Perturbation-Theory Machine Learning (PTML) Multilabel Model of the ChEMBL Dataset of Preclinical Assays for Antisarcoma Compounds

In Silico Approach for Antibacterial Discovery: PTML Modeling of Virtual Multi-Strain Inhibitors Against Staphylococcus aureus

Background/Objectives: Infectious diseases caused by Staphylococcus aureus (S. aureus) have become alarming health issues worldwide due to the ever-increasing emergence of multidrug resistance. In silico approaches can accelerate the identification and/or design of versatile antibacterial chemicals with the ability to target multiple S. aureus strains with varying degrees of drug resistance. Here, we develop a perturbation theory machine learning model based on a multilayer perceptron neural network (PTML-MLP) for the prediction and design of versatile virtual inhibitors against S. aureus strains. Methods: To develop the PTML-MLP model, chemical and biological data associated with antibacterial activity against S. aureus strains were retrieved from the ChEMBL database. We applied the Box-Jenkins approach to convert the topological indices into multi-label graph-theoretical indices; the latter were used as inputs for the creation of the PTML-MLP model. Results: The PTML-MLP model exhibited accuracy higher than 80% in both training and test sets. The physicochemical and structural interpretation of the PTML-MLP model was performed through the fragment-based topological design (FBTD) approach. Such interpretations permitted the analysis of different molecular fragments with favorable contributions to the multi-strain antibacterial activity and the design of four new drug-like molecules using different fragments as building blocks. The designed molecules were predicted/confirmed by our PTML model as multi-strain inhibitors of diverse S. aureus strains, thus representing promising chemotypes to be considered for future synthesis and biological testing of versatile anti-S. aureus agents. Conclusions: This work envisages promising applications of PTML modeling for early antibacterial drug discovery and related antimicrobial research areas.

Artificial Intelligence-Driven Modeling for Hydrogel Three-Dimensional Printing: Computational and Experimental Cases of Study

Determining the values of various properties for new bio-inks for 3D printing is a very important task in the design of new materials. For this purpose, a large number of experimental works have been consulted, and a database with more than 1200 bioprinting tests has been created. These tests cover different combinations of conditions in terms of print pressure, temperature, and needle values, for example. These data are difficult to deal with in terms of determining combinations of conditions to optimize the tests and analyze new options. The best model demonstrated a specificity (Sp) of 88.4% and a sensitivity (Sn) of 86.2% in the training series while achieving an Sp of 85.9% and an Sn of 80.3% in the external validation series. This model utilizes operators based on perturbation theory to analyze the complexity of the data. For comparative purposes, neural networks have been used, and very similar results have been obtained. The developed tool could easily be applied to predict the properties of bioprinting assays in silico. These findings could significantly improve the efficiency and accuracy of predictive models in bioprinting without resorting to trial-and-error tests, thereby saving time and funds. Ultimately, this tool may help pave the way for advances in personalized medicine and tissue engineering.

From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine

Prostate cancer is the most common cancer in men worldwide and has a high mortality rate. The complex and heterogeneous development of prostate cancer has become a core obstacle in the treatment of prostate cancer. Simultaneously, the issues of overtreatment in early-stage diagnosis, oligometastasis and dormant tumor recognition, as well as personalized drug utilization, are also specific concerns that require attention in the clinical management of prostate cancer. Some typical genetic mutations have been proved to be associated with prostate cancer's initiation and progression. However, single-omic studies usually are not able to explain the causal relationship between molecular alterations and clinical phenotypes. Exploration from a systems genetics perspective is also lacking in this field, that is, the impact of gene network, the environmental factors, and even lifestyle behaviors on disease progression. At the meantime, current trend emphasizes the utilization of artificial intelligence (AI) and machine learning techniques to process extensive multidimensional data, including multi-omics. These technologies unveil the potential patterns, correlations, and insights related to diseases, thereby aiding the interpretable clinical decision making and applications, namely intelligent medicine. Therefore, there is a pressing need to integrate multidimensional data for identification of molecular subtypes, prediction of cancer progression and aggressiveness, along with perosonalized treatment performing. In this review, we systematically elaborated the landscape from molecular mechanism discovery of prostate cancer to clinical translational applications. We discussed the molecular profiles and clinical manifestations of prostate cancer heterogeneity, the identification of different states of prostate cancer, as well as corresponding precision medicine practices. Taking multi-omics fusion, systems genetics, and intelligence medicine as the main perspectives, the current research results and knowledge-driven research path of prostate cancer were summarized.

Perturbation Theory Machine Learning Model for Phenotypic Early Antineoplastic Drug Discovery: Design of Virtual Anti-Lung-Cancer Agents

Lung cancer is the most diagnosed malignant neoplasm worldwide and it is associated with great mortality. Currently, developing antineoplastic agents is a challenging, time-consuming, and costly process. Computational methods can speed up the early discovery of anti-lung-cancer chemicals. Here, we report a perturbation theory machine learning model based on a multilayer perceptron (PTML-MLP) model for phenotypic early antineoplastic drug discovery, enabling the rational design and prediction of new molecules as virtual versatile inhibitors of multiple lung cancer cell lines. The PTML-MLP model achieved an accuracy above 80%. We applied the fragment-based topological design (FBTD) approach to physicochemically and structurally interpret the PTML-MLP model. This enabled the extraction of suitable fragments with a positive influence on anti-lung-cancer activity against the different lung cancer cell lines. By following the aforementioned interpretations, we could assemble several suitable fragments to design four novel molecules, which were predicted by the PTML-MLP model as versatile anti-lung-cancer agents. Such predictions of potent multi-cellular anticancer activity against diverse lung cancer cell lines were rigorously confirmed by a well-established virtual screening tool reported in the literature. The present work envisages new opportunities for the application of PTML models to accelerate early antineoplastic discovery from phenotypic assays.

A breast cancer-specific combinational QSAR model development using machine learning and deep learning approaches

Breast cancer is the most prevalent and heterogeneous form of cancer affecting women worldwide. Various therapeutic strategies are in practice based on the extent of disease spread, such as surgery, chemotherapy, radiotherapy, and immunotherapy. Combinational therapy is another strategy that has proven to be effective in controlling cancer progression. Administration of Anchor drug, a well-established primary therapeutic agent with known efficacy for specific targets, with Library drug, a supplementary drug to enhance the efficacy of anchor drugs and broaden the therapeutic approach. Our work focused on harnessing regression-based Machine learning (ML) and deep learning (DL) algorithms to develop a structure-activity relationship between the molecular descriptors of drug pairs and their combined biological activity through a QSAR (Quantitative structure-activity relationship) model. 11 popularly known machine learning and deep learning algorithms were used to develop QSAR models. A total of 52 breast cancer cell lines, 25 anchor drugs, and 51 library drugs were considered in developing the QSAR model. It was observed that Deep Neural Networks (DNNs) achieved an impressive R2 (Coefficient of Determination) of 0.94, with an RMSE (Root Mean Square Error) value of 0.255, making it the most effective algorithm for developing a structure-activity relationship with strong generalization capabilities. In conclusion, applying combinational therapy alongside ML and DL techniques represents a promising approach to combating breast cancer.

Optimizing drug discovery using multitasking models for quantitative structure-biological effect relationships: an update of the literature

INTRODUCTION

Drug discovery has provided modern societies with the means to fight against many diseases. In this sense, computational methods have been at the forefront, playing an important role in rationalizing the search for novel drugs. Yet, tackling phenomena such as the multi-genic nature of diseases and drug resistance are limitations of the current computational methods. Multi-tasking models for quantitative structure-biological effect relationships (mtk-QSBER) have emerged to overcome such limitations.

AREAS COVERED

The present review describes an update on the fundamentals and applications of the mtk-QSBER models as tools to accelerate multiple stages/substages of the drug discovery process.

EXPERT OPINION

Computational approaches are extremely important for the rationalization of the search for novel and efficacious therapeutic agents. However, they need to focus more on the multi-target drug discovery paradigm. In this sense, mtk-QSBER models are particularly suited for multi-target drug discovery, offering encouraging opportunities across multiple therapeutic areas and scientific disciplines associated with drug discovery.