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This Perspective summarizes successful fragment-to-lead (F2L) studies that were published in 2023 and is the ninth installment in an annual series. A tabulated summary of the relevant articles published in 2023 is provided (17 entries from 16 articles), and a comparison of the target classes, screening methods, and overall fragment or lead property trends for 2023 examples and for the combined entries over the years 2015-2023 is discussed. In addition, we identify several trends and innovations in the 2023 literature that promise to further increase the success of fragment-based drug discovery (FBDD), particularly in the areas of NMR and virtual screening, fragment library design, and fragment linking.

Tyrosine kinases (TKs) are emerging as important targets in cancer therapy and some of their inhibitors, TKIs ( e.g. imatinib and nilotinib), are FDA-approved drugs that are used as selective anti-cancer therapeutics against cell lines that overexpress TKs. Many examples of metal-based complexes functionalised with TKIs are reported in the literature but very few have been functionalised with platinum. Here we report the design, a detailed computational analysis/simulation, the complete chemical characterisation and the preliminary biological evaluation of two novel Pt(IV) anticancer pro-drugs based on cisplatin tethered with a derivative of either imatinib or nilotinib in the axial position. Pt(IV) complexes are a strategic scaffold in combination therapy due to their axial ligands that can be functionalised to form dual action drugs. The activation by reduction releases the Pt(II) core and the axial ligands upon cellular internalisation. The antiproliferative activity and the TK inhibition properties of the novel adducts are analysed with a theoretical approach and confirmed in vitro with preliminary biological assays.

Considering the importance of the 2019 outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulting in the coronavirus disease 2019 (COVID-19) pandemic, an overview of two proteases that play an important role in the infection by SARS-CoV-2, the main protease of SARS-CoV-2 (M Pro ) and the host transmembrane protease serine 2 (TMPRSS2), is presented in this review. After summarising the viral replication cycle to identify the relevance of these proteases, the therapeutic agents already approved are presented. Then, this review discusses some of the most recently reported inhibitors first for the viral M Pro and next for the host TMPRSS2 explaining the mechanism of action of each protease. Afterward, some computational approaches to design novel M Pro and TMPRSS2 inhibitors are presented, also describing the corresponding crystallographic structures reported so far. Finally, a brief discussion on a few reports found some dual-action inhibitors for both proteases is given. This review provides an overview of two proteases of different origins (viral and human host) that have become important targets for the development of antiviral agents to treat COVID-19.

The rapid development of applications relying on magnetism at the nanoscale has put a spotlight on nanoparticles with novel morphologies that are associated with enhanced electronic and magnetic properties. In this quest, nanoalloys combining highly magnetic cobalt and weakly reactive gold could offer many application-specific advantages, such as strong magnetic anisotropy. In the present study, we have employed density functional theory (DFT) calculations to provide a systematic overview of the size- and morphology-dependence of the energetic order and magnetic properties of AuCo nanoparticles up to 2.5 nm in diameter. The core-shell icosahedron was captured as the most favourable morphology, showing a small preference over the core-shell decahedron. However, the magnetic properties (total magnetic moments and magnetic anisotropy) were found to be significantly improved within the L1 0 ordered structures, even in comparison to monometallic Co nanoparticles. Atom-resolved charges and orbital moments accessed through the DFT analysis of the electronic level properties permitted insight into the close interrelation between the AuCo nanoparticle morphology and their magnetism. These results are expected to assist in the design of tailored magnetic AuCo nanoalloys for specific applications.

Zinc phosphides (ZnP 2 and Zn 3 P 2 ) are emerging absorber materials for photovoltaic applications owing to their abundancy and non-toxic nature. Herein, we provide a comprehensive characterisation of the surface structure, composition, stabilities, morphology, and electronic properties of both bare and hydrated/hydroxylated low-Miller index surfaces of β-ZnP 2 by means of density functional theory (DFT) calculations. Mechanistic insights into the fundamental aspects of water adsorption and dissociation, including the adsorption geometries, energetics, and structural parameters along the reaction path are systematically characterised. The stabilities of the surfaces under dry and wet conditions are discussed in detail and the predicted phase diagrams for the water adsorption are presented. Using calculated surface energies, we have derived the equilibrium morphology of the β-ZnP 2 nanocrystals under vacuum and upon hydration or hydroxylation. Atomic-level insights into the origin of the incipient oxidation of β-ZnP 2 surfaces are provided through analysis of Bader charges, which reveal that the Zn sites to which H 2 O and OH species are bound undergo oxidation due to the transfer of charge to the adsorbed species. Adsorption-induced changes to the electronic properties before and after hydration/hydroxylation were characterised by the work function and partial density of states. The results highlight the need for protection of β-ZnP 2 nanocrystals against possible oxidation in the presence of water through post-synthesis organic functionalisation.

Implementation of magnetic nanoparticles in biomedicine requires their passivation, which often comes at a cost of diminished magnetic properties. For the design of nano-agents with targeted magnetic behaviour, it is important to distinguish between ligands which can improve desired performance, and those that reduce it. Carboxylic acid-, thiol-, and amine-protected cobalt nanoparticles were studied by density functional theory calculations to model the impact of ligand coverage on the magnetic properties. The simulations show that the functional group, arrangement, and coverage density of the ligand coating control both the total magnetic moment and magnetic anisotropy energy of the nanoparticle, as well as the distribution of local spin magnetic moments across the metallic core. Captured effects of ligand binding on the orbital moments of cobalt atoms were insignificant. Out of the three ligand families, only carboxylic acid coatings increased the magnetic moments of cobalt nanoparticles, while amines and thiols quenched them. Calculated anisotropy energies of protected nanoparticles consistently increased with the growing ligand density, reaching the highest values for a 100% coverage of both carboxylic acid and thiol coatings. However, the binding nature of the two functional groups showed opposite impacts on the d-states of interacting cobalt atoms. This study has thus established important principles for the design of biocompatible magnetic nanocomposites, highlighting different routes to achieve desired magnetic behaviour.

The focus of this review is on the physical and magnetic properties that are related to the efficiency of monometallic magnetic nanoparticles used in biomedical applications, such as magnetic resonance imaging (MRI) or magnetic nanoparticle hyperthermia, and how to model these by theoretical methods, where the discussion is based on the example of cobalt nanoparticles. Different simulation systems (cluster, extended slab, and nanoparticle models) are critically appraised for their efficacy in the determination of reactivity, magnetic behaviour, and ligand-induced modifications of relevant properties. Simulations of the effects of nanoscale alloying with other metallic phases are also briefly reviewed.

The promise of biocompatible magnetic nanoparticles with high magnetic saturation in the implementation as drug carriers and hyperthermia agents has generated significant interest in functionalised cobalt nanoparticles. Carboxylic acid coatings on metallic nanoparticles have been shown as an attractive option owing to their respectable stability and biocompatibility. However, only limited information is available on the molecular mechanism leading to the formation of such protective coatings. In this study, ab initio molecular dynamics simulations have been used to unravel the functionalisation mechanism starting from a neutral cobalt cluster and valeric acid molecules. Three stages were detected in the coating process: (i) rapid initial adsorption of acid molecules, (ii) simultaneous adsorption of new molecules and dissociation of those already interacting with the cluster, and, finally, (iii) grouping of dissociated hydrogen atoms and subsequent desorption of acid molecules. The fate of the hydrogen atoms was probed through a combination of static and dynamic ab initio modelling approaches, which predicted H2 generation with favourable energetics. A better understanding of the functionalisation and interaction mechanisms will aid the rational design of biocompatible cobalt nanoparticles for various applications.

Platinum, when used as a cathode material for the oxygen reduction reaction, suffers from high overpotential and possible dissolution, in addition to the scarcity of the metal and resulting cost. Although the introduction of cobalt has been reported to improve reaction kinetics and decrease the precious metal loading, surface segregation or complete leakage of Co atoms causes degradation of the membrane electrode assembly, and either of these scenarios of structural rearrangement eventually decreases catalytic power. Ternary PtCo alloys with noble metals could possibly maintain activity with a higher dissolution potential. First-principles-based theoretical methods are utilized to identify the critical factors affecting segregation in Pt-Co binary and Pt-Co-Au ternary nanoparticles in the presence of oxidizing species. With a decreasing share of Pt, surface segregation of Co atoms was already found to become thermodynamically viable in the PtCo systems at low oxygen concentrations, which is assigned to high charge transfer between species. While the introduction of gold as a dopant caused structural changes that favor segregation of Co, creation of CoAu alloy core is calculated to significantly suppress Co leakage through modification of the electronic properties. The theoretical framework of geometrically different ternary systems provides a new route for the rational design of oxygen reduction catalysts., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

Cobalt nanoparticles with diameters of 8 nm have recently shown promising performance for biomedical applications. However, it is still unclear how the shape of cobalt clusters changes with size when reaching the nanoparticle range. In the present work, density functional theory calculations have been employed to compare the stabilities of two non-crystalline (icosahedron and decahedron) shapes, and three crystalline motifs (hcp, fcc, and bcc) for magic numbered cobalt clusters with up to 1500 atoms, based on the changes in the cohesive energies, coordination numbers, and nearest-neighbour distances arising from varying geometries. Obtained trends were extrapolated to a 10 4 size range, and an icosahedral shape was predicted for clusters up to 5500 atoms. Larger sized clusters adopt hcp stacking, in correspondence with the bulk phase. To explain the crystalline/non-crystalline crossovers, the contributions of the elastic strain density and twin boundary from the specimen surfaces to the cohesive energy of different motifs were evaluated. These results are expected to aid the design and synthesis of cobalt nanoparticles for applications ranging from catalysis to biomedical treatments.

Owing to their high saturation magnetisation, cobalt nanoparticles hold significant potential for the hyperthermia treatment of tumours. Covalent binding of carboxylic acids to the nanoparticles can induce biocompatibility, whilst also preventing the formation of surface oxides which reduce the magnetic properties of cobalt. Understanding the origin of the acid-metal interaction is key, yet probably the most experimentally challenging step, for the rational design of such entities. In this density functional theory study, we use static calculations to establish that a 57-atom Co cluster is the smallest model able to reproduce the adsorption behaviour of carboxylic acids, and ab initio metadynamics to obtain the structure and the free energy landscape for its interaction with valeric acid. Our simulations show that a bridging bidentate binding mode has a stronger affinity compared to monodentate binding, with energetically high transition barriers between the two. A chelate interaction mode of two carboxyl oxygen atoms can be formed as an intermediate. These results clarify the organic-inorganic interactions in the cobalt-acid system, providing a basis for the rational design of biocompatible metallic nanoparticles.

Binary II-V semiconductors are highly optically active materials, possess high intrinsic mechanical and chemical durability, and have electronic properties ideal for optoelectronic applications. Among them, zinc diphosphide (ZnP 2 ) is a promising earth-abundant absorber material for solar energy conversion. We have investigated the structural, mechanical, and optoelectronic properties of both the tetragonal (α) and monoclinic (β) phases of ZnP 2 using standard, Hubbard-corrected and screened hybrid density functional theory methods. Through the analysis of bond character, band gap nature, and absorption spectra, we show that there exist two polymorphs of the β phase (denoted as β 1 and β 2 ) with distinct differences in the photovoltaic potential. While β 1 exhibits the characteristics of metallic compounds, β 2 is a semiconductor with predicted thin-film photovoltaic absorbing efficiency of almost 10%. The α phase is anticipated to be an indirect gap material with a calculated efficiency limited to only 1%. We have also analysed and gained insights into the electron localization function, projected density of states and projected crystal orbital Hamilton populations for the analogue bonds between the α and β-ZnP 2 . In light of these calculations, a number of previous discrepancies have been solved and a solid ground for future employment of zinc diphosphides in photovoltaics has been established.