Cell‐Based Optimization of Covalent Reversible Ketoamide Inhibitors Bridging the Unprimed to the Primed Site of the Proteasome β5 Subunit

Stubba, Daniel; Bensinger, Dennis; Steinbacher, Janika; Proskurjakov, Lilia; Gómez, Álvaro Salcedo; Schmidt, Uwe; Roth, Stefan; Schmitz, Katja; Schmidt, Boris

doi:10.1002/cmdc.201900472

Cited by 4 publications

(4 citation statements)

References 40 publications

(123 reference statements)

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“…Many previous studies have demonstrated that targeting the primed site can be an effective strategy for developing potent or selective inhibitors of proteases of viruses such as human immunodeficiency virus and hepatitis C virus [ [25] , [26] , [27] ]. Recently, several groups have reported α-keto phenylamide and epoxyketone based proteasome inhibitors targeting the primed site to increase potency or overcome resistance [ 21 , 45 ]. It was shown that the targeting of the primed site by 3-phenoxy phenyl could increase β5 inhibition of a compound.…”

Section: Discussionmentioning

confidence: 99%

A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities

Wang

Liang²,

Chan

et al. 2021

European Journal of Medicinal Chemistry

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Inhibitors of the proteasome have been extensively studied for their applications in the treatment of human diseases such as hematologic malignancies, autoimmune disorders, and viral infections. Many of the proteasome inhibitors reported in the literature target the non-primed site of proteasome's substrate binding pocket. In this study, we designed, synthesized and characterized a series of novel α-keto phenylamide derivatives aimed at both the primed and non-primed sites of the proteasome. In these derivatives, different substituted phenyl groups at the head group targeting the primed site were incorporated in order to investigate their structure-activity relationship and optimize the potency of α-keto phenylamides. In addition, the biological effects of modifications at the cap moiety, P1、P2 and P3 side chain positions were explored. Many derivatives displayed highly potent biological activities in proteasome inhibition and anticancer activity against a panel of six cancer cell lines, which were further rationalized by molecular modeling analyses. Furthermore, a representative α-ketoamide derivative was tested and found to be active in inhibiting the cellular infection of SARS-CoV-2 which causes the COVID-19 pandemic. These results demonstrate that this new class of α-ketoamide derivatives are potent anticancer agents and provide experimental evidence of the anti-SARS-CoV-2 effect by one of them, thus suggesting a possible new lead to develop antiviral therapeutics for COVID-19.

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Section: Discussionmentioning

confidence: 99%

A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities

Wang

Liang²,

Chan

et al. 2021

European Journal of Medicinal Chemistry

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“…The crystal structures show that its phenylamide moiety projects into the primed site (S1′) that was rarely investigated in past drug development efforts (Figure ). Previous studies imply that optimization of the α-keto phenylamide with different substitutions at its phenyl group increases the β5 binding potency and reduces the adverse events, such as peripheral neuropathy. , Exploiting the primed site has been shown as an effective strategy for improving the specificity and potency of protease inhibitors. − Furthermore, α-ketoamide’s electrophile shows a reversible inhibition against the enzyme with the potential for the treatment of solid tumors . The reversible inhibition may make it a safer option compared to irreversible covalent inhibitors .…”

Section: Introductionmentioning

confidence: 99%

“…8 Previous studies imply that optimization of the α-keto phenylamide with different substitutions at its phenyl group increases the β5 binding potency and reduces the adverse events, such as peripheral neuropathy. 9,10 Exploiting the primed site has been shown as an effective strategy for improving the specificity and potency of protease inhibitors. 11−13 Furthermore, α-ketoamide's electrophile shows a reversible inhibition against the enzyme with the potential for the treatment of solid tumors.…”

Section: ■ Introductionmentioning

confidence: 99%

Elucidation of the α-Ketoamide Inhibition Mechanism: Revealing the Critical Role of the Electrostatic Reorganization Effect of Asp17 in the Active Site of the 20S Proteasome

Zhou,

Sang,

Wang

et al. 2023

ACS Catal.

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The 20S proteasome is an attractive drug target for the development of anticancer agents because it plays an important role in cellular protein degradation. It has a threonine residue that can act as a nucleophile to attack inhibitors with an electrophilic warhead, forming a covalent adduct. Fundamental understanding of the reaction mechanism between covalent inhibitors and the proteasome may assist the design and refinement of compounds with the desired activity. In this study, we investigated the covalent inhibition mechanism of an α-keto phenylamide inhibitor of the proteasome. We calculated the noncovalent binding free energy using the PDLD/S-LRA/β method and the reaction free energy through the empirical valence bond method (EVB). Several possible reaction pathways were explored. Subsequently, we validated the calculated activation and reaction free energies of the most plausible pathways by performing kinetic experiments. Furthermore, the effects of different ionization states of Asp17 on the activation energy at each step were also discussed. The results revealed that the ionization states of Asp17 remarkably affect the activation energies and there is an electrostatic reorganization of Asp17 during the course of the reaction. Our results demonstrate the critical electrostatic effect of Asp17 in the active site of the 20S proteasome.

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“…In recent years, bortezomib has been gradually applied to fish. Stubba et al (2019) explored the effect of bortezomib on tactile response using a zebrafish embryo model and observed that the tactile response of embryos treated with bortezomib was significantly decreased [ 22 ]. Jin et al (2018) discovered that bortezomib inhibited hypoxia-induced degeneration of ILCM (interlamellar cell mass) in goldfish and affected gill remodeling [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

The transcriptomic responses of blunt snout bream (Megalobrama amblycephala) to acute hypoxia stress alone, and in combination with bortezomib

Zhao

Pan

et al. 2022

BMC Genomics

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Background Blunt snout bream (Megalobrama amblycephala) is sensitive to hypoxia. A new blunt snout bream strain, “Pujiang No.2”, was developed to overcome this shortcoming. As a proteasome inhibitor, bortezomib (PS-341) has been shown to affect the adaptation of cells to a hypoxic environment. In the present study, bortezomib was used to explore the hypoxia adaptation mechanism of “Pujiang No.2”. We examined how acute hypoxia alone (hypoxia-treated, HN: 1.0 mg·L− 1), and in combination with bortezomib (hypoxia-bortezomib-treated, HB: Use 1 mg bortezomib for 1 kg fish), impacted the hepatic ultrastructure and transcriptome expression compared to control fish (normoxia-treated, NN). Results Hypoxia tolerance was significantly decreased in the bortezomib-treated group (LOEcrit, loss of equilibrium, 1.11 mg·L− 1 and 1.32 mg·L− 1) compared to the control group (LOEcrit, 0.73 mg·L− 1 and 0.85 mg·L− 1). The HB group had more severe liver injury than the HN group. Specifically, the activities of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) in the HB group (52.16 U/gprot, 32 U/gprot) were significantly (p < 0.01) higher than those in the HN group (32.85 U/gprot, 21. 68 U/gprot). In addition, more severe liver damage such as vacuoles, nuclear atrophy, and nuclear lysis were observed in the HB group. RNA-seq was performed on livers from the HN, HB and NN groups. KEGG pathway analysis disclosed that many DEGs (differently expressed genes) were enriched in the HIF-1, FOXO, MAPK, PI3K-Akt and AMPK signaling pathway and their downstream. Conclusion We explored the adaptation mechanism of “Pujiang No.2” to hypoxia stress by using bortezomib, and combined with transcriptome analysis, accurately captured the genes related to hypoxia tolerance advantage.

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Cell‐Based Optimization of Covalent Reversible Ketoamide Inhibitors Bridging the Unprimed to the Primed Site of the Proteasome β5 Subunit

Cited by 4 publications

References 40 publications

A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities

A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities

Elucidation of the α-Ketoamide Inhibition Mechanism: Revealing the Critical Role of the Electrostatic Reorganization Effect of Asp17 in the Active Site of the 20S Proteasome

The transcriptomic responses of blunt snout bream (Megalobrama amblycephala) to acute hypoxia stress alone, and in combination with bortezomib

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