Structural basis of IL-23 antagonism by an Alphabody protein scaffold

Protein scaffolds can provide a promising alternative to antibodies for various biomedical and biotechnological applications, including therapeutics. Here we describe the design and development of the Alphabody, a protein scaffold featuring a single-chain antiparallel triple-helix coiled-coil fold. We report affinity-matured Alphabodies with favourable physicochemical properties that can specifically neutralize human interleukin (IL)-23, a pivotal therapeutic target in autoimmune inflammatory diseases such as psoriasis and multiple sclerosis. The crystal structure of human IL-23 in complex with an affinity-matured Alphabody reveals how the variable interhelical groove of the scaffold uniquely targets a large epitope on the p19 subunit of IL-23 to harness fully the hydrophobic and hydrogen-bonding potential of tryptophan and tyrosine residues contributed by p19 and the Alphabody, respectively. Thus, Alphabodies are suitable for targeting protein-protein interfaces of therapeutic importance and can be tailored to interrogate desired design and binding-mode principles via efficient selection and affinity-maturation strategies

Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting

The therapeutic scope of antibody and nonantibody protein scaffolds is still prohibitively limited against intracellular drug targets. Here, we demonstrate that the Alphabody scaffold can be engineered into a cell-penetrating protein antagonist against induced myeloid leukemia cell differentiation protein MCL-1, an intracellular target in cancer, by grafting the critical B-cell lymphoma 2 homology 3 helix of MCL-1 onto the Alphabody and tagging the scaffold’s termini with designed cell-penetration polypeptides. Introduction of an albumin-binding moiety extended the serum half-life of the engineered Alphabody to therapeutically relevant levels, and administration thereof in mouse tumor xenografts based on myeloma cell lines reduced tumor burden. Crystal structures of such a designed Alphabody in complex with MCL-1 and serum albumin provided the structural blueprint of the applied design principles. Collectively, we provide proof of concept for the use of Alphabodies against intracellular disease mediators, which, to date, have remained in the realm of small-molecule therapeutics

Heterosubtypic Neutralizing Monoclonal Antibodies Cross-Protective against H5N1 and H1N1 Recovered from Human IgM+ Memory B Cells

Background: The hemagglutinin (HA) glycoprotein is the principal target of protective humoral immune responses to influenza virus infections but such antibody responses only provide efficient protection against a narrow spectrum of HA antigenic variants within a given virus subtype. Avian influenza viruses such as H5N1 are currently panzootic and pose a pandemic threat. These viruses are antigenically diverse and protective strategies need to cross protect against diverse viral clades. Furthermore, there are 16 different HA subtypes and no certainty the next pandemic will be caused by an H5 subtype, thus it is important to develop prophylactic and therapeutic interventions that provide heterosubtypic protection. Methods and Findings: Here we describe a panel of 13 monoclonal antibodies (mAbs) recovered from combinatorial display libraries that were constructed from human IgM+ memory B cells of recent (seasonal) influenza vaccinees. The mAbs have broad heterosubtypic neutralizing activity against antigenically diverse H1, H2, H5, H6, H8 and H9 influenza subtypes. Restriction to variable heavy chain gene IGHV1-69 in the high affinity mAb panel was associated with binding to a conserved hydrophobic pocket in the stem domain of HA. The most potent antibody (CR6261) was protective in mice when given before and after lethal H5N1 or H1N1 challenge. Conclusions: The human monoclonal CR6261 described in this study could be developed for use as a broad spectrum agent for prophylaxis or treatment of human or avian influenza infections without prior strain characterization. Moreover, the CR6261 epitope could be applied in targeted vaccine strategies or in the design of novel antivirals. Finally our approach of screening the IgM+ memory repertoire could be applied to identify conserved and functionally relevant targets on other rapidly evolving pathogens

Explanation of Benveniste

SCOPUS: le.jinfo:eu-repo/semantics/publishe

Reduction methods for logical control networks

SCOPUS: ar.jinfo:eu-repo/semantics/publishe

The design of idealized α/β-barrels: Analysis of β-sheet closure requirements

SCOPUS: ar.jFLWNAinfo:eu-repo/semantics/publishe

Basic design features of the parallel αβ barrel, a ubiquitous protein-folding motif

SCOPUS: cp.jinfo:eu-repo/semantics/publishe

BIOINFORMATICS APPLICATIONS NOTE Sequence analysis SABmark—a benchmark for sequence alignment that covers the entire known fold space

Summary: The Sequence Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These sets, Twilight Zone and Superfamilies, both cover the entire known fold space using sequences with very low to low, and low to intermediate similarity, respectively. In addition, each set has an alternate version in which unalignable but apparently similar sequences are added to each problem. Availability: SABmark is available fro

Immunogénicité de protéines d’intérêt thérapeutique

Le potentiel thérapeutique des anticorps monoclonaux ne cesse de croître avec d’indiscutables succès. Mais le bénéfice clinique de leur utilisation peut être compromis par l’induction d’anticorps contre ces anticorps, réalisant une réponse de type ADA (anti-drug antibodies) bien connue pour d’autres agents médicamenteux. Si la conception d’anticorps chimères contenant des séquences humaines, humanisés voire totalement humains, a substantiellement réduit leur immunogénicité, ce risque ne pourra pas être entièrement éradiqué. Nous discutons dans cette revue les aspects spécifiques aux réactions induites par l’administration d’Acm, qu’ils soient inhérents au produit thérapeutique ou au patient ; nous évoquerons aussi le programme de gestion des risques mis en place par les instances réglementaires et notamment l’European Medicines Agency (EMEA), et dont le rôle est d’évaluer, chez le patient, mais aussi en amont lors des étapes de recherche et développement précédant la mise sur le marché du produit (démarche prédictive), non seulement la probabilité d’une réponse immune dirigée contre cette protéine mais aussi son intensité. Cela implique le développement de méthodes in silico, de tests in vitro détectant l’activation T et finalement l’analyse fine des ADA à la recherche de l’épitope immunogène

Modelling the polypeptide backbone with 'spare parts' from known protein structures.

SCOPUS: ar.jinfo:eu-repo/semantics/publishe