Table 2.
Molecular docking analysis for NITD-related and potential inhibitor compounds (candidate molecules in this study) at the binding site of NS5 RdRp located in the RNA template tunnel
| Ligand name | ΔG (kcal/mol) mean ± SD | Ligand name | ΔG (kcal/mol) mean ± SD | Ligand name | ΔG (kcal/mol) mean ± SD | Ligand name | ΔG (kcal/mol) mean ± SD |
|---|---|---|---|---|---|---|---|
| NS5 RdRp of DENV-1 | NS5 RdRp of DENV-2 | ||||||
| NITD-1 | −8.6±0.5 | NITD-1 | −8.5±0.6 | 11999940 | −11.2±0.9 | 11612450 | −11.0±0.7 |
| NITD-2 | −9.6±0.5 | NITD-2 | −9.9±0.8 | 71815510 | −11.2±0.6 | 22867347 | −11.0±1.0 |
| NITD-29 | −10.1±0.8 | NITD-29 | −10.8±1.2 | 53019114 | −11.2±1.3 | 53834657 | −11.0±0.7 |
| 91166410 | −11.5±1.2 | 53019095 | −11.8±1.2 | 68563659 | −11.2±0.9 | 86608192 | −11.0±1.1 |
| 88881717 | −11.5±1.1 | 53019000 | −11.7±1.6 | 90644640 | −11.2±0.8 | 58550574 | −11.0±0.6 |
| 53019095 | −11.4±1.0 | 58847065 | −11.6±0.6 | 74937125 | −11.2±1.0 | 87254969 | −11.0±1.0 |
| 58509828 | −11.4±1.3 | 58847008 | −11.6±0.6 | 5330687 | −11.2±1.0 | 91982228 | −11.0±0.8 |
| 86592137 | −11.4±0.7 | 59558635 | −11.5±0.6 | 53019157 | −11.1±1.0 | 58117326 | −11.0±1.0 |
| 87254969 | −11.4±0.7 | 53019136 | −11.5±1.7 | 53019118 | −11.1±1.1 | 86592137 | −11.0±1.0 |
| 58847008 | −11.4±0.6 | 91166410 | −11.5±1.3 | 57483735 | −11.1±0.9 | 46228828 | −11.0±0.8 |
| 24320265 | −11.4±0.8 | 53019046 | −11.5±1.2 | 42623761 | −11.1±1.1 | 57590479 | −11.0±0.8 |
| 5330687 | −11.3±1.0 | 58509828 | −11.5±1.3 | 58847188 | −11.1±0.6 | 24818217 | −11.0±1.1 |
| 71815510 | −11.3±0.6 | 57883147 | −11.4±0.8 | 11612953 | −11.1±1.0 | 58716236 | −11.0±0.9 |
| 53019000 | −11.3±1.0 | 88881717 | −11.4±1.2 | 59120485 | −11.1±0.9 | 53019023 | −11.0±1.4 |
| 58847188 | −11.3±0.3 | 76724063 | −11.4±0.8 | 71815570 | −11.1±0.7 | 99173129 | −11.0±1.0 |
| 58847065 | −11.3±0.7 | 4982894 | −11.4±1.1 | 60118013 | −11.1±0.9 | 16749692 | −11.0±0.6 |
| 46228732 | −11.3±0.9 | 90644642 | −11.4±1.0 | 46228732 | −11.1±0.9 | 53019026 | −11.0±1.5 |
| 4982894 | −11.2±1.1 | 75237511 | −11.3±1.1 | 90644637 | −11.1±1.0 | 10163912 | −11.0±0.9 |
| 58550574 | −11.2±0.7 | 60138427 | −11.3±0.9 | 53098093 | −11.1±0.9 | 53019135 | −11.0±1.6 |
| 71815377 | −11.2±0.5 | 21114517 | −11.3±0.9 | 99437562 | −11.1±1.2 | 11503697 | −11.0±1.1 |
| 16749628 | −11.2±0.5 | 60118830 | −11.3±0.9 | 68490845 | −11.1±0.8 | 58117469 | −11.0±0.9 |
| 53019136 | −11.2±0.9 | 53019143 | −11.3±1.3 | 17240799 | −11.1±0.9 | 67017052 | −11.0±1.1 |
| 66966190 | −11.1±0.3 | 11591299 | −11.3±1.0 | 10116388 | −11.1±0.9 | 83275648 | −11.0±1.3 |
| 53019046 | −11.1±0.9 | 46926790 | −11.2±0.8 | 60402568 | −11.1±1.0 | 21598341 | −11.0±1.0 |
| 66661763 | −11.1±0.6 | 67023200 | −11.2±0.8 | 59508095 | −11.1±1.2 | 44419986 | −11.0±0.9 |
| 57955372 | −11.1±0.3 | 44605230 | −11.2±1.4 | 51038723 | −11.1±1.1 | 58518208 | −11.0±0.4 |
| 16749692 | −11.1±0.6 | 60250081 | −11.2±1.1 | 69707773 | −11.0±0.9 | 11547552 | −11.0±0.8 |
| 71815441 | −11.1±0.5 | 59558530 | −11.2±0.6 | 57955382 | −11.0±0.6 | 59558378 | −11.0±0.9 |
| 58044822 | −11.1±0.8 | 66662216 | −11.2±0.7 | 22556722 | −11.0±1.0 | 59508029 | −11.0±1.1 |
| 21598341 | −11.0±1.2 | 24672975 | −11.2±0.6 | 22587546 | −11.0±0.9 | 53019073 | −11.0±1.1 |
| 22556747 | −11.0±1.0 | 59069323 | −11.2±1.2 | 58044822 | −11.0±0.6 | 53310399 | −11.0±1.0 |
| 42598694 | −11.0±0.5 | 9804722 | −11.2±1.2 | 10239163 | −11.0±0.7 | 86608190 | −11.0±1.0 |
| 71815570 | −11.0±0.6 | 5330694 | −11.2±1.1 | 56085441 | −11.0±1.4 | 59113200 | −11.0±1.1 |
| 11591299 | −11.0±0.7 | 66661763 | −11.2±0.7 | 44068150 | −11.0±1.2 | 2307085 | −11.0±0.9 |
| 90644637 | −11.0±0.9 | 88881725 | −11.2±0.2 | 2408779 | −11.0±0.8 | 58847051 | −11.0±0.6 |
| 53239274 | −11.0±1.0 | 71815377 | −11.2±0.4 | 60117771 | −11.0±1.0 | ||
| 90644642 | −11.0±1.0 | 88884325 | −11.2±0.4 | 58094574 | −11.0±0.9 | ||
| NS5 RdRp of DENV-4 | |||||||
| NITD-1 | −8.9±0.3 | 22556722 | −11.3±1.3 | 5330659 | −11.1±1.1 | 56244330 | −11.0±1.0 |
| NITD-2 | −10.2±0.5 | 58187960 | −11.3±0.7 | 53041346 | −11.1±1.0 | 4498761 | −11.0±0.9 |
| NITD-29 | −10.8±0.7 | 71016043 | −11.3±0.6 | 58117268 | −11.1±0.6 | 6129755 | −11.0±0.8 |
| 4982894 | −12.2±1.4 | 58117308 | −11.3±0.5 | 66605204 | −11.1±0.7 | 10410064 | −11.0±0.7 |
| 2408779 | −12.0±1.1 | 59121600 | −11.3±0.8 | 25065563 | −11.1±0.9 | 23627602 | −11.0±0.8 |
| 59558635 | −11.9±1.0 | 6524590 | −11.2±1.1 | 53884638 | −11.1±1.3 | 26283419 | −11.0±0.9 |
| 44605230 | −11.9±0.5 | 55797299 | −11.2±0.8 | 57483798 | −11.1±0.8 | 45167069 | −11.0±1.2 |
| 71815510 | −11.8±0.8 | 11525541 | −11.2±1.2 | 9930411 | −11.1±1.3 | 51925674 | −11.0±0.6 |
| 59558530 | −11.8±0.6 | 76810150 | −11.2±1.8 | 25138236 | −11.1±0.7 | 55790271 | −11.0±1.0 |
| 88881717 | −11.8±1.3 | 56085441 | −11.2±0.9 | 25154812 | −11.1±0.9 | 57467031 | −11.0±1.0 |
| 91166410 | −11.8±1.3 | 68698259 | −11.2±1.0 | 58117332 | −11.1±0.4 | 59558574 | −11.0±0.8 |
| 58509828 | −11.7±1.2 | 99173125 | −11.2±0.7 | 59962443 | −11.1±0.6 | 60118484 | −11.0±0.4 |
| 16749692 | −11.6±1.1 | 11999813 | −11.2±0.9 | 77152204 | −11.1±0.7 | 66662021 | −11.0±1.1 |
| 46228732 | −11.6±1.0 | 25138230 | −11.2±0.8 | 99501210 | −11.1±1.3 | 69707178 | −11.0±0.7 |
| 68701918 | −11.6±1.2 | 53098094 | −11.2±0.3 | 16749694 | −11.1±1.0 | 22063077 | −11.0±0.6 |
| 60402568 | −11.6±0.9 | 59875861 | −11.2±1.1 | 19288807 | −11.1±1.0 | 56022032 | −11.0±0.4 |
| 25065772 | −11.6±1.0 | 68496294 | −11.2±1.3 | 46926790 | −11.1±1.2 | 59558479 | −11.0±0.9 |
| 68702576 | −11.6±1.1 | 60205770 | −11.2±0.9 | 58787557 | −11.1±1.3 | 66662543 | −11.0±0.6 |
| 66661763 | −11.6±1.0 | 21114517 | −11.2±0.6 | 76541785 | −11.1±0.7 | 4498763 | −11.0±0.8 |
| 58094574 | −11.6±0.9 | 25065362 | −11.2±1.0 | 20765416 | −11.1±1.0 | 10392307 | −11.0±0.9 |
| 76724063 | −11.6±1.4 | 54127944 | −11.2±0.8 | 25066204 | −11.1±1.1 | 46377852 | −11.0±0.7 |
| 66662686 | −11.6±0.7 | 44303726 | −11.2±1.0 | 27563621 | −11.1±1.1 | 50848671 | −11.0±0.9 |
| 57955382 | −11.5±1.3 | 53098093 | −11.2±0.4 | 46602120 | −11.1±1.1 | 59212388 | −11.0±0.9 |
| 88884325 | −11.5±1.8 | 56925033 | −11.2±1.9 | 53098102 | −11.1±0.5 | 66604901 | −11.0±0.8 |
| 57883147 | −11.5±1.4 | 66606315 | −11.2±1.0 | 16431302 | −11.1±1.0 | 68894072 | −11.0±1.1 |
| 60250081 | −11.5±0.8 | 86608190 | −11.2±1.2 | 3554749 | −11.1±0.8 | 89886799 | −11.0±0.9 |
| 11591299 | −11.5±1.1 | 89361165 | −11.2±0.6 | 25174057 | −11.1±1.0 | 44605022 | −11.0±0.7 |
| 17240799 | −11.5±0.6 | 89361072 | −11.2±0.6 | 58509782 | −11.1±1.3 | 60402552 | −11.0±0.9 |
| 25065775 | −11.5±1.0 | 20765428 | −11.2±1.0 | 69144161 | −11.1±0.9 | 76808085 | −11.0±1.2 |
| 44176508 | −11.5±1.2 | 58044822 | −11.2±0.8 | 23627601 | −11.1±1.1 | 17359718 | −11.0±0.6 |
| 46885243 | −11.5±0.9 | 59239811 | −11.2±1.0 | 69579276 | −11.1±0.9 | 35767226 | −11.0±1.1 |
| 15605185 | −11.5±0.6 | 146429 | −11.2±1.3 | 10116388 | −11.0±0.9 | 58768495 | −11.0±0.9 |
| 5330687 | −11.5±1.3 | 11612450 | −11.2±1.0 | 25065360 | −11.0±1.0 | 4710567 | −11.0±0.7 |
| 25065774 | −11.5±1.0 | 44068150 | −11.2±0.9 | 76310566 | −11.0±0.8 | 9799922 | −11.0±1.2 |
| 66662216 | −11.5±1.1 | 53098204 | −11.2±0.4 | 46833812 | −11.0±1.8 | 11756868 | −11.0±1.0 |
| 60118013 | −11.5±1.1 | 25065776 | −11.2±0.9 | 10206429 | −11.0±0.8 | 16589824 | −11.0±1.0 |
| 88881725 | −11.5±1.1 | 53310399 | −11.2±0.8 | 30870527 | −11.0±0.8 | 44155098 | −11.0±0.7 |
| 53019000 | −11.4±1.0 | 18710168 | −11.2±0.7 | 44580357 | −11.0±1.1 | 44159652 | −11.0±0.7 |
| 60118830 | −11.4±0.5 | 50848824 | −11.2±1.0 | 59304633 | −11.0±0.5 | 57483735 | −11.0±0.7 |
| 11612953 | −11.4±0.9 | 98939207 | −11.2±0.6 | 66694881 | −11.0±0.9 | 59121601 | −11.0±1.0 |
| 86592137 | −11.4±0.4 | 59375041 | −11.2±1.8 | 9537955 | −11.0±1.6 | 58117321 | −11.0±0.4 |
| 87254969 | −11.4±0.4 | 60494790 | −11.2±0.6 | 10069263 | −11.0±0.8 | 9886055 | −11.0±1.2 |
| 60117771 | −11.4±0.4 | 5330699 | −11.2±1.4 | 41273686 | −11.0±1.1 | 52886452 | −11.0±0.5 |
| 25138229 | −11.4±0.8 | 25065773 | −11.2±0.8 | 46228828 | −11.0±0.9 | 66604312 | −11.0±0.9 |
| 46228865 | −11.4±0.7 | 56057109 | −11.2±0.6 | 57483762 | −11.0±0.4 | 68714559 | −11.0±1.1 |
| 10342132 | −11.4±1.0 | 58550574 | −11.2±0.9 | 68701232 | −11.0±1.0 | 6129075 | −11.0±0.6 |
| 67133415 | −11.4±1.4 | 10228015 | −11.2±0.9 | 53018993 | −11.0±0.5 | 11752081 | −11.0±0.6 |
| 71815570 | −11.4±0.6 | 39906246 | −11.2±0.5 | 58069426 | −11.0±1.0 | 16065158 | −11.0±1.2 |
| 16675341 | −11.4±1.0 | 58064300 | −11.2±1.2 | 11760627 | −11.0±1.1 | 18710165 | −11.0±0.7 |
| 24320265 | −11.4±1.0 | 60402580 | −11.2±1.1 | 16583630 | −11.0±0.6 | 19665288 | −11.0±1.0 |
| 68695702 | −11.4±1.2 | 68698167 | −11.2±0.9 | 20637893 | −11.0±1.0 | 22556747 | −11.0±1.3 |
| 50848923 | −11.4±0.9 | 20765438 | −11.2±1.1 | 22909360 | −11.0±0.9 | 24512675 | −11.0±0.8 |
| 87254968 | −11.4±1.3 | 51038723 | −11.2±0.5 | 57483761 | −11.0±0.4 | 25138237 | −11.0±0.9 |
| 16749628 | −11.4±1.1 | 60481456 | −11.2±0.8 | 58607039 | −11.0±1.1 | 57483734 | −11.0±0.5 |
| 25066203 | −11.4±0.9 | 56085277 | −11.2±1.2 | 59615666 | −11.0±0.9 | 57878492 | −11.0±1.0 |
| 86608192 | −11.4±1.3 | 56025347 | −11.1±1.3 | 59986516 | −11.0±0.9 | 88042824 | −11.0±0.8 |
| 362451 | −11.3±1.3 | 11999940 | −11.1±0.7 | 60481455 | −11.0±0.8 | 90299314 | −11.0±0.9 |
| 10477276 | −11.3±0.9 | 53019143 | −11.1±0.9 | 66599533 | −11.0±0.6 | 5330694 | −11.0±1.4 |
| 71815377 | −11.3±0.5 | 58117326 | −11.1±0.2 | 69138857 | −11.0±0.4 | 45856807 | −11.0±0.6 |
| 59375107 | −11.3±1.9 | 67023384 | −11.1±0.7 | 76541767 | −11.0±0.9 | 2647295 | −11.0±0.8 |
| 67023200 | −11.3±0.7 | 44251670 | −11.1±1.0 | 89856954 | −11.0±1.4 | 6197109 | −11.0±0.7 |
| 68490845 | −11.3±0.9 | 44178168 | −11.1±1.0 | 10002281 | −11.0±0.8 | 9804722 | −11.0±1.3 |
| 44419986 | −11.3±0.8 | 53019026 | −11.1±1.1 | 42623761 | −11.0±0.9 | 20637894 | −11.0±0.7 |
| 5280143 | −11.3±0.8 | 58064137 | −11.1±1.1 | 51035546 | −11.0±0.6 | 21378092 | −11.0±0.6 |
| 57878498 | −11.3±0.8 | 16327670 | −11.1±0.8 | 51035547 | −11.0±0.4 | 25070620 | −11.0±1.5 |
| 18710166 | −11.3±1.2 | 24548686 | −11.1±0.9 | 56214202 | −11.0±1.1 | 31895387 | −11.0±0.8 |
| 59880286 | −11.3±1.2 | 86608206 | −11.1±1.3 | 59558378 | −11.0±1.0 | 54347717 | −11.0±1.3 |
| 59144489 | −11.3±1.2 | 68700123 | −11.1±1.2 | 71149319 | −11.0±0.6 | 55760732 | −11.0±1.0 |
| 18710167 | −11.3±1.5 | 46885245 | −11.1±1.0 | 25065560 | −11.0±1.1 | 57955372 | −11.0±1.0 |
| 60402567 | −11.3±0.9 | 53019136 | −11.1±0.9 | 58117279 | −11.0±0.6 | 58975131 | −11.0±0.5 |
| 71815441 | −11.3±0.6 | 60621794 | −11.1±0.8 | 90731410 | −11.0±1.0 | 59121588 | −11.0±1.1 |
| 25065987 | −11.3±1.2 | 68559862 | −11.1±1.0 | 102119533 | −11.0±1.1 | 59558337 | −11.0±0.8 |
| 11317629 | −11.3±1.0 | 85874649 | −11.1±1.0 | 44605023 | −11.0±0.7 | 59880283 | −11.0±1.2 |
| 44419982 | −11.3±0.9 | 5330697 | −11.1±1.4 | 46231533 | −11.0±0.6 | 66605319 | −11.0±0.7 |
| 47037799 | −11.3±0.7 | 16376567 | −11.1±0.8 | 54087042 | −11.0±0.5 | 66661799 | −11.0±0.9 |
| 50848762 | −11.3±0.8 | 53019095 | −11.1±0.9 | 57391501 | −11.0±0.5 | 74937104 | −11.0±0.5 |
| 53019046 | −11.3±0.9 | 20765417 | −11.1±1.2 | 59973115 | −11.0±1.4 | ||
| 58518208 | −11.3±1.8 | 22556882 | −11.1±1.2 | 69707773 | −11.0±0.9 | ||
| 89856935 | −11.3±1.2 | 99455350 | −11.1±0.9 | 59212517 | −11.0±0.6 | ||
| 10239163 | −11.3±1.1 | 2947808 | −11.1±0.8 | 41927843 | −11.0±0.7 | ||
Notes: The name of each ligand was obtained from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/).22 The name of the compounds NITD-1, -2, and -29 was taken from Niyomrattanakit et al.21 The table shows the estimated binding free energy variation31 (mean ± SD). The maps of the interacting residues of the protein with the best ligands and ΔG values among the candidate compounds are available at http://docking.umh.es/
Abbreviations: NS5, nonstructural protein 5; RdRp, RNA-dependent RNA polymerase; SD, standard deviation.