Fluorine in Medicinal Chemistry: In Perspective to COVID-19

Recent progress in therapeutic applications of fluorinated five-membered heterocycles and their benzo-fused systems

Heterocyclic derivatives grafted with fluorine atom(s) have attracted the attention of scientists due to the unique physicochemical properties of the C-F bond. The inclusion of fluorine atom(s) into organic compounds often increases their lipophilicity and metabolic stability, enhancing their bioavailability and affinity for target proteins. Therefore, it is not surprising to find that more than 20% of the medications on the market contain fluorine, and nearly 300 fluorine-containing drugs have been officially approved for use as medicines. In this review article, we are interested in classifying and describing the reports comprising varied therapeutic activities of the directly fluorinated five-membered heterocycles and their fused systems during the last two decades. These therapeutic activities included antiviral, anti-inflammatory, enzymatic inhibitory, antimalarial, anticoagulant, antipsychotic, antioxidant, antiprotozoal, histamine-H3 receptor, serotonin receptor, chemokine receptor, prostaglandin-D2 receptor, and PBR inhibition activities. In many cases, the activities of fluorinated azoles were almost equal to or exceeded the potency of reference drugs.

Inhibiting SARS-CoV-2 viral entry by targeting spike:ACE2 interaction with O-modified quercetin derivatives

The cell entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is mediated by the interaction between the receptor-binding domain of its spike (S) protein and human angiotensin-converting enzyme 2 (ACE2). Quercetin, a flavonoid found abundantly in plants, shows potential as a SARS-CoV-2 S:ACE2 inhibitor but is known to have low bioavailability. Modification of quercetin by capping its hydroxyl moieties could enhance the metabolic stability, solubility, and bioavailability, and reduce toxicity. In this study, sixteen (16) O-modified quercetin derivatives were synthesized by incorporating alkyl and acyl moieties of varying lengths, sizes, and polarities to the hydroxyl groups. The SARS-CoV-2 S:ACE2 inhibitory activity and toxicity of the synthesized derivatives were assessed in vitro, and their physicochemical properties, pharmacokinetics, and drug-likeness were predicted and evaluated using the SwissADME web tool. Results showed that functionalization of the hydroxyl moieties of quercetin generally resulted in more potent inhibitors (>50% inhibition). Five (5) derivatives displayed a dose-dependent inhibition against the SARS-CoV-2 S:ACE2 interaction with promising IC50 values (i.e., 2e (IC50 = 7.52 μM), 3a (IC50 = 5.00 μM), 3b (IC50 = 25.70 μM), 3c (IC50 = 2.22 μM), and 4b (IC50 = 3.28 μM)). Moreover, these compounds exhibited low hepato-, nephro-, and cardiotoxicity, and their SwissADME profiles indicated favorable physicochemical, pharmacokinetic, and drug-like properties, suggesting their potential as promising lead SARS-CoV-2 S:ACE2 inhibitors.

Fluorinated Protein-Ligand Complexes: A Computational Perspective

Fluorine is an element renowned for its unique properties. Its powerful capability to modulate molecular properties makes it an attractive substituent for protein binding ligands; however, the rational design of fluorination can be challenging with effects on interactions and binding energies being difficult to predict. In this Perspective, we highlight how computational methods help us to understand the role of fluorine in protein-ligand binding with a focus on molecular simulation. We underline the importance of an accurate force field, present fluoride channels as a showcase for biomolecular interactions with fluorine, and discuss fluorine specific interactions like the ability to form hydrogen bonds and interactions with aryl groups. We put special emphasis on the disruption of water networks and entropic effects.

Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery

The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).

A Novel 3-meta-Pyridine-1,2,4-oxadiazole Derivative of Glycyrrhetinic Acid as a Safe and Promising Candidate for Overcoming P-Glycoprotein-Mediated Multidrug Resistance in Tumor Cells

Given the pharmacophore properties of the nitrogen-containing moiety in the molecular structure of P-glycoprotein (P-gp) inhibitors, we report the evaluation of the P-gp inhibitory and MDR reversal activities of 2g, a 3-meta-pyridin-1,2,4-oxadiazole derivative of 18βH-glycyrrhetinic acid. Through molecular docking, we have shown that 2g has the potential to directly interact with the transmembrane domain of P-gp with a low free binding energy (-10.2 kcal/mol). Using KB-8-5 human cervical carcinoma cells and RLS40 murine lymphosarcoma cells, both of which exhibit a multidrug-resistant (MDR) phenotype mediated by P-gp activation, we have shown that 2g, at nontoxic concentrations, effectively increased the intracellular accumulation of fluorescent P-gp substrates (rhodamine 123 or doxorubicin (DOX)), leading to a marked sensitization of the model cells to the cytotoxic effect of DOX. Considering the comparable activity of 2g with verapamil, a known P-gp inhibitor, 2g can be considered as a promising candidate for the development of agents capable of overcoming P-gp-mediated MDR in tumor cells.

A review: FDA-approved fluorine-containing small molecules from 2015 to 2022

Fluorine-containing small molecules have occupied a special position in drug discovery research. The successful clinical use of fluorinated corticosteroids in the 1950s and fluoroquinolones in the 1980s led to an ever-increasing number of approved fluorinated compounds over the last 50 years. They have shown various biological properties such as antitumor, antimicrobial, and anti-inflammatory activities. Fluoro-pharmaceuticals have been considered a strong and practical tool in the rational drug design approach due to their benefits from potency and ADME (absorption, distribution, metabolism, and excretion) points of view. Herein, approved fluorinated drugs from 2015 to 2022 were reviewed.

Selective Synthesis of (Z)- and (E)-β-Fluoro-α,β-Unsaturated Amides Using Palladium-Catalyzed Aminocarbonylation

The selective synthesis of (Z)- and (E)-β-fluoro-α,β-unsaturated amides via the palladium-catalyzed aminocarbonylation of 1-fluoro-2,2-diiodovinylarenes is described in the present study. Using {Pd(allyl)Cl}2 as a catalyst and DBU as a base in DMF, the primary product is (Z)-isomers. Conversely, the use of a Xantphos ligand along with {Pd(allyl)Cl}2 and Et3N as the bases in 1,4-dioxane leads to the selective formation of (E)-isomers. Notably, 1-fluoro-2,2-diiodovinylarenes with various substituents on the phenyl ring react with various secondary amines, producing the corresponding (Z)-isomeric amides with a high yield and selectivity. In contrast, (E)-isomeric amides exhibit lower yields and restricted applicability.

Electrochemical or Photoelectrochemical Alkenylpolyfluoroalkylation of 3-Aza-1,5-dienes: Regioselective Entry to Polyfluoroalkylated 4-Pyrrolin-2-ones

An electrochemical or photoelectrochemical regioselective polyfluoroalkylation/cyclization cascade of 3-aza-1,5-dienes with sodium fluoroalkanesulfinates is presented. This protocol proceeds with a broad substrate scope and good functional group tolerance under mild, oxidant-free, transition-metal-free, and electrolyte-free conditions to provide 3-polyfluoroalkylated 4-pyrrolin-2-ones in one step from readily available N-vinylacrylamides, and it is readily scalable to the Gram scale.

Fluorinated Imines in Tandem and Cycloaddition Reactions

The chemistry of fluorinated compounds has experienced extraordinary growth in recent decades due to the many and varied properties which many of the compounds that contain fluorinated groups possess. Among all of them, fluorinated chiral imines, in particular the Ellman's imines, are of great importance since they are some of the most interesting building blocks for the synthesis of a large number of enantioenriched carbocycles and heterocycles with extraordinary biological and synthetic properties. This personal account covers the most significant results obtained in our research group in the last two decades concerning asymmetric tandem reactions, paying special attention to the intramolecular aza-Michael reaction (IMAMR), diversity oriented synthesis (DOS), asymmetric tandem reactions involving a p-tolylsulfinyl group as chiral inducer and cycloaddition processes, in particular, the Pauson-Khand reaction, [2+2+2]-cycloadditions and metathesis reactions, starting mainly from enyne compounds and through the use of fluorinated chiral N-sulfinyl imines and their derivatives as starting materials.

Divergent Fluorinations of Vinylcyclopropanes: Ring-Opening 1,5-Hydrofluorination and Ring-Retaining 1,2-Difluorination

Organofluorine compounds have been widely used in pharmaceutical, agrochemical, and material sciences. Reported herein are divergent fluorination reactions of vinylcyclopropanes with different electrophiles, which allow the facile synthesis of homoallylic monofluorides and vicinal-difluorides through ring-opening 1,5-hydrofluorination and ring-retaining 1,2-difluorination, respectively. Both protocols feature mild conditions, simple operations, good functional group tolerance, and generally good yields. The practicality of these reactions is demonstrated by their scalability, as well as the successful conversion of the formed homoallylic monofluorides into other complex fluorinated molecules.

Redox-Neutral Decarboxylative and Desulfonylative C(sp3) Trifluoromethylation: Method Development and Mechanistic Inquiry

Sodium triflinate (CF₃SO₂Na) is an inexpensive bench-stable radical CF₃ source that is often activated by external oxidants such as peroxides. However, despite the commercial accessibility of CF₃SO₂Na, the salt has never been applied to decarboxylative trifluoromethylation due to challenges in controlled cross-radical coupling. We report a redox-neutral approach to decarboxylative C(sp³) trifluoromethylation of carboxylic acid derivatives. Mechanistic inquiry is performed to address the limitations in scope.

Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.

Enantioselective Synthesis of Fluorinated Indolizidinone Derivatives

The enantioselective synthesis of fluorinated indolizidinone derivatives has been developed. The process involved an enantioselective intramolecular aza-Michael reaction of conjugated amides bearing a pendant α,β-unsaturated ketone moiety, catalyzed by the (S)-TRIP-derived phosphoric acid, followed by dimethyltitanocene methylenation and ring closing metathesis (RCM). Final indolizidine-derived products comprise a fluorine-containing tetrasubstituted double bond generated by the RCM reaction, which is a challenging task. The whole synthetic sequence took place in acceptable overall yields with excellent enantioselectivities.

Fluorine-a small magic bullet atom in the drug development: perspective to FDA approved and COVID-19 recommended drugs

During the last twenty years, organic fluorination chemistry established itself as an important tool to get a biologically active compound. This belief can be supported by the fact that every year, we are getting fluorinated drugs in the market in extremely significant numbers. Last year, also ten fluorinated drugs have been approved by FDA and during the COVID-19 pandemic, fluorinated drugs played a very crucial role to control the disease and saved many lives. In this review, we surveyed all ten fluorinated drugs approved by FDA in 2021 and all fluorinated drugs which were directly-indirectly used during the COVID-19 period, and emphasis has been given particularly to their synthesis, medicinal chemistry, and development process. Out of ten approved drugs, one drug pylarify, a radioactive diagnostic agent for cancer was approved for use in positron emission tomography imaging. Also, very briefly outlined the significance of fluorinated drugs through their physical, and chemical properties and their effect on drug development.

Graphical abstract

Novel Investigational Anti-SARS-CoV-2 Agent Ensitrelvir "S-217622": A Very Promising Potential Universal Broad-Spectrum Antiviral at the Therapeutic Frontline of Coronavirus Species

Lately, nitrogenous heterocyclic antivirals, such as nucleoside-like compounds, oxadiazoles, thiadiazoles, triazoles, quinolines, and isoquinolines, topped the therapeutic scene as promising agents of choice for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying ailment, the coronavirus disease 2019 (COVID-19). At the same time, the continuous emergence of new strains of SARS-CoV-2, like the Omicron variant and its multiple sublineages, resulted in a new defiance in the enduring COVID-19 battle. Ensitrelvir (S-217622) is a newly discovered orally active noncovalent nonpeptidic agent with potential strong broad-spectrum anticoronaviral activities, exhibiting promising nanomolar potencies against the different SARS-CoV-2 variants. S-217622 effectively and nonspecifically hits the main protease (M^pro) enzyme of a broad scope of coronaviruses. Herein, in the present computational/biological study, we tried to extend these previous findings to prove the universal activities of this investigational agent against any coronavirus, irrespective of its type, through synchronously acting on most of its main unchanged replication enzymes/proteins, including (in addition to the M^pro), e.g., the highly conserved RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN). Biochemical evaluation proved, using the in vitro anti-RdRp/ExoN bioassay, that S-217622 can potently inhibit the replication of coronaviruses, including the new virulent strains of SARS-CoV-2, with extremely minute in vitro anti-RdRp and anti-RdRp/ExoN half-maximal effective concentration (EC₅₀) values of 0.17 and 0.27 μM, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico results greatly supported these biochemical results, proposing that the S-217622 molecule strongly and stabilizingly strikes the key catalytic pockets of the SARS-CoV-2 RdRp's and ExoN's principal active sites predictably via the nucleoside analogism mode of anti-RNA action (since the S-217622 molecule can be considered as a uridine analog). Moreover, the idealistic druglikeness and pharmacokinetic characteristics of S-217622 make it ready for pharmaceutical formulation with the expected very good clinical behavior as a drug for the infections caused by coronaviruses, e.g., COVID-19. To cut it short, the current critical findings of this extension work significantly potentiate and extend the S-217622's previous in vitro/in vivo (preclinical) results since they showed that the striking inhibitory activities of this novel anti-SARS-CoV-2 agent on the M^pro could be extended to other replication enzymes like RdRp and ExoN, unveiling the possible universal use of the compound against the next versions of the virus (i.e., disclosing the nonspecific anticoronaviral properties of this compound against almost any coronavirus strain), e.g., SARS-CoV-3, and encouraging us to rapidly start the compound's vast clinical anti-COVID-19 evaluations.

Synthesis of gem-Diboromethyl-Substituted Bicyclo[1.1.1]pentanes and Their Application in Palladium-Catalyzed Cross Couplings

We describe the first general transition-metal-free synthesis of gem-diboromethyl-substituted bicyclo[1.1.1]pentane (BCP) and other related C(sp³)-rich carbocyclic benzene bioisosteres from their corresponding p-tosylhydrazones. These novel functionalized benzene bioisosteres demonstrated unique reactivities toward palladium-catalyzed C(sp²)-C(sp³) cross couplings. The overall transformation can be applied to relatively complex substrates with potential utility in drug discovery.

Understanding and combating COVID-19 using the biology and chemistry of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptoms of COVID-19 can range from asymptomatic to severe, which could lead to fatality. Like other pathogenic viruses, the infection of SARS-CoV-2 relies on binding its spike glycoprotein to the host receptor angiotensin-converting enzyme 2 (ACE 2). Molecular studies suggested that there is a high affinity between the spike glycoprotein and ACE 2 that might arise due to their hydrophobic interaction. This property is mainly responsible for making this virus highly infectious. Apart from this, the transmissibility of the virus, prolonged viability in certain circumstances, and rapid mutations also contributed to the current pandemic situation. Nanotechnology provides potential alternative solutions to combat COVID-19 with the development of i. nanomaterial-based COVID-19 detection technology, ii. nanomaterial-based disinfectants, iii. nanoparticle-based vaccines, and iv. nanoparticle-based drug delivery. Hence, this review provides diverse insight into understanding COVID-19.