Variants of the Antibody Herceptin That Interact with HER2

Extracellular region of HER2 alone and in complex with the Herceptin Fab

Increased in Vivo Stability
The HER2 breast cancers (~20%) are characterized by amplification of the HER2/neu gene, which is also known as ErbB2. Like EGFR
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The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer
trastuzumab, has a higher binding affinity for HER2 (Kd=0.1 nM) than murine MAb 4D5
he ErbB receptor tyrosine kinase 2 (ErbB2 or HER2) belongs to the ErbB (HER) family of receptor tyrosine kinases along with three other members, including epithelial growth factor receptor (EGFR), ErbB3 (HER3), and ErbB4 (HER4) . Generally, these receptors consist of three main domains: (1) the extracellular domain that contains the four subdomains that mediate HER receptor ligand-dependent or -independent dimerization,
Trastuzumab has been shown to bind three distinct regions of domain IV of the HER2 extracellular domain through electrostatic and hydrophobic bindings
maps of genomic changes
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HER2 monomer. Mutation Profile via Cancer Genom Atlas
The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer
The HER2 (also known as ERBB2 or HER2/neu) is a member of the epidermal growth factor receptor (EGFR) family
Mutation Table DownLoad Excel
Unnamed: 0 lg(cond(W)) ΔWd,kcal/Mol lg[Kd] ΔG,kcal/Mol ΔP,kcal/Mol TΔH,kcal/Mol
WT 7.010160 0.130717 11.895411 - - -
S310F 7.010408 0.130717 11.895518 0.0 0.000604 0.000604
S310TYR 7.010266 0.130717 11.895456 0.0 0.000253 0.000253
G222C 7.010514 0.130717 11.896008 0.0 0.003396 0.003396
R226HIS 7.011194 0.130717 11.894228 0.0 -0.006731 -0.006731
S250F 7.010262 0.130717 11.895538 0.0 0.000723 0.000723
A87T 7.009984 0.130717 11.895154 -0.0 -0.001466 -0.001466
S250K 7.010425 0.130717 11.895866 0.0 0.002587 0.002587
S413L 7.010315 0.130717 11.895380 0.0 -0.000178 -0.000178
P122L 7.010160 0.130717 11.895446 -0.0 0.000196 0.000196
V308M 7.010004 0.130717 11.895355 -0.0 -0.00032 -0.00032
T182I 7.010012 0.130717 11.895206 -0.0 -0.001167 -0.001167
P197L 7.010110 0.130717 11.895300 -0.0 -0.000633 -0.000633
Q329L 7.010151 0.130717 11.895410 -0.0 -0.00001 -0.00001
Q106R 7.010203 0.130717 11.895541 0.0 0.00074 0.00074
R138W 7.010177 0.130717 11.895411 0.0 0.000681 0.000681
L149F 7.010162 0.130717 11.895485 0.0 0.00042 0.00042
A241V 7.010147 0.130717 11.895477 -0.0 0.000376 0.000376
Trastuzumab binds to the juxtamembrane domain of HER2 and upon receptor binding, the antibody downregulates the expression of HER2
When Herceptin binds to HER2 it is able to flag these cells for destruction.
[Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab]
23
520
628
Herceptin Fab
A
breast tumor development and progression, strategies were developed to therapeutically target HER2 activity. The first successful approach began with the development of a mouse monoclonal antibody (mAb) called 4D5, which targets an extracellular epitope of the HER2 protein . HER2-specific monoclonal antibody 4D5 blocked phosphorylation of HER2 and suppressed growth of HER2-positive breast cancer cell lines and xenografts. In order to translate 4D5 clinically, a derivative that includes the antigen binding loops of 4D5 and the human variable region and immunoglobulin G1 constant domains was constructed [35]. The recombinant humanized anti-HER2 antibody that resulted from this effort is called trastuzumab (Herceptin; Genentech, San Francisco, CA, USA).
Trastuzumab achieved significant regression of human HER2-overexpressing tumor xenografts as monotherapy or in combination with cytotoxic chemotherapeutic agents. The mechanisms underlying the anticancer activity of trastuzumab are not completely known, but several have been proposed . Some studies have suggested that trastuzumab downregulates total levels of HER2 on the cell surface , which may ultimately reduce downstream PI3K and MAPK signaling. Trastuzumab has been shown to block cleavage of the extracellular domain of HER2, thus, preventing formation of the constitutively active membrane-bound 95-kiloDalton HER2 protein called p95 HER2 . Trastuzumab may also selectively inhibit HER2-HER3 heterodimerization , reducing PI3K signaling. Induction of cell cycle arrest by trastuzumab is mediated by p27kip1 and inhibition of cdk2 activity . Furthermore, trastuzumab appears to reduce angiogenesis, which may result in increased permeability of blood vessels, potentially increasing delivery of drugs to the tumor. Finally, HER2-positive cells that become “coated” in trastuzumab will be recognized by specific immune cells, causing antibody-dependent cellular cytotoxicity (ADCC), or lysis of the antibody-bound cells . This last mechanism may be quite important to the overall activity of trastuzumab, as trastuzumab was unable to achieve an antitumor response in mice that lacked Fc gamma receptors present on the ADCC-promoting immune cells, natural killer cells and macrophages, and is discussed in detail below as a mechanism of trastuzumab resistance .
The past decade of research into HER2-overexpressing breast cancer has provided significant insight into the mechanisms by which HER2 signaling drives tumor progression, as well as potential mechanisms by which cancer cells escape the anticancer activity of HER2-targeted therapy. Many of these preclinical findings have been translated into clinical development, resulting in novel combinations of HER2-targeted therapies and combinations of trastuzumab plus inhibitors of resistance pathways
Molecular Mechanisms of Trastuzumab-Based Treatment in HER2-Overexpressing
The interface between antibody and antigen is often depicted as a lock and key, suggesting that an antibody surface can accommodate only one antigen. Here, we describe an antibody with an antigen binding site
Herceptin to HER2 protein in breast cancer
520-CWGPGPTQCV_NCSQFLRGQE_CVEECRVLQGL_PREYVN
ARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCV
ARCPSGVKPDLSYMPIWKFPDEE_GACQPCPINC -630
P04626 · ERBB2_HUMAN
HER2 monomer [520-628]-Fab_blue
HER2 monomer [520-628]-Fab_yell
HER2 monomer [520-628]
B
Mutation Results Table
Mutation lg(cond(W)) Wd, kcal/Mol lg[Kd(wt)] ΔG, kcal/Mol ΔP, kcal/Mol TΔH, kcal/Mol
wt6.2514087190.76500648511.431784517---
P594SER6.2516299940.76500648511.4318548157.36E-100.0004000.000400
wt3.5816461870.55858549613.406445120---
P594SER3.5830406320.55858652513.4066011621.03E-060.0008930.000892
F595L3.5815155280.55858539913.406424011-9.65E-08-0.000121-0.000120
3.8410111880.55394969013.409833610---
P594SER3.8422268950.55395014113.4099475744.51E-070.0006510.000650
F595L3.8407689630.55394960013.409809693-9.00E-08-0.000136-0.000136

Data Tables: Cancer Genome Atlas Mutation Profile

Discussion and conclusions

Сalculated data discussion: HER2 mutational profile was used in the case of monomeric and antibody-antigen binding
HER2 [23-630] monomer.
Oncological profile

The HER2 [520-628] region

Trastazumab Fabs binding
How to read and interpret data?
Let's take two "symmetrical" from the point of analysis quantities lg(cond(W)) and lg[Kd] for which we are looking for a minimum of values. The values ​​of these quantities should tend to a minimum.

We will also take various biological associations, both complete formations and truncated domains, and for each formation we will sign the value of these two quantities.

Next, we analyze similar formations in order to find the minimum values ​​of the calculated quantities.

We draw "flow" arrows for biological formations.
This diagram summarizes the stability (lg(cond(W))) and dissociation constant (lg(Kd)) parameters for different HER2 regions and Fab combinations.
Visual annotations indicate levels of stability: most unstable, unstable, average, and most stable.
C
Trastuzumab Fragments Acquire an Increased in Vivo Stability
Trastuzumab, the first anti-HER2 agent that was developed, is a humanized mAb that binds to the extracellular, juxtamembrane portion of the HER2. rastuzumab only binds to HER2, not EGFR. Therefore, any effects of trastuzumab on EGF-induced activation of EGFR, HER2, and downstream signaling. Trastuzumab binds to the HER2 receptor, blocking its homodimerization. This inhibits cell proliferation and replication, and ultimately slows the growth of HER . Synergy between trastuzumab and pertuzumab for human . Herceptin contains the active substance trastuzumab (anti-p185, rhuMab HER2), which is a humanised monoclonal antibody that binds to the HER2 protein. Pertuzumab binds to a different epitope of the HER2 extracellular domain than trastuzumab and is able to block HER2 dimerization.Herceptin is a monoclonal antibody that binds to the extracellular portion of the HER2 gene, preventing dimerization. Trastuzumab is a clinically approved monoclonal antibody therapy which targets HER2 (or ErbB2) for treatment of HER2-overexpressing breast and gastric cancers. Safety studies are important in the development of antibody therapeutics and should use animal species which bind the target antigen (HER2) to understand target-mediated effects, in addition to a non-binding species to observe non-targeted effects. It is acknowledged that trastuzumab does not bind to the rodent equivalent of HER2 (called ‘neu’), but researchers still use rodent species to study toxicities of trastuzumab-based therapeutics. In their studies, Dr Gail Lewis Phillips and colleagues from Genentech Oncology demonstrate how future safety studies for trastuzumab-based therapeutics should be conducted to generate better understanding of toxicities, and to potentially reduce animal experimentation

Application of Alanine Scanning to Determination of Amino Acids Essential for Peptide Adsorption
Combinatorial alanine scanning mutagenesis is a powerful tool for the exploration of protein structure-function relationships
 three antibodies using alanine-scanning mutagenesis and structural analyses.
Fab_blue
HER2(cut)

Fab alanine scaning

Mutation Results Table – Fab_bl
Fab_bl lg(cond(W)) ΔWd, kcal/Mol lg[Kd] ΔG, kcal/Mol ΔP, kcal/Mol TΔS, kcal/Mol
WT3.58164620.558585513.4064451---
H91A3.60344650.558601213.40972030.00001570.01870850.0186928
Y92A3.61545450.558609013.41033590.00002350.02225030.0222268
T93A3.59115860.558592413.40921590.00000690.01579470.0157877
T94A3.58427890.558587413.40904860.00000190.01481730.0148154
The best stability and affinity are characterized by the smallest values ​​of the lg(cond(W)) and Kd quantities. Especially if the overall nature of the change on the two graphs is repeated.

Also, to increase accuracy, you can compare only alanine substitutions separately without taking into account the "wt"
Combinatorial libraries of alanine-substituted proteins can be used to rapidly identify residues important for protein function, stability and shape.
D
PDB ID Structure Description Resolution Mutations Binding Affinity Reference
1N8Z HER2 extracellular domain with Herceptin Fab 2.52 Å None Not specified Cho et al., 2003
3PP0 HER2 kinase domain with selective inhibitor 2.25 Å Yes (3 mutations) Not specified Aertgeerts et al., 2011
3RCD HER2 kinase domain with TAK-285 3.21 Å None Not specified Ishikawa et al., 2011
3MZW HER2 with engineered Zher2 affibody 2.60 Å None KD = 22 pM Eigenbrot et al., 2010
3BE1 bH1 Fab in complex with HER2 2.70 Å None Not specified Bostrom et al., 2009
6LBX HER2 domain IV with Rb-H2 binder 2.03 Å None Not specified Kim et al., 2021
2GJJ scA21 single-chain antibody against HER2 2.10 Å None Not specified Hu et al., 2007
6J71 HuA21-scFv with HER2 extracellular domain 2.92 Å None Not specified Wang et al., 2019
3N85 HER2 trimer with Fab37 3.20 Å None Sub-nanomolar Fisher et al., 2010
2KS1 ErbB1-ErbB2 transmembrane heterodimer N/A (NMR) None Not specified Mineev et al., 2010
DNA Change Protein Change Consequence # Affected Cases in ERBB2
chr17:g.39717426A>CERBB2K615TMissense1/3 913(0.03 %)
chr17:g.39717362C>TERBB2P594SMissense1/3 913(0.03 %)
chr17:g.39712008A>CERBB2T328PMissense1/3 913(0.03 %)
chr17:g.39727755C>TERBB2A1160VMissense1/3 913(0.03 %)
chr17:g.39723330C>GERBB2S653CMissense1/3 913(0.03 %)
chr17:g.39727734G>AERBB2R1153QMissense1/3 913(0.03 %)
chr17:g.39711952G>CERBB2G309AMissense1/3 913(0.03 %)
chr17:g.39726824T>GERBB2L994VMissense1/3 913(0.03 %)
chr17:g.39717417C>AERBB2P612HMissense1/3 913(0.03 %)
chr17:g.39715470C>AERBB2P416QMissense1/3 913(0.03 %)
chr17:g.39724795A>GERBB2T793AMissense1/3 913(0.03 %)
chr17:g.39726860C>TERBB2R1006CMissense1/3 913(0.03 %)
chr17:g.39727466C>TERBB2R1111WMissense1/3 913(0.03 %)
chr17:g.39723330C>TERBB2S653FMissense1/3 913(0.03 %)
chr17:g.39728008G>TERBB2E1244DMissense1/3 913(0.03 %)
chr17:g.39709828C>TERBB2P197LMissense1/3 913(0.03 %)
chr17:g.39710191C>AERBB2S250YMissense1/3 913(0.03 %)
chr17:g.39726618T>AERBB2S977TMissense1/3 913(0.03 %)
chr17:g.39707122C>TERBB2A69VMissense1/3 913(0.03 %)
chr17:g.39724808T>CERBB2V797AMissense1/3 913(0.03 %)
chr17:g.39715345T>CERBB2L403PMissense1/3 913(0.03 %)
chr17:g.39708397T>GERBB2I101SMissense1/3 913(0.03 %)
chr17:g.39712012A>TERBB2Q329LMissense1/3 913(0.03 %)
chr17:g.39708412A>GERBB2Q106RMissense1/3 913(0.03 %)
chr17:g.39727859G>AERBB2E1195KMissense1/3 913(0.03 %)
chr17:g.39725151C>AERBB2L866MMissense1/3 913(0.03 %)
chr17:g.39708507C>TERBB2R138WMissense1/3 913(0.03 %)
chr17:g.39715338G>CERBB2E401QMissense1/3 913(0.03 %)
chr17:g.39717345C>TERBB2A588VMissense1/3 913(0.03 %)
chr17:g.39709325G>TERBB2L149FMissense1/3 913(0.03 %)
chr17:g.39710368T>CERBB2I263TMissense1/3 913(0.03 %)
chr17:g.39727370G>AERBB2E1079KMissense1/3 913(0.03 %)
chr17:g.39710164C>TERBB2A241VMissense1/3 913(0.03 %)

ERBB2 Missense Mutations – Block 2

DNA Change Protein Change Consequence Affected Cases
chr17:g.39723966T>AERBB2 L755MMissense2 / 3
chr17:g.39710418G>CERBB2 E280QMissense2 / 3
chr17:g.39724745G>TERBB2 G776VMissense2 / 3
chr17:g.39717367C>AERBB2 F595LMissense1 / 3
chr17:g.39712035C>TERBB2 P337SMissense1 / 3
chr17:g.39723652G>AERBB2 V734IMissense1 / 3
chr17:g.39715461C>TERBB2 S413LMissense1 / 3
chr17:g.39710191C>TERBB2 S250FMissense1 / 3
chr17:g.39727838G>AERBB2 G1188RMissense1 / 3
chr17:g.39727839G>AERBB2 G1188EMissense1 / 3
chr17:g.39710418G>AERBB2 E280KMissense1 / 3
chr17:g.39725119G>TERBB2 S855IMissense1 / 3
chr17:g.39719834G>CERBB2 S649TMissense1 / 3
chr17:g.39726905G>CERBB2 E1021QMissense1 / 3
chr17:g.39723323C>GERBB2 L651VMissense1 / 3
chr17:g.39708460C>TERBB2 P122LMissense1 / 3
chr17:g.39723342C>TERBB2 A657VMissense1 / 3
chr17:g.39711948G>AERBB2 V308MMissense1 / 3
chr17:g.39709423C>TERBB2 T182IMissense1 / 3
chr17:g.39715822G>AERBB2 A466TMissense1 / 3
chr17:g.39724768C>TERBB2 R784CMissense1 / 3
chr17:g.39727976C>TERBB2 P1234SMissense1 / 3

Data source: GDC Portal: ERBB2

ERBB2 Missense Mutations (GDC Portal)

DNA Change Protein Change Consequence Affected Cases
chr17:g.39711955C>TERBB2 S310FMissense43 / 3
chr17:g.39725079G>AERBB2 V842IMissense20 / 3
chr17:g.39723967T>CERBB2 L755SMissense18 / 3
chr17:g.39723405G>AERBB2 R678QMissense16 / 3
chr17:g.39724747G>TERBB2 V777LMissense11 / 3
chr17:g.39711955C>AERBB2 S310YMissense9 / 3
chr17:g.39724747G>AERBB2 V777MMissense4 / 3
chr17:g.39710106G>TERBB2 G222CMissense4 / 3
chr17:g.39724008G>TERBB2 D769YMissense4 / 3
chr17:g.39723650C>TERBB2 T733IMissense3 / 3
chr17:g.39724004C>GERBB2 I767MMissense3 / 3
chr17:g.39710119G>AERBB2 R226HMissense2 / 3
chr17:g.39711963C>GERBB2 L313VMissense2 / 3
chr17:g.39716337G>AERBB2 R517QMissense2 / 3
chr17:g.39725139A>GERBB2 T862AMissense2 / 3
chr17:g.39708354G>AERBB2 A87TMissense2 / 3
chr17:g.39724008G>CERBB2 D769HMissense2 / 3
chr17:g.39727917G>AERBB2 S1214NMissense2 / 3
chr17:g.39726610C>TERBB2 S974FMissense2 / 3
chr17:g.39708403G>AERBB2 R103QMissense2 / 3
chr17:g.39725070G>AERBB2 V839MMissense2 / 3

Data source: GDC Portal: ERBB2

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