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Fragment-Based Drug Design (FBDD) plays a pivotal role in the field of drug discovery and development. The construction of high-quality fragment libraries is a critical step in FBDD. Conventional fragmentation approaches often rely on rigid rules and chemical intuition, limiting their adaptability to diverse molecular structures. The rapid development of Artificial Intelligence (AI) technology offers a transformative opportunity to rethink traditional methods. Here, we present DigFrag, a digital fragmentation method that highlights important substructures by focusing locally within the molecular graph. In addition, we feed the fragments segmented by machine intelligence and human expertise into the deep generative model to compare the preference for data from different sources. Experimental results show that the structural diversity of fragments segmented by DigFrag is higher, and more desirable compounds are generated based on these fragments. These results also demonstrate that data generated based on AI methods may be more suitable for AI models. Moreover, a user-friendly platform called MolFrag ( https://dpai.ccnu.edu.cn/MolFrag/ ) is developed based on various fragmentation techniques to support molecular segmentation., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Pesticide molecules, such as insecticides, play a critical role in modern agricultural production. Traditional pesticide development methods are often inefficient and expensive, while data-driven artificial intelligence (AI) techniques have emerged as a useful tool to facilitate drug discovery. However, currently available commercial pesticide data is limited, which makes the trained models unsatisfactory in terms of performance and generalization. From a domain knowledge perspective, insect toxicity data were incorporated to improve the insecticide recognition of AI models. Compared to the models trained with the original data set, the new models performed better in the external validation, and their generalization was more desirable. In addition, by integrating different types of individual models, we obtained an ensemble model with better performance. Based on this, an online platform was developed to provide researchers with free access to insecticide screening (https://dpai.ccnu.edu.cn/InsectiVS/). Finally, two potential insecticide molecules with insecticidal activity against Plutella xylostella were successfully identified in a real-world scenario. In conclusion, this idea connects the fields of AI and agricultural chemistry and is expected to have wide application in pesticide research.

Adaptive behavior requires the ability to shift responding within (intra-dimensional) or between (extra-dimensional) stimulus dimensions when reward contingencies change. Studies of shifting in humans have focused mainly on the prefrontal cortex and/ or have been restricted to indirect measures of neural activity such as fMRI and lesions. Here, we demonstrate the importance of the amygdala and hippocampus by recording local field potentials directly from these regions intracranially in human epilepsy patients. Reward signals were coded in the high frequency gamma activity (HFG; 60-250 Hz) of both regions and synchronised via low frequency (3-5 Hz) phase-locking only after a shift when patients did not already know the rule and it signalled to stop shifting ("Win-Stay"). In contrast, HFG punishment signals were only seen in the amygdala when the rule then changed and it signalled to start shifting ("Lose-Shift"). During decision-making, hippocampal HFG was more inhibited on non-shift relative to shift trials, suggesting a role in preventing interference in rule representation and amygdala HFG was sensitive to stimulus novelty. The findings expand our understanding of human amygdala-hippocampal function and shifting processes, the disruption of which could contribute to shifting deficits in neuropsychiatric disorders., (© 2024. The Author(s).)

Determination of protein-ligand binding affinity (PLA) is a key technological tool in hit discovery and lead optimization, which is critical to the drug development process. PLA can be determined directly by experimental methods, but it is time-consuming and costly. In recent years, deep learning has been widely applied to PLA prediction, the key of which lies in the comprehensive and accurate representation of proteins and ligands. In this study, we proposed a multi-modal deep learning model based on the early fusion strategy, called DeepLIP, to improve PLA prediction by integrating multi-level information, and further used it for virtual screening of extracellular signal-regulated protein kinase 2 (ERK2), an ideal target for cancer treatment. Experimental results from model evaluation showed that DeepLIP achieved superior performance compared to state-of-the-art methods on the widely used benchmark dataset. In addition, by combining previously developed machine learning models and molecular dynamics simulation, we screened three novel hits from a drug-like natural product library. These compounds not only had favorable physicochemical properties, but also bound stably to the target protein. We believe they have the potential to serve as starting molecules for the development of ERK2 inhibitors., (© 2024. The Author(s).)

Neurons in the primate lateral habenula fire in response to punishments and are inhibited by rewards. Through its modulation of midbrain monoaminergic activity, the habenula is believed to play an important role in adaptive behavioural responses to punishment and underlie depressive symptoms and their alleviation with ketamine. However, its role in value-based decision-making in humans is poorly understood due to limitations with non-invasive imaging methods which measure metabolic, not neural, activity with poor temporal resolution. Here, we overcome these limitations to more closely bridge the gap between species by recording local field potentials directly from the habenula in 12 human patients receiving deep brain stimulation treatment for bipolar disorder (n = 4), chronic pain (n = 3), depression (n = 3) and schizophrenia (n = 2). This allowed us to record neural activity during value-based decision-making tasks involving monetary rewards and losses. High-frequency gamma (60-240 Hz) activity, a proxy for population-level spiking involved in cognitive computations, increased during the receipt of loss and decreased during receipt of reward. Furthermore, habenula high gamma also encoded risk during decision-making, being larger in amplitude for high compared to low risk. For both risk and aversion, differences between conditions peaked approximately between 400 and 750 ms after stimulus onset. The findings not only demonstrate homologies with the primate habenula but also extend its role to human decision-making, showing its temporal dynamics and suggesting revisions to current models. The findings suggest that habenula high gamma could be used to optimize real-time closed-loop deep brain stimulation treatment for mood disturbances and impulsivity in psychiatric disorders., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Guarantors of Brain.)

Matrix metalloproteinase-2 (MMP-2) is capable of degrading Collage TypeIV in the vascular basement membrane and extracellular matrix. Studies have shown that MMP-2 is tightly associated with the biological behavior of malignant tumors. Therefore, the identification of inhibitors targeting MMP-2 could be effective in treating the disease by maintaining extracellular matrix homeostasis. In the pharmaceutical and biomedical fields, many computational tools are widely used, which improve the efficiency of the whole process to some extent. Apart from the conventional cheminformatics approaches (e.g., pharmacophore model and molecular docking), virtual screening strategies based on machine learning also have promising applications. In this study, we collected 2871 compound activity data against MMP-2 from the ChEMBL database and divided the training and test sets in a 3:1 ratio. Four machine learning algorithms were then selected to construct the classification models, and the best-performing model, i.e., the stacking-based fusion model with the highest AUC value in both training and test datasets, was used for the virtual screening of ZINC database. Next, we screened 17 potential MMP-2 inhibitors from the results predicted by the machine learning model via ADME/T analysis. The interactions between these compounds and the target protein were explored through molecular docking calculations, and the results showed that ZINC712249, ZINC4270723, and ZINC15858504 had lower binding free energies than the co-crystal ligand. To further examine the binding stability of the complexes, we performed molecular dynamics simulations and finally identified these three hits as the most promising natural products for MMP-2 inhibitors., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

The amygdala, orbitofrontal cortex (OFC) and medial prefrontal cortex (mPFC) form a crucial part of the emotion circuit, yet their emotion induced responses and interactions have been poorly investigated with direct intracranial recordings. Such high-fidelity signals can uncover precise spectral dynamics and frequency differences in valence processing allowing novel insights on neuromodulation. Here, leveraging the unique spatio-temporal advantages of intracranial electroencephalography (iEEG) from a cohort of 35 patients with intractable epilepsy (with 71 contacts in amygdala, 31 in OFC and 43 in mPFC), we assessed the spectral dynamics and interactions between the amygdala, OFC and mPFC during an emotional picture viewing task. Task induced activity showed greater broadband gamma activity in the negative condition compared to positive condition in all the three regions. Similarly, beta activity was increased in the negative condition in the amygdala and OFC while decreased in mPFC. Furthermore, beta activity of amygdala showed significant negative association with valence ratings. Critically, model-based computational analyses revealed unidirectional connectivity from mPFC to the amygdala and bidirectional communication between OFC-amygdala and OFC-mPFC. Our findings provide direct neurophysiological evidence for a much-posited model of top-down influence of mPFC over amygdala and a bidirectional influence between OFC and the amygdala. Altogether, in a relatively large sample size with human intracranial neuronal recordings, we highlight valence-dependent spectral dynamics and dyadic coupling within the amygdala-mPFC-OFC network with implications for potential targeted neuromodulation in emotion processing., (© 2022. The Author(s).)

The integration of multiple virtual screening strategies facilitates the balance of computational efficiency and prediction accuracy. In this study, we constructed an efficient and reliable "multi-stage virtual screening-in vitro biological validation" system to identify potential inhibitors targeting extracellular signal-regulated protein kinase 2 (ERK2). Firstly, we rapidly obtained 10 candidate ERK2 inhibitors with desirable pharmacokinetic characteristics from thousands of named natural products in ZINC database based on machine learning classification models and ADME/T prediction. The structure-based molecular docking approach was then used to obtain four further hits with lower binding free energy compared to the positive control molecule Magnolipin. Subsequently, the two compounds were purchased for in vitro biological validation considering commercial availability and economic cost, and the results showed that Dodoviscin A exhibited acceptable inhibitory activity on ERK2 (IC 50 = 10.79 μm). Finally, the mechanism of action and binding stability of this natural product inhibitor were investigated by binding mode analysis and molecular dynamics simulation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Yang, Zhao, Zhang, Xia, Yu, Yan and Cheng.)

Ginseng is an important medicinal plant benefiting human health for thousands of years. Root disease is the main cause of ginseng yield loss. It is difficult to detect ginseng root disease by manual observation on the changes of leaves, as it takes a long time until symptoms appear on leaves after the infection on roots. In order to detect root diseases at early stages and limit their further spread, an efficient and non-destructive testing (NDT) method is urgently needed. Hyperspectral remote sensing technology was performed in this study to discern whether ginseng roots were diseased. Hyperspectral reflectance of leaves at 325-1,075 nm were collected from the ginsengs with no symptoms on leaves at visual. These spectra were divided into healthy and diseased groups according to the symptoms on roots after harvest. The hyperspectral data were used to construct machine learning classification models including random forest, extreme random tree (ET), adaptive boosting and gradient boosting decision tree respectively to identify diseased ginsengs, while calculating the vegetation indices and analyzing the region of specific spectral bands. The precision rates of the ET model preprocessed by savitzky golay method for the identification of healthy and diseased ginsengs reached 99% and 98%, respectively. Combined with the preliminary analysis of band importance, vegetation indices and physiological characteristics, 690-726 nm was screened out as a specific band for early detection of ginseng root diseases. Therefore, underground root diseases can be effectively detected at an early stage by leaf hyperspectral reflectance. The NDT method for early detection of ginsengs root diseases is proposed in this study. The method is helpful in the prevention and control of root diseases of ginsengs to prevent the reduction of ginseng yield., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhao, Pei, Yang, Xiang, Fang, Wang, Yin, Wu, Gao, Yu and Li.)

c-Jun N-terminal kinase 1 (JNK1) is currently considered a critical therapeutic target for type-2 diabetes. In recent years, there has been a great interest in naturopathic molecules, and the discovery of active ingredients from natural products for specific targets has received increasing attention. Based on the above background, this research aims to combine emerging Artificial Intelligence technologies with traditional Computer-Aided Drug Design methods to find natural products with JNK1 inhibitory activity. First, we constructed three machine learning models (Support Vector Machine, Random Forest, and Artificial Neural Network) and performed model fusion based on Voting and Stacking strategies. The integrated models with better performance (AUC of 0.906 and 0.908, respectively) were then employed for the virtual screening of 4112 natural products in the ZINC database. After further drug-likeness filtering, we calculated the binding free energy of 22 screened compounds using molecular docking and performed a consensus analysis of the two methodologies. Subsequently, we identified the three most promising candidates (Lariciresinol, Tricin, and 4'-Demethylepipodophyllotoxin) according to the obtained probability values and relevant reports, while their binding characteristics were preliminarily explored by molecular dynamics simulations. Finally, we performed in vitro biological validation of these three compounds, and the results showed that Tricin exhibited an acceptable inhibitory activity against JNK1 (IC 50 = 17.68 μM). This natural product can be used as a template molecule for the design of novel JNK1 inhibitors.

p38α is a mitogen-activated protein kinase (MAPK), and the signaling pathways involved are closely related to the inflammation, apoptosis and differentiation of cells, which also makes it an attractive target for drug discovery. With the high efficiency and low cost, virtual screening technology is becoming an indispensable part of drug development. In this study, a novel multi-stage virtual screening method based on machine learning, molecular docking and molecular dynamics simulation was developed to identify p38α MAPK inhibitors from natural products in ZINC database, which improves the prediction accuracy by considering and utilizing both ligand and receptor information compared to any individual approach. Ultimately, we screened out two candidate inhibitors with acceptable ADMET properties (ZINC4260400 and ZINC8300300). Among the generated machine learning models, Random Forest (RF) and Support Vector Machine (SVM) performed better, with the area under the receiver operating characteristic curve (AUC) values of 0.932 and 0.931 on the test set, as well as 0.834 and 0.850 on the external validation set. In addition, the results of molecular docking and ADMET prediction showed that two compounds with appropriate pharmacokinetic properties had binding free energies less than -8.0 kcal/mol for the target protein, and the results of molecular dynamics simulations further confirmed that they were stable during the process of inhibition., Competing Interests: The authors declare no conflict of interest., (© 2022 The Author(s).)

Neurophysiological work in primates and rodents have shown the amygdala plays a central role in reward processing through connectivity with the orbitofrontal cortex (OFC) and hippocampus. However, understanding the role of oscillations in each region and their connectivity in different stages of reward processing in humans has been hampered by limitations with noninvasive methods such as poor spatial and temporal resolution. To overcome these limitations, we recorded local field potentials (LFPs) directly from the amygdala, OFC and hippocampus simultaneously in human male and female epilepsy patients performing a monetary incentive delay (MID) task. This allowed us to dissociate electrophysiological activity and connectivity patterns related to the anticipation and receipt of rewards and losses in real time. Anticipation of reward increased high-frequency gamma (HFG; 60-250 Hz) activity in the hippocampus and theta band (4-8 Hz) synchronization between amygdala and OFC, suggesting roles in memory and motivation. During receipt, HFG in the amygdala was involved in outcome value coding, the OFC cue context-specific outcome value comparison and the hippocampus reward coding. Receipt of loss decreased amygdala-hippocampus theta and increased amygdala-OFC HFG amplitude coupling which coincided with subsequent adjustments in behavior. Increased HFG synchronization between the amygdala and hippocampus during reward receipt suggested encoding of reward information into memory for reinstatement during anticipation. These findings extend what is known about the primate brain to humans, showing key spectrotemporal coding and communication dynamics for reward and punishment related processes which could serve as more precise targets for neuromodulation to establish causality and potential therapeutic applications. SIGNIFICANCE STATEMENT Dysfunctional reward processing contributes to many psychiatric disorders. Neurophysiological work in primates has shown the amygdala, orbitofrontal cortex (OFC), and hippocampus play a synergistic role in reward processing. However, because of limitations with noninvasive imaging, it is unclear whether the same interactions occur in humans and what oscillatory mechanisms underpin them. We addressed this issue by recording local field potentials (LFPs) from all three regions in human epilepsy patients during monetary reward processing. There was increased amygdala-OFC high-frequency coupling when losing money which coincided with subsequent adjustments in behavior. In contrast, increased amygdala-hippocampus high-frequency phase-locking suggested a role in reward memory. The findings highlight amygdala networks for reward and punishment processes that could act as more precise neuromodulation targets to treat psychiatric disorders., (Copyright © 2022 the authors.)