SDSC Researchers Develop Potential COVID-19 Protease Inhibitors

April 16, 2020

April 16, 2020 — San Diego Supercomputer Center (SDSC) researchers Valentina Kouznetsova and Igor Tsigelny recently created a pharmacophore model and conducted data mining of the conformational database of FDA-approved drugs that identifies 64 compounds as potential inhibitors of the COVID-19 protease. Among the selected compounds are two HIV protease inhibitors, two hepatitis C protease inhibitors, and three drugs that have already shown positive results in testing with COVID-19.

This image illustrates azithromycin in the pharmacophore model of a potential protease inhibitor. The model contains nine functional centers: two donors, two acceptors, one donor/acceptor center, and three hydrophobic centers. Image courtesy of V. Kouznetsova, I. Tsigelny, D. Huang, San Diego Supercomputer Center/UC San Diego.

The conformations of these compounds underwent three-dimensional fingerprint similarity clusterization. The researchers also conducted docking of possible conformers of these drugs to the binding pocket of protease and then conducted the same docking of random compounds.

“This cocktail of inhibitors could help save thousands of lives,” said Tsigelny. “We have now published our findings with Chemrxiv so that we can move on with proper testing that would next allow this concept to be utilized during the current pandemic crisis.”

“There are several lines of defense when a virus like this attacks the organism and one of them is the siege of the fortress of the cell with a virus – there are inhibitors and antibodies that prevent COVID-19 to bind a receptor ACE2 to infuse to the human cell,” explained Kouznetsova. “To help visualize this, it is as if people on the fortress moor are throwing cobblestones and pouring hot tar on the heads of enemies. The second line of defense is when the enemies arrive and hand-to-hand combat begins. This latter line is what protease inhibitors do – they don’t allow the virus to produce needed viral proteins for a further attack.”

Tsigelny further explained that the main point of this study is elucidation of FDA-approved drugs that can be immediately tried and used on patients – and avenue supported by other COVID-19 research.

“The possibility that existing drugs could be useful immediately for countering this infection is a very important topic,” said Roberto Burioni, a professor of microbiology and virology at Milan’s Vita-Salute San Raffaele University and author of the recently released Virus: The Great Challenge: From Coronavirus to the Plague: How Science Can Save Mankind. “To fight an epidemic you need speed and strategy. The later the reaction, the more likely the defeat.”

In addition to their positions at SDSC, Tsigelny, and Kouznetsova are also affiliated with UC San Diego’s Moores Cancer Center. Tsigelny is also affiliated with the UC San Diego Department of Neurosciences and CureMatch, Inc. High school student David Huang, a participant in SDSC’s Research Experience for High School Students (REHS) program, conducted the computational docking.

About SDSC

As an Organized Unit of the University of California San Diego, SDSC is considered a leader in data-intensive computing and cyberinfrastructure, providing resources, services, and expertise to the national research community, including industry and academia. Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics, and health IT. SDSC’s petascale Comet supercomputer is a key resource within the National Science Foundation’s XSEDE (Extreme Science and Engineering Discovery Environment) program.

About CureMatch

Tsigelny, along with his work at UC San Diego, is the Chief Science Officer and co-founder of CureMatch, Inc., a company which provides decision support for doctors in personalized cancer medicine. With 4.5 million possibilities to combine around 300 FDA-approved cancer drugs, CureMatch targets multiple cancer mutations at the same time and determines the best combination treatment for each patient. The company also intends to propose new treatments for coronavirus patients.


Source: Kimberly Mann Bruch, The University of California San Diego

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industry updates delivered to you every week!

A Big Memory Nvidia GH200 Next to Your Desk: Closer Than You Think

February 22, 2024

Students of the microprocessor may recall that the original 8086/8088 processors did not have floating point units. The motherboard often had an extra socket for an optional 8087 math coprocessor. The math coprocessor ma Read more…

IonQ Reports Advance on Path to Networked Quantum Computing

February 22, 2024

IonQ reported reaching a milestone in its efforts to use entangled photon-ion connectivity to scale its quantum computers. IonQ’s quantum computers are based on trapped ions which feature long coherence times and qubit Read more…

Apple Rolls out Post Quantum Security for iOS

February 21, 2024

Think implementing so-called Post Quantum Cryptography (PQC) isn't important because quantum computers able to decrypt current RSA codes don’t yet exist? Not Apple. Today the consumer electronics giant started rolling Read more…

GenAI Having Major Impact on Data Culture, Survey Says

February 21, 2024

While 2023 was the year of GenAI, the adoption rates for GenAI did not match expectations. Most organizations are continuing to invest in GenAI but are yet to derive any substantial value from it. However, the GenAI hyp Read more…

QED-C Issues New Quantum Benchmarking Paper

February 20, 2024

The Quantum Economic Development Consortium last week released a new paper on benchmarking – Quantum Algorithm Exploration using Application-Oriented Performance Benchmarks – that builds on earlier work and is an eff Read more…

AWS Solution Channel

Shutterstock 2283618597

Deep-dive into Ansys Fluent performance on Ansys Gateway powered by AWS

Today, we’re going to deep-dive into the performance and associated cost of running computational fluid dynamics (CFD) simulations on AWS using Ansys Fluent through the Ansys Gateway powered by AWS (or just “Ansys Gateway” for the rest of this post). Read more…

Atom Computing Reports Advance in Scaling Up Neutral Atom Qubit Arrays

February 15, 2024

The scale-up challenge facing quantum computing (QC) is daunting and varied. It’s commonly held that 1 million qubits (or more) will be needed to deliver practical fault tolerant QC. It’s also a varied challenge beca Read more…

A Big Memory Nvidia GH200 Next to Your Desk: Closer Than You Think

February 22, 2024

Students of the microprocessor may recall that the original 8086/8088 processors did not have floating point units. The motherboard often had an extra socket fo Read more…

Apple Rolls out Post Quantum Security for iOS

February 21, 2024

Think implementing so-called Post Quantum Cryptography (PQC) isn't important because quantum computers able to decrypt current RSA codes don’t yet exist? Not Read more…

QED-C Issues New Quantum Benchmarking Paper

February 20, 2024

The Quantum Economic Development Consortium last week released a new paper on benchmarking – Quantum Algorithm Exploration using Application-Oriented Performa Read more…

The Pulse of HPC: Tracking 4.5 Million Heartbeats of 3D Coronary Flow

February 15, 2024

Working in Duke University's Randles Lab, Cyrus Tanade, a National Science Foundation graduate student fellow and Ph.D. candidate in biomedical engineering, is Read more…

It Doesn’t Get Much SWEETER: The Winter HPC Computing Festival in Corpus Christi

February 14, 2024

(Main Photo by Visit Corpus Christi CrowdRiff) Texas A&M University's High-Performance Research Computing (HPRC) team hosted the "SWEETER Winter Comput Read more…

Q-Roundup: Diraq’s War Chest, DARPA’s Bet on Topological Qubits, Citi/Classiq Explore Optimization, WEF’s Quantum Blueprint

February 13, 2024

Yesterday, Australian start-up Diraq added $15 million to its war chest (now $120 million) to build a fault tolerant computer based on quantum dots. Last week D Read more…

2024 Winter Classic: Razor Thin Margins in HPL/HPCG

February 12, 2024

The first task for the 11 teams in the 2024 Winter Classic student cluster competition was to run and optimize the LINPACK and HPCG benchmarks. As usual, the Read more…

2024 Winter Classic: We’re Back!

February 9, 2024

The fourth edition of the Winter Classic Invitational Student Cluster Competition is up and running. This year, we have 11 teams of eager students representin Read more…

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

Leading Solution Providers

Contributors

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire