Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue

Monoclonal antibody therapeutics have revolutionized the treatment of diseases such as cancer and autoimmune disorders, and also serve as research reagents for diverse and unparalleled applications. To extend their utility in both contexts, we have begun development of tunable antibodies, whose activity can be controlled by addition of a small molecule. Conceptually, we envision that incorporating cavity-forming mutations into an antibody can disrupt its structure, thereby reducing its affinity for antigen; addition of a small molecule may then restore the active structure, and thus rescue antigen binding. As a first proof of concept toward implementing this strategy, we have incorporated individual tryptophan to glycine mutations into FITC-E2, an anti-fluorescein single-chain variable fragment (scFv). We find that these can disrupt the protein structure and diminish antigen binding, and further that both structure and function can be rescued by addition of indole to complement the deleted side chain. While the magnitude of the affinity difference triggered by indole is modest in this first model system, it nonetheless provides a framework for future mutation/ligand pairs that may induce more dramatic responses. Disrupting and subsequently rescuing antibody activity, as exemplified by this first example, may represent a new approach to "design in" fine-tuned control of antibody activity for a variety of future applications.

Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression

Activating KRAS mutations frequently occur in pancreatic, colorectal, and lung adenocarcinomas. While many attempts have been made to target oncogenic KRAS, no clinically useful therapies currently exist. Most efforts to target KRAS have focused on inhibiting the mutant protein; a less explored approach involves targeting KRAS at the transcriptional level. The promoter element of the KRAS gene contains a GC-rich nuclease hypersensitive site with three potential DNA secondary structure-forming regions. These are referred to as the Near-, Mid-, and Far-regions, on the basis of their proximity to the transcription start site. As a result of transcription-induced negative superhelicity, these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. While the G-quadruplexes have been well characterized, the i-motifs have not been investigated as thoroughly. Here we show that the i-motif that forms in the C-rich Mid-region is the most stable and exists in a dynamic equilibrium with a hybrid i-motif/hairpin species and an unfolded hairpin species. The transcription factor heterogeneous nuclear ribonucleoprotein K (hnRNP K) was found to bind selectively to the i-motif species and to positively modulate KRAS transcription. Additionally, we identified a benzophenanthridine alkaloid that dissipates the hairpin species and destabilizes the interaction of hnRNP K with the Mid-region i-motif. This same compound stabilizes the three existing KRAS G-quadruplexes. The combined effect of the compound on the Mid-region i-motif and the G-quadruplexes leads to downregulation of KRAS gene expression. This dual i-motif/G-quadruplex-interactive compound presents a new mechanism to modulate gene expression.

Targeting mutant KRAS for anticancer therapeutics: a review of novel small molecule modulators

The RAS proteins play a role in cell differentiation, proliferation, and survival. Aberrant RAS signaling has been found to play a role in 30% of all cancers. KRAS, a key member of the RAS protein family, is an attractive cancer target, as frequent point mutations in the KRAS gene render the protein constitutively active. A number of attempts have been made to target aberrant KRAS signaling by identifying small molecule compounds that (1) are synthetic lethal to mutant KRAS, (2) block KRAS/GEF interactions, (3) inhibit downstream KRAS effectors, or (4) inhibit the post-translational processing of RAS proteins. In addition, inhibition of novel targets outside the main KRAS signaling pathway, specifically the cell cycle related kinase PLK1, has been shown have an effect in cells that harbor mutant KRAS. Herein we review the use of various high-throughput screening assays utilized to identify new small-molecule compounds capable of targeting mutant KRAS-driven cancers.

Abstract 1829: Small molecule stabilization of the kRAS promoter G-quadruplex as a target for novel pancreatic cancer therapeutics

kRAS is one of, if not the, most prevalent oncogenic aberrations identified to date. It is either upregulated or mutationally activated in a multitude of cancers, including close to 100% of pancreatic adenocarcinomas. Pancreatic cancer carries the highest mortality rate of all cancers, with only a 3-6 month median survival, and a 5-year survival of <5%. There is a desperate need for new therapeutics, particularly those targeting kRAS. This is not a new concept; due to the common nature of the kRAS mutation a significant effort has been made to develop drugs that target its activated form. However, the clinical activity of those drugs has been disappointing due to a variety of mechanistic hurdles. The presented works describe a novel target to downregulate kRAS expression - secondary structures within the proximal promoter, which contains a unique string of G-rich DNA. Negative superhelicity induced by transcription results in this region opening up to form unique secondary structures called G-quadruplexes (G4s). These G4s most often act as silencer elements, forming globular structures that mask binding sites for transcriptional factors, allowing for specific molecular targeting by small molecule drugs, modulating transcription, and protein expression. Using the confirmed major isoform - a unique ‘kinked’ structure - as the primary target, we undertook a screening effort in order to identify potential G4-stabilizing small molecules. Several hundred compounds were screened, and two chemical classes consistently emerged: ellipticines (E) and quindolines (Q). The lead compounds from each pharmacophore are NSC176327 (E-14) and Quindoline i (Q-i), respectively, each of which has previously been demonstrated to stabilize other G4 structures (such as the parallel structure found within the MYC promoter.) What is most intriguing is the clear difference in isoform stabilization with these compounds; E-14 stabilizes the major kinked isoform, whereas Q-i is a bit more promiscuous and stabilizes several isoforms as demonstrated by FRET melt, the Polymerase Stop Assay and DMS footprinting. Both of these compounds demonstrate cytotoxicity, as measured by MTS, at 24 and 72 h, in a variety of pancreatic cell lines, with E-14 being notably more potent. Cytotoxicity is is being correlated to changes in kRAS mRNA expression. G4s have emerged as a potential DNA target with great potential for specificity as they are more globular than nascent DNA, and each carry some degree of distinctiveness. Using the kRAS proximal promoter G4 structure as the primary target, a drug discovery program will have great potential to develop a potent, specifically targeted small molecule to be used in the treatment of pancreatic adenocarcinomas, as well as childhood leukemias, ovarian, lung, and colon cancers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1829. doi:1538-7445.AM2012-1829

Gaining insights into the small molecule targeting of the G-quadruplex in the c-MYC promoter using NMR and an allele-specific transcriptional assay

G-quadruplexes (four-stranded DNA secondary structures) are showing promise as new targets for anticancer therapies. Specifically, G-quadruplexes in the proximal promoter region of regulatory genes have the potential to act as silencer elements and thereby turn off transcription. Thus, compounds that are capable of binding to and stabilizing G-quadruplexes would be of great benefit. In this chapter we describe two recent studies from our labs. In the first case, we use NMR to elucidate the structure of a 2:1 complex between a small molecule and the G-quadruplex in the c-MYC promoter. In the second case, we use an allele-specific transcription assay to demonstrate that the effect of a G-quadruplex-interactive compound is mediated directly through the G-quadruplex. Finally, we use this information to propose models for the interaction of various small molecules with the c-MYC G-quadruplex.

4-(Piperidin-1-yl)-4H-benzo[b]tetra-zolo[1,5-d][1,4]diazepin-5(6H)-one

There are two crystallographically unique mol­ecules present in the asymmetric unit of the title compound, C₁₄H₁₆N₆O; in both mol­ecules, the seven-membered diazepinone ring adopts a boat-like conformation and the chair conformation piperidine ring is an axial substituent on the diazepinone ring. In the crystal, each mol­ecule forms hydrogen bonds with its respective symmetry equivalents. Hydrogen bonding between mol­ecule A and symmetry equivalents forms two ring motifs, the first formed by inversion-related N—H⋯O inter­actions and the second formed by C—H⋯O and C—H⋯N inter­actions. The combination of both ring motifs results in the formation of an infinite double tape, which propagates in the a-axis direction. Hydrogen bonding between mol­ecule B and symmetry equivalents forms one ring motif by inversion-related N—H⋯O inter­actions and a second ring motif by C—H⋯O inter­actions, which propagate as a single tape parallel with the c axis.

Interrelationship amongst the avian orders Galliformes, Columbiformes, and Anseriformes as evinced by the fiber types in the pectoralis muscle

The three types of fiber red, white, and intermediate have been characterized from a study of the pectoralis muscle of some representative species of birds of the orders Galliformes, Columbiformes, and Anseriformes. The presence of all the three types was characteristic of the Galliformes except for the Japanese quail, which had only two types, red and white, the former predominating. All the columbiform and anseriform birds studied had similar fiber composition as the Japanese quail. It is postulated that these three orders of birds are closely related phylogenetically.The small red fibers which are known to be adapted for aerobic metabolism metabolizing fat as the main fuel for energy indulge in sustained flight activity whereas the large white fibers, which are adapted for anaerobic metabolism utilizing glycogen, are responsible for quick and short-term activity as in takeoff and in manoeuvring quick and sudden turns while in flight. In the heaviest birds such as the Canada geese, which have a heavy load to lift in the takeoff and also to keep afloat while in the air, were found to possess the largest white and red fibers.