Recent Advances in the Scaffold Engineering of Protein Binders.

In recent years, extensive attention has been given to the generation of new classes of ligand- specific binding proteins to supplement monoclonal antibodies. A combination of protein engineering and display technologies has been used to manipulate non-human antibodies for humanization and stabilization purposes or even the generation of new binding proteins. Engineered protein scaffolds can now be directed against therapeutic targets to treat cancer and immunological disorders. Although very few of these scaffolds have successfully passed clinical trials, their remarkable properties such as robust folding, high solubility, and small size motivate their employment as a tool for biology and applied science studies. Here, we have focused on the generation of new non-Ig binding proteins and single domain antibody manipulation, with a glimpse of their applications.

Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing.

CRISPR technology is a universal tool for genome engineering that has revolutionized biotechnology. Recently identified unique CRISPR/Cas systems, as well as re-engineered Cas proteins, have rapidly expanded the functions and applications of CRISPR/Cas systems. The structures of Cas proteins are complex, containing multiple functional domains. These protein domains are evolutionarily conserved polypeptide units that generally show independent structural or functional properties. In this review, we propose using protein domains as a new way to classify protein engineering strategies for these proteins and discuss common ways to engineer key domains to modify the functions of CRISPR/Cas systems.

Molecular advancements on over-expression, stability and catalytic aspects of endo-ß-mannanases.

The hydrolysis of mannans by endo-ß-mannanases continues to gather significance as exemplified by its commercial applications in food, feed, and a rekindled interest in biorefineries. The present review provides a comprehensive account of fundamental research and fascinating insights in the field of endo-ß-mannanase engineering in order to improve over-expression and to decipher molecular determinants governing activity-stability during harsh conditions, substrate recognition, polysaccharide specificity, endo/exo mode of action and multi-functional activities in the modular polypeptide. In-depth analysis of the available literature has also been made on rational and directed evolution approaches, which have translated native endo-ß-mannanases into superior biocatalysts for satisfying industrial requirements.

Harnessing the Power of Proteolysis for Targeted Protein Inactivation.

Two decades into the twenty-first century, a confluence of breakthrough technologies wielded at the molecular level is presenting biologists with unique opportunities to unravel the complexities of the cellular world. CRISPR/Cas9 allows gene knock-outs, knock-ins, and single-base editing at chromosomal loci. RNA-based tools such as siRNA, antisense oligos, and morpholinos can be used to silence expression of specific genes. Meanwhile, protein knockdown tools that draw inspiration from natural regulatory mechanisms and facilitate elimination of native or degron-tagged proteins from cells are rapidly emerging. The acute and reversible reduction in protein levels enabled by these methods allows for precise determination of loss-of-function phenotypes free from secondary effects or compensatory adaptation that can confound nucleic-acid-based methods that involve slow depletion or permanent loss of a protein. In this Review, we summarize the ingenious ways biologists have exploited natural mechanisms for protein degradation to direct the elimination of specific proteins at will. This has led to advancements not only in basic research but also in the therapeutic space with the introduction of PROTACs into clinical trials for cancer patients.

[Bispecific antibodies, novel therapeutic candidates harnessing the immune system]. / Les anticorps et scaffold bispécifiques, des médicaments innovants en oncologie impliquant le ciblage des cellules immunitaires.

Over the past ten years, an increased knowledge of tumor biology and immunology allowed the design and development of novel therapeutic antibody and protein scaffold formats, where bispecific antibodies (Abs) play a major role. The latter molecules can (1) bring novel pharmacological properties through the co-engagement of two targets, (2) increase the safety profile as compared to a combination of two antibodies thanks to a targeted relocation to the tumor and (3) reduce development and manufacturing costs associated with single drug product. This review analyzes the different bispecific antibodies and scaffolds described in the field of immuno-oncology, their structure and major pharmacological and physico-chemical properties.

TITLE: Les anticorps et scaffold bispécifiques, des médicaments innovants en oncologie impliquant le ciblage des cellules immunitaires. ABSTRACT: Une connaissance approfondie de la biologie et de l'immunologie des tumeurs, mais aussi la conception de formats innovants d'anticorps et d'autres charpentes (ou scaffolds) protéiques ont permis de générer une véritable explosion de nouvelles molécules à visée thérapeutique au cours de ces 10 dernières années. Dans ce cadre, les anticorps bispécifiques (Abs) tiennent une place de choix. Ils permettent en effet, (1) d'apporter des propriétés biologiques et pharmacologiques nouvelles qui dépendent de l'engagement simultané des deux cibles, (2) d'améliorer le profil de sécurité par rapport à une combinaison d'anticorps en favorisant sa localisation tumorale en oncologie, et également (3) de combiner en une seule molécule les activités de deux anticorps conventionnels, réduisant ainsi les coûts de développement clinique et de fabrication. Cet article de revue a pour objectif d'analyser les différentes molécules bispécifiques décrites à ce jour dans le domaine de l'immuno-oncologie, et de présenter leurs différents formats et principales propriétés.

[The hinge region of therapeutic antibodies: major importance of a short sequence]. / La région charnière des anticorps thérapeutiques - L'importance capitale d'une courte séquence.

The hinge region is a short sequence of the heavy chains (H) of antibodies linking the Fab (Fragment antigen binding) region to the Fc (Fragment crystallisable) region. The functional properties of the four IgG subclasses partly result from the sequence differences of their hinge regions as some amino acids of the lower hinge region are located within or in the close vicinity of the C1q and FcγR binding sites on the IgG H chains. In addition, the hinge is susceptible to proteolytic cleavage by many proteases present in tumor and/or inflammatory microenvironment capable of affecting functional responses. Thus, an optimal format of the hinge region remains a major challenge for the development of new therapeutic antibodies.

TITLE: La région charnière des anticorps thérapeutiques - L'importance capitale d'une courte séquence. ABSTRACT: La région charnière est une courte séquence des chaînes lourdes (H) d'anticorps liant le Fab (fragment antigen binding) au Fc (fragment crystallisable). Les propriétés fonctionnelles des quatre sous-classes d'immunoglobulines d'isotype G (IgG) résultent en partie des différences de séquence de leurs régions charnières. En effet, certains acides aminés de la partie C-terminale de ces régions charnières (« partie basse ¼) sont situés au sein ou à proximité des sites de liaison de la molécule C1q de la voie classique du complément et des récepteurs pour la région Fc des IgG (RFcγ) sur les chaînes H d'IgG. Les régions charnières sont également sensibles au clivage protéolytique par de nombreuses protéases du microenvironnement tumoral et/ou inflammatoire pouvant altérer les réponses fonctionnelles. Le format optimal de la charnière reste donc un défi majeur pour le développement de nouveaux anticorps thérapeutiques.

Current progress in innovative engineered antibodies.

As of May 1, 2017, 74 antibody-based molecules have been approved by a regulatory authority in a major market. Additionally, there are 70 and 575 antibody-based molecules in phase III and phase I/II clinical trials, respectively. These total 719 antibody-based clinical stage molecules include 493 naked IgGs, 87 antibody-drug conjugates, 61 bispecific antibodies, 37 total Fc fusion proteins, 17 radioimmunoglobulins, 13 antibody fragments, and 11 immunocytokines. New uses for these antibodies are being discovered each year. For oncology, many of the exciting new approaches involve antibody modulation of T-cells. There are over 80 antibodies in clinical trials targeting T cell checkpoints, 26 T-cell-redirected bispecific antibodies, and 145 chimeric antigen receptor (CAR) cell-based candidates (all currently in phase I or II clinical trials), totaling more than 250 T cell interacting clinical stage antibody-based candidates. Finally, significant progress has been made recently on routes of delivery, including delivery of proteins across the blood-brain barrier, oral delivery to the gut, delivery to the cellular cytosol, and gene- and viral-based delivery of antibodies. Thus, there are currently at least 864 antibody-based clinical stage molecules or cells, with incredible diversity in how they are constructed and what activities they impart. These are followed by a next wave of novel molecules, approaches, and new methods and routes of delivery, demonstrating that the field of antibody-based biologics is very innovative and diverse in its approaches to fulfill their promise to treat unmet medical needs.

A new insight in chimeric antigen receptor-engineered T cells for cancer immunotherapy.

Adoptive cell therapy using chimeric antigen receptor (CAR)-engineered T cells has emerged as a very promising approach to combating cancer. Despite its ability to eliminate tumors shown in some clinical trials, CAR-T cell therapy involves some significant safety challenges, such as cytokine release syndrome (CRS) and "on-target, off-tumor" toxicity, which is related to poor control of the dose, location, and timing of T cell activity. In the past few years, some strategies to avoid the side effects of CAR-T cell therapy have been reported, including suicide gene, inhibitory CAR, dual-antigen receptor, and the use of exogenous molecules as switches to control the CAR-T cell functions. Because of the advances of the CAR paradigm and other forms of cancer immunotherapy, the most effective means of defeating the cancer has become the integration therapy with the combinatorial control system of switchable dual-receptor CAR-T cell and immune checkpoint blockade.

Engineered bifunctional proteins and stem cells: next generation of targeted cancer therapeutics.

Redundant survival signaling pathways and their crosstalk within tumor and/or between tumor and their microenvironment are key impediments to developing effective targeted therapies for cancer. Therefore developing therapeutics that target multiple receptor signaling pathways in tumors and utilizing efficient platforms to deliver such therapeutics are critical to the success of future targeted therapies. During the past two decades, a number of bifunctional multi-targeting antibodies, fusion proteins, and oncolytic viruses have been developed and various stem cell types have been engineered to efficiently deliver them to tumors. In this review, we discuss the design and efficacy of therapeutics targeting multiple pathways in tumors and the therapeutic potential of therapeutic stem cells engineered with bifunctional agents.

Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins.

Methods to prepare proteins that include a specific modification at a desired position are essential for understanding their cellular functions and physical properties in living systems. Chemical protein synthesis, which relies on the chemoselective ligation of unprotected peptides, enables the preparation of modified proteins that are not easily fabricated by other methods. In contrast to recombinant approaches, chemical synthesis can be used to prepare protein analogues such as D-proteins, which are useful in protein structure determination and the discovery of novel therapeutics. Post-translationally modifying proteins is another example where chemical protein synthesis proved itself as a powerful approach for preparing samples with high homogeneity and in workable quantities. In this Review, we discuss the basic principles of the field, focusing on novel chemoselective peptide ligation approaches such as native chemical ligation and the recent advances based on this method with a proven record of success in the synthesis of highly important protein targets.

Elastin-like polypeptides and their applications in anticancer drug delivery systems: a review.

Elastin-like polypeptides (ELPs) are large molecular weight biopolymers. They have been widely studied as macromolecular carriers for targeted delivery of drugs. The aim of the present article is to review the available information on ELPs (including our recent investigations), their properties, drug delivery applications to tumor sites and future perspectives. This review also provides information on the use of short synthetic ELPs for making ELP-drug conjugates, for targeted delivery of anticancer drugs. In the present review we also focus on the point that short ELPs can also be used for targeting anticancer drugs to tumor sites as they behave similar to long ELPs regarding their capacity to undergo inverse temperature transition (ITT) behavior.

Engineering α-fetoprotein-based gene vaccines to prevent and treat hepatocellular carcinoma: review and future prospects.

Activation of a patient's immune system offers an attractive approach to prevent and treat hepatocellular carcinoma (HCC). However, the antitumor efficacy of current HCC vaccines was weak owing to insufficient immune activation of targeting self/tumor antigens. We recently found that epitope-optimized α-fetoprotein effectively activated CD8 T cells and generated potent antitumor effects in the carcinogen-induced autochthonous HCC mouse model. We predict that the same antigen engineering approach of epitope-optimization will enable us to develop effective human vaccines to prevent HCC recurrence after liver resection. The engineered human HCC vaccines may also allow us to identify high-affinity T-cell receptors and antibodies that can be used to reprogram T cells to treat HCC tumors via adoptive transfer.

Novel protein scaffolds as emerging therapeutic proteins: from discovery to clinical proof-of-concept.

Recent advances in combinatorial protein engineering have made it possible to develop immunoglobulin (Ig)-based and non-Ig protein scaffolds that can potentially substitute for most whole antibody-associated properties and currently translate into biologicals with drug-like properties. During the past 10 years, the most validated scaffolds have reached the clinical development phase and, recently, one of them [Kalbitor(®) (Dyax)] has made it to the market, making these alternative scaffold proteins viable drug candidates in a post-antibody landscape. Interestingly, several scaffolds include an immune-active component as part of their therapeutic mode of action, which yielded spectacular clinical efficacy in some hematological malignancies. Here, we review the most recent clinical advances and analyze their benefits for patients.

Fourth World Antibody-Drug Conjugate Summit: February 29-March 1, 2012, Frankfurt, Germany.

The 4th World Antibody Drug Conjugate (WADC) Summit, organized by Hanson Wade was held on February 29­March 1, 2012 in Frankfurt, Germany, which was also the location for the Antibody Drug Conjugate Summit Europe held in February 2011. During the one year between these meetings, antibody drug conjugates (ADCs) have confirmed their technological maturity and their clinical efficacy in oncology. Brentuximab vedotin (ADCETRIS (TM) ) gained approval by the US Food and Drug Administration in August 2011 and trastuzumab emtansine (T-DM1) confirmed impressive clinical efficacy responses in a large cohort of breast cancer patients. During the 4th WADC meeting, antibody-maytansinoid conjugates were showcased by representatives of ImmunoGen (T-DM1, SAR3419, lorvotuzumab mertansine/IMGN801, IMGN529 and IMG853) and Biotest (BT-062). Data on antibody-auristatin conjugates were presented by scientists and clinicians from Seattle Genetics and Takeda (brentuximab vedotin), Pfizer (5T4-MMAF), Agensys/Astella (AGS-16M8F), Progenics (PSMA-ADC) and Genmab (anti-TF ADCs). Alternative payloads such as calicheamicins and duocarmycin used for preparation of ADCs were discussed by Pfizer and Synthon representatives, respectively. In addition, emerging technologies, including site-directed conjugation (Ambrx), a protein toxin as payload (Viventia), hapten-binding bispecific antibodies (Roche), and use of light activated drugs (Photobiotics), were also presented. Last but not least, progresses in solving Chemistry Manufacturing and Control, and pharmacokinetic issues were addressed by scientists from Genentech, Pfizer, Novartis and Pierre Fabre.

7th cancer scientific forum of theCancéropôle Lyon Auvergne Rhône-Alpes: March 20-21, 2012, Lyon, France.

The Innovative Approaches in Anti-Cancer Monoclonal Antibodies meeting, held on March 20, 2012 in Lyon, was organized by Cancéropôle Lyon Auvergne-Rhône-Alps in partnership with the French competitiveness cluster Lyonbiopôle. CLARA is one of the seven cancer research clusters within France in charge of facilitating Translational Oncology Research by taking into account the objectives of the French National Cancer Plans I and II and, in coordination with the French National Cancer Institute and local authorities (mainly Grand Lyon, Rhône County and Rhône-Alpes Region), to perform economic development of research findings. The contribution of lectures by outstanding speakers as described in this report, the organization of two-round tables: "Antibody treatment in cancer: Unmet needs in solid tumors and hematological malignancies," and "From chimeric to more than human antibodies," together with face-to-face meetings, was shared by over 230 participants. The lectures provided an overview of the commercial pipeline of monoclonal antibody (mAb) therapeutics for cancer; discussion of the distinction between biosimilar, biobetter and next generation therapeutic antibodies for cancer; updates on obinutuzumab and the use of mAbs in lymphoma; and discussion of antibody-drug conjugates.

Molecular engineering of antibodies for therapeutic and diagnostic purposes.

During the past ten years, monoclonal antibodies (mAbs) have taken center stage in the field of targeted therapy and diagnosis. This increased interest in mAbs is due to their binding accuracy (affinity and specificity) together with the original molecular and structural rules that govern interactions with their cognate antigen. In addition, the effector properties of antibodies constitute a second major advantage associated with their clinical use. The development of molecular and structural engineering and more recently of in vitro evolution of antibodies has opened up new perspectives in the de novo design of antibodies more adapted to clinical and diagnostic use. Thus, efforts are regularly made by researchers to improve or modulate antibody recognition properties, to adapt their pharmacokinetics, engineer their stability, and control their immunogenicity. This review presents the latest molecular engineering results on mAbs with therapeutic and diagnostic applications.

DARPins and other repeat protein scaffolds: advances in engineering and applications.

Antibodies have long been regarded as the only class of binding proteins. With the emergence of protein engineering techniques, new binding proteins based on alternative scaffolds have been designed. Additionally, modern technologies for selection and evolution from libraries are independent of the antibody scaffold and could thus be readily used for obtaining specific binding proteins. One important group of alternative scaffolds is based on repeat proteins. Nature is widely using these proteins to modulate protein-protein interactions, and even in the adaptive immune system of jawless vertebrates; the step to their application as an alternative to antibodies seems therefore logical. In this review, progress on DARPins and other repeat protein scaffolds will be discussed. Advances in their design as well as novel applications will be highlighted.