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Surgical management of colon cancer in ulcerative colitis patients with orthotopic liver transplant for primary sclerosing cholangitis. A systematic review. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2023; 49:106922. [PMID: 37210276 DOI: 10.1016/j.ejso.2023.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/13/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
INTRODUCTION Colon cancer in ulcerative colitis patients with liver transplant (UCCOLT) due to primary sclerosing cholangitis carries significant treatment challenges. Aim of this literature search is to review management strategies and provide a framework to facilitate the decisional process in this clinical setting. METHODS PRISMA-compliant systematic search was followed by critical expert commentary of the results and development of a surgical management algorithm. Endpoints included surgical management, operative strategies, functional and survival outcomes. Technical and strategics aspects with particular regard to the choice of reconstruction were evaluated to tentatively develop an integrated algorithm. RESULTS Ten studies reporting treatment of 20 UCCOLT patients were identified after screening. Nine patients underwent proctocolectomy and end-ileostomy (PC) and eleven had restorative ileal pouch-anal anastomosis (IPAA). Reported results for perioperative outcomes, oncological outcomes, and graft loss were comparable for both procedures. There were no reports of subtotal colectomies and ileo-rectal anastomosis (IRA). CONCLUSIONS Literature in the field is scarce and decision-making is particularly complex. PC and IPAA have been reported with good results. Nevertheless, IRA may also be considered in UCCOLT patients in selected cases, reducing the risks of sepsis, OLT and pouch failure; furthermore, in young patients, it has the advantage of preserving fertility or sexual function. The proposed treatment algorithm may represent a valuable support in guiding surgical strategy.
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Strigolactones as Broad-Spectrum Antivirals against β-Coronaviruses through Targeting the Main Protease M pro. ACS Infect Dis 2023; 9:1310-1318. [PMID: 37358826 DOI: 10.1021/acsinfecdis.3c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
The current SARS-CoV-2 pandemic and the likelihood that new coronavirus strains will emerge in the immediate future point out the urgent need to identify new pan-coronavirus inhibitors. Strigolactones (SLs) are a class of plant hormones with multifaceted activities whose roles in plant-related fields have been extensively explored. Recently, we proved that SLs also exert antiviral activity toward herpesviruses, such as human cytomegalovirus (HCMV). Here we show that the synthetic SLs TH-EGO and EDOT-EGO impair β-coronavirus replication including SARS-CoV-2 and the common cold human coronavirus HCoV-OC43. Interestingly, in silico simulations suggest the binding of SLs in the SARS-CoV-2 main protease (Mpro) active site, and this was further confirmed by an in vitro activity assay. Overall, our results highlight the potential efficacy of SLs as broad-spectrum antivirals against β-coronaviruses, which may provide the rationale for repurposing this class of hormones for the treatment of COVID-19 patients.
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Targeting protein-protein interactions with low molecular weight and short peptide modulators: insights on disease pathways and starting points for drug discovery. Expert Opin Drug Discov 2023:1-16. [PMID: 37246811 DOI: 10.1080/17460441.2023.2218641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
INTRODUCTION Protein-protein interactions (PPIs) have been often considered undruggable targets although they are attractive for the discovery of new therapeutics. The spread of artificial intelligence and machine learning complemented with experimental methods is likely to change the perspectives of protein-protein modulator research. Noteworthy, some novel low molecular weight (LMW) and short peptide modulators of PPIs are already in clinical trials for the treatment of relevant diseases. AREAS COVERED This review focuses on the main molecular properties of protein-protein interfaces and on key concepts pertaining to the modulation of PPIs. The authors survey recently reported state-of-the-art methods dealing with the rational design of PPI modulators and highlight the role of several computer-based approaches. EXPERT OPINION Interfering specifically with large protein interfaces is still an open challenge. The initial concerns about the unfavorable physicochemical properties of many of these modulators are nowadays less acute with several molecules lying beyond the rule of 5, orally available and successful in clinical trials. As the cost of biologics interfering with PPIs is very high, it would seem reasonable to put more effort, both in academia and the private sectors, on actively developing novel low molecular weight compounds and short peptides to perform this task.
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Influence of COVID-19 Pandemic on Colorectal Cancer Presentation, Management and Outcome during the COVID-19 Pandemic. J Clin Med 2023; 12:jcm12041425. [PMID: 36835958 PMCID: PMC9962694 DOI: 10.3390/jcm12041425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
The aim of the study was to investigate whether the COVID-19 pandemic and related measures had an influence on colorectal cancer (CRC) presentation, management, and outcomes; it was a retrospective monocentric study. CRC patients undergoing surgery during the COVID-19 pandemic (1 March 2020-28 February 2022) (group B) were compared with patients operated on in the previous two years (1 March 2018-29 February 2020) in the same unit (group A). The primary outcome was to investigate whether there were differences in concern regarding the stage at presentation, as a whole and after dividing groups based on cancer location (right colon cancer, left colon cancer, rectal cancer). Secondary outcomes included differences in the number of patients admitted from emergency departments and emergency surgeries between periods, and differences in the postoperative outcomes. A subanalysis within the pandemic group was conducted on the same outcomes, dividing the aforementioned group based on pandemic trends. Two hundred and eighty (280) were operated on during the study period: 147 in group A and 133 in group B. Stage at presentation was similar between groups; however, the subgroups analysis showed that in the pandemic group, the number of early-stage left colon cancer occurrences almost halves, yet not significantly. Emergency department referral was more common in group B (p-value: 0.003); in group B, they also had longer operations and there was a more frequent use of ostomy. No differences in the number of postoperative complications nor in the postoperative outcomes were found. Patients with CRC were more frequently referred through the emergency department during the COVID-19 pandemic and left-sided cancers appear to be generally diagnosed at a more advanced stage. Postoperative outcomes showed that high specialized colorectal units can deliver standard high-level treatment under high-pressure external conditions.
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ELIOT: A platform to navigate the E3 pocketome and aid the design of new PROTACs. Chem Biol Drug Des 2023; 101:69-86. [PMID: 35857806 DOI: 10.1111/cbdd.14123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 12/15/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) are novel therapeutics for the treatment of human disease. They exploit the enormous potential of the E3 ligases, a class of proteins that mark a target protein for degradation via the ubiquitin-proteasome system. Despite the existence of several E3 ligase-related databases, the choice of the functioning ligase is limited to only 1.6% of those available, probably due to the fragmentary understanding of their structures and their known ligands; in fact, none of the existing databases report detailed studies covering their 3D structure or their pockets. Here, we report ELIOT (E3 LIgase pocketOme navigaTor), an accurate and complete platform containing the E3 ligase pocketome to enable navigation and selection of new E3 ligases and new ligands for the design of new PROTACs. All E3 ligase pockets were characterized with innovative 3D descriptors including their PROTAC-ability score, and similarity analyses between E3 pockets are presented. Tissue specificity and their degree of involvement in patients with specific cancer types are also annotated for each E3 ligase, enabling appropriate selection for the design of a PROTAC with improved specificity. All data are available at https://eliot.moldiscovery.com.
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An Integrated Machine Learning Model To Spot Peptide Binding Pockets in 3D Protein Screening. J Chem Inf Model 2022; 62:6812-6824. [PMID: 36320100 DOI: 10.1021/acs.jcim.2c00583] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The prediction of peptide-protein binding sites is of utmost importance to tackle the onset of severe neurodegenerative diseases and cancer. In this work, we detail a novel machine learning model based on Linear Discriminant Analysis (LDA) demonstrating to be highly predictive in detecting the putative protein binding regions of small peptides. Starting from 439 high-quality pockets derived from peptide-protein crystallographic complexes, three sets of well-established peptide-binding regions were first selected through a Partitioning Around Medoids (PAM) clustering algorithm based on morphological and energetic 3D GRID-MIF molecular descriptors. Next, the best combination between all the putative interacting peptide pockets and related GRID-MIF scores was automatically explored by using the LDA-based protocol implemented in BioGPS. This approach proved successful to recognize the actual interacting peptide regions (that is, AUC = 0.86 and partial ROC enrichment at 5% of 0.48) from all the other pockets of the protein. Validated on two external collections sets, including 445 and 347 crystallographic peptide-protein complexes, our LDA-based model could be effective to further run peptide-protein virtual screening campaigns.
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Discovery of a new class of triazole based inhibitors of acetyl transferase KAT2A. J Enzyme Inhib Med Chem 2022; 37:1987-1994. [PMID: 35880250 PMCID: PMC9331200 DOI: 10.1080/14756366.2022.2097447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
We have recently developed a new synthetic methodology that provided both N-aryl-5-hydroxytriazoles and N-pyridine-4-alkyl triazoles. A selection of these products was carried through virtual screening towards targets that are contemporary and validated for drug discovery and development. This study determined a number of potential structure target dyads of which N-pyridinium-4-carboxylic-5-alkyl triazole displayed the highest score specificity towards KAT2A. Binding affinity tests of abovementioned triazole and related analogs towards KAT2A confirmed the predictions of the in-silico assay. Finally, we have run in vitro inhibition assays of selected triazoles towards KAT2A; the ensemble of binding and inhibition assays delivered pyridyl-triazoles carboxylates as the prototype of a new class of inhibitors of KAT2A.
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Exploring Ligand Binding Domain Dynamics in the NRs Superfamily. Int J Mol Sci 2022; 23:ijms23158732. [PMID: 35955864 PMCID: PMC9369052 DOI: 10.3390/ijms23158732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Nuclear receptors (NRs) are transcription factors that play an important role in multiple diseases, such as cancer, inflammation, and metabolic disorders. They share a common structural organization composed of five domains, of which the ligand-binding domain (LBD) can adopt different conformations in response to substrate, agonist, and antagonist binding, leading to distinct transcription effects. A key feature of NRs is, indeed, their intrinsic dynamics that make them a challenging target in drug discovery. This work aims to provide a meaningful investigation of NR structural variability to outline a dynamic profile for each of them. To do that, we propose a methodology based on the computation and comparison of protein cavities among the crystallographic structures of NR LBDs. First, pockets were detected with the FLAPsite algorithm and then an "all against all" approach was applied by comparing each pair of pockets within the same sub-family on the basis of their similarity score. The analysis concerned all the detectable cavities in NRs, with particular attention paid to the active site pockets. This approach can guide the investigation of NR intrinsic dynamics, the selection of reference structures to be used in drug design and the easy identification of alternative binding sites.
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19 disease, has rapidly imposed an urgent need to identify effective drug candidates. In this context, the high resolution and non-redundant beta-Coronavirus protein cavities database is pivotal to help virtual screening protocols. Furthermore, the cross-relationship among cavities can lead to highlighting multitarget therapy chances. Here, we first collect all protein cavities on SARS-CoV-2, SARS-CoV, and MERS-CoV X-ray structures, and then, we compute a similarity map by using molecular interaction fields (MIFs). All the results come together in CROMATIC (CROss-relationship MAp of CaviTIes from Coronaviruses). CROMATIC encloses both a comprehensive and a non-redundant version of the cavities collection and a similarity map revealing, on the one hand, cavities that are conserved among the three Coronaviruses and, on the other hand, unexpected similarities among cavities that can represent a key starting point for multitarget therapy strategies. Similarity analysis was also performed for the available structures of SARS-CoV-2 spike variants, linking sequence mutations to three-dimensional interaction alterations. The CROMATIC repository is freely available to the scientific community at https://github.com/moldiscovery/sars-cromatic.
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Getting Insights into Structural and Energetic Properties of Reciprocal Peptide-Protein Interactions. J Chem Inf Model 2022; 62:1113-1125. [PMID: 35148095 DOI: 10.1021/acs.jcim.1c01343] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptide-protein interactions play a key role for many cellular and metabolic processes involved in the onset of largely spread diseases such as cancer and neurodegenerative pathologies. Despite the progress in the structural characterization of peptide-protein interfaces, the in-depth knowledge of the molecular details behind their interactions is still a daunting task. Here, we present the first comprehensive in silico morphological and energetic study of peptide binding sites by focusing on both peptide and protein standpoints. Starting from the PixelDB database, a nonredundant benchmark collection of high-quality 3D crystallographic structures of peptide-protein complexes, a classification analysis of the most representative categories based on the nature of each cocrystallized peptide has been carried out. Several interpretable geometrical and energetic descriptors have been computed both from peptide and target protein sides in the attempt to unveil physicochemical and structural causative correlations. Finally, we investigated the most frequent peptide-protein residue pairs at the binding interface and made extensive energetic analyses, based on GRID MIFs, with the aim to study the peptide affinity-enhancing interactions to be further exploited in rational drug design strategies.
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Indomethacin-based PROTACs as pan-coronavirus antiviral agents. Eur J Med Chem 2021; 226:113814. [PMID: 34534839 PMCID: PMC8416298 DOI: 10.1016/j.ejmech.2021.113814] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 11/29/2022]
Abstract
Indomethacin (INM), a well-known non-steroidal anti-inflammatory drug, has recently gained attention for its antiviral activity demonstrated in drug repurposing studies against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Although the mechanism of action of INM is not yet fully understood, recent studies have indicated that it acts at an early stage of the coronaviruses (CoVs) replication cycle. In addition, a proteomic study reported that the anti-SARS-CoV-2 activity of INM could be also ascribed to its ability to inhibit human prostaglandin E synthase type 2 (PGES-2), a host protein which interacts with the SARS-CoV-2 NSP7 protein. Although INM does not potently inhibit SARS-CoV-2 replication in infected Vero E6 cells, here we have explored for the first time the application of the Proteolysis Targeting Chimeras (PROTACs) technology in order to develop more potent INM-derived PROTACs with anti-CoV activity. In this study, we report the design, synthesis, and biological evaluation of a series of INM-based PROTACs endowed with antiviral activity against a panel of human CoVs, including different SARS-CoV-2 strains. Two PROTACs showed a strong improvement in antiviral potency compared to INM. Molecular modelling studies support human PGES-2 as a potential target of INM-based antiviral PROTACs, thus paving the way toward the development of host-directed anti-CoVs strategies. To the best of our knowledge, these PROTACs represent the first-in-class INM-based PROTACs with antiviral activity and also the first example of the application of PROTACs to develop pan-coronavirus agents.
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Abstract
In the nineteenth century the idea of a correct surgical approach in oncologic surgery moved towards a good lymphadenectomy. In colon cancer the segment is removed with adjacent mesentery, in gastric cancer or pancreatic cancer a good oncologic resection is obtained with adequate lymphadenectomy. Many guidelines propose a minimal lymph node count that the surgeon must obtain. Therefore, it is essential to understand the adequate extent of lymphadenectomy to be performed in cancer surgery. In this review of the current literature, the focus is on "central vascular ligation", understood as radical lymphadenectomy in upper and lower gastrointestinal cancer, the evolution of this approach during the years and the improvement of laparoscopic techniques. For what concerns laparoscopic surgery, the main goal is to minimize post-operative trauma introducing the "less is more" concept whilst preserving attention for oncological outcomes. This review will demonstrate the importance of a scientifically based standardization of oncologic gastrointestinal surgery, especially in relation to the expansion of minimally invasive surgery and underlines the importance to further investigate through new randomized trials the role of extended lymphadenectomy in the new era of a multimodal approach, and most importantly, an era where minimally invasive techniques and the idea of "less is more" are becoming the standard thought for the surgical approach.
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Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase. J Chem Inf Model 2021; 61:2706-2719. [PMID: 34061520 DOI: 10.1021/acs.jcim.1c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stress testing is one of the most important parts of the drug development process, helping to foresee stability problems and to identify degradation products. One of the processes involving stress testing is represented by forced degradation studies, which can predict the impact of certain conditions of pH, moisture, heat, or other negative effects due to transportation or packaging issues on drug potency and purity, ensuring patient safety. Regulatory agencies have been working on a standardization of laboratory procedures since the past two decades. One of the results of those years of intensive research is the International Conference on Harmonization (ICH) guidelines, which clearly define which forced degradation studies should be performed on new drugs, which become a routine work in pharmaceutical laboratories. Since used techniques based on high-performance liquid chromatography coupled with high-resolution mass spectrometry have been developed years ago and are now mastered by pharmaceutical scientists, automation of data analysis, and thus data processing, is becoming a hot topic nowadays. In this work, we present MassChemSite and WebChembase as a tandem to automatize the routine analysis studies without missing information quality, using as a case study the degradation of lansoprazole under acidic, oxidative, basic, and neutral stress conditions.
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Abstract
INTRODUCTION Hospital centralization effect is reported to lower complications and mortality for high risk and complex surgery operations, including colorectal surgery. However, no linear relation between volume and outcome has been demonstrated. Aim of the study was to evaluate the increased surgical volume effect on early outcomes of patient undergoing laparoscopic restorative anterior rectal resection (ARR). METHODS A retrospective analysis of all consecutive patients undergoing ARR with primary anastomosis between November 2016 and December 2020 after centralization of rectal cancer cases in an academic Centre. Short-term outcomes are compared to those of patients operated in the same unit during the previous 10 years before service centralization. The primary outcome was estimated anastomotic leak rate. Mean operative time, need of conversion, postoperative use of blood transfusion, radicality, in-hospital stay, number and type of complications, readmission and reoperation rate, mortality and 1-year and stoma persistence rates were evaluated as secondary outcomes. RESULTS 86 patients were operated in the study period and outcomes compared to those of 101 patients operated during the previous ten years. Difference in volume of surgery was significant between the two periods (p 0.019) and the estimated leak rate was significantly lower in the higher volume unit (p 0.047). Mean operative time, need of conversion, postoperative use of blood transfusion and in-hospital stay (p < 0.05) were also significantly reduced in Group A. CONCLUSION This study suggests that the shift toward higher volume in rectal cancer surgery is associated to decreased anastomotic leak rate. Potentiation of lower volume surgical units may yield optimal perioperative outcomes.
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Abstract
Non-structural protein 9 (Nsp9) plays a key role in viral replication of coronavirus and represents a promising target for anti-SARS-CoV-2 strategies.
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Abstract
Chron’s Disease is a chronic inflammatory intestinal disease, first described at the beginning of the last century. The disease is characterized by the alternation of periods of flares and remissions influenced by a complex pathogenesis in which inflammation plays a key role. Crohn’s disease evolution is mediated by a complex alteration of the inflammatory response which is characterized by alterations of the innate immunity of the intestinal mucosa barrier together with a remodeling of the extracellular matrix through the expression of metalloproteins and increased adhesion molecules expression, such as MAcCAM-1. This reshaped microenvironment enhances leucocytes migration in the sites of inflammation, promoting a TH1 response, through the production of cytokines such as IL-12 and TNF-α. IL-12 itself and IL-23 have been targeted for the medical treatment of CD. Giving the limited success of medical therapies, the treatment of the disease is invariably surgical. This review will highlight the role of inflammation in CD and describe the surgical approaches for the prevention of the almost inevitable recurrence.
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Impact of asymptomatic COVID-19 patients in global surgical practice during the COVID-19 pandemic. Br J Surg 2020; 107:e364-e365. [PMID: 32767367 PMCID: PMC7929295 DOI: 10.1002/bjs.11800] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 02/05/2023]
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Mid-transverse colon cancer and extended versus transverse colectomy: Results of the Italian society of surgical oncology colorectal cancer network (SICO CCN) multicenter collaborative study. Eur J Surg Oncol 2020; 46:1683-1688. [PMID: 32220542 DOI: 10.1016/j.ejso.2020.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Transverse colon cancer (TCC) is poorly studied, and TCC cases are often excluded from large prospective randomized trials because of their complexity and their potentially high complication rate. The best surgical approach for TCC has yet to be established. The aim of this large retrospective multicenter Italian series is to investigate the advantages and disadvantages of both hemicolectomy and transverse colectomy in order to identify the best surgical approach. MATERIALS AND METHODS This was a retrospective cohort study of patients with mid-transverse colon cancer treated with a segmental colon resection or an extended hemicolectomy (right or left) between 2006 and 2016 in 28 high-volume (more than 70 procedures/year) Italian referral centers for colorectal surgery. RESULTS The study included 1529 patients, 388 of whom underwent a segmental resection while 1141 underwent an extended resection. A higher number of complications has been reported in the segmental group than in the extended group (30.1% versus 23.6%; p 0.010). In 42 cases the main complication was the anastomotic leak (4.4% versus 2.2%; p 0.020). Recovery outcomes also showed statistical differences: time to first flatus (p 0.014), time to first mobilization (p 0.040), and overall hospital stay (p < 0.001) were significantly shorter in the extended group. Even if overall survival were similar between the groups (95.1% versus 97%; p 0.384), 3-year disease-free survival worsened after segmental resection (78.1% versus 86.2%; p 0.001). CONCLUSIONS According to our results, an extended right colon resection for TCC seems to be surgically safer and more oncologically valid.
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Bisphenol A binding promiscuity: A virtual journey through the universe of proteins. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION 2019; 37:85-94. [PMID: 31707420 DOI: 10.14573/altex.1906141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/23/2019] [Indexed: 11/23/2022]
Abstract
Significant efforts are currently being made to move toxicity testing from animal experimentation to human relevant, mechanism-based approaches. In this context, the identification of molecular target(s) responsible for mechanisms of action is an essential step. Inspired by the recent concept of polypharmacology (the ability of drugs to interact with multiple targets) we argue that whole proteome virtual screening might become a breakthrough tool in toxicology reflecting the real complexity of chemical-biological interactions. Therefore, we investigated the value of performing ligand-protein binding prediction screening across the full proteome to identify new mechanisms of action for food chemicals. We applied the new approach to make a broader comparison between bisphenol A (BPA) (food-packaging chemical) and the endogenous estrogen, 17β-estradiol (EST). Applying a novel high-throughput ligand-protein binding prediction tool (BioGPS) by the Amazon Web Services (AWS) cloud (to speed-up the calculation), we investigated the value of performing in silico screening across the full proteome (all human and rodent x-ray protein structures available in the Protein Data Bank). The strong correlation between in silico predictions and available in vitro data demonstrates the high predictive power of the method used. The most striking results obtained was that BPA was predicted to bind to many more proteins than the ones already known, most of which were common to EST. Our findings provide a new and unprecedented insight on the complexity of chemical-protein interactions, highlighting the binding promiscuity of BPA and its broader similarity compared to the female sex hormone, EST.
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Abstract
Virtual screening represents an effective computational strategy to rise-up the chances of finding new bioactive compounds by accelerating the time needed to move from an initial intuition to market. Classically, the most pursued approaches rely on ligand- and structure-based studies, the former employed when structural data information about the target is missing while the latter employed when X-ray/NMR solved or homology models are instead available for the target. The authors will focus on the most advanced techniques applied in this area. In particular, they will survey the key concepts of virtual screening by discussing how to properly select chemical libraries, how to make database curation, how to applying and- and structure-based techniques, how to wisely use post-processing methods. Emphasis will be also given to the most meaningful databases used in VS protocols. For the ease of discussion several examples will be presented.
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Detecting similar binding pockets to enable systems polypharmacology. PLoS Comput Biol 2017; 13:e1005522. [PMID: 28662117 PMCID: PMC5490940 DOI: 10.1371/journal.pcbi.1005522] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 04/15/2017] [Indexed: 01/19/2023] Open
Abstract
In the era of systems biology, multi-target pharmacological strategies hold promise for tackling disease-related networks. In this regard, drug promiscuity may be leveraged to interfere with multiple receptors: the so-called polypharmacology of drugs can be anticipated by analyzing the similarity of binding sites across the proteome. Here, we perform a pairwise comparison of 90,000 putative binding pockets detected in 3,700 proteins, and find that 23,000 pairs of proteins have at least one similar cavity that could, in principle, accommodate similar ligands. By inspecting these pairs, we demonstrate how the detection of similar binding sites expands the space of opportunities for the rational design of drug polypharmacology. Finally, we illustrate how to leverage these opportunities in protein-protein interaction networks related to several therapeutic classes and tumor types, and in a genome-scale metabolic model of leukemia. Traditionally, the fact that most drugs are promiscuous binders has been a major concern in pharmacology, due to the occurrence of undesired off-target clinical events. In the recent years, however, the realization that many diseases are the result of complex biological processes has encouraged rethinking of drug promiscuity as a promising feature, since it is sometimes necessary to interfere with multiple receptors in order to overcome the robustness of disease-related networks. One way to identify groups of proteins that could be targeted simultaneously is to look for similar binding sites. We have massively done so for all human proteins with a known high-resolution three-dimensional structure, unveiling a vast space of ‘polypharmacology’ opportunities. Of these, we know, a great majority is not of therapeutic interest. To pinpoint promising multi-target combinations, we advocate for the use of computational tools that are able to rapidly simulate the effect of drug-target interactions on biological networks.
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Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case. ChemMedChem 2016; 11:1653-66. [PMID: 27404817 DOI: 10.1002/cmdc.201600121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/08/2016] [Indexed: 12/14/2022]
Abstract
Repurposing and repositioning drugs has become a frequently pursued and successful strategy in the current era, as new chemical entities are increasingly difficult to find and get approved. Herein we report an integrated BioGPS/FLAPdock pipeline for rapid and effective off-target identification and drug repurposing. Our method is based on the structural and chemical properties of protein binding sites, that is, the ligand image, encoded in the GRID molecular interaction fields (MIFs). Protein similarity is disclosed through the BioGPS algorithm by measuring the pockets' overlap according to which pockets are clustered. Co-crystallized and known ligands can be cross-docked among similar targets, selected for subsequent in vitro binding experiments, and possibly improved for inhibitory potency. We used human thymidylate synthase (TS) as a test case and searched the entire RCSB Protein Data Bank (PDB) for similar target pockets. We chose casein kinase IIα as a control and tested a series of its inhibitors against the TS template. Ellagic acid and apigenin were identified as TS inhibitors, and various flavonoids were selected and synthesized in a second-round selection. The compounds were demonstrated to be active in the low-micromolar range.
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Exploring Basic Tail Modifications of Coumarin-Based Dual Acetylcholinesterase-Monoamine Oxidase B Inhibitors: Identification of Water-Soluble, Brain-Permeant Neuroprotective Multitarget Agents. J Med Chem 2016; 59:6791-806. [DOI: 10.1021/acs.jmedchem.6b00562] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1462-71. [PMID: 25839357 DOI: 10.1016/j.bbamem.2015.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/26/2015] [Accepted: 03/23/2015] [Indexed: 11/30/2022]
Abstract
Neuromyelitis optica (NMO) is a multiple sclerosis-like immunopathology disease affecting optic nerves and the spinal cord. Its pathological hallmark is the deposition of a typical immunoglobulin, called NMO-IgG, against the water channel Aquaporin-4 (AQP4). Preventing NMO-IgG binding would represent a valuable molecular strategy for a focused NMO therapy. The recent observation that aspartate in position 69 (D69) is determinant for the formation of NMO-IgG epitopes prompted us to carry out intensive Molecular Dynamics (MD) studies on a number of single-point AQP4 mutants. Here, we report a domino effect originating from the point mutation at position 69: we find that the side chain of T62 is reoriented far from its expected position leaning on the lumen of the pore. More importantly, the strength of the H-bond interaction between L53 and T56, at the basis of the loop A, is substantially weakened. These events represent important pieces of a clear-cut mechanistic rationale behind the failure of the NMO-IgG binding, while the water channel function as well as the propensity to aggregate into OAPs remains unaltered. The molecular interaction fields (MIF)-based analysis of cavities complemented MD findings indicating a putative binding site comprising the same residues determining epitope reorganization. In this respect, docking studies unveiled an intriguing perspective to address the future design of small drug-like compounds against NMO. In agreement with recent experimental observations, the present study is the first computational attempt to elucidate NMO-IgG binding at the molecular level, as well as a first effort toward a less elusive AQP4 druggability.
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BioGPS: Navigating biological space to predict polypharmacology, off-targeting, and selectivity. Proteins 2015; 83:517-32. [DOI: 10.1002/prot.24753] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 12/09/2014] [Accepted: 12/13/2014] [Indexed: 12/12/2022]
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BioGPS: The Music for the Chemo- and Bioinformatics Walzer. Mol Inform 2014; 33:446-53. [DOI: 10.1002/minf.201400028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/19/2014] [Indexed: 01/09/2023]
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From student to professional nurse. THE CANADIAN NURSE 1996; 92:55-6. [PMID: 8788335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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