Diverse Scaffolds Research Articles

Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays

Although small molecule superposition is a standard technique in drug discovery, a rigorous performance assessment of the corresponding methods is currently challenging. Datasets in this field are sparse, small, tailored to specific applications, unavailable, or outdated. The newly developed LOBSTER set described herein offers a publicly available and method-independent dataset for benchmarking and method optimization. LOBSTER stands for “Ligand Overlays from Binding SiTe Ensemble Representatives”. All ligands were derived from the PDB in a fully automated workflow, including a ligand efficiency filter. So-called ligand ensembles were assembled by aligning identical binding sites. Thus, the ligands within the ensembles are superimposed according to their experimentally determined binding orientation and conformation. Overall, 671 representative ligand ensembles comprise 3583 ligands from 3521 proteins. Altogether, 72,734 ligand pairs based on the ensembles were grouped into ten distinct subsets based on their volume overlap, for the benefit of introducing different degrees of difficulty for evaluating superposition methods. Statistics on the physicochemical properties of the compounds indicate that the dataset represents drug-like compounds. Consensus Diversity Plots show predominantly high Bemis–Murcko scaffold diversity and low median MACCS fingerprint similarity for each ensemble. An analysis of the underlying protein classes further demonstrates the heterogeneity within our dataset. The LOBSTER set offers a variety of applications like benchmarking multiple as well as pairwise alignments, generating training and test sets, for example based on time splits, or empirical software performance evaluation studies. The LOBSTER set is publicly available at https://doi.org/10.5281/zenodo.12658320, representing a stable and versioned data resource. The Python scripts are available at https://github.com/rareylab/LOBSTER, open-source, and allow for updating or recreating superposition sets with different data sources. Graphical abstractSimplified illustration of the LOBSTER dataset generation.

High potency 3-carboxy-2-methylbenzofuran pendrin inhibitors as novel diuretics

Pendrin (SLC26A4) is an anion exchanger expressed in epithelial cells of kidney and lung. Pendrin inhibition is a potential treatment approach for edema, hypertension and inflammatory lung diseases. We have previously identified first-in-class pendrin inhibitors by high-throughput screening, albeit with low potency for pendrin inhibition (IC50 ∼10 μM). Here, we performed a de novo small molecule screen with follow-on structure-activity studies to identify more potent pendrin inhibitors. Screening of 50,000 synthetic small molecules identified four novel classes of pendrin inhibitors with diverse scaffolds, including 5-benzyloxy-2-methylbenzofurans, N-aryl urea substituted 5-methyltryptamines, N-aryl urea substituted anthranilic acid, and substituted N-benzyl 3-carboxyindoles. The most potent inhibitor from the initial screen, a 3-carboxy-2-methylbenzofuran (1a), had IC50 of 4.1 μM. Structure-activity studies using 732 benzofuran analogs identified 1d with IC50 ∼ 0.5 μM for pendrin inhibition. Selectivity studies showed that 1d has minimal or no activity against related ion channels/transporters including SLC26A3, SLC26A6, SLC26A9 and CFTR at high concentrations. 1d administration to mice at 10 mg/kg had no effect on urine volume when used alone, but potentiated the diuretic effect of furosemide by 45%. In conclusion, we have identified novel pendrin inhibitors with greatly improved potency and good in vivo efficacy. These compounds can be used as pharmacological tools to study the roles of pendrin, and potentially developed as drug candidates for edema, hypertension and lung diseases.

Aza-Michael addition-elimination led synthesis, characterization and X-ray crystallography of novel trifluoromethylated-enaminone derivatives

Enaminones are important synthetic intermediates for the construction of diverse heterocyclic scaffolds owing to their push-pull electronic structures. A series of novel (Z)-1-(3,5-bis(trifluoromethyl)phenyl)-3-(aryl/alkyl)prop-2-en-1-ones (5, 6) and (Z)-3-(aryl/alkylamino)-1-(4-(trifluoromethyl)phenyl)prop-2-en-1-ones (9, 10) were synthesized with (E)-1-(3,5-bis(trifluoromethyl)phenyl)-3-(dimethylamino)prop-2-en-1-one (2) & (E)-3-(dimethylamino)-1-(4-(trifluoromethyl)phenyl) prop-2-en-1-one (8) as starting materials. The structures of the fluorinated enaminones were established with the help of spectral and analytical data. X-ray crystallographic study for a model compound (6a) gave a vivid image showing the existence of the product in Z-form unlike the corresponding intermediate that exists in E-form.

Systematic, computational discovery of multicomponent and one-pot reactions

Discovery of new types of reactions is essential to organic chemistry because it expands the scope of accessible molecular scaffolds and can enable more economical syntheses of existing structures. In this context, the so-called multicomponent reactions, MCRs, are of particular interest because they can build complex scaffolds from multiple starting materials in just one step, without purification of intermediates. However, for over a century of active research, MCRs have been discovered rather than designed, and their number remains limited to only several hundred. This work demonstrates that computers taught the essential knowledge of reaction mechanisms and rules of physical-organic chemistry can design – completely autonomously and in large numbers – mechanistically distinct MCRs. Moreover, when supplemented by models to approximate kinetic rates, the algorithm can predict reaction yields and identify reactions that have potential for organocatalysis. These predictions are validated by experiments spanning different modes of reactivity and diverse product scaffolds.

Structurally Diverse Nitrogen-Rich Scaffolds via Continuous Photo-Click Reactions.

Continuous flow technology was exploited for the effective generation of nitrile imines via photolysis of substituted aryl tetrazoles. The resulting photo-click process rapidly affords advanced nitrogen-rich scaffolds upon the subsequent trapping of the reactive dipole with alkenes, alkynes, and benzylic amines. Crucially, this approach uncovers the differential reactivity for ether vs amine tethers, thus providing facile and scalable access to underexplored medicinally relevant heterocyclic entities.

Homobarrelenones: Versatile Building Blocks for the Construction of Novel and Structurally Diverse Scaffolds

AbstractWe describe the derivatization of tropolone–based homobarrelenones through simple transformations, including catalytic hydrogenations, base‐catalyzed solvolysis, and hydride reductions. Despite being structurally complex and highly functionalized, the novel compounds had no significant cytotoxicity in sperm motility assays, underscoring the importance of Michael acceptor moieties in the biological activity of this class of compounds.

Hydrogel-Enhanced Autologous Chondrocyte Implantation for Cartilage Regeneration-An Update on Preclinical Studies.

Autologous chondrocyte implantation (ACI) and matrix-induced ACI (MACI) have demonstrated improved clinical outcomes and reduced revision rates for treating osteochondral and chondral defects. However, their ability to achieve lasting, fully functional repair remains limited. To overcome these challenges, scaffold-enhanced ACI, particularly utilizing hydrogel-based biomaterials, has emerged as an innovative strategy. These biomaterials are intended to mimic the biological composition, structural organization, and biomechanical properties of native articular cartilage. This review aims to provide comprehensive and up-to-date information on advancements in hydrogel-enhanced ACI from the past decade. We begin with a brief introduction to cartilage biology, mechanisms of cartilage injury, and the evolution of surgical techniques, particularly looking at ACI. Subsequently, we review the diversity of hydrogel scaffolds currently undergoing development and evaluation in preclinical studies for articular cartilage regeneration, emphasizing chondrocyte-laden hydrogels applicable to ACI. Finally, we address the key challenges impeding effective clinical translation, with particular attention to issues surrounding fixation and integration, aiming to inform and guide the future progression of tissue engineering strategies.

Cascade Cyclization/Annulation of β-Enamino Diketones and o-Phenylenediamine: A Strategy to Access Pyrrole-fused 1,5-Benzodiazepines.

Herein, we introduce an unprecedented cascade reaction for the assembly of pyrrole-fused 1,5-benzodiazepine frameworks. These diverse privileged scaffolds were controllably constructed by intramolecular cyclization of β-enamino diketone, followed by annulation with o-phenylenediamine. The protocol features efficient one-pot cascade cyclization/annulation, performed under simple and mild reaction conditions. The products are obtained in a metal-free manner, in good to excellent yields (65-91%), and represent a fused heterocyclic scaffold that is not yet found in nature.

Diffusion-based generative drug-like molecular editing with chemical natural language

Recently, diffusion models have emerged as a promising paradigm for molecular design and optimization. However, most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geometries, with limited research on molecular sequence diffusion models. The International Union of Pure and Applied Chemistry (IUPAC) names are more akin to chemical natural language than the Simplified Molecular Input Line Entry System (SMILES) for organic compounds. In this work, we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language (SMILES) and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language. We propose DiffIUPAC, a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings. Evaluation results demonstrate that our model outperforms existing methods and successfully captures the semantic rules of both chemical languages. Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints. Additionally, to illustrate the model's applicability in drug design, we conducted case studies in functional group editing, analogue design and linker design.

Enantioselective Borylative Functionalization of Internal Alkenes: A Platform for Constructing Vicinal Stereocenters†

Comprehensive SummaryVicinal stereogenic centers are ubiquitous structural scaffolds in both natural products and synthetic compounds, yet their enantioselective construction remains a significant challenge in organic synthesis. Organoboron compounds are of paramount importance in synthetic chemistry due to their ability to undergo facile transformations, yielding diverse essential chemical bonds such as carbon‐carbon, carbon‐oxygen, carbon‐nitrogen, and carbon‐halogen bonds. Transition‐metal‐catalyzed asymmetric borylative functionalizations of internal alkenes offer a promising strategy for the enantioselective installation of two adjacent chiral centers across carbon‐carbon bonds. By leveraging the versatile transformations of the newly introduced boryl unit, this approach holds great potential for expanding the structural diversity of vicinal stereogenic scaffolds. In this concise review, we aim to highlight recent advancements in transition‐metal‐catalyzed asymmetric borylative functionalizations of internal alkenes, underscore their utility as a versatile approach for constructing vicinal stereogenic centers, and discuss unsolved challenges and future directions in this field. Key Scientists

H2S scavenger as a broad-spectrum strategy to deplete bacteria-derived H2S for antibacterial sensitization

Bacteria-derived H2S plays multifunctional protective roles against antibiotics insult, and the H2S biogenesis pathway is emerging as a viable target for the antibacterial adjuvant design. However, the development of a pan-inhibitor against H2S-synthesizing enzymes is challenging and underdeveloped. Herein, we propose an alternative strategy to downregulate the H2S levels in H2S-producing bacteria, which depletes the bacteria-derived H2S chemically by H2S scavengers without acting on the synthesizing enzymes. After the screening of chemically diversified scaffolds and a structural optimization campaign, a potent and specific H2S scavenger is successfully identified, which displays efficient H2S depletion in several H2S-producing bacteria, potentiates both bactericidal agents and photodynamic therapy, enhances the bacterial clearance of macrophages and polymorphonuclear neutrophils, disrupts the formation of bacterial biofilm and increases the sensitivity of bacterial persister cells to antibiotics. Most importantly, such an H2S scavenger exhibits sensitizing effects with gentamicin in Pseudomonas aeruginosa -infected pneumonia and skin wound female mouse models. In aggregate, our results not only provide an effective strategy to deplete bacteria-derived H2S and establish the H2S biogenesis pathway as a viable target for persisters and drug-resistant bacteria, but also deliver a promising antibacterial adjuvant for potential clinical translation.

Robust whole‐cell‐based chemoenzymatic synthesis of site‐selective deuterated α‐hydroxy acids and α‐amino acids

Deuterated hydroxyl acids and amino acids have been widely utilized in life science, biochemistry and drug development. Site‐selective and stereoselective synthesis of deuterated hydroxyl acids and amino acids remains a significant challenge. Here, we report the development of a robust whole‐cell‐based chemoenzymatic platform for the synthesis of deuterated hydroxyl acids and amino acids from off‐the‐shelf aldehydes in high yields with excellent selectivities and levels of deuteration. The platform delivers products with diverse scaffolds and deuteration patterns, as well as broad scopes with both aromatic and aliphatic side chains. The application of the platform was demonstrated by the concise synthesis of a deuterium‐containing antiparkinson's disease candidate. This platform provides a concrete foundation for accessing amino acid isotopologs for potential applications in research and drug discovery and development.

Improving docking and virtual screening performance using AlphaFold2 multi-state modeling for kinases

Structure-based virtual screening (SBVS) is a crucial computational approach in drug discovery, but its performance is sensitive to structural variations. Kinases, which are major drug targets, exemplify this challenge due to active site conformational changes caused by different inhibitor types. Most experimentally determined kinase structures have the DFGin state, potentially biasing SBVS towards type I inhibitors and limiting the discovery of diverse scaffolds. We introduce a multi-state modeling (MSM) protocol for AlphaFold2 (AF2) kinase structures using state-specific templates to address these challenges. Our comprehensive benchmarks evaluate predicted model qualities, binding pose prediction accuracy, and hit compound identification through ensemble SBVS. Results demonstrate that MSM models exhibit comparable or improved structural accuracy compared to standard AF2 models, enhancing pose prediction accuracy and effectively capturing kinase-ligand interactions. In virtual screening experiments, our MSM approach consistently outperforms standard AF2 and AF3 modeling, particularly in identifying diverse hit compounds. This study highlights the potential of MSM in broadening kinase inhibitor discovery by facilitating the identification of chemically diverse inhibitors, offering a promising solution to the structural bias problem in kinase-targeted drug discovery.

Semisynthetic Phage Display Library Construction: Design and Synthesis of Diversified Single-Chain Variable Fragments and Generation of Primary Libraries.

Display of antibody fragments on the surface of M13 filamentous bacteriophages is a well-established approach for the identification of antibodies binding to a target of interest. Here, we describe the first of a three-step method to construct Antibody Libraries for Therapeutic Antibody Discovery (ALTHEA) Libraries. The three-step method involves (1) primary library (PL) construction, (2) filtered library construction, and (3) secondary library construction. The first step, described here, entails design, synthesis, and cloning of four PLs. These PLs are designed with specific properties amenable to therapeutic antibody development using one universal variable heavy (VH) scaffold and four distinct variable light (VL) scaffolds. The scaffolds are diversified in positions that bind both protein and peptide targets identified in antibody-antigen complexes of known structure using the amino acid frequencies found in those positions in known human antibody sequences, avoiding residues that may lead to developability liabilities. The diversified scaffolds are combined with 90 synthetic neutral HCDR3 sequences designed with developable human diversity genes (IGHD) and joining heavy genes (IGHJ) in germline configuration, and assembled as single-chain variable fragments (scFvs) in a VL-linker-VH orientation. The four designed PLs are synthesized using trinucleotide phosphoramidites (TRIMs) and cloned independently into a phagemid vector for M13 pIII display. Quality control of the cloning of the four PLs is also described, which involves sequencing scFvs in each library.

Photoinduced Transformations with Diverse Maleimide Scaffolds

Maleimides serve as crucial components in various synthetic processes and are of significant interest to researchers in bioorganic chemistry and biotechnology. Although thermal reactions involving maleimides have been studied extensively, light-mediated reactions with maleimides remain relatively underutilized. This review focuses on understanding the behavior of maleimides in their excited state, particularly their role as synthetic scaffolds for excited-state reactions. Specific emphasis is placed on the diverse photoreactions involving maleimides and photophysical evaluation from our research group.

Supramolecular Guest Exchange in Cucurbit[7]uril for Bioorthogonal Fluorogenic Imaging across the Visible Spectrum.

Fluorogenic probes that unmask fluorescence signals in response to bioorthogonal reactions are a powerful new addition to biological imaging. They can significantly reduce background fluorescence and minimize nonspecific signals, potentially enabling real-time, high-contrast imaging without the need to wash out excess fluorophores. While diverse classes of highly refined synthetic fluorophores are now readily available, integrating them into a bioorthogonal fluorogenic scheme still requires extensive design efforts and customized structural alterations to optimize quenching mechanisms for each specific fluorophore scaffold. Herein, we present a highly generalizable strategy that can produce an efficient bioorthogonal fluorogenic response from essentially any readily available fluorophore without further structural alterations. We designed this strategy based on the macrocyclic cucurbit[7]uril (CB7) host, where a fluorogenic response is achieved by programming a guest exchange reaction within the macrocyclic cavity. We employed this strategy to rapidly create fluorogenic probes across the visible spectrum from diverse fluorophore scaffolds, which enabled no-wash imaging in live cells and tissues with minimal background signal. Finally, we demonstrated that this strategy can be combined with metabolic labeling for fluorogenic detection of metabolically tagged mycobacteria under no-wash conditions and paired with covalently clickable probes for high-contrast super-resolution and multiplexed imaging in cells and tissues.

Synthesis and biological evaluation of some new heterocyclic compounds incorporating sulfapyridine as potential antimicrobial agents

This study investigated the cyanoacylation of the sulfapyridine moiety using cyanoacetyl pyrazole as a key synthetic intermediate for the construction of diverse bioactive scaffolds. The intermediate, 2-cyano-N-(4-(N-pyridin-2-yl) sulfamoyl) phenylacetamide, served as a valuable precursor for the synthesis of acrylamide, thiophene, thiazole, chromene, pyridone, 1,2,4-triazine, and hydrazone derivatives all incorporating the sulfapyridine core. The structural elucidation of the synthesized compounds was achieved using infrared (IR), nuclear magnetic resonance (1H and 13C), and mass spectrometry techniques. The biological activity of the newly synthesized compounds was evaluated against a panel of microorganisms, including Gram-positive bacteria (Staphylococcus aureus, Bacillus subtilis), Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa), and the fungus Candida albicans. Notably, the thiol derivative (compound 12), the pyrazole derivative (compound 15), and the 1,2,4-triazine derivatives (compound 21) exhibited significant to good antibacterial and antifungal activity. Interestingly, compounds 12 and 15 displayed a broader spectrum of activity, demonstrating efficacy against all tested microbial strains.

Stereoselective Construction of the ABCDE Pentacyclic Motif of Phainanoids via Norrish-Yang Photocyclization Reaction.

A Norrish-Yang photocyclization reaction has been applied to regio- and stereoselective construction of the ABCDE pentacyclic motif of natural product phainanoids. The observed substrate conformation control implicates this powerful reaction could be applied to the construction of structurally diverse natural product scaffolds.

Development of Mycobacterium tuberculosis Enoyl Acyl Reductase (InhA) Inhibitors: A Mini-Review

This review article delves into the critical role of Enoyl acyl carrier protein Reductase (InhA; ENR), a vital enzyme in the NADH-dependent acyl carrier protein reductase family, emphasizing its significance in fatty acid synthesis and, more specifically, the biosynthesis of mycolic acid. The primary objective of this literature review is to elucidate diverse scaffolds and their developmental progression targeting InhA inhibition, thereby disrupting mycolic acid biosynthesis. Various scaffolds, including thiourea, piperazine, thiadiazole, triazole, quinazoline, benzamide, rhodanine, benzoxazole, and pyridine, have been systematically explored for their potential as InhA inhibitors. Noteworthy findings highlight thiadiazole and triazole derivatives, demonstrating promising IC50 values within the nanomolar concentration range. The review offers comprehensive insights into InhA's structure, structure-activity relationships, and a detailed overview of distinct scaffolds as effective inhibitors of InhA.

Finding the most potent compounds using active learning on molecular pairs.

Active learning allows algorithms to steer iterative experimentation to accelerate and de-risk molecular optimizations, but actively trained models might still exhibit poor performance during early project stages where the training data is limited and model exploitation might lead to analog identification with limited scaffold diversity. Here, we present ActiveDelta, an adaptive approach that leverages paired molecular representations to predict improvements from the current best training compound to prioritize further data acquisition. We apply the ActiveDelta concept to both graph-based deep (Chemprop) and tree-based (XGBoost) models during exploitative active learning for 99 Ki benchmarking datasets. We show that both ActiveDelta implementations excel at identifying more potent inhibitors compared to the standard exploitative active learning implementations of Chemprop, XGBoost, and Random Forest. The ActiveDelta approach is also able to identify more chemically diverse inhibitors in terms of their Murcko scaffolds. Finally, deep models such as Chemprop trained on data selected through ActiveDelta approaches can more accurately identify inhibitors in test data created through simulated time-splits. Overall, this study highlights the large potential for molecular pairing approaches to further improve popular active learning strategies in low data regimes by enabling faster and more accurate identification of more diverse molecular hits against critical drug targets.