t typically takes many years of experiments to develop a new medicine. Although vaccines to protect against disease from the novel coronavirus are starting to reach clinics around the world, patients and doctors will still need treatments to manage COVID-19 symptoms for some time.
At Pacific Northwest National Laboratory (PNNL), computational biologists, structural biologists, and analytical chemists are using their expertise to safely accelerate the design step of the COVID-19 drug discovery process.
Rather than finding a new drug by trial and error, scientists are taking the three-dimensional structures of proteins from the novel coronavirus and using computer modeling and machine learning to identify a unique molecule that best fits inside a binding pocket on a protein’s surface. Ideally, that molecule clogs the viral protein and prevents it from functioning.
“Drug research and development is a complex, costly, and time-consuming process, particularly considering the majority of molecules advanced from the design phase fail in clinical trials,” said PNNL computational data scientist Neeraj Kumar. “Computer-based screening incorporates chemical information during the design process to increase a drug candidate’s potential for success in clinical testing.”
Developing an approach to speed drug discovery during this pandemic could also reveal new design steps that might be useful during the next outbreak.
Clogging coronavirus proteins
There are almost 30 different proteins in this novel coronavirus that are potential targets for COVID-19 drug discovery. Combine that with millions of molecules that are potential drug candidates, and the possibilities for matching molecules to specific proteins are mind-boggling.
To narrow the options towards molecules with potential to become medicines, Kumar and his team first use molecular docking to virtually screen libraries of known molecules and regulatory-approved drugs. Ones that fit in the binding pocket of a particular coronavirus protein make the short list for the next step of the process: testing the fit with actual proteins and molecules.
Experimental scientists then combine the molecules on this short list with purified coronavirus protein and “weigh them” with native mass spectrometry to see if the protein picked up the molecule. This technique measures interactions between the protein and the molecules and can confirm the predicted binding.
Image Credit: Timothy Holland | Pacific Northwest National Laboratory
A new type of ultra-efficient, nano-thin material could advance self-powered electronics, wearable technologies and even deliver pacemakers powered by heart beats. The flexible and printable piezoelectric material, which can convert mechanical pressure into electrical energy, [...]
For about one in 13 children in the U.S., normally harmless foodstuffs such as milk, eggs and peanuts can send the body's natural defenses into overdrive. Symptoms of food allergies can vary widely, but at [...]
Frank Boehm (Nanoapps Medical Inc. Founder) has contributed to 'Platelet-Rich Plasma Applications for Achilles Tendon Repair: A Bridge between Biology and Surgery', published by International Journal of Molecular Sciences/ MDP. Abstract: Achilles tendon ruptures [...]
Using both mouse and human brain tissue, researchers at Yale School of Medicine have discovered that SARS-CoV-2 can directly infect the central nervous system and have begun to unravel some of the virus’s effects on [...]
A deep learning algorithm developed at MIT has discovered new antibiotics that can treat drug-resistant diseases by killing 35 powerful bacteria. The pathogens that the halicin antibiotic has targetted include Acinetobacter baumannii, which was nicknamed [...]
In our transforming world, digital technology has the critical mass to push our frontiers and release unlimited potential. As the wave of digital transformation soars high, improving our lives, industries and economies, we must not [...]
Scientists Discover a Way to Control the Immune System’s “Natural Killer” Cells With “Invisible” Stem Cells
UC San Francisco scientists have discovered a new way to control the immune system’s “natural killer” (NK) cells, a finding with implications for novel cell therapies and tissue implants that can evade immune rejection. The [...]
A team led by scientists at Georgia State University simulates the precise transition between the processes of DNA synthesis and proofreading DNA replication is one of the most important processes in biology, responsible for ensuring [...]
Everybody loves Neandertals, those big-brained brutes we supposedly outcompeted and ultimately replaced using our sharp tongues and quick, delicate minds. But did we really, though? Is it mathematically possible that we could yet be them, [...]
From a small discovery to producing at scale, photojournalist David Levene documents the groundbreaking work of the scientists of Oxford University during the development of a vaccine which is now poised for approval by medicines regulators. [...]
Optical tweezers are a rapidly growing technology, and have opened up a wide variety of research applications in recent years. The devices operate by trapping particles at the focal points of tightly focused laser beams, [...]
In what is believed to be a medical first, researchers from Johns Hopkins Medicine (JHM) and the Johns Hopkins University Applied Physics Laboratory (APL) have enabled a quadriplegic man to control a pair of prosthetic [...]