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Investigation of changes in protein stability and substrate affinity of 3CL-protease of SARS-CoV-2 caused by mutations

Abstract

3CLpro of SARS-CoV-2 is one of the enzymes required for the replication process of the virus responsible for the COVID-19 pandemic. In this study, changes in protein stability and substrate affinity caused by mutations were investigated to stir the development of potent inhibitors. Sequence data of samples were obtained from the NCBI Virus database. Mutation analyses were performed with RDP4 and MegaX. 3CLpro tertiary models were created using Robetta. Molecular docking for peptidomimetic substrate and inhibitor ligand was done with Autodock v4.2 and Haddock v2.4. Protein stability analysis was performed using mCSM stability and DynaMut2. Twenty-four missense mutations in 3CLpro were identified in this study. Changes in the 3CLpro structure induced by the mutations Met49Thr, Leu167Ser, and Val202Ala resulted in significant levels of instability (-2.029,-2.612,-2.177 kcal.mol-1, respectively). The lowest interaction energy for substrate was -58.7 kcal.mol-1 and -62.6 kcal.mol-1 in wild-type and mutant, respectively. The lowest docking energy for ligand was -6.19 and -9.52 kcal.mol-1 for wild-type and mutant, respectively. This study reports for the first time that mutations cause increased substrate affinity of 3CLpro from SARS-CoV-2. This research provides important data for the development of potent peptidomimetic inhibitors for the treatment of COVID-19.

Keywords:
3CL-protease; mutation analysis; protein stability; SARS-CoV-2 genome; substrate affinity

Introduction

The etiologic agent of coronavirus disease 2019 (COVID-19), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed more than 4.97 million people worldwide (Wu et al., 2020Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, Hu Y, Tao Z-W, Tian J-H, Pei Y-Y et al. (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265-269.; Worldometer, 2021Worldometer (2021) Coronavirus case report, Worldometer (2021) Coronavirus case report, https://www.worldometers.info/coronavirus (accessed 30 Nowember 2021)
https://www.worldometers.info/coronaviru...
). SARS-CoV-2 is the third zoonotic coronavirus outbreak after the emergence of SARS-CoV and the Middle East Respiratory Syndrome (MERS-CoV) in the last two decades. SARS-CoV-2 is a positive-sense RNA virus (Drosten et al., 2003Drosten C, Günther S, Preiser W, Van der Werf S, Brodt HR, Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RAM et al. (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348:1967-1976.; Zaki et al., 2012Zaki AM, Van Boheemen S, Bestebroer TM, Osterhaus ADME and Fouchier RAM (2012) Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 367:1814-1820.). The SARS-CoV-2 genome is noted for its high similarity to SARS-CoV and MERS-CoV (Akbulut, 2020aAkbulut E (2020a) Comparative genomic and proteomic analysis of SARS CoV-2 - with potential mutation probabilities and drug targeting. J Sci Technol 13:1187-1197.). Once the SARS-CoV-2 viral genome has entered the host cell, it is translated to yield two overlapping polyproteins (polyprotein1a and polyprotein1ab) (Zhu et al., 2020Zhu W, Xu M, Chen CZ, Guo H, Shen M, Hu X, Shinn P, Klumpp-Thomas C, Michael SG and Zheng W (2020) Identification of SARS-CoV-2 3CL protease inhibitors by a quantitative high-throughput screening. ACS Pharmacol Transl Sci 3:1008-1016.). 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro) contribute to the activation of 15 different non-structural proteins (nsp) by processing polyprotein1ab from 14 different points (Gao et al., 2021Gao X, Qin B, Chen P, Zhu K, Hou P, Wojdyla JA, Wang M and Cui S (2021) Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharm Sin B 11:237-245.). The critical role of 3CLpro, a cysteine protease, in converting polyproteins into individual functional proteins for viral replication, as well as the enzyme’s highly conserved substrate selectivity among Coronaviruses, make it an attractive target for inhibitor screening (Su et al., 2020Su H-X, Yao S, Zhao W-F, Li M-J, Liu J, Shang W-J, Xie H, Ke C-Q, Hu H-C, Gao M-N et al. (2020) Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients. Acta Pharmacol Sin 41:1167-1177.). The active site of 3CLpro is sandwiched between two β-barrel domains, domain I (residue 10-99) and domain II (residue 100-182). Domain III (residue 198-306), forms a bundle of alpha-helices and is proposed to regulate dimerization (Douangamath et al., 2020Douangamath A, Fearon D, Gehrtz P, Krojer T, Lukacik P, Owen CD, Resnick E, Strain-Damerell C, Aimon A, Ábrányi-Balogh P et al. (2020) Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun 11:5047.).

Mutations can trigger changes in protein structure and stability, causing changes in protein functional properties, substrate/ligand affinity, and protein-protein interactions (Manolaridis et al., 2018Manolaridis I, Jackson SM, Taylor NMI, Kowal J, Stahlberg H and Locher KP (2018) Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states. Nature 563:426-430.; Kalathiya et al., 2019Kalathiya U, Padariya M and Baginski M (2019) Structural, functional, and stability change predictions in human telomerase upon specific point mutations. Sci Rep 9:8707.; Akbulut, 2021aAkbulut E (2021a) Mutations in the SARS CoV-2 spike protein may cause functional changes in the protein quaternary structure. Turk J Biochem 46:137-144., bAkbulut E (2021b) Changes in interaction between accessory protein 8 and IL-17RA in UK isolates caused by mutations in the SARS-CoV-2 open reading frame 8. Int J Comput Exp Sci Eng 7:76-83.).

Understanding the molecular-level mechanism of peptide cleavage catalyzed by cysteine proteases after mutations are crucial for designing strong structure-based inhibitors (Mengist et al., 2021Mengist HM, Dilnessa T and Jin T (2021) Structural basis of potential inhibitors targeting SARS-CoV-2 main protease. Front Chem 9:622898.). Here, changes in the structure and functional properties of 3CLpro caused by mutations in the nsp5 of SARS CoV-2 were determined. To aid in the creation of efficient 3CLpro inhibitors, structural alterations in proteins were studied.

Materials and Methods

Mutation data and protein stability analysis

Sequence data of 1,536,489 individuals were searched from the NCBI Virus database for the analysis of 3CLpro mutations of SARS CoV-2. The study included 1,474 complete sequence data from the 2,950 sequence data from the Africa. Reference 3CLpro accesion codes are YP_009725301_1 and NC_045512.2. Protein sequence information was aligned with the MAFFT (v7.487) multiple sequence alignment program FFT-NS-i algorithm (Katoh et al., 2018Katoh K, Rozewicki J and Yamada KD (2018) MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 20:1160-1166.). The scoring matrix BLOSUM 80 and 1 PAM/k=2 was chosen for the amino acid sequences and nucleotide, respectively (Mount, 2008aMount DW (2008a) Using BLOSUM in sequence alignments. CSH Protoc 2008:pdb.top39.,bMount DW (2008b) Using PAM matrices in sequence alignments. CSH Protoc 2008:pdb.top38.). The gap opening penalty was used as 2.0. The mutated residues were analyzed with RDP4 and MegaX tools (Martin et al., 2015Martin DP, Murrell B, Golden M, Khoosal A and Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003.; Kumar et al., 2018Kumar S, Stecher G, Li M, Knyaz C and Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547-1549.). Analysis of changes in protein stability after the mutation was performed using mCSM stability and DynaMut2 (Pires et al., 2014Pires DEV, Ascher DB and Blundell TL (2014) mCSM: Predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics 30:335-342.; Rodrigues et al., 2021Rodrigues CHM, Pires DEV and Ascher DB (2021) DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Sci 30:60-69.). The results were viewed with the NGL viewer (Rodrigues et al., 2021).

Mutant protein modeling

The homology model of the mutant 3CLpro was created using Rosetta algorithms applying the deep residual neural network approach (Yang et al., 2020Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S and Baker D (2020) Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci U S A 117:1496-1503.). 7K3T (PDB code) was selected as a template. ProSA was used for the structural quality of 3CLpro models (Wiederstein and Sippl, 2007Wiederstein M and Sippl MJ (2007) ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:407-410.). Superimpose and conformational analyses of wild-type and mutant proteins were performed with PyMOL (ver2.4.1). Topological differences were calculated with the i-Tasser TM-Score and root mean square deviation (RMSD) algorithm (Xu and Zhang, 2010Xu J and Zhang Y (2010) How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26:889-895.).

Molecular docking

The wild-type and mutant of 3CLpro were used as targets, and GC376 alpha-ketoamide analog-VR4 (CID 155804578) was used as an inhibitor ligand for molecular docking using AutoDock 4.2 (Steffen et al., 2010Steffen C, Thomas K, Huniar U, Hellweg A, Rubner O and Schroer A (2010) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 31:2967-2970.). Molecular docking was performed with a grid box of 70x74x80 (−11.333, −3.139, 5.833) with a grid spacing of 0.375 Å around the binding pocket. The simulations were performed with the Lamarckian genetic algorithm (LGA) (Morris et al., 1998Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK and Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662.). The LGA parameters were 100 runs, 2.7x104 generations, and 500 population size. A maximum of 2.5x107 energy evaluations was applied for each experiment.

The change in substrate affinity after the mutation was tested with the protein-peptide docking using Haddock v2.4 (Van Zundert et al., 2016Van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, Van Dijk M, De Vries SJ and Bonvin AMJJ (2016) The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428:720-725.). The active site for the 3CLpro was residues number 41,49,140, 144,145,163,165,166,168,172, and 189. Octa-peptide -SAVLQ/SGF- was used as a substrate to represent the nsp4/nsp5 cleavage site. The number of structures for rigid-body docking was set to 1000. The number of trials for rigid body minimization was set to 5. The number of structures for semi-flexible refinement was set to 200. Refined with short molecular dynamics in open solvent using water. The clustering method was selected Fraction of Common Contacts (FCC). RMSD cutoff for clustering was set to 0.6 Å. Kyte-Doolittle hydrophobicity scale method was used for solvating. Cutoff distance (proton-acceptor) to define a hydrogen bond was set to 2.5 Å. Cutoff distance (carbon-carbon) to define a hydrophobic contact was set to 3.9 Å. Docking parameters were performed as blind docking with default values. Docking results were visualized with Discovery SV (ver20.1, DDS Biovia).

Results

The results showed that a decrease in protein stability increased substrate and ligand affinity. Twenty-four missense mutations were detected in South African isolates of SARS CoV-2 in this study (Table 1). The protein tertiary structure of the mutant 3CLpro was created with trRosetta, a deep neural network-based modeling algorithm. The Z-score of the homology model of mutant 3CLpro was -7.36. The model was within the NMR quality limits. TM-score was 0.97. RMSD of the common residues was 1.601 Å. RMSD in superposition was 0.93 Å. Two of these mutations were shown to improve the stability of the 3CLpro structure, whereas twenty-two were found to destabilize it. Changes in the 3CLpro structure induced by the mutations Met49Thr, Leu167Ser, and Val202Ala resulted in significant levels of instability (-2.029, -2.612, and -2.177 kcal.mol-1, respectively) (Table 1). It was observed that the stable structure formed by Met49, which is involved in the stabilization of the active site with its strong bond network, in the wild protein with 5 hydrophobic, 7 polar interactions, and 2 hydrogen bonds, weakens in the mutant protein (Figure 1a,b). After the Met49Thr mutation, the hydrophobic interactions between the catalytic residue His41 and the Met49 residue were removed. After the Met165Ile and Leu167Ser mutations of Met165 and Leu167 residues, which play an important role in the formation of the substrate-binding pocket with their polar, hydrophobic, and Van der Walls interactions, significant weakening occurred in the interaction networks (Figure 1). The stable structure formed by Val202 in domain III, which is involved in dimerization, with five hydrophobic, three polar, one Van der Walls, and one hydrogen bond interactions were reduced to three polar, one Van der Walls, and one hydrogen bond interactions after mutation (Figure 1g,h). The Asn238Tyr/Ser mutations increased protein stability in its location.

Table 1 -
Changes in stability of 3CLpro of SARS-CoV2.

Figure 1-
Surface-stick illustration of changes in protein stability induced by highly destabilizing mutations of 3CLpro of SARS-CoV-2. a) Met49/wild-type, b) Thr49/mutant, c) Met165/wild-type, d) Ile165/mutant, e) Leu167/ wild-type, f) Ser167/mutant, g) Val202/wild-type, h) Ala202/mutant. Bond legends; red-hydrogen, green-hydrophobic, orange-polar, blue-van der walls, navy blue-carbonyl.

The results of mutations in molecular interaction were tested with molecular docking. The lowest binding energy for ligand was -6.19 kcal.mol-1 and -9.52 kcal.mol-1 for wild-type and mutant 3CLpro, respectively (Table 2). The minimum inhibitory concentration was 28.54 µM and 0.105 µM for wild-type and mutant 3CLpro, respectively. The wild-type 3CLpro provided hydrogen bond interaction with the ligand at His41:CD2 - VR4:O14, Asn142:CA - A:VR4:O27, and Gln189:NE2 - VR4 positions, and hydrophobic interaction with residues Met49, Met165, Pro168, and His163 (Figure 2). The mutant 3CLpro provided hydrogen bond interaction with the ligand at VR4:N03 - Cys145:SG, VR4:N06 - His41:NE2, Asn142:CA - VR4:O32, VR4:C12 - Asp187:O, VR4:C18 - Thr49:OG1, Ser46:OG - VR4, and Ser144:OG - VR4 positions, and hydrophobic interaction with residues Leu27, His41, Cys145, Ile165,and Glu166.

Table 2-
Docking results of wild and mutant 3CLpro of SARS-CoV-2 with inhibitor ligand.

Figure 2-
Representation of binding interaction of VR4 inhibitor ligand with 3CLpro of SARS CoV-2. a) Hydrophobic surface illustration of wild-type 3CLpro-ligand complex, b) Diagram illustration of mutant 3CLpro-ligand complex, c) Hydrophobic surface illustration of wild-type 3CLpro-ligand complex, d) Diagram illustration of the mutant 3CLpro-ligand complex .

Changes in protein structure induced by mutations resulted in increased interest in substrate affinity. FCC and interface-RMSD (i-RMSD) values indicate that the structure with the lowest energy differs significantly from other clusters and that Cluster-1 for wild-type and Cluster-6 for mutant were the correct binding model. While the lowest substrate interaction energy was -58.7 kcal.mol-1 in wild-type, the interaction was achieved with -62.6 kcal.mol-1 in mutant protein (Figure 3). Z-scores were -1.8 and -2.0 for wild-type/substrate and mutant/substrate complexes, respectively (Table 3). The interaction with the catalytic residues (His41 and Cys145) was stronger in the mutant protein, and the formation of the substrate in the mutant protein binding groove was more successful (Figure 4).

Figure 3-
The quality parameters of 3CLpro-substrate interaction.

Table 3-
Docking results of wild and mutant 3CLpro of SARS-CoV-2 with the substrate.

Figure 4-
Representation of interaction of the substrate with 3CLpro of SARS-CoV-2. a) Hydrophobic surface illustration of wild-type 3CLpro-substrate complex, b) Stick illustration of wild-type 3CLpro-substrate complex, c) Diagram illustration of wild-type 3CLpro-substrate complex, d) Hydrophobic surface illustration of mutant 3CLpro-substrate complex, e) Stick illustration of mutant 3CLpro-substrate complex, f) Diagram illustration of mutant 3CLpro-substrate complex.

Discussion

SARS-CoV-2 will perhaps be one of the most devastating health problems of this century. Despite the success of vaccine studies to prevent the disease, the high mutation rate of SARS-CoV-2 made the current preventive efforts only partially successful, making the studies on the development of therapeutic drugs even more important. In this context, the most important drug targets are cysteine proteases, which provide the functional structure of the SARS-CoV-2 proteome. Cysteine proteases are attractive targets for covalent inhibitors (Kathman et al., 2014Kathman SG, Xu Z and Statsyuk AV (2014) A fragment-based method to discover irreversible covalent inhibitors of cysteine proteases. J Med Chem 57:4969-4974.). In this study, changes in 3CLpro stability and activity caused by mutations in South African isolates were investigated in silico. Mutations can cause changes in the structure and stability of drug target proteins, resulting in changes in substrate and ligand affinity (Akbulut, 2020Akbulut E (2020b) SARS CoV-2 spike glycoprotein mutations and changes in protein structure. Trak Univ J Nat Sci 22:23-33.b; Xavier et al., 2021Xavier JS, Nguyen T-B, Karmarkar M, Portelli S, Rezende PM, Velloso JPL, Ascher DB and Pires DEV (2021) ThermoMutDB: A thermodynamic database for missense mutations. Nucleic Acids Res 49:D475-D479.). In silico studies have achieved great success in recent years due to their contributions to the design and development of effective drug molecules in a short time, taking these changes into account (Prabhavathi et al., 2020Prabhavathi H, Dasegowda KR, Renukananda KH, Lingaraju K and Naika HR (2020) Exploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach. J Biomol Struct Dyn 39:5471-5485.; Das et al., 2021Das P, Majumder R, Mandal M and Basak P (2021) In silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis. J Biomol Struct Dyn 39:6265-6280.). In this study, the data obtained showed that the decrease in protein stability due to mutations increased the affinity for the substrate and VR4 ligand, a cysteine protease inhibitor.

SARS-CoV-2 3CLpro has two catalytic residues, His41 and Cys145. The residues 49, 140, 144, 163, 165, 166, 168, 172 and 189 are the main structures in the active site formation. The charge change near the active site can alter the energetic barrier to attaining oxyanion transition states (Simón and Goodman, 2010Simón L and Goodman JM (2010) Enzyme catalysis by hydrogen bonds: The balance between transition State binding and substrate binding in oxyanion holes. J Org Chem 75:1831-1840.). The altered electrical charge and hydrophobic interactions as a result of mutations concentrated around the active site may explain the increased ligand and substrate affinity, and catalytic activity (Table 1). In dimerization, Glu166 gets close to the N-terminus of the protein. This movement contributes to the completion of the active site formation by providing the formation of the substrate specificity pocket and the oxyanion hole (Hilgenfeld, 2014Hilgenfeld R (2014) From SARS to MERS: Crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J 281:4085-4096.). Conservation of the conformations of Glu166 and Phe140 involved in dimerization may indicate successful dimerization despite increased instability by mutations.

The distance between His41:CE1 and Cys145:SG resulting in 0.1 Å divergence after mutation resulted in a narrowing of approximately 1 degree (0.9°) in the angle between His41:NE2-Cys145:SG and His41:CE1--Cys145:SG (Figure 5). The conformational structure and topology of the substrate-binding groove are one of the most fundamental factors determining the catalytic efficiency of 3CLpro. The changes in the substrate-binding groove and the changing topological structure caused by the mutations detected in South African isolates, most of which concern the active site residues and the surrounding area, may explain the increased activity. This might also explain the exponential increase in the number of instances after new mutations (Deparment Health Republic of South Africa, 2021Deparment Health Republic of South Africa (2021) COVID19 Daily Cases, Deparment Health Republic of South Africa (2021) COVID19 Daily Cases, https://sacoronavirus.co.za/covid-19-daily-cases (accessed 21 September 2021)
https://sacoronavirus.co.za/covid-19-dai...
).

Figure 5-
Conformational change in catalytic residues His41 and Cys145 a) wild-type 3CLpro, b) mutant 3CLpro.

The binding patterns presented in this study revealed a high degree of similarity with the high-resolution crystallographic substrate-binding patterns. (MacDonald et al., 2021MacDonald EA, Frey G, Namchuk MN, Harrison SC, Hinshaw SM and Windsor IW (2021) Recognition of divergent viral substrates by the SARS-CoV-2 main protease. ACS Infect Dis 7:2591-2595.). 3CLpro-substrate interactions contribute to fine-tuned substrate geometry that results in substrate-specific catalytic efficiency (Kneller et al., 2020Kneller DW, Phillips G, O’Neill HM, Jedrzejczak R, Stols L, Langan P, Joachimiak A, Coates L and Kovalevsky A (2020) Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography. Nat Commun 11:3202.). The point of interest here is whether SARS-CoV-2 functional proteins, organized by a mechanism that we can evaluate sequentially depending on the variability in substrate affinity, can act in coordination with increased protease activity. The differential affinity of 3CLpro to nonstructural protein substrates for SARS-CoV-2 supports cleavage of pp1ab by a cascading mechanism. Despite the invariance of P1 (Gln) in substrates, the sequences before and after it are thought to play a role in programming this gradual cleavage by limiting the rate of catalytic activity (Snijder et al., 2016Snijder EJ, Decroly E and Ziebuhr J (2016) The non-structural proteins directing Coronavirus RNA synthesis and processing. Adv Virus Res 96:59-126.; Gildenhuys, 2020Gildenhuys S (2020) Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle. Biochem J 477:1479-1482.).

The process of formation of SARS-CoV-2 functional proteins begins with the autocleavage of 3CLpro. Phe305Val mutation detected in the C-terminal autocleavage site (Ser301-Gln306) increased unstable structure and motility in the autocleavage region (Table 1). Whether the Phe305Val mutation results in increased autocleavage activity is a further question to be answered.

The high instability caused by the Met49Thr mutation seen in the substrate-binding site results in increased substrate-enzyme interaction due to increased mobility. The S2 sub-binding site is formed by the Met49 and Met165 residues of 3CLpro. Mutations in Met49Thr and Met165Ile induced alterations in the active site’s conformation and topology (Figure 1a,b,c,d).

Glu166 is one of the key residues in both dimerization and substrate binding (Świderek and Moliner, 2020Świderek K and Moliner V (2020) Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mpro by QM/MM computational methods. Chem Sci 11:10626-10630.; Ullrich et al., 2021Ullrich S, Sasi VM, Mahawaththa MC, Ekanayake KB, Morewood R, George J, Shuttleworth L, Zhang X, Whitefield C, Otting G, et al. (2021) Challenges of short substrate analogues as SARS-CoV-2 main protease inhibitors. Bioorg Med Chem Lett 50:128333.). Unstable mutant neighboring residues (162,164,165,167, 168,169 and 170), which have a role in substrate localization, may be considered to be involved in the increase in substrate interaction of Glu166.

Conclusion

This study was the first to report that mutations cause increased substrate affinity of 3CLpro from SARS-CoV-2. Although mutations indicate increased substrate affinity and viral activity, the positional accuracy and increased affinity of the inhibitory ligand after mutations in the active site may also lead to increased success of therapeutic drugs. In addition, increased substrate affinity inspires efforts to use peptidomimetics without warheads as inhibitors against 3CLpro of SARS-CoV-2.

References

  • Akbulut E (2020a) Comparative genomic and proteomic analysis of SARS CoV-2 - with potential mutation probabilities and drug targeting. J Sci Technol 13:1187-1197.
  • Akbulut E (2020b) SARS CoV-2 spike glycoprotein mutations and changes in protein structure. Trak Univ J Nat Sci 22:23-33.
  • Akbulut E (2021a) Mutations in the SARS CoV-2 spike protein may cause functional changes in the protein quaternary structure. Turk J Biochem 46:137-144.
  • Akbulut E (2021b) Changes in interaction between accessory protein 8 and IL-17RA in UK isolates caused by mutations in the SARS-CoV-2 open reading frame 8. Int J Comput Exp Sci Eng 7:76-83.
  • Das P, Majumder R, Mandal M and Basak P (2021) In silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis J Biomol Struct Dyn 39:6265-6280.
  • Douangamath A, Fearon D, Gehrtz P, Krojer T, Lukacik P, Owen CD, Resnick E, Strain-Damerell C, Aimon A, Ábrányi-Balogh P et al (2020) Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun 11:5047.
  • Drosten C, Günther S, Preiser W, Van der Werf S, Brodt HR, Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RAM et al (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348:1967-1976.
  • Gao X, Qin B, Chen P, Zhu K, Hou P, Wojdyla JA, Wang M and Cui S (2021) Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharm Sin B 11:237-245.
  • Gildenhuys S (2020) Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle. Biochem J 477:1479-1482.
  • Hilgenfeld R (2014) From SARS to MERS: Crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J 281:4085-4096.
  • Kalathiya U, Padariya M and Baginski M (2019) Structural, functional, and stability change predictions in human telomerase upon specific point mutations. Sci Rep 9:8707.
  • Kathman SG, Xu Z and Statsyuk AV (2014) A fragment-based method to discover irreversible covalent inhibitors of cysteine proteases. J Med Chem 57:4969-4974.
  • Katoh K, Rozewicki J and Yamada KD (2018) MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 20:1160-1166.
  • Kneller DW, Phillips G, O’Neill HM, Jedrzejczak R, Stols L, Langan P, Joachimiak A, Coates L and Kovalevsky A (2020) Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography. Nat Commun 11:3202.
  • Kumar S, Stecher G, Li M, Knyaz C and Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547-1549.
  • MacDonald EA, Frey G, Namchuk MN, Harrison SC, Hinshaw SM and Windsor IW (2021) Recognition of divergent viral substrates by the SARS-CoV-2 main protease. ACS Infect Dis 7:2591-2595.
  • Manolaridis I, Jackson SM, Taylor NMI, Kowal J, Stahlberg H and Locher KP (2018) Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states. Nature 563:426-430.
  • Martin DP, Murrell B, Golden M, Khoosal A and Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003.
  • Mengist HM, Dilnessa T and Jin T (2021) Structural basis of potential inhibitors targeting SARS-CoV-2 main protease. Front Chem 9:622898.
  • Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK and Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662.
  • Mount DW (2008a) Using BLOSUM in sequence alignments. CSH Protoc 2008:pdb.top39.
  • Mount DW (2008b) Using PAM matrices in sequence alignments. CSH Protoc 2008:pdb.top38.
  • Pires DEV, Ascher DB and Blundell TL (2014) mCSM: Predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics 30:335-342.
  • Prabhavathi H, Dasegowda KR, Renukananda KH, Lingaraju K and Naika HR (2020) Exploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach. J Biomol Struct Dyn 39:5471-5485.
  • Rodrigues CHM, Pires DEV and Ascher DB (2021) DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Sci 30:60-69.
  • Simón L and Goodman JM (2010) Enzyme catalysis by hydrogen bonds: The balance between transition State binding and substrate binding in oxyanion holes. J Org Chem 75:1831-1840.
  • Snijder EJ, Decroly E and Ziebuhr J (2016) The non-structural proteins directing Coronavirus RNA synthesis and processing. Adv Virus Res 96:59-126.
  • Steffen C, Thomas K, Huniar U, Hellweg A, Rubner O and Schroer A (2010) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 31:2967-2970.
  • Su H-X, Yao S, Zhao W-F, Li M-J, Liu J, Shang W-J, Xie H, Ke C-Q, Hu H-C, Gao M-N et al (2020) Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients. Acta Pharmacol Sin 41:1167-1177.
  • Świderek K and Moliner V (2020) Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mpro by QM/MM computational methods. Chem Sci 11:10626-10630.
  • Ullrich S, Sasi VM, Mahawaththa MC, Ekanayake KB, Morewood R, George J, Shuttleworth L, Zhang X, Whitefield C, Otting G, et al (2021) Challenges of short substrate analogues as SARS-CoV-2 main protease inhibitors. Bioorg Med Chem Lett 50:128333.
  • Van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, Van Dijk M, De Vries SJ and Bonvin AMJJ (2016) The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428:720-725.
  • Wiederstein M and Sippl MJ (2007) ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:407-410.
  • Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, Hu Y, Tao Z-W, Tian J-H, Pei Y-Y et al (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265-269.
  • Xavier JS, Nguyen T-B, Karmarkar M, Portelli S, Rezende PM, Velloso JPL, Ascher DB and Pires DEV (2021) ThermoMutDB: A thermodynamic database for missense mutations. Nucleic Acids Res 49:D475-D479.
  • Xu J and Zhang Y (2010) How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26:889-895.
  • Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S and Baker D (2020) Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci U S A 117:1496-1503.
  • Zaki AM, Van Boheemen S, Bestebroer TM, Osterhaus ADME and Fouchier RAM (2012) Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 367:1814-1820.
  • Zhu W, Xu M, Chen CZ, Guo H, Shen M, Hu X, Shinn P, Klumpp-Thomas C, Michael SG and Zheng W (2020) Identification of SARS-CoV-2 3CL protease inhibitors by a quantitative high-throughput screening. ACS Pharmacol Transl Sci 3:1008-1016.

Internet Resources

Edited by

Associate Editor:

Rogério Margis

Publication Dates

  • Publication in this collection
    29 Apr 2022
  • Date of issue
    2022

History

  • Received
    16 Dec 2021
  • Accepted
    05 Mar 2022
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