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Shrivastava A, Magani SKJ, Lokhande KB, Chintakhindi M, Singh A. Exploring the role of TLK2 mutation in tropical calcific pancreatitis: an in silico and molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-20. [PMID: 38500246 DOI: 10.1080/07391102.2024.2329797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Tropical calcific pancreatitis (TCP) is a juvenile form of non-alcoholic chronic pancreatitis seen exclusively in tropical countries. The disease poses a high risk of complications, including pancreatic diabetes and cancer, leading to significant mortality due to poor diagnosis and ineffective treatments. This study employed whole exome sequencing (WES) of 5 TCP patient samples to identify genetic variants associated with TCP. Advanced computational techniques were used to gain atomic-level insights into disease progression, including microsecond-scale long MD simulations and essential dynamics. In silico virtual screening was performed to identify potential therapeutic compounds targeting the mutant protein using the Asinex and DrugBank compound library. WES analysis predicted several single nucleotide variants (SNVs) associated with TCP, including a novel missense variant (c.T1802A or p.V601E) in the TLK2 gene. Computational analysis revealed that the p.V601E mutation significantly affected the structure of the TLK2 kinase domain and its conformational dynamics, altering the interaction profile between ATP and the binding pocket. These changes could impact TLK2's kinase activity and functions, potentially correlating with TCP progression. Promising lead compounds that selectively bind to the TLK2 mutant protein were identified, offering potential for therapeutic interventions in TCP. These findings hold great potential for future research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Sri Krishna Jayadev Magani
- Cancer Biology Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Kiran Bharat Lokhande
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | | | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
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Thirunavukkarasu MK, Karuppasamy R. Drug repurposing combined with MM/PBSA based validation strategies towards MEK inhibitors screening. J Biomol Struct Dyn 2022; 40:12392-12403. [PMID: 34459701 DOI: 10.1080/07391102.2021.1970629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Emergence of oncogenic mutations in the MAPK pathway gaining more impact in the recent years. Importantly, MEK is a core element of this pathway as it is easy to inhibit and is a gatekeeper of multiple malignancies. Therefore, we performed in-silico strategy to screen repurposed candidate for MEK protein using a library of 11,808 compounds from different clusters in the DrugBank database. Glide docking, Prime-MM/GBSA and QikProp analysis were implemented to retrieve the hits with high precision. The stability of the binding mode and binding affinity of the resultant hit were explored using molecular dynamic simulations and MM/PBSA approach. The results highlight that Nebivolol (DB04861) not only achieved a stable conformation in the MEK binding pocket but also displayed highest binding affinity than the other molecules investigated in our study. Taken together, we hypothesized that Nebivolol is an excellent candidate for the inhibition of MEK in NSCLC patients in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muthu Kumar Thirunavukkarasu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Nivetha R, Bhuvaragavan S, Muthu Kumar T, Ramanathan K, Janarthanan S. Inhibition of multiple SARS-CoV-2 proteins by an antiviral biomolecule, seselin from Aegle marmelos deciphered using molecular docking analysis. J Biomol Struct Dyn 2022; 40:11070-11081. [PMID: 34431451 DOI: 10.1080/07391102.2021.1955009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Our earlier experimental and computational report produced evidence on the antiviral nature of the compound seselin purified from the leaf extracts of Aegle marmelos against Bombyx mori Nuclear Polyhedrosis Virus (BmNPV). In the pandemic situation of COVID-19 caused by the SARS-COV-2 virus, an in silico effort to evaluate the potentiality of the seselin was made to test its efficacy against multiple targets of SARS-COV-2 such as spike protein S2, COVID-19 main protease and free enzyme of the SARS-CoV-2 (2019-nCoV) main protease. The ligand seselin showed the best interaction with receptors, spike protein S2, COVID-19 main protease and free enzyme of the SARS-CoV-2 (2019-nCoV) main protease with a binding energy of -6.3 kcal/mol, -6.9 kcal/mol and -6.7 kcal/mol, respectively. Docking analysis with three different receptors identified that all the computationally predicted lowest energy complexes were stabilized by intermolecular hydrogen bonds and stacking interactions. The amino acid residues involved in interactions were ASP1184, GLU1182, ARG1185 and SER943 for spike protein, SER1003, ALA958 and THR961 for COVID-19 main protease, and for SARS-CoV-2 (2019-nCoV) main protease, it was THR111, GLN110 and THR292. The MD simulation and MM/PBSA analysis showed that the compound seselin could effectively bind with the target receptors. The outcome of pharmacokinetic analysis suggested that the compound had favourable drugability properties. The results suggested that the seselin had inhibitory potential over multiple SARS-COV-2 targets and hold a high potential to work effectively as a novel drug for COVID-19 if evaluated in experimental setups in the foreseeable future. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Thirunavukkarasu Muthu Kumar
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Karuppasamy Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
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Du S, Lu XH, Li WY, Li LP, Ma YC, Zhou L, Wu JW, Ma Y, Wang RL. Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2 E69K. Mol Divers 2021; 25:1873-1887. [PMID: 33392964 DOI: 10.1007/s11030-020-10179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
The E69K mutation is one of the most frequent protein tyrosine phosphatase-2 (SHP2) mutations in leukemia, and it can cause the increase in the protein activity. Recent studies have shown that the E69K mutation was fairly sensitive to the allosteric inhibitor of SHP2 (SHP099). However, the molecular mechanism of the allosteric drug SHP099 inhibiting SHP2E69K remains unclear. Thus, the molecular dynamic simulations and the post-dynamics analyses (RMSF, PCA, DCCM, RIN and the binding free energies) for SHP2WT, SHP2WT-SHP099, SHP2E69K and SHP2E69K-SHP099 were carried out, respectively. Owing to the strong binding affinity of SHP099 to residues Thr219 and Arg220, the flexibility of linker region (residues Val209-Arg231) was reduced. Moreover, the presence of SHP099 kept the autoinhibition state of the SHP2 protein through enhancing the interactions between the linker region and Q loop in PTP domain, such as Thr219/Val490, Thr219/Asn491, Arg220/Ile488 and Leu254/Asn491. In addition, it was found that the residues (Thr219, Arg220, Leu254 and Asn491) might be the key residues responsible for the conformational changes of protein. Overall, this study may provide an important basis for understanding how the SHP099 effectively inhibited the SHP2E69K activity at the molecular level.
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Affiliation(s)
- Shan Du
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, 050015, Hebei, China
| | - Wei-Ya Li
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Li-Peng Li
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Yang-Chun Ma
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Liang Zhou
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Jing-Wei Wu
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Ying Ma
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory On Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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