Peptide Designing using Quantum Computing

Kanikah Mehndiratta, MSc

Introduction:

Quantum computing can be considered a revolutionary and transformative technology that is coming but nowhere close yet, especially when it comes to biomedical research. The science of the living has always been intertwined with other areas, be it by studying biochemical properties, or use of biostatistics to quantify biological phenomena, or understanding the physicality of biological molecules through biophysics. Naturally, quantum computing has become one such arena that molecular biologists, bioinformaticians, and biophysicists find very fascinating in structural and functional studies at the molecular level. In a simple yet complex way, DNA has been quoted to be just like a quantum computer that simply localizes a ubiquitous spirit or consciousness into energy, time and space information, and matter. The famous physicist Erwin Schrodinger believed that quantum ‘leaps’ of electrons between different states of energy were essential for the natural adaptation of living beings. Watson and Crick also based the discovery of double-helical DNA structure on the ‘aperiodic crystal’ comparison he made with genetic material. Similarly, structural analysis of other biological molecules like enzymes, or simply proteins is being approached in recent times, keeping the same laws in mind.

The field of Quantum computing

A supercomputer might be better at arithmetic, but a quantum computer when assessed for a specific task of random number generation took 200 seconds. A supercomputer could have taken 10,000 years to do the same, supporting how fast quantum computing works. Quantum Leap is all about observation, manipulation, and controlling the behaviour of particles and associated energy at atomic and subatomic levels in order to develop next-gen advancements in the field of computing, modelling, sensing, and communicating. A lot of prominent institutes, particularly the EU Quantum Flagship and the US National Science Foundation have been investing a lot into related research. Companies such as Google, Microsoft, Zapata Computing, IonQ etc. are developing related products and services. The US National Institute of Health recently discussed the approach of quantum computing to machine learning and deep learning. Quantum bits or the qubits can be both 1 and 0, meaning a superposition of states. The oddness of the theory is explained through Schrodinger’s ‘Cats in Boxes’ experiment where the apparatus holds a 50% chance of killing the cat but until someone checks that cat in theory stays both alive and dead.

Peptide designing using quantum computing:

In a 2021 article by V. Marx in Nature Methods, peptide designing is approached using quantum mechanics for molecular bond creation and breaking studies. Folding of proteins involves ‘monster calculations’ which could be simplified using quantum computing. He discussed the application of quantum computing in drug design where at the atomic level, a protein would acquire a structure that corresponds with the lowest energy conformation. They mapped the peptide designing issues to a quantum computer where the Packer module of the software Rosetta was used for trying many positions per rotamers for appropriate optimization.

In comparison to a classical computer, this helped consideration of all possible rotamer combinations, with an initial equal superposition of every possible string of 0s and 1s. The sequence design part was then mapped using D-Wave with 5000 bits, according to which molecular peptides were designed and characterized in the lab.

Conclusion:

With a lot of controversies associated with quantum supremacy, the advantages it offers, considering them overhyped, there is still a lot of research and investment needed in the area.

Biological sequence analysis, quantum sensing, and biological process simulation would probably be the next major areas of application for quantum computing.

Also read: Tarantula toxin- the Key to Future Chronic pain medications?

References:

1. Marx, V. Biology begins to tangle with quantum computing. Nat Methods (2021). https://doi.org/10.1038/s41592-021-01199-z

2.  Emani, P. S., Warrell, J., Anticevic, A., et al. Quantum computing at the frontiers of biological sciences. Nature Methods, 1-9.(2019) https://doi.org/10.1038/s41592-020-01004-3

About Author:

Kanikah Mehndiratta is an avid researcher in the field of Genetics with a background in Biotechnology. She is a post-graduate from the University of Glasgow in their Medical Genetics and Genomics program. Currently, based in Chandigarh as a Scientific Writer, she involves herself mainly in projects related to neurological disorders. Outside of academics, she likes to read novels, travel and is involved in volunteer work mostly.

LinkedIn profile– https://www.linkedin.com/in/kanikah-mehndiratta-301830171

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