Human parainfluenza viruses (hPIVs) cause upper and lower respiratory tract disease in children that results in a significant number of hospitalizations and impacts health systems worldwide. To date, neither antiviral drugs nor vaccines are approved for clinical use against parainfluenza virus, which reinforces the urgent need for new therapeutic discovery strategies. Here we use a multidisciplinary approach to develop potent inhibitors that target a structural feature within the hPIV type 3 haemagglutinin-neuraminidase (hPIV-3 HN). These dual-acting designer inhibitors represent the most potent designer compounds and efficiently block both hPIV cell entry and virion progeny release. We also define the binding mode of these inhibitors in the presence of whole-inactivated hPIV and recombinantly expressed hPIV-3 HN by Saturation Transfer Difference NMR spectroscopy. Collectively, our study provides an antiviral preclinical candidate and a new direction towards the discovery of potential anti-parainfluenza drugs.

Human parainfluenza virus type 3 (hPIV-3) is one of the leading causes for lower respiratory tract disease in children, with neither an approved antiviral drug nor vaccine available to date. Understanding the catalytic mechanism of human parainfluenza virus haemagglutinin-neuraminidase (HN) protein is key to the design of specific inhibitors against this virus. Herein, we used (1) H NMR spectroscopy, X-ray crystallography, and virological assays to study the catalytic mechanism of the HN enzyme activity and have identified the conserved Tyr530 as a key amino acid involved in catalysis. A novel 2,3-difluorosialic acid derivative showed prolonged enzyme inhibition and was found to react and form a covalent bond with Tyr530. Furthermore, the novel derivative exhibited enhanced potency in virus blockade assays relative to its Neu2en analogue. These outcomes open the door for a new generation of potent inhibitors against hPIV-3 HN.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged virus that causes coronavirus infectious disease 2019 (COVID-19). SARS-CoV-2 spike protein, like SARS-CoV-1, uses the angiotensin converting enzyme 2 (ACE2) as a cellular receptor to initiate infection. Compounds that interfere with the SARS-CoV-2 spike protein receptor binding domain protein (RBD)-ACE2 receptor interaction may function as entry inhibitors. Here, we used a dual strategy of molecular docking and surface plasmon resonance (SPR) screening of compound libraries to identify those that bind to human ACE2 or the SARS-CoV-2 spike protein receptor binding domain (RBD). Molecular modeling screening interrogated 57,641 compounds and focused on the region of ACE2 that is engaged by RBD of the SARS-CoV-2 spike glycoprotein and vice versa. SPR screening used immobilized human ACE2 and SARS-CoV-2 Spike protein to evaluate the binding of these proteins to a library of 3,141 compounds. These combined screens identified compounds from these libraries that bind at KD (equilibrium dissociation constant) <3 μM affinity to their respective targets, 17 for ACE2 and 6 for SARS-CoV-2 RBD. Twelve ACE2 binders and six of the RBD binders compete with the RBD-ACE2 interaction in an SPR-based competition assay. These compounds included registered drugs and dyes used in biomedical applications. A Vero-E6 cell-based SARS-CoV-2 infection assay was used to evaluate infection blockade by candidate entry inhibitors. Three compounds demonstrated dose-dependent antiviral in vitro potency—Evans blue, sodium lifitegrast, and lumacaftor. This study has identified potential drugs for repurposing as SARS-CoV-2 entry inhibitors or as chemical scaffolds for drug development. IMPORTANCE SARS-CoV-2, the causative agent of COVID-19, has caused more than 60 million cases worldwide with almost 1.5 million deaths as of November 2020. Repurposing existing drugs is the most rapid path to clinical intervention for emerging diseases. Using an in silico screen of 57,641 compounds and a biophysical screen of 3,141 compounds, we identified 22 compounds that bound to either the angiotensin converting enzyme 2 (ACE2) and/or the SARS-CoV-2 spike protein receptor binding domain (SARS-CoV-2 spike protein RBD). Nine of these drugs were identified by both screening methods. Three of the identified compounds, Evans blue, sodium lifitegrast, and lumacaftor, were found to inhibit viral replication in a Vero-E6 cell-based SARS-CoV-2 infection assay and may have utility as repurposed therapeutics. All 22 identified compounds provide scaffolds for the development of new chemical entities for the treatment of COVID-19.

• Human parainfluenza viruses (hPIVs) cause significant disease in infants, the elderly and immunocompromised persons. • Haemagglutinin-neuraminidase (HN) has multiple roles in the hPIV lifecycle, making it an attractive antiviral drug target. • Computational modelling and structure-based inhibitor studies have enhanced the development of potent hPIV3 HN inhibitors. • Current inhibitor strategies targeting HN are primarily based on sialic acid analogues. • Identification of new targets and inhibitor scaffolds could prove worthwhile in the fight against hPIVs.

Human parainfluenza viruses represent a leading cause of lower respiratory tract disease in children, with currently no available approved drug or vaccine. The viral surface glycoprotein haemagglutininneuraminidase (HN) represents an ideal antiviral target. Herein, we describe the first structure-based study on the rearrangement of key active site amino acid residues by an induced opening of the 216-loop, through the accommodation of appropriately functionalised neuraminic acid-based inhibitors. We discovered that the rearrangement is influenced by the degree of loop opening and is controlled by the neuraminic acid's C-4 substituent's size (large or small). In this study, we found that these rearrangements induce a butterfly effect of paramount importance in HN inhibitor design and define criteria for the ideal substituent size in two different categories of HN inhibitors and provide novel structural insight into the druggable viral HN protein.Human parainfluenza virus (hPIV) is one of the leading causes of respiratory tract disease in infants and children 1, 2 and is estimated to result in over 1.5 million cases per year in the United States alone 3 . Despite continuous efforts 4, 5 , there are neither specific antiviral therapy nor vaccines available against hPIV-3 to date. The viral surface glycoprotein haemagglutinin-neuraminidase (HN) represents an ideal target for the development of urgently needed antiviral agents. The viral HN protein encompasses three key functions in virus infection and spread. The hPIV HN recognizes and attaches to N-acetylneuraminic acid-containing glycoconjugates present on the host cell and subsequently activates the fusion machinery, facilitating infection. Upon virus replication, hPIV HN enzymatically cleaves the neuraminic acid (Neu), N-acetylneuraminic acid (Neu5Ac, 1) from host cell receptors allowing viral spread to uninfected cells 3 . A number of Neu2en (2)-based inhibitors (e.g. BCX 2798, 3) 6, 7 , as well as a novel approach that uses two well-established drugs 8 in a combinatorial manner, have been used to target the hPIV-3 HN protein. However, none of these agents have progressed to the clinic.Recently, we have reported 9 the first structural investigation into the catalytic mechanism of the hPIV-3 HN protein using the 2,3-difluoro-N-acylneuraminic acid derivative, 4. This study demonstrated that the protein forms a covalent adduct with the substrate as a result of a nucleophilic attack at the Neu moiety's anomeric carbon (C-2) by the hydroxyl group of the key catalytic amino acid, Tyr530. Hence, it was verified 9 that hPIV-3 HN can be targeted by reactive substrate-like inhibitors such as 4.We have also recently described the design and synthesis of novel potent 4-deoxy-4-triazolo-Neu2en-based inhibitors (5 and 6, Fig. 1) 10 . These inhibitors carry bulky C-4 substituents on the Neu2en template and target the proposed 216-cavity formed by movement of the flexible 216-loop 11 , a unique feature in hPIV-3 HN. Taken together these developments inspired further structural ...