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Quantum Calculations

[Interview] The Rise of Quantum Physics in Drug Discovery

   by Andrii Buvailo    148
[Interview] The Rise of Quantum Physics in Drug Discovery

Computer-aided drug design (CADD) is a central part of so-called “rational drug design”, pioneered in the last century by companies like Vertex. Over the last decades, CADD had great influence on the way new therapeutics are discovered, however, it also showed limitations due to modest accuracy of computational tools.  

The majority of software tools used for computational chemistry and biology rely on molecular mechanics -- a simplified representation of molecules, essentially reducing them down to “balls and sticks”: atoms and bonds between them. In this way it is easier to compute, but accuracy suffers greatly.

In order to gain adequate accuracy, one has to account for the electronic behavior of atoms and molecules, i.e. consider subatomic particles -- electrons and protons. This is what quantum mechanical (QM) methods are all about -- and the theory is not new, dating back to the early decades of the 20th century.  

8 Startups Using Quantum Theory To Accelerate Drug Discovery

   by Andrii Buvailo    605
8 Startups Using Quantum Theory To Accelerate Drug Discovery

Molecular mechanics (MM) is a traditional computational approach when it comes to modeling in synthetic organic chemistry, medicinal chemistry and versatile aspects of drug design. However, MM methods have significant limitations, for example, when used to study electron-based properties within the drug-receptor microenvironment. Quantum mechanical (QM) methods allow to substantially increase the accuracy of predictions and provide much more relevant models of chemical and biological objects and their interactions, but QM methods are extremely (often prohibitively) computationally costly.

However, a series of advancements over recent years allowed to expand horizons in this direction, for example, the emergence of density functional theory (DFT), the overall increase in the computation power and the emergence of distributed cloud-based computational infrastructures.

ConstruQt - a Reliable Molecular Structure Predictor in the Cloud

   by Peter Jarowski    651
ConstruQt - a Reliable Molecular Structure Predictor in the Cloud

Since August Kekulé’s proposal for the tetrahedral configuration of carbon or his more famous realization that benzene was a cyclic molecule, a snake biting its tale, molecular structure has been the leading consideration for the design of new molecules as drugs or performance materials. For the former, it is said that 70% of drug design is based on molecular shape with the remainder attributed to electrostatic or non-bonded interactions.

Structural chemistry began around the 1860 with these dual assignments by Kekulé but it wasn’t until one hundred years later with Allinger’s initial force field approaches that the first classical molecular mechanics (MM) models became available to make computer-assisted prediction of molecular structure. These models themselves are based on principles derived by Robert Hooke, a contemporary of Isaac Newton, in the mid 17th century with additional layers from van der Waals (19th century) etc.

[White paper] High Throughput Quantum Chemistry for Drug Discovery - Towards Reaction Screening

   by Peter Jarowski    3167

In the domain of drug discovery, there can be a world of difference between a computer-generated hit compound, which is predicted to bind well to a drug target and what can be reliably synthesized at scale, or indeed synthesized at all. This discrepancy has been a lingering point of discord between the Discovery and R&D efforts in the chemical industry. Computer-aided drug design (CADD) has become an increasingly valuable tool by providing essential screening data and unique insight into drug action and mechanism, but it does not model the more complex world of chemical reactivity and synthetic chemistry.