Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines

Difunctionalization of gem-difluoroalkenes for amination and heteroarylation via metal-free photocatalysis

gem-Difluoroalkenes are widely used building blocks in fluorine chemistry. Herein, a metal-free photocatalytic amination and heteroarylation method of gem-difluoroalkenes with heteroaryl carboxylic acid oxime esters as substrates is reported. This environmentally benign reaction proceeds via radical-radical cross-coupling in energy-transfer-mediated photocatalysis and can be used in the rapid construction of heteroaryl difluoroethylamine scaffolds and late-stage modification of complex pharmaceutical structures.

Recent Advancements in the Synthesis of α-fluoroalkylated Azine-derived Heterocycles through Direct Fluorination

The review highlights recent advancements in the synthesis of α-fluoro and α,α- difluoroalkylated azines, focusing on two main approaches. The first approach involves nucleophilic deoxofluorination, wherein α-hydroxy- or α-oxoalkylated azines are treated with diethylaminosulfur trifluoride or other S-F reagents to introduce fluorine atoms. The second approach employs direct electrophilic benzylic fluorination, whereby alkylazines undergo fluorination using N-F reagents. Both methods provide flexibility in designing and synthesizing fluoroalkylated heterocycles.

Visible-Light-Induced Cascade Cyclization of 1-Acryloyl-2-cyanoindole: Access of Difluoroalkylated Pyrrolo[1,2-a]indolediones

An effective method for accessing diverse difluoroalkylated pyrrolo[1,2-a]indolediones via visible-light-induced PhI(OAc)2-promoted cascade difluoroalkylation/cyclization reaction under mild conditions has been established. This method is noteworthy for its use of DMSO-H2O as a green medium at room temperature and avoidance of photocatalysts. The reactions are straightforward to execute and convenient to expand on, provide good to excellent yields, and have good functional group tolerance.

Copper-Catalyzed Regio- and Enantioselective Hydroboration of Difluoroalkyl-Substituted Internal Alkenes

Catalytic asymmetric hydroboration of fluoroalkyl-substituted alkenes is a straightforward approach to access chiral small molecules possessing both fluorine and boron atoms. However, enantioselective hydroboration of fluoroalkyl-substituted alkenes without fluorine elimination has been a long-standing challenge in this field. Herein, a copper-catalyzed hydroboration of difluoroalkyl-substituted internal alkenes with high levels of regio- and enantioselectivities is reported. The native carbonyl directing group, copper hydride system, and bisphosphine ligand play crucial roles in suppressing the undesired fluoride elimination. This atom-economic protocol provides a practical synthetic platform to obtain a wide scope of enantioenriched secondary boronates bearing the difluoromethylene moieties under mild conditions. Synthetic applications including functionalization of biorelevant molecules, versatile functional group interconversions, and preparation of difluoroalkylated Terfenadine derivative are also demonstrated.

Chemistry and Pharmacology of Fluorinated Drugs Approved by the FDA (2016-2022)

Fluorine is characterized by high electronegativity and small atomic size, which provide this molecule with the unique property of augmenting the potency, selectivity, metabolic stability, and pharmacokinetics of drugs. Fluorine (F) substitution has been extensively explored in drug research as a means of improving biological activity and enhancing chemical or metabolic stability. Selective F substitution onto a therapeutic or diagnostic drug candidate can enhance several pharmacokinetic and physicochemical properties such as metabolic stability and membrane permeation. The increased binding ability of fluorinated drug target proteins has also been reported in some cases. An emerging line of research on F substitution has been addressed by using 18F as a radiolabel tracer atom in the extremely sensitive methodology of positron emission tomography (PET) imaging. This review aims to report on the fluorinated drugs approved by the US Food and Drug Administration (FDA) from 2016 to 2022. It cites selected examples from a variety of therapeutic and diagnostic drugs. FDA-approved drugs in this period have a variety of heterocyclic cores, including pyrrole, pyrazole, imidazole, triazole, pyridine, pyridone, pyridazine, pyrazine, pyrimidine, triazine, purine, indole, benzimidazole, isoquinoline, and quinoline appended with either F-18 or F-19. Some fluorinated oligonucleotides were also authorized by the FDA between 2019 and 2022.

Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M-1 s-1, achieves sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

Defluoroalkylation of Trifluoromethylarenes with Hydrazones: Rapid Access to Benzylic Difluoroarylethylamines

Here, we report an efficient and modular approach toward the formation of difluorinated arylethylamines from simple aldehyde-derived N,N-dialkylhydrazones and trifluoromethylarenes (CF₃-arenes). This method relies on selective C-F bond cleavage via reduction of the CF₃-arene. We show that a diverse set of CF₃-arenes and CF₃-heteroarenes react smoothly with a range of aryl and alkyl hydrazones. The β-difluorobenzylic hydrazine product can be selectively cleaved to form the corresponding benzylic difluoroarylethylamines.

2(1H)-Pyrazinones from acyclic building blocks: methods of synthesis and further derivatizations

Pyrazinones (2(1H)-pyrazinones) are found as components of a range of natural substances and are involved in the preparation of a great number of bioactive molecules. Synthesis of such compounds, and analogues, requires knowledge of the heterocyclic properties of pyrazinones and, in particular, methods for their ring construction. This review deals with the strategies that have been developed for the synthesis of pyrazinones from acyclic precursors, especially α-amino acid-derived units, from the first examples in 1905 up to the most recent in 2021.

Transition-metal-free radical difluorobenzylation/cyclization of unactivated alkenes: access to ArCF2-substituted ring-fused quinazolinones

A mild and efficient transition-metal-free radical difluorobenzylation/cyclization of unactivated alkenes toward the synthesis of difluorobenzylated polycyclic quinazolinone derivatives with easily accessible α,α-difluoroarylacetic acids has been developed. This transformation has the advantages of wide functional group compatibility, a broad substrate scope, and operational simplicity. This methodology provided a highly attractive access to pharmaceutically valuable ArCF₂-containing polycyclic quinazolinones.

Potent and Selective Covalent Inhibition of the Papain-like Protease from SARS-CoV-2

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein (ISG15) from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we have designed a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibited PLpro with kinact/KI = 10,000 M- 1 s- 1, achieved sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and did not inhibit a panel of human deubiquitinases at > 30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validated our design strategy and established the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

Organocatalytic difluorobenzylation of 1,2-diketones via mild cleavage of carbon–carbon bonds

Difluoroacetophenones (DFAPs) are developed as a class of novel and practical reagents for organocatalytic difluorobenzylation reactions.

Insertion of Diazo Esters into C-F Bonds toward Diastereoselective One-Carbon Elongation of Benzylic Fluorides: Unprecedented BF3 Catalysis with C-F Bond Cleavage and Re-formation

Selective transformation of C-F bonds remains a significant goal in organic chemistry, but C-F insertion of a one-carbon-atom unit has never been established. Herein we report the BF₃-catalyzed formal insertion of diazo esters as one-carbon-atom sources into C-F bonds to accomplish one-carbon elongation of benzylic fluorides. A DFT calculation study revealed that the BF₃ catalyst could contribute to both C-F bond cleavage and re-formation. This elongation provided α-fluoro-α,β-diaryl esters with a high level of diastereoselectivity. Various benzylic fluorides and diazo esters were applicable. The synthetic utility of this method was demonstrated by the synthesis of a fluoro analogue of a compound that is used as a transient receptor and potential canonical channel inhibitor.

Optimization of peptide-based inhibitors targeting the HtrA serine protease in Chlamydia: Design, synthesis and biological evaluation of pyridone-based and N-Capping group-modified analogues

The obligate intracellular bacterium Chlamydia trachomatis (C. trachomatis) is responsible for the most common bacterial sexually transmitted infection and is the leading cause of preventable blindness, representing a major global health burden. While C. trachomatis infection is currently treatable with broad-spectrum antibiotics, there would be many benefits of a chlamydia-specific therapy. Previously, we have identified a small-molecule lead compound JO146 [Boc-Val-Pro-Val^P(OPh)₂] targeting the bacterial serine protease HtrA, which is essential in bacterial replication, virulence and survival, particularly under stress conditions. JO146 is highly efficacious in attenuating infectivity of both human (C. trachomatis) as well as koala (C. pecorum) species in vitro and in vivo, without host cell toxicity. Herein, we present our continuing efforts on optimizing JO146 by modifying the N-capping group as well as replacing the parent peptide structure with the 2-pyridone scaffold at P3/P2. The drug optimization process was guided by molecular modelling, enzyme and cell-based assays. Compound 18b from the pyridone series showed improved inhibitory activity against CtHtrA by 5-fold and selectivity over human neutrophil elastase (HNE) by 109-fold compared to JO146, indicating that 2-pyridone is a suitable bioisostere of the P3/P2 amide/proline for developing CtHtrA inhibitors. Most pyridone-based inhibitors showed superior anti-chlamydial potency to JO146 especially at lower doses (25 and 50 μM) in C. trachomatis and C. pecorum cell culture assays. Modifications of the N-capping group of the peptidyl inhibitors did not have much influence on the anti-chlamydial activities, providing opportunities for more versatile alterations and future optimization. In summary, we present 2-pyridone based analogues as a new generation of non-peptidic CtHtrA inhibitors, which hold better promise as anti-chlamydial drug candidates.

α-(Imino)pyridyldifluoroethyl Phosphonates: Novel Promising Building Blocks in Synthesis of Biorelevant Aminophosphonic Acids Derivatives

A convenient synthetic approach to previously unknown NH-iminophosphonates bearing 2-, 3-, and 4-pyridyldifluoromethyl groups at the imine carbon atom was developed. The synthetic potential of these novel building blocks was demonstrated by their conversion into highly functionalized acyclic and heterocyclic aminophosphonates and phosphonic acids combining in their structure biorelevant aminophosphonic fragment, difluoromethyl group, and pyridyl, piperidyl, thiazolidin-4-one, or thiazidinan-4-one heterocyclic moieties in a single molecular platform.

Silver-catalyzed decarboxylative radical allylation of α,α-difluoroarylacetic acids for the construction of CF2-allyl bonds

An efficient silver-catalyzed method of decarboxylative radical allylation of α,α-difluoroarylacetic acids to build CF2-allyl bonds has been developed. Using allylsulfone as an allyl donor, α,α-difluorine substituted arylacetic acids bearing various functional groups are successfully allylated to access a series of 3-(α,α-difluorobenzyl)-1-propylene compounds in moderate to excellent yields in aqueous CH3CN solution under the mild conditions. Experimental studies disclosed that the α-fluorine substitution of arylacetic acid has a great influence on free radical activity and reactivity.

Into the Fray! A Beginner's Guide to Medicinal Chemistry

Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.

Synthetic applications of α,α-difluoroarylacetic acids and salts via decarboxylative functionalization

α,α-Difluoroarylacetic acids are stable, inexpensive and readily available building blocks which can be used to access various difluoromethylated aryl motifs via decarboxylative functionalization for the formation of carbon–carbon and carbon-heteroatom (F, O, S) bonds.

Visible light induced deaminative alkylation of difluoroenoxysilanes: a transition metal free strategy

Visible-light-promoted deaminative alkylation of difluoroenoxysilanes utilizing Hantzsch ester as a catalyst or through substrate-induced pathway have been demonstrated.

Visible-light Promoted Atom Transfer Radical Addition-Elimination (ATRE) Reaction for the Synthesis of Fluoroalkylated Alkenes Using DMA as Electron-Donor

Here, we describe a mild, catalyst-free and operationally-simple strategy for the direct fluoroalkylation of olefins driven by the photochemical activity of an electron donor−acceptor (EDA) complex between DMA and fluoroalkyl iodides. The significant advantages of this photochemical transformation are high efficiency, excellent functional group tolerance, and synthetic simplicity, thus providing a facile route for further application in pharmaceuticals and life sciences.

Ag-Catalyzed minisci C–H difluoromethylarylation of N-heteroarenes

A mild silver-catalyzed decarboxylative C–H difluoromethylarylation of electron-deficient N-heteroarenes.

A general and green fluoroalkylation reaction promoted via noncovalent interactions between acetone and fluoroalkyl iodides

The first example of visible light promoted fluoroalkylation reactions initiated via noncovalent interactions between solvents and R_FI is presented.

The Research Progress of Direct Thrombin Inhibitors

Blood coagulation is the process of changing the blood from the flowing state to the gel state. It is an important part of the hemostatic function. Coagulation is a process by which a series of coagulation factors are sequentially activated, and finally thrombin is formed to form fibrin clot. Direct thrombin inhibitors are important anticoagulant drug. These drugs can selectively bind to the active site of thrombin, inhibit thrombin activity, have strong action and high specificity, and have important significance in the clinical treatment of thrombus diseases. Some of them come from natural products of animals or plants, and many of them have been applied in the clinic. The other part is derived from the design, synthesis and activity studies of small molecule inhibitors. This review discusses the progress of direct thrombin inhibitors in recent years.

Copper-mediated cascade radical cyclization of olefins with naphthalenyl iododifluoromethyl ketones

Copper-mediated radical cyclization of naphthalenyl iododifluoromethyl ketones with olefins was developed to generate a series of unprecedented gem-difluorodihydrophenanthrenones with excellent regioselectivity.

Transition-metal-free decarboxylative C3-difluoroarylmethylation of quinoxalin-2(1H)-ones with α,α-difluoroarylacetic acids

A facile and efficient transition-metal-free decarboxylative radical coupling reaction of α,α-difluoroarylacetic acids with quinoxalin-2(1H)-ones has been developed under mild conditions.

Direct heterobenzylic fluorination, difluorination and trifluoromethylthiolation with dibenzenesulfonamide derivatives

Functionalization of heterocyclic scaffolds with mono- or difluoroalkyl groups provides unique opportunities to modulate drug pKa, influence potency and membrane permeability, and attenuate metabolism. While advances in the addition of fluoroalkyl radicals to heterocycles have been made, direct C(sp3)-H heterobenzylic fluorination is comparatively unexplored. Here we demonstrate both mono- and difluorination of a range of alkyl heterocycles using a convenient process that relies on transient sulfonylation by the electrophilic fluorinating agent N-fluorobenzenesulfonimide. We also report heterobenzylic trifluoromethylthiolation and 18F-fluorination, providing a suite of reactions for late-stage C(sp3)-H functionalization of drug leads and radiotracer discovery.

Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design

The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.

The selectivity and bioavailability improvement of novel oral anticoagulants: An overview

Anticoagulants have exhibited a critical role in the prevention and/or treatment of thrombotic diseases. Up to now, kinds of novel oral anticoagulants, inhibiting plasma serine proteases in the coagulation cascade, have been developed to overcome the clinical limitations of classical anticoagulants (like warfarin and heparins). Some of them, such as Apixaban, Rivaroxaban, Edoxaban, and Dabigatran, have been approved by FDA in recent years. This review summarizes the discovery and optimization of representative novel oral anticoagulants with the aim to improve selectivity and bioavailability of compounds. The impact of different targets in the cascade on bleeding risk also is discussed. We hope some more effective, selective, and safer anticoagulants can be developed in the future on the basis of these design experiences.

Bioisosteric Exchange of Csp3 -Chloro and Methyl Substituents: Synthesis and Initial Biological Studies of Atpenin A5 Analogues

Asymmetric synthesis and initial biological studies of two analogues of a naturally occurring chlorinated antifungal agent, atpenin A5, are described. These analogues were selected on the basis of Cl→CH3 or H3 C→Cl exchanges in the side-chain of atpenin A5. The interchange of chloro and methyl substituents led to complex II inhibitors with equal IC50 values. This suggests that Cl↔Me bioisosteric exchange can be realized in aliphatic settings.

Pd-catalyzed gem-difluoroallylation of arylboronic acids with γ,γ-difluoroallylic acetates

A highly regio- and stereo-selective palladium-catalyzed gem-difluoroallylation of arylboronic acids with γ,γ-difluoroallylic acetates has been described. The method allows the synthesis of a variety of gem-difluoroallylated arenes with a tosyloxy group on the CC double bond, thus providing a good opportunity for down-stream transformations.

Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods

Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico modeling during the lead optimization phase of a drug discovery campaign. Here, we present a large-scale study of the efficacy of data fusion strategies to leverage results from end-point MM/GBSA calculations in multiple receptors to identify potent inhibitors among an ensemble of congeneric ligands. The retrospective analysis of 13 congeneric ligand series curated from publicly available data across seven biological targets demonstrates that in 90% of the individual receptor structures MM/GBSA scores successfully identify subsets of inhibitors that are more potent than a random selection, and data fusion strategies that combine MM/GBSA scores from each of the receptors significantly increase the robustness of the predictions. Among nine different data fusion metrics based on consensus scores or receptor rankings, the SumZScore (i.e., converting MM/GBSA scores into standardized Z-Scores within a receptor and computing the sum of the Z-Scores for a given ligand across the ensemble of receptors) is found to be a robust and physically meaningful metric for combining results across multiple receptors. Perhaps most surprisingly, even with relatively low to modest overall correlations between SumZScore and experimental binding affinities, SumZScore tends to reliably prioritize subsets of inhibitors that are at least as potent as those that are prioritized from a "best" single receptor identified from known compounds within the congeneric series.

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.

Enhanced ligand sampling for relative protein-ligand binding free energy calculations

Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM.

Synthesis of diaryldifluoromethanes by Pd-catalyzed difluoroalkylation of arylboronic acids

The first example of Pd-catalyzed aryldifluoromethylation of arylboronic acids with readily available aryldifluoromethyl bromides has been described. Preliminary mechanistic studies revealed that a Pd(0)L_n-initiated single electron transfer (SET) pathway is involved in the catalytic cycle.

Accelerated adaptive integration method

Conformational changes that occur upon ligand binding may be too slow to observe on the time scales routinely accessible using molecular dynamics simulations. The adaptive integration method (AIM) leverages the notion that when a ligand is either fully coupled or decoupled, according to λ, barrier heights may change, making some conformational transitions more accessible at certain λ values. AIM adaptively changes the value of λ in a single simulation so that conformations sampled at one value of λ seed the conformational space sampled at another λ value. Adapting the value of λ throughout a simulation, however, does not resolve issues in sampling when barriers remain high regardless of the λ value. In this work, we introduce a new method, called Accelerated AIM (AcclAIM), in which the potential energy function is flattened at intermediate values of λ, promoting the exploration of conformational space as the ligand is decoupled from its receptor. We show, with both a simple model system (Bromocyclohexane) and the more complex biomolecule Thrombin, that AcclAIM is a promising approach to overcome high barriers in the calculation of free energies, without the need for any statistical reweighting or additional processors.

The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems

The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.