OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding

Pantazes, Robert J.; Maranas, Costas D.

doi:10.1093/protein/gzq061

Cited by 80 publications

(73 citation statements)

References 42 publications

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“…Such computational methods allow for the consideration of large numbers of amino acid-amino acid interactions simultaneously. Computational design has been used to design inhibitors against H1N1 influenza hemagglutinin [56], to switch cofactor specificity of an enzyme [57], for generalized antibody design for recognition of a target epitope [58], for the design of entry inhibitors of HIV-1 gp41 [59], for the design of C3a receptor agonists for medicinal use [54], and for the design of inhibitors of the histone methyltransferase EZH2 [55]. See Fung et al [51], Pantazes et al [60], Samish et al [61], and Khoury et al [62] for reviews of the recent advances and successes in the area.…”

Section: Introductionmentioning

confidence: 99%

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

Smadbeck

Chan²,

Khoury³

et al. 2014

PLoS Comput Biol

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Self-association is a common phenomenon in biology and one that can have positive and negative impacts, from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases. Understanding the nature and mechanisms of self-association is important for modulating these systems and in creating biologically-inspired materials. Here, we present a two-stage de novo peptide design framework that can generate novel self-associating peptide systems. The first stage uses a simulated multimeric template structure as input into the optimization-based Sequence Selection to generate low potential energy sequences. The second stage is a computational validation procedure that calculates Fold Specificity and/or Approximate Association Affinity (K*association) based on metrics that we have devised for multimeric systems. This framework was applied to the design of self-associating tripeptides using the known self-associating tripeptide, Ac-IVD, as a structural template. Six computationally predicted tripeptides (Ac-LVE, Ac-YYD, Ac-LLE, Ac-YLD, Ac-MYD, Ac-VIE) were chosen for experimental validation in order to illustrate the self-association outcomes predicted by the three metrics. Self-association and electron microscopy studies revealed that Ac-LLE formed bead-like microstructures, Ac-LVE and Ac-YYD formed fibrillar aggregates, Ac-VIE and Ac-MYD formed hydrogels, and Ac-YLD crystallized under ambient conditions. An X-ray crystallographic study was carried out on a single crystal of Ac-YLD, which revealed that each molecule adopts a β-strand conformation that stack together to form parallel β-sheets. As an additional validation of the approach, the hydrogel-forming sequences of Ac-MYD and Ac-VIE were shuffled. The shuffled sequences were computationally predicted to have lower K*association values and were experimentally verified to not form hydrogels. This illustrates the robustness of the framework in predicting self-associating tripeptides. We expect that this enhanced multimeric de novo peptide design framework will find future application in creating novel self-associating peptides based on unnatural amino acids, and inhibitor peptides of detrimental self-aggregating biological proteins.

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Section: Introductionmentioning

confidence: 99%

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

Smadbeck

Chan²,

Khoury³

et al. 2014

PLoS Comput Biol

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“…This procedure is based on the identification of a peptide complementary to a target region and on its grafting on to the CDR of an antibody scaffold. Related methods of altering rationally antibodies have been discussed in the literature, which include the exploration of specificity-enhancing mutations (27,28), the design of CDRs to bind structured epitopes (28,29), and the grafting of peptides extracted from aggregation prone proteins (30-32) or from other antibodies (33) in the CDR of an antibody scaffold. Here we show that designed antibodies can be obtained by the method that we present for essentially any disordered epitope.…”

mentioning

confidence: 99%

Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins

Sormanni

Aprile

Vendruscolo

2015

Proc. Natl. Acad. Sci. U.S.A.

116

164

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Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions.protein design | protein aggregation | complementary peptides A ntibodies are versatile molecules that are increasingly used in therapeutic and diagnostic applications, as they can be used to treat a wide range of diseases, including cancer and autoimmune disorders (1-5). These molecules can be obtained with well-established methods, such as immunization or phage and associated display methods, against a wide variety of targets (6-11). In some cases, however, these procedures may require significant amounts of time and resources, in particular if one is interested in targeting weakly immunogenic epitopes in protein molecules. In this work, we introduce a computational method of rational design of complementarity determining regions (CDRs) that makes it possible to obtain antibody against virtually any target epitope within intrinsically disordered peptides and proteins or within disordered regions in structured proteins.Intrinsically disordered proteins, in particular, play major roles in a wide range of biochemical processes in living organisms. A range of recent studies has revealed that the functional diversity provided by disordered regions complements that of ordered regions of proteins, in particular in terms of key cellular functions such as signaling and regulation (12-18). The high flexibility and lack of stable secondary and tertiary structures allow intrinsically disordered proteins to have multiple interactions with multiple partners, often placing them at the hubs of proteinprotein interaction networks (19-21). It has also been realized that the failure of the regulatory processes responsible for the corre...

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“…This differs from previous attempts where iterations of insertion and crosslinking conditions had to be considered in order to identify functional crosslinks. Further studies will be needed to test the utility of these approaches with antibody homology models (e.g., (Marcatili et al, 2008; Pantazes and Maranas, 2010; Sivasubramanian et al, 2009)) or docked structures (e.g., (Sircar and Gray, 2010)).…”

Section: Discussionmentioning

confidence: 99%

“…With the development of computational techniques and a number of successful experiences in protein modeling and design (Lippow and Tidor, 2007; Mandell and Kortemme, 2009), computational antibody design has begun to play an important role in predicting improvements to antibody function. Computational design of antibodies has been used to enhance binding affinity (Barderas et al, 2008; Clark et al, 2006; Lippow et al, 2007), to improve stability by improvement of thermal/aggregation resistance (Chennamsetty et al, 2009; Miklos et al, 2012), and to alter binding specificity (Farady et al, 2009), and others (Caravella et al, 2010; Kuroda et al, 2012; Midelfort et al, 2004; Pantazes and Maranas, 2010). …”

Section: Introductionmentioning

confidence: 99%

Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex

Tack

Hughes

et al. 2014

Journal of Structural Biology

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Engineering antibodies to utilize non-canonical amino acids (NCAA) should greatly expand the utility of an already important biological reagent. In particular, introducing crosslinking reagents into antibody complementarity determining regions (CDRs) should provide a means to covalently crosslink residues at the antibody–antigen interface. Unfortunately, finding the optimum position for crosslinking two proteins is often a matter of iterative guessing, even when the interface is known in atomic detail. Computer-aided antibody design can potentially greatly restrict the number of variants that must be explored in order to identify successful crosslinking sites. We have therefore used Rosetta to guide the introduction of an oxidizable crosslinking NCAA, l-3,4-dihydroxyphenylalanine (l-DOPA), into the CDRs of the anti-protective antigen scFv antibody M18, and have measured crosslinking to its cognate antigen, domain 4 of the anthrax protective antigen. Computed crosslinking distance, solvent accessibility, and interface energetics were three factors considered that could impact the efficiency of l-DOPA-mediated crosslinking. In the end, 10 variants were synthesized, and crosslinking efficiencies were generally 10% or higher, with the best variant crosslinking to 52% of the available antigen. The results suggest that computational analysis can be used in a pipeline for engineering crosslinking antibodies. The rules learned from l-DOPA crosslinking of antibodies may also be generalizable to the formation of other crosslinked interfaces and complexes.

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OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding

Cited by 80 publications

References 42 publications

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides

Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins

Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex

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