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Understand KRAS and the Quest for Anti-Cancer Drugs

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Understand KRAS and the Quest for Anti-Cancer Drugs cells Review Understand KRAS and the Quest for Anti-Cancer Drugs Chang Woo Han 1 , Mi Suk Jeong 2,* and Se Bok Jang 3,* 1 Institute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea; [email protected] 2 Institute for Plastic Information and Energy Materials and Sustainable Utilization of Photovoltaic Energy Research Center, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea 3 Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea * Correspondence: [email protected] (M.S.J.); [email protected] (S.B.J.); Tel.: +82-51-510-2523 (M.S.J. & S.B.J.) Abstract: The KRAS oncogene is mutated in approximately ~30% of human cancers, and the targeting of KRAS has long been highlighted in many studies. Nevertheless, attempts to target KRAS directly have been ineffective. This review provides an overview of the structure of KRAS and its characteristic signaling pathways. Additionally, we examine the problems associated with currently available KRAS inhibitors and discuss promising avenues for drug development. Keywords: KRAS; cancer; signaling pathway; inhibitors 1. Introduction RAS HRAS KRAS NRAS genes ( , , and ) encode 21 kDa monomeric small guanosine triphosphate (GTP)-hydrolases (GTPases) that function as regulators of intracellular signal- Citation: Han, C.W.; Jeong, M.S.; ing transduction cascades involved in cell growth, differentiation, and survival. Normally, Jang, S.B. Understand KRAS and the the cycling of RAS protein by GTPases is tightly regulated by the binding of guanosine Quest for Anti-Cancer Drugs. Cells triphosphate (GTP) to nucleotide exchange factors (GEFs) and by the hydrolysis of GTP 2021, 10, 842. https://doi.org/ to guanosine diphosphate (GDP) by GTPase activating proteins (GAPs) [1,2]. KRAS is 10.3390/cells10040842 frequently mutated in pancreatic, colorectal, endometrial, biliary tract, lung, and cervical cancer. For example, oncogenic missense mutations in the KRAS gene frequently occur Academic Editor: Bor Luen Tang at glycine (Gly) 12 or 13 or glutamine (Gln) 61 codons located on the P loop and Switch II region and are related to the impairment of stable nucleotide-binding in its active site. Received: 11 March 2021 These mutations impair GTPase cycling and result in accumulations of bound and active Accepted: 6 April 2021 GTP, which result in activation of multiple downstream effectors [3,4]. In this review, Published: 8 April 2021 we examine aberrant activated KRAS signaling in tumors and place focus on promising KRAS inhibitors. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in 2. Structure published maps and institutional affil- iations. KRAS is a 21 kDa monomeric, membrane-localized GTPase with a conserved domain, known as the G domain (residues 1–165, Figure1A), and a less conserved C-terminal tail, called the hypervariable domain (residues 166–188, Figure1A) [ 5]. KRAS consists of five α2-helixes (α1–α5) and six β-sheets (β1–β6). GTPase has two switches— switches I (residues 30–38) and II (residues 60–76)—which undergo major conformational changes in Copyright: © 2021 by the authors. response to changes in guanine nucleotide (GTP to GDP or vice versa) [6]. The phosphate- Licensee MDPI, Basel, Switzerland. binding loop (P-loop, residues 10–17) of KRAS participates in the induction of the confor- This article is an open access article distributed under the terms and mational change that occurs during its GDP-bound (inactive) and the GTP-bound (active) conditions of the Creative Commons states (Figure1B). The γ-phosphate of GTP interacts with tyrosine (Tyr) 32 and threonine Attribution (CC BY) license (https:// (Thr) 35 residues of the switch I region. Additionally, conserved Gly 60 in the switch creativecommons.org/licenses/by/ II region interacts with γ-phosphate [7]. KRAS is the most frequently mutated proto- 4.0/). oncogene in human cancers, and mutated KRAS remains locked in an active state, relaying Cells 2021, 10, 842. https://doi.org/10.3390/cells10040842 https://www.mdpi.com/journal/cells Cells 2021, 10, x 2 of 11 Cells 2021, 10, 842 2 of 10 (active) states (Figure 1B). The γ-phosphate of GTP interacts with tyrosine (Tyr) 32 and threonine (Thr) 35 residues of the switch I region. Additionally, conserved Gly 60 in the switch Ⅱ region interacts with γ-phosphate [7]. KRAS is the most frequently mutated uncontrolledproto-oncogene proliferative in human cancers, signals. and Jonathanmutated KRAS M. Ostrem remains et locked al. identified in an active that state, oncogenic mutationsrelaying uncontrolled result in conformational proliferative signals. change Jonathan and functionalM. Ostrem et activation al. identified of RAS that proteinson- by impairingcogenic mutations both intrinsic result in GTPase conformational activity change and GAP-stimulated and functional activation GTP hydrolysis of RAS [pro-6]. Recently, manyteins by studies impairing have both focused intrinsic on GTPase attempts activity that and target GAP exchange-stimulated nucleotide. GTP hydrolysis Recent [6]. studies haveRecently, focused many onstudies attempts have focus to blocked on nucleotideattempts that exchange target exchange [8,9]. nucleotide. Several structure-based Recent inhibitorsstudies have (e.g., focused SML-8-73-1, on attempts H-REV107 to block peptide, nucleotide BAY-293, exchange or BI-3406)[8,9]. Several have structure been reported- to targetbased inhibitors the guanine (e.g., nucleotide SML-8-73-1, binding H-REV107 site peptide, of the BAY KRAS-293 mutant, or BI-3406) and have inhibit been GDP re- to GTP exchangeported to target[10– 13the]. guanine The Cys-A-A-X nucleotide C-terminalbinding site of motif, the KRAS where mutant A is and isoleucine, inhibit GDP leucine, or valine,to GTP exchange and X is [10 either–13]. methionine The Cys-A-A or-X serine,C-terminal is located motif, where in the A KRAS is isoleucine, hypervariable leucine, region (HVR).or valine, KRAS and X traffickingis either methionine on the plasma or serine, membrane is located in plays the KRAS essential hypervariable roles in multiple region signal- (HVR). KRAS trafficking on the plasma membrane plays essential roles in multiple sig- ing pathways that control various processes, and the Cys-A-A-X C-terminal motif of KRAS naling pathways that control various processes, and the Cys-A-A-X C-terminal motif of undergoesKRAS undergoes several several post-translational post-translational modifications modifications (PTMs) (PTMs) that that facilitate facilitate itsits traffickingtraf- to theficking inner to the surface inner of surface the plasma of the plasma membrane membrane [14–16 [14].–16]. Cells 2021, 10, x 3 of 11 FigureFigure 1.1. DomainDomain structuresstructures and the three three-dimensional-dimensional structure structure.. (A ()A Domain) Domain structure structure of offull full-length- length KRAS. (B) Ribbon representation of the monomeric crystal structure of KRAS (PDB ID: 7C40) KRAS. (B) Ribbon representation of the monomeric crystal structure of KRAS (PDB ID: 7C40) using using the program PyMOL. The Mg2+ ion is indicated by a gray circle and guanosine diphosphate 2+ the(GDP program) by a yellow PyMOL. rod. TheThe MgGDP Mg ion molecule is indicated is color by-coded a gray as circlefollows and: C yellow, guanosine O red, diphosphate N blue, P (GDP) bypurple, a yellow and rod.Mg2+ Thegray. MgGDP molecule is color-coded as follows: C yellow, O red, N blue, P purple, and Mg2+ gray. (i) KRAS is synthesized as a biologically inactive cytosolic propeptide (Pro-Ras). (ii) The first modification of this propeptide is catalyzed by farnesyltransferase (FTase) and involves covalent addition of the 15-carbon farnesyl group (C-15) from farnesyl diphos- phate (FDP) onto the cysteine residue of the CAAX sequence. (iii) Next, the -AAX se- quence is cleaved by a CAAX protease RAS converting CAAX endopeptidase 1 also known as RAS converting enzyme 1 (RCE1), and this is followed by methylation of the carboxyl-prenylated cysteine residue through isoprenylcysteine carboxyl methyltransfer- ase (ICMT). (iv) Finally, palmitoyl transferase (PTase) catalyzes the addition of palmitic acid (a 16-carbon fatty acid) to upstream cysteine residues. These KRAS modifications enhance protein hydrophobicity and plasma membrane anchoring, and membrane-anchored KRAS proteins cycle between the GTP-bound active form and the GDP-bound inactive form. The associated conformational changes of KRAS serve as master moderators of a large number of signaling pathways involved in various cellular processes. 3. Oncogenic KRAS Signaling Pathways in Human Cancer 3.1. GEFs and GAPs KRAS-associated signaling pathways are persistently activated in many cancers, where they participate in cellular growth and proliferation, differentiation, protein syn- thesis, glucose metabolism, cell survival, and inflammation (Figure 2) [3]. KRAS is acti- vated by GEFs: SOS1 and SOS2 (two sons of sevenless 1 and 2), GRB2 (growth factor re- ceptor-bound protein 2), RASGRF2 (Ras protein-specific guanine nucleotide releasing fac- tor 2), or RasGRPs (Ras guanine nucleotide releasing proteins). GEFs are activated by Cells 2021, 10, 842 3 of 10 (i) KRAS is synthesized as a biologically inactive cytosolic propeptide (Pro-Ras). (ii) The first modification of this propeptide is catalyzed by farnesyltransferase (FTase) and involves covalent addition of the 15-carbon farnesyl group (C-15) from farnesyl diphos- phate (FDP) onto
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