Table 3.
Comparative analysis of binding specificity of protein variants from Indian SARS-CoV-2 isolates with FDA-approved antiviral drugs.
| Genotype | Isolate | Gene | Mutant | Drug name | DrugBank/PubChem | PMID | Score |
Area |
ACE |
|||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ref. | Var. | Ref. | Var. | Ref. | Var. | |||||||
| 1 | IND/29 (Kerala) | Nsp2 | I671T | Ribostamycin sulfate | DB03615 | 31443266 | 5334 | 5334 | 687.7 | 687.7 | −72.19 | −72.19 |
| E−64 | 123985 | 31443266 | 4606 | 4606 | 537.8 | 537.8 | −286.28 | −286.28 | ||||
| PLPro | P2144S | Simeprevir | DB06290 | 18678486 | 6956 | 6956 | 944.4 | 944.4 | −306.29 | −306.29 | ||
| RdRp | A4798V | Remdesivir | DB14761 | 32020029 | 6472 | 6460 | 862.6 | 858.6 | −297.68 | −298.62 | ||
| Hydroxychloroquine | DB01611 | 32020029 | 5546 | 5602 | 642.2 | 646.5 | −200.07 | −34.74 | ||||
| Spike | R407I | Emodin | DB07715 | 32194980 | 4022 | 4242 | 507.4 | 518.8 | −159.29 | −169.22 | ||
| 2 | IND/166 (Kerala) | Nsp2 | I476V | Ribostamycin sulfate | DB03615 | 31443266 | 5334 | 5334 | 687.7 | 687.7 | −72.19 | −72.19 |
| E−64 | 123985 | 31443266 | 4606 | 4606 | 537.8 | 537.8 | −286.28 | −286.28 | ||||
| Helicase | T5538I | Artenimol | DB11638 | 32696720 | 4102 | 4190 | 507.9 | 515.1 | −250.26 | −77.86 | ||
| Spike | A930V | Emodin | DB07715 | 32194980 | 4022 | 4220 | 507.4 | 532.9 | −159.29 | −157.1 | ||
| Orf8 | L84S | Azacitidine | DB00928 | 15899874 | 3324 | 3130 | 367.6 | 361 | −165.95 | −51.28 | ||
| 3 | GMCKN318 (Telangana: Hyderabad) | RdRp | P4715L | Remdesivir | DB14761 | 32020029 | 6472 | 6266 | 862.6 | 829.2 | −297.68 | −272.29 |
| Hydroxychloroquine | DB01611 | 32020029 | 5546 | 5568 | 642.2 | 665.9 | −200.07 | −198.71 | ||||
| Spike | D614G | Emodin | DB07715 | 32194980 | 4022 | 4042 | 507.4 | 515.2 | −159.29 | −150.58 | ||
| 4 | GBRC97b (Himachal Pradesh: Una) | Nsp2 | L204F | Ribostamycin sulfate | DB03615 | 31443266 | 5334 | 5334 | 687.7 | 687.7 | −72.19 | −72.19 |
| E−64 | 123985 | 31443266 | 4606 | 4606 | 537.8 | 537.8 | −286.28 | −286.28 | ||||
| PLPro | A1812D | Simeprevir | DB06290 | 18678486 | 6956 | 7080 | 944.4 | 884 | −306.29 | −259.49 | ||
| Nsp6 | L3606F | Loratadine | DB00455 | 25318072 | 3896 | 3896 | 518.3 | 518.3 | −216.58 | −216.58 | ||
| RdRp | K4451 N | Remdesivir | DB14761 | 32020029 | 6472 | 6308 | 862.6 | 849 | −297.68 | −349.93 | ||
| P4715L | Hydroxychloroquine | DB01611 | 32020029 | 5546 | 5430 | 642.2 | 635 | −200.07 | −28.24 | |||
| Helicase | P5624L | Artenimol | DB11638 | 32696720 | 4102 | 4228 | 507.9 | 529.5 | −250.26 | −113.65 | ||
| Exonuclease | K6274 N | 2-(N-Morpholino)ethanesulfonate | 4599203 | 32470577 | 3074 | 3152 | 343.4 | 352.6 | −112.57 | −112.60 | ||
| Migalastat | DB05018 | 32353859 | 2714 | 2714 | 311.1 | 311.5 | −81.75 | −88.36 | ||||
| Mycophenolic acid | DB01024 | 32353859 | 5338 | 5264 | 605 | 595.8 | −182.69 | −159.11 | ||||
| Ribavirin | DB00811 | 32353859 | 3938 | 3784 | 439.8 | 457.7 | −85.04 | −153.66 | ||||
| Spike | D614G | Emodin | DB07715 | 32194980 | 4022 | 4042 | 507.4 | 515.2 | −159.29 | −150.58 | ||
| N | R203K | Silmitasertib | DB15408 | 21159648 | 4516 | 4514 | 487.8 | 582.6 | −170.62 | −330.15 | ||
| G204R | ||||||||||||
| 5 | GBRC98 (Himachal Pradesh: Una) | Nsp2 | G519S | Ribostamycin sulfate | DB03615 | 31443266 | 5334 | 5334 | 687.7 | 687.7 | −72.19 | −72.19 |
| E−64 | 123985 | 31443266 | 4606 | 4606 | 537.8 | 537.8 | −286.28 | −286.28 | ||||
| PLPro | S2015R | Simeprevir | DB06290 | 18678486 | 6956 | 6956 | 944.4 | 944.4 | −306.29 | −306.29 | ||
| T2016K | ||||||||||||
| P2739L | ||||||||||||
| Nsp6 | L3606F | Loratadine | DB00455 | 25318072 | 3896 | 3896 | 518.3 | 518.3 | −216.58 | −216.58 | ||
| RdRp | A4489V | Remdesivir | DB14761 | 32020029 | 6472 | 6572 | 862.6 | 808.8 | −297.68 | −0.23 | ||
| Hydroxychloroquine | DB01611 | 32020029 | 5546 | 5534 | 642.2 | 629.9 | −200.07 | −29.61 | ||||
| Spike | Q677H | Emodin | DB07715 | 32194980 | 4022 | 4154 | 507.4 | 518.2 | −159.29 | −150.90 | ||
| N | P13L | Silmitasertib | DB15408 | 21159648 | 4516 | 4514 | 487.8 | 582.6 | −170.62 | −330.15 | ||
| A152S | ||||||||||||
| 6 | GBRC275b (Gujarat: Surat) | Exonuclease | W6152R | 2-(N-Morpholino)ethanesulfonate | 4599203 | 32470577 | 3074 | 2982 | 343.4 | 324 | −112.57 | −108.46 |
| Migalastat | DB05018 | 32353859 | 2714 | 2608 | 311.1 | 298.4 | −81.75 | −43.19 | ||||
| Mycophenolic acid | DB01024 | 32353859 | 5338 | 4426 | 605 | 514.2 | −182.69 | −159.56 | ||||
| Ribavirin | DB00811 | 32353859 | 3938 | 3452 | 439.8 | 414.7 | −85.04 | −150.4 | ||||
| Spike | L54F | Emodin | DB07715 | 32194980 | 4022 | 4170 | 507.4 | 505.3 | −159.29 | −166.39 | ||
| D614G | ||||||||||||
| H1088R | ||||||||||||
| F1089V | ||||||||||||
| 7 | GBRC258b (Gujarat: Gondal) | 2′-O-MTase | D6900Y | Sinefungin | DB01910 | 17139284 | 1168 | 1074 | 134.6 | 111.7 | −350.22 | −377.34 |
| 8 | GBRC245 (Gujarat: Modasa) | Orf3a | P42R | Tranilast | DB07615 | 32190290 | 4992 | 5098 | 583 | 580.9 | −124.1 | −120.40 |
| Q57H | ||||||||||||
| 9 | GBRC273b (Gujarat: Choryasi) | N | S202 N | Silmitasertib | DB15408 | 21159648 | 4516 | 4514 | 487.8 | 582.6 | −170.62 | −330.15 |
| 10 | GBRC242 (Gujarat: Himatnagar) | 3CLPro | V3475F | Raltegravir | DB06817 | 32266873 | 5840 | 5786 | 724.2 | 723.2 | −214.91 | −205.25 |
| 11 | GBRC239 (Gujarat: Gandhinagar) | Exonuclease | N5928H | 2-(N-Morpholino)ethanesulfonate | 4599203 | 32470577 | 3074 | 3084 | 343.4 | 349.9 | −112.57 | −110.08 |
| Migalastat | DB05018 | 32353859 | 2714 | 2792 | 311.1 | 325.9 | −81.75 | −110.33 | ||||
| Mycophenolic acid | DB01024 | 32353859 | 5338 | 5328 | 605 | 605.5 | −182.69 | −181.98 | ||||
| Ribavirin | DB00811 | 32353859 | 3938 | 3712 | 439.8 | 444.5 | −85.04 | −130.46 | ||||
| 12 | GBRC244 (Gujarat: Ahmadabad) | N | S194L | Silmitasertib | DB15408 | 21159648 | 4516 | 4514 | 487.8 | 582.6 | −170.62 | −330.15 |