In this paper, we introduce research results from our network-approach-based investigation of the European Union defence cooperation projects. After brief remarks on the background, the research ...problem, the conceptual and methodological issues, we focus on the structure of the cooperation network and introduce the territorial, institutional, and (sub)regional patterns of partnerships. The data analyses illustrate that an integrated but fragmented cooperation network could be explored, and in several aspects remarkable differences can be measured on country-, regional, and sub-regional levels implying that territorial and institutional factors might have an important role in this specific area as well.
COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite ...previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.
Herein, we present a novel one‐pot aqueous reaction for the synthesis of 2‐iminothiazolines and 2‐aminothiazoles using isocyanides, amines, sulfur, and 2′‐bromoacetophenones. The three‐component ...preparation of thioureas is followed by the one‐pot cyclization leading to the heterocyclic product. This efficient and mild procedure features excellent step‐ and atom‐economy and enables the chromatography‐free preparation of diversely substituted 2‐iminothiazoline and 2‐aminothiazole derivatives.
A multicomponent one‐pot process led to the formation of diversely trisubstituted 2‐iminothiazolines and disubstituted 2‐aminothiazoles under aqueous conditions. Starting from isocyanides, amines, 2’‐bromoacetophenones, and aqueous polysulfide solution or sulfur powder, this efficient procedure enabled the chromatography‐free separation of solid products.
Immunolabeling and autoradiography have traditionally been applied as the methods-of-choice to visualize and collect molecular information about physiological and pathological processes. Here, we ...introduce PharmacoSTORM super-resolution imaging that combines the complementary advantages of these approaches and enables cell-type- and compartment-specific nanoscale molecular measurements. We exploited rational chemical design for fluorophore-tagged high-affinity receptor ligands and an enzyme inhibitor; and demonstrated broad PharmacoSTORM applicability for three protein classes and for cariprazine, a clinically approved antipsychotic and antidepressant drug. Because the neurobiological substrate of cariprazine has remained elusive, we took advantage of PharmacoSTORM to provide in vivo evidence that cariprazine predominantly binds to D
dopamine receptors on Islands of Calleja granule cell axons but avoids dopaminergic terminals. These findings show that PharmacoSTORM helps to quantify drug-target interaction sites at the nanoscale level in a cell-type- and subcellular context-dependent manner and within complex tissue preparations. Moreover, the results highlight the underappreciated neuropsychiatric significance of the Islands of Calleja in the ventral forebrain.
-phosphonates,
-phosphinates and secondary phosphine oxides may be preligands, and are important building blocks in the synthesis of pharmaceuticals, pesticides, and
-ligands. The prototropic ...tautomerism influenced by substituent effects plays an important role in the reactivity of these species. The main goal of our research was to study the tautomerism of the >P(O)H reagents by means of computational investigations applying several DFT methods at different levels. We focused on the effect of implicit solvents, and on explaining the observed trends with physical chemical molecular descriptors. In addition, multiple reaction pathways incorporating three
-molecules were elucidated for the mechanism of the interconversion.
•Overview on available covalent warheads.•Design principles of covalent fragment libraries.•Surrogate assay methodologies for testing reactivity.•Covalent screening protocols against proteins and the ...proteome.•Collection of recent drug discovery applications.
Targeted covalent inhibitors and chemical probes have become integral parts of drug discovery approaches. Given the advantages of fragment-based drug discovery, screening electrophilic fragments emerged as a promising alternative to discover and validate novel targets and to generate viable chemical starting points even for targets that are barely tractable. In this review, we present recent principles and considerations in the design of electrophilic fragment libraries from the selection of the appropriate covalent warhead through the design of the covalent fragment to the compilation of the library. We then summarize recent screening methodologies of covalent fragments against surrogate models, proteins, and the whole proteome, or living cells. Finally, we highlight recent drug discovery applications of covalent fragment libraries.
We discuss design principles, screening methodologies, and successful applications of electrophilic fragment libraries for the covalent modification and functional modulation of protein targets of pharmacological interest.
Targeted covalent inhibitors have become an integral part of a number of therapeutic protocols and are the subject of intense research. The mechanism of action of these compounds involves the ...formation of a covalent bond with protein nucleophiles, mostly cysteines. Given the abundance of cysteines in the proteome, the specificity of the covalent inhibitors is of utmost importance and requires careful optimization of the applied warheads. In most of the cysteine targeting covalent inhibitor programs the design strategy involves incorporating Michael acceptors into a ligand that is already known to bind non-covalently. In contrast, we suggest that the reactive warhead itself should be tailored to the reactivity of the specific cysteine being targeted, and we describe a strategy to achieve this goal. Here, we have extended and systematically explored the available organic chemistry toolbox and characterized a large number of warheads representing different chemistries. We demonstrate that in addition to the common Michael addition, there are other nucleophilic addition, addition-elimination, nucleophilic substitution and oxidation reactions suitable for specific covalent protein modification. Importantly, we reveal that warheads for these chemistries impact the reactivity and specificity of covalent fragments at both protein and proteome levels. By integrating surrogate reactivity and selectivity models and subsequent protein assays, we define a road map to help enable new or largely unexplored covalent chemistries for the optimization of cysteine targeting inhibitors.
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•A broad library of cysteine targeting warheads was explored and characterized.•Diverse chemical reactions are suitable for specific covalent protein modification.•Warheads impact the reactivity and specificity of covalent fragments.•A road map for the optimization of cysteine targeting inhibitors is proposed.
Covalent fragment approaches targeting non-cysteine residues Csorba, Noémi; Ábrányi-Balogh, Péter; Keserű, György M.
Trends in pharmacological sciences (Regular ed.),
November 2023, 2023-11-00, 20231101, Volume:
44, Issue:
11
Journal Article
Peer reviewed
Open access
The available collection of warheads has been extended to target a wider range of amino acid residues beyond cysteine enabling the identification of a larger pool of proteins.Covalent labeling can be ...achieved by noncatalytic chemical reactions; however, catalytic labeling achieved by heterogenous catalysts, photo- or electrocatalysis is an emerging field increasing the toolkit of specific labeling reactions. Photo- and electrocatalysis provide additional options for conditional labeling.Covalent fragments allow target identification by chemoproteomic techniques and enable identifying new (allosteric) binding sites.Covalent fragments can be considered as viable chemical starting points of targeted covalent ligands for target validation, molecular glues, and proteolysis-targeting chimeras (PROTACs).
Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.
Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimaeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.
The microwave (MW)-assisted direct esterification of certain P-acids is a green method. Quantum chemical calculations revealed that the activation enthalpy (ΔH#) for the exothermic monoalkylphosphate ...→ dialkylphosphate transformation was on the average 156.6 kJ mol−1, while ΔH# for the dialkylphosphate → trialkylphosphate conversion was somewhat higher, 171.2 kJ mol−1, and the energetics of the elemental steps of this esterification was less favorable. The direct monoesterification may be performed on MW irradiation in the presence of a suitable ionic liquid additive. However, the second step, with the less favorable energetics as a whole, could not be promoted by MWs. Hence, dialkylphosphates had to be converted to triesters by another method that was alkylation. In this way, it was also possible to synthesize triesters with different alkyl groups. Eventually a green, P-chloride free MW-promoted two-step method was elaborated for the synthesis of phosphate triesters.
Covalent drugs have been used for more than hundred years, but gathered larger interest in the last two decades. There are currently over a 100 different electrophilic warheads used in covalent ...ligands, and there are several considerations tailoring their reactivity against the target of interest, which is still a challenging task.
This review aims to give an overview of electrophilic warheads used for protein labeling in chemical biology and medicinal chemistry. The warheads are discussed by targeted residues, mechanism and selectivity, and analyzed through three different datasets including our collection of warheads, the CovPDB database, and the FDA approved covalent drugs. Moreover, the authors summarize general practices that facilitate the selection of the appropriate warhead for the target of interest.
In spite of the numerous electrophilic warheads, only a fraction of them is used in current drug discovery projects. Recent studies identified new tractable residues by applying a wider array of warhead chemistries. However, versatile, selective warheads are not available for all targetable amino acids, hence discovery of new warheads for these residues is needed. Broadening the toolbox of the warheads could result in novel inhibitors even for challenging targets developing with significant therapeutic potential.
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