Publications

Peer reviewed articles (33) + Peer reviewed book chapters (2)

Computational Drug Design (Method development and application)

1. Schimunek, J.; Seidl, P.; Elez, K.; et.al. A community effort in SARS-CoV-2 drug discovery. (2024) Mol. Inform. 43:e202300262 [IF*: 3.6]

2. Mukherjee, G.; Braka, A.; Wu, S. Quantifying Functional-Group-like Structural Fragments in Molecules and Its Applications in Drug Design. (2023) J. Chem. Inf. Model. 63, 2073–2083. [IF*: 6.162] [Conceived the project, carried out all the experiments, analyzed the results and wrote the computer program].

3. Holderbach, S.; Adam, L.; Jayaram, B.; Wade, R. C.; Mukherjee, G@. (2020) RASPD+: Fast protein-ligand binding free energy prediction using simplified physicochemical features. Front. Mol. Biosci. 7, 601065. [IF*: 4.188] [Conceived the project, carried out protein and ligand structure preparation, developed the descriptor pipeline and performed enrichment analysis, analyzed the data, guidance and supervised the work].

4. Mukherjee G., Gupta, P. L., Jayaram, B. (2015): Predicting the binding modes and sites of metabolism of xenobiotics. Mol. Biosyst. 11, 1914-1924. [IF**: 3.336] [I and Prof. B Jayaram conceived the project. I carried out all the experiments, analyzed the results and wrote the computer program]

5. Jayaram, B., Dhingra, P., Mishra, A., Kaushik, R., Mukherjee, G., Singh, A., Shekhar S. (2014): Bhageerath-H: A homology ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. BMC Bioinformatics 15, S7. [IF*: 3.242] [I carried out quantum mechanics (PM6) based loop bond angle refinement of protein structure]

6. Arya, P., Srivastava, A., Vasaikar, S. V., Mukherjee, G., Mishra, P., Kundu, B. (2014): Selective Interception of Gelsolin Amyloidogenic Stretch Results in Conformationally Distinct Aggregates with Reduced Toxicity.  ACS Chem. Neurosci. 5, 982–992. [IF*: 4.486] [I carried out virtual screening of 40 bioactive small molecules and suggested two potential hit molecules out of 40 to the experimentalists]

7. Mukherjee G., Jayaram, B. (2013): A rapid identification of hit molecules for target proteins via physico-chemical descriptors. Phys. Chem. Chem. Phys. 15, 9107-9116. [IF*: 3.430] [I and Prof. B Jayaram  conceived the project. I carried out all the experiments, analyzed the results and wrote the computer program]

8. Jayaram, B., Singh, T., Mukherjee, G., Mathur, A., Shekhar, S., Shekhar, V. (2012): Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics 13, S7. [IF*: 3.242] [I collected the data for Zn-containing protein-ligand binding free energies]

9. B. Jayaram, P. Dhingra, G. Mukherjee, and V. Perumal. “Genome to Hits: The emerging assembly line in silico.” New Frontiers in Drug Design, Discovery and Development, Ranbaxy Science Foundation, Ed. Jalali, R.K., 2011, Chapter 3, 17-40. [I carried out virtual screening of small molecules and suggested a few hit molecules for the target protein]

10. Mukherjee G., Patra, N., Barua, P., Jayaram, B. (2011): A Fast Empirical GAFF Compatible Partial Atomic Charge Assignment Scheme for Modeling Interactions of Small Molecules with Biomolecular Targets. J. Comput. Chem. 32, 893-907. [IF*: 2.976] [I and Prof. B Jayaram conceived the project. I carried out all the experiments along with writing the computer program]

(Bio)molecular Modelling

1. Han, S. B.; Teuffel, J.; Mukherjee, G.; Wade, R. C. (2024) Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4. Protein Science (Accepted). [IF*: 4.5] [Along with Sungho Bosco Han, Jonathan Teuffel, I designed and performed the calculations.]

2. Mukesh, S.; Mukherjee, G.; Singh, R.; Steenbuck, N.; Demidova, C.; Joshi, P.; Sangamwar, A.; Wade, R. C. (2023) Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance. Communications Chemistry 6 (1), 201. [IF*: 5.9] [Along with Prof. Wade and I designed the strategy for computational modelling, performed trajectory analysis along with Nathan and Caroline and wrote the computational part of the manuscript along with Prof. Wade].

3. Mukherjee, G.; Nandekar, P. P.; Wade, R. C. (2021) An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase. Communications Biology, 4(55), 1-13. [IF*: 6.268] [Prof. Wade and Prajwal Nandekar and I conceived the project. I carried out the experiments and analyzed the results and wrote the manuscript with input from all authors].

4. Mustafa, G.; Nandekar, P. P.; Mukherjee, G.; Bruce, N. J.; Wade, R. C. (2020): The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics. Sci. Rep. 10, 1-11. [IF*: 3.998] [I performed MD simulations and analyzed the results].

5. Mukherjee, G.; Nandekar, P.; Mustafa, G.; Richter, S.; Wade, R. C. (2019) : A Multi-Resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer. In High Performance Computing in Science and Engineering’18; Springer, 505–514. [Prof. Wade and Prajwal Nandekar and I conceived the project. I carried out the experiments and analyzed the results and wrote the book chapters with input from all authors].

6. Mukherjee G., Pal, A., Levy, Y. (2017): Mechanism of the formation of the RecA–ssDNA nucleoprotein filament structure: a coarse-grained approach. Mol. Biosyst. 13, 2697-2703. [IF**: 3.336] [I and Prof. Y. Levy conceived the project. I carried out the experiments and analyzed the      results]

7. Nishikawa, J. L., Boeszoermenyi, A., Vale-Silva, L. A., Torelli, R., Posteraro, B., Sohn, Y.-J., Ji, F., Gelev, V., Sanglard, D., Sanguinetti, M., Sadreyev, R. I., Mukherjee, G., Jayaram, B., Buhrlage, S. J., Gray, N. S., Wagner, G., Näär, A. M., Arthanari, H. (2016): Inhibiting Fungal Multidrug Resistance by Disrupting an Activator-Mediator Interaction. Nature, 530, 485–489. [IF*: 42.778] [I carried out the docking calculations and analyzed the results]

8. Bansal, S., Srivastava, A., Mukherjee, G., Pandey, R., Verma, A. K., Mishra, P., Kundu, B. (2012): Hyperthermophilic asparaginase mutants with enhanced substrate affinity and antineoplastic activity: structural insights on their mechanism of action. FASEB J. 26, 1161-1171. [IF*: 4.966] [I carried out the molecular dynamics simulation studied and analyzed the results]

Quantum Mechanical applications 

1. Mahawar, P.; Shukla, P.; Joshi, P. J.; Singh, D.; Kumar, H.; Mukherjee, G.; Nagendran, S (2022) Air and Water Stable Germacarbonyl Compounds. Chem. Sci., Accepted Manuscript (DOI: 10.1039/D2SC01869A) [IF*: 9.346] [I analyzed the QM calculations (NBO donor-acceptor interactions, Free energy) along with Pritam Mahawar]

2. Mahawar, P.; Wasson, M. K.; Sharma, M. K.; Jha, C. K.; Mukherjee, G.; Vivekanandan, P.; Nagendran, S. (2020): A Prelude to Biogermylene Chemistry. Angew. Chem. Int. Ed. 59, 1-6. [IF*: 12.959] [I carried out the molecular orbital calculations].

3. Sharma, M. K., Sinhababu, S., Mahawar, P., Mukherjee, G., Pandey, B., Rajaraman, G., Nagendran, S. (2019): Donor–acceptor-stabilized germanium analogues of acid chloride, ester, and acyl pyrrole compounds: synthesis and reactivity. Chem. Sci. 10, 4402-4411 [IF*: 9.346] [I carried out the quantum mechanical calculations and analyzed the results]

4. Sharma M. K.,  Sinhababu, S.,  Yadav, D.,  Mukherjee, G., Rajaraman, G., Nagendran, S. (2018): Pseudohalogenogermylenes versus Halogenogermylenes: Difference in their Complexation Behavior towards Group 6 Metal Carbonyls. Chem. Asian J. 13, 1357–1365. [IF*: 4.056] [I carried out the quantum mechanical calculations and analyzed the results]

5. Sharma, M. K., Sinhababu, S., Mukherjee, G., Rajaraman, G. Nagendran, S. (2017): A cationic aluminium complex: an efficient mononuclear main-group catalyst for the cyanosilylation of carbonyl compounds. Dalton Trans. 46, 7672-7676. [IF*: 4.174] [I carried out the quantum mechanical calculations and analyzed the results]

6. Sinhababu, S., Yadav, D., Karwasara, S., Sharma, M. K., Mukherjee, G., Rajaraman, G., Nagendran, S. (2016): The Preparation of Complexes of Germanone from a Germanium μ-Oxo Dimer. Angew. Chem. Int. Ed. 55, 7742–7746. [IF: 12.959] [I carried out the quantum mechanical calculations and analyzed the results]

7. Siwatch, R. K., Karwasara, S., Sharma, M. K., Mondal, S., Mukherjee, G., Rajaraman, G., Nagendran, S. (2016): Reactivity of LGe–NR2 and LGe(E)–NR2 over LGe–Cl and LGe(E)–Cl toward Me3SiX (L = Aminotroponiminate; NR2 = N(SiMe3)2/NC4H4; E = S/Se; X = Br/CN). Organometallics 35, 429–438. [IF*: 3.804] [I carried out the quantum mechanical calculations and analyzed the results]

8. Rao, G. K., Kumar, A., Saleem, F., Singh, M. P., Kumar, S., Kumar, B., Mukherjee, G., Singh, A. K. (2015): Palladium(II)-1-phenylthio-2-arylchalcogenoethane complexes: palladium phosphide nano-peanut and ribbon formation controlled  by chalcogen and Suzuki coupling activation. Dalton Trans. 44, 6600-6612. [IF*: 4.174] [I carried out the quantum mechanical calculations and analyzed the results]

9. Yadav, D., Siwatch, R. K., Mukherjee, G., Rajaraman, G., Nagendran, S. (2014): Use of Thio and Seleno Germanones as Ligands: Silver(I) Halide Complexes with Ge═E→Ag–I (E = S, Se) Moieties and Chalcogen-Dependent Argentophilic Interaction. Inorg. Chem. 53, 10054–10059. [IF*: 4.825] [I carried out the quantum mechanical calculations and analyzed the results]

10. Siwatch, R. K., Yadav, D., Mukherjee, G., Rajaraman, G., Nagendran, S. (2014): Are Ligand-Stabilized Carboxylic Acid Derivatives with Ge═Te Bonds Isolable? Inorg. Chem. 53, 5073–5079. [IF*: 4.825] [I carried out the quantum mechanical calculations and analyzed the results]

11. Saleem, F., Rao, G. K., Kumar, A., Mukherjee, G., Singh, A. K. (2014): Catalyst Activation with Cp*RhIII/IrIII–1,2,3-Triazole-Based Organochalcogen Ligand Complexes: Transfer Hydrogenation via Loss of Cp* and N-Methylmorpholine N-Oxide Based vs Oppenauer-Type Oxidation. Organometallics 33, 2341–2351. [IF*: 3.804] [I carried out the quantum mechanical calculations and analyzed the results]

12. Siwatch, R. K., Yadav, D., Mukherjee, G., Rajaraman, G., Nagendran, S. (2013): Digermylene Oxide Complexes: Facile Synthesis and Reactivity. Inorg. Chem. 52, 13384–13391. [IF*: 4.825] [I carried out the quantum mechanical calculations and analyzed the results]

13. Saleem, F., Rao, G. K., Kumar, A., Mukherjee, G., Singh, A. K. (2013): Half-Sandwich Ruthenium(II) Complexes of Click Generated 1,2,3-Triazole Based Organosulfur/-selenium Ligands: Structural and Donor Site Dependent Catalytic Oxidation and Transfer Hydrogenation Aspects. Organometallics 32, 3595–3603. [IF*: 3.804] [I carried out the quantum mechanical calculations and analyzed the results]

14. Sinhababu, S., Siwatch, R. K., Mukherjee, G., Rajaraman, G., Nagendran, S. (2012): Aminotroponiminatogermaacid Halides with a Ge(E)X Moiety (E = S, Se; X = F, Cl). Inorg. Chem. 51, 9240–9248. [IF*: 4.825] [I carried out the quantum mechanical calculations and analyzed the results]

15. Singh, P., Mukherjee, G., Singh, A. K. (2012): Unprecedented oxidation of half-sandwiched ruthenium(II) in the excess of ammonium hexafluorophosphate and formation of nanosized Ru–RuS2. J. Organomet. Chem. 715, 33-38. [IF*: 2.304] [I carried out the quantum mechanical calculations and analyzed the results]

16. Prakash, O., Singh, P., Mukherjee, G., Singh, A. K. (2012): Efficient Catalysis of Transfer Hydrogenation of Ketones and Oxidation of Alcohols with Newly Designed Half-Sandwich Rhodium(III) and Iridium(III) Complexes of Half-Pincer Chalcogenated Pyridines. Organometallics 31, 3379–3388. [IF*: 3.804] [I carried out the quantum mechanical calculations and analyzed the results]

Experimental synthesis (M.Sc. Project)

Mukherjee G., Singh, P., Ganguri, C., Sharma, S., Singh, H. B., Goel, N., Singh, U. P., Butcher, R. J. (2012): Selenadiazolopyridine: A Synthon for Supramolecular Assembly and Complexes with Metallophilic Interactions. Inorg. Chem. 51, 8128–8140. [IF*: 4.825] [I and Prof. H. B. Singh conceived the project. I carried out the synthesis of the ligand molecule (Pubchem ID: 129875670) and its metal (Ag1+, Cu2+, Cu1+) complexes, and characterized the ligand and metal complexes by various spectroscopic techniques] 

@Corresponding author

*IF of journals were collected from the journal home pages.

**IF of Molecular Biosystem in 2019 was collected from the following website: https://www.bioxbio.com/journal/MOL-BIOSYST