Homologation: A Versatile Molecular Modification Strategy to Drug Discovery

Homologous Design and Three-Dimensional Quantitative Structure-Activity Relationship Study of Acaricidal 2,4-Diphenyloxazolines Containing Different Heteroatoms and Alkyl Chains

In order to speculate the three-dimensional structure of the potential binding pocket of the chitin synthase inhibitor, a series of 2,4-diphenyloxazoline derivatives with different lengths of alkyl chains and heteroatoms were designed and synthesized by a homologous strategy. The bioassay results indicate that both the length of the alkyl chains and the type of substituents can affect the acaricidal activity against mite eggs. Compounds containing chloropropyl, alkoxyalkyl, and para-substituted phenoxyalkyl or phenylthioalkyl groups exhibit good activity, while those containing steric hindrance substituents or carbonyl substituents on the benzene ring exhibit reduced activity. Three-dimensional quantitative structure-activity relationship (3D-QSAR) study showed that there may be a narrow hydrophobic region deep in the pocket, and the steric effect plays a more important role than the electrostatic effect. The current work will provide assistance for future molecular design and target binding research.

Direct Access to Quinone-Fused 5-Substituted-1,4-Benzodiazepine Scaffolds from Azidoquinones with/without [1,2]-Azide-Nitrogen Migration: Mechanistic Insights

Seven-membered nitrogen heterocycles have a strong influence in drug discovery due to their inherent 3D character, which allows the ability to explore a vast conformational space with a biological target. Notably, the privileged 1,4-benzodiazepine scaffold is dominant in treating the central nervous system due to its binding affinity with the GABAA receptor. Herein, we report a protocol for the transformation of azidoquinones to p-quinone fused 5-substituted-1,4-benzodiazepines (p-QBZDs) from InCl3-catalyzed intermolecular tandem cycloannulation of azidoquinones with amines and aldehydes. Detailed mechanistic studies reveal that the EDA complex between azidoquinones and InCl3 is crucial in determining the reaction pathway. In the absence of EDA complex formation, the reaction proceeds via the intermediacy of 2,3-bridged-2H-azirine followed by regiospecific addition of an amine to C═N/ring opening/cyclization to deliver p-QBZD with 1,2-azide-nitrogen migration. In the case of EDA complex formation, the reaction proceeds through regioselective aza-Michael addition/nitrene insertion with aldehyde and subsequent cyclization to deliver p-QBZD and p-quinone fused imidazole as a secondary product without 1,2-azide-nitrogen migration. This protocol provides straightforward access to redox-active quinone embedded 5-substituted-1,4-benzodiazepines from azidoquinones with diverse substrate scopes that would find potential applications in medicinal chemistry and drug discovery.

Rhodium catalyzed tunable amide homologation through a hook-and-slide strategy

Preparation of diverse homologs from lead compounds has been a common and important practice in medicinal chemistry. However, homologation of carboxylic acid derivatives, particularly amides, remains challenging. Here we report a hook-and-slide strategy for homologation of tertiary amides with tunable lengths of the inserted carbon chain. Alkylation at the α-position of the amide (hook) is followed by highly selective branched-to-linear isomerization (slide) to effect amide migration to the end of the newly introduced alkyl chain; thus, the choice of alkylation reagent sets the homologation length. The key step involves a carbon-carbon bond activation process by a carbene-coordinated rhodium complex with assistance from a removable directing group. The approach is demonstrated for introduction of chains as long as 16 carbons and is applicable to derivatized carboxylic acids in complex bioactive molecules.

Base-mediated homologative rearrangement of nitrogen-oxygen bonds of N-methyl-N-oxyamides

Due to the well known reactivity of C(O)-N functionalities towards canonical C1-homologating agents (e.g. carbenoids, diazomethane, ylides), resulting in the extrusion of the N-centered fragment en route to carbonyl compounds, formal C1-insertions within N-O bonds still remain obscure. Herein, we document the homologative transformation of N-methyl-N-oxyamides - with high tolerance for diverse O-substituents - into N-acyl-N,O-acetals. Under controlled basic conditions, the N-methyl group of the same starting materials acts as a competent precursor of the methylene synthon required for the homologation. The logic is levered on the formation of an electrophilic iminium ion (via N-O heterolysis) susceptible to nucleophilic attack by the alkoxide previously expulsed. The procedure documents genuine chemocontrol and flexibility, as judged by the diversity of substituents placed on both amide and nitrogen linchpins. The mechanistic rationale was validated through experiments conducted on D-labeled materials which unambiguously attributed the origin of the methylene fragment to the N-methyl group of the starting compounds.

The Magic Methyl and Its Tricks in Drug Discovery and Development

One of the key scientific aspects of small-molecule drug discovery and development is the analysis of the relationship between its chemical structure and biological activity. Understanding the effects that lead to significant changes in biological activity is of paramount importance for the rational design and optimization of bioactive molecules. The "methylation effect", or the "magic methyl" effect, is a factor that stands out due to the number of examples that demonstrate profound changes in either pharmacodynamic or pharmacokinetic properties. In many cases, this has been carried out rationally, but in others it has been the product of serendipitous observations. This paper summarizes recent examples that provide an overview of the current state of the art and contribute to a better understanding of the methylation effect in bioactive small-molecule drug candidates.

In vitro and ex vivo antibiofilm activity of riparin 1, and its nor and dinor homologs, against dermatophytes

Dermatophytosis is one of the most frequent superficial mycoses in the world. They are mainly caused by the dermatophytes Trichophyton rubrum and Microsporum canis. Biofilm production is an essential factor in the pathogenesis of dermatophytes; it confers drug resistance and significantly impairs antifungal effectiveness. Therefore, we evaluated the antibiofilm activity of an alkamide-type alkaloid called riparin 1 (RIP1) against clinically relevant dermatophytes. We also produced synthetic nor (NOR1) and dinor (DINOR1) homologs for pharmacological evaluation, with a 61-70% yield. We used in vitro (96-well polystyrene plates) and ex vivo (hair fragments) models to verify the effects of these compounds on the formation and viability of biofilms. RIP1 and NOR1 showed antifungal activity against strains of T. rubrum and M. canis, but DINOR1 showed no significant antifungal activity against the dermatophytes. Furthermore, RIP1 and NOR1 significantly reduced the viability of biofilms in vitro and ex vivo (P < 0.05). RIP1 was more potent than NOR1, possibly due to the distance between the p-methoxyphenyl and the phenylamide moieties in these compounds. Due to the significant antifungal and antibiofilm activities observed for RIP1 and NOR1, we suggest that they could be useful in the treatment of dermatophytosis.

Design, Synthesis and Phenotypic Profiling of Simplified Gedatolisib Analogues

Targeted antitumour therapy has revolutionized the treatment of several types of tumours. Among the validated targets, phosphatidylinositol-3 kinase (PI3K) deserves to be highlighted. Several PI3K inhibitors have been developed for the treatment of cancer, including gedatolisib (4). This inhibitor was elected as a prototype and molecular modifications were planned to design a new series of simplified gedatolisib analogues (5a-f). The analogues were synthesised, and the comparative cytotoxic activity profile was studied in phenotypic models employing solid and nonadherent tumour cell lines. Compound 5f (LASSBio-2252) stood out as the most promising of the series, showing good aqueous solubility (42.38 μM (pH = 7.4); 39.33 μM (pH = 5.8)), good partition coefficient (cLogP = 2.96), cytotoxic activity on human leukemia cell lines (CCRF-CEM, K562 and MOLT-4) and an excellent metabolic stability profile in rat liver microsomes (t1/2 = 462 min; Clapp = 0.058 mL/min/g). The ability of 5f to exert its cytotoxic effect through modulation of the PI3K pathway was demonstrated by flow cytometry analysis in a comparative manner to gedatolisib.

An algorithm to classify homologous series within compound datasets

Homologous series are groups of related compounds that share the same core structure attached to a motif that repeats to different degrees. Compounds forming homologous series are of interest in multiple domains, including natural products, environmental chemistry, and drug design. However, many homologous compounds remain unannotated as such in compound datasets, which poses obstacles to understanding chemical diversity and their analytical identification via database matching. To overcome these challenges, an algorithm to detect homologous series within compound datasets was developed and implemented using the RDKit. The algorithm takes a list of molecules as SMILES strings and a monomer (i.e., repeating unit) encoded as SMARTS as its main inputs. In an iterative process, substructure matching of repeating units, molecule fragmentation, and core detection lead to homologous series classification through grouping of identical cores. Three open compound datasets from environmental chemistry (NORMAN Suspect List Exchange, NORMAN-SLE), exposomics (PubChemLite for Exposomics), and natural products (the COlleCtion of Open NatUral producTs, COCONUT) were subject to homologous series classification using the algorithm. Over 2000, 12,000, and 5000 series with CH₂ repeating units were classified in the NORMAN-SLE, PubChemLite, and COCONUT respectively. Validation of classified series was performed using published homologous series and structure categories, including a comparison with a similar existing method for categorising PFAS compounds. The OngLai algorithm and its implementation for classifying homologues are openly available at: https://github.com/adelenelai/onglai-classify-homologues .

Discovery of Putative Dual Inhibitor of Tubulin and EGFR by Phenotypic Approach on LASSBio-1586 Homologs

Combretastatin A-4 (CA-4, 1) is an antimicrotubule agent used as a prototype for the design of several synthetic analogues with anti-tubulin activity, such as LASSBio-1586 (2). A series of branched and unbranched homologs of the lead-compound 2, and vinyl, ethinyl and benzyl analogues, were designed and synthesized. A comparison between the cytotoxic effect of these homologs and 2 on different human tumor cell lines was performed from a cell viability study using MTT with 48 h and 72 h incubations. In general, the compounds were less potent than CA-4, showing CC50 values ranging from 0.030 μM to 7.53 μM (MTT at 72 h) and 0.096 μM to 8.768 μM (MTT at 48 h). The antimitotic effect of the target compounds was demonstrated by cell cycle analysis through flow cytometry, and the cellular mechanism of cytotoxicity was determined by immunofluorescence. While the benzyl homolog 10 (LASSBio-2070) was shown to be a microtubule stabilizer, the lead-compound 2 (LASSBio-1586) and the methylated homolog 3 (LASSBio-1735) had microtubule destabilizing behavior. Molecular docking studies were performed on tubulin protein to investigate their binding mode on colchicine and taxane domain. Surprisingly, the benzyl homolog 10 was able to modulate EGFR phosphorylate activity in a phenotypic model. These data suggest LASSBio-2070 (10) as a putative dual inhibitor of tubulin and EGFR. Its binding mode with EGFR was determined by molecular docking and may be useful in lead-optimization initiatives.

Camphor nitroimine: a key building block in unusual transformations and its applications in the synthesis of bioactive compounds

The development of new drugs requires a lot of time and high financial investments. It involves a research network in which there is the participation of several researchers from different areas. For a new drug to reach the market, thousands of substances must be evaluated. There are several tools for this and the use of suitable building blocks can facilitate the process by allowing a lead compound to have suitable parameters. These compounds are key structures containing special functional groups that also permit adequate synthetic transformations, leading to several structures of interest in a short period of time. In this review, the use of camphor nitroimine as a potential key building block is explored. Derived from camphor, an abundant natural product present in various plant species, this nitroimine has proved to be quite versatile, allowing the access to substances with miscellaneous biological activities, ligands to asymmetric catalysis, asymmetric oxidants, O-N transfer agents and other applications. Its easy conversion to camphecene and other derivatives is described, as well as their applications in medicinal chemistry. Druglikeness analyses were performed on these studied agents as well as on their bioactive derivatives in order to assess their use in the development of potential drugs.

Synthesis and Application of Constrained Amidoboronic Acids Using Amphoteric Boron-Containing Building Blocks

Amidoboronic acid-containing peptidomimetics are an important class of scaffolds in chemistry and drug discovery. Despite increasing interest in boron-based enzyme inhibitors, constrained amidoboronic acids have received little attention due to the limited options available for their synthesis. We describe a new methodology to prepare both α- and β-amidoboronic acids that impose restrictions on backbone angles. Lewis acid-promoted Boyer-Schmidt-Aube lactam ring expansions using an azidoalkylboronate enabled generation of constrained α-amidoboronic acid derivatives, whereas assembly of the homologous β-amidoboronic acids was achieved through a novel boronic acid-mediated lactamization process stemming from an α-boryl aldehyde. The results of quantum chemical calculations suggest carboxylate-boron coordination to be rate-limiting for small ring sizes, whereas the tetrahedral intermediate formation is rate limiting in the case of larger rings. As part of this study, an application of β-amidoboronic acid derivatives as novel VIM-2 metallo-β-lactamase inhibitors has been demonstrated.

Hydrofluoromethylation of alkenes with fluoroiodomethane and beyond

A process for the direct hydrofluoromethylation of alkenes is reported for the first time. This straighforward silyl radical-mediated reaction utilises CH₂FI as a non-ozone depleting reagent, traditionally used in electrophilic, nucleophilic and carbene-type chemistry, but not as a CH₂F radical source. By circumventing the challenges associated with the high reduction potential of CH₂FI being closer to CH₃I than CF₃I, and harnessing instead the favourable bond dissociation energy of the C–I bond, we demonstrate that feedstock electron-deficient alkenes are converted into products resulting from net hydrofluoromethylation with the intervention of (Me₃Si)₃SiH under blue LED activation. This deceptively simple yet powerful methodology was extended to a range of (halo)methyl radical precursors including ICH₂I, ICH₂Br, ICH₂Cl, and CHBr₂F, as well as CH₃I itself; this latter reagent therefore enables direct hydromethylation. This versatile chemistry was applied to ¹⁸F-, ¹³C-, and D-labelled reagents as well as complex biologically relevant alkenes, providing facile access to more than fifty products for applications in medicinal chemistry and positron emission tomography.

Herein, we report the direct hydro(halo)methylation of alkenes from a variety of (halo)methyl iodides (including F-18, C-13, D-2 isotopologues), enabling the incorporation of a plethora of C-1 fragments into complex biologically active molecules.

Design and Synthesis In Silico Drug-like Prediction and Pharmacological Evaluation of Cyclopolymethylenic Homologous of LASSBio-1514

Acylhydrazones are still an important framework to the design of new bioactive compounds. As treatment of chronic pain represents a clinical challenge, we decided to modify the structure of LASSBio-1514 (1), previously described as anti-inflammatory and analgesic prototype. Applying the homologation as a strategy for molecular modification, we designed a series of cyclopentyl- (2a-e), cyclobutyl- (3a-e), and cyclopropylacylhydrazones (4a-e) that were synthetized and evaluated in murine models of inflammation and pain. A comparison of their in silico physicochemical and drug-like profile was conducted, as well as their anti-inflammatory and analgesic effect. Compounds 4a (LASSBio-1755) and 4e (LASSBio-1757) displayed excellent in silico drug-like profiles and were identified as new analgesic lead-candidates in acute and chronic model of pain, through oral administration.