In silico Prediction of the Roccustyrna ADMET Properties and Bioactivity Score.
To predict important molecular properties such as logP, polar surface area, drug - likeness and bioactivity of our new prototype and small - sized Roccustyrna ligand 2 - ({ (fluoro ({ ((2E) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene) cyano - lambda6 - sulfanyl}) methyl) - phospho - rylidene} amino) - 4, 6 - dihydro - 1H - purin - 6 - one (1S, 2r, 3S) - 2 - ({ ((1S, 2S, 4S, 5r) - 4 - ethenyl - 4 - sulfonyl ‐ bicyclo (1S, 2r, 3S) - 2 - ({ ((1S, 2S, 4S, 5r) - 4 - ethenyl - 4 - sulfonyl - bicyclo (3.2.0) heptan - 2 - yl) oxy} amino) - 3 - ((2r, 5r) - 5 - (2 - methyl - 6 - methylidene - 6, 9 - dihydro - 3H - purin - 9 - yl) - 3 - methylideneoxolan - 2 - yl) phosphirane - 1 - carbonitrile (3.2.0) heptan - 2 - yl) oxy} amino) - 3 - ((2r, 5r) - 5 - (2 - methyl - 6 - methylidene - 6, 9 - dihydro - 3H - purin - 9 - yl) - 3 - methyli deneoxolan - 2 - yl) phosphirane - 1 - carbonitrile, the Molinspiration tool was employed as customized on the basis of this rational anti - viral drug design study. The milogP (Octanol - water partition coefficient logP) and TPSA (Topological polar surface area) values were calculated by utilizing the same online tool using Bayesian statistics. These In - Silico results indicated that the milogP value of the Roccustyrna small molecule was predicted as having optimum lipophilicity properties (logP < 5) (Han et al, 2019) in the aspect of dermal absorption and parallel artificial permeation (Table S1), (Table S2), (Table S3), (Table S4).
Screening of the Roccustyrna Inhibitor for Spike Protein - rBD - ACE2 Interaction.
In this study, we have shown that the QMMM designed Roccustyrna small molecule which was designed in silico by using Topology Euclidean Geometric and Artificial Intelligence - Driven Predictive Neural Networks was engaged in the binding domains of the protein targets of of the (PDB:1xak) (Figure S2) with the docking energy values of (T.Energy, I.Energy, vdW, Coul, Numrotors, rMSD, Score), ( - 19.625, - 35.483, 7.633, - 43.116, 7, - 5.813) Kcal/mol, (Table S4), (Table S5) The Roccustyrna chemical structure interacted into the binding sites of the protein targets of (PDB:6w9c), (Figure S2) with the negative docking energies of the (T.Energy, I.Energy, vdW, Coul, Numrotors, rMSD, Score), ( - 36.678, - 55.648, - 7.519, - 48.129, 7, - 6.762) Kcal/Mol. The same combination of small molecules also generated hydrophobic interactions when docked onto the A1, 02J C binding cavities of the amino acid of 168 PrO with the docking energy values of ( - 3.53, - 2369, - 1303, - 10.425, - 3.42, - 72.447, - 13.394, - 3.19, - 70.551) Kcal/mol. Our new QMMM designed cluster of quantum thinking small molecules additionally involved in the generation of the hydrogen bonding within the PJE: C:5 (PJE - 010) 010:C:6 Interacting chain (s) while generating hydrophobic interactions when docked into the A6, 010 C binding domains of the amino acid of the 25THr with the docking energy values of ( - 3.73, - 2415, 179, - 7.156, - 21.406, - 66.898 - 8.709, - 22.779) Kcal/mol. The combination of GisitorviffirnaTM, Roccustyrna_gs1_TM, and Roccustyrna_fr1_TM cluster of active pharmacophoric sites of the 2 - ({ (fluoro ({ ((2E) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene) cyano - lambda6 - sulfanyl}) methyl) phosphorylidene} amino) - 4, 6 - dihydro - 1H - purin - 6 - one (methylamino) - 1, 6 - diazabicyclo (3.2.0) heptan - 4 - yl) oxy} imino) interacted into the A6 010C binding cavities of the amino acid of the 26 THr with the docking energy values of ( - 3.81, - 2415, - 186, - 7.156, - 21.406, - 66.898, - 6.155, - 24.392, - 64.757) Kcal/mol. The combination of the same cluster of active pharmacophoric sites of the 2 - ({ (fluoro ({ ((2E) - 5 - dimethyl - 7 - oxo - 4 - thia - 1 - azabicyclo (3.2.0)heptane - 2 - carbonyloxy) ({ ((2 - amino - 6 - oxo - 6,9 - dihydro - 3H - purin - 9 - yl) oxy) (hydroxy) phosphoryl} oxy) phosphinic acid - ylidene+,*cyano (2,6 - diazabicyclo*3.1.0+hex - 1 - oxabicyclo (2.1.0) pentan - 2 - ylidene) cyano - lambda6 - sulfanyl}) methyl) phosphor - rylidene} amino) - 4, 6 - dihydro - 1H - purin - 6 - onedihydro - 3H - purin - 9 - yl) - 3 - hydroxy - oxolan generated a docking effect which was involved in the generation of hydrogen bonds when docked into the A 6 010 C binding cavities of the amino acid of 143 GLY with the docking energy values of ( - 62.905) Kcal/mol. In addition, the CoMFA contour map of electrostatic regions around Roccustyrna chemical structure indicated to us that contact residues from the Roccustyrna ligand when docked onto the SARS - COV - 2 protein targets of (PDB:2zu5) around the Roccustyrna chemical structure hit the entire sequence of the amino acid of the V - M - THr - 25, V - S - THr - 25, V - M - THr - 26, V - S - HIS - 41, V - M - LEU - 141, V - M - ASN - 142, V - S - ASN - 142, V - M - GLY - 143, V - S - CYS - 145, V - M - MET - 165 with the binding energy values of the - 97.2 and - 5.16512, - 4.15949, - 9.8487, - 4.77062, - 4.72901, - 6.7295, - 5.82428, - 5.35883, - 4.2588, - 5.37491 Kcal/mol respectively. (Figure S2d) The same prototype pharmacophoric element named Roccustyrna when docked into the A5, PJE C2 binding sites of the amino acid sequence of V - S - HIS - 41, V - M - LEU - 141, V - M - ASN - 142, generated hydrogen interactions with the binding energy values of the ( - 16 3.07, - 153.73, - 2408) Kcal/mol/A, in the coupled atoms of the N3 and O2 with the docking energy values of ( - 12.282, - 14.994, - 67.123) Kcal/Mol. The binding patterns of the 02J:C:1 (02J) active sites of the amino acid sequence of V - S - THr - 25, V - M - THr - 26, V - S - HIS - 41, V - M - LEU - 141, V - M - ASN - 142, V - S - ASN - 142, V - M - GLY - 143, V - S - CYS - 145, V - M - MET – 165 onto the 168 PrO, A1, 02J C binding domains generated hydrophobic interactions with the docking energy values of ( - 3.53, - 2369, - 1303, - 10.425, - 3.42, - 72.447, - 13.394, - 3.19, - 70.551) Kcal/mol/A inside the PJE:C:5 (PJE - 010) 010:C:6 A5, PJE C2 interacting chain (s) : A C. (Figure S3) D10 - C - 1099 DMS: A: 402 (DMS) binding sites were also constructed when the combined pharmacophoric elements of the combination of GisitorviffirnaTM, Roccustyrna _gs1_TM, and the Roccustyrna_fr1_TM ligands docked inside the (PDB: 6lu7) protein targets. Hydrogen Bonds were then identified when the RoccustyrnaTM’s chemical coupled atoms interacted within the 298 ArG A amino acid into the 402 DMS A Ng+ 2377 O2 binding cavities with the docking energy values of ( - 1.76, - 2.73, - 166.89, - 2331, - 6.971, - 0.756, - 7.541 - 9.7, - 0.883, - 7.581) Kcal/mol/A. Salt Bridges were also shown to be involved in the generation of the Sulfonium bonding when docked inside the DMS A 5.49 binding cavities within the 295 ASP A amino acid domains with the docking energy values of ( - 402, - 2376, - 6.081,-6.367 -10.436, -2.231, -5.560) Kcal/mol/A. Pi - Cation Interactions of sulfonium bonding within our small molecule whole residue subsurface were also constructed within the amino acid 8 PHE A inside the 402 DMS A pharmacophoric sites with the docking energy values of ( - 4.70, - 1.01, - 2376, - 6.081, - 6.367, - 8.339, - 4.556, - 4.264) Kcal/mo/A. (Figure S3), Hydrophobic Interactions were simultaneously generated by the Roccustyrna chemical residues when docked in the (PDB:6lu7) protein targets of inside the D10 - H - 1099. X77:A:401 (X77) side domains within the active sites of the amino acid cavities of the 41 HIS A 401 X77 A, 165 MET A 401 X77 A, and 166 GLU A 401 X77 A with the docking energy values of ( - 3.75, - 4670, - 609, - 20.444, - 13.613, - 29.034, - 19.778, - 13.574, - 32.721 - 3.90, - 4673, - 2529, - 19.389, - 17.775, - 28.688, - 16.611, 16.152, - 26.489, - 3.86, - 4661, - 2546, - 17.350, - 23.138, - 25.438 - 16.439, - 20.244, - 23.055, - 18.9, - 3.90, - 4657, - 2881, - 21.763, - 15.894, - 23.429, - 24.934, - 13.635, - 23.312) Kcal/mol/A showing that my AI - quantum thinking chemical structure named Roccustyrna is capable of generating Hydrogen Bonds when docked onto the 41 HIS A 401 X77 A, 143 GLY A 401 X77 A, 144 SEr A 401 X77 A, and 166 GLU A 401 X77 A, sequence of amino acids while targeting the Npl 4680 N2, O3 4679 N2 Nam 4682 O2, and Nam 4683 O2 binding sites with the binding free energy values of the ( - 3.46, - 3.79, - 106.13, - 611, - 20.860, - 19.573, - 32.52, - 19.394, - 16.086, - 32.767, - 2.17, - 2.94, - 148.03, - 2216 - 19.635, - 22.244, - 29.036 - 18.779, - 24.455, - 30.773, - 3.14, - 3.42, - 101.78, - 2228 - 16.096, - 21.679, - 26.816, - 14.503, - 23.707, - 29.056, - 1.98, - 2.80, - 158.32, - 2542 - 18.546, - 18.654, - 26.028 - 16.172, - 18.348, - 24.583) Kcal/molA respectively. (Figure S3) The 2 - ({ (fluoro ({ ((2E) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene) cyano - lambda6 - sulfanyl}) methyl) phosphorylidene} amino) - 4, 6 - dihydro - 1H - purin - 6 - one (1Z) - 2 - { ((2S, 3S, 5r) - 5 - (2 - amino - 6 - oxo - 6, 9 - dihydro - 1H - purin - 9 - yl) - 3 - hydroxyoxolan - 2 - yl) methylidene} - 2 - cyano - 1 - ({ ((2S, 4r, 5r) - 2 - methyl - 2 - (methylamino) - 1, 6 - diazabicyclo (3.2.0) heptan - 4 - yl) oxy} imino) - 1lambda5, 2lambda5 - azaphosphiridin - 1 - ylium druggable scaffold of the Roccustyrna small molecule therefore competes with endogenous SARS - CoV2 PLpro for binding to Lys711 and Arg355 targeting into the binding domains of the critical SARS - CoV2 PLpro residues onto the SARS - COV - 2 protein targets of (PDB:2zu5) within the binding sites of the amino acid of the V - M - THr - 25, V - S - THr - 25, V - M - THr - 26, V - S - HIS - 41, V - M - LEU - 141, V - M - ASN - 142, V - S - ASN - 142, V - M - GLY - 143, V - S - CYS - 145, V - M - MET - 165 with the binding energy values of the ( - 97.2 and - 5.16512, - 4.15949, - 9.8487, - 4.77062, - 4.72901, - 6.7295, - 5.82428, - 5.35883, - 4.2588, - 5.37491) Kcal/mol respectively. CoMFA analysis of electrostatic regions around the Roccustyrna small molecule a chemical structure indicated to us that Hydrogen bonds, Salt bridges and Metal complexes containing Diphosphate, dihydrogen and ION binding sites were generated into the contact residues of the Roccustyrna’s small molecule when docked onto the SARS - COV - 2 protein targets of the (PDB:2zu5) within the sequence of the amino acids of V - M - THr - 25, V - S - THr - 25, V - M - THr - 26, V - S - HIS - 41, V - M - LEU - 141, V - M - ASN - 142, V - S - ASN - 142, V - M - GLY - 143, V - S - CYS - 145, V - M - MET - 165 with the negative docking values of ( - 97.2, and - 5.16512, - 4.15949, - 9.8487, - 4.77062, - 4.72901, - 6.7295, - 5.82428, - 5.35883, - 4.2588, - 5.37491) Kcal/mol/A respectively. (Figure S4a), (Table S4), (Table S5) DMS:A:402 (DMS) binding sites into the 524 Nam 2578 O2 02J (5 - Methylisoxazole - 3 - carboxylic acid) domains were generated inside the 65 ASN A 402 DMS A cavities when RoccustyrnaTM drug deisgn interactred with the PDB:6lu7 protein targets with the docking energy values of ( - 2.05, - 2.94, - 148.0, - 8.211, - 20.857, - 29.787 - 11.058, - 20.242, - 30.160 298) Kcal/mol/A. Salt Bridges were also constructed when our prototype’s surface sites docked inside the DMS - A, Ng+ 2582 O2 binding pocket cavities of the amino acid of the ArG A 403 with the docking energy values of ( - 1.93, - 2.87, - 160.38, - 2512, - 7.044, - 0.753, - 7.469, - 9.865, - 1.270, - 7.327) Kcal/mol/A. Sulfonium bondings were also constructed when our small molecule interacted within the 403 DMS A contact residues of the binding sites of the 295 ASP amino acid with the docking energy values of ( - 5.31, - 2581, - 6.227, - 1.042, - 6.293, - 10.460, - 2.019, - 5.344) Kcal/mol/A. (Figure S4) 999 ZN D 20947 Zn, ZN:A:998 (ZN), and 998 ZN A 20940 Zn 470 S Metal Complexes were also constructed into the 02J (5 - Methylisoxazole - 3 - carboxylic acid) PJE - C – 5 residues when the Roccustyrna’s chemical fragment of (1Z) - 2 - { ((2S, 3S, 5r) - 5 - (2 - amino - 6 - oxo - 6, 9 - + - 6 - fluoro - 3, 4 - dihydropyrazine - 2 - carboxamide (7aR) - 5 - amino - N - * (S) - , 2 - * (3 - oxabicyclo (2.1.0) (1S, 4S) - 5 - oxabicyclo*2.1.0 +pentan - 2 ((2S, 5R, 6R) - 6 - ((2S) - 2 - amino - 2 - phenylacetamido) - 3, 3 - dihydro - 1H - purin - 9 - yl - 4 - yl) oxy} - imino) - 1lambda5, 2lambda5 - azaphosphiridin - 1 - ylium generated tetrahedral side chains inside the 117 CYS D, 74 CYS A amino acids with the docking energy values of ( - 1103.746, - 101.848, - 13.968, - 103.306, - 102.613, - 1118.874, - 104.964, - 32.313 - 118.938, - 103.573, - 30.6090Kcal/mol/A indicating that our multi - targeted drug design has the ability of generating a self - assembled monolayer inside the 1: Mg, NA (1), 1, 10P, G Metal Complexes when docked onto the 1, 553A binding cavities of the amino acid of the ArG into the PDB:7bv2 protein targets. The combination of GisitorviffirnaTM, Roccustyrna_gs1_TM, and Roccustyrna_fr1_TM cluster of pharmacophoric (1Z) - 2 - { ((2S, 3S, 5r) - 5 - (2 - amino - 6 - 2 - yl) methylidene} - 2 - cyano - 12 - ({ (fluoro ({ ((2E) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene) cyano - lambda6 - sulfanyl}) methyl) phosphorylidene} amino) - 4, 6 - dihydro - 1H - purin - 6 - one - ({ ((2S, 4r, 5r) - 2 - methyl - 2 - (methylamino) - 1, 6 - dia - zabicyclo (3.2.0) heptan - 4 - yl) oxy} imino) - 1lambda5, 2lambda5 - azaphosphiridin - 1 - ylium active site of the 2 - lambda5 - azaphosphiridin - 1 - ylium was engaged in hydrogen bonding interactions with the formation of hydrogen bonds inside the N3 1266 O2 binding cavities within the amino acid sequence of V ‐ S ‐ HIS ‐ 159, V ‐ S ‐ ARG ‐ 160, V ‐ S ‐ ARG ‐ 112 V ‐ M ‐ GLU ‐ 148 V ‐ M ‐ PHE ‐ 150, V ‐ S ‐ PHE ‐ 150, V ‐ S ‐ HIS ‐ 159, and V ‐ M ‐ TYR ‐ 161 with the docking energy values of ( - 1.93, - 2.80, - 145.29, - 1105, - 3.81, - 2415, - 186, - 7.156, - 21.406, - 66.898 - 6.155, - 24.392, - 64.757, - 2411, - 8.911, - 17.849, - 65.703 - 8.918, - 17.918, - 62.905, - 2.16, - 3.07, - 153.73, - 2408, - 12.282, - 14.994, - 67.123, - 15.161, - 15.336, - 68.144) Kcal/mol. The Roccustyrna small molecule involved also in the generation of the hydrophobic interactions within the binding domains of the amino acid of the V ‐ M ‐ LYS ‐ 557, V ‐ S ‐ LYS ‐ 557, V ‐ M ‐ ARG ‐ 567, V ‐ M ‐ ASP ‐ 568, V ‐ S ‐ ASP ‐ 574, V ‐ S ‐ PHE ‐ 43, V ‐ M ‐ ARG ‐ 44, V ‐ M ‐ SER ‐ 45, V ‐ S ‐ SER ‐ 45 with the docking energy values of ( - 3.73, - 2415, - 179, - 7.156, - 21.406, - 66.898 - 8.709, - 22.779) Kcal/mol as illustrated in the (Figure S4). In this drug designing project the electrostatic regions around the combinationof GisitorviffirnaTM, Roccustyrna_gs1_TM, and Roccustyrna_fr1_ TM pharmacophoric elements of (7ar) - 5 - amino - N - ((S) - {2 - ((S) - ((E) - (amino - methylidene) amino) (cyano) methyl) hydrazin - 1 - yl} (aziridin - 1 - yl) phosphoryl) - 1 - ((2E) - 2 - ((fluoro - methanimidoyl) imino) acetyl) - 7 - oxo - 1H, 7H, 7aH - pyrazolo (4, 3 - d) pyrimidine - 3 - carboxamide; N - { ((2 - amino - 6 - oxo - 6, 9 - dihydro - 1H - purin - 9 - yl) amino) ({1 - (5 - ({ (cyano ({1 - ((diamino methylidene) amino) ethenyl}) amino) oxy} methyl) - 3, 4 - dihydroxyoxolan - 2 - yl) - 1H - 1, 2, 4 - triazol - 3 - yl} (formamido) phosphoryl} - 6 - fluoro - 3, 4 - dihydropyrazine - 2 - carboxamide; (3 - (2 - amino - 5 - sulfanylidene - 1, 2, 4 - triazolidin - 3 - yl) oxaziridin - 2 - yl) ({3 - sulfanylidene - 1, 2, 4, 6 - tetraaza bicyclo (3.1.0) hexan - 6 - yl}) phosphoroso1 - (3, 4, 5 - trifluorooxolan - 2 - yl) - 1H - 1, 2, 4 - triazole - 3 - carboxylate 3 - hydroxyoxolan - 2 - yl) methylidene} - 2 - cyano - 1 - ({ ((2S, 4r, 5r) - 2 - methyl - 2 - (methylamino) - 1, 6 - diazabicyclo (3.2.0) heptan - 4 - yl) oxy} imino) - 1lambda5, 2 - lambda5 - azaphosphiridin - 1 - ylium (Figure S4a), (Figure S4f) showing that the combination of GisitorviffirnaTM, Roccustyrna_gs1_TM, and Roccustyrna_fr1_TM binding site (s) inside the (PDB:6lu7) binding domains of the 02J:C:1 (02J) regions while co - generating Hydrophobic Interactions and Hydrogen Bonds against the coupled atoms of the Nam 2411 O3 inside the cavities of the crucial entering amino acids of the 25 THr A 6 010 C and 143 GLY A 6 010 C with the docking energy values of ( - 3.73, - 2415, - 179, - 7.156, ‐ 21.406, - 66.898, - 8.709, - 22.779, - 70, - 26, - 81, - 2415, - 186, - 7.156, - 21.406, - 66.898, - 6.155, - 24.392, - 64.757, - 1.93, - 2.80, - 145, - 29, - 1105, - 8.911, ‐ 17.849, - 65.703, - 8.918, - 17.918, - 62.905) Kcal/mol/A respectively. Electrostatic CoMFA analysis of the contact residues of the best docking poses of the contact chemical residues indicated also that the entire Roccustyrna chemical structure when docked onto the SARS - COV - 2 protein targets of (PDB:3fqq) hits the positively charged SARS ‐ CoV Mpro ‐ N1 groups and SARS ‐ CoV Mpro ‐ N3 regions favored by negatively charged groups within the amino acid sequence of the V - S - HIS - 159, V - S - ArG - 16, V - S - ArG - 112, V - M - GLU - 148, V - M - PHE - 15, V - S - PHE - 15, V - S - HIS - 159, V - M - TYr - 161 with the docking energy values of ( - 101, - 14.0762, - 5.11094, - 7.98447, - 4.17314, - 4.43549, - 9.66939, - 9.42926, - 7.32) Kcal/mol/A. (Figure S2b) Other QSAR/CoMFA experiments have shown to us that the entire pharmacophoric residues of the Roccustyrna chemical design when docked onto the Mpro ‐ N9 binding sites inside the SARS - COV - 2 protein targets of (PDB:6xs6), interacted negatively with the Cys145 catalytic site of SARS ‐ CoV ‐ 2 Mpro charged groups within the sequence of the amino acid of V - M - LYS - 557, V - S - LYS - 557, V - M - ArG - 567, V - M - ASP - 568, V - S - ASP - 574, V - S - PHE - 43, V - M - ArG - 44, V - M - SEr - 45, and V - S - SEr - 45 with the docking energy values of ( - 85.8, and - 5.56, - 8.38956, - 5.77168, - 6.13664, - 12.8661, - 5.37546, - 6.10391, - 5, 928) Kcal/mol respectively. (Figure S2c) Moreover, Cluster of the QSAR/QMMM/CoMFA map analysis of the electrostatic regions around the (rboximidoyl - 3 - fluoro - (1S, 4S) ((diaminomethylidene) amino) ethenyl}) amino+oxy - methyl) - 3, 4 - dihydroxyoxolan - 2 - yl+ - 1, 2, 4 - triazol - 3 - yl - (formamido) phosphoryl + - 6 - fluoro - 3, 4 - dihydropyrazine - 2 - carboxamide (7ar) - 5 - amino - N - * (S) - , 2 - * (3 - oxabicyclo (2.1.0) (1S, 4S) - 5 - oxabicyclo*2.1.0 +pentan - 2 ((2S, 5r, 6r) - 6 - ((2S) - 2 - amino - 2 - phenylacetamido) - 3, 3 - dimethyl - 7 - oxo - 4 - thia - 1 - azabicyclo (3.2.0) heptane - 2 - carbonyloxy) ({ ((2 - amino - 6 - oxo - 6, 9 - dihydro - 3H - purin - 9 - yl) oxy) (hydroxy) phosphoryl} oxy) phosphinic acid - ylidene+, *cyano ( 2, 6 - diazabicyclo*3.1.0+hex - 1 - en - 6 - yl) (rboximidoyl - 3 - fluoro - (1S, 4S) ((diaminomethylidene) amino) ethenyl}) amino+oxy - methyl) - 3, 4 - dihydroxyoxolan - 2 - yl+ - 1, 2, 4 - triazol - 3 - yl - (formamido) phosphoryl + - 6 - fluoro - 3, 4 - dihydropyrazine - 2 - carboxamide (7ar) - 5 - amino - N - * (S) - , 2 - * (3 - { ((1S, 4S) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene) { (cyano ({2, 6 - diazabicyclo (3.1.0) hex - 1 - en - 6 - yl}) phosphanyl - (fluoro) methyl} - lambda6 - sulfanyl}one pentan - 2 - ylidene) { (cyano ({2, 6 - diazabicyclo (3.1.0) hex - 1 - en - 6 - yl}) phosphanyl - lambda6 - (rboximidoyl - 3 - { ((1S,4S) - 5 - oxabicyclo (2.1.0)pentan - 2 - ylidene){ (cyano ({2,6 - diazabicyclo (3.1.0)hex - 1 - en - 6 - yl}) phosphanyl) (fluoro)methyl} - lambda6 - su lfanyl}one (rboximidoyl - 3 - oxabicyclo (2.1.0)pentan - 2 - ylidene){ (cyano ({2,6 - diazabicyclo (3.1.0)hex - sulfanyl}oneboximidoyl - 3 - { ((1S, 4S) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene) contact residues of the Roccustyrna small molecule when docked onto the SARS - COV - 2 protein targets of (PDB:2ghv) after solving the (id ⋱⋯⊗⋱⋯ ε) ◦ ∆ == == √q𝜌0 ⟨ Ψ∣∣T̂∣∣Ψ ⟩ (id ⋱⋯⊗⋱⋯ ε) ◦ ∆ == == (ε ⋱⋯⊗⋱⋯ id) e Zˆ, zˆ 0 :== == ∇ ∇ 𝑁𝑎𝐼rr H∂M ⋱⋯⊗⋱⋯ H∂N ∼A ∧ (m0−xi)rA⋱⋯∇ ∇ ∇ 𝑉𝑛𝑒 as parameterized input for 2/3∫rrrˆ0rr ∫rA ∧ rA ∧ rA𝜌 ⋱⋯⊗⋱⋯ ik 4π Z M A ∧ rA𝜌0£∑∑∑∑∑∑ √q𝜌0 ⟨ Ψ∣∣T̂∣∣Ψ ⟩ (−1)ω+ˆωe2πbωe Zˆ, zˆ 0 :== == ∇ ∇ 𝑁𝑎𝐼rr H∂M ⋱⋯⊗⋱⋯ H∂N ∼A ∧ (m0−xi) rA⋱⋯∇ ∇ ∇ 𝑉𝑛𝑒 2/3∫rrrˆ0rr ∫rA ∧ rA ∧ rA𝜌 ⋱⋯⊗⋱⋯ ik 4π Z M A ∧ rA𝜌0£∑∑∑ ∑∑∑ (−1) ω+ˆωe2πbω when combined with(METHODS AND MATERIALS) (Scheme of Eqs.1 ‐ 44), (Group of Eqs.1 ‐ 128), (Cluster of Eqs.1 - 81) as a chemical block for the generation of the chemical scaffold of lambda6 - sulfanyl}oneboximidoyl - 3 - (rboximidoyl - 3 - fluoro - (1S, 4S) ((diaminomethylidene) amino) ethenyl}) amino+oxy - methyl) - 3, 4 - dimethyl - 7 - oxo - 4 - thia - 1 - azabicyclo (3.2.0) heptane - 2 - carbonyloxy) ({ ((2 - amino - 6 - oxo - 6, 9 - dihydro - 3H - purin - 9 - yl)oxy) (hydroxy) phosphoryl} oxy) phosphinic acid - ylidene +, *cyano ( 2, 6 - diazabicyclo *3.1.0+hex - 1 - en - 6 - yl ‐ ) (rboximidoyl - 3 - fluoro ‐ (1S, 4S) ((diamino methylidene) amino) ethenyl}) amino+oxy ‐ methyl) - 3, 4 - dihydroxyoxolan - 2 - yl+ - 1, 2, 4 - triazol - 3 - yl ‐ formamido)dihydroxyoxolan - 2 - yl+ - 1, 2, 4 - triazol - 3 - yl - (formamido) phosphoryl + - 6 - fluoro - 3, 4 - dihydropyrazine - 2 - carboxamide (7ar) - 5 - amino - N - * (S) - , 2 - * (3 - oxabicyclo (2.1.0) (1S, 4S) - 5 - oxabicyclo*2.1.0+pentan - 2 ((2S, 5r, 6r) - 6 - ((2S) - 2 - amino - 2 - phenylacetamido) - 3, 3 - dimethyl - 7 - oxo - 4 - thia - 1 - azabicyclo (3.2.0) heptane - 2 - carbonyloxy) ({ ((2 - amino - 6 - oxo - 6, 9 - dihydro - 3H - purin - 9 - yl) oxy) (hydroxy) phosphoryl} oxy) phosphinic acid - ylidene+, *cyano ( 2, 6 - diazabicyclo*3.1.0+hex - 1 - en - 6 - yl) (rboximidoyl - 3 - fluoro - (1S, 4S) ((diaminomethylidene) amino) ethenyl}) amino+oxy - methyl) - 3, 4 - dihydroxyoxolan - 2 - yl+ - 1, 2, 4 - triazol - 3 - yl - (formamido) phosphoryl + - 6 - fluoro - 3, 4 - dihydropyrazine - 2 - carboxamide (7ar) - 5 - amino - N - * (S) - , 2 - * (3 - { ((1S, 4S) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene) { (cyano ({2, 6 - diazabicyclo (3.1.0) hex - 1 - en - 6 - yl}) phosphanyl - (fluoro) methyl} - lambda6 - sulfanyl}one pentan - 2 - ylidene) { (cyano ({2, 6 - diazabicyclo (3.1.0) hex - 1 - en - 6 - yl}) phosphanyl { ((1S, 4S) - 5 - oxabicyclo (2.1.0) pentan - 2 - ylidene).(METHODS AND MATERIALS) (Cluster of Eqs. 70) Our innovative drug design generated also negatively charged groups within the sequence of the amino acid of the H - M - ASN - 33, H - S - ASN - 33, H - S - TYr - 356, H - M - ASN - 424, V - M - ASN - 33, V - M - ALA - 331, V - M - THr - 332, V - S - THr - 332, V - S - TYr - 356, V - S - TrP - 423, V - S - ILE - 428, and V - S - ArG - 495 with the docking energy values of ( - 104.7 and - 3.45708, - 3.5, - 3.97711, - 3.5, - 5.33228, - 6.79753, - 7.9376, - 6.69969, - 12.2528, - 7.66989, - 8.15072, - 7.332) Kcal/mol respectively. The Roccustyrna small molecule hits also the entire binding domains of the SARS - COV - 2 (PDB:6w9c) protein targets within the amino acid sequence of V - S - PrO - 59, V - S - ArG - 65, V - M - THr - 75, V - S - THr - 75, V - M - PrO - 77, V - S - PrO - 77, V - M - HIS - 47, and V - S - HIS - 47 with the docking energies of the ( - 83.9, - 4.21999, - 12.6164, - 7.60372, - 6.69528, - 5.89416, - 6.40663, - 5.51621, - 7.99273) Kcal/mol. (Figure S2e) As illustrated in the (Figure S3) the Roccustyrna small molecule generated also negative docking energy values with a potential inhibitory effect when docked against the sequence of the amino acids of the protein targets of (PDB: 6YI3) of the N - terminal RNA - binding domain of the SARS - CoV - 2 nucleocapsid phosphoprotein which is essential for linking the viral genome to the viral membrane. (Figure S4d), (Figure S4e) In this project for the first time we generated a Comparative Docking Cluster Analysis between the remdesivir and our prototype Roccustyrna small molecule when docked onto the SARS - COV - 2 protein targets of (PDB:7bv2), with the docking energy values of (Num_Members == == 40, Total_Energy == == 2.103, vdW == == - 5.122, Coulomb == == - 4.977, Internal == == 12.203, rmsd == == 3.183 and $Number of Clusters == == 10, $Seed == == - 1985, $Leader_Info 1 { Num_Members == == 63 Total_Energy == == - 0.883, vdW == == - 6.041, Coulomb == == - 7.045, Internal == == 12.203) respectively. More specifically, in this project we unified generalized k - nearest values and topology geometric methods for generalized formalisms of k - nearest neighbors of Molecular Pairs (MMP) and von Neumann formulations for Dirac formulation states as a Tipping–Ogilvie and Machine Learning application within the quantum computing context with algebraic multi - metrics characteristics targeting the atomistic level of the protein apparatus of the SARS - COV - 2 viral characteristics. An Adaptive Weighted KNN Positioning approach through nonlinear electrodynamics to simulate an advanced quantum mechanical inverse docking algorithm was applied in this unified protocol by providing further insight on a ℓneuron (ι) : == == φ∘D∘r2∘S∘r1 improver for Chern - Simons Topology Euclidean Geometrics for generating a negative docking energy effect of the highest docking energy value. By performing stationary phase approximations around these pharmacophore merging critical points, I obtained the asymptotic expansions of the Roccustyrna’s merged holomorphic chemical block systems against a specific (PDB: 6XS6) protein target. (Illustration1) As a result, Entangled Neural Networks and Quantum - Inspired Kappa - Symmetrizing frameworks were mixed together and by using Chern - Simons normalized Shannon entropy quantities through Tipping–Ogilvie potentials I generated the combination of GisitorviffirnaTM, Roccustyrna_gs1_TM, and Roccustyrna_fr1_TM small molecules. That annotated cluster of druggable scaffolds were able of producing the highest rates of negative docking energy values when virtually compined with Amprenavir, Asunaprevir, Atazanavir, Boceprevir, Cytarabine, Darunavir, ritonavir, Sorivudine, Taribavirin, Tenofovir, Valganciclovir, Vidarabine, Lopinavir, Sofosbuvir, Zanamivir, Penciclovir, Nelfinavir, Merimepodib, Maribavir, Indinavir, Inarigivir, Galidesivir, Famciclovir, and Faldaprevir FDA approved antiviral drugs against the SARS - COV - 2 protein binding sites of the (PDB: 6M2Q) SARS - CoV - 2 3CL protease (3CL pro) apo structure (space group C21) inside the amino acid sequence of V - M - ArG - 4, V - S - ArG - 4, V - S - MET - 6, V - M - ALA - 7, V - S - PHE - 8, V - M - GLY - 11, V - M - LYS - 12, V - S - LYS - 12, V - M - GLU - 14, V - S - GLU - 14, V - M - GLY - 15, V - M - THr - 24, V - S - THr - 24, V - M - THr - 25, V - S - THr - 25, V - M - THr - 26, V - S - THr - 26, V - M - VAL - 35, V - S - VAL - 35, V - S - ArG - 40, V - S - HIS - 41, V - M - THr - 45, V - M - SEr - 46, V - S - SEr - 46, V - S - MET - 49, V - M - ASN - 53, V - S - ASN - 53, V - S - TYr - 54, V - M - ALA - 70, V - M - GLY - 71, V - M - ASN - 95, V - S - LYS - 97, V - M - PrO - 99, V - S - LYS - 102, V - S - VAL - 104, V - M - ILE - 106, V - S - GLN - 107, V - M - PrO - 108, V - M - GLY - 109, V - S - GLN - 110, V - M - THr - 111, V - S - ASN - 119, V - M - GLY - 124, V - S - TYr - 126, V - M - GLN - 127, V - M - CYS - 128, V - S - ArG - 131, V - S - LYS - 137, V - M - LEU - 141, V - M - ASN - 142, V - S - ASN - 142, V - M - GLY - 143, V - M - ASN - 151, V - S - ASN - 151, V - M - ILE - 152, V - M - ASP - 153, V - S - ASP - 153, V - S - SEr - 158, V - M - MET - 165, V - S - MET - 165, V - M - GLU - 166, V - S - GLU - 166, V - M - LEU - 167, V - S - PrO - 168, V - M - GLU - 178, V - M - VAL - 186, V - S - VAL - 186, V - S - ArG - 188, V - M - GLN - 189, V - S - GLN - 189, V - M - THr - 190, V - S - TrP - 218, V - M - LEU - 220, V - M - ASN - 221, V - S - PHE - 223, V - M - TYr - 237, V - S - TYr - 237, V - S - TYr - 239, V - M - ASP - 245, V - S - ASP - 245, V - S - HIS - 246, V - S - ILE - 249, V - M - GLU - 270, V - S - GLU - 270, V - S - LEU - 271, V - M - LEU - 272, V - M - GLN - 273, V - M - ASN - 274, V - S - ASN - 274, V - M - GLY - 275, V - M - MET - 276, V - M - ASN - 277, V - S - ASN - 277, V - M - GLY - 278, V - M - LEU - 286, V - S - LEU - 286, V - M - LEU - 287, V - S - LEU - 287, V - S - ASP - 289, V - S - GLU - 290, V - S - THr - 292, V - S - PrO - 293, V - M - PHE - 294, V - S - PHE - 294, V - S - ArG - 298, V - M - GLN - 299, V - S - GLN - 299, V - M - GLY - 302, V - M - VAL - 303, V - M - PHE - 305. More precisely, I generally made use of the vector field ∂/∂t which is globally well defined, as the kernel of dz and dz at each point can be viewed as a topological theory of class H. So in this sense our topological theory here is generating a well defined direction which can be identified with the diffeomorphism generated by ∂/∂t. Additionally, the same combination of our drug design novelties interacted with the highest docking energy values onto the binding sites of the (PDB: 6WOJ) protein targets of the SARS - CoV - 2 macrodomain (NSP3) in complex with ADP - ribose of the targeting sequence of V - M - ALA - 21, V - M - ASP - 22, V - S - ASP - 22, V - M - GLU - 25, V - S - GLU - 25, V - M - ALA - 38, V - M - ALA - 39, V - S - ASN - 40, V - M - TYr - 42, V - M - GLY - 46, V - M - GLY - 47, V - M - GLY - 48, V - M - VAL - 49, V - S - VAL - 49, V - M - ALA - 50, V - M - GLY - 51, V - M - ALA - 52, V - S - LEU - 53, V - M - VAL - 95, V - S - VAL - 95, V - M - VAL - 96, V - M - PrO - 98, V - S - ASN - 101, V - S - LEU - 109, V - S - PrO - 125, V - M - LEU - 126, V - S - LEU - 126, V - M - SEr - 128, V - M - ALA - 129, V - M - GLY - 130, V - M - ILE - 131, V - S - ILE - 131, V - S - PHE - 132, V - M - GLY - 133, V - M - ALA - 134, V - S - PrO - 136, V - M - SEr - 139, V - M - ALA - 154, V - M - VAL - 155, V - S - VAL - 155, V - M - PHE - 156, V - S - PHE - 156, V - M - ASP - 157, V - M - LEU - 160, V - S - LEU - 160, V - M - GLU - 120 amino acids respectively when compared with Amprenavir, Asunaprevir, Atazanavir, Boceprevir, Cytarabine, Darunavir, ritonavir, Sorivudine, Taribavirin, Tenofovir, Valganciclovir, Vidarabine, Lopinavir, Sofosbuvir, Zanamivir, Penciclovir, Nelfinavir, Merimepodib, Maribavir, Indinavir, Inarigivir, Galidesivir, Famciclovir, and Faldaprevir FDA approved antiviral drugs while targeting the PDB:7khp (Figure S9A), PDB: 6WOJ (Figure S9B), PDB: 7B3D (Figure S9C), PDB:6M2Q Figure S9D), PDB:6lu7 (Figure S9E), PDB: 6wzu (Figure S9F), PDB:1XU9 (Figure S9G), PDB: 3TWU (Figure S9H), PDB:7BEO (Figure S9H), PDB:1XAK (Figure S9I) protein targets. (Figure S4f), (Figure S4g), (Figure S4h) Finally, the Roccustyrna chemical structure generated an inhibitory docking effect of high negative binding energy docking values of the - 66, 7 Kcal/mol when docked onto the cav7bv2_POP binding domains within the amino acids of the V - M - LYS - 551, V - S - LYS - 551, V - S - ArG - 553, V - S - ASP - 618, V - M - TYr - 619, and V - M - PrO - 620 with the docking energy values of ( - 4.71516, - 10.4842, - 4.7999, - 6.65538, - 5.1339, - 6.28532) Kcal/mol. (Figure S5a), (Figure S5b), (Figure S5c), (Figure S6) On the other hand the remdesivir drug when combined to the Roccustyrna small molecule interacted at the same binding domains of the amino acids of the V - M - LYS - 551, V - S - LYS - 551, V - S - ArG - 553, V - S - ASP - 618, V - M - TYr - 619, and V - M - PrO - 620 with positive and zero docking values of the +42.1, - 0.104885, - 0.19986, +25.0575, Kcal/mol. That means that the remdesivir drug could induce in same the COVID19 disease.