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Bidault X, Chaudhuri S. How Accurate Can Crystal Structure Predictions Be for High-Energy Molecular Crystals? Molecules 2023; 28:molecules28114471. [PMID: 37298947 DOI: 10.3390/molecules28114471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Molecular crystals have shallow potential energy landscapes, with multiple local minima separated by very small differences in total energy. Predicting molecular packing and molecular conformation in the crystal generally requires ab initio methods of high accuracy, especially when polymorphs are involved. We used dispersion-corrected density functional theory (DFT-D) to assess the capabilities of an evolutionary algorithm (EA) for the crystal structure prediction (CSP) of well-known but challenging high-energy molecular crystals (HMX, RDX, CL-20, and FOX-7). While providing the EA with the experimental conformation of the molecule quickly re-discovers the experimental packing, it is more realistic to start instead from a naïve, flat, or neutral initial conformation, which reflects the limited experimental knowledge we generally have in the computational design of molecular crystals. By doing so, and using fully flexible molecules in fully variable unit cells, we show that the experimental structures can be predicted in fewer than 20 generations. Nonetheless, one must be aware that some molecular crystals have naturally hindered evolutions, requiring as many attempts as there are space groups of interest to predict their structures, and some may require the accuracy of all-electron calculations to discriminate between closely ranked structures. To save resources in this computationally demanding process, we showed that a hybrid xTB/DFT-D approach could be considered in a subsequent study to push the limits of CSP beyond 200+ atoms and for cocrystals.
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Affiliation(s)
- Xavier Bidault
- Department of Civil, Materials and Environmental Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Santanu Chaudhuri
- Department of Civil, Materials and Environmental Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
- Applied Materials Division, Argonne National Laboratory, Lemont, IL 60439, USA
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Shawish I, Barakat A, Aldalbahi A, Malebari AM, Nafie MS, Bekhit AA, Albohy A, Khan A, Ul-Haq Z, Haukka M, de la Torre BG, Albericio F, El-Faham A. Synthesis and Antiproliferative Activity of a New Series of Mono- and Bis(dimethylpyrazolyl)- s-triazine Derivatives Targeting EGFR/PI3K/AKT/mTOR Signaling Cascades. ACS OMEGA 2022; 7:24858-24870. [PMID: 35874229 PMCID: PMC9301957 DOI: 10.1021/acsomega.2c03079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Here, we synthesized a newseries of mono- and bis(dimethylpyrazolyl)-s-triazine derivatives. The synthetic methodology involved the reaction of different mono- and dihydrazinyl-s-triazine derivatives with acetylacetone in the presence of triethylamine to produce the corresponding target products in high yield and purity. The antiproliferative activity of the novel mono- and bis(dimethylpyrazolyl)-s-triazine derivatives was studied against three cancer cell lines, namely, MCF-7, HCT-116, and HepG2. N-(4-Bromophenyl)-4-(3,5-dimethyl-1H-pyrazol-1-yl)-6-morpholino-1,3,5-triazin-2-amine 4f, N-(4-chlorophenyl)-4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl)-1,3,5-triazin-2-amine 5c, and 4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl)-N-(4-methoxyphenyl)-1,3,5-triazin-2-amine 5d showed promising activity against these cancer cells: 4f [(IC50 = 4.53 ± 0.30 μM (MCF-7); 0.50 ± 0.080 μM (HCT-116); and 3.01 ± 0.49 μM (HepG2)]; 5d [(IC50 = 3.66 ± 0.96 μM (HCT-116); and 5.42 ± 0.82 μM (HepG2)]; and 5c [(IC50 = 2.29 ± 0.92 μM (MCF-7)]. Molecular docking studies revealed good binding affinity with the receptor targeting EGFR/PI3K/AKT/mTOR signaling cascades. Compound 4f exhibited potent EGFR inhibitory activity with an IC50 value of 61 nM compared to that of Tamoxifen (IC50 value of 69 nM), with EGFR inhibition of 83 and 84%, respectively, at a concentration of 10 μM. Interestingly, 4f showed remarkable PI3K/AKT/mTOR inhibitory activity with 0.18-, 0.27-, and 0.39-fold decrease in their concentration (reduction in controls from 6.64, 45.39, and 86.39 ng/mL to 1.24, 12.35, and 34.36 ng/mL, respectively). Hence, the synthetic 1,3,5-triazine derivative 4f exhibited promising antiproliferative activity in HCT-116 cells through apoptosis induction by targeting the EGFR and its downstream pathway.
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Affiliation(s)
- Ihab Shawish
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Department
of Math and Sciences, College of Humanities and Sciences, Prince Sultan University, P.O. Box 66833, Riyadh 11586, Saudi Arabia
| | - Assem Barakat
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ali Aldalbahi
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Azizah M. Malebari
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohamed S. Nafie
- Department
of Chemistry, Faculty of Science, Suez Canal
University, Ismailia 41522, Egypt
| | - Adnan A. Bekhit
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
- Pharmacy
Program, Allied Health Department, College of Health and Sport Sciences, University of Bahrain, Zallaq, Kingdom of Bahrain
| | - Amgad Albohy
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt (BUE), El-Sherouk City, Suez Desert Road, Cairo 11837, Egypt
- The Center
for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
| | - Alamgir Khan
- H.E.J. Research
Institute of Chemistry, International Center for Chemical and Biological
Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Zaheer Ul-Haq
- H.E.J. Research
Institute of Chemistry, International Center for Chemical and Biological
Sciences, University of Karachi, Karachi 75270, Pakistan
- Dr. Panjwani
Center for Molecular Medicine and Drug Research, International Center
for Chemical and Biological Sciences, University
of Karachi, Karachi 75270, Pakistan
| | - Matti Haukka
- Department
of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Beatriz G. de la Torre
- KwaZulu-Natal
Research Innovation and Sequencing Platform (KRISP), School of Laboratory
Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Peptide
Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4000, South
Africa
| | - Fernando Albericio
- Peptide
Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4000, South
Africa
- Institute
for Advanced Chemistry of Catalonia (IQAC−CSIC), 08034 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine,
and Department of Organic Chemistry, University
of Barcelona, 08028 Barcelona, Spain
| | - Ayman El-Faham
- Department
of Chemistry, Faculty of Science, Alexandria
University, P.O. Box 426,
Ibrahimia, Alexandria 21321, Egypt
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