# Discovery and Development of Broad-spectrum Protease Inhibitors of Flaviviruses of Significant Public Health Threats

> **NIH NIH R43** · PLEX PHARMACEUTICALS, INC. · 2020 · $300,000

## Abstract

Project Summary
 Mosquito-borne members of the Flavivirus family including Zika virus (ZKV), Dengue virus (DNV) and West Nile
virus (WNV), are classified as re-emerging pathogens due to the frequency and severity of recent epidemics. Also known
as arboviruses, these viruses are the etiologic agents of many debilitating diseases affecting the human population
worldwide. Consequently, vector borne diseases now account for 17% of all infections worldwide. DNV is the fastest
growing arboviral disease currently affecting 400 million annually with 96 million cases manifesting into clinical severity
and 22,000 deaths, mainly children. WNV is considered the most important causative agent of viral encephalitis worldwide.
The recent ZKV infection outbreak has been associated with congenital microcephaly and intracranial calcification and, in
adults, with GBS and severe thrombocytopenia. Currently there is no effective treatment for infections caused by these
viruses, which highlights the urgent need to find preventive and therapeutic interventions.
 The Flaviviridae genome is translated into a single polyprotein which is processed to yield 3 structural and 7
nonstructural proteins. The correct processing of the polyprotein is essential for replication of all flaviviruses, which requires
both host proteases and the highly conserved viral NS2B-NS3 protease (NS2B-NS3pro). Hence, the viral protease is a
rational target for development of small molecule inhibitors that block flavivirus replication. Small molecule antivirals
targeting HIV-1-encoded and HCV-encoded proteases have been successfully developed, which supports the concept of
developing chemotherapeutic agents targeting the flavivirus NS2B-NS3pro. The innovation of our proposal is: (i)
optimization of a highly-sensitive screening assay for the identification of low binding fragment hits; (ii) evolution of
fragment and compound hits into broad-spectrum leads; (iii) the use of replicon and plaque assays to test for cellular efficacy
and guide optimization. Our preliminary results and the use of multiple cell-based models supports the feasibility of the
discovery of broad-spectrum anti-flaviviral therapeutics. The specific aims are: Aim 1: Complete the screening of fragment
and compound libraries for the identification of broad-spectrum NS2B-NS3pro hits. Milestone 1: Identify 6-8 structurally
distinct broad-spectrum NS2B-NS3pro hits with an IC50 ≤ 25μM. Aim 2a: Iterative 3D-structure and SAR-based discovery
of three non-overlapping broad-spectrum NS2B-NS3pro inhibitor series, using a combination of: (i) commercial analogues
and (ii) med-chem design and synthesis approach. Milestone 2: Identify three non-overlapping broad-spectrum NS2B-
NS3pro inhibitor series with an IC50 ≤ 200nM. Aim 2b: Characterize biochemically potent inhibitors for: (a) mode of
inhibition and (b) enzyme:ligand interactions and prioritize compounds with IC50 ≤ 200nM, for cellular efficacy studies.
Aim 3a: In vitro evaluation and opti...

## Key facts

- **NIH application ID:** 9907267
- **Project number:** 1R43AI145617-01A1
- **Recipient organization:** PLEX PHARMACEUTICALS, INC.
- **Principal Investigator:** Sridhar G Prasad
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $300,000
- **Award type:** 1
- **Project period:** 2020-02-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9907267

## Citation

> US National Institutes of Health, RePORTER application 9907267, Discovery and Development of Broad-spectrum Protease Inhibitors of Flaviviruses of Significant Public Health Threats (1R43AI145617-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9907267. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*