A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation

Abstract

RAF inhibitors have transformed treatment for patients with BRAFV600-mutant cancers, but clinical benefit is limited by adaptive induction of ERK signaling, genetic alterations that induce BRAFV600 dimerization, and poor brain penetration. Next-generation pan-RAF dimer inhibitors are limited by a narrow therapeutic index. PF-07799933 (ARRY-440) is a brain-penetrant, selective, pan-mutant BRAF inhibitor. PF-07799933 inhibited signaling in vitro, disrupted endogenous mutant-BRAF:wild-type-CRAF dimers, and spared wild-type ERK signaling. PF-07799933 ± binimetinib inhibited growth of mouse xenograft tumors driven by mutant BRAF that functions as dimers and by BRAFV600E with acquired resistance to current RAF inhibitors. We treated patients with treatment-refractory BRAF-mutant solid tumors in a first-in-human clinical trial (NCT05355701) that utilized a novel, flexible, pharmacokinetics-informed dose escalation design that allowed rapid achievement of PF-07799933 efficacious concentrations. PF-07799933 ± binimetinib was well-tolerated and resulted in multiple confirmed responses, systemically and in the brain, in patients with BRAF-mutant cancer who were refractory to approved RAF inhibitors. Significance: PF-07799933 treatment was associated with antitumor activity against BRAFV600- and non-V600-mutant cancers preclinically and in treatment-refractory patients, and PF-07799933 could be safely combined with a MEK inhibitor. The novel, rapid pharmacokinetics (PK)-informed dose escalation design provides a new paradigm for accelerating the testing of next-generation targeted therapies early in clinical development.

Figure 1.

Preclinical characterization of pan-mutant BRAF selective monomer/dimer inhibitor PF-07799933. A, Heatmap of 50% inhibitory concentration (IC₅₀) values for inhibition of pERK in human cancer cell lines for PF-07799933 and comparator RAF inhibitors, as derived from dose–response curves in Supplementary Fig. S1. Each cell line with specific BRAF mutation is summarized in Supplementary Table S1. Note color scaling for BRAF wild-type cell lines is distinct from BRAF-mutant cell lines. Unsupervised clustering of compounds is shown using Euclidean distance as a similarity metric. B, Immunoprecipitation of BRAF and CRAF dimer complexes in the MEL21514 (p61 BRAF splice variant) melanoma cell line. Comparison of dimer-breaking effects of PF-07799933 and encorafenib are shown at indicated drug concentrations for a 1-hour incubation period. C, Efficacy curves of mean tumor volumes in mice (n = 8–10) bearing subcutaneous xenografts (left) and change in flux measurements of intracranial xenografts (right) of Class I A375 (BRAF^V600E) melanoma cells following oral treatment with the indicated agents. D, Efficacy curves of mean tumor volumes in mice (n = 8–10) bearing subcutaneous patient-derived or cell line xenografts of Class II, indel, and Class I acquired resistance models following oral treatment with the indicated agents. IC₅₀, 50% inhibitory concentration; nM, nanomolar; INDEL, insertion/deletion; WT, wild-type; IP, immunoprecipitated; FL, full-length; mm³, cubic millimeter; SEM, standard error of mean; QD, once daily; BID, twice daily; mpk, milligrams per kilogram; NSCLC, non–small cell lung cancer; PDAC, pancreatic adenocarcinoma.

Figure 2.

PF-07799933 safety and rapid PK-guided dose escalation. A, Examples of traditional (left) vs. PK-guided dose escalation (right) for a drug with a wide therapeutic index based on preclinical data and available clinical data for similar drugs. With traditional dose escalation (example of modified Fibonacci dose escalation design with decreasing dose increments at higher dose levels), even without DLTs, it can require many dose levels and patients to reach a potentially efficacious exposure (C_eff). In contrast, PK-guided dose escalation may require fewer dose levels, time, and patients to reach a potentially efficacious exposure. An example shown is a threefold dose increase in the absence of DLTs and if drug exposures are lower than the potentially toxic exposure (C_tox) by at least a prespecified safety margin (C_marg); otherwise, a twofold dose increase. B, Preliminary C_max, AUC_tau, and MOE values for each patient on Cycle 1 Day 15 (C1D15) of dosing for patients with available PK at the time of dose escalation. At a given dose level, if MOEs (rat value at STD₁₀/human value for C_max and AUC_tau) are >40 in at least two out of three participants, and no DLTs are observed at the current and all prior dose levels, a threefold dose increase is allowed; otherwise, the maximum dose increase is twofold. C, Preliminary plasma concentration vs. time data (mean ± standard deviation for n = 3–5 per dose level) on C1D15. Horizontal reference lines show plasma concentrations for IC₉₀BRAF-mutant protein target coverage based on the cell-based pERK assay, the average concentration (C_av) in the mouse xenograft at a 30-mg/kg dose (shown to be efficacious for multiple tumor types), the C_max at the rat (sensitive tox species) STD₁₀ and the C_max at the cutoff allowing a threefold dose increase (i.e., C_max/40). To enroll patients with symptomatic brain metastases, C_trough on C1D15 had to exceed the G469A IC₉₀ in at least one-half of patients, achieved at 150 mg QD. PK, pharmacokinetics; DLT, dose-limiting toxicity; DL, dose level; PT, patient; AUC_tau, area under the dose–response curve to end of dosing interval; MOE, margin of exposure; mg, milligrams; QD, daily; BID, twice daily; ng, nanograms; conc, concentration; ml, milliliters; STD₁₀, severely toxic dose in 10% animals; mpk, milligrams per kilogram; C_av, average concentration; C_max, maximum concentration; IC₉₀, 90% inhibitory concentration.

Figure 3.

Efficacy in patients with BRAF^V600E/Class I-mutant cancer. A, A waterfall plot of the maximum change in tumor size by treatment, dose, and tumor. Preliminary summary of select cooccurring mutations (known activating for oncogenes, known inactivating for tumor suppressor genes, green—tumor, blue—ctDNA) is shown at the bottom (see Supplementary Table S5). B, A swimmer plot representing the overall treatment duration. Two patients are not shown in A due to the absence of a target lesion (n = 1) or the absence of postbaseline imaging assessment (n = 1). + indicates patient with BRAF^V600E+ thyroid cancer who achieved sustained tumor decrease consistent with a confirmed PR with the addition of binimetinib, after progression on PF-07799933 monotherapy. # indicates patient with BRAF^V600E+ primary brain tumor who achieved a confirmed PR after the data cutoff. Note: response categories are per RECIST 1.1 except for primary brain tumor, which is categorized by RANO. B, binimetinib combination; C, cetuximab combination; CR, complete response; PR, partial response; SD, stable disease; PD, progressive disease; NE, not evaluable; NCNP, non-CR/non-PD; p48, BRAF p48 splice variant; gain, BRAF copy number gain.

Figure 4.

PF-07799933 overcomes de novo and acquired resistance and intracranial progression in patients with BRAF-mutant cancer. A, Previous therapies (best overall response to each systemic therapy shown in parenthesis) and timing of lymph node biopsy that showed a p48 splice variant for a patient with BRAF^V600E+ papillary thyroid cancer. B, Structure of the BRAF p48 in-frame BRAF splice-variant detected by tumor mRNA analysis. The table shows details of the spliced mRNA identified in 15% of all BRAF transcripts in a biopsy sample with 13% V600E MAF (Supplementary Table S5), likely representing the acquisition of the splice variant in cis in all V600E transcripts. C, Change in the sum of longest tumor diameters of target lesions (blue, normalized to baseline) and in BRAF^V600E ctDNA (green). Note: ctDNA assay cannot detect splice variants in mRNA. Imaging for weeks 36 to 48 was obtained after the data cutoff. D, Images of a large left neck target lesion mass during treatment. E, Previous therapies for a patient with a BRAF^V600E+ primary brain tumor. PF-07284890 is an investigational, brain-penetrant BRAF monomer inhibitor. F, Change in the sum of target lesion diameters (no ctDNA was detected in this patient). G, Images of a right temporal lobe target lesion during treatment. H, Change in the sum of the longest tumor diameters and mutations detected in ctDNA for a patient with BRAF^G466E-mutant ACC. * indicates BRAF^V600E or BRAF^G469A detected with BRAF gene-specific ctDNA assay. ACC, adenoid cystic carcinoma; CR, complete response; PR, partial response; SD, stable disease; PD, progressive; L, lenvatinib; MAF, mean allele frequency.