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Acta Pharmaceutica Sinica B

Elsevier BV

All preprints, ranked by how well they match Acta Pharmaceutica Sinica B's content profile, based on 11 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
A new long-acting GLP-1 derivative 6- KTP ameliorates body weight and lipid metabolism in DIO mice

peixiu, w.; Ran, Y.

2019-11-18 physiology 10.1101/846717 medRxiv
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As a global epidemic, obesity has become the biggest challenge facing global and public health. Glucagon-like peptide-1(GLP-1) has been able to inhibit appetite, slow gastric emptying and reduce body weight. We designed a novel long-acting GLP-1 derivative 6-KTP based on wild-type GLP-1 and performed its pharmacodynamics study on obesity in DIO mice. DIO mice were treated once daily with subcutaneous injections of 6-KTP (1.8 mg/kg body weight), Liraglutide (0.4 mg/kg body weight) or vehicle (phosphate buffered saline (PBS), pH 7.4) for 12 weeks. The results show that 6-KTP decreased food intake, induced anorexia and weight loss, and improved blood lipid and lipid metabolism in DIO mice.

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Celastrol directly inhibits PFKM to induce weight loss and leptin sensitization

Wang, K.; wu, x.; zhuang, y.; sun, h.; Wang, F.; wang, t.; Zhang, Z.

2020-09-08 physiology 10.1101/2020.09.06.284752 medRxiv
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Despite the prevalence of obesity and related health consequences around the globe, effective treatments for inducing healthy weight loss are still lacking. Celastrol is a pentacyclic triterpene that was recently identified as a potent anti-obesity agent. Celastrol increases sensitivity to leptin, but the molecular target of celastrol is unknown. Therefore, the mechanisms by which this agent exerts its anti-obesity effect remain elusive. Using tissue-specific ABPP (activity-based protein profiling), we found that PFKM, a rate-limiting enzyme for glycolysis in skeletal muscle, is a direct target of celastrol. Celastrol inhibited PFKM enzymatic activity, and Pfkm knockout mice were resistant to a high fat diet, were hypersensitive to exogenous leptin, and were unresponsive to celastrol. PFKM inhibition led to activation of AMPK and inactivation of ACC in cultured myotubes and mouse skeletal muscle. Specific loss of AMPK in muscle significantly attenuated the anti-obesity effects of celastrol. Further, PFKM inhibition and subsequent activation of the AMPK/ACC signaling pathway reduced levels of free fatty acids by switching energy expenditure and consequently decreasing levels of SOCS1 expression, which are both required for leptin sensitization in 293t/hLepRb cells and mice. Finally, using a high throughput compound screen we identified an alternative PFKM inhibitor, 3-79, which exhibits a strong anti-obesity effect and non-covalent binding capacity. This compound is a promising agent for treating obesity in the clinic.

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Resveratrol targets G-quadruplexes to exert its pharmacological effects

Soriano-Lerma, A.; Sanchez-Martin, V.; Murciano-Calles, J.; Ortiz-Gonzalez, M.; Tello-Lopez, M. J.; Perez-Carrasco, V.; Linde-Rodriguez, A.; Ramirez-Macias, I.; Gomez-Pinto, I.; Lopez-Aliaga, I.; Soriano, M.; Garcia-Salcedo, J. A.

2024-08-02 physiology 10.1101/2024.07.29.605564 medRxiv
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Resveratrol (RSV) is one of the most studied and used biomolecules, for which many pharmacological effects targeting multiple tissues have been described. However, a common underlying mechanism driving its full pharmacological activity has not been elucidated to date. G-quadruplexes (G4s) are non-canonical nucleic acid structures found in promoters and involved in controlling gene transcription. This study demonstrates a G4-dependent mode of action for RSV, explaining its multi-target traits. RSV was shown to stabilise cellular G4s, which accumulate around double strand breaks (DSBs) in the promoters of differentially expressed genes (DEGs). G4 targeting triggers DNA damage and controls gene expression. Unravelling the main mode of action of RSV will be helpful to improve its therapeutic potential in a wide variety of health scenarios.

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Novel circadian clock activators display anti-obesity efficacy via suppression of adipocyte development and hypertrophy

Xiong, X.; Pangemanan, J.; Kiperman, T.; Tang, L.; Fang, Z.; Agua, A.; Huang, W.; Horne, D.; Ma, K.

2026-01-09 physiology 10.64898/2026.01.08.698495 medRxiv
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The circadian clock exerts temporal coordination of metabolic processes to maintain homeostasis, and its disruption predisposes to the development of obesity and insulin resistance. Despite the established genetic basis of clock modulation in adipocyte development, whether it can be targeted for anti-obesity interventions remains to be explored. Here we report the novel actions of clock-activating molecules, chlorhexidine and a new derivative CM002, on inhibiting adipocyte development and hypertrophy that results in anti-obesity efficacy in vivo. Both chlorhexidine and CM002 were sufficient to activate clock in adipocytes with induction of core clock components and shortening of clock period length. Consistent with their clock-activating properties, these compounds suppressed the distinct lineage commitment and terminal differentiation stages of adipogenic precursor cells mediated via activation of the Wnt signaling pathway. Furthermore, CM002 attenuated lipid storage and adipocyte hypertrophy by suppressing the lipogenic and adipogenic program in a clock-dependent manner. Most importantly, CM002 administration in mice with diet-induced obesity was sufficient to induce clock activation in adipose depots, leading to robust suppression of adipogenic factors and lipogenic enzymes with marked effect on reducing fat mass and promoting insulin sensitivity. Collectively, our findings uncovered the anti-adipogenic properties of novel small molecule clock activators with demonstrated anti-obesity efficacy. These compounds provide novel chemical probes to dissect clock function in metabolic regulations with translational potential toward development of first-in-class clock-targeting drugs for anti-obesity therapy. HighlightsO_LIDiscovery of the anti-adipogenic properties of the clock activator chlorhexidine C_LIO_LIIdentification of a new clock-activating molecule CM002 C_LIO_LICM002 inhibits the lineage commitment and terminal differentiation of adipocytes C_LIO_LIClock activation by CM002 suppresses lipid storage in mature adipocytes C_LIO_LICM002 displays anti-obesity efficacy in diet-induced obesity model C_LI

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SIRT5-mediated GLS and GDH desuccinylation attenuates autophagy in MAC-T cells induced by ammonia

Wang, Y.; Yang, H.; Gao, S.; Lu, G.; He, J.; Dong, J.; Zhang, X.; Liu, L.; Zhong, K.; Zha, G.; Han, L.; Guo, S.; Li, H.

2024-08-26 physiology 10.1101/2024.08.26.609685 medRxiv
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Our previous research revealed that NH3 regulated autophagy dependent on SIRT5 in MAC-T cells. Interestingly, SIRT5 reduced the content of NH3 and glutamate by inhibiting GLS activity, ADP/ATP value also declined. In this study, SIRT5 interacted with endogenous GLS and GDH, and had no effect on endogenous GLS and GDH expression. SIRT5 declined significantly the succinylation levels of GLS and GDH, and further reduced the enzymatic activity of GLS and GDH. SIRT5 declined the glutamine metabolism, which attenuated ammonia release in MAC-T cells, accompanying with cellular autophagy decline, reducing the formation of autophagosome. Deletion of SIRT5 increased the content of NH3 and glutamate, as well as promotes autophagy, which could be alleviated by SIRT5 overexpression. SIRT5 KO was associated with increased succinylation and activity of GLS and GDH, as well as autophagy response in MAC-T cells. Furthermore, SIRT5 promoted the maintenance of mitochondria homeostasis. Mechanistically, SIRT5 modulated the succinylation levels and enzymatic activities of GLS and GDH in mitochondria and promoted the maintenance of mitochondria homeostasis, further attenuating ammonia-stimulated autophagy in MAC-T cells. HighlightsO_LISIRT5 catalyzed lysine desuccinylation of GLS and GDH. C_LIO_LIGLS and GDH enzymatic activity were enhanced by lysine succinylation. C_LIO_LIGLS and GDH were required for SIRT5 to regulate ammonia-induced cellular autophagy. C_LIO_LISIRT5 promoted the maintenance of mitochondrial homeostasis C_LI

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The P3 O-Tert-Butyl-Threonine is Key to High Cellular and Antiviral Potency for Aldehyde-Based SARS-CoV-2 Main Protease Inhibitors

Ma, Y.; Yang, K.; Geng, Z. Z.; Alugubellia, Y. R.; Shaabani, N.; Vatansever, E. C.; Ma, X. R.; Cho, C.-C.; Khatua, K.; Blankenship, L.; Yu, G.; Sankaran, B.; Li, P.; Allen, R.; Ji, H.; Xu, S.; Liu, W. R.

2021-12-21 biochemistry 10.1101/2021.12.18.473326 medRxiv
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As an essential enzyme to SARS-CoV-2, main protease (MPro) is a viable target to develop antivirals for the treatment of COVID-19. By varying chemical compositions at both P2 and P3 sites and the N-terminal protection group, we synthesized a series of MPro inhibitors that contain {beta}-(S-2-oxopyrrolidin-3-yl)-alaninal at the P1 site. These inhibitors have a large variation of determined IC50 values that range from 4.8 to 650 nM. The determined IC50 values reveal that relatively small side chains at both P2 and P3 sites are favorable for achieving high in vitro MPro inhibition potency, the P3 site is tolerable toward unnatural amino acids with two alkyl substituents on the -carbon, and the inhibition potency is sensitive toward the N-terminal protection group. X-ray crystal structures of MPro bound with 16 inhibitors were determined. All structures show similar binding patterns of inhibitors at the MPro active site. A covalent interaction between the active site cysteine and a bound inhibitor was observed in all structures. In MPro, large structural variations were observed on residues N142 and Q189. All inhibitors were also characterized on their inhibition of MPro in 293T cells, which revealed their in cellulo potency that is drastically different from their in vitro enzyme inhibition potency. Inhibitors that showed high in cellulo potency all contain O-tert-butyl-threonine at the P3 site. Based on the current and a previous study, we conclude that O-tert-butyl-threonine at the P3 site is a key component to achieve high cellular and antiviral potency for peptidyl aldehyde inhibitors of MPro. This finding will be critical to the development of novel antivirals to address the current global emergency of concerning the COVID-19 pandemic.

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An Azapeptide Platform in Conjunction with Covalent Warheads to Uncover High-Potency Inhibitors for SARS-CoV-2 Main Protease

Khatua, K.; Alugubelli, Y. R.; Yang, K.; Reddy, V.; Blankenship, L.; Coleman, D.; Atla, S.; Chaki, S.; Geng, Z.; Ma, X.; Xiao, J.; Chen, P.-H.; Cho, C.-C.; Vatansever, E. C.; Ma, Y.; Yu, G.; Neuman, B.; Xu, S.; Liu, W. R.

2023-04-12 biochemistry 10.1101/2023.04.11.536467 medRxiv
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Main protease (MPro) of SARS-CoV-2, the viral pathogen of COVID-19, is a crucial nonstructural protein that plays a vital role in the replication and pathogenesis of the virus. Its protease function relies on three active site pockets to recognize P1, P2, and P4 amino acid residues in a substrate and a catalytic cysteine residue for catalysis. By converting the P1 C atom in an MPro substrate to nitrogen, we showed that a large variety of azapeptide inhibitors with covalent warheads targeting the MPro catalytic cysteine could be easily synthesized. Through the characterization of these inhibitors, we identified several highly potent MPro inhibitors. Specifically, one inhibitor, MPI89 that contained an aza-2,2-dichloroacetyl warhead, displayed a 10 nM EC50 value in inhibiting SARS-CoV-2 from infecting ACE2+ A549 cells and a selectivity index of 875. The crystallography analyses of MPro bound with 6 inhibitors, including MPI89, revealed that inhibitors used their covalent warheads to covalently engage the catalytic cysteine and the aza-amide carbonyl oxygen to bind to the oxyanion hole. MPI89 represents one of the most potent MPro inhibitors developed so far, suggesting that further exploration of the azapeptide platform and the aza-2,2-dichloroacetyl warhead is needed for the development of potent inhibitors for the SARS-CoV-2 MPro as therapeutics for COVID-19.

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KYLO-0603, a novel liver-targeting, thyroid hormone recep-tor-β agonist for the treatment of MASH

Lu, X.; Wang, S.; Du, Y.; Xie, B.; Chen, Q.; Lin, J.; Chen, B.; Cui, K.

2025-02-11 biochemistry 10.1101/2025.02.09.637336 medRxiv
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Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive liver disease associated with liver-related complications and death. Kylo-0603 is a novel agonist for the thyroid hormone receptor {beta} (THR-{beta}) that has been developed by merging the structures of three acetylgalactosamine (GalNAc)-modified ASPGR ligands with a triiodothyronine (T3) analog. This unique design allows for both THR-{beta} activation and targeted delivery to hepatocytes, significantly reducing the risk of adversed effects related to increased systemic thyroid hormone-like effects. Additionally, it effectively lowers serum cholesterol by as much as 69.2% and low-density lipoprotein cholesterol (LDL-C) levels by up to 88.2% in the MASH mouse model. Meanwhile, Kylo-0603 was shown to reduce steatosis by up to 1.3 points (P < 0.001), inflammation by 1.8 points (P < 0.0001), and ballooning by 0.8 points (P < 0.01). The non-alcoholic steatohepatitis (NASH) activity score (NAS) decreased by up to 3.7 points (P < 0.0001), and the fibrosis score dropped by 0.6 points (P < 0.05). These findings suggest that Kylo-0603 is effective in enhancing liver tissue NASH status and inhibiting fibrosis progression. In summary, Kylo-0603, as a highly both tissue and target selective and low-toxicity THR-{beta} agonist, shows significant promise for treating MASH and is likely to emerge as a new therapeutic option for patients with this condition.

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Discovery of potent inhibitors of PLproCoV2 by screening libraries of selen-containing compounds

Weglarz-Tomczak, E.; Tomczak, J. M.; Giurg, M.; Burda-Grabowska, M.

2020-05-20 biochemistry 10.1101/2020.05.20.107052 medRxiv
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A collection of twelve organoselenium compounds, structural analogues of antioxidant drug ebselen were screened for inhibition of the papain-like protease (PLpro) from the acute respiratory syndrome coronavirus 2 (SARS-CoV-2, CoV2). This cysteine protease, being responsible for the hydrolysis of peptide bonds between specific amino acids, plays a critical role in CoV2 replication and in assembly of new viral particles within human cells. The activity of the PLpro CoV2 is essential for the progression of coronavirus disease 2019 (COVID-19) and it constitutes a key target for the development of anti-COVID-19 drugs. Here, we identified four strong inhibitors that bind favorably to the PLpro CoV2 with the IC50 in the nanomolar range.

10
Identification of PTGR2 inhibitors as a new therapy for diabetes and obesity

Chang, Y.-C.; Chuang, L.-M.

2024-12-20 physiology 10.1101/2024.12.17.629058 medRxiv
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Peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) is a master transcriptional regulator of systemic insulin sensitivity and energy balance. The anti-diabetic drug thiazolidinediones (TZDs) are potent synthetic PPAR{gamma} ligands with undesirable side effects, including obesity, fluid retention, and osteoporosis. 15-keto prostaglandin E2 (15-keto-PGE2) is an endogenous PPAR{gamma} ligand metabolized by prostaglandin reductase 2 (PTGR2). Here, we confirmed that 15-keto-PGE2 binds and activates PPAR{gamma} via covalent binding. In patients with type 2 diabetes and obese mice, serum 15-keto-PGE2 levels were decreased. Administration of 15-keto-PGE2 improves glucose homeostasis and prevented diet-induced obesity in mice. Either genetic inhibition of PTGR2 or PTGR2 inhibitor BPRPT0245 protected mice from diet-induced obesity, insulin resistance, and hepatic steatosis without fluid retention and osteoporosis. In conclusion, inhibition of PTGR2 is a new therapeutic approach to treat diabetes and obesity through increasing endogenous PPAR{gamma} ligands without side effects of synthetic PPAR{gamma} ligands TZDs.

11
Cellular Activities of SARS-CoV-2 Main Protease Inhibitors Reveal Their Unique Characteristics

Cao, W.; Cho, C.-C. D.; Geng, Z. Z.; Ma, X. R.; Allen, R.; Shaabani, N.; Vatansever, E. C.; Alugubelli, Y. R.; Ma, Y.; Ellenburg, W. H.; Yang, K. S.; Qiao, Y.; Ji, H.; Xu, S.; Liu, W. R.

2021-06-09 biochemistry 10.1101/2021.06.08.447613 medRxiv
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As an essential enzyme of SARS-CoV-2, the pathogen of COVID-19, main protease (MPro) triggers acute toxicity to its human cell host, an effect that can be alleviated by an MPro inhibitor with cellular potency. By coupling this toxicity alleviation with the expression of an MPro-eGFP fusion protein in a human cell host for straightforward characterization with fluorescent flow cytometry, we developed an effective method that allows bulk analysis of cellular potency of MPro inhibitors. In comparison to an antiviral assay in which MPro inhibitors may target host proteases or other processes in the SARS-CoV-2 life cycle to convene strong antiviral effects, this novel assay is more advantageous in providing precise cellular MPro inhibition information for assessment and optimization of MPro inhibitors. We used this assay to analyze 30 literature reported MPro inhibitors including MPI1-9 that were newly developed aldehyde-based reversible covalent inhibitors of MPro, GC376 and 11a that are two investigational drugs undergoing clinical trials for the treatment of COVID-19 patients in United States, boceprevir, calpain inhibitor II, calpain inhibitor XII, ebselen, bepridil that is an antianginal drug with potent anti-SARS-CoV-2 activity, and chloroquine and hydroxychloroquine that were previously shown to inhibit MPro. Our results showed that most inhibitors displayed cellular potency much weaker than their potency in direct inhibition of the enzyme. Many inhibitors exhibited weak or undetectable cellular potency up to 10 M. On contrary to their strong antiviral effects, 11a, calpain inhibitor II, calpain XII, ebselen, and bepridil showed relatively weak to undetectable cellular MPro inhibition potency implicating their roles in interfering with key steps other than just the MPro catalysis in the SARS-CoV-2 life cycle to convene potent antiviral effects. characterization of these molecules on their antiviral mechanisms will likely reveal novel drug targets for COVID-19. Chloroquine and hydroxychloroquine showed close to undetectable cellular potency to inhibit MPro. Kinetic recharacterization of these two compounds rules out their possibility as MPro inhibitors. Our results also revealed that MPI5, 6, 7, and 8 have high cellular and antiviral potency with both IC50 and EC50 values respectively below 1 M. As the one with the highest cellular and antiviral potency among all tested compounds, MPI8 has a remarkable cellular MPro inhibition IC50 value of 31 nM that matches closely to its strong antiviral effect with an EC50 value of 30 nM. Given its strong cellular and antiviral potency, we cautiously suggest that MPI8 is ready for preclinical and clinical investigations for the treatment of COVID-19.

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Oolonghomobisflavans from Camellia sinensis disaggregate tau fibrils across Alzheimer's disease models

Duangjan, C.; Chang, X.; Seidler, P. M.; Curran, S. P.

2024-03-01 physiology 10.1101/2024.02.26.582120 medRxiv
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Alzheimers disease (AD) is a common debilitating neurodegenerative disease with limited treatment options. Amyloid-{beta} (A{beta}) and tau fibrils are well-established hallmarks of AD, which can induce oxidative stress, neuronal cell death, and are linked to disease pathology. Here, we describe the effects of Oolonghomobisflavan A (OFA) and Oolonghomobisflavan B (OFB) on tau fibril disaggregation and prionogenic seeding. Transcriptomic analysis of OF-treated animals reveals the induction of a proteostasis-enhancing and health-promoting signature. OFA treatment reduced the burden of Tau protein aggregation in a C. elegans model expressing pathogenic human tau ("hTau-expressing") and promoted Tau disaggregation and inhibited seeding in assays using ex vivo brain-derived paired helical filament tau protein fibrils from Alzheimers disease brain donors. Correspondingly, treatment with OF improved multiple fitness and aging-related health parameters in the hTau-expressing C. elegans model, including reproductive output, muscle function, and importantly, reversed the shortened lifespan stemming from pathogenic Tau expression. Collectively, this study provides new evidence supporting the neuroprotective effects of OFs and reveal a new therapeutic strategy for targeting AD and other neurodegenerative diseases characterized by tauopathy.

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Mitorubin, berberrubine-based compounds that improve mitochondrial function, exhibit cardioprotective effects against age-related cardiac dysfunction

Sato, M.; Tanabu, D.; Torigoe, D.; Kadomatsu, T.; Taniwaka, K.; Ogata, Y.; Shiiba, I.; Suzuki, Y.; Inatome, R.; Tokuyama, T.; Takeiwa, T.; Inoue, S.; Kanai, E.; Hamano, T.; Hirata, H.; Kanamitsu, K.; Kusuhara, H.; Yokosuka, A.; Mimaki, Y.; Abe, H.; Oike, Y.; Yanagi, S.

2025-05-03 biochemistry 10.1101/2025.05.01.651794 medRxiv
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Mitochondria play a central role in cellular energy metabolism and homeostasis, and their dysfunction is closely linked to the progression of age-related diseases. The mitochondrial ubiquitin ligase MITOL (also known as MARCHF5) is a key regulator of mitochondrial dynamics and function, and reduced MITOL expression in the mouse heart has been implicated in mitochondrial dysfunction and cardiac aging. In this study, we identified berberrubine as a compound that promotes MITOL expression and activates mitochondria. We further assembled a group of berberrubine-based compounds, including its quinoid form and a newly developed water-soluble derivative, and collectively named them "Mitorubin" as mitochondria-activating compounds with therapeutic potential. While conventional berberrubine has poor water solubility, the addition of acetic acid significantly improved its solubility, enabling formulation as a solution. Mitorubin enhanced MITOL expression in cultured cells, increased mitochondrial DNA content and expression of mitochondrial proteins, and promoted mitochondrial respiration. In a model of age-related cardiac dysfunction, oral administration of Mitorubin restored mitochondrial function, improved cardiac performance, suppressed myocardial hypertrophy, and alleviated pulmonary congestion. Moreover, Mitorubin did not shorten lifespan in aged mice and significantly extended lifespan in high-fat diet-fed mice, suggesting both safety and efficacy under chronic administration. These findings suggest that Mitorubin is a promising mitochondrial activator and may represent a novel therapeutic strategy for age-related diseases.

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Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro

Su, H.; Yao, S.; Zhao, W.; Li, M.; Liu, J.; Shang, W.; Xie, H.; Ke, C.; Gao, M.; Yu, K.; Liu, H.; Shen, J.; Tang, W.; Zhang, L.; Zuo, J.; Jiang, H.; Bai, F.; Wu, Y.; Ye, Y.; Xu, Y.

2020-04-14 molecular biology 10.1101/2020.04.13.038687 medRxiv
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Human infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause coronavirus disease 19 (COVID-19) and there is currently no cure. The 3C-like protease (3CLpro), a highly conserved protease indispensable for replication of coronaviruses, is a promising target for development of broad-spectrum antiviral drugs. To advance the speed of drug discovery and development, we investigated the inhibition of SARS-CoV-2 3CLpro by natural products derived from Chinese traditional medicines. Baicalin and baicalein were identified as the first non-covalent, non-peptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography is distinctly different from those of known inhibitors. Baicalein is perfectly ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a "shield" in front of the catalytic dyad to prevent the peptide substrate approaching the active site. The simple chemical structure, unique mode of action, and potent antiviral activities in vitro, coupled with the favorable safety data from clinical trials, emphasize that baicalein provides a great opportunity for the development of critically needed anti-coronaviral drugs.

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ACIS, A Novel KepTide™, Binds to ACE-2 Receptor and Inhibits the Infection of SARS-CoV2 Virus in vitro in Primate Kidney Cells: Therapeutic Implications for COVID-19

Roy, A.; Gottschalk, G.; Knox, K.; Luan, C. H.; Keating, J.; Kesler, K.

2020-10-14 biochemistry 10.1101/2020.10.13.337584 medRxiv
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Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a virus known as SARS-Coronavirus 2 (SARS-CoV2). Without a targeted-medicine, this disease has been causing a massive humanitarian crisis not only in terms of mortality, but also imposing a lasting damage to social life and economic progress of humankind. Therefore, an immediate therapeutic strategy needs to be intervened to mitigate this global crisis. Here, we report a novel KepTide (Knock-End Peptide) therapy that nullifies SARS-CoV2 infection. SARS-CoV2 employs its surface glycoprotein "spike" (S-glycoprotein) to interact with angiotensin converting enzyme-2 (ACE-2) receptor for its infection in host cells. Based on our in-silico-based homology modeling study validated with a recent X-ray crystallographic structure (PDB ID:6M0J), we have identified that a conserved motif of S-glycoprotein that intimately engages multiple hydrogen-bond (H-bond) interactions with ACE-2 enzyme. Accordingly, we designed a peptide, termed as ACIS (ACE-2 Inhibitory motif of Spike), that displayed significant affinity towards ACE-2 enzyme as confirmed by biochemical assays such as BLItz and fluorescence polarization assays. Interestingly, more than one biochemical modifications were adopted in ACIS in order to enhance the inhibitory action of ACIS and hence called as KEpTide. Consequently, a monolayer invasion assay, plaque assay and dual immunofluorescence analysis further revealed that KEpTide efficiently mitigated the infection of SARS-CoV2 in vitro in VERO E6 cells. Finally, evaluating the relative abundance of ACIS in lungs and the potential side-effects in vivo in mice, our current study discovers a novel KepTide therapy that is safe, stable, and robust to attenuate the infection of SARS-CoV2 virus if administered intranasally.

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Structural basis of nirmatrelvir and ensitrelvir resistance profiles against SARS-CoV-2 Main Protease naturally occurring polymorphisms

Noske, G. D.; Silva, E. S.; Godoy, M. O.; Dolci, I.; Fernandes, R. S.; Guido, R. V. C.; Sjo, P.; Oliva, G.; Godoy, A. S.

2022-09-01 biochemistry 10.1101/2022.08.31.506107 medRxiv
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SARS-CoV-2 is the causative agent of COVID-19. Mpro is the main viral protease, with a critical role in replication and, therefore, an attractive target for antiviral drug discovery. The clinically approved drug nirmatrelvir from Pfizer, and the clinical candidate ensitrelvir from Shionogi Pharmaceuticals had so far showed great potential for treatment of viral infections. Despite the importance of new therapeutics, the broad use of antivirals is often associated with mutation selection and resistance generation. Herein, we characterized 14 naturally occurring polymorphisms that are already in circulation and are within the radius of action of these two antivirals. Nirmatrelvir retained most of its in vitro activity against most polymorphism tested, while mutants G143S and Q189K were associated with higher resistance. For ensitrelvir, higher resistance was observed for polymorphisms M49I, G143S and R188S, but not for Q189K, suggesting a distinct resistance profile difference between the two inhibitors. The crystal structures of selected polymorphism reveal the structural basis for resistance generation. Our data will assist the monitoring of potential resistant strains, support the design of combined therapy to avoid resistance, as well as assist the development of a next generation of Mpro inhibitors

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Structure-Based Design, Synthesis and Biological Evaluation of Peptidomimetic Aldehydes as a Novel Series of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease

Dai, W.; Zhang, B.; Jiang, X.-M.; Su, H.; Li, J.; Zhao, Y.; Xie, X.; Jin, Z.; Peng, J.; Liu, F.; Li, C.; Li, Y.; Bai, F.; Wang, H.; Cheng, X.; Cen, X.; Hu, S.; Yang, X.; Wang, J.; Liu, X.; Xiao, G.; Jiang, H.; Rao, Z.; Zhang, L.; Xu, Y.; Yang, H.; Liu, H.

2020-03-28 biochemistry 10.1101/2020.03.25.996348 medRxiv
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SARS-CoV-2 is the etiological agent responsible for the COVID-19 outbreak in Wuhan. Specific antiviral drug are urgently needed to treat COVID-19 infections. The main protease (Mpro) of SARS-CoV-2 is a key CoV enzyme that plays a pivotal role in mediating viral replication and transcription, which makes it an attractive drug target. In an effort to rapidly discover lead compounds targeting Mpro, two compounds (11a and 11b) were designed and synthesized, both of which exhibited excellent inhibitory activity with an IC50 value of 0.05 M and 0.04 M respectively. Significantly, both compounds exhibited potent anti-SARS-CoV-2 infection activity in a cell-based assay with an EC50 value of 0.42 M and 0.33 M, respectively. The X-ray crystal structures of SARS-CoV-2 Mpro in complex with 11a and 11b were determined at 1.5 [A] resolution, respectively. The crystal structures showed that 11a and 11b are covalent inhibitors, the aldehyde groups of which are bound covalently to Cys145 of Mpro. Both compounds showed good PK properties in vivo, and 11a also exhibited low toxicity which is promising drug leads with clinical potential that merits further studies.

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A small molecule drug screening identifies colistin sulfate as an enhancer of Natural Killer cell cytotoxicity.

Cortes-Kaplan, S.; Hasim, M.; Kaczmarek, S.; Taha, Z.; Maznyi, G.; McComb, S.; Lee, S.-H.; Diallo, J.-S.; Ardolino, M.

2021-08-21 immunology 10.1101/2021.08.20.457155 medRxiv
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Because of their crucial role in tumor immunity, NK cells have quickly become a prime target for immunotherapies, with adoptive transfer of NK cells and the use of NK cell engagers quickly moving to clinical stage. On the other hand, only few studies have focused on small molecule drugs capable of unleashing NK cell against cancer. In this context, repurposing small molecule is an attractive strategy to identify new immunotherapies from already approved drugs. Here, we screened 1,200 FDA-approved drugs from the Prestwick Chemical Library, to identify compounds that increase NK cell cytotoxic potential. Using a high-throughput luciferase-release cytotoxicity assay, we found that the antibiotic colistin sulfate increased cytotoxicity of human NK cells towards cancer cells. The effect of colistin was short lived and was not observed when NK cells were pretreated with the drug, showing how NK cell activity was potentiated only when the compound was present at the time of recognition of cancer cells. Further studies are needed to uncover the mechanism of action and the pre-clinical efficacy of colistin sulfate in mouse cancer models.

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Crystal structure and activity profiling of deubiquitinating inhibitors-bound to SARS-CoV-2 papain like protease revealed new allosteric sites for antiviral therapies

Choudhary, S.; Nehul, S.; Kumar, K. A.; Sharma, S.; Rani, R.; Saha, A.; Sharma, G. K.; Tomar, S.; Kumar, P.

2022-11-11 molecular biology 10.1101/2022.11.11.516107 medRxiv
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SARS-CoV-2 papain-like protease (PLpro) is a key antiviral target as it plays a dual role in viral replication and in modulation of innate immune responses by deubiquitinating or deISGylating host proteins. Thus, therapeutic targeting of PLpro serves as a two-pronged approach to abate SARS-CoV-2. Interestingly, PLpro shares structural and functional similarities with the cellular deubiquitinating enzymes (DUBs) and in this study this fact has been exploited to identify DUBs inhibitors that target the Ubiquitin/ISG15 binding site and the known catalytic substrate binding pocket of PLpro. Among these identified compounds, flupenthixol, lithocholic acid, teneligliptin, and linagliptin markedly inhibited the proteolytic activity of purified PLpro and demonstrated potent antiviral efficacies against SARS-CoV-2 infection in a dose dependent manner. Treatment with lithocholic acid and linagliptin suppressed the expression levels of inflammatory mediators, thereby, restoring immune responses. Crystal structures of SARS-CoV-2 PLpro in complex with linagliptin and with lithocholic acid determined in this study, revealed insights into the inhibition mechanism with unique interactions within the Ubiquitin/ISG15 binding site (S2 site; Phe69, His73, Asn128, His175) and the substrate binding cleft. Additionally, oral and intraperitoneal treatments with linagliptin increased survival, reduced lung viral load, and ameliorated histopathological damage in mouse-adapted model of SARS-CoV-2 infection. The study for the first time demonstrates a two-pronged strategy using DUB inhibitors that target the proteolytic activity of PLpro and simultaneously reinstates the hosts immune response against SARS-CoV-2.

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Nucleotide Analogues as Inhibitors of Viral Polymerases

Ju, J.; Kumar, S.; Li, X.; Jockusch, S.; Russo, J. J.

2020-01-31 pharmacology and toxicology 10.1101/2020.01.30.927574 medRxiv
Top 0.1%
14.4%
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Coronaviruses such as the newly discovered virus from Wuhan, China, 2019-nCoV, and the viruses that cause SARS and MERS, have resulted in regional and global public health emergencies. Based on our molecular insight that the hepatitis C virus and the coronavirus use a similar viral genome replication mechanism, we reasoned that the FDA-approved drug EPCLUSA (Sofosbuvir/Velpatasvir) for the treatment of hepatitis C will also inhibit the above coronaviruses, including 2019-nCoV. To develop broad spectrum anti-viral agents, we further describe a novel strategy to design and synthesize viral polymerase inhibitors, by combining the ProTide Prodrug approach used in the development of Sofosbuvir with the use of 3-blocking groups that we have previously built into nucleotide analogues that function as polymerase terminators.