Long-time scale molecular dynamics simulations run on specialized computational hardware allow us to see biologically relevant conformational changes of proteins upon ligand binding.


New computing architectures accelerate our physics-based simulations dramatically. GPUs alone represent a 100x increase in speed (FGPAs and ASICs are orders of magnitude faster).


Rigorous quantum mechanical methods, which also run on GPU hardware, give us the ability accurately model challenging chemistries, including metal interactions and covalent bonding.


Silicon Therapeutics is an integrated computational drug discovery company using rigorous physics-based simulations to significantly accelerate the drug discovery process. We are building our company around a core platform that leverages quantum mechanics and molecular dynamics, which we are deploying on massive computational resources, including internal clusters and the cloud to attack previously undruggable targets highly implicated in a number of human diseases.

STX was founded on the premise that ultimately, "...everything that is living can be understood in terms of the jiggling and wiggling of atoms" (Richard Feynman). while we are a long way off from rigorously simulating cells, organs, and organisms, with current state-of-the-art approaches we can accurately simulate proteins and protein-ligand binding. Using all-atom simulations with explicit waters and an accurate representation of molecules in the system, we can predict relative binding energies to on-targets and off-targets, allowing for in

silico affinity and selectivity profiling much more rapidly and efficiently than experimental approaches. Tightly coupling these simulations experimental synthesis and assays allows us to shorten the time between design cycles and increase the fraction of desirable compounds made. This gives STX a significant advantage both in the accuracy with which it can solve extremely difficult biochemical problems and in the speed.

Our scientific leadership team has published seminal papers in the field of computer-aided drug design related to the above topics, with an emphasis on rigorous all-atom simulations to compute binding affinity, selectivity, water thermodynamics, and virtual screening. The below publications highlight our work and approach.



Binding Affinity

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of modern free-energy calculation protocol and force field

--L Wang et al., J. Am.
Chem. Soc., 137 (7), 2695-2703, 2015

Accurate binding free energy predictions in fragment optimization.

--TB Steinbrecher, et al., J.
Chem. Inf.  Model., 55 (11), 2411-2420, 2015

Predicting binding affinities for GPCR ligands using free-energy perturbation.

-- EB Lenselink, et al.,
ACS Omega, 1  (2), 293-304, 2016

Relative Binding Free Energy Calculations Apllied to Protein Homology Models.

--D Cappel, ML Hall, EB Lenselink, T Beuming, J Qi, J Bradner, W Sherman,
J. Chem. Inf. Model., 56 (12), 2388-2400, 2016

Water Thermodynamics

Differential water thermodynamics determine PI3K-Beta/Delta selectivity for solvent-exposed ligan modifications.

--D Robinson, et al.,
J. Chem. Inf. Model., 56 (5), 886-894, 2016

Mechanism of the hydrophobic effect in the bio-molecular recognition of aryl-sulfonamides by carbonic anhydrase

--PW Snyder, et al.,
Proc. Nat. Acad. Sci., 108 (44), 17889-17894, 2011

Water networks contribute to enthalpy.entropy compensation in protein-ligand binding.

--B Breiten, et al.
J. Am. Chem. Soc., 135 (41), 15579-15584, 2013

RInteractions between Hofmeister anions and the binding pocket of a protein.

-- JM Fox, et al.,
J. Am. Chem. Soc., 137 (11), 3859-3866 2015

Thermodynamic analysis of water molecules at the surface of proteins and applications to bind site prediction and characterization.

-- T Beuming, Y Che, R Abel, B Kim, V Shanmugasundaram, W Sherman,
Prot. Struct. Funct, Bioinf., 80 (3), 871-883, 2012

High-energy water sites determine peptide binding affinity and specificity of PDZ domains.

-- T Beuming, R Farid, W Sherman,
Prot. Sci., 18 (8), 1609-1619, 2009

Hydration site thermodynamics explain SARs for triazolypurines analogues binding to the A2A receptor.

-- C Higgs, T Beuming, W Sherman,
ACS Med. Chem. Lett., 1 (4), 160-164, 2010


Binding Selectivity

Novel method for probing the specificity binding profile of ligands: applications to HIV Protease.

-- W Sherman, B Tidor,
Chem. Bio. Drug Des., 71 (5), 387-407, 2006

Rational approaches to improving selectivity in drug design.

-- DJ Huggins, W Sherman, B Tidor,
J. Med. Chem., 55(4), 1424-1444, 2012

Understanding kinase selectivity through energetic analysis of binding site waters.

-- DD Robinson, W Sherman, R  Farid,
ChemMedChem, 5 (4), 618-627, 2010

Solvation Free Energy Calculations

Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field.

--D Shivakumar, J Williams, Y Wu, W Damm, J Shelley, W Sherman,
J. Chem. Theory Comput., 6 (5), 1509-1519, 2010

Improving the prediction of absolute solvation free energies using the next generation OPLS force field.

-- D Shivakumar, E Harder, W Damm, RA Friesnerm, W Sherman,
J. Chem. Theory Comput., 8 (8), 2553-2558, 2012

Virtual Screening and Drug Design

Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering.

-- DJ Osguthorpe, W Sherman, AT Hagler,
Chem. Bio. Drug Des., 80 (2), 182-193, 2012

Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols.

-- DJ Osguthorpe, W Sherman, AT Hagler,
J. Phys. Chem. B, 116 (23), 6952-6959, 2012

Boosting virtual screening enrichment with data fusion: coalescing hits from two-dimensional fingerprints, shape, and docking.

-- GM Sastry, VSS Inakollu, W Sherman,
J. Chem. Inf. Model., 53 (7), 1531-1542. 2013

Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.

-- EB Lenselink, T Beuming, W Sherman, HWT van Vlikmen, AP Ijzerman,
J. Chem. Inf. Model., 54 (6), 1737-1746, 2014

 Discovery of furan carboxylate derivatives as novel inhibitors of ATP-citrate lyase via virtual high-throughput screening.

--Jernigan FE, Hanai J, Sukhatme VP, Sun L, Bioorg. Med. Chem. Lett. 27 (4), 929-935, 2017

 Design and synthesis of emodin derivatives as novel inhibitors of ATP-citrate lyase. 

--Koerner SK, Hanai J, Bai S, Jernigan FE, Oki M, Komaba C, Shuto E, Sukhatme VP, Sun L, Eur. J. Med. Chem. 126, 920-928, 2017

Glycopeptide analogues of PSGL-1 inhibit P-selectin in vitro and in vivo.

 ---Krishnamurthy VR, et al. Nat. Commun. 6, 6387, 2015

Ganetespib, a unique triazolone-containing Hsp90 inhibitor, exhibits potent antitumor activity and a superior safety profile for cancer therapy.

--Ying W, et al. Mol. Cancer Ther. 11, 475, 2012.