Molecular Modeling and Affinity Determination of scFv Antibody: Proper Linker Peptide Enhances Its Activity

One of existing strategies to engineer active antibody is to link VH and VL domains via a linker peptide. How the composition, length, and conformation of the linker affect antibody activity, however, remains poorly understood. In this study, a dual approach that coordinates molecule modeling, biological measurements, and affinity evaluation was developed to quantify the binding activity of a novel stable miniaturized anti-CD20 antibody or singlechain fragment variable (scFv) with a linker peptide. Upon computer-guided homology modeling, distance geometry analysis, and molecular superimposition and optimization, three new linker peptides PT1, PT2, and PT3 with respective 7, 10, and 15 residues were proposed and three engineered antibodies were then constructed by linking the cloned VH and VL domains and fusing to a derivative of human IgG1. The binding stability and activity of scFv-Fc chimera to CD20 antigen was quantified using a micropipette adhesion frequency assay and a Scatchard analysis. Our data indicated that the binding affinity was similar for the chimera with PT2 or PT3 and ~24-fold higher than that for the chimera with PT1, supporting theoretical predictions in molecular modeling. These results further the understanding in the impact of linker peptide on antibody structure and activity.

Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

A biologically active peptide in the skin of lampreys (Eudontomyzon danfordi vladykovi). [Translation from: Z.Naturforsch. (B), 26(10), 1021-1023, 1971. ]

In recent years interest in the production and description of kinin-type substances has been greatly intensified. So, for example, bradykinin, phyllokinin, physalaemin, ranatensin and caerulein could be extracted from the skin of amphibians as well as. eledoisin out of the salivary glands of Eledon moschata. An examination of lampreys seemed to us particularly profitable in the search for the incidence of further kinins. Ammocoetes of different sizes and also adults of both sexes of the species Eudontomyzon danfordi vladykovi were studied in this research. This species is found in many tributaries of the Danube. Skin extracts were tested on on isolated rat uterus, rat duodenum, guinea pig ileum and rabbit jejunum, further tests were done in order to determine a peptide character of the biologically active substance.

The structure specificity of alpha-chymotrypsin. I. Polypeptides as substrates. II. N-acylated peptide esters as substrates. III. Some reactive esters of N-acylated amino acids as substrates

The structural specificity of α-chymotrypsin for polypeptides and denatured proteins has been examined. The primary specificity of the enzyme for these natural substrates is shown to closely correspond to that observed for model substrates. A pattern of secondary specificity is proposed.

A series of N-acetylated peptide esters of varying length have been evaluated as substrates of α-chymotrypsin. The results are interpreted in terms of proposed specificity theories.

The α-chymotrypsin-catalyzed hydrolyses of a number of N-acetylated dipeptide methyl esters were studied. The results are interpreted in terms of the available specificity theories and are compared with results obtained in the study of polypeptide substrates. The importance of non-productive binding in determining the kinetic parameters of these substrates is discussed. A partial model of the locus of the active site which interacts with the R’₁CONH- group of a substrate of the form R’₁CONHCHR₂COR’₃ is proposed.

Finally, some reactive esters of N-acetylated amino acids have been evaluated as substrates of α-chymotrypsin. Their reactivity and stereo-chemical behavior are discussed in terms of the specificity theories available. The importance of a binding interaction between the carboxyl function of the substrate and the enzyme is suggested by the results obtained.

Expressão da leptina e seu receptor no câncer de próstata

O câncer de próstata é o tumor não cutâneo mais comum entre homens e responsável pela segunda maior mortalidade entre os tumores neste sexo. Diferentes métodos são utilizados com o objetivo de determinar o prognóstico do paciente portador de câncer de próstata, contudo existe grande heterogeneidade quando estes são usados individualmente. A leptina é um hormônio peptídico envolvido na regulação da ingestão alimentar, do metabolismo, do gasto energético, além de função neuroendócrina. Este hormônio parece estar envolvido na patogênese de alguns tipos de tumores, inclusive os adenocarcinomas de próstata. Até o presente não se tem certeza se a leptina e seu receptor possam ser utilizados como fatores prognósticos no cancer de próstata. O objetivo do trabalho foi correlacionar os perfis de imunomarcação da leptina e seu receptor em adenocarcinomas de próstata com diferentes fatores prognósticos e comparar as análises de imunomarcação da leptina e seu receptor em adenocarcinomas de próstata por métodos semiquantitativos e quantitativos (morfometria). Foram analisadas 532 peças cirúrgicas de prostatectomias radicais por câncer prostático. A partir destas amostras, após estudo histopatológico, foi montado um arranjo de matriz tecidual, contendo fragmentos de áreas tumorais e não tumorais (peritumorais) destas amostras. Estas foram imunomarcadas com anticorpos antileptina e antirreceptor de leptina. Análises subjetivas (feitas por dois observadores) e objetivas (através da contagem de pontos) foram realizadas em cada uma das imunomarcações. Estes resultados foram comparados e correlacionados com os seguintes fatores prognósticos: invasão perineural, embolização neoplásica vascular, comprometimento bilateral da próstata, invasão das vesículas seminais, comprometimento de margem vesical, de margem uretral e de margem cirúrgica de ressecção. Houve diferença significativa entre as análises subjetivas dos dois observadores e, portanto, estas não foram utilizadas para as demais comparações. Em relação às análises objetivas, foi verificado que a expressão do receptor de leptina estava diminuída nos tumores com comprometimento de margem cirúrgica, de margem uretral e de vesículas seminais. Ainda foi observado correlação entre a expressão desse receptor e o somátório dos fatores prognósticos analisados. Para as demais análises não foi verificada diferença significativa. Métodos semiquantitativos podem ter grande variação e devem ser preteridos em relação a métodos quantitativos para as análises realizadas neste estudo. Nem a leptina nem o seu receptor apresentaram alterações de sua expressão em amostras neoplásicas de próstata quando comparado àquelas não neoplásicas. O receptor de leptina apresentou uma diminuição da sua expressão em tumores com margem cirúrgica comprometida, margem uretral comprometida e com vesículas seminais comprometidas. Houve correlação negativa entre o percentual de área imunomarcada com o anticorpo antirreceptor de leptina e o somatório dos fatores prognósticos analisados.

The protein, peptide and free amino-acid contents of some species of Gracilaria from south-east coast of India

Four species of Gracilaria are investigated for their free amino-acid contents, as well as amino-acid constituents in the proteins and the peptides, using quantitative paper chromatographic technique. Amino-acid constituents of different species of Gracilaria differ only in amount, while free amino-acids and the amino-acids in the peptides vary both in quality and quantity. A number of amino-acids recorded as protein constituents have even escaped detection in the peptides, while in the free state they occur either in all the species or in some only except homocystine. Moreover, some amino-acids occur exclusively in the free state.

A novel bradykinin-related peptide from skin secretions of toad Bombina maxima and its precursor containing six identical copies of the final product

Amphibian skin contains rich bradykinin-related peptides, but the mode of biosynthesis of these peptides is unknown. In the present study, a novel bradykinin-related peptide, termed bombinakinin M, was purified from skin secretions of the Chinese red bell