Complex I inhibitor of oxidative phosphorylation in advanced solid tumors and acute myeloid leukemia: phase I trials

Abstract

Although targeting oxidative phosphorylation (OXPHOS) is a rational anticancer strategy, clinical benefit with OXPHOS inhibitors has yet to be achieved. Here we advanced IACS-010759, a highly potent and selective small-molecule complex I inhibitor, into two dose-escalation phase I trials in patients with relapsed/refractory acute myeloid leukemia (NCT02882321, n = 17) and advanced solid tumors (NCT03291938, n = 23). The primary endpoints were safety, tolerability, maximum tolerated dose and recommended phase 2 dose (RP2D) of IACS-010759. The PK, PD, and preliminary antitumor activities of IACS-010759 in patients were also evaluated as secondary endpoints in both clinical trials. IACS-010759 had a narrow therapeutic index with emergent dose-limiting toxicities, including elevated blood lactate and neurotoxicity, which obstructed efforts to maintain target exposure. Consequently no RP2D was established, only modest target inhibition and limited antitumor activity were observed at tolerated doses, and both trials were discontinued. Reverse translational studies in mice demonstrated that IACS-010759 induced behavioral and physiological changes indicative of peripheral neuropathy, which were minimized with the coadministration of a histone deacetylase 6 inhibitor. Additional studies are needed to elucidate the association between OXPHOS inhibition and neurotoxicity, and caution is warranted in the continued development of complex I inhibitors as antitumor agents.

Extended Data Fig. 1. Effect of IACS-010759 on venous lactate and blood pH.

a-d, Relationship between venous lactate and IACS-010759 concentrations in AML (a) cohort 1, (b) cohort 2, (c) cohort 3, and (d) cohort 4. Dotted line indicates 8 nM of plasma IACS-010759. e-h, Relationship between blood pH and plasma IACS-010759 concentrations in AML (e) cohort 1, (f) cohort 2, (g) cohort 3, and (h) cohort 4. Dotted line indicates 8 nM of plasma IACS-010759. i-m, Relationship between venous lactate and IACS-010759 concentrations in Solid Tumor (i) cohort 1, (j) cohort 2, (k) cohort 3, (l) cohort 4, and (m) cohort 5. Dotted line indicates 8 nM of plasma IACS-010759. n-r, Relationship between blood pH and plasma IACS-010759 concentrations in Solid Tumor (n) cohort 1, (o) cohort 2, (p) cohort 3, (q) cohort 4, and (r) cohort 5. Dotted line indicates 8 nM of plasma IACS-010759.

Extended Data Fig. 2. Treatment-induced peripheral neuropathy.

a, b, (a) Ultrastructural examination and (b) electronic microscopy analysis of a biopsy collected from the left superficial peroneal upper leg nerve root of a Cohort 4 patient from the Solid Tumor trial. The patient developed Grade 3–4 peripheral neuropathy while on a treatment regimen of 2.5 mg of IACS-010759 daily during the induction phase (Day 1–7), and 2.5 mg bi-weekly during the maintenance phase. Images indicate severe vacuolar changes in myelin sheath with axonal degenerative changes and atrophy.

Extended Data Fig. 3. Pharmacokinetics of IACS-010759 in AML and Solid Tumor cohorts.

Dosing regimens are detailed in Fig. 1, Supplementary Table 1. a, b, Plasma IACS-010759 concentrations over time in (a) AML Cohort 1 (blue) and Cohort 2 (red); (b) AML Cohort 3 (green) and 4 (purple). c, d, Plasma IACS-010759 concentrations (nM) over time in Solid Tumor (c) Cohort 1 (blue), Cohort 2 (red), and Cohort 3 (green); (d) Cohort 4 (purple), Cohort 5 (orange), and Cohort 6 (black). Each dot represents the mean plasma IACS-010759 concentration at one collection point for one patient.

Extended Data Figure 4.. Plasma IACS-010759 concentrations in individual patients.

(a-b) Plasma IACS-010759 concentrations AML patients in (a) cohorts 1 (red) and 2 (blue), which received once daily (QD) dosing, and in (b) cohorts 3–4, which each received an induction and maintenance phase. (e-f) Plasma IACS-010759 concentrations in Solid Tumor (c) cohorts 1 and 5, (d) cohorts 2 and 4, (e) cohort 3, and (f) cohort 6. All cohorts received induction and maintenance phases.

Extended Data Figure 5.. Correlations between plasma IACS-010759 concentration and baseline oxygen consumption rate (OCR) from AML blasts.

Baseline OCR has been normalized to cell number. Each symbol represents the mean +/− 95% confidence interval derived from 2–6 technical replicates. Closed circles are predose and open circles indicate post dose values. Blue indicates pre-dose (C1D1). Red indicates after one week of QD dosing (C1D7 - Cohorts 3, 4; C1D14 - Cohorts 1, 2). Black closed circles are other timepoints collected during cycle 1. Correlations analyzed by a Pearson’s correlation coefficient test; p < 0.05. (a) n= 3 at C1D8(6), C1D10; n = 5 at C1D1, C1D1(6) C1D8, and C1D14; n = 6 at all other times. (b) n = 5 at C1D8, C1D8(6), C1D22(6), C1D28, C1D28(6); n = 6 at all other times. (c) n = 6. (d) n = 2 at C1D9, C1D14(6), C1D25(6), C1D28, C1D28(6); n = 3 at C1D8, C1D8(6), C1D14, C1D17, C1D17(6); n = 4 at C1D2, C1D10; n = 5 at C1D1, C1D1(6). (e) n = 5 at C1D10; n = 6 at all other times. (f) n = 4 at C1D8(6); n = 6 at all other times. (g) n = 4 at C1D1(4); n = 5 at C1D1; n = 6 at all other times. (h) n = 6. (i) n = 2 at C1D7(4); n = 3 at C1D7, C1D15, C1D15(4), n = 6 at C1D1, C1D1(4). (j-k) n = 6. (l) n = 3 at C1D1, C1D1(4); n = 4 C1D7, C1D7(4); n = 6 at all other times.

Extended Data Figure 6.. Correlations between plasma IACS-010759 concentration and maximal oxygen consumption rate (OCR) from AML blasts.

Maximal OCR has been normalized to cell number. Each symbol represents the mean +/− 95% confidence interval derived from 2–6 technical replicates. Closed circles are predose and open circles are post dose values. Blue indicates pre-dose (C1D1). Red indicates after one week of QD dosing (C1D7 - Cohorts 3, 4; C1D14 - Cohorts 1, 2). Black closed circles are other timepoints collected during cycle 1. Correlations analyzed by a Pearson’s correlation coefficient test; p < 0.05. (a) n = 3 at C1D8(6), C1D10; n = 4 at C1D1, C1D2, C1D8; n = 5 at C1D1(6), C1D14, C1D14(6), n = 6 at all other times. (b) n = 4 at C1D28, C1D28(6); n = 5 at C1D8, C1D8(6), C1C14, C1C14(6), C1D22(6); n = 6 at all other times. (c) n = 6. (d) n = 1 at C1D17; n = 2 at C1D9, C1D14, C1D14(6), C1D25(6), C1D28, C1D28(6); n = 3 at C1D8, C1D8(6), C1D17(6); n = 4 at C1D2, C1D10; n = 5 at C1D1, C1D1(6). (e) n = 4 at C1D10; n = 6 at all other times. (f) n = 4 at C1D8(6); n = 5 at all other times. (g) n = 4 at C1D1(4), C1D15; n = 5 at C1D1, C1D15(4), C1D21, n = 6 at C1D7, C1D7(4). (h), n = 5 at C1D15, C1D15(4); n = 6 at all other times. (i), n = 2 at C1D7(4), C1D15; n = 3 at C1D7, C1D15(4); n = 6 at C1D1, C1D1(4). (j) n = 5 at C1D1, C1D1(4), C1D21, unscheduled collection time point; n = 6 at all other times. (k) n = 3 at C1D15, C1D15(4); n = 6 at all other times. (l) n = 2 at C1D1; n = 3 at C1D1(4); n = 4 at C1D7, C1D7(4); n = 5 at C1D21; n = 6 at C1D15, C1D15(4), end of study.

Extended Data Figure 7.. Evidence of target inhibition in AML blasts.

(a-e) Effect of IACS-010759 on levels of (a) NAD+, (b) nicotinamide, (c) tryptophan, (d) glutamine, or (e) alanine in AML blasts from Patients 16, 17, and 19 from AML Cohort 4. Y-axis shows metabolite levels relative to pre-dose levels. Differences from pre-trial levels analyzed by linear regression; *p < 0.05, **p < 0.01, ***p < 0.001. (f-g) Effect of IACS-010759 exposure on NMP, NDP, and NTP levels in AML blasts from (f) Patient 19 and (g) Patient 16 and from AML cohort 4. Y-axis shows nucleotide levels respective to pre-dose levels. Differences from pre-trial levels analyzed by linear regression; *p < 0.05; **p < 0.01, ***p < 0.001.

Extended Data Figure 8.. Drug-induced effects on gene expression in AML blasts.

(a) Gene Ontology enrichment analysis on RNA-sequencing (RNA-seq) results from AML blasts collected from Patients 16, 17, and 19 of AML Cohort 4 at several pre- and post-dose timepoints across Cycle 1. (b) Pathway analysis ranking deregulated biological pathways upon IACS-010759 treatment from patients described in (a).

Extended Data Fig. 9. IACS-010759 elevates plasma lactate as well as induces behavioral and physiological changes indicative of peripheral neuropathy in preclinical models

(a) Effect of escalating doses of IACS-010759 or vehicle on plasma lactate in NSG and B6 mice. n = 4 or n = 5 biologically independent samples from vehicle-treated mice or all other groups, respectively. Data analyzed by two-tailed unpaired Student’s T-test; n.s. = non-significant. Mean ± SE shown. (b) Schematic of the Conditioned Place Preference (CPP) Test. (c) Spontaneous pain assessed with a CPP test (b) after the last dose of IACS-010759 (n = 6) or vehicle (n = 6). Data analyzed by two-sided unpaired Student’s T-test. Mean ± SE shown. (d) Sensorimotor function of mice in (c) assessed with a beam walk test. n = 12 biologically independent samples. Data analyzed with a two-way ANOVA with Tukey’s multiple comparison test. Mean ± SE shown. (e) Oxygen consumption rate (OCR) in the dorsal root ganglion (DRG) from mice in (c) measured under basal conditions (Basal) and after addition of oligomycin (ATP, H + leak), FCCP (Max), or actinomycin + rotenone (spare capacity).; n = 8, n = 4, or n = 8 biologically independent mice for 0 (vehicle), 0.3, or 1 mg/kg IACS-010759, respectively. Data analyzed by two-way ANOVA with Dunnett’s Multiple comparison test. Mean ± SE shown. (f) Density of intraepidermal nerve fibers (IENF) from mice in (b) assessed by quantifying PGP9.5 and nerve fibers crossing into the hind paw epidermis per length (mm) of the basement membrane. n = 12, n = 8, or n = 8 biologically independent samples for vehicle, 1 mg/kg, or 5 mg/kg IACS-010759, respectively. Data analyzed by one-way ANOVA followed by Dunnett’s multiple comparison test. Mean ± SE shown. (g) Immunohistochemistry (IHC) analysis of DRG ATF3 expression (pink) in of mice treated with vehicle, or 1 mg/kg or 5 mg/kg IACS-010759. Positive control = spare nerve injury (SNI) with ATF3 staining. Scale bar = 167.2 μm. Independently repeated three times with similar results. (h) (top) Representative transmission electron microscopy cross sections of the sciatic nerve from mice in (c) after the last dose of vehicle or IACS-010759. Scale bar=2 μm. (h)(bottom) Effects of 5 mg/kg IACS-010759 (n = 131 axons/4 mice) or vehicle (n = 205 axons/4 mice) on myelin. Differences from vehicle group analyzed by a two-tailed Fisher’s exact test; ***p = 0.0003, **p = 0.0031, *p = 0.0447.

Extended Data Fig. 10. Co-administration of an HDAC inhibitor mitigates the behavioral symptoms of IACS-010759-induced peripheral neuropathy.

a, Spontaneous pain assessed with a Conditioned Place Preference test (Extended Data Fig. 9b) after the last dose of IACS-010759 or vehicle +/- ACY-1215. n = 11, n = 8, or n = 12 biologically independent mice for vehicle, vehicle + ACY-1215, or 1 mg/kg IACS-010759 + vehicle/ACY-1215, respectively. Data were analyzed by a two-way ANOVA. Mean ± SE shown. b, Sensorimotor function of mice in (a) was assessed with a beam walk test after the last dose of IACS-010759 or vehicle +/- ACY-1215. Data represent time to cross the beam. n = 8 or n = 12 biologically independent mice for vehicle + ACY-1215 or all other groups, respectively. Data analyzed by two-way ANOVA with Tukey’s Multiple comparison test. Mean ± SE shown. (c) (left) Representative transmission electron microscopy cross sections of the sciatic nerve from mice in (a) after the last dose of vehicle (top), IACS-010759 (center), or IACS-010759 + ACY-1215 (bottom). Scale bar=2 μm. (Right) Comparison of effects induced by vehicle (n = 184 axons/4 mice), 0.3 mg/kg IACS-010759 (n = 233 axons/4 mice), 1 mg/kg IACS 010759 (n = 158 axons/4 mice), 1 mg/kg IACS-010759 + ACY1215 (n = 201 axons/4 mice), or ACY-1215 (n = 255 axons/4 mice) on myelin. Analysis by two-tailed Fisher’s exact test; **p = 0.0016 vs vehicle; ##p = 0.0041 vs 1 mg/kg IACS-010759.

Figure 1.. Flow diagram summarizing the AML and Solid Tumor trials and clinical analyses.

Flow diagram summarizing the enrollment and dose scheduling of the AML (left) and Solid Tumor (right) trials as well as the pharmacokinetic and pharmacodynamic analyses performed on blasts from AML patients. QD, once daily. OCR, oxygen consumption rate.

Figure 2.. Drug-related toxicity.

a-b, Change in venous lactate levels across plasma IACS-010759 concentrations in AML (a) and Solid Tumor (b) cohorts. Each dot represents the mean value of all samples collected from the cohort at the same time point. c, Study timelines of patients from the Solid Tumor (red) and AML (blue) trials. Diamonds, onset of peripheral neuropathy; circles, onset of myalgia. Patients with SMARCA1-null or ENO1-null tumors are noted. Dosing regimen indicated on the right. d, (left) Plasma lactate levels in Solid Tumor patients who developed (red) or did not develop (blue) peripheral neuropathy. Data analyzed by two-way ANOVA, *P = 0.0040. Data show mean ± SE; n=11 biologically independent samples. Individual comparisons of plasma lactate levels in Solid Tumor patients who (center) developed or (right) did not develop peripheral neuropathy. e, (left) Plasma IACS-010759 concentrations in Solid Tumor patients who developed (red; n=11 biologically independent samples) or did not develop (blue; n=9 biologically independent samples) peripheral neuropathy. Data analyzed by two-way ANOVA, showing mean ± SE. Individual comparisons of plasma IACS-010759 levels in Solid Tumor patients who (center) developed or (right) did not develop peripheral neuropathy.

Figure 3.. Evidence of target inhibition in AML blasts.

a-b, Change in (a) baseline and (b) maximal oxygen consumption rate (OCR) prior to dosing (C1D1), after one week of QD dosing (C1D7/C1D14), or extended dosing (C1D15/21/28). n=12 biologically independent samples. Data analyzed by a two-sided paired Student’s t-test. c, The ratio of mitochondrial (mtDNA) to genomic DNA (gDNA) from AML blasts collected pre- and post-dose on Day 16/21/27/28. Data analyzed with a two-sided paired Student’s T-test; mean ± SE shown. Paired patient samples are indicated; n=8 biologically independent samples. d, Baseline OCR across IACS-010759 concentrations in AML blasts from Patients 16, 17, and 19. Grey line indicates expected modulation of baseline OCR by IACS-010759. All samples are biologically independent. Patients 16 and 17: n=6. Patient 19: n=3 at C1D1, C1D1(4); n=4 at C1D7, C1D7(4); n=6 at all other times. Mean ± SE shown. e, Schematic depicting effects of IACS-010759 on oxidative metabolism and alternative fuel pathways. TCA = The tricarboxylic acid cycle; GSH = glutathione; ETC = electron transport chain. f-h, IACS-010759 exposure on (f) NMP, (g) NDP, and (h) NTP in AML blasts from Patient 17. n=7, n=6, or n=7 biologically independent samples for (f), (g), and (h), respectively. Data analyzed by a simple linear regression. i, IACS-010759 exposure on aspartate in AML blasts from patients 16, 17, and 19. N=4, n=7, or n=5 biologically independent samples for Patients 16, 17, or 19 respectively. Data analyzed by a simple linear regression. j, IACS-010759 exposure on lactate in AML blasts from patients 16, 17, and 19. N=4, n=7, or n=5 biologically independent samples for Patients 16, 17, or 19 respectively. Data analyzed by a simple linear regression. k, (top) The OXPHOS signature was generated from published preclinical data and applied to AML blasts from Patients 16, 17, and 19. (bottom) The 1065 signature was established using mRNAs significantly modulated in AML blasts from Patients 16, 17, and 19 upon IACS-010759 treatment.

Figure 4.. IACS-010759 induces physiological and behavioral symptoms of peripheral neuropathy in preclinical models.

a, Plasma IACS-010759 concentrations in NSG mice treated with escalating doses of IACS-010759. Mean ± SE shown. Data analyzed with a 2-way analysis of variance (ANOVA) with a Tukey’s multiple comparison test; n=3 biologically independent samples. At 2 hr: ***p<0.0001 for 5 vs 0.1, 0.3, or 1 mg/kg; *p=0.0129 for 1 vs 0.1 mg/kg; **p=0.0059 for 1 vs 0.3 mg/kg. At 4 hr: **p<0.0001 for 5 vs 0.1, 0.3, or 1 mg/kg; *p=0.0004 for 1 vs 0.1 mg/kg; ***p=0.0003 for 1 vs 0.03 mg/kg. At 8 hr: ***p<0.0001 for 5 vs 0.1, 0.3, or 1 mg/kg; *p=0.340 for 1 vs 0.3 mg/kg. n.s. = non-significant. b, Baseline oxygen consumption rates (OCR) from blasts from the spleen of NSG mice treated with vehicle or escalating doses of IACS-010759. N=5 biologically independent samples. Data analyzed with a two-sided unpaired Student’s t-tests; ns = non-significant. c, Kaplan-Meier survival analysis of NSG mice treated with escalating doses of IACS-010759 or vehicle. N=9 mice/group. Data analyzed with a Log-rank test; vehicle vs 0.03 mg/kg: **p=0.0059; vs 1 mg/kg *p=0.0070; vs 5 mg/kg ***p=0.0004. d, Mechanical sensitivity of hind paws of mice (n=4/group) treated with IACS-010759 or vehicle for 5 days on (grey), 2 days off. Differences from controls (vehicle) were analyzed with a two-way ANOVA with a Dunnett’s multiple comparison test. Mean ± SE shown. e, OCR of murine dorsal root ganglion (DRG) after the last dose of IACS-010759 or vehicle +/− ACY-1215. n=8 biologically independent samples. Data analyzed by two-way ANOVA with Sidak’s multiple comparison test; n.s. = non-significant. Mean ± SE shown. f, Mean maximal OCR of murine DRG neurons after the last dose of IACS-010759 or vehicle. n=8 or n=4 biologically independent samples for 0 and 1 mg/kg or 0.3 mg/kg IACS-010759, respectively. Data analyzed by one-way ANOVA with Dunnett’s multiple comparison test. Mean ± SE shown. g, Mechanical sensitivity of murine hind paws (n=4/group) treated with IACS-010759 (0.3 mg/kg or 1 mg/kg) or vehicle +/− ACY-1215 for 5 days on (grey) and 2 days off. Mean ± SE shown. Data analyzed by two-way ANOVA with Sidak’s multiple comparison test.