Medicinal Chemistry Research Articles

Site-Selective Distal C(sp3)-H Bromination of Aliphatic Amines as a Gateway for Forging Nitrogen-Containing sp3 Architectures.

Herein, we disclose a new strategy that rapidly and reliably incorporates bromine atoms at distal, secondary C(sp3)-H sites in aliphatic amines with excellent and predictable site-selectivity pattern. The resulting halogenated building blocks serve as versatile linchpins to enable a series of carbon-carbon and carbon-heteroatom bond-formations at remote C(sp3) sites, thus offering a new modular and unified platform that expedites the access to advanced sp3 architectures possessing valuable nitrogen-containing saturated heterocycles of interest in medicinal chemistry settings.

Site Identification and Next Choice Protocol for Hit-to-Lead Optimization.

Time efficiency and cost savings are major challenges in drug discovery and development. In this process, the hit-to-lead stage is expected to improve efficiency because it primarily exploits the trial-and-error approach of medicinal chemists. This study proposes a site identification and next choice (SINCHO) protocol to improve the hit-to-lead efficiency. This protocol selects an anchor atom and growth site pair, which is desirable for a hit-to-lead strategy starting from a 3D complex structure. We developed and fine-tuned the protocol using a training data set and assessed it using a test data set of the preceding hit-to-lead strategy. The protocol was tested for experimentally determined structures and molecular dynamics (MD) ensembles. The protocol had a high prediction accuracy for applying MD ensembles, owing to the consideration of protein flexibility. The SINCHO protocol enables medicinal chemists to visualize and modify functional groups in a hit-to-lead manner.

Incorporating Synthetic Accessibility in Drug Design: Predicting Reaction Yields of Suzuki Cross-Couplings by Leveraging AbbVie's 15-Year Parallel Library Data Set.

Despite the increased use of computational tools to supplement medicinal chemists' expertise and intuition in drug design, predicting synthetic yields in medicinal chemistry endeavors remains an unsolved challenge. Existing design workflows could profoundly benefit from reaction yield prediction, as precious material waste could be reduced, and a greater number of relevant compounds could be delivered to advance the design, make, test, analyze (DMTA) cycle. In this work, we detail the evaluation of AbbVie's medicinal chemistry library data set to build machine learning models for the prediction of Suzuki coupling reaction yields. The combination of density functional theory (DFT)-derived features and Morgan fingerprints was identified to perform better than one-hot encoded baseline modeling, furnishing encouraging results. Overall, we observe modest generalization to unseen reactant structures within the 15-year retrospective library data set. Additionally, we compare predictions made by the model to those made by expert medicinal chemists, finding that the model can often predict both reaction success and reaction yields with greater accuracy. Finally, we demonstrate the application of this approach to suggest structurally and electronically similar building blocks to replace those predicted or observed to be unsuccessful prior to or after synthesis, respectively. The yield prediction model was used to select similar monomers predicted to have higher yields, resulting in greater synthesis efficiency of relevant drug-like molecules.

Synthesis, structure of the N-(Alkyl/Arylsulfonyl) substituted 5-(Bromo/Iodo)-3-methylindazoles and bioactivity screening against some of the biochemical targets linked to type 2 diabetes mellitus

The indazole scaffold and sulfonamide moiety have evoked high interest in medicinal chemistry especially in the context of antidiabetic drug development. A series of the C-5 unsubstituted (2a–f), 5‑bromo (2g–l) and 5-iodo (2m–r) substituted 1-(alkyl/arylsulfonyl)-3-methylindazoles were prepared, characterized and then evaluated through enzymatic assay in vitro for anti-α-glucosidase activity and for potential free radical scavenging properties. Compounds 2b, 2d, 2f–h, 2k, 2p and 2q exhibited strong activity against α-glucosidase compared to acarbose (IC50 = 1.30 ± 0.02 µM) with IC50 values in the range of 0.72 ± 0.03 – 1.20 ± 0.01 µM. These compounds exhibited increased or strong 2,2-diphenyl-1-picrylhydrazyl (DPPH) and/or nitric oxide (NO) free radical scavenging activities. The compounds were, in turn, evaluated through enzymatic assays in vitro for the potential to inhibit or activate superoxide dismutase (SOD), lipoxygenase-15 (LOX-15) and/or vascular endothelial growth factor receptor-2 (VEGFR-2) activities. An in vitro cell-based antioxidant activity assay involving lipopolysaccharide induced reactive oxygen species (ROS) production in the human breast (MCF-7) cancer cell line revealed that compounds 2d, 2f and 2h exhibit moderate activity (35.5 %, 47 % and 28 %, respectively) compared to staurosporine (24 %). Compounds 2d, 2f and 2h significantly reduced the ROS level in the human embryonic kidney (HEK293-T) cells (65.5 %, 58 % and 48 %, respectively) compared to staurosporine (34 %). The planar benzo-fused heterocyclic scaffold and the distorted tetrahedral geometry of the N-sulfonyl moiety are predicted to facilitate hydrophobic and/or hydrogen bonding interactions to stabilize protein-ligand interaction in the receptors. The ADME analysis predicted that the test compounds have drug-like properties, a safe toxicity profile in silico without any carcinogenic and mutagenicity side effect. Molecular modelling was also used to attempt to rationalize the biological activity of these compounds and to correlate the results of in vitro and in silico studies.

Experimental biological studies of novel tetradentate hydrazone Cu(II) complexes for potential applications in medicinal chemistry

A series of mononuclear Cu(II) complexes were synthesized using a potential tetradentate hydrazone ligand obtained from the reaction between phenylhydrazine groups and 2,5-thiophenedicarboxaldehyde. The structures of ligands and complexes were elucidated through various spectroscopic techniques, confirming their composition. All complexes were found to adopt four-coordinated geometries, indicating the formation of stable structures. Spectroscopic analysis revealed that the hydrazone ligand coordinated with the Cu(II) metal ions as a dibasic tetradentate ligand by utilizing the phenolic oxygen and azomethine nitrogen atoms. The binding affinity of the complexes with calf thymus DNA (CT-DNA) was investigated using absorption and viscosity measurements, demonstrating their interaction through the intercalation mode. The binding studies showed that the Cu(II) complexes exhibited varying degrees of binding affinity, with Cu(L4) demonstrating the highest affinity, followed by Cu(L1), Cu(L2), and Cu(L3). Moreover, the DNA fragmentation properties of the Cu(II) complexes were evaluated, suggesting their potential utilization in pharmaceutical applications. The obtained results highlight the significance of these novel complexes in the field of medicinal chemistry.

Discovery of N-X anomeric amides as electrophilic halogenation reagents.

Electrophilic halogenation is a widely used tool employed by medicinal chemists to either pre-functionalize molecules for further diversity or incorporate a halogen atom into drugs or drug-like compounds to solve metabolic problems or modulate off-target effects. Current methods to increase the power of halogenation rely on either the invention of new reagents or activating commercially available reagents with various additives such as Lewis or Brønsted acids, Lewis bases and hydrogen-bonding activators. There is a high demand for new reagents that can halogenate otherwise unreactive compounds under mild conditions. Here we report the invention of a class of halogenating reagents based on anomeric amides, taking advantage of the energy stored in the pyramidalized nitrogen of N-X anomeric amides as a driving force. These robust halogenating methods are compatible with a variety of functional groups and heterocycles, as exemplified on over 50 compounds (including 13 gram-scale examples and 1 flow chemistry scale-up).

STOPLIGHT: A Hit Scoring Calculator.

We introduce STOPLIGHT, a web portal to assist medicinal chemists in prioritizing hits from screening campaigns and the selection of compounds for optimization. STOPLIGHT incorporates services to assess 6 physiochemical and structural properties, 6 assay liabilities, and 11 pharmacokinetic properties, for any small molecule represented by its SMILES string. We briefly describe each service and illustrate the utility of this portal with a case study. The STOPLIGHT portal provides a user-friendly tool to guide hit selection in early drug discovery campaigns, whereby compounds with unfavorable properties can be quickly recognized and eliminated.

The emergence of sulfo-click amidation in kinetic target-guided synthesis

AbstractSulfo-click is a chemoselective and biocompatible reaction between thioacids and sulfonyl azides that forms highly versatile N-acylsulfonamides, interesting bioisosteres of carboxylic acids. This reaction is useful for chemists and biologists and has many applications in medicinal chemistry, drug discovery, bioconjugation chemistry, and chemical biology. Sulfo-click amidations have been extensively used in kinetic target-guided synthesis (KTGS) to identify modulators of protein-protein interactions (PPIs). Different variants of KTGS screening, such as binary and multi-fragments, as well as one-pot deprotection/amidation strategies, have been successfully performed using sulfo-click chemistry. In this mini-review, we discuss the recent developments of sulfo-click amidation in KTGS and provide directions for future research.

Visible-Light-Induced Radical Sulfonylative-Cyclization Cascade of 1,6-Enynol Derivatives with Sulfinic Acids: A Sustainable Approach for the Synthesis of 2,3-Disubstituted Benzoheteroles.

Benzoheteroles are promising structural scaffolds in the realm of medicinal chemistry, but sustainable synthesis of 2,3-difunctionalized benzoheterole derivatives is still in high demand. Indeed, we have conceptually rationalized the intrinsic reactivity of propargylic-enyne systems for the flexible construction of 2,3-disubstituted benzoheteroles through radical sulfonylative-cyclization cascade under organophotoredox catalysis. We hereby report an efficient visible-light-induced sulfonyl radical-triggered cyclization of 1,6-enynols with sulfinic acids under the dual catalytic influence of 4CzIPN and NiBr2⋅DME, which led to the formation of 2,3-disubstituted benzoheteroles in good to high yields. Additionally, the Rose Bengal (RB)-catalyzed radical sulfonylative-cycloannulation of acetyl-derived 1,6-enynols with sulfinic acids under blue LED irradiation allowed to access 3-(E-styryl)-derived benzofurans and benzothiophenes in moderate to good yields. The scope and limitations of the present strategies were successfully established using different classes of 1,6-enynols and sulfinic acids bearing various sensitive functional groups, yielding the desired products in a highly stereoselective fashion. Plausible mechanistic pathways were also proposed based on the current experimental and control experiments.

Naphthyl‐Based Chalcone Derivatives: A Multifaceted Player in Medicinal Chemistry

AbstractResearch has placed a great deal of emphasis on molecule development and discovery with substantial biological profiling in recent years. Despite the significant side effects, medicinal chemists have long strived to synthesize drug molecules with the highest level of therapeutic activity and the lowest possible level of toxicity. The naphthyl‐based chalcone derivatives have drawn attention due to their simple structures and wide range of pharmacological effects. The main focus of this review is to outline the biologically active molecules based on naphthyl moiety‐substituted chalcone derivatives developed over the years. A synopsis of pharmacological screening, including relevant structure‐activity relationships, action mechanisms, and possible therapeutic applications, is provided in this article. It is true that prospective hybrids combining the naphthyl moiety with different chalcone pharmacophores are needed to address drug resistance and improve specificity. Therefore, this review may be useful in the development and design of new, highly successful therapeutic drugs based on previously reported methodologies.

Transition‐Metal‐Free Annulation of Sulfonyl‐Derived 1,3‐Enynes: Simple and Efficient Construction of 2,4‐Disubstituted Thiophenes and Vinyl Sulfone‐Tethered 1,2,3‐NH‐Triazoles

Thiophenes and 1,2,3‐NH‐triazoles are important frameworks in pharmaceuticals and advanced functional materials. Vinyl sulfones are also blueprint motifs in medicinal chemistry, but hybrid analogues of 1,2,3‐NH‐triazole‐derived from vinyl sulfones still need to be explored. In this report, we present an efficient and transition‐metal‐free [4+1]‐thioannulation of sulfonyl‐tethered 1,3‐enynes with Na2S in the presence of Cs2CO3 to generate 2,4‐disubstituted thiophenes in good to high yields. We also established a formal [3+2]‐cycloaddition of 1,3‐sulfonylenynes with NaN3 under metal‐ and base‐free conditions to synthesize vinyl sulfone‐containing 1,2,3‐NH‐triazole derivatives in moderate to high yields. The scope of these protocols was successfully showcased with various types of 1,3‐enynes bearing sensitive functional groups and complex structural scaffolds. The desired products were readily obtained with good functional group tolerance and compatibility. Based on the existing results and control experiments, plausible mechanistic pathways are also presented.

Rhodium‐Catalyzed C–H Bond Annulation for the Synthesis of 5‐ and 6‐Membered N‐Heterocyclic Building Blocks

The sustainable preparation of N‐heterocycles is one of the most active research areas owing to their predominance as synthetics building blocks with extensive applications in organic, pharmaceutical, and material chemistry fields. Among the various catalytic protocols, the C–H bond functionalization with the concomitant C–N bond formation, so‐called C–H bond annulation, has become one of the most sustainable routes to access N‐heterocycles because it starts from low‐functionalized materials and generates a limited amount of waste, all respecting the concept of atom economy. Rhodium complexes often catalyze these reactions. This review focuses on the synthesis of 5‐ and 6‐membered ring N‐containing heterocycles such as indoles, pyrroles, indolines, (iso)quinolinones, dihydroquinolines, and pyrrolidones from readily available starting materials, with an emphasis on the novel C–H bond cascade synthetic methodologies via C–N/C–C bond formation, as well as on the mechanisms of these reactions, especially the oxidation steps. We hope this review will help researchers looking to prepare N‐heterocycles in a minimum of steps and those who want to develop new methodologies based on C–H bond activation/functionalizations.

Hydrosulfonylation of Alkynes for Stereodivergent Synthesis of Vinyl Sulfones: Synthetic Strategy and Mechanistic Insights.

Direct synthesis of thermodynamically less favorable (Z)-vinyl sulfones presents a notable challenge in organic synthesis. In addition, the development of a stereodivergent synthesis for (E)- and (Z)-vinyl sulfones is crucial but remains elusive. In this study, we present a hydrosulfonylation of aryl-substituted alkynes, achieving a stereodivergent synthesis of (E)- and (Z)-vinyl sulfones by leveraging both thermodynamic and kinetic controls. Notably, the synthesis of challenging (Z)-vinyl sulfones was achieved through a kinetically controlled process without the need for a catalyst. To synthesize (E)-vinyl sulfones, unconventional visible light-mediated isomerization was employed as a means of facilitating the transition to the thermodynamically favored form. The present study encompasses a comprehensive experimental and computational investigation, which provides valuable insights into the reaction mechanism. This investigation reveals two plausible isomerization pathways: a novel double spin-flip mechanism and a hydrogen atom transfer process in the presence of eosin Y. This study not only advances our understanding of isomerization mechanisms beyond conventional energy-transfer routes but also offers a robust and switchable strategy for synthesizing (E)- and (Z)-vinyl sulfones, thereby providing a versatile avenue for the creation of valuable compounds in the fields of organic synthesis and medicinal chemistry.

Ultrasound-Assisted, BF3·OEt2-Promoted, Multicomponent Synthesis of Chromene-Based Podophyllotoxin Analogues

AbstractA novel method was developed to synthesise chromene-lactone analogues of podophyllotoxin using an ultrasound-assisted multicomponent reaction (MCR). The MCR involved tetronic acid, phenols, and aromatic aldehydes and was promoted by BF3·OEt2, resulting in the production of ten derivatives with different substituents on the aromatic rings in yields ranging from 32% to 93%. These compounds are of interest due to their reported activity against tumour cells. Their ease of synthesis through the MCR may allow for more in-depth studies on anticancer activity, as well as investigations of other biological targets. The synthesised derivatives contain important pharmacophoric groups for potential applications in medicinal chemistry.

Recent Advances in Metal-Catalyzed Approaches for the Synthesis of Quinazoline Derivatives.

Quinazolines are an important class of heterocyclic compounds that have proven their significance, especially in the field of organic synthesis and medicinal chemistry because of their wide range of biological and pharmacological properties. Thus, numerous synthetic methods have been developed for the synthesis of quinazolines and their derivatives. This review article briefly outlines the new synthetic methods for compounds containing the quinazoline scaffold employing transition metal-catalyzed reactions.

Ortho-Halobenzyl Halides as Precursors for the Synthesis of Five- to Nine-Membered Ring Structures Employing Transition Metals as Catalysts

AbstractThis review highlights the multifaceted usefulness of o-halobenzyl halides as pivotal substrates for the construction of five- to nine-membered cyclic structures with the aid of transition metals as catalysts. These privileged entities engage dual active sites, enabling the combination of both intermolecular benzylation and intramolecular arylation strategies that directs the formation of a diverse repository of cyclic structures. The introduction of transition-metal catalysis in cross-coupling transformations sparked a revolution in forging aryl–heteroatom bonds, culminating in the evolution of more potent methodologies for the synthesis of a wide spectrum of valuable compounds. Furthermore, the associated pharmaceutical and biological attributes of these cyclic structures augment their significance in medicinal chemistry research. This review aims to showcase the importance of this synthetic methodology and its far-reaching applications in synthesis.1 Introduction2 Synthesis of Five-Membered Rings3 Synthesis of Six-Membered Rings4 Synthesis of Seven-Membered Rings5 Synthesis of Eight- and Nine-Membered Rings6 Conclusion

Ultrapotent influenza hemagglutinin fusion inhibitors developed through SuFEx-enabled high-throughput medicinal chemistry

Seasonal and pandemic-associated influenza strains cause highly contagious viral respiratory infections that can lead to severe illness and excess mortality. Here, we report on the optimization of our small-molecule inhibitor F0045(S) targeting the influenza hemagglutinin (HA) stem with our Sulfur-Fluoride Exchange (SuFEx) click chemistry-based high-throughput medicinal chemistry (HTMC) strategy. A combination of SuFEx- and amide-based lead molecule diversification and structure-guided design led to identification and validation of ultrapotent influenza fusion inhibitors with subnanomolar EC50 cellular antiviral activity against several influenza A group 1 strains. X-ray structures of six of these compounds with HA indicate that the appended moieties occupy additional pockets on the HA surface and increase the binding interaction, where the accumulation of several polar interactions also contributes to the improved affinity. The compounds here represent the most potent HA small-molecule inhibitors to date. Our divergent HTMC platform is therefore a powerful, rapid, and cost-effective approach to develop bioactive chemical probes and drug-like candidates against viral targets.

Nonclassical Zwitterions as a Design Principle to Reduce Lipophilicity without Impacting Permeability.

The ionization of bioactive molecules impacts many ADME-relevant physicochemical properties, in particular, solubility, lipophilicity, and permeability. Ampholytes contain both acidic and basic groups and are distinguished as ordinary ampholytes and zwitterions. An influential review states that zwitterions only exist if the acidic pKa is significantly lower than the basic pKa. Through concordance of measured and calculated pKa and log P, we show that the zwitterionic behavior of several marketed drugs and natural products occurs despite a low or negative ΔpKa. These nonclassical zwitterions are characterized by a weak acidic and basic pKa and conjugation through an extended aromatic system, often including pseudorings via intramolecular hydrogen bonds. In contrast to most classical zwitterions, nonclassical zwitterions can exhibit excellent permeability. As permeability and lipophilicity are typically correlated, the combination of low lipophilicity and high permeability makes nonclassical zwitterions an attractive design principle in medicinal chemistry.

Introduction of the difluoromethyl group at the meta- or para-position of pyridines through regioselectivity switch

Difluoromethyl pyridines have gained significant attention in medicinal and agricultural chemistry. The direct C−H-difluoromethylation of pyridines represents a highly efficient economic way to access these azines. However, the direct meta-difluoromethylation of pyridines has remained elusive and methods for site-switchable regioselective meta- and para-difluoromethylation are unknown. Here, we demonstrate the meta-C−H-difluoromethylation of pyridines through a radical process by using oxazino pyridine intermediates, which are easily accessed from pyridines. The selectivity can be readily switched to para by in situ transformation of the oxazino pyridines to pyridinium salts upon acid treatment. The preparation of various meta- and para-difluoromethylated pyridines through this approach is presented. The mild conditions used also allow for the late-stage meta- or para-difluoromethylation of pyridine containing drugs. Sequential double functionalization of pyridines is presented, which further underlines the value of this work.

Synthesis of Azo-Substituted Bicyclo[1.1.1]pentanes (BCPs) via Base-Promoted Halogen Atom Transfer.

Because of the three-dimensional bioisosteric feature, bicyclo[1.1.1]pentylamines (BCPAs) are valuable scaffolds in synthetic chemistry and medicinal chemistry. Here, we report a Halogen Atom Transfer (XAT) mediated radical C-N coupling between C3-iodo-BCPs and diazonium salts in the presence of base. Similarly, a multicomponent reaction (MCR) enables the simultaneous construction of the C-C bond and C-N bond simultaneously. Versatile roles of diazonium salts were also explored.