Wednesday, January 18, 2012

stapled peptides| What is stapled peptides|Papers on stapled peptides|Research on stapled peptides | Publications on stapled peptides


1.
Methods Enzymol. 2012;503:3-33.

Stapled peptides for intracellular drug targets.

Source

Departments of Chemistry and Chemical Biology, Stem Cell and Regenerative Biology, and Molecular and Cellular Biology, Harvard University, and Program in Cancer Chemical Biology, Dana - Farber Cancer Institute, Boston, Massachusetts, USA.

Abstract

Proteins that engage in intracellular interactions with other proteins are widely considered among the most biologically appealing yet chemically intractable targets for drug discovery. The critical interaction surfaces of these proteins typically lack the deep hydrophobic involutions that enable potent, selective targeting by small organic molecules, and their localization within the cell puts them beyond the reach of protein therapeutics. Considerable interest has therefore arisen in next-generation targeting molecules that combine the broad target recognition capabilities of protein therapeutics with the robust cell-penetrating ability of small molecules. One type that has shown promise in early-stage studies is hydrocarbon-stapled α-helical peptides, a novel class of synthetic miniproteins locked into their bioactive α-helical fold through the site-specific introduction of a chemical brace, an all-hydrocarbon staple. Stapling can greatly improve the pharmacologic performance of peptides, increasing their target affinity, proteolytic resistance, and serum half-life while conferring on them high levels of cell penetration through endocytic vesicle trafficking. Here, we discuss considerations crucial to the successful design and evaluation of potent stapled peptide interactions, our intention being to facilitate the broad application of this technology to intractable targets of both basic biologic interest and potential therapeutic value.

Copyright © 2012 Elsevier Inc. All rights reserved.

PMID:
22230563
[PubMed - in process]
2.
J Med Chem. 2011 Dec 23. [Epub ahead of print]

Design of Triazole-stapled BCL9 α-Helical Peptides to Target the β-Catenin/B-cell CLL/lymphoma 9 (BCL9) Protein-Protein Interaction.

Abstract

The interaction between β-catenin and B-cell CLL/lymphoma 9 (BCL9), critical for the transcriptional activity of β-catenin, is mediated by a helical segment from BCL9 and a large binding groove in β-catenin. Design of potent, metabolically stable BCL9 peptides represents an attractive approach to inhibit the activity of β-catenin. In this study, we report the use of the Huisgen 1,3-dipolar cycloaddition reaction to generate triazole-stapled BCL9 α-helical peptides. The high efficiency and mild conditions of this "click" reaction combined with the ease of synthesis of the necessary unnatural amino acids allows for facile synthesis of triazole-stapled peptides. We have performed extensive optimization of this approach and identified the optimal combinations of azido and alkynyl linkers necessary for stapling BCL9 helices. The unsymmetrical nature of the triazole staple also allowed the synthesis of double-stapled BCL9 peptides, which show a marked increase in helical character and an improvement in binding affinity and metabolic stability relative to wild-type and linear BCL9 peptides. This study lays the foundation for further optimization of these triazole-stapled BCL9 peptidesas potent, metabolically stable and cell-permeable inhibitors to target the β-catenin and BCL9 interaction.

PMID:
22196480
[PubMed - as supplied by publisher]
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3.
Biopolymers. 2011 Dec 14. doi: 10.1002/bip.22015. [Epub ahead of print]

Novel structures of self-associating stapled peptides.

Source

New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027. sbhattacharya@nysbc.org.

Abstract

Hydrocarbon stapling of peptides is a powerful technique to transform linear peptides into cell-permeable helical structures that can bind to specific biological targets. In this study, we have used high resolution solution NMR techniques complemented by Dynamic Light Scattering to characterize extensively a family of hydrocarbon stapledpeptides with known inhibitory activity against HIV-1 capsid assembly to evaluate the various factors that modulate activity. The helical peptides share a common binding motif but differ in charge, the length and position of the staple. An important outcome of the study was to show the peptides share a propensity to self-associate into organized polymeric structures mediated predominantly by hydrophobic interactions between the olefinic chain and the aromatic side-chains from the peptide. We have also investigated in detail the structural significance of the length and position of the staple, and of olefinic bond isomerization in stabilizing the helical conformation of the peptides as potential factors driving polymerization. This study presents the numerous challenges of designing biologically active stapled peptides and the conclusions have broad implications for optimizing a promising new class of compounds in drug discovery. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011.

Copyright © 2011 Wiley Periodicals, Inc.

PMID:
22170623
[PubMed - as supplied by publisher]
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4.
J Am Chem Soc. 2012 Jan 11;134(1):103-6. Epub 2011 Dec 14.

Structure of the Stapled p53 Peptide Bound to Mdm2.

Source

Max Planck Institute for Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.

Abstract

Mdm2 is a major negative regulator of the tumor suppressor p53 protein, a protein that plays a crucial role in maintaining genome integrity. Inactivation of p53 is the most prevalent defect in human cancers. Inhibitors of the Mdm2-p53 interaction that restore the functional p53 constitute potential nongenotoxic anticancer agents with a novel mode of action. We present here a 2.0 Å resolution structure of the Mdm2 protein with a bound stapled p53 peptide. Suchpeptides, which are conformationally and proteolytically stabilized with all-hydrocarbon staples, are an emerging class of biologics that are capable of disrupting protein-protein interactions and thus have broad therapeutic potential. The structure represents the first crystal structure of an i, i + 7 stapled peptide bound to its target and reveals that rather than acting solely as a passive conformational brace, a staple can intimately interact with the surface of a protein and augment the binding interface.

PMID:
22148351
[PubMed - in process]
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5.
Bioorg Med Chem Lett. 2011 Dec 15;21(24):7412-5. Epub 2011 Oct 12.

Conjugation of spermine enhances cellular uptake of the stapled peptide-based inhibitors of p53-Mdm2 interaction.

Source

Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA.

Abstract

We report the first synthesis of the C-terminally spermine-conjugated stapled peptide-based inhibitors of the p53-Mdm2 interaction. Subsequent biological, biophysical and cellular uptake assays with the spermine-conjugated stapledpeptides revealed that spermine conjugation minimally affects biological activity while significantly increases peptide helicity and cellular uptake without apparent cytotoxicity.

Copyright © 2011 Elsevier Ltd. All rights reserved.

PMID:
22047690
[PubMed - in process]
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6.
Biochem Biophys Res Commun. 2011 Jul 8;410(3):446-51. Epub 2011 Jun 6.

Helix stabilization of amphipathic peptides by hydrocarbon stapling increases cholesterol efflux by the ABCA1 transporter.

Source

Lipoprotein Metabolism Section, Cardiopulmonary Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892-1508, USA.

Abstract

Apolipoprotein mimetic peptides are short amphipathic peptides that efflux cholesterol from cells by the ABCA1 transporter and are being investigated as therapeutic agents for cardiovascular disease. We examined the role of helix stabilization of these peptides in cholesterol efflux. A 23-amino acid long peptide (Ac-VLEDSFKVSFLSALEEYTKKLNTQ-NH2) based on the last helix of apoA-I (A10) was synthesized, as well as two variants, S1A10 and S2A10, in which the third and fourth and third and fifth turn of each peptide, respectively, were covalently joined by hydrocarbon staples. By CD spectroscopy, the stapled variants at 24 °C were more helical in aqueous buffer than A10 (A10 17%, S1A10 62%, S2A10 97%). S1A10 and S2A10 unlike A10 were resistant to proteolysis by pepsin and chymotrypsin. S1A10 and S2A10 showed more than a 10-fold increase in cholesterol efflux by the ABCA1 transporter compared to A10. In summary, hydrocarbon stapling of amphipathic peptides increases their helicity, makes them resistant to proteolysis and enhances their ability to promote cholesterol efflux by the ABCA1 transporter, indicating that this peptide modification may be useful in the development of apolipoprotein mimeticpeptides.

Published by Elsevier Inc.

PMID:
21672528
[PubMed - indexed for MEDLINE]
PMCID: PMC3253552
[Available on 2012/7/8]
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7.
Nat Protoc. 2011 Jun;6(6):761-71. doi: 10.1038/nprot.2011.324. Epub 2011 May 12.

Synthesis of all-hydrocarbon stapled α-helical peptides by ring-closing olefin metathesis.

Source

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

Abstract

This protocol provides a detailed procedure for the preparation of stapled α-helical peptides, which have proven their potential as useful molecular probes and as next-generation therapeutics. Two crucial features of this protocol are (i) the construction of peptide substrates containing hindered α-methyl, α-alkenyl amino acids and (ii) the ring-closing olefin metathesis (RCM) of the resulting resin-bound peptide substrates. The stapling systems described in this protocol, namely bridging one or two turns of an α-helix, are highly adaptable to most peptide sequences, resulting in favorable RCM kinetics, helix stabilization and promotion of cellular uptake.

PMID:
21637196
[PubMed - indexed for MEDLINE]
Click here to read
8.
J Am Chem Soc. 2011 Jun 29;133(25):9696-9. Epub 2011 Jun 6.

Design and structure of stapled peptides binding to estrogen receptors.

Source

Department of Chemistry, Pfizer, Sandwich CT13 9NJ, UK. Chris.Phillips@famco.co.uk

Abstract

Synthetic peptides that specifically bind nuclear hormone receptors offer an alternative approach to small molecules for the modulation of receptor signaling and subsequent gene expression. Here we describe the design of a series of novelstapled peptides that bind the coactivator peptide site of estrogen receptors. Using a number of biophysical techniques, including crystal structure analysis of receptor-stapled peptide complexes, we describe in detail the molecular interactions and demonstrate that all-hydrocarbon staples modulate molecular recognition events. The findings have implications for the design of stapled peptides in general.

PMID:
21612236
[PubMed - indexed for MEDLINE]
Click here to read
9.
Retrovirology. 2011 May 3;8:28.

Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain.

Source

Laboratory of Molecular Modeling & Drug Design; Lindsley F, Kimball Research Institute of the New York Blood Center, 310 E 67th Street, New York, NY 10065, USA.

Abstract

BACKGROUND:

The C-terminal domain (CTD) of HIV-1 capsid (CA), like full-length CA, forms dimers in solution and CTD dimerization is a major driving force in Gag assembly and maturation. Mutations of the residues at the CTD dimer interface impair virus assembly and render the virus non-infectious. Therefore, the CTD represents a potential target for designing anti-HIV-1 drugs.

RESULTS:

Due to the pivotal role of the dimer interface, we reasoned that peptides from the α-helical region of the dimer interface might be effective as decoys to prevent CTD dimer formation. However, these small peptides do not have any structure in solution and they do not penetrate cells. Therefore, we used the hydrocarbon stapling technique to stabilize the α-helical structure and confirmed by confocal microscopy that this modification also made these peptides cell-penetrating. We also confirmed by using isothermal titration calorimetry (ITC), sedimentation equilibrium and NMR that these peptides indeed disrupt dimer formation. In in vitro assembly assays, the peptides inhibited mature-like virus particle formation and specifically inhibited HIV-1 production in cell-based assays. These peptides also showed potent antiviral activity against a large panel of laboratory-adapted and primary isolates, including viral strains resistant to inhibitors of reverse transcriptase and protease.

CONCLUSIONS:

These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind CA-CTD.

PMID:
21539734
[PubMed - indexed for MEDLINE]
PMCID: PMC3097154
Free PMC Article
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10.
Bioorg Med Chem Lett. 2011 Mar 1;21(5):1472-5. Epub 2011 Jan 7.

Synthesis of cell-permeable stapled peptide dual inhibitors of the p53-Mdm2/Mdmx interactions via photoinduced cycloaddition.

Source

Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA.

Abstract

We report the first application of a photoinduced 1,3-dipolar cycloaddition reaction to 'staple' a peptide dual inhibitor of the p53-Mdm2/Mdmx interactions. A series of stapled peptide inhibitors were efficiently synthesized and showed excellent dual inhibitory activity in ELISA assay. Furthermore, the positively charged, stapled peptides showed enhanced cellular uptake along with modest in vivo activity.

Copyright © 2011 Elsevier Ltd. All rights reserved.

PMID:
21277201
[PubMed - indexed for MEDLINE]
PMCID: PMC3057119
[Available on 2012/3/1]
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11.
J Org Chem. 2011 Mar 4;76(5):1228-38. Epub 2011 Jan 28.

Stapling of a 3(10)-helix with click chemistry.

Source

School of Pharmacy, University of Oslo, P.O. Box 1068 Blindern, 0316 Oslo, Norway. oyvind.jacobsen@farmasi.uio.no

Abstract

Short peptides are important as lead compounds and molecular probes in drug discovery and chemical biology, but their well-known drawbacks, such as high conformational flexibility, protease lability, poor bioavailability and short half-lives in vivo, have prevented their potential from being fully realized. Side chain-to-side chain cyclization, e.g., by ring-closing olefin metathesis, known as stapling, is one approach to increase the biological activity of short peptides that has shown promise when applied to 3(10)- and α-helical peptides. However, atomic resolution structural information on the effect of side chain-to-side chain cyclization in 3(10)-helical peptides is scarce, and reported data suggest that there is significant potential for improvement of existing methodologies. Here, we report a novel stapling methodology for 3(10)-helical peptides using the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction in a model aminoisobutyric acid (Aib) rich peptide and examine the structural effect of side chain-to-side chain cyclization by NMR, X-ray diffraction, linear IR and femtosecond 2D IR spectroscopy. Our data show that the resulting cyclic peptide represents a more ideal 3(10)-helix than its acyclic precursor and other stapled 3(10)-helical peptides reported to date. Side chain-to-side chain stapling by CuAAC should prove useful when applied to 3(10)-helical peptides and protein segments of interest in biomedicine.

PMID:
21275402
[PubMed - indexed for MEDLINE]
Click here to read
12.
Chem Commun (Camb). 2011 Mar 7;47(9):2589-91. Epub 2010 Dec 21.

End-stapled homo and hetero collagen triple helices: a click chemistry approach.

Source

School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, UK.

Abstract

A CuAAC reaction was established for modular synthesis of end-stapled homo- and hetero-triple helical peptides, generating "clicked" macro-assemblies with enhanced thermal stability.

PMID:
21173963
[PubMed - indexed for MEDLINE]
13.
Chem Biol. 2010 Dec 22;17(12):1325-33.

Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome.

Source

Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA.

Abstract

Defining protein interactions forms the basis for discovery of biological pathways, disease mechanisms, and opportunities for therapeutic intervention. To harness the robust binding affinity and selectivity of structured peptides for interactome discovery, we engineered photoreactive stapled BH3 peptide helices that covalently capture their physiologic BCL-2 family targets. The crosslinking α helices covalently trap both static and dynamic protein interactors, and enable rapid identification of interaction sites, providing a critical link between interactome discovery and targeted drug design.

Copyright © 2010 Elsevier Ltd. All rights reserved.

PMID:
21168768
[PubMed - indexed for MEDLINE]
PMCID: PMC3048092
Free PMC Article
Click here to readClick here to read
14.
Cell Cycle. 2010 Nov 15;9(22):4560-8. Epub 2010 Nov 15.

Stapled peptides in the p53 pathway: computer simulations reveal novel interactions of the staples with the target protein.

Source

Bioinformatics Institute, Matrix, Singapore.

Abstract

Atomistic simulations of a set of stapled peptides derived from the transactivation domain of p53 (designed by Verdine & colleagues, JACS 2007 129:2456) and complexed to MDM2 reveal that the good binders are uniquely characterized by higher helicity and by extensive interactions between the hydrocarbon staples and the MDM2 surface; in contrast the poor binders have reduced helicity and their staples are mostly solvent exposed. Our studies also find that the best binders can also potentially inhibit MDMX with similar affinities, suggesting that such stapled peptides can be evolved for dual inhibition with therapeutic potential.

PMID:
21088491
[PubMed - indexed for MEDLINE]
Click here to read
16.
Transplantation. 2010 Sep 27;90(6):622-9.

Reduced ischemia-reoxygenation injury in rat intestine after luminal preservation with a tailored solution.

Source

Department of Surgery, University Medical Center Groningen, Groningen, The Netherlands. a.m.roskott@chir.umcg.nl

Abstract

BACKGROUND:

The intestine is extremely sensitive to ischemic preservation and reoxygenation injury. Current vascular perfusion and cold storage with University of Wisconsin (UW) solution neglect the intestinal lumen and the ongoing mucosal metabolism during hypothermia. This study was designed to test the effects of luminal preservation with an alternative preservation solution in addition to the common vascular flush with UW solution on graft viability after preservation and ex vivo reoxygenation.

METHODS:

Rat intestine was preserved on ice for 6 hr in UW solution or Williams Medium E with additional buffering, impermeants, and a colloid (WMEplus) after being stapled or after flushing and filling the lumen with the respective preservation solution. Tissue slices were prepared from fresh and preserved intestines and were incubated with oxygen for 6 hr at 37°C to assess the viability after reoxygenation.

RESULTS:

Directly after preservation, histologic damage was mild and unaffected by preservation strategy. Contrary to luminal preservation, closed preservation resulted in significantly decreased ATP levels compared with control. Reoxygenation aggravated damage and revealed differences between the strategies. Luminal preservation better maintained the ATP levels and histologic integrity (vs. closed preservation) for both solutions. Histomorphologic integrity was superior after preservation with WMEplus (vs. UW solution). Expression of stress responsive genes was least up-regulated in the slices from tissue preserved luminally with WMEplus.

CONCLUSIONS:

In conclusion, preservation and reoxygenation injury can be attenuated by luminal preservation with WMEplus.

PMID:
20689496
[PubMed - indexed for MEDLINE]
18.
Am Surg. 2010 Jun;76(6):614-7.

Role of growth factors in improved skin flap viability caused by phosphodiesterase-5 inhibitor.

Source

Department of Surgery, Dwight D. Eisenhower Army Medical Center, 300 Hospital Road, Augusta, Georgia 30905, USA. Bradley.Bandera@amedd.army.mil

Abstract

Flap necrosis is one of the major complications of reconstructive surgery and sildenafil citrate has been shown to decrease flap necrosis in preclinical animal models. However, the mechanisms underlying sildenafil's therapeutic efficacy are not known. As with other phosphodiesterase 5 selective inhibitors, sildenafil causes vasodilation and enhanced blood flow. In addition, sildenafil can also alter gene expression. This study is designed to test the hypothesis that increased expression of angiogenic growth factors may be responsible for therapeutic efficacy of sildenafil. A modified McFarlane flap measuring 3 x 10 cm was created on the dorsal skin of male Sprague-Dawley rats. For growth factor expression experiment, rats were administered either vehicle or sildenafil 10 mg/Kg intraperitoneal (IP). Ribonucleic acid (RNA) extracted from skin flap was analyzed to assess the messenger ribonucleic acid (mRNA) levels of different angiogenic growth factors. For skin flap viability experiment, fibrin film impregnated with vehicle, fibroblast growth factor (FGF) (5.0 microg) or vascular endothelial growth factor (VEGF) (2.0 microg) was applied to the wound. The skin flap was then returned to its native position and stapled in place. Total affected area (area of necrosis and blood flow stasis) of each rat on postoperative day 14 was analyzed with orthogonal polarization spectral imaging. Daily systemic treatment with sildenafil significantly (P < 0.05) increased the expression of FGF1 and FGF Receptor 3 on postoperative day 3 by 5.08- and 4.78-fold, respectively. In addition, sildenafil increased the expression of VEGF-A, VEGF-B, and VEGF-C by 2.66-, 2.02-, and 2.00-fold, respectively. Subcutaneous treatment with FGF but not VEGF-A tended to decrease total affected area in rats. These data demonstrate that sildenafil altered the expression of FGF and VEGF. Altered expression of growth factors may be, at least partly, responsible for the beneficial effects of sildenafil citrate on skin viability.

PMID:
20583517
[PubMed - indexed for MEDLINE]
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19.
Chem Biol Drug Des. 2010 Apr;75(4):348-59.

Probing the alpha-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis.

Source

Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.

Abstract

Reactivation of the p53 cell apoptosis pathway through inhibition of the p53-hDM2 interaction is a viable approach to suppress tumor growth in many human cancers and stabilization of the helical structure of synthetic p53 analogs via a hydrocarbon cross-link (staple) has been found to lead to increased potency and inhibition of protein-protein binding (J. Am. Chem. Soc. 129: 5298). However, details of the structure and dynamic stability of the stapled peptides are not well understood. Here, we use extensive all-atom molecular dynamics simulations to study a series of stapled alpha-helicalpeptides over a range of temperatures in solution. The peptides are found to exhibit substantial variations in predicted alpha-helical propensities that are in good agreement with the experimental observations. In addition, we find significant variation in local structural flexibility of the peptides with the position of the linker, which appears to be more closely related to the observed differences in activity than the absolute alpha-helical stability. These simulations provide new insights into the design of alpha-helical stapled peptides and the development of potent inhibitors of alpha-helical protein-protein interfaces.

PMID:
20331649
[PubMed - indexed for MEDLINE]
Click here to read
20.
World J Surg. 2010 Jul;34(7):1615-26.

Postsurgical recurrence of ileal Crohn's disease: an update on risk factors and intervention points to a central role for impaired host-microflora homeostasis.

Source

Surgical Professorial Unit, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland.

Abstract

BACKGROUND:

A pressing need exists to identify factors that predispose to recurrence after terminal ileal resection for Crohn's disease (CD) and to determine effective prophylactic strategies. This review presents an up-to-date summary of the literature in the field and points to a role for bacterial overproliferation in recurrence.

METHODS:

The literature (Medline, Embase, and the Cochrane Library, 1971-2009) on ileal CD and postoperative recurrence was searched, and 528 relevant articles were identified and reviewed.

RESULTS:

Smoking is a key independent risk factor for recurrence. NOD2/CARD15 polymorphisms and penetrating phenotype are associated with aggressive disease and higher reoperation rates. Age at diagnosis, disease duration, gender, and family history are inconsistent predictors of recurrence. Prophylactic 5-aminosalicylic acid therapy and nitromidazole antibiotics are beneficial. Combination therapies with immunosuppressants are also effective. Anti-TNFalpha-based regimens show benefit but the evidence base is small. Corticosteroid, interleukin-10, and probiotic therapies are not effective. Wider, stapled anastomotic configurations are associated with reduced recurrence rates. Strictureplasty and laparoscopic approaches have similar long-term recurrence rates to open resection techniques. Length of resection and presence of microscopic disease at resection margins do not influence recurrence. A lack of consensus exists regarding whether the presence of granulomas or plexitis affects outcome.

CONCLUSIONS:

Current evidence points to defects in mucosal immunity and intestinal dysbiosis of either innate (NOD2/CARD15) or induced (smoking) origin in postoperative CD recurrence. Prophylactic strategies should aim to limit dysbiosis (antibiotics, side-to-side anastomoses) or prevent downstream chronic inflammatory sequelae (anti-inflammatory, immunosuppressive, and immunomodulatory therapy).


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