Fragment optimization and elaboration strategies - the discovery of two lead series of PRMT5/MTA inhibitors from five fragment hits

Here we describe the early stages of a fragment-based lead discovery (FBLD) project for a recently elucidated synthetic lethal target, the PRMT5/MTA complex, for the treatment of MTAP-deleted cancers. Starting with five fragment/PRMT5/MTA X-ray co-crystal structures, we employed a two-phase fragment elaboration process encompassing optimization of fragment hits and subsequent fragment growth to increase potency, assess synthetic tractability, and enable structure-based drug design. Two lead series were identified, one of which led to the discovery of the clinical candidate MRTX1719.

Design and evaluation of achiral, non-atropisomeric 4-(aminomethyl)phthalazin-1(2H)-one derivatives as novel PRMT5/MTA inhibitors

MRTX1719 is an inhibitor of the PRMT5/MTA complex and recently entered clinical trials for the treatment of MTAP-deleted cancers. MRTX1719 is a class 3 atropisomeric compound that requires a chiral synthesis or a chiral separation step in its preparation. Here, we report the SAR and medicinal chemistry design strategy, supported by structural insights from X-ray crystallography, to discover a class 1 atropisomeric compound from the same series that does not require a chiral synthesis or a chiral separation step in its preparation.

Anti-tumor efficacy of a potent and selective non-covalent KRASG12D inhibitor

Recent progress in targeting KRAS^G12C has provided both insight and inspiration for targeting alternative KRAS mutants. In this study, we evaluated the mechanism of action and anti-tumor efficacy of MRTX1133, a potent, selective and non-covalent KRAS^G12D inhibitor. MRTX1133 demonstrated a high-affinity interaction with GDP-loaded KRAS^G12D with K_D and IC₅₀ values of ~0.2 pM and <2 nM, respectively, and ~700-fold selectivity for binding to KRAS^G12D as compared to KRAS^WT. MRTX1133 also demonstrated potent inhibition of activated KRAS^G12D based on biochemical and co-crystal structural analyses. MRTX1133 inhibited ERK1/2 phosphorylation and cell viability in KRAS^G12D-mutant cell lines, with median IC₅₀ values of ~5 nM, and demonstrated >1,000-fold selectivity compared to KRAS^WT cell lines. MRTX1133 exhibited dose-dependent inhibition of KRAS-mediated signal transduction and marked tumor regression (≥30%) in a subset of KRAS^G12D-mutant cell-line-derived and patient-derived xenograft models, including eight of 11 (73%) pancreatic ductal adenocarcinoma (PDAC) models. Pharmacological and CRISPR-based screens demonstrated that co-targeting KRAS^G12D with putative feedback or bypass pathways, including EGFR or PI3Kα, led to enhanced anti-tumor activity. Together, these data indicate the feasibility of selectively targeting KRAS mutants with non-covalent, high-affinity small molecules and illustrate the therapeutic susceptibility and broad dependence of KRAS^G12D mutation-positive tumors on mutant KRAS for tumor cell growth and survival.

Design and Discovery of MRTX0902, a Potent, Selective, Brain-Penetrant, and Orally Bioavailable Inhibitor of the SOS1:KRAS Protein-Protein Interaction

SOS1 is one of the major guanine nucleotide exchange factors that regulates the ability of KRAS to cycle through its “on” and “off” states. Disrupting the SOS1:KRAS^G12C protein–protein interaction (PPI) can increase the proportion of GDP-loaded KRAS^G12C, providing a strong mechanistic rationale for combining inhibitors of the SOS1:KRAS complex with inhibitors like MRTX849 that target GDP-loaded KRAS^G12C. In this report, we detail the design and discovery of MRTX0902—a potent, selective, brain-penetrant, and orally bioavailable SOS1 binder that disrupts the SOS1:KRAS^G12C PPI. Oral administration of MRTX0902 in combination with MRTX849 results in a significant increase in antitumor activity relative to that of either single agent, including tumor regressions in a subset of animals in the MIA PaCa-2 tumor mouse xenograft model.

Abstract LB505: Design and discovery of MRTX0902, a potent, selective, and orally bioavailable SOS1 inhibitor

KRAS mutations are the most common activating mutations in human cancer that ultimately lead to hyperactivation of the MAPK pathway and uncontrolled growth. KRAS functions as a small GTPase that cycles through its GTP-loaded “on” state and its GDP-loaded “off” state, a highly regulated process that is crucial for normal cell proliferation and survival. The guanine nucleotide exchange factor (GEF) SOS1 plays a critical role in this process by regulating the “on/off” state of KRAS. The protein-protein interaction between SOS1 and KRAS facilitates turnover of KRAS from the GDP-loaded inactive state to its activated and GTP-loaded state, a critical step to enable productive KRAS effector binding and activation of downstream signaling. The KRASG12C inhibitor, adagrasib (MRTX849), irreversibly binds to the GDP-loaded inactive conformation of KRASG12C and has recently shown encouraging clinical activity across several cancer types. As adagrasib binds preferentially to the inactive state of KRAS, blockade of SOS1 is anticipated to shift KRASG12C into the adagrasib-susceptible GDP-loaded state. Furthermore, this combination strategy could be used to target other mutant-driven cancers within the MAPK pathway using the appropriate KRASmut inhibitors and/or inhibitors of other targets within the MAPK pathway including MEK or EGFR. MRTX0902 was identified using iterative structure-based design as a selective inhibitor of SOS1 that demonstrates an IC50 value of 2 nM in a SOS1 HTRF binding assay and 30 nM in an MKN1 cellular assay. In pharmacokinetic evaluation across species, MRTX0902 demonstrated low extraction ratios and moderate to high bioavailability in mice, rats, and dogs. In preclinical models, MRTX0902 augmented the antitumor activity of adagrasib and other selected therapies. The design, discovery, and preclinical characterization of the potential best-in-class candidate MRTX0902 will be described.

Citation Format: John M. Ketcham, David M. Briere, Aaron C. Burns, James G. Christensen, Robin J. Gunn, Jacob Haling, Anthony Ivetac, Shilpi Khare, Jon Kuehler, Svitlana Kulyk, Jade Laguer, John D. Lawson, Krystal Moya, Natalie Nguyen, Peter Olson, Lisa Rahbaek, Christopher R. Smith, Niranjan Sudhakar, Nicole C. Thomas, Darin Vanderpool, Xiaolun Wang, Matthew A. Marx. Design and discovery of MRTX0902, a potent, selective, and orally bioavailable SOS1 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB505.

Abstract ND02: MRTX0902: A SOS1 inhibitor for therapeutic intervention of KRAS-driven cancers

KRAS is the most frequently mutated oncogene in cancer and drives uncontrolled growth through hyperactivation of the MAPK pathway. Significant progress has been made in the past several years to directly target KRASG12C with the FDA approval of sotorasib and the reported clinical activity of adagrasib (MRTX849). Despite these remarkable breakthroughs, additional therapies that enhance the depth and duration of response to KRASG12C inhibitors provide the opportunity to build upon the initial progress. SOS proteins are guanine nucleotide exchange factors (GEFs) that transduce receptor tyrosine kinase (RTK) signaling from the cell surface and facilitate the activation of RAS family proteins. In addition, SOS1 is a target of negative feedback signaling following RAS-mediated activation of the RAF-MEK-ERK cascade. Thus, SOS proteins represent a significant therapeutic node that maintains RAS pathway equilibrium as well as oncogenic signaling dynamics. Here we highlight the discovery and preclinical evaluation of MRTX0902, a potent, selective, and orally bioavailable inhibitor of SOS1 presently in IND-enabling studies. A structure-based approach was used to identify a novel chemical series that disrupts the protein-protein interaction between SOS1 and KRAS, thereby preventing SOS1-mediated GTP-exchange on GDP-bound KRAS. Considering MRTX849 preferentially binds to inactive GDP-bound KRASG12C, targeting SOS1 in this genetic context increases the ability of MRTX849 to bind and inhibit KRASG12C. The combination of MRTX0902 with MRTX849 enhances the depth and durability of an anti-tumor response when compared to MRTX849 alone in pre-clinical KRASG12C tumor models. MRTX0902 augments additional targeted therapies across a variety of RAS-addicted tumors, indicating that SOS1 inhibition is effective against a broad spectrum of mutations within the MAPK pathway. Furthermore, drug-anchored CRISPR experiments with MRTX0902 and MRTX849 uncovered a previously underappreciated functional role of the SOS1 paralog, SOS2, in KRAS-addicted tumors. In addition to aiding in the understanding of SOS and RAS family signaling dynamics, these studies implicate SOS2 as a potential cancer drug target in the context of SOS1/KRASG12C inhibition. In summary, we have used a structure-based approach to discover a SOS1 inhibitor that augments the anti-tumor activity of MRTX849 and additional targeted MAPK pathway inhibitors. We anticipate our findings to translate into the clinic and make an impact in patients with RAS-addicted tumors.

Citation Format: John M. Ketcham, Shilpi Khare, Niranjan Sudhakar, David M. Briere, Larry Yan, Jade Laguer, Laura Vegar, Darin Vanderpool, Jill Hallin, Lauren Hargis, Vickie Bowcut, David Lawson, Robin J. Gunn, Anthony Ivetac, Nicole C. Thomas, Barbara Saechao, Natalie Nguyen, Jeffrey Clarine, Lisa Rahbaek, Christopher R. Smith, Aaron C. Burns, Matthew A. Marx, James G. Christensen, Peter Olson, Jacob R. Haling. MRTX0902: A SOS1 inhibitor for therapeutic intervention of KRAS-driven cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr ND02.

Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP-Deleted Cancers

The PRMT5•MTA complex has recently emerged as a new synthetically lethal drug target for the treatment of MTAP-deleted cancers. Here, we report the discovery of development candidate MRTX1719. MRTX1719 is a potent and selective binder to the PRMT5•MTA complex and selectively inhibits PRMT5 activity in MTAP-deleted cells compared to MTAP-wild-type cells. Daily oral administration of MRTX1719 to tumor xenograft-bearing mice demonstrated dose-dependent inhibition of PRMT5-dependent symmetric dimethylarginine protein modification in MTAP-deleted tumors that correlated with antitumor activity. A 4-(aminomethyl)phthalazin-1(2H)-one hit was identified through a fragment-based screen, followed by X-ray crystallography, to confirm binding to the PRMT5•MTA complex. Fragment growth supported by structural insights from X-ray crystallography coupled with optimization of pharmacokinetic properties aided the discovery of development candidate MRTX1719.

Identification of MRTX1133, a Noncovalent, Potent, and Selective KRASG12D Inhibitor

KRAS^G12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of solid tumors. However, when compared to KRAS^G12C, selective inhibition of KRAS^G12D presents a significant challenge due to the requirement of inhibitors to bind KRAS^G12D with high enough affinity to obviate the need for covalent interactions with the mutant KRAS protein. Here, we report the discovery and characterization of the first noncovalent, potent, and selective KRAS^G12D inhibitor, MRTX1133, which was discovered through an extensive structure-based activity improvement and shown to be efficacious in a KRAS^G12D mutant xenograft mouse tumor model.

Evaluation of β-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure

β-Amino acids have a backbone that is expanded by one carbon atom relative to α-amino acids, and β residues have been investigated as subunits in protein-like molecules that adopt discrete and predictable conformations. Two classes of β residue have been widely explored in the context of generating α-helix-like conformations: β³ -amino acids, which are homologous to α-amino acids and bear a side chain on the backbone carbon adjacent to nitrogen, and residues constrained by a five-membered ring, such the one derived from trans-2-aminocyclopentanecarboxylic acid (ACPC). Substitution of α residues with their β³  homologues within an α-helix-forming sequence generally causes a decrease in conformational stability. Use of a ring-constrained β residue, however, can offset the destabilizing effect of α→β substitution. Here we extend the study of α→β substitutions, involving both β³ and ACPC residues, to short loops within a small tertiary motif. We start from previously reported variants of the Pin1 WW domain that contain a two-, three-, or four-residue β-hairpin loop, and we evaluate α→β replacements at each loop position for each variant. By referral to the ϕ,ψ angles of the native structure, one can choose a stereochemically appropriate ACPC residue. Use of such logically chosen ACPC residues enhances conformational stability in several cases. Crystal structures of three β-containing Pin1 WW domain variants show that a native-like tertiary structure is maintained in each case.

Toward a Soluble Model System for the Amyloid State

The formation and deposition of amyloids is associated with many diseases. β-Sheet secondary structure is a common feature of amyloids, but the packing of sheets against one another is distinctive relative to soluble proteins. Standard methods that rely on perturbing a polypeptide's sequence and evaluating impact on folding can be problematic for amyloid aggregates because a single sequence can adopt multiple conformations and diverse packing arrangements. We describe initial steps toward a minimum-sized, soluble model system for the amyloid state that supports comparisons among sequence variants. Critical to this goal is development of a new linking strategy to enable intersheet association mediated by side chain interactions, which is characteristic of the amyloid state. The linker design we identified should ultimately support exploration of relationships between sequence and amyloid state stability for specific strand-association modes.

Quasiracemate Crystal Structures of Magainin 2 Derivatives Support the Functional Significance of the Phenylalanine Zipper Motif

Quasiracemic crystallography has been used to explore the significance of homochiral and heterochiral associations in a set of host-defense peptide derivatives. The previously reported racemic crystal structure of a magainin 2 derivative displayed a homochiral antiparallel dimer association featuring a "phenylalanine zipper" notable for the dual roles of phenylalanines in mediating dimerization and formation of an exposed hydrophobic swath. This motif is seen as well in two new quasiracemate crystals that contain the d form of the magainin 2 derivative along with an l-peptide in which one Ala has been replaced by a β-amino acid residue. This structural trend supports the hypothesis that the Phe zipper motif has functional significance.

Crystallization of the NADP-dependent beta-keto acyl-carrier protein reductase from Brassica napus

The NADP-dependent beta-keto acyl-carrier protein reductase (BKR) from Brassica napus has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol of average molecular weight 1500 as the precipitant. The crystals belong to the hexagonal space group P6(4)22, with unit-cell parameters a = b = 129. 9, c = 93.1 A, alpha = beta = 90, gamma = 120 degrees. Calculated values for V(m), the use of rotation and translation functions and consideration of the packing suggest that the asymmetric unit contains a monomer. The crystals diffract to beyond 2.8 A resolution and are more amenable to X-ray diffraction analysis than those reported previously for the Escherichia coli enzyme. The structure determination of B. napus BKR will provide important insights into the catalytic mechanism of the enzyme and into the evolution of the fatty-acid elongation cycle by comparisons with the other oxidoreductase of the pathway, enoyl acyl-carrier protein reductase (ENR).

Crystallization of the NADP-dependent beta-keto acyl carrier protein reductase from Escherichia coli

The NADP-dependent beta-keto acyl carrier protein reductase (BKR) from E. coli has been crystallized by the hanging-drop method of vapour diffusion using poly(ethylene glycol) of average molecular weight 1450. The crystals belong to the hexagonal space group P6122 or P6522 with unit-cell dimensions a = b = 67.8, c = 355.8 A. Calculated values for Vm and consideration of the packing suggest that the asymmetric unit contains a dimer. BKR catalyses the first reductive step in the elongation cycle of fatty-acid biosynthesis. It shares extensive sequence homology with the enzyme which catalyzes the second reductive step in the cycle, enoyl acyl carrier protein reductase (ENR), and thus provides an opportunity to study the evolution of enzyme function in a metabolic pathway. The structure determination will permit the analysis of the molecular basis of its catalytic mechanism and substrate specificity.

Case report: reporting anti-G as anti-C+D may have misleading clinical implications

Four months after a D- male was transfused with four units of D- red blood cells (RBCs), the results of a standard pretransfusion antibody screen and alloantibody identification panel detected anti-C+D in his serum. This report was interpreted by his physician to be evidence of alloimmunization to the D antigen, which triggered concern that the patient had been transfused previously with D+ RBCs as the result of an error in blood typing or personal identification. After a review of hospital records failed to identify such an error, consultation with a reference laboratory technologist confirmed that the serologic reactions resembled those of anti-C+D but were also consistent with anti- C + anti-G. Additional testing confirmed that the reactions were due to anti-G, not anti-C+D. One of the four donors was identified to have the C+D- RBC phenotype, which is typically G+, thus identifying the stimulus for anti-G. Routine reporting of the detection of anti-C+D in the serum of D- people, without confirmatory testing or commentary about the possibility that anti-G may resemble anti-C+D, may mislead health care providers who are not familiar with the pertinent blood group serology.

A quantitative assay for subclassing IgG alloantibodies implicated in hemolytic disease of the newborn

Traditionally, IgG subclassing has been performed using qualitative assays. Quantitation of IgG subclasses may have prognostic value in evaluating alloimmunized pregnancies. A quantitative enzyme-linked immunosorbent assay (ELISA) was implemented for measuring IgG subclasses of red blood cell (RBC) antibodies (AB) isolated by adsorption/elution from the sera of alloimmunized pregnant women. The assay is a sandwich enzyme immunoassay using monoclonal antibodies specific for the relevant IgG subclasses and anti-human IgG peroxidase conjugate to quantitate the amount of bound IgG. The sensitivities of the assay for IgG1, 2, 3, and 4, respectively, were 4, 23, 4 and 2 micrograms/l. The results for each subclass for a given AB were expressed as a percentage of the total. In a series of pregnant mothers with ABs: E (4), Fya (2), Jka (1) and S (1), the mean percentage +/- 1SD of each subclass was: IgG1 61 +/- 34; IgG2 14 +/- 22; IgG3 18 +/- 28 and IgG4 4 +/- 17. IgG1 or IgG3 accounted for greater than 50% of the AB subclass distribution in 5 cases that resulted in hemolytic disease of the newborn (HDN). Although only a small number of samples was studied, changes in the concentrations of IgG1 or IgG3 during gestation suggest a correlation with the presence or absence of HDN. The ELISA may be used to quantitate the IgG subclasses of RBC ABs and may be valuable in predicting the severity of HDN in alloimmunized pregnancies.

Ruthenium carbonyl complexes. III. Peparations, properties and structures of Dicarbonyl- and Monocarbonyl-(2,2':6',2''-terpyridyl)ruthenium(II) complexes

Reaction of 2,2':6',2''-terpyridyl (tpy) with ruthenium dicarbonyl dihalides yields the complexes Ru(CO)2X2(tpy) (X = Br or Cl), which can be protonated giving [Ru(CO)2X2(tpyH)]ClO4. Crystal structures of the two forms (red and yellow) of Ru(CO)2Br2(tpy) show each to have octahedral stereo-chemistry with cis-carbonyls, trans-bromines, and bidentate tpy. Treatment of Ru(CO)2X2(tpy) complexes with trimethylamine N-oxide in dichloromethane at room temperature gives cis-Ru(CO)X2(tpy) complexes. The presence of cis halogens and tridentate terpyridyl in the chloro complex has been established by X-ray crystallography. Reaction of terpyridyl with ruthenium trichloride in dimethylformamide yields trans-Ru(CO)Cl2(tpy), the crystal structure of which has been determined.

Ruthenium carbonyl complexes. I. Synthesis of [Ru(CO)2(bidentate)2]2+ complexes

The complexes RU(CO)2Cl2L [L = 1,l0-phenanthroline (phen) or 2,2'-bipyridyl (bpy)] react with silver carboxylates to yield Ru(CO)2(OCOR)2L derivatives (R = Me or CF3). Reactions of Ru(CO)2(OAc)2L and Ru(CO)2(OAc)2(phen) with trifluoroacetic and trifluoromethanesulfonic acid give Ru(CO)2(OCOCF3)2L and Ru(CO)2(OSO2CF3)2(phen) respectively. In acetonitrile, Ru(CO)2(OAC)2L complexes react with trifluoromethanesulfonic acid to give [Ru(CO)2(MeCN)2L] (O3SCF3)2. The complexes [RU(CO)2L2]2+, [Ru(CO)2(phen)(bpy)]2+, and [Ru(C02(phen)(tmp)]2+ (tmp = 3,4,7,8-tetramethyl-1,l0-phenanthroline) have been prepared by reaction of [Ru(CO)2- (MeCN)2L]2+ and/or Ru(CO)2(OSO2CF3)2 phen with an excess of the appropriate bidentate ligand. A similar series of reactions has yielded Ru(C0)2(OAc)2(py)2, [Ru(CO)2(MeCN)2(py)2] (O3SCF3)2, and [RU(CO)2(py)2L]2+ from Ru(CO)2Cl2(py)2. Stereochemical assignments have been made for all complexes.

Localization of acetylcholinesterase via production of osmiophilic polymers: new benzenediazonium salts with thiolacetate functions

By incorporating an enzyme-susceptible thiolester group and a diazonium group into the same molecule, it has been possible to obtain an osmiophilic polymer upon enzymatic hydrolysis of the thiolester, via diazothioether formation linking the units. The thiolacetates with diazonium groups are specific substrates for cholinesterase because of the strong positive charge on the diazonium group. Following osmication, sites of acetylcholinesterase in motor end plate are notable as black deposits in light microscopy and opaque deposits in electron microscopy. This is the first cytochemical demonstration of a hydrolytic enzyme using a single agent as both substrate and capture reagent to form a polymer. The insolubility of the polymer in both water and lipid before osmication provides precision of localization needed for the high resolution of electron microscopy. However, the effectiveness of the new principle for electron microscopy depends as well upon the rate of the capture reaction (polymerization), which in turn depends upon the pK a of the thiol and pH and temperature at which the cytochemical reaction is conducted.