Skip to main content

Advertisement

Log in

A Review of the in Silico Design and Development Approaches of Ras-Specific Anticancer Therapeutics

  • Published:
International Journal of Peptide Research and Therapeutics Aims and scope Submit manuscript

Abstract

Ras Proteins, play a pivotal role in the proliferation pathways, and Ras mutant forms are well-established cancer drivers. Ras mutations are found in about 30% of all human cancers widely known as challenging diseases to control and treat. The direct inhibition of Ras is challenging and makes Ras an “undruggable” target for many years. The important reason is, that Ras protein has a unique smooth surface and shows different dynamicity upon binding GDP and GTP. As a result, interfering peptides (IPs) targeting the Ras family protein-protein interactions (PPIs) are considered more likely to bind Ras effectively and inhibit the downstream signaling. In this review, we aimed to cover the recent approaches to design the peptides that target Ras family proteins, focusing on in silico methods. In this regard, the anti-cancer peptide development approaches including design and delivery strategies are discussed. Later, more specific methods regarding Ras-specific peptide design are presented. In conclusion, IPs are a promising group of cancer therapeutics to combat Ras mutant cancers. For future perspectives to have these peptides in clinical use, co-inhibition of other cancer targets as well as improving the pharmacokinetic features of peptides are suggested.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Data Availability

There is no original data as this is a review article.

References

  • Asati V, Mahapatra DK, Bharti SK (2016) PI3K/Akt/mTOR and Ras/Raf/MEK/ERK signaling pathways inhibitors as anticancer agents: structural and pharmacological perspectives. Eur J Med Chem 109:314–341

    Article  PubMed  CAS  Google Scholar 

  • Baek S et al (2012) Structure of the stapled p53 peptide bound to Mdm2. J Am Chem Soc 134(1):103–106

    Article  PubMed  CAS  Google Scholar 

  • Bakail M, Ochsenbein F (2016) Targeting protein–protein interactions, a wide open field for drug design. C R Chim 19(1):19–27

    Article  CAS  Google Scholar 

  • Bird GH et al (2016) Biophysical determinants for cellular uptake of hydrocarbon-stapled peptide helices. Nat Chem Biol 12(10):845–852

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Boohaker RJ et al (2018) Rational design and development of a peptide inhibitor for the PD-1/PD-L1 interaction. Cancer Lett 434:11–21

    Article  PubMed  CAS  Google Scholar 

  • Bos JL (1989) Ras oncogenes in human cancer: a review. Cancer Res 49(17):4682–4689

    PubMed  CAS  Google Scholar 

  • Bos JL, Rehmann H, Wittinghofer A (2007) GEFs and GAPs: critical elements in the control of small G proteins. Cell 129(5):865–877

    Article  PubMed  CAS  Google Scholar 

  • Bruzzoni-Giovanelli H et al (2018) Interfering peptides targeting protein-protein interactions: the next generation of Drugs? Drug Discov Today 23(2):272–285

    Article  PubMed  CAS  Google Scholar 

  • Bullock BN, Jochim AL, Arora PS (2011) Assessing helical protein interfaces for inhibitor design. J Am Chem Soc 133(36):14220–14223

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Burns MC et al (2014) Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange. Proc Natl Acad Sci U S A 111(9):3401–3406

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cao Q et al (2008) Evaluation of biodistribution and anti-tumor effect of a dimeric RGD peptide-paclitaxel conjugate in mice with Breast cancer. Eur J Nucl Med Mol Imaging 35(8):1489–1498

    Article  PubMed  CAS  Google Scholar 

  • Chatterjee J et al (2008) N-methylation of peptides: a new perspective in medicinal chemistry. Acc Chem Res 41(10):1331–1342

    Article  PubMed  CAS  Google Scholar 

  • Chatterjee J, Rechenmacher F, Kessler H (2013) N-methylation of peptides and proteins: an important element for modulating biological functions. Angew Chem Int Ed Engl 52(1):254–269

    Article  PubMed  CAS  Google Scholar 

  • Cho KJ, van der Hoeven D, Hancock JF (2013) Inhibitors of K-Ras plasma membrane localization Enzymes, 33 Pt A: p. 249 – 65

  • Deng Y, Li J (2017) Rational optimization of Tumor suppressor-derived peptide inhibitor selectivity between Oncogene Tyrosine Kinases ErbB1 and ErbB2. Arch Pharm 350(12):1700181

    Article  Google Scholar 

  • Fairlie DP, Dantas de A, Araujo (2016) Rev Stapling Peptides Using Cysteine Crosslink Biopolymers 106(6):843–852

    CAS  Google Scholar 

  • Ford B et al (2009) Characterization of a ras mutant with identical GDP-and GTP-bound structures. Biochemistry 48(48):11449–11457

    Article  PubMed  CAS  Google Scholar 

  • Furet P et al (2019) Structure-based design of potent linear peptide inhibitors of the YAP-TEAD protein-protein interaction derived from the YAP omega-loop sequence. Bioorg Med Chem Lett 29(16):2316–2319

    Article  PubMed  CAS  Google Scholar 

  • Gabernet G et al (2019) In silico design and optimization of selective membranolytic anticancer peptides. Sci Rep 9(1):1–11

    Article  CAS  Google Scholar 

  • Green M, Loewenstein PM (1988) Autonomous functional domains of chemically synthesized human immunodeficiency virus tat trans-activator protein. Cell 55(6):1179–1188

    Article  PubMed  CAS  Google Scholar 

  • Gunderwala AY et al (2019) Development of allosteric BRAF peptide inhibitors targeting the dimer interface of BRAF. ACS Chem Biol 14(7):1471–1480

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gupta UK, Mahanta S, Paul S (2013) Silico design of small peptide-based Hsp90 inhibitor: a novel anticancer agent. Med Hypotheses 81(5):853–861

    Article  PubMed  CAS  Google Scholar 

  • Ho AL et al (2018) Preliminary results from a phase II trial of tipifarnib in squamous cell carcinomas (SCCs) with HRAS mutations. Ann Oncol 29:viii373

    Article  Google Scholar 

  • Jing H et al (2016) Novel cell-penetrating peptide-loaded nanobubbles synergized with ultrasound irradiation enhance EGFR siRNA delivery for triple negative Breast cancer therapy. Colloids Surf B Biointerfaces 146:387–395

    Article  PubMed  CAS  Google Scholar 

  • Kamagata K et al (2019) Rational design using sequence information only produces a peptide that binds to the intrinsically disordered region of p53 Scientific reports, 9(1): p. 1–10

  • Karnoub AE, Weinberg RA (2008) Ras oncogenes: split personalities. Nat Rev Mol Cell Biol 9(7):517–531

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kato K et al (1992) Isoprenoid addition to Ras protein is the critical modification for its membrane association and transforming activity. Proc Natl Acad Sci U S A 89(14):6403–6407

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kim YW, Grossmann TN, Verdine GL (2011) Synthesis of all-hydrocarbon stapled α-helical peptides by ring-closing olefin metathesis. Nat Protoc 6(6):761–771

    Article  PubMed  CAS  Google Scholar 

  • Lelle M et al (2015) Octreotide-mediated tumor-targeted drug delivery via a cleavable doxorubicin-peptide conjugate. Mol Pharm 12(12):4290–4300

    Article  PubMed  CAS  Google Scholar 

  • Li Z, Buck M (2019) Computational design of myristoylated cell-penetrating peptides targeting oncogenic K-Ras. G12D at the effector-binding membrane interface. J Chem Inf Model 60(1):306–315

    Article  Google Scholar 

  • Li HM et al (2017) De novo computational design for development of a peptide ligand oriented to VEGFR-3 with high affinity and long circulation. Mol Pharm 14(7):2236–2244

    Article  PubMed  CAS  Google Scholar 

  • Lim KJ et al (2013) A cancer specific cell-penetrating peptide, BR2, for the efficient delivery of an scFv into cancer cells. PLoS ONE 8(6):e66084

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Marqus S, Pirogova E, Piva TJ (2017) Evaluation of the use of therapeutic peptides for cancer treatment. J Biomed Sci 24(1):21

    Article  PubMed  PubMed Central  Google Scholar 

  • Matsson P et al (2016) Cell permeability beyond the rule of 5. Adv Drug Deliv Rev 101:42–61

    Article  PubMed  CAS  Google Scholar 

  • Nakajima EC et al (2022) FDA approval Summary: Sotorasib for KRAS G12C-Mutated metastatic NSCLC. Clin Cancer Res 28(8):1482–1486

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nevola L, Giralt E (2015) Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 51(16):3302–3315

    Article  PubMed  CAS  Google Scholar 

  • Nomura TK et al (2021) Specific inhibition of oncogenic RAS using cell-permeable RAS-binding domains. Cell Chem Biology 28(11):1581–1589e6

    Article  CAS  Google Scholar 

  • Novotny CJ et al (2017) Farnesyltransferase-mediated delivery of a covalent inhibitor overcomes alternative Prenylation to mislocalize K-Ras. ACS Chem Biol 12(7):1956–1962

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Oliveira S et al (2007) Fusogenic peptides enhance endosomal Escape improving siRNA-induced silencing of oncogenes. Int J Pharm 331(2):211–214

    Article  PubMed  CAS  Google Scholar 

  • Ostrem JM et al (2013) K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions. Nature 503(7477):548–551

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Papke B, Der CJ (2017) Drugging RAS: know the enemy. Science 355(6330):1158–1163

    Article  PubMed  CAS  Google Scholar 

  • Patgiri A et al (2011) An orthosteric inhibitor of the ras-sos interaction. Nat Chem Biol 7(9):585–587

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Qian Z, Dougherty PG, Pei D (2017) Targeting intracellular protein-protein interactions with cell-permeable cyclic peptides. Curr Opin Chem Biol 38:80–86

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Regina A et al (2008) Antitumour activity of ANG1005, a conjugate between paclitaxel and the new brain delivery vector Angiopep-2. Br J Pharmacol 155(2):185–197

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sakamoto K et al (2017) K-Ras (G12D)-selective inhibitory peptides generated by random peptide T7 phage display technology. Biochem Biophys Res Commun 484(3):605–611

    Article  PubMed  CAS  Google Scholar 

  • Sakamoto K, Masutani T, Hirokawa T (2020) Generation of KS-58 as the first K-Ras (G12D)-inhibitory peptide presenting anti-cancer activity in vivo. Sci Rep 10(1):1–16

    Article  Google Scholar 

  • Samec T et al (2022) Peptide-based delivery of therapeutics in cancer treatment. Mater Today Bio 14:100248

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sang P et al (2019) Inhibition of β-catenin/B cell lymphoma 9 protein – protein interaction using α-helix–mimicking sulfono-γ-AApeptide inhibitors Proceedings of the National Academy of Sciences, 116(22): p. 10757–10762

  • Sung H et al (2021) Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. Cancer J Clin 71(3):209–249

    Article  Google Scholar 

  • Tang S et al (2019) Structure-based Discovery of Novel CK2α-Binding cyclic peptides with anti-cancer activity. Mol Inf 38(3):e1800089

    Article  Google Scholar 

  • Trinh TB et al (2016) Discovery of a direct ras inhibitor by screening a Combinatorial Library of cell-permeable bicyclic peptides. ACS Comb Sci 18(1):75–85

    Article  PubMed  CAS  Google Scholar 

  • Upadhyaya P et al (2014) Direct Ras inhibitors identified from a structurally rigidified bicyclic peptide library. Tetrahedron 70(42):7714–7720

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Upadhyaya P et al (2015) Inhibition of Ras signaling by blocking Ras–effector interactions with cyclic peptides. Angew Chem Int Ed 54(26):7602–7606

    Article  CAS  Google Scholar 

  • Uprety D, Adjei AA (2020) KRAS: from undruggable to a druggable Cancer target. Cancer Treat Rev 89:102070

    Article  PubMed  CAS  Google Scholar 

  • Vadevoo SMP et al (2023) Peptides as multifunctional players in cancer therapy. Exp Mol Med 55(6):1099–1109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Walensky LD, Bird GH (2014) Hydrocarbon-stapled peptides: principles, practice, and progress. J Med Chem 57(15):6275–6288

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Weinberg RA (1996) How cancer arises. Sci Am 275(3):62–70

    Article  PubMed  CAS  Google Scholar 

  • Whyte DB et al (1997) K- and N-Ras are geranylgeranylated in cells treated with farnesyl protein transferase inhibitors. J Biol Chem 272(22):14459–14464

    Article  PubMed  CAS  Google Scholar 

  • Wu XL et al (2010) Tumor-targeting peptide conjugated pH-responsive micelles as a potential drug carrier for cancer therapy. Bioconjug Chem 21(2):208–213

    Article  PubMed  Google Scholar 

  • Xu W et al (2018) P1c peptide decorated liposome targeting alphavbeta3-expressing Tumor cells in vitro and in vivo. RSC Adv 8(45):25575–25583

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xue S et al (2021) Cartilage-targeting peptide-modified dual-drug delivery nanoplatform with NIR laser response for osteoarthritis therapy. Bioact Mater 6(8):2372–2389

    PubMed  PubMed Central  CAS  Google Scholar 

  • Yoo DY et al (2020) Covalent targeting of ras G12C by rationally designed peptidomimetics. ACS Chem Biol 15(6):1604–1612

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zeitouni D et al (2016) KRAS mutant Pancreatic cancer: no lone path to an effective treatment. Cancers 8(4):45

    Article  PubMed  PubMed Central  Google Scholar 

  • Zeng J et al (2001) Design of inhibitors of ras–raf interaction using a computational combinatorial algorithm. Protein Eng 14(1):39–45

    Article  PubMed  CAS  Google Scholar 

  • Zenonos K, Kyprianou K (2013) RAS signaling pathways, mutations and their role in Colorectal cancer. World J Gastrointest Oncol 5(5):97

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Z et al (2020) GTP-state-selective cyclic peptide ligands of K-Ras (G12D) block its interaction with Raf. ACS Cent Sci 6(10):1753–1761

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhou P et al (2018) Disrupting the intramolecular interaction between proto-oncogene c-Src SH3 domain and its self-binding peptide PPII with rationally designed peptide ligands Artificial Cells, Nanomedicine, and Biotechnology, 46(6): p. 1122–1131

  • Zinatizadeh MR et al (2019) The role and function of ras-association domain family in Cancer: a review, vol 6. Genes & Diseases, pp 378–384. 4

Download references

Funding

This manuscript is supported by the grant of the National Institute for Medical Research Development (NIMAD), with grant number 972544.

Author information

Authors and Affiliations

Authors

Contributions

All authors have made a contribution to the concept or design of the article. P.M. and H.R.H. drafted the manuscript and interpret the relevant literature. M.S.H. and O.M revised the manuscript. E.M.A. conceptualize and draft the manuscript and interpret the relevant literature.

Corresponding author

Correspondence to Elnaz Mehdizadeh Aghdam.

Ethics declarations

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Competing interests

The authors declare no competing interests.

Conflict of interest

The authors declare no conflict of interest.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Motiei, P., Heidari, H.R., Hejazi, M.S. et al. A Review of the in Silico Design and Development Approaches of Ras-Specific Anticancer Therapeutics. Int J Pept Res Ther 30, 2 (2024). https://doi.org/10.1007/s10989-023-10578-3

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10989-023-10578-3

Keywords

Navigation