1
|
Mookkan M, Kandasamy S, Al-Odayni AB, Abduh NAY, Srinivasan S, Revannasidappa BC, Kumar V, Chinnasamy K, Aravindhan S, Shankar MK. A Structural and In Silico Investigation of Potential CDC7 Kinase Enzyme Inhibitors. ACS OMEGA 2023; 8:47187-47200. [PMID: 38107948 PMCID: PMC10719926 DOI: 10.1021/acsomega.3c07059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
A crucial role in the regulation of DNA replication is played by the highly conserved CDC kinase. The CDC7 kinase could serve as a target for therapeutic intervention in cancer. The primary heterocyclic substance is pyrazole, and its derivatives offer great potential as treatments for cancer cell lines. Here, we synthesized the two pyrazole derivatives: 4-(2-(4-chlorophenyl)hydrazinyl)-5-methyl-2-tosyl-1H-pyrazol-3(2H)-one (PYRA-1) and 4-(2-(2,4-difluorophenyl)hydrazinyl)-5-methyl-2-tosyl-1H-pyrazol-3(2H)-one (PYRA-2). The structural confirmation of both the compounds at the three-dimensional level is characterized using single crystal X-ray diffraction and density functional theory. Furthermore, the in silico chemical biological properties were derived using molecular docking and molecular dynamics (MD) simulations. PYRA-1 and PYRA-2 crystallize in the P-1 (a = 8.184(9), b = 14.251(13), c = 15.601(15), α = 91.57(8), β = 97.48(9), 92.67(9), V = 1801.1(3) 3, and Z = 2) and P21/n (a = 14.8648(8), b = 8.5998(4), c = 15.5586(8), β = 116.47(7), V = 1780.4(19) 3, and Z = 4), space groups, respectively. In both PYRA-1 and PYRA-2 compounds, C-H···O intermolecular connections are common to stabilize the crystal structure. In addition, short intermolecular interactions stabilizes with C-H···π and π-π stacking. Crystal packing analysis was quantified using Hirshfeld surface analysis resulting in C···H, O···H, and H···H contacts in PYRA-1 exhibiting more contribution than in PYRA-2. The conformational stabilities of the molecules are same in the gas and liquid phases (water and DMSO). The docking scores measured for PYRA-1 and PYRA-2 with CDC7 kinase complexes are -5.421 and -5.884 kcal/mol, respectively. The MD simulations show that PYRA-2 is a more potential inhibitor than PYRA-1 against CDC7 kinase.
Collapse
Affiliation(s)
- Mohanbabu Mookkan
- Department
of Physics, Presidency College (Autonomous), University of Madras, Chennai 600 005, India
| | - Saravanan Kandasamy
- Faculty
of Chemistry, University of Warsaw, Ludwika Pasteura 1, Warsaw 02-093, Poland
| | - Abdel-Basit Al-Odayni
- Department
of Restorative Dental Science, College of Dentistry, King Saud University, P.O. Box 60169, Riyadh 11545, Saudi Arabia
| | - Naaser Ahmed Yaseen Abduh
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sugarthi Srinivasan
- Department
of Physics and Nanotechnology, SRM Institute
of Science and Technology, Kattankulathur 603203, India
| | - Bistuvalli Chandrashekara Revannasidappa
- Department
of Pharmaceutical Chemistry, NGSM Institute
of Pharmaceutical Sciences of Nitte - Deemed to be University, Paneer, Deralakatte, Mangalore 575018, Karnataka India
| | - Vasantha Kumar
- Department
of P.G. Chemistry, Sri Dharmasthala Manjunatheshwara
College (Autonomous), Ujire 574240, India
| | | | - Sanmargam Aravindhan
- Department
of Physics, Presidency College (Autonomous), University of Madras, Chennai 600 005, India
| | - Madan Kumar Shankar
- Department
of Chemistry-BMC, University of Uppsala, Husargatan 3, Uppsala 75237, Sweden
| |
Collapse
|
2
|
Structural, Hirshfeld, spectroscopic, quantum chemical and molecular docking studies on 6b′, 7′, 8′, 9′-Tetrahydro-2H,6′H-spiro[acenaphthylene-1,11′-chromeno [3,4-a]pyrrolizine]-2,6′(6a′H,11a′H)-dione. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
3
|
Balasubramanian PK, Balupuri A, Kang HY, Cho SJ. Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors. BMC SYSTEMS BIOLOGY 2017; 11:6. [PMID: 28361711 PMCID: PMC5374705 DOI: 10.1186/s12918-017-0385-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
BACKGROUND Bruton tyrosine kinase (Btk) plays an important role in B-cell development, differentiation, and signaling. It is also found be in involved in male immunodeficiency disease such as X-linked agammaglobulinemia (XLA). Btk is considered as a potential therapeutic target for treating autoimmune diseases and hematological malignancies. RESULTS In this work, a combined molecular modeling study was performed on a series of thieno [3,2-c] pyridine-4-amine derivatives as Btk inhibitors. Receptor-guided COMFA (q 2 = 0.574, NOC = 3, r 2 = 0.924) and COMSIA (q 2 = 0.646, NOC = 6, r 2 = 0.971) models were generated based on the docked conformation of the most active compound 26. All the developed models were tested for robustness using various validation techniques. Furthermore, a 5-ns molecular dynamics (MD) simulation and binding free energy calculations were carried out to determine the binding modes of the inhibitors and to identify crucial interacting residues. The rationality and stability of molecular docking and 3D-QSAR results were validated by MD simulation. The binding free energies calculated by the MM/PBSA method showed the importance of the van der Waals interaction. CONCLUSIONS A good correlation between the MD results, docking studies, and the contour map analysis were observed. The study has identified the key amino acid residues in Btk binding pocket. The results from this study can provide some insights into the development of potent, novel Btk inhibitors.
Collapse
Affiliation(s)
- Pavithra K Balasubramanian
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 61452, Republic of Korea
| | - Anand Balupuri
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 61452, Republic of Korea
| | - Hee-Young Kang
- Department of Nursing, Chosun University, Gwangju, 61452, Republic of Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 61452, Republic of Korea.
- Department of Cellular Molecular Medicine, College of Medicine, Chosun University, Gwangju, 61452, Republic of Korea.
| |
Collapse
|