interactions and a multi-source feature interaction learning controller for managing information transfer between different data sources, accommodating both drug and cell line features. Comparative studies with benchmark datasets demonstrate MFSynDCP's superiority over existing methods. Additionally, its adaptive attention mechanism graph aggregation module identifies drug chemical substructures crucial to the synergy mechanism. Overall, MFSynDCP is a robust tool for predicting synergistic drug combinations. The source code is available from GitHub at https://github.com/kkioplkg/MFSynDCP .


Assuntos
Benchmarking , Treinamento por Simulação , Combinação de Medicamentos , Quimioterapia Combinada , Linhagem Celular
9.
Antimicrob Agents Chemother ; 68(7): e0011424, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38780260

RESUMO

Schistosomiasis, a widespread parasitic disease caused by the blood fluke of the genus Schistosoma, affects over 230 million people, primarily in developing countries. Praziquantel, the sole drug currently approved for schistosomiasis treatment, demonstrates effectiveness against patent infections. A recent study highlighted the antiparasitic properties of amiodarone, an anti-arrhythmic drug, exhibiting higher efficacy than praziquantel against prepatent infections. This study assessed the efficacy of amiodarone and praziquantel, both individually and in combination, against Schistosoma mansoni through comprehensive in vitro and in vivo experiments. In vitro experiments demonstrated synergistic activity (fractional inhibitory concentration index ≤0.5) for combinations of amiodarone with praziquantel. In a murine model of schistosomiasis featuring prepatent infections, treatments involving amiodarone (200 or 400 mg/kg) followed by praziquantel (200 or 400 mg/kg) yielded a substantial reduction in worm burden (60%-70%). Given the low efficacy of praziquantel in prepatent infections, combinations of amiodarone with praziquantel may offer clinical utility in the treatment of schistosomiasis.


Assuntos
Amiodarona , Praziquantel , Schistosoma mansoni , Esquistossomose mansoni , Amiodarona/farmacologia , Amiodarona/uso terapêutico , Animais , Praziquantel/farmacologia , Praziquantel/uso terapêutico , Schistosoma mansoni/efeitos dos fármacos , Camundongos , Esquistossomose mansoni/tratamento farmacológico , Esquistossomose mansoni/parasitologia , Feminino , Anti-Helmínticos/farmacologia , Anti-Helmínticos/uso terapêutico , Sinergismo Farmacológico , Quimioterapia Combinada , Masculino , Modelos Animais de Doenças
10.
Brief Bioinform ; 23(1)2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34477201

RESUMO

Combination therapy has shown an obvious efficacy on complex diseases and can greatly reduce the development of drug resistance. However, even with high-throughput screens, experimental methods are insufficient to explore novel drug combinations. In order to reduce the search space of drug combinations, there is an urgent need to develop more efficient computational methods to predict novel drug combinations. In recent decades, more and more machine learning (ML) algorithms have been applied to improve the predictive performance. The object of this study is to introduce and discuss the recent applications of ML methods and the widely used databases in drug combination prediction. In this study, we first describe the concept and controversy of synergism between drug combinations. Then, we investigate various publicly available data resources and tools for prediction tasks. Next, ML methods including classic ML and deep learning methods applied in drug combination prediction are introduced. Finally, we summarize the challenges to ML methods in prediction tasks and provide a discussion on future work.


Assuntos
Algoritmos , Aprendizado de Máquina , Bases de Dados Factuais , Combinação de Medicamentos , Interações Medicamentosas
11.
Brief Bioinform ; 23(1)2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34505623

RESUMO

Drug combination is a sensible strategy for disease treatment because it improves the treatment efficacy and reduces concomitant side effects. Due to the large number of possible combinations among candidate compounds, exhaustive screening is prohibitive. Currently, a large number of studies have focused on predicting potential drug combinations. However, these methods are not entirely satisfactory in terms of performance and scalability. In this paper, we proposed a Network Embedding frameWork in MultIplex Network (NEWMIN) to predict synthetic drug combinations. Based on a multiplex drug similarity network, we offered alternative methods to integrate useful information from different aspects and to decide the quantitative importance of each network. For drug combination prediction, we found seven novel drug combinations that have been validated by external sources among the top-ranked predictions of our model. To verify the feasibility of NEWMIN, we compared NEWMIN with other five methods, for which it showed better performance than other methods in terms of the area under the precision-recall curve and receiver operating characteristic curve.


Assuntos
Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Combinação de Medicamentos , Humanos , Curva ROC
12.
Brief Bioinform ; 23(5)2022 09 20.
Artigo em Inglês | MEDLINE | ID: mdl-35915050

RESUMO

Drug combination therapies are superior to monotherapy for cancer treatment in many ways. Identifying novel drug combinations by screening is challenging for the wet-lab experiments due to the time-consuming process of the enormous search space of possible drug pairs. Thus, computational methods have been developed to predict drug pairs with potential synergistic functions. Notwithstanding the success of current models, understanding the mechanism of drug synergy from a chemical-gene-tissue interaction perspective lacks study, hindering current algorithms from drug mechanism study. Here, we proposed a deep neural network model termed DTSyn (Dual Transformer encoder model for drug pair Synergy prediction) based on a multi-head attention mechanism to identify novel drug combinations. We designed a fine-granularity transformer encoder to capture chemical substructure-gene and gene-gene associations and a coarse-granularity transformer encoder to extract chemical-chemical and chemical-cell line interactions. DTSyn achieved the highest receiver operating characteristic area under the curve of 0.73, 0.78. 0.82 and 0.81 on four different cross-validation tasks, outperforming all competing methods. Further, DTSyn achieved the best True Positive Rate (TPR) over five independent data sets. The ablation study showed that both transformer encoder blocks contributed to the performance of DTSyn. In addition, DTSyn can extract interactions among chemicals and cell lines, representing the potential mechanisms of drug action. By leveraging the attention mechanism and pretrained gene embeddings, DTSyn shows improved interpretability ability. Thus, we envision our model as a valuable tool to prioritize synergistic drug pairs with chemical and cell line gene expression profile.


Assuntos
Biologia Computacional , Redes Neurais de Computação , Algoritmos , Biologia Computacional/métodos , Combinação de Medicamentos , Curva ROC
13.
Brief Bioinform ; 23(2)2022 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-35062018

RESUMO

Combination therapy has shown an obvious curative effect on complex diseases, whereas the search space of drug combinations is too large to be validated experimentally even with high-throughput screens. With the increase of the number of drugs, artificial intelligence techniques, especially machine learning methods, have become applicable for the discovery of synergistic drug combinations to significantly reduce the experimental workload. In this study, in order to predict novel synergistic drug combinations in various cancer cell lines, the cell line-specific drug-induced gene expression profile (GP) is added as a new feature type to capture the cellular response of drugs and reveal the biological mechanism of synergistic effect. Then, an enhanced cascade-based deep forest regressor (EC-DFR) is innovatively presented to apply the new small-scale drug combination dataset involving chemical, physical and biological (GP) properties of drugs and cells. Verified by the dataset, EC-DFR outperforms two state-of-the-art deep neural network-based methods and several advanced classical machine learning algorithms. Biological experimental validation performed subsequently on a set of previously untested drug combinations further confirms the performance of EC-DFR. What is more prominent is that EC-DFR can distinguish the most important features, making it more interpretable. By evaluating the contribution of each feature type, GP feature contributes 82.40%, showing the cellular responses of drugs may play crucial roles in synergism prediction. The analysis based on the top contributing genes in GP further demonstrates some potential relationships between the transcriptomic levels of key genes under drug regulation and the synergism of drug combinations.


Assuntos
Inteligência Artificial , Biologia Computacional , Biologia Computacional/métodos , Combinação de Medicamentos , Aprendizado de Máquina , Redes Neurais de Computação
14.
Brief Bioinform ; 23(1)2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34571537

RESUMO

MOTIVATION: Drug combination therapy has become an increasingly promising method in the treatment of cancer. However, the number of possible drug combinations is so huge that it is hard to screen synergistic drug combinations through wet-lab experiments. Therefore, computational screening has become an important way to prioritize drug combinations. Graph neural network has recently shown remarkable performance in the prediction of compound-protein interactions, but it has not been applied to the screening of drug combinations. RESULTS: In this paper, we proposed a deep learning model based on graph neural network and attention mechanism to identify drug combinations that can effectively inhibit the viability of specific cancer cells. The feature embeddings of drug molecule structure and gene expression profiles were taken as input to multilayer feedforward neural network to identify the synergistic drug combinations. We compared DeepDDS (Deep Learning for Drug-Drug Synergy prediction) with classical machine learning methods and other deep learning-based methods on benchmark data set, and the leave-one-out experimental results showed that DeepDDS achieved better performance than competitive methods. Also, on an independent test set released by well-known pharmaceutical enterprise AstraZeneca, DeepDDS was superior to competitive methods by more than 16% predictive precision. Furthermore, we explored the interpretability of the graph attention network and found the correlation matrix of atomic features revealed important chemical substructures of drugs. We believed that DeepDDS is an effective tool that prioritized synergistic drug combinations for further wet-lab experiment validation. AVAILABILITY AND IMPLEMENTATION: Source code and data are available at https://github.com/Sinwang404/DeepDDS/tree/master.


Assuntos
Neoplasias , Redes Neurais de Computação , Combinação de Medicamentos , Humanos , Aprendizado de Máquina , Neoplasias/tratamento farmacológico , Software
15.
J Transl Med ; 22(1): 572, 2024 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-38880914

RESUMO

BACKGROUND: Accurately identifying the risk level of drug combinations is of great significance in investigating the mechanisms of combination medication and adverse reactions. Most existing methods can only predict whether there is an interaction between two drugs, but cannot directly determine their accurate risk level. METHODS: In this study, we propose a multi-class drug combination risk prediction model named AERGCN-DDI, utilizing a relational graph convolutional network with a multi-head attention mechanism. Drug-drug interaction events with varying risk levels are modeled as a heterogeneous information graph. Attribute features of drug nodes and links are learned based on compound chemical structure information. Finally, the AERGCN-DDI model is proposed to predict drug combination risk level based on heterogenous graph neural network and multi-head attention modules. RESULTS: To evaluate the effectiveness of the proposed method, five-fold cross-validation and ablation study were conducted. Furthermore, we compared its predictive performance with baseline models and other state-of-the-art methods on two benchmark datasets. Empirical studies demonstrated the superior performances of AERGCN-DDI. CONCLUSIONS: AERGCN-DDI emerges as a valuable tool for predicting the risk levels of drug combinations, thereby aiding in clinical medication decision-making, mitigating severe drug side effects, and enhancing patient clinical prognosis.


Assuntos
Redes Neurais de Computação , Humanos , Interações Medicamentosas , Combinação de Medicamentos , Medição de Risco , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos , Reprodutibilidade dos Testes , Gráficos por Computador
16.
J Med Virol ; 96(1): e29354, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38180134

RESUMO

The Mpox virus can cause severe disease in the susceptible population with dermatologic and systemic manifestations. Furthermore, ophthalmic manifestations of mpox infection are well documented. Topical trifluridine (TFT) eye drops have been used for therapy of ophthalmic mpox infection in patients, however, its efficacy against mpox virus infection in this scenario has not been previously shown. In the present study, we have established ophthalmic cell models suitable for the infection with mpox virus. We show, that TFT is effective against a broad range of mpox isolates in conjunctival epithelial cells and keratocytes. Further, TFT remained effective against a tecovirimat-resistant virus strain. In the context of drug combinations, a nearly additive effect was observed for TFT combinations with brincidofovir and tecovirimat in conjunctival epithelial cells, while a slight antagonism was observed for both combinations in keratocytes. Altogether, our findings demonstrate TFT as a promising drug for treatment of ophthalmic mpox infection able to overcome tecovirimat resistance. However, conflicting results regarding the effect of drug combinations with approved compounds warrant close monitoring of such use in patients.


Assuntos
Mpox , Trifluridina , Humanos , Trifluridina/farmacologia , Trifluridina/uso terapêutico , Olho , Combinação de Medicamentos , Benzamidas , Isoindóis , Monkeypox virus
17.
Cancer Cell Int ; 24(1): 285, 2024 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-39135053

RESUMO

BACKGROUND: Olaparib is a PARP inhibitor inducing synthetic lethality in tumors with deficient homologous recombination (HRD) caused by BRCA1/2 mutations. The FDA has approved monotherapy for first-line platinum-sensitive, recurrent high-grade epithelial ovarian cancer. Combination therapy alongside DNA-damaging therapeutics is a promising solution to overcome the limited efficacy in patients with HRD. The present study was designed to develop topotecan- and olaparib-loaded liposomes (TLL and OLL) and assess the effectiveness of their combination in patient-derived ovarian cancer samples. METHODS: We used HEOC, four clear-cell tumors (EOC 1-4), malignant ascites, and an OCI-E1p endometrioid primary ovarian cancer cell line and performed NGS analysis of BRCA1/2 mutation status. Antiproliferative activity was determined with the MTT assay. The Chou-Talalay algorithm was used to investigate the in vitro pharmacodynamic interactions of TLLs and OLLs. RESULTS: The OLL showed significantly higher efficacy in all ovarian cancer types with wild-type BRCA1/2 than a conventional formulation, suggesting potential for increased in vivo efficacy. The TLL revealed substantially higher toxicity to EOC 1, EOC 3, ascites and lower toxicity to HEOC than the standard formulation, suggesting better therapeutic efficacy and safety profile. The combination of studied compounds showed a higher reduction in cell viability than drugs used individually, demonstrating a synergistic antitumor effect at most of the selected concentrations. CONCLUSIONS: The concentration-dependent response of different ovarian cancer cell types to combination therapy confirms the need for in vitro optimization to maximize drug cytotoxicity. The OLL and TLL combination is a promising formulation for further animal studies, especially for eliminating epithelial ovarian cancer with wild-type BRCA1/2.

18.
BMC Cancer ; 24(1): 335, 2024 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-38475728

RESUMO

BACKGROUND: The development of drug resistance is a major cause of cancer therapy failures. To inhibit drug resistance, multiple drugs are often treated together as a combinatorial therapy. In particular, synergistic drug combinations, which kill cancer cells at a lower concentration, guarantee a better prognosis and fewer side effects in cancer patients. Many studies have sought out synergistic combinations by small-scale function-based targeted growth assays or large-scale nontargeted growth assays, but their discoveries are always challenging due to technical problems such as a large number of possible test combinations. METHODS: To address this issue, we carried out a medium-scale optical drug synergy screening in a non-small cell lung cancer cell line and further investigated individual drug interactions in combination drug responses by high-content image analysis. Optical high-content analysis of cellular responses has recently attracted much interest in the field of drug discovery, functional genomics, and toxicology. Here, we adopted a similar approach to study combinatorial drug responses. RESULTS: By examining all possible combinations of 12 drug compounds in 6 different drug classes, such as mTOR inhibitors, HDAC inhibitors, HSP90 inhibitors, MT inhibitors, DNA inhibitors, and proteasome inhibitors, we successfully identified synergism between INK128, an mTOR inhibitor, and HDAC inhibitors, which has also been reported elsewhere. Our high-content analysis further showed that HDAC inhibitors, HSP90 inhibitors, and proteasome inhibitors played a dominant role in combinatorial drug responses when they were mixed with MT inhibitors, DNA inhibitors, or mTOR inhibitors, suggesting that recessive drugs could be less prioritized as components of multidrug cocktails. CONCLUSIONS: In conclusion, our optical drug screening platform efficiently identified synergistic drug combinations in a non-small cell lung cancer cell line, and our high-content analysis further revealed how individual drugs in the drug mix interact with each other to generate combinatorial drug response.


Assuntos
Antineoplásicos , Carcinoma Pulmonar de Células não Pequenas , Neoplasias Pulmonares , Humanos , Inibidores de Histona Desacetilases/farmacologia , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Inibidores de MTOR , Linhagem Celular Tumoral , Inibidores de Proteassoma/uso terapêutico , Neoplasias Pulmonares/tratamento farmacológico , Antineoplásicos/uso terapêutico , Pirimidinas/uso terapêutico , Serina-Treonina Quinases TOR/metabolismo , Combinação de Medicamentos , DNA/uso terapêutico , Sinergismo Farmacológico
19.
Diabetes Obes Metab ; 26(11): 5065-5077, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-39223856

RESUMO

AIM: To evaluate the efficacy and safety of dapagliflozin versus placebo as an add-on in patients with type 2 diabetes who did not achieve adequate glycaemic control with evogliptin and metformin combination. PATIENTS AND METHODS: In this multicentre, randomized, double-blind, placebo-controlled Phase 3 trial, patients with glycated haemoglobin (HbA1c) levels ≥7.0% (≥53 mmol/mol) and ≤10.5% (≤91 mmol/mol) who had received stable-dose metformin (≥1000 mg) and evogliptin (5 mg) for at least 8 weeks were randomized to receive dapagliflozin 10 mg or placebo once daily for 24 weeks. Participants continued treatment with metformin and evogliptin. The primary endpoint was change in HbA1c level after 24 weeks of treatment from baseline level. RESULTS: In total, 198 patients were randomized, and 195 patients were included in the efficacy analyses (dapagliflozin: 96, placebo: 99). At Week 24, dapagliflozin significantly reduced HbA1c levels. The least squares mean difference in HbA1c level change from baseline after 24 weeks of treatment was -0.70% (-7.7 mmol/mol) (p < 0.0001). The proportion of participants achieving HbA1c <7.0% (≥53 mmol/mol) was higher in the dapagliflozin group than in the placebo group. Compared to placebo, dapagliflozin significantly reduced fasting plasma glucose, mean daily glucose, 2-h postprandial plasma glucose, fasting insulin, uric acid and gamma-glutamyl transferase levels, homeostatic model assessment for insulin resistance index, body weight, hepatic steatosis index, and albuminuria. Adiponectin level significantly increased from baseline level after 24 weeks of dapagliflozin treatment. Adverse event rates were similar in the two groups. CONCLUSION: Dapagliflozin add-on to evogliptin plus metformin improved glycaemic control and was well tolerated by the target patients.


Assuntos
Compostos Benzidrílicos , Glicemia , Diabetes Mellitus Tipo 2 , Quimioterapia Combinada , Glucosídeos , Hemoglobinas Glicadas , Hipoglicemiantes , Metformina , Humanos , Diabetes Mellitus Tipo 2/tratamento farmacológico , Diabetes Mellitus Tipo 2/sangue , Metformina/uso terapêutico , Glucosídeos/uso terapêutico , Glucosídeos/efeitos adversos , Glucosídeos/administração & dosagem , Compostos Benzidrílicos/uso terapêutico , Compostos Benzidrílicos/efeitos adversos , Método Duplo-Cego , Masculino , Feminino , Pessoa de Meia-Idade , Hemoglobinas Glicadas/análise , Hemoglobinas Glicadas/efeitos dos fármacos , Hipoglicemiantes/uso terapêutico , Hipoglicemiantes/efeitos adversos , Idoso , Glicemia/efeitos dos fármacos , Resultado do Tratamento , Adulto , Controle Glicêmico/métodos , Piperazinas
20.
Eur J Clin Microbiol Infect Dis ; 43(8): 1579-1587, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38811482

RESUMO

PURPOSE: Amongst all etiologic hospital-acquired infection factors, K. pneumoniae strains producing New Delhi metallo-ß-lactamase (KP-NDM) belong to pathogens with the most effective antibiotic resistance mechanisms. Clinical guidelines recommend using ceftazidime/avibactam with aztreonam (CZA + AT) as the preferred option for NDM-producing Enterobacterales. However, the number of observations on such treatment regimen is limited. This retrospective study reports the clinical and microbiological outcomes of 23 patients with KP-NDM hospital-acquired infection treated with CZA + AT at a single center in Poland. METHODS: The isolates were derived from the urine, lungs, blood, peritoneal cavity, wounds, and peritonsillar abscess. In microbiological analysis, mass spectrometry for pathogen identification, polymerase chain reaction, or an immunochromatographic assay for detection of carbapenemase, as well as VITEK-2 system, broth microdilution, and microdilution in agar method for antimicrobial susceptibility tests were used, depending of the pathogens' nature. CZA was administered intravenously (IV) at 2.5 g every eight hours in patients with normal kidney function, and aztreonam was administered at 2 g every eight hours IV. Such dosage was modified when renal function was reduced. RESULTS: KP-NDM was eradicated in all cases. Four patients (17.4%) died: three of them had a neoplastic disease, and one - a COVID-19 infection. CONCLUSION: The combination of CZA + AT is a safe and effective therapy for infections caused by KP-NDM, both at the clinical and microbiological levels. The synergistic action of all compounds resulted in a good agreement between the clinical efficacy of CZA + AT and the results of in vitro susceptibility testing.


Assuntos
Antibacterianos , Compostos Azabicíclicos , Aztreonam , Ceftazidima , Combinação de Medicamentos , Infecções por Klebsiella , Klebsiella pneumoniae , beta-Lactamases , Humanos , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/enzimologia , Aztreonam/farmacologia , Aztreonam/uso terapêutico , beta-Lactamases/metabolismo , Masculino , Compostos Azabicíclicos/uso terapêutico , Compostos Azabicíclicos/farmacologia , Feminino , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/microbiologia , Pessoa de Meia-Idade , Estudos Retrospectivos , Idoso , Ceftazidima/uso terapêutico , Ceftazidima/farmacologia , Antibacterianos/uso terapêutico , Antibacterianos/farmacologia , Polônia , Testes de Sensibilidade Microbiana , Adulto , Idoso de 80 Anos ou mais , Resultado do Tratamento , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/microbiologia
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