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Khairnar S, Sonawane A, Cheke RS, Kharkar PS, Gaikwad V, Patil S, Aware V. Hit discovery of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines as potential anti-glioblastoma therapeutics: Design, synthesis, biological evaluation, and computational screening. Drug Dev Res 2023; 84:561-578. [PMID: 36823756 DOI: 10.1002/ddr.22046] [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: 12/11/2022] [Revised: 01/15/2023] [Accepted: 01/28/2023] [Indexed: 02/25/2023]
Abstract
Glioblastoma multiforme (GBM) is a highly-aggressive, dreadful disease with poor prognosis and disappointing clinical success. There is an unmet medical need of molecularly-targeted therapeutics for GBM treatment. In the present work, a series of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines was designed, synthesized, purified, characterized, and evaluated for cytotoxicity against glioblastoma cell line U87-MG. The design process (virtual library enumeration around the core, physicochemical and molecular property prediction/calculation of the designs, filtering the undesirable ones, and the diversity analyses of the lead-like designs), was carefully curated so as to obtain a set of structurally-diverse, novel molecules (total 20), with a particular focus on the relatively unexplored core structure, 6,7-dihydro-5H-cyclopenta[d]pyrimidine. The preliminary screening was done using MTT assay at 10 and 100 μM concentrations of the title compounds F1 -F20 and positive control cisplatin, which yielded six hits (% inhibition at 10 μM: ~50%)-F2 , F3 , F5 , F7 , F15 , and F20 , which were taken up for IC50 determination. The top hits F2 and F7 (IC50 < 10 μM) were further used for computational studies such as target prediction, followed by their molecular docking in the binding sites of the top-3 predicted targets (epidermal growth factor receptor kinase domain, cyclin-dependent kinase 2 [CDK2]) /cyclin E, and anaplastic lymphoma kinase [ALK]). The docking pose analyses revealed interesting trends. The relatively planar core structure, presence of favorable hinge-binding substructures, basic groups, all added up, and culminated in appreciable cytotoxicity against GBM cell line.
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Affiliation(s)
- Sanjay Khairnar
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, India.,Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Anjali Sonawane
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Rameshwar S Cheke
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Prashant S Kharkar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Vishwas Gaikwad
- Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Sambhaji Patil
- Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Valmik Aware
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, India
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Bamou FZ, Le TM, Tayeb BA, Tahaei SAS, Minorics R, Zupkó I, Szakonyi Z. Antiproliferative Activity of (-)-Isopulegol-based 1,3-Oxazine, 1,3-Thiazine and 2,4-Diaminopyrimidine Derivatives. Chemistry 2022; 11:e202200169. [PMID: 36200514 PMCID: PMC9535514 DOI: 10.1002/open.202200169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/25/2022] [Indexed: 11/08/2022]
Abstract
A series of novel heterocyclic structures, namely 1,3‐oxazines, 1,3‐thiazines and 2,4‐diaminopyrimidines, were designed and synthesised. The bioassay tests demonstrated that, among these analogues, 2,4‐diaminopyridine derivatives showed significant antiproliferative activity against different human cancer cell lines (A2780, SiHa, HeLa, MCF‐7 and MDA‐MB‐231). Pyrimidines substituted with N2‐(p‐trifluoromethyl)aniline, in particular, displayed a potent inhibitory effect on the growth of cancer cells. Structure–activity relationships were also studied from the aspects of stereochemistry on the aminodiol moiety as well as exploring the effects of substituents on the pyrimidine scaffold.
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Affiliation(s)
- Fatima Z. Bamou
- Institute of Pharmaceutical Chemistry andMTA-SZTE Stereochemistry Research GroupHungarian Academy of SciencesUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Tam M. Le
- Institute of Pharmaceutical Chemistry andMTA-SZTE Stereochemistry Research GroupHungarian Academy of SciencesUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Bizhar A. Tayeb
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Seyyed A. S. Tahaei
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Renáta Minorics
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - István Zupkó
- Department of Pharmacodynamics and BiopharmacyUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Zsolt Szakonyi
- Institute of Pharmaceutical Chemistry andMTA-SZTE Stereochemistry Research GroupHungarian Academy of SciencesUniversity of SzegedEötvös u. 66720SzegedHungary
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SNAr Reactions on 2-Amino-4,6-dichloropyrimidine-5-carbaldehyde. MOLBANK 2022. [DOI: 10.3390/m1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We report the experimental results of unexpected aromatic nucleophilic substitution reaction products on 2-amino-4,6-dichloropyrimidine-5-carbaldehyde. The isolated compounds are products of amination, solvolysis, and condensation processes under mild and environmentally friendly conditions, due to the influence of structural factors of the starting pyrimidine and a high concentration of alkoxide ions. This method allows the building of pyrimidine-based compound precursors of N-heterocyclic systems.
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Development of Pyrimidine- Cinnamamide Hybrids as Potential Anticancer agents: A Rational Design Approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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El-Shamy NT, Alkaoud AM, Hussein RK, Ibrahim MA, Alhamzani AG, Abou-Krisha MM. DFT, ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6,6'-Diamino-1,1',3,3'-tetramethyl-5,5'-(4-chlorobenzylidene)bis[pyrimidine-2,4(1H,3H)-dione]. Molecules 2022; 27:620. [PMID: 35163880 PMCID: PMC8839838 DOI: 10.3390/molecules27030620] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/05/2022] [Accepted: 01/15/2022] [Indexed: 12/24/2022] Open
Abstract
Heterocyclic compounds, including pyrimidine derivatives, exhibit a broad variety of biological and pharmacological activities. In this paper, a previously synthesized novel pyrimidine molecule is proposed, and its pharmaceutical properties are investigated. Computational techniques such as the density functional theory, ADMET evaluation, and molecular docking were applied to elucidate the chemical nature, drug likeness and antibacterial function of molecule. The viewpoint of quantum chemical computations revealed that the molecule was relatively stable and has a high electrophilic nature. The contour maps of HOMO-LUMO and molecular electrostatic potential were analyzed to illustrate the charge density distributions that could be associated with the biological activity. Natural bond orbital (NBO) analysis revealed details about the interaction between donor and acceptor within the bond. Drug likeness and ADMET analysis showed that the molecule possesses the agents of safety and the effective combination therapy as pharmaceutical drug. The antimicrobial activity was investigated using molecular docking. The investigated molecule demonstrated a high affinity for binding within the active sites of antibacterial and antimalarial proteins. The high affinity of the antibacterial protein was proved by its low binding energy (-7.97 kcal/mol) and a low inhibition constant value (1.43 µM). The formation of four conventional hydrogen bonds in ligand-protein interactions confirmed the high stability of the resulting complexes. When compared to known standard drugs, the studied molecule displayed a remarkable antimalarial activity, as indicated by higher binding affinity (B.E. -5.86 kcal/mol & Ki = 50.23 M). The pre-selected molecule could be presented as a promising drug candidate for the development of novel antimicrobial agents.
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Affiliation(s)
- Nesreen T. El-Shamy
- Physics Department, Faculty of Science, Taibah University, Al-Madina Al Munawarah 44256, Saudi Arabia; or
- Physics Department, Faculty of Women, Ain Shams University, Cairo 11865, Egypt
| | - Ahmed M. Alkaoud
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Rageh K. Hussein
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Moez A. Ibrahim
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Abdulrahman G. Alhamzani
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.G.A.); (M.M.A.-K.)
| | - Mortaga M. Abou-Krisha
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.G.A.); (M.M.A.-K.)
- Department of Chemistry, Faculty of Science, South Valley University, Qena 83523, Egypt
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