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Esther Rubavathy SM, Rajapandian V, Prakash M. Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics. J Biomol Struct Dyn 2024:1-12. [PMID: 38456827 DOI: 10.1080/07391102.2024.2325104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/24/2024] [Indexed: 03/09/2024]
Abstract
Overexpression of histone deacetylase (HDAC) enzymes is linked to a wide variety of illnesses, including malignancies and neurological disorders, which makes HDAC inhibitors potentially therapeutic. However, most HDAC inhibitors lack subclass or isoform selectivity, which can be dangerous. Featuring both enhanced selectivity and toxicity profiles, slow-binding HDAC inhibitors offer promising treatment options for a variety of disorders. Diseases like cardiac, neurodegenerative disorders and diabetes are mainly associated with the HDAC1, HDAC2 and HDAC3 enzymes. The AI-based virtual screening tool PyRMD is implemented to identify the potential inhibitors from ∼2 million compounds. Based on the IC50 values, the top 10 compounds were selected for molecular docking. From the docking and ADMET study, the top-ranked three compounds were selected for molecular dynamics (MD) simulations. Further, to get more insights into the binding/unbinding mechanism of the ligand, we have employed the steered molecular dynamics (SMD) simulations. This study assists in developing Amber force field parameters for the HDAC1, HDAC2 and HDAC3 proteins and sheds light on the discovery of a potent drug. Our study suggests that hydroxamic acid derivative (i.e. referred to as Comp-1, CHEMBL600072) is the potential inhibitor for the series of HDAC-related diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S M Esther Rubavathy
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - V Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - M Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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Priyankha S, Rajapandian V, Palanisamy K, Esther Rubavathy SM, Thilagavathi R, Selvam C, Prakash M. Identification of indole-based natural compounds as inhibitors of PARP-1 against triple-negative breast cancer: a computational study. J Biomol Struct Dyn 2024; 42:2667-2680. [PMID: 37154583 DOI: 10.1080/07391102.2023.2208215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive kind of breast cancer known to mankind. It is a heterogeneous disease that is formed due to the missing estrogen, progesterone and human epidermal growth factor 2 receptors. Poly(ADP-ribose) polymerase-1 (PARP-1) protein helps in the development of TNBC by repairing the cancer cells, which proliferate and spread metastatically. To determine the potential PARP-1 inhibitors (PARPi), 0.2 million natural products from Universal Natural Product Database were screened using molecular docking and six hit compounds were selected based on their binding affinity towards PARP-1. The bio-availability and drug-like properties of these natural products were evaluated using ADMET analysis. Molecular dynamics simulations were conducted for these complexes for 200 ns to examine their structural stability and dynamic behaviour and further compared with the complex of talazoparib (TALA), an FDA-approved PARPi. Using MM/PBSA calculations, we conclude that the complexes HIT-3 and HIT-5 (-25.64 and -23.14 kcal/mol, respectively) show stronger binding energies with PARP-1 than TALA with PARP-1 (-10.74 kcal/mol). Strong interactions were observed between the compounds and hotspot residues, Asp770, Ala880, Tyr889, Tyr896, Ala898, Asp899 and Tyr907, of PARP-1 due to the existence of various types of non-covalent interactions between the compounds and PARP-1. This research offers critical information about PARPi, which could potentially be incorporated into the treatment of TNBC. Moreover, these findings were validated by comparing them with an FDA-approved PARPi.
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Affiliation(s)
- Sridhar Priyankha
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Varatharaj Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - S M Esther Rubavathy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education, Coimbatore, India
| | - Chelliah Selvam
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas, USA
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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Karuppasamy P, Senthilkumar S, Ganeshbabu O, Pitchaimuthu S, Sennappan M, Rajapandian V. Sonochemical Synthesis and Characterization of Visible Light Driven CuO@g-C3N4 Nano-Photocatalyst for Eriochrome Black T Dye Degradation in Industrial Dye Effluent. RUSS J INORG CHEM+ 2022. [DOI: 10.1134/s0036023622100631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Karuppasamy P, Thiruppathi D, Ganesan M, Rajendran T, Rajagopal S, Sivasubramanian VK, Rajapandian V. Electrocatalytic Oxidation of L-Cysteine, L-Methionine, and Methionine–Glycine Using [Oxoiron(IV)–Salen] Ion Immobilized Glassy Carbon Electrode. Electrocatalysis (N Y) 2021. [DOI: 10.1007/s12678-021-00652-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Karuppasamy P, Thiruppathi D, Sundar JV, Ganesan M, Rajendran T, Meena SS, Rajagopal S, Sivasubramanian VK, Rajapandian V. Insight into structural aspects and study of reaction kinetics of model [oxo(salen)iron(IV)] complexes with dipeptides. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Palanisamy K, Prakash M, Rajapandian V. Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids. NEW J CHEM 2020. [DOI: 10.1039/d0nj03085f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The hydrated clusters of protonated imidazole (ImH+) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.
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Affiliation(s)
- Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Varatharaj Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science
- Coimbatore-641020
- India
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Azhagiya Singam ER, Rajapandian V, Subramanian V. Molecular dynamics simulation study on the interaction of collagen-like peptides with gelatinase-A (MMP-2). Biopolymers 2016; 101:779-94. [PMID: 24374600 DOI: 10.1002/bip.22457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/21/2013] [Accepted: 12/21/2013] [Indexed: 12/19/2022]
Abstract
Although several models have been proposed for the interaction of collagen with gelatinase-A (matrix metalloproteinases-2 (MMP-2)), the extensive role of each domain of gelatinase A in hydrolyzing the collagens with and without interruptions is still elusive. Molecular docking, molecular dynamics (MD) simulation, normal mode analysis (NMA) and framework rigidity optimized dynamics algorithm (FRODAN) based analysis were carried out to understand the function of various domains of MMP-2 upon interaction with collagen like peptides. The results reveal that the collagen binding domain (CBD) binds to the C-terminal of collagen like peptide with interruption. CBD helps in unwinding the loosely packed interrupted region of triple helical structure to a greater extent. It can be possible to speculate that the role of hemopexin (HPX) domain is to prevent further unwinding of collagen like peptide by binding to the other end of the collagen like peptide. The catalytic (CAT) domain then reorients itself to interact with the part of the unwound region of collagen like peptide for further hydrolysis. In conclusion the CBD of MMP-2 recognizes the collagen and aids in unwinding the collagen like peptide with interruptions, and the HPX domain of MMP-2 binds to the other end of the collagen allowing CAT domain to access the cleavage site. This study provides a comprehensive understanding of the structural basis of collagenolysis by MMP-2.
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Affiliation(s)
- E R Azhagiya Singam
- Chemical Laboratory, Council of Scientific and Industrial Research, Central Leather Research Institute, Adyar, Chennai, 600 020, Tamil Nadu, India
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Karuppasamy P, Thiruppathi D, Vijaya Sundar J, Rajapandian V, Ganesan M, Rajendran T, Rajagopal S, Nagarajan N, Rajendran P, Sivasubramanian VK. Spectral, Computational, Electrochemical and Antibacterial Studies of Iron(III)–Salen Complexes. Arab J Sci Eng 2015. [DOI: 10.1007/s13369-015-1599-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kalva S, Azhagiya Singam ER, Rajapandian V, Saleena LM, Subramanian V. Discovery of potent inhibitor for matrix metalloproteinase-9 by pharmacophore based modeling and dynamics simulation studies. J Mol Graph Model 2014; 49:25-37. [PMID: 24473069 DOI: 10.1016/j.jmgm.2013.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 12/17/2013] [Accepted: 12/20/2013] [Indexed: 12/21/2022]
Abstract
Matrix metalloproteinase-9 (MMP-9) is an attractive target for anticancer therapy. In the present study ligand based pharmacophore modeling was performed to elucidate the structural elements for a diverse class of MMP-9 inhibitors. The pharmacophore model was validated through Güner-Henry (GH) scoring method. The final pharmacophore model consisted of three hydrogen bond acceptors (HBA), and two ring aromatic regions (RA). This model was utilized to screen the natural compound database to seek novel compounds as MMP-9 inhibitors. The identified hits were validated using molecular docking and molecular dynamics simulation studies. Finally, one compound named Hinokiflavone from Juniperus communis had high binding free energy of -26.54kJ/mol compared with the known inhibitors of MMP-9. Cytotoxicity for hinokiflavone was evaluated by MTT assay. Inhibition of MMP-9 in the presence of hinokiflavone was detected by gelatin zymography and gelatinolytic inhibition assay. Results revealed that the natural compounds derived based on the developed pharmacophore model would be useful for further design and development of MMP-9 inhibitors.
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Affiliation(s)
- Sukesh Kalva
- Department of Bioinformatics, SRM University, Kattankulathur, Kancheepuram District 603 203, India
| | - E R Azhagiya Singam
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - Lilly M Saleena
- Department of Bioinformatics, SRM University, Kattankulathur, Kancheepuram District 603 203, India.
| | - V Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India.
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Indumathy R, Weyhermüller T, Rajapandian V, Subramanian V, Nair BU. An unusual oxidation of the imidazolyl ring in a cobalt terpyridyl complex: Crystal structure and photonuclease activity of the transformed cobalt terpyridyl complex. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Manikandamathavan VM, Rajapandian V, Freddy AJ, Weyhermüller T, Subramanian V, Nair BU. Effect of coordinated ligands on antiproliferative activity and DNA cleavage property of three mononuclear Cu(II)-terpyridine complexes. Eur J Med Chem 2012; 57:449-58. [PMID: 22846797 DOI: 10.1016/j.ejmech.2012.06.039] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 06/15/2012] [Accepted: 06/20/2012] [Indexed: 01/18/2023]
Abstract
Three mononuclear copper(II) complexes, [Cu(tpy)Cl(2)] 1, [Cu(tpy)(NO(3))(2)(H(2)O)] 2 and [Cu(Ptpy)Cl(2)]·H(2)O·HCl 3 have been synthesised and characterized by various spectroscopic techniques and single crystal X-ray diffraction. Complexes 1 and 3 have five coordinate geometry in solid state, whereas complex 2 has six coordinate geometry. Mass spectral and EPR evidence suggest that in solution all the three complexes exist predominantly as a four coordinate species. Molecular modelling and DNA cleavage studies indicate that complexes 1 and 2 are DNA minor groove binders, whereas 3 is an intercalator. All the three complexes show nuclease activity in the presence of hydrogen peroxide. The three complexes have been found to be cytotoxic towards A549 lung adenocarcinoma cells.
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Affiliation(s)
- Verasuntharam M Manikandamathavan
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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Rajapandian V, Subramanian V. Calculations on the Structure and Spectral Properties of Cytochrome c551 Using DFT and ONIOM Methods. J Phys Chem A 2011; 115:2866-76. [DOI: 10.1021/jp110983v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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Rajapandian V, Hakkim V, Subramanian V. Molecular Dynamics Studies on Native, Loop-Contracted, and Metal Ion-Substituted Azurins. J Phys Chem B 2010; 114:8474-86. [DOI: 10.1021/jp911301v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Hakkim
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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Rajapandian V, Raman SS, Hakkim V, Parthasarathi R, Subramanian V. Molecular mechanics and molecular dynamics study on azurin using extensible and systematic force field (ESFF). ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Hakkim
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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