The live biotherapeutic SYNB1353 decreases plasma methionine via directed degradation in animal models and healthy volunteers

Methionine is an essential proteinogenic amino acid, but its excess can lead to deleterious effects. Inborn errors of methionine metabolism resulting from loss of function in cystathionine β-synthase (CBS) cause classic homocystinuria (HCU), which is managed by a methionine-restricted diet. Synthetic biotics are gastrointestinal tract-targeted live biotherapeutics that can be engineered to replicate the benefits of dietary restriction. In this study, we assess whether SYNB1353, an E. coli Nissle 1917 derivative, impacts circulating methionine and homocysteine levels in animals and healthy volunteers. In both mice and nonhuman primates (NHPs), SYNB1353 blunts the appearance of plasma methionine and plasma homocysteine in response to an oral methionine load. A phase 1 clinical study conducted in healthy volunteers subjected to an oral methionine challenge demonstrates that SYNB1353 is well tolerated and blunts plasma methionine by 26%. Overall, SYNB1353 represents a promising approach for methionine reduction with potential utility for the treatment of HCU.

Elucidating Substrate Promiscuity within the FabI Enzyme Family

The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead to their expanded use in the fields of chemical synthesis and industrial biotechnology. Here, we explore the substrate promiscuity of enoyl-acyl carrier protein reductases (commonly known as FabI) and how that promiscuity is a function of inherent reactivity and the geometric demands of the enzyme's active site. We demonstrate that these enzymes catalyze the reduction of a wide range of substrates, particularly α,β-unsaturated aldehydes. In addition, we demonstrate that a combination of quantum mechanical hydride affinity calculations and molecular docking can be used to rapidly categorize compounds that FabI can use as substrates. The results here provide new insight into the determinants of catalysis for FabI and set the stage for the development of a new assay for drug discovery, organic synthesis, and novel biocatalysts.

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs shows that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. These results are directly applicable to rational enzyme design and engineering.

Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants

The use of computational modeling algorithms to guide the design of novel enzyme catalysts is a rapidly growing field. Force-field based methods have now been used to engineer both enzyme specificity and activity. However, the proportion of designed mutants with the intended function is often less than ten percent. One potential reason for this is that current force-field based approaches are trained on indirect measures of function rather than direct correlation to experimentally-determined functional effects of mutations. We hypothesize that this is partially due to the lack of data sets for which a large panel of enzyme variants has been produced, purified, and kinetically characterized. Here we report the kcat and KM values of 100 purified mutants of a glycoside hydrolase enzyme. We demonstrate the utility of this data set by using machine learning to train a new algorithm that enables prediction of each kinetic parameter based on readily-modeled structural features. The generated dataset and analyses carried out in this study not only provide insight into how this enzyme functions, they also provide a clear path forward for the improvement of computational enzyme redesign algorithms.

Extensive adenocarcinoma and large cell undifferentiated carcinoma of the lung treated with 5-FU, vindesine, and mitomycin (FEMi): a Southwest Oncology Group Study

Sixty-three previously untreated patients with metastatic non-small cell lung cancer (40 patients with adenocarcinoma and 23 with large cell undifferentiated carcinoma) were treated with combination chemotherapy consisting of 5-FU (300 mg/m2) given as an iv bolus on Days 1-4 and vindesine (3 mg/m2) and mitomycin (10 mg/m2), both given as an iv bolus on Day 1 of each treatment course (FEMi). FEMi was repeated at 3-week intervals for three treatment courses and thereafter at 6-week intervals until disease progression. Major objective responses were seen in 13 of 63 patients (21%). Minor responses were seen in an additional 12 patients (19%). The median survival for all patients was 23 weeks and for responding patients was 38 weeks. The pretreatment performance status had a significant effect on both the response rate and survival time. Patients having an initial Karnofsky performance score greater than or equal to 70% had a 54% response rate, with a median survival of 42 weeks for responding patients. FEMi was well-tolerated: 18 patients (29%) did not have any side effects and only five (8%) experienced vomiting.

Expression of silver-stained nucleolar organizing regions (Ag-NORs) in human cancer

Five cases of ovarian adenocarcinoma, three cases of endometrial adenocarcinoma, and one case of transitional cell carcinoma of the bladder have been studied for expression of silver-stained nucleolar organizing regions (Ag-NORs). The modal chromosome number of these tumors varied from 37 to 72, with a wide range of chromosome numbers (13 to 150). The modal number of Ag-NORs in this sample varied from 3 to 7. Regression analysis among and between tumors demonstrated a proportionate increase in the number of Ag-NORs with increasing number of total chromosomes and increasing number of acrocentric chromosomes (r = 0.64 and 0.75, respectively). Modal assessment of Ag-NORs in both peripheral blood lymphocytes (PBLs) and cultured tumor cells in one patient revealed identical modes in normal and malignant cells. Also, no difference in the expression of Ag-NORs was observed between tumor cells obtained at biopsy and placed for 48 h in agar culture and tumor cells established in finite monolayer culture. Our study provides further evidence for a proportionate increase in Ag-NORs with increasing numbers of acrocentric chromosomes and total chromosomes.