Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase.

There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.

Expansive discovery of chemically diverse structured macrocyclic oligoamides.

Small macrocycles with four or fewer amino acids are among the most potent natural products known, but there is currently no way to systematically generate such compounds. We describe a computational method for identifying ordered macrocycles composed of alpha, beta, gamma, and 17 other amino acid backbone chemistries, which we used to predict 14.9 million closed cycles composed of >42,000 monomer combinations. We chemically synthesized 18 macrocycles predicted to adopt single low-energy states and determined their x-ray or nuclear magnetic resonance structures; 15 of these were very close to the design models. We illustrate the therapeutic potential of these macrocycle designs by developing selective inhibitors of three protein targets of current interest. By opening up a vast space of readily synthesizable drug-like macrocycles, our results should considerably enhance structure-based drug design.

A Tag-Free Platform for Synthesis and Screening of Cyclic Peptide Libraries.

In the realm of high-throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post-screening. Our innovation introduces a tag-free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity-enhancing derivatization method, utilized in tandem with nano LC-MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays.

Design and structural validation of peptide-drug conjugate ligands of the kappa-opioid receptor.

Despite the increasing number of GPCR structures and recent advances in peptide design, the development of efficient technologies allowing rational design of high-affinity peptide ligands for single GPCRs remains an unmet challenge. Here, we develop a computational approach for designing conjugates of lariat-shaped macrocyclized peptides and a small molecule opioid ligand. We demonstrate its feasibility by discovering chemical scaffolds for the kappa-opioid receptor (KOR) with desired pharmacological activities. The designed De Novo Cyclic Peptide (DNCP)-ß-naloxamine (NalA) exhibit in vitro potent mixed KOR agonism/mu-opioid receptor (MOR) antagonism, nanomolar binding affinity, selectivity, and efficacy bias at KOR. Proof-of-concept in vivo efficacy studies demonstrate that DNCP-ß-NalA(1) induces a potent KOR-mediated antinociception in male mice. The high-resolution cryo-EM structure (2.6 Å) of the DNCP-ß-NalA-KOR-Gi1 complex and molecular dynamics simulations are harnessed to validate the computational design model. This reveals a network of residues in ECL2/3 and TM6/7 controlling the intrinsic efficacy of KOR. In general, our computational de novo platform overcomes extensive lead optimization encountered in ultra-large library docking and virtual small molecule screening campaigns and offers innovation for GPCR ligand discovery. This may drive the development of next-generation therapeutics for medical applications such as pain conditions.

The Effect of Illumination on Positive Fusional Vergence.

Background: Positive fusional vergence (PFV) is vital in maintaining fusion in critical and continuous near tasks such as reading or performing digital screen tasks. This study investigated how PFV changed under various lighting conditions. Methods: This cross-sectional study recruited 34 participants aged between 21 and 25 years, with best corrected visual acuity (BCVA) 0.0 logMAR and insignificant refractive error. Three different illuminations-low illumination (50 lux), medium lighting (100 lux), and high illumination (150 lux)-were used to examine the ocular parameters PFV (blur, break, and recovery points), contrast sensitivity and pupil diameter. Results: Pupil diameter changed significantly in different room illuminations (p = 0.00). There was no significant difference in contrast sensitivity across the three levels of room illumination (p = 0.368). Mean PFV (SD) (blur) was 14.5 (2.5) in 50 lux, 10.2 (2.2) in 100 lux, and 8.2 (2.1) in 150 lux. Under 50, 100 and 150 lux, respectively, the mean PFV (SD) (break) values were 16.7 (2.4), 13.4 (1.8), and 10.8 (2.2), and the mean PFV (SD) (recovery) values were 13.3 (2.1), 10.7 (2.1), and 7.5 (2.7). With increased illumination levels, PFV blur, break, and recovery values were significantly lower (p < 0.001). Conclusions: PFV values were significantly higher in lower illumination. Clinicians should be aware that room illumination affected the PFV values measured.

Cell-permeable chameleonic peptides: Exploiting conformational dynamics in de novo cyclic peptide design.

Membrane-traversing peptides offer opportunities for targeting intracellular proteins and oral delivery. Despite progress in understanding the mechanisms underlying membrane traversal in natural cell-permeable peptides, there are still several challenges to designing membrane-traversing peptides with diverse shapes and sizes. Conformational flexibility appears to be a key determinant of membrane permeability of large macrocycles. We review recent developments in the design and validation of chameleonic cyclic peptides, which can switch between alternative conformations to enable improved permeability through cell membranes, while still maintaining reasonable solubility and exposed polar functional groups for target protein binding. Finally, we discuss the principles, strategies, and practical considerations for rational design, discovery, and validation of permeable chameleonic peptides.

Cyclic peptide structure prediction and design using AlphaFold.

Deep learning networks offer considerable opportunities for accurate structure prediction and design of biomolecules. While cyclic peptides have gained significant traction as a therapeutic modality, developing deep learning methods for designing such peptides has been slow, mostly due to the small number of available structures for molecules in this size range. Here, we report approaches to modify the AlphaFold network for accurate structure prediction and design of cyclic peptides. Our results show this approach can accurately predict the structures of native cyclic peptides from a single sequence, with 36 out of 49 cases predicted with high confidence (pLDDT > 0.85) matching the native structure with root mean squared deviation (RMSD) less than 1.5 Å. Further extending our approach, we describe computational methods for designing sequences of peptide backbones generated by other backbone sampling methods and for de novo design of new macrocyclic peptides. We extensively sampled the structural diversity of cyclic peptides between 7-13 amino acids, and identified around 10,000 unique design candidates predicted to fold into the designed structures with high confidence. X-ray crystal structures for seven sequences with diverse sizes and structures designed by our approach match very closely with the design models (root mean squared deviation < 1.0 Å), highlighting the atomic level accuracy in our approach. The computational methods and scaffolds developed here provide the basis for custom-designing peptides for targeted therapeutic applications.

Accommodative spasm and its different treatment approaches: A systematic review.

This article is about the accommodation spasm. The primary rule for near vision is ciliary muscle constriction, synchronised convergence of both eyes, and pupil constriction. Any weaknesses in these components could result in an accommodative spasm. Variable retinoscopic reflex, unstable refractive error, and lead of accommodation in near retinoscopy are common causes of spasm. We conducted a thorough literature search in the PubMed and Google Scholar databases for published journals prior to June 2022, with no data limitations. This review contains twenty-eight case reports, six cohort studies, four book references, four review articles, and two comparative studies after applying the inclusion and exclusion criteria. The majority of studies looked at accommodative spasm, near reflex spasm, and pseudomyopia. The most common causes of accommodative spasm are excessive close work, emotional distress, head injury, and strabismus. Despite side effects or an insufficient regimen, cycloplegic drops are effective in diagnosing accommodation spasm. The modified optical fogging technique is also effective and may be an option for treating accommodative spasm symptoms. Bifocals for near work, manifest refraction, base-in prisms, and vision therapy are some of the other management options. As a result, it requires a comprehensive clinical treatment strategy. This review aims to investigate the various aetiology and treatments responsible for accommodative spasm and proposes widely implementing the modified optical fogging method and vision therapy in clinics as comprehensive management to reduce the future upward trend of accommodative spasm.

Accurate de novo design of membrane-traversing macrocycles.

We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6-12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6-12 residue size range cross membranes with an apparent permeability greater than 1 × 10-6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.

Neuroendocrine Carcinoma of the Colon: Emergency Presentation of a Rare Disease With Poor Biology.

Neuroendocrine tumors (NETs) are rare entities. Most common among them are gastroenteropancreatic neuroendocrine tumors (GEP-NETs) and pulmonary NETs. Most of them are indolent in nature. Colonic NETs are rare among GEP-NETs and mostly present with large size and with metastasis. Emergency presentation with hematochezia is rare in colonic NETs. This case report discusses a rare emergency presentation of colonic NETs and highlights their poor biological nature.

Diabetic myonecrosis in end-stage renal disease.

Diabetic myonecrosis or muscle infarction (DMI), a clinicoradiological entity is an underdiagnosed complication of diabetes mellitus. It refers to spontaneous aseptic necrosis of skeletal muscles commonly of the lower limb without evidence of any large vessel disease. It presents as painful swollen limb without any external insult in patients with long-standing diabetes mellitus with other microvascular complications especially nephropathy. We present four instances of DMI in our patients who had end-stage renal disease with a varied course.

Clinical presentations and surgical outcomes of intraocular foreign body presenting to an ocular trauma unit.

OBJECTIVES: To describe, evaluate, and identify the characteristics, prognostic factors, and visual outcomes in patients with intraocular foreign body (IOFB) in a Latin American population. METHODS: A retrospective, observational case-series of patients with a diagnosis of IOFB. Variables analyzed included age, gender, initial and final best correct visual acuity (BCVA), ocular trauma score, intraocular pressure, mechanism of injury, material and number of IOFB, zone of injury, timing of primary repair and IOFB removal, complications, and follow up. RESULTS: Sixty-one patients with IOFB were identified of which 97% were male with a mean age of 37.9 years (SD 2.16). The most common IOFB location was intravitreal (43%). IOFBs were metallic in 78%, vegetal in 3%, and other materials in 11%. Primary repair and secondary IOFB removal were performed at a mean timepoint of 3 days and 5 days, respectively. Systemic and topical antibiotics were administered to all patients. The initial BCVA was 1.62 logMAR and the final was 0.6 logMAR, which was statistically significant (Pearson's chi-squared test, p value 0.01). No cases of endophthalmitis were seen. CONCLUSION: IOFB removal can be delayed when there are no signs of infection or evidence of retinal detachment, without an increased risk of endophthalmitis and a negative impact on visual outcomes. Use of topical and systemic antibiotics appear sufficient to prevent endophthalmitis in these cases.

Internal Medicine Resident Work Absence During the COVID-19 Pandemic at a Large Academic Medical Center in New York City.

BACKGROUND: Montefiore Medical Center (MMC) is a large tertiary care center in the Bronx, New York City, with 245 internal medicine residents. Beginning on February 29, 2020, residents became ill with COVID-19-like illness (CLI), which required absence from work. There was initially a shortage of personal protective equipment and delays in SARS-CoV-2 testing, which gradually improved during March and April 2020. OBJECTIVE: We evaluated the relationship between CLI-related work absence rates of internal medicine residents and MMC's COVID-19 hospital census over time. METHODS: Data on resident work absence between February 29 and May 22 were reviewed along with MMC's COVID-19 hospital census data. To determine the effect of patient exposure on resident CLI incidence, we compared the mean incidence of CLI per patient exposure days (PED = daily hospital census × days pre- or post-peak) before and after peak COVID-19 hospital census. RESULTS: Forty-two percent (103 of 245) of internal medicine residents were absent from work, resulting in 875 missed workdays. At the peak of resident work absence, 16% (38 of 245) were out sick. Residents were absent for a median of 7 days (IQR 6-9.5 days). Mean resident CLI incidence per PED (CLI/PED) was 13.9-fold lower post-peak compared to pre-peak (P = .003). CONCLUSIONS: At the beginning of the COVID-19 pandemic in New York City, a large portion of internal medicine residents at this single center became ill. However, the incidence of CLI decreased over time, despite ongoing exposure to patients with COVID-19.

MANAGEMENT OF GIANT RETINAL TEARS USING TRANSSCLERAL DIODE LASER RETINOPEXY AND SHORT-TERM POSTOPERATIVE TAMPONADE WITH PERFLUORO-N-OCTANE.

PURPOSE: To determine the results of pars plana vitrectomy for giant retinal tear detachments using transscleral diode laser retinopexy and short-term postoperative tamponade with perfluoro-n-octane (PFnO). METHODS: Twenty consecutive patients with fresh giant retinal tears were enrolled in a single-arm prospective study. One case was withdrawn for technical reasons. The remainder all underwent pars plana vitrectomy, PFnO injection, transscleral diode laser retinopexy to the edge of the giant retinal tear, and short-term postoperative heavy liquid tamponade. None of the cases had scleral buckling or lensectomy. RESULTS: Nineteen cases (18 male and 1 female) with a mean age of 41 years (range 10-69 years) were followed up for a period of 6 months. Postoperative tamponade with PFnO was maintained for a mean of 7.6 days (range 4-21 days), after which it was exchanged for sulfur hexafluoride (SF6), perfluoropropane (C3F8) gas, or balanced salt solution. Final reattachment rate was 100%, with 3 (15.7%) patients requiring additional surgery. Best-corrected visual acuity at final follow-up was 20/40 or better in 11 eyes (58%), between 20/60 and 20/200 in 7 (37%), and 20/400 in 1 (5%). CONCLUSION: In this series of acute giant retinal tears, transscleral diode laser retinopexy together with the use of PFnO for short-term postoperative tamponade achieved excellent anatomical and visual results.

Acute kidney injury is associated with higher mortality and healthcare costs in hospitalized patients with cirrhosis.

INTRODUCTION AND OBJECTIVES: AKI is known to be associated with increased risk of mortality, however limited information is available on how AKI impacts healthcare costs and resource utilization in hospitalized patients with cirrhosis. Previous studies have had variable definitions of AKI, resulting in inconsistent reporting of the true impact of AKI in patients with cirrhosis. METHODS: Data from the Nationwide Inpatient Sample (NIS) which contains data from 44 states and 4378 hospitals, accounting for over 7 million discharges were analyzed. The inclusion data were all discharges in the 2012 NIS dataset with a discharge diagnosis of cirrhosis. RESULTS: A total of 32,605 patients were included in the analysis, incidence of AKI was 12.12% in patients with cirrhosis. Crude mortality was much higher for patients with cirrhosis and AKI (14.9% vs. 1.8%, OR 9.42, p<0.001) than for patients without AKI. In addition, mean LOS was longer (8.5 vs. 4.3 days, p<0.001) and median total hospital charges were higher for patients with AKI ($43,939 vs. $22,270, p<0.001). In multivariate logistic regression, controlling for covariates and mortality risk score, sepsis, ascites and SBP were predictors of AKI. CONCLUSIONS: AKI is relatively common in hospitalized patients with cirrhosis. Presence of AKI results in significantly higher inpatient mortality as well as LOS and resource utilization. Median hospitalization cost was twice as high in AKI patients. Early identification of patients at high risk for AKI should be implemented to reduce mortality and contain costs. Prognosis could be enhanced by utilizing biomarkers which could rapidly detect AKI.

A 21-Year Study of Vitreoretinal Surgery for Aphakic Retinal Detachment: Long-Term Surgical Outcomes and Complications.

PURPOSE: To determine the characteristics and outcomes of primary retinal detachment (RD) surgery in aphakic patients. DESIGN: Retrospective case series. PARTICIPANTS: Sixty eyes with primary aphakic RD (ARD) in 51 patients. METHODS: A consecutive series of patients who underwent vitreoretinal surgery for primary rhegmatogenous ARD was analyzed retrospectively between 1997 and 2018 at Moorfields Eye Hospital. MAIN OUTCOME MEASURES: Best-corrected visual acuity (BCVA), surgical outcomes, and complications. RESULTS: Mean BCVA improved from 1.31 to 1.08 logarithm of the minimum angle of resolution (logMAR; P = 0.081) over a mean follow-up period of 8.2 years. Macula-off retinal detachments showed significantly improved BCVA from 1.72 to 1.1 logMAR (P = 0.007). Mean age was 38.8 years, and the most common cause of aphakia was congenital cataract surgery (55%). The macula was attached in 45% eyes, and grade C proliferative vitreoretinopathy (PVR) was present in 12%. Operations performed were vitrectomy (88%), combined vitrectomy and scleral buckle (8%), and encirclement (3%). The final anatomic success rate was 88%, and PVR was a significant predictor of redetachment (P = 0.03; odds ratio, 20.7; 95% confidence interval, 2.8-152.2). Raised intraocular pressure was the most common postoperative complication at 30%, with a rate of de novo postoperative glaucoma of 6.7% at final follow-up. CONCLUSIONS: We report high rates of primary and overall anatomic success for surgery in ARD surgery. Grade C PVR was a positive predictor for surgical failure. Final visual outcomes were limited by ocular comorbidity, and we report significant improved visual outcomes for macula-off ARD.

Comprehensive computational design of ordered peptide macrocycles.

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l- and d-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.

Upper Gastrointestinal Bleed as a Manifestation of Poorly Differentiated Metastatic Squamous Cell Carcinoma of the Lung.

Gastrointestinal (GI) metastasis from primary lung cancer is a rare clinical finding. Lung cancer most often metastasizes to the brain, bone, liver, and adrenal glands; with gastrointestinal involvement being very rare. We report a case of a 39-year-old female with a diagnosis of poorly differentiated Squamous Cell Carcinoma (SCC) of the lung presenting with dizziness and melena. Esophagogastroduodenoscopy (EGD) showed a bleeding mass in the stomach. Final biopsy report and Immunohistochemistry (IHC) of the specimen were consistent with SCC lung metastasis. While it is imperative to have a high clinical suspicion for GI metastasis in patients with primary lung cancer presenting with GI symptoms, it may be challenging to establish diagnosis. Endoscopy along with pathology and immunohistochemistry play a crucial role in differentiating primary GI malignancies from metastasis.

Bleeding ectopic duodenal varix: use of a new microvascular plug (MVP) device along with transjugular intrahepatic portosystemic shunt (TIPSS).

Ectopic varices (ECV) occur along the gastrointestinal (GI) tract outside the common variceal sites and represent 2%-5% of all GI variceal bleeds with mortality rates up to 40%. Management is challenging because of inaccessibility and increased risk of rebleeding. We report what is to our knowledge the first clinical use of a new microvascular plug (MVP) with transjugular intrahepatic portosystemic shunt (TIPSS) for a bleeding duodenal varix (DV). A 68-year-old man presented with melena. Endoscopy demonstrated a grade II varix in the second part of the duodenum with red wale sign. TIPSS was performed and portogram revealed a single DV. Poststent placement venogram revealed a persistent varix and hence a 5-7 mm MVP was deployed. Subsequent imaging showed cessation of blood through the DV. The patient had no further bleeding. TIPSS with embolisation is an effective treatment for ECV. This MVP offers advantages due to its size and compatibility and can be redeployed in case of suboptimal placement.