Engineered Protein Scaffolds as Next-Generation Therapeutics

2020 ◽  
Vol 60 (1) ◽  
pp. 391-415 ◽  
Author(s):  
Michaela Gebauer ◽  
Arne Skerra
Keyword(s):  
Recombinant Antibody ◽  
Clinical Stage ◽  
Protein A ◽  
Protein Scaffolds ◽  
Next Generation ◽  
Current State ◽  
Repeat Proteins ◽  
Human Fibronectin ◽  
Active Research ◽  
Ankyrin Repeat Proteins

The concept of engineering robust protein scaffolds for novel binding functions emerged 20 years ago, one decade after the advent of recombinant antibody technology. Early examples were the Affibody, Monobody (Adnectin), and Anticalin proteins, which were derived from fragments of streptococcal protein A, from the tenth type III domain of human fibronectin, and from natural lipocalin proteins, respectively. Since then, this concept has expanded considerably, including many other protein templates. In fact, engineered protein scaffolds with useful binding specificities, mostly directed against targets of biomedical relevance, constitute an area of active research today, which has yielded versatile reagents as laboratory tools. However, despite strong interest from basic science, only a handful of those protein scaffolds have undergone biopharmaceutical development up to the clinical stage. This includes the abovementioned pioneering examples as well as designed ankyrin repeat proteins (DARPins). Here we review the current state and clinical validation of these next-generation therapeutics.

Designed Ankyrin Repeat Proteins as Novel Binders for Ultrasound Molecular Imaging

2021 ◽  
Author(s):  
Alexandra Kosareva ◽  
Mukesh Punjabi ◽  
Amanda Ochoa-Espinosa ◽  
Lifen Xu ◽  
Jonas V. Schaefer ◽  
...  
Keyword(s):  
Molecular Imaging ◽  
Ankyrin Repeat ◽  
Repeat Proteins ◽  
Ultrasound Molecular Imaging ◽  
Ankyrin Repeat Proteins

scholarly journals Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs

2021 ◽  
Author(s):  
Johannes Schilling ◽  
Christian Jost ◽  
Ioana Mariuca Ilie ◽  
Joachim Schnabl ◽  
Oralea Buechi ◽  
...  
Keyword(s):  
Melting Temperature ◽  
Building Blocks ◽  
Ankyrin Repeat ◽  
Internal Repeat ◽  
Repeat Proteins ◽  
Repeat Domain ◽  
Ankyrin Repeat Proteins ◽  
Classical Immunoglobulin ◽  
Dynamics Simulations ◽  
Innovative Drugs

AbstractDesigned Ankyrin Repeat Proteins (DARPins) are a class of antibody mimetics with a high and mostly unexplored potential in drug development. They are clinically validated and thus represent a true alternative to classical immunoglobulin formats. In contrast to immunoglobulins, they are built from solenoid protein domains comprising an N-terminal capping repeat, one or more internal repeats and a C-terminal capping repeat. By using in silico analysis and a rationally guided Ala-Scan, we identified position 17 of the N-terminal capping repeat to play a key role for the overall protein thermostability. The melting temperature of a DARPin domain with a single full-consensus internal repeat was increased by about 8°C to 10°C when the original Asp17 was replaced by Leu, Val, Ile, Met, Ala or Thr, as shown by high-temperature unfolding experiments at equilibrium. We then transferred the Asp17Leu mutation to various backgrounds, including different N- and C-terminal capping repeats and clinically validated DARPin domains, such as the VEGF-binding ankyrin repeat domain of abicipar pegol. In all cases, the proteins remained monomeric and showed improvements in the thermostability of about 8°C to 16°C. Thus, the replacement of Asp17 seems to be generically applicable to this drug class. Molecular dynamics simulations show that the Asp17Leu mutation reduces electrostatic repulsion and improves van-der-Waals packing, rendering the DARPin domain less flexible and more stable. Interestingly, such a beneficial Asp17Leu mutation is present in the N-terminal caps of three of the five DARPin domains of ensovibep, a SARS-CoV-2 entry inhibitor currently in clinical development. This mutation is likely responsible, at least in part, for the very high melting temperature (>90°C) of this promising anti-Covid-19 drug. Overall, such N-terminal capping repeats with increased thermostability seem to be beneficial for the development of innovative drugs based on DARPins.

scholarly journals A Robust Context-Based Deep Learning Approach for Highly Imbalanced Hyperspectral Classification

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Juan F. Ramirez Rochac ◽  
Nian Zhang ◽  
Lara A. Thompson ◽  
Tolessa Deksissa
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Mineral Exploration ◽  
Classification Models ◽  
Noise Resistance ◽  
Deep Convolutional Neural Networks ◽  
Current State ◽  
Feature Augmentation ◽  
Active Research ◽  
Hyperspectral Classification

Hyperspectral imaging is an area of active research with many applications in remote sensing, mineral exploration, and environmental monitoring. Deep learning and, in particular, convolution-based approaches are the current state-of-the-art classification models. However, in the presence of noisy hyperspectral datasets, these deep convolutional neural networks underperform. In this paper, we proposed a feature augmentation approach to increase noise resistance in imbalanced hyperspectral classification. Our method calculates context-based features, and it uses a deep convolutional neuronet (DCN). We tested our proposed approach on the Pavia datasets and compared three models, DCN, PCA + DCN, and our context-based DCN, using the original datasets and the datasets plus noise. Our experimental results show that DCN and PCA + DCN perform well on the original datasets but not on the noisy datasets. Our robust context-based DCN was able to outperform others in the presence of noise and was able to maintain a comparable classification accuracy on clean hyperspectral images.

scholarly journals Rigid fusions of designed helical repeat binding proteins efficiently protect a binding surface from crystal contacts

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Patrick Ernst ◽  
Annemarie Honegger ◽  
Floor van der Valk ◽  
Christina Ewald ◽  
Peer R. E. Mittl ◽  
...  
Keyword(s):  
Protein Design ◽  
Binding Proteins ◽  
Peptide Binding ◽  
Binding Mode ◽  
Equilibrium Structure ◽  
Repeat Proteins ◽  
Binding Surface ◽  
Crystal Contacts ◽  
Armadillo Repeat ◽  
Ankyrin Repeat Proteins

Abstract Designed armadillo repeat proteins (dArmRPs) bind extended peptides in a modular way. The consensus version recognises alternating arginines and lysines, with one dipeptide per repeat. For generating new binding specificities, the rapid and robust analysis by crystallography is key. Yet, we have previously found that crystal contacts can strongly influence this analysis, by displacing the peptide and potentially distorting the overall geometry of the scaffold. Therefore, we now used protein design to minimise these effects and expand the previously described concept of shared helices to rigidly connect dArmRPs and designed ankyrin repeat proteins (DARPins), which serve as a crystallisation chaperone. To shield the peptide-binding surface from crystal contacts, we rigidly fused two DARPins to the N- and C-terminal repeat of the dArmRP and linked the two DARPins by a disulfide bond. In this ring-like structure, peptide binding, on the inside of the ring, is very regular and undistorted, highlighting the truly modular binding mode. Thus, protein design was utilised to construct a well crystallising scaffold that prevents interference from crystal contacts with peptide binding and maintains the equilibrium structure of the dArmRP. Rigid DARPin-dArmRPs fusions will also be useful when chimeric binding proteins with predefined geometries are required.

Arpp/Ankrd2, a member of the muscle ankyrin repeat proteins (MARPs), translocates from the I-band to the nucleus after muscle injury

2007 ◽  
Vol 129 (1) ◽  
pp. 55-64 ◽  
Author(s):  
Yoshiyuki Tsukamoto ◽  
Naoki Hijiya ◽  
Shinji Yano ◽  
Shigeo Yokoyama ◽  
Chisato Nakada ◽  
...  
Keyword(s):  
Muscle Injury ◽  
Ankyrin Repeat ◽  
Repeat Proteins ◽  
Ankyrin Repeat Proteins

scholarly journals Antimicrobial resistance in enteric bacteria: current state and next-generation solutions

Gut Microbes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 1799654 ◽  
Author(s):  
M. J. Wallace ◽  
S. R. S. Fishbein ◽  
G. Dantas
Keyword(s):  
Antimicrobial Resistance ◽  
Enteric Bacteria ◽  
Next Generation ◽  
Current State

scholarly journals The evolution of the cancer stem cell state in glioblastoma: emerging insights into the next generation of functional interactions

2020 ◽  
Author(s):  
Kelly Mitchell ◽  
Katie Troike ◽  
Daniel J Silver ◽  
Justin D Lathia
Keyword(s):  
Cellular Heterogeneity ◽  
Next Generation ◽  
Cell State ◽  
Functional Interactions ◽  
Current State ◽  
Key Concepts ◽  
Discrete Population ◽  
A Cell ◽  
Stem Cell State ◽  
Primary Malignant Brain Tumor

Abstract Cellular heterogeneity is a hallmark of advanced cancers and has been ascribed in part to a population of self-renewing, therapeutically resistant cancer stem cells (CSCs). Glioblastoma (GBM), the most common primary malignant brain tumor, has served as a platform for the study of CSCs. In addition to illustrating the complexities of CSC biology, these investigations have led to a deeper understanding of GBM pathogenesis, revealed novel therapeutic targets, and driven innovation towards the development of next-generation therapies. While there continues to be an expansion in our knowledge of how CSCs contribute to GBM progression, opportunities have emerged to revisit this conceptual framework. In this review, we will summarize the current state of CSCs in GBM using key concepts of evolution as a paradigm (variation, inheritance, selection, and time) to describe how the CSC state is subject to alterations of cell intrinsic and extrinsic interactions that shape their evolutionarily trajectory. We identify emerging areas for future consideration, including appreciating CSCs as a cell state that is subject to plasticity, as opposed to a discrete population. These future considerations will not only have an impact on our understanding of this ever-expanding field but will also provide an opportunity to inform future therapies to effectively treat this complex and devastating disease.

Lenvatinib plus checkpoint inhibitors in patients (pts) with advanced intrahepatic cholangiocarcinoma (ICC): Preliminary data and correlation with next-generation sequencing.

2018 ◽  
Vol 36 (4_suppl) ◽  
pp. 500-500 ◽  
Author(s):  
Jianzhen Lin ◽  
Weiwei Shi ◽  
Songhui Zhao ◽  
Jinwei Hu ◽  
Zheng Hou ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Checkpoint Inhibitors ◽  
Clinical Stage ◽  
Objective Response ◽  
Stage Iv ◽  
Progression Free Survival ◽  
Cancer Genes ◽  
Next Generation ◽  
Multikinase Inhibitor ◽  
Generation Sequencing

500 Background: Lenvatinib (Len) is a multikinase inhibitor targeting VEGFR 1-3, FGFR 1-4 and other kinases. Pembrolizumab (Pem) and nivolumab (Nivo) are antibodies inhibiting programmed cell death 1 (PD-1) and reactivate T-cell cytotoxic effect. Len plus PD-1 inhibitors have shown promising results in treating various solid tumors. The role of this combination in ICC is undefined. Methods: 14 ICC pts (median age 49 years, range 34-68; 7 males and 7 females) with treatment of enrolled in a single center, observational study of Len plus Pem/Nivo. Objective response rate (ORR), disease control rate (DCR) and progression-free survival (PFS) were measured according to RECIST 1.1. Next generation sequencing (NGS) with deep coverage on 450 cancer genes and whole exome sequencing were performed in 7 pts to detect all classes of genomic alterations, tumor mutational burden (TMB) and microsatellite instability (MSI) status. Results: All 14 pts had > = 2 prior anticancer therapy with clinical stage IV. ORR was 21.4% with 3 pts achieved partial response (PR), DCR was 92.9% and clinical benefit rate (ORR + durable stable disease > = 5 months) was 64.3%. Median PFS was 5.9 months (95% CI: 4.2-6.2). The most common adverse events (AEs) included hypertension, aminotransferase elevation and fatigue. The grade-3 AEs were occurred at 14% while no grade-4 AE was observed. The most altered genes in the 7 sequenced tumors were IDH1 (3 pts), ARID1A (3 pts), PIK3CA (3 pts), TP53 (2 pts) and BAP1 (2 pts). 4 out of the 7 pts had high TMB ( > 12 mut/Mb) and all responded to Len plus Pem/Nivo with 2 PR. One pt with low TMB and FGFR2 mutation had a response of 27% decreased target lesion. Two low TMB pts were progressed, including one with FGFR2 rearrangement. A responder harbored a 399 bp deletion on MLH1, and was identified as MSI-H. More data will be presented. Conclusions: Our study preliminarily indicates that combining Len with PD-1 inhibitors results in promising efficacy in advanced ICC. High TMB from 450-gene NGS panel was strongly associated with a better therapeutic response.

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