Discovery of 1-(3'-aminobenzisoxazol-5'-yl)-3-trifluoromethyl-N-[2-fluoro-4- [(2'-dimethylaminomethyl)imidazol-1-yl]phenyl]-1H-pyrazole-5-carboxyamide hydrochloride (razaxaban), a highly potent, selective, and orally bioavailable factor Xa inhibitor

Unexpected effect of halogenation on the water solubility of small organic compounds

Halogenation is an indispensable method in the structural modification of lead compounds. It is known to increase lipophilicity and is hence used to improve membrane permeability and thus bioavailability. In this study, we compare the water solubility (logS) of organohalogen compounds and their non-halogenated parent compounds using the molecular matched pair (MMP) analysis method. Unexpectedly, 19.9% of the compounds increased their water solubility upon halogenation. Iodination was observed to have the greatest effect on solubility, followed by chlorination, bromination, and fluorination. Introducing amino, hydroxyl and carboxyl groups into organohalogens improves their aqueous solubilities, whereas introducing a trifluoromethyl group has the opposite effect. According to our quantum chemical calculations, the increased water solubility upon halogenation is, at least partially, attributed to an increased polarity and polarizability. These results improve our understanding of the influence of halogenation on bioactivity.

Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)

Cosolvent molecular dynamics (MD) simulations are molecular dynamics simulations used to identify preferable locations of small organic fragments on a protein target. Most cosolvent molecular dynamics workflows make use of only water-soluble fragments, as hydrophobic fragments would cause lipophilic aggregation. To date the two approaches that allow usage of hydrophobic cosolvent molecules are to use a low (0.2 M) concentration of hydrophobic probes, with the disadvantage of a lower sampling speed, or to use force field modifications, with the disadvantage of a difficult and inflexible setup procedure. Here we present a third alternative, that does not suffer from low sampling speed nor from cumbersome preparation procedures. We have built an easy-to-use open source command line tool PART (Plumed Automatic Restraining Tool) to generate a PLUMED file handling all intermolecular restraints to prevent lipophilic aggregation. We have compared restrained and unrestrained cosolvent MD simulations, showing that restraints are necessary to prevent lipophilic aggregation at hydrophobic probe concentrations of 0.5 M. Furthermore, we benchmarked PART generated restraints on a test set of four proteins (Factor-Xa, HIV protease, P38 MAP kinase and RNase A), showing that cosolvent MD with PART generated restraints qualitatively reproduces binding features of cocrystallised ligands.

Trifluoromethyl-β-dicarbonyls as Versatile Synthons in Synthesis of Heterocycles

Trifluoromethyl group relishes a privileged position in the realm of medicinal chemistry because its incorporation into organic molecules often enhances the bioactivity by altering pharmacological profile of molecule. Trifluoromethyl-β-dicarbonyls have emerged as pivotal building blocks in synthetic organic chemistry due to their facile accessibility, stability and remarkable versatility. Owing to presence of nucleophilic and electrophilic sites, they offer multifunctional sites for the reaction. This review covers a meticulous exploration of their multifaceted role, encompassing an in-depth analysis of mechanism, extensive scope, limitations and wide-ranging applications in diverse organic synthesis, covering the literature from the 21st century. This comprehensive review encapsulates the applications of trifluoromethyl-β-dicarbonyls and their synthetic equivalents as precursors of complex and diverse heterocyclic scaffolds, fused heterocycles and spirocyclic compounds having medicinal and material importance. Their potent synthetic utility in cyclocondensation reactions with binucleophiles, cycloaddition reactions, C-C bond formations, asymmetric multicomponent reactions using classical/solvent-free/catalytic synthesis have been presented. Influence of unsymmetrical trifluoromethyl-β-diketones on regioselectivity of transformation is also reviewed. This review will benefit the synthetic and pharmaceutical communities to explore trifluoromethyl-β-dicarbonyls as trifluoromethyl building blocks for fabrication of heterocyclic scaffolds having implementation into drug discovery programs in the imminent future.

Applications of Bioisosteres in the Design of Biologically Active Compounds

The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.

Regio- and Stereoselective Switchable Synthesis of (E)- and (Z)-N-Carbonylvinylated Pyrazoles

Regio- and stereoselective switchable synthesis of (E)- and (Z)-N-carbonylvinylated pyrazoles is first developed by using the Michael addition reaction of pyrazoles and conjugated carbonyl alkynes. Ag₂CO₃ plays a key role in the switchable synthesis of (E)- and (Z)-N-carbonylvinylated pyrazoles. Ag₂CO₃-free reactions lead to thermodynamically stable (E)-N-carbonylvinylated pyrazoles in excellent yields whereas reactions with Ag₂CO₃ give (Z)-N-carbonylvinylated pyrazoles in good yields. It is noteworthy that (E)- or (Z)-N¹-carbonylvinylated pyrazoles are obtained with high regioselectivity when asymmetrically substituted pyrazoles react with conjugated carbonyl alkynes. The method can also extend to the gram scale. A plausible mechanism is proposed on the basis of the detailed studies, wherein Ag⁺ acts as coordination guidance.

Highlights on U.S. FDA-approved fluorinated drugs over the past five years (2018-2022)

The objective of this review is to provide an update on the fluorine-containing drugs approved by U.S. Food and Drug Administration in the span of past five years (2018-2022). The agency accepted a total of fifty-eight fluorinated entities to diagnose, mitigate and treat a plethora of diseases. Among them, thirty drugs are for therapy of various types of cancers, twelve for infectious diseases, eleven for CNS disorders, and six for some other diseases. These are categorized and briefly discussed based on their therapeutic areas. In addition, this review gives a glimpse about their trade name, date of approval, active ingredients, company developers, indications, and drug mechanisms. We anticipate that this review may inspire the drug discovery and medicinal chemistry community in both industrial and academic settings to explore the fluorinated molecules leading to the discovery of new drugs in the near future.

Copper-Promoted Aerobic Oxidative [3+2] Cycloaddition Reactions of N,N-Disubstituted Hydrazines with Alkynoates: Access to Substituted Pyrazoles

A copper-promoted aerobic oxidative [3+2] cycloaddition reaction for the synthesis of various substituted pyrazoles from N,N-disubstituted hydrazines with alkynoates in the presence of bases is developed. This work involves a direct C(sp³)-H functionalization and the formation of new C-C/C-N bonds. In this strategy, inexpensive and easily available Cu₂O serves as the promoter and air acts as the green oxidant. The reaction exhibits the advantages of high atom and step economy, high regioselectivity, and easy operation.

Pyrazole-containing pharmaceuticals: target, pharmacological activity, and their SAR studies

Pyrazole is a five-membered heterocycle bearing two adjacent nitrogen atoms. Both pharmaceutical agents and natural products with pyrazole as a nucleus have exhibited a broad spectrum of biological activities. In the last few decades, more than 40 pyrazole-containing drugs have been approved by the FDA for the treatment of a broad range of clinical conditions including celecoxib (anti-inflammatory), CDPPB (antipsychotic), difenamizole (analgesic), etc. Owing to the unique physicochemical properties of the pyrazole core, pyrazole-containing drugs may exert better pharmacokinetics and pharmacological effects compared with drugs containing similar heterocyclic rings. The purpose of this paper is to provide an overview of all the existing drugs bearing a pyrazole nucleus that have been approved or in clinical trials, involving their pharmacological activities and SAR studies.

Quadruple Functionalized Pyrazole Pharmacophores via One-pot Regioselective [3 + 2] Cycloaddition of Fluorinated Nitrile Imines and Dicyanoalkenes

Here we present a quadruple functionalization approach for the modular construction of fully substituted N 1 -aryl 3-di/trifluoro-methyl-4/5-cyanopyrazole pharmacophores from readily available hydrazonyl chlorides and dicyanoalkenes. The realization of this [3 + 2] cycloaddition reaction hinges upon the employment of N -aryl di/trifluoromethyl nitrile imines as the 1,3-dipoles to bypass external synthetic steps and dicyanoalkenes as the dipolarophiles to tune the regioselectivity. This one-pot strategy offers access to a divergent library of cyano analogues of prevalent 3-di/trifluoromethyl pyrazole pharmacophores, among which several compounds have shown potent inhibitory activity towards cyclooxygenase 2 (COX-2) compared with marketed drug Celecoxib.

Design, synthesis, and biological evaluation of C6-difluoromethylenated epoxymorphinan Mu opioid receptor antagonists

The recent widespread abuse of high potency synthetic opioids, such as fentanyl, presents a serious threat to individuals affected by substance use disorder. Synthetic opioids generally exhibit prolonged in vivo circulatory half-lives that can outlast the reversal effects of conventional naloxone-based overdose antidotes leading to a life-threatening relapse of opioid toxicity known as renarcotization. In this manuscript, we present our efforts to combat the threat of renarcotization by attempting to extend the half-life of traditional MOR antagonists through the design of novel, fluorinated 4,5-epoxymorphinans possessing increased lipophilicity. Analogues were prepared via a concise synthetic strategy highlighted by decarboxylative Wittig olefination of the C6 ketone to install a bioisosteric 1,1-difluoromethylene unit. C6-difluoromethylenated compounds successfully maintained in vitro potency against an EC90 challenge of fentanyl and were predicted to have enhanced circulatory half-life compared to the current standard of care, naloxone. Subsequent in vivo studies demonstrated the effective blockade of fentanyl-induced anti-nociception in mice.

Polyfluoroalkylated antipyrines in Pd-catalyzed transformations

In the direct C–H arylation with arylhalogenides in the presence of Pd(OAc)₂, trifluoromethyl-containing antipyrine reacts very slowly and incompletely owing to the low nucleophilicity of its C4 center. However, it was effective in modifying polyfluoroalkyl-substituted 4-bromo- and 4-iodo antipyrines by the Suzuki and Sonogashira reactions. It was established that using Pd₂(dba)₃ as catalyst and XPhos as phosphine ligand was the optimal catalytic system for the synthesis of 4-aryl- and 4-phenylethynyl-3-polyfluoroalkyl-antipyrines. Moreover, iodo-derivatives as the initial reagents were found to be more advantageous compared to bromo-containing analogs. It was found that 4-phenylethynyl-5-CF₃-antipyrine has a moderate activity against the influenza virus A/Puerto Rico/8/34 (H1N1) and 4-iodo-5-CF₃-antipyrine reveals a weak activity against the vaccine virus (strain Copenhagen) and bovine diarrhea virus (strain VC-1).

Peculiarities of heterocyclic systems with electron-withdrawing groups (polyfluoroalkyl-containing antipyrines) in Pd-catalyzed C–H arylation and cross-coupling reactions.

Berotralstat (BCX7353): Structure-Guided Design of a Potent, Selective, and Oral Plasma Kallikrein Inhibitor to Prevent Attacks of Hereditary Angioedema (HAE)

Hereditary angioedema (HAE) is a rare and potentially life-threatening disease that affects an estimated 1 in 50 000 individuals worldwide. Until recently, prophylactic HAE treatment options were limited to injectables, a burdensome administration route that has driven the need for an oral treatment. A substantial body of evidence has shown that potent and selective plasma kallikrein inhibitors that block the generation of bradykinin represent a promising approach for the treatment of HAE. Berotralstat (BCX7353, discovered by BioCryst Pharmaceuticals using a structure-guided drug design strategy) is a synthetic plasma kallikrein inhibitor that is potent and highly selective over other structurally related serine proteases. This once-daily, small-molecule drug is the first orally bioavailable prophylactic treatment for HAE attacks, having successfully completed a Phase III clinical trial (meeting its primary end point) and recently receiving the U.S. Food and Drug Administration's approval for the prophylactic treatment of HAE attacks in patients 12 years and older.

From basic science to life-saving therapy: the rationale, and drug discovery efforts that led to the direct factor Xa inhibitor eliquis

Over the past few decades, drug discovery directed at the treatment and prevention of thromboembolic diseases has been challenged by the need to balance robust efficacy with improved safety relative to the standard of care. To this end, the most impactful advance to date has been the discovery and development of oral factor Xa inhibitors. In this essay, a brief account of the program that culminated in the discovery of Eliquis (apixaban) and the commitment to identify a compound with an optimal profile are described.

The Critical Role of Passive Permeability in Designing Successful Drugs

Passive permeability is a key property in drug disposition and delivery. It is critical for gastrointestinal absorption, brain penetration, renal reabsorption, defining clearance mechanisms and drug-drug interactions. Passive diffusion rate is translatable across tissues and animal species, while the extent of absorption is dependent on drug properties, as well as in vivo physiology/pathophysiology. Design principles have been developed to guide medicinal chemistry to enhance absorption, which combine the balance of aqueous solubility, permeability and the sometimes unfavorable compound characteristic demanded by the target. Permeability assays have been implemented that enable rapid development of structure-permeability relationships for absorption improvement. Future advances in assay development to reduce nonspecific binding and improve mass balance will enable more accurately measurement of passive permeability. Design principles that integrate potency, selectivity, passive permeability and other ADMET properties facilitate rapid advancement of successful drug candidates to patients.

Surfing the Blood Coagulation Cascade: Insight into the Vital Factor Xa

Factor Xa (FXa) plays a key role in haemostasis, it is a central part of the blood coagulation cascade which catalyzes the production of thrombin and leads to clot formation and wound closure. Therefore, FXa is an attractive target for the development of new anticoagulant agents. In this review, we will first describe the molecular features of this fundamental protein in order to understand its mechanism of action, an essential background for the design of novel inhibitors by means of synthetic organic chemistry or using peptides obtained from recombinant methodologies. Then, we will review the current state of the synthesis of novel direct FXa inhibitors along with their mechanisms of action. Finally, approved reversal agents that aid in maintaining blood haemostasis by using these commercial drugs will also be discussed.

CoII immobilized on an aminated magnetic metal–organic framework catalyzed C–N and C–S bond forming reactions: a journey for the mild and efficient synthesis of arylamines and arylsulfides

The catalytic activity of Fe₃O₄@AMCA-MIL53(Al)-NH₂-Co^II NPs as a novel and inexpensive catalyst was investigated in the C–N and C–S cross coupling reactions.

Modulating ADME Properties by Fluorination: MK2 Inhibitors with Improved Oral Exposure

MAP-activated protein kinase 2 (MK2) plays an important role in the regulation of innate immune response as well as in cell survival upon DNA damage. Despite its potential for the treatment of inflammation and cancer, to date no MK2 low molecular weight inhibitors have reached the clinic, mainly due to inadequate absorption, distribution, metabolism, and excretion (ADME) properties. We describe here an approach based on specifically placed fluorine within a recently described pyrrole-based MK2 inhibitor scaffold for manipulation of its physicochemical and ADME properties. While preserving target potency, the novel fluoro-derivatives showed greatly improved permeability as well as enhanced solubility and reduced in vivo clearance leading to significantly increased oral exposure.

CuCl heterogenized on metformine-modified multi walled carbon nanotubes as a recyclable nanocatalyst for Ullmann-type C–O and C–N coupling reactions

Herein, a novel MWCNTs-Met/CuCl nanocatalyst synthesis method by metformine covalent grafting on the surface of carbon nanotubes and subsequent coordination with a CuCl catalyst is described.

Pyrazole synthesis via a cascade Sonogashira coupling/cyclization of N-propargyl sulfonylhydrazones

An efficient approach for the preparation of pyrazoles via a Pd(ii)/Cu(i)-catalyzed Sonogashira coupling/cyclization of N-propargyl sulfonylhydrazones has been established.

Optimization of Substrate-Analogue Furin Inhibitors

The proprotein convertase furin is a potential target for drug design, especially for the inhibition of furin-dependent virus replication. All effective synthetic furin inhibitors identified thus far are multibasic compounds; the highest potency was found for our previously developed inhibitor 4-(guanidinomethyl)phenylacetyl-Arg-Tle-Arg-4-amidinobenzylamide (MI-1148). An initial study in mice revealed a narrow therapeutic range for this tetrabasic compound, while significantly reduced toxicity was observed for some tribasic analogues. This suggests that the toxicity depends at least to some extent on the overall multibasic character of this inhibitor. Therefore, in a first approach, the C-terminal benzamidine of MI-1148 was replaced by less basic P1 residues. Despite decreased potency, a few compounds still inhibit furin in the low nanomolar range, but display negligible efficacy in cells. In a second approach, the P2 arginine was replaced by lysine; compared to MI-1148, this furin inhibitor has slightly decreased potency, but exhibits similar antiviral activity against West Nile and Dengue virus in cell culture and decreased toxicity in mice. These results provide a promising starting point for the development of efficacious and well-tolerated furin inhibitors.

Poly[tris{μ-2-[(dimethylamino)methyl]imidazolato-κ3 N 1,N 2:N 3}(nitrato-κO)dizinc(II)]

In the title coordination polymer, [Zn2(C6H10N3)3(NO3)] n , two independent ZnII ions are tetrahedrally coordinated by the anionic ligands, viz. 2-[(dimethylamino)methyl]imidazolate or nitrate ions. One ZnII ion is coordinated by the imidazolate N atoms of three anions and an O atom of the nitrate ion. The second ZnII ion is coordinated by imidazolate N atoms of three anions and one amino N atom of one such ligand. The 2-[(dimethylamino)methyl]imidazolate anions are bridging the ZnII ions to form a helical chain structure along [001]. The chains are further linked by the bridging ligands into a three-dimensional framework structure. The nitrate anion is disordered over two sets of sites and was refined with two pairs of three O atoms using half-occupancy for each O atom.

Fluoroalkyl-Substituted Diazomethanes and Their Application in a General Synthesis of Pyrazoles and Pyrazolines

A novel continuous-flow approach for the synthesis of fluoroalkyl-substituted diazomethanes has been developed. Utilizing a cheap, self-made microreactor fluoroalkyl-substituted amines were transformed into the corresponding diazomethanes using tert-butyl nitrite and acetic acid as catalyst. These diazomethanes were employed in [2+3] cycloaddition reactions with olefins and alkynes, yielding valuable pyrazolines and pyrazoles in good to excellent yields.

Contemporary developments in the discovery of selective factor Xa inhibitors: A review

Thrombosis is a leading cause of death in cardiovascular diseases such as myocardial infarction (MI), unstable angina and acute coronary syndrome (ACS) in the industrialized world. Venous thromboembolism is observed in about 1 million people every year in United States causing significant morbidity and mortality. Conventional antithrombotic therapy has been reported to have several disadvantages and limitations like inconvenience in oral administration, bleeding risks (heparin analogs), narrow therapeutic window and undesirable interactions with food and drugs (vitamin K antagonist-warfarin). The unmet medical demand for orally active safe anticoagulants has generated widespread interest among the medicinal chemists engaged in this field. To modulate blood coagulation, various enzymes involved in the coagulation process have received great attention as potential targets by various research groups for the development of oral anticoagulants. Among these enzymes, factor Xa (FXa) has remained the centre of attention in the last decade. Intensive research efforts have been made by various research groups for the development of small, safe and orally bioavailable FXa inhibitors. This review is an attempt to compile the research work of various researchers in the direction of development of FXa inhibitors reported since 2010 onward.

Fluorinated diazoalkanes – a versatile class of reagents for the synthesis of fluorinated compounds

Fluorinated diazo compounds were long neglected in organic synthesis. This review discusses the flourishing chemistry of these reagents, ranging from C–H activation to cycloadditions for the synthesis of fluorinated compounds.

1,4-Dihydroxyanthraquinone–copper(ii) supported on superparamagnetic Fe3O4@SiO2: an efficient catalyst for N-arylation of nitrogen heterocycles and alkylamines with aryl halides and click synthesis of 1-aryl-1,2,3-triazole derivatives

1,4-Dihydroxyanthraquinone–copper(ii) supported on superparamagnetic Fe₃O₄@SiO₂ catalyst was employed for the N-arylation of nitrogen heterocycles and alkylamines.

K. N, P. D, N. H, Pai K. SR, Biswas S, S. K. P. Design, synthesis, characterization of some new 1,2,3-triazolyl chalcone derivatives as potential anti-microbial, anti-oxidant and anti-cancer agents via a Claisen–Schmidt reaction approach

A new series of 1,2,3-triazolyl chalcone derivatives (5a–k) and (6a–e) were synthesized and evaluated for their anti-microbial, anti-oxidant and anti-cancer activities.

Applications of Fluorine in Medicinal Chemistry

The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, (18)F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in positron emission tomography.

Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets

Accurately predicting relative binding affinities and biological potencies for ligands that interact with proteins remains a significant challenge for computational chemists. Most evaluations of docking and scoring algorithms have focused on enhancing ligand affinity for a protein by optimizing docking poses and enrichment factors during virtual screening. However, there is still relatively limited information on the accuracy of commercially available docking and scoring software programs for correctly predicting binding affinities and biological activities of structurally related inhibitors of different enzyme classes. Presented here is a comparative evaluation of eight molecular docking programs (Autodock Vina, Fitted, FlexX, Fred, Glide, GOLD, LibDock, MolDock) using sixteen docking and scoring functions to predict the rank-order activity of different ligand series for six pharmacologically important protein and enzyme targets (Factor Xa, Cdk2 kinase, Aurora A kinase, COX-2, pla2g2a, β Estrogen receptor). Use of Fitted gave an excellent correlation (Pearson 0.86, Spearman 0.91) between predicted and experimental binding only for Cdk2 kinase inhibitors. FlexX and GOLDScore produced good correlations (Pearson>0.6) for hydrophilic targets such as Factor Xa, Cdk2 kinase and Aurora A kinase. By contrast, pla2g2a and COX-2 emerged as difficult targets for scoring functions to predict ligand activities. Although possessing a high hydrophobicity in its binding site, β Estrogen receptor produced reasonable correlations using LibDock (Pearson 0.75, Spearman 0.68). These findings can assist medicinal chemists to better match scoring functions with ligand-target systems for hit-to-lead optimization using computer-aided drug design approaches.

Insights into the impact of N- and O-methylation on aqueous solubility and lipophilicity using matched molecular pair analysis

The impact of N- and O-methylation on aqueous solubility and measured lipophilicity for several chemically diverse structural classes is described.

Palladium nanoparticles supported on modified single-walled carbon nanotubes: a heterogeneous and reusable catalyst in the Ullmann-type N-arylation of imidazoles and indoles

Application of SWCNT-Met/Pd as an efficient and heterogeneous catalyst in the Ullmann coupling of imidazoles and indoles with aryl iodides.