2 weeks ago

Baudry Lab finds 125 naturally occurring compounds with potential against COVID-19

The Baudry Lab at The University of Alabama in Huntsville (UAH) has identified 125 naturally occurring compounds that have a computational potential for efficacy against the COVID-19 virus from the first batch of 50,000 rapidly assessed by a supercomputer.

It’s the first time a supercomputer has been used to assess the treatment efficacy of naturally occurring compounds against the proteins made by COVID-19. Located in UAH’s Shelby Center for Science and Technology, the lab is searching for potential precursors to drugs that will help combat the global pandemic using the Hewlett Packard Enterprise (HPE) Cray Sentinel supercomputer.

The UAH team is led by molecular biophysicist Dr. Jerome Baudry (pronounced Bō-dre), the Mrs. Pei-Ling Chan Chair in the Department of Biological Sciences. Dr. Baudry is video blogging about his COVID-19 research journey using HPE’s Cray Sentinel system. His research is in collaboration with the National Center for Natural Products Research at the University of Mississippi School of Pharmacy and HPE.

“We have used supercomputers to predict natural products most likely to bind to three proteins of the SARS-CoV-2 virus,” says Dr. Baudry. SARS-CoV-2 is the scientific name for COVID-19.

“Out of the 50,000 natural products that we have looked at using supercomputers, we find several hundred to be predicted to be potentially binding on the proteins of interest,” he says.

“We further found 125 – but there may be more – that are particularly interesting because they bind right where we want to, they are not too big, not too small and they have the chemical profiles of pharmaceuticals.”

There are many diverse natural sources for the chemicals of interest, Dr. Baudry says.

“Many are from relatively common medicinal plants that can be found in the U.S., and many are from more distant plants from Southeast Asia and South America, as well as from some ground and oceanic bacteria strains and fungi.”

Promising compounds will undergo a computational technique called pharmacophore analysis to find what the chemicals have in common and flag chemical features important for future research.

The next phase for the compounds is in vitro testing by a partner laboratory that will use live virus and live cells. Those chemical molecules found most efficacious will form the basis for future drug research and development processes that include testing for efficacy, tolerance and adverse effects in human trials. That process might also include chemical modifications to make the drug more efficient, better tolerated or both.

“Maybe we will need a cocktail of drugs, as is the case in many anti-AIDS treatments. But every drug that ends up surviving this long and winding road of development and testing starts as a hit that binds to a protein. It is this initial event that we are modeling here using supercomputers,” Dr. Baudry says.

“Normally it would take a very long time and a lot of money to achieve that, but with the supercomputers we can perform this initial hit discovery step much faster and cheaper,” he says. “Everything is being accelerated for COVID-19, so the whole process that can take up to a decade may end up being shorter here.”

More batches are being prepared for supercomputer testing, according to Baudry Lab researcher Dr. Kendall Byler, who is running the calculations on Sentinel. Dr. Byler is highly experienced in using computational approaches for natural product research.

“Actually, there are over 400,000 compounds we’d like to test,” Dr. Byler says.

Blocking proteins

In the initial batch, naturally occurring compounds were found that seem likely to bind to two important proteins, COVID-19’s papain-like protease, or PLpro, and the main protease, or Mpro. The proteins are enzymes from the virus’ genome that are responsible for processing all the virus’ proteins in infected cells. Infected cells are forced to manufacture them so that the virus can replicate.“If we can block these viral proteins from self-assembling and performing their functions inside the cell, we may not have been able to save that one infected cell, but we will prevent the virus from replicating and it will die with that cell,” Dr. Baudry says. “If we find a chemical that ‘sticks’ in these reactive regions of the proteins, the processing reactions will not be possible anymore and we will stop the infected cells from making and releasing more virus.”

The third protein of interest is COVID-19’s spike protein, which is how the virus attaches itself to a cell to initiate the infection process. This spike protein is present on the surface of the virus and gives the virus its characteristic crown-like (corona in Latin) appearance. It binds to a protein called ACE2 on the cell surface to begin the infection process.

“We are trying to find chemicals that would bind on the surface of the virus’ spike protein and prevent it from locking itself with the cell’s ACE2,” Dr. Baudry says.

In the initial batch modeled, scientists found the interactions of 24 compounds interesting in the spike protein, 41 molecules interesting in the main protein and 60 compounds interesting in the PL-pro protein.

“We can then have a good idea of what the natural products exhibit that makes them successful in these different proteins, and that is the starting point for screening larger databases of millions of chemicals much faster, helping chemists to synthesize novel molecules down the road, maybe more potent and more selective than the original natural products against these proteins,” Dr. Baudry says.

AI and ancient knowledge

Located in a Microsoft Azure data center in Texas, the Sentinel supercomputer makes the work more rapid than ever before possible and an HPE team is helping facilitate it. Dr. Baudry’s UAH team has access to Sentinel’s powerful capabilities through the cloud with Microsoft Azure.

Sentinel, which features HPE’s Cray XC50 end-to-end high-performance computing (HPC) system, is capable of computing 147 trillion floating point operations per second and can store 830,000 gigabytes of data.

Sentinel helps to cut compound testing time from months or even years to weeks, Dr. Baudry says. The supercomputer is as fast as the Earth’s entire population doing 20,000 calculations every second and has storage capacity for more than 45 years of high definition video.

The fight to prevent COVID-19’s sometimes devastating health consequences has created a new meeting of modern high-capacity artificial intelligence with humankind’s most ancient healing knowledge, Dr. Baudry says.

“Even five years ago, this would not have been possible,” he says. “It is fortunate for us that this kind of very advanced, very rapid computational power is available at this time when we need it so much.”

At UAH, the Baudry Lab collaborates on machine learning and big data in drug discovery with the laboratory of Dr. Vineetha Menon, an assistant professor of computer science.

The lab also collaborates in a separate COVID-19 compound search led by Oak Ridge National Laboratory (ORNL) in Tennessee and is working with the Alabama Supercomputer Center on COVID treatment compound research.

(Courtesy of UAH)

15 hours ago

Brooks: ‘I oppose the Socialist Democrat and racist efforts to deface and destroy Mount Rushmore’

Count Congressman Mo Brooks (AL-05) as a steadfast supporter of Mount Rushmore.

Ahead of President Donald Trump’s planned Friday trip to the national memorial in South Dakota for a pre-Independence Day fireworks show and patriotic tribute, Brooks released a statement emphasizing his cosponsorship of H.R. 7358.

This bill, known as the Mount Rushmore Protection Act, was authored by Congressman Dusty Johnson (R-SD) and would prohibit federal funds from being used to alter, change, destroy or remove, in whole or in part, any name, face or other feature on the namesake memorial.

Liberal organizations in recent days have begun to target Mount Rushmore, with the Democratic National Committee even claiming the monument is “glorifying white supremacy.”

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Brooks pushed back on this, saying, “Thomas Jefferson, George Washington, Teddy Roosevelt, and Abraham Lincoln are exceptional American heroes. Each contributed monumentally to America’s greatness and share a common legacy of spreading freedom and liberty throughout the world. Their places on Mount Rushmore are well-deserved as exemplars of what it took to make America great, and efforts to denigrate their contributions are beyond reprehensible.”

The North Alabama Republican also outlined the contributions of each American icon memorialized on Mount Rushmore.

“Thomas Jefferson drafted the Declaration of Independence, the document that officially kicked off America’s quest for independence,” he continued. “George Washington won the Revolutionary War, served as America’s first president, and set the high standards of honor and leadership that have molded the republic to this day. Teddy Roosevelt protected America’s beautiful and special lands for public enjoyment forever. Abraham Lincoln held our young nation together through the most tumultuous period in American history, freed the slaves and gave his life perfecting of union. These men represent the best of us. Generations of Americans have celebrated their contributions to our nation. They embody American exceptionalism, freedom and liberty.”

Brooks said this issue exemplifies larger societal issues that are ongoing in America.

“With the exception of the Civil War, America has never faced greater internal threats,” the congressman warned.

“Socialist Democrats and racists, as evidenced by a recent Democrat National Committee tweet that said Mount Rushmore is ‘glorifying white supremacy’, are dead set on undermining American’s freedom and liberty,” Brooks continued. “In a frenzy of delirious ‘wokeness’, Socialist Democrats and those who promote racial division are hellbent on destroying the very fabric of our republic.”

“I oppose the Socialist Democrat and racist efforts to deface and destroy Mount Rushmore,” he stressed to conclude his statement.

Sean Ross is the editor of Yellowhammer News. You can follow him on Twitter @sean_yhn

17 hours ago

Auburn University gets $3 million grant to increase innovative conservation practices

AUBURN, Ala. – Auburn University College of Agriculture research and extension faculty will be using a $3 million grant to help forge a future for Alabama agriculture by encouraging the use of innovative conservation practices among the state’s row crop farmers.

The grant comes from the USDA Natural Resources Conservation Service (NRCS) On-Farm Conservation Innovation Trials (On-Farm Trials), a new component of the Conservation Innovation Grants first authorized in the 2018 Farm Bill.

Auburn’s $3 million grant is the largest to a single entity of the more than $24 million awarded. The grants are designed to help partners implement and evaluate innovative approaches that have demonstrated conservation benefits on farmland.

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These conservation practices are sorely needed on Alabama farms for several reasons, said Rishi Prasad, assistant professor and Alabama Extension specialist in the Department of Crop, Soil and Environmental Sciences and leader of the research project.

“Many soils in Alabama are severely degraded and have low organic matter content,” Prasad said. “It is important to rebuild soil health to conserve soil for use by future generations. Increased adoption of cover crops by Alabama farmers can create sustainable row-crop production systems while protecting the state’s soil and water resources.”

Another aspect of the grant will be the demonstration of water-smart irrigation practices, he said.

“Summer droughts in Alabama are very common, often causing yield losses,” Prasad said. “The adoption of water-smart irrigation in Alabama is considered one of the most important strategies for mitigating the negative impacts of drought. This project will demonstrate the use of these technologies and help increase the adoption of irrigation in Alabama.”

The project also will help farmers evaluate nutrient losses and demonstrate the agronomic, economic and environmental benefits of improved conservation practices compared to farmers’ “business-as-usual” practices, he said.

“Fertilizer is one of the major inputs used in crop production,” Prasad said. “However, more than 50 percent of the purchased fertilizers ends up getting lost in air or water. This project will help farmers evaluate those losses.”

Three Alabama farms have been selected as cooperators for this project: Posey Farms in north Alabama, Lazenby Farms in central Alabama and L.C. Farms in south Alabama. These farms will be used to demonstrate the innovative conservation practices.

“The interesting part of this project is that any farmer who wants to adopt cover crops or smart irrigation technologies will receive incentive payments that include assistance for cover crop seed, planting and termination costs, labor charges and forgone income,” Prasad said. “Farmers also can borrow inter-seeder, roller crimper and soil moisture sensors from selected NRCS offices as a part of this project.”

A network of learning sites will be established at the extension offices located in Lawrence, Geneva and Lee counties, said Audrey Gamble, assistant professor and Alabama Extension specialist in the Department of Crop, Soil and Environmental Sciences, who also is involved in the grant. Project meetings with cooperating farmers and neighboring farmers will be organized, and information on the project will be presented.

“Farmers will be called for face-to-face meetings, dinner meetings, workshops and field days where information on topics related to cover crops, water-smart irrigation strategies, nutrient budgets and nutrient-use efficiencies will be presented,” Gamble said. “As project data becomes available, information will be shared with farmers at learning sites. The project already is underway, and we will be instrumenting these demonstration farms in the fall of 2020.”

For Brenda Ortiz, professor and Alabama Extension specialist in the Department of Crop, Soil and Environmental Sciences, the grant marks the continuation of on-farm irrigation projects she initiated in 2017.

“The important thing about this project is that we will look at the whole system—the impact of cover crops on soil health and soil structure that will impact soil water storage and movement which, in the end, will impact water availability for the crops and improved nutrient and water-use efficiency,” Ortiz said.

While technological changes take time, there is a greater awareness in Alabama now of what technology can do to increase irrigation efficiency, she said.

“Farmers and consultants have gained knowledge on the use of soil sensors for irrigation scheduling, and we have been able to demonstrate the impact of variable-rate irrigation at some sites,” Ortiz said. “However, more work is needed.”

Ortiz hopes the innovation grant will increase the adoption of practices such as irrigation scheduling.

“If we can accomplish this, it will be a great success story and will result in possible environmental and economic benefits,” she said. “The other piece of the puzzle is nutrient management. This project has a strong emphasis on environmental stewardship.”

Leah Duzy of the National Soil Dynamics Laboratory is working on the economic aspects of the grant. Innovation grant awardees are required to evaluate the economic and conservation outcomes from these practices and systems, giving NRCS critical information to inform conservation work in the future. That’s where Michelle Worosz, professor of rural sociology in the Department of Agricultural Economics and Rural Sociology, will play a role in implementing the grant.

“Production agriculture by its very nature is sociological—there is nothing that is not a product of human activity and/or social interaction,” Worosz said. “In the case of our grant, I will examine the conservation-based decision-making processes that take place on the three selected farms. These farms will serve as case studies of technological change, adoption and adaptation.

“I also will observe the extension team as they interact with a broader range of participants during workshops and field days. It is hoped that data from the case studies and the observations can be used by the team to improve conservation technology. In other words, this feedback loop is a means of co-developing knowledge about conservation strategies, particularly smart irrigation and cover cropping.

The grant’s implementation on “real” farms is important to its success, Worosz said.

“Understandably, producers can be quite skeptical of experimental plots on research farms,” she said. “Because research plots are often smaller, they may receive an unrealistic amount or type of care, they may not be subject to the same rules or regulations, the farm manager and researchers might have access to more or different resources such as advanced technologies, the plots are not required to produce the same yields or produce the same return on investment, and they may be located in a place that is not comparable to producers’ farms.”

It’s also important that the conservation technologies will be co-developed by faculty and extension specialists working alongside farmers, Worosz said.

“This is a way to develop a more robust set of bundled technologies—technologies that will be more user-friendly and better able to meet the needs of the user while also meeting larger environmental goals,” she said. “If the user has input, it will help with a broader buy-in of these conservation technologies by other producers.”

(Courtesy of Auburn University)

18 hours ago

Lara Trump: ‘We actually had never confirmed a rally in Alabama’

Senior campaign adviser Lara Trump has rebutted reporting from CNN that the president’s reelection campaign canceled a July 11 rally in Mobile, Alabama.

Trump — who is married to the president’s son, Eric — told Fox News’ Martha MacCallum this week that the rally was never finalized.

Rumors had been swirling in previous weeks that President Donald J. Trump would come to the state to campaign in person for his endorsed Republican Senate candidate, former Auburn University head football coach Tommy Tuberville.

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RELATED: Watch: Trump, Tuberville depart Air Force One together

MacCallum asked Lara Trump if the Alabama rally was canceled and, if so, why it was canceled.

“Well, we actually had never confirmed a rally in Alabama,” she responded. “We never talked about it, never announced anything. So, I’m not sure why everybody got so excited about an Alabama rally.”

The show host then interjected to followed up with, “So there never was an Alabama rally? That’s what you’re saying?”

Shaking her head to indicate a negative response, Trump added, “There was nothing official from the campaign. We never announced anything on that.”

It should be noted that the Tuberville campaign never confirmed the rally, either.

He will face former U.S. Attorney General Jeff Sessions in Alabama’s July 14 Republican primary runoff.

Sean Ross is the editor of Yellowhammer News. You can follow him on Twitter @sean_yhn

22 hours ago

New public pavilion opens at Smith Lake

Anglers and tournament staff now have a shaded place on Smith Lake to host their weigh-ins.

A new public weigh-in pavilion is open at the Lewis Smith Lake Dam boat ramp in Walker County. The pavilion was funded through a partnership between B.A.S.S. and Alabama Power, and constructed with the help of many others.

“Our great partnership with Alabama Power continues with this pavilion,” B.A.S.S. CEO Bruce Akin said. “It was exciting to see this come together, and we look forward to future tournaments that will benefit the local community.”

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New fishing weigh-in pavilion opens on Smith Lake from Alabama NewsCenter on Vimeo.

The pavilion provides shade for fish holding tanks during tournament weigh-ins, which reduces stress and increases survival rates of the fish.

“This facility was designed to make setting up for weigh-ins easier and more efficient for all sizes of tournament organizations,” said B.A.S.S. Conservation Director Gene Gilliland. “Having the pavilion close to the water, the boat ramp and the courtesy docks will improve the survival of fish released following weigh-ins – and that means more bass for everyone to catch in the future.”

Construction began in January and was initially scheduled to be completed by April but was delayed due to the COVID-19 pandemic. Volunteer labor was coordinated by the Union Sportsmen’s Alliance that provided apprentices for all phases of the build.

“The Union Sportsmen’s Alliance was privileged to be a part of this great partnership to benefit local anglers and the community,” said Robert Stroede, conservation manager for the Union Sportsmen’s Alliance. “Our union volunteers donated more than 1,000 hours of their time and trade skills to help make this facility possible and benefit not only the community but also the valuable resources of Smith Lake. Partnerships like this one between corporate, public and nonprofit organizations are now, and will continue to be, a huge asset to the future of conservation.”

The new pavilion is the latest in a growing list of amenities offered at Alabama Power’s 65 public recreation sites. It is the second pavilion Alabama Power and B.A.S.S. have worked together to build. In 2014, B.A.S.S., Alabama Power, the Alabama Department of Conservation and Natural Resources, Shelby County and volunteers from Alabama B.A.S.S. Nation teamed to open a similar weigh-in pavilion at Beeswax Landing on Lay Lake.

“We were thrilled to work with B.A.S.S., the Union Sportsmen’s Alliance, the Alabama Department of Conservation and Natural Resources and the local community to construct this pavilion,” said Zeke Smith, Alabama Power executive vice president of External Affairs. “Not only does this pavilion enhance this access point on Smith Lake, it also helps showcase the state of Alabama’s beautiful waterways.”

The Alabama Department of Conservation and Natural Resources donated engineering expertise to the project, and added a ramp and docks to the nearby boat launch.

“We are very excited about the pavilion and the upgrades we have made to the access point at Smith Dam,” said Alabama Department of Conservation Deputy Commissioner Ed Poolos. “It all works together nicely and will offer a great experience for anyone interested in visiting this beautiful lake.”

Project leaders said the pavilion will boost the Smith Lake community.

“I have been involved with high school fishing for a number of years and the sport is rapidly growing,” said Casey Shelton, business manager, International Brotherhood of Electrical Workers (IBEW) System Council U-19. “This has been a great partnership to see come together and will benefit the local community for years to come.”

Community leaders said the pavilion will attract more fishing tournaments, especially among high schools and amateurs.

“I am pleased to be involved in this project alongside Alabama Power and know that those that enjoy bass fishing, especially high school anglers in our community, will enjoy this pavilion and the facilities,” said Alabama Senate Majority Leader Greg Reed. “This partnership with B.A.S.S., IBEW, Alabama Department of Conservation and Natural Resources, Union Sportsmen’s Alliance and Alabama Power is a wonderful opportunity for Smith Lake and will promote the sport of angling for many years to come.”

“We so appreciate the investment Alabama Power has made in the Smith Lake Dam Pavilion,” added State Rep. Connie Rowe. “For several years this area has been utilized by The Chamber of Commerce of Walker County for fishing tournaments, which bring thousands of visitors and their tax dollars into our area. This pavilion will serve as a hub for those tournaments and other events.”

For up-to-date information about Alabama lakes, download the Smart Lakes app to your smartphone at smartlakes.com. For more information on this or other Alabama Power public recreation sites, visit apcshorelines.com.

(Courtesy of Alabama NewsCenter)

23 hours ago

7 Things: No confirmed ‘coronavirus parties’ in Tuscaloosa, Tuberville’s handling of a 2nd-degree rape case becomes political fodder, Ivey open to changing Confederate holidays and more …

7. Pelosi is just out here ‘trying to save the world’

  • Recently, House Minority Leader Kevin McCarthy (R-CA) criticized House Speaker Nancy Pelosi (D-CA) for not commenting on protestors who have taken to tearing down statues like the one of St. Junipero Serra at the Golden Gate Park in Pelosi’s district.
  • Pelosi said that McCarthy “hasn’t had the faintest idea of our dynamic in our district,” and that she’s “trying to save the world from coronavirus.” Now, as coronavirus cases have increased across the country, the Senate will take up the relief package HEROES Act, which Senate Majority Leader Mitch McConnell (R-KY) has called a “liberal wish list.”

6. Coronavirus cases in Madison County jail, Clanton mayor also positive

  • In Madison County, an employee at the jail has tested positive for the coronavirus, which is the first case at the facility, and Madison County Sheriff Kevin Turner has said that they are taking “precautions” within the facility “concerning the affected employee’s contact with the inmates prior to the positive test result.”
  • Mayor Billy Joe Driver in Clanton has also tested positive for the coronavirus and is currently at St. Vincent’s Birmingham for treatment. At 84-years-old, the mayor is at higher risk regarding the virus.
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5. More than 1,100 coronavirus cases in one day

  • The Alabama Department of Public Health has added 1,162 coronavirus cases in the state in just one day. There were also 22 more hospitalizations bringing the total currently to 797, and there were 14 people who died, bringing total deaths to 961.
  • Ten counties have 57% of the new cases, which includes Mobile, Madison, Jefferson, Tuscaloosa, Marshall, Morgan, Baldwin, DeKalb and Montgomery counties. There were 5,788 tests conducted across the state in one day.

4. Record jobs numbers as economy continue to recover

  • The headlines screamed of June numbers far better than the experts expected. Much to MSNBC’s Rachel Maddow’s chagrin, there were 4.8 million jobs created and an unemployment rate that fell to 11.1%, with President Donald Trump saying, “Today’s announcement proves that our economy is roaring back. It’s coming back extremely strong.”
  • But tens of millions are still out of work as the American economy continues to reel from the effects of rising coronavirus numbers and a patchwork of economic lockdowns that seem to be increasing in number again.

3. Ivey open to making changes

  • Governor Kay Ivey’s spokesperson Gina Maiola said that “Ivey is certainly open to the discussion” of changing Confederate holidays, but those decisions have to go “through the Legislature.”
  • Maiola added that Ivey “believes that while we cannot change the past or erase our history, she is confident that we can build a future that values the worth of each and every citizen,” and the holidays in question would be Robert E. Lee’s birthday, Confederate Memorial Day and Jefferson Davis Day.

2. Tuberville attacked for his handling of a player’s rape case from Auburn

  • With less than two weeks to go before the run-off for the Republican U.S. Senate nomination, voters are starting to see what type of attacks former Auburn football coach Tommy Tuberville could see in November from U.S. Senator Doug Jones and the media.
  • The attack stems from the 1999 season when wide receiver Clifton Robinson received a one-game suspension after pleading guilty to contributing to the delinquency of a minor (a misdemeanor) as a plea deal following being charged with the second-degree rape of a 15-year-old girl. Robinson would later be arrested on assault charges and subsequently convicted for the battery of an off-duty police officer years after leaving Auburn.

1. No, there were not coronavirus parties in Tuscaloosa

  • A Tuscaloosa City councilwoman repeated a stupid rumor that students at Alabama colleges and universities were hosting parties with bowls full of money as prizes for getting the coronavirus, and the national media ran with the story as if it was fact, but don’t expect a retraction.
  • There is obviously no evidence that any such events actually took place — not a single Facebook post, tweet or Instagram story supports this narrative, but the narrative was helpful for the media and the desires for a mandatory mask ordinance from Tuscaloosa’s leaders.