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Molecular Mechanisms of Targeted Cancer Therapies

Understanding Cancer

The resource Exploring the Structural Biology of Cancer is a comprehensive guide on the molecular mechanisms of cancer. Using this resource, you will gain understanding of how cancer originates, grows, and spreads in the body, as well as what treatments are available to the cancer patients.

Understanding Targeted Cancer Therapies

A section of your video should introduce the viewers the concept of targeted cancer therapies. One overview can be found at National Cancer Institute Targeted Therapy to Treat Cancer, another at American Cancer Society How Targeted Therapies Are Used to Treat Cancer.

Topic-related PDB Structures and Molecular Visualization Resources

For each of the 2023 topics you will find a list of learning resources along with a table that contains short description of topic-relevant proteins along with an image enhanced with labels. In each of the rows, you will find a link to a UCSF Chimera session that was used to create the images shown in the right column of each of the tables. Use the UCSF Chimera tutorial to learn how to edit the sessions, create animations, or save pictures.

In addition, we provide a link to the 3D view in Mol* (MolStar) for each PDB structure discussed. Mol* is a web-based molecular viewer. Use these tutorials to learn its basic functionality. Access the full documentation to learn about more advanced features. Mol* is accessible from each structure summary page, from the “3D View” tab.

2023 Topics Overview

Topic 1: Fighting breast cancer by targeting HER2 receptor

HER2 stands for Human Epidermal growth factor Receptor 2. The protein in humans is encoded by the ERBB2 gene. The gene is overexpressed in about 20% of breast cancers. Because the activation of the HER2 receptor initiates many cell proliferative and anti-apoptotic pathways, the targeted cancer therapies aim at maintaining the receptor in the inactive state.

Learning Resources about HER2:

Table 1: Relevant PDB Structures and Visualization Resources for Topic 1

Topic-relevant Structures Description with PDB IDs	Visual Guide
Inactive HER2 Receptor The HER2 receptors exist as monomers on the cell surface (cellular membrane indicated for clarity on the visual guide). The HER2 protein has three portions: a receptor that extends outside the cell (shown from the PDB Structure 1n8z, chain C); a single helix that spans the membrane (shown from the PDB structure 2ks1, chain A); and a tyrosine kinase domain inside the cell (shown from the PDB structure 3pp0, chain B). The kinase features a long C-terminal tail with multiple tyrosine residues (shown using a part of AlphaFold Model AF_AFP04626F1.) The illustration shown here was created from the UCSF Chimera session available here for download. To visualize each individual structure using Mol*, access the links below: 1n8z, 2ks1, 3pp0, AF_AFP04626F1
Activated HER2 Receptor When HER2 is activated, it provides the cell with potent proliferative and anti-apoptosis signals. Activation occurs through dimerization with other receptors from HER family, including HER1, HER3, and HER4. The HER2/HER3 dimer is shown on the left from PDB Structure 7mn6; the membrane helices are shown from the PDB Structure 2ks1 and the kinase domains are shown from PDB structure 3pp0. This dimerization activates the kinase domains. They bind ATP and tyrosine residues from the C-terminal tails and phosphorylate them. The phosphorylated tyrosines bind other proteins enabling forming protein complexes that drive the cell division and antiapoptotic pathways. Two ATP-like molecules are shown in yellow in the binding sites (PDB Structure 3pp0) The illustration shown here was created based on the UCSF Chimera session available here for download. To visualize each individual structure using Mol*, access the links below: 7mn6, 2ks1, 3pp0
HER2 Receptor with trastuzumab HER2 is the target of the monoclonal antibody trastuzumab. The illustration shows the antibody bound HER2 monomer from the PDB structure 1n8z. The binding prevents dimerization thus inhibiting the signaling pathways initiated by HER2. The illustration shown here was created based on the UCSF Chimera session available here for download. To visualize each individual structure using Mol*, access the links below: 1n8z, 2ks1, 3pp0

Topic 2: Preventing blood vessel formation in tumors by targeting VegF

VegF stands for Vascular Endothelial Growth Factor. In healthy humans, the release of the VegF into blood stream promotes creation of new blood vessels in embryonic development and is important for wound healing in adults. This process is kidnapped by the cancer cells which release VegF to form new blood vessels providing nutrients to the growing tumor. The vasculature formed by tumor is leaky causing suboptimal blood flow, resulting in further release of VegF. This essential role in tumor vessel formation makes VegF a target for cancer therapy.

Learning Resources about HER2:

Table 2: Relevant PDB Structures and Visualization Resources for Topic 2

Topic-relevant Structures Description with PDB IDs	Visual Guide
VegF signaling protein VegF is a small signal protein secreted by many cells that stimulates the formation of blood vessels. The protein is shown here from PDB entry 1bj1, chains V and W. The illustration shown here was created from the UCSF Chimera session available here for download. To visualize this structure using Mol*, access the link below: 1bj1
Inactive VegF receptor The inactive VegF receptor (VegFR) is a monomer. The VegFR has three portions: a receptor that extends outside the cell (shown from the PDB Structure 5t89, chain Y); a single helix that spans the membrane (shown from the PDB structure 2m59, chain A); and a tyrosine kinase domain inside the cell (shown from the PDB structure 3hng). The kinase features a long C-terminal tail with multiple tyrosine residues (shown in atom representation) using a part of AlphaFold Model AF_AFP17948F1. The illustration shown here was created based on the UCSF Chimera session available here for download. To visualize each individual structure using Mol*, access the links below: 5t89, 2m59, 3hng, AF_AFP17948F
Activated VegF Receptor When VegF binds to the receptor, it pairs off with another copy of itself, creating an active dimer. This dimerization activates the kinase domains. They bind ATP and tyrosine residues from the C-terminal tails and phosphorylate them. The phosphorylated tyrosines bind other proteins enabling pathways that are relevant for angiogenesis. The VegFR extracellular portion is shown from the PDB Structure 5t89, the membrane portion is shown from PDB structure 2m59; the tyrosine kinase domains are shown from 2 copies of PDB structure 3hng, and the kinase's C-terminal tail is shown from a part of AlphaFold Model AF_AFP17948F1. The illustration shown here was created based on the UCSF Chimera session available here for download. To visualize each individual structure using Mol*, access the links below: 5t89, 2m59, 3hng, AF_AFP17948F
VegF with bevacizumab antibody bound The bevacizumab antibody binds to the VegF proteins. This prevents the activation of VegFR. VegF with 2 bevacizumab antibodies bound is shown here from PDB entry 1bj1. The illustration shown here was created from the UCSF Chimera session available here for download. To visualize this structure using Mol*, access the link below: 1bj1

Topic 3: Interrupting cancer cell growth by targeting the G12C variant of ras protein

The ras protein family is a group of four enzymes that function as molecular switches regulating cellular proliferation in growth factor signaling pathways (see Section 3 in Exploring the Structural Biology of Cancer for an example pathway). The protein cycles between the GDP-bound, inactive state and the GTP-bound, active state.

Three genes, HRAS, KRAS, and NRAS encode for all the ras proteins in humans. KRAS is the most frequently mutated oncogene in human cancer.

One of the common carcinogenic mutations in KRAS is the mutation of Guanine to Cysteine at position 12 (G12C). This mutation disrupts the GDP/GTP exchange cycle which in turn drives tumorigenic signals. In 2021, the first drug, sotorasib, was approved by the FDA to target this mutation.

Learning Resources about targeting the G12C variant of ras protein :

Table 3: Relevant PDB Structures and Visualization Resources for Topic 3

Topic-relevant Structures Description with PDB IDs	Visual Guide
Ras/GEF Complex The guanine nucleotide exchange factors (GEFs) modify the GDP binding site promoting GDP disassociation and GTP binding. The illustration here shows the GEF (chain B, dark blue) in complex with ras (chain A, cyan) form PDB structure 1xd2. The mutation site at residue 12 (Guanine) is highlighted in red. The illustration shown here was created from the UCSF Chimera session available here for download. To visualize the structure using Mol*, access the link below: 1xd2
KRAS with G12C Mutation The Guanine to Cysteine mutation at position 12 (highlighted) disrupts the guanine exchange cycle, thereby locking the protein in the GTP-bound, active state, which concurrently disrupts the signal in the cellular pathway. The KRAS mutant is shown here from PDB entry 4ldj with the mutation site highlighted. The illustration shown here was created from the UCSF Chimera session available here for download. To visualize the structure using Mol*, access the link below: 4ldj
G12C Mutant with Inhibitor Tetrahydropyridopyrimidines are inhibitors that bind covalently to the cysteine in the mutant protein and lock the protein in the inactive GDP-bound state. An example inhibitor is shown here in purple form PDB structure 6n2j. The illustration shown here was created based on the UCSF Chimera session available here for download. To visualize each individual structure using Mol*, access the link below: 6n2j