MYC-Targeting Inhibitors Generated from a Stereodiversified Bicyclic Peptide Library

Here, we present the second generation of our bicyclic peptide library (NTB), featuring a stereodiversified structure and a simplified construction strategy. We utilized a tandem ring-opening metathesis and ring-closing metathesis reaction (ROM-RCM) to cyclize the linear peptide library in a single step, representing the first reported instance of this reaction being applied to the preparation of macrocyclic peptides. Moreover, the resulting bicyclic peptide can be easily linearized for MS/MS sequencing with a one-step deallylation process. We employed this library to screen against the E363-R378 epitope of MYC and identified several MYC-targeting bicyclic peptides. Subsequent in vitro cell studies demonstrated that one candidate, NT-B2R, effectively suppressed MYC transcription activities and cell proliferation.

What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks

Identifying residues critical to protein-protein binding and efficient design of stable and specific protein binders are challenging tasks. Extending beyond the direct contacts in a protein-protein binding interface, our study employs computational modeling to reveal the essential network of residue interactions and dihedral angle correlations critical in protein-protein recognition. We hypothesized that mutating residues exhibiting highly correlated dynamic motion within the interaction network could efficiently optimize protein-protein interactions to create tight and selective protein binders. We tested this hypothesis using the ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complex, since Ub is a central player in multiple cellular functions and PLpro is an antiviral drug target. Our designed ubiquitin variant (UbV) hosting three mutated residues displayed a ∼3,500-fold increase in functional inhibition relative to wild-type Ub. Further optimization of two C-terminal residues within the Ub network resulted in a KD of 1.5 nM and IC50 of 9.7 nM for the five-point Ub mutant, eliciting 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study highlights residue correlation and interaction networks in protein-protein interactions, and introduces an effective approach to design high-affinity protein binders for cell biology research and future therapeutics.

What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks

Identifying critical residues in protein-protein binding and efficiently designing stable and specific protein binders is challenging. In addition to direct contacts in a protein-protein binding interface, our study employs computation modeling to reveal the essential network of residue interaction and dihedral angle correlation critical in protein-protein recognition. We propose that mutating residues regions exhibited highly correlated motions within the interaction network can efficiently optimize protein-protein interactions to create tight and selective protein binders. We validated our strategy using ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complexes, where Ub is one central player in many cellular functions and PLpro is an antiviral drug target. Our designed UbV with 3 mutated residues resulted in a ~3,500-fold increase in functional inhibition, compared with the wild-type Ub. Further optimization by incorporating 2 more residues within the network, the 5-point mutant achieved a KD of 1.5 nM and IC50 of 9.7 nM. The modification led to a 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study highlights residue correlation and interaction networks in protein-protein interaction, introduces an effective approach to design high affinity protein binders for cell biology and future therapeutics solutions.

What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks

Identifying critical residues in protein-protein binding and efficiently designing stable and specific protein binders to target another protein is challenging. In addition to direct contacts in a protein-protein binding interface, our study employs computation modeling to reveal the essential network of residue interaction and dihedral angle correlation critical in protein-protein recognition. We propose that mutating residues regions exhibited highly correlated motions within the interaction network can efficiently optimize protein-protein interactions to create tight and selective protein binders. We validated our strategy using ubiquitin (Ub) and MERS coronaviral papain-like protease (PLpro) complexes, where Ub is one central player in many cellular functions and PLpro is an antiviral drug target. Molecular dynamics simulations and experimental assays were used to predict and verify our designed Ub variant (UbV) binders. Our designed UbV with 3 mutated residues resulted in a ~3,500-fold increase in functional inhibition, compared with the wild-type Ub. Further optimization by incorporating 2 more residues within the network, the 5-point mutant achieved a KD of 1.5 nM and IC50 of 9.7 nM. The modification led to a 27,500-fold and 5,500-fold enhancements in affinity and potency, respectively, as well as improved selectivity, without destabilizing the UbV structure. Our study illustrates the importance of residue correlation and interaction networks in protein-protein interaction and introduces a new approach that can effectively design high affinity protein binder for cell biology studies and future therapeutic solution.

Dual endoscopic-assisted endoluminal colostomy reversal: a feasibility study

BACKGROUND

Emergent colostomies are associated with increased morbidity related to second closure operations. The purpose of this canine pilot study was to create a minimally invasive procedure that would reduce the time interval and morbidity involved with colostomy reversals after left colon end colostomies.

METHODS

Six mongrel dogs underwent modified laparoscopic Hartmann's procedures in which the stapled end of the rectal stump was approximated to the left colon proximal to the stoma. After 1 week, they underwent an endoluminal colostomy reversal with a computer-mediated, circular stapling device and varying anvil insertion methods. Variables recorded included anvil insertion technique and feasibility, OR time, complications, and number of days to first meal and bowel movement. A contrast enema performed 1 week post colostomy reversal ruled out anastomosis leaks and stenosis. The dogs were euthanized and subjected to necropsy.

RESULTS

Of four anvil insertion techniques tested, the most feasible employed a large-bore needle to perforate through the stapled end of the Hartmann pouch into the lumen of the left colon. Simultaneous endoluminal views of the rectal stump with a sigmoidoscope and the left colon lumen with an endoscope permitted a controlled and safe needle puncture. Through the needle, a guide wire was inserted to withdraw the anvil via the colostomy into place. A transanally inserted stapler was then married to the anvil under fluoroscopic guidance, thus completing the anastomosis. The colostomy was then taken down and transected at the level of the colocolostomy. Average operating time was 126 min (range 90-180), diet was tolerated within 1.5 days, and average number of days to first bowel movement was 2.5. The absence of stenosis, leaks, and inadvertent visceral injuries confirmed feasibility.

CONCLUSIONS

In this canine model, a dual endoscopic-assisted colostomy reversal with a computer-mediated, circular stapling device is feasible. Using this technique, colostomy reversals can possibly be performed 1 week post-colostomy without entering the peritoneal cavity, thus reducing the number of invasive operations and subsequent morbidity required to manage emergent colon perforations.

Laparoscopic harvesting of small bowel graft for small bowel transplantation

BACKGROUND

Small bowel transplantation represents a valid therapeutic option for patients with intestinal failure, obviating the need for long-term total parenteral nutrition. Recently, reports have shown the feasibility of performing living related intestinal transplantation using segmental small bowel grafts. The limitations of this technique include inadequate harvested small bowel lengths, as compared with the lengths obtained in cadaveric small bowel harvests, and large incisions for the donor. In this pilot study, we evaluated the feasibility of laparoscopically harvesting long segments of proximal jejunum for small bowel transplantation using a porcine model. The results can be used to evaluate the potential for applying this technique in human cases.

METHODS

For this study 10 yorkshire pigs were used. Under general anesthesia, each pig underwent laparoscopic segmental resection of 200 cm of proximal jejunum on a vascular pedicle. The harvested graft then was autoreimplanted using an open technique by anastomosing the vascular pedicle to the superior mesenteric vessels. Success was determined 2 hours after anastomosis by visually identifying a pink graft with viable-appearing mucosa, an artery with a strong thrill, and palpable venous flow. The animals were then sacrificed.

RESULTS

The mean operation time required to laparoscopically harvest the small bowel graft was 80 min (range, 35-120 min), and the mean length of harvested graft was 220 cm (range, 200-260 cm). The mean length of the graft's vascular pedicle was 4.5 cm (range, 4-5 cm). All 10 grafts were successfully harvested laparoscopically and then reimplanted using an open technique. All the grafts maintained good vascular flow, and showed no evidence of mucosal necrosis at necropsy. Obviously, further studies would be required to examine the long-term results of reimplanting a laparoscopically harvested small bowel graft, but proposals for such studies is beyond the scope of this report.

CONCLUSION

Minimally invasive techniques can be used to harvest proximal small bowel grafts for living related small bowel transplantation.