DH MOTM Fenebrutinib
DH MOTM Fenebrutinib
com
Case Study
fenebrutinib
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fenebrutinib
oral BTK inhibitor
Ph. III for multiple sclerosis
from ATP site-directed compound libraries + optimization
Clinical data release, May 16, 2023
GENENTECH, SOUTH SAN FRANCISCO, CA
VIEW ONLINE
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Reviewer Comments
Reviewer Charles Cole notes, “BTK is a well-known target in medicinal chemistry - in fact,
a recent book by Nathaniel Vardi, ‘For Blood and Money,’ grippingly details the discovery
and development of the first-to-market BTK inhibitors, ibrutinib and acalabrutinib. The
most notable feature of fenebrutinib is the selected indications in clinical trials. Most
BTKi’s focus primarily on the treatment of mantle cell lymphoma and similar oncology
indications. Fenebrutinib, rather, is currently under investigation in multiple traditional
autoimmune disease indications, including multiple sclerosis, rheumatoid arthritis, systemic
lupus erythematosus and chronic spontaneous urticaria. While these indications are tough,
requiring strict safety profiles due to long-term treatment, fenebrutinib has the chance to
become the first approved BTKi for an autoimmune disorder.”
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Mechanism Of Action In Multiple Sclerosis
In brain autospies from MS patients, BTK+ cells have been found to be increased
around brain lesions, attributable to BTK protein in microglia. Microglia recruit
and maintain adaptive immune cells into the CNS, including brain-homing B
cells, which drive CNS damage in MS. While B cell-depleting anti-CD20 antibodies
like ocrelizumab and rituximab have long been effective in MS, they are not brain penetrant
and likely cannot target CNS-resident B cells. Since small molecules are more likely to be
CNS-penetrant than antibodies, small molecule inhibition of intracellular BTK offers the
potential to target CNS-resident B cells, since BTK inhibition blocks B cell receptor (BCR)
signalling. Additionally, BTK inhibition reduces Fcγ receptor (FcγR) signaling in macrophages
and microglia, potentially addressing several mechanisms that drive immunopathology in
the CNS. BTK inhibition can suppress key processes in relapsing and progressive forms of
MS, including pathological activation of B cells, infiltration of the CNS by lymphocytes,
leptomeningeal inflammation, pro-inflammatory microglial activation, and demyelination.
O N
O N H
H N S
N N N HN N
H HN N
O
N O
HN N
O
H
O
N
N O
N
O
O N HO
O N HO O N HO N
N N
N
N N HN
HN HN
O
N O N O N
N N
F
N
N N
N
N N
O
O O
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against, with >980x-selectivity over the next most sensitive kinase, BMX. The 1.8 Å crystal
structure of the molecule bound to the human BTK kinase domain (PDB: 3OCS) revealed that
CGI1746 bound to the enzyme in an inactive conformation in which the activating tyrosine
residue (Tyr551) was unphosphorylated and sequestered from solvent. Binding of CGI1746
induced the formation of a large pocket in the SH3 domain, dubbed the H3 pocket, which
was occupied by the critical t-butylphenyl moiety of CGI1746.
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Mitigating Amide Hydrolysis Through Cyclization
The Genentech/CGI team was able to identify more metabolically stable compounds
by cyclizing the amide onto the thiophene or related heterocycles, forming 6-5-5 tricycles.
Removing the exposed N-H hydrogen bond donor and increasing the molecules’ rigidity
increased potency and permeability.
H-bonding
(potency) reduce amide hydrolysis
O N HO
N
O N N
H HN
N S O
HN N N
O
F
GDC-0834 G-278
improved preclinical PK improved metabolic profile
rapid amide hydrolysis in clinic dog hepatotoxicity
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Lowering LogD And Avoiding Strongly Basic Groups To
Address Hepatotoxicity
A hepatocyte cytotoxicity assay with cryopreserved human hepatocytes to was used to
identify high-risk compounds, and an in silico model was generated based on 70 molecules
to help predict hepatocyte cytotoxicity. The model suggested that the pKa of most basic
nitrogen, the logP, and plasma protein binding (PPB) were cytotoxic risk factors with
a strongly basic nitrogen being the most significant risk factor. Optimization therefore
focused on lowering logD while avoiding strongly basic groups. Replacing the central aryl
ring with a pyridine heterocycle lowered the logD (pH 7.4) from 3.1 to 2.0 and an increased
predicted stability in human liver microsomes from 12.3 to 8.1 mL/min/kg. Incorporating the
dimethyl-substituted cyclopentyl group improved whole blood (WB) potency, lowering the
WB CD69 IC50 from 55 to 15 nM while maintaining metabolic stability and physicochemical
properties. These modifications resulted in compound 12, which successfully avoided toxicity
in primary human hepatocytes but unfortunately exhibited high plasma clearance with a Clp
of 165 mL/min/kg and a short half-life of 0.4h in cassette rat PK study, so SAR evaluation
continued to improve in vivo stability.
O N HO
O N HO O N HO N
N N N
N N HN
HN HN WB N O
O N O potency N
N N
F
lower
N
N N logD
O
O O
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Binding Mode
PDB: 5VFI - A 1.59-Å resolution X-ray cocrystal structure of fenebrutinib bound to BTK was
solved. The central pyridone is the hinge binder, and the hydrophobic tricyclic ring system
of the drug displaces Tyr551 of the activation loop 18 Å from its position in apo-Btk which
contributes substantially to its potency and kinase selectivity.
• Primary cell activity: The drug inhibited anti-IgM induced BTK phosphorylation (IC50 =
3.1 nM) and FcγRIII-triggered TNFα production in monocytes (IC50 = 1.3 nM).
• In vivo efficacy in rat B and myeloid cell-dependent inflammatory arthritis model (2
mpk PO BID)
• Favorable PK: 85% bioavailability in dogs, 3.8 h half-life (Clp = 10.9 mL/min/kg, Vd =
2.96 L/kg), 65% F in rats, 2.2 h half-life (Clp = 27.4 mL/min/kg, Vd = 5.42 L/kg)
• In vivo safety: a high no observed adverse effect level (NOAEL) in dogs (most sensitive
species), >80-fold higher than targeted efficacious exposure (human WB CD69 IC70
coverage for >12 h)
• Clean in vitro safety profile: no binding >50% in 41 receptor panel at 10 µM, hERG
channel inhibition (functional) IC50 > 30 µM, hNav1.5 channel inhibition = 0.6% at 1
µM and 1.9% at 10 µM, hCav1.2 channel inhibition (functional) = 1.5% at 1 µM
and 3.8% at 10 µM, Ames negative, MNT (HPBLs) negative, cytotoxicity in human
hepatocytes IC50 > 300 µM, CYP 3A4, 1A2, 2C19, 2D6, 2D9 inhibition IC50s > 5 µM
• Physicochemical properties: MW = 664.8, pKa (25 ˚C) = 5.03, 3.69, 1.05; logP (neutral) =
3.3, logP (cationic) = 1.34, solubility (0.1 N HCl, 37 ˚C) = 35.9 mg/mL, (water, 37 ˚C) =
0.003 mg/mL
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Safety And Efficacy Demonstrated In Ph. I And Ph. II Clinical Trials
Fenebrutinib was well-tolerated with no serious or dose-limiting effects in a placebo-
controlled Ph. I study with healthy volunteers, which indicated suitability for its
development as a treatment for autoimmune diseases, with PK/PD data supporting oral
activity of fenebrutinib at 100 mg QD, though 200 mg BID was used in later studies. A Ph.
II study (FenOPTA, NCT05119569) in MS recently showed the drug reduces the number of
new gadolinium-enhancing T1 brain lesions and significantly reduce new or enlarging T2
brain lesions. The human half-life is 4.9-6.0 hours at 60-250 mg BID. Across clinical trials
including more than 2,500 people as of Oct. 2023, rates of adverse events were 38% with
fenebrutinib and 33% with placebo, with the most common differential adverse events being
abnormal liver enzyme levels (5.5% for fenebrutinib vs. 0% for placebo), headache (4.1% vs.
2.8%), nasopharyngitis (2.7% vs. 0%), and upper abdominal pain (2.7% vs. 0%).
Is Fenebrutinib Brain-Penetrant?
In a ACTRIMS 2022 presentation, Sanofi shared preclinical CNS pharmacology for various
BTK inhibitors evaluated in MS, including fenebrutinib, suggesting significant CNS
penetration. The following properties were reported:
• Fenebrutinib: Kp,uu (CSF, day 4, 10 mpk in NHPs): 0.147, 12.9 ng/mL Cmax; MPO score =
3.5, ~8 h CSF IC50 coverage, no IC90 coverage
• Tolebrutinib: Kp,uu (CSF, day 4, 10 mpk in NHPs): 0.397, 4.8 ng/mL Cmax; MPO score =
4.7, ~3 h IC90 coverage
Given the long residence time of fenebrutinib, it is plausible that in humans, fenebrutinib
sufficiently engages BTK in the CNS for pharmacological activity in the CNS compartment,
though the data suggests that it is likely that future inhibitors can improve upon the total
dose required to achieve optimal target coverages in the CNS.
What’s Next?
Genentech is recruiting for two Ph. III clinical trials to compare fenebrutinib to teriflunomide
in patients with RMS (relapsing multiple sclerosis) and PPMS (primary-progressive multiple
sclerosis) (NCT04586023, NCT04586010) at 200 mg BID, with estimated completion dates
into 2026. The safety profile of fenebrutinib has remained consistent with its profile in
previous and ongoing clinical trials involving over 2,400 people, and no new safety concerns
were identified. The results of these studies suggest fenebrutinib may soon be evaluated for
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other autoimmune indications. Fenebrutinib’s positive clinical signal is likely to trigger more
effort into reversible BTK inhibitors outside of oncology, as well as in alternative modalities
for targeting BTK like targeted protein degradation.
Lessons Learned
Fenebrutinib provides a valuable case study highlighting the potential safety advantages
of reversible inhibitors outside of oncology, how to deal with various forms of preclinical
toxicology, how drug-receptor residence time can impart covalent-like properties, how
the selection of a selective starting point can make a tremendous downstream impact, and
how a molecule of high quality against a target with myriad applications can lead to an
opportunity for success outside of an initially intended indication. The medicinal chemistry
campaign also highlights how small, single heavy-atom changes can lead to remarkable
pharmacological improvements with respect to PK, residence time, safety, and beyond.
Synthesis Highlights
The initial medicinal chemistry route to fenebrutinib and its precursors was highly
convergent allowing the route for process development to remain similar. One notable route
modification in a process route was in the synthesis of the tricyclic lactam intermediate
on the left side of the molecule. The medicinal chemists performed a Wittig olefination
extension of chlorovinyl aldehyde to yield the intermediate in 5 steps and 8% overall yield.
In process development, this route was replaced with a 1,4-aza-Michael addition and
cyclization of oxo-piperazine affording 51% yield in 1 step from the same starting material
to give the desired tricyclic lactam product on a >300kg scale. The tricyclic lactam was
then C-N coupled with the 2,4-dichloronicotinaldehyde in 95% yield. The right half of the
molecule was synthesized from chiral starting material (S)-2-methylpiperazine in 7 steps in
39% yield to provide the borylated Intermediate. These two halves were then coupled using a
Suzuki coupling and subsequently reduced to yield the final product in 70% over 2 steps.
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Overall, the route was not greatly changed but the reactions were optimized and scaled to
provide a process for synthesizing fenebrutinib on a hundred kg scale.
O
Routes to Fenebrutinib: N
O
N
N
N NH N
O
O
N NH
Cl C-N coupling N HO
Cl N O Bpin N O
N +
NH N 85% yield N Cl N N
Suzuki Coupling
O O N and Reduction O N
2 steps, 70% yield
CO2Et
(Ph3)P
4 steps
Med. Chem. Route: Cl Cl N 5 steps, 8% overall yield
Wittig olefination NH
CHO
CO2Et O
HN
NH
Cl O
Process Route: N
1 step, 51% overall yield
CHO base-mediated NH
annulation
O
Relevant Patents
Heteroaryl pyridone and aza-pyridone compounds (USRE48239E1). Therapeutic compounds
and compositions, and methods of use thereof (US10307426B2). Dosage form compositions
comprising an inhibitor of bruton’s tyrosine kinase (US10246461B2).
10/15/23 Update:
Introduction and brain-penetration sections updated to include human CSF data reported by
Genentech at the 9th Joint ECTRIMS-ACTRIMS meeting.
6/6/24 Update:
Fenebrutinib was placed on a partial clinical hold by the FDA in Dec. 2023. The decision was
made based on two recent cases of suggesting potential DILI risk, characterized by elevation
of hepatic transaminases in conjunction with elevated bilirubin levels during the blinded Ph.
III trials in relapsing MS. Both patients were asymptomatic and bilirubin as well as ALT/AST
levels returned to normal after drug discontinuation. As a result, enrollment in the US was
paused but continued outside of the US. Patients who received fenebrutinib 70 days or longer
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in the US are continuing the trial. Only a small number of patients who received fenebrutinib
70 days or less discontinued treatment. Fenebrutinib remains in Genentech’s development
pipeline as of Jun. 6, 2024. It is possible that the FDA’s caution was heightened with FDA
clinical holds of several BTK inhibitors including orelabrutinib (Biogen, Ph. II, 2022),
tolebrutinib (Sanofi, Ph. III, 2022), evobrutinib (Merck KGaA, Ph. III, 2023). The pattern is
similar in all cases (reversible lab-based observations).
In Mar. 2024 Merck KGaA announced that they will discontinue development of evobrutinib
for the treatment of MS. The decision was made based on the non-superiority of evobrutinib
compared to Sanofi’s DHODH (dihydroorotate dehydrogenase) inhibitor teriflunomide.
BTK appears to remain an actively pursued target for MS. Biogen just disclosed the discovery
campaign of their covalent BTK inhibitor BIIB129, which is a Molecule of the Month in May
2024, and has a peripheral BTK inhibitor listed in its pipeline for MS in Ph. II as of Jun. 6,
2024 (BIIB091).
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