Accelerating therapeutic protein design

Protein structures provide for defined microenvironments that can support complex pharmacological functions, otherwise unachievable by small molecules. The advent of therapeutic proteins has thus greatly broadened the range of manageable disorders. Leveraging the knowledge and recent advances in de novo protein design methods has the prospect of revolutionizing how protein drugs are discovered and developed. This review lays out the main challenges facing therapeutic proteins discovery and development, and how present and future advancements of protein design can accelerate the protein drug pipelines.

Evaluation of feeding behaviour traits to predict efficiency traits in pigs using partial least square regression

The improvement of efficiency traits, such as protein efficiency (PE), digestible energy efficiency (EnE) and lipid gain (LipG), are relevant given their associations with environmental pollution, cost of production, and the quality of meat. However, these traits are difficult to measure and usually require slaughtering of pigs. Efficiency traits are complex, and several factors, such as genetic predisposition, feed composition, but also individual feeding behaviour may contribute to efficiency. The objective of this study was therefore to evaluate the potential of using feeding behaviour traits to predict efficiency traits under dietary protein restriction. A total of 587 Swiss Large White pigs, consisting of 312 females and 275 castrated males, had ad libitum access to feed and water, and were fed a protein-reduced diet (80% of recommended digestible protein and essential amino acids) from 22.5 ± 1.6 to 106.6 ± 4.6 kg BW. Individual feed intake was monitored and carcass composition (lean and fat mass) at slaughter was determined by dual-energy X-ray absorptiometry. The PE and EnE were calculated as the ratio of protein or energy in the carcass (estimated by dual-energy X-ray absorptiometry) to the total protein or energy consumed. Feeding behaviour traits monitored were daily feed intake, feed intake per meal, number of daily meals, duration per meal, feeding rate, and feeder occupation. A partial least square (PLS) regression was used to predict PE, EnE and LipG from feeding behaviour traits, while including farrowing series (for PE only), age at slaughter and BW at slaughter. Accuracy of PLS regression was assessed based on RMSE and R² for calibration and validation sets, and on concordance correlation coefficient, which were estimated over 100 replicates of calibration and validation sets. Models with a number of latent variables of 5, 2 and 3 were identified as optimal for PE, EnE, and LipG, which explained 34.64%, 55.42% and 82.68% of the total variation in PE, EnE, and LipG, respectively. Significant concordance correlation coefficient was found between predicted and observed values for PE (0.50), EnE (0.70), and LipG (0.90). In conclusion, individual feeding behaviour traits can better predict EnE and LipG than for PE under dietary protein restriction when fed ad libitum.

Comparison of absorption kinetics and utilisation of DL-methionine (DL-Met), Met-Met product (AQUAVI® Met-Met), and protein-bound methionine (PB-Met) by female broiler chickens

1. Two experiments were conducted to determine the effects of different methionine (Met) sources regarding their absorption kinetics and utilisation in female single-meal-fed broiler chickens.2. A total of 340, one day old female Ross 308 broiler chickens were fed commercial starter and grower diets for 38 d. Birds were then allocated to treatment diets in two experiments as a completely randomised design with four replicates of five chicks per each until 60 d of age. In experiment 1, a 2 × 5 factorial design was used to investigate the effect of two sources (DL-Met and AQUAVI®Met-Met) and five equimolar levels (0.4, 0.8, 1.2, 1.6, and 2 g/kg) in the diet. In experiment 2, different proportions of protein-bound methionine (PB-Met) to DL-Met (0.4:1.6, 0.8:1.2, 1.2:0.8: 1.6:0.4, and 2:0 g/kg) were incorporated into a basal diet deficient in Met. During the experiment, chickens received 90 g of pelleted feed for a time period of 17 ± 2.5 min, once daily.3. The results indicated that chickens fed diets supplemented with DL-Met and Met-Met showed a rapid rise in plasma Met 1 h after feeding, with a sudden drop at 2 h after feeding. In contrast, chickens fed PB-Met substituted diets showed a gradual plasma peak at 1 and 2 h postprandial (P < 0.01). Plasma homocysteine (HCY) content increased to 34.38 and 40.43 μmol/l with DL-Met_2.0 and Met-Met_2.0 diets, while it decreased to 25.68 μmol/l with PB-Met_2.0(P ≤ 0.01). Chickens that received the PB-Met_2.0 diet had higher (P ≤ 0.01) protein utilisation (0.54 g/g) and lower excreta nitrogen content (4.04 g/100 g excreta), which demonstrated the benefits of feeding a protein-bound Met source. The efficiency of Met utilisation was 0.69 g/g in chickens fed PB-Met_2.0 diet, but only 0.36 and 0.41 g/g in those fed DL-Met_2.0 and Met-Met_2.0 (P ≤ 0.01).4. The observed utilisation coefficient of DL-Met and Met-Met for single-meal meat-type chickens was lower than expected. The synchronisation of intestinal Met absorption maintained the efficiency of utilisation, which was related to the sources of added Met, with protein-bound Met showing the best utilisation and least excretion.

De novo assembly and characterization of seabass Lateolabrax japonicus transcriptome and expression of hepatic genes following different dietary phosphorus/calcium levels

Fish farming seriously influences the aquatic environment because most dietary phosphorus (P) is excreted in the effluent. To increase the P utilization in fish, molecular techniques should be explored given the remarkable development of these techniques. Thus, to identify the candidate genes related to P utilization and molecular alterations following administration of a P-deficient diet in seabass Lateolabrax japonicus, we assessed the de novo pituitary, gill, intestine, liver, kidney, scales and vertebra transcriptomes, and we compared the expression of hepatic genes with three diets varying in P and Ca levels: diet I (0.4% P, 0.3% Ca), diet II (0.8% P, 0.3% Ca), and diet III (0.8% P, 3% Ca). In total, we identified 99,392 unigenes, and 37,086 (37.31%) unigenes were annotated. The results showed that 48 unigenes were significantly (P<0.05) up-regulated, while 55 genes were significantly down-regulated in the liver of group I compared with group II. Offering the P-sufficient and high Ca diet, diet III significantly up-regulated 24 unigenes and down-regulated 46 genes in the liver. There were significant differences in the regulation of 8 unigenes (3 up-regulated and 5 down-regulated) between groups II and III. Gene ontology (GO) functional enrichment and KEGG pathway analysis of differently expressed genes were performed for each pair of groups. The GO analysis showed that a large number of biological processes were significantly altered between P-deficient and P-sufficient treatments (I vs II and I vs III). Comparing group I and group II, seven KEGG terms were enriched significantly: glycine, serine and threonine metabolism, one carbon pool by folate, arginine and proline metabolism, the biosynthesis of unsaturated fatty acids, fatty acid elongation, drug metabolism-cytochrome P450, and fatty acid metabolism. There was no significantly enriched KEGG pathway between groups II and III. In conclusion, our study revealed that a P-deficient diet could increase catabolism and decrease anabolism of protein, as highlighted by low protein efficiency in fish fed the P-deficient diet. Furthermore, P-deficiency could motivate the biosynthesis of fatty acids. However, the dietary Ca level had no significant effect on the growth and expression of hepatic genes in L. japonicus.