TCMSSD: A comprehensive database focused on syndrome standardization

BACKGROUD

Quantitative and standardized research on syndrome differentiation has always been at the forefront of modernizing Traditional Chinese Medicine (TCM) theory. However, the majority of existing databases primarily concentrate on the network pharmacology of herbal prescriptions, and there are limited databases specifically dedicated to TCM syndrome differentiation.

PURPOSE

In response to this gap, we have developed the Traditional Chinese Medical Syndrome Standardization Database (TCMSSD, http://tcmssd.ratcm.cn).

METHODS

TCMSSD is a comprehensive database that gathers data from various sources, including TCM literature such as TCM Syndrome Studies (Zhong Yi Zheng Hou Xue) and TCM Internal Medicine (Zhong Yi Nei Ke Xue) and various public databases such as TCMID and ETCM. In our study, we employ a deep learning approach to construct the knowledge graph and utilize the BM25 algorithm for syndrome prediction.

RESULTS

The TCMSSD integrates the essence of TCM with the modern medical system, providing a comprehensive collection of information related to TCM. It includes 624 syndromes, 133,518 prescriptions, 8,073 diseases (including 1,843 TCM-specific diseases), 8,259 Chinese herbal medicines, 43,413 ingredients, 17,602 targets, and 8,182 drugs. By analyzing input data and comparing it with the patterns and characteristics recorded in the database, the syndrome prediction tool generates predictions based on established correlations and patterns.

CONCLUSION

The TCMSSD fills the gap in existing databases by providing a comprehensive resource for quantitative and standardized research on TCM syndrome differentiation and laid the foundation for research on the biological basis of syndromes.

Cornus officinalis with high pressure wine steaming enhanced anti-hepatic fibrosis: Possible through SIRT3-AMPK axis

Cornus officinalis, a medicinal and edible plant known for its liver-nourishing properties, has shown promise in inhibiting the activation of hepatic stellate cells (HSCs), crucial indicators of hepatic fibrosis, especially when processed by high pressure wine steaming (HPWS). Herein, this study aims to investigate the regulatory effects of cornus officinalis, both in its raw and HPWS forms, on inflammation and apoptosis in liver fibrosis and their underlying mechanisms. In vivo liver fibrosis models were established by subcutaneous injection of CCl4, while in vitro HSCs were exposed to transforming growth factor-β (TGF-β). These findings demonstrated that cornus officinalis with HPWS conspicuously ameliorated histopathological injury, reduced the release of proinflammatory factors, and decreased collagen deposition in CCl4-induced rats compared to its raw form. Utilizing ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometer (UHPLC-QTOF-MS) combined with network analysis, we identified that the pharmacological effects of the changed components of cornus officinalis before and after HPWS, primarily centered on the adenosine phosphate (AMP)-activated protein kinase (AMPK) pathway. Of note, cornus officinalis activated AMPK and Sirtuin 3 (SIRT3), promoting the apoptosis of activated HSCs through the caspase cascade by regulating caspase3, caspase6 and caspase9. siRNA experiments showed that cornus officinalis could regulate AMPK activity and its mediated-apoptosis through SIRT3. In conclusion, cornus officinalis exhibited the ability to reduce inflammation and apoptosis, with the SIRT3-AMPK signaling pathway identified as a potential mechanism underlying the synergistic effect of cornus officinalis with HPWS on anti-liver fibrosis.

Detoxification and underlying mechanisms towards toxic alkaloids by Traditional Chinese Medicine processing: A comprehensive review

BACKGROUND

Alkaloids have attracted enduring interest worldwide due to their remarkable therapeutic effects, including analgesic, anti-inflammatory, and anti-tumor properties, thus offering a rich source for lead compound design and new drug discovery. However, some of these alkaloids possess intrinsic toxicity. Processing (Paozhi) is a pre-treatment step before the application of herbal medicines in traditional Chinese medicine (TCM) clinics, which has been employed for centuries to mitigate the toxicity of alkaloid-rich TCMs.

PURPOSE

To explore the toxicity phenotypes, chemical basis, mode of action, detoxification processing methods, and underlying mechanisms, we can gain crucial insights into the safe and rational use of these toxic alkaloid-rich herbs. Such insights have the great potential to offer new strategies for drug discovery and development, ultimately improving the quality of life for millions of people.

METHODS

Literatures published or early accessed until December 31, 2023, were retrieved from databases including PubMed, Web of Science, and CNKI. The following keywords, such as "toxicity", "alkaloid", "detoxification", "processing", "traditional Chinese medicine", "medicinal plant", and "plant", were used in combination or separately for screening.

RESULTS

Toxicity of alkaloids in TCM includes hepatotoxicity, nephrotoxicity, neurotoxicity, cardiotoxicity, and other forms of toxicity, primarily induced by pyrrolizidines, quinolizidines, isoquinolines, indoles, pyridines, terpenoids, and amines. Factors such as whether the toxic-alkaloid enriched part is limited or heat-sensitive, and whether toxic alkaloids are also therapeutic components, are critical for choosing appropriate detoxification processing methods. Mechanisms of alkaloid detoxification includes physical removal, chemical decomposition or transformation, as well as biological modifications.

CONCLUSION

Through this exploration, we review toxic alkaloids and the mechanisms underlying their toxicity, discuss methods to reduce toxicity, and unravel the intricate mechanisms behind detoxification. These offers insights into the quality control of herbs containing toxic alkaloids, safe and rational use of alkaloid-rich TCMs in clinics, new strategies for drug discovery and development, and ultimately helping improve the quality of life for millions of people.

The pathogenesis of organ fibrosis: Focus on necroptosis

Fibrosis is a common process of tissue repair response to multiple injuries in all chronic progressive diseases, which features with excessive deposition of extracellular matrix. Fibrosis can occur in all organs and tends to be nonreversible with the progress of the disease. Different cells types in different organs are involved in the occurrence and development of fibrosis, that is, hepatic stellate cells, pancreatic stellate cells, fibroblasts and myofibroblasts. Various types of programmed cell death, including apoptosis, autophagy, ferroptosis and necroptosis, are closely related to organ fibrosis. Among these programmed cell death types, necroptosis, an emerging regulated cell death type, is regarded as a huge potential target to ameliorate organ fibrosis. In this review, we summarize the role of necroptosis signalling in organ fibrosis and collate the small molecule compounds targeting necroptosis. In addition, we discuss the potential challenges, opportunities and open questions in using necroptosis signalling as a potential target for antifibrotic therapies. LINKED ARTICLES: This article is part of a themed issue on Translational Advances in Fibrosis as a Therapeutic Target. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v180.22/issuetoc.

Expanding annotation of chemical compounds in hawthorn fruits and their variations in thermal processing using integrated mass spectral similarity networking

Chemical structural characterization of chemical compounds from hawthorn fruits and its thermal processed products was carried out in present study. By linking Global Natural Products Social (GNPS) Molecular Networking and MolNetEnhancer workflow, seventy-four chemical compounds in hawthorn fruits and its thermal processed products were tentatively identified. Three quercetagetin derivatives (quercetagetin-3-O-glucoside, quercetagetin-di-glucoside and its isomer), five quercetin or kaempferol derivatives (quercetin-acetylapiosyl-hexoside, quercetin-3-O-(6″-malonyl-hexoside), quercetin-3-O-(6″-malonyl-hexoside)-(1 → 2)-O-hexoside, quercetin-3-O-(6″-malonyl-hexoside)-(1 → 2)-O-deoxyhexoside, kaempferol-3-O-(6″-malonyl-hexoside)), six procyanidins including four (E)C-ethyl-procyanidins and two A-type procyanidins digallate, as well as 13 triterpenoids including ursolic aldehyde, triterpenoid glycosides, and triterpene acids were reported for the first time in hawthorn fruits. In addition, triterpenoids exhibited considerable thermal stability, while all of flavonoid glycosides, proanthocyanidins and 10 in 13 organic acids showed dramatic decrease after thermal processing.

The Ferroptosis Induced by Palmitic Acid via CD36 Activating ER Stress to Break Calcium-Iron Balance in Colon Cancer Cells

PURPOSE/OBJECTIVE(S)

There have been numerous studies to date on the treatment of tumors by saturated fatty acids. But the role that ferroptosis plays in this is not clear. Palmitic acid (PA) is a common saturated fatty acid with huge application prospects for inducing tumor cell ferroptosis.

MATERIALS/METHODS

In vivo and in vitro experiments were performed to verify changes in cell proliferation, apoptosis and ferroptosis after PA treatment of colon cancer cells. Changes in ROS, lipid peroxidation, ferric ions, calcium ions, endoplasmic reticulum (ER) stress, endocytosis recycling trafficking of transferrin after PA treatment of colon cancer cells were detected. Further using necrosis inhibitor (Necrostatin-1), apoptosis inhibitor (Z-VAD-FMK), autophagy inhibitor (CQ), iron death inhibitor (Fer-1), calcium / ferric ion chelator (BAPTA-AM / DFP), iron supplement (FAC), calcium ion agonist (thapsigargin) for positive and negative verification. The association of CD36 expression and patient prognosis in colon cancer patients was subsequently evaluated by bioinformatics analysis. Detect the difference of CD36 expression in different colon cancer cells induced by PA, and further knock down or over express CD36 to explore the change of sensitivity to PA induced ferroptosis.

RESULTS

PA inhibited colon cancer cell viability in vitro and in vivo, in conjunction with an accumulation of ROS and lipid peroxidation. The ferroptosis inhibitor Ferrostatin-1 but not Z-VAD-FMK, Necrostatin-1, or CQ rescued the cell death induced by PA. Subsequently, we verified that PA-induced ferroptosis through excess iron as cell death was inhibited by iron chelator deferiprone (DFP) but exacerbated by a supplement of ferric ammonium citrate (FAC). Mechanistically, PA leads to endoplasmic reticulum calcium release by inducing ER stress, and the increase of cytosolic calcium level positively regulates the endocytosis recycling transport of transferrin to promote the increase of intracellular iron content. Furthermore, we observed that cells with high expression of CD36 were more vulnerable to PA-induced ferroptosis. Knocking down the expression of CD36 can inhibit the sensitivity of colon cancer cells to PA induced ferroptosis, and vice versa.

CONCLUSION

In general, we report for the first time that PA can selectively induce ferroptosis in colon cancer cells with high expression of CD36 by activating ER stress/ER calcium release/transferrin-dependent ferroptosis. This provides a new strategy and basis for the precise treatment of tumors.

Prognostic Significance of Serum Lipids in Patients with Non-Small Cell Lung Cancer Treated with Radiotherapy: A Multicenter Prospective Study

PURPOSE/OBJECTIVE(S)

Although lipids have been assessed for their possible roles in cancer survival prediction, studies on the association between serum lipids levels and the prognosis of non-small cell lung cancer (NSCLC) patients are limited. This study aimed to evaluate whether serum lipids are associated with outcomes in patients with NSCLC treated with radiotherapy.

MATERIALS/METHODS

We conducted a multicenter prospective study on patients diagnosed with NSCLC between January 2018 and February 2021. Participants received thoracic radiotherapy of 60ཞ80 Gy to the primary lung tumor and positive lymph node metastases. We measured patients' serum lipids levels (serum triglyceride, TGs; total cholesterol, TC, high density lipoprotein cholesterol, HDL-C; low density lipoprotein cholesterol, LDL-C) before radiotherapy. The association between serum lipids levels and overall survival (OS) was evaluated using hazard ratios. We sought to determine a threshold point using optimal stratification. Survival analysis was performed using Kaplan-Meier curves.

RESULTS

Of the 300 participants diagnosed with NSCLC treated with radiotherapy, 165 (55.0%) were men. Median follow-up time was 24.4 months (range 1.0- 101.9 months). Using univariate and multivariate Cox proportional hazard analysis, among those serum lipids, only serum TG was shown to be independent prognostic factors for OS (hazard ratio: 1.203, 95% confidence interval: 1.038 - 1.393, p = 0.014). The cut-off for TG associated with OS was 2.04 mmol/L. Based on the TG cut-off value, 55 NSCLC patients were categorized into the high TG group (>2.04 mmol/L) and 245 in the low TG group (<2.04 mmol/L). The NSCLC patients in the low TG group exhibited higher OS than the high group (median OS, not reach vs 41.4 months, p = 0.025).

CONCLUSION

TG levels were found to be a significant negative prognostic biomarker for OS in NSCLC patients treated with radiotherapy.

Nanodrug rescues liver fibrosis via synergistic therapy with H2O2 depletion and Saikosaponin b1 sustained release

Hypoxia and hydrogen peroxide (H₂O₂) accumulation form the profibrogenic liver environment, which involves fibrogenesis and chronic stimulation of hepatic stellate cells (HSCs). Catalase (CAT) is the major antioxidant enzyme that catalyzes H₂O₂ into oxygen and water, which loses its activity in different liver diseases, especially in liver fibrosis. Clinical specimens of cirrhosis patients and liver fibrotic mice are collected in this work, and results show that CAT decrease is closely correlated with hypoxia-induced transforminmg growth factor β1 (TGF-β1). A multifunctional nanosystem combining CAT-like MnO₂ and anti-fibrosis Saikosaponin b1 (Ssb1) is subsequently constructed for antifibrotic therapy. MnO₂ catalyzes the accumulated H₂O₂ into oxygen, thereby ameliorating the hypoxic and oxidative stress to prevent activation of HSCs, and assists to enhance the antifibrotic pharmaceutical effect of Ssb1. This work suggests that TGF-β1 is responsible for the diminished CAT in liver fibrosis, and our designed MnO₂@PLGA/Ssb1 nanosystem displays enhanced antifibrotic efficiency through removing excess H₂O₂ and hypoxic stress, which may be a promising therapeutic approach for liver fibrosis treatment.

A deep clustering-based mass spectral data visualization strategy for anti-renal fibrotic lead compound identification from natural products

We present a deep clustering-based MS data visualization strategy (MCnebula), integrated with the influential open-source automatic MS annotation platform SIRIUS and in vivo and in vitro methods, to screen and validate potential lead compounds from natural products.

Automated ASPECTS on Noncontrast CT Scans in Patients with Acute Ischemic Stroke Using Machine Learning

BACKGROUND AND PURPOSE

Alberta Stroke Program Early CT Score (ASPECTS) was devised as a systematic method to assess the extent of early ischemic change on noncontrast CT (NCCT) in patients with acute ischemic stroke (AIS). Our aim was to automate ASPECTS to objectively score NCCT of AIS patients.

MATERIALS AND METHODS

We collected NCCT images with a 5-mm thickness of 257 patients with acute ischemic stroke (<8 hours from onset to scans) followed by a diffusion-weighted imaging acquisition within 1 hour. Expert ASPECTS readings on DWI were used as ground truth. Texture features were extracted from each ASPECTS region of the 157 training patient images to train a random forest classifier. The unseen 100 testing patient images were used to evaluate the performance of the trained classifier. Statistical analyses on the total ASPECTS and region-level ASPECTS were conducted.

RESULTS

For the total ASPECTS of the unseen 100 patients, the intraclass correlation coefficient between the automated ASPECTS method and DWI ASPECTS scores of expert readings was 0.76 (95% confidence interval, 0.67-0.83) and the mean ASPECTS difference in the Bland-Altman plot was 0.3 (limits of agreement, -3.3, 2.6). Individual ASPECTS region-level analysis showed that our method yielded κ = 0.60, sensitivity of 66.2%, specificity of 91.8%, and area under curve of 0.79 for 100 × 10 ASPECTS regions. Additionally, when ASPECTS was dichotomized (>4 and ≤4), κ = 0.78, sensitivity of 97.8%, specificity of 80%, and area under the curve of 0.89 were generated between the proposed method and expert readings on DWI.

CONCLUSIONS

The proposed automated ASPECTS scoring approach shows reasonable ability to determine ASPECTS on NCCT images in patients presenting with acute ischemic stroke.

Radiomics-Based Intracranial Thrombus Features on CT and CTA Predict Recanalization with Intravenous Alteplase in Patients with Acute Ischemic Stroke

BACKGROUND AND PURPOSE

Thrombus characteristics identified on non-contrast CT (NCCT) are potentially associated with recanalization with intravenous (IV) alteplase in patients with acute ischemic stroke (AIS). Our aim was to determine the best radiomics-based features of thrombus on NCCT and CT angiography associated with recanalization with IV alteplase in AIS patients and proximal intracranial thrombi.

MATERIALS AND METHODS

With a nested case-control design, 67 patients with ICA/M1 MCA segment thrombus treated with IV alteplase were included in this analysis. Three hundred twenty-six radiomics features were extracted from each thrombus on both NCCT and CTA images. Linear discriminative analysis was applied to select features most strongly associated with early recanalization with IV alteplase. These features were then used to train a linear support vector machine classifier. Ten times 5-fold cross-validation was used to evaluate the accuracy of the trained classifier and the stability of the selected features.

RESULTS

Receiver operating characteristic curves showed that thrombus radiomics features are predictive of early recanalization with IV alteplase. The combination of radiomics features from NCCT, CTA, and radiomics changes is best associated with early recanalization with IV alteplase (area under the curve = 0.85) and was significantly better than any single feature such as thrombus length (P < .001), volume (P < .001), and permeability as measured by mean attenuation increase (P < .001), maximum attenuation in CTA (P < .001), maximum attenuation increase (P < .001), and assessment of residual flow grade (P < .001).

CONCLUSIONS

Thrombus radiomics features derived from NCCT and CTA are more predictive of recanalization with IV alteplase in patients with acute ischemic stroke with proximal occlusion than previously known thrombus imaging features such as length, volume, and permeability.

Oxygen defect engineering by the current effect assisted with temperature cycling in a perovskite-type La0.7Sr0.3CoO3 film

Introducing and modulating the oxygen deficiency concentration have been received as an effective way to obtain high catalytic activity in perovskite oxides. However, it is difficult to control the oxygen vacancy in conventional oxygen defect engineering due to harsh reaction conditions at elevated temperatures and the reducing atmosphere, which make it impractical for many technological applications. Herein, we report a new approach to oxygen defect engineering based on the combination of the current effect and temperature cycling at low temperature. Our investigations revealed that the electrical conductivity of the (011)-La_0.7Sr_0.3CoO₃/PMN-PT film changes continuously from metallicity to insulativity under repeated transport measurements below room temperature, which indicates the transformation of the Co⁴⁺ state to Co³⁺ in the film. Further experiments and analysis revealed that oxygen vacancies can be well regulated by the combined current effect and temperature cycling in repeated measurements, which results in a decrease of Co⁴⁺/Co³⁺ and thus the remarkable variation of conductive properties of the film. Our work provides a simple and highly efficient method to engineer oxygen vacancies in perovskite-type oxides and brings new opportunities in designing high-efficiency oxidation catalysts.

Withasteroid B from D. metel L. regulates immune responses by modulating the JAK/STAT pathway and the IL-17+ RORγt+ /IL-10+ FoxP3+ ratio

Datura metel L. is a medicinal herb that contains withasteroids and has a wide range of biological activities. We isolated seven withasteroids from the flowers of D. metel L and examined their ability to inhibit immune responses in vitro and in vivo. Among the withasteroids, withasteroid B2 exhibited the strongest inhibitory effect on immune responses comparing B2 with other isolated compounds from D. metel L., including suppressing the differentiation of CD4⁺ T cells by inhibiting the expression and production of T cell lineage-specific master regulators and cytokines and directly suppressing the cytokine-induced Janus kinase/signal transducer and activator of transcription (JAK/STAT) signalling pathways. In the interleukin (IL)-23-induced mouse ear model of skin disease, B2 repressed disease development by inhibiting the expression of proinflammatory mediators in murine ear skin. Moreover, B2 affected the maturation of dendritic cells (DCs) in vitro which, in turn, induced T cell differentiation with an increased regulatory T cell (T_reg ) phenotype and decreased T helper type 17 (Th17) phenotype. This study provides new evidence that B2 might ameliorate chronic inflammatory skin diseases by suppressing pathogenic CD4⁺ T cell differentiation and the IL-17⁺ retinoic-acid-receptor-related orphan receptor gamma t (RORγt)⁺ /IL-10⁺ forkhead box protein 3 (FoxP3)⁺ ratio. These findings suggest that B2 might mediate the therapeutic effects observed in psoriasis patients following treatment with D. metel L.

G-protein coupled receptor 120 is involved in glucose metabolism in fat cells

Free fatty acids (FFA) are closely related to insulin resistance in which proteins such as insulin receptor substrate 1 (IRS-1), phosphatidylinositol 3 kinase (PI3K) and glucose transporter type 4 (GLUT4) are involved. Recent researches have shown that G-protein coupled receptor 120 (GPR120) is a receptor for medium and long chain FFA. This study aimed to evaluate the relationship between GPR120 and proteins related to the glucose metabolism. We used siRNA technique to down-regulate the GPR120 expression in 3T3-L1 cells before incubation with palmitic acid (PA), and evaluated the effect of GPR120 expression on the levels of IRS-1, PI3K and GLUT4 after PA induction. RT-PCR and western blot were performed to detect gene and protein levels in differentiated cells. RT-PCR result showed that GPR120 mRNA significantly increased in differentiated cells. GPR120-SiRNA transfection significantly down-regulated GPR120 gene and protein level in differentiated 3T3-L1 cells on day 5 after PA-induced and also decreased lipid droplets accumulated within the cells. SiRNA-mediated decreased of GRP120 was associated with significant reductions in gene and protein levels of IRS-1 and GLUT4. Our results showed that the expression level of GPR120 affected the expression of proteins related to the glucose metabolism, suggesting a contribution of GPR120 in the insulin resistance.

Development of an enzyme-linked immunosorbent assay for the alpha-cyano pyrethroids multiresidue in Tai lake water

A general and broad class selective competitive enzyme-linked immunosorbent assay (ELISA) for the detection of the alpha-cyano pyrethroids was developed. One class specific hapten, the 5-(3-benzylphenyl)-5-cyanopentanoic acid (CPBA-BE), was conjugated with BSA as an immunogen. Polyclonal antibodies, PY-antibodies, were generated. The assay with the most selectivity for the family alpha-cyano pyrethroids such as cyphenothrin was further optimized and tested for tolerance to cosolvent, pH, and ionic strength changes. The IC(50) values of the optimized immunoassay were 4.58 microg L(-1) for cyphenothrin, 5.62 microg L(-1) for fenpropathrin, 7.08 microg L(-1) for deltamethrin, 10.72 microg L(-1) for cypermethrin, 19.95 microg L(-1) for flucythrinate, and 28.18 microg L(-1) for esfenvalerate. The cross-reactivities of cyphenothrin, fenpropathrin, deltamethrin, cypermethrin, flucythrinate, and esfenvalerate were 100%, 81.49%, 64.68%, 42.72%, 22.96%, and 16.25%, respectively. The low detection limit (LDL) of this assay was 0.107 microg L(-1) for cyphenothrin. This method was used for the detection of the alpha-cyano pyrethroids in Tai lake water.

Synthesis of a cationic pyridoxamine conjugation reagent and application to the mechanistic analysis of an artificial transaminase

An N-methylated, cationic pyridoxamine conjugation reagent was synthesized and tethered via a disulfide bond to a cysteine residue inside the cavity of intestinal fatty acid binding protein. The conjugate was characterized and the kinetic parameters compared to its nonmethylated pyridoxamine analogue. Kinetic isotope effects were used for further mechanistic analysis. Taken together, these experiments suggest that a step distinct from deprotonation of the ketimine in the pyridoxamine to pyridoxal reaction is what limits the rate of the artificial transaminase IFABP-Px. However, the internal energetics of reactions catalyzed by the conjugate containing the N-methylated cofactor appear to be different suggesting that the MPx reagent will be useful in future experiments designed to alter the catalytic properties of semisynthetic transaminases.

Artificial metalloenzymes based on protein cavities: exploring the effect of altering the metal ligand attachment position by site directed mutagenesis

In an effort to construct catalysts with enzyme-like properties, we are employing a small, cavity-containing protein as a scaffold for the attachment of catalytic groups. In earlier work we demonstrated that a phenanthroline ligand could be introduced into the cavity of the protein ALBP and used to catalyze ester hydrolysis. To examine the effect of positioning the phenanthroline catalyst at different locations within the protein cavity, three new constructs--Phen60, Phen72 and Phen104--were prepared. Each new conjugate was characterized by UV/vis spectroscopy, fluorescence spectroscopy, guanidine hydrochloride denaturation, gel filtration chromatography, and CD spectroscopy to confirm the preparation of the desired construct. Analysis of reactions containing Ala-OiPr showed that Phen60 catalyzed ester hydrolysis with less selectivity than ALBP-Phen while Phen72 promoted this same reaction with higher selectivity. Reactions with Tyr-OMe were catalyzed with higher selectivity by Phen60 and more rapidly by Phen104. These results demonstrate that both the rates and selectivities of hydrolysis reactions catalyzed by these constructs are dependent on the precise site of attachment of the metal ligand within the protein cavity.

The design of protein-based catalysts using semisynthetic methods

The combination of site-directed mutagenesis and chemical modification has resulted in the preparation of protein conjugates with new and useful properties. Proteins modified with metal-chelating groups are proving useful for mapping tertiary and quaternary interactions using the technique of affinity cleavage. The attachment of cofactors, including pyridoxal and pyridoxamine, has resulted in the preparation of semisynthetic transaminases that display enzyme-like properties, including enantioselectivity, substrate specificity and reaction-rate acceleration.

Effects of metal ions on the rates and enantioselectivities of reactions catalyzed by a series of semisynthetic transaminases created by site directed mutagenesis

Fatty acid binding proteins are a class of small 15 kDa proteins with a simple architecture that forms a large solvent sequestered cavity. In previous work, we demonstrated that reductive amination reactions could be performed in this cavity by covalent attachment of a pyridoxamine cofactor and that the rate, enantioselectivity and substrate specificity of these reactions could be altered by site directed mutagenesis. Herein, we show that the chemistry performed by these conjugates can be extended to include catalytic transamination and describe the effects of added metal ions on reaction rate and enantioselectivity. We conclude that metal ions can be used to increase the rate of reactions catalyzed by semisynthetic transaminases; however, the addition of metal ions can also retard the reaction rate. Furthermore, it appears that the presence of metal ions almost always results in an erosion of reaction enantioselectivity. This limits their utility as a practical means of increasing reaction rate. The results reported here, for four independent systems, should be considered in future designs of artificial transaminases.

Structural characterization of two synthetic catalysts based on adipocyte lipid-binding protein

Adipocyte lipid-binding protein (ALBP) is a small (14.5 kDa) 10-stranded beta-barrel protein found in mammalian fat cells. The crystal structures of various holo-forms of ALBP have been solved and show the fatty acid ligand bound in a large (approximately 400 A3) cavity isolated from bulk solvent. Examination of the cavity suggests that it would be a good site for the creation of an artificial catalyst, as numerous well defined crystal structures of ALBP are available and past studies have shown the conformation to be reasonably tolerant to modification and mutagenesis. Previous work has shown ALBP to be a good protein scaffold for exploring enantio- and stereoselective reactions; two constructs, ALBP attached to either a pyridoxamine or a phenanthroline group at C117, have been chemically characterized. Both modified proteins have been crystallized and their structures solved and refined. The X-ray models have been used to examine the origin of the chiral selectivity seen in the products. It is apparent that these covalent adducts reduce the internal cavity volume, sterically limiting substrate interactions with the reactive groups, as well as solvent access to potential intermediates in the reaction pathway.