we’re joined by Dr. Andrey Kovalevsky, Senior Scientist in Structural Biology & Biochemistry at Oak Ridge National Laboratory. Andrey and his team used neutrons and x-rays to map part of the internal structure of the coronavirus to create an accurate 3-D model. Specifically, the scientists mapped the main protease (Mpro), an enzyme involved in the virus replication, to which they had added a preliminary small molecule discovered using high-speed computer screening and virtual reality (VR). Using the MedChem tool in Nanome to look at the enzyme model, the scientists virtually constructed different small molecules by modifying their structures to see if any newly designed compounds could fit, or bind, to a key site on the Mpro enzyme surface. A strong enough binding could inhibit, or block, the enzyme from functioning, which is vital to stopping the virus from multiplying in patients with COVID-19.

References:

Kneller et al. (2021). Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. J. Med. Chem. 64, 8, 4991–5000.
DOI: 10.1021/acs.jmedchem.1c01475

https://neutrons.ornl.gov/content/jou...

https://www.pfizer.com/news/press-rel...

https://www.rcsb.org/structure/7SI9

VIVE Focus 3 gets Facial Tracker, and Eye Tracker

https://blog.vive.com/us/vive-focus-3-gets-facial-tracker-and-eye-tracker/?utm_source=blog&utm_medium=social+media&utm_campaign=vive_focus_3_gets_facial_tracker_and_eye_tracker

Meta Connect will be a virtual event starting on October 11, 2022

https://www.metaconnect.com/en-us

Parsing natural speech and writing to specific commands by using GPT3 -and it's all web! 

https://youtu.be/IrOUyazOzHk

The Merge: Ethereum upgrade Bellatrix is live, what comes next? 

https://www.theblock.co/post/166799/the-merge-ethereum-upgrade-bellatrix-is-live-what-comes-next

What exascale computing could mean for chemistry

https://cen.acs.org/physical-chemistry/computational-chemistry/exascale-computing-mean-chemistry/100/i31

Meta accounts - https://www.oculus.com/blog/getting-started-with-meta-accounts/

Sony says the PlayStation VR2 is coming in early 2023 - https://www.theverge.com/2022/8/22/23317342/sony-playstation-ps-vr2-release-date-early-2023

VDP-54.1 Expression of Interest: Pfizer Ventures  https://gov.vitadao.com/t/vdp-54-1-expression-of-interest-pfizer-ventures/832

Discngine Labs: Virtual Reality for Structure-Based Drug Discovery

Ever wondered how Virtual Reality for Drug Design looks like in practice? 

In the second session of our Discngine Labs, they host industry experts Wilian Cortopassi and Dr. Rishi Gupta from Novartis Institutes for BioMedical Research (NIBR) will present the “NIBR”Verse: the multidimensional space that brings together data and peers from all over the world in a single (virtual) place for effective collaborations in structure-based drug design. 

The presentation will be followed by the panel discussion on the current and future opportunities of Virtual Reality for Drug Discovery. Steve McCloskey, from the leading VR software company Nanome, will chair the discussion where industry experts and early adopters will share their thoughts and experiences on the topic.  

Recording with video here: 
https://www.discngine.com/event/2022/06/23/discngine-labs-virtual-reality-for-collaborative-sbdd

Meta is shutting down one of its biggest VR games — but only for Quest 1 owners
https://www.theverge.com/2022/8/7/23295691/meta-quest-1-population-one-shutting-down-biggest-vr-game-virtual-reality-battle-royale

Major chemical database investigates hundreds of suspicious crystal structures
https://www.nature.com/articles/d41586-022-02100-4

New plugins from Nanome
https://blog.matryx.ai/hot-new-plugins-for-hot-new-summer-250ef97a23cb

this week’s topics

• alphafold - ‘The entire protein universe’: AI predicts shape of nearly every known protein
  • https://www.nature.com/articles/d41586-022-02083-2
• Two decades of Alzheimer’s research was based on deliberate fraud by 2 scientists that has cost billions of dollars and millions of lives
  • https://wallstreetpro.com/2022/07/23/two-decades-of-alzheimers-research-was-based-on-deliberate-fraud-by-2-scientists-that-has-cost-billions-of-dollars-and-millions-of-lives/
• 3-Year-Old Conjoined Twins with Fused Brains Separated in Historic Virtual Reality Surgery
  • https://people.com/health/conjoined-twins-with-fused-brains-separated-in-historic-virtual-reality-surgery/?utm_source=facebook&utm_medium=news_tab&mibextid=GwLpAq

Quest 2 prices going up https://twitter.com/metaquestvr/status/1551975828442910720?s=21&t=AYmHwjCEWLEz5BmlblPGxQ

Acquisition is expected to accelerate the development of Ginkgo's innovative horizontal synthetic biology platform Expect integration of Zymergen's... (38 kB)

https://www.prnewswire.com/news-releases/ginkgo-to-acquire-zymergen-301592281.html

@Cadence to acquire OpenEye, combining our molecular modeling software with their leading AI/ML, cloud solutions

https://twitter.com/openeyesoftware/status/1551555197264187394?s=21&t=gXuRIl9uOVivwHyPXPeKNg

• meta facebook login deprecation
  • https://www.oculus.com/blog/meta-accounts/
• Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold
  • https://www.science.org/doi/10.1126/science.abm9326

Dr. Michael Kuiper, a bio-molecular modeler at an Australian government research lab (Data61/CSIRO), is using Nanome & VR to analyze and help against the fight with the Coronavirus (COVID-19). 
Dr. Kuiper’s colleagues at CSIRO are working on a vaccine at Geelong, and also some diagnostics at VIDRL (Victorian Infectious Diseases Reference Laboratory). Dr. Kuiper is generating models and analyzing molecular simulations in Nanome that could help gain insights into potential vaccines. 
Relevant articles/references to info above:
https://www.csiro.au/en/News/News-releases/2020/CSIRO-scientists-start-work-on-coronavirus
https://www.goldcentralvictoria.com.au/news/current-events/100839-contained-csiro-lab-to-tackle-coronavirus
More info on the corona virus protease: http://pdb101.rcsb.org/motm/242
If you’d like to see the structures in this livestream for yourself, you can load them from within Nanome via the PDB code 6LU7. Nanome is free to download through Oculus, Steam, Sidequest, or nanome.ai/setup

Nanome scientists are joined by Dr. Robert Pearlstein and Dr. Hongbin Wan, of Novartis, who share with us their recent publication on the application of biodynamics theory to characterize the structural dynamics of substrate-induced activation under non-equilibrium conditions. Biodynamics is a first principles multi-scale physics-based theory on the general mechanisms by which cellular functions are conveyed by dynamic multi-molecular/ionic systems and by which molecular and multi-molecular systems are powered by covalent and non-covalent forms of free energy (solvation free energy in the latter case). In this video, we cover the transduction of solvation free energy into dynamic molecular structure and drug-target binding exemplified by COVID Mpro inhibition.

Reference: Wan, H., Aravamuthan, V. & Pearlstein, R. A. Probing the dynamic structure-function and structure-free energy relationships of the corona virus main protease with Biodynamics theory. http://biorxiv.org/lookup/doi/10.1101... (2020) doi:10.1101/2020.07.19.211185.