Machine learning-based solubility prediction and methodology evaluation of active pharmaceutical ingredients in industrial crystallization

Advancements in small molecule drug design: A structural perspective

In this review, we outline recent advancements in small molecule drug design from a structural perspective. We compare protein structure prediction methods and explore the role of the ligand binding pocket in structure-based drug design. We examine various structural features used to optimize drug candidates, including functional groups, stereochemistry, and molecular weight. Computational tools such as molecular docking and virtual screening are discussed for predicting and optimizing drug candidate structures. We present examples of drug candidates designed based on their molecular structure and discuss future directions in the field. By effectively integrating structural information with other valuable data sources, we can improve the drug discovery process, leading to the identification of novel therapeutics with improved efficacy, specificity, and safety profiles.

Yield and Properties Prediction Based on the Multicondition LSTM Model for the Solvent Deasphalting Process

Solvent deasphalting (SDA) is a complex multiscale continuous process. The operation mode of the SDA process is not considered in the related data-driven model. Therefore, this paper proposes a time lag process prediction model with multiple operation modes to solve the above problem. First, based on random forests, the relative importance of initial input variables in the SDA process on DAO yield and Conradson carbon residual are studied and features are selected according to the results. Then, the stack denoising autoencoder (SDAE) is used to reconstruct the data and obtain the nonlinear mapping information of hidden layers of SDAE and achieve feature dimension reduction. SDAE can improve clustering accuracy of fuzzy c-means, and the operation mode of SDA process is accurately divided. Long short-term memory (LSTM) is used to establish a multicondition LSTM model. Compared with the traditional LSTM model, the multicondition LSTM model has a higher prediction accuracy with R ² > 0.95. The sensitivity analyses of the properties of feed and operating conditions on DAO yield are consistent with the principle of two-phase countercurrent extraction in the SDA process. In addition, the benchmark test of the Tennessee Eastman process shows that the proposed method is also effective in the fault detection of other processes. Because the multicondition LSTM can predict the future process measurement data according to operating mode, it can better avoid the false alarm problem and predict the fault earlier.

An Integrated Method of Bayesian Optimization and D-Optimal Design for Chemical Experiment Optimization

The smart chemical laboratory has recently emerged as a promising trend for future chemical research, where experiment optimization is of vital importance. The traditional Bayesian optimization (BO) algorithm focuses on exploring the dependent variable space while overlooking the independent variable space. Consequently, the BO algorithm suffers from becoming stuck at local optima, which severely deteriorates the optimization performance, especially with bad-quality initial points. Herein, we propose a novel stochastic framework of Bayesian optimization with D-optimal design (BODO) by integrating BO with D-optimal design. BODO can balance the exploitation in the dependent variable space and the exploration in the independent variable space. We highlight the excellent performance of BODO even with poor initial points on the benchmark alpine2 function. Meanwhile, BODO demonstrates a better average objective function value than BO on the benchmark Summit SnAr chemical process, showing its advantage in chemical experiment optimization and potential application in future chemical experiments.

Cocrystal Prediction of Bexarotene by Graph Convolution Network and Bioavailability Improvement

Bexarotene (BEX) was approved by the FDA in 1999 for the treatment of cutaneous T-cell lymphoma (CTCL). The poor aqueous solubility causes the low bioavailability of the drug and thereby limits the clinical application. In this study, we developed a GCN-based deep learning model (CocrystalGCN) for in-silico screening of the cocrystals of BEX. The results show that our model obtained high performance relative to baseline models. The top 30 of 109 coformer candidates were scored by CocrystalGCN and then validated experimentally. Finally, cocrystals of BEX-pyrazine, BEX-2,5-dimethylpyrazine, BEX-methyl isonicotinate, and BEX-ethyl isonicotinate were successfully obtained. The crystal structures were determined by single-crystal X-ray diffraction. Powder X-ray diffraction, differential scanning calorimetry, and thermogravimetric analysis were utilized to characterize these multi-component forms. All cocrystals present superior solubility and dissolution over the parent drug. The pharmacokinetic studies show that the plasma exposures (AUC_0−8h) of BEX-pyrazine and BEX-2,5-dimethylpyrazine are 1.7 and 1.8 times that of the commercially available BEX powder, respectively. This work sets a good example for integrating virtual prediction and experimental screening to discover the new cocrystals of water-insoluble drugs.

Applications of Artificial Intelligence and Machine Learning Algorithms to Crystallization

Artificial intelligence and specifically machine learning applications are nowadays used in a variety of scientific applications and cutting-edge technologies, where they have a transformative impact. Such an assembly of statistical and linear algebra methods making use of large data sets is becoming more and more integrated into chemistry and crystallization research workflows. This review aims to present, for the first time, a holistic overview of machine learning and cheminformatics applications as a novel, powerful means to accelerate the discovery of new crystal structures, predict key properties of organic crystalline materials, simulate, understand, and control the dynamics of complex crystallization process systems, as well as contribute to high throughput automation of chemical process development involving crystalline materials. We critically review the advances in these new, rapidly emerging research areas, raising awareness in issues such as the bridging of machine learning models with first-principles mechanistic models, data set size, structure, and quality, as well as the selection of appropriate descriptors. At the same time, we propose future research at the interface of applied mathematics, chemistry, and crystallography. Overall, this review aims to increase the adoption of such methods and tools by chemists and scientists across industry and academia.