Computational attributes of protein kinase-C gamma C2-domain &amp; virtual screening for small molecules: elucidation from meta-dynamics simulations &amp; free-energy calculations

Singh, Harvinder; Raja, Anupam; Shekhar, Nishant; Chauhan, Arushi; Prakash, Ajay; Avti, Pramod K.; Medhi, Bikash

doi:10.1080/07391102.2022.2077447

Cited by 3 publications

(5 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…11,18 Our study focused on three compounds emixustat, sitagliptin, and distigmine bromide identified through computational simulations for their inhibitory potential against PKC-γ. 13 Emixustat emerged as the most potent inhibitor, boasting an impressive IC 50 value of 0.48 nM, followed closely by sitagliptin with an IC 50 value of 0.73 nM. Distigmine bromide, however, exhibited less efficiency.…”

Section: ■ Discussionmentioning

confidence: 99%

“…These might be key contributors to the shortcomings of valproate. Earlier studies have indicated that increased PKC-γ levels in general seizures and pain scenarios, combined with its control over LTP, position it as a promising candidate for addressing drug-resistant epilepsy. , Our study focused on three compounds emixustat, sitagliptin, and distigmine bromide identified through computational simulations for their inhibitory potential against PKC-γ …”

Section: Discussionmentioning

confidence: 99%

“…As per the drug design and development pipeline, each and every hit/lead molecule has to go through wet-lab validation, i.e., in vitro. 13 In our case, we targeted the PKC-γ C2 domain, which might regulate the activity of the kinase domain. So, the primary requisite property of the hits has to be inhibitory against PKCγ's kinase activity.…”

Section: ■ Materials and Methodologiesmentioning

confidence: 99%

See 2 more Smart Citations

Unlocking the Therapeutic Potential: Sitagliptin’s Multifaceted Approach in Drug-Resistant Epilepsy through a Novel Mechanism Inhibiting Protein Kinase C-γ and a Long-Term Potentiation Pathway

Singh,

Raja,

Chauhan

et al. 2024

ACS Pharmacol. Transl. Sci.

Self Cite

View full text Add to dashboard Cite

Drug-resistant epilepsy is a prominent challenge in chronic neurological disorders. Valproate, commonly used to treat epilepsy, can fail due to various side effects and interactions, necessitating the exploration of alternative treatments. Our study primarily investigated sitagliptin’s potential as a therapeutic agent for drug-resistant epilepsy. Employing computational modeling and enzyme assay testing, three lead compounds, emixustat, sitagliptin, and distigmine bromide, were evaluated against the target enzyme protein kinase C-γ. In vivo, experiments on a pentylenetetrazolium-induced lamotrigine-resistant epilepsy model were conducted to test sitagliptin’s antiseizure effects, compared with the standard phenobarbital treatment. Emixustat and sitagliptin showcased strong inhibitory properties, while distigmine bromide was less effective in the enzyme assay. Mechanistic insights revealed sitagliptin’s ability to modulate the seizure grade and first myoclonic jerk latency via oxidative stress markers, like reduced glutathione and glutathione peroxidase emphasizing its antioxidative role in epilepsy. Additionally, it demonstrated anti-inflammatory effects by significantly reducing proinflammatory markers interleukin-1β and interleukin-6. The modulation of key genes of the long-term potentiation pathway, particularly protein kinase C-γ and metabotropic glutamate receptor 5, was evident through mRNA expression levels. Finally, sitagliptin showed potential neuroprotective properties, limiting pentylenetetrazolium-induced neuronal loss in the hippocampal region. Collectively, our findings suggest sitagliptin’s multidimensional therapeutic potential for drug-resistant epilepsy specifically via a long-term potentiation pathway by inhibiting protein kinase C-γ.

show abstract

Section: ■ Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: ■ Materials and Methodologiesmentioning

confidence: 99%

See 1 more Smart Citation

Unlocking the Therapeutic Potential: Sitagliptin’s Multifaceted Approach in Drug-Resistant Epilepsy through a Novel Mechanism Inhibiting Protein Kinase C-γ and a Long-Term Potentiation Pathway

Singh,

Raja,

Chauhan

et al. 2024

ACS Pharmacol. Transl. Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The protein–ligand complex used in a study that was recently published was tested using dipeptidyl peptidase-4 (DPP-4) and its inhibitor sitagliptin. The data set used to simulate this complex is available in the supplementary data on the GitHub repository at . , The protein structure was obtained from the RCSB database with PDB ID 1X70, and the ligand parameter files used were the same as those described above. In brief, water, ligands, and identical chains were removed using CHARMM-GUI.…”

Section: Methodsmentioning

confidence: 99%

“…The data set used to simulate this complex is available in the supplementary data on the GitHub repository at https:// github.com/harry-maan/gmx_qk. 16,17 The protein structure was obtained from the RCSB database with PDB ID 1X70, and the ligand parameter files used were the same as those described above. In brief, water, ligands, and identical chains were removed using CHARMM-GUI.…”

Section: Energy Minimization For the User-defined Nanostepsmentioning

confidence: 99%

Gmx_qk: An Automated Protein/Protein–Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study

Singh

Raja

Prakash

et al. 2023

J. Chem. Inf. Model.

Self Cite

View full text Add to dashboard Cite

Open-source MD simulation tools provide academics and low-income countries with the ability to compete in drug discovery advancements. Gromacs is a well-known and established MD simulation tool, among others. Although command-line tools offer full flexibility to users, they require expertise and familiarity with the UNIX operating system. In this context, we have developed an automated bash workflow that enables users with minimal knowledge of UNIX or command-line tools to run protein/protein–ligand complex simulations bridged to MM/PBSA calculations. The workflow provides information to the user using Zenity widgets and requires minimal intervention, such as energy minimization, simulation duration, and output file naming. It initiates MD simulations within a few seconds (energy minimization, NVT, NPT, and MD) after taking input files and parameters, which takes 20–30 min in a command-line-based protocol. The single workflow also helps users to produce reproducible research results with fewer errors. The workflow is available at the GitHub repository: .

show abstract

Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein–protein interactions

Kaur¹,

Prajapat²,

Singh³

et al. 2023

Sci Rep

View full text Add to dashboard Cite

Protein–protein interactions (PPIs) play a critical role in all biological processes. Menin is tumor suppressor protein, mutated in multiple endocrine neoplasia type 1 syndrome and has been shown to interact with multiple transcription factors including (RPA2) subunit of replication protein A (RPA). RPA2, heterotrimeric protein required for DNA repair, recombination and replication. However, it’s still remains unclear the specific amino acid residues that have been involved in Menin-RPA2 interaction. Thus, accurately predicting the specific amino acid involved in interaction and effects of MEN1 mutations on biological systems is of great interests. The experimental approaches for identifying amino acids in menin-RPA2 interactions are expensive, time-consuming, and challenging. This study leverages computational tools, free energy decomposition and configurational entropy scheme to annotate the menin-RPA2 interaction and effect on menin point mutation, thereby proposing a viable model of menin-RPA2 interaction. The menin–RPA2 interaction pattern was calculated on the basis of different 3D structures of menin and RPA2 complexes, constructed using homology modeling and docking strategy, generating three best-fit models: Model 8 (− 74.89 kJ/mol), Model 28 (− 92.04 kJ/mol) and Model 9 (− 100.4 kJ/mol). The molecular dynamic (MD) was performed for 200 ns and binding free energies and energy decomposition analysis were calculated using Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) in GROMACS. From binding free energy change, model 8 of Menin-RPA2 exhibited most negative binding energy of − 205.624 kJ/mol, followed by model 28 of Menin-RPA2 with − 177.382 kJ/mol. After S606F point mutation in Menin, increase of BFE (ΔGbind) by − 34.09 kJ/mol in Model 8 of mutant Menin-RPA2 occurs. Interestingly, we found a significant reduction of BFE (ΔGbind) and configurational entropy by − 97.54 kJ/mol and − 2618 kJ/mol in mutant model 28 as compared the o wild type. Collectively, this is the first study to highlight the configurational entropy of protein–protein interactions thereby strengthening the prediction of two significant important interaction sites in menin for the binding of RPA2. These predicted sites could be vulnerable for structural alternation in terms of binding free energy and configurational entropy after missense mutation in menin.

show abstract

Computational attributes of protein kinase-C gamma C2-domain & virtual screening for small molecules: elucidation from meta-dynamics simulations & free-energy calculations

Cited by 3 publications

References 41 publications

Unlocking the Therapeutic Potential: Sitagliptin’s Multifaceted Approach in Drug-Resistant Epilepsy through a Novel Mechanism Inhibiting Protein Kinase C-γ and a Long-Term Potentiation Pathway

Unlocking the Therapeutic Potential: Sitagliptin’s Multifaceted Approach in Drug-Resistant Epilepsy through a Novel Mechanism Inhibiting Protein Kinase C-γ and a Long-Term Potentiation Pathway

Gmx_qk: An Automated Protein/Protein–Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study

Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein–protein interactions

Contact Info

Product

Resources

About