New Dual Inhibitors of SARS-CoV-2 Based on Metal Complexes with Schiff-Base 4-Chloro-3-Methyl Phenyl Hydrazine: Synthesis, DFT, Antibacterial Properties and Molecular Docking Studies
Round 1
Reviewer 1 Report
The present study is devoted to the urgent problem of searching for new inhibitors of non-structural proteins of the SARS-CoV-2 virus. The paper presents newly synthesized chelate complexes of some transition metals that exhibit antibacterial activity and may also be potential candidates for inhibitors of Mpro and NSP16. In general, the work may be of some interest in this area of research. However, a number of remarks must be taken into account:
1. Since the complexes under study contain heavy atoms of transition metals, one should expect manifestations of relativistic effects for them. The B3LYP/6-31+G(d,p)//LANL2DZ geometry optimization level used does not allow taking these effects into account. Reference 34, however, has nothing to do with the use for the objects under study. Since the article [34] discusses algorithms based on the calculation of molecular properties in the framework of AMBER force fields, and not DFT. In this case, it is necessary to refer, for example, to the publications of Rusakovs, in which such effects are considered in detail.
Have there been any attempts to use at least specialized basis sets, such as Dyall relativistic basis sets?
2. What is the reason for the choice of not the most relevant Mpro and NSP16 structures dating back to 2020?
3. It is necessary to more particularly describe the details of the performed molecular docking in Section 2.6.
4. The phrases on lines 118-120, 234-237 are inconsistent.
5. It is probably a typo in the size of the grid box (–16.0 × -24.0 × 17.0) (line 119)? The edge size of the grid box cannot be a negative number.
6. Reference [34] on line 122 has nothing to do with the text.
7. Scheme 1 (on page 3) does not show the temperature conditions of the reaction, and does not indicate the leaving group (H2O).
8. Scheme 1 (on page 3), Figures 1(Cmpy), 1(5), 3, 4c are horizontally compressed/expanded, and Figure 5d is low resolution. Needs to be redrawn.
9. Scheme 1 on page 4 should have serial number 2.
10. What do the “n” in Chart 1 on page 4 mean? And why are they not given for Pd and Pt?
11. Despite the fact that the authors carried out an extensive analysis of data on IR and NMR spectroscopy, nevertheless, the arbitration method in proving the structure of transition metal complexes is the single crystal X-ray diffraction. As you understand, in a solution we are dealing with an equilibrium mixture of several substances, including, in addition to the reagents and the product (complex), also other structures. Thus, in the NMR spectrum (by the way, where is SI?), we observe an average pattern from this equilibrium mixture, and not only signals from the complex under study. It is highly desirable to obtain crystals of the complexes in order to be able to judge their true structure.
12. Tables 3 and 4 are much more conveniently presented in column form, where the signal value in one column corresponds to a specific atom in another column.
13. The indexes of nuclei 1H and 13C are missing in the headers of Tables 3 and 4.
14. It is very useful to give an assigned of aromatic carbon atoms in the Table 4.
15. Line 209 shows 5 compounds (1-5), and line 210 shows only 3: (3) > (1) > (2).
16. As far as I understand, Chart 1 is a complete counterpart of the data shown in Table 5. Does it make sense to duplicate this information? The given graphs are connected by solid lines. What functional dependency do they have? Obviously none, so the lines should be dashed.
17. References [30,31] on line 316 are given out of context. Parr and Fukui should be quoted when describing the reactivity descriptors.
18. “There is a remarkable correlation between estimated quantum chemical parameters and experimental inhibitory activities in much recent research.” (lines 319-320) - several references should be cited as evidence.
19. “Molecular electrostatic potential (MEP) is a visual technique for knowing the shape of molecules presented with graduated color clouds.” (lines 338-339) - a more scientific and rigorous definition of MESP is needed.
21. Why were only Ni and Zn complexes investigated during molecular docking, and not all other Pd(II), Pt(II), and Hg(II) complexes?
22. Has an ADMET analysis of the synthesized complexes been carried out? If not, why not?
23. Figure 4 is not of great scientific importance, as it has been repeatedly shown in other studies.
24. “ligand does not dock to the active sites of Mpro, unlike the complexes” (line 438) – which specific ligand?
25. The section on possible dual inhibition (lines 440-447) is very promising and can be expanded with additional explanatory details on the mechanism of inhibition and the interaction of complexes with target proteins.
26. Line 447: "CoV-SARS-2" is a typo.
27. “Our results from molecular docking may represent for the first time the role of metalorganic in the inhibition of Mpro and NSP16.” – this study is far from the first in this area, check out, for example, the links:
10.1002/anie.202016768
10.1002/cbic.202100186
10.1039/D1CC02956H
10.1371/journal.pone.0240079
10.1016/j.jinorgbio.2020.111179
10.26434/chemrxiv.12673436
Author Response
RESPONSES TO REFEREE #1’s COMMENTS:
Comments and Suggestions for Authors
The present study is devoted to the urgent problem of searching for new inhibitors of non-structural proteins of the SARS-CoV-2 virus. The paper presents newly synthesized chelate complexes of some transition metals that exhibit antibacterial activity and may also be potential candidates for inhibitors of Mpro and NSP16. In general, the work may be of some interest in this area of research. However, a number of remarks must be taken into account:
1# Since the complexes under study contain heavy atoms of transition metals, one should expect manifestations of relativistic effects for them. The B3LYP/6-31+G(d,p)//LANL2DZ geometry optimization level used does not allow taking these effects into account. Reference 34, however, has nothing to do with the use for the objects under study. Since the article [34] discusses algorithms based on the calculation of molecular properties in the framework of AMBER force fields, and not DFT. In this case, it is necessary to refer, for example, to the publications of Rusakovs, in which such effects are considered in detail.
Have there been any attempts to use at least specialized basis sets, such as Dyall relativistic basis sets?
Response:
We are delighted to hear your positive opinion about our manuscript and that is a valuable one. We are grateful for the time and energy you expended on our behalf.
First, I want to thank reviewer very much for such observation and valuable comments which will add great scientific value for the manuscript. We apologize for the confusion for reference 34 which is modified to [35] P.J. Hay, W.R. Wadt, Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg, J. Chem. Phys. 82 (1985) 270–283.
I agree with reviewer comment that specialized basis set such as Relativistic effective core potential basis set of double zeta quality LANL2DZ, mixed basis set denoted GEN (LanL2DZ) are more accurate in such calculations. But It is very expensive and take too much time and now is not suitable to do.
However the results of such methods may be acceptable as we compare experimental results as IR, But I still agree that your comments is true and more better.
2. What is the reason for the choice of not the most relevant Mpro and NSP16 structures dating back to 2020?
Response:
Lines 54-56: The justification has been added.
3# It is necessary to more particularly describe the details of the performed molecular docking in Section 2.6.
Response:
Lines 120-125: done.
4# The phrases on lines 118-120, 234-237 are inconsistent.
Response:
I did not find the intended phrases
It is probably a typo in the size of the grid box (–16.0 × -24.0 × 17.0) (line 119)? The edge size of the grid box cannot be a negative number.
Response:
Lines 124-125: corrected.
- Reference [34] on line 122 has nothing to do with the text.
Response:
Line 120: The missing phrase was added
- Scheme 1 (on page 3) does not show the temperature conditions of the reaction, and does not indicate the leaving group (H2O).
Response:
Done
- Scheme 1 (on page 3), Figures 1(Cmpy), 1(5), 3, 4c are horizontally compressed/expanded, and Figure 5d is low resolution. Needs to be redrawn.
Response:
Done
Figure 4c has been clarified
9. Scheme 1 on page 4 should have serial number 2.
Response:
Done
What do the “n” in Chart 1 on page 4 mean? And why are they not given for Pd and Pt?
Response:
n number of water molecules but are not given for Pd and Pt because these salt does not contain water molecules
Despite the fact that the authors carried out an extensive analysis of data on IR and NMR spectroscopy, nevertheless, the arbitration method in proving the structure of transition metal complexes is the single crystal X-ray diffraction. As you understand, in a solution we are dealing with an equilibrium mixture of several substances, including, in addition to the reagents and the product (complex), also other structures. Thus, in the NMR spectrum (by the way, where is SI?), we observe an average pattern from this equilibrium mixture, and not only signals from the complex under study. It is highly desirable to obtain crystals of the complexes in order to be able to judge their true structure.
Response:
We thank the reviewer for raising this point and we fully agree that it is better to have X-ray single crystal structure of these complexes; however, our attempts to grow X-ray quality single crystals of these complexes by dissolving them in many solvents were failed. Unfortunately, all our trials were unsuccessful and no crystals suitable for X-ray diffraction studies were obtained.
Tables 3 and 4 are much more conveniently presented in column form, where the signal value in one column corresponds to a specific atom in another column.
Response:
In accordance with the referees’ wishes. We update the Tables 3 and 4
13. The indexes of nuclei 1H and 13C are missing in the headers of Tables 3 and 4.
Response:
In accordance with the referees’ wishes. We update the Tables 3 and 4
14. It is very useful to give an assigned of aromatic carbon atoms in the Table 4.
Response:
In accordance with the referees’ wishes. We gave the chemical shift assignments of carbon atoms in Table 4.
15. Line 209 shows 5 compounds (1-5), and line 210 shows only 3: (3) > (1) > (2).
Response:
We checked and corrected.
- As far as I understand, Chart 1 is a complete counterpart of the data shown in Table 5. Does it make sense to duplicate this information? The given graphs are connected by solid lines. What functional dependency do they have? Obviously none, so the lines should be dashed.
Response:
Chart has been removed
References [30,31] on line 316 are given out of context. Parr and Fukui should be quoted when describing the reactivity descriptors.
Response:
Done.
[30] Fukui, K. (1982) Role of Frontier Orbitals in Chemical Reactions. Science, 218, 747-754.
[31] Yang, W. and Parr, R.G. (1985) Hardness, Softness, and the Fukui Function in the Electronic Theory of Metals and Catalysis. Proceedings of the National Academy of Sciences of the United States of America, 82, 6723-6726.
18. “There is a remarkable correlation between estimated quantum chemical parameters and experimental inhibitory activities in much recent research.” (lines 319-320) - several references should be cited as evidence.
19. “Molecular electrostatic potential (MEP) is a visual technique for knowing the shape of molecules presented with graduated color clouds.” (lines 338-339) - a more scientific and rigorous definition of MESP is needed.
Response:
We checked and modified.
Why were only Ni and Zn complexes investigated during molecular docking, and not all other Pd(II), Pt(II), and Hg(II) complexes?
Response:
For the other metals, their atom types did not included into autodock vina software.
Has an ADMET analysis of the synthesized complexes been carried out? If not, why not?
Response:
ADMET analysis was carried out and added.
Figure 4 is not of great scientific importance, as it has been repeatedly shown in other studies.
Response:
The Figure has been removed.
“ligand does not dock to the active sites of Mpro, unlike the complexes” (line 438) – which specific ligand?
Response:
Line 440: corrected.
25. The section on possible dual inhibition (lines 440-447) is very promising and can be expanded with additional explanatory details on the mechanism of inhibition and the interaction of complexes with target proteins.
Response:
The discussion of this point was supported with Fig. 5c.
Line 447: "CoV-SARS-2" is a typo.
Response:
Line 449: corrected.
“Our results from molecular docking may represent for the first time the role of metalorganic in the inhibition of Mpro and NSP16.” – this study is far from the first in this area, check out, for example, the links:
10.1002/anie.202016768
10.1002/cbic.202100186
10.1039/D1CC02956H
10.1371/journal.pone.0240079
10.1016/j.jinorgbio.2020.111179
10.26434/chemrxiv.12673436
Reviewer 2 Report
The manuscript submitted by Al-Janabi and its co-workers is intended to bring a new class of metal complexes of Schiff base ligands as potential inhibitors of the non-structural protein NSP16 and of the main protease MPro of the SARS-COV-2 virus. The subject of the manuscript is a part of the nowadays trend to assign as many ligands and metal complexes as efficient fighters against a virus.
As a whole, the manuscript does not suffer from bad English language and grammar, or from a poor description of the methods and techniques.The manuscript is of average quality, the synthesis of the Schiff base ligand and its tranzitional metal complexes is not difficult, and the characterization goes smoothly as well.
I failed to see the Supplementary Information, there is no link to it, so I cannot pronounce on the quality of the IR and NMR spectra and other issues.
I do have several issues, as listed bellow:
11. The authors claim that the metal complexes have been obtained as crystals. I do not see any evidence of the claimed structures, the X-ray data are missing, still the authors claim the correspondence with the DFT calculations.
22. Pag. 5, lines 149 – 150 – the frequency at which the CH=N stretching vibration is missing
33. Pag. 5, line 150 – “the n(C=N) of pyridyl ring displayed at 1689cm-1.” The frequency is much too high for this type of vibration. Please re-assign the vibrations
I I suggest the authors to fix the problems from above and the manuscript can be afterwards published in Inorganics.
I
Author Response
RESPONSES TO REFEREE #2’s COMMENTS:
The manuscript submitted by Al-Janabi and its co-workers is intended to bring a new class of metal complexes of Schiff base ligands as potential inhibitors of the non-structural protein NSP16 and of the main protease MPro of the SARS-COV-2 virus. The subject of the manuscript is a part of the nowadays trend to assign as many ligands and metal complexes as efficient fighters against a virus.
As a whole, the manuscript does not suffer from bad English language and grammar, or from a poor description of the methods and techniques. The manuscript is of average quality, the synthesis of the Schiff base ligand and its transitional metal complexes is not difficult, and the characterization goes smoothly as well.
I failed to see the Supplementary Information, there is no link to it, so I cannot pronounce on the quality of the IR and NMR spectra and other issues.
Response:
We added the supplementary information (IR and NMR spectra)
I do have several issues, as listed below:
- The authors claim that the metal complexes have been obtained as crystals. I do not see any evidence of the claimed structures, the X-ray data are missing, still the authors claim the correspondence with the DFT calculations.
Response:
We thank the reviewer for raising this point and we fully agree that it is better to have X-ray single crystal structure of these complexes; however, our attempts to grow X-ray quality single crystals of these complexes by dissolving them in many solvents were failed. Unfortunately, all our trials were unsuccessful and no crystals suitable for X-ray diffraction studies were obtained.
So in absence of X-ray single crystal structure , DFT calculations were carried out to obtain more information about structures.
- Pag. 5, lines 149 – 150 – the frequency at which the CH=N stretching vibration is missing.
Response:
Done
- Pag. 5, line 150 – “the n(C=N) of pyridyl ring displayed at 1689cm-1.” The frequency is much too high for this type of vibration. Please re-assign the vibrations
Response:
We agree with referee in this comment, but the frequency range of nC=N is very wide in IR spectroscopy. some published papers as following assigned the frequency of C=N within ( 1680 - 1630)cm-1 range.
1- A. Menteş et al. Turkish Journal of Chemistry. 31(2007)667 – 676.
2- https://doi.org/10.1016/j.molstruc.2021.131830.
3- https://doi.org/10.3390/molecules20010822.
4- https://doi.org/ 10.1007/s11243-007-0276-5
I suggest the authors to fix the problems from above and the manuscript can be afterwards published in Inorganics.
Round 2
Reviewer 1 Report
The authors significantly supplemented the manuscript with new data. The article can be recommended for publication. There is one small clarification: In Scheme 2, the number of water molecules is indicated as "x" on the left side of this Scheme, while on the right side of this Scheme it is indicated as "n".
