Iridium(III)-based minor groove binding complexes as DNA photocleavage agents

Transition metal complexes containing the qtpy ligand (2':4,4'':4',4'''-quaterpyridyl) are known to be DNA intercalators or minor groove binders. In this study, new tricationic iridium(III) complexes of qtpy are reported. Both [Ir(bpy)2(qtpy)]3+1 and [Ir(phen)2(qtpy)]3+2 display good water solubility as chloride salts. The complexes possess high-energy excited states, which are quenched in the presence of duplex DNA and even by the mononucleotides guanosine monophosphate and adenosine monophosphate. Further studies reveal that although the complexes bind to quadruplex DNA, they display a preference for duplex structures, which are bound with an order of magnitude higher affinities than their isostructural dicationic RuII-analogues. Detailed molecular dynamics simulations confirm that the complexes are groove binders through the insertion of, predominantly, the qtpy ligand into the minor groove. Photoirradiation of 1 in the presence of plasmid DNA confirms that this class of complexes can function as synthetic photonucleases by cleaving DNA.

Molecular Insights into the Dynamics of Amyloid Fibril Growth: Elongation and Lateral Assembly of GNNQQNY Protofibrils

The self-assembly of peptides and proteins into β-sheet rich amyloid fibrils is linked to both functional and pathological states. In this study, the growth of fibrillar structures of the short peptide GNNQQNY, a fragment from the yeast prion Sup35 protein, was examined. Molecular dynamics simulations were used to study alternative mechanisms of fibril growth, including elongation through binding of monomers as well as fibril self-assembly into larger, more mature structures. It was found that after binding, monomers diffused along preformed fibrils toward the ends, supporting the mechanism of fibril growth via elongation. Lateral assembly of protofibrils was found to occur readily, suggesting that this could be the key to transitioning from isolated fibrils to mature multilayer structures. Overall, the work provides mechanistic insights into the competitive pathways that govern amyloid fibril growth.

Engaging Early-Career Scientists in Global Policy-Making

Pressing global challenges, such as climate change, the COVID-19 pandemic, or antibiotic resistance, require coordinated international responses guided by evidence-informed decisions. For this purpose, it is critical that scientists engage in providing insights during the decision-making process. However, the mechanisms for the engagement of scientists in policy-making are complex and vary internationally, which often poses significant challenges to their involvement. Herein, we address some of the mechanisms and barriers for scientists to engage in policy-making with a global perspective by early-career scientists. We highlight the importance of scientific academies, societies, universities, and early-career networks as stakeholders and how they can adapt their structures to actively contribute to shaping global policies, with representative examples from chemistry-related disciplines. We showcase the importance of raising awareness, providing resources and training, and leading discussions about connecting emerging scientists with global decision-makers to address societal challenges through policies.

Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism

The self-assembly of peptides into supramolecular structures has been linked to neurodegenerative diseases but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly cellular membrane lipids. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of membrane models that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid β (1-40) peptide (Aβ40), linked to Alzheimer's disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While Aβ40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an α-helical conformation compared to Aβ40. Different peptide-to-lipid ratios resulted in different effects. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predicting how cellular changes might impact peptide self-assembly in vivo.

Peptide Self-Assembly into Amyloid Fibrils at Hard and Soft Interfaces-From Corona Formation to Membrane Activity

Peptides and proteins are exposed to a variety of interfaces in a physiological environment, such as cell membranes, protein nanoparticles (NPs), or viruses. These interfaces have a significant impact on the interaction, self-assembly, and aggregation mechanisms of biomolecular systems. Peptide self-assembly, particularly amyloid fibril formation, is associated with a wide range of functions; however, there is a link with neurodegenerative diseases, such as Alzheimer's disease. This review highlights how interfaces affect peptide structure and the kinetics of aggregation leading to fibril formation. In nature, many surfaces are nanostructures, such as liposomes, viruses, or synthetic NPs. Once exposed to a biological medium, nanostructures are coated with a corona, which then determines their activity. Both accelerating and inhibiting effects on peptide self-assembly have been observed. When amyloid peptides adsorb to a surface, they typically concentrate locally, which promotes aggregation into insoluble fibrils. Starting from a combined experimental and theoretical approach, models that allow for a better understanding of peptide self-assembly near hard and soft matter interfaces are introduced and reviewed. Research results from recent years are presented and relationships between biological interfaces, such as membranes and viruses, and amyloid fibril formation are proposed.

Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation

The aggregation of peptides into amyloid fibrils has been linked to ageing-related diseases, such as Alzheimer's and type 2 diabetes. Interfaces, particularly those with large nanostructured surfaces, can affect the kinetics of peptide aggregation, which ranges from complete inhibition to strong acceleration. While a number of physiochemical parameters determine interfacial effects, we focus here on the role of nanoparticle (NP) size and curvature. We used thioflavin T (ThT) fluorescence assays to demonstrate the size-dependent effects of NPs on amyloid fibril formation for the peptides Aβ₄₀, NNFGAIL, GNNQQNY and VQIYVK. While 5 nm gold NPs (AuNP-5) retarded or inhibited the aggregation of all peptides except NNFGAIL, larger 20 nm gold NPs (AuNP-20) tended to accelerate or not influence peptide aggregation. Differences in the NP effects for the peptides resulted from the different peptide properties (size, tendency to aggregate) and associated surface binding affinities. Additional dynamic light scattering (DLS), electron microscopy, and atomic force microscopy (AFM) experiments with the Aβ₄₀ peptide confirmed size-dependent NP effects on peptide aggregation, and also suggested a structural influence on the formed fibrils. NPs can serve as a surface for the adsorption of peptide monomers and enable nucleation to oligomers and fibril formation. However, molecular dynamics (MD) simulations showed that peptide oligomers were less stable at smaller NPs. High surface curvatures destabilized prefibrillar structures, which provides a possible explanation for inhibitory effects on fibril growth, provided that peptide-NP surface binding was relevant for fibril formation. These mechanistic insights can support the design of future nanostructured materials.

Planar 2D wireframe DNA origami

Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo-electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.

ESMO expert consensus statements on the management of EGFR mutant non-small-cell lung cancer

The European Society for Medical Oncology (ESMO) held a virtual consensus-building process on epidermal growth factor receptor (EGFR)-mutant non-small-cell lung cancer in 2021. The consensus included a multidisciplinary panel of 34 leading experts in the management of lung cancer. The aim of the consensus was to develop recommendations on topics that are not covered in detail in the current ESMO Clinical Practice Guideline and where the available evidence is either limited or conflicting. The main topics identified for discussion were: (i) tissue and biomarkers analyses; (ii) early and locally advanced disease; (iii) metastatic disease and (iv) clinical trial design, patient's perspective and miscellaneous. The expert panel was divided into four working groups to address questions relating to one of the four topics outlined above. Relevant scientific literature was reviewed in advance. Recommendations were developed by the working groups and then presented to the entire panel for further discussion and amendment before voting. This manuscript presents the recommendations developed, including findings from the expert panel discussions, consensus recommendations and a summary of evidence supporting each recommendation.

Epidemiology and routine care treatment of patients with hip or knee osteoarthritis and chronic lower back pain: real-world evidence from Germany

Aim

Musculoskeletal disorders are a major public health problem in most developed countries. As a main cause of chronic pain, they have resulted in an increasing prescription of opioids worldwide. With regard to the situation in Germany, this study aimed at estimating the prevalence of musculoskeletal diseases such as chronic low back pain (CLBP) and hip/knee osteoarthritis (OA) and at depicting the applied treatment patterns.

Subject and methods

German claims data from the InGef Research Database were analyzed over a 6-year period (2011–2016). The dataset contains over 4 million people, enrolled in German statutory health insurances. Inpatient and outpatient diagnoses were considered for case identification of hip/knee OA and CLBP. The World Health Organization (WHO) analgesic ladder was applied to categorize patients according to their pain management interventions. Information on demographics, comorbidities, and adjuvant medication was collected.

Results

In 2016, n = 2,693,481 individuals (50.5% female, 49.5% male) were assigned to the study population; 62.5% of them were aged 18–60 years. In 2016, n = 146,443 patients (5.4%) with CLBP and n = 307,256 patients (11.4%) with hip/knee OA were identified. Of those with pre-specified pain management interventions (CLBP: 66.3%; hip/knee OA: 65.1%), most patients received WHO I class drugs (CLBP: 73.6%; hip/knee OA: 68.7%) as the highest level.

Conclusion

This study provides indications that CLBP and hip/knee OA are common chronic pain conditions in Germany, which are often subjected to pharmacological pain management. Compared to non-opioid analgesic prescriptions of the WHO I class, the dispensation of WHO class II and III opioids was markedly lower, though present to a considerable extent.

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

First-line nivolumab plus ipilimumab with two cycles of chemotherapy versus chemotherapy alone (four cycles) in advanced non-small-cell lung cancer: CheckMate 9LA 2-year update

BACKGROUND

To further characterize survival benefit with first-line nivolumab plus ipilimumab with two cycles of chemotherapy versus chemotherapy alone, we report updated data from the phase III CheckMate 9LA trial with a 2-year minimum follow-up.

PATIENTS AND METHODS

Adult patients were treatment naïve, with stage IV/recurrent non-small-cell lung cancer, no known sensitizing EGFR/ALK alterations, and an Eastern Cooperative Oncology Group performance status ≤1. Patients were randomized 1 : 1 to nivolumab 360 mg every 3 weeks plus ipilimumab 1 mg/kg every 6 weeks with two cycles of chemotherapy, or four cycles of chemotherapy. Updated efficacy and safety outcomes are reported, along with progression-free survival (PFS) after next line of treatment (PFS2), treatment-related adverse events (TRAEs) by treatment cycle, and efficacy outcomes in patients who discontinued all treatment components in the experimental arm due to TRAEs.

RESULTS

With a median follow-up of 30.7 months, nivolumab plus ipilimumab with chemotherapy continued to prolong overall survival (OS) versus chemotherapy. Median OS was 15.8 versus 11.0 months [hazard ratio 0.72 (95% confidence interval 0.61-0.86)]; 2-year OS rate was 38% versus 26%. Two-year PFS rate was 20% versus 8%. ORR was 38% versus 25%, respectively; 34% versus 12% of all responses were ongoing at 2 years. Median PFS2 was 13.9 versus 8.7 months. Improved efficacy outcomes in the experimental versus control arm were observed across most subgroups, including by programmed death-ligand 1 and histology. No new safety signals were observed; onset of grade 3/4 TRAEs was mostly observed during the first two treatment cycles in the experimental arm. In patients who discontinued all components of nivolumab plus ipilimumab with chemotherapy treatment due to TRAEs (n = 61) median OS was 27.5 months; 56% of responders had an ongoing response ≥1 year after discontinuation.

CONCLUSIONS

With a 2-year minimum follow-up, nivolumab plus ipilimumab with two cycles of chemotherapy provided durable efficacy benefits over chemotherapy with a manageable safety profile and remains an efficacious first-line treatment of advanced non-small-cell lung cancer.

The Role of Early-Career Chemists in European Policy-Making

Global societal challenges emphasize the importance of collaboration between scientists and policy-makers, while the participation of a diverse group of professionals, including early-career scientists, is critical towards a sustainable future. The European Young Chemists' Network (EYCN) has been actively working with the European Chemical Society (EuChemS) to create a platform for early-career chemists in policy advice. This article comments on the possible roles of scientists in policy-making and provides an overview of relevant initiatives and platforms at the European level that could facilitate involvement. Opportunities for participation in policy advice from the perspective of early-career chemists are discussed and examples of impact are provided, hoping to stimulate further discussions and engagement in policy-making.

Diagnostic Challenges And Clinical Implications For Systemic EBV-Associated T-Cell Lymphoproliferative Disorders Of Childhood

Introduction/Objective

Systemic EBV-associated T-cell lymphoproliferative disorders of childhood (S-EBV-T-LPD) comprise three major forms: EBV-positive hemophagocytic lymphohistiocytosis (EBV-HLH), systemic EBV-positive T- cell lymphoma (S-EBV-TCL), and systemic T-cell chronic active EBV infection (S-T-CAEBV). These disorders are rare in children and young adults in Western countries and are associated with poor outcomes. Frequently patients were treated initially for EBV-HLH and subsequently found to have relapsed/refractory EBV-HLH vs S-EBV-TCL or overt EBV+ TCL, the latter of which requires different therapy than EBV-HLH. We report the clinicopathologic findings of 13 cases, including 8 previously reported. (PMID: 31099136)

Methods

Thirteen cases of S-EBV-T-LPD were identified at Texas Children’s Hospital from 1990 to 2020. Clinicopathologic and relevant laboratory parameters were recorded.

Results

Patients included six females and seven males of Hispanic (n=6), Asian (4), and Caucasian origins (3) ages 1-22 years (median 2). All had fever, hepatosplenomegaly, cytopenias, abnormal EBV serologies, and significantly elevated peripheral blood EBV- DNA load by quantitative PCR. Histologic features were variable ranging from EBV+ T-cell infiltrates with subtle architectural distortion and mild atypia to overt morphologic appearance of lymphoma.

Consistent findings were aberrant T-cell populations identified by immunohistochemistry (n=4) or bone marrow flow cytometry (n=9, 1-50%, mean 16%). Five patients were classified as overt EBV+ TCL with abnormal karyotyping identified in 3. Seven patients had pathology findings indistinguishable between EBV-HLH and S-EBV-TCL and were classified as EBV-HLH/S-EBV-TCL. One patient had S-T-CAEBV. Outcomes were dismal after HLH-directed immuno/chemotherapy protocols with/without bone marrow transplant as only three EBV-HLH/S-EBV-TCL patients were alive at 1.5, 2.5 months, and 9 years follow-up.

Conclusion

This series from North America demonstrate challenges in the diagnosis and management of S-EBV-T- LPD cases. Particularly, EBV-HLH and S-EBV-TCL, which require vastly different treatment strategies, may initially present with overlapping clinicopathological features. Further studies are needed to address clear diagnostic criteria to guide appropriate management.

A Diverse View of Science to Catalyse Change

Valuing diversity leads to scientific excellence, the progress of science and most importantly, it is simply the right thing to do. We can value diversity not only in words, but also in actions.

Growth, Polymorphism, and Spatially Controlled Surface Immobilization of Biotinylated Variants of IAPP21-27 Fibrils

The islet amyloid polypeptide (IAPP) is a regulatory peptide that can aggregate into fibrillar structures associated with type 2 diabetes. In this study, the IAPP_21-27 segment was modified with a biotin linker at the N-terminus (Btn-GNNFGAIL) to immobilize peptide fibrils on streptavidin-coated surfaces. Key residues for fibril formation of the N-terminal biotinylated IAPP_21-27 segment were identified by using an alanine scanning approach combined with molecular dynamics simulations, thioflavin T fluorescence measurements, and scanning electron microscopy. Significant contributions of phenylalanine (F23), leucine (L27), and isoleucine (I26) for the fibrillation of the short peptide segment were identified. The fibril morphologies of the peptide variants differed depending on their primary sequence, ranging from flexible and semiflexible to stiff and crystal-like structures. These insights could advance the design of new functional hybrid bionanomaterials and fibril-engineered surface coatings using short peptide segments. To validate this concept, the biotinylated fibrils were immobilized on streptavidin-coated surfaces under spatial control.

A diverse view of science to catalyse change

Valuing diversity leads to scientific excellence, the progress of science and, most importantly, it is simply the right thing to do. We must value diversity not only in words, but also in actions.

Adsorption of Amyloidogenic Peptides to Functionalized Surfaces Is Biased by Charge and Hydrophilicity

Surfaces are abundant in living systems, such as in the form of cellular membranes, and govern many biological processes. In this study, the adsorption of the amyloidogenic model peptides GNNQQNY, NNFGAIL, and VQIVYK as well as the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5) were studied at low concentrations (100 μM) to different surfaces. The technique of a quartz crystal microbalance with dissipation monitoring (QCM-D) was applied as it enables the monitoring of mass binding to sensors at nanogram sensitivity. Gold-coated quartz sensors were used as unmodified gold surfaces or functionalized with self-assembled monolayers (SAMs) of alkanethiols (terminated as methyl, amino, carboxyl, and hydroxyl) resulting in different adsorption affinities of the peptides. Our objective was to evaluate the underlying role of the nature and feature of interfaces in biological systems which could concentrate peptides and impact or trigger peptide aggregation processes. In overall, the largely hydrophobic peptides adsorbed with preference to hydrophobic or countercharged surfaces. Further, the glycoprotein lubricin (LUB) was tested as an antiadhesive coating. Despite its hydrophilicity, the adsorption of peptides to LUB coated sensors was similar to the adsorption to unmodified gold surfaces, which indicates that some peptides diffused through the LUB layer to reach the underlying gold sensor surface. The LUB protein-antiadhesive is thus more effective as a biomaterial coating against larger biomolecules than small peptides under the conditions used here. This study provides directions toward a better understanding of amyloid peptide adsorption to biologically relevant interfaces, such as cellular membranes.