Discovery of SARS-CoV-2 M<sup>pro</sup> peptide inhibitors from modelling substrate and ligand binding

Chan, H. T. Henry; Moesser, Marc A.; Walters, Rebecca K.; Malla, Tika R.; Twidale, Rebecca; John, Tobias; Deeks, Helen M.; Johnston-Wood, Tristan; Mikhailov, Victor A.; Sessions, Richard B.; Dawson, William; Salah, E.; Lukacik, P.; Strain-Damerell, Claire; Owen, C.D.; Nakajima, Takahito; Świderek, Katarzyna; Lodola, Alessio; Moliner, Vicent; Glowacki, David R.; Spencer, James; Walsh, M.A.; Schofield, Christopher J.; Genovese, Luigi; Shoemark, Deborah K.; Mulholland, Adrian J.; Duarte, Fernanda; Morris, Garrett M.

doi:10.1039/d1sc03628a

Cited by 65 publications

(116 citation statements)

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“… 15 Thus, for instance, the initial enzyme:substrate complex would not be the ion pair dyad C145 – /H41 + ( E (±) :I ) but rather the neutral C145/H41 dyad ( E:I ). This result is in agreement with studies carried out by us, and others, using different inhibitors and substrates (except for B1 mentioned above), 13 , 16 , 18 but in contrast with the protonation state of the catalytic dyad suggested from the ligand-free SARS-CoV-2 M pro recently solved by neutron crystallography at pH 6.6. 19 Nevertheless, as has already been pointed out, questions remain about how pH or the presence of an inhibitor or substrate influence the protonation state of the dyad in SARS-CoV-2 M pro .…”

Section: Introductionsupporting

confidence: 93%

“… 19 Nevertheless, as has already been pointed out, questions remain about how pH or the presence of an inhibitor or substrate influence the protonation state of the dyad in SARS-CoV-2 M pro . 16 Moreover, while the formation of the ion pair dyad C145 – /H41 + ( E (±) :I ) and the nucleophilic attack of sulfur atom of C145 to the carbonyl carbon atom of the peptide take place concertedly in the proteolysis reaction catalyzed by M pro , 15 in the inhibition reaction by N3 , our designed B1 and B2 MA compounds, 13 or the simulation with M pro –substrate peptide models, 16 the formation of the ion pair dyad and the sulfur–carbon covalent bond formation appear to proceed in a stepwise manner. In any event, the rate-limiting step of the process, in all three studied inhibitors, was the enzyme–inhibitor covalent bond formation, with activation free energies ranging from 11.8 to 9.8 kcal mol –1 .…”

Section: Introductionmentioning

confidence: 99%

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Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M^pro Explored by QM/MM Simulations

et al. 2021

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The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a simulation study of the inhibition of the SARS-CoV-2 main protease (M pro ), a cysteine hydrolase essential for the life cycle of the virus. The free energy landscape for the mechanism of the inhibition process is explored by QM/MM umbrella sampling and free energy perturbation simulations at the M06-2X/MM level of theory for two proposed peptidyl covalent inhibitors that share the same recognition motif but feature distinct cysteine-targeting warheads. Regardless of the intrinsic reactivity of the modeled inhibitors, namely a Michael acceptor and a hydroxymethyl ketone activated carbonyl, our results confirm that the inhibitory process takes place by means of a two-step mechanism, in which the formation of an ion pair C145/H41 dyad precedes the protein–inhibitor covalent bond formation. The nature of this second step is strongly dependent on the functional groups in the warhead: while the nucleophilic attack of the C145 sulfur atom on the Cα of the double bond of the Michael acceptor takes place concertedly with the proton transfer from H41 to C β , in the compound with an activated carbonyl, the sulfur attacks the carbonyl carbon concomitant with a proton transfer from H41 to the carbonyl oxygen via the hydroxyl group. An analysis of the free energy profiles, structures along the reaction path, and interactions between the inhibitors and the different pockets of the active site on the protein shows a measurable effect of the warhead on the kinetics and thermodynamics of the process. These results and QM/MM methods can be used as a guide to select warheads to design efficient irreversible and reversible inhibitors of SARS-CoV-2 M pro .

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Section: Introductionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M^pro Explored by QM/MM Simulations

et al. 2021

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“…We have verified that the sum of these terms correlates very well with the QM interaction energy between the subsystems F and G, thereby proving that they capture the essential contributions of the interactions in our analysis [25].…”

Section: A4 Details Of the Fragmentation Proceduressupporting

confidence: 62%

“…Each of the calculations presented here requires about 2 h of wall-time on 32 compute nodes of the IRENE-Rome supercomputer, at the TGCC Supercomputing center in Saclay (Paris, France). A similar approach has been previously used, in conjunction with the other atomistic techniques described in the introduction, to investigate the interaction patterns of the SARS-CoV-2 main protease with natural peptidic substrates and to design peptide inhibitors tested in vitro [25].…”

Section: Methodsmentioning

confidence: 99%

Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling

Zaccaria

Genovese

Farzan

et al. 2021

Preprint

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Evolved SARS-CoV-2 variants are currently challenging the efficacy of first-generation vaccines, largely through the emergence of spike protein mutants. Among these variants, Delta is presently the most concerning. We employ an ab initio quantum mechanical model based on Density Functional Theory to characterize the spike protein Receptor Binding Domain (RBD) interaction with host cells and gain mechanistic insight into SARS-CoV-2 evolution. The approach is illustrated via a detailed investigation of the role of the E484K RBD mutation, a signature mutation of the Beta and Gamma variants. The simulation is employed to: predict the depleting effect of the E484K mutation on binding the RBD with select antibodies; identify residue E484 as a weak link in the original interaction with the human receptor hACE2; and describe SARS-CoV-2 Wuhan strand binding to the bat Rhinolophus macrotis ACE2 as more optimized than the human counterpart. Finally, we predict the hACE2 binding efficacy of a hypothetical E484K mutation added to the Delta variant RBD, identifying a potential future variant of concern. Results can be generalized to other mutations, and provide useful information to complement existing experimental datasets of the interaction between randomly generated libraries of hACE2 and viral spike mutants. We argue that ab initio modeling is at the point of being aptly employed to inform and predict events pertinent to viral and general evolution.

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“…These calculations allow us to investigate inter-molecular interactions. The approach employed here is identical to the one described in our previous contribution [2], and has also been employed to investigate the interaction of SARS-CoV-2's main protease with natural peptidic substrates to design peptide inhibitors [4].…”

Section: Methodsmentioning

confidence: 99%

Mechanistic investigation of SARS-CoV-2 Omicron variant spike mutants via full quantum mechanical modeling

Zaccaria

Genovese

Lawhorn

et al. 2021

Preprint

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SARS-CoV-2 variant “Omicron” B1.1.529 was first identified in South Africa in November 2021. Given the large number of mutations in Omicron’s spike protein compared to the original Wuhan strain, its binding efficacy to the ACE2 receptor and its potential to escape antibodies are in the spotlight. Recently, we presented an ab initio quantum mechanical model to characterize the interactions of spike protein’s Receptor Binding Domain (RBD) with select antibodies and ACE2 variants. The model identified weak links among the residues constituting interactions with the human ACE2 receptor (hACE2), and also enabled us to characterize in silico mutated RBDs to identify potential Variants of Concern (VOC). In particular, we focused on the role of RBD residue 484 in the interaction of the Delta variant with ACE2 and neutralizing antibodies (nAbs). In this report, we apply our model to the Omicron VOC, and characterize its interaction pattern with hACE2. Our results show that (i) binding affinity with hACE2, compared to Delta, is considerably increased, possibly contributing to increased infectivity. (ii) The interaction pattern between B1.1.529 and hACE2 differs from previous variants by shifting the hot-spot interaction residues on hACE2, and potentially affecting nAbs efficacy. (iii) A K mutation in the RBD residue 484 can further improve Omicron’s binding of hACE2 and evasion of nAbs. Finally, we argue that a library of hot-spots for point-mutations can predict binding interaction energies of complex variants.

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Discovery of SARS-CoV-2 M^pro peptide inhibitors from modelling substrate and ligand binding

Abstract: The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its...

Cited by 65 publications

References 69 publications

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M^pro Explored by QM/MM Simulations

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M^pro Explored by QM/MM Simulations

Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling

Mechanistic investigation of SARS-CoV-2 Omicron variant spike mutants via full quantum mechanical modeling

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Discovery of SARS-CoV-2 Mpro peptide inhibitors from modelling substrate and ligand binding

Abstract: The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its...

Cited by 65 publications

References 69 publications

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations

Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling

Mechanistic investigation of SARS-CoV-2 Omicron variant spike mutants via full quantum mechanical modeling

Contact Info

Product

Resources

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Discovery of SARS-CoV-2 M^pro peptide inhibitors from modelling substrate and ligand binding

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M^pro Explored by QM/MM Simulations

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M^pro Explored by QM/MM Simulations