| Literature DB >> 34188160 |
Tarun Jairaj Narwani1, Narayanaswamy Srinivasan2, Sohini Chakraborti1.
Abstract
Computational methods accelerate the drug repurposing pipelines that are a quicker and cost-effective alternative to discovering new molecules. However, there is a paucity of web servers to conduct fast, focussed, and customized investigations for identifying new uses of old drugs. We present the NOD web server, which has the mentioned characteristics. NOD uses a sensitive sequence-guided approach to identify close and distant homologs of a protein of interest. NOD then exploits this evolutionary information to suggest potential compounds from the DrugBank database that can be repurposed against the input protein. NOD also allows expansion of the chemical space of the potential candidates through similarity searches. We have validated the performance of NOD against available experimental and/or clinical reports. In 65.6% of the investigated cases in a control study, NOD is able to identify drugs more effectively than the searches made in DrugBank. NOD is freely-available at http://pauling.mbu.iisc.ac.in/NOD/NOD/ .Entities:
Year: 2021 PMID: 34188160 PMCID: PMC8241987 DOI: 10.1038/s41598-021-92903-8
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Few selected examples from validation of NOD’s predictions.
| Sl. No. | Disease (causative pathogen, if applicable) | Query protein (gene) | Target homolog protein (organism, gene) | Potential candidate (DrugBank ID) | Reference to laboratory and/ or clinical evidence |
|---|---|---|---|---|---|
| 1 | Tuberculosis ( | G0ZF27 (rpoB) | P0A8V2 ( | Rifabutin (DB00615) | [ |
| 2 | P9WPL3 (cyp143) | P08684 (Human, CYP3A4) | Isoniazid (DB00951) | [ | |
| 3 | P9WH63 (rpsL) | P0A7S3 ( | Kanamycin (DB01172) | [ | |
| 4 | P9WH63 (rpsL) | P0A7S3 ( | Amikacin (DB00479) | [ | |
| 5 | G0ZF23 (rpoB) | P0A8V2 ( | Rifampicin (DB01045) | [ | |
| 6 | Malaria ( | Q8ILQ7 (GST) | P09210 (Human, GSTA2) | Chloroquine (DB00608) | [ |
| 7 | Q8I4X0 (PFL2215w) | P63261 (Human, ACTG1) | Artenimol (DB11638) | [ | |
| 8 | Candidiasis ( | A0A1D8PDL5 (GSL1) | A2QLK4 ( | Anidulafungin (DB00362) | [ |
| 9 | P10613 (ERG11) | P50859 ( | Isavuconazole (DB11633) | [ | |
| 10 | Q5A7M3 (BNA4) | Q14534 (Human, SQLE) | Terbinafine (DB00857) | [ | |
| 11 | A0A1D8PJ01 (PMA1) | P05023 (Human, ATP1A1) | Ciclopirox (DB01188) | [ | |
| 12 | Q5A7M3 (BNA4) | Q14534 (Human, SQLE) | Naftifine (DB00735) | [ | |
| 13 | AIDS ( | Q72874 (pol) | O90777 ( | Nelfinavir (DB00220) | [ |
| 14 | Covid-19 ( | P0DTD1 (rep) | P0C6X7 ( | Remdesivir (DB14761) | [ |
| 15 | Cancer | O14965 (AURKA) | P24941 (Human, CDK2) | N-[3-(1H-benzimidazol-2-yl)-1H-pyrazol-4-yl]benzamide (DB08066) | [ |
P.S.: In the case where the candidate molecules are associated with more than one query-target pairs, only a single non-trivial (i.e., non-self hit) pair is selected for reporting in this table. Information on detailed validation results of NOD could be found in the Table S1.
Figure 1Performance statistics for MODE-1 and MODE-2 runs of NOD server with default settings. MODE-1 (left) is run against multiple sequence input data with different number of sequences (y2-axis) and run-time (y1-axis) is catalogued. With a gradual increase in No. of sequences (from 10 to 6035) using Candida albicans proteome, a non-linear increase in run-time is observed at Ca_1000 to Ca_2000. However, a comparison between the mode-1 runs of Ca_4000 and 4081 sequences of Mtb (Mtb_4081) shows that the run-time complexity is not essentially linear. It takes longer for Ca_4000 than Mtb_4081. Other protein sequence input includes: Plasmodium falciparum (Pf), nSARS-Cov2 (Sc), and miscellaneous set of 3 sequences comprising an Aurora Kinase and two GPCRs. For MODE-2 (right), it is evident that the computation time is independent of the sequence length as well. While Aurora-A Kinase (AurKinase), Beta-2 Adernergic Receptor (β2-AR) are relatively short sequences of 403 and 413 residues, their run-time ranges are very high in the order of 95 min to 197 min, respectively. Other sequences include: protease of HIV and HCV, RNA polymerase of Ebola, and Genome polyprotein of Zika virus.
Figure 2Workflow involved in NOD pipeline. Steps—1 and 2 are common to both MODE-1 and 2. Step 3 is executed only in MODE-2. The user submits the input sequence/s (query) using the forms available in ‘Run-Options’ page of NOD server. The homologs of the query protein/s are then searched and subsequently the relevant information of associated compounds is fetched to suggest a list of potential candidates which could be considered for further probing in the drug repurposing pipeline. MODE-2 offers an additional analysis by allowing an expansion of the primary chemical space through similarity search quantified using Tanimoto coefficient (Tc). Q. cov. indicates Query coverage.