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

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.

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The repurposed drugs suramin and quinacrine inhibit cooperatively in vitro SARS-CoV-2 3CLpro

10.1101/2020.11.11.378018 ◽

2020 ◽

Author(s):

Raphael J. Eberle ◽

Danilo S. Olivier ◽

Marcos S. Amaral ◽

Dieter Willbold ◽

Raghuvir K. Arni ◽

...

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Drug Repositioning ◽

Binding Mode ◽

Main Protease ◽

Repurposed Drugs ◽

Inhibitory Potential ◽

Dynamics Simulations ◽

Synergistic Drug Combinations

AbstractSince the first report of a new pneumonia disease in December 2019 (Wuhan, China) up to now WHO reported more than 50 million confirmed cases and more than one million losses, globally. The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide resulting in a pandemic of unprecedented magnitude. To date, no clinically safe drug or vaccine is available and the development of molecules to combat SARS-CoV-2 infections is imminent. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is the repurposing of clinically developed drugs, e.g., anti-parasitic drugs. The results described in this study demonstrate the inhibitory potential of quinacrine and suramin against SARS-CoV-2 main protease (3CLpro). Quinacrine and suramin molecules present a competitive and non-competitive mode of inhibition, respectively, with IC50 and KD values in low μM range. 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. The identification of effective, synergistic drug combinations could lead to the design of better treatments for the COVID-19 disease. Drug repositioning offers hope to the SARS-CoV-2 control.

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Molecular insights into the inhibition of plasmepsins by HIV-1 protease inhibitors: Implications for antimalarial drug discovery

10.1101/2021.09.27.461917 ◽

2021 ◽

Author(s):

Vandana Mishra ◽

Ishan Rathore ◽

Anuradha Deshmukh ◽

Swati Patankar ◽

Alla Gustchina ◽

...

Keyword(s):

Protease Inhibitors ◽

Drug Targets ◽

Drug Repurposing ◽

Binding Mode ◽

Ic50 Values ◽

Multiple Regions ◽

Potential Drug Targets ◽

Hiv 1 ◽

Micromolar Range

Malaria is a deadly disease, and the worldwide emergence of drug resistance in the Plasmodium parasites demands the development of novel and potent antimalarials. HIV-1 protease inhibitors (HIV-1 PIs) alleviate the Plasmodium pathogenesis during malaria/HIV-1 co-infection plausibly by inhibiting vacuolar plasmepsins (PMs), the hemoglobin degrading proteases from P. falciparum. All five FDA-approved HIV-1 PIs tested against PMII exhibit the Ki values in the low micromolar range of which RTV and LPV display the highest inhibition activity. Both inhibitors impede in vitro growth of P. falciparum at low micromolar IC50 values. We report the first crystal structures of PMII complexed with RTV and LPV that reveal the binding mode and interactions of the inhibitors in the active site as well as elucidate the mechanism underlying their differential potency. The conformational flexibility of the P4 group in RTV allows it to explore multiple regions of the S4 pocket. The present study establishes vacuolar PMs as potential drug targets of HIV-1 PIs. The molecular details explaining the inhibitory mechanism of HIV-1 PIs might be crucial in designing novel and potent antimalarial analogs. This work strengthens the prospect of drug repurposing as an alternative strategy towards antimalarial treatments and provides an opportunity to tackle malaria and HIV-1 co-infection.

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Discrimination of Naturally-Occurring 2-Arylbenzofurans as Cyclooxygenase-2 Inhibitors: Insights into the Binding Mode and Enzymatic Inhibitory Activity

Biomolecules ◽

10.3390/biom10020176 ◽

2020 ◽

Vol 10 (2) ◽

pp. 176 ◽

Cited By ~ 1

Author(s):

Ericsson Coy-Barrera

Keyword(s):

Three Dimensional ◽

3D Qsar ◽

Binding Mode ◽

Binding Energies ◽

Wide Range ◽

Ic50 Values ◽

Structure Relationship ◽

Cox 2 ◽

Dynamics Simulations

2-arylbenzofuran-containing compounds are chemical entities that can be naturally produced by several organisms. A wide-range of activities is described for several compounds of this kind and they are, therefore, valuable moieties for a lead finding from nature. Although there are in-vitro data about the activity of 2-arylbenzofuran-related compounds against cyclooxygenase (COX) enzymes, the molecular level of these COX-inhibiting constituents had not been deeply explored. Thus, 58 2-arylbenzofurans were initially screened through molecular docking within the active site of nine COX-2 crystal structures. The resulting docking scores were statistically analyzed and good reproducibility and convergence were found to discriminate the best-docked compounds. Discriminated compounds exhibited the best performance in molecular dynamics simulations as well as the most-favorable binding energies and the lowest in-vitro IC50 values for COX-2 inhibition. A three-dimensional quantitative activity-structure relationship (3D-QSAR) was also demonstrated, which showed some crucial structural requirements for enhanced enzyme inhibition. Therefore, four hits are proposed as lead structures for the development of COX-2 inhibitors based on 2-arylbenzofurans in further studies.

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Novel hybrids of oxoisoaporphine-tryptamine as acetylcholinesterase-induced β-amyloid aggregation inhibitors with improved antioxidant properties

Journal of the Serbian Chemical Society ◽

10.2298/jsc140319092z ◽

2015 ◽

Vol 80 (2) ◽

pp. 127-136 ◽

Cited By ~ 3

Author(s):

Hai-Tao Zhao ◽

Shu-Ming Zhong ◽

Jiang-Ke Qin ◽

Huang Tang

Keyword(s):

Inhibitory Activity ◽

Antioxidant Properties ◽

Drug Candidates ◽

Ache Inhibitors ◽

Ache Inhibitory Activity ◽

Ic50 Values ◽

Aggregation Inhibitors ◽

Β Amyloid ◽

Micromolar Range

A series of dual binding site acetylcholinesterase (AChE) inhibitors have been designed, synthesized, and tested for their antioxidant ability and inhibitory potency on AChE and AChE-induced b-amyloid (Ab) aggregation. The new hybrids consist of a unit of 1-azabenzanthrone and a tryptamine or its derivative, connected through a a,w - alkyldiamide bridge. These hybrids exhibit moderate AChE inhibitory activity with IC50 values in the micromolar range and significant in vitro inhibitory activity toward the AChE-induced Ab aggregation. Moreover, six out of the nine hybrids of this series exhibit a higher oxygen radical absorbance capacity than trolox, which makes them promising anti-Alzheimer drug candidates.

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Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp5 main protease

Biochemical Journal ◽

10.1042/bcj20210197 ◽

2021 ◽

Vol 478 (13) ◽

pp. 2499-2515 ◽

Cited By ~ 2

Author(s):

Jennifer C. Milligan ◽

Theresa U. Zeisner ◽

George Papageorgiou ◽

Dhira Joshi ◽

Christelle Soudy ◽

...

Keyword(s):

Economic Effects ◽

Calpain Inhibitor ◽

Chemical Library ◽

Antiviral Compounds ◽

Main Protease ◽

The World ◽

Ic50 Values ◽

Global Population ◽

Micromolar Range

The coronavirus 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread around the world with unprecedented health and socio-economic effects for the global population. While different vaccines are now being made available, very few antiviral drugs have been approved. The main viral protease (nsp5) of SARS-CoV-2 provides an excellent target for antivirals, due to its essential and conserved function in the viral replication cycle. We have expressed, purified and developed assays for nsp5 protease activity. We screened the nsp5 protease against a custom chemical library of over 5000 characterised pharmaceuticals. We identified calpain inhibitor I and three different peptidyl fluoromethylketones (FMK) as inhibitors of nsp5 activity in vitro, with IC50 values in the low micromolar range. By altering the sequence of our peptidomimetic FMK inhibitors to better mimic the substrate sequence of nsp5, we generated an inhibitor with a subnanomolar IC50. Calpain inhibitor I inhibited viral infection in monkey-derived Vero E6 cells, with an EC50 in the low micromolar range. The most potent and commercially available peptidyl-FMK compound inhibited viral growth in Vero E6 cells to some extent, while our custom peptidyl FMK inhibitor offered a marked antiviral improvement.

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Rutin Is a Low Micromolar Inhibitor of SARS-CoV-2 Main Protease 3CLpro: Implications for Drug Design of Quercetin Analogs

Biomedicines ◽

10.3390/biomedicines9040375 ◽

2021 ◽

Vol 9 (4) ◽

pp. 375

Author(s):

Bruno Rizzuti ◽

Fedora Grande ◽

Filomena Conforti ◽

Ana Jimenez-Alesanco ◽

Laura Ceballos-Laita ◽

...

Keyword(s):

Drug Design ◽

Simulation Techniques ◽

Model Combining ◽

Main Protease ◽

Experimental Spectroscopy ◽

Dynamics Simulations ◽

Catalytic Dyad ◽

Micromolar Range

The pandemic, due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has stimulated the search for antivirals to tackle COVID-19 infection. Molecules with known pharmacokinetics and already approved for human use have been demonstrated or predicted to be suitable to be used either directly or as a base for a scaffold-based drug design. Among these substances, quercetin is known to be a potent in vitro inhibitor of 3CLpro, the SARS-CoV-2 main protease. However, its low in vivo bioavailability calls for modifications to its molecular structure. In this work, this issue is addressed by using rutin, a natural flavonoid that is the most common glycosylated conjugate of quercetin, as a model. Combining experimental (spectroscopy and calorimetry) and simulation techniques (docking and molecular dynamics simulations), we demonstrate that the sugar adduct does not hamper rutin binding to 3CLpro, and the conjugated compound preserves a high potency (inhibition constant in the low micromolar range, Ki = 11 μM). Although showing a disruption of the pseudo-symmetry in the chemical structure, a larger steric volume and molecular weight, and a higher solubility compared to quercetin, rutin is able to associate in the active site of 3CLpro, interacting with the catalytic dyad (His41/Cys145). The overall results have implications in the drug-design of quercetin analogs, and possibly other antivirals, to target the catalytic site of the SARS-CoV-2 3CLpro.

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Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease

10.1101/2021.04.07.438806 ◽

2021 ◽

Author(s):

Clovis Basier ◽

Rupert Beale ◽

Ganka Bineva-Todd ◽

Berta Canal ◽

Joseph F Curran ◽

...

Keyword(s):

Economic Effects ◽

Calpain Inhibitor ◽

Chemical Library ◽

Antiviral Compounds ◽

Main Protease ◽

The World ◽

Ic50 Values ◽

Global Population ◽

Micromolar Range

The coronavirus 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread around the world with unprecedented health and socio-economic effects for the global population. While different vaccines are now being made available, very few antiviral drugs have been approved. The main viral protease (nsp5) of SARS-CoV-2 provides an excellent target for antivirals, due to its essential and conserved function in the viral replication cycle. We have expressed, purified and developed assays for nsp5 protease activity. We screened the nsp5 protease against a custom chemical library of over 5,000 characterised pharmaceuticals. We identified calpain inhibitor I and three different peptidyl fluoromethylketones (FMK) as inhibitors of nsp5 activity in vitro, with IC50 values in the low micromolar range. By altering the sequence of our peptidomimetic FMK inhibitors to better mimic the substrate sequence of nsp5, we generated an inhibitor with a subnanomolar IC50. Calpain inhibitor I inhibited viral infection in monkey-derived Vero E6 cells, with an EC50 in the low micromolar range. The most potent and commercially available peptidyl-FMK compound inhibited viral growth in Vero E6 cells to some extent, while our custom peptidyl FMK inhibitor offered a marked antiviral improvement.

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In vitro Antidiabetic, anti-obesity and antioxidant proprities of Rosemary extracts

JOURNAL OF ADVANCES IN CHEMISTRY ◽

10.24297/jac.v10i2.5497 ◽

2014 ◽

Vol 10 (2) ◽

pp. 2305-2316 ◽

Cited By ~ 4

Author(s):

Manel Ben Ali ◽

Kais Mnafgui ◽

Abdelfattah Feki ◽

Mohamed Damak ◽

Noureddine Allouche

Keyword(s):

Essential Oil ◽

Ethyl Acetate ◽

Pancreatic Lipase ◽

Antioxidant Properties ◽

Methanolic Extracts ◽

Ic50 Values ◽

Inhibitory Potential ◽

Prevention Of Diabetes ◽

First Time

Diabetes mellitus is a serious health problem worldwide that has adverse and long-lasting consequences for individuals, families, and communities. Hence, this study sought to investigate the inhibitory potential of rosemary extracts on key-enzymes related to diabetes such as α-amylase and pancreatic lipase activities, as well as to assess their antioxidant properties in vitro. The IC50 values of Rosemary essential oil, ethyl acetate and methanolic extracts against α-amylase were 28.36, 34.11 and 30.39 µg/mL respectively, and those against pancreatic lipase were 32.25, 36.64 and 34.07 µg/mL, suggesting strong anti-diabetic and anti-obesity effects of Rosemary. The methanolic extract was found to be the highest in levels of phenolic (282.98 µgGAE/mg extract) and flavonoids (161.05 µg QE /mg extract) contents as well as in the antioxidant activity (IC50 = 15.82 µg/mL) as compared to other extracts ethyl acetate (IC50 = 32.23 µg/mL) and essential oil (IC50 = 96.12 µg/mL).Antioxidant efficacy of Rosemary extracts has been estimated in the stabilization of sunflower oil (SFO) at three different concentrations, i.e. 200 (SFO-200), 500 (SFO-500) and 1000 ppm (SFO-1000). Results showed the highest efficiency of SFO-1000.The results obtained in this study demonstrated for the first time that Rosemary is a potent source of natural inhibitors of α-amylase and pancreatic lipase with powerful antioxidants proprieties that might be used in the food stabilization and the prevention of diabetes and obesity complications as a complementary pharmacological drug.

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Identification of inhibitors of SARS-CoV-2 3CL-Pro enzymatic activity using a small molecule in-vitro repurposing screen

10.1101/2020.12.16.422677 ◽

2020 ◽

Author(s):

Maria Kuzikov ◽

Elisa Costanzi ◽

Jeanette Reinshagen ◽

Francesca Esposito ◽

Laura Vangeel ◽

...

Keyword(s):

Enzymatic Activity ◽

Small Molecules ◽

Drug Target ◽

Treatment Options ◽

Cleavage Sites ◽

X Ray ◽

Binding Characteristics ◽

Main Protease ◽

Ic50 Values

Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro, and have identified 62 additional compounds with IC50 values below 1 uM and profiled their selectivity towards Chymotrypsin and 3CL-Pro from the MERS virus. A subset of 8 inhibitors showed anti-cytopathic effect in a Vero-E6 cell line and the compounds thioguanosine and MG-132 were analysed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Angs., showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.

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In Silico Analysis of the Subtype Selective Blockage of KCNA Ion Channels through the µ-Conotoxins PIIIA, SIIIA, and GIIIA

Marine Drugs ◽

10.3390/md17030180 ◽

2019 ◽

Vol 17 (3) ◽

pp. 180 ◽

Cited By ~ 4

Author(s):

Desirée Kaufmann ◽

Alesia Tietze ◽

Daniel Tietze

Keyword(s):

In Silico Analysis ◽

Binding Mode ◽

Dynamic Simulations ◽

Drug Candidates ◽

Toxin Binding ◽

Subtype Specificity ◽

Pore Blockage ◽

Natural Peptide ◽

Dynamics Simulations ◽

Subtype Selective

Understanding subtype specific ion channel pore blockage by natural peptide-based toxins is crucial for developing such compounds into promising drug candidates. Herein, docking and molecular dynamics simulations were employed in order to understand the dynamics and binding states of the µ-conotoxins, PIIIA, SIIIA, and GIIIA, at the voltage-gated potassium channels of the KV1 family, and they were correlated with their experimental activities recently reported by Leipold et al. Their different activities can only adequately be understood when dynamic information about the toxin-channel systems is available. For all of the channel-bound toxins investigated herein, a certain conformational flexibility was observed during the molecular dynamic simulations, which corresponds to their bioactivity. Our data suggest a similar binding mode of µ-PIIIA at KV1.6 and KV1.1, in which a plethora of hydrogen bonds are formed by the Arg and Lys residues within the α-helical core region of µ-PIIIA, with the central pore residues of the channel. Furthermore, the contribution of the K+ channel’s outer and inner pore loops with respect to the toxin binding. and how the subtype specificity is induced, were proposed.

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