1
|
Chagaleti BK, Saravanan V, Vellapandian C, Kathiravan MK. Exploring cyclin-dependent kinase inhibitors: a comprehensive study in search of CDK-6 inhibitors using a pharmacophore modelling and dynamics approach. RSC Adv 2023; 13:33770-33785. [PMID: 38019988 PMCID: PMC10655667 DOI: 10.1039/d3ra05672d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Cancer prevalence and resistance issues in cancer treatment are a significant public health concern globally. Among the existing strategies in cancer therapy, targeting cyclin-dependent kinases (CDKs), especially CDK-6 is found to be one of the most promising targets, as this enzyme plays a pivotal role in cell cycle stages and cell proliferation. Cell proliferation is the characteristic feature of cancer giving rise to solid tumours. Our research focuses on creating novel compounds, specifically, pyrazolopyrimidine fused azetidinones, using a groundbreaking molecular hybridization approach to target CDK-6. Through computational investigations, ligand-based pharmacophore modelling, pharmacokinetic studies (ADMET), molecular docking, and dynamics simulations, we identified 18 promising compounds. The pharmacophore model featured one aromatic hydrophobic centre (F1: Aro/Hyd) and two H-bond acceptors (F2 and F3: Acc). Molecular docking results showed favourable binding energies (-6.5 to -8.0 kcal mol-1) and effective hydrogen bonds and hydrophobic interactions. The designed compounds demonstrated good ADMET profiles. Specifically, B6 and B18 showed low energy conformation (-7.8 kcal and -7.6 kcal), providing insights into target inhibition compared to the standard drug Palbociclib. Extensive molecular dynamics simulations confirmed the stability of these derivatives. Throughout the 100 ns simulation, the ligand-protein complexes maintained structural stability, with acceptable RMSD values. These compounds hold promise as potential leads in cancer therapy.
Collapse
Affiliation(s)
- Bharath Kumar Chagaleti
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur-603203 India
| | - Venkatesan Saravanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur-603203 India
| | - Chitra Vellapandian
- Department of Pharmacology, SRM College of Pharmacy SRMIST, Kattankulathur Chennai Tamil Nadu - 603 203 India
| | - Muthu K Kathiravan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur-603203 India
- Dr A. P. J. Abdul Kalam Research Lab, Department of Pharmaceutical Chemistry, SRM College of Pharmacy SRMIST, Kattankulathur Chennai Tamil Nadu - 603 203 India
| |
Collapse
|
2
|
Kausar N, Murtaza S, Khalid M, Shoukat U, Asad M, Arshad MN, Asiri AM, Braga AA. Experimental and Quantum Chemical Approaches for Hydrazide-based Crystalline Organic Chromophores: Synthesis, SC-XRD, Spectroscopic and Nonlinear Optical Properties. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
3
|
Asati V, Anant A, Patel P, Kaur K, Gupta GD. Pyrazolopyrimidines as anticancer agents: A review on structural and target-based approaches. Eur J Med Chem 2021; 225:113781. [PMID: 34438126 DOI: 10.1016/j.ejmech.2021.113781] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 07/31/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022]
Abstract
Pyrazolopyrimidine scaffold is one of the privileged heterocycles in drug discovery. This scaffold produced numerous biological activities in which anticancer is important one. Previous studies showed its importance in interactions with various receptors such as growth factor receptor, TGFBR2 gene, CDK2/cyclin E and Abl kinase, adenosine receptor, calcium-dependent Protein Kinase, Pim-1 kinase, Potent Janus kinase 2, BTK kinase, P21-activated kinase 1, extracellular signal-regulated kinase 2, histone lysine demethylase and Human Kinesin-5. However, there is a need of numerous studies for the discovery of target based potential compounds. The structure activity relationship studies may help to explore the generation of potential compounds in short time period. Therefore, in the present review we tried to explore the structural aspects of Pyrazolopyrimidine with their structure activity relationship against various targets for the development of potential compounds. The current review is the compilation of significant advances made on Pyrazolopyrimidines reported between 2015 and 2020.
Collapse
Affiliation(s)
- Vivek Asati
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India.
| | - Arjun Anant
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Preeti Patel
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Kamalpreet Kaur
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - G D Gupta
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| |
Collapse
|
4
|
Palafox MA, Chalanchi SM, Isasi J, Premkumar R, Franklin Benial AM, Rastogi VK. Effect of bromine atom on the different tautomeric forms of microhydrated 5-bromouracil, in the DNA:RNA microhelix and in the interaction with human proteins. J Biomol Struct Dyn 2020; 38:5443-5463. [DOI: 10.1080/07391102.2019.1704878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Fisica, Universidad Complutense de Madrid, Madrid, Spain
| | - S. M. Chalanchi
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - J. Isasi
- Facultad de Ciencias Químicas, Departamento de Química Inorgánica, Universidad Complutense de Madrid, Madrid, Spain
| | - R. Premkumar
- PG and Research Department of Physics, N.M.S.S.V.N. College, Madurai, Tamil Nadu, India
| | | | | |
Collapse
|
5
|
Ponikvar-Svet M, Zeiger DN, Liebman JF. Interplay of thermochemistry and Structural Chemistry: the journal (volume 29, 2018, issues 1–2) and the discipline. Struct Chem 2019. [DOI: 10.1007/s11224-019-01344-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
6
|
Alcolea Palafox M. Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs. Biopolymers 2019; 110:e23247. [PMID: 30676643 DOI: 10.1002/bip.23247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/03/2018] [Accepted: 11/07/2018] [Indexed: 02/06/2023]
Abstract
The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in 3 E-envelope C3' -endo, and B-type in 2 E-envelope C2' -endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.
Collapse
Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
7
|
Base-free benzylation of 1,3-dicarbonyl compounds using sulfamic acid supported on silica by linker: a combined experimental and theoretical approach. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2284-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
8
|
Karimzadeh M, Manouchehri N, Saberi D, Niknam K. FT-IR study and solvent-implicit and explicit effect on stepwise tautomerism of Guanylurea: M06-2X as a case of study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 199:1-11. [PMID: 29558700 DOI: 10.1016/j.saa.2018.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/10/2018] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
All 66 conformers of guanylurea were optimized and frequency calculations were performed at M06-2X/6-311++G(d,p) level of theory. Theses conformers were categorized into five tautomers, and the most stable conformer of each tautomer were found. Geometrical parameters indicated that these tautomers have almost planar structure. Complete stepwise tautomerism were studied through both intramolecular proton transfer routs and internal rotations. Results indicated that the proton transfer routs involving four-membered heterocyclic structures were rate-determining steps. Also, intramolecular proton movement having six-membered transition state structures had very low energy barrier comparable to the transition states of internal rotation routs. Differentiation of studied tautomers could easily be done through their FT-IR spectra in the range of 3200 to 3900cm-1 by comparing absorption bands and intensity of peaks. Solvent-implicit effects on the stability of tautomers were also studied through re-optimization and frequency calculation in four solvents. Water, DMSO, acetone and toluene had stabilization effect on all considered tautomers, but the order of stabilization effect was as follows: water>DMSO>acetone>toluene. Finally, solvent-explicit, base-explicit and acid-explicit effect were also studied by taking place of studied tautomer nearside of acid, base or solvent and optimization of them. Frequency calculation for proton movement by contribution of explicit effect showed that formic acid had a very strong effect on proton transfer from tautomer A1 to tautomer D8 by lowering the energy barrier from 42.57 to 0.8kcal/mol. In addition, ammonia-explicit effect was found to lower the barrier from 42.57 to 22.46kcal/mol, but this effect is lower than that of water and methanol-explicit effect.
Collapse
Affiliation(s)
- Morteza Karimzadeh
- Department of Chemistry, Faculty of Sciences, Persian Gulf University, Bushehr 75169, Iran.
| | - Neda Manouchehri
- Department of Chemistry, Faculty of Sciences, Persian Gulf University, Bushehr 75169, Iran
| | - Dariush Saberi
- Fisheries and Aquaculture Department, College of Agriculture and Natural Resources, Persian Gulf University, Bushehr 75169, Iran
| | - Khodabakhsh Niknam
- Department of Chemistry, Faculty of Sciences, Persian Gulf University, Bushehr 75169, Iran.
| |
Collapse
|