A New Fingerprint and Graph Hybrid Neural Network for Predicting Molecular Properties.

Machine learning plays a role in accelerating drug discovery, and the design of effective machine learning models is crucial for accurately predicting molecular properties. Characterizing molecules typically involves the use of molecular fingerprints and molecular graphs. These are input into a multilayer perceptron (MLP) and variants of graph neural networks, such as graph attention networks (GATs). Due to the diverse types and large dimension of fingerprints, models may contain many features that are relatively irrelevant or redundant; meanwhile, although the GAT excels in handling heterogeneous graph tasks, it lacks the ability to extract collaborative information from neighboring nodes, which is crucial in scenarios where it cannot capture the joint influence of adjacent groups on atoms. To overcome these challenges, we introduce a hybrid model, combining improved GAT and MLP. In GAT, the recurrent neural network is employed to capture collaborative information. To address the dimensionality issue, we propose a feature selection algorithm, which is based on the principle of maximizing relevance while minimizing redundancy. Through experiments on 13 public data sets and 14 breast cell lines, our model demonstrates superior performance compared to state-of-the-art deep learning and traditional machine learning algorithms. Additionally, a series of ablation experiments were conducted to demonstrate the advantages of our improved version, as well as its antinoise capability and interpretability. These results indicate that our model holds promising prospects for practical applications.

Proteomic Analysis of Staphylococcus aureus Treated with ShangKeHuangShui.

Staphylococcus aureus (SAU) stands as the prevailing pathogen in post-traumatic infections, with the emergence of antibiotic resistance presenting formidable treatment hurdles. The pressing need is to explore novel antibiotics to address this challenge. ShangKeHuangShui (SKHS), a patented traditional Chinese herbal formula, has gained widespread use in averting post-traumatic infections, but its biological effects remain incomplete understanding. This study's primary objective was to delve into the antibacterial properties, potential antibacterial compounds within SKHS, and their associated molecular targets. In vitro SKHS antibacterial assays demonstrated that the minimum inhibitory concentration (MIC) was 8.625 mg/mL and the minimum bactericide concentration (MBC) was 17.25 mg/mL. Proteomic analysis based on tandem mass tag (TMT) showed significant changes in the expression level of 246 proteins in SKHS treated group compared to control group, with 79 proteins upregulated and 167 proteins downregulated (>1.5-fold, p < 0.05). Subsequently, thirteen target proteins related to various biological processes and multiple metabolic pathways were selected to conduct parallel reaction monitoring (PRM) and molecular docking screen. In protein tyrosine phosphatase PtpA (ptpA) docking screening, phellodendrine and obacunone can bind to ptpA with the binding energy of - 8.4 and - 8.3 kcal/mol, respectively. This suggests their potential impact on antibacterial activity by modulating the two-component system of SAU. The discovery lays a groundwork for future research endeavors for exploring new antibacterial candidates and elucidating specific active chemical components within SKHS that match target proteins. Further investigations are imperative to unveil the biological effects of these monomers and their potential synergistic actions.

Unexpectedly resisting protein adsorption on self-assembled monolayers terminated with two hydrophilic hydroxyl groups.

OH-terminated self-assembled monolayers, as protein-resistant surfaces, have significant potential in biocompatible implant devices, which can avoid or reduce adverse reactions caused by protein adhesion to biomaterial surfaces, such as thrombosis, immune response and inflammation. Here, molecular dynamics simulations were performed to evaluate the degree of protein adsorption on the self-assembled monolayer terminated with two hydrophilic OH groups ((OH)2-SAM) at packing densities (Σ) of 4.5 nm-2 and 6.5 nm-2, respectively. The results show that the structure of the (OH)2-SAM itself, i.e., a nearly perfect hexagonal-ice-like hydrogen bond structure in the OH matrix of the (OH)2-SAM at Σ = 4.5 nm-2 sharply reduces the number of hydrogen bonds (i.e., 0.7 ± 0.27) formed between the hydrophobic (OH)2-SAM surface and protein. While for Σ = 6.5 nm-2, the hydrophilic (OH)2-SAM surface can provide more hydrogen bonding sites to form hydrogen bonds (i.e., 6.2 ± 1.07) with protein. The number of hydrogen bonds formed between the (OH)2-SAM and protein at Σ = 6.5 nm-2 is ∼8 times higher than that at Σ = 4.5 nm-2, reflecting the excellent resistance to protein adsorption exhibited by the structure of the (OH)2-SAM itself at Σ = 4.5 nm-2. Compared with a traditional physical barrier effect formed by a large number of hydrogen bonds between the (OH)2-SAM and water at Σ = 6.5 nm-2, the structure of the (OH)2-SAM itself at Σ = 4.5 nm-2 proposed in this study significantly improves the performance of the (OH)2-SAM resistance to protein adsorption, which provides new insights into the mechanism of resistance to protein adsorption on the (OH)2-SAM.

Nonselective Intercalation of G-Quadruplex-Targeting Ligands into Double-Stranded DNA Quantified by Single-Molecule Stretching.

Most G-quadruplex (G4)-targeting ligands reported so far contain planar heteroaromatic groups and can intercalate into adjacent base pairs of double-stranded DNA (dsDNA). However, quantitative data on the binding number γ (ligands/bp) of G4 ligands that intercalate into long dsDNA remain lacking, which are essential for understanding the selectivity of G4 ligands. Here, using a single-molecule stretching assay based on the lengthening of dsDNA, we analyzed the dissociation constants and the binding number of eight most commonly used G4 ligands that intercalate into dsDNA. We showed that five ligands (CX-5461, BRACO-19, RHPS4, TrisQ, and Phen-DC3) intercalate into dsDNA avidly (Kd = 0.5-2.1 µM, saturated γ > 0.2 ligands/bp), which was similar to the typical dsDNA intercalator EB. Two bisquinolines, PDS and 360A, showed moderate intercalation ability (Kd = 22.5 and 48.7 µM) and γ < 0.01 ligands/bp in the presence of 1 µM ligands. Porphyrin NMM showed no intercalative binding even at 200 µM. Molecular docking and molecular dynamics simulations were carried out to further evaluate the intercalative binding of these G4 ligands with dsDNA by calculating the binding energies and π-π stacking probability.

Identification of Andrographolide as a novel FABP4 inhibitor for osteoarthritis treatment.

BACKGROUND AND PURPOSE: Fatty acid binding protein 4 (FABP4) has been identified as a contributor to cartilage degradation in osteoarthritis (OA) patients, and inhibiting FABP4 using small molecules has emerged as a promising approach for developing OA drugs. Our previous research showed that Andrographis paniculata, a medicinal plant, strongly inhibits FABP4 activity. This led us to hypothesize that Andrographis paniculata ingredients might have protective effects on OA cartilage through FABP4 inhibition. METHODS: We analyzed scRNA-seq data from joint tissue of OA patients (GSE152805; GSE145286) using Scanpy 1.9.1 and Single Cell Portal. We conducted docking analysis of FABP4 inhibitors using Autodock Vina v.1.0.2. We evaluated the anti-FABP4 activity using a fluorescence displacement assay and measured the fatty acid oxidation (FAO) activity using the FAOBlue assay. We used H2DCF-DA to measure reactive oxygen species (ROS) levels. We studied signaling pathways using bulk RNA sequencing and western blot analysis in human C28/I2 chondrocytes. We evaluated anti-OA activity in monosodium iodoacetate (MIA)-induced rats. RESULTS: We identified Andrographolide (AP) as a novel FABP4 inhibitor. Bulk RNA-sequencing analysis revealed that FABP4 upregulated FAO and ROS in chondrocytes, which was inhibited by AP. ROS generation activated the NF-κB pathway, leading to overexpression of a disintegrin and metalloproteinase with thrombospondin motifs 4 (ADAMTS4), which is a responsible factor for cartilage degradation in OA patients. AP inhibited FABP4, thereby reducing the overexpression of ADAMTS4 by inhibiting the NF-κB pathway. In MIA rats, AP treatment reduced the overexpression of ADAMTS4, repaired cartilage and subchondral bone, and promoted cartilage regeneration. CONCLUSION: Our results indicate that the inhibition of FABP4 activity by AP explains the anti-OA properties of Andrographis paniculata by protecting against cartilage degradation in OA patients. Additionally, our findings suggest that AP may be a promising therapeutic agent for OA treatment due to its ability to alleviate cartilage damage and bone erosion.

Tissue-Specific Downregulation of Fatty Acid Synthase Suppresses Intestinal Adenoma Formation via Coordinated Reprograming of Transcriptome and Metabolism in the Mouse Model of Apc-Driven Colorectal Cancer.

Altered lipid metabolism is a potential target for therapeutic intervention in cancer. Overexpression of Fatty Acid Synthase (FASN) correlates with poor prognosis in colorectal cancer (CRC). While multiple studies show that upregulation of lipogenesis is critically important for CRC progression, the contribution of FASN to CRC initiation is poorly understood. We utilize a C57BL/6-Apc/Villin-Cre mouse model with knockout of FASN in intestinal epithelial cells to show that the heterozygous deletion of FASN increases mouse survival and decreases the number of intestinal adenomas. Using RNA-Seq and gene set enrichment analysis, we demonstrate that a decrease in FASN expression is associated with inhibition of pathways involved in cellular proliferation, energy production, and CRC progression. Metabolic and reverse phase protein array analyses demonstrate consistent changes in alteration of metabolic pathways involved in both anabolism and energy production. Downregulation of FASN expression reduces the levels of metabolites within glycolysis and tricarboxylic acid cycle with the most significant reduction in the level of citrate, a master metabolite, which enhances ATP production and fuels anabolic pathways. In summary, we demonstrate the critical importance of FASN during CRC initiation. These findings suggest that targeting FASN is a potential therapeutic approach for early stages of CRC or as a preventive strategy for this disease.

Unexpected hydrophobicity on self-assembled monolayers terminated with two hydrophilic hydroxyl groups.

Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules onto the surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of 82° on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ((OH)2-SAM). This hydrophobicity, verified by a water slip phenomenon characterizing the friction on the (OH)2-SAM surface, is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of (OH)2-SAM, which sharply reduces the hydrogen bonds between the surface and the water molecules above. The unique simple interface presented here offers a significant molecular-level platform for examining the bio-interfacial interactions ranging from biomolecule binding to cell adhesion.

Selectivity mechanism of magnesium and calcium in cation-binding pocket structures of phosphotyrosine.

Magnesium (Mg^{2+}) and calcium (Ca^{2+}) are of essential importance in biological activity, but the molecular understanding of their selectivity is still lacking. Here, based on density functional theory calculations and ab initio molecular dynamics simulations, we show that Mg^{2+} binds more tightly to phosphotyrosine (pTyr) and stabilizes the conformation of pTyr, while Ca^{2+} binds more flexibly to pTyr with less structural stability. The key for the selectivity is attributed to the cation-π interactions between the hydrated cations and the aromatic ring together with the synergic interaction between the cations and the side groups in pTyr to form a cation-binding pocket structure, which we refer as side-group-synergetic hydrated cation-π interaction. The existence and relative strength of the cation-π interactions in the pocket structures as well as their structural stability have been demonstrated experimentally with ultraviolet (UV) absorption spectra and ^{1}H NMR spectra. The findings offer insight into understanding the selectivity of Mg^{2+} and Ca^{2+} in a variety of biochemical and physiological essential processes.

Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex.

Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg2+ can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg2+ solutions. Our calculations show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg2+], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg2+]. Our analyses show that Mg2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg2+ is much stronger for tsDNA. Such stronger external binding of Mg2+ for tsDNA favors more apparent ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging ions, as a special part of external binding ions, are tightly and positively coupled to ion-mediated attraction between DNAs.

Radial distribution function of semiflexible oligomers with stretching flexibility.

The radial distribution of the end-to-end distance Ree is crucial for quantifying the global size and flexibility of a linear polymer. For semiflexible polymers, several analytical formulas have been derived for the radial distribution of Ree ignoring the stretching flexibility. However, for semiflexible oligomers, such as DNA or RNA, the stretching flexibility can be rather pronounced and can significantly affect the radial distribution of Ree. In this study, we obtained an extended formula that includes the stretch modulus to describe the distribution of Ree for semiflexible oligomers on the basis of previous formulas for semiflexible polymers without stretching flexibility. The extended formula was validated by extensive Monte Carlo simulations over wide ranges of the stretch modulus and persistence length, as well as all-atom molecular dynamics simulations of short DNAs and RNAs. Additionally, our analyses showed that the effect of stretching flexibility on the distribution of Ree becomes negligible for DNAs longer than ∼130 base pairs and RNAs longer than ∼240 base pairs.

Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.

The flexibility of double-stranded (ds) RNA and dsDNA is crucial for their biological functions. Recent experiments have shown that the flexibility of dsRNA and dsDNA can be distinctively different in the aspects of stretching and twist-stretch coupling. Although various studies have been performed to understand the flexibility of dsRNA and dsDNA, there is still a lack of deep understanding of the distinctive differences in the flexibility of dsRNA and dsDNA helices as pertains to their stretching and twist-stretch coupling. In this work, we have explored the relative flexibility in stretching and twist-stretch coupling between dsRNA and dsDNA by all-atom molecular dynamics simulations. The calculated stretch modulus and twist-stretch coupling are in good accordance with the existing experiments. Our analyses show that the differences in stretching and twist-stretch coupling between dsRNA and dsDNA helices are mainly attributed to their different (A- and B-form) helical structures. Stronger basepair inclination and slide in dsRNA is responsible for the apparently weaker stretching rigidity versus that of dsDNA, and the opposite twist-stretch coupling for dsRNA and dsDNA is also attributed to the stronger basepair inclination in dsRNA than in dsDNA. Our calculated macroscopic elastic parameters and microscopic analyses are tested and validated by different force fields for both dsRNA and dsDNA.

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.

Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Co(NH3)6 (3+) (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive. However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become 'internal binding' into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit 'external binding' to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.

Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs.

Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5-50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with lp ∼ 50 nm.

A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect.

To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (≤45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 Å and an overall minimum RMSD of 1.9 Å from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ∼ 1.0 °C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition.

Salt contribution to the flexibility of single-stranded nucleic acid offinite length.

Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this article, the salt effects on the flexibility of single-stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse-grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual-bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and both trivalent/small divalent ions can induce more compact state than a random relaxation state. We found that monovalent, divalent, and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion-exclusion-volume effect to ion Coulomb correlations. In addition, the predicted Na(+) and Mg(2+)-dependent persistence length l(p)'s of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for l(p) as a function of [Na(+)], [Mg(2+)] and chain length.

[Preliminary study on rDNA ITS sequencing and characteristics of Citrus grandis var. tomentosa].

OBJECTIVE: To study the difference of rDNA ITS sequences between Cirtus grandis var. tomentosa and its relatives. METHODS: The rDNA ITS gene fragment was amplified by PCR with universal primers of rDNA ITS and sequenced. RESULTS: The DNA sequences of ITS ranged from 675 to 683 bp and the 5.8S gene of all of the samples are 165 bp in size. Distance values of ITS sequence, estimated according to Kimura two-parameter models between C. grandis var. tomentosa and C. grandis var. shatin-you, C. grandis var. tomentosa and C. reticulata were 1.05 and 2.29 respectively. CONCLUSION: There are some differences in rDNA ITS sequences among C. grandis var. tomentosa and its relatives.