First experimental identification of Ras-inhibitor binding interface using a water-soluble Ras ligand

Palmioli, Alessandro; Sacco, Elena; Abraham, Sherwin J.; Thomas, Ciza; Domizio, Alessandro Di; Gioia, Luca De; Gaponenko, Vadim; Vanoni, Marco; Peri, Francesco

doi:10.1016/j.bmcl.2009.05.107

Cited by 35 publications

(36 citation statements)

References 32 publications

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“…Although several previous studies have reported potential small-molecule association with Ras, none have characterized the binding site by a high-resolution structure analysis and none reported a defined binding pocket (3)(4)(5)(6)(7). The best-characterized Ras-binding compounds reported so far are SCH54292 (16) and its more water-soluble derivative (7).…”

Section: Discussionmentioning

confidence: 99%

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Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

Maurer¹,

Garrenton²,

Oh³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

540

575

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The Ras gene is frequently mutated in cancer, and mutant Ras drives tumorigenesis. Although Ras is a central oncogene, small molecules that bind to Ras in a well-defined manner and exert inhibitory effects have not been uncovered to date. Through an NMR-based fragment screen, we identified a group of small molecules that all bind to a common site on Ras. High-resolution cocrystal structures delineated a unique ligand-binding pocket on the Ras protein that is adjacent to the switch I/II regions and can be expanded upon compound binding. Structure analysis predicts that compound-binding interferes with the Ras/SOS interactions. Indeed, selected compounds inhibit SOS-mediated nucleotide exchange and prevent Ras activation by blocking the formation of intermediates of the exchange reaction. The discovery of a small-molecule binding pocket on Ras with functional significance provides a new direction in the search of therapeutically effective inhibitors of the Ras oncoprotein.small G protein | guanine nucleotide exchange | nuclear magnetic resonance | crystal structure | small-molecule inhibitors R as is a small GTP-binding protein that functions as a nucleotide-dependent switch for central growth signaling pathways (1, 2). In response to extracellular signals, Ras is converted from a GDP-bound (Ras GDP ) to a GTP-bound (Ras GTP ) state, as catalyzed by guanine nucleotide exchange factors (GEFs), notably the SOS1 protein. Active Ras GTP mediates its diverse growth-stimulating functions through its direct interactions with effectors including Raf, PI3K, and Ral guanine nucleotide dissociation stimulator. The intrinsic GTPase activity of Ras then hydrolyzes GTP to GDP to terminate Ras signaling. The Ras GTPase activity can be further accelerated by its interactions with GTPase-activating proteins (GAPs), including the neurofibromin 1 tumor suppressor (2).Ras, a human oncogene identified and characterized over 30 y ago, is mutated in more than 20% of human cancers. Among the three Ras isoforms (K, N, and H), KRas is most frequently mutated (2). Mutant Ras has a reduced GTPase activity, which prolongs its activated conformation, thereby promoting Rasdependent signaling and cancer cell survival or growth (1, 2).Mutations of Ras in cancer are associated with poor prognosis (2). Inactivation of oncogenic Ras in mice results in tumor shrinkage. Thus, Ras is widely considered an oncology target of exceptional importance. However, development of small-molecule inhibitors against Ras has thus far proven unsuccessful. Given the picomolar affinity between guanine nucleotides and Ras and the high cytosolic concentration of guanine nucleotides, it is very challenging to develop a conventional inhibitor competitive against nucleotide binding (1, 2). Outside of the nucleotide-binding pocket, the Ras protein does not contain obvious cavities for small-molecule binding. A number of small molecules have been reported to bind to Ras (3-7), but their mechanisms of action and the structural basis to achieve Ras inhibition remain elusive.Fra...

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Section: Discussionmentioning

confidence: 99%

“…The best-characterized Ras-binding compounds reported so far are SCH54292 (16) and its more water-soluble derivative (7). In silico calculation based on NMR mapping suggests that these compounds bind to a region between switch II and helix 4 of Ras GDP , although other binding areas cannot be ruled out.…”

Section: Discussionmentioning

confidence: 99%

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

Maurer¹,

Garrenton²,

Oh³

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

540

575

View full text Add to dashboard Cite

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“…Judged from our HADDOCK docking models and the available co-crystal structures, it seems highly likely, that these different ligands, including Bisphenol A, bind to GDP-Ras and interfere with SOS complex formation due to steric reasons. Interestingly, the observed affinity of Bisphenol A is in the same micromolar range as the affinity between Ras-GDP and the SOS molecule itself (Palmioli et al, 2009). …”

Section: Low Molecular Weight Compounds As Functional Modulators Of Smentioning

confidence: 99%

“…Moreover, on the basis of these measurements only, the Ras protein was believed to be undruggable, since it lacks hydrophobic cavities on its molecular surface (Cox et al, 2014). Nevertheless, during the past years several small molecules and zinc-chelating compounds have been identified and characterised as Sos antagonists of K-Ras (Palmioli et al, 2009;Rosnizeck et al, 2012). In 2012, co-crystal structures of several ligands bound to the fulllength and truncated Ras were published (Maurer et al, 2012;Sun et al, 2012).…”

Section: Low Molecular Weight Compounds As Functional Modulators Of Smentioning

confidence: 99%

The small GTPases Ras and Rheb studied by multidimensional NMR spectroscopy: structure and function

Schöpel

Potheraveedu

Al-Harthy

et al. 2017

Biological Chemistry

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Ras GTPases are key players in cellular signalling because they act as binary switches. These states manifest through toggling between an active (GTP-loaded) and an inactive (GDP-loaded) form. The hydrolysis and replenishing of GTP is controlled by two additional protein classes: GAP (GTPase-activating)-and GEF (Guanine nucleotide exchange factors)-proteins. The complex interplay of the proteins is known as the GTPase-cycle. Several point mutations of the Ras protein deregulate this cycle. Mutations in Ras are associated with up to one-third of human cancers. The three isoforms of Ras (H, N, K) exhibit high sequence similarity and mainly differ in a region called HVR (hypervariable region). The HVR governs the differential action and cellular distribution of the three isoforms. Rheb is a Ras-like GTPase that is conserved from yeast to mammals. Rheb is mainly involved in activation of cell growth through stimulation of mTORC1 activity. In this review, we summarise multidimensional NMR studies on Rheb and Ras carried out to characterise their structure-function relationship and explain how the activity of these small GTPases can be modulated by low molecular weight compounds. These might help to design GTPaseselective antagonists for treatment of cancer and brain disease.

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“…Some small-molecule inhibitors of KRAS have been identified [53], including development of potential irreversible inhibitors of KRAS G12C mutant protein [54,55]. Although these new drugs seem to be effective in vitro, there is a need for further clinical studies and new drugs with increased affinity [56].…”

Section: Inhibition Of Ras Functionmentioning

confidence: 99%

Targeting the KRAS Pathway in Non-Small Cell Lung Cancer

et al. 2016

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Lung cancer remains the leading cause of cancer‐related deaths worldwide. However, significant progress has been made individualizing therapy based on molecular aberrations (e.g., EGFR, ALK) and pathologic subtype. KRAS is one of the most frequently mutated genes in non‐small cell lung cancer (NSCLC), found in approximately 30% of lung adenocarcinomas, and is thus an appealing target for new therapies. Although no targeted therapy has yet been approved for the treatment of KRAS‐mutant NSCLC, there are multiple potential therapeutic approaches. These may include direct inhibition of KRAS protein, inhibition of KRAS regulators, alteration of KRAS membrane localization, and inhibition of effector molecules downstream of mutant KRAS. This article provides an overview of the KRAS pathway in lung cancer and related therapeutic strategies under investigation. Implications for Practice: The identification of oncogene‐addicted cancers and specific inhibitors has revolutionized non‐small cell lung cancer (NSCLC) treatment and outcomes. One of the most commonly mutated genes in adenocarcinoma is KRAS, found in approximately 30% of lung adenocarcinomas, and thus it is an appealing target for new therapies. This review provides an overview of the KRAS pathway and related targeted therapies under investigation in NSCLC. Some of these agents may play a key role in KRAS‐mutant NSCLC treatment in the future.

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First experimental identification of Ras-inhibitor binding interface using a water-soluble Ras ligand

Cited by 35 publications

References 32 publications

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

The small GTPases Ras and Rheb studied by multidimensional NMR spectroscopy: structure and function

Targeting the KRAS Pathway in Non-Small Cell Lung Cancer

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