scholarly journals Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2

2022 ◽  
Author(s):  
Lucianna H. Santos ◽  
Thales Kronenberger ◽  
Renata G Almeida ◽  
Elany Barbosa da Silva ◽  
Rafael E O Rocha ◽  
...  
Keyword(s):  
Active Site ◽  
Drug Targets ◽  
Inhibitory Concentration ◽  
Binding Modes ◽  
Fluorogenic Substrate ◽  
Biochemical Assays ◽  
Main Protease ◽  
Ic50 Values ◽  
Biochemical Approach ◽  
Dynamics Simulations

The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 μM and 66 μM. In addition, eight compounds inhibited PLpro with IC50 ranging from 1.7 μM to 46 μM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.

scholarly journals The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CLpro In Vitro

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 873
Author(s):  
Raphael J. Eberle ◽  
Danilo S. Olivier ◽  
Marcos S. Amaral ◽  
Ian Gering ◽  
Dieter Willbold ◽  
...  
Keyword(s):  
Binding Mode ◽  
Drug Candidates ◽  
Main Protease ◽  
Ic50 Values ◽  
Repurposed Drugs ◽  
Antiparasitic Drugs ◽  
Inhibitory Potential ◽  
Dynamics Simulations ◽  
Micromolar Range

Since the first report of a new pneumonia disease in December 2019 (Wuhan, China) the WHO reported more than 148 million confirmed cases and 3.1 million losses globally up to now. The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide, resulting in a pandemic of unprecedented magnitude. To date, several clinically safe and efficient vaccines (e.g., Pfizer-BioNTech, Moderna, Johnson & Johnson, and AstraZeneca COVID-19 vaccines) as well as drugs for emergency use have been approved. However, increasing numbers of SARS-Cov-2 variants make it imminent to identify an alternative way to treat SARS-CoV-2 infections. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is repurposing clinically developed drugs, e.g., antiparasitic drugs. The results described in this study demonstrated the inhibitory potential of quinacrine and suramin against SARS-CoV-2 main protease (3CLpro). Quinacrine and suramin molecules presented a competitive and noncompetitive inhibition mode, respectively, with IC50 values in the low micromolar range. Surface plasmon resonance (SPR) experiments demonstrated that quinacrine and suramin alone possessed a moderate or weak affinity with SARS-CoV-2 3CLpro but suramin binding increased quinacrine interaction by around a factor of eight. Using docking and molecular dynamics simulations, we identified a possible binding mode and the amino acids involved in these interactions. Our results suggested that suramin, in combination with quinacrine, showed promising synergistic efficacy to inhibit SARS-CoV-2 3CLpro. We suppose that the identification of effective, synergistic drug combinations could lead to the design of better treatments for the COVID-19 disease and repurposable drug candidates offer fast therapeutic breakthroughs, mainly in a pandemic moment.

scholarly journals Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin

2020 ◽  
Author(s):  
Jian Li ◽  
Xuelan Zhou ◽  
Yan Zhang ◽  
Fanglin Zhong ◽  
Cheng Lin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Drug Targets ◽  
Chinese Herb ◽  
Binding Modes ◽  
High Potency ◽  
Main Protease ◽  
Covalent Inhibitors ◽  
Catalytic Dyad ◽  
Important Drug

AbstractMain protease (Mpro, also known as 3CLpro) has a major role in the replication of coronavirus life cycle and is one of the most important drug targets for anticoronavirus agents. Here we report the crystal structure of main protease of SARS-CoV-2 bound to a previously identified Chinese herb inhibitor shikonin at 2.45 angstrom resolution. Although the structure revealed here shares similar overall structure with other published structures, there are several key differences which highlight potential features that could be exploited. The catalytic dyad His41-Cys145 undergoes dramatic conformational changes, and the structure reveals an unusual arrangement of oxyanion loop stabilized by the substrate. Binding to shikonin and binding of covalent inhibitors show different binding modes, suggesting a diversity in inhibitor binding. As we learn more about different binding modes and their structure-function relationships, it is probable that we can design more effective and specific drugs with high potency that can serve as effect SARS-CoV-2 anti-viral agents.

scholarly journals Activity of phytochemical constituents of Curcuma longa (turmeric) and Andrographis paniculata against coronavirus (COVID-19): an in silico approach

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Kalirajan Rajagopal ◽  
Potlapati Varakumar ◽  
Aparma Baliwada ◽  
Gowramma Byran
Keyword(s):  
Active Site ◽  
In Silico ◽  
Chemical Constituents ◽  
Curcuma Longa ◽  
Andrographis Paniculata ◽  
Significant Activity ◽  
Binding Modes ◽  
Main Protease ◽  
In Silico Admet ◽  
In Silico Studies

Abstract Background In early 2020, many scientists are rushing to discover novel drugs and vaccines against the coronavirus, and treatments for COVID-19, because coronavirus disease 2019 (COVID-19), a life-threatening viral disease, affected first in China and quickly spread throughout the world. In this article, in silico studies have been performed to explore the binding modes of chemical constituents for natural remedies like Curcuma longa (turmeric) and Andrographis paniculata against COVID-19 (PDB ID 5R82) targeting coronavirus using Schrodinger suit 2019-4. The molecular docking studies are performed by the Glide module, in silico ADMET screening was performed by the QikProp module, and binding energy of ligands was calculated using the Prime MM-GB/SA module. Results The chemical constituents from turmeric like cyclocurcumin and curcumin and from Andrographis paniculata like andrographolide and dihydroxy dimethoxy flavone are significantly binding with the active site of SARS CoV-2 main protease with Glide score more than − 6 when compared to the currently used drugs hydroxychloroquine (− 5.47) and nelfinavir (− 5.93). When compared to remdesivir (− 6.38), cyclocurcumin from turmeric is significantly more active. The docking results of the compounds exhibited similar mode of interactions with SARS CoV-2. Main protease and the residues THR24, THR25, THR26, LEU27, SER46, MET49, HIE41, GLN189, ARG188, ASP187, MET165, HIE164, PHE181, and THR54 play a crucial role in binding with ligands. Conclusion Based on in silico investigations, the chemical constituents from turmeric like cyclocurcumin and curcumin and from Andrographis paniculata like andrographolide and dihydroxy dimethoxy flavone, significantly binding with the active site of SARS CoV-2 main protease, may produce significant activity and be useful for further development.

scholarly journals Identification of Kaurane-Type Diterpenes as Inhibitors of Leishmania Pteridine Reductase I

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3076
Author(s):  
Chonny Herrera-Acevedo ◽  
Areli Flores-Gaspar ◽  
Luciana Scotti ◽  
Francisco Jaime Bezerra Mendonça-Junior ◽  
Marcus Tullius Scotti ◽  
...  
Keyword(s):  
Active Sites ◽  
Leishmania Major ◽  
Inhibitory Concentration ◽  
Chemical Space ◽  
Leishmania Species ◽  
Ic50 Values ◽  
Docking Calculations ◽  
Dynamics Simulations ◽  
Potential Inhibitors ◽  
Leishmania Parasites

The current treatments against Leishmania parasites present high toxicity and multiple side effects, which makes the control and elimination of leishmaniasis challenging. Natural products constitute an interesting and diverse chemical space for the identification of new antileishmanial drugs. To identify new drug options, an in-house database of 360 kauranes (tetracyclic diterpenes) was generated, and a combined ligand- and structure-based virtual screening (VS) approach was performed to select potential inhibitors of Leishmania major (Lm) pteridine reductase I (PTR1). The best-ranked kauranes were employed to verify the validity of the VS approach through LmPTR1 enzyme inhibition assay. The half-maximal inhibitory concentration (IC50) values of selected bioactive compounds were examined using the random forest (RF) model (i.e., 2β-hydroxy-menth-6-en-5β-yl ent-kaurenoate (135) and 3α-cinnamoyloxy-ent-kaur-16-en-19-oic acid (302)) were below 10 μM. A compound similar to 302, 3α-p-coumaroyloxy-ent-kaur-16-en-19-oic acid (302a), was also synthesized and showed the highest activity against LmPTR1. Finally, molecular docking calculations and molecular dynamics simulations were performed for the VS-selected, most-active kauranes within the active sites of PTR1 hybrid models, generated from three Leishmania species that are known to cause cutaneous leishmaniasis in the new world (i.e., L. braziliensis, L. panamensis, and L. amazonensis) to explore the targeting potential of these kauranes to other species-dependent variants of this enzyme.

scholarly journals Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are non-specific promiscuous SARS-CoV-2 main protease inhibitors

2020 ◽  
Author(s):  
Chunlong Ma ◽  
Yanmei Hu ◽  
Julia Alma Townsend ◽  
Panagiotis I. Lagarias ◽  
Michael Thomas Marty ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Drug Targets ◽  
Cysteine Proteases ◽  
Native Mass Spectrometry ◽  
Main Protease ◽  
Enterovirus A71 ◽  
Dynamics Simulations ◽  
Hit Validation ◽  
Viral Polyprotein ◽  
Inhibition Potency

AbstractThere is an urgent need for vaccines and antiviral drugs to combat the COVID-19 pandemic. Encouraging progress has been made in developing antivirals targeting SARS-CoV-2, the etiological agent of COVID-19. Among the drug targets being investigated, the viral main protease (Mpro) is one of the most extensively studied drug targets. Mpro is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites and it is highly conserved among coronaviruses. In addition, Mpro has a unique substrate preference for glutamine in the P1 position. Taken together, it appears that Mpro inhibitors can achieve both broad-spectrum antiviral activity and a high selectivity index. Structurally diverse compounds have been reported as Mpro inhibitors, with several of which also showed antiviral activity in cell culture. In this study, we investigated the mechanism of action of six previously reported Mpro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. Collectively, the results showed that the inhibition of Mpro by these six compounds is non-specific and the inhibition is abolished or greatly reduced with the addition of reducing reagent DTT. In the absence of DTT, these six compounds not only inhibit Mpro, but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease, the 2Apro and 3Cpro from enterovirus A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymatic inhibition potency IC50 values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity. Overall, we provide compelling evidence suggesting that ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 are non-specific SARS-CoV-2 Mpro inhibitors, and urge the scientific community to be stringent with hit validation.

scholarly journals Deciphering the Binding Mechanism of Dexamethasone Against SARS-CoV-2 Main Protease: Computational Molecular Modelling Approach

2020 ◽  
Author(s):  
Shafi Ullah Khan ◽  
Thet.thet Htar
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Binding Mechanism ◽  
Protein Targets ◽  
High Affinity ◽  
Main Protease ◽  
Dynamics Simulations ◽  
Covalent Inhibitor ◽  
Modelling Approach

<p>At present, there are no proven agents for the treatment of 2019 coronavirus disease (COVID-19). The available evidence has not allowed guidelines to clearly recommend any drugs outside the context of clinical trials. One of the most important SARS-CoV-2 protein targets for therapeutics is the 3C-like protease (main protease, Mpro). Here in this study we utilize the recently published 6W63 crystal structure of Mpro complexed with a non-covalent inhibitor X77. Various docking methods FRED, HYBRID, CDOCKER and LEADFINDER tools were benchmark to optimally re-dock the co-crystal ligand within the active site of SARS-COV-2 Mpro. This study was restricted to molecular docking without validation by molecular dynamics simulations. CDOCKER was found to depict the exact binding of co-crystal ligand having lowest RMSD of less than 2 A. Interactions with the SARS-COV-2 Mpro may play a key role in fighting against viruses. Dexamethasone was found to bind with a high affinity to the same sites of the SARS-COV-2 Mpro than the Remdesivir. Dexamethasone was forming six hydrogen bonds compared to the three hydrogen bonds formed by Remdesivir within the active site of SARS-COV-2 Mpro. LEU141, GLY143, HIS163, GLU166, GLN192 were the key amino acid residue of SAR-COV-2 Mpro involved in stabilizing the complex between Dexamethasone and SARS-COV-2 Mpro. The results suggest the effectiveness of Dexamethasone as potent drugs against SARS-CoV-2 since it bind tightly to its Mpro. In addition, the results also suggest that dexamethasone as top antiviral treatments option than the Remdesivir with high potential to fight the SARS-CoV-2.</p>

scholarly journals MPI8 is Potent Against SARS-CoV-2 by Inhibiting Dually and Selectively the SARS-CoV-2 Main Protease and the Host Cathepsin L

2021 ◽  
Author(s):  
Xinyu R Ma ◽  
Yugendar R Alugubelli ◽  
Yuying Ma ◽  
Erol Can Vatansever ◽  
Danielle A Scott ◽  
...  
Keyword(s):  
Active Site ◽  
Cathepsin L ◽  
Critical Role ◽  
Cathepsin K ◽  
Host Cells ◽  
High Potency ◽  
Active Site Cysteine ◽  
Cellular Analysis ◽  
Main Protease ◽  
Ic50 Values

A number of inhibitors have been developed for the SARS-CoV-2 main protease (MPro) as potential COVID-19 medications but little is known about their selectivity. Using enzymatic assays, we characterized inhibition of TMPRSS2, furin, and cathepsins B/K/L by more than a dozen of previously developed MPro inhibitors including MPI1-9, GC376, 11a, 10-1, 10-2, and 10-3. MPI1-9, GC376 and 11a all contain an aldehyde for the formation of a reversible covalent hemiacetal adduct with the MPro active site cysteine and 10-1, 10-2 and 10-3 contain a labile ester to exchange with the MPro active site cysteine for the formation of a thioester. Our data revealed that all these inhibitors are inert toward TMPRSS2 and furin. Diaryl esters also showed low inhibition of cathepsins. However, all aldehyde inhibitors displayed high potency in inhibiting three cathepsins. Their determined IC50 values vary from 4.1 to 380 nM for cathepsin B, 0.079 to 2.3 nM for cathepsin L, and 0.35 to 180 nM for cathepsin K. All aldehyde inhibitors showed similar inhibition levels toward cathepsin L. A cellular analysis indicated high potency of MPI5 and MPI8 in inhibiting lysosomal activity, which is probably attributed to their inhibition of cathepsins. Among all aldehyde inhibitors, MPI8 shows the best selectivity toward cathepsin L. With respect to cathepsins B and K, the selective indices are 192 and 150, respectively. MPI8 is the most potent compound among all aldehyde inhibitors in cellular MPro inhibition potency and anti-SARS-CoV-2 activity in Vero E6 cells. Cathepsin L has been demonstrated to play a critical role in the SARS-CoV-2 cell entry. By selectively inhibiting both SARS-CoV-2 MPro and the host cathepsin L, MPI8 potentiates dual inhibition effects to synergize its overall antiviral potency and efficacy. Due to its high selectivity toward cathepsin L that reduces potential toxicity toward host cells and high cellular and antiviral potency, we urge serious consideration of MPI8 for preclinical and clinical investigations for treating COVID-19.

scholarly journals Deciphering the Binding Mechanism of Dexamethasone Against SARS-CoV-2 Main Protease: Computational Molecular Modelling Approach

2020 ◽  
Author(s):  
Shafi Ullah Khan ◽  
Thet.thet Htar
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Binding Mechanism ◽  
Protein Targets ◽  
High Affinity ◽  
Main Protease ◽  
Dynamics Simulations ◽  
Covalent Inhibitor ◽  
Modelling Approach

<p>At present, there are no proven agents for the treatment of 2019 coronavirus disease (COVID-19). The available evidence has not allowed guidelines to clearly recommend any drugs outside the context of clinical trials. One of the most important SARS-CoV-2 protein targets for therapeutics is the 3C-like protease (main protease, Mpro). Here in this study we utilize the recently published 6W63 crystal structure of Mpro complexed with a non-covalent inhibitor X77. Various docking methods FRED, HYBRID, CDOCKER and LEADFINDER tools were benchmark to optimally re-dock the co-crystal ligand within the active site of SARS-COV-2 Mpro. This study was restricted to molecular docking without validation by molecular dynamics simulations. CDOCKER was found to depict the exact binding of co-crystal ligand having lowest RMSD of less than 2 A. Interactions with the SARS-COV-2 Mpro may play a key role in fighting against viruses. Dexamethasone was found to bind with a high affinity to the same sites of the SARS-COV-2 Mpro than the Remdesivir. Dexamethasone was forming six hydrogen bonds compared to the three hydrogen bonds formed by Remdesivir within the active site of SARS-COV-2 Mpro. LEU141, GLY143, HIS163, GLU166, GLN192 were the key amino acid residue of SAR-COV-2 Mpro involved in stabilizing the complex between Dexamethasone and SARS-COV-2 Mpro. The results suggest the effectiveness of Dexamethasone as potent drugs against SARS-CoV-2 since it bind tightly to its Mpro. In addition, the results also suggest that dexamethasone as top antiviral treatments option than the Remdesivir with high potential to fight the SARS-CoV-2.</p>

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

2021 ◽  
Author(s):  
Yuying Ma ◽  
Kai Yang ◽  
Zhi Zachary Geng ◽  
Yugendar R. Alugubellia ◽  
Namir Shaabani ◽  
...  
Keyword(s):  
Active Site ◽  
Unnatural Amino Acids ◽  
Chemical Compositions ◽  
Structural Variations ◽  
Covalent Interaction ◽  
Tert Butyl ◽  
Main Protease ◽  
Ic50 Values ◽  
Inhibition Potency

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 𝛽-(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 𝛼-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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