We’re at the dawn of a new era in medicine. At Silicon Therapeutics we perform accurate, all-atom, quantum physics-based simulations fast enough and at the scale necessary to break through the bottlenecks preventing effective discovery of therapeutics for biologically validated but chemically intractable targets.

Silicon Therapeutics is founded on the principle that accurate physics-based simulations, which rigorously account for full system flexibility (proteins, ligands, cofactors and water molecules), enable us to address difficult protein targets through an atomic-level understanding of the conformational mechanism driving the disease. We believe our integrated in-house experimental efforts in chemistry and biology, combined with our high-performance computing environment, will lead to the design and delivery of new medicines for cancers, the flu and other diseases to improve the lives of patients.

Then to Now

Until recently, drug discovery has followed the well-defined path of rational drug design: identify a relevant receptor or enzyme investigate the structure; design a molecule to interact with the receptor or enzyme in a therapeutically beneficial way.

Rational drug design has resulted in important therapeutics, but its methodology supplies only part of the picture. Rational drug design addresses enthalpy, the total heat content of the system, but does not address entropy, the unavailability of thermal energy for conversion into mechanical work. This omission leads to bottlenecks in drug design, including inefficiencies that add years, high costs and high failure rates in drug discovery.

Designing Better Medicines: Atom-by-Atom

Silicon Therapeutics approaches today’s vast chemical space and most challenging disease targets by leveraging our proprietary quantum physics-based simulations, experimentation through our in-house laboratories and industry-leading high-performance computing to run our highly predictive models at scale. By combining these computational breakthroughs with quantum physics, our integrated team of chemists, biologists, physicists, biophysicists, force field developers, software engineers and parallel computing experts can build three-dimensional time-based simulations that guide their molecular designs at the atomic level. Our insights from this logical and elegant approach will pioneer a new path for drug design and deliver novel medicines for cancers, the flu and other diseases to treat patients.

Fully Integrated Drug Discovery

Silicon Therapeutics’ proprietary quantum physics-driven platform is the foundation for realizing this commitment to create and deliver novel therapeutics. Owning the platform technology allows us to customize applications and workflows in real-time. Our algorithms go beyond static binding as we analyze the conformational mechanism and motion of biological targets.

As a fully integrated company and leader in quantum physics-driven molecular design, Silicon Therapeutics possesses capabilities throughout the full value chain for creation of novel therapeutics. We believe our end-to-end expertise will lead to design and delivery of new medicines to improve the lives of patients.

Beyond Binding

The power of the Silicon Therapeutics platform arises from the precision of our in silico conformation modulation assays, which take us beyond the traditional static representation of binding and open up extraordinary potential associated with understanding the free energy landscape of protein motion. Using proprietary algorithms, we gain insights into not only how each molecule modulates the conformational state of a target protein, but also a clearer understanding of how a molecule impacts the underlying disease biology. Our platform also includes in-house biophysical operations such as NMR, HDX-MS, and SPR to complement our simulations and produce actionable insights that allow us to target protein motion on an atom-by-atom basis.

By combining in-house high-performance computing (HPC), the expertise of our integrated biophysical teams and insights derived through our proprietary platforms and molecular simulations, Silicon Therapeutics is pioneering a new way of doing science. We’ve advanced beyond analysis of static binding and are now navigating the rugged, dynamic landscape of the free energy surface that links protein motion to disease biology.

Navigating the Free Energy Surface

Silicon Therapeutics is sharply focused on scientific insights directed toward designing medicines, atom-by-atom, to treat diseases. Protein function is governed by the complex, multidimensional free energy surface that results from the quantum mechanical interactions among and between all of the atoms in the system. While the dimensions of this vast free energy landscape are so large that the entire space cannot be exhaustively sampled, Silicon Therapeutics is focused on identifying and navigating the critical difference between active and inactive states of target proteins.

We customize our proprietary algorithms to predict the specific motions that modulate the target protein function and design molecules atom-by-atom that shift the conformational equilibrium of the free energy landscape in a way that directly affects the biology of disease. By carefully defining the free energy landscape directly associated with biological targets, we more clearly address the affinity of a molecule to bind to its target based on the change in energy. We analyze the atomic contribution of each interaction between the potential drug and target protein, including the entropy, to precisely design medicines atom-by-atom. From these insights, we build our physics-driven model to recapitulate atomic level interactions and produce in-house experimental measurements to validate and guide our drug discovery process.