scholarly journals Potent and Selective Covalent Inhibitors of the Papain-like Protease from SARS-CoV-2

2021 ◽  
Author(s):  
Jerry Parks ◽  
Brian Sanders ◽  
Suman Pohkrel ◽  
Audrey Labbe ◽  
Irimpan Mathews ◽  
...  
Keyword(s):  
Protease Inhibition ◽  
Host Proteins ◽  
Promising Target ◽  
Covalent Inhibitors ◽  
Polymerase Inhibitor ◽  
Interferon Stimulated Gene 15 ◽  
Viral Proliferation ◽  
Direct Acting ◽  
Small Molecule Therapeutics ◽  
Further Development

Abstract Direct-acting antivirals for the treatment of COVID-19, which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), are needed to complement vaccination efforts. The papain-like protease (PLpro) of SARS-CoV-2 is essential for viral proliferation. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein (ISG15) from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we have designed a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophilic “warheads” onto analogs of the noncovalent PLpro inhibitor GRL0617. We show that the most promising PLpro inhibitor is potent and selective, with activity in cell-based antiviral assays rivaling that of the RNA-dependent RNA polymerase inhibitor remdesivir. An X-ray crystal structure of the most promising lead compound bound covalently to PLpro establishes the molecular basis for protease inhibition and selectivity against structurally similar human deubiquitinases. These findings present an opportunity for further development of potent and selective covalent PLpro inhibitors.

scholarly journals Novel Selective IDO1 Inhibitors with Isoxazolo[5,4-d]pyrimidin-4(5H)-one Scaffold

2021 ◽  
Vol 14 (3) ◽  
pp. 265
Author(s):  
Ana Dolšak ◽  
Tomaž Bratkovič ◽  
Larisa Mlinarič ◽  
Eva Ogorevc ◽  
Urban Švajger ◽  
...  
Keyword(s):  
Systematic Investigation ◽  
The Novel ◽  
Indoleamine 2,3 Dioxygenase ◽  
Tryptophan Dioxygenase ◽  
Promising Target ◽  
Synthetic Procedure ◽  
Ic50 Values ◽  
Novel Scaffold ◽  
Further Development ◽  
Micromolar Range

Indoleamine 2,3-dioxygenase 1 (IDO1) is a promising target in immunomodulation of several pathological conditions, especially cancers. Here we present the synthesis of a series of IDO1 inhibitors with the novel isoxazolo[5,4-d]pyrimidin-4(5H)-one scaffold. A focused library was prepared using a 6- or 7-step synthetic procedure to allow a systematic investigation of the structure-activity relationships of the described scaffold. Chemistry-driven modifications lead us to the discovery of our best-in-class inhibitors possessing p-trifluoromethyl (23), p-cyclohexyl (32), or p-methoxycarbonyl (20, 39) substituted aniline moieties with IC50 values in the low micromolar range. In addition to hIDO1, compounds were tested for their inhibition of indoleamine 2,3-dioxygenase 2 and tryptophan dioxygenase, and found to be selective for hIDO1. Our results thus demonstrate a successful study on IDO1-selective isoxazolo[5,4-d]pyrimidin-4(5H)-one inhibitors, defining promising chemical probes with a novel scaffold for further development of potent small-molecule immunomodulators.

scholarly journals Rethinking protein drug design with highly accurate structure prediction of anti-CRISPR proteins

2021 ◽  
Author(s):  
Ho-min Park ◽  
Yunseol Park ◽  
Joris Vankerschaver ◽  
Arnout Van Messem ◽  
Wesley De Neve ◽  
...  
Keyword(s):  
Protein Structure ◽  
Drug Design ◽  
Structure Prediction ◽  
Modern Medicine ◽  
Protein Therapeutics ◽  
Protein Drug ◽  
Host Proteins ◽  
Small Proteins ◽  
Small Molecule Therapeutics ◽  
Host Parasite

Protein therapeutics play an important role in controlling the functions and activities of disease-causing proteins in modern medicine. Despite protein therapeutics having several advantages over traditional small-molecule therapeutics, further development has been hindered by drug complexity and delivery issues. However, recent progress in deep learning-based protein structure prediction approaches such as AlphaFold opens new opportunities to exploit the complexity of these macro-biomolecules for highly-specialised design to inhibit, regulate or even manipulate specific disease-causing proteins. Anti-CRISPR proteins are small proteins from bacteriophages that counter-defend against the prokaryotic adaptive immunity of CRISPR-Cas systems. They are unique examples of natural protein therapeutics that have been optimized by the host-parasite evolutionary arms race to inhibit a wide variety of host proteins. Here, we show that these Anti-CRISPR proteins display diverse inhibition mechanisms through accurate structural prediction and functional analysis. We find that these phage-derived proteins are extremely distinct in structure, some of which have no homologues in the current protein structure domain. Furthermore, we find a novel family of Anti-CRISPR proteins which are structurally homologous to the recently-discovered mechanism of manipulating host proteins through enzymatic activity, rather than through direct inference. Using highly accurate structure prediction, we present a wide variety of protein-manipulating strategies of anti-CRISPR proteins for future protein drug design.

scholarly journals Identification of Potent VHZ Phosphatase Inhibitors with Structure-Based Virtual Screening

2012 ◽  
Vol 18 (2) ◽  
pp. 226-231 ◽  
Author(s):  
Hwangseo Park ◽  
So Ya Park ◽  
Jung Jin Oh ◽  
Seong Eon Ryu
Keyword(s):  
Virtual Screening ◽  
Active Site ◽  
Structural Features ◽  
Drug Candidate ◽  
The Novel ◽  
Anticancer Activities ◽  
Phosphatase Inhibitors ◽  
Structure Activity ◽  
Promising Target ◽  
Further Development

VH1-like phosphatase Z (VHZ) has proved to be a promising target for the development of therapeutics for the treatment of human cancers. Here, we report the first example for a successful application of structure-based virtual screening to identify the novel small-molecule inhibitors of VHZ. These inhibitors revealed high potencies with the associated IC50 values ranging from 3 to 20 µM and were also screened for having desirable physicochemical properties as a drug candidate. Therefore, they deserve consideration for further development by structure-activity relationship studies to optimize inhibitory and anticancer activities. Structural features relevant to the stabilization of the newly identified inhibitors in the active site of VHZ are discussed in detail.

scholarly journals Design, Synthesis and Biological Evaluation of Novel SARS-CoV-2 3CLpro Covalent Inhibitors

2021 ◽  
Author(s):  
Julia Stille ◽  
Jevgenijs Tjutrins ◽  
Guanyu Wang ◽  
Felipe A. Venegas ◽  
Christopher Hennecker ◽  
...  
Keyword(s):  
Biological Evaluation ◽  
Antiviral Drugs ◽  
Design Synthesis ◽  
Design And Synthesis ◽  
Promising Target ◽  
Starting Point ◽  
Covalent Inhibitors ◽  
Screening Platform ◽  
And Function ◽  
Synthesis And Biological Evaluation

Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CLpro> has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. We report herein our efforts in design and synthesis which led to submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.

scholarly journals Design, Synthesis and Biological Evaluation of Novel SARS-CoV-2 3CLpro Covalent Inhibitors

2020 ◽  
Author(s):  
Julia Stille ◽  
Jevgenijs Tjutrins ◽  
Guanyu Wang ◽  
Felipe A. Venegas ◽  
Christopher Hennecker ◽  
...  
Keyword(s):  
Biological Evaluation ◽  
Antiviral Drugs ◽  
Design Synthesis ◽  
Design And Synthesis ◽  
Promising Target ◽  
Starting Point ◽  
Covalent Inhibitors ◽  
Screening Platform ◽  
And Function ◽  
Synthesis And Biological Evaluation

Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CLpro has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. We report herein our efforts in design and synthesis which led to submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.

scholarly journals Favipiravir May Acts as COVID-19 Main Protease PDB ID 6LU7 Inhibitor: Docking Analysis

2020 ◽  
Vol 10 (6) ◽  
pp. 6821-6828 ◽  
Keyword(s):  
Amino Acids ◽  
Protease Inhibitor ◽  
Essential Amino Acids ◽  
Antiviral Drugs ◽  
Binding Pattern ◽  
Protease Inhibition ◽  
Docking Analysis ◽  
Protease Enzyme ◽  
Main Protease ◽  
Polymerase Inhibitor

Coronavirus is a well-known threat to the human being in the form of COVID-19. Virus replication may be controlled by inhibition of protease enzyme. Hence, well known 13 antiviral drugs have been observed by docking analysis for understanding the binding pattern of drugs with COVID-19 main protease PDB ID: 6LU7 for any possibilities of protease inhibition. For docking analysis PyRx- Python Prescription 0.8 was used. This analysis reveals that the essential amino acids involved in binding of antiviral drugs to COVID-19 main protease PDB ID: 6LU7 are Glycine (Gly), Serine (Ser), Cysteine (Cys), Leucine (Leu), Asparagine (Asn), Glutamine (Gln), Glutamic acid (Glu) and Threonine (Thr). After docking analysis, it was observed that Favipiravir maybe act as COVID-19 main protease inhibitor despite being vRNA polymerase inhibitor and may further be used in the treatment of COVID-19 infection.

scholarly journals A comparative analysis of SARS-CoV-2 antivirals characterizes 3CLpro inhibitor PF-00835231 as a potential new treatment for COVID-19

2021 ◽  
Author(s):  
Maren de Vries ◽  
Adil S. Mohamed ◽  
Rachel A. Prescott ◽  
Ana M. Valero-Jimenez ◽  
Ludovic Desvignes ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Life Cycle ◽  
Comparative Analysis ◽  
Airway Epithelium ◽  
Antiviral Drug ◽  
Viral Polymerase ◽  
Direct Acting Antiviral ◽  
Polymerase Inhibitor ◽  
Direct Acting

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of Coronavirus Disease 2019 (COVID-19). There is a dire need for novel effective antivirals to treat COVID-19, as the only approved direct-acting antiviral to date is remdesivir, targeting the viral polymerase complex. A potential alternate target in the viral life cycle is the main SARS-CoV-2 protease 3CLpro (Mpro). The drug candidate PF-00835231 is the active compound of the first anti-3CLpro regimen in clinical trials. Here, we perform a comparative analysis of PF-00835231, the pre-clinical 3CLpro inhibitor GC-376, and the polymerase inhibitor remdesivir, in alveolar basal epithelial cells modified to express ACE2 (A549+ACE2 cells). We find PF-00835231 with at least similar or higher potency than remdesivir or GC-376. A time-of-drug-addition approach delineates the timing of early SARS-CoV-2 life cycle steps in A549+ACE2 cells and validates PF-00835231’s early time of action. In a model of the human polarized airway epithelium, both PF-00835231 and remdesivir potently inhibit SARS-CoV-2 at low micromolar concentrations. Finally, we show that the efflux transporter P-glycoprotein, which was previously suggested to diminish PF-00835231’s efficacy based on experiments in monkey kidney Vero E6 cells, does not negatively impact PF-00835231 efficacy in either A549+ACE2 cells or human polarized airway epithelial cultures. Thus, our study provides in vitro evidence for the potential of PF-00835231 as an effective SARS-CoV-2 antiviral and addresses concerns that emerged based on prior studies in non-human in vitro models. Importance: The arsenal of SARS-CoV-2 specific antiviral drugs is extremely limited. Only one direct-acting antiviral drug is currently approved, the viral polymerase inhibitor remdesivir, and it has limited efficacy. Thus, there is a substantial need to develop additional antiviral compounds with minimal side effects and alternate viral targets. One such alternate target is its main protease, 3CLpro (Mpro), an essential component of the SARS-CoV-2 life cycle processing the viral polyprotein into the components of the viral polymerase complex. In this study, we characterize a novel antiviral drug, PF-00835231, which is the active component of the first-in-class 3CLpro-targeting regimen in clinical trials. Using 3D in vitro models of the human airway epithelium, we demonstrate the antiviral potential of PF-00835231 for inhibition of SARS-CoV-2.

scholarly journals RSP5 Positively Regulates the Osteogenic Differentiation of Mesenchymal Stem Cells by Activating the K63-Linked Ubiquitination of Akt

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Changxiang Liang ◽  
Guoyan Liang ◽  
Xiaoqing Zheng ◽  
Yongxiong Huang ◽  
Shuaihao Huang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Osteogenic Differentiation ◽  
Bone Repair ◽  
Multipotent Stem Cells ◽  
Cell Therapies ◽  
Ubiquitin Protein Ligase ◽  
Promising Target ◽  
Further Development

Mesenchymal stem cells (MSCs) are multipotent stem cells that have a strong osteogenic differentiation capacity. However, the molecular mechanism underlying the osteogenic differentiation of MSCs remains largely unknown and thus hinders further development of MSC-based cell therapies for bone repair in the clinic. RSP5, also called NEDD4L (NEDD4-like E3 ubiquitin protein ligase), belongs to the HECT (homologous to E6-AP carboxyl terminus) domain-containing E3 ligase family. Nevertheless, although many studies have been conducted to elucidate the role of RSP5 in various biological processes, its effect on osteogenesis remains elusive. In this study, we demonstrated that the expression of RSP5 was elevated during the osteogenesis of MSCs and positively regulated the osteogenic capacity of MSCs by inducing K63-linked polyubiquitination and activation of the Akt pathway. Taken together, our findings suggest that RSP5 may be a promising target to improve therapeutic efficiency by using MSCs for bone regeneration and repair.

scholarly journals Mitochondrial Modulations, Autophagy Pathways Shifts in Viral Infections: Consequences of COVID-19

2021 ◽  
Vol 22 (15) ◽  
pp. 8180
Author(s):  
Shailendra Pratap Singh ◽  
Salomon Amar ◽  
Pinky Gehlot ◽  
Sanjib K. Patra ◽  
Navjot Kanwar ◽  
...  
Keyword(s):  
Cell Death ◽  
Essential Role ◽  
Viral Infections ◽  
Mitochondrial Dynamics ◽  
Mitochondrial Fission ◽  
Innate Immune ◽  
Innate Immune Signaling ◽  
Promising Target ◽  
Intracellular Organelles ◽  
Viral Proliferation

Mitochondria are vital intracellular organelles that play an important role in regulating various intracellular events such as metabolism, bioenergetics, cell death (apoptosis), and innate immune signaling. Mitochondrial fission, fusion, and membrane potential play a central role in maintaining mitochondrial dynamics and the overall shape of mitochondria. Viruses change the dynamics of the mitochondria by altering the mitochondrial processes/functions, such as autophagy, mitophagy, and enzymes involved in metabolism. In addition, viruses decrease the supply of energy to the mitochondria in the form of ATP, causing viruses to create cellular stress by generating ROS in mitochondria to instigate viral proliferation, a process which causes both intra- and extra-mitochondrial damage. SARS-COV2 propagates through altering or changing various pathways, such as autophagy, UPR stress, MPTP and NLRP3 inflammasome. Thus, these pathways act as potential targets for viruses to facilitate their proliferation. Autophagy plays an essential role in SARS-COV2-mediated COVID-19 and modulates autophagy by using various drugs that act on potential targets of the virus to inhibit and treat viral infection. Modulated autophagy inhibits coronavirus replication; thus, it becomes a promising target for anti-coronaviral therapy. This review gives immense knowledge about the infections, mitochondrial modulations, and therapeutic targets of viruses.

scholarly journals Assessing the in vitro resistance development in Enterovirus 71 in the context of combination antiviral treatment

2020 ◽  
Author(s):  
Kristina Lanko ◽  
Chenyan Shi ◽  
Shivaprasad Patil ◽  
Leen Delang ◽  
Jelle Matthijnssens ◽  
...  
Keyword(s):  
Antiviral Treatment ◽  
Enterovirus 71 ◽  
Sequencing Analysis ◽  
Resistance Development ◽  
Development Of Resistance ◽  
Enterovirus A71 ◽  
Polymerase Inhibitor ◽  
Direct Acting ◽  
Deep Sequencing Analysis

AbstractThere are currently no antivirals available to treat infection with enterovirus A71 (EV-A71) or any other enterovirus. The extensively studied capsid binders select rapidly for drug-resistant variants. We here explore whether the combination of two direct-acting enterovirus inhibitors with a different mechanism of action may delay or prevent resistance development to the capsid binders. To that end, the in vitro dynamics of resistance development to the capsid binder pirodavir was studied either alone or in combination with (i) a viral 2C-targeting compound (SMSK_0213), (ii) a viral 3C-protease inhibitor (rupintrivir) or (iii) a viral RNA-dependent RNA polymerase (RdRp) inhibitor [7-deaza-2’C-methyladenosine (7DMA)]. We demonstrate that combining pirodavir with either rupintrivir or the nucleoside analogue 7DMA delays the development of resistance to pirodavir and that no resistance to the protease or polymerase inhibitor develops. The combination of pirodavir with the 2C inhibitor results in a double-resistant virus population. The deep sequencing analysis of resistant populations revealed that even though resistant mutations are present in less than 30% of the population, this still provides the resistant phenotype.

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