Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

Berger, Stephanie; Procko, Erik; Margineantu, Daciana; Lee, Erinna F.; Shen, Betty; Zelter, Alex; Silva, Daniel‐Adriano; Chawla, Kusum; Herold, Marco J.; Garnier, Jean Marc; Johnson, Richard S.; MacCoss, Michael J.; Lessène, Guillaume; Davis, Trisha N.; Stayton, Patrick S.; Stoddard, Barry; Fairlie, W. Douglas; Hockenbery, David M.; Baker, David

doi:10.7554/elife.20352

Cited by 76 publications

(94 citation statements)

References 58 publications

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“…To match the mini-protein scaffolds with the desired target helix-binding motifs, we used the Rosetta MotifGraft Mover 7,24 . The inputs were composed of: (1) HB36, HB80 or Syt-II helical binding motifs (Protein Databank (PDB) IDs: 3R2X, 4EEF and 2NM1, respectively); (2) the context target protein (influenza HA or BoNT H C B); and (3) the above described library of de novo mini-protein scaffolds.…”

Section: Methodsmentioning

confidence: 99%

“…Computational protein design has the potential to overcome these limitations by efficiently sampling both shape and sequence space on a much larger scale, and by generating readily producible proteins, as recently demonstrated by the design of stapled mini-protein scaffolds with a wide range of shapes 5 . Despite this potential, the high cost of synthesizing genes for each designed protein has, until recently 6 , limited testing to small numbers (tens) of designs for any one application, which is too few to systematically explore the determinants of protein binding and folding and provide feedback to improve the computational model 7,8 .…”

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confidence: 99%

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Massively parallel de novo protein design for targeted therapeutics

Chevalier

Silva

Rocklin

et al. 2017

Nature

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399

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De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37–43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Massively parallel de novo protein design for targeted therapeutics

Chevalier

Silva

Rocklin

et al. 2017

Nature

Self Cite

399

383

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show abstract

“…Berger et al used a 3-helix bundle protein, BINDI that utilizes a BH3-like central helix with two flanking helices for additional contacts [46]. Computational mutagenesis and docking was used to develop a series of mutants capable of selectively inhibiting each of the six anti-apoptotic BCL-2 proteins.…”

Section: Non-canonical Targeting Of Anti-apoptotic Bcl-2 Proteinsmentioning

confidence: 99%

Progress in targeting the BCL-2 family of proteins

Garner

López

Reyna

et al. 2017

Current Opinion in Chemical Biology

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The network of protein-protein interactions among the BCL-2 protein family plays a critical role in regulating cellular commitment to mitochondrial apoptosis. Anti-apoptotic BCL-2 proteins are considered promising targets for drug discovery and exciting clinical progress has stimulated intense investigations in the broader family. Here, we discuss recent developments in small molecules targeting anti-apoptotic proteins and alternative approaches to targeting BCL-2 family interactions. These studies advance our understanding of the role of BCL-2 family proteins in physiology and disease, providing unique tools for dissecting these functions. The BCL-2 family of proteins is a prime example of targeting protein-protein interactions and further chemical biology approaches will increase opportunities for novel targeted therapies in cancer, autoimmune and aging-associated diseases.

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“…62 In summary, we have identified non-natural protein ligands that exhibit selectivity for different BCL-2 family members. Although computational protein design has been applied to discovery of BCL-2 family selective binders, 63 to our knowledge non-antibody based binding proteins have not previously been shown to differentiate between these proteins notably BCL-xL and MCL-1; this is noteworthy given the role of MCL-1 in driving several cancers. 64,65 We note the attrition rate that is a consequence of applying a variety of activity criteria as we progressed along this pipeline.…”

Section: Discussion (Without Subheadings)mentioning

confidence: 99%

Selective Affimers Recognize BCL-2 Family Proteins Through Non-Canonical Structural Motifs

Miles¹,

Hóbor²,

Taylor³

et al. 2019

Preprint

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no more than 200 words)The BCL-2 family is a challenging set of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are desirable as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL, BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective and potent recognition of their target BCL-2 protein. For anti-apoptotic targets, competitive inhibition of their canonical protein-protein interactions is demonstrated. Cocrystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug bound like conformation. These results indicate Affimers can be used as alternative templates to inspire design of selective BCL-2 family modulators, and provide proof-ofconcept for the elaboration of selective non-antibody binding reagents for use in cell-biology applications. [198 words]

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Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

Cited by 76 publications

References 58 publications

Massively parallel de novo protein design for targeted therapeutics

Massively parallel de novo protein design for targeted therapeutics

Progress in targeting the BCL-2 family of proteins

Selective Affimers Recognize BCL-2 Family Proteins Through Non-Canonical Structural Motifs

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