Targeting Receptor Binding Domain and Cryptic Pocket of Spike glycoprotein from SARS-CoV-2 by biomolecular modeling
Kewin Otazu, Manuel E. Chenet-Zuta, Georcki Ropon-Palacios, Gustavo E. Olivos-Ramirez, Gabriel M. Jimenez-Avalos, Cleidy Osorio-Mogollon, Frida Sosa-Amay, Rosa Vargas-Rodriguez, Tania P. Nina-Larico, Riccardo Concu, Ihosvany Camps
TTargeting Receptor Binding Domain and Cryptic Pocket of Spikeglycoprotein from SARS-CoV-2 by biomolecular modeling
Kewin Otazu , Manuel E. Chenet-Zuta , Georcki Rop´on-Palacios ∗ , Gustavo E.Olivos-Ram´ırez , Gabriel M. Jimenez-Avalos , Cleidy Osorio-Mogoll´on , FridaSosa-Amay , Rosa Vargas-Rodr´ıguez , Tania P. Nina-Larico , Riccardo Concu , IhosvanyCamps ∗ Laborat´orio de Modelagem Computacional - La Model, Instituto de Ciˆencias Exatas- ICEx. UniversidadeFederal de Alfenas - UNIFAL-MG, Alfenas, Minas Gerais, Brasil Escuela de Posgrado, Universidad San Ignacio de Loyola, Lima, Per´u Facultad de Ciencias y Filosof´ıa, Universidad Peruana Cayetano Heredia, Lima, Per´u Faculdade de Medicina de Ribeir˜ao Preto, Universidade de S˜ao Paulo, S˜ao Paulo, Brasil Facultad de Farmacia y Bioqu´ımica, Universidad Nacional de la Amazon´ıa Peruana, Iquitos, Per´u LAQV-REQUINTE of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto,Portugal
Abstract
SARS-CoV-2, the causative agent of the disease known as Covid-19, has so far reportedaround 3,435,000 cases of human infections, including more than 239,000 deaths in 187countries, with no effective treatment currently available. For this reason, it is necessary toexplore new approaches for the development of a drug capable of inhibiting the entry of thevirus into the host cell. Therefore, this work includes the exploration of potential inhibitorycompounds for the Spike protein of SARS-CoV-2 (PDB ID: 6VSB), which were obtainedfrom The Patogen Box. Later, they were filtered through virtual screening and moleculardocking techniques, thus obtaining a top of 1000 compounds, which were used against abinding site located in the Receptor Binding Domain (RBD) and a cryptic site located inthe N-Terminal Domain (NTD), resulting in good pharmaceutical targets for the blockingthe infection. From the top 1000, the best compound (TCMDC-124223) was selected forthe binding site. It interacts with specific residues that intervene in the recognition andsubsequent entry into the host cell, resulting in a more favorable binding free energy incomparison to the control compounds (Hesperidine and Emodine). In the same way, the1 a r X i v : . [ q - b i o . B M ] J un ompound TCMDC-133766 was selected for the cryptic site. These identified compounds arepotential inhibitors that can be used for the development of new drugs that allow effectivetreatment for the disease. Keywords:
SARS-CoV-2, molecular docking, spike, cryptic site
1. Introduction
Coronaviruses (CoV) are a large family of enveloped positive chain RNA viruses, whichbelong to the Nidoviral order and are primarily responsible for upper respiratory and di-gestive tract infections, both in domestic animals and in humans [1, 2]. In the last 20years, multiples CoVs have been transmitted from animal hosts to humans, causing severeoutbreaks of respiratory diseases and coming to be considered as pandemic on two occa-sions [3, 4]. Since then, multiple efforts have been made to study these viruses in differentanimals in order to identify potential infectious agents who affect humans [5, 6, 7].In December 2019, a new type of CoV (SARS-CoV-2), causing the disease called COVID-19, was reported in the city of Wuhan, China, which has been spreading rapidly throughoutChina and all the world. Currently (May 2020), the World Health Organization has reportedmore than 3,435,000 cases of human infections, including more than 239,000 deaths in 187countries. That is why, since its emergence, various investigations have been carried out tounderstand the phylogenetic relationships of this virus, as well as the structural character-istics of its proteins, mainly those that are involved in the processes of viral replication andpathogenesis, in order to discover inhibitors thereof [8, 9, 10].The Spike (S) protein is a multifunctional molecular machinery that mediates the entryof CoV into host cells, in addition to promoting transmission between species, especially inBetacoronaviruses ( β CoV) [11]. This protein belongs to class I of viral fusion proteins. Thatis, it needs to be cleaved by a cellular protease to bind to the host receptor [12, 13, 14, 15, 16]. ∗ Corresponding author
Email addresses: [email protected] (Georcki Rop´on-Palacios ), [email protected] (Ihosvany Camps ) Preprint submitted to Elsevier June 12, 2020 he S protein is a 180 kDa homotrimer consisting of an extracellular domain, an inter-membrane domain, and an intracellular domain [17]. The extracellular domain contains the S S S S S β sheets ( β β β β β α helices connected by loops that form the coreof the structure [24]. Between sheets β β β sheets 5 and 6, α α
2. Material and methods
A library of chemical compounds was obtained from The Pathogen Box (Van Voorhis etal., 2016), frequently used in the search for treatment against malaria. This box originallycontains around 20,000 compounds in SMILE format, stored in a XLSX file, which were usedfor virtual screening tests. The compounds were filtered based on the criteria established inLipinsky’s rule of 5 [31], selecting only those molecules that do not show any violation of therule. Subsequently, the compounds were converted to SDF, PDB and PDBQT formats, inthis order consecutively, using OpenBabel v2.4.1 software [32], adding polar hydrogens forpH 7.4, following the methodology described in Ref. [33]. In addition, the three-dimensional4tructures of the compounds were minimized using the MMFF96 force field, implementedin the OpenBabel software, in order to optimize their geometry. This entire procedure wasperformed using an in-house
Python script that automates each of the steps described foreach compound.
The CryoEM-resolved structure of the SARS-CoV-2 Spike (S) protein was obtained fromthe Protein Data Bank [34]in PDB format (PDB ID: 6VSB, 3 .
46 ˚ A resolution) [17]. After-wards, the structure was repaired by adding missing loops and missing atoms with Swiss-Model [35], followed by adding di-sulfide bridges (C131-C166, C291-C301, C336-C361, C379-C432, C391-C525 C538-C590, C617-C649, C662-C671, C738-C760, C743-C749, C1032-C1043and C1082-C1126) using the PDB Reader module available from Charmm-GUI [36]. Subse-quently, the structure was prepared with MGLTools v1.5.7 [37], with which Gasteiger-Marsilifillers and polar hydrogens are added, and finally it was converted to .PDBQT format.For virtual screening assays, the RBD region, located in the S S
1) of Sprotein, was considered as a potential site of inhibition, since this region has been reportedin various studies as the region binding to the human ACE2 receptor, mediating the onsetof infection [38, 39, 40, 41, 20]. Amino acids Y396, S399 and F400 were selected as theproximal, central and distal reference point in the RBD to cover this entire domain, whenconfiguring the simulation box both in virtual screening and in molecular docking. Likewise,putative cryptic sites were predicted, using the CryptoSite server [30], keeping those crypticsites that had a score of ≥
20. Both the RBD site and the predicted cryptic site were usedfor the virtual screening trials. The coordinates, and the size of the simulation box wereconfigured on the two sites using MGLTools v1.5.7.
With the database of the filtered chemical compounds, a virtual screening was per-formed on the RBD- S .
00 ˚ A , for5oth. Furthermore, in this procedure, a second in-house Python script was used to auto-matically run the virtual screening and select, from the results, the top 1000 compoundswith the best binding energy for a second filtering using molecular docking.
Using the Autodock GPU software [37, 43], a molecular docking was performed with thetop 1000 molecules. This new Autodock uses the Solis-Wets algorithm. A new gridbox wasprepared on the previously described binding sites, using a spacing of 0 .
375 in both cases.The parameters of the molecular docking were: population size of 350, number of evaluationsof 2500000, number of generations of 27000, a mutation ratio of 0 .
02, a crossover ratio of0 . DS = N pop − N M BE ,where N pop is the population of the cluster where the pose of the ligand was classified, and N M BE is the average coupling energy. This procedure was carried out in the same wayusing another in-house
Python script, to automate the procedures and make a new selectionof the top 10 best compounds based on binding energies, both for the RBD and for thecryptic site. Each selected pose was extracted with PyMol v2.3.5 and converted to PDBformat for subsequent simulations.
The resulting data from virtual screening was treated using a Python and C++ in-house scripts. The first one was used to select the top of the best ligands based on thebinding energy and the second one, to convert the binding energy (∆ G ) to the dissociationconstant ( k d ), through the equation ∆ G = RT ln ( k d ) ( R is the gas constant and T is thetemperature, taken equal to 300 K ).The generated poses that showed the best interactionenergies were analyzed with PLIP [44] to determine the type and number of interactionsbetween compounds and receptor. The figures were rendered with VMD software [45].6 . Results The untimely appearance of SARS-CoV-2, as a result of a kind of global crisis, has af-fected not only China, but hundreds of other countries, where the impact has been worse.Therefore, many research groups in the world are putting all their interest and efforts on it.The main interest is to block the virus from entering the host cell, and give the immune sys-tem time to recognize and eliminate it. For this purpose, multiple approaches are explored.The one we explored here was to identify potential small molecules with the ability to in-teract with key residues involved in the molecular recognition of the ACE2-RBD complex,which was successfully achieved, and it is shown in the following paragraphs of this section.
As reported in various studies, the Recognition Binding Domain of SARS-Cov-2 spikeprotein mediates the entry of the virus into the host cell through the human ACE2 recep-tor [12, 13, 14, 19, 15, 16, 20]. Therefore, this domain was considered the binding site forvirtual screening evaluations, since the main amino acids involved in the interaction arefound in this region (Y396, S399 and F400) (figure 1A), and, which are also points of accessto the distal and proximal regions of the domain that allowed us to cover most of the do-main. On the other hand, we introduced the search for another region of the protein as aninteraction site with small molecules, this site is called cryptic site, which was predicted withthe Cryptosite server [30], managing to observe this cryptic site with potential drugability,located in the N-Terminal Domain (figure 1C).In the virtual screening, the compounds were classified based on their free binding en-ergy, ∆ G , obtaining the top 1000 compounds with the best binding and cryptic site affinity.Subsequently, the evaluation of the top 1000 compounds, by molecular docking, allowed iden-tifying the top 10 ligands that have high affinity with the RBD of S protein, in the bindingsite and cryptic site (∆ G ≤ − . kcal/mol and ∆ G ≤ − . kcal/mol , respectively).To determine the molecular recognition and test that these interact with key residues,the analysis was performed with PLIP software, where it was observed that the ligandsinteracted forming hydrogen bonds, salt bridges, aromatic interactions and hydrophobic7 B C
Figure 1: Anatomy and binding site of Spike glycoprotein. (A) Front view of the monomeric protein S isshown, where the receptor-binding motif (RBM) is colored in green, receptor-binding domain (RBD) in blueand S2 domain in silver. Moreover, the lateral view (left) of the protein shows the S1 domain colored indark-silver and N-terminal domain (NTD) in red. (B) The three referential residues Y396, S399, and F400are represented in yellow-sticks. The proximal region, the core and distal region are signalized in dottedlines. (C) The cryptic pocket is shown in cartoon while the principal residues are shown in surface. G = − . kcal/mol , k d = 530 . nM ) at the binding site (RBD) of S protein. This compoundis molecularly recognized by the formation of hydrogen bonds with residues N487, Y489and L492, at distances of 2 .
14 ˚ A , 3 .
37 ˚ A and 3 .
43 ˚ A , respectively (figure 2A). Furthermore,it presents an aromatic interaction with residue Y489 and hydrophobic interactions withresidues F456, Y473, A475, Q484, Y489, F490 and L492 (table 1).9 modin Hespiridine
A B CD E F
G H I
J K L
TCMDC-124223 GNF-Pf-2151 GNF-Pf-209
GNF-Pf-4334 TCMDC-124284 TCMDC-141509TCMDC-140895 TCMDC-140646
TCMDC-123460TCMDC-137673
Figure 2: Molecular recognition in RBD. The binding modes of the top 10 ligands obtained from themolecular docking assays, and positive controls are represented in black-sticks. The receptor residues arerepresented in white-sticks, and the ligands are shown in different colors. The hydrogen bonds are shown insky blue dotted lines. able 1: Ligand interactions with the Recognition Binding Domain of domain S S
1) Spike from SARS-CoV-2.
Ligand Interactions∆
G k d H-Bond Aromatic HydrophobicNumber Residue Functional group Distance Number Residue Number ResidueTCMDC-124223 − .
53 530 .
53 3 Asn487(O-OH) hydroxyl 2 .
14 1 Tyr489 7 Phe456,Tyr473,Ala475,Tyr489(OH-N) secondary amino 3 .
37 Glu484, Tyr489, Phe490,Leu492(O-HN) secondary amino 3 .
43 Leu492GNF-Pf-2151 − .
49 567 .
73 2 Asn487(NH-O) ester 2 .
45 3 Phe456, Glu484, Tyr489Phe490(NH-O) ester 2 . − .
41 650 .
12 3 Glu484(O-HN) carboxamide 3 .
02 1 Tyr489 5 Phe456, GLu484, Phe486,Asn487(NH-O) carboxamide 2 .
27 Tyr489, Phe490Phe490(NH-O) secondary amino 2 . − .
35 719 .
67 3 Arg457(NH-O) hydroxyl 1 .
63 2 Tyr421, 3 Lys417, Phe456, Ala475Arg457(O-HO) hydroxyl 1 .
90 Tyr473Tyr473(OH-N) secondary amino 2 . − .
31 770 .
13 3 Leu455(O-HN) secondary amino 1 .
97 5 Lys417, Tyr421, Leu455,Asn487(O-HN) secondary amino 1 .
78 Phe456, Tyr489Tyr489(OH-N) secondary amino 3 . − .
29 796 .
66 2 Asn487(NH-O) ketone 2 .
54 2 Phe456, 5 Glu484, Phe486, Tyr489,Cys488(NH-O) ketone 2 .
59 Phe490 Phe490, Gln493TCMDC-123460 − .
24 867 .
08 1 Gly485(O-HN) secondary amino 2 .
18 6 Glu484, Phe486, Tyr489,Phe490, Leu492, Gln493TCMDC-140895 − .
22 896 .
96 4 Glu484(OH-O) carboxamide 3 .
32 2 Phe456, 4 Phe456, Glu484, Tyr489,Glu484(O-HN) secondary amino 2 .
09 Tyr489 Phe490Tyr489(OH-O) hydroxyl 3 . . − .
18 959 .
84 2 Arg457(NH-O) carboxamide 1 .
98 1 Phe456 5 Lys417, Leu455, Phe456,Tyr489(O-HN) secondary amino 2 .
34 Tyr489, Phe490TCMDC-137673 − .
15 1009 . .
91 1 Phe486 5 Lys417, Tyr421, Leu455,Asn487(O-HN) secondary amino 2 .
13 Phe456, Tyr489Tyr489(OH-N) tertiary amino 3 . G is in units of kcal/mol. k d is in units of nM and distances are in ˚ A . t the cryptic site, compound TCMDC-133766 presented the best interaction energy(∆ G = − . kcal/mol , k d = 14 . nM ), which exceeds the compounds evaluated in thebinding site. The mode of binding of this compound is mediated by the formation of ahydrogen bridge with residue I101, at a distance of 1 .
98 ˚ A . Likewise, in the formation of thecomplex, aromatic interactions with residues F92, T104, F192 and R190 and hydrophobicinteractions with residues F92, I101, T104, F106, V126, F175, F192, F194, L226 and Y240(Figure 3A, and table 2). A B C
D E F
G H I
TCMDC-135260 TCMDC-124284TCMDC-133766 TCMDC-132194 TCMDC-125125
TCMDC-137793
TCMDC-135884 TCMDC-132494GNF-Pf-5368
Figure 3: Interactions in the cryptic site. The binding modes obtained from molecular docking assays arerepresented in sticks. The receptor residues are represented in white-sticks, and the ligands are shown indifferent colors. able 2: Ligand interactions in the predicted Spike cryptic pocket from SARS-CoV-2. Ligand Interactions∆
G k d H-Bond Aromatic HydrophobicNumber Residue Functional group Distance Number Residue Number ResidueTCMDC-133766 − .
66 14 .
37 1 Ile101(NH-O) secondary amino 1 .
98 4 Phe92, Trp104, 10 Phe92, Ile101, Trp104, Phe106,Phe192, Arg190 Val126, Phe175, Phe192, Phe194,Leu226, Thr240TCMDC-135260 − .
24 29 .
28 2 Ile101(OH-N) secondary amino 1 .
83 10 Phe92, Ile101, Trp104, Ile119,Ser172(O-HO) sulfone 2 .
60 Phe175, Phe192, Phe194, Ile203,Leu226, Val227TCMDC-124284 − .
21 30 .
81 3 Asn121(O-HN) secondary amino 3 .
17 1 Phe192 10 Phe92, Ile101, Trp104, Val126,Leu189(NH-N) tertiary amino 1 .
94 Gln173, Phe175, Phe192, Ile203,His207(NH-N) tertiary amino 2 .
66 Leu226, Val227TCMDC-135232 − .
14 34 .
69 2 Phe92, 8 Ile101, Trp104, Ile119, Val126,Arg190 Gln173, Phe175, Phe192, Leu226TCMDC-137793 − .
09 37 .
76 2 Leu189(NH-N) tertiary amino 1 .
90 2 Arg190, 9 Glu96, Trp104, Val126, Phe175,His207(NH-N) tertiary amino 2 .
49 His207 Asn188, Arg190, Ile203, His207,Val227TCMDC-132194 − .
94 41 .
10 6 Glu96(O-HN) primary amino 3 .
23 9 Ile101, Trp104, Ile119,Ile101(NH-N) primary amino 2 .
65 Val126, Gln173, Phe175,Gln173(NH-N) tertiary amino 2 .
07 Phe192, Leu226, Val227Arg190(NH-N) primary amino 2 . . . − .
96 47 .
06 3 Gln173(NH-O) ether 2 .
57 1 Arg190 10 Ile101, Trp104, Ile119, Val126,Arg190(NH-N) secondary amino 3 .
24 Gln173, Phe175, Phe192, Ile203,Arg190(NH-N) secondary amino 2 .
43 Leu226, Val227GNF-Pf-5368 − .
93 49 .
51 5 Asn99(NH-O) ether 3 .
28 2 Phe175, 6 Gln173, Phe175, Asn188, Phe192,Arg190(NH-O) ketone 2 .
41 His207 His207, Leu226Arg190(NH-O) ether 2 . . . − .
91 51 .
22 3 Ser172(OH-O) carboxamine 3 .
51 1 Phe192 10 Phe92, Ile101, Trp104, Val126,Arg190(NH-N) carboxamine 2 .
32 Gln173, Phe175, Phe192, Ile203,Arg190(NH-N) carboxamine 2 .
63 Leu226, Val227TCMDC-132494 − .
84 57 .
67 3 Asn121(NH-N) secondary amino 3 .
40 1 Arg190 7 Arg102, Trp104, Val126, Phe175,Gln173(NH-O) carboxamine 1 .
94 Phe192, Leu226, Val227Leu226(O-HN) secondary amino 3 . G is in units of kcal/mol. k d is in units of nM and distances are in ˚ A . dditionally, two drugs (Hespiridine and Emodin), approved by the FDA, were takenas controls for the analysis of molecular docking. Emodin presented a binding energy − . kcal/mol ; while, the compound Hespidiridine, presented an energy of − . kcal/mol (table 3). Similarly, analysis with PLIP software found that these drugs form hydrogenbridge-type interactions with important residues, such as Y473 and N487, and hydrophobicinteractions (figure 2K). 14 able 3: Ligand-control interactions with the Recognition Binding Domain of domain S Ligand Interactions∆ G H-Bond Aromatic HydrophobicNumber Residue Distance Number Residue Number ResidueEmodin − .
62 4 Arg457(NH-O) 2 .
16 4 Tyr421, Leu455,Tyr473(O-HO) 3 .
14 Tyr473, Ala475Tyr473(OH-O) 2 . . − .
46 4 Tyr473(OH-O) 1 .
89 4 Lys417, Tyr421,Asn487(NH-O) 3 .
32 Leu455, Phe456Asn487(O-HO) 2 . . G is in units of kcal/mol. k d is in units of nM and distances are in ˚ A . . Discussion The current SARS-CoV-2 pandemic represents one of the greatest challenges due to itseasy transmission [25]. Despite various investigations being conducted, so far no treatmentis effective in fighting this virus. Computational approaches are promising alternatives forfinding potential inhibitors through drug repositioning. Therefore, this research focusedon the search for RBD inhibitors for S protein that can prevent recognition by the ACE2receptor.The results of the virtual screening of 13 ,
102 compounds allowed the identification ofpotential inhibitors that can be used in the treatment of Covid-19, including TCMDC-124223, GNF-Pf-2151 and GNF-Pf-209 for the binding site (RBD) and TCMDC-133766,TCMDC-135260 and TCMDC-124284 for the cryptic site (NTD). These compounds havepreviously been used as antimalarial potentials [46], which demonstrates their versatility.Various studies indicate that the amino acids located in the RBM contribute substantiallyto the recognition and subsequent entry of the virus into the cell [26, 47, 48]. Our analyzesdemonstrate that six compounds manage to interact by forming hydrogen bonds with residueN487 (table 1), and polar contacts with residue Y83 of the ACE2 receptor [49]. Likewise,eight compounds show hydrophobic interactions with the Y489 residue (table 1). This typeof interaction with the K31 residue of ACE2 has been shown to be conserved among variantsof this protein [50]. This suggests that the interactions formed could cause modifications inthe contact surface, preventing recognition.Furthermore, the formation of hydrophobic interactions with the K417 residue was ob-served in at least four compounds in the top 10. This residue is known to be located in theloop of the proximal part of the RBM and has a high-energy contribution ( − . kcal/mol )during molecular recognition with ACE2 [51]. In this sense, those compounds that presentsome form of favorable interaction with this residue could promote a competitive type inhi-bition on the contact surface. However, chemical modifications could be introduced, to raisethe binding energy. Similar studies have highlighted the importance of this residue in theinhibition of RBD [27, 24]. 16s other studies point out, the drugability of cryptic sites allows modifying the thermo-dynamic or structural characteristics of proteins [30]. In this study, we report a potentialdrugable cryptic site, located in the N-Terminal domain of the Spike protein. The structurethat makes up this cryptic site allows the virus to merge with the cell membrane [27, 23],so its inhibition could indirectly prevent the entry of the virus. The drug that presentedthe best mode of coupling on this cryptic site (TCMDC-133766) has shown a higher affinity( − . kcal/mol ) compared to the best compounds tested in the RBD. In this sense, it ispossible to evaluate the synergism of the inhibition of RBD and NTD, in such a way thatthe activity of the Spike protein can be suppressed with greater effectiveness.On the other hand, it was observed that the compounds with the best interaction energyhave common functional chemical groups of other inhibitor molecules [52]. The functionalgroups of the top compounds in the binding site (RBD) are mainly of the secondary amino,hydroxyl, and carboxamine type. In the cryptic site, the most representative functionalgroups are the secondary amines, tertiary amino and carboxamines (tables 1 and 2). Thesefunctional groups, which form hydrogen bonds, can be considered for rational drug designbased on a pharmacophore model, as has been proposed for other drugable targets [53].For the control of molecular docking evaluations, two compounds were used, Emodineand Hespiridine, which are approved by the FDA [54, 55]. These drugs interact with im-portant residues in the RBD (N487 and Y489). However, it has been observed that thesecompounds present lower interaction energies ( − . kcal/mol and − . kcal/mol respec-tively) compared to the top of the evaluated compounds. This suggests that the compoundsreported in this work could improve the inhibitory activity on the Spike protein.Finally, our studies suggest a pharmacological potential of the present molecules againstthe Spike protein of SARS-CoV-2. In-vivo studies can confirm the inhibitory activity ofthese compounds. Furthermore, the functional groups of these drugs can be used to searchfor similar compounds in different databases.17 . Conclusion
Our approach has allowed us to identify a set of small molecules with the capacity tointerrupt the interaction of ACE2-RBD, since their molecular recognition is associated withkey residues in the interaction of the ACE2-RBD complex, and that these can also interactwith the cryptic site and can reduce the interaction of this complex, through synergism.In therapy, that it is called combination therapy , which has shown better benefits in thetreatment of the disease. However, these compounds must be tested in-vitro to demonstratetheir activity, and undergo the respective clinical tests. It is worth mentioning that thefunctional groups of these compounds could be used to perform pharmacophore models,and to identify FDA-approved drugs and speed up clinical tests.
6. Acknowledgments
Part of the results presented here were developed with the help of CENAPAD-SP (CentroNacional de Processamento de Alto Desempenho em S˜ao Paulo) grant UNICAMP/FINEP-MCT and CENAPAD-UFC (Centro Nacional de Processamento de Alto Desempenho, atUniversidade Federal do Cear´a). 18 eferences [1] M. P. Cruz, E. Santos, M. V. Cervantes, M. L. Ju´arez, COVID-19, una emergencia de salud p´ublicamundial, Revista Cl´ınica Espa˜nola (mar 2020). doi:10.1016/j.rce.2020.03.001 .[2] V. L´opez, T. V´azquez, J. Alonso-Titos, M. Cabello, A. Alonso, I. Beneyto, M. Crespo, C. D´ıaz-Corte,A. Franco, F. Gonz´alez-Roncero, E. Guti´errez, L. Guirado, C. Jim´enez, C. Jironda, R. Lauzurica,S. Llorente, A. Mazuecos, J. Paul, A. Rodr´ıguez-Benot, J. C. Ruiz, A. S´anchez-Fructuoso, E. Sola,V. Torregrosa, S. Z´arraga, D. 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