Predicting drug/phospholipid complexation by the lightGBM method

Recent advancements toward the incremsent of drug solubility using environmentally-friendly supercritical CO2: a machine learning perspective

Inadequate bioavailability of therapeutic drugs, which is often the consequence of their unacceptable solubility and dissolution rates, is an indisputable operational challenge of pharmaceutical companies due to its detrimental effect on the therapeutic efficacy. Over the recent decades, application of supercritical fluids (SCFs) (mainly SCCO2) has attracted the attentions of many scientists as promising alternative of toxic and environmentally-hazardous organic solvents due to possessing positive advantages like low flammability, availability, high performance, eco-friendliness and safety/simplicity of operation. Nowadays, application of different machine learning (ML) as a versatile, robust and accurate approach for the prediction of different momentous parameters like solubility and bioavailability has been of great attentions due to the non-affordability and time-wasting nature of experimental investigations. The prominent goal of this article is to review the role of different ML-based tools for the prediction of solubility/bioavailability of drugs using SCCO2. Moreover, the importance of solubility factor in the pharmaceutical industry and different possible techniques for increasing the amount of this parameter in poorly-soluble drugs are comprehensively discussed. At the end, the efficiency of SCCO2 for improving the manufacturing process of drug nanocrystals is aimed to be discussed.

Computer-driven formulation development of Ginsenoside Rh2 ternary solid dispersion

(20 S)-Ginsenoside Rh2 is a natural saponin derived from Panax ginseng Meyer (P. ginseng), which showed significantly potent anticancer properties. However, its low water solubility and bioavailability strongly restrict its pharmaceutical applications. The aim of current research is to develop a modified (20 S)-Ginsenoside Rh2 formulation with high solubility, dissolution rate and bioavailability by combined computational and experimental methodology. The "PharmSD" model was employed to predict the optimal polymer for (20 S)-Ginsenoside Rh2 solid dispersion formulations. The solubility of (20 S)-Ginsenoside Rh2 in various polymers was assessed, and the optimal ternary solid dispersion was evaluated across different dissolution mediums. Characterization techniques included the Powder X-ray diffraction (PXRD) and Fourier transform infrared spectroscopy (FTIR). Molecular dynamics simulations were employed to elucidate the formation mechanism of the solid dispersion and the interactions among active pharmaceutical ingredient (API) and excipient molecules. Cell and animal experiments were conducted to evaluate the in vivo performance of the modified formulation. The "PharmSD" solid dispersion model identified Gelucire 44/14 as the most effective polymer for enhancing the dissolution rate of Rh2. Subsequent experiment also confirmed that Gelucire 44/14 outperformed the other selected polymers. Moreover, the addition of the third component, sodium dodecyl sulfate (SDS), in the ternary solid dispersion formulation significantly amplified dissolution rates than the binary systems. Characterization experiments revealed that the API existed in an amorphous state and interacted via hydrogen bonding with SDS and Gelucire. Moreover, molecular modeling results provided additional evidence of hydrogen bonding interactions between the API and excipient molecules within the optimal ternary solid dispersion. Cell experiments demonstrated efflux ratio (EfR) of Rh2 ternary solid dispersion was lower than that of pure Rh2. In vivo experiments revealed that the modified formulation substantially improved the absorption of Rh2 in rats. Our research successfully developed an optimal ternary solid dispersion for Rh2 with high solubility, dissolution rate and bioavailability by integrated computational and experimental tools. The combination of Artificial Intelligence (AI) technology and molecular dynamics simulation is a wise way to support the future formulation development.

The Millennia-Long Development of Drugs Associated with the 80-Year-Old Artificial Intelligence Story: The Therapeutic Big Bang?

The journey of drug discovery (DD) has evolved from ancient practices to modern technology-driven approaches, with Artificial Intelligence (AI) emerging as a pivotal force in streamlining and accelerating the process. Despite the vital importance of DD, it faces challenges such as high costs and lengthy timelines. This review examines the historical progression and current market of DD alongside the development and integration of AI technologies. We analyse the challenges encountered in applying AI to DD, focusing on drug design and protein-protein interactions. The discussion is enriched by presenting models that put forward the application of AI in DD. Three case studies are highlighted to demonstrate the successful application of AI in DD, including the discovery of a novel class of antibiotics and a small-molecule inhibitor that has progressed to phase II clinical trials. These cases underscore the potential of AI to identify new drug candidates and optimise the development process. The convergence of DD and AI embodies a transformative shift in the field, offering a path to overcome traditional obstacles. By leveraging AI, the future of DD promises enhanced efficiency and novel breakthroughs, heralding a new era of medical innovation even though there is still a long way to go.

FormulationAI: a novel web-based platform for drug formulation design driven by artificial intelligence

Today, pharmaceutical industry faces great pressure to employ more efficient and systematic ways in drug discovery and development process. However, conventional formulation studies still strongly rely on personal experiences by trial-and-error experiments, resulting in a labor-consuming, tedious and costly pipeline. Thus, it is highly required to develop intelligent and efficient methods for formulation development to keep pace with the progress of the pharmaceutical industry. Here, we developed a comprehensive web-based platform (FormulationAI) for in silico formulation design. First, the most comprehensive datasets of six widely used drug formulation systems in the pharmaceutical industry were collected over 10 years, including cyclodextrin formulation, solid dispersion, phospholipid complex, nanocrystals, self-emulsifying and liposome systems. Then, intelligent prediction and evaluation of 16 important properties from the six systems were investigated and implemented by systematic study and comparison of different AI algorithms and molecular representations. Finally, an efficient prediction platform was established and validated, which enables the formulation design just by inputting basic information of drugs and excipients. FormulationAI is the first freely available comprehensive web-based platform, which provides a powerful solution to assist the formulation design in pharmaceutical industry. It is available at https://formulationai.computpharm.org/.

AmorProt: Amino Acid Molecular Fingerprints Repurposing-Based Protein Fingerprint

As protein therapeutics play an important role in almost all medical fields, numerous studies have been conducted on proteins using artificial intelligence. Artificial intelligence has enabled data-driven predictions without the need for expensive experiments. Nevertheless, unlike the various molecular fingerprint algorithms that have been developed, protein fingerprint algorithms have rarely been studied. In this study, we proposed the amino acid molecular fingerprints repurposing-based protein (AmorProt) fingerprint, a protein sequence representation method that effectively uses the molecular fingerprints corresponding to 20 amino acids. Subsequently, the performances of the tree-based machine learning and artificial neural network models were compared using (1) amyloid classification and (2) isoelectric point regression. Finally, the applicability and advantages of the developed platform were demonstrated through a case study and the following experiments: (3) comparison of dataset dependence with feature-based methods, (4) feature importance analysis, and (5) protein space analysis. Consequently, the significantly improved model performance and data-set-independent versatility of the AmorProt fingerprint were verified. The results revealed that the current protein representation method can be applied to various fields related to proteins, such as predicting their fundamental properties or interaction with ligands.

Deep Learning for Identifying Promising Drug Candidates in Drug-Phospholipid Complexes

Drug-phospholipid complexing is a promising formulation technology for improving the low bioavailability of active pharmaceutical ingredients (APIs). However, identifying whether phospholipid and candidate drug can form a complex through in vitro tests can be costly and time-consuming due to the physicochemical properties and experimental environment. In a previous study, the authors developed seven machine learning models to predict drug-phospholipid complex formation, and the lightGBM model demonstrated the best performance. However, the previous study was unable to sufficiently address the degradation of test performance caused by the small size of the training data with class imbalance, and it had the limitation of considering only machine learning techniques. To overcome these limitations, we propose a new deep learning-based prediction model that employs variational autoencoder (VAE) and principal component analysis (PCA) techniques to improve prediction performance. The model uses a multi-layer one-dimensional convolutional neural network (CNN) with a skip connection to effectively capture the complex relationship between drugs and lipid molecules. The computer simulation results demonstrate that our proposed model performs better than the previous model in all performance metrics.

Machine Learning-Enabled NIR Spectroscopy in Assessing Powder Blend Uniformity: Clear-Up Disparities and Biases Induced by Physical Artefacts

NIR spectroscopy is a non-destructive characterization tool for the blend uniformity (BU) assessment. However, NIR spectra of powder blends often contain overlapping physical and chemical information of the samples. Deconvoluting the information related to chemical properties from that associated with the physical effects is one of the major objectives of this work. We achieve this aim in two ways. Firstly, we identified various sources of variability that might affect the BU results. Secondly, we leverage the machine learning-based sophisticated data analytics processes. To accomplish the aforementioned objectives, calibration samples of amlodipine as an active pharmaceutical ingredient (API) with the concentrations ranging between 67 and 133% w/w (dose ~ 3.6% w/w), in powder blends containing excipients, were prepared using a gravimetric approach and assessed using NIR spectroscopic analysis, followed by HPLC measurements. The bias in NIR results was investigated by employing data quality metrics (DQM) and bias-variance decomposition (BVD). To overcome the bias, the clustered regression (non-parametric and linear) was applied. We assessed the model's performance by employing the hold-out and k-fold internal cross-validation (CV). NIR-based blend homogeneity with low mean absolute error and an interval estimates of 0.674 (mean) ± 0.218 (standard deviation) w/w was established. Additionally, bootstrapping-based CV was leveraged as part of the NIR method lifecycle management that demonstrated the mean absolute error (MAE) of BU ± 3.5% w/w and BU ± 1.5% w/w for model generalizability and model transferability, respectively. A workflow integrating machine learning to NIR spectral analysis was established and implemented. Impact of various data learning approaches on NIR spectral data.

A Strategy for the Effective Optimization of Pharmaceutical Formulations Based on Parameter-Optimized Support Vector Machine Model

Engineering pharmaceutical formulations is governed by a number of variables, and the finding of the optimal preparation is intricately linked to the exploration of a multiparametric space through a variety of optimization tasks. As a result, making such optimization activities simpler is a significant undertaking. For the purposes of this study, we suggested a prediction model that was based on least square support vector machine (LSSVM) and whose parameters were optimized using the particle swarm optimization algorithm (PSO-LSSVM model). Other in silico optimization methods were used and compared, including the LSSVM and the back propagation (BP) neural networks algorithm. PSO-LSSVM demonstrated the highest performance on the test dataset, with the lowest mean square error. In addition, two dosage forms, quercetin solid dispersion and apigenin nanoparticles, were selected as model formulations due to the wide range of formulation compositions and manufacturing factors used in their production. Three different models were used to predict the ideal formulations of two different dosage forms, and in real world, the Taguchi orthogonal design arrays were used to optimize the formulations of each dosage form. It is clear that the predicted performance of two formulations using PSO-LSSVM was both consistent with the outcomes of the Taguchi orthogonal planned experiment, demonstrating the model's good reliability and high usefulness. Together, our PSO-LSSVM prediction model has the potential to accurately predict the best possible formulations, reduce the reliance on experimental effort, accelerate the process of formulation design, and provide a low-cost solution to drug preparation optimization.

In silico formulation prediction of drug/cyclodextrin/polymer ternary complexes by machine learning and molecular modeling techniques

Ternary cyclodextrin (CD) complexes (drug/CD/polymer) can effectively improve the solubility of water-insoluble drugs with large size than binary CD formulations. However, ternary formulations are screened by a trial-and-error approach, which is laborious and material-wasting. Current research aims to develop a prediction model for ternary CD formulations by combined machine learning and molecular modeling. 596 ternary formulations data were collected to build a prediction model by machine learning. The random forest model achieved good performance with R² = 0.887 in S_T prediction and R² = 0.815 in S_T/S_B prediction. Two ternary formulations (Hydrocortisone/β-CD/HPMC and dovitinib/γ-CD/CMC) were used to validate the prediction model. Molecular modeling results showed that HPMC not only warped around hydrocortisone but also prevented CD molecules from self-aggregation to increase solubility. In conclusion, a prediction model for the ternary CD formulations was successfully developed, which will significantly accelerate the formulation screening process to benefit the formulation development of water-insoluble drugs.

Prediction of small-molecule compound solubility in organic solvents by machine learning algorithms

Rapid solvent selection is of great significance in chemistry. However, solubility prediction remains a crucial challenge. This study aimed to develop machine learning models that can accurately predict compound solubility in organic solvents. A dataset containing 5081 experimental temperature and solubility data of compounds in organic solvents was extracted and standardized. Molecular fingerprints were selected to characterize structural features. lightGBM was compared with deep learning and traditional machine learning (PLS, Ridge regression, kNN, DT, ET, RF, SVM) to develop models for predicting solubility in organic solvents at different temperatures. Compared to other models, lightGBM exhibited significantly better overall generalization (logS  ± 0.20). For unseen solutes, our model gave a prediction accuracy (logS  ± 0.59) close to the expected noise level of experimental solubility data. lightGBM revealed the physicochemical relationship between solubility and structural features. Our method enables rapid solvent screening in chemistry and may be applied to solubility prediction in other solvents.

Integrated in silico formulation design of self-emulsifying drug delivery systems

The drug formulation design of self-emulsifying drug delivery systems (SEDDS) often requires numerous experiments, which are time- and money-consuming. This research aimed to rationally design the SEDDS formulation by the integrated computational and experimental approaches. 4495 SEDDS formulation datasets were collected to predict the pseudo-ternary phase diagram by the machine learning methods. Random forest (RF) showed the best prediction performance with 91.3% for accuracy, 92.0% for sensitivity and 90.7% for specificity in 5-fold cross-validation. The pseudo-ternary phase diagrams of meloxicam SEDDS were experimentally developed to validate the RF prediction model and achieved an excellent prediction accuracy (89.51%). The central composite design (CCD) was used to screen the best ratio of oil-surfactant-cosurfactant. Finally, molecular dynamic (MD) simulation was used to investigate the molecular interaction between excipients and drugs, which revealed the diffusion behavior in water and the role of cosurfactants. In conclusion, this research combined machine learning, central composite design, molecular modeling and experimental approaches for rational SEDDS formulation design. The integrated computer methodology can decrease traditional drug formulation design works and bring new ideas for future drug formulation design.

Development of Arteannuin B Sustained-Release Microspheres for Anti-Tumor Therapy by Integrated Experimental and Molecular Modeling Approaches

Arteannuin B (AB) has been found to demonstrate obvious anti-tumor activity. However, AB is not available for clinical use due to its very low solubility and very short half-life. This study aimed to develop AB long sustained-release microspheres (ABMs) to improve the feasibility of clinical applications. Firstly, AB-polylactic-co-glycolic acid (PLGA) microspheres were prepared by a single emulsification method. In vitro characterization studies showed that ABMs had a low burst release and stable in vitro release for up to one week. The particle size of microspheres was 69.10 μm (D50). The drug loading is 37.8%, and the encapsulation rate is 85%. Moreover, molecular dynamics modeling was firstly used to simulate the preparation process of microspheres, which clearly indicated the molecular image of microspheres and provided in-depth insights for understanding several key preparation parameters. Next, in vivo pharmacokinetics (PK) study was carried out to evaluate its sustained release effect in Sprague-Dawley (SD) rats. Subsequently, the methyl thiazolyl tetrazolium (MTT) method with human lung cancer cells (A549) was used to evaluate the in vitro efficacy of ABMs, which showed the IC50 of ABMs (3.82 μM) to be lower than that of AB (16.03 μM) at day four. Finally, in vivo anti-tumor activity and basic toxicity studies were performed on BALB/c nude mice by subcutaneous injection once a week, four times in total. The relative tumor proliferation rate T/C of AMBs was lower than 40% and lasted for 21 days after administration. The organ index, organ staining, and tumor cell staining indicated the excellent safety of ABMs than Cis-platinum. In summary, the ABMs were successfully developed and evaluated with a low burst release and a stable release within a week. Molecular dynamics modeling was firstly applied to investigate the molecular mechanism of the microsphere preparation. Moreover, the ABMs possess excellent in vitro and in vivo anti-tumor activity and low toxicity, showing great potential for clinical applications.

Machine learning directed drug formulation development

Machine learning (ML) has enabled ground-breaking advances in the healthcare and pharmaceutical sectors, from improvements in cancer diagnosis, to the identification of novel drugs and drug targets as well as protein structure prediction. Drug formulation is an essential stage in the discovery and development of new medicines. Through the design of drug formulations, pharmaceutical scientists can engineer important properties of new medicines, such as improved bioavailability and targeted delivery. The traditional approach to drug formulation development relies on iterative trial-and-error, requiring a large number of resource-intensive and time-consuming in vitro and in vivo experiments. This review introduces the basic concepts of ML-directed workflows and discusses how these tools can be used to aid in the development of various types of drug formulations. ML-directed drug formulation development offers unparalleled opportunities to fast-track development efforts, uncover new materials, innovative formulations, and generate new knowledge in drug formulation science. The review also highlights the latest artificial intelligence (AI) technologies, such as generative models, Bayesian deep learning, reinforcement learning, and self-driving laboratories, which have been gaining momentum in drug discovery and chemistry and have potential in drug formulation development.

PharmDE: A new expert system for drug-excipient compatibility evaluation

Drug-excipient compatibility study is the essential basis for excipient selection at the pre-formulation stage. According to the pharmaceutical Quality by Design (QbD) principles, a comprehensive understanding of the ingredients' physicochemical properties and a theoretical evaluation of the interaction risk between the drugs and excipients are required for conducting rational compatibility experimental design. Currently, there is an urgent need to establish an artificial intelligence system for researchers to easily get through the problem because it is very inconvenient and hard to utilize those drug-excipient incompatibility data scattered in scientific literature. Here, we designed a knowledge-driven expert system named PharmDE for drug-excipient incompatibility risk evaluation. PharmDE firstly developed an information-rich database to store incompatibility data, covering 532 data items from 228 selected articles. Then, 60 drug-excipient interaction rules were created based on our knowledge and formulation research experiences. Finally, the expert system was developed by organically integrating the database searching and rule-based incompatibility risk prediction, which resulted in four main functionalities: basic search of incompatibility database, data matching by similarity search, drug incompatibility risk evaluation, and formulation incompatibility risk evaluation. PharmDE is expected to be a useful tool for drug-excipient compatibility study and accelerate drug formulation design. It is now freely available at https://pharmde.computpharm.org.

Review of machine learning algorithms' application in pharmaceutical technology

Machine learning algorithms, and artificial intelligence in general, have a wide range of applications in the field of pharmaceutical technology. Starting from the formulation development, through a great potential for integration within the Quality by design framework, these data science tools provide a better understanding of the pharmaceutical formulations and respective processing. Machine learning algorithms can be especially helpful with the analysis of the large volume of data generated by the Process analytical technologies. This paper provides a brief explanation of the artificial neural networks, as one of the most frequently used machine learning algorithms. The process of the network training and testing is described and accompanied with illustrative examples of machine learning tools applied in the context of pharmaceutical formulation development and related technologies, as well as an overview of the future trends. Recently published studies on more sophisticated methods, such as deep neural networks and light gradient boosting machine algorithm, have been described. The interested reader is also referred to several official documents (guidelines) that pave the way for a more structured representation of the machine learning models in their prospective submissions to the regulatory bodies.

Succinylation Site Prediction Based on Protein Sequences Using the IFS-LightGBM (BO) Model

Succinylation is an important posttranslational modification of proteins, which plays a key role in protein conformation regulation and cellular function control. Many studies have shown that succinylation modification on protein lysine residue is closely related to the occurrence of many diseases. To understand the mechanism of succinylation profoundly, it is necessary to identify succinylation sites in proteins accurately. In this study, we develop a new model, IFS-LightGBM (BO), which utilizes the incremental feature selection (IFS) method, the LightGBM feature selection method, the Bayesian optimization algorithm, and the LightGBM classifier, to predict succinylation sites in proteins. Specifically, pseudo amino acid composition (PseAAC), position-specific scoring matrix (PSSM), disorder status, and Composition of k-spaced Amino Acid Pairs (CKSAAP) are firstly employed to extract feature information. Then, utilizing the combination of the LightGBM feature selection method and the incremental feature selection (IFS) method selects the optimal feature subset for the LightGBM classifier. Finally, to increase prediction accuracy and reduce the computation load, the Bayesian optimization algorithm is used to optimize the parameters of the LightGBM classifier. The results reveal that the IFS-LightGBM (BO)-based prediction model performs better when it is evaluated by some common metrics, such as accuracy, recall, precision, Matthews Correlation Coefficient (MCC), and F-measure.

Digital Pharmaceutical Sciences

Artificial intelligence (AI) and machine learning, in particular, have gained significant interest in many fields, including pharmaceutical sciences. The enormous growth of data from several sources, the recent advances in various analytical tools, and the continuous developments in machine learning algorithms have resulted in a rapid increase in new machine learning applications in different areas of pharmaceutical sciences. This review summarizes the past, present, and potential future impacts of machine learning technologies on different areas of pharmaceutical sciences, including drug design and discovery, preformulation, and formulation. The machine learning methods commonly used in pharmaceutical sciences are discussed, with a specific emphasis on artificial neural networks due to their capability to model the nonlinear relationships that are commonly encountered in pharmaceutical research. AI and machine learning technologies in common day-to-day pharma needs as well as industrial and regulatory insights are reviewed. Beyond traditional potentials of implementing digital technologies using machine learning in the development of more efficient, fast, and economical solutions in pharmaceutical sciences are also discussed.