Targeting the Essential Transcription Factor HP1043 of Helicobacter pylori: A Drug Repositioning Study

Antibiotic-resistant bacterial pathogens are a very challenging problem nowadays. Helicobacter pylori is one of the most widespread and successful human pathogens since it colonizes half of the world population causing chronic and atrophic gastritis, peptic ulcer, mucosa-associated lymphoid tissue-lymphoma, and even gastric adenocarcinoma. Moreover, it displays resistance to numerous antibiotics. One of the H. pylori pivotal transcription factors, HP1043, plays a fundamental role in regulating essential cellular processes. Like other bacterial transcription factors, HP1043 does not display a eukaryote homolog. These characteristics make HP1043 a promising candidate to develop novel antibacterial strategies. Drug repositioning is a relatively recent strategy employed in drug development; testing approved drugs on new targets considerably reduces the time and cost of this process. The combined computational and in vitro approach further reduces the number of compounds to be tested in vivo. Our aim was to identify a subset of known drugs able to prevent HP1043 binding to DNA promoters. This result was reached through evaluation by molecular docking the binding capacity of about 14,350 molecules on the HP1043 dimer in both conformations, bound and unbound to the DNA. Employing an ad hoc pipeline including MMGBSA molecular dynamics, a selection of seven drugs was obtained. These were tested in vitro by electrophoretic mobility shift assay to evaluate the HP1043–DNA interaction. Among these, three returned promising results showing an appreciable reduction of the DNA-binding activity of HP1043. Overall, we applied a computational methodology coupled with experimental validation of the results to screen a large number of known drugs on one of the H. pylori essential transcription factors. This methodology allowed a rapid reduction of the number of drugs to be tested, and the drug repositioning approach considerably reduced the drug design costs. Identified drugs do not belong to the same pharmaceutical category and, by computational analysis, bound different cavities, but all display a reduction of HP1043 binding activity on the DNA

Age above 70 years and Charlson Comorbidity Index higher than 3 are associated with reduced survival probabilities after radical cystectomy for bladder cancer. Data from a contemporary series of 334 consecutive patients.

Objective: To assess the joint effect of age and comorbidities on clinical outcomes of radical cystectomy (RC).Methods: 334 consecutive patients undergoing open RC for bladder cancer (BC) during the years 2005-2015 were analyzed. Pre-, peri- and post-operative parameters, including age at RC (ARC) and Charlson Comorbidity Index (CCI), were evaluated. Overall and cancer-specific survivals (OS, CSS) were assessed by univariate and multivariate modelling. Furthermore, a three-knot restricted cubic spline (RCS) was fitted to survival data to detect dependency between death-rate ratio (HR) and ARC. Results: Median follow-up time was 3.8 years (IQR = 1.3-7.5) while median OS was 5.9 years (95%CL = 3.8-9.1). Globally, 180 patients died in our cohort (53.8%), 112 of which (62.2%) from BC and 68 patients (37.8%) for unrelated causes. After adjusting for preoperative, pathological and perioperative parameters, patients with CCI > 3 showed significantly higher death rates (HR = 1.61; p = 0.022). The highest death rate was recorded in ARC = 71-76 years (HR = 2.25; p = 0.034). After fitting an RCS to both OS and CSS rates, two overlapping nonlinear trends, with common highest risk values included in ARC = 70-75 years, were observed. Conclusions: Age over 70 years and CCI > 3 were significant factors limiting the survival of RC and should both be considered when comparing current RC outcomes

Challenging Scenarios and Debated Indications for Laparoscopic Liver Resections for Hepatocellular Carcinoma

Simple Summary Minimally invasive liver resections are nowadays performed worldwide for both benign and malignant lesions. Good short-term and safe long-term outcomes have been reported. Despite this growing implementation of the technique, challenging scenarios and debated indications still exist. There is currently a lack of high-quality evidence regarding minimally invasive liver resections in portal hypertension, advanced cirrhosis, lesions in the posterosuperior segments and large and recurrent tumors. Laparoscopic liver resections (LLRs) have been increasingly adopted for the treatment of hepatocellular carcinoma (HCC), with safe short- and long-term outcomes reported worldwide. Despite this, lesions in the posterosuperior segments, large and recurrent tumors, portal hypertension, and advanced cirrhosis currently represent challenging scenarios in which the safety and efficacy of the laparoscopic approach are still controversial. In this systematic review, we pooled the available evidence on the short-term outcomes of LLRs for HCC in challenging clinical scenarios. All randomized and non-randomized studies reporting LLRs for HCC in the above-mentioned settings were included. The literature search was run in the Scopus, WoS, and Pubmed databases. Case reports, reviews, meta-analyses, studies including fewer than 10 patients, non-English language studies, and studies analyzing histology other than HCC were excluded. From 566 articles, 36 studies dated between 2006 and 2022 fulfilled the selection criteria and were included in the analysis. A total of 1859 patients were included, of whom 156 had advanced cirrhosis, 194 had portal hypertension, 436 had large HCCs, 477 had lesions located in the posterosuperior segments, and 596 had recurrent HCCs. Overall, the conversion rate ranged between 4.6% and 15.5%. Mortality and morbidity ranged between 0.0% and 5.1%, and 18.6% and 34.6%, respectively. Full results according to subgroups are described in the study. Advanced cirrhosis and portal hypertension, large and recurrent tumors, and lesions located in the posterosuperior segments are challenging clinical scenarios that should be carefully approached by laparoscopy. Safe short-term outcomes can be achieved provided experienced surgeons and high-volume centers

Definition of the Binding Architecture to a Target Promoter of HP1043, the Essential Master Regulator of Helicobacter pylori

HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (Php1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the Php1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase