Inhibition of Coronavirus main protease using natural compounds

This is an ongoing project in collaboration with Dr. Chris Stobart at Butler University. Newly emerging coronaviruses pose a significant public health concern. There have been three new coronaviruses emerge since 2001. While we have developed many treatment options for SARS-CoV 2 (cause of COVID-19), these options may not cross-react with a future emergent coronavirus. This leads to a need for broadly acting antivirals for coronaviruses. Herbal medicines have been used for centuries to treat viral infections. More recently, there have been studies into which components of these preps are exerting these effects. As part of this project, we start by identifying compounds that are in natural products/herbal remedies that have been shown to have antiviral activity against the nsp5 protease of SARS-CoV 2 (and sometimes other human coronaviruses). We test these compounds against the nsp5 protease of 2 human coronaviruses that cause the common cold (HKU-1 and OC-43).  We had previously developed chimeric viruses to study nsp5 proteases from coronaviruses that infected humans in a non-human virus background (Mouse hepatitis virus, MHV).

Testing whether different brew methods alters the antibacterial properties of coffee

There have been studies that show that coffee has antimicrobial properties, but the brew method was not tested. We have tested 8 brew methods including:espresso, french press, pour-over, drip-pot, instant, cold brew, Moka pot, and Keurig brewing methods. Preliminary data showed that brew method did seem to change the antibacterial activity against S. aureus, but we saw no activity against other bacteria tested.

Prevalence of Borrelia burgdorferi in deer ticks on DeSales University campus

Tick borne diseases, caused by microbial infectious agents, are a prominent issue across the state of Pennsylvania. Ticks acquire these pathogens through blood meals of small mammals and transmit them via blood meals of larger hosts such as animals and humans. Tick borne diseases are commonly transmitted in the spring and summer months when these ticks are most active. At DeSales University, pesticide use was decreased and “grow zones” were introduced to improve the environment, however, this has led to an noticeable increase of ticks on campus. In a pilot study, nymph, larva, and adult stage ticks were collected from wooded and grassy areas at DeSales University. The ticks collected are Ixodes scapularis, commonly known as deer ticks, and Dermacentor variabilis, or American dog tick. Ticks were sized and the species identified before performing DNA extraction, PCR, and agarose gel electrophoresis to detect the presence of multiple different microbial infectious agents. These infectious agents include Borrelia burgdorferi, Anaplasma phagocytophilum, Ehrlichiosis chaffeensis, Babesiosia microti, and Rickettsia rickettsii. In the pilot study, 3 ticks tested positive for B. burgdorferi. Expanding the scope of this research to include more tick samples and test for more pathogens will improve the understanding of the likelihood of contracting a tick-borne illness in Pennsylvania and can help determine what proactive measures can be taken to prevent these diseases.  

Tiny Earth – Identifying Novel Antibiotics from Soil Bacteria

The Tiny Earth Project (previously small world initiative) is a nationally run CURE for microbiology. The goal of the project is to isolate bacteria from various soil sources (groups are starting to also branch out from soil) and test for the production of novel antibiotics. Antibiotic resistance is of major global health concern and pharmaceutical companies do not prioritize identifying new antibiotics. The Tiny Earth project is basically using crowd sourcing to identify new antibiotics. This CURE is also used in the Medical Microbiology lab.

Antibacterial properties of skunk cabbage

In collaborated with Dr. Fan Mayville we performed organic extractions of the skunk cabbage plant with the goal of testing for antimicrobial activity. We are currently testing these extracts for antibacterial activity against the ESKAPE pathogens.

Phylogenetic signature of gut microbiomes in 6 Pennsylvania bat species

In the summer of 2023, we started the collaborated with the Pennsylvania Bat Rescue to collect fecal samples from bats at the rescue. One of the things we wanted was to get samples before bats were treated with antibiotics.  Throughout the 2024-2025 academic year, we got multiple samples from 3 of the 6 bat species. We have samples ready to submit for sequencing but will need more samples from the other species to do the analysis we want. Austin presented this work internally at the Sciences poster session. We hope to continue this collaboration in the future.

Coronavirus Evasion of Innate Immunity

When a virus enters a host cell it can be sensed by pattern recognition receptors (PRRs) that sensed conserved features of a virus called a pathogen associated molecular pattern (PAMP). For RNA viruses, this is often double stranded RNA, in the form of a replication intermediate or a structured region of the viral genome. Activation of PRRs lead to downstream signaling that induces type I interferons (IFNs)  (Fig. 1 A and C) that can then activate the IFN-response pathway (Fig. 1 B) to induces hundreds of IFN-stimulated genes, which can have direct antiviral properties.  As innate immunity is the first line of defense against viruses, they have evolved several strategies to evade sensing by the host cell. One mechanism that is commonly used is cleavage of host innate immune proteins by viral proteases. The most well studied is the HCV protease complex, NS3/4A, cleavage of MAVS, an innate immune adaptor protein. There has been limited study of Coronavirus cleavage of host innate immune proteins by the viral protease 3Cysteine-like protease (3CLpro, nsp5).  It is known that two porcine coronaviruses use the 3CLpro to cleave NEMO, an NF-kB inhibitor protein, but other host targets have not been studied. Our research focuses on testing whether the coronavirus 3CLpro is involved in innate immune evasion,  cleaves predicted host targets within the innate immune pathways, and whether there are host species differences in the ability of 3CLpro to cleave the target protein. 

Coronavirus genomes contains ~10 open reading frames (ORFs). The first 2 overlapping ORFs (ORF1a and ORF1an) encode the nonstructural proteins (nsps) and the remaining ORFs encode structural and accessory proteins. There are 16 nsps that are translated into 2 large polyproteins. The individual proteins are then cleaved by viral proteases (nsp3 and nsp5) to generate mature proteins. Nsp5 is responsible for 11 cleavages (dark grey arrow heads). Projects in the Beachboard lab will focus on the role of nsp5 in evading host innate immunity.