A non-canonical vitamin K cycle is a potent ferroptosis suppressor.

Ferroptosis, a non-apoptotic form of cell death marked by iron-dependent lipid peroxidation1, has a key role in organ injury, degenerative disease and vulnerability of therapy-resistant cancers2. Although substantial progress has been made in understanding the molecular processes relevant to ferroptosis, additional cell-extrinsic and cell-intrinsic processes that determine cell sensitivity toward ferroptosis remain unknown. Here we show that the fully reduced forms of vitamin K-a group of naphthoquinones that includes menaquinone and phylloquinone3-confer a strong anti-ferroptotic function, in addition to the conventional function linked to blood clotting by acting as a cofactor for γ-glutamyl carboxylase. Ferroptosis suppressor protein 1 (FSP1), a NAD(P)H-ubiquinone reductase and the second mainstay of ferroptosis control after glutathione peroxidase-44,5, was found to efficiently reduce vitamin K to its hydroquinone, a potent radical-trapping antioxidant and inhibitor of (phospho)lipid peroxidation. The FSP1-mediated reduction of vitamin K was also responsible for the antidotal effect of vitamin K against warfarin poisoning. It follows that FSP1 is the enzyme mediating warfarin-resistant vitamin K reduction in the canonical vitamin K cycle6. The FSP1-dependent non-canonical vitamin K cycle can act to protect cells against detrimental lipid peroxidation and ferroptosis.

Role of 8-hydroxyguanine DNA glycosidase 1 deficiency in exacerbating diabetic cardiomyopathy through the regulation of insulin resistance.

Diabetic cardiomyopathy (DCM) is a heart failure syndrome, and is one of the major causes of morbidity and mortality in diabetes. DCM is mainly characterized by ventricular dilation, myocardial hypertrophy, myocardial fibrosis and cardiac dysfunction. Clinical studies have found that insulin resistance is an independent risk factor for DCM. However, its specific mechanism of DCM remains unclear. 8-hydroxyguanine DNA glycosylase 1(OGG1)is involved in DNA base repair and the regulation of inflammatory genes. In this study, we show that OGG1 was associated with the occurrence of DCM. for the first time. The expression of OGG1 was increased in the heart tissue of DCM mice, and OGG1 deficiency aggravated the cardiac dysfunction of DCM mice. Metabolomics show that OGG1 deficiency resulted in obstruction of glycolytic pathway. At the molecular level, OGG1 regulated glucose uptake and insulin resistance by interacting with PPAR-γ in vitro. In order to explore the protective effect of exogenous OGG1 on DCM, OGG1 adeno-associated virus was injected into DCM mice through tail vein in the middle stage of the disease. We found that the overexpression of OGG1 could improve cardiac dysfunction of DCM mice, indicating that OGG1 had a certain therapeutic effect on DCM. These results demonstrate that OGG1 is a new molecular target for the treatment of DCM and has certain clinical significance.

Interrupted Homolytic Substitution Enables Organoboron Compounds to Inhibit Radical Chain Reactions Rather than Initiate Them.

The reactions of organoboranes with peroxyl radicals are key to their use as radical initiators for a vast array of radical chain reactions, particularly at low temperatures where high stereoselectivity or regioselectivity is desired. Whereas these reactions generally proceed via concerted homolytic substitution (SH2) mechanisms, organoboranes that bear groups that can stabilize tetracoordinate boron radical "ate" complexes (e.g., catecholboranes) undergo this reaction via a stepwise addition/fragmentation sequence and serve as useful stoichiometric alkyl radical precursors. Here we show that arylboronic esters and amides derived from catecholborane and diaminonaphthaleneborane, respectively, are potent radical-trapping antioxidants (RTAs). Mechanistic studies reveal that this is because the radical "ate" complexes derived from peroxyl radical addition to boron are sufficiently persistent to trap another radical in an interrupted SH2 reaction. Remarkably, the reactivity of these organoboranes as inhibitors of autoxidation was shown to translate from simple hydrocarbons to the phospholipids of biological membranes such that they can inhibit ferroptosis, the cell death modality driven by lipid autoxidation and relevant in neurodegeneration and other major pathologies. The unique mechanism of these organoboranes is one of only a handful of RTA mechanisms that are not based on H-atom transfer processes and provide a new dimension to boron chemistry and its applications.

8-Oxoguanine DNA glycosylase protects cells from senescence via the p53-p21 pathway.

Cellular senescence is an important factor leading to pulmonary fibrosis. Deficiency of 8-oxoguanine DNA glycosylase (OGG1) in mice leads to alleviation of bleomycin (BLM)-induced mouse pulmonary fibrosis, and inhibition of the OGG1 enzyme reduces the epithelial mesenchymal transition (EMT) in lung cells. In the present study, we find decreased expression of OGG1 in aged mice and BLM-induced cell senescence. In addition, a decrease in OGG1 expression results in cell senescence, such as increases in the percentage of SA-ß-gal-positive cells, and in the p21 and p-H2AX protein levels in response to BLM in lung cells. Furthermore, OGG1 promotes cell transformation in A549 cells in the presence of BLM. We also find that OGG1 siRNA impedes cell cycle progression and inhibits the levels of telomerase reverse transcriptase (TERT) and LaminB1 in BLM-treated lung cells. The increase in OGG1 expression results in the opposite phenomenon. The mRNA levels of senescence-associated secretory phenotype (SASP) components, including IL-1α, IL-1ß, IL-6, IL-8, CXCL1/CXCL2, and MMP-3, in the absence of OGG1 are obviously increased in A549 cells treated with BLM. Interestingly, we demonstrate that OGG1 binds to p53 to inhibit the activation of p53 and that silencing of p53 reverses the inhibition of OGG1 on senescence in lung cells. Additionally, the augmented cell senescence is shown in vivo in OGG1-deficient mice. Overall, we provide direct evidence in vivo and in vitro that OGG1 plays an important role in protecting tissue cells against aging associated with the p53 pathway.

Apurinic/apyrimidinic endonuclease 1 regulates palmitic acid-mediated apoptosis in cardiomyocytes via endoplasmic reticulum stress.

Cardiomyocyte apoptosis caused by fat metabolism disorder plays an essential role in the pathogenesis of diabetic cardiomyopathy (DCM). Apurinic/apyrimidinic endonuclease 1 (APE1) has multiple functions, including regulating redox and DNA repair. However, the role of APE1 in the pathogenesis of DCM remains unclear. To investigate the mechanism of APE1 on high-fat induced apoptosis in H9C2 cells, we treated H9C2 cells with palmitic acid (PA) as an apoptosis model caused by hyperlipidemia. We found that PA reduced the viability and increased apoptosis of H9C2 cells by inducing up-regulation of APE1 protein and endoplasmic reticulum (ER) stress. APE1 knockdown enhanced PA-induced apoptosis, and ER stress and overexpression of APE1 demonstrated the opposite effect. Furthermore, APE1 regulated PA-induced apoptosis via ER stress. The APE1 mutant (C65A, lack of redox regulation) loses its protective effect against ER stress and apoptosis. These findings indicate that APE1 protects PA-induced H9C2 cardiomyocyte apoptosis through ER stress via its redox-regulated function. This study provided new insights into the therapy for DCM.

Oncolytic virotherapy evolved into the fourth generation as tumor immunotherapy.

BACKGROUND: Oncolytic virotherapy (OVT) is a promising anti-tumor modality that utilizes oncolytic viruses (OVs) to preferentially attack cancers rather than normal tissues. With the understanding particularly in the characteristics of viruses and tumor cells, numerous innovative OVs have been engineered to conquer cancers, such as Talimogene Laherparepvec (T-VEC) and tasadenoturev (DNX-2401). However, the therapeutic safety and efficacy must be further optimized and balanced to ensure the superior safe and efficient OVT in clinics, and reasonable combination therapy strategies are also important challenges worthy to be explored. MAIN BODY: Here we provided a critical review of the development history and status of OVT, emphasizing the mechanisms of enhancing both safety and efficacy. We propose that oncolytic virotherapy has evolved into the fourth generation as tumor immunotherapy. Particularly, to arouse T cells by designing OVs expressing bi-specific T cell activator (BiTA) is a promising strategy of killing two birds with one stone. Amazing combination of therapeutic strategies of OVs and immune cells confers immense potential for managing cancers. Moreover, the attractive preclinical OVT addressed recently, and the OVT in clinical trials were systematically reviewed. CONCLUSION: OVs, which are advancing into clinical trials, are being envisioned as the frontier clinical anti-tumor agents coming soon.

Screening of rosmarinic acid from Salvia miltiorrhizae acting on the novel target TRPC1 based on the 'homology modelling-virtual screening-molecular docking-affinity assay-activity evaluation' method.

CONTEXT: Salvia miltiorrhizae Bunge (Lamiaceae) is a traditional Chinese medicine (TCM) for the treatment of 'thoracic obstruction'. Transient receptor potential canonical channel 1 (TRPC1) is a important target for myocardial injury treatment. OBJECTIVE: This work screens the active component acting on TRPC1 from Salvia miltiorrhizae. MATERIALS AND METHODS: TCM Systems Pharmacology Database and Analysis Platform (TCMSP) was used to retrieve Salvia miltiorrhiza compounds for preliminary screening by referring to Lipinski's rule of five. Then, the compound group was comprehensively scored by AutoDock Vina based on TRPC1 protein. Surface plasmon resonance (SPR) was used to determine the affinity of the optimal compound to TRPC1 protein. Western blot assay was carried out to observe the effect of the optimal compound on TRPC1 protein expression in HL-1 cells, and Fura-2/AM detection was carried out to observe the effect of the optimal compound on calcium influx in HEK293 cells. RESULTS: Twenty compounds with relatively good characteristic parameters were determined from 202 compounds of Salvia miltiorrhiza. Rosmarinic acid (RosA) was obtained based on the molecular docking scoring function. RosA had a high binding affinity to TRPC1 protein (KD value = 1.27 µM). RosA (50 µM) could reduce the protein levels (417.1%) of TRPC1 after oxygen-glucose deprivation/reperfusion (OGD/R) in HL-1 cells and it could inhibit TRPC1-mediated Ca2+ influx injury (0.07 ΔRatio340/380) in HEK293 cells. DISCUSSION AND CONCLUSIONS: We obtained the potential active component RosA acting on TRPC1 from Salvia miltiorrhizae, and we speculate that RosA may be a promising clinical candidate for myocardial injury therapy.

Hydropersulfides Inhibit Lipid Peroxidation and Protect Cells from Ferroptosis.

Hydropersulfides (RSSH) are believed to serve important roles in vivo, including as scavengers of damaging oxidants and electrophiles. The α-effect makes RSSH not only much better nucleophiles than thiols (RSH), but also much more potent H-atom transfer agents. Since HAT is the mechanism of action of the most potent small-molecule inhibitors of phospholipid peroxidation and associated ferroptotic cell death, we have investigated their reactivity in this context. Using the fluorescence-enabled inhibited autoxidation (FENIX) approach, we have found RSSH to be highly reactive toward phospholipid-derived peroxyl radicals (kinh = 2 × 105 M-1 s-1), equaling the most potent ferroptosis inhibitors identified to date. Related (poly)sulfide products resulting from the rapid self-reaction of RSSH under physiological conditions (e.g., disulfide, trisulfide, H2S) are essentially unreactive, but combinations from which RSSH can be produced in situ (i.e., polysulfides with H2S or thiols with H2S2) are effective. In situ generation of RSSH from designed precursors which release RSSH via intramolecular substitution or hydrolysis improve the radical-trapping efficiency of RSSH by minimizing deleterious self-reactions. A brief survey of structure-reactivity relationships enabled the design of new precursors that are more efficient. The reactivity of RSSH and their precursors translates from (phospho)lipid bilayers to cell culture (mouse embryonic fibroblasts), where they were found to inhibit ferroptosis induced by inactivation of glutathione peroxidase-4 (GPX4) or deletion of the gene encoding it. These results suggest that RSSH and the pathways responsible for their biosynthesis may act as a ferroptosis suppression system alongside the recently discovered FSP1/ubiquinone and GCH1/BH4/DHFR systems.

Intrinsic and Extrinsic Limitations to the Design and Optimization of Inhibitors of Lipid Peroxidation and Associated Cell Death.

The archetype inhibitors of ferroptosis, ferrostatin-1 and liproxstatin-1, were identified via high-throughput screening of compound libraries for cytoprotective activity. These compounds have been shown to inhibit ferroptosis by suppressing propagation of lipid peroxidation, the radical chain reaction that drives cell death. Herein, we present the first rational design and optimization of ferroptosis inhibitors targeting this mechanism of action. Engaging the most potent radical-trapping antioxidant (RTA) scaffold known (phenoxazine, PNX), and its less reactive chalcogen cousin (phenothiazine, PTZ), we explored structure-reactivity-potency relationships to elucidate the intrinsic and extrinsic limitations of this approach. The results delineate the roles of inherent RTA activity, H-bonding interactions with phospholipid headgroups, and lipid solubility in determining activity/potency. We show that modifications which increase inherent RTA activity beyond that of the parent compounds do not substantially improve RTA kinetics in phospholipids or potency in cells, while modifications that decrease intrinsic RTA activity lead to corresponding erosions to both. The apparent "plateau" of RTA activity in phospholipid bilayers (kinh ∼ 2 × 105 M-1 s-1) and cell potency (EC50 ∼ 4 nM) may be the result of diffusion-controlled reactivity between the RTA and lipid-peroxyl radicals and/or the potential limitations on RTA turnover/regeneration by endogenous reductants. The metabolic stability of selected derivatives was assessed to identify a candidate for in vivo experimentation as a proof-of-concept. This PNX-derivative demonstrated stability in mouse liver microsomes comparable to liproxstatin-1 and was successfully used to suppress acute renal failure in mice brought on by tissue-specific inactivation of the ferroptosis regulator GPX4.

Metformin Hydrochloride Mucosal Nanoparticles-Based Enteric Capsule for Prolonged Intestinal Residence Time, Improved Bioavailability, and Hypoglycemic Effect.

Metformin hydrochloride enteric-coated capsule (MH-EC) is a commonly used clinical drug for the treatment of type 2 diabetes. In this study, we described a metformin hydrochloride mucosal nanoparticles enteric-coated capsule (MH-MNPs-EC) based on metformin hydrochloride chitosan mucosal nanoparticles (MH-CS MNPs) and its preparation method to improve the bioavailability and hypoglycemic effect duration of MH-EC. In intestinal adhesion study, the residue rates of free drugs and mucosal nanoparticles were 10.52% and 67.27%, respectively after cleaned with PBS buffer. MH-CS MNPs could significantly improve the efficacy of MH and promote the rehabilitation of diabetes rats. In vitro release test of MH-MNPs-EC showed continuous release over 12 h, while commercial MH-EC released completely within about 1 h in intestinal environment (pH 6.8). Pharmacokinetic study was performed in beagle dogs compared to the commercial MH-EC. The durations of blood MH concentration above 2 µg/mL were 9 h for MH-MNPs-EC versus 2 h for commercial MH-EC. The relative bioavailability of MH-MNPs-EC was determined as 185.28%, compared with commercial MH-EC. In conclusion, MH-CS MNPs have good intestinal adhesion and can significantly prolong the residence time of MH in the intestine. MH-MNPs-EC has better treatment effect compared with MH-EC, and it is expected to be a potential drug product for the treatment of diabetes because of its desired characteristics.

A Divergent Strategy for Site-Selective Radical Disulfuration of Carboxylic Acids with Trisulfide-1,1-Dioxides.

The direct conversion of carboxylic acids into disulfides is described. The approach employs oxidative photocatalysis for base-promoted decarboxylation of the substrate, which yields an alkyl radical that reacts with a trisulfide dioxide through homolytic substitution. The trisulfide dioxides are easily prepared by a newly described approach. 1°, 2°, and 3° carboxylic acids with varied substitution are good substrates, including amino acids and substrates with highly activated C-H bonds. Trisulfide dioxides are also used to achieve the γ-C(sp3 )-H disulfuration of amides through a radical relay sequence. In both reactions, the sulfonyl radical that results from substitution propagates the reaction. Factors governing the selectivity of substitution at S2 versus S3 of the trisulfide dioxides have been explored.

Radical Substitution Provides a Unique Route to Disulfides.

Radical substitution on tetrasulfides is demonstrated to be a highly effective means to prepare unsymmetric disulfides. Alkyl and aryl radicals generated thermally or photochemically underwent substitution on readily prepared dialkyl, diaryl, and diacyl tetrasulfides to yield the corresponding disulfides in good to excellent yields. Classic and contemporary thermal and photochemical radical sources could be employed; while photoredox catalysis approaches led to either oxidation or reduction of the tetrasulfide, energy transfer photocatalysis was particularly useful. The success of the approach is driven by the thermodynamic stability of the perthiyl radicals formed upon substitution on the tetrasulfide; they simply combine under the reaction conditions to provide the starting tetrasulfide. Competition kinetic experiments reveal that alkyl radical substitution on tetrasulfides is a rapid reaction (6 × 105 M-1 s-1) that is enhanced at least 6-fold upon moving from dialkyl tetrasulfide to diacyl tetrasulfide due to favorable polar effects. This unique and versatile reaction enables introduction of disulfide moieties from a variety of radical precursors and straightforward access to hydropersulfides.

Co-occurrence patterns of microbial communities affected by inoculants of plant growth-promoting bacteria during phytoremediation of heavy metal-contaminated soils.

Phytoremediation assisted by plant growth-promoting bacteria (PGPB) is an alternative method of cleaning up toxic metals from soil. However, the interactions among indigenous soil microorganisms following PGPB inoculation are far from fully understood, although these interactions are conducive to evaluate the effectiveness of PGPB. Here, we used Illumina Miseq sequencing and network analysis to decipher the co-occurrence patterns of bacterial communities following PGPB inoculation during phytoremediation of heavy metal contaminated soil. Miseq sequencing revealed that PGPB inoculation changed the bacterial community composition one day after inoculation, with minor changes continuing to be observed ten days after inoculation. This suggested that PGPB inoculants did not proliferate extensively in a new environment. Network analysis showed that PGPB inoculation altered the co-occurrence patterns, dominant modules and topological roles of individual OTUs. In the presence of PGPB inoculants the bacterial community had more complex and compact associations. Moreover, PGPB inoculation increased the percentage of connectors, indicating that PGPB may contribute to more intensified interactions among OTUs from different modules; consequently, the microbial community would be more ordered and efficient. The enhanced co-occurrence associations in the PGPB-inoculated bacterial network may contribute to the plant growth-promoting effects of PGPB during phytoremediation of heavy metal-contaminated soil.

CYP450s-Activity Relations of Celastrol to Interact with Triptolide Reveal the Reasons of Hepatotoxicity of Tripterygium wilfordii.

Celastrol and triptolide, as the two main bio-activity ingredients in Tripterygium wilfordii, have wide anticancer pharmacological potency, as well as anti-inflammatory and immunosuppression effects. However, they have potential hepatotoxicity and underlying mechanisms of them-induced toxicity mediated by hepatic CYP450s have not been well delineated. In the present study, we accessed the toxic effects and possible mechanism of celastrol and triptolide on primary rat hepatocytes. Models of subdued/enhanced activity of CYP450 enzymes in primary rat hepatocytes were also constructed to evaluate the relationship between the two ingredients and CYP450s. LC-MS/MS was used to establish a detection method of the amount of triptolide in rat hepatocytes. As the results, cell viability, biochemical index, and mitochondrial membrane potential indicated that celastrol and triptolide had toxic potencies on hepatocytes. Moreover, the toxic effects were enhanced when the compounds combined with 1-aminobenzotriazole (enzyme inhibitor) while they were mitigated when combined with phenobarbital (an enzyme inducer). Meanwhile, celastrol could affect the amount of triptolide in the cell. We therefore put forward that increase of triptolide in the cell might be one of the main causes of hepatotoxicity caused by Tripterygium wilfordii.

A cascade C-H functionalization/cyclization reaction of N-arylpyridin-2-amines with α,ß-unsaturated aldehydes for the synthesis of dihydroquinolinone derivatives under rhodium catalysis.

A novel cascade C-H functionalization/cyclization reaction of N-arylpyridin-2-amines with α,ß-unsaturated aldehydes has been developed under rhodium catalysis, affording dihydroquinolinone derivatives in moderate to excellent yields. A plausible mechanism of dual catalytic cycles by rhodium(iii) catalysis is also proposed.

Coordination Mechanism and Bio-Evidence: Reactive γ-Ketoenal Intermediated Hepatotoxicity of Psoralen and Isopsoralen Based on Computer Approach and Bioassay.

Psoralen and isopsoralen are secondary plant metabolites found in many fruits, vegetables, and medicinal herbs. Psoralen-containing plants (Psoralea corylifolia L.) have been reported to cause hepatotoxicity. Herein, we found that psoralen and isopsoralen were oxidized by CYP450s to reactive furanoepoxide or γ-ketoenal intermediates, causing a mechanism-based inhibition of CYP3A4. Furthermore, in GSH-depleted mice, the hepatotoxicity of these reactive metabolites has been demonstrated by pre-treatment with a well-known GSH synthesis inhibitor, L-buthionine-S, Rsulfoxinine (BSO). Moreover, a molecular docking simulation of the present study was undertaken to understand the coordination reaction that plays a significant role in the combination of unstable intermediates and CYP3A4. These results suggested that psoralen and isopsoralen are modest hepatotoxic agents, as their reactive metabolites could be deactivated by H2O and GSH in the liver, which partly contributes to the ingestion of psoralen-containing fruits and vegetables being safe.

Reactive metabolite activation by CYP2C19-mediated rhein hepatotoxicity.

1. Rhein, an active ingredient in the root of rhubarb, is used for its beneficial effects in a variety of clinical applications including the treatment of osteoarthritis and diabetic nephropathy. However, its hepatotoxicity has been reported in recent years. Rhein belongs to the conjugate structure which could be activated to reactive metabolites (RMs) inducing side-effects. This study is to explore the relationship between RMs and hepatotoxicity. 2. Based on the early detection of RMs, we have established a series of key technologies to research rhein hepatotoxicity mechanism: IC50 shift experiments and reduced glutathione (GSH) trapping experiment are adopted to identify RMs. The model of low activity of CYP450 enzymes (CYPs) in primary rat hepatocyte is constructed to analyze the relationship between the primary metabolic enzyme and hepatotoxicity of rhein better. 3. The IC50 shift value for CYP2C19 is 1.989, it suggests that CYP2C19 could activate rhein to RM. The structure of RM is epoxide intermediate. Besides, it is found that CYP2C19 is a primary metabolic enzyme for rhein. In the cytotoxicity assay, it is reported that rhein could cause mitochondrial dysfunction. Furthermore, mitochondrial membrane potential (Δψm) and AST levels could be restored by adding inhibitor of CYP2C19 together with rhein, which further shows that CYP2C19 could mediate the hepatotoxicity of rhein. 4. We put forward the possible mechanism that reactive metabolite activation by CYP2C19 mediated rhein hepatotoxicity, it provides important information on predicting in vivo drug-induced liver injury (DILI).

Oxidative enantioselective α-fluorination of aliphatic aldehydes enabled by N-heterocyclic carbene catalysis.

Described is the first study on oxidative enantioselective α-fluorination of simple aliphatic aldehydes enabled by N-heterocyclic carbene catalysis. N-fluorobis(phenyl)sulfonimide serves as a an oxidant and as an "F" source. The C-F bond formation occurs directly at the α position of simple aliphatic aldehydes, thus overcoming nontrivial challenges, such as competitive difluorination and nonfluorination, and proceeds with high to excellent enantioselectivities.

Intermolecular dynamic kinetic resolution cooperatively catalyzed by an N-heterocyclic carbene and a Lewis acid.

The ubiquitous structure of δ-lactones makes the development of new methods for their enantioselective and stereoselective synthesis an important ongoing challenge. The intermolecular dynamic kinetic resolution (DKR) of ß-halo-α-ketoesters cooperatively catalyzed by an N-heterocyclic carbene and a Lewis acid generates two contiguous stereocenters with remarkable diastereoselectivity through an oxidation/lactonization sequence.

SPREd: a simulation-supervised neural network tool for gene regulatory network reconstruction.

Summary: Reconstruction of gene regulatory networks (GRNs) from expression data is a significant open problem. Common approaches train a machine learning (ML) model to predict a gene's expression using transcription factors' (TFs') expression as features and designate important features/TFs as regulators of the gene. Here, we present an entirely different paradigm, where GRN edges are directly predicted by the ML model. The new approach, named "SPREd," is a simulation-supervised neural network for GRN inference. Its inputs comprise expression relationships (e.g. correlation, mutual information) between the target gene and each TF and between pairs of TFs. The output includes binary labels indicating whether each TF regulates the target gene. We train the neural network model using synthetic expression data generated by a biophysics-inspired simulation model that incorporates linear as well as non-linear TF-gene relationships and diverse GRN configurations. We show SPREd to outperform state-of-the-art GRN reconstruction tools GENIE3, ENNET, PORTIA, and TIGRESS on synthetic datasets with high co-expression among TFs, similar to that seen in real data. A key advantage of the new approach is its robustness to relatively small numbers of conditions (columns) in the expression matrix, which is a common problem faced by existing methods. Finally, we evaluate SPREd on real data sets in yeast that represent gold-standard benchmarks of GRN reconstruction and show it to perform significantly better than or comparably to existing methods. In addition to its high accuracy and speed, SPREd marks a first step toward incorporating biophysics principles of gene regulation into ML-based approaches to GRN reconstruction. Availability and implementation: Data and code are available from https://github.com/iiiime/SPREd.