Reviewer #1 (Public review):
Summary:
Polymyxins are the last line of drugs to treat gram-negative bacteria-induced multi-drug resistance; however, they cause nephrotoxicity in 60% of patients. In this work, the authors have studied the structure-interaction relationship (SIR) of polymyxins with hPepT2 using computational and experimental methods. Moreover, it is observed that the electrostatic interactions coordinate the hPepT2-Polymyxin interactions; hence, an alanine scanning strategy is used to understand the interactions and derive the polymyxin variants.
Computational methods such as molecular modeling, coarse-grained and all-atom MD simulations, and interaction studies are performed, while the results are validated in the mouse model, which is a great strategy to prove the hypothesis.
Strengths:
A clear understanding of the hPepT2-Polymyxin interactions and the role of electrostatic interactions is one of the very important strengths of the paper. In addition, this work proposes a great pipeline for using computational approaches and experimental validation methods to guide the development of newer antibiotics.
Overall, the study proposes novel polymyxin analogues with reduced or no nephrotoxicity, thereby providing a promising foundation for the rational development of safer lipopeptide antibiotics.
Weaknesses:
This work is very well executed and presented; however, addressing the following concerns might improve the presentation of the work:
(1) The introduction is well articulated; however, including a paragraph on the known inhibitors might be helpful in understanding the current status. In addition, it might also help to introduce Dabs, FADDI variants, Gly-sar and MIPS.
(2) The following details of modeling with AlphaFold2 should be included: how the final structure was selected, what the RMSD and structure alignment of the template are, and the final selected structure. A section on modeling with all the parameter details might be useful for reproducing the structure. In addition, specify how the alanine scanning was performed alongside the structure prediction of polymyxins.
(3) In the all-atom MD simulation method, detailing several parameters might help in reproducing the results: simulation time for each system, water model, system composition, protonation state, box type and dimensions, salt ions and concentration, membrane parameters and ligand parameterization methods. Also, the following details on energy minimization might be useful: minimization algorithm, number of steps for minimization and structure restraints in place.
(4) On page 6, line 210, the MIC is used for the first time; although MIC is given in the abbreviation list, the first occurrence should have a complete name. A one-line explanation of MIC in the introduction or wherever suitable might be better but is not mandatory.
(5) Similarly, Gly-sar is first mentioned on page 8, line 301, but its complete name is only mentioned later on page 10, line 368. This can be addressed if a short description is included in the introduction section.
(6) For coarse-grained MD simulation, why were 2 replicates performed? Most studies perform 3 replicates, which are also good in terms of statistics and error bar calculations. In addition, the authors should specify whether an independent minimization is done for each of the two replicates or whether the minimization step is common for both.
(7) For MD simulation results, giving simulation movies in supplementary results might be a better way to show how the trajectories behaved.
(8) The description of visualisation software such as VMD or PyMol is missing. The authors should specify if any visualization tool is used.
(9) For the mouse model study, the authors claim that FADDI-795 has no observable nephrotoxicity; however, the n=3 shows that a very small number of mouse models were used to make the assumption. In addition, the number of mice used in each experiment is not explicitly mentioned in the methods section.
(10) In Table 2, the column 8 header is not visible.