SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.

Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields the HIV structural proteins and enzymes. Structures of the mature enzymes PR, reverse transcriptase (RT), and integrase (IN) aided understanding of catalysis and design of antiretrovirals, but knowledge of the Pol precursor architecture and function before PR cleavage is limited. We developed a system to produce stable HIV-1 Pol and determined its cryo–electron microscopy structure. RT in Pol has a similar arrangement to the mature RT heterodimer, and its dimerization may draw together two PR monomers to activate proteolytic processing. HIV-1 thus may leverage the dimerization interfaces in Pol to regulate assembly and maturation of polyprotein precursors.

In most cases, proteolytic processing of the retroviral Pol portion of the Gag-Pol polyprotein precursor produces protease (PR), reverse transcriptase (RT), and integrase (IN). However, foamy viruses (FVs) express Pol separately from Gag and, when Pol is processed, only the IN domain is released. Here, we report a 2.9 Å resolution crystal structure of the mature PR-RT from prototype FV (PFV) that can carry out both proteolytic processing and reverse transcription but is in a configuration not competent for proteolytic or polymerase activity. PFV PR-RT is monomeric and the architecture of PFV PR is similar to one of the subunits of HIV-1 PR, which is a dimer. There is a C-terminal extension of PFV PR (101-145) that consists of two helices which are adjacent to the base of the RT palm subdomain, and anchors PR to RT. The polymerase domain of PFV RT consists of fingers, palm, thumb, and connection subdomains whose spatial arrangements are similar to the p51 subunit of HIV-1 RT. The RNase H and polymerase domains of PFV RT are connected by flexible linkers. Significant spatial and conformational (sub)domain rearrangements are therefore required for nucleic acid binding. The structure of PFV PR-RT provides insights into the conformational maturation of retroviral Pol polyproteins.

Some 2H-chromen-2-one and imine derivatives have been synthesized through a one-pot condensation of aldehydes, diethyl malonate, and amine compounds. The compounds obtained have been characterized using FTIR, NMR, GC-MS, and elemental analysis. The single-crystal X-ray structure of 3-[piperidine-1-carbonyl]-2H-chromen-2-one (2) has been presented. Compound 2, recrystallized in the monoclinic space C2/c (no. 15), a = 16.654(15) Å, b = 8.789(7) Å, c = 18.460(18) Å, β = 102.89(5)°, V = 2634(4) Å3, Z = 8, T = 296(2) K, μ(MoKα) = 0.091 mm-1, Dcalc = 1.298 g/cm3, 17626 reflections measured (4.528° ≤ 2Θ ≤ 57.446°), 3321 unique (Rint = 0.0313, Rsigma = 0.0257) which were used in all calculations. The final R1 was 0.0441 (I > 2σ(I)) and wR2 was 0.1329 (all data). The experimental bond lengths, bond angles, and other topological properties of compound 2 were compared with the DFT calculated results, the comparison showed good agreement with each other with varying level deviations. The energy levels of HOMO and LUMO, as well as the global chemical reactivity descriptors of representative compound 2, have been presented. A discussion of the Hirshfeld surface analysis of compound 2 has been carried out to provide insight into its structural properties.

Parinari is a genus of woody medicinal plants with expansive ethnomedicinal uses. While extensive data are available for several members of this genus, this information is generally scattered. This review therefore crystallizes major reports relating to the ethnomedicinal uses, phytochemistry, and biological activities of this genus for easy accessibility. The rich therapeutic applications of this genus include their use as antimalarial, antidiabetic, anti-inflammatory, antimicrobial, anti-snake venom, and anticancer agents. However, the overarching biological theme for this genus appears to be their application in treating infection and infection-related diseases. These bioactivities have largely been attributed to molecules isolated from this genus and categorized under; kaurene-type diterpenoids, triterpenoids (ursane, oleanane, and lupane types), flavonoids, steroids, and phenolic compounds. While data is available for most parts of the plants, the stem appears to be the most used part. Given the varied medicinal uses of this genus, and yet the scarcity of information on many Parinari species, studies on the ethnomedicine, phytochemistry, and biological activities that fully explore the medicinal potential of this genus for drug discovery are critical. These include the need for comprehensive phytochemical profiling to uncover novel compounds, detailed studies on mechanisms of action, and translational research to validate clinical efficacy. Additionally, comparative ethnobotanical studies, standardization of extraction methods, and sustainable harvesting practices are critical to fully realizing the medicinal potential of Parinari species.

SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its ∼30 kb RNA genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11 polyprotein, whose mature products are cofactors of the viral replicase, identifying the order of cleavages as: 1) nsp9-10, 2) nsp8-9/nsp10-11, and 3) nsp7-8. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and X-ray scattering yielded three-dimensional models of the nsp7-10/11 polyprotein. Our data suggest that the nsp7- 10/11 structure in complex with Mpro strongly resembles the unbound polyprotein, and that both polyprotein conformation and junction accessibility determine the preference and order of cleavages. Finally, we used limited proteolysis assays to characterize the effect of a series of inhibitors/binders on Mpro processing of nsp7-11 and Mpro inhibition using a polyprotein substrate. Teaser: We elucidated the structural basis of order of cleavage of SARS-CoV-2 nsp7-11 polyprotein, with implications for Mpro inhibition.