scholarly journals A Microscopic Description of SARS-CoV-2 Main Protease Inhibition with Michael Acceptors. Strategies for Improving Inhibitors Design

2020 ◽  
Author(s):  
Carlos A. Ramos-Guzmán ◽  
J. Javier Ruiz-Pernía ◽  
Iñaki Tuñón
Keyword(s):  
Free Energy ◽  
Enzyme Inhibitor ◽  
Multiscale Simulation ◽  
Ion Pair ◽  
Protease Inhibition ◽  
Microscopic Description ◽  
Inhibitor Complex ◽  
Main Protease ◽  
Michael Acceptors ◽  
Catalytic Dyad

The irreversible inhibition of the main protease of SARS-CoV-2 by a Michael acceptor compound known as N3 has been investigated using multiscale simulation methods. The noncovalent enzyme-inhibitor complex was simulated using classical Molecular Dynamics techniques and the pose of the inhibitor in the active site was compared to that of the natural substrate, a peptide containing the Gln-Ser scissile bond. The formation of the covalent enzyme-inhibitor complex was then simulated using hybrid QM/MM free energy methods. After binding, the reaction mechanism was found to be composed of two steps: i) the activation of the catalytic dyad (Cys145 and His41) to form an ion pair and ii) a Michael addition where the attack of the Sg atom of Cys145 to the Cb atom of the inhibitor precedes the water-mediated proton transfer from His41 to the Ca atom. The microscopic description of protease inhibition by N3 obtained from our simulations is strongly supported by the excellent agreement between the estimated activation free energy and the value derived from kinetic experiments. Comparison with the acylation reaction of a peptide substrate suggest that that N3-based inhibitors could be improving adding chemical modifications that could facilitate the formation of the catalytic dyad ion pair.

scholarly journals A Microscopic Description of SARS-CoV-2 Main Protease Inhibition with Michael Acceptors. Strategies for Improving Inhibitors Design

2020 ◽  
Author(s):  
Carlos A. Ramos-Guzmán ◽  
J. Javier Ruiz-Pernía ◽  
Iñaki Tuñón
Keyword(s):  
Free Energy ◽  
Enzyme Inhibitor ◽  
Multiscale Simulation ◽  
Ion Pair ◽  
Protease Inhibition ◽  
Microscopic Description ◽  
Inhibitor Complex ◽  
Main Protease ◽  
Michael Acceptors ◽  
Catalytic Dyad

The irreversible inhibition of the main protease of SARS-CoV-2 by a Michael acceptor compound known as N3 has been investigated using multiscale simulation methods. The noncovalent enzyme-inhibitor complex was simulated using classical Molecular Dynamics techniques and the pose of the inhibitor in the active site was compared to that of the natural substrate, a peptide containing the Gln-Ser scissile bond. The formation of the covalent enzyme-inhibitor complex was then simulated using hybrid QM/MM free energy methods. After binding, the reaction mechanism was found to be composed of two steps: i) the activation of the catalytic dyad (Cys145 and His41) to form an ion pair and ii) a Michael addition where the attack of the Sg atom of Cys145 to the Cb atom of the inhibitor precedes the water-mediated proton transfer from His41 to the Ca atom. The microscopic description of protease inhibition by N3 obtained from our simulations is strongly supported by the excellent agreement between the estimated activation free energy and the value derived from kinetic experiments. Comparison with the acylation reaction of a peptide substrate suggest that that N3-based inhibitors could be improving adding chemical modifications that could facilitate the formation of the catalytic dyad ion pair.

scholarly journals A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design

2021 ◽  
Author(s):  
Carlos A. Ramos-Guzmán ◽  
J. Javier Ruiz-Pernía ◽  
Iñaki Tuñón
Keyword(s):  
Water Molecule ◽  
Transition State ◽  
Inhibitor Design ◽  
Protease Inhibition ◽  
Microscopic Description ◽  
Main Protease ◽  
Michael Acceptor ◽  
Michael Acceptors ◽  
3Cl Protease ◽  
Catalytic Dyad

Inhibition of SARS-CoV-2 3CL protease by a Michael acceptor is studied using classical and QM/MM simulations. Results point out to a transition state with a key water molecule stabilizing the catalytic dyad and assisting the protonation step.

scholarly journals Potential Binding Efficiency of Antiviral Drug Lopinavir Targeted to the Catalytic Dyad, His41 - Cys145 of SARS CoV -2 Main Protease

2020 ◽  
Author(s):  
Muthu Raj S ◽  
Manohar M ◽  
Mohan M ◽  
Ganesh P ◽  
Marimuthu K
Keyword(s):  
Antiviral Drug ◽  
Emergency Situation ◽  
Viral Disease ◽  
New Drugs ◽  
Viral Population ◽  
Protease Inhibition ◽  
Main Protease ◽  
Model Drug ◽  
Approved Drugs ◽  
Catalytic Dyad

<p>The spread of SARS CoV 2 across the globe rushed the scientific community to find out the potential inhibitor for controlling the viral disease. The main protease (Mpro) or Chymotrypsin protease (3CLpro) is involved in the cleavage of polyproteins, duplication of intracellular materials and release of nonstructural proteins. Cys-His catalytic dyad is located in the SARS-CoV Mpro which is the substrate-binding site located in domains I and II. There are many approved drugs that have their active protease inhibition capability. The targeting of the active site of the main protease is the better option to fight against the viral population. Lopinavir, ritonavir, Remdesivir and Chloroquine are some of the drug candidates considered to be involved in the treatment of SARS CoV 2 under emergency situation as a trial basis. In the present investigation we used lopinavir as a drug to bind the catalytic dyad His41, Cys145 of main protease. The minimum binding of energy of -11.45 kcal/mol observed with the binding of Cys145 and -10.93 kcal/mol was noted with the residue His41. The inhibition constant was also found to be relevant to the binding efficiency of the drug. This is considered to be a model drug target which is initiating the finding of many new drugs to target the current outbreak created by the virus SARS.CoV - 2.</p>

scholarly journals Potential Binding Efficiency of Antiviral Drug Lopinavir Targeted to the Catalytic Dyad, His41 - Cys145 of SARS CoV -2 Main Protease

2020 ◽  
Author(s):  
Muthu Raj S ◽  
Manohar M ◽  
Mohan M ◽  
Ganesh P ◽  
Marimuthu K
Keyword(s):  
Antiviral Drug ◽  
Emergency Situation ◽  
Viral Disease ◽  
New Drugs ◽  
Viral Population ◽  
Protease Inhibition ◽  
Main Protease ◽  
Model Drug ◽  
Approved Drugs ◽  
Catalytic Dyad

<p>The spread of SARS CoV 2 across the globe rushed the scientific community to find out the potential inhibitor for controlling the viral disease. The main protease (Mpro) or Chymotrypsin protease (3CLpro) is involved in the cleavage of polyproteins, duplication of intracellular materials and release of nonstructural proteins. Cys-His catalytic dyad is located in the SARS-CoV Mpro which is the substrate-binding site located in domains I and II. There are many approved drugs that have their active protease inhibition capability. The targeting of the active site of the main protease is the better option to fight against the viral population. Lopinavir, ritonavir, Remdesivir and Chloroquine are some of the drug candidates considered to be involved in the treatment of SARS CoV 2 under emergency situation as a trial basis. In the present investigation we used lopinavir as a drug to bind the catalytic dyad His41, Cys145 of main protease. The minimum binding of energy of -11.45 kcal/mol observed with the binding of Cys145 and -10.93 kcal/mol was noted with the residue His41. The inhibition constant was also found to be relevant to the binding efficiency of the drug. This is considered to be a model drug target which is initiating the finding of many new drugs to target the current outbreak created by the virus SARS.CoV - 2.</p>

m-[o-(2-Chloro-5-Fluorosulfonylphenylureido)Phenoxybutoxy]Benzamidine: Affinity Labeling Reagent Which Can Identify Secondary Binding Sites of Coagulation Complement and Fibrinolytic Serine Proteases

1979 ◽  
Author(s):  
D Bing ◽  
D Robison ◽  
J Andrews ◽  
R Laura
Keyword(s):  
Binding Sites ◽  
Serine Proteases ◽  
Enzyme Inhibitor ◽  
Molecular Model ◽  
Factor Xa ◽  
Affinity Labeling ◽  
Catalytic Center ◽  
Inhibitor Complex ◽  
Polypeptide Chains ◽  
Kinetics Of

We have determined that m-[o-(2-chloro-5-fluorosulfonylphenylureido)phenoxybutoxy]benza-midine [mCP(PBA)-F] is an affinity labeling reagent which labels both polypeptide chains of thrombin, factor Xa, complement component CIS and plasmin. As this means it is reacting outside of the catalytic center, we have called this reagent an exo-site affinity labeling reagent. Progressive irreversible inhibition of these enzymes by this reagent is rapid (k1st 2.5-4.6 x 10-3sec-1), the kinetics of inactivation are consistent with inhibition proceding via formation of a specific enzyme-inhibitor complex analogous to a Michaelis-Menton complex (KL - 115-26 μM), and diisopropylfluorophosphate or p-amidino-phenylmethanesulfonyfluoride Prevent labeling by [3H]mCP(PBA)-F. A molecular model of mCP(PBA)-F shows that the reactive SO2F group can be 17 A from the cationic amidine. The data are consistent with the hypothesis that both peptide chains are required for the specific proteolytic activity exhibited by these proteases and that the peptide chain which does not contain the active site serine is close to the catalytic center. (Supported by NIH and AHA grants

Optimal Duration of the Preincubation Phase in Enzyme Inhibition Experiments

2020 ◽  
Author(s):  
Petr Kuzmic
Keyword(s):  
Enzyme Inhibition ◽  
Dose Response ◽  
Enzyme Inhibitor ◽  
Single Point ◽  
Association Rate ◽  
Weakly Bound ◽  
Inhibitor Complex ◽  
Dissociation Equilibrium ◽  
Optimal Duration ◽  
Algebraic Formula

This report describes an algebraic formula to calculate the optimal duration of the pre-incubation phase in enzyme-inhibition experiments, based on the assumed range of expected values for the dissociation equilibrium constant of the enzyme–inhibitor complex and for the bimolecular association rate constant. Three typical experimental scenarios are treated, namely, (1) single-point primary screening at relatively high inhibitor concentrations; (2) dose-response secondary screening of relatively weakly bound inhibitors; (3) dose-response screening of tightly-bound inhibitors.

Identification of Main Protease of Coronavirus SARS-CoV-2 (Mpro)Inhibitors from Melissa officinalis

2020 ◽  
Vol 17 ◽  
Author(s):  
Olusola O. Elekofehinti ◽  
Opeyemi Iwaloye ◽  
Courage D. Famusiwa ◽  
Olanrewaju Akinseye ◽  
Joao B. T. Rocha
Keyword(s):  
Qsar Model ◽  
Computational Approach ◽  
Melissa Officinalis ◽  
Lead Compounds ◽  
Main Protease ◽  
The World ◽  
Recent Outbreak ◽  
Global Concern ◽  
Catalytic Dyad ◽  
Potential Therapeutic Intervention

Background: he recent outbreak of Coronavirus SARS-CoV-2 (Covid-19) which has rapidly spread around the world in about three months with tens of thousands of deaths recorded so far is a global concern. An urgent need for potential therapeutic intervention is of necessity. Mpro is an attractive druggable target for the development of anti-COVID-19 drug development. Compounds previously characterized from Melissa officinalis were queried against main protease of coronavirus SARS-CoV-2 using computational approach. Results: Melitric acid A and salvanolic acid A had higher affinity than lopinavir and ivermectin using both AutodockVina and XP docking algorithms. The computational approach was employed in the generation of QSAR model using automated QSAR, and in the docking of ligands from Melissa officinalis with SARS-CoV-2 Mpro inhibitors. The best model obtained was KPLS_Radial_28 (R2 = 0.8548 and Q2=0.6474, and was used in predicting the bioactivity of the lead compounds. Molecular mechanics based MM-GBSA confirmed salvanolic acid A as the compound with the highest free energy and predicted bioactivity of 4.777; it interacted with His-41 of the catalytic dyad (Cys145-His41) of SARS-CoV-2 main protease (Mpro), as this may hinder the cutting of inactive viral protein into active ones capable of replication. Conclusion: Salvanolic acid A can be further evaluated as potential Mpro inhibitor.

scholarly journals Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

2021 ◽  
Vol 7 (3) ◽  
pp. 467-475 ◽  
Author(s):  
Chun-Hui Zhang ◽  
Elizabeth A. Stone ◽  
Maya Deshmukh ◽  
Joseph A. Ippolito ◽  
Mohammad M. Ghahremanpour ◽  
...  
Keyword(s):  
Free Energy ◽  
Free Energy Perturbation ◽  
Main Protease ◽  
Energy Perturbation

Kinetics of Ion-Pair Effect of Aquation of Bromopentaammine Cobalt(III) Complex in Different Dicarboxylate Media

2011 ◽  
Vol 324 ◽  
pp. 166-169 ◽  
Author(s):  
Farah Zeitouni ◽  
Gehan El-Subruiti ◽  
Ghassan Younes ◽  
Mohammad Amira
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Compensation Effect ◽  
Ion Pairing ◽  
Reaction Rates ◽  
Ion Pair ◽  
Free Energy Of Activation ◽  
Different Types ◽  
Different Temperatures ◽  
Kinetics Of

The rate of aquation of bromopentaammine cobalt(III) ion in the presence of different types of dicarboxylate solutions containing tert-butanol (40% V/V) have been measured spectrophotometrically at different temperatures (30-600°C) in the light of the effects of ion-pairing on reaction rates and mechanism. The thermodynamic and extrathermodynamic parameters of activation have been calculated and discussed in terms of solvent effect on the ion-pair aquation reaction. The free energy of activation ∆Gip* is more or less linearly varied among the studied dicarboxylate ion-pairing ligands indicating the presence of compensation effect between ∆Hip* and ∆Sip*. Comparing the kip values with respect of different buffers at 40% of ter-butanol is introduced.

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