Engineering a therapeutic IgG molecule to address cysteinylation,aggregation and enhance thermal stability and expression

Antibodies can undergo a variety of covalent and non-covalent degradation reactions that have adverse effects on efficacy, safety, manufacture and storage. We had identified an antibody to Angiopoietin 2 (Ang2 mAb) that neutralizes Ang2 binding to its receptor in vitro and inhibits tumor growth in vivo. Despite favorable pharmacological activity, the Ang2 mAb preparations were heterogeneous, aggregated rapidly and were poorly expressed. Here, we report the engineering of the antibody variable and constant domains to generate an antibody with reduced propensity to aggregate, enhanced homogeneity, 11°C elevated T_m, 26-fold improved level of expression and retained activity. The engineered molecule, MEDI-3617, is now compatible with the large scale material supply required for clinical trials and is currently being evaluated in Phase 1 in cancer patients. This is the first report to describe the stability engineering of a therapeutic antibody addressing non canonical cysteine residues and the design strategy reported here is generally applicable to other therapeutic antibodies and proteins.     

Effects of sodium nitroprusside in aortic stenosis associated with severe heart failure: pressure-volume loop analysis using a numerical model

In the recently published clinical study [Use of Nitroprusside in Left Ventricular Dysfunction and Obstructive Aortic Valve Disease (UNLOAD)], sodium nitroprusside (SNP) improved cardiac function in patients with severe aortic stenosis (AS) and left ventricular (LV) systolic dysfunction. We explored the possible mechanisms of these findings using a series of numerical simulations. A closed-loop lumped parameters model that consists of 24 differential equations relating pressure and flow throughout the circulation was used to analyze the effects of varying hemodynamic conditions in AS. Hemodynamic data from UNLOAD study subjects were used to construct the initial simulation. Systemic vascular resistance (SVR), heart rate, and aortic valve area were directly entered into the model while end-systolic and end-diastolic pressure-volume (P-V) relationships were adjusted using previously published data to match modeled and observed end-systolic and end-diastolic pressures and volumes. Initial simulation of SNP treatment by a reduction of SVR was not adequate. To obtain realistic model hemodynamics that reliably reproduce SNP treatment effects, we performed a series of simulations while simultaneously changing end-systolic elastance (E(es)), end-systolic volume at zero pressure (V(0)), and diastolic P-V shift. Our data indicate that either an E(es) increase or V(0) decrease is necessary to obtain realistic model hemodynamics. In five patients, we corroborated our findings by using the model to duplicate individual P-V loops obtained before and during SNP treatment. In conclusion, using a numerical model, we identified ventricular function parameters that are responsible for improved hemodynamics during SNP infusion in AS with LV dysfunction.     

Living organisms from Prigogine’s perspective: an opportunity to introduce students to biological entropy balance

All living structures, from archaea to human, are open thermodynamic systems analysed through nonequilibrium thermodynamics. Nonequilibrium thermodynamics is a field with important applications to life sciences, which is very often left out of life science courses. A three-step method is suggested to make an easy introduction of nonequilibrium thermodynamics to life science students. The first step is to introduce the Prigogine equation dS = d_eS + d_iS, and explain the meaning of the entropy exchange with the surroundings d_eS and internal entropy generation in the system d_iS. The second step is to show that the Prigogine equation is connected to the equilibrium thermodynamics already known to students. This can be done by deriving the Clausius inequality dS ≥ dq/T, from the Prigogine equation applied to reversible and irreversible processes in closed systems. Reversible and irreversible processes are discussed separately and the results are then combined into the Clausius inequality. The third step is to introduce the fact that the Prigogine equation has a variety of applications in life sciences. This would give the students an opportunity to understand the entropy balance of physiological processes in cells and organisms. The import and accumulation of entropy, entropy generation, and entropy export could be made easier for students to adopt.     

Glycolipoprotein extract (G-90) from earthworm Eisenia foetida exerts some antioxidative activity

Antioxidants protect DNA, proteins and lipids in the body from damage. These types of damages are a major contributor to aging and to degenerative diseases such as cancer, cardiovascular disease, immune-system decline, brain dysfunction and cataracts. The effect of glycolipoprotein extract of Eisenia foetida (G-90) as an antioxidant was investigated in cultured human fibroblasts and epithelial cells. After treatment of the cells with H2O2 for 4 h, G-90 completely allows the cells to recover and stimulated their growth. When the cells were incubated with G-90 48 h before the treatment with H2O2, the oxidative damage of the cells did not occur. Thus, G-90 had an apparent protective effect against the toxicity of H2O2 and stimulated the growth of the cells. Ascorbic acid, a known antioxidant, did not allow the growth of the cells to recover after damage nor did it protect them, unless it was added simultaneously with H2O2. The antioxidative activity of G-90, together with its antibacterial and mitogen activities, could be useful in the study of G-90 as a wound-healing agent.     

Folding,stability, and secondary structure of a new dimeric cysteine proteinase inhibitor

Clitocypin, a new type of cysteine proteinase inhibitor from the mushroom Clitocybe nebularis, is a 34-kDa homodimer lacking disulphide bonds, reported to have unusual stability properties. Sequence similarity is limited solely to certain proteins from mushrooms. Infrared spectroscopy shows that clitocypin is a high beta-structure protein which was lost at high temperatures. The far UV circular dichroism spectrum is not that of classical beta-structure, but similar to those of a group of small beta-strand proteins, with a peak at 189nm and a trough at 202nm. An aromatic peak at 232nm and infrared bands at 1633 and 1515cm(-1) associated with the peptide backbone and the tyrosine microenvironment, respectively, were used to characterize the thermal unfolding. The reversible transition has a midpoint at 67 degrees C, with DeltaG=34kJ/mol and DeltaH=300kJ/mol, and is, unusually, independent of protein concentration. The kinetics of thermal unfolding and refolding are slow, with activation energies of 167 and 44kJ/mol, respectively. A model for folding and assembly is discussed.     

Diverse enzymatic specificities of digestive proteases, 'intestains', enable Colorado potato beetle larvae to counteract the potato defence mechanism

In response to insect attack, high levels of proteinase inhibitors are synthesised in potato leaves. This can cause inefficient protein digestion in insects, leading to reduced growth, delayed development and lower fecundity. It has been suggested that Colorado potato beetle overcomes this defence mechanism by inducing the production of a set of cysteine proteases that are resistant to potato proteinase inhibitors. Experiments with gut extracts showed that these proteases have unusual inhibition profiles as they are not inhibited by most of the cystatins but are strongly inhibited by thyropins. In this study we have isolated three cysteine proteases from adapted guts of Colorado potato beetle larvae, named intestains 1, 2 and 3, the first cysteine proteases known to be involved in extracellular protein digestion. The N-terminal sequences suggest their classification into the papain family. Intestains differ in substrate specificities and inhibitory profiles. Their substrate specificities suggest that intestains 1 and 2 are general digestive enzymes, while intestain 3 has a more specific function. The inhibitory profile of intestain 1 is similar to that of proteases of the papain family. However, the Ki values for the interaction of intestain 2 with the same set of inhibitors are several hundred fold higher, which would enable the enzyme to circumvent the potato defence mechanism characterised by high concentrations of protease inhibitors in attacked potato leaves. A further, different strategy of the Colorado potato beetle to avoid potato defence is exhibited by intestain 3, which is able to cleave off the N-terminus of model cystatin and thus inactivate the inhibitor. These results suggest that the Colorado potato beetle combines different strategies to counteract plant defence mechanisms.     

Myostatin-deficient mice lose more skeletal muscle mass than wild-type controls during hindlimb suspension

Myostatin inhibits myogenesis. Therefore, we sought to determine if mice lacking the myostatin gene [Mstn(-/-)] would lose less muscle mass than wild-type mice during 7 days of hindlimb suspension (HS). Male Mstn(-/-) and wild-type (C57) mice were subjected to HS or served as ground-based controls (n = 6/group). Wild-type mice lost 8% of body mass and approximately 13% of wet mass from biceps femoris, quadriceps femoris, and soleus, whereas the mass of extensor digitorum longus (EDL) was unchanged after HS. Unexpectedly, Mstn(-/-) mice lost more body (13%, P < 0.05) and quadriceps femoris (17%, P < 0.05) mass than wild-type mice and lost 33% of EDL mass (P < 0.01) after HS. Protein expression of myostatin in biceps femoris and quadriceps femoris was not altered, whereas expression of MyoD, Myf-5, and myogenin increased in wild-type mice and tended to decrease in muscles of Mstn(-/-) mice. These data suggest that HS induced myogenesis in wild-type mice to counter atrophy, whereas myogenesis was not induced in Mstn(-/-) mice, thereby resulting in a greater loss of muscle mass.     

Organic anion transporting polypeptides (OATP) in zebrafish (Danio rerio): Phylogenetic analysis and tissue distribution

The aim of our study was the initial characterization of Organic anion transporting polypeptides (SLCO gene superfamily) in zebrafish (Danio rerio) as an important model species in biomedical and ecotoxicological research, using phylogenetic analysis, membrane topology prediction and tissue expression profiling. The phylogenetic tree of Oatp superfamily in vertebrates was constructed in Mega 3.1. Software, membrane topology was predicted using HMMTOP algorithm, while qRT-PCR was used to determine tissue-specific gene expression levels. Phylogenetic analysis revealed that Oatp superfamily in zebrafish consists of five families that include 14 SLCO genes. Eight out of 14 transporters do have orthologs or co-orthologs in other vertebrates, while 6 members are found only in fish lineage. Topology analysis showed that all zebrafish Oatps consist of 12 transmembrane domains (TMD) with the large fifth extracellular loop (LP5). Tissue distribution analysis revealed that the expression patterns of Oatp2a1, Oatp2b1 and Oatp3a1 follow tissue distribution patterns of their mammalian (co)orthologs. Expression pattern of a newly identified Oatp1d1 is similar to mouse Oatp1a4, while other new zebrafish Oatps (Oatp1e1, 1f2) do not resemble any of the mammalian Oatps. In summary, the described comprehensive analysis of Oatp superfamily in fish represents a first step towards research on toxicological relevance of uptake transporters in aquatic organisms.     

INCIPIENT SPECIATION OF SEA STAR POPULATIONS BY ADAPTIVE GAMETE RECOGNITION COEVOLUTION

Reproductive isolation—the key event in speciation—can evolve when sexual conflict causes selection favoring different combinations of male and female adaptations in different populations. Likely targets of such selection include genes that encode proteins on the surfaces of sperm and eggs, but no previous study has demonstrated intraspecific coevolution of interacting gamete recognition genes under selection. Here, we show that selection drives coevolution between an egg receptor for sperm (OBi1) and a sperm acrosomal protein (bindin) in diverging populations of a sea star (Patiria miniata). We found positive selection on OBi1 in an exon encoding part of its predicted substrate‐binding protein domain, the ligand for which is found in bindin. Gene flow was zero for the parts of bindin and OBi1 in which selection for high rates of amino acid substitution was detected; higher gene flow for other parts of the genome indicated selection against immigrant alleles at bindin and OBi1. Populations differed in allele frequencies at two key positively selected sites (one in each gene), and differences at those sites predicted fertilization rate variation among male–female pairs. These patterns suggest adaptively evolving loci that influence reproductive isolation between populations.