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Scientists at The Wistar Institute Discover Novel Series of SARS-CoV-2 Mpro Inhibitors for Potential New COVID-19 Treatments

PRESS RELEASE

PHILADELPHIA — (Oct. 8, 2024) — New research from The Wistar Institute’s Salvino lab — led by professor Joseph Salvino, Ph.D. — has identified a novel series of SARS-CoV-2 Mpro inhibitors that may lead to potential new COVID-19 treatments that, according to preclinical testing, effectively inhibits COVID-19 and synergizes with existing anti-COVID therapies. Their new discovery is detailed in the paper, “Design of novel and highly selective SARS-CoV-2 main protease inhibitors,” published in the journal Antimicrobial Agents and Chemotherapy.

Despite effective vaccines approved for use worldwide, COVID-19 continues to contribute to mortality and morbidity — an issue compounded by the problems of vaccine & therapy access. However, the existing drug designs in use for COVID-19 therapy lend themselves to drug interactions and the risk of incomplete viral inhibition.

To address this problem, Salvino — a medicinal chemist at Wistar — led a drug discovery team with the goal of improving upon the existing Mpro inhibitor design, an approach to viral therapy that seeks to prevent both viral replication and mutation-based drug resistance by targeting a component of the virus that regulates its ability to spread. And because Mpro is not an easy-to-mutate biological feature like a spike protein, inhibiting Mpro can help retain antiviral effectiveness even between different variations.

The team used a drug discovery technique that applied an “acyloxymethyl ketone electrophilic warhead” — in essence, a molecule designed to identify the important binding regions that a drug candidate compound would interact with. Using their drug discovery process, Salvino and the team identified a novel series of Mpro inhibitors with greater selectivity — that is, more reliable at producing an inhibitory effect — than the existing Mpro inhibitor for COVID-19 on the market.

The group’s novel compounds successfully inhibited viral replication in vitro against three different COVID variants, including within lung tissue. The compound also synergized (i.e., achieved greater-than-the-sum-of-its-parts strength) with other existing antivirals in fighting the virus. In the preclinical testing, no apparent toxicities were observed — a positive indication of the compound’s safety.

“We’re very excited to have identified such a promising new pathway for developing future therapies,” said Salvino. “As we continue to refine the chemistry through further testing and optimization, we look forward to achieving improved potency in anti-coronaviral therapies.”

Co-authors: Adi N. R. Poli, Ian Tietjen, Nitesh K. Nandwana, Joel Cassel, Troy E. Messick, Emery T. Register, Frederick Keeney, Luis J. Montaner, and Joseph M. Salvino of The Wistar Institute; and Rajesh Rajaiah, Atul K. Verma, Kabita Pandey, Arpan Acharya, and Siddappa N. Byrareddy of The University of Nebraska Medical Center.

Work supported by: NIH grants S10OD030245 and P30CA010815; Canadian Institutes of Health Research grant CIHR PJT-153057; and Commonwealth of Pennsylvania Special Initiatives Grant – COVID-19 Funding, SAP #4100089371

Publication information: “Design of novel and highly selective SARS-CoV-2 main protease inhibitors,” from Antimicrobial Agents and Chemotherapy.

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ABOUT THE WISTAR INSTITUTE:

The Wistar Institute is the nation’s first independent nonprofit institution devoted exclusively to foundational biomedical research and training. Since 1972, the Institute has held National Cancer Institute (NCI)-designated Cancer Center status. Through a culture and commitment to biomedical collaboration and innovation, Wistar science leads to breakthrough early-stage discoveries and life science sector start-ups. Wistar scientists are dedicated to solving some of the world’s most challenging problems in the field of cancer and immunology, advancing human health through early-stage discovery and training the next generation of biomedical researchers. wistar.org


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Wistar’s Medicinal Chemist Dr. Joe Salvino and the Journey to Drug Discovery

Joseph Salvino, Ph.D., medicinal chemist and professor in the Molecular & Cellular Oncogenesis Program and scientific director of the Molecular Screening & Protein Expression facility at The Wistar Institute, spent more than 20 years in the pharmaceutical industry’s drug discovery before coming to Wistar. Dr. Salvino collaborates with many Wistar scientists on programs to help identify novel small molecule lead compounds that could evolve into future drugs.

Here at the intersection of biology and chemistry is where Dr. Salvino and his team work best. Their medicinal and synthetic chemistry skills complement our investigators’ biology expertise. It’s a process wherein Dr. Salvino helps to optimize a hit compound our Wistar scientists identified or tries to identify a new lead compound for an interesting new target.

When Wistar scientists want to identify a compound that can produce a certain desired effect, Dr. Salvino works to optimize that compound’s ability to achieve its target effect. These early-stage compounds that show promise are called “hits,” and Dr. Salvino investigates these hits in a variety of biochemical settings.

Dr. Salvino’s expertise is in optimizing early-stage hits by improving target binding affinity and functional activity. His aim is to increase a compound’s biological potency and improve drug-like properties. To achieve this goal Dr. Salvino works closely with biologists to understand the molecular target. He focuses on how a small molecule will engage the target to elicit a biological response.

This crucial foundational research is the bedrock of the drug discovery process. It’s here that assays are developed with the throughput to support iterative medicinal chemistry optimization efforts that can quickly evaluate twenty or so compounds in a few days. The goal of lead optimization is to identify a suitable compound that could become a therapy to treat cancer and other disease. This is the compelling fundamental work that Wistar basic researchers accomplish before a drug discovery company considers translating what Wistar scientists have identified and potentially converts a Wistar discovery into a drug useful in health care.

As Wistar’s medicinal chemist, describe how you fit into Wistar’s scientific efforts?

I work in collaboration with Wistar scientists and scientists at neighboring universities to help identify a series of compounds suitable as a pharmacological means to modulate their target of interest. My job is to identify a suitable compound, part of a “hit-to-lead” series usually identified from a screening campaign, to test pharmacologically the effects of small molecule treatment both in vitro and in vivo.

In a lay friendly way tell us your process working with the scientists.

We work with other scientists by identifying and improving on small molecules that engage their protein target of interest. These small molecules may inhibit, stimulate, or degrade their protein and be biologically active in a cell expressing their protein, or where their protein is the cause for the disease we are trying to treat. My team needs to learn as much as we can about the molecular target from our collaborator.

We work with many Wistar investigators—typically those who are looking to identify or improve on a small molecule as a potential therapeutic agent for a disease related to their target. Often the investigator has already identified a small molecule to test their hypothesis. My team works in collaboration to improve or develop a new molecule, focusing on improving selectivity, potency, or its in vivo drug-like properties.

The Wistar Institute Molecular Screening & Protein Expression Core is under my direction. This group can develop assays that typically can be run in a plate-based format to provide a high-throughput approach to support our medicinal chemistry efforts. For example, when medicinal chemists are trying to identify an optimized compound, we need to synthesize and evaluate 10-50 different analogs that are related but have slight differences in their structure. We do this to probe for “structure activity relationships”—the changes required to improve binding affinity to a protein target or to improve its functional activity. Both binding affinity and functional efficacy are very important to optimize a molecule, even though its functional efficacy is what a biologist wants to study.

Interestingly, a typical drug discovery effort from a pharmaceutical company requires the synthesis of about 2000-3000 compounds per target to identify a development candidate.

How do you start working with scientists?

We start to work together because of a common interest in a target or a disease, such as treatment of melanoma, ovarian, or breast cancer or EBV associated cancer, or others. We normally start collaborating because of our common interests and complementary skills.

What aspects of your work do you like most?

I enjoy the interface between chemistry and biology. I love finding new compounds with interesting biological activity in collaboration with my colleagues, especially for interesting new targets. I like working with the screening core to help develop new methods to test compounds. We spend a lot of time synthesizing chemical probes, such as a binding probe, which greatly facilitate assay development. A binding probe, or also sometimes called a tracer, is used in a competitive binding assay, where an unlabeled compound will compete for binding with the tracer. For this type of study, we can determine the binding affinity of an unlabeled test compound.

Wistar does not make drugs or therapies but advances discoveries that can move into drug discovery as future therapeutics.

Spotlight on Wistar COVID-19 Researchers: Luis Montaner, D.V.M., D.Phil., & Joseph Salvino, Ph.D.

Dr. Luis Montaner is an HIV expert focused on finding new ways to boost the natural function of the immune system to combat infection or viral-associated disease. Dr. Joseph Salvino is a medicinal chemist and an expert in drug discovery and identification of novel small molecule lead compounds. The two have combined their expertise to design a strategy to modulate the immune response to viral infections using novel small molecules. They discuss the basis of this approach and how they are advancing it.

Montaner: We are born programmed to resist viral infections. One of the key weapons our immune system uses to respond to viruses is interferon, which “interferes” with the viral replication. However, sometimes our system is not effective. Our goal is to amp up the natural immune response to COVID-19 in a targeted way without inducing greater inflammatory damage in the lung.

Salvino: Interferons activate the immune response by engaging a specific receptor present on the cell surface. We are developing compounds that stimulate binding of interferons to their receptor and activate signaling to the cell to initiate an antiviral response. We have some interesting lead compounds that we are testing to confirm they have the intended biological effect without toxicity.

Montaner: Joe and I have been collaborating for the past three years to find small molecules that can modulate immunity in HIV by acting on the interferon response, as one of my lab’s interests is what happens when this response becomes chronic and poses problems.

Salvino: For this project, we have now tested about 20-30 thousand compounds based on computer models and predictions. We were looking for inhibitory compounds that block the interaction of interferons with their receptor, but we have also come across stimulatory compounds that have the opposite effect and can actually serve as a glue between ligand and receptor.

Montaner: When the COVID-19 outbreak started, we realized we had those molecules in our hands that could potentially be helpful and limit the disease by amplifying the interferon antiviral response. These small molecules act as cement between interferon and receptor, making the interaction more stable and, as a consequence, strengthening the stimulation provided on the immune cell. We don’t want to make it irreversible, though. We want to maintain an off switch because the immune cells are not programmed to be on a constant inflammatory state and that could lead to tissue damage, for example to the lungs in the case of COVID-19.

So, we looked back at several molecules that in our studies made the interferon response better. The platform we developed to test our inhibitory compounds in vitro and in vivo gives us the advantage of time because we don’t need to set up new systems and assays; we already have them in place. Basically, we are steps ahead in the process because we already have candidate molecules and the appropriate tools to test them. We are evaluating these compounds to track their effect on the immune response in vivo.

Salvino: There are limited small molecule drugs available to fight viral infections and, in general, they work by directly interacting with the virus. For example, a compound could bind to the “Spike” of COVID-19 to block the virus from entering the host cells; or it could directly bind to an essential component in the virus to reduce its ability to function. However, viruses have the ability to mutate and become resistant to drugs, and that small molecule could lose effectiveness. Our approach is different because it targets the host and has a reduced likelihood of causing resistance compared to virus-directed approaches.

Montaner: These small molecule drugs can potentially amplify the natural antiviral response and prevent the COVID-19 virus from establishing an infection, or rapidly fight it off. In theory, such therapeutic booster could be used alone at onset of symptoms or later on in combination with other antiviral drugs.

Salvino: This work is very collaborative. Our labs complement each other, since my expertise in organic and synthetic chemistry is combined with Luis’s immunology and biology expertise.

Montaner: As a basic biomedical research institute, Wistar makes fundamental discoveries and generates proofs of concepts for potential new therapies. For example, after identifying new compounds, we study their activity and test them in preclinical models. Once these steps are complete, partnerships with industry become critical in order to translate our discoveries into new medicines.

We believe our work to identify small molecules to boost the immune response against viral infection could potentially be important in the COVID-19 crisis, and for other diseases, but even getting to the point at which a new candidate drug is attractive to industry partners requires extensive work and robust financial support.