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1.
Oncoimmunology ; 13(1): 2372886, 2024.
Article in English | MEDLINE | ID: mdl-38952672

ABSTRACT

The randomized METIMMOX trial (NCT03388190) examined if patients with previously untreated, unresectable abdominal metastases from microsatellite-stable (MSS) colorectal cancer (CRC) might benefit from potentially immunogenic, short-course oxaliplatin-based chemotherapy alternating with immune checkpoint blockade (ICB). Three of 38 patients assigned to this experimental treatment had metastases from BRAF-mutant MSS-CRC, in general a poor-prognostic subgroup explored here. The ≥70-year-old females presented with ascending colon adenocarcinomas with intermediate tumor mutational burden (6.2-11.8 mutations per megabase). All experienced early disappearance of the primary tumor followed by complete response of all overt metastatic disease, resulting in progression-free survival as long as 20-35 months. However, they encountered recurrence at previously unaffected sites and ultimately sanctuary organs, or as intrahepatic tumor evolution reflected in the terminal loss of initially induced T-cell clonality in liver metastases. Yet, the remarkable first-line responses to short-course oxaliplatin-based chemotherapy alternating with ICB may offer a novel therapeutic option to a particularly hard-to-treat MSS-CRC subgroup.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols , Colorectal Neoplasms , Immune Checkpoint Inhibitors , Oxaliplatin , Proto-Oncogene Proteins B-raf , Humans , Oxaliplatin/therapeutic use , Oxaliplatin/administration & dosage , Female , Proto-Oncogene Proteins B-raf/genetics , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Immune Checkpoint Inhibitors/therapeutic use , Immune Checkpoint Inhibitors/pharmacology , Aged , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Mutation , Microsatellite Instability/drug effects , Treatment Outcome , Aged, 80 and over
2.
RSC Med Chem ; 15(6): 2037-2044, 2024 Jun 19.
Article in English | MEDLINE | ID: mdl-38911155

ABSTRACT

Functional dyspepsia (FD) is a gastrointestinal disorder characterized by postprandial fullness, upper abdominal bloating, and early satiation. Peripheral acetylcholinesterase (AChE) inhibitors such as acotiamide have shown efficacy in FD treatment, but their limited affinity towards the enzyme has hindered their effectiveness. Conversely, AChE inhibitors developed for Alzheimer's disease have high potency but exhibit strong central activity, making them unsuitable for FD treatment. In this study, we developed potent AChE inhibitors based on a donepezil and a phthalimide scaffold that contain additional amine groups. Our compounds demonstrate IC50 values in the low to mid-nanomolar range. Computational modelling was employed to determine important molecular interactions with AChE. The compounds show low membrane permeability, which indicates a significantly reduced central activity. These findings suggest that the developed inhibitors could potentially serve as promising treatments for functional dyspepsia.

3.
Br J Cancer ; 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-38909137

ABSTRACT

BACKGROUND: Chemotherapy has limited efficacy in advanced digestive high-grade neuroendocrine neoplasms (HG-NEN) and prognosis is dismal. Predictive markers for palliative chemotherapy are lacking, and prognostic markers are limited. METHODS: Digestive HG-NEN patients (n = 229) were prospectively included 2013-2017. Pathological re-assessment revealed 188 neuroendocrine carcinomas (NEC) and 41 neuroendocrine tumours (NET G3). Tumour-DNA was sequenced across 360 cancer-related genes, assessing mutations (mut) and copy number alterations. We linked sequencing results to clinical information and explored potential markers for first-line chemotherapy efficacy and survival. RESULTS: In NEC given cis/carboplatin and etoposide (PE), TP53mut predicted inferior response rate in multivariate analyses (p = 0.009) and no BRAFmut NEC showed response. In overall assessment of PE-treated NEC, no genetic alterations were prognostic for OS. For small-cell NEC, TP53mut were associated with longer OS (p = 0.011) and RB1 deletions predicted lack of immediate-progression (p = 0.003). In non-small cell NEC, APC mut were associated with immediate-progression and shorter PFS (p = 0.008/p = 0.004). For NET G3, ATRXmut, ARID1A- and ERS1 deletions were associated with shorter PFS. CONCLUSION: Correlations between genetic alterations and response/immediate-progression to PE were frequent in NEC but affected PFS or OS only when subdividing for cell-type. The classification of digestive NEC into large- and small-cell seems therefore molecularly and clinically relevant.

4.
J Chem Inf Model ; 64(11): 4485-4499, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38766733

ABSTRACT

With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.


Subject(s)
Nucleic Acid Conformation , Quantum Theory , RNA , Ligands , RNA/chemistry , Models, Molecular , Protons , Drug Design
5.
RSC Med Chem ; 15(5): 1527-1538, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38784459

ABSTRACT

Targeting RNA including viral RNAs with small molecules is an emerging field. The hepatitis C virus internal ribosome entry site (HCV IRES) is a potential target for translation inhibitor development to raise drug resistance mutation preparedness. Using RNA-focused and unbiased molecule libraries, a structure-based virtual screening (VS) by molecular docking and pharmacophore analysis was performed against the HCV IRES subdomain IIa. VS hits were validated by a microscale thermophoresis (MST) binding assay and a Förster resonance energy transfer (FRET) assay elucidating ligand-induced conformational changes. Ten hit molecules were identified with potencies in the high to medium micromolar range proving the suitability of structure-based virtual screenings against RNA-targets. Hit compounds from a 2-guanidino-quinazoline series, like the strongest binder, compound 8b with an EC50 of 61 µM, show low molecular weight, moderate lipophilicity and reduced basicity compared to previously reported IRES ligands. Therefore, it can be considered as a potential starting point for further optimization by chemical derivatization.

6.
Br J Cancer ; 130(12): 1921-1928, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38664577

ABSTRACT

BACKGROUND: We evaluated first-line treatment of metastatic microsatellite-stable colorectal cancer with short-course oxaliplatin-based chemotherapy alternating with immune checkpoint blockade. METHODS: Patients were randomly assigned to chemotherapy (the FLOX regimen; control group) or alternating two cycles each of FLOX and nivolumab (experimental group). Radiographic response assessment was done every eight weeks with progression-free survival (PFS) as the primary endpoint. Cox proportional-hazards regression models estimated associations between PFS and relevant variables. A post hoc analysis explored C-reactive protein as signal of responsiveness to immune checkpoint blockade. RESULTS: Eighty patients were randomised and 38 in each group received treatment. PFS was comparable-control group: median 9.2 months (95% confidence interval (CI), 6.3-12.7); experimental group: median 9.2 months (95% CI, 4.5-15.0). The adjusted Cox model revealed that experimental-group subjects aged ≥60 had significantly lowered progression risk (p = 0.021) with hazard ratio 0.17 (95% CI, 0.04-0.76). Experimental-group patients with C-reactive protein <5.0 mg/L when starting nivolumab (n = 17) reached median PFS 15.8 months (95% CI, 7.8-23.7). One-sixth of experimental-group cases (all KRAS/BRAF-mutant) achieved complete response. CONCLUSIONS: The investigational regimen did not improve the primary outcome for the intention-to-treat population but might benefit small subgroups of patients with previously untreated, metastatic microsatellite-stable colorectal cancer. TRIAL REGISTRATION: ClinicalTrials.gov number, NCT03388190 (02/01/2018).


Subject(s)
Antineoplastic Combined Chemotherapy Protocols , Colorectal Neoplasms , Nivolumab , Oxaliplatin , Humans , Nivolumab/therapeutic use , Nivolumab/administration & dosage , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Oxaliplatin/administration & dosage , Oxaliplatin/therapeutic use , Male , Female , Middle Aged , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Aged , Microsatellite Instability , Progression-Free Survival , Adult , Neoplasm Metastasis , Immune Checkpoint Inhibitors/therapeutic use , Proto-Oncogene Proteins p21(ras)/genetics
7.
Chem Sci ; 14(36): 9827-9837, 2023 Sep 20.
Article in English | MEDLINE | ID: mdl-37736627

ABSTRACT

Microscale Thermophoresis (MST) is a powerful biophysical technique that measures the mobility of biomolecules in response to a temperature gradient, making it useful for investigating the interactions between biological molecules. This study presents a novel methodology for studying RNA-containing samples using non-covalent nucleic acid-sensitive dyes in MST. This "mix-and-measure" protocol uses non-covalent dyes, such as those from the Syto or Sybr series, which lead to the statistical binding of one fluorophore per RNA oligo showing key advantages over traditional covalent labelling approaches. This new approach has been successfully used to study the binding of ligands to RNA molecules (e.g., SAM- and PreQ1 riboswitches) and the identification of modifications (e.g., m6A) in short RNA oligos which can be written by the RNA methyltransferase METTL3/14.

8.
Endocr Relat Cancer ; 30(10)2023 10 01.
Article in English | MEDLINE | ID: mdl-37410378

ABSTRACT

High-grade gastroenteropancreatic (HG-GEP) neuroendocrine neoplasms (NENs) are highly aggressive cancers. The molecular etiology of these tumors remains unclear, and the prevalence of pathogenic germline variants in patients with HG-GEP NENs is unknown. We assessed sequencing data of 360 cancer genes in normal tissue from 240 patients with HG-GEP NENs; 198 patients with neuroendocrine carcinomas (NECs) and 42 with grade 3 neuroendocrine tumors (NET G3). Applying strict criteria, we identified pathogenic germline variants and compared the frequency with previously reported data from 33 different cancer types. We found a recurrent MYOC variant in three patients and a recurrent MUTYH variant in two patients, indicating that these genes may be important underlying risk factors for HG-GEP NENs when mutated. Further, germline variants were found in canonical tumor-suppressor genes, such as TP53, RB1, BRIP1 and BAP1. Overall, we found that 4.5% of patients with NEC and 9.5% of patients with NET G3 carry germline pathogenic or highly likely pathogenic variants. Applying identical criteria for variant classification in silico to mined data from 33 other cancer types, the median percentage of patients carrying pathogenic or highly likely pathogenic variants was 3.4% (range: 0-17%). The patients with NEC and pathogenic germline variants had a median overall survival of 9 months, similar to what is generally expected for metastatic GEP NECs. A patient with NET G3 and pathogenic MUTYH variant had much shorter overall survival than expected. The fraction of HG-GEP NENs with germline pathogenic variants is relatively high, but still <10%, meaning that that germline mutations cannot be the major underlying cause of HG-GEP NENs.


Subject(s)
Carcinoma, Neuroendocrine , Gastrointestinal Neoplasms , Intestinal Neoplasms , Neuroendocrine Tumors , Pancreatic Neoplasms , Stomach Neoplasms , Humans , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Germ-Line Mutation , Gastrointestinal Neoplasms/genetics , Neuroendocrine Tumors/pathology , Carcinoma, Neuroendocrine/pathology , Intestinal Neoplasms/genetics , Intestinal Neoplasms/pathology , Stomach Neoplasms/genetics , Stomach Neoplasms/pathology
9.
BMC Cancer ; 23(1): 650, 2023 Jul 12.
Article in English | MEDLINE | ID: mdl-37438741

ABSTRACT

BACKGROUND: Recent reports have demonstrated that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological attributes of this cell-free mitochondrial DNA (mtDNA) remain insufficiently understood. We used next-generation sequencing to compare plasma EV-derived mtDNA to that of whole blood (WB), peripheral blood mononuclear cells (PBMCs), and formalin-fixed paraffin-embedded (FFPE) tumor tissue from eight rectal cancer patients and WB and fresh-frozen (FF) tumor tissue from eight colon cancer patients. METHODS: Total DNA was isolated before the mtDNA was enriched by PCR with either two primer sets generating two long products or multiple primer sets (for the FFPE tumors), prior to the sequencing. mtDNA diversity was assessed as the total variant number, level of heteroplasmy (mutant mtDNA copies mixed with wild-type copies), variant distribution within the protein-coding genes, and the predicted functional effect of the variants in the different sample types. Differences between groups were compared by paired Student's t-test or ANOVA with Dunnett's multiple comparison tests when comparing matched samples from patients. Mann-Whitney U test was used when comparing differences between the cancer types and patient groups. Pearson correlation analysis was performed. RESULTS: In both cancer types, EV mtDNA presented twice as many variants and had significantly more low-level heteroplasmy than WB mtDNA. The EV mtDNA variants were clustered in the coding regions, and the proportion of EV mtDNA variants that were missense mutations (i.e., estimated to moderately affect the mitochondrial protein function) was significantly higher than in WB and tumor tissues. Nonsense mutations (i.e., estimated to highly affect the mitochondrial protein function) were only observed in the tumor tissues and EVs. CONCLUSION: Taken together, plasma EV mtDNA in CRC patients exhibits a high degree of diversity. TRIAL REGISTRATION: ClinicalTrials.gov: NCT01816607 . Registered 22 March 2013.


Subject(s)
Cell-Free Nucleic Acids , Colonic Neoplasms , Extracellular Vesicles , Genome, Mitochondrial , Humans , Leukocytes, Mononuclear , High-Throughput Nucleotide Sequencing , DNA, Mitochondrial/genetics , Cell-Free Nucleic Acids/genetics , Extracellular Vesicles/genetics , Mitochondrial Proteins
10.
Cancer Immunol Res ; 11(8): 1137-1155, 2023 08 03.
Article in English | MEDLINE | ID: mdl-37309673

ABSTRACT

Intraepithelial lymphocytes (IEL) expressing γδ T-cell receptors (γδTCR) play key roles in elimination of colon cancer. However, the precise mechanisms by which progressing cancer cells evade immunosurveillance by these innate T cells are unknown. Here, we investigated how loss of the Apc tumor suppressor in gut tissue could enable nascent cancer cells to escape immunosurveillance by cytotoxic γδIELs. In contrast with healthy intestinal or colonic tissue, we found that γδIELs were largely absent from the microenvironment of both mouse and human tumors, and that butyrophilin-like (BTNL) molecules, which can critically regulate γδIEL through direct γδTCR interactions, were also downregulated in tumors. We then demonstrated that ß-catenin activation through loss of Apc rapidly suppressed expression of the mRNA encoding the HNF4A and HNF4G transcription factors, preventing their binding to promoter regions of Btnl genes. Reexpression of BTNL1 and BTNL6 in cancer cells increased γδIEL survival and activation in coculture assays but failed to augment their cancer-killing ability in vitro or their recruitment to orthotopic tumors. However, inhibition of ß-catenin signaling via genetic deletion of Bcl9/Bcl9L in either Apc-deficient or mutant ß-catenin mouse models restored Hnf4a, Hnf4g, and Btnl gene expression and γδ T-cell infiltration into tumors. These observations highlight an immune-evasion mechanism specific to WNT-driven colon cancer cells that disrupts γδIEL immunosurveillance and furthers cancer progression.


Subject(s)
Colonic Neoplasms , Intraepithelial Lymphocytes , Mice , Animals , Humans , beta Catenin/genetics , beta Catenin/metabolism , Intraepithelial Lymphocytes/metabolism , Butyrophilins/genetics , Butyrophilins/metabolism , Colonic Neoplasms/genetics , Receptors, Antigen, T-Cell, gamma-delta/genetics , Receptors, Antigen, T-Cell, gamma-delta/metabolism , Tumor Microenvironment
11.
ACS Med Chem Lett ; 14(6): 777-787, 2023 Jun 08.
Article in English | MEDLINE | ID: mdl-37312859

ABSTRACT

The DNA methyltransferase 2 (DNMT2) is an RNA modifying enzyme associated with pathophysiological processes, such as mental and metabolic disorders or cancer. Although the development of methyltransferase inhibitors remains challenging, DNMT2 is not only a promising target for drug discovery, but also for the development of activity-based probes. Here, we present covalent SAH-based DNMT2 inhibitors decorated with a new type of aryl warhead. Based on a noncovalent DNMT2 inhibitor with N-benzyl substituent, the Topliss scheme was followed for optimization. The results showed that electron-deficient benzyl moieties highly increased affinity. By decorating the structures with strong electron-withdrawing moieties and leaving groups, we adjusted the electrophilicity to create covalent DNMT2 inhibitors. A 4-bromo-3-nitrophenylsulfonamide-decorated SAH derivative (80) turned out to be the most potent (IC50 = 1.2 ± 0.1 µM) and selective inhibitor. Protein mass spectrometry confirmed the covalent reaction with the catalytically active cysteine-79.

12.
RSC Med Chem ; 14(5): 969-982, 2023 May 25.
Article in English | MEDLINE | ID: mdl-37252099

ABSTRACT

Understanding different contributions to the binding entropy of ligands is of utmost interest to better predict affinity and the thermodynamic binding profiles of protein-ligand interactions and to develop new strategies for ligand optimization. To these means, the largely neglected effects of introducing higher ligand symmetry, thereby reducing the number of energetically distinguishable binding modes on binding entropy using the human matriptase as a model system, were investigated. A set of new trivalent phloroglucinol-based inhibitors that address the roughly symmetric binding site of the enzyme was designed, synthesized, and subjected to isothermal titration calorimetry. These highly symmetric ligands that can adopt multiple indistinguishable binding modes exhibited high entropy-driven affinity in line with affinity-change predictions.

13.
Int J Mol Sci ; 24(8)2023 Apr 13.
Article in English | MEDLINE | ID: mdl-37108388

ABSTRACT

Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.


Subject(s)
Peptidomimetics , Protease Inhibitors , Protease Inhibitors/pharmacology , Protease Inhibitors/chemistry , Peptidomimetics/pharmacology , Molecular Docking Simulation , Amino Acids/chemistry , Cysteine/metabolism
14.
Front Immunol ; 14: 1170443, 2023.
Article in English | MEDLINE | ID: mdl-37006231

ABSTRACT

Background: Systemic inflammation, diagnostically ascribed by measuring serum levels of the acute phase reactant C-reactive protein (CRP), has consistently been correlated with poor outcomes across cancer types. CRP exists in two structurally and functionally distinct isoforms, circulating pentameric CRP (pCRP) and the highly pro-inflammatory monomeric isoform (mCRP). The aim of this pilot study was to map the pattern of mCRP distribution in a previously immunologically well-defined colon cancer (CC) cohort and explore possible functional roles of mCRP within the tumor microenvironment (TME). Methods: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from 43 stage II and III CC patients, including 20 patients with serum CRP 0-1 mg/L and 23 patients with serum CRP >30 mg/L were immunohistochemically (IHC) stained with a conformation-specific mCRP antibody and selected immune and stromal markers. A digital analysis algorithm was developed for evaluating mCRP distribution within the primary tumors and adjacent normal colon mucosa. Results: mCRP was abundantly present within tumors from patients with high serum CRP (>30 mg/L) diagnostically interpreted as being systemically inflamed, whereas patients with CRP 0-1 mg/L exhibited only modest mCRP positivity (median mCRP per area 5.07‰ (95%CI:1.32-6.85) vs. 0.02‰ (95%CI:0.01-0.04), p<0.001). Similarly, tissue-expressed mCRP correlated strongly with circulating pCRP (Spearman correlation 0.81, p<0.001). Importantly, mCRP was detected exclusively within tumors, whereas adjacent normal colon mucosa showed no mCRP expression. Double IHC staining revealed colocalization of mCRP with endothelial cells and neutrophils. Intriguingly, some tumor cells also colocalized with mCRP, suggesting a direct interaction or mCRP expression by the tumor itself. Conclusion: Our data show that the pro-inflammatory mCRP isoform is expressed in the TME of CC, primarily in patients with high systemic pCRP values. This strengthens the hypothesis that CRP might not only be an inflammatory marker but also an active mediator within tumors.


Subject(s)
C-Reactive Protein , Colonic Neoplasms , Humans , C-Reactive Protein/metabolism , Endothelial Cells/metabolism , Pilot Projects , Colonic Neoplasms/metabolism , Protein Isoforms/metabolism , Tumor Microenvironment
15.
Int J Mol Sci ; 24(7)2023 Mar 24.
Article in English | MEDLINE | ID: mdl-37047081

ABSTRACT

Targeting RNA methyltransferases with small molecules as inhibitors or tool compounds is an emerging field of interest in epitranscriptomics and medicinal chemistry. For two challenging RNA methyltransferases that introduce the 5-methylcytosine (m5C) modification in different tRNAs, namely DNMT2 and NSUN6, an ultra-large commercially available chemical space was virtually screened by physicochemical property filtering, molecular docking, and clustering to identify new ligands for those enzymes. Novel chemotypes binding to DNMT2 and NSUN6 with affinities down to KD,app = 37 µM and KD,app = 12 µM, respectively, were identified using a microscale thermophoresis (MST) binding assay. These compounds represent the first molecules with a distinct structure from the cofactor SAM and have the potential to be developed into activity-based probes for these enzymes. Additionally, the challenges and strategies of chemical space docking screens with special emphasis on library focusing and diversification are discussed.


Subject(s)
Methyltransferases , RNA , Molecular Docking Simulation , RNA, Transfer/chemistry , DNA (Cytosine-5-)-Methyltransferases , tRNA Methyltransferases
16.
J Chem Inf Model ; 63(7): 2218-2225, 2023 04 10.
Article in English | MEDLINE | ID: mdl-36884022

ABSTRACT

AlphaFold2 and RoseTTAfold impress with their high accuracy in protein structure prediction. However, for structure-based virtual screenings, not only the overall structure but especially the binding sites need to be accurately predicted. In this work, the docking performance for 66 targets with known ligands but without experimental structures available in the protein data bank was elucidated. The results suggest that using an experimental surrogate-ligand complex is often superior over homology models, and only at low sequence identity to the closest homologue AlphaFold2 structures show an equal performance. The generally high fluctuation of receiver operating characteristic area under the curve values obtained for different homology models suggests that multiple combinations of docking programs and homology models should be tested prior to prospective virtual screenings, and in some cases post-processing of crude models might be necessary.


Subject(s)
Molecular Docking Simulation , Protein Folding , Ligands , Binding Sites , Proteins/chemistry , Proteins/metabolism , Models, Molecular , Protein Structure, Tertiary
17.
JCO Precis Oncol ; 7: e2200336, 2023 02.
Article in English | MEDLINE | ID: mdl-36753687

ABSTRACT

PURPOSE: Gastroenteropancreatic neuroendocrine carcinomas (GEP-NEC) are rare and have a poor prognosis. Most GEP-NEC are diagnosed with metastatic disease, with only minor biopsies available for molecular diagnostics. We assessed the applicability of liquid biopsies for molecular profiling of GEP-NEC. MATERIALS AND METHODS: We performed massive parallel sequencing of 76 cancer-related genes in circulating tumor DNA from 50 patients with advanced GEP-NEC and compared findings to previous analyses of solid tumor biopsies from the same patients. Plasma samples were collected before therapy, and the median time span between blood and tissue sampling was 25 days. RESULTS: We detected 178 somatic mutations in the liquid biopsies, 127 (71%) were also detected in the solid biopsies, whereas 51 (29%) were unique to the liquid biopsies. In the same 76 genes, we previously detected 199 somatic mutations (single nucleotide variants) in solid biopsies, of which 127 (64%) were also now detected in liquid biopsies. In exploratory subgroup assessments, concordance was higher in patients with liver metastases (P = 1.5 × 10-5) and increasing with level of liver involvement (P = 1.2 × 10-4). The concordance was similar between GEP-NEC with different primary sites, except being lower in esophageal cases (P = .001). Concordance was not associated with tumor mutation burden. Tumor tissue mutations also detected in liquid biopsies was lower for MSI (40%) versus MSS tumors (70%; P = 7.8 × 10-4). We identified potentially targetable mutations in plasma of 26 (52%) of patients with GEP-NEC; nine patients (18%) had potentially targetable mutation detected only in liquid biopsies. CONCLUSION: Liquid biopsy analyses may be an applicable alternative to solid biopsies in GEP-NEC. Liquid biopsies may add additional mutations compared with tumor biopsies alone and could be useful for biomarker assessment in clinical trials for these patients.


Subject(s)
Carcinoma, Neuroendocrine , Pancreatic Neoplasms , Humans , Pancreatic Neoplasms/drug therapy , Carcinoma, Neuroendocrine/drug therapy , Biomarkers, Tumor/genetics , Mutation , Biopsy
18.
Arch Pharm (Weinheim) ; 356(4): e2200518, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36480352

ABSTRACT

Cyclization of small molecules is a widely applied strategy in drug design for ligand optimization to improve affinity, as it eliminates the putative need for structural preorganization of the ligand before binding, or to improve pharmacokinetic properties. In this work, we provide a deeper insight into the binding thermodynamics of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its linear analogs. Characterization of the thermodynamic binding profiles by isothermal titration calorimetry experiments revealed an unfavorable entropy of the macrocycle compared to the open linear reference ligands. Molecular dynamic simulations and X-ray crystal structure analysis indicated only minor benefits from macrocyclization to fixate a favorable conformation, while linear ligands retained some flexibility even in the protein-bound complex structure, possibly explaining the initially surprising effect of a higher entropic penalty for the macrocyclic ligand.


Subject(s)
Zika Virus Infection , Zika Virus , Humans , Zika Virus/metabolism , Ligands , Viral Nonstructural Proteins , Protein Conformation , Structure-Activity Relationship , Serine Endopeptidases/chemistry , Serine Endopeptidases/metabolism , Serine Endopeptidases/pharmacology , Thermodynamics , Protease Inhibitors/pharmacology , Protease Inhibitors/chemistry
19.
Br J Cancer ; 127(12): 2227-2233, 2022 12.
Article in English | MEDLINE | ID: mdl-36229579

ABSTRACT

BACKGROUND: Immune checkpoint blockade (ICB) results in radiologic tumour response dynamics that differ from chemotherapy efficacy measures and require an early signal of clinical utility. METHODS: Previously untreated, unresectable microsatellite-stable (MSS)/mismatch repair-proficient (pMMR) colorectal cancer (CRC) patients were randomly assigned to the oxaliplatin-based Nordic FLOX regimen (control arm) or repeat sequential two FLOX cycles and two ICB cycles (experimental arm). The radiologic response was assessed every 8 weeks. In this post hoc analysis, we explored early target lesion (TL) dynamics as indicator of ICB responsiveness. Progression-free survival (PFS) was the primary endpoint. RESULTS: Using a landmark analysis approach, we categorised experimental-arm patients into ≥10% (N = 19) or <10% (N = 16) TL reduction at the first post-baseline response assessment. Median PFS for the groups was 16.0 (95% confidence interval (CI), 12.3-19.7) and 3.9 months (95% CI, 2.3-5.5), respectively, superior and inferior (both P < 0.01) to the median PFS of 9.8 months (95% CI, 4.9-14.7) for control arm patients (N = 31). CONCLUSIONS: Radiologic TL reduction of ≥10% at the first post-baseline response assessment identified patients with ICB-responsive metastatic MSS/pMMR-CRC. This pragmatic measure may be used to monitor patients in investigational ICB schedules, enabling early treatment adaptation for unresponsive cases. TRIAL REGISTRATION: ClinicalTrials.gov number, NCT03388190 (02/01/2018).


Subject(s)
Colorectal Neoplasms , Immune Checkpoint Inhibitors , Humans , Colorectal Neoplasms/diagnostic imaging , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , DNA Mismatch Repair
20.
Acta Oncol ; 61(10): 1248-1255, 2022 Oct.
Article in English | MEDLINE | ID: mdl-36068730

ABSTRACT

INTRODUCTION: The presence of preoperative systemic inflammatory response (SIR) is an established negative prognostic factor for patients diagnosed with colorectal cancer (CRC). C-reactive protein (CRP) is known to be implicated in detrimental immune responses. The biological differences between right-sided and left-sided CRC are gaining increasing attention. Our aim was to analyse the prognostic value of CRP and explore the association between tumour location and SIR. MATERIAL AND METHODS: A total of 2059 patients treated for stage I-III CRC, identified from the prospectively sampled ScotScan Collaborative dataset, were included. The clinical and prognostic value of five CRP levels (<10/11-30/31-60/61-100/>100 mg/l) were examined. Additionally, the relationship between SIR and tumour location was explored. RESULTS: Increasing levels of CRP were associated with impaired overall and cancer-specific outcome. Presence of SIR was independently associated with right-sided tumour location (p<0.001). However, the impact of SIR on cancer-specific survival (CSS) was greater for left-sided tumour location, even when adjusted for other clinicopathological factors. CONCLUSIONS: This study confirms CRP as a routinely available, valid, and clinically relevant strong prognostic marker of SIR in CRC patients. Right-sided tumours were more often associated with SIR, but the prognostic impact was stronger in left-sided tumours.


Subject(s)
C-Reactive Protein , Colorectal Neoplasms , Humans , C-Reactive Protein/analysis , Colorectal Neoplasms/pathology , Prognosis
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