Structure of SARS-CoV-2 main protease in the apo state reveals the inactive conformation

AbstractMpro is of considerable interest as a drug target in the treatment of COVID-19 since the proteolytic activity of this viral protease is essential for viral replication. Here we report the first insight of the structure Mpro for SARS-CoV-2 in the inactive conformation under conditions close to the physiological state (pH 7.5) to an overall resolution of 1.9 Å. The comparisons of Mpro in different states reveal that substrate binding site and the active site are more flexible in the inactive conformation than that in the active conformations. Notably, compared with the active conformation of the apo state structure in pH7.6 of SARS, the SARS-CoV-2 apo state is in the inactive conformation under condition close to physiological state (pH7.5). Two water molecules are present in the oxyanion hole in our apo state structure, whereas in the ligand-bound structure, water molecular is absence in the same region. This structure provides novel and important insights that have broad implications for understanding the structural basis underlying enzyme activity, and can facilitate rational, structure-based, approaches for the design of specific SARS-CoV-2 ligands as new therapeutic agents.

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Molecular docking identification of plant-derived inhibitors of the COVID-19 main protease

Bulletin of the Karaganda University Chemistry series ◽

10.31489/2021ch3/37-46 ◽

2021 ◽

Vol 103 (3) ◽

pp. 37-46

Author(s):

S.S. Bhujbal ◽

◽

M. Kale ◽

B. Chawale ◽

◽

...

Keyword(s):

Bioactive Compounds ◽

Drug Target ◽

Viral Proteins ◽

Natural Compounds ◽

Therapeutic Agents ◽

High Rate ◽

Therapeutic Drug ◽

Research Organizations ◽

Main Protease ◽

Modeling Techniques

COVID-19 cases increase at a high rate and become dangerous in recent months. As a consequence, some healthcare and research organizations are attempting to find an effective cure for the COVID-19 outbreak. Many natural products have been reported to have powerful activity against COVID-19 in recent research studies. The primary aim of this article is to establish natural bioactive compounds with suitable antiviral properties. Lui et al. have reported in their study that SARS-Cov-2 main protease is present in a crystalline structure known as a novel therapeutic drug target. It is important to inhibit SARS-Cov-2 main protease to stop the replication of viral proteins. In this study natural compounds were screened using molecular modeling techniques to investigate probable bioactive compounds that block SARS-Cov-2. From these studies many natural compounds were found to have the potential to interact with viral proteins and show inhibitory activity against COVID-19 main protease (Mpro) and these natural compounds were also compared to known antiviral drugs such as Saquinavir and Remdesivir. Besides that, additional research is needed before these potential leads can be developed into natural therapeutic agents against COVID-19 to fight the epidemic.

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The Possible Molecular Mechanism of SARS-CoV-2 Main Protease: New Structural Insights from Computational Methods

SciMedicine Journal ◽

10.28991/scimedj-2020-02-si-11 ◽

2021 ◽

Vol 2 ◽

pp. 108-126

Author(s):

Alvea Tasneem ◽

Gyan Prakash Rai ◽

Saima Reyaz ◽

Hridoy R. Bairagya

Keyword(s):

Drug Target ◽

Computational Study ◽

Vital Role ◽

Testable Hypothesis ◽

Water Molecules ◽

Main Protease ◽

Definition Of ◽

Imidazolium Ion ◽

Catalytic Dyad ◽

Structural Insights

Main protease (Mpro) is one of the key enzymes in the life cycle of SARS-CoV-2 that plays a pivotal role in mediating viral replication, transcription, and makes it an attractive drug target for this virus. The catalytic site of this enzyme comprises of a dyad His41 and Cys145 and lacks the third catalytic residue, which is replaced by a stable water molecule (W). The computational structural analysis on crystal data for Mpro protein suggests that W1, W2, His163, and Tyr161 may also play a vital role in the activity of this enzyme and they may act as catalytic partners along with Cys(145)-His(41) catalytic dyad. The thiolate–imidazolium ion-pair between Cys145 (-SH---NE2-) His41 and Cys145 (-SH---NE2-) His163 have been stabilized by W1 (with W2) and Tyr161, respectively. Therefore, unique interactions of W2---W1---ND1-His41-NE2---SH-Cys145 or Cys145-SH---NE2-His163-ND1---OH-Tyr161 in Mpro serve as an excellent drug target for this enzyme and suggest a rethink of the conventional definition of chemical geometry of inhibitor binding site, its shape, and complementarities. Our computational hypothesis suggests two essential clues that may be implemented to design a new inhibitor for Mpro protein. The strategies are: (i) ligand should be occupied either W1 or W2 or both of these position to displace these water molecules from the catalytic region, and (ii) ligand should be made H-bonds with Cys145 (-SH), His41 (NE2/ND1) and His163(NE2) to inhibit Mpro. The results from this computational study could be of interest to the experimental community and also provide a testable hypothesis for experimental validation. Doi: 10.28991/SciMedJ-2020-02-SI-11 Full Text: PDF

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Current Status in the Design and Development of Agonists and Antagonists of Adenosine A3 Receptor as Potential Therapeutic Agents

Current Pharmaceutical Design ◽

10.2174/1381612825666190716114056 ◽

2019 ◽

Vol 25 (25) ◽

pp. 2772-2787 ◽

Cited By ~ 6

Author(s):

Raghu P. Mailavaram ◽

Omar H.A. Al-Attraqchi ◽

Supratik Kar ◽

Shinjita Ghosh

Keyword(s):

Drug Target ◽

Therapeutic Agents ◽

G Protein Coupled Receptors ◽

Current Status ◽

Renal Diseases ◽

Adenosine A3 Receptor ◽

Drug Candidates ◽

Novel Drugs ◽

The Family ◽

G Protein Coupled

Adenosine receptors (ARs) belongs to the family of G-protein coupled receptors (GPCR) that are responsible for the modulation of a wide variety of physiological functions. The ARs are also implicated in many diseases such as cancer, arthritis, cardiovascular and renal diseases. The adenosine A3 receptor (A3AR) has emerged as a potential drug target for the progress of new and effective therapeutic agents for the treatment of various pathological conditions. This receptor’s involvement in many diseases and its validity as a target has been established by many studies. Both agonists and antagonists of A3AR have been extensively investigated in the last decade with the goal of developing novel drugs for treating diseases related to immune disorders, inflammation, cancer, and others. In this review, we shall focus on the medicinal chemistry of A3AR ligands, exploring the diverse chemical classes that have been projected as future leading drug candidates. Also, the recent advances in the therapeuetic applications of A3AR ligands are highlighted.

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Small Molecule Inhibitors of Influenza Virus Entry

Pharmaceuticals ◽

10.3390/ph14060587 ◽

2021 ◽

Vol 14 (6) ◽

pp. 587

Author(s):

Zhaoyu Chen ◽

Qinghua Cui ◽

Michael Caffrey ◽

Lijun Rong ◽

Ruikun Du

Keyword(s):

Influenza Virus ◽

Membrane Fusion ◽

Small Molecule ◽

Drug Target ◽

Small Molecule Inhibitors ◽

Virus Entry ◽

Critical Role ◽

Structural Basis ◽

Future Directions ◽

The Past

Hemagglutinin (HA) plays a critical role during influenza virus receptor binding and subsequent membrane fusion process, thus HA has become a promising drug target. For the past several decades, we and other researchers have discovered a series of HA inhibitors mainly targeting its fusion machinery. In this review, we summarize the advances in HA-targeted development of small molecule inhibitors. Moreover, we discuss the structural basis and mode of action of these inhibitors, and speculate upon future directions toward more potent inhibitors of membrane fusion and potential anti-influenza drugs.

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Drug Repurposing for Candidate SARS-CoV-2 Main Protease Inhibitors by a Novel in Silico Method

10.26434/chemrxiv.12248561.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Milan Sencanski ◽

Vladimir Perovic ◽

Snezana Pajovic ◽

Miroslav Adzic ◽

Slobodan Paessler ◽

...

Keyword(s):

Protease Inhibitors ◽

In Silico ◽

Drug Target ◽

Transmission Rate ◽

Experimental Testing ◽

Drug Repurposing ◽

Global Public Health ◽

Main Protease ◽

Additional Approach ◽

Drugbank Database

The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening (VS) protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the ISM applied for Small Molecules was used for searching the Drugbank database and further followed by molecular docking. After in silico screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.

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Effects of the Temperature and the pH on the Main Protease of SARS-CoV-2: A Molecular Dynamics Simulation Study

Biointerface Research in Applied Chemistry ◽

10.33263/briac126.72397248 ◽

2021 ◽

Vol 12 (6) ◽

pp. 7239-7248

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Root Mean Square ◽

Dynamics Simulation ◽

Effect Of Temperature ◽

Water Molecules ◽

Mean Square ◽

Main Protease ◽

Decreasing Ph ◽

Increasing Temperature

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

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Structural basis for SARM1 inhibition and activation under energetic stress

eLife ◽

10.7554/elife.62021 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Michael Sporny ◽

Julia Guez-Haddad ◽

Tami Khazma ◽

Avraham Yaron ◽

Moshe Dessau ◽

...

Keyword(s):

Cell Death ◽

Axonal Degeneration ◽

Structural Basis ◽

Allosteric Site ◽

Inactive Conformation ◽

Catalytic Domains ◽

Energetic Stress ◽

Catalytic Sites ◽

Peripheral Ring ◽

Cellular Metabolite

SARM1, an executor of axonal degeneration, displays NADase activity that depletes the key cellular metabolite, NAD+, in response to nerve injury. The basis of SARM1 inhibition and its activation under stress conditions are still unknown. Here, we present cryo-EM maps of SARM1 at 2.9 and 2.7 Å resolutions. These indicate that SARM1 homo-octamer avoids premature activation by assuming a packed conformation, with ordered inner and peripheral rings, that prevents dimerization and activation of the catalytic domains. This inactive conformation is stabilized by binding of SARM1’s own substrate NAD+ in an allosteric location, away from the catalytic sites. This model was validated by mutagenesis of the allosteric site, which led to constitutively active SARM1. We propose that the reduction of cellular NAD+ concentration contributes to the disassembly of SARM1's peripheral ring, which allows formation of active NADase domain dimers, thereby further depleting NAD+ to cause an energetic catastrophe and cell death.

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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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Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur

Nature Structural & Molecular Biology ◽

10.1038/s41594-020-0440-6 ◽

2020 ◽

Vol 27 (6) ◽

pp. 529-532 ◽

Cited By ~ 72

Author(s):

Zhenming Jin ◽

Yao Zhao ◽

Yuan Sun ◽

Bing Zhang ◽

Haofeng Wang ◽

...

Keyword(s):

Antineoplastic Drug ◽

Structural Basis ◽

Main Protease

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Solid-state structure and antimicrobial and cytotoxicity studies of a cucurbit[6]uril-like Cu6 L 4 constructed from 3,5-bis[(1H-tetrazol-5-yl)methyl]-4H-1,2,4-triazol-4-amine

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229618013670 ◽

2018 ◽

Vol 74 (11) ◽

pp. 1413-1419

Author(s):

Serhii Vasylevskyi ◽

Anja Holzheu ◽

Katharina M. Fromm

Keyword(s):

Solid State ◽

Distorted Octahedral Geometry ◽

Water Molecules ◽

State Structure ◽

Sulfate Anion ◽

E Coli ◽

Cytotoxicity Studies ◽

Distorted Octahedral ◽

Sulfate Hydrate ◽

Coordinated Water

3,5-Bis[(1H-tetrazol-5-yl)methyl]-4H-1,2,4-triazol-4-amine (H2 L) associates under deprotonation with CuSO4 in aqueous medium to form a new waisted barrel-shaped M 6 L 4 cluster, namely hexaaquatetrakis{μ4-3,5-bis[(1H-tetrazol-5-yl)methyl]-4H-1,2,4-triazol-4-amine}-μ4-sulfato-hexacopper(II) sulfate hydrate, [Cu6(SO4)(C6H6N12)4(H2O)6]SO4·nH2O (n = ∼23) (1). Cluster 1 resembles concave cucurbit[6]uril and has one disordered sulfate anion trapped inside the cage, which additionally stabilizes the Cu6 unit. The CuII ions have either a square-pyramidal or a distorted octahedral geometry. The equatorial positions are filled by N atoms from the L 2− ligand, while the axial positions are occupied by coordinated water molecules and O atoms of the sulfate counter-ion. In the solid state, the Cu6 clusters are connected through a large number of hydrogen bonds formed by uncoordinated water molecules and an additional sulfate anion. The compound shows good antimicrobial activity against E. coli tested with the Kirby Bauer approach. In addition, the cell viability towards HeLa and L-929 cells was studied.

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