Project 1

Development of ALG-097558 as a broad-spectrum 3CL pro inhibitor Four novel series of compounds with potent and selective SARS-CoV-2 3CLpro inhibition were identified with demonstrated broad-spectrum activity. This program is on track to move toward IND enabling studies.

Project Leader: Julian Symons, D.Phil.
Institution: Aligos Therapeutics
Location: South San Francisco, CA

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Project 2

Accelerated development of advanced Leads against SARS-CoV-2 and other pandemic viruses

Boceprevir, an FDA-approved orally active serine protease inhibitor, is used to treat hepatitis C virus. Structure-based modeling combined with extensive medicinal chemistry mimicking the interactions of Boceprevir with the protease (3CLpro) structure in SARS-CoV-2 yielded lead compounds with exceptional therapeutic indices and forms the basis for this highly promising discovery effort that is producing Optimized Leads with selection for an IND enabling and de-risking program with Merck. The Optimized Lead Compounds will be evaluated against MERS, other coronaviruses and flaviviruses.

Project Leader: David Perlin, Ph.D.
Institution: Center for Discovery and Innovation, Hackensack Meridian Health
Industry Partner: Merck
Locations: Nutley, NJ; Kenilworth, NJ

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Project 3

Discovery of new antiviral methylase, protease and helicase inhibitors of corona-, flavi-, and alphaviruses

Robust advanced hit-to-lead development program of inhibitors against SARS-CoV-2 PLpro and Nsp14 MTase, 3CLpro and Nsp13 helicase. Screening of inhouse (>430,000 member) RU library resulted in the identification of non-covalent hit-to-lead series of PLpro and Nsp14 inhibitors with promising translational potential. This project is highly robust and encompasses high-throughput screening and development of pre-lead and lead compounds. The compounds possess strong broad-spectrum potential and target viral proteases (3CLpro, PLpro), methylases (including 2’-O-MTase), and helicases in MERS, flavi- and alphaviruses.

Project Leader: Tom Tuschl, Ph.D.
Institution: Rockefeller University
Industry Partner: Tri-Institutional Therapeutics Discovery Institute - Takeda
Location: New York, NY

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Project 4

Discovery and optimization of inhibitors for SARS-CoV-2 RNA synthesis

The Program uses synthetic chemistry, structural, functional and computational approaches to discover RNA polymerase (RdRp) and exonuclease (ExoN) inhibitors of SARS-CoV-2. Preliminary data support the thesis that simultaneous inhibition of both the viral RdRp and ExoN have synergistic effects in blocking SARS-CoV-replication. Implementing two high resolution molecular assays using mass-spectrometry detection to assess SARS-CoV-2 RdRp and ExoN activities for screening inhibitors and identified unique structure activity relationship information for inhibitors for RdRp and ExoN complexes. Based on this, new inhibitors with improved potency and reduced toxicity will be designed and synthesized. This project will develop early lead compounds (RdRp and ExoN inhibitors) with strong potential for broad-spectrum activity.

Project Leader: Jingyue Ju, Ph.D.
Institution: Columbia University
Industry Partner: TBD
Location: New York, NY

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Project 5

Discovery and characterization of synBNP antivirals

Over the past two decades, the world has witnessed various deadly viral pandemics, including the ongoing crisis caused by SARS-CoV-2. While vaccines provide hope, challenges such as persistent reservoirs, emerging variants, and vaccine hesitancy necessitate additional therapeutic options. Bacterial-derived small molecules offer a promising avenue to combat viral pandemics. To tap into the vast potential of unexplored natural products, Dr Brady’s group has developed a unique approach that combines bioinformatics and total chemical synthesis to create synthetic Bioinformatic Natural Products (synBNPs). He will use this pipeline to discover and optimize novel small molecules with activity against pandemic viruses. By exploring a greater fraction of bacterial biosynthetic diversity, his research aims to identify nature-derived antiviral compounds.

Project Leader: Sean Brady, Ph.D.
Institution: The Rockefeller University
Location: New York, NY

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Project 6

Identification and characterization of small molecule inhibitors of yellow fever virus Yellow fever (YF), caused by the yellow fever virus (YFV), poses a significant threat to human health. Recent reemergence events in non-endemic and historically low-activity areas highlight the urgent need to address YFV as a serious infectious disease. Currently, vaccination campaigns with the live-attenuated YFV-17D vaccine are the primary defense against YF and future outbreaks. The objective of Dr Ploss’s project is to identify novel inhibitors of YFV that can also suppress other flaviviruses. Through technical advancements, including full-length and subgenomic YFV genomes for high-throughput screening, he aims to discover potential antiviral compounds. His research team will validate hits using genetically diverse YFV strains, investigate resistance mutations, and assess the inhibitors' activity against other related viruses.

Project Leader: Alexander Ploss, Ph.D.
Institution: Princeton University
Location: Princeton, NJ

Multiplex Small Molecule Discovery to Identify Broad-Acting Viral Protease Inhibitors This program will utilize a novel approach to small molecule screening to uncover broadly active protease (CLpro) inhibitors against human and animal pathogens capable of studying >40 viral proteases at a time. An approach to in-depth resistance profiling was established to identify and optimize Leads that are not only potent and safe but for which viral escape is minimized. Tools produced are highly valuable to other programs.

Project Leaders: David Ho, Ph.D.; Alejandro Chavez, Ph.D.; Yosef Sabo, Ph.D.
Institution: Columbia University
Location: New York, NY

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Past Projects supported by MAVDA

Multiplex Small Molecule Discovery to Identify Broad-Acting Viral Protease Inhibitors

This program will utilize a novel approach to small molecule screening to uncover broadly active protease (CLpro) inhibitors against human and animal pathogens capable of studying >40 viral proteases at a time. An approach to in-depth resistance profiling was established to identify and optimize Leads that are not only potent and safe but for which viral escape is minimized. Tools produced are highly valuable to other programs.

Project Leaders: David Ho, Ph.D.; Alejandro Chavez, Ph.D.; Yosef Sabo, Ph.D.
Institution: Columbia University
Location: New York, NY

Developmental Research Projects

Developmental Research Projects (DRPs) are intended to expand the scope and range of current research and investigators involved in antiviral discovery, allowing for testing of novel ideas and development of new technologies.

DRP project: Multiplex genome editing of MAVDA-prioritized positive-strand RNA viruses

As viruses evolve, acquiring mutations, some advantageous and others incidental, the emergence of drug resistance poses a significant challenge for antiviral treatments. By utilizing a yeast genome-editing technique called eukaryotic multiplex automated genome engineering (eMAGE), this project will focus on efficient reverse genetics of positive-strand RNA viruses, specifically targeting MAVDA-prioritized CoVs, flaviviruses, and alphaviruses. The aims of this program include developing stable cDNA vectors, establishing renewable libraries for testing against DAA compounds, and optimizing the eMAGE workflow for generating virus variants integrated with mammalian cell culture assays. This innovative approach will enhance understanding of complex viral phenotypes and support research and therapeutic endeavors.

Project Leader: Brett Lindenbach, Ph.D.
Institution: Yale University
Location: New Haven, CT

DRP project: Interfering with SARS-CoV-2 RNA capping: Discovery and characterization of nidovirus RdRp associated nucleotidyltransferase (NiRAN) inhibitors

Coronaviruses (CoVs) are RNA viruses responsible for deadly zoonotic events, including the current COVID-19 pandemic caused by SARS-CoV-2. Nidoviruses, including CoVs, possess a conserved RNA-dependent RNA polymerase (RdRp) responsible for viral RNA synthesis. Dr Campbell’s recent structural studies have identified a crucial pocket in the NiRAN domain, an N-terminal region of nidoviral RdRps, which plays a vital role in viral propagation and RNA capping. In this project, Dr Campbell aims to conduct a large-scale structure-based in silico docking screen targeting the NiRAN GTP/GDP binding site to identify potential drug or chemical leads. Validated hits will undergo further biochemical and structural characterization. This approach holds promise for the development of early therapeutics or chemical probes against CoVs.

Project Leader: Elizabeth Campbell, Ph.D.
Institution: The Rockefeller University
Location: New York, NY

Mentored Research Projects

Mentored Research Projects (MRPs) are intended to increase the availability of qualified researchers and other personnel for antiviral discovery research by providing opportunities to further their professional advancement. MRPs must relate to the Center objectives and may be used to support post-doctoral fellows, early career investigators, or senior investigators new to the field of antiviral discovery and development.

MRP Project: Targeting the SARS-CoV-2 RdRp for antiviral discovery efforts

Coronaviruses (CoV) have caused major zoonotic events, including SARS and MERS, and the ongoing Covid-19 pandemic. The high mutation rate of SARS-CoV-2 threatens current treatments. The RNA-dependent RNA polymerase (RdRp) protein, specifically the nsp12 subunit, is crucial for viral replication and an attractive target for antiviral therapies. However, nsp12 purification has been challenging, hindering drug target identification. This project aims to optimize nsp12 purification using established techniques, enabling the production of active holo-RdRp for inhibitor screening. A plate-based assay for transcriptional activity is being developed for high-throughput screening. Validated hits will undergo biochemical and structural analyses. This study aligns with MAVDA's objectives and aims to lay the foundation for SARS-CoV-2 drug development, benefiting future coronavirus outbreaks.

Project Leader: Wamiah Chowdhury, Ph.D.
Institution: The Rockefeller University
Location: New York, NY

MRP Project: Development of inhibitors against Chikungunya NSP2 protease

Chikungunya fever, caused by the Chikungunya virus (CHIKV), has become a global arboviral concern with no approved vaccination or antiviral treatment available. The CHIKV nsP2 protease, crucial for viral replication, presents an attractive therapeutic target. This project aims to purify the CHIKV nsP2 protease and establish a high throughput screening assay to identify potential drug molecules. Antiviral activity will be evaluated using in vitro and in vivo models. Molecular interactions between the protein target and drug candidates will be studied using techniques such as surface plasmon resonance (SPR), microscale thermophoresis (MST), and X ray crystallography. The MAVDA mentored research program will provide valuable training in structure

activity relationship studies and expertise in structure-guided drug discovery, establishing a foundation for a career in drug development.

Project Leader: Subodh Samrat, Ph.D.
Institution: University of Arizona
Location: Tucson, AZ

MRP Project: Rapid high-throughput identification of SARS-COV2 drug resistance

The global impact of the COVID-19 pandemic, with 650 million cases and 6.5 million deaths, underscores the need for effective therapeutics. While monoclonal antibodies and small molecules have shown promise, the emergence of drug resistance poses a significant challenge. Several SARS-CoV-2 strains exhibit complete resistance to authorized monoclonal antibodies, raising concerns. In contrast, limited studies have explored resistance to small molecules, with only a few resistance-conferring mutations identified. To address this gap, we aim to investigate mechanisms of SARS-CoV-2 resistance to small molecule inhibitors, focusing on 3CL protease inhibitors like nirmatrelvir and ensitrelvir. Traditional resistance profiling methods are costly and time-consuming, hindering comprehensive studies. Therefore, we propose two innovative approaches utilizing attenuated viral strains to rapidly and systematically identify drug resistance, enabling informed next-generation drug design.

Project Leader: Sho Iketani, Ph.D.
Institution: Columbia University
Location: New York, NY