Diverse Scaffolds Research Articles

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

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

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.

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.

NMR structures and magnetic force spectroscopy studies of small molecules binding to models of an RNA CAG repeat expansion.

RNA repeat expansions fold into stable structures and cause microsatellite diseases such as Huntington's disease (HD), myotonic dystrophy type 1 (DM1), and spinocerebellar ataxias (SCAs). The trinucleotide expansion of r(CAG), or r(CAG)exp, causes both HD and SCA3, and the RNA's toxicity has been traced to its translation into polyglutamine (polyQ; HD) as well as aberrant pre-mRNA alternative splicing (SCA3 and HD). Previously, a small molecule, 1, was discovered that binds to r(CAG)exp and rescues aberrant pre-mRNA splicing in patient-derived fibroblasts by freeing proteins bound to the repeats. Here, we report the structures of single r(CAG) repeat motif (5'CAG/3'GAC where the underlined adenosines form a 1×1 nucleotide internal loop) in complex with 1 and two other small molecules via nuclear magnetic resonance (NMR) spectroscopy combined with simulated annealing. Compound 2 was designed based on the structure of 1 bound to the RNA while 3 was selected as a diverse chemical scaffold. The three complexes, although adopting different 3D binding pockets upon ligand binding, are stabilized by a combination of stacking interactions with the internal loop's closing GC base pairs, hydrogen bonds, and van der Waals interactions. Molecular dynamics (MD) simulations performed with NMR-derived restraints show that the RNA is stretched and bent upon ligand binding with significant changes in propeller-twist and opening. Compound 3 has a distinct mode of binding by insertion into the helix, displacing one of the loop nucleotides into the major groove and affording a rod-like shape binding pocket. In contrast, 1 and 2 are groove binders. A series of single molecule magnetic force spectroscopy studies provide a mechanistic explanation for how bioactive compounds might rescue disease-associated cellular phenotypes.

Hexafluoroisopropanol (HFIP)-Mediated Intramolecular Cyclization of Allenamides To Access C1-Vinyl Tetrahydro-β-carbolines.

The construction of biologically interesting N-heterocycles under metal-free conditions is a constant goal in industry and academia. Herein, we have developed an hexafluoroisopropanol (HFIP)-mediated intramolecular cyclization of allenamides, providing tetrahydro-β-carboline derivatives embedded with a C1-vinyl functionality. The metal-free protocol provided tetrahydro-β-carboline derivatives atom-efficiently under room temperature with a broad substrate scope in good to excellent yields. The potential impact of the protocol is further highlighted by synthesizing derivatives of biologically important molecules and diversified scaffolds via postsynthetic modifications.

Mechanochemically Induced Thianthrenium Salts-Based Arylation of Diverse Heterocyclic Scaffolds

Mechanochemically Induced Thianthrenium Salts-Based Arylation of Diverse Heterocyclic Scaffolds

Combining (CH2O)n and (NH4)2CO3 as a Formamidine Equivalent for "Four-in-One" Synthesis of Fluoroalkylated 2-H-Pyrimidines.

Multicomponent reactions hold the potential to maximize the synthetic efficiency in the preparation of diverse and complex molecular scaffolds. An unprecedented formal [3+1+1+1] annulation approach for the one-step synthesis of fluoroalkylated 2-H-pyrimidines commencing from perfluoroalkyl alkenes, paraformaldehyde, and ammonium carbonate is described. By harnessing readily accessible (CH2O)n and cheap (NH4)2CO3 as a formamidine surrogate, this method effectively replaces traditionally preformed amidines with a pyrimidine assembly. The multicomponent reaction proceeds in a step-economical, operationally simple, metal-free, and additive-free manner, featuring a broad substrate scope, excellent functional group compatibility, and scalability. The potential for the synthetic elaboration of the obtained 2-H-pyrimidine is further demonstrated in the alkylation and vinylation of its C2 position.

Synthesis of Isatin-derived Heterocycles with Promising Anticancer Activities.

Isatin or 1H-indole-2,3-dione skeleton has been playing a significant role in drug de-sign and development. Isatin itself and many of its derivatives are widely distributed in naturally occurring bioactive compounds. Various synthetic isatin derivatives were found to possess a broad range of significant pharmacological efficacies especially anti-cancer activity against a wide variety of cancer cell lines. Interestingly, on a few occasions, some isatin-derived scaffolds were reported as more potent than the tested reputed drug molecules. As a result, isatin-derived compounds have been gaining significant attention in cancer-based drug developments. In this re-view, we have summarized literature reported during the last two decades related to the synthesis of structurally diverse isatin-derived scaffolds with promising anti-cancer activities.

Metal-free internal nucleophile-triggered domino route for synthesis of fused quinoxaline [1,4]-diazepine hybrids and the evaluation of their DNA binding properties

An unprecedented metal-free synthesis of fused quinoxaline 1,5-disubstituted-[1,4]-diazepine hybrids have been reported under mild conditions through a domino intermolecular SNAr followed by an internal nucleophile-triggered intramolecular SNAr pathway. Our strategy offers the flexibility for the introduction of a broad variety of functionalities at the N-1 position of fused diazepine moiety by using suitable diamine tails to design structurally diverse scaffolds. The DNA binding properties of representative quinoxaline diazepine hybrids were studied using UV–vis absorbance and EtBr displacement assay and were found to be governed by the functionalities at the N-1 position. Interestingly, compound 11f containing the N-1 benzyl substitution demonstrated significant DNA binding (KBH ∼ 2.15 ± 0.25 × 104 M−1 and Ksv ∼ 12.6 ± 1.41 × 103 M−1) accompanied by a bathochromic shift (Δλ ∼ 5 nm). In silico studies indicated possible binding of diazepine hybrid 11f at the GC-rich major groove in the ct-DNA hexamer duplex and showed comparable binding energies to that of ethidium bromide. The antiproliferative activity of compounds was observed in the given order in different cell lines: (HeLa > HT29 > SKOV 3 > HCT116 > HEK293). Lead compound 11f demonstrated maximum cytotoxicity (IC50 value of 13.30 μM) in HeLa cell lines and also caused early apoptosis-mediated cell death in cancer cell lines. We envision that our work will offer newer methodologies for the construction of fused quinoxaline 1,5-disubstituted-[1,4]-diazepine class of molecules.

Structurally Diverse Stilbenoids as Potent α-Glucosidase Inhibitors with Antidiabetic Effect from Morus alba.

Fifteen stilbenoid derivatives, including five previously undescribed ones (albaphenols A-E, 1-5) with diverse scaffolds, were obtained from the well-known agricultural economic tree Morus alba. Their structures, including absolute stereochemistries, were fully characterized by detailed interpretation of spectroscopic data and quantum chemical computational analyses of nuclear magnetic resonance (NMR) and electric circular dichroism (ECD). Albaphenol A (1) features an unprecedented rearranged carbon skeleton incorporating a novel 2-oxaspiro[bicyclo[3.2.1]octane-6,3'-furan] motif; albaphenol C (3) is likely derived from a cometabolite through an interesting intramolecular transesterification reaction; and albaphenol E (5) bears a cleavage-reconnection scaffold via a dioxane ring. All of the compounds exhibited significant inhibition against the diabetic target α-glucosidase, with low to submicromole IC50 values (0.70-8.27 μM), and the binding modes of selected molecules with the enzyme were further investigated by fluorescence quenching, kinetics, and molecular docking experiments. The antidiabetic effect of the most active and abundant mulberrofuran G (6) was further assessed in vivo in diabetic mice, revealing potent antihyperglycemic activity and comparable antidiabetic efficacy to the clinical drug acarbose.

Therapeutic Potential and Pharmacological Activities of Bioflavonoid ‘Ochnaflavone’ in Medicine: Diverse Scaffolds and Promise Leads for Drug Discovery

Background: Biflavonoids are natural phytocompounds that received enormous at-tention in various remedies due to their diverse biological activities. Biflavonoids have anti-inflammatory, anti-leishmanial, anti-plasmodial, anti-viral and β-secretase inhibitory activity in medicine. Ochnaflavone is a biflavone class natural phytochemical isolated from plants belong-ing to the Ochnaceae family. Methods:: Scientific information on ochnaflavone was collected and analyzed in the present investigation to investigate the biological activities of ochnaflavone. The present paper de-scribes the pharmacological activities and bioanalytical aspects of ochnaflavone based on the available scientific research on ochnaflavone in research work, books and other literature data-bases. Scientific data on ochnaflavone were collected from various scientific databases (Google, Science Direct, Scopus and PubMed) in this paper in order to investigate the health-beneficial potential of ochnaflavone in medicine. Further, the pharmacological activity of ochnaflavone was also collected in a detailed manner and discussed here in order to know the health-beneficial aspects of ochnaflavone. Results:: The therapeutic importance of ochnaflavone has been summarized in the present paper through available literature data on ochnaflavone in the scientific fields. Ochnaflavone was found to be an active phytochemical of Campylospermum excavatum, Cespedesia spathulata, Godoya antioquiensis, Lonicera japonica, Lonicerae Japonicae, Ochna afzelii, Ochna bed-domei, Ochna beddomi, Ochna integerrima, Ochna kibbiensis, Ochna pretoriensis, Ochna squarrosa Linn., Selaginella trichoclada and Triclisia gilletii. Scientific data revealed the bio-logical importance of ochnaflavone for its effectiveness on inflammation, SARS-CoV-2, fungal arthritis, enzymes, mutagenic effect, lymphocyte proliferation, and inhibition of arachidonate release. However, its antimycobacterial activity, cytotoxic effect, anti-HIV-1 activity, and anti-oxidant potential were also presented in this work. Further, analytical data on ochnaflavone has also been described. Conclusion: The present paper describes the therapeutic role of ochnaflavone in human disor-ders with their analytical aspects.