Shining a Light on Cancer Therapy: Benchmarking DFT Functionals for Enhanced Optical Probing of Tyrosine Kinase Inhibitors


Epidermal growth factor receptor (EGFR) is a transmembrane protein that plays a major role in cell growth, differentiation, and survival. Overexpression or mutation of EGFR is implicated in the development and progression of various cancers and inhibiting EGFR’s tyrosine kinase activity (TKIs) by molecules such as AG-1478 can interrupt these processes by blocking the ATP binding site. This inhibition prevents the phosphorylation and activation of downstream signaling pathways that are vital for cell proliferation and survival. AG-1478 has been extensively used in medical research as a tool to understand the role of EGFR in the development of cancers and elucidating the pathways involved and in the development of other more potent and specific EGFR inhibitors. Indeed, AG-1478 has paved the way for the development of other EGFR inhibitors that are currently used in cancer treatment. FDA approved drugs like Gefitinib and Erlotinib, which are used to treat non-small cell lung cancer and other malignancies, were developed based on the understanding gained from compounds like AG-1478. Understanding the mechanism of action of AG-1478 has also helped in addressing issues like drug resistance. It has led to the development of second and third-generation EGFR inhibitors and the exploration of combination therapies to overcome resistance.

The use of optical spectroscopy, specifically UV-vis and fluorescence spectroscopy, plays an important role in understanding the chemical environment and conformation of fluorophores. These techniques are exceptionally sensitive to changes in their surroundings, making them ideal for probing the conformation and solvent responses of various substances. AG-1478, which contain a quinazolinamine scaffold, are fluorophores and exhibit distinct optical properties that are influenced by their environment. In a new study published in the Journal Electronic Structures by Sallam Alagawani and Professor Feng Wang from the Swinburne University of Technology together with Dr. Vladislav Vasilyev from the Australian National University, the researchers in the study conducted computational analyses to investigate the optical properties of the AG-1478, particularly focusing on its behavior in dimethyl sulfoxide (DMSO) solvent.

The researchers simulated the absorption spectrum of AG-1478 in DMSO UV-vis Spectroscopy to understand how it absorbs light while the emission spectrum of AG-1478 in DMSO was recorded to study its fluorescence characteristics. The researchers used Density Functional Theory (DFT) to predict the electronic structure and optical properties of AG-1478. They employed Time-Dependent DFT (TD-DFT) for simulating the excited-state properties and to understand the absorption and emission spectra of AG-1478. They also benchmarked up to 22 different DFT functionals against experimentally measured properties, to find which ones most accurately predict the optical spectra of AG-1478. The fluorescence spectrum of AG-1478 was found to be highly sensitive to the solvent environment, suggesting its potential as a probe for studying solvent effects on electronic states. Among the 22 DFT functionals they tested, seven were identified as the top performers: B3PW91, B3LYP, B3P86, PBE1PBE, APFD, HSEH1PBE, and N12SX. These functionals showed the highest accuracy in reproducing the experimental optical spectra of AG-1478 in DMSO.

According to the authors, they recommended B3PW91 for studying the overall optical properties of 4-quinazolinamine TKIs, while B3LYP was found to be excellent for modeling the absorption spectrum, on the other hand B3P86 was Identified as the best for emission spectrum predictions. They highlighted the significance of including electron correlation energy in the calculations for accurate optical spectra predictions. The researchers suggested that these DFT functionals could be reliable tools in designing new TKIs with larger Stokes shifts, which is beneficial for medical imaging applications. Moreover, modifications to the B3LYP functional, like CAM-B3LYP, LC-B3LYP, and B3LYP-D3, resulted in larger errors, emphasizing the complexity of functional selection in theoretical calculations. Furthermore, AG-1478 showed a significant stokes shift in DMSO, which is advantageous for fluorescence-based applications, as it helps in enhancing signal clarity.

The authors successfully provided a comprehensive understanding of the optical properties of TKIs, especially AG-1478 by examining experimental spectroscopy with extensive computational benchmarking, and set a precedent for using computational methods to aid in the design of new drugs and diagnostic agents. Moreover, the use of quantum mechanics, particularly the frequency-dependent linear response (LR) TD-DFT method, is a cornerstone of their research. TD-DFT, being an exact theory, is important for analyzing the TD LR of the exact ground-state density to a TD external perturbation. However, the accuracy of TD-DFT calculations is contingent upon the selection of the appropriate exchange-correlation (VXC) functional. The study’s benchmarking of 22 DFT VXC functionals against the experimental optical spectra of AG-1478 in DMSO is a testament to this. It underscores the need for precise VXC functional selection for modeling ES properties. The findings of Professor Feng Wang and her colleagues are groundbreaking in several respects. Firstly, it identified the top seven DFT-VXC functionals for accurately reproducing the optical properties of AG-1478. These include B3PW91, B3LYP, B3P86, PBE1PBE, APFD, HSEH1PBE, and N12SX DFT-VXC functionals. Notably, Becke’s three-parameter exchange functional (B3) emerged as a key player in generating accurate optical spectra. Secondly, they recommended specific functionals for studying different aspects of the optical properties of 4-quinazolinamine TKIs. For instance, B3PW91 is recommended for studying the overall optical properties, B3LYP for absorption spectra, and B3P86 for emission spectra.

An intriguing finding of this research is the impact of further corrections to B3LYP, such as CAM-B3LYP, LC-B3LYP, and B3LYP-D3, which result in larger errors in the optical spectra of AG-1478 in DMSO. This highlights the delicacy of the balance between theoretical corrections and empirical observations. These best-performing functionals are reliable tools for studying the optical properties of TKIs, aiding in the design of new agents with larger Stokes shifts for medical imaging applications. The new study also emphasizes the importance of including the electron correlation energy in obtaining reliable optical spectra for this class of 4-quinazolinamine-based TKIs. This aspect is important as it indicates the need to go beyond mere electron exchange considerations for accurate optical spectral simulations in these systems. In conclusion, the study by Alagawani, Vasilyev and Wang marks a significant advancement in our understanding of the optical properties of TKIs, particularly those with a quinazolinamine scaffold. By benchmarking various DFT functionals against experimental data, they have not only provided a reliable methodology for studying these compounds but also opened new avenues for the development of TKIs with improved optical properties for medical applications. The new study highlights the synergy between computational and experimental methods in advancing our understanding of complex molecular systems, with far-reaching implications for drug development and medical imaging.

Shining a Light on Cancer Therapy: Benchmarking DFT Functionals for Enhanced Optical Probing of Tyrosine Kinase Inhibitors - Medicine Innovates Shining a Light on Cancer Therapy: Benchmarking DFT Functionals for Enhanced Optical Probing of Tyrosine Kinase Inhibitors - Medicine Innovates

About the author

Ms Sallam Alagawani
PhD researcher at Swinburne University of Technology
E-mail: [email protected]

Sallam holds a bachelor’s degree of Doctor of Pharmacy from Jordan University of Science and Technology in Jordan. Sallam is recognized as a highly skilled individual proficient in efficiently designing, recommending, activating, monitoring, and evaluating patient-specific pharmacotherapy to ensure optimal outcomes. As a pharmaceutical caregiver, she ensures the accurate and timely distribution of medications to patients, playing a vital role in implementing pharmaceutical care plans.

In August 2020, she embarked on a higher degree research program, initiating a Master of Science with a Tuition Fee Scholarship, later elevating her academic pursuits to an integrated PhD program in December 2022. Sallam’s research focuses on Drug Design, medicinal chemistry, molecular modelling, and computational chemistry, particularly in the realm of anti-cancer drugs. Her notable research project is titled “In silico study of halogen impact on quinazoline-based EGFR-TKIs,” conducted at the Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology in Melbourne, Australia.

In addition to her research pursuits, Sallam serves as an experienced Laboratory Demonstrator, imparting knowledge to undergraduate students in both introductory and computational chemistry. Her academic interests lie in new drug development, pharmaceutical chemistry, drug design and delivery, and molecular modelling. Sallam’s multifaceted expertise positions her as a valuable asset in the realm of pharmaceutical research and education.

Useful links about Sallam Alagawani:


About the author

Dr Vladislav Vassiliev

Dr Vladislav Vassiliev is a computational chemist at National Computational Infrastructure (NCI) at Australian National University.  (Information from

E: [email protected]

About the author

Professor Feng Wang (corresponding author)

Feng Wang is Professor of Chemistry at Swinburne University of Technology (Australia). She received her PhD Degree from University of Newcastle (Australia).  Feng has had academic appointments as an NESRC Canada International Postdoctoral Fellowship of University of Waterloo (Canada), The University of Melbourne (Australia) and Swinburne University of Technology. Feng’s expertise covers computational chemistry, molecule spectroscopy and molecular physics for systems including drug candidates, bioactive compounds, functional organic compounds, energy storage materials and catalysts.

Feng serves the Australian Research Council (ARC) as a College of Expert (CoE) and Chairs Scientific Adversary Committee (SAC) of National Computational Merit Allocation Scheme (NCMAS), Department of Education (Australia).

E:  [email protected]


Sallam Alagawani, Vladislav Vasilyev and Feng Wang. Optical spectra of EGFR inhibitor AG-1478 for benchmarking DFT functionals2023 Electron. Struct. 5, 024011

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