Hiroaki Iwata

Spliced alignment plays a central role in the precise identification of eukaryotic gene structures. Even though many spliced alignment programs have been developed, recent rapid progress in DNA sequencing technologies demands further improvements in software tools. Benchmarking algorithms under various conditions is an indispensable task for the development of better software; however, there is a dire lack of appropriate datasets usable for benchmarking spliced alignment programs. In this study,

Drug repositioning, or the application of known drugs to new indications, is a challenging issue in pharmaceutical science. In this study, we developed a new computational method to predict unknown drug indications for systematic drug repositioning in a framework of supervised network inference. We defined a descriptor for each drug-disease pair based on the phenotypic features of drugs (e.g., medicinal effects and side effects) and various molecular features of diseases (e.g., disease-causing g

Pharmacokinetic research plays an important role in the development of new drugs. Accurate predictions of human pharmacokinetic parameters are essential for the success of clinical trials. Clearance (CL) and volume of distribution (Vd) are important factors for evaluating pharmacokinetic properties, and many previous studies have attempted to use computational methods to extrapolate these values from nonclinical laboratory animal models to human subjects. However, it is difficult to obtain suffi

Overall, the present study indicates that both splicing signals themselves and their relative contributions to short intron recognition are rather susceptible to evolutionary changes, while some poorly characterized properties seem to be preserved within the mammalian intron subtypes. Our findings may afford additional clues to understanding of evolution of splicing mechanisms.

The identification of beneficial drug combinations is a challenging issue in pharmaceutical and clinical research toward combinatorial drug therapy. In the present study, we developed a novel computational method for large-scale prediction of beneficial drug combinations using drug efficacy and target profiles. We designed an informative descriptor for each drug-drug pair based on multiple drug profiles representing drug-targeted proteins and Anatomical Therapeutic Chemical Classification System

Research into pharmacokinetics plays an important role in the development process of new drugs. Accurately predicting human pharmacokinetic parameters from preclinical data can increase the success rate of clinical trials. Since clearance (CL) which indicates the capacity of the entire body to process a drug is one of the most important parameters, many methods have been developed. However, there are still rooms to be improved for practical use in drug discovery research; "improving CL predictio

Phenotypic and target-based approaches are useful methods in drug discovery. The phenotypic approach is an experimental approach for evaluating the phenotypic response. The target-based approach is a rational approach for screening drug candidates targeting a biomolecule that causes diseases. These approaches are widely used for drug discovery. However, two serious problems of target deconvolution and polypharmacology are encountered in these conventional experimental approaches. To overcome the

Drug discovery is researched and developed through many processes, but its overall success rate is extremely low, requiring a very long period of development and considerable costs. Clearly, there is a need to reduce research and development costs by improving the probability of success and increasing process efficiency. One promising approach to this challenge is so-called "in silico drug discovery," which is drug discovery utilizing information and communications technologies (ICT) such as art

Scanning electron microscopy (SEM) images are the most widely used tool for evaluating particle morphology; however, quantitative evaluation using SEM images is time-consuming and often neglected. In this study, we aimed to extract features related to particle morphology of pharmaceutical excipients from SEM images using a convolutional neural network (CNN). SEM images of 67 excipients were acquired and used as models. A classification CNN model of the excipients was constructed based on the SEM

Recent research has increasingly focused on using machine learning for covariate selection in population pharmacokinetics (PPK) analysis. However, few studies have explored the prediction of plasma concentration profiles of drugs using nonlinear mixed-effect models combined with machine learning. This gap includes limited validation of prediction accuracy and applicability to diverse patient populations and dosing conditions. This study addresses these gaps by using remifentanil as a model drug

Understanding the molecular mechanisms governing sweetness and bitterness is essential for identifying desirable taste characteristics in natural and synthetic compounds. In this study, we developed graph neural network (GNN)-based artificial intelligence (AI) models to predict bitterness and sweetness based on chemical structure. GNNs utilize deep learning to capture relationships among molecular components within a graph, extracting latent molecular vectors. Unlike conventional methods relying

The pharmaceutical industry has increasingly adopted model-informed drug discovery and development (MID3) to enhance productivity in drug discovery and development. Quantitative systems pharmacology (QSP), which integrates drug action mechanisms and disease complexities to predict clinical endpoints and biomarkers is central to MID3. QSP modeling has proven successful in metabolic and cardiovascular diseases and has expanded into oncology, immunotherapy, and infectious diseases. Despite its bene

The process of developing new drugs in the pharmaceutical industry is both time-consuming and costly, making efficiency crucial. Recent advances in hardware and computational methods have led to the widespread application of computational science approaches in drug discovery. These approaches, including artificial intelligence and molecular simulations, span from target identification to pharmacokinetics research, aiming to reduce the likelihood of failure and present lower costs. Machine learni

Abstract Molecular generation is crucial for advancing drug discovery, materials science, and chemical exploration. It expedites the search for new drug candidates, facilitates tailored material creation, and enhances our understanding of molecular diversity. By employing artificial intelligence techniques, such as molecular generative models based on molecular graphs, researchers have tackled the challenge of identifying efficient molecules with desired properties. Here, we propose a new molecu