Page 88 - TD-4-1

Tumor Discovery Identification of a potential KRAS(G12C) inhibitor

the tumor microenvironment. These characteristics need to identify novel pharmacophores targeting the
1,2
collectively contribute to the development and progression KRAS(G12C), we performed a covalent docking-based
of cancer, making it a difficult and complex disease to virtual screening in conjunction with molecular dynamics
treat. Understanding these characteristics is critical for (MD) simulations to investigate the stability of compounds
developing cancer therapies that target specific aspects binding to the target protein. Based on scaffold-hopping
of the disease’s biology, as cancer is greatly influenced approach with Sotorasib as a template, we identified 174
by evolutionary principles, particularly through tumor molecules exhibiting structural similarities to Sotorasib
evolution. Genetic mutations and natural selection among billions of compounds. Our covalent docking-
3-6
drive the development of diverse cell populations within based virtual screening revealed potential putative binders
a tumor, resulting in genetic diversity and heterogeneity. of KRAS(G12C), namely, C01, C02a, C02b, and C03,
7
This diversity enables cancer cells to adapt to various with notable Glide score similarities to Sotorasib. MD
environmental challenges, such as treatments or changes simulations further demonstrated that the KRAS(G12C)-
in the microenvironment, resulting in the survival of drug- C02b complex exhibited stable binding interactions
resistant and more aggressive cell clones. 8-11 with a low root-mean-square deviation (RMSD) value,
Kirsten rat sarcoma viral oncogene homolog (KRAS) comparable to the reference FDA-approved drug Sotorasib.
signaling regulates important cellular functions through Moreover, the calculations of binding free energy
a network of intracellular signaling pathways. KRAS indicated that these favorable interactions were highly
12
functions normally as a molecular switch, cycling between preserved from the last 50 nanoseconds (ns) up to 500 ns
an inactive (GDP-bound) and active (GTP-bound) form. of simulation time. To further investigate the dynamics
When activated, GTP-bound KRAS drives downstream of the KRAS(G12C)-Sotorasib and KRAS(G12C)-C02b
signaling pathways that regulate cell growth, survival, and complexes, we conducted post-MD analyses, including
proliferation, such as the MAPK/ERK and PI3K/AKT dynamic cross-correlation matrix (DCCM) and principal
pathways. KRAS mutations, such as the common G12C component analysis (PCA). These analyses aimed to
13
mutation, maintain KRAS in an active state, resulting in elucidate the movements of the two switches and identify
uncontrolled signaling and cellular responses, ultimately the flexible regions within the complexes. These findings
driving cancer development and progression by promoting suggest that C02b may serve as a promising inhibitor
cell growth, inhibiting apoptosis, enhancing metastasis, candidate for the KRAS(G12C) mutation, and further
and modulating the tumor microenvironment. 14 advanced studies are needed to validate its potential.
KRAS gene mutations, particularly the G12C variant, 2. Materials and methods
are prevalent in a variety of cancers, including non-
small cell lung cancer (NSCLC) and colorectal cancer. 15,16 2.1. Similarity search
KRAS(G12C) inhibitors are an emerging class of targeted Sotorasib served as a template to identify similar
cancer therapy that targets a specific mutation (G12C) in compounds within various chemical spaces including
17
the KRAS gene. KRAS(G12C) inhibitors aim to address eXplore, Freedom Space, GalaXi, and KnowledgeSpace.
a long-standing problem in cancer treatment, as KRAS The scaffold-hopping search was conducted using the
mutations were previously considered “undruggable” infiniSee software (version 5.0.1; BioSolveIT GmbH,
18
.
Sotorasib (AMG 510) was the first KRAS(G12C) inhibitor Sankt Augustin, Germany, 2023, www.biosolveit.de/
to receive accelerated FDA approval in May 2021 for infiniSee). The chemical spaces encompassing both
the treatment of adult patients with NSCLC harboring building blocks and reactions allowed for the creation of a
the KRAS(G12C) mutation. This marked a significant maximum number of virtual product molecules. Scaffold
19
milestone in cancer therapy by introducing the first drug Hopper was executed using the infiniSee software.
25
approved to target KRAS mutations. Sotorasib functions by The acrylamide warhead was selected from Sotorasib 22
irreversibly binding to the mutant KRAS(G12C), inhibiting (Figure A1 in Appendix). The target similarity was set at
its activity. Specifically, Sotorasib forms a covalent bond 1.00 to ensure a precise match, while a minimum similarity
20
with cysteine 12 in the switch II pocket of KRAS(G12C), threshold was established at 90% to guarantee a significant
21
preventing its ability to activate downstream signaling level of similarity. Furthermore, a total diversity score of
pathways that promote cell growth and proliferation. 13 1.00 was ensured to uncover compounds with a high degree
Although Sotorasib has been approved as a drug for of similarity with Sotorasib. As a result, 174 compounds
targeting KRAS(G12C), there are still a limited number containing the acrylamide warhead and showing structural
19
of virtual screening approaches to identify potential similarities to Sotorasib were identified and saved in the
inhibitors for the KRAS(G12C). 22-24 Given this urging structure-data file (SDF) format.

Volume 4 Issue 1 (2025) 80 doi: 10.36922/td.5163