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Abstract Spin glass theory, as a paradigm for describing disordered magnetic systems, constitutes a prominent subject of study within statistical physics. Replica symmetry breaking (RSB), as one of the pivotal concepts for the understanding of spin glass theory, means that under identical conditions, disordered systems can yield distinct states with nontrivial correlations. Random fiber laser (RFL) based on Rayleigh scattering (RS) is a complex disordered system, owing to the disorder and stochasticity of RS. In this work, for the first time, a precise theoretical model is elaborated for studying the photonic phase transition via the platform of RS-based RFL, in which we clearly reveal that, apart from the pump power, the photon phase variation in RFL is also an analogy to the temperature term in spin-glass phase transition, leading to a novel insight into the intrinsic mechanisms of photonic phase transition. In addition, based on this model and real-time high-fidelity detection spectral evolution, we theoretically predict and experimentally observe the mode-asymmetric characteristics of photonic phase transition in RS-based RFL. This finding contributes to a deeper understanding of the photonic RSB regime and the dynamics of RS-based RFL.

Mitochondria can contact lipid droplets (LDs) to form peridroplet mitochondria (PDM) which trap fatty acids in LDs by providing ATP for triglyceride synthesis and prevent lipotoxicity. However, the role of PDM in metabolic dysfunction associated steatotic liver disease (MASLD) is not clear. Here, the features of PDM in dietary MASLD models with different severity in mice were explored. Electron microscope photographs show that LDs and mitochondria rarely come into contact with each other in normal liver. In mice fed with high-fat diet, PDM can be observed in the liver as early as the beginning of steatosis in hepatocytes. For the first time, we show that PDM in mouse liver varies with the severity of MASLD. PDM and cytosolic mitochondria were isolated from the liver tissue of MASLD and analyzed by quantitative proteomics. Compared with cytosolic mitochondria, PDM have enhanced mitochondrial respiration and ATP synthesis. Diethyldithiocarbamate (DDC) alleviates choline-deficient, L-amino acid–defined diet-induced MASLD, while increases PDM in the liver. Similarly, DDC promotes the contact of mitochondria-LDs in steatotic C3A cells in vitro. Meanwhile, DDC promotes triglyceride synthesis and improves mitochondrial dysfunction in MASLD. In addition, DDC upregulates perilipin 5 both in vivo and in vitro, which is considered as a key regulator in PDM formation. Knockout of perilipin 5 inhibits the contact of mitochondria-LDs induced by DDC in C3A cells. These results demonstrate that PDM might be associated with the progression of MASLD and the prevention of MASLD by DDC.

IntroductionType 2 diabetes mellitus (T2DM) is a major cause of atherosclerosis (AS). However, definitive evidence regarding the common molecular mechanisms underlying these two diseases are lacking. This study aimed to investigate the mechanisms underlying the association between T2DM and AS.MethodsThe gene expression profiles of T2DM (GSE159984) and AS (GSE100927) were obtained from the Gene Expression Omnibus, after which overlapping differentially expressed gene identification, bioinformatics enrichment analyses, protein–protein interaction network construction, and core genes identification were performed. We confirmed the discriminatory capacity of core genes using receiver operating curve analysis. We further identified transcription factors using TRRUST database to build a transcription factor–mRNA regulatory network. Finally, the immune infiltration and the correlation between core genes and differential infiltrating immune cells were analyzed.ResultsA total of 27 overlapping differentially expressed genes were identified under the two-stress conditions. Functional analyses revealed that immune responses and transcriptional regulation may be involved in the potential pathogenesis. After protein–protein interaction network deconstruction, external datasets, and qRT-PCR experimental validation, four core genes (IL1B, C1QA, CCR5, and MSR1) were identified. ROC analysis further showed the reliable value of these core genes. Four common differential infiltrating immune cells (B cells, CD4+ T cells, regulatory T cells, and M2 macrophages) between T2DM and AS datasets were selected based on immune cell infiltration. A significant correlation between core genes and common differential immune cells. Additionally, five transcription factors (RELA, NFκB1, JUN, YY1, and SPI1) regulating the transcription of core genes were mined using upstream gene regulator analysis.DiscussionIn this study, common target genes and co-immune infiltration landscapes were identified between T2DM and AS. The relationship among five transcription factors, four core genes, and four immune cells profiles may be crucial to understanding T2DM complicated with AS pathogenesis and therapeutic direction.

Summary: We previously reported that loss of function of TYW1 led to cerebral palsy with severe intellectual disability through reduced neural proliferation. However, whether TYW1 loss affects neural differentiation is unknown. In this study, we first demonstrated that TYW1 loss blocked the formation of OHyW in tRNAphe and therefore affected the translation efficiency of UUU codon. Using the brain organoid model, we showed impaired neuron differentiation when TYW1 was depleted. Interestingly, retrotransposons were differentially regulated in TYW1−/− hESCs (human embryonic stem cells). In particular, one kind of human-specific endogenous retrovirus-K (HERVK/HML2), whose reactivation impaired human neurodevelopment, was significantly up-regulated in TYW1−/− hESCs. Consistently, a UUU codon-enriched protein, SMARCAD1, which was a key factor in controlling endogenous retroviruses, was reduced. Taken together, TYW1 loss leads to up-regulation of HERVK in hESCs by down-regulated SMARCAD1, thus impairing neuron differentiation.

Abstract Background The Zhizi Chuanxiong herb pair (ZCHP) can delay pathological progression of atherosclerosis (AS); however, its pharmacological mechanism remains unclear because of its complex components. The purpose of current study is to systematically investigate the anti-AS mechanism of ZCHP. Methods The databases of TCMSP, STITCH, SwissTargetPrediction, BATMAN-TCM, and ETCM were searched to predict the potential targets of ZCHP components. Disease targets associated with AS was retrieved from the GEO database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analyses were executed using DAVID 6.8. Molecular docking method was employed to evaluate the core target binding to blood components, and animal experiments were performed to test action mechanism. Results A ZCHP-components-targets-AS network was constructed by using Cytoscape, included 11 main components and 52 candidate targets. Crucial genes were shown in the protein–protein interaction network, including TNF, IL-1β, IGF1, MMP9, COL1A1, CCR5, HMOX1, PTGS1, SELE, and SYK. KEGG enrichment illustrated that the NF-κB, Fc epsilon RI, and TNF signaling pathways were important for AS treatment. These results were validated by molecular docking. In ApoE−/− mice, ZCHP significantly reduced intima-media thickness, pulse wave velocity, plaque area, and serum lipid levels while increasing the difference between the end-diastolic and end-systolic diameters. Furthermore, ZCHP significantly decreased the mRNA and protein levels of TNF-α and IL-1β, suppressed NF-κB activation, and inhibited the M1 macrophage polarization marker CD86 in ApoE−/− mice. Conclusion This study combining network pharmacology, molecular biology, and animal experiments showed that ZCHP can alleviate AS by suppressing the TNF/NF-κB axis and M1 macrophage polarization. Graphical Abstract

Background: Abnormal cardiac metabolism is a key factor in the development of cardiovascular diseases. Consequently, there has been considerable emphasis on researching and developing drugs that regulate metabolism. This study employed bibliometric methods to comprehensively and objectively analyze the relevant literature, offering insights into the knowledge dynamics in this field. Methods: The data source for this study was the Web of Science Core Collection (WoSCC), from which the collected data were imported into bibliometric software for analysis. Results: The United States was the leading contributor, accounting for 38.33 % of publications. The University of Washington and Damian J. Tyler were the most active institution and author, respectively. The American Journal of Physiology-Heart and Circulatory Physiology, Journal of Molecular and Cellular Cardiology, Cardiovascular Research, Circulation Research, and American Journal of Physiology-Endocrinology and Metabolism were highly influential journals that published numerous high-quality articles on cardiac metabolism. Common keywords in this research area included heart failure, insulin resistance, skeletal muscle, mitochondria, as well as topic words such as cardiac metabolism, fatty acid oxidation, glucose metabolism, and myocardial metabolism. Co-citation analysis has shown that research on heart failure and in vitro modeling of cardiovascular disease has gained prominence in recent years and making it a research hotspot. Conclusion: Research on cardiac metabolism is steadily growing, with a specific focus on heart failure and the interplay between mitochondrial dysfunction, insulin resistance, and cardiac metabolism. An emerging trend in this field involves the enhancement of maturation in human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) through the manipulation of cardiac metabolism.

Broadband low-coherence light is considered to be an effective way to suppress laser plasma instability. Recent studies have demonstrated the ability of low-coherence laser facilities to reduce back-scattering during beam–target coupling. However, to ensure simultaneous low coherence and high energy, complex spectral modulation methods and amplification routes have to be adopted. In this work, we propose the use of a random fiber laser (RFL) as the seed source. The spectral features of this RFL can be carefully tailored to provide a good match with the gain characteristics of the laser amplification medium, thus enabling efficient amplification while maintaining low coherence. First, a theoretical model is constructed to give a comprehensive description of the output characteristics of the spectrum-tailored RFL, after which the designed RFL is experimentally realized as a seed source. Through precise pulse shaping and efficient regenerative amplification, a shaped random laser pulse output of 28 mJ is obtained, which is the first random laser system with megawatt-class peak power that is able to achieve low coherence and efficient spectrum-conformal regenerative amplification.

Abstract Human oral bioavailability (HOB) is a key factor in determining the fate of new drugs in clinical trials. HOB is conventionally measured using expensive and time-consuming experimental tests. The use of computational models to evaluate HOB before the synthesis of new drugs will be beneficial to the drug development process. In this study, a total of 1588 drug molecules with HOB data were collected from the literature for the development of a classifying model that uses the consensus predictions of five random forest models. The consensus model shows excellent prediction accuracies on two independent test sets with two cutoffs of 20% and 50% for classification of molecules. The analysis of the importance of the input variables allowed the identification of the main molecular descriptors that affect the HOB class value. The model is available as a web server at www.icdrug.com/ICDrug/ADMET for quick assessment of oral bioavailability for small molecules. The results from this study provide an accurate and easy-to-use tool for screening of drug candidates based on HOB, which may be used to reduce the risk of failure in late stage of drug development. Graphical Abstract

Low–coherence laser is regarded as the key to mitigating laser–plasma instability (LPI) in laser–driven inertial confinement fusion (ICF), where LPI can decrease the laser energy coupled to the target. With the merits of low coherence, high spectral stability, and flexible output characteristics, the Raman random fiber laser (RRFL) is considered to be a candidate light source in ICF. In this paper, the 1054 nm RRFL with high slope efficiency is achieved for the first time. In the RRFL pump source design section, we have optimized the ytterbium–doped fiber (YDF) length by simulation and amplified the power by Master Oscillator Power Amplifier (MOPA) to realize a 1011 nm YDF laser with 47.3 dB optical signal–to–noise ratio (OSNR). In terms of RRFL cavity design, a fiber loop mirror and Rayleigh scattering in the HI 1060 Flex fiber provide wideband point feedback and random distributed feedback, respectively. Based on this system, we achieve an RRFL output with 0.4 nm half–maximum full width, 182% slope efficiency, and 41.3 dB OSNR. This work will provide guidance for the application of RRFL in high–energy–density physics research.

Soil macrofauna is an important component of soil biodiversity and plays a key role in soil ecosystem function. Little work, however, has explored how macrofauna may contribute, directly or indirectly, to soil microfauna communities. In this study, we explored the impact of two classes of common soil macrofauna, earthworms (Eisenia foetida) and millipedes (Spirobolus walkeri), on soil nematode community diversity and structure. We found that earthworms and millipedes play an important role in maintaining soil nematode communities and increasing soil nutrients. Both earthworms and millipedes act as hosts for soil nematodes, and play a valuable role in dispersing and distributing these important microfauna throughout the soil landscape. We tested the efficacy of this strategy on multiple soil layers and found that layer does not have a significant influence on soil nematode community. These results suggest that soil nematode abundance, diversity, and structure are tightly linked to the existence of soil macrofauna, which may contribute to the maintenance mechanism of forest soil biodiversity.

As artificially designed two-dimensional (2D) arrays of subwavelength nanostructures, metasurfaces provide a new avenuefor the design of static planar optics. However, one would prefer a dynamic modulation of the metasurface in the event of practical applications. As a potentially important technique for information security, meta-holographic encryption has the characteristics of subwavelength pixels, precise control, and high safety factor. In this paper, by integrating birefringent liquid crystals (LCs) with all-dielectric metasurfaces in combination with visual cryptography (VC), we demonstrate a tunable metasurface with an information encryption function in the visible range. In the encryption process, the secret image is hidden in a set of unidentifiable and orthogonal arranged phase-only meta-holograms with high security of concealment. In the decryption process, the generated meta-hologram is illuminated by a plane wave and an electric field across the LC layer is applied to superimpose the reconstructed holographic patterns, thus we could acquire the secret image. Therefore, the decryption method can be flexibly and sufficiently adjusted with applied field under monitorable condition. For this reason, it is useful in enhancing the diversity of information hiding methods and improving the security of information. Our method can be extended to other similar applications.

AimChinese medicine Danhong injection (DHI) is an effective pharmaceutical preparation for treating cerebral infarction. Our previous study shows that DHI can remarkably reduce the ischemic stroke-induced infarct volume in a dose-dependent manner, but the pharmacological mechanism of the DHI dose-dependent relationship is not clear. Therefore, the dose-dependent efficacy of DHI on cerebral ischemia and the underlying mechanisms were further investigated in this study.MethodsA middle cerebral artery occlusion (MCAO) model was established and the rats were randomly divided into six groups: sham, vehicle, DHI dose-1, DHI dose-2, DHI dose-3, and DHI dose-4. Forty-one metabolites in serum were selected as candidate biomarkers of efficacy phenotypes by the Agilent 1290 rapid-resolution liquid chromatography system coupled with the Agilent 6550 Q-TOF MS system. Then, the metabolic networks in each group were constructed using the Weighted Correlation Network analysis (WGCNA). Moreover, the Yang and Yin transformation of six patterns (which are defined by up- and downregulation of metabolites) and synchronous modules divided from a synchronous network were used to dynamically analyze the mechanism of the drug’s effectiveness.ResultsThe neuroprotective effect of DHI has shown a dose-dependent manner, and the high-dose group (DH3 and DH4) effect is better. The entropy of the metabolic network and the Yin/Yang index both showed a consistent dose–response relationship. Seven dose-sensitive metabolites maintained constant inverse upregulation or downregulation in the four dose groups. Three synchronous modules for the DH1–DH4 full-course network were identified. Glycine, N-acetyl-L-glutamate, and tetrahydrofolate as a new emerging module appeared in DH2/DH3 and enriched in glutamine and glutamate metabolism-related pathways.ConclusionThis study takes the DHI metabolic network as an example to provide a new method for the discovery of multiple targets related to pharmacological effects. Our results show that the three conservative allosteric module nodes, taurine, L-tyrosine, and L-leucine, may be one of the basic mechanisms of DHI in the treatment of cerebral infarction, and the other three new emerging module nodes glyoxylate, L-glutamate, and L-valine may participate in the glutamine and glutamate metabolism pathway to improve the efficacy of DHI.

Peroxymonosulfate (PMS) has been intensively used to enhance the photocatalytic activity of catalysts, which is adopted as an electron acceptor to inhibit the recombination of electrons and holes. However, the effect of holes generated by visible light (VL) on PMS activation is always overlooked. Herein, the VL/Bi2WO6/PMS process was constructed for the efficient removal of organics, in which the degradation rate of carbamazepine (CBZ) increased by over 33.0 times by the introduction of PMS into Bi2WO6 under visible light. The radical quenching and determination experiments confirmed that the photogenerated holes could firstly oxidize PMS to form SO5•− and react with HSO5− to produce 1O2, then inducing the formation of other reactive species to greatly enhance the performance of pollutant removal by the VL/Bi2WO6/PMS process. Density functional theory (DFT) predicted that sites with high Fukui index (f0) on CBZ were more susceptible to being attacked, resulting in hydroxylation, ring closure, and C=C bond cleavage of CBZ. Toxicity estimation indicated that photocatalysis degradation products from CBZ were less toxic compared to the parent compound. This study provides a potential avenue for improving photocatalytic efficiency and widening the application of photocatalytic technology in wastewater purification.

Summary: N6-methyladenosine (m6A) is emerging as a vital factor regulating neural differentiation. Here, we report that deficiency of Arhgef2, a novel cause of a neurodevelopmental disorder we identified recently, impairs neurogenesis, neurite outgrowth, and synaptic formation by regulating m6A methylation. Arhgef2 knockout decreases expression of Mettl14 and total m6A level significantly in the cerebral cortex. m6A sequencing reveals that loss of Arhgef2 reduces m6A methylation of 1,622 mRNAs, including Npdc1 and Cend1, which are both strongly associated with cell cycle exit and terminal neural differentiation. Arhgef2 deficiency decreases m6A methylations of the Npdc1 and Cend1 mRNAs via down-regulation of Mettl14, and thereby inhibits the translation of Npdc1 and nuclear export of Cend1 mRNAs. Overexpression of Mettl14, Npdc1, and Cend1 rescue the abnormal phenotypes in Arhgef2 knockout mice, respectively. Our study provides a critical insight into a mechanism by which defective Arhgef2 mediates m6A-tagged target mRNAs to impair neural differentiation.

Androgen receptor (AR) is an important therapeutic target for the treatment of diseases such as prostate cancer, hypogonadism, muscle wasting, etc. In this study, the complex structures of the AR ligand-binding domain (LBD) with fifteen ligands were analyzed by molecular dynamics simulations combined with the alanine-scanning-interaction-entropy method (ASIE). The quantitative free energy contributions of the pocket residues were obtained and hotspot residues are quantitatively identified. Our calculation shows that that these hotspot residues are predominantly hydrophobic and their interactions with binding ligands are mainly van der Waals interactions. The total binding free energies obtained by summing over binding contributions by individual residues are in good correlation with the experimental binding data. The current quantitative analysis of binding mechanism of AR to ligands provides important insight on the design of future inhibitors.

The nuclear protein poly (ADP-ribose) polymerase-1 (PARP-1) inhibitors have been proven effective to potentiate both chemotherapeutic agents and radiotherapy. However, a major problem of most current PARP inhibitors is their lack of selectivity for PARP-1 and its closest isoform PARP-2. NMS-P118 is a highly selective PARP inhibitor that binds PARP-1 stronger than PARP-2 and has many advantages such as excellent pharmacokinetic profiles. In this study, molecular dynamics (MD) simulations of NMS-P118 in complex with PARP-1 and PARP-2 were performed to understand the molecular mechanism of its selectivity. Alanine scanning together with free energy calculation using MM/GBSA and interaction entropy reveal key residues that are responsible for the selectivity. Although the conformation of the binding pockets and NMS-P118 are very similar in PARP-1 and PARP-2, most of the hot-spot residues in PARP-1 have stronger binding free energy than the corresponding residues in PARP-2. Detailed analysis of the binding energy shows that the 4′4-difluorocyclohexyl ring on NMS-P118 form favorable hydrophobic interaction with Y889 in PARP-1. In addition, the H862 residue in PARP-1 has stronger binding free energy than H428 in PARP-2, which is due to shorter distance and stronger hydrogen bonds. Moreover, the negatively charged E763 residue in PARP-1 forms stronger electrostatic interaction energy with the positively charged NMS-P118 than the Q332 residue in PARP-2. These results rationalize the selectivity of NMS-P118 and may be useful for designing novel selective PARP inhibitors.

Abstract Background Increased collagen expression and deposition are associated with cancer progression and poor prognosis in breast cancer patients. However, function and regulation of membrane-associated collagen in breast cancer have not been determined. Collagen XIII is a type II transmembrane protein within the collagen superfamily. Experiments in tissue culture and knockout mouse models show that collagen XIII is involved in cell adhesion and differentiation of certain cell types. In the present study, we determined roles of collagen XIII in breast cancer progression and metastasis. Methods We analyzed the association of collagen XIII expression with breast cancer development and metastasis using published gene expression profiles generated from human breast cancer tissues. Utilizing gain- and loss- of function approaches and 3D culture assays, we investigated roles of collagen XIII in regulating invasive tumor growth. Using the tumorsphere/mammosphere formation assay and the detachment cell culture assay, we determined whether collagen XIII enhances cancer cell stemness and induces anoikis resistance. We also inhibited collagen XIII signaling with β1 integrin function-blocking antibody. Finally, using the lung colonization assay and the orthotopic mammary tumor model, we investigated roles of collagen XIII in regulating breast cancer colonization and metastasis. Cox proportional hazard (log-rank) test, two-sided Student’s t-test (two groups) and one-way ANOVA (three or more groups) analyses were used in this study. Results Collagen XIII expression is significantly higher in human breast cancer tissue compared with normal mammary gland. Increased collagen XIII mRNA levels in breast cancer tissue correlated with short distant recurrence free survival. We showed that collagen XIII expression promoted invasive tumor growth in 3D culture, enhanced cancer cell stemness, and induced anoikis resistance. Collagen XIII expression induced β1 integrin activation. Blocking β1 integrin activation significantly reduced collagen XIII-induced invasion and mammosphere formation. Importantly, silencing collagen XIII in MDA-MB-231 cells reduced lung colonization and metastasis. Conclusions Our results demonstrate a novel function of collagen XIII in promoting cancer metastasis, cell invasion, and anoikis resistance.

Under the oxidative stress condition, the small RNA (sRNA) OxyS that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in the defection of gene regulation. However, how the Hfq protein interacts with sRNA OxyS and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result was correlated with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly came from the increased van der Waals interactions (vdW). This research explored the binding mechanism between Oxys and chaperone protein Hfq and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights into the mechanism of gene expression regulation affected by protein mutations.

Collagen is the major component of extracellular matrix. Collagen cross-link and deposition depend on lysyl hydroxylation, which is catalyzed by procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD). Aberrant lysyl hydroxylation and collagen cross-link contributes to the progression of many collagen-related diseases, such as fibrosis and cancer. Three lysyl hydroxylases (LH1, LH2, and LH3) are identified, encoded by PLOD1, PLOD2, and PLOD3 genes. Expression of PLODs is regulated by multiple cytokines, transcription factors and microRNAs. Dysregulation of PLODs promotes cancer progression and metastasis, suggesting that targeting PLODs is potential strategy for cancer treatment. Here, we summarize the recent progress in the investigation of function and regulation of PLODs in normal tissue development and disease progression, especially in cancer.

The anthrax lethal toxin consists of protective antigen (PA) and lethal factor (LF). Understanding both the PA pore formation and LF translocation through the PA pore is crucial to mitigating and perhaps preventing anthrax disease. To better understand the interactions of the LF-PA engagement complex, the structure of the LFN-bound PA pore solubilized by a lipid nanodisc was examined using cryo-EM. CryoSPARC was used to rapidly sort particle populations of a heterogeneous sample preparation without imposing symmetry, resulting in a refined 17 Å PA pore structure with 3 LFN bound. At pH 7.5, the contributions from the three unstructured LFN lysine-rich tail regions do not occlude the Phe clamp opening. The open Phe clamp suggests that, in this translocation-compromised pH environment, the lysine-rich tails remain flexible and do not interact with the pore lumen region.

D-3-phosphoglycerate dehydrogenase (PGDH) from Escherichia coli catalyzes the first critical step in serine biosynthesis, and can be allosterically inhibited by serine. In a previous study, we developed a computational method for allosteric site prediction using a coarse-grained two-state Gō Model and perturbation. Two potential allosteric sites were predicted for E. coli PGDH, one close to the active site and the nucleotide binding site (Site I) and the other near the regulatory domain (Site II). In the present study, we discovered allosteric inhibitors and activators based on site I, using a high-throughput virtual screen, and followed by using surface plasmon resonance (SPR) to eliminate false positives. Compounds 1 and 2 demonstrated a low-concentration activation and high-concentration inhibition phenomenon, with IC50 values of 34.8 and 58.0 µM in enzymatic bioassays, respectively, comparable to that of the endogenous allosteric effector, L-serine. For its activation activity, compound 2 exhibited an AC50 value of 34.7 nM. The novel allosteric site discovered in PGDH was L-serine- and substrate-independent. Enzyme kinetics studies showed that these compounds influenced Km, kcat, and kcat/Km. We have also performed structure-activity relationship studies to discover high potency allosteric effectors. Compound 2-2, an analog of compound 2, showed the best in vitro activity with an IC50 of 22.3 µM. Compounds targeting this site can be used as new chemical probes to study metabolic regulation in E. coli. Our study not only identified a novel allosteric site and effectors for PGDH, but also provided a general strategy for designing new regulators for metabolic enzymes.