**1. Introduction**

Cross-coupling reactions have made an impressive impact in medicinal chemistry, and drug discovery and development for more than two decades. The success and popularity of this type of methodology comes from the fact that during the drug discovery phase, chemists are attracted to reactions that are reliable and reproducible. In drug discovery, medicinal chemists are designing and synthesizing novel compounds that could meet the criteria envisioned for the specific target product profile (TPP) to advance the eventual selected compound (referred to as Development Candidate) into clinical trials. During this period, medicinal chemists look for approaches to modify the structure in multiple ways to impart the corresponding pharmacological activity, pharmacokinetic and physicochemical attributes, in addition to a suitable safety profile, in general known as structure–activity relationships (SAR) and structure–property relationships (SPR). The cross-coupling methodology is a reliable and versatile approach that allows for the bond-formation of a sp2-hybridized aromatic halide (acting as an electrophile or **1**) with an organometallic (nucleophile or **2**) using a metal catalyst (Figure 1). In particular, palladium-catalyzed cross-coupling reactions have been demonstrated as an extraordinary resource and robust class of reactions [1] for the creation of carbon–carbon and carbon–heteroatom bonds in the pharmaceutical industry. In this review, we want to highlight the impactful applications of cross-coupling reactions in medicinal chemistry with a few recent examples from the field, with an emphasis on the Suzuki–Miyaura and Buchwald–Hartwig methodologies due to their versatility to generate carbon–carbon and carbon–heteroatom bonds and their prevalence as the two most common coupling reactions that contribute to medicinal chemistry [2] (For a broader

scope of other cross-coupling reactions beyond the goals of this review, like Negishi [3,4], Kumada [5], Stille [6] and Chan-Lam [7], the reader is referred to additional reading.) Furthermore, we present specific recent cases for the identification of clinical candidates that incorporate cross-coupling reactions during their large-scale manufacturing process. As a forward outlook of these applications, we review several examples of broader utilization of cross-coupling reactions to new chemical modalities, such as DNA-encoded libraries (DELs), synthesis of novel cyclopeptides, allosteric modulators, and proteolysis targeting chimera (PROTAC) approaches.

**Figure 1.** (**a**) Fundamentals of cross-coupling methodology; (**b**) example of Suzuki–Miyaura Csp2-Csp2 coupling.

The nomenclature for cross-coupling reactions is based on the type of nucleophile utilized. For example, using organoboranes as nucleophiles is referred to as Suzuki–Miyaura reactions (Figure 1), while using organozinc nucleophiles is known as the Negishi reaction.

French chemist Andre Job was the first person to combine organometallic reagents with catalysis in an effective fashion [8]. He reported mixing the Grignard PhMgBr with NiCl2 to incorporate CO, NO, C2H4, C2H2, or H2. Building on this initial discovery, in 1941, Kharasch published on metal-catalyzed homo-couplings of organomagnesium reagents [9]. Kharasch used catalytic amounts of FeCl3, CoCl2, MnCl2, or NiCl2 with Grignard reagents and alkyl or aryl halides for the homo-coupling reaction. After key contributions from Heck and others, Kochi [10] disclosed an FeCl3-catalyzed reaction between Csp2–Br electrophiles and Grignard reagents. In 1976, Negishi [11] demonstrated that other organometallic reagents could be used instead of Grignard reagents. Due to its bench stability and high reactivity, palladium was considered the preferred metal for cross-coupling reactions, and is now utilized in a routine basis across medicinal chemistry therapeutic areas.

#### **2. C-C Reaction: Suzuki–Miyaura Reaction**

In a recent study analyzing the most common reactions in medicinal chemistry [2], it was revealed that, in 2014, the Suzuki–Miyaura coupling was the second most utilized transformation after the amide bond formation. As a testimony to the impact of this reaction, it is possible to see a biphenyl moiety or aryl-heterocycle groups in a variety of approved drugs (Figure 2).

**Figure 2.** Examples of approved drugs where Suzuki–Miyaura coupling is employed to form critical carbon–carbon bonds with aromatic or heterocyclic groups.

As an example, the synthesis of Losartan (**4**) [12] is shown in Scheme 1 [13]. Losartan (**4**), one of the most prescribed medicines in the world, is the first angiotensin II receptor antagonist discovered by scientists at Dupont to treat high blood pressure. A key cross-coupling step in the synthetic route required further optimization in order to obtain a high yield. It was found that heating Pd(OAc)2 and triphenylphosphine in tetrahydrofuran (THF) led to the preparation of an active catalyst, instead of using tetrakis (triphenylphosphine) palladium, which was air-sensitive and not cost-effective for large-scale. The high temperature required for the coupling reaction led to the identification of a solvent system that mixed well with the water/base. A 1: 4 mixture of THF/Diethoxymethane (DEM) was identified as the most favorable for the catalyst preparation, affording a 95% yield.

**Scheme 1.** Example of the Suzuki–Miyaura coupling for the synthesis of Losartan (**4**).

A more recent example shown in Figure 2 is abemaciclib (**9**) [14], a CDK 4/6 inhibitor to treat advanced breast cancer with specific mutations HR+/HER2−, approved by the U.S. Food and Drug Administration (FDA) in 2017. The synthesis of abemaciclib (**9**) [15] incorporates a Suzuki cross-coupling reaction using a boronic ester followed by a palladium-mediated Buchwald–Hartwig amination to form the C-N bond with the pyrimidine ring.

The broad scope of the reaction to generate Csp2-Csp2 bonds, non-toxicity, tolerance toward varied functional groups, air- and moisture-stable properties, and straightforward synthesis made the Suzuki–Miyaura the top transformation of choice for SAR exploration in drug discovery. The research investment, mainly by academics, in developing new ligands and reaction conditions facilitated the synthetic feasibility and applicability to a large number of medicinal chemistry projects. This is one of the critical factors on how organic chemistry influences medicinal chemistry [16], helping to reduce the cycle times of the fundamental hypothesis, synthesis, and testing iterative processes in drug discovery.

The appealing use of Suzuki–Miyaura coupling led to multiple development candidates with these biphenyl groups. However, those biphenyls or "flat sp2-sp2 biaryls" introduced significant challenges in the developability [17] of this new chemical space. The molecules tended to be more lipophilic, with "flat" structure lattice resulting in high melting points and poor solubility. These developability issues created significant attrition [18] in clinical development. In a seminal paper, Humblet [19] and colleagues unveiled the concept of fraction sp<sup>3</sup> (Fsp3, defined as number of sp3 hybridized carbons/total carbon count) as a measure of molecular complexity and established its correlation with the probability of technical success for compounds to transition from drug discovery to clinical testing and eventually becoming drugs. The higher the Fsp3 value, the higher probability of advancing the discovery candidate compound further into drug development, with approved small-molecule drugs having an average Fsp3 value of 0.47 [20]. This study marked the start of a paradigm shift in drug discovery towards increasing the three dimensionality (3D) of the molecules to minimize pharmaceutical development issues and increase the opportunities in clinical development.

The development of synthetic methodology has evolved [21] to meet the need for preparing 3D-type molecules, including rhodium-catalyzed asymmetric Suzuki–Miyaura reaction with aryls, vinyls, heteroaryls, and heterocycles. Application of the asymmetric sp2-sp3 Suzuki–Miyaura methodology [22] enabled the synthesis of clinical candidates preclamol (**15**, a dopamine D2 receptor partial agonist studied for the treatment of schizophrenia), niraparib (**16**, MK−4827, a 2017 approved poly-(ADP ribose) polymerase (PARP) inhibitor indicated for ovarian cancer), and natural product isoanabasine (**17**), which are all presented in Figure 3 with their corresponding Fsp<sup>3</sup> values calculated using SwissADME [23] online tool.

**Figure 3.** Clinical candidates synthesized via asymmetric Suzuki–Miyaura coupling reactions.

An example of the trend to increase Fsp3 during the Lead Optimization phase, leveraging cross-coupling reactions in drug design, comes from the evolution of the SAR approach for novel E-prostanoid receptor 4 (EP4) antagonists (Figure 4) [24,25] that eventually led to the discovery of LY3127760 [26]. An initial lead (naphthalene derivative, **18**) [27] was identified through an early medicinal chemistry effort, possessing modest human whole blood activity (hWB, IC50 = 243 nM) and low Fsp3. The central core was further explored to increase ligand efficiency and sp3 character. Replacement of the naphthalene core with 2-methyl benzene or 3-methyl-pyridine led to the discovery of **19** (hWB IC50 = 39 nM, Fsp3 = 0.17), a compound with suitable pharmacokinetic profile to test in vivo. Additional SAR optimization to augment Fsp3 led to clinical candidate **20** with an Fsp<sup>3</sup> of 0.38. The crucial synthetic steps for the preparation of compounds **18** and **19** are Pd-mediated cross-coupling reactions (Scheme 2). Suzuki–Miyaura coupling of quinoline or naphthalene (**21**) with 3-chloro-phenyl-boronic acid using PdCl2(dppf)·CH2Cl2 and potassium carbonate led to the corresponding ester derivatives (**22**) as penultimate compounds in the synthesis. This approach led to a route that enabled a rapid exploration of analogs for SAR optimization. In a similar fashion, Suzuki cross-coupling of 3-(hydroxymethyl)-phenyl-boronic acid with halogen-substituted phenyl or pyridine derivatives (**23**), using PdCl2(dppf)·CH2Cl2, provided the bi-aryl-ester analogs **24**.

**Figure 4.** EP4 antagonists and their corresponding Fsp3 values.

**Scheme 2.** Synthetic approach for the preparation of EP4 antagonists.

#### **3. C-N Reaction: Buchwald–Hartwig Reaction**

Another breakthrough cross-coupling transformation in drug discovery is the Buchwald–Hartwig reaction that enables the C–N bond formation [28]. The introduction of nitrogen atoms is a fundamental approach in drug design [29] to modulate the lipophilicity of the molecules and their attributes like pharmacokinetic profile, brain penetration, solubility, permeability, etc. The versatile scope of the reaction resulted in it being one of the most used reactions in medicinal chemistry [30].

The major contributions by Stephen Buchwald and John Hartwig towards palladium-catalyzed cross-coupling reactions of amines with aryl halides between 1994 and 2000's led to the methodology being known as Buchwald–Hartwig amination (Figure 5). The cross-coupling reaction fulfilled a need in medicinal chemistry of effectively generating aromatic C–N bonds, as other traditional methods, such as nucleophilic substitution, reductive amination, and amide coupling, as a few examples, have limited applicability.

**Figure 5.** Buchwald-Hartwig Amination.

The investment into developing structurally distinct ligands led to multiple novel catalyst systems that enabled an increase in the scope of the reaction to hindered amines or moderately reactive ones. The catalysts diphenylphosphinobinapthyl (BINAP, **25**) and diphenylphosphinoferrocene (DPPF, **26**) (Figure 6) enabled the initial extension to primary amines and the application to use aryl iodides or triflates. One of the advantages of those bidentate ligands was the prevention of generating the palladium iodide dimer after the oxidative addition step, thus accelerating the reaction and lowering the amount of palladium required. Large, bulky, sterically hindered tri- and di-alkyl phosphine ligands have demonstrated their ability to be resourceful catalysts, enabling the coupling of a vast variety of amines (primary, secondary, electron deficient, heterocyclic, etc.) with aryl or heteroaryl chlorides, bromides, iodides, and triflates. Further investigation into reaction conditions using different bases (e.g., hydroxide, carbonate, and phosphate bases) allowed for the development of stronger or milder conditions depending on the functional moieties in the substrates. The Buchwald group has focused mainly on generating a large variety of biaryl phosphine ligands, whereas the Hartwig group has directed their research towards ferrocene-derived phosphine ligands. In the last two decades, the interest in these transformations has led to general approaches and reliable protocols that are considered essential for SAR exploration and medicinal chemistry efforts.

**Figure 6.** Key ligands used in palladium-mediated cross-coupling reactions.

One of the biggest challenges for the Buchwald–Hartwig reaction is the use of ammonia as a coupling partner, as it can bind tightly to palladium complexes. The generation of primary aniline derivatives is often found in the synthetic routes for more elaborated medicinal chemistry analogs, as it is a versatile precursor for the synthesis of *n*-based heterocycles or further elaboration of the aniline to amide derivatives. The direct use of ammonia gas as a coupling partner has significant limitations from a safety and handling perspective, even generating polyarylated side products. To overcome this issue, it has been disclosed an approach using ammonia equivalents [31]. This strategy is based on the utilization of benzophenone imine (**30)** [32] or silylamide [33] as coupling partners in the palladium-catalyzed cross-coupling reaction, and subsequent hydrolysis to yield the corresponding primary aniline (**32**, Figure 7). This method of employing ammonia surrogates is a milder synthetic alternative in comparison to other well-known routes like nitration and corresponding reduction steps.

**Figure 7.** General strategy of using benzophenone imine as an ammonia equivalent.

Palladium-catalyzed amination using a benzophenone imine is widely used in medicinal chemistry. As an example, this methodology was applied in the SAR exploration for selective 5-HT1F receptor agonists [34] (Scheme 3) that eventually led to the 2019 approved drug for acute migraine, Lasmiditan (**38**) [35]. Treatment of the key precursor halo-pyridinyl-(1-methyl-piperidin-4-yl)-methanone (**34**) with benzophenone imine, Pd2(dba)3, BINAP in the presence of *t*BuONa, led to the corresponding (6-((diphenylmethylene)amino)pyridin-2-yl) (1-methylpiperidin-4-yl) methanone derivative (**35**) in situ, that was hydrolyzed with hydrochloric acid to afford the desired amino-pyridine **36**. Acylation with substituted benzoyl chloride led to compound **37**, a selective 5-HT1F agonist displaying >90-fold in vitro selectivity over 5-HT1A and 5-HT1D, minimizing potential side effects of broad activation of those serotonin receptors.

**Scheme 3.** Example of 5-HT1F receptor analogs.

Cross-coupling reactions have been employed in medicinal chemistry campaigns across therapeutic areas, including the development of novel antiviral compounds as in the next example. In 2019, Akaji and colleagues [36] reported their efforts to evaluate decahydroisoquinoline inhibitors as severe acute respiratory syndrome (SARS) 3-chymotrypsin-like (3CL) protease inhibitors. The campaign aimed for the treatment of the SARS caused by a beta coronavirus (CoV) back in 2003, and so prevalent unfortunately in 2020 [37]. The CoV contains an RNA genome that encodes two polyproteins with a 3CL cysteine protease (SARS 3CLPRO). This protease is critical for viral replication and is not found in humans (or host cells), and therefore constitutes an attractive target for novel antivirals as there is no current available treatment. Applying structure-based drug design and to further optimize potency of a previous decahydroisoquinoline derivative, the researchers hypothesized that the 4-position carbon of the decahydroisoquinoline is the ideal place to incorporate a non-prime substituent (Figure 8). A key step of the synthesis is the Pd-catalyzed diastereoselective cyclization to generate the appropriate substituted decahydroisoquinoline **40**. Treatment of compound **39** with bis-acetonitrile palladium chloride led to the desired crucial intermediate **40** in 78% yield. This approach resulted in four analogs that were tested for their inhibitory activity against SARS 3CLPRO and the discovery of compound **41** as the most potent analog among them.

**Figure 8.** Cross-coupling reaction in the synthesis of SARS 3CLPRO inhibitors.

#### **4. Cross-Coupling Reactions and Process Chemistry**

Palladium cross-coupling reactions have a profound impact in the drug discovery phase, enabling the rapid functionalization of key precursors and exploration of SAR, as we have reviewed several cases in previous sections. The impact of this synthetic methodology is also appreciated in process chemistry during the large scale-up for clinical studies of development candidates. In particular, in process chemistry there are examples of specific cross-coupling reactions that are yield-efficient on a kilogram scale with cost-effective low catalyst loading. Purification of the desired product on a large-scale might become more complex, and the development of new technologies like metal scavenging or fixed-bed absorption processes enable the isolation of the desired cross-coupling product with minimal levels of palladium residue (<1 ppm) [38] to meet guidelines from regulatory agencies for active pharmaceutical ingredients (API). In addition of new methodology to remove traces of palladium or other catalysts, there is a strong trend to develop more "green" or environmentally friendly approaches to minimize potential toxicity to the ecosystem. We refer the reader to additional resources [39,40] for in depth focus of green chemistry metrics for development of pharmaceutics.

As an example, exploration into these alternate "green" [41] conditions (Figure 9) led to the use of a biphasic reaction medium composed of 2-methyltetrahydrofuran (MeTHF) and water, to assist solubilizing the inorganic base. This helped overcome a common issue encountered with scalability of Buchwald–Hartwig aminations.

**Figure 9.** Strategies which enable "green chemistry" approach toward Buchwald–Hartwig amination.

In this section, we highlight several recent examples of application of cross-coupling reactions to process chemistry. In 2020, the Genentech process group [42] reported the research to overcome a difficult palladium-catalyzed C–N bond formation for the scale-up synthesis of their clinical candidate GDC−0022 (**46**), an inhibitor of the nuclear hormone retinoic acid-related orphan receptor γ (RORγ). The clinical compound contains a sultam moiety with two chiral centers, and the coupling of the bromide-derivative containing the sultam is needed to proceed under mild conditions to ensure chiral integrity. The team explored the initial route developed by the discovery group that included a late-stage Buchwald–Hartwig C–N coupling. Upon initial exploration of that sequence, the process group found out that even 10 mol% of Pd(OAc)2 led to poor overall yields and produced epimerization leading to the undesired cis-(3*S*, 6*S*) diastereomer **47** (Scheme 4). Another challenge was the hydrodehalogenation by-products of the reagents. Initial attempts to scale-up to 150 g led to poor conversion (25% yield) and substantial amounts of the corresponding epimer **47** (12%). To make matters worse, the separation of GDC−0022 (**46**) vs. **47** was not easy and required expensive and time-consuming chiral supercritical fluid chromatography (SFC) methods. This approach was not suitable for a kilogram development campaign. The team used a creative multiparameter optimization effort on a microscale to screen ~300 different Pd-cross-coupling conditions varying the solvent, using different bases (K3PO4 or K2CO3) to minimize the risk for epimerization, and Pd(OAc)2 with mono- and bidentate phosphine ligands (XantPhos, XPhos, RuPhos, DPEPhos, DPPF, and BrettPhos). Based on this exploration, the combination of XantPhos and Pd(OAc)2 using K3PO4 in 1,4-dioxane demonstrated to be superior and was applied to early development manufacturing work, successfully enabling the reaction on an 8 kg scale.

**Scheme 4.** Initial results for the Buchwald–Hartwig C–N cross-coupling last step synthesis of GDC-0022 (**46**).

In the next example, the researchers applied a ligandless coupling approach using palladium supported on charcoal to synthesize a key biaryl moiety for a promising dual B cell lymphoma (Bcl)−2/-/Bcl-xL inhibitor [43]. Antiapoptotic Bcl-2 family members have received great attention based on the clinical success of ABT−199 [44] (Venetoclax, **50**), which was approved by the FDA in 2016 for chronic lymphocytic leukemia [45]. However, Bcl inhibitors of this chemical class, for example, ABT−737 (**48**) and ABT−263 (**49**) (Figure 10), are large molecules with potential developability issues like low solubility that can reduce oral absorption. Scientists at Servier identified compound **51** (Figure 10) as a tricyclic analog of ABT−737 (**48**), specifically designed to decrease planarity of the central core and minimize solubility issues.

**Figure 10.** Bcl inhibitors ABT−737 (**48**), ABT−263 (**49**), Venetoclax (**50**), and **51**.

The authors tackle the challenge of a kilogram scale synthesis of **51**, and in particular the Suzuki coupling reaction of precursor **54** (Scheme 5), in an efficient manner. Although previously the reaction was carried out using Pd(OAc)2, the researchers wanted to develop a greener process exploring Pd/C type 91 as catalyst in water (Scheme 5). Based on their preliminary work, it was necessary to heat the reaction mixture, otherwise the reaction would stall. The use of K2CO3 as a base gave the best yields for compound **54**. The use of hexadecyl-trimethyl ammonium bromide (CTAB) did not further improve the conversion of the reaction. This is an interesting approach for large-scale synthesis in water for palladium mediated reactions.

Another impactful example of application of cross-coupling reactions to the development of meaningful medicines for patients comes from the synthesis of Lumacaftor (**57**) (Figure 11). Vertex has changed the landscape for cystic fibrosis with the recent approvals of Ivacaftor (**56**), Lumacaftor (**57**), Tezacaftor (**58**), and Elexacaftor (**59**) (Figure 11), and their corresponding combinations [46]. The rapid discovery and development of these four drugs since 2012 have been a game changer for science and patients [47]. A genetic mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) [48] protein reduces its function leading to less chloride secretion with consequent increase of mucus in the airways, gastrointestinal tract, and other organs. These effects manifest clinically with gradual loss of pulmonary function, dietary deficits, and, eventually, could be fatal with respiratory failure. The most frequent genetic defect is the deletion of phenylalanine 508 (F508del). More than one CFTR modulator is needed to overcome the genetic defects in the CFTR protein. Positive allosteric modulators of the CFTR channel increase the probability of the open-channel state improving the ion

gating through the channel. Small-molecule correctors such as Lumacaftor (**57**) behave as chaperones enabling protein folding and enhancing the trafficking of the CFTR proteins to the cell surface.

*<sup>a</sup>*Water 10 mL/g, 10% Pd/C type 91 (0.25 mol%). *<sup>b</sup>*Determined as HPLC % *a/a* of species. *<sup>c</sup>*On 0.2 g of **52**. *<sup>d</sup>*On 3 g of **52**.

**Scheme 5.** Reaction and screening conditions for Suzuki cross-coupling in water.

**Figure 11.** Cystic fibrosis transmembrane conductance regulator (CFTR)-modulator drugs for the treatment of cystic fibrosis.

In the synthesis of Lumacaftor [49] (**57**, Scheme 6) there are two critical Pd-mediated cross-coupling reactions. For the assembly of the acid fragment **65**, the Pd-mediated carbonylation of the aromatic bromide **60** using Pd(PPh3)4, Et3N in methanol provided the corresponding methyl ester **61**. Further functionalization gave the desired acid **65** in 1.6% yield over the final four steps. After amide formation via an acid chloride to afford precursor **67**, the final step of the synthesis includes a Suzuki–Miyaura transformation. Cross-coupling using Pd(dppf)Cl2 in dimethylformamide (DMF) (at 150 ◦C, in the microwave for a short period of time) led to lumacaftor (**57**) (no yield was disclosed in the original synthesis) [50]. This initial synthesis was most likely used during the discovery phase to allow for an efficient synthesis of different analogs. However, once lumacaftor (**57**) was identified for clinical development, the synthesis was streamlined. Instead, the critical biaryl formation was performed first in the synthesis as displayed in Scheme 7. The Suzuki coupling of the boronic acid with 2-bromo-3-picoline **69** in toluene/water using Pd(dppf)Cl2 and K2CO3 at 80 ◦C provided a functionalized biaryl precursor **70** in an 82% yield.
