GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning

Fragment-based drug discovery (FBDD) is widely used in drug design. One useful strategy in FBDD is designing linkers for linking fragments to optimize their molecular properties. In the current study, we present a novel generative fragment linking model, GRELinker, which utilizes a gated-graph neural network combined with reinforcement and curriculum learning to generate molecules with desirable attributes. The model has been shown to be efficient in multiple tasks, including controlling log P, optimizing synthesizability or predicted bioactivity of compounds, and generating molecules with high 3D similarity but low 2D similarity to the lead compound. Specifically, our model outperforms the previously reported reinforcement learning (RL) built-in method DRlinker on these benchmark tasks. Moreover, GRELinker has been successfully used in an actual FBDD case to generate optimized molecules with enhanced affinities by employing the docking score as the scoring function in RL. Besides, the implementation of curriculum learning in our framework enables the generation of structurally complex linkers more efficiently. These results demonstrate the benefits and feasibility of GRELinker in linker design for molecular optimization and drug discovery

Overexpression of <i>OsSWEET5</i> in Rice Causes Growth Retardation and Precocious Senescence

<div><p>As a novel sugar transporter family, SWEETs play important roles in plant growth and development. Here, we characterized a SWEET gene named <i>OsSWEET5</i> through its overexpression in rice. Heterologous expression assay indicated that <i>OsSWEET5</i> encoded a galactose transporter in yeast. <i>OsSWEET5</i>-overexpressing plants displayed the phenotypes of growth retardation and precocious senescence at seedling stage. GC-MS analysis showed that the sugar levels were largely altered in the leaves of the <i>OsSWEET5</i>-overexpressing plants. Molecular analysis revealed that these phenotypes might be due to the transcriptional changes of the genes involved in sugar metabolism and transport. In addition, the transgenic plants showed a lower level of auxin with altered transcription of genes involved in auxin signaling and translocation pathways. However, no obvious phenotype was observed between the <i>amiRNA</i>-<i>OsSWEET5</i> transgenic lines and WT plants, which could be a result of the functional redundancy of the galactose transporters in rice. Taken together, our findings suggest that OsSWEET5 plays a crucial role in regulating the crosstalk between sugar and auxin in rice.</p></div

Additional file 1 of Willingness to pay for HPV vaccine among female health care workers in a Chinese nationwide survey

Additional file 1: Supplementary Table 1. Response to diverse initial bid amounts across sociodemographics among Chinese female health care workers. Supplementary Table 2. Attitude shift towards HPVvaccines between two payment scenarios across sociodemographics

Sugar metabolism and transport were disordered in <i>OsSWEET5</i>-overexpressing plants.

<p>(A) Sugar levels in leaves of OX2 and WT at three-leaf stage at the end of the light periods. Gal, galactose; Suc, sucrose; Glc, glucose; Fru, fructose. Statistical significance is indicated by * (<i>P</i><0.05) and ** (<i>P</i><0.01) (<i>t</i>-test, <i>n</i> = 3). FW, Fresh weight. (B) Expression analysis of key genes involved in sugar metabolism in OX2 and WT plants. The first-strand cDNAs were prepared using RNAs extracted from the second leaves of OX2 and WT plants at three-leaf stage. c qRT-PCR analysis of genes involved in sugar transport in OX2 and WT plants. The first-strand cDNAs were prepared using RNAs extracted from the second leaves of OX2 and WT plants at three-leaf stage.</p

DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design

Fragment-based drug discovery is a widely used strategy for drug design in both academic and pharmaceutical industries. Although fragments can be linked to generate candidate compounds by the latest deep generative models, generating linkers with specified attributes remains underdeveloped. In this study, we presented a novel framework, DRlinker, to control fragment linking toward compounds with given attributes through reinforcement learning. The method has been shown to be effective for many tasks from controlling the linker length and log P, optimizing predicted bioactivity of compounds, to various multiobjective tasks. Specifically, our model successfully generated 91.0% and 93.9% of compounds complying with the desired linker length and log P and improved the 7.5 pChEMBL value in bioactivity optimization. Finally, a quasi-scaffold-hopping study revealed that DRlinker could generate nearly 30% molecules with high 3D similarity but low 2D similarity to the lead inhibitor, demonstrating the benefits and applicability of DRlinker in actual fragment-based drug design

Phenotype and physiological characterization of <i>OsSWEET5</i>-overexpressing transgenic plants.

<p>(A) Photographs of WT and <i>OsSWEET5</i>-overexpressing lines (T₂) at 15 days after germination. The bar indicates 10 cm. (B) Measurement of chlorophyll content in <i>OsSWEET5</i>-overexpressing lines and WT plants. The samples were from the second leaves in (A). The results shown are the means of three independent measurements. Significant differences are calculated by <i>t</i>-test and shown by asterisks. *, <i>P</i><0.05 or **, <i>P</i><0.01. FW, Fresh weight. (C) Northern blot analysis of <i>OsSWEET5</i>-overexpressing lines. RNA was extracted from the second leaves in (A). (D) RT-PCR analysis of <i>SGR</i> in <i>OsSWEET5</i>-overexpressing lines (OX1 and OX2) and WT plants. The first-strand cDNAs were prepared using RNAs extracted from the second leaves of OX1, OX2 and WT plants at three-leaf stage.</p

Histochemical localization of <i>GUS</i> expression in <i>P_OsSWEET5</i>::GUS transgenic rice.

<p>(A) flag leaf at 40 days after heading; (B) stamen; (C) pistil; (D) hull; (E) stem; (F) root at flowering stage.</p

Subcellular localization of OsSWEET5 in rice cell protoplasts.

<p>Rice cell protoplasts were transformed using 35S::OsSWEET5-GFP (A–D) and 35S::GFP (E–G). (B) red autofluorescence signals. (C) and (F) bright field. (D) and (G) merged image. 35S::GFP was transformed as a control. The bar indicates 20 μm.</p

OsSWEET5 had sugar transporter activity involved in galactose.

<p>Growth complementation of the yeast mutant strain EBY.VW4000 was restored by OsSWEET5 on the culture medium containing galactose. N, negative control; P, positive control; OsSWEET5, p413-pHXT7-OsSWEET5.</p

FMN protects against liver injury in APAP-overdose mice.

<p>(A, B) Serum AST and ALT levels in control group, APAP group, APAP + 50 mg/kg FMN group and APAP + 100 mg/kg FMN group. (C, D) Hepatic MDA and GSH contents in control group, APAP group, APAP + 50 mg/kg FMN group and APAP + 100 mg/kg FMN group. (E) Representative photomicrograph of H&E stained liver tissues from control group, APAP group, APAP + 50 mg/kg FMN group and APAP + 100 mg/kg FMN group. Values represent the means ± SE; <i>n</i> = 4–6. (*) the APAP group <i>vs</i> control; (#) APAP+ 50 mg/kg or APAP+ 100 mg/kg <i>vs</i> the APAP group. #, <i>p</i> < 0.05; ** or ##, <i>p</i> < 0.05; *** or ###, <i>p</i> < 0.001.</p