De novo drug design through gradient-based regularized search in information-theoretically controlled latent space.

Over the last decade, automatic chemical design frameworks for discovering molecules with drug-like properties have significantly progressed. Among them, the variational autoencoder (VAE) is a cutting-edge approach that models the tractable latent space of the molecular space. In particular, the usage of a VAE along with a property estimator has attracted considerable interest because it enables gradient-based optimization of a given molecule. However, although successful results have been achieved experimentally, the theoretical background and prerequisites for the correct operation of this method have not yet been clarified. In view of the above, we theoretically analyze and rigorously reconstruct the entire framework. From the perspective of parameterized distribution and the information theory, we first describe how the previous model overcomes the limitations of the beta VAE in discovering molecules with the desired properties. Furthermore, we describe the prerequisites for training the above model. Next, from the log-likelihood perspective of each term, we reformulate the objectives for exploring latent space to generate drug-like molecules. The distributional constraints are defined in this study, which will break away from the invalid molecular search. We demonstrated that our model could discover a novel chemical compound for targeting BCL-2 family proteins in de novo approach. Through the theoretical analysis and practical implementation, the importance of the aforementioned prerequisites and constraints to operate the model was verified.

Prediction of inherited genomic susceptibility to 20 common cancer types by a supervised machine-learning method.

Prevention and early intervention are the most effective ways of avoiding or minimizing psychological, physical, and financial suffering from cancer. However, such proactive action requires the ability to predict the individual's susceptibility to cancer with a measure of probability. Of the triad of cancer-causing factors (inherited genomic susceptibility, environmental factors, and lifestyle factors), the inherited genomic component may be derivable from the recent public availability of a large body of whole-genome variation data. However, genome-wide association studies have so far showed limited success in predicting the inherited susceptibility to common cancers. We present here a multiple classification approach for predicting individuals' inherited genomic susceptibility to acquire the most likely phenotype among a panel of 20 major common cancer types plus 1 "healthy" type by application of a supervised machine-learning method under competing conditions among the cohorts of the 21 types. This approach suggests that, depending on the phenotypes of 5,919 individuals of "white" ethnic population in this study, (i) the portion of the cohort of a cancer type who acquired the observed type due to mostly inherited genomic susceptibility factors ranges from about 33 to 88% (or its corollary: the portion due to mostly environmental and lifestyle factors ranges from 12 to 67%), and (ii) on an individual level, the method also predicts individuals' inherited genomic susceptibility to acquire the other types ranked with associated probabilities. These probabilities may provide practical information for individuals, heath professionals, and health policymakers related to prevention and/or early intervention of cancer.

Seminal CD38 is a pivotal regulator for fetomaternal tolerance.

A successful pregnancy depends on a complex process that establishes fetomaternal tolerance. Seminal plasma is known to induce maternal immune tolerance to paternal alloantigens, but the seminal factors that regulate maternal immunity have yet to be characterized. Here, we show that a soluble form of CD38 (sCD38) released from seminal vesicles to the seminal plasma plays a crucial role in inducing tolerogenic dendritic cells and CD4(+) forkhead box P3(+) (Foxp3(+)) regulatory T cells (Tregs), thereby enhancing maternal immune tolerance and protecting the semiallogeneic fetus from resorption. The abortion rate in BALB/c females mated with C57BL/6 Cd38(-/-) males was high compared with that in females mated with Cd38(+/+) males, and this was associated with a reduced proportion of Tregs within the CD4(+) T-cell pool. Direct intravaginal injection of sCD38 to CBA/J pregnant mice at preimplantation increased Tregs and pregnancy rates in mice under abortive sonic stress from 48 h after mating until euthanasia. Thus, sCD38 released from seminal vesicles to the seminal plasma acts as an immunoregulatory factor to protect semiallogeneic fetuses from maternal immune responses.

The critical role of uterine CD31 as a post-progesterone signal in early pregnancy.

CD31 has been shown to play a role in endothelial cell migration and angiogenesis, which are critical to the formation and function of the endometrium and myometrium in uterine development during early pregnancy. However, the role of CD31 in uterine receptivity during blastocyst implantation is poorly understood. The pregnancy rate in CD31-/- female mice mated with CD31+/+ male mice was higher than that observed in CD31+/+ female mice mated with CD31+/+ male mice. During the receptive phase of implantation, uterine glands were more developed in CD31-/- mice than in CD31+/+ mice, and the uterine weights of CD31-/- mice were increased. Leukemia inhibitory factor (LIF) was highly expressed in the CD31-/- mice during implantation and the expression of LIF was up-regulated by estradiol-17ß (E2 ) + progesterone (P4 ) in ovariectomized CD31-/- mice, compared with CD31+/+ mice at 8 h after hormone treatment. E2 -induced protein synthesis was inhibited by P4 in the CD31+/+ uterus, but not in the uterus of CD31-/- mice. Also, STAT3, HAND2, LIF, and mTOR signals were enhanced in CD31-/- mice. Stromal DNA replication was highly activated in the uterus of CD31-/- mice, manifested by upregulated cyclin series signaling and PCNA expression after E2 + P4 treatment. Collectively, CD31 inhibits E2 -mediated epithelial proliferation via recruitment and phosphorylation of SHP-2 upon receiving P4 signal in early pregnancy.

H1 linker histone promotes epigenetic silencing by regulating both DNA methylation and histone H3 methylation.

Epigenetic silencing in mammals involves DNA methylation and posttranslational modifications of core histones. Here we show that the H1 linker histone plays a key role in regulating both DNA methylation and histone H3 methylation at the H19 and Gtl2 loci in mouse ES cells. Some, but not all, murine H1 subtypes interact with DNA methyltransferases DNMT1 and DNMT3B. The interactions are direct and require a portion of the H1 C-terminal domain. Expression of an H1 subtype that interacts with DNMT1 and DNMT3B in ES cells leads to their recruitment and DNA methylation of the H19 and Gtl2 imprinting control regions. H1 also interferes with binding of the SET7/9 histone methyltransferase to the imprinting control regions, inhibiting production of an activating methylation mark on histone H3 lysine 4. H1-dependent recruitment of DNMT1 and DNMT3B and interference with the binding of SET7/9 also were observed with chromatin reconstituted in vitro. The data support a model in which H1 plays an active role in helping direct two processes that lead to the formation of epigenetic silencing marks. The data also provide evidence for functional differences among the H1 subtypes expressed in somatic mammalian cells.

Critical role for NAD glycohydrolase in regulation of erythropoiesis by hematopoietic stem cells through control of intracellular NAD content.

NAD glycohydrolases (NADases) catalyze the hydrolysis of NAD to ADP-ribose and nicotinamide. Although many members of the NADase family, including ADP-ribosyltransferases, have been cloned and characterized, the structure and function of NADases with pure hydrolytic activity remain to be elucidated. Here, we report the structural and functional characterization of a novel NADase from rabbit reticulocytes. The novel NADase is a glycosylated, glycosylphosphatidylinositol-anchored cell surface protein exclusively expressed in reticulocytes. shRNA-mediated knockdown of the NADase in bone marrow cells resulted in a reduction of erythroid colony formation and an increase in NAD level. Furthermore, treatment of bone marrow cells with NAD, nicotinamide, or nicotinamide riboside, which induce an increase in NAD content, resulted in a significant decrease in erythroid progenitors. These results indicate that the novel NADase may play a critical role in regulating erythropoiesis of hematopoietic stem cells by modulating intracellular NAD.

OCIAD2 activates γ-secretase to enhance amyloid ß production by interacting with nicastrin.

The gamma (γ)-secretase holoenzyme is composed of four core proteins and cleaves APP to generate amyloid beta (Aß), a key molecule that causes major neurotoxicity during the early stage of Alzheimer's disease (AD). However, despite its important role in Aß production, little is known about the regulation of γ-secretase. OCIAD2, a novel modulator of γ-secretase that stimulates Aß production, and which was isolated from a genome-wide functional screen using cell-based assays and a cDNA library comprising 6,178 genes. Ectopic expression of OCIAD2 enhanced Aß production, while reduction of OCIAD2 expression suppressed it. OCIAD2 expression facilitated the formation of an active γ-secretase complex and enhanced subcellular localization of the enzyme components to lipid rafts. OCIAD2 interacted with nicastrin to stimulate γ-secretase activity. OCIAD2 also increased the interaction of nicastrin with C99 and stimulated APP processing via γ-secretase activation, but did not affect Notch processing. In addition, a cell-permeable Tat-OCIAD2 peptide that interfered with the interaction of OCIAD2 with nicastrin interrupted the γ-secretase-mediated AICD production. Finally, OCIAD2 expression was significantly elevated in the brain of AD patients and PDAPP mice. This study identifies OCIAD2 as a selective activator of γ-secretase to increase Aß generation.

Autocrine/paracrine function of nicotinic acid adenine dinucleotide phosphate (NAADP) for glucose homeostasis in pancreatic ß-cells and adipocytes.

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a second messenger for mobilizing Ca(2+) from intracellular stores in various cell types. Extracellular application of NAADP has been shown to elicit intracellular Ca(2+) signals, indicating that it is readily transported into cells. However, little is known about the functional role of this NAADP uptake system. Here, we show that NAADP is effectively transported into selected cell types involved in glucose homeostasis, such as adipocytes and pancreatic ß-cells, but not the acinar cells, in a high glucose-dependent manner. NAADP uptake was inhibitable by Ned-19, a NAADP mimic; dipyridamole, a nucleoside inhibitor; or NaN3, a metabolic inhibitor or under Ca(2+)-free conditions. Furthermore, NAADP was found to be released from pancreatic islets upon stimulation by high glucose. Consistently, administration of NAADP to type 2 diabetic mice improved glucose tolerance. We propose that NAADP is functioning as an autocrine/paracrine hormone important in glucose homeostasis. NAADP is thus a potential antidiabetic agent with therapeutic relevance.

Whole-genome demography of COVID-19 virus during its pandemic period and on "panvalent" vaccine design.

With over 16 million submitted genomic sequences, the SARS-CoV-2 (SC2) virus, the cause of the most recent worldwide COVID-19 pandemic, has become the most sequenced genome of all known viruses, revealing, for example, a vast number of expanding viral lineages. Since the pandemic phase appears to be over, we performed a retrospective re-examination of the demographic grouping pattern and their genomic characteristics during the entire pandemic period up to the peak of the last pandemic wave. For our study, we extracted from the NCBI only unique viral sequences and converted each sequence data to a relational vector, indicating the presence/absence of each variational event compared to a "reference" sequence. Our study revealed several genomic features that are unexpected or different from those of previous studies. For example, approximately 44,000 variants with unique sequences emerged during the pandemic period; they group into only four major viral-genomic groups and each has a set of mostly unique highly-conserved variant-genotypes (HCVGs); and a small set from the first ("ancestral") group was inherited by the three ("descendant") groups, suggesting that HCVGs in the next group may be predictable from the current group(s). Such a concept may be potentially important in designing "panvalent" vaccines against the current and future waves of viral infections.

PIDiff: Physics informed diffusion model for protein pocket-specific 3D molecular generation.

Designing drugs capable of binding to the structure of target proteins for treating diseases is essential in drug development. Recent remarkable advancements in geometric deep learning have led to unprecedented progress in three-dimensional (3D) generation of ligands that can bind to the protein pocket. However, most existing methods primarily focus on modeling the geometric information of ligands in 3D space. Consequently, these methods fail to consider that the binding of proteins and ligands is a phenomenon driven by intrinsic physicochemical principles. Motivated by this understanding, we propose PIDiff, a model for generating molecules by accounting in the physicochemical principles of protein-ligand binding. Our model learns not only the structural information of proteins and ligands but also to minimize the binding free energy between them. To evaluate the proposed model, we introduce an experimental framework that surpasses traditional assessment methods by encompassing various essential aspects for the practical application of generative models to actual drug development. The results confirm that our model outperforms baseline models on the CrossDocked2020 benchmark dataset, demonstrating its superiority. Through diverse experiments, we have illustrated the promising potential of the proposed model in practical drug development.

On whole-genome demography of world's ethnic groups and individual genomic identity.

All current categorizations of human population, such as ethnicity, ancestry and race, are based on various selections and combinations of complex and dynamic common characteristics, that are mostly societal and cultural in nature, perceived by the members within or from outside of the categorized group. During the last decade, a massive amount of a new type of characteristics, that are exclusively genomic in nature, became available that allows us to analyze the inherited whole-genome demographics of extant human, especially in the fields such as human genetics, health sciences and medical practices (e.g., 1,2,3), where such health-related characteristics can be related to whole-genome-based categorization. Here we show the feasibility of deriving such whole-genome-based categorization. We observe that, within the available genomic data at present, (a) the study populations form about 14 genomic groups, each consisting of multiple ethnic groups; and (b), at an individual level, approximately 99.8%, on average, of the whole autosomal-genome contents are identical between any two individuals regardless of their genomic or ethnic groups.

Monitoring Immune Modulation in Season Population: Identifying Effects and Markers Related to Apis mellifera ligustica Honey Bee Health.

Honey bees play a significant role in ecology, producing biologically active substances used to promote human health. However, unlike humans, the molecular markers indicating honey bee health remain unknown. Unfortunately, numerous reports of honey bee collapse have been documented. To identify health markers, we analyzed ten defense system genes in Apis mellifera ligustica honey bees from winter (Owb) and spring (Fb for foragers and Nb for newly emerged) populations sampled in February and late April 2023, respectively. We focused on colonies free from SBV and DWV viruses. Molecular profiling revealed five molecular markers of honey bee health. Of these, two seasonal molecular markers-domeless and spz genes-were significantly downregulated in Owb compared to Nb and Fb honey bees. One task-related marker gene, apid-1, was identified as being downregulated in Owb and Nb compared to Fb honey bees. Two recommended general health markers, SOD and defensin-2, were upregulated in honey bees. These markers require further testing across various honey bee subspecies in different climatic regions. They can diagnose bee health without colony intervention, especially during low-temperature months like winter. Beekeepers can use this information to make timely adjustments to nutrients or heating to prevent seasonal losses.

ReBADD-SE: Multi-objective molecular optimisation using SELFIES fragment and off-policy self-critical sequence training.

The discovery of drugs to selectively remove disease-related cells is challenging in computer-aided drug design. Many studies have proposed multi-objective molecular generation methods and demonstrated their superiority using the public benchmark dataset for kinase inhibitor generation tasks. However, the dataset does not contain many molecules that violate Lipinski's rule of five. Thus, it remains unclear whether existing methods are effective in generating molecules violating the rule, such as navitoclax. To address this, we analysed the limitations of existing methods and propose a multi-objective molecular generation method with a novel parsing algorithm for molecular string representation and a modified reinforcement learning method for the efficient training of multi-objective molecular optimisation. The proposed model had success rates of 84% in GSK3b+JNK3 inhibitor generation and 99% in Bcl-2 family inhibitor generation tasks.

Synthesis and properties of 1-(3'-dihydroxyboryl-2',3'-dideoxyribosyl)pyrimidines.

Nucleoside analogues having a boronic acid in place of the 3-hydroxyl group of deoxyribose have been synthesized. The synthesis of 3'-dihydroxyboryl-2',3'-dideoxyribose was based on asymmetric homologation of boronic esters with (dihalomethyl)lithium, beginning from a (silyloxymethyl)boronic ester. A change of chiral director is required before introduction of the second stereocenter, and the direct displacement of (S,S)-1,2-dicyclohexyl-1,2-ethanediol by (1S,2S,3R,5S)-pinanediol was used for this purpose. Coupling of the pinanediol ester of the 1-acetoxy-3-dioxyboryl-5-tert-butylsilyloxy deoxyribose analogue with silylated pyrimidine bases was accomplished with trimethylsilyl bromide. The boronic acid nucleoside analogues were not cytotoxic toward Hep G2 (human hepatocarcinoma) cells. Decomposition occurred over a period of several hours at 37 °C, pH 7.4, with liberation of free pyrimidine base.

Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder.

In this paper, a reinforcement learning model is proposed that can maximize the predicted binding affinity between a generated molecule and target proteins. The model used to generate molecules in the proposed model was the Stacked Conditional Variation AutoEncoder (Stack-CVAE), which acts as an agent in reinforcement learning so that the resulting chemical formulas have the desired chemical properties and show high binding affinity with specific target proteins. We generated 1000 chemical formulas using the chemical properties of sorafenib and the three target kinases of sorafenib. Then, we confirmed that Stack-CVAE generates more of the valid and unique chemical compounds that have the desired chemical properties and predicted binding affinity better than other generative models. More detailed analysis for 100 of the top scoring molecules show that they are novel ones not found in existing chemical databases. Moreover, they reveal significantly higher predicted binding affinity score for Raf kinases than for other kinases. Furthermore, they are highly druggable and synthesizable.

Association between obesity and the prevalence of allergic diseases, atopy, and bronchial hyperresponsiveness in Korean adolescents.

BACKGROUND: Although several mechanisms underlying the asthma-obesity connection have been proposed, debates still remain. This study was to determine whether overweight is associated with a higher prevalence of atopy, asthma symptoms, airway obstruction, bronchial hyperresponsiveness (BHR) or biomarkers of inflammation in a sample of Korean adolescents. METHODS: We conducted a cross-sectional survey involving questionnaires, skin tests, spirometry and methacholine challenge tests among 717 adolescents from Seoul (South Korea). Overweight status was defined as a BMI greater than the local age- and gender-specific 85th percentile. RESULTS: Overweight subjects more frequently reported ever having wheezing (24.6 vs. 14.0%, p = 0.001) and wheezing in the previous 12 months (11.5 vs. 6.3%, p = 0.02) than normal-weight subjects, especially in boys. Atopy was more common among overweight adolescents than among those of normal weight (61.5 vs. 49.2%, p = 0.002), especially in boys (65.0 vs. 52.8%, p = 0.005). Overweight subjects had higher total WBC counts and eosinophil counts, especially boys. The presence of BHR was more common only among overweight girls (32.8 vs. 18.0%, p = 0.028). Overweight status was a significant risk factor for the presence of atopy (odds ratio = 1.49; 95% CI 1.06-2.10), after adjusting for various confounders by logistic regression analysis. CONCLUSIONS: An association was found between overweight status and both atopy and an increased prevalence of wheezing in adolescent Korean boys. These findings suggest that being overweight in puberty may be one of several risk factors responsible for atopy, BHR, and asthma symptoms.

Disruption of nucleocytoplasmic trafficking as a cellular senescence driver.

Senescent cells exhibit a reduced response to intrinsic and extrinsic stimuli. This diminished reaction may be explained by the disrupted transmission of nuclear signals. However, this hypothesis requires more evidence before it can be accepted as a mechanism of cellular senescence. A proteomic analysis of the cytoplasmic and nuclear fractions obtained from young and senescent cells revealed disruption of nucleocytoplasmic trafficking (NCT) as an essential feature of replicative senescence (RS) at the global level. Blocking NCT either chemically or genetically induced the acquisition of an RS-like senescence phenotype, named nuclear barrier-induced senescence (NBIS). A transcriptome analysis revealed that, among various types of cellular senescence, NBIS exhibited a gene expression pattern most similar to that of RS. Core proteomic and transcriptomic patterns common to both RS and NBIS included upregulation of the endocytosis-lysosome network and downregulation of NCT in senescent cells, patterns also observed in an aging yeast model. These results imply coordinated aging-dependent reduction in the transmission of extrinsic signals to the nucleus and in the nucleus-to-cytoplasm supply of proteins/RNAs. We further showed that the aging-associated decrease in Sp1 transcription factor expression was critical for the downregulation of NCT. Our results suggest that NBIS is a modality of cellular senescence that may represent the nature of physiological aging in eukaryotes.

Enzyme-catalyzed transfer of a ketone group from an S-adenosylmethionine analogue: a tool for the functional analysis of methyltransferases.

S-adenosylmethionine (AdoMet or SAM)-dependent methyltransferases belong to a large and diverse family of group-transfer enzymes that perform vital biological functions on a host of substrates. Despite the progress in genomics, structural proteomics, and computational biology, functional annotation of methyltransferases remains a challenge. Herein, we report the synthesis and activity of a new AdoMet analogue functionalized with a ketone group. Using catechol O-methyltransferase (COMT, EC 2.1.1.6) and thiopurine S-methyltransferase (TPMT, EC 2.1.1.67) as model enzymes, this robust and readily accessible analogue displays kinetic parameters that are comparable to AdoMet and exhibits multiple turnovers with enzyme. More importantly, this AdoMet surrogate displays the same substrate specificity as the natural methyl donor. Incorporation of the ketone group allows for subsequent modification via bio-orthogonal labeling strategies and sensitive detection of the tagged ketone products. Hence, this AdoMet analogue expands the toolbox available to interrogate the biochemical functions of methyltransferases.

Effect of artemisinin derivatives on apoptosis and cell cycle in prostate cancer cells.

Artemisinin is a plant-derived anti-malarial drug that has relatively low toxicity in humans and is activated by heme and/or intracellular iron leading to intracellular free radical formation. Interestingly, artemisinin has displayed anti-cancer activity, with artemisinin dimers being more potent than monomeric artemisinin. Intracellular iron uptake is regulated by the transferrin receptor (TfR), and the activity of artemisinin depends on the availability of iron. We examined the level of TfR in prostate cancer (PCa) tumor cells, synthesized two new artemisinin dimers, and evaluated the effect of dihydroartemisinin and artemisinin dimers, ON-2Py and 2Py, on proliferation and apoptosis in PCa cells. TfR was expressed in the majority of PCa bone and soft tissue metastases, all 24 LuCaP PCa xenografts, and PCa cell lines. After treatment with dihydroartemisinin, ON-2Py, or 2Py all PCa cell lines displayed dose-dependent decrease in cell number. 2Py was most effective in decreasing cell number. An increase in apoptotic events and growth arrest was observed in the C4-2 and LNCaP cell lines. Growth arrest was observed in PC-3 cells, but no significant change was observed in DU 145 cells. Treatment with 2Py resulted in a loss of the anti-apoptotic protein survivin in all four cell lines. 2Py treatment also decreased androgen receptor and prostate-specific antigen expression in C4-2 and LNCaP cells, with a concomitant loss of cell cycle regulatory proteins cyclin D1 and c-Myc. This study shows the potential use of artemisinin derivatives as therapeutic candidates for PCa and warrants the initiation of preclinical studies.

Caspase-mediated cleavage of importin-alpha increases its affinity for MCM and downregulates DNA synthesis by interrupting the binding of MCM to chromatin.

Importin-alpha is essential for classical nucleocytoplasmic transport of nuclear proteins. Here, we report that importin-alpha is cleaved by caspases during apoptosis, generating importin-alpha lacking an IBB domain. This truncated importin-alpha binds tightly to the MCM replication licensing factor and, thus, prevents its binding to chromatin and downregulates DNA synthesis. Together, our data reveal for the first time that a dying cell effectively salvages limited supplies of cellular energy to ensure an orderly process of its own demise by simultaneously downregulating nucleocytoplasmic protein transport and DNA synthesis. Strikingly, cells can achieve this multi-task process by simply cleaving-off a key nuclear import protein.