P1 Moiety Research Articles

Design and biological evaluation of candidate drugs against zoonotic porcine deltacoronavirus (PDCoV)

Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus with zoonotic potential. PDCoV spillovers were recently detected in Haitian children with acute undifferentiated febrile illness, underscoring the urgent need to develop anti-PDCoV therapeutics. Coronavirus 3C-like protease (CoV 3CLpro) is essential for viral replication, and therefore provides an attractive target for drugs directed against CoV. Here, we initially evaluated the anti-PDCoV effect of Nirmatrelvir (PF-07321332), an FDA-approved anti-SARS-CoV-2 drug targeting viral 3CLpro. Regrettably, a very limited anti-PDCoV effect was achieved. By analyzing the binding modes of Nirmatrelvir with PDCoV 3CLpro and SARS-CoV-2 3CLpro, we demonstrated that the S2 pocket of 3CLpro is the primary factor underlying the differential inhibitory potency of Nirmatrelvir against different CoV 3CLpros. Based on the specific characteristics of the S2 pocket of PDCoV 3CLpro, four derivatives of Nirmatrelvir (compounds T1–T4) with substituted P2 moieties were synthesized. Compound T1, with an isobutyl at the P2 site, displayed improved anti-PDCoV activity invitro (cell infection model) and invivo (embryonated chicken egg infection model), and therefore is a potential candidate drug to combat PDCoV. Together, our results identify the substrate-binding mode and substrate specificity of PDCoV 3CLpro, providing insight into the optimization of Nirmatrelvir as an antiviral therapeutic agent against PDCoV.

Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2

Coronaviruses not only pose significant global public health threats but also cause extensive damage to livestock-based industries. Previous studies have shown that 5-benzyloxygramine (P3) targets the Middle East respiratory syndrome coronavirus (MERS-CoV) nucleocapsid (N) protein N-terminal domain (N-NTD), inducing non-native protein-protein interactions (PPIs) that impair N protein function. Moreover, P3 exhibits broad-spectrum antiviral activity against CoVs. The sequence similarity of N proteins is relatively low among CoVs, further exhibiting notable variations in the hydrophobic residue responsible for non-native PPIs in the N-NTD. Therefore, to ascertain the mechanism by which P3 demonstrates broad-spectrum anti-CoV activity, we determined the crystal structure of the SARS-CoV-2 N-NTD:P3 complex. We found that P3 was positioned in the dimeric N-NTD via hydrophobic contacts. Compared with the interfaces in MERS-CoV N-NTD, P3 had a reversed orientation in SARS-CoV-2 N-NTD. The Phe residue in the MERS-CoV N-NTD:P3 complex stabilized both P3 moieties. However, in the SARS-CoV-2 N-NTD:P3 complex, the Ile residue formed only one interaction with the P3 benzene ring. Moreover, the pocket in the SARS-CoV-2 N-NTD:P3 complex was more hydrophobic, favoring the insertion of the P3 benzene ring into the complex. Nevertheless, hydrophobic interactions remained the primary stabilizing force in both complexes. These findings suggested that despite the differences in the sequence, P3 can accommodate a hydrophobic pocket in N-NTD to mediate a non-native PPI, enabling its effectiveness against various CoVs.

Substrate Peptidomimetic Inhibitors of P. falciparum Plasmepsin X with Potent Antimalarial Activity.

Plasmepsin X (PMX) is an aspartyl protease that processes proteins essential for Plasmodium parasites to invade and egress from host erythrocytes during the symptomatic asexual stage of malaria. PMX substrates possess a conserved cleavage region denoted by the consensus motif, SFhE (h=hydrophobic amino acid). Peptidomimetics reflecting the P3 -P1 positions of the consensus motif were designed and showed potent and selective inhibition of PMX. It was established that PMX prefers Phe in the P1 position, di-substitution at the β-carbon of the P2 moiety and a hydrophobic P3 group which was supported by modelling of the peptidomimetics in complex with PMX. The peptidomimetics were shown to arrest asexual P. falciparum parasites at the schizont stage by impairing PMX substrate processing. Overall, the peptidomimetics described will assist in further understanding PMX substrate specificity and have the potential to act as a template for future antimalarial design.

An Isolable 2,5-Disila-3,4-Diphosphapyrrole and a Conjugated Si=P-Si=P-Si=N Chain Through Degradation of White Phosphorus with a N,N-Bis(Silylenyl)Aniline.

White phosphorus (P4) undergoes degradation to P2 moieties if exposed to the new N,N‐bis(silylenyl)aniline PhNSi 2 1 (Si=Si[N(tBu)]2CPh), furnishing the first isolable 2,5‐disila‐3,4‐diphosphapyrrole 2 and the two novel functionalized Si=P doubly bonded compounds 3 and 4. The pathways for the transformation of the non‐aromatic 2,5‐disila‐3,4‐diphosphapyrrole PhNSi 2P2 2 into 3 and 4 could be uncovered. It became evident that 2 reacts readily with both reactants P4 and 1 to afford either the polycyclic Si=P‐containing product [PhNSi 2P2]2P2 3 or the unprecedented conjugated Si=P−Si=P−Si=NPh chain‐containing compound 4, depending on the employed molar ratio of 1 and P4 as well as the reaction conditions. Compounds 3 and 4 can be converted into each other by reactions with 1 and P4, respectively. All new compounds 1–4 were unequivocally characterized including by single‐crystal X‐ray diffraction analysis. In addition, the electronic structures of 2–4 were established by Density Functional Theory (DFT) calculations.

Assessing the Role of a Malonamide Linker in the Design of Potent Dual Inhibitors of Factor Xa and Cholinesterases.

The rational discovery of new peptidomimetic inhibitors of the coagulation factor Xa (fXa) could help set more effective therapeutic options (to prevent atrial fibrillation). In this respect, we explored the conformational impact on the enzyme inhibition potency of the malonamide bridge, compared to the glycinamide one, as a linker connecting the P1 benzamidine anchoring moiety to the P4 aryl group of novel selective fXa inhibitors. We carried out structure–activity relationship (SAR) studies aimed at investigating para- or meta-benzamidine as the P1 basic group as well as diversely decorated aryl moieties as P4 fragments. To this end, twenty-three malonamide derivatives were synthesized and tested as inhibitors of fXa and thrombin (thr); the molecular determinants behind potency and selectivity were also studied by employing molecular docking. The malonamide linker, compared to the glycinamide one, does significantly increase anti-fXa potency and selectivity. The meta-benzamidine (P1) derivatives bearing 2′,4′-difluoro-biphenyl as the P4 moiety proved to be highly potent reversible fXa-selective inhibitors, achieving inhibition constants (Ki) in the low nanomolar range. The most active compounds were also tested against cholinesterase (ChE) isoforms (acetyl- or butyrylcholinesterase, AChE, and BChE), and some of them returned single-digit micromolar inhibition potency against AChE and/or BChE, both being drug targets for symptomatic treatment of mild-to-moderate Alzheimer’s disease. Compounds 19h and 22b were selected as selective fXa inhibitors with potential as multimodal neuroprotective agents.

Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance

Third generation Hepatitis C virus (HCV) NS3/4A protease inhibitors (PIs), glecaprevir and voxilaprevir, are highly effective across genotypes and against many resistant variants. Unlike earlier PIs, these compounds have fluorine substitutions on the P2-P4 macrocycle and P1 moieties. Fluorination has long been used in medicinal chemistry as a strategy to improve physicochemical properties and potency. However, the molecular basis by which fluorination improves potency and resistance profile of HCV NS3/4A PIs is not well understood. To systematically analyze the contribution of fluorine substitutions to inhibitor potency and resistance profile, we used a multi-disciplinary approach involving inhibitor design and synthesis, enzyme inhibition assays, co-crystallography, and structural analysis. A panel of inhibitors in matched pairs were designed with and without P4 cap fluorination, tested against WT protease and the D168A resistant variant, and a total of 22 high-resolution co-crystal structures were determined. While fluorination did not significantly improve potency against the WT protease, PIs with fluorinated P4 caps retained much better potency against the D168A protease variant. Detailed analysis of the co-crystal structures revealed that PIs with fluorinated P4 caps can sample alternate binding conformations that enable adapting to structural changes induced by the D168A substitution. Our results elucidate molecular mechanisms of fluorine-specific inhibitor interactions that can be leveraged in avoiding drug resistance.

Iodine-induced stepwise reactivity of coordinated white phosphorus: A mechanistic overview

The main role of the Ruthenium metal in the stepwise demolition of the P4 ligand upon the reaction with I2 is to enhance the basicity of the phosphorus atoms. The first step of reaction goes through the η2 coordination of the P4 moiety. The bounded phosphorus atoms are able to interact with the di-iodine molecule allowing the formation of tri-iodide anions. The latter, once released, may exert their nucleophilic action toward the transient unsaturated coordinated phosphorus centre. Such a vacancy is partially fulfilled by the metal through the formation of a partial Ru=P double bond. A detailed analysis of the evolution of the electronic structure at the various intermediates allows to discriminate in between the possible different initial adducts and to predict the most stable product. In contrast with the unassisted reaction, no concerted mechanism has been pointed out but the process evolves through a stepwise cleavage of the three PP bonds involving the coordinated phosphorus up to the final PI3 ligand formation and a cyclo-P3I3 moiety.

A convenient P- source.

White phosphorus is a prominent source of P atoms but has remained difficult to activate without using transition metals. Now, a bidentate ligand based on silicon(ii) donors has successfully stabilized a P2 moiety, and the resulting complex acts as a transfer reagent for P– anions.

Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.

This manuscript describes the discovery of a series of macrocyclic inhibitors of FXIa with oral bioavailability. Assisted by structure based drug design and ligand bound X-ray crystal structures, the group linking the P1 moiety to the macrocyclic core was modified with the goal of reducing H-bond donors to improve pharmacokinetic performance versus 9. This effort resulted in the discovery of several cyclic P1 linkers, exemplified by 10, that are constrained mimics of the bioactive conformation displayed by the acrylamide linker of 9. These cyclic P1 linkers demonstrated enhanced bioavailability and improved potency.

Insights into resistance mechanism of hepatitis C virus nonstructural 3/4A protease mutant to boceprevir using umbrella sampling simulation study

Hepatitis C virus can cause inflammation in human liver cells, leading to liver cirrhosis and liver cancer. Based on the World Health Organization reports, about 228 million people in the world have hepatitis C. To date, some inhibitory medicines against the hepatitis C virus nonstructural 3/4A protease, such as boceprevir, have entered clinical trial phases. However, several hepatitis C virus nonstructural 3/4A protease mutations have been recognized to decrease susceptibility of boceprevir to hepatitis C virus. The molecular details behind inhibitor resistance of these single-point mutations are not still understood. Thus, in this research, computational strategies were applied to clarify the inhibitor resistance mechanism. From umbrella sampling simulation and energy profiles, the polar interactions are the main driving force for boceprevir binding. Based on the analyzed R155T mutant, the main reason for the occurrence of boceprevir resistance is the conformation alterations of S4 and extended S2 binding pockets. These changes, lead to decreased binding ability of the key residues to P2 and P4 moieties of boceprevir. Moreover, structural results show that the disappearance of important salt bridges can bring about the great conformation changes of the binding pockets in R155T.Communicated by Ramaswamy H. Sarma

Metal-Assisted Opening of Intact P4 Tetrahedra.

The reactivity of ruthenium and manganese complexes bearing intact white phosphorus in the coordination sphere was investigated towards the low-valent transition-metal species [Cp'''Co] (Cp'''=η5 -C5 H2 -1,2,4-tBu3 ) and [L0 M] (L0 =CH[CHN(2,6-Me2 C6 H3 )]2 ; M=Fe, Co). Remarkably, and irrespective of the metal species, the reaction proceeds by the selective cleavage of two P-P edges and the formation of a square-planar cyclo-P4 ligand. The reaction products [{CpRu(PPh3 )2 }{CoCp'''}(μ,η1:4 -P4 )][CF3 SO3 ] (5), [{CpBIG Mn(CO)2 }2 {CoCp'''}(μ,η1:1:4 -P4 )] (6) and [{CpBIG Mn(CO)2 }2 {ML0 }(μ,η1:1:4 -P4 )] (CpBIG =C5 (C6 H4 nBu)5 ; L0 =CH[CHN(2,6-Me2 C6 H3 )]2 ; M=Fe (7 a), Co (7 b)), respectively, were fully characterized by single-crystal X-ray diffraction and spectroscopic methods. The electronic structure of the cyclo-P4 ligand in the complexes 5-7 is best described as a π-delocalized P4 2- system, which is further stabilized by two and three metal moieties, respectively. DFT calculations envisaged a potential intermediate in the reaction to form 5, in which a quasi-butterfly-shaped P4 moiety bridges the two metals and behaves as an η3 -coordinated ligand towards the cobalt center.

Rapid thermal-acid hydrolysis of spiramycin by silicotungstic acid under microwave irradiation

Spiramycin is a widely used macrolide antibiotic and exists at high concentration in production wastewater. A thermal-acid hydrolytic pretreatment using silicotungstic acid (STA) under microwave (MW) irradiation was suggested to mitigate spiramycin from production wastewater. Positive correlations were observed between STA dosage, MW power, interaction time and the hydrolytic removal efficiencies, and an integrative equation was generalized quantitively. Rapid and complete removal 100 mg/L of spiramycin was achieved after 8 min of reaction with 1.0 g/L of STA under 200 W of MW irradiation, comparing to 30.1% by MW irradiation or 15.9% by STA alone. The synergetic effects of STA and MW irradiation were originated from the dissociated-proton catalysis by STA and the dipolar rotation heating effect of MW. STA performed much better than the mineral acid H2SO4 under MW, due to the much stronger Brönsted acidity and higher Hammett acidity. After 8 min, 98.0% of antibacterial potency was also reduced. The m/z 558.8614 fragment (P1) and m/z 448.1323 fragment (P2) were identified as the primary products, which were formed by breaking glucosidic bonds and losing mycarose and forosamine for P1 and further mycaminose moiety for P2. Finally, production wastewater with 433 mg/L of spiramycin was effectively treated using this thermal-acid hydrolytic method. Spiramycin and its antibacterial potency both dropped to 0 after 6 min. The potency drop was supposed from the losing of mycarose and/or forosamine. To decrease both the concentration of spiramycin and its antibacterial potency, combinedly using STA and MW was suggested in this work to break down the structural bonds of the functional groups rather than to destroy the whole antibiotic molecules. It is promising for pretreating spiramycin-contained production wastewater to mitigate both the antibiotic and its antibacterial potency.

Structures of Zika virus NS2B-NS3 protease in complex with peptidomimetic inhibitors

Zika virus NS2B-NS3 protease plays an essential role in viral replication by processing the viral polyprotein into individual proteins. The viral protease is therefore considered as an ideal antiviral drug target. To facilitate the development of protease inhibitors, we report three high-resolution co-crystal structures of bZiPro with peptidomimetic inhibitors composed of a P1-P4 segment and different P1′ residues. Compounds 1 and 2 possess small P1′ groups that are split off by bZiPro, which could be detected by mass spectrometry. On the other hand, the more potent compound 3 contains a bulky P1′ benzylamide structure that is resistant to cleavage by bZiPro, demonstrating that presence of an uncleavable C-terminal cap contributes to a slightly improved inhibitory potency. The N-terminal phenylacetyl residue occupies a position above the P1 side chain and therefore stabilizes a horseshoe-like backbone conformation of the bound inhibitors. The P4 moieties show unique intra- and intermolecular interactions. Our work reports the detailed binding mode interactions of substrate-analogue inhibitors within the S4-S1′ pockets and explains the preference of bZiPro for basic P1-P3 residues. These new structures of protease-inhibitor complexes will guide the design of more effective NS2B-NS3 protease inhibitors with improved potency and bioavailability.

Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants.

A series of linear HCV NS3/4A protease inhibitors was designed by eliminating the P2-P4 macrocyclic linker in grazoprevir, which, in addition to conferring conformational flexibility, allowed structure-activity relationship (SAR) exploration of diverse quinoxalines at the P2 position. Biochemical and replicon data indicated preference for small hydrophobic groups at the 3-position of P2 quinoxaline for maintaining potency against resistant variants R155K, A156T, and D168A/V. The linear inhibitors, though generally less potent than the corresponding macrocyclic analogues, were relatively easier to synthesize and less susceptible to drug resistance. Three inhibitor cocrystal structures bound to wild-type NS3/4A protease revealed a conformation with subtle changes in the binding of P2 quinoxaline, depending on the 3-position substituent, likely impacting both inhibitor potency and resistance profile. The SAR and structural analysis highlight inhibitor features that strengthen interactions of the P2 moiety with the catalytic triad residues, providing valuable insights to improve potency against resistant variants.

Synthesis and antiviral evaluation of novel peptidomimetics as norovirus protease inhibitors

A series of tripeptidyl transition state inhibitors with new P1 and warhead moieties were synthesized and evaluated in a GI-1 norovirus replicon system and against GII-4 and GI-1 norovirus proteases. Compound 19, containing a 6-membered ring at the P1 position and a reactive aldehyde warhead exhibited sub-micromolar replicon inhibition. Retaining the same peptidyl scaffold, several reactive warheads were tested for protease inhibition and norovirus replicon inhibition. Of the six that were synthesized and tested, compounds 42, 43, and 45 potently inhibited the protease in biochemical assay and GI-1 norovirus replicon in the nanomolar range.

Facile Phenylphosphinidene Transfer Reactions from Carbene-Phosphinidene Zinc Complexes.

Phosphinidenes [R-P] are convenient P1 building blocks for the synthesis of a plethora of organophosphorus compounds. Thus far, transition-metal-complexed phosphinidenes have been used for their singlet ground-state reactivity to promote selective addition and insertion reactions. One disadvantage of this approach is that after transfer of the P1 moiety to the substrate, a challenging demetallation step is required to provide the free phosphine. We report a simple method that enables the Lewis acid promoted transfer of phenylphosphinidene, [PhP], from NHC=PPh adducts (NHC=N-heterocyclic carbene) to various substrates to produce directly uncoordinated phosphorus heterocycles that are difficult to obtain otherwise.

Facile Phenylphosphinidene Transfer Reactions from Carbene–Phosphinidene Zinc Complexes

AbstractPhosphinidenes [R‐P] are convenient P1 building blocks for the synthesis of a plethora of organophosphorus compounds. Thus far, transition‐metal‐complexed phosphinidenes have been used for their singlet ground‐state reactivity to promote selective addition and insertion reactions. One disadvantage of this approach is that after transfer of the P1 moiety to the substrate, a challenging demetallation step is required to provide the free phosphine. We report a simple method that enables the Lewis acid promoted transfer of phenylphosphinidene, [PhP], from NHC=PPh adducts (NHC=N‐heterocyclic carbene) to various substrates to produce directly uncoordinated phosphorus heterocycles that are difficult to obtain otherwise.

Design and Synthesis of P2-P4 Macrocycles Containing a Unique Spirocyclic Proline: A New Class of HCV NS3/4A Inhibitors.

A new class of hepatitis C NS3/4A inhibitors was identified by introducing a novel spirocyclic proline-P2 surrogate onto the P2-P4 macrocyclic core of MK-5172 (grazoprevir). The potency profile of new analogues showed excellent pan-genotypic activity for most compounds. The potency evaluation included the most difficult genotype 3a (EC50 values ≤10 nM) and other key genotype 1b mutants. Molecular modeling was used to design new target compounds and rationalize our results. A synthetic approach based on the Julia-Kocienski olefination and macrolactamization to assemble the P2-P4 macrocyclic core containing the novel spirocyclic proline-P2 moiety is presented as well.

Density Functional Study of Oxygen Insertion into Niobium–Phosphorus Bonds: Novel Mechanism for Liberating P3– Synthons

We explore the mechanism of oxygen insertion into niobium–phosphorus bonds to liberate synthetically relevant, phosphorus-containing molecules. Oxygen insertion mechanisms generally proceed through either direct oxygen insertion from an oxo ligand, M═O (oxy-insertion), or an insertion of an oxygen atom from an external oxidant, OY (Baeyer–Villiger, BV). Computational methods were employed to elucidate the preferred mechanism for the liberation of the phosphorus moiety from [(η2-P3)Nb(ODipp)3] (Dipp = 2,6-iPr2C6H3, P3 = P3-SnPh3) when treated with pyridine-N-oxide as an external oxidant. Careful analysis of conformational isomers and energies clearly suggests that the BV mechanism is the preferred pathway toward phosphorus liberation. Once free, the P3 moiety can react with 1,3-cyclohexadiene to form the Diels–Alder product, which is also modeled in the computational study.

A Modified P1 Moiety Enhances In Vitro Antiviral Activity against Various Multidrug-Resistant HIV-1 Variants and In Vitro Central Nervous System Penetration Properties of a Novel Nonpeptidic Protease Inhibitor, GRL-10413.

We report here that GRL-10413, a novel nonpeptidic HIV-1 protease inhibitor (PI) containing a modified P1 moiety and a hydroxyethylamine sulfonamide isostere, is highly active against laboratory HIV-1 strains and primary clinical isolates (50% effective concentration [EC50] of 0.00035 to 0.0018 μM), with minimal cytotoxicity (50% cytotoxic concentration [CC50] = 35.7 μM). GRL-10413 blocked the infectivity and replication of HIV-1NL4-3 variants selected by use of atazanavir, lopinavir, or amprenavir (APV) at concentrations of up to 5 μM (EC50 = 0.0021 to 0.0023 μM). GRL-10413 also maintained its strong antiviral activity against multidrug-resistant clinical HIV-1 variants isolated from patients who no longer responded to various antiviral regimens after long-term antiretroviral therapy. The development of resistance against GRL-10413 was significantly delayed compared to that against APV. In addition, GRL-10413 showed favorable central nervous system (CNS) penetration properties as assessed with an in vitro blood-brain barrier (BBB) reconstruction system. Analysis of the crystal structure of HIV-1 protease in complex with GRL-10413 demonstrated that the modified P1 moiety of GRL-10413 has a greater hydrophobic surface area and makes greater van der Waals contacts with active site amino acids of protease than in the case of darunavir. Moreover, the chlorine substituent in the P1 moiety interacts with protease in two distinct configurations. The present data demonstrate that GRL-10413 has desirable features for treating patients infected with wild-type and/or multidrug-resistant HIV-1 variants, with favorable CNS penetration capability, and that the newly modified P1 moiety may confer desirable features in designing novel anti-HIV-1 PIs.