Synthetic Access Research Articles

Synthesis of α-Hydroxy-1,2,3-Triazole-linked Sialyltransferase Inhibitors and Evaluation of Selectivity Towards ST3GAL1, ST6GAL1 and ST8SIA2.

Tumour-derived sialoglycans, bearing the charged nonulosonic sugar sialic acid at their termini, play a critical role in tumour cell adhesion and invasion, as well as evading cell death and immune surveillance. Sialyltransferases (ST), the enzymes responsible for the biosynthesis of sialylated glycans, are highly upregulated in cancer, with tumour hypersialylation strongly correlated with tumour growth, metastasis and drug resistance. As a result, desialylation of the tumour cell surface using either targeted delivery of a pan-ST inhibitor (or sialidase) or systemic delivery of a non-toxic selective ST inhibitors are being pursued as potential new anti-metastatic strategies against multiple cancers including pancreatic, ovarian, breast, melanoma and lung cancer. Herein, we have employed molecular modelling to give insights into the selectivity observed in a series of selective ST inhibitors that incorporate a uridyl ring in place of the cytidine of the natural donor (CMP-Neu5Ac) and replace the charged phosphodiester linker of classical ST inhibitors with a neutral α-hydroxy-1,2,3-triazole linker. The inhibitory activities of the nascent compounds were determined against recombinant human ST enzymes (ST3GAL1, ST6GAL1, ST8SIA2) showing promising activity and selectivity towards specific ST sub-types. Our ST inhibitors are non-toxic and show improved synthetic accessibility and drug-likeness compared to earlier nucleoside-based ST inhibitors.

Divergent synthesis of complex withanolides enabled by a scalable route and late-stage functionalization.

Withanolides are a group of naturally occurring C28 steroids based on an ergostane skeleton. They have a high degree of polyoxygenation, and the abundance of O-functional groups has enabled various natural alterations to both the carbocyclic skeleton and the side chain. Consequently, these molecules have intricate structural features that lead to their highly varied display of biological activities including anticancer, anti-inflammatory, and immunomodulating properties. Despite being intriguing leads for further discovery research, synthetic access to the withanolides remains highly challenging-compounds for current biological research are mainly isolated from plants, often inefficiently. Here, we report the divergent synthesis of 11 withanolides in 12 to 20 steps, enabled by a gram-scale route and a series of late-stage functionalizations, most notably a bioinspired photooxygenation-allylic hydroperoxide rearrangement sequence. This approach enables further biological research disconnected from a reliance on minute quantities of the parent natural products or their simple derivatives.

Network Models of BACE-1 Inhibitors: Exploring Structural and Biochemical Relationships.

This study investigates the clustering patterns of human β-secretase 1 (BACE-1) inhibitors using complex network methodologies based on various distance functions, including Euclidean, Tanimoto, Hamming, and Levenshtein distances. Molecular descriptor vectors such as molecular mass, Merck Molecular Force Field (MMFF) energy, Crippen partition coefficient (ClogP), Crippen molar refractivity (MR), eccentricity, Kappa indices, Synthetic Accessibility Score, Topological Polar Surface Area (TPSA), and 2D/3D autocorrelation entropies are employed to capture the diverse properties of these inhibitors. The Euclidean distance network demonstrates the most reliable clustering results, with strong agreement metrics and minimal information loss, indicating its robustness in capturing essential structural and physicochemical properties. Tanimoto and Hamming distance networks yield valuable clustering outcomes, albeit with moderate performance, while the Levenshtein distance network shows significant discrepancies. The analysis of eigenvector centrality across different networks identifies key inhibitors acting as hubs, which are likely critical in biochemical pathways. Community detection results highlight distinct clustering patterns, with well-defined communities providing insights into the functional and structural groupings of BACE-1 inhibitors. The study also conducts non-parametric tests, revealing significant differences in molecular descriptors, validating the clustering methodology. Despite its limitations, including reliance on specific descriptors and computational complexity, this study offers a comprehensive framework for understanding molecular interactions and guiding therapeutic interventions. Future research could integrate additional descriptors, advanced machine learning techniques, and dynamic network analysis to enhance clustering accuracy and applicability.

A Monometallic Bis(cyaphido) Complex.

The first example of a bis(cyaphido) complex, trans-[Ru(dppe)2(C≡P)2], is described, unequivocally demonstrating the synthetic accessibility and stability of complexes that feature more than one cyaphido ligand. Synthesis is achieved from the precedent cation [Ru(dppe)2(C≡P)]+ via sequential coordination and desilylation of the phosphaalkyne Me3SiC≡P. The heteroleptic analogue trans-[Ru(dppe)2(C≡N)(C≡P)] is also prepared from the same cation and NaCN; both cyaphido complexes are structurally characterized, enabling the first direct comparison of cyaphide with cyanide, its isoelectronic and isolobal counterpart. This demonstrates an enhanced π-acidity for -C≡P over -C≡N, while computational studies reveal also a higher π-donor character for the cyaphido ligand.

Total Synthesis of Nona-decasaccharide Motif from Ganoderma sinense Polysaccharide Enabled by Modular and One-Pot Stereoselective Glycosylation Strategy.

Polysaccharides from a medicinal fungus Ganoderma sinense represent important and adjunctive therapeutic agents for treating various diseases, including leucopenia and hematopoietic injury. However, the synthetic accessibility to long, branched, and complicated carbohydrates chains from Ganoderma sinense polysaccharides remains a challenging task in chemical synthesis. Here, we report the modular chemical synthesis of nona-decasaccharide motif from Ganoderma sinense polysaccharide GSPB70-S with diverse biological activities for the first time through one-pot stereoselective glycosylation strategy on the basis of glycosyl ortho-(1-phenyvinyl)benzoates, which not only sped up carbohydrates synthesis but also reduced chemical waste and avoided aglycones transfer issues inherent to one-pot glycosylation on the basis of thioglycosides. The synthetic route also highlights the following key steps: (1) preactivation-based one-pot glycosylation for highly stereoselective constructions of several 1,2-cis-glycosidic linkages, including three α-d-GlcN-(1 → 4) linkages and one α-d-Gal-(1 → 4) bond via the reagent N-methyl-N-phenylformamide modulation; (2) orthogonal one-pot assembly of 1,2-trans-glycosidic linkages in various linear and branched glycans fragments by strategic combinations of glycosyl N-phenyltrifluoroacetimidates, glycosyl ortho-alkynylbenzoates, and glycosyl ortho-(1-phenyvinyl)benzoates; and (3) the final [1 × 4 + 15] Yu glycosylation for efficient assembly of nona-decasaccharide target. Additionally, shorter sequences of 4-mer, 5-mer, and 6-mer are also prepared for structure-activity relationship biological studies. The present work shows that this one-pot stereoselective glycosylation strategy can offer a reliable and effective means to streamline chemical synthesis of long, branched, and complex carbohydrates with many 1,2-cis-glycosidic bonds.

Biobased polysulfides prepared via inverse vulcanization with properties of intrinsic self-extinguishment and thermal remodeling

Developing high-performance polymers with intrinsic self-extinguishment and thermal remodeling from biobased resources has attracted increasing attention due to both safety and environmental concerns. In this work, two biobased crosslinkers, trieugenylcyanuric (TEC) and trieugenylphosphate (TEP), were designed and synthesized, and then five novel biobased polysulfides were synthesized via inverse vulcanization with different combinations of elemental sulfur, eugenol (Eug) and crosslinkers. The chemical structure of crosslinkers and polysulfides were confirmed by nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopies (FT-IR), respectively. In addition, molecular weight of the linear polysulfide was measured by gel permeation chromatography (GPC). Various techniques, such as thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), microscale combustion calorimeter (MCC) and scanning electron microscopy (SEM) were used to characterize the properties of the polysulfides. Notably, the crosslinked polysulfide (P(S-TEP)) shows self-extinguishment with heat release apacity (HRC) value of 165 J/g⋅K and total heat release (THR) value of 7.9 kJ/g, and it can melt completely at 180℃ (thermal remodeling) without any extra treatment. Overall, the current work provides a high-efficiency and sustainable synthetic route access to a series biobased polysulfides with self-extinguishment and thermal remodeling.

Highly Condensed and Super-Incompressible Be2PN3.

Although beryllium and its compounds show outstanding properties, owing to its toxic potential and extreme reaction conditions the chemistry of Be under high-pressure conditions has only been investigated sparsely. Herein, we report on the highly condensed wurtzite-type Be2PN3, which was synthesized from Be3N2 and P3N5 in a high-pressure high-temperature approach at 9 GPa and 1500 °C. It is the missing member in the row of formula type M2PN3 (M=Mg, Zn). The structure was elucidated by powder X-ray diffraction (PXRD), revealing that Be2PN3 is a double nitride, rather than a nitridophosphate. The structural model was further corroborated by 9Be and 31P solid-state nuclear magnetic resonance (NMR) spectroscopy. We present 9Be NMR data for tetrahedral nitride coordination for the first time. Infrared and energy-dispersive X-ray spectroscopy (FTIR and EDX), as well as temperature dependent PXRD complement the analytical characterization. Density functional theory (DFT) calculations reveal super-incompressible behavior and the remarkable hardness of this low-density material. The formation of Be2PN3 through a high-pressure high-temperature approach expands the synthetic access to Be-containing compounds and may open access to various multinary beryllium nitrides.

Highly Condensed and Super‐Incompressible Be2PN3

AbstractAlthough beryllium and its compounds show outstanding properties, owing to its toxic potential and extreme reaction conditions the chemistry of Be under high‐pressure conditions has only been investigated sparsely. Herein, we report on the highly condensed wurtzite‐type Be2PN3, which was synthesized from Be3N2 and P3N5 in a high‐pressure high‐temperature approach at 9 GPa and 1500 °C. It is the missing member in the row of formula type M2PN3 (M = Mg, Zn). The structure was elucidated by powder X‐ray diffraction (PXRD), revealing that Be2PN3 is a double nitride, rather than a nitridophosphate. The structural model was further corroborated by 9Be and 31P solid‐state nuclear magnetic resonance (NMR) spectroscopy. We present 9Be NMR data for tetrahedral nitride coordination for the first time. Infrared and energy‐dispersive X‐ray spectroscopy (FTIR and EDX), as well as temperature dependent PXRD complement the analytical characterization. Density functional theory (DFT) calculations reveal super‐incompressible behavior and the remarkable hardness of this low‐density material. The formation of Be2PN3 through a high‐pressure high‐temperature approach expands the synthetic access to Be‐containing compounds and may open access to various multinary beryllium nitrides.

Rapid Peptide Cyclization Inspired by the Modular Logic of Nonribosomal Peptide Synthetases.

Nonribosomal cyclic peptides (NRcPs) are structurally complex natural products and a vital pool of therapeutics, particularly antibiotics. Their structural diversity arises from the ability of the multidomain enzyme assembly lines, nonribosomal peptide synthetases (NRPSs), to utilize bespoke nonproteinogenic amino acids, modify the linear peptide during elongation, and catalyze an array of cyclization modes, e.g., head to tail, side chain to tail. The study and drug development of NRcPs are often limited by a lack of easy synthetic access to NRcPs and their analogues, with selective macrolactamization being a major bottleneck. Herein, we report a generally applicable chemical macrocyclization method of unprecedented speed and selectivity. Inspired by biosynthetic cyclization, it combines the deprotected linear biosynthetic precursor peptide sequence with a highly reactive C-terminus to produce NRcPs and analogues in minutes. The method was applied to several NRcPs of varying sequences, ring sizes, and cyclization modes including rufomycin, colistin, and gramicidin S with comparable success. We thus demonstrate that the linear order of modules in NRPS enzymes that determines peptide sequence encodes the key structural information to produce peptides conformationally biased toward macrocyclization. To fully exploit this conformational bias synthetically, a highly reactive C-terminal acyl azide is also required, alongside carefully balanced pH and solvent conditions. This allows for consistent, facile cyclization of exceptional speed, selectivity, and atom efficiency. This exciting macrolactamization method represents a new enabling technology for the biosynthetic study of NRcPs and their development as therapeutics.

Enantioselective Aminative Dearomatization of Indoles via Electrophilic 1,6-Addition of p-Quinone Diimides (p-QDIs).

Herein we report the first use of p-quinone diimide for the aminative dearomatization of 2,3-disubstituted indoles to furnish C3 aza-quaternary chiral indolenines. This approach, which proceeds via an electrophilic 1,6-addition of p-quinone diimide, allows the synthesis of an array of optically active aza-quaternary indolenines with high yields and excellent enantioselectivities. A one-pot approach of the same has also been established to further improve the synthetic accessibility of this protocol.

An Introductory Guide to Protease Sensitive Linker Design Using Matrix Metalloproteinase 13 as an Example.

Proteases play a crucial role, not only in physiological, but also in pathological processes, such as cancer, inflammation, arthritis, Alzheimer's, and infections, to name but a few. Their ability to cleave peptides can be harnessed for a broad range of biotechnological purposes. To do this efficiently, it is essential to find an amino acid sequence that meets the necessary requirements, including interdependent factors like specificity, selectivity, cleavage kinetics, or synthetic accessibility. Cleavage sequences from natural substrates of the protease may not be optimal in terms of specificity and selectivity, which is why these frequently require arduous and sometimes unsuccessful optimization such as by iterative exchange of single amino acids. Hence, here we describe the systematic design of protease sensitive linkers (PSLs)─peptide sequences specifically cleaved by a target protease─guided by the mass spectrometry based determination of target protease specific cleavage sites from a proteome-based peptide library. It includes a procedure for identifying bespoke PSL sequences, their optimization, synthesis, and validation and introduces a program that can indicate potential cleavage sites by hundreds of enzymes in any arbitrary amino acid sequence. Thereby, we provide an introduction to PSL design, illustrated by the example of matrix metalloproteinase 13 (MMP13). This introduction can serve as a guide and help to greatly accelerate the development and use of protease-sensitive linkers in diverse applications.

Representations of lipid nanoparticles using large language models for transfection efficiency prediction.

Lipid nanoparticles (LNPs) are the most widely used vehicles for mRNA vaccine delivery. The structure of the lipids composing the LNPs can have a major impact on the effectiveness of the mRNA payload. Several properties should be optimized to improve delivery and expression including biodegradability, synthetic accessibility, and transfection efficiency. To optimize LNPs, we developed and tested models that enable the virtual screening of LNPs with high transfection efficiency. Our best method uses the lipid Simplified Molecular-Input Line-Entry System (SMILES) as inputs to a large language model. Large language model-generated embeddings are then used by a downstream gradient-boosting classifier. As we show, our method can more accurately predict lipid properties, which could lead to higher efficiency and reduced experimental time and costs. Code and data links available at: https://github.com/Sanofi-Public/LipoBART.

Efficient Synthetic Access to Stable Isotope Labelled Pseudouridine Phosphoramidites for RNA NMR Spectroscopy.

Here we report the efficient synthetic access to 13C/15N-labelled pseudouridine phosphoramidites, which were incorporated into a binary H/ACA box guide RNA/product complex comprising 77 nucleotides (nts) in total and into a 75 nt E. coli tRNAGly. The stable isotope (SI) labelled pseudouridines were produced via a highly efficient chemo-enzymatic synthesis. 13C/15N labelled uracils were produced via chemical synthesis and enzymatically converted to pseudouridine 5'-monophosphate (ΨMP) by using YeiN, a Ψ-5'-monophosphate C-glycosidase. Removal of the 5'-phosphate group yielded the desired pseudouridine nucleoside (Ψ), which was transformed into a phosphoramidite building suitable for RNA solid phase synthesis. A Ψ -building block carrying both a 13C and a 15N label was incorporated into a product RNA and the complex formation with a 63 nt H/ACA box RNA could be observed via NMR. Furthermore, the SI labelled pseudouridine building block was used to determine imino proton bulk water exchange rates of a 75 nt E. coli tRNAGly CCmnm5U, identifying the TΨC-loop 5-methyluridine as a modifier of the exchange rates. The efficient synthetic access to SI-labelled Ψ building blocks will allow the solution and solid-state NMR spectroscopic studies of Ψ containing RNAs and will facilitate the mass spectrometric analysis of Ψ-modified nucleic acids.

ADME Studies of Phytochemicals in Stachys pilifera Benth plant species

Medicinal chemistry is a constantly changing and developing field. It is a successful and prosperous branch due to the new technologies, the changing complexities of medicine, and the expansion of medicinal chemistry knowledge. In drug design, many aspects need to be checked. The first step in drug development is discovering when new insights and technologies become available. Discovery is possible to find new treatments for diseases. This can begin with thousands of different computational methods, including under Computer-aided drug design (CADD). It provides a no. of tools and techniques that assist the various stages of drug design which can minimize the cost of drug research and development time. For this particular project, we use the SwissADME web tool it is a free web tool, easily assessable and convenient. It can characterize any chemical compound within a min. it allows you to compute physiochemical descriptors also to predict ADME parameters, pharmacokinetic properties, drug like nature of our compound, and medicinal chemistry friendliness of many small molecules to support drug discovery. For ADME analysis we chose a plant in which the isolation of its chemical compound is already done. i.e. stachys pilifera benth plant species. We did the ADME study of their chemical compounds using SwissADME and concluded its drug-like nature, its bioavailability, its synthetic accessibility, and many medicinal properties. We can say that Swiss ADME is the Asset for medicinal chemistry.

Inside Back Cover: Easy Synthetic Access to High‐Melting Sulfurated Copolymers and their Self‐Assembling Diblock Copolymers from Phenylisothiocyanate and Oxetane (Angew. Chem. Int. Ed. 25/2024)

Inside Back Cover: Easy Synthetic Access to High‐Melting Sulfurated Copolymers and their Self‐Assembling Diblock Copolymers from Phenylisothiocyanate and Oxetane (Angew. Chem. Int. Ed. 25/2024)

Innenrücktitelbild: Easy Synthetic Access to High‐Melting Sulfurated Copolymers and their Self‐Assembling Diblock Copolymers from Phenylisothiocyanate and Oxetane (Angew. Chem. 25/2024)

Innenrücktitelbild: Easy Synthetic Access to High‐Melting Sulfurated Copolymers and their Self‐Assembling Diblock Copolymers from Phenylisothiocyanate and Oxetane (Angew. Chem. 25/2024)

Silylimidazolium Hexafluorophosphate Salts as Synthetic Precursors to N-Heterocyclic Carbene Pentafluorophosphorus Adducts.

N-Heterocyclic carbene pentafluorophosphorus (NHC-PF5) adducts are six-coordinate phosphorus(v) compounds with emerging applications but poor synthetic accessibility. We have developed a simple and high yielding protocol for synthesizing imidazolylidene NHC-PF5 adducts from silylimidazolium hexafluorophosphate salts. Using this methodology, we have prepared a series of NHC-PF5 adducts in high yields, including new NHC-PF5 building blocks amenable to subsequent synthetic diversification. We also demonstrate that a similar approach enables access to analogous, synthetically elusive NHC-BF3 and NHC-SbF5 adducts.

Development of scoring-assisted generative exploration (SAGE) and its application to dual inhibitor design for acetylcholinesterase and monoamine oxidase B

De novo molecular design is the process of searching chemical space for drug-like molecules with desired properties, and deep learning has been recognized as a promising solution. In this study, I developed an effective computational method called Scoring-Assisted Generative Exploration (SAGE) to enhance chemical diversity and property optimization through virtual synthesis simulation, the generation of bridged bicyclic rings, and multiple scoring models for drug-likeness. In six protein targets, SAGE generated molecules with high scores within reasonable numbers of steps by optimizing target specificity without a constraint and even with multiple constraints such as synthetic accessibility, solubility, and metabolic stability. Furthermore, I suggested a top-ranked molecule with SAGE as dual inhibitors of acetylcholinesterase and monoamine oxidase B through multiple desired property optimization. Therefore, SAGE can generate molecules with desired properties by optimizing multiple properties simultaneously, indicating the importance of de novo design strategies in the future of drug discovery and development.Scientific contribution The scientific contribution of this study lies in the development of the Scoring-Assisted Generative Exploration (SAGE) method, a novel computational approach that significantly enhances de novo molecular design. SAGE uniquely integrates virtual synthesis simulation, the generation of complex bridged bicyclic rings, and multiple scoring models to optimize drug-like properties comprehensively. By efficiently generating molecules that meet a broad spectrum of pharmacological criteria—including target specificity, synthetic accessibility, solubility, and metabolic stability—within a reasonable number of steps, SAGE represents a substantial advancement over traditional methods. Additionally, the application of SAGE to discover dual inhibitors for acetylcholinesterase and monoamine oxidase B not only demonstrates its potential to streamline and enhance the drug development process but also highlights its capacity to create more effective and precisely targeted therapies. This study emphasizes the critical and evolving role of de novo design strategies in reshaping the future of drug discovery and development, providing promising avenues for innovative therapeutic discoveries.

Amine-Terminated Phenanthroline Diimides as Aqueous Masking Agents for Am(III)/Eu(III) Separation: An Alternative Ligand Design Strategy for Water-Soluble Lanthanide/Actinide Chelating Ligands.

Selective actinide coordination (from lanthanides) is critical for both nuclear waste management and sustainable development of nuclear power. Hydrophilic ligands used as masking agents to withhold actinides in the aqueous phase are currently highly pursued, while synthetic accessibility, water solubility, acid resistance, and extraction capability are the remaining problems. Most reported hydrophilic ligands are only effective at low acidity. We recently proved that the phenanthroline diimide skeleton was an efficient building block for the construction of highly efficient acid-resistant hydrophilic lanthanide/actinide separation agents, while the limited water solubility hindered the loading capability of the ligand. Herein, amine was introduced as the terminal solubilizing group onto the phenanthroline diimide backbone, which after protonation in acid showed high water solubility. The positively charged terminal amines enhanced the ligand water solubility to a large extent, which, on the other side, was believed to be detrimental for the coordination and complexation of the metal cations. We showed that by delicately adjusting the alkyl chain spacing, this intuitive disadvantage could be relieved and superior extraction performances could be achieved. This work holds significance for both hydrophilic lanthanide/actinide separation ligand design and, concurrently, offers insights into the development of water-soluble lanthanide/actinide complexes for biomedical and bioimaging applications.

(Hetero)Arene Ring-Fused [1,2,4]Triazines

Synthetic access to a five (hetero)arene ring-fused 3-phenyl[1,2,4]triazines is described. The resulting compounds were characterized via 1H and 13C NMR, IR, UV–vis spectroscopy and HRMS. The structure of 3-phenyl[1,2,4]triazino[5,6-c]quinoline was unambiguously confirmed by single crystal XRD.