NMR strategies to support medicinal chemistry workflows for primary structure determination

Porphyrin Atropisomerism as a Molecular Engineering Tool in Medicinal Chemistry, Molecular Recognition, Supramolecular Assembly, and Catalysis

Porphyrin atropisomerism, which arises from restricted σ-bond rotation between the macrocycle and a sufficiently bulky substituent, was identified in 1969 by Gottwald and Ullman in 5,10,15,20-tetrakis(o-hydroxyphenyl)porphyrins. Henceforth, an entirely new field has emerged utilizing this transformative tool. This review strives to explain the consequences of atropisomerism in porphyrins, the methods which have been developed for their separation and analysis and present the diverse array of applications. Porphyrins alone possess intriguing properties and a structure which can be easily decorated and molded for a specific function. Therefore, atropisomerism serves as a transformative tool, making it possible to obtain even a specific molecular shape. Atropisomerism has been thoroughly exploited in catalysis and molecular recognition yet presents both challenges and opportunities in medicinal chemistry.

NMR spectroscopy can help accelerate antiviral drug discovery programs

Small molecule drugs have an important role to play in combating viral infections, and biophysics support has been central for contributing to the discovery and design of direct acting antivirals. Perhaps one of the most successful biophysical tools for this purpose is NMR spectroscopy when utilized strategically and pragmatically within team workflows and timelines. This report describes some clear examples of how NMR applications contributed to the design of antivirals when combined with medicinal chemistry, biochemistry, X-ray crystallography and computational chemistry. Overall, these multidisciplinary approaches allowed teams to reveal and expose compound physical properties from which design ideas were spawned and tested to achieve the desired successes. Examples are discussed for the discovery of antivirals that target HCV, HIV and SARS-CoV-2.

Aporphine and amide alkaloids from Illigera parviflora

Three undescribed alkaloids (+)-9-hydroxy-N-acetylnordicentrine (1), illigeparvinine (2), and deca-(2E,4Z)-2,4-dienoic acid 4-hydroxy-2-phenethyl amide (3), along with 19 known analogues (4-22), were isolated from the ethnic medicinal plant Illigera parviflora. Their structures were established using NMR, MS, and other spectroscopic analyses as well as X-ray diffraction. Moderate inhibition of human gastric carcinoma (MGC-803) and breast adenocarcinoma (T-47D) cell lines proliferation was observed for actinodaphnine (4) with IC50 values of 28.74 and 11.65 μM, respectively. These findings contribute new anticancer potential compounds and expand the chemical diversity known from the valuable traditional medicinal plant I. parviflora.

Determining the Predominant Conformations of Mortiamides A-D in Solution Using NMR Data and Molecular Modeling Tools

Macrocyclic peptidomimetics have been seriously contributing to our arsenal of drugs to combat diseases. The search for nature's discoveries led us to mortiamides A-D (found in a novel fungus from Northern Canada), which is a family of cyclic peptides that clearly have demonstrated impressive pharmaceutical potential. This prompted us to learn more about their solution-state properties as these are central for binding to target molecules. Here, we secured and isolated mortiamide D, and then acquired high-resolution nuclear magnetic resonance (NMR) data to learn more about its structure and dynamics attributes. Sets of two-dimensional NMR experiments provided atomic-level (through-bond and through-space) data to confirm the primary structure, and NMR-driven molecular dynamics (MD) simulations suggested that more than one predominant three-dimensional (3D) structure exist in solution. Further steps of MD simulations are consistent with the finding that the backbones of mortiamides A-C also have at least two prominent macrocyclic shapes, but the side-chain structures and dynamics differed significantly. Knowledge of these solution properties can be exploited for drug design and discovery.

Design and synthesis optimization of novel diimide indoles derivatives for ameliorating acute lung injury through modulation of NF-κB signaling pathway

Acute lung injury (ALI) is a common respiratory disease caused by local or systemic inflammatory reaction. Based on the natural 7-chain diaryl anti-inflammatory framework, a series of diimide indoles derivatives were designed by combining curcumin and indole in this study. The synthesis of diimide compounds was extended using dichloromethane (DCM) as solvent and 1,1'-carbonyldiimidazole (CDI) and sodium hydride (NaH) as double activators, and a total of 40 diimide-indole derivatives were obtained. The results of in vitro anti-inflammatory activity showed that most compounds could inhibit the production of interleukin-6 (IL-6) better than curcumin and indomethacin. Among the compounds, the IC₅₀ of compound 11f on IL-6 reached 1.05 μM with no obvious cytotoxic side effects. Mechanistically, compound 11f could block the expression of NF-κB P65 phosphorylation, and nuclear translocation of P65. The acute toxicity tests in-vivo also showed no obvious toxicity in mice after the intragastric administration of 1000 mg/kg. In addition, the compound 11f could significantly inhibit the LPS-induced inflammatory response in mice and reduce the number of neutrophils and wet/dry lung weight ratio, thereby alleviating ALI. These results indicated that the novel diimide indoles were promising anti-inflammatory agents for the treatment of ALI.

Extraction, Purification, and Elucidation of Six Ginkgol Homologs from Ginkgo biloba Sarcotesta and Evaluation of Their Anticancer Activities

Ginkgols are active constituents from Ginkgo biloba L. (GB) and have pharmacological activities, such as antibacterial and antioxidant activities. In our previous report, only five ginkgols were separated. However, ginkgol C17:1 had two isomers, for which their separation, identification, and bioactivities have not yet been investigated. Hence, this research reports the successful isolation of six ginkgol homologs with alkyl substituents-C17:1-Δ¹², C15:1-Δ⁸, C13:0, C17:2, C17:1-Δ¹⁰, and C15:0-for the first time using HPLC. This was followed by the identification of their chemical structures using Fourier transform infrared (FTIR), ultraviolet (UV), gas chromatography and mass spectrometry (GC-MS), carbon-13 nuclear magnetic resonance (¹³C-NMR), and proton nuclear magnetic resonance (¹H-NMR) analysis. The results showed that two ginkgol isomers, C17:1-Δ¹² and C17:1-Δ¹⁰, were obtained simultaneously from the ginkgol C17:1 mixture and identified entirely for the first time. That aside, the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay showed that the six ginkgol homologs possessed significant antiproliferation effects against HGC and HepG2 cells. Furthermore, the ginkgols with unsaturated side chains (C17:2, C15:1-Δ⁸, C17:1-Δ¹², and C17:1-Δ¹⁰) exhibited more potent inhibitory effects than ginkgols with saturated side chains (C13:0, C15:0). In addition, unsaturated ginkgol C15:1-Δ⁸ showed the most potent cytotoxicity on HepG2 and HGC cells, of which the half-maximal inhibition concentrations (IC₅₀) were 18.84 ± 2.58 and 13.15 ± 2.91 μM, respectively. The IC₅₀ for HepG2 and HGC cells for the three unsaturated ginkgols (C17:1-Δ¹⁰, C17:2 and C17:1-Δ¹²) were ~59.97, ~60.82, and ~68.97 μM for HepG2 and ~30.97, ~33.81, and ~34.55 μM for HGC cells, respectively. Comparing the ginkgols' structure-activity relations, the findings revealed that the position and number of the double bonds of the ginkgols with 17 side chain carbons in length had no significant difference in anticancer activity.

Atropisomerism in Drug Discovery: A Medicinal Chemistry Perspective Inspired by Atropisomeric Class I PI3K Inhibitors

Atropisomerism is a type of axial chirality resulting from hindered rotation about a σ bond that gives rise to nonsuperimposable stereoisomers (termed "atropisomers"). The inversion of chirality of an atropisomeric axis is a time- and temperature-dependent dynamic process occurring by simple bond rotation. For this reason, the rotational energy barrier (ΔE_rot) and the interconversion rate between an atropisomeric pair of biologically active molecules are important parameters to consider in drug discovery.Many compounds with atropisomeric axes advance into development every year. The vast majority of them have low rotational energy barriers (ΔE_rot lower than 20 kcal/mol), meaning they are rapidly equilibrating conformers and considered achiral (class 1 atropisomers). Compounds in class 2 (ΔE_rot = 20 to 30 kcal/mol) can be challenging to develop given that the stereochemical integrity of the atropisomeric axes can be compromised over time. It has been recommended that small molecule drug candidates containing one or more atropisomeric axes with rotational energy barriers greater than 30 kcal/mol (class 3 atropisomers) should be developed as single atropisomers.In medicinal chemistry, a σ bond with restricted rotation is engineered into a bioactive molecule primarily to limit its number of accessible conformations, thereby minimizing entropic and/or enthalpic energy penalties associated with biological target binding. In addition to enhanced pharmacology, potential positive outcomes of introducing atropisomerism include improved physicochemical properties and superior pharmacokinetics/ADME profiles. The application of atropisomerism in medicinal chemistry has become increasingly enabled due to recent advances in synthesis, purification, and analysis, as described in this special issue and recent review articles.Herein, we discuss two case studies from our own work in which restricting rotation about axes of atropisomerism led to significant improvements in pharmacological, physicochemical, and ADME properties for different series of PI3K inhibitors. In the first instance, a restricted axis of rotation was designed to mitigate an acid-mediated hydrolytic degradation pathway observed in a series of PI3Kδ inhibitors. The conformational constraint disrupts conjugation between a quinazolinone and a pyridine, leading to improved chemical stability under acidic conditions. In the second case study, introduction of a restricted axis of rotation between two heteroaromatic systems in a series of PI3Kβ inhibitors generated pairs of atropisomeric compounds with significantly different biological activities. Advanced profiling also demonstrated clear substrate stereospecificity in regard to metabolism by aldehyde oxidase. Gratifyingly, the eutomer (more active atropisomer) shows significantly less susceptibility for oxidative metabolism relative to the distomer (less active atropisomer). The improvements in potency, selectivity, chemical stability, and metabolic stability discussed in this manuscript are all directly related to the concept of atropisomerism.

Application of 2D EXSY and qNMR Spectroscopy for Diastereomeric Excess Determination Following Chiral Resolution of β-Lactams

Trans-β-lactam isomers have garnered much attention as anti-cancer microtubule targeting agents. Currently available synthetic methods are available for the preparation of enantiopure β-lactams and favour isomeric cis/trans β-lactam mixtures. Indirect chiral resolution offers the opportunity for isolation of exclusively enantiopure trans-β-lactams. In this study, liquid chromatography chiral resolution of β-lactams derivatized as diastereomer mixtures with a panel of N-protected amino acids is explored, where N-(Boc)-L-proline served as the optimal chiral derivatising reagent. High-performance liquid chromatography failed to adequately determine diastereomeric excess (de) of resolved diastereomers. Variable temperature, ¹ H NMR and 2D EXSY spectroscopic analyses of proline-derivatised diastereomers were successfully employed to characterise equilibrating rotamers of resolved diastereomers and determine their de. Integration of resolved resonances corresponding to H₃ and H₄ of the β-lactam ring served as a quantitative qNMR tool for the calculation of de following resolution.

Discovery of novel tubulin inhibitors targeting the colchicine binding site via virtual screening, structural optimization and antitumor evaluation

The colchicine binding site of tubulin is a promising target for discovering novel antitumor agents which exert the antiangiogenic effect and are not susceptible to multidrug resistance. For identifying novel tubulin inhibitors, structure-based virtual screening was applied to identify hit 9 which displayed moderate tubulin polymerization inhibition and broad-spectrum in vitro antitumor activity. Structural optimization was performed, and biological assay revealed analog E27 displayed the best antitumor activity with IC₅₀ values ranging from 7.81 μM to 10.36 μM, and improved tubulin polymerization inhibitory activity (IC₅₀ = 16.1 μM). It significantly inhibited cancer cell migration and invasion, induced cell apoptosis and arrested the cell cycle at G2/M phase. Moreover, the apoptotic effect of E27 is related to the increased ROS level, the decrease of MMP, and the abnormal expression of apoptosis-related proteins. Taken together, these results suggested E27 was a promising lead compound for discovering novel tubulin-targeted antitumor agents.

Discovery and optimization of 2-((1H-indol-3-yl)thio)-N-benzyl-acetamides as novel SARS-CoV-2 RdRp inhibitors

The emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the global pandemic coronavirus disease (COVID-19), but no specific antiviral drug has been proven effective for controlling this pandemic to date. In this study, several 2-((indol-3-yl)thio)-N-benzyl-acetamides were identified as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibitors. After a two-round optimization, a new series of 2-((indol-3-yl)thio)-N-benzyl-acetamides was designed, synthesized, and evaluated for SARS-CoV-2 RdRp inhibitory effect. Compounds 6b2, 6b5, 6c9, 6d2, and 6d5 were identified as potent inhibitors with IC₅₀ values of 3.35 ± 0.21 μM, 4.55 ± 0.2 μM, 1.65 ± 0.05 μM, 3.76 ± 0.79 μM, and 1.11 ± 0.05 μM, respectively; the IC₅₀ of remdesivir (control) was measured as 1.19 ± 0.36 μM. All of the compounds inhibited RNA synthesis by SARS-CoV-2 RdRp. The most potent compound 6d5, which showed a stronger inhibitory activity against the human coronavirus HCoV-OC43 than remdesivir, is a promising candidate for further investigation.

Describing Polytopal Rearrangement Processes of Octacoordinate Structures. I. Renewed Insights into Fluxionality of the Rhenium Polyhydride Complex ReH5(PPh3)2(Pyridine)

Hydride ligands of transition metal polyhydride complexes with a high coordination number are prone to fluxionality leading to interesting structural dynamics. However, the underlying polytopal rearrangement pathways have been rarely studied. Based on quantum chemical calculations carried out in this work with density functional theory and coupled-cluster theory, two new fluxional mechanisms have been identified for the rhenium polyhydride complex ReH₅(PPh₃)₂(pyridine) to jointly account for two consecutive coalescence events in the variable-temperature NMR spectra upon heating: lateral and basal three-arm turnstile rotation. The frequently cited pseudorotation in ReH₅(PPh₃)₂(pyridine) (Lee et al. Inorg. Chem. 1996, 35, 695) turns out to be a three-step process including two lateral three-arm turnstile steps and one basal turnstile step in between. The new fluxional mechanisms discovered in this work may also exist in other transition metal polyhydrides.

Reactions in NMR Tubes as Key Weapon in Rational Drug Design

NMR spectroscopy is a powerful technique suitable for obtaining detailed structural and dynamic data at atomic resolution. Progress in NMR instrumentation has led the scientific community to produce novel techniques which provide valuable information to resolve demanding and crucial questions of molecular biology and rational drug design. This chapter outlines the progress of NMR spectroscopy in the rational drug design. In addition, it offers an example of a reaction in NMR tube for achieving rational drug design.