Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity

Arafet, Kemel; Serrano-Aparicio, Natalia; Lodola, Alessio; Mulholland, Adrian J.; González, Florenci V.; Świderek, Katarzyna; Moliner, Vicent

doi:10.26434/chemrxiv.12941819

Cited by 7 publications

(12 citation statements)

References 36 publications

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“…From the MD-PMM calculations we obtain that, in the presence of the inhibitor N3 in the active-site, the PT reaction free energy is significantly lower, changing from Δ G 0 = 34 ± 6 kJ/mol to Δ G 0 = 20 ± 6 kJ/mol (see Table 1 and Figure 2 ). The positive free energy difference upon PT estimated here is in agreement with previous recent computational works 11 , 12 showing that in the presence of N3 the ionic couple is at a higher energy with respect to the reactant state. In these previous calculations free-energy changes upon PT of ∼5.5 kJ/mol 12 and ∼43 kJ/mol 11 were reported.…”

supporting

confidence: 92%

“…Diverse binding mechanisms between inhibitors and enzymes featuring an active-site cysteine have been reported, either involving a direct PT reaction between the inhibitor and the cysteine 9 or requiring a PT reaction from the cysteine to a protein base prior to the binding reaction. 10 In the case of SARS-CoV-2 M pro previous computational works, wherein Michael acceptors 11 , 12 and ketoamides 6 , 13 were investigated, suggested that the physiological PT reaction from Cys145 to His41 occurs prior to covalent binding of the inhibitor. These computational works 6 , 11 also showed that the PT reaction free energy in the presence of two potent inhibitors of SARS-CoV-2 M pro , namely the peptidomimetic N3 and the α-ketoamide 13b , 2 , 8 accounts for 50% and 37%, respectively, of the total activation free energy for the formation of the covalent complex and thus the PT relevantly contributes to the rate-determining step.…”

mentioning

confidence: 99%

“…As commonly done in hybrid multiscale approaches, 24 − 27 also for the investigation of enzyme catalysis, 3 , 5 , 12 , 28 − 31 the portion of the system in which the chemical event takes place is treated quantum mechanically (the quantum center, QC) while the rest of the system is treated classically and atomistically and exerts an electrostatic perturbation on the QC electronic states. However, the main difference with other hybrid methods is that in the MD-PMM the whole system configurational space (including the QC) is sampled by fully classical MD simulations and the electrostatic perturbation of the environment on the electronic properties of the QC is included a posteriori .…”

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confidence: 99%

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Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Zanetti-Polzi

Smith

Chipot

et al. 2021

J. Phys. Chem. Lett.

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The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT is likely also required for the covalent binding of some inhibitors. Here we use a multiscale computational approach to investigate the PT thermodynamics in the apo enzyme and in complex with two potent inhibitors, N3 and the α-ketoamide 13b . We show that with the inhibitors the free energy cost to reach the charge-separated state of the active-site dyad is lower, with N3 inducing the most significant reduction. We also show that a few key sites (including specific water molecules) significantly enhance or reduce the thermodynamic feasibility of the PT reaction, with selective desolvation of the active site playing a crucial role. The approach presented is a cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction and is thus also useful to guide the design of inhibitors.

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supporting

confidence: 92%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Zanetti-Polzi

Smith

Chipot

et al. 2021

J. Phys. Chem. Lett.

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“…A semiempirical QM/MM DFT calculation of the hydrolytic reaction of M Pro dimer with the fluorogenic substrate Ac-Val-Lys-Leu-Gln-ACC exhibited four transition states, with excellent agreement of computed and experimental ∆G ‡ values [ 114 ]. DFT based approaches were applied to a large set of pyridine N-oxide compounds as potential inhibitors of SARS-CoV-2 M Pro , peptidic Michael acceptor compounds, as well as to small molecule Schiff bases [ 115 , 116 , 117 ]. Moreover, SARS-2 M Pro was virtually screened for inhibition by several hundred natural compounds [ 118 ].…”

Section: Mechanisms Of Cysteine Proteasesmentioning

confidence: 99%

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Elsässer

Goettig

2021

IJMS

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Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.

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“…Computational simulations of SARS-CoV-2 3CL protease have been devoted to study its reactivity with peptide substrates, including the acylation and deacylation steps. 16 , 17 Regarding covalent inhibition, QM/MM methods have been also used to analyze the reaction with irreversible Michael acceptors 18 , 19 and α-ketoamide inhibitors. 20 This last study provides a complete evaluation of the binding free energy of the covalent inhibitor as the sum of the noncovalent binding and the reaction steps.…”

Section: Introductionmentioning

confidence: 99%

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism

2021

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We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those containing an aldehyde group as a warhead. These compounds are covalent inhibitors that inactivate the protease, forming a stable hemithioacetal complex. Inhibitor 11a is a potent inhibitor that has been already tested in vitro and in animals. Using a combination of classical and QM/MM simulations, we determined the binding mode of the inhibitor into the active site and the preferred rotameric state of the catalytic histidine. In the noncovalent complex, the aldehyde group is accommodated into the oxyanion hole formed by the NH main-chain groups of residues 143 to 145. In this pose, P1–P3 groups of the inhibitor mimic the interactions established by the natural peptide substrate. The reaction is initiated with the formation of the catalytic dyad ion pair after a proton transfer from Cys145 to His41. From this activated state, covalent inhibition proceeds with the nucleophilic attack of the deprotonated Sγ atom of Cys145 to the aldehyde carbon atom and a water-mediated proton transfer from the Nε atom of His41 to the aldehyde oxygen atom. Our proposed reaction transition-state structure is validated by comparison with X-ray data of recently reported inhibitors, while the activation free energy obtained from our simulations agrees with the experimentally derived value, supporting the validity of our findings. Our study stresses the interplay between the conformational dynamics of the inhibitor and the protein with the inhibition mechanism and the importance of including conformational diversity for accurate predictions about the inhibition of the main protease of SARS-CoV-2. The conclusions derived from our work can also be used to rationalize the behavior of other recently proposed inhibitor compounds, including aldehydes and ketones with high inhibitory potency.

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Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity

Cited by 7 publications

References 36 publications

Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism

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