Keywords
diabetes, Bacillus cereus, PI-PLC, serine protease, lipase
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Chakraborty S, Rendón-Ramírez A, Ásgeirsson B et al. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.12688/f1000research.2-286.v3)
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Research Article
Revised
The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins
[version 3; peer review: 2 approved]
PUBLISHED 29 Jan 2015
OPEN PEER REVIEW
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Abstract
Corresponding author:
Sandeep Chakraborty
Competing interests:
No competing interests were disclosed.
Grant information:
FMG thanks the Spanish Ministerio de Ciencia e Innovacion for grant No. BFU 2012-36241, and the University of the Basque Country for grant No. IT 849-13. BJ and RV acknowledge financial support from Tata Institute of Fundamental Research (Department of Atomic Energy). Additionally, BJR is thankful to the Department of Science and Technology for the JC Bose Award Grant. BA extends gratitude to the University of Iceland Research Found for supporting the project financially. AMD wishes to acknowledge grant #12-0130-SA from California Department of Food and Agriculture CDFA PD/GWSS Board. MO was supported in part by a Grant-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan; (grant No. 21790431). The work in Liege was supported by an IUAP program funded by the Belgian federal government.
Copyright:
© 2015 Chakraborty S et al.
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions.
Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
How to cite: Chakraborty S, Rendón-Ramírez A, Ásgeirsson B et al. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.12688/f1000research.2-286.v3)
First published: 27 Dec 2013, 2:286 (https://doi.org/10.12688/f1000research.2-286.v1)
Latest published: 29 Jan 2015, 2:286 (https://doi.org/10.12688/f1000research.2-286.v3)
Revised Amendments from Version 2
In the current version, we have changed the title, and cited previous research (ref 41 and 54) based on referee suggestions.
We have also included some minor corrections as suggested by a co-author.
See the authors' detailed response to the review by Rodney Rouse
See the authors' detailed response to the review by Mark D Gorrell
Introduction
Oral glucose elicits a greater insulin response than intravenous glucose infusion, a phenomenon known as the incretin effect1. This effect is mostly attributed to the intestinally derived hormones glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptide (GIP)2. These hormones have a very short half-life as they are rapidly inactivated by the ubiquitous enzyme dipeptidyl peptidase-IV (DPP4)3. The finding that the incretin effect is impaired in subjects with type 2 diabetes4 led to two major types of GLP-1 based therapies5 - intravenously or sub-cutaneously administered GLP-1 mimetics that are resistant to DPP4 (exenatide, liraglutide, etc.)6, and the orally administered gliptins that prolong the physiological actions of incretin hormones by inhibiting DPP4 (sitagliptin, vildagliptin, etc.)7–9. Due to the multifarious roles played by the DPP4 enzyme10–12, the possible side effects of these drugs (acute pancreatitis, pancreatic cancer, etc.13–15) are strongly contested by researchers who argue that current statistics are insufficient16,17 to conclusively attribute these side effects to the otherwise beneficial GLP-1 drugs18. Compound promiscuity is another phenomenon that might play a crucial role in determining the side effects of these therapies, although this aspect has rarely been pursued intensively19.
Previous work by our group has established the spatial and electrostatic congruence in cognate residue pairs of the active site in proteins with the same functionality (CLASP)20,21. CLASP analysis indicated that the phosphoinositide-specific phospholipase C (PI-PLC) from Bacillus cereus has spatial and electrostatic congruence with a serine protease motif22. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). The specificity of the protease activity was for a proline in the amino terminal, suggesting that PI-PLC is a prolyl peptidase, similar to the DPP4 enzyme. This finding led us to believe that the gliptins would have similar inhibitory effect on PI-PLC. In the current work, we have confirmed the inhibition of the native phospholipase activity of PI-PLC using two gliptins - vildagliptin23 (at µ-molar concentrations) and K57924 (at nano-molar concentrations).
Subsequently, we used a motif derived from a DPP4 protein25, in addition to the trypsin motif used previously22, to query a comprehensive and non-redundant (50% sequence identity) list of ~5000 human proteins with known structures using CLASP, intending to identify other proteins that might be inhibited by the gliptins. From the set of proteins with significant congruent matches with these two motifs, we identified a pancreatic lipase26 and a gastric lipase27, keeping the context of lipases, acute pancreatitis and GLP-1 based therapies in mind. Our findings rationalize the elevated levels of serum lipase found in patients undergoing DPP4 inhibitor based therapies28,29, although these reports are in disagreement with other findings30,31. While it is logical and expected to find scaffolds that are congruent to trypsin and DPP4 active sites in lipases based on the current results and our previous findings22, we also show the presence of the serine catalytic triad in close proximity to the active site residues of proteins which have a completely different enzymatic mechanism (for example, in glutaminyl cyclase which is a transferase32). This corroborates the current belief that convergent evolution occurs more frequently than previously believed33. Thus, we propose a rational method to identify proteins that might have unintended and undesirable interactions with newly introduced compounds, and substantiate our claims by demonstrating the inhibition of the native phospholipase activity of PI-PLC from B. cereus using gliptins that are used in type 2 diabetes therapy.
Results
The active site motifs
The active sites of serine proteases differ in their specificities owing to residues other than the conserved catalytic triad. Thus, in addition to the trypsin motif used previously (Asp102, Ser195 and His57 - PDBid 1A0J)22 (Motif1), we choose another motif from a DPP4 enzyme (Asp708, Ser630 and His740 - PDBid:1N1M) (Motif2) (Table 1). Apart from the catalytic triad, we chose another non-polar residue in order to increase the specificity of the matches (Ala56 in Motif1 and Val711 in Motif2). This fourth residue is chosen as the closest residue to any one of the catalytic triad residues. Using the ability of CLASP to include stereochemically equivalent residues, this last residue could be matched by another non-polar residue - one of Gly, Ala, Val, Leu, Ile or Met. Further, it has been seen that the second (ac) and fifth (bd) (Table 1) pairwise electrostatic potential differences (EPD) are not discriminatory - thus, this pair is not used to score the EPD difference (although it is included in the distance deviation score).
Table 1. Potential and spatial congruence of the active site residues in proteins queried using two motifs - Motif1 from Trypsin and Motif2 from DPP4.
Rmsd1 and Rmsd2 are the root mean square deviation of the scaffold with respect to Motif1 and Motif2. DPP4 - dipeptidyl peptidase-IV, PI-PLC - phosphoinositide-specific phospholipase C, PLASE - human pancreatic lipase-Related Protein 2, GPASE - human gastric lipase, QC - glutaminyl cyclase. D = Pairwise distance in Å. PD = Pairwise potential difference. APBS writes out the electrostatic potential in dimensionless units of kT/e where k is Boltzmann’s constant, T is the temperature in K and e is the charge of an electron.
Table 2. Best matches in the set of ~5000 human proteins.
(a) Motif1 (Asp102, Ser195, His57, Ala56) from Trypsin (b) Motif2 (Asp708, Ser630, His740, Val711) from DPP4.
Inhibition of phosphoinositide-specific phospholipase C (PI-PLC) using dipeptidyl peptidase-IV (DPP4) inhibitors. DPP4 (EC 3.4.14.5), a serine protease that is expressed in many tissues (kidney, liver, lung, intestinal membranes, lymphocytes and endothelial cells), cleaves peptides with Pro or Ala residues in the second amino terminal position. Previously, we have experimentally demonstrated the existence of the serine protease domain in PI-PLC from Bacillus cereus - both by virtue of its proteolytic activity, and the inhibition of its native activity on phospholipids in the presence of serine protease inhibitors22. Furthermore, the specificity of the proteolytic activity indicated that it was a prolyl peptidase - thus, leading us to believe that DPP4 inhibitors should have a similar inhibitory effect on the PI-PLC enzyme. Table 1 shows the presence of a congruent motif in the PI-PLC protein with both Motif1 and Motif2. His32 and Asp67 are known to be a part of the active site scaffold in PI-PLC22. These proteins have completely different folds, and thus a superimposition (using both MUSTANG34 and DECAAF35) does not show any detectable similarity in their structures (Supplementary Figure 1). Figure 1 shows the active sites of these proteins, and the superimposition of these proteins based on their catalytic residues35. It can be seen that the closest non-polar residue to the catalytic triad in trypsin and PI-PLC (Ala56 in PDBid:1A0J, Ile68 in PDBid:1PTD) is differently placed from Val711 in DPP4 (PDBid:1N1M). This is also indicated by the greater RMSD (root mean square deviation) of the scaffold in PI-PLC to Motif2 as compared to Motif1. The differences in the position of peripheral residues is the source of the diverse specificities exhibited by these proteases. Figure 2 shows the inhibition of PI-PLC using two gliptins - vildagliptin (LAF-237)23 and K57924. PI-PLC catalyzes hydrolysis of phospholipids to yield diacylglycerol and a phosphoryl alcohol. In the absence of inhibitors enzyme addition to the vesicle suspension causes an increase in turbidity due to vesicle aggregation (Figure 2 a,c). Aggregation in turn occurs as a result of formation of the enzyme endproduct diacylglycerol36,37. A steady-state is reached under our conditions after 6–8 min. Addition of either LAF-237 (vildagliptin) or K579 leads to an obvious inhibition of the enzyme activity. Dose-response curves for the inhibitors are shown in Figure 2 (b,d). K579 is two orders of magnitude more potent than LAF-237 as a PI-PLC inhibitor, with half-maximal inhibitory concentrations IC50 respectively of 1 µM and 100 µM.
Figure 2. PI-PLC inhibition using DPP4 inhibitors.
(a,c) Time courses of enzyme activity in the presence of varying amounts of inhibitors, respectively LAF-237 and K579. The trace marked LIPOSOMES corresponds to a control in the absence of PI-PLC. (b,d) Dose-response effect of inhibitors on PI-PLC activity. Activity was computed as the extent of vesicle aggregation after 10 min enzyme activity.
Querying a non-redundant set of human proteins using Motif1 and Motif2. Currently, the PDB database has about 25,000 human proteins. Using a identity cutoff of 50%, we chose a set of ~5000 proteins (Supplementary Table 1) as the target proteins. Table 2 shows ten proteins which have signicant matches with Motif1 and Motif2. Given the context of lipases, acute pancreatitis and GLP-1 based therapies, we picked two proteins - the human pancreatic lipase-related protein 2 (PDBid:2OXE)26 and a human gastric lipase (PDBid:1HLG)27 - to demonstrate the distinct possibility that these proteins might be inhibited by DPP4 inhibitors. Table 1 shows the congruence of the DPP4 motif to these proteins using Motif1 and Motif2. It is interesting to note that the gastric lipase (PDBid:1HLG) has a good match with both motifs - Leu326 in PDBid:1HLG is congruent to Ala56 in PDBid:1A0J, and Ala237 (PDBid:1HLG) is congruent to Val711 (PDBid:1N1M).
Since both these proteins are lipases (hydrolases), this congruence to Motif1 and Motif2 is expected based on our previous results with PI-PLC22. However, our methodology also detects other proteins, often with a completely different enzymatic mechanism from hydrolases. A glutaminyl cyclase (PDBid:3PB432), a transferase, has a significantly congruent domain with Motif1 (lesser congruence with Motif2, as indicated by the RMSD) (Table 1). Figure 3 shows the proximity of the promiscuous scaffold to the active site of the cyclase, and also the congruence of the scaffold to Motif1.
Figure 3. A scaffold congruent to the active site of Trypsin (PDBid:1A0J) in a glutaminyl cyclase (PDBid:3PB4).
(a) The active site residues are marked in magenta. They are seen to be proximal to the identified scaffold. (b) Superimposition of Motif1 and the scaffold in glutaminyl cyclase. The exact pairwise interatomic distance and electrostatic potential differences are specified in Table 1.
Docking vildagliptin to the PIPLC structure. Since there are no DPP4 structures solved which ligand K-579, a DPP4 protein structure in complex with vildagliptin (PDBid:3W2TA)38 was used to dock vildagliptin to the PIPLC structure complexed with myo-inositol (PDBid:1PTG39) using DOCLASP40 (Figure 4). The Pymol script for visualizing the docking (SupplementaryPymol.p1m) is provided as Supplementary information.
Figure 4. Docking vildagliptin to the PI-PLC structure in complex with myo-inositol (PDBid:1PTGA).
Docking done using DOCLASP40. The Pymol script for visualizing the docking (SupplementaryPymol.p1m) is provided as Supplementary information.
Statistics of atoms making contact with inhibitors. There are 76 unique DPP4 inhibitors, defined by three letter codes, for which the ligand-DPP4 structure is solved (Supplementary Table 2). For uniformity, we chose the first four closest atoms from the protein that make contacts to the ligand, excluding hydrophobic interactions. Table 3 shows the number of times each residue in DPP4 makes contact to the ligand. Three residues are ubiquitous in making contacts in all these ligands: Glu205, Glu206 and Tyr662 made contacts in 71, 68 and 63 ligands, respectively. Interestingly, Glu205 and Glu206 have been implicated as critical residues for the enzymatic activity of DPP4 through point mutations41. Note, that since only the first four residues were considered, these counts are conservative (and might be more). A recent study has found that inhibitors that bind to residues beyond the extensive subsite (defined as Val207, Ser209, Phe357 and Arg358) increases DPP4 inhibition, as compared to those inhibitors that form a covalent bond with Ser63038. Table 3 shows that very few inhibitors make such contacts. We created a library of motifs from these structures that can be used to query any protein using CLASP to determine the possibility that DPP4 inhibitors might bind to it (Supplementary Table 3), after removing equivalent ones to eliminate redundancy. This table shows the final list of 39 motifs (pruned from the initial 76): this is a comprehensive set of motifs that encapsulates the current knowledge about protein ligand interactions for the DPP4 enzyme. A facet of ligand binding that needs to be accounted for while choosing a motif is the spatial and electrostatic changes that can be induced by ligand binding. Thus, we obtain the residues involved in binding from the holo enzyme, but extract the motif values (pairwise distance and EPD) from the apo enzyme.
Table 3. Number of times residues from the DPP4 enzyme ligand an inhibitor.
Three residues - Glu205, Glu206 and Tyr662 - make contacts in 71, 68 and 63 ligands, respectively. Note, that since we only choose the first four residues based on proximity of the atoms closest to the ligand, these counts are conservative (and might be actually more).
| Residue | Number of ligands |
|---|---|
| ARG125 | 11 |
| GLU205 | 71 |
| GLU206 | 68 |
| VAL207 | 1 |
| SER209 | 3 |
| ARG358 | 6 |
| TYR547 | 18 |
| GLN553 | 1 |
| TYR585 | 1 |
| TRP629 | 1 |
| SER630 | 10 |
| TYR631 | 12 |
| TYR662 | 63 |
| ASN710 | 15 |
Discussion
The controversy regarding the side effects of the dpp4 inhibitors, particularly with respect to acute pancreatitis and pancreatic cancer, continues unabated. While some researchers feel that it is not acceptable to assume that ‘absence of evidence is evidence of absence’42,43, others believe that current data are not conclusive and the ‘benefits by far outweigh the potential risks’16. Adding to the uncertainties are conflicting reports presented by different groups28–31. Notwithstanding the antagonistic views on the subject, it is unanimously accepted that current data are insufficient to establish a causal pathogenic effect of these drugs on such side effects44.
Various database studies have been undertaken in order to ascertain the effects of the GLP-1 therapies. Some studies ‘did not find an association between the use of exenatide or sitagliptin and acute pancreatitis’ with the caveat that the ‘limitations of this observational claims-based analysis cannot exclude the possibility of an increased risk’45. On the other hand, other studies have shown that the use of ‘sitagliptin or exenatide increased the odds ratio for reported pancreatitis 6-fold as compared with other therapies’14. Further, they reported that ‘pancreatic cancer was more commonly reported among patients who took sitagliptin or exenatide as compared with other therapies’14. Although these studies concern the usage of both GLP-1 mimetics and the orally administered gliptins, and our study exclusively focusses on gliptins, and is not concerned with the GLP-1 mimetics data. The close relationship between chronic pancreatitis and pancreatic cancer is also a subject of intense research46. Another administrative database study of US adults with type 2 diabetes reported increased odds of hospitalization for acute pancreatitis for patients undergoing GLP-1 based therapies sitagliptin13. Once again, such correlation of GLP-1 based therapies to acute pancreatitis is contested by other studies47.
Our findings rationalize the elevated levels of serum lipase found in patients undergoing DPP4 inhibitor based therapies28,29, keeping in mind that other studies contradict these reports30,31. While several studies have reported that the GLP-1 mimetics do not induce pancreatitis in rats, mouse and/or monkey48–50, these studies did not include DPP4 inhibitors, which are the compounds that might be responsible for interactions with pancreatic proteins according to our study. It is to be noted however that these mimetics may have other physiological effects and ‘the long-term consequences of sustained GLP-1 receptor activation in the human thyroid remain unknown and merit further investigation’51. Once again, the previous study51 has been challenged by another group who note that ‘findings previously reported in rodents may not apply to humans’52.
The orally administered gliptins differ in many aspects such as potency, excretion mechanism, target selectivity, half-life, metabolism and possible drug-drug interactions9,53,54. This difference is also highlighted in the different concentrations of vildagliptin and K579 that inhibit PI-PLC. A recent study has also noted the differential off-target inhibition of enzymes by vildagliptin and sitagliptin using a high-throughput, multiplexed assay55. Interestingly, the PI-PLC scaffold has a better match with the trypsin motif than with the DPP4 motif (Table 1). In order to be able to model these differences in our in silico search, it is important to be able to provide flexibility in the scoring mechanism.
To summarize, it has been noted in the case of GLP-1 based therapies that as ‘evidence of harm accumulates, but is vigorously discounted’ the ‘burden of proof now rests with those who wish to convince us of their safety’43. Surveillance programs, real-life cohort studies and case-control studies can be supplemented by rational investigations of relevant proteins based on anecdotal reports56. The methodology proposed in the current work, which specifically demonstrates the effects of the DPP4 inhibitors, also presents a rational way of determining the inadvertent interactions of newly designed compounds with proteins, and thus prevent the recurrence of drug induced diseases being detected after considerable damage has already been inflicted on humans subjected to these drugs57.
Materials and methods
In silico analysis
A comprehensive, non-redundant set of ~5000 human proteins (50% identity cutoff) was obtained from the PDB database58. The CLASP package (http://www.sanchak.com/clasp) used for querying these proteins using motifs from trypsin and DPP4 is written in Perl on Ubuntu20. Hardware requirements are modest - all results here are from a simple workstation (8GB ram), and runtimes for analyzing the ~5000 proteins was about 24 hours. Adaptive Poisson-Boltzmann Solver (APBS) and PDB2PQR packages were used to calculate the potential difference between the reactive atoms of the corresponding proteins59,60. The APBS parameters and electrostatic potential units were set as described previously in Chakraborty et al.20. All protein structures were rendered by PyMol (http://www.pymol.org/). Protein structures have been superimposed using MUSTANG34 and DECAAF35.
Protein, substrate and reagents
PI-PLC was purchased from Sigma. Vildagliptin (LAF-237) was obtained from Selleckchem, and K579 was obtained from Santa Cruz.
PI-PLC assay and inhibition using DPP4 inhibitors
Vesicle preparation and characterization. The appropriate lipids were mixed in organic solution, and the solvent was evaporated to dryness under N2. Solvent traces were removed by evacuating the lipids for at least 2 hours. The lipids were then swollen in 10 mM Hepes, 150 mM NaCl, pH 7.5 buffer. Large unilamellar vesicles (LUV) were prepared from the swollen lipids by extrusion and sized by using 0.1 µm poresize Nuclepore filters, as described by Ahyayauch et al.36. LUV composition was egg phosphatidylcholine: egg phosphatidylethanolamine: cholesterol at a 2:1:1 mole ratio. The average size of LUV was measured by quasi-elastic light scattering, using a Malvern Zeta-sizer instrument. Lipid concentration, determined by phosphate analysis, was 0.3 mM in all experiments.
Aggregation Assay. Enzyme activity was assayed measuring enzyme-induced vesicle aggregation. All assays were carried out at 39°C with continuous stirring, in 10 mM Hepes, 150 mM NaCl buffer (pH 7.5), in the presence of 0.1% BSA for optimum catalytic activity. Enzyme concentration was 0.16 U/mL, and liposomal concentration was 0.3 mM. Lipid aggregation was monitored in a Cary Varian UV-vesicle spectrometer as an increase in turbidity (absorbance at 450 nm) of the sample, as described by Villar et al.37. The data are average values of two closely similar experiments.
Analyzing known DPP4 inhibitors with solved structures. In order to obtain all known structures of DPP4 with inhibitors bound to the active site, we did a search for the keyword dipeptidyl-peptidase on the PDB database, and choose proteins with DPP4 inhibitors as ligands. There are 76 such unique compounds (defined by three letter codes) that are reported to date (May 2014). We docked the DPP4 inhibitor to the PIPLC active site using DOCLASP40.
Data availability
figshare: Phosphoinositide-specific phospholipase C inhibition data using the dipeptidyl peptidase-IV inhibitors K-579 and LAF-237, http://dx.doi.org/10.6084/m9.figshare.880620
Author contributions
SC, ARR and BA performed the experiments. All authors analyzed the data, and contributed equally to the writing and subsequent refinement of the manuscript.
Grant information
FMG thanks the Spanish Ministerio de Ciencia e Innovacion for grant No. BFU 2012-36241, and the University of the Basque Country for grant No. IT 849-13. BJ and RV acknowledge financial support from Tata Institute of Fundamental Research (Department of Atomic Energy). Additionally, BJR is thankful to the Department of Science and Technology for the JC Bose Award Grant. BA extends gratitude to the University of Iceland Research Found for supporting the project financially. AMD wishes to acknowledge grant #12-0130-SA from California Department of Food and Agriculture CDFA PD/GWSS Board. MO was supported in part by a Grant-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan; (grant No. 21790431). The work in Liege was supported by an IUAP program funded by the Belgian federal government.
Acknowledgements
We are grateful to Jean-Marie Frère, Centre for Protein Engineering, Universite de Liège, Institut de Chimie B6, Sart Tilman, B-4000 Liège, Belgium for critical inputs.
Supplementary information
Supplementary Pymol scripts. Click here to access the files. http://dx.doi.org/10.5256/f1000research.3002.s40929
Supplementary Table 1. PDB IDs of ∼5000 human proteins analyzed in this study.
Supplementary Table 2. Residues of DPP4 closest to the bound ligand with possible hydrogen bonds.
Interactions sorted based on the distance. N: Number of atoms in the ligand, R/A/LA/D: Residue number/Atom of the residue/Atom of ligand/distance between the interacting atoms (in Å). For example, ‘E205/OE1/N25/2.7’ means that the atom OE1 from Glu205 is at 2.7 Å from the N25 atom of W94 in PDBid:3VJLA. For uniformity, we choose the first four closest atoms. This might result in choosing some atoms which are unlikely to form a hydrogen bond (for example, in PDBid:4J3JA S209/OG is at 4.8 Å from NAQ).
Supplementary Table 3. Library of non-redundant motifs.
This library of motifs can be used to query any protein using CLASP to determine the possibility that DPP4 inhibitors might bind to it.
Faculty Opinions recommended
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Chakraborty S, Rendón-Ramírez A, Ásgeirsson B et al. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.12688/f1000research.2-286.v3)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations
A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 2
VERSION 2
PUBLISHED 14 Jan 2015
Revised
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How to cite this report:
Gorrell MD. Reviewer Report For: The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.5256/f1000research.6371.r7383)
The direct URL for this report is:
https://f1000research.com/articles/2-286/v2#referee-response-7383
https://f1000research.com/articles/2-286/v2#referee-response-7383
NOTE: it is important to ensure the information in square brackets after the title is included in this citation.
Reviewer Report 20 Jan 2015
Mark D Gorrell,
Molecular Hepatology, Centenary Institute, Newtown, NSW, Australia
Approved
VIEWS 29
Thank you to the authors for developing this paper.
I have some further comments.
I have some further comments.
- The primary issue now is the speculation in the title.
The title seeks to extrapolate the obtained data on two compounds to suggest that it is applicable to all
CITE
HOW TO CITE THIS REPORT
Gorrell MD. Reviewer Report For: The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.5256/f1000research.6371.r7383)
The direct URL for this report is:
https://f1000research.com/articles/2-286/v2#referee-response-7383
https://f1000research.com/articles/2-286/v2#referee-response-7383
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
-
Author Response 29 Jan 2015Sandeep Chakraborty, Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India29 Jan 2015Author ResponseWe would like to thank you for your positive comments, and your informative suggestions.
We agree with your suggested change in the title. In the latest version, we have also cited ... Continue reading
COMMENTS ON THIS REPORT
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Author Response 29 Jan 2015Sandeep Chakraborty, Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India29 Jan 2015Author ResponseWe would like to thank you for your positive comments, and your informative suggestions.
We agree with your suggested change in the title. In the latest version, we have also cited ... Continue reading
Version 1
VERSION 1
PUBLISHED 27 Dec 2013
Views
60
How to cite this report:
Gorrell MD. Reviewer Report For: The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.5256/f1000research.3236.r4249)
The direct URL for this report is:
https://f1000research.com/articles/2-286/v1#referee-response-4249
https://f1000research.com/articles/2-286/v1#referee-response-4249
NOTE: it is important to ensure the information in square brackets after the title is included in this citation.
Reviewer Report 26 Mar 2014
Mark D Gorrell,
Molecular Hepatology, Centenary Institute, Newtown, NSW, Australia
Approved with Reservations
VIEWS 60
The successful targeting of DPP4 using small molecule compounds to treat type 2 diabetes has attracted a great deal of attention towards the study of this protease.
The authors applied sophisticated techniques that they have developed in order to discover that ... Continue reading
The authors applied sophisticated techniques that they have developed in order to discover that ... Continue reading
CITE
HOW TO CITE THIS REPORT
Gorrell MD. Reviewer Report For: The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.5256/f1000research.3236.r4249)
The direct URL for this report is:
https://f1000research.com/articles/2-286/v1#referee-response-4249
https://f1000research.com/articles/2-286/v1#referee-response-4249
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
-
Author Response 14 Jan 2015Sandeep Chakraborty, Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India14 Jan 2015Author ResponseWe would like to thank you for taking the time to review this paper, and also for your insightful comments. We also apologize for the inordinate time taken to respond ... Continue reading
COMMENTS ON THIS REPORT
-
Author Response 14 Jan 2015Sandeep Chakraborty, Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India14 Jan 2015Author ResponseWe would like to thank you for taking the time to review this paper, and also for your insightful comments. We also apologize for the inordinate time taken to respond ... Continue reading
Views
52
How to cite this report:
Rouse R. Reviewer Report For: The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.5256/f1000research.3236.r3818)
The direct URL for this report is:
https://f1000research.com/articles/2-286/v1#referee-response-3818
https://f1000research.com/articles/2-286/v1#referee-response-3818
NOTE: it is important to ensure the information in square brackets after the title is included in this citation.
Reviewer Report 06 Mar 2014
Rodney Rouse,
Division of Applied Regulatory Science, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
Approved
VIEWS 52
Disclaimer: I lack the protein chemistry expertise to comment on the assumptions and protein chemistry used in the computational method described in this article.
The title and abstract are appropriate.The overall experimental design is simple but strong and well suited for this project. The methods were ... Continue reading
The title and abstract are appropriate.The overall experimental design is simple but strong and well suited for this project. The methods were ... Continue reading
CITE
HOW TO CITE THIS REPORT
Rouse R. Reviewer Report For: The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins [version 3; peer review: 2 approved]. F1000Research 2015, 2:286 (https://doi.org/10.5256/f1000research.3236.r3818)
The direct URL for this report is:
https://f1000research.com/articles/2-286/v1#referee-response-3818
https://f1000research.com/articles/2-286/v1#referee-response-3818
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
-
Author Response 10 Mar 2014Adela Rendón-Ramirez, Unidad de Biofisica CSIC UPV, Spain10 Mar 2014Author ResponseDear Dr Rouse,
We would like to thank you for taking the time and reviewing our paper. Your positive comments encourage us to further our research in this area.
We concur with ... Continue reading
COMMENTS ON THIS REPORT
-
Author Response 10 Mar 2014Adela Rendón-Ramirez, Unidad de Biofisica CSIC UPV, Spain10 Mar 2014Author ResponseDear Dr Rouse,
We would like to thank you for taking the time and reviewing our paper. Your positive comments encourage us to further our research in this area.
We concur with ... Continue reading
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