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Benghanem S, Mesli F, Fatima Zohra HA, Nacereddine C, Hadjer C, Abdellatif M. Discovery of novel and highly potential inhibitors of glycogen synthase kinase 3-beta (GSK-3β) through structure-based pharmacophore modeling, virtual computational screening, docking and in silico ADMET analysis. J Biomol Struct Dyn 2024; 42:7091-7106. [PMID: 37498130 DOI: 10.1080/07391102.2023.2238062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
The protein Glycogen Synthase Kinase 3-Beta (GSK-3β), is a promising therapeutic target for treating various diseases such as neurodegenerative disorders, diabetes, inflammation and cancer. This study aims to investigate the potential of compounds targeting inflammation or carbohydrate metabolism to selectively inhibit GSK3β by binding to its ATP site. To achieve this goal, we filtered a database of 49367 molecules involved in carbohydrate metabolism or targeting inflammation using various computational analyses, including pharmacophore modeling, molecular docking, dynamic simulation, prime MM-GBSA calculation, and in silico ADME studies. We generated a pharmacophore model (hypo S: AADDHRR) using two different crystallographic complexes of GSK3β and evaluated the model's performance in identifying hits using various parameters, including EF, GH, ROC, AUC and BEDROC. Subsequently, we performed various dockings (HTVS, SP, XP and IFD) for the retrieved hits and found that, 5 out of the top 10 ranked compounds had the scaffold of pyrazolidine 3,5-dione, which has never been reported to inhibit kinases. We also conducted ADMET studies to and concluded that compound N6 exhibited the best pharmacokinetic profile passing the blood-brain barrier, possessing high lipophilicity and a high coefficient of skin permeability in the intestines, along with good bioavailability and low toxicity risk assessment. Dynamic simulation were also performed indicating that compounds N6 derived from pyrazolidine 3,5-dione demonstrated better binding potential for GSK3β during the simulation period. Therefore, we propose that compounds derived from pyrazolidine-3,5-dione, which modulate the activity of lysosomal alpha-glucosidase could serve as a novel scaffold for the selective inhibition of GSK-3β.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumia Benghanem
- Faculty of Medicine, Laboratory of Therapeutic Chemistry, Tlemcen University, Tlemcen, Algeria
| | - Fouzia Mesli
- Faculty of Science, Laboratory of Natural and Bio-Actives Substances, Tlemcen University, Tlemcen, Algeria
| | - Hadjadj Aoul Fatima Zohra
- Faculty of Pharmacy, Laboratory of Therapeutic Chemistry, Benyoucef Benkhadda University, Tlemcen, Algeria
| | - Chaida Nacereddine
- Faculty of Medicine, Laboratory of Therapeutic Chemistry, Tlemcen University, Tlemcen, Algeria
| | - Chenaffa Hadjer
- Faculty of Medicine, Laboratory of Therapeutic Chemistry, Tlemcen University, Tlemcen, Algeria
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2
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Tamang JSD, Banerjee S, Baidya SK, Ghosh B, Adhikari N, Jha T. Employing comparative QSAR techniques for the recognition of dibenzofuran and dibenzothiophene derivatives toward MMP-12 inhibition. J Biomol Struct Dyn 2024; 42:7304-7320. [PMID: 37498149 DOI: 10.1080/07391102.2023.2239923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Among various matrix metalloproteinases (MMPs), MMP-12 is one of the potential targets for cancer and other diseases. However, none of the MMP-12 inhibitors has passed the clinical trials to date. Therefore, designing potential MMP-12 inhibitors as new drug molecules can provide effective therapeutic strategies for several diseases. In this study, a series of dibenzofuran and dibenzothiophene derivatives were subjected to different 2D and 3D-QSAR techniques to point out the crucial structural contributions highly influential toward the MMP-12 inhibitory activity. These techniques identified some structural attributes of these compounds that are responsible for influencing their MMP-12 inhibition. The carboxylic group may enhance proper binding with catalytic Zn2+ ion at the MMP-12 active site. Again, the i-propyl sulfonamido carboxylic acid function contributed positively toward MMP-12 inhibition. Moreover, the dibenzofuran moiety conferred stable binding at the S1' pocket for higher MMP-12 inhibition. The steric and hydrophobic groups were found favourable near the furan ring substituted at the dibenzofuran moiety. Besides these ligand-based approaches, molecular docking and molecular dynamic (MD) simulation studies not only elucidated the importance of several aspects of these MMP-12 inhibitors while disclosing the significance of the finding of these QSAR studies and their influences toward MMP-12 inhibition. The MD simulation study also revealed stable and compact binding between such compounds at the MMP-12 active site. Therefore, the findings of these validated ligand-based and structure-based molecular modeling studies can aid the development of selective and potent lead molecules that can be used for the treatment of MMP-12-associated diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jigme Sangay Dorjay Tamang
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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3
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Bultum LE, Kim G, Lee SW, Lee D. Data Mining and in Silico Analysis of Ethiopian Traditional Medicine: Unveiling the Therapeutic Potential of Rumex abyssinicus Jacq. Cell Biochem Biophys 2024:10.1007/s12013-024-01478-4. [PMID: 39154130 DOI: 10.1007/s12013-024-01478-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2024] [Indexed: 08/19/2024]
Abstract
Multicomponent traditional medicine prescriptions are widely used in Ethiopia for disease treatment. However, inconsistencies across practitioners, cultures, and locations have hindered the development of reliable therapeutic medicines. Systematic analysis of traditional medicine data is crucial for identifying consistent and reliable medicinal materials. In this study, we compiled and analyzed a dataset of 505 prescriptions, encompassing 567 medicinal materials used for treating 106 diseases. Using association rule mining, we identified significant associations between diseases and medicinal materials. Notably, wound healing-the most frequently treated condition-was strongly associated with Rumex abyssinicus Jacq., showing a high support value. This association led to further in silico and network analysis of R. abyssinicus Jacq. compounds, revealing 756 therapeutic targets enriched in various KEGG pathways and biological processes. The Random-Walk with Restart (RWR) algorithm applied to the CODA PPI network identified these targets as linked to diseases such as cancer, inflammation, and metabolic, immune, respiratory, and neurological disorders. Many hub target genes from the PPI network were also directly associated with wound healing, supporting the traditional use of R. abyssinicus Jacq. for treating wounds. In conclusion, this study uncovers significant associations between diseases and medicinal materials in Ethiopian traditional medicine, emphasizing the therapeutic potential of R. abyssinicus Jacq. These findings provide a foundation for further research, including in vitro and in vivo studies, to explore and validate the efficacy of traditional and natural product-derived medicines.
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Affiliation(s)
- Lemessa Etana Bultum
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.
- Bio-Synergy Research Center, Daejeon, South Korea.
- Institute of Agricultural Life Sciences, Dong-A University, Busan, South Korea.
| | - Gwangmin Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
- Bio-Synergy Research Center, Daejeon, South Korea
| | - Seon-Woo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan, South Korea
| | - Doheon Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.
- Bio-Synergy Research Center, Daejeon, South Korea.
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4
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Samy A, Hassan A, Hegazi NM, Farid M, Elshafei M. Network pharmacology, molecular docking, and dynamics analyses to predict the antiviral activity of ginger constituents against coronavirus infection. Sci Rep 2024; 14:12059. [PMID: 38802394 PMCID: PMC11130167 DOI: 10.1038/s41598-024-60721-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
COVID-19 is a global pandemic that caused a dramatic loss of human life worldwide, leading to accelerated research for antiviral drug discovery. Herbal medicine is one of the most commonly used alternative medicine for the prevention and treatment of many conditions including respiratory system diseases. In this study, a computational pipeline was employed, including network pharmacology, molecular docking simulations, and molecular dynamics simulations, to analyze the common phytochemicals of ginger rhizomes and identify candidate constituents as viral inhibitors. Furthermore, experimental assays were performed to analyze the volatile and non-volatile compounds of ginger and to assess the antiviral activity of ginger oil and hydroalcoholic extract. Network pharmacology analysis showed that ginger compounds target human genes that are involved in related cellular processes to the viral infection. Docking analysis highlighted five pungent compounds and zingiberenol as potential inhibitors for the main protease (Mpro), spike receptor-binding domain (RBD), and human angiotensin-converting enzyme 2 (ACE2). Then, (6)-gingerdiacetate was selected for molecular dynamics (MD) simulations as it exhibited the best binding interactions and free energies over the three target proteins. Trajectories analysis of the three complexes showed that RBD and ACE2 complexes with the ligand preserved similar patterns of root mean square deviation (RMSD) and radius of gyration (Rg) values to their respective native structures. Finally, experimental validation of the ginger hydroalcoholic extract confirmed the existence of (6)-gingerdiacetate and revealed the strong antiviral activity of the hydroalcoholic extract with IC50 of 2.727 μ g / ml . Our study provides insights into the potential antiviral activity of (6)-gingerdiacetate that may enhance the host immune response and block RBD binding to ACE2, thereby, inhibiting SARS-CoV-2 infection.
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Affiliation(s)
- Asmaa Samy
- Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Afnan Hassan
- Biomedical Sciences Program, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Nesrine M Hegazi
- Department of Phytochemistry and Plant Systematics, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, 12622, Egypt
| | - Mai Farid
- Department of Phytochemistry and Plant Systematics, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Cairo, 12622, Egypt
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5
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Nayana P, Manjunatha H, Gollapalli P, Ashok AK, Karal Andrade P, V V. A combined in vitro and molecular dynamics simulation studies unveil the molecular basis of the anticancer potential of piperine targeting AKT1 against prostate cancer. J Biomol Struct Dyn 2024; 42:3616-3629. [PMID: 37272194 DOI: 10.1080/07391102.2023.2220045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023]
Abstract
The present study investigates the activity of the natural compound piperine on prostate cancer cell line (PC-3), followed by exploring its mechanistic inhibition on the RAC-alpha serine/threonine-protein kinase (AKT1) protein. The 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay showed that after 24 hrs of exposure to piperine (15 µmol/ml), cell viability fell to 50% compared to the standard drug flutamide (SDF) (51 µmol/ml) with a lower IC50 concentration. However, the Dual acridine orange/ethidium bromide (AO/EtBr) staining demonstrated that, as compared to the SDF, piperine caused substantial cellular death in PC-3 cells, presumably by triggering DNA fragmentation. In addition, compared to untreated cells, the proportion of the sub-G0/G1 and G2/M stages population increased considerably in piperine-treated cells. The cell cycle's sub-G0/G1 and G2/M phases were also arrested in piperine-treated cells compared to the SDF in cell cycle analysis. Based on our systems pharmacology and molecular docking studies, AKT1 is predicted as a potential target against piperine. The complementary charge between AKT1 and piperine was emphasized in the transient ligand-protein binding interaction in molecular dynamic modeling over 100 ns, and stable hydrogen bond interaction between Lys268 and Ser205 amino acid residues of the active pocket was hypothesized. Overall, the findings from our in vitro and MD simulations provide insights into the mechanism of piperine targeting AKT1 and offer a possible candidate for future prostate cancer therapeutic development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prakash Nayana
- Department of PG studies and research in Biotechnology, Kuvempu University, Shivamogga, Karnataka, India
| | | | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, India
| | - Avinash Karkada Ashok
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India
| | - Preema Karal Andrade
- Department of PG studies and research in Biotechnology, Kuvempu University, Shivamogga, Karnataka, India
| | - Vijayalaksmi V
- Department of PG studies and research in Biotechnology, Kuvempu University, Shivamogga, Karnataka, India
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6
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Aslam M, Rahman J, Iqbal A, Mujtaba S, Ashok AK, Kaouche FC, Hayat MM, Nisa MU, Ashraf M. Antiurease Activity of Antibiotics: In Vitro, In Silico, Structure Activity Relationship, and MD Simulations of Cephalosporins and Fluoroquinolones. ACS OMEGA 2024; 9:14005-14016. [PMID: 38559955 PMCID: PMC10975586 DOI: 10.1021/acsomega.3c09355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Helicobacter pylori infection is widespread in 50% of the world's population and is associated with gastric ulcers and related disorders that ultimately culminate in gastric cancer. Levofloxacin-based, or clarithromycin-based, triple therapy is frequently used to inhibit the bacterial urease enzyme for the eradication of H. pylori. A comprehensive investigation based on the urease inhibitory profiles of antibiotics and their computational implications is lacking in the scientific literature. The present study was aimed specifically to determine the antiurease activities within the realms of cephalosporins and fluoroquinolones by in vitro methods supported with in silico investigations. The results demonstrate the jack bean urease inhibitory activity of cephalosporins, wherein cefadroxil, cefpodoxime, cefotaxime, and cefaclor displayed inhibitions (IC50 21.35 ± 0.64 to 62.86 ± 0.78 μM) compared with the standard thiourea (IC50 21.25 ± 0.15 μM). Among fluoroquinolones, levofloxacin, ofloxacin, and gemifloxacin (IC50 7.24 ± 0.29 to 16.53 ± 0.85 μM) unveiled remarkable inhibitory profiles. Levofloxacin and ofloxacin exhibited competitive inhibition against the said enzyme. Ciprofloxacin and moxifloxacin displayed weak urease inhibitions. During molecular docking studies, Asp362, Gly279, Arg338, Asn168, Asp223, Gln364, and Met366 were involved in hydrogen bonding in fluoroquinolones, and hydrogen bonding was established with Arg338, His248, Asn168 residues, and metal Ni601 and Ni602 of the enzyme. MD simulations and MMPBSA results demonstrated the existence of significant protein-ligand binding. Overall, these results warrant further investigations into the significance of these active molecules in relation to their inhibitory potential against the targeted urease enzyme.
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Affiliation(s)
- Misbah Aslam
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Jameel Rahman
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Ambar Iqbal
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
- Department
of Biochemistry and Molecular Biology, Institute of Biochemistry,
Biotechnology, Bioinformatics (IBBB), B.J. Campus, The Islamia University of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Sara Mujtaba
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
| | - Avinash Karkada Ashok
- Department
of Biotechnology, Siddaganga Institute of
Technology, Tumakuru 572103, Karnataka, India
| | - Farah Chafika Kaouche
- Department
of Chemistry, Faculty of Sciences of Mater, Ibn Khaldoun University, BP 78 zaaoura, 14000 Tiaret, Algeria
| | - Muhammad Munawar Hayat
- P
& SH Department, Punjab Drug Testing
Laboratory, 1-Bird Wood
Road, Lahore 631000, Pakistan
| | - Mouqadus-Un Nisa
- Multan Drug
Testing Laboratory, near Multan Institute
of Kidney Disease, Muzaffargarh
Road, Multan 261000, Pakistan
| | - Muhammad Ashraf
- Institute
of Chemistry, B.J. Campus, The Islamia University
of Bahawalpur, Bahawalpur 36000, Pakistan
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Abdullah S, Iqbal A, Ashok AK, Kaouche FC, Aslam M, Hussain S, Rahman J, Hayat MM, Ashraf M. Anti-enzymatic and DNA docking studies of montelukast: A multifaceted molecular scaffold with in vitro investigations, molecular expression analysis and molecular dynamics simulations. Heliyon 2024; 10:e24470. [PMID: 38298631 PMCID: PMC10828691 DOI: 10.1016/j.heliyon.2024.e24470] [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: 09/27/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Montelukast, an approved leukotriene receptor 1 (Cys-LT 1) antagonist with anti-inflammatory properties is used for the treatment of asthma and allergic rhinitis. In the present studies, montelukast was subjected to in vitro inhibitory assays followed by kinetic and in silico investigations. Montelukast demonstrated inhibitory activity against yeast α-glucosidase (IC50 44.31 ± 1.21 μM), jack bean urease (JB urease, IC50 8.72 ± 0.23 μM), human placental alkaline phosphatase (hPAP, IC50 17.53 ± 0.19 μM), bovine intestinal alkaline phosphatase (bIAP, IC50 15.18 ± 0.23 μM) and soybean 15-lipoxygenase (15-LOX, IC50 2.41 ± 0.13 μM). Kinetic studies against α-glucosidase and urease enzymes revealed its competitive mode of inhibition. Molecular expression analysis of montelukast in breast cancer cell line MCF-7 down-regulated AP by a factor of 0.27 (5 μM) compared with the 0.26 value for standard inhibitor levamisole (10 μM). Molecular docking estimated a binding affinity ranging -8.82 to -15.65 kcal/mol for the enzymes. Docking against the DNA dodecamer (ID: 1BNA) observed -9.13 kcal/mol via minor groove binding. MD simulations suggested stable binding between montelukast and the target proteins predicting strong inhibitory potential of the ligand. Montelukast features a chloroquinoline, phenyl ring, a cyclopropane group, a carboxylic group and a sulfur atom all of which collectively enhance its inhibitory potential against the said enzymes. These in vitro and computational investigations demonstrate that it is possible and suggested that the interactions of montelukast with more than one targets presented herein may be linked with the side effects presented by this drug and necessitate additional work. The results altogether suggest montelukast as an important structural scaffold possessing multitargeted features and warrant further investigations in repurposing beyond its traditional pharmacological use.
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Affiliation(s)
- Shawana Abdullah
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Ambar Iqbal
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
- Department of Biochemistry and Molecular Biology, Institute of Biochemistry, Biotechnology & Bioinformatics, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Avinash Karkada Ashok
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, 572103, India
| | - Farah Chafika Kaouche
- Department of Chemistry, Faculty of Sciences of Mater, Ibn Khaldoun University, BP 78 Zaaoura, 14000, Tiaret, Algeria
| | - Misbah Aslam
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Safdar Hussain
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Jameel Rahman
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | | | - Muhammad Ashraf
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
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8
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Ren FD, Liu YZ, Ding KW, Chang LL, Cao DL, Liu S. Finite temperature string by K-means clustering sampling with order parameters as collective variables for molecular crystals: application to polymorphic transformation between β-CL-20 and ε-CL-20. Phys Chem Chem Phys 2024; 26:3500-3515. [PMID: 38206084 DOI: 10.1039/d3cp05389j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Polymorphic transformation of molecular crystals is a fundamental phase transition process, and it is important practically in the chemical, material, biopharmaceutical, and energy storage industries. However, understanding of the transformation mechanism at the molecular level is poor due to the extreme simulating challenges in enhanced sampling and formulating order parameters (OPs) as the collective variables that can distinguish polymorphs with quite similar and complicated structures so as to describe the reaction coordinate. In this work, two kinds of OPs for CL-20 were constructed by the bond distances, bond orientations and relative orientations. A K-means clustering algorithm based on the Euclidean distance and sample weight was used to smooth the initial finite temperature string (FTS), and the minimum free energy path connecting β-CL-20 and ε-CL-20 was sketched by the string method in collective variables, and the free energy profile along the path and the nucleation kinetics were obtained by Markovian milestoning with Voronoi tessellations. In comparison with the average-based sampling, the K-means clustering algorithm provided an improved convergence rate of FTS. The simulation of transformation was independent of OP types but was affected greatly by finite-size effects. A surface-mediated local nucleation mechanism was confirmed and the configuration located at the shoulder of potential of mean force, rather than overall maximum, was confirmed to be the critical nucleus formed by the cooperative effect of the intermolecular interactions. This work provides an effective way to explore the polymorphic transformation of caged molecular crystals at the molecular level.
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Affiliation(s)
- Fu-de Ren
- School of Chemical Engineering and Technology, North University of China, Taiyuan 030051, China.
| | - Ying-Zhe Liu
- Xi'an Modern Chemistry Research Institute, Xi'an 710065, China
| | - Ke-Wei Ding
- Xi'an Modern Chemistry Research Institute, Xi'an 710065, China
| | - Ling-Ling Chang
- School of Chemical Engineering and Technology, North University of China, Taiyuan 030051, China.
| | - Duan-Lin Cao
- School of Chemical Engineering and Technology, North University of China, Taiyuan 030051, China.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA.
- Depaertment of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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9
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Raut B, Upadhyaya SR, Bashyal J, Parajuli N. In Silico and In Vitro Analyses to Repurpose Quercetin as a Human Pancreatic α-Amylase Inhibitor. ACS OMEGA 2023; 8:43617-43631. [PMID: 38027372 PMCID: PMC10666247 DOI: 10.1021/acsomega.3c05082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Human pancreatic α-amylase (HPA), situated at the apex of the starch digestion hierarchy, is an attractive therapeutic approach to precisely regulate blood glucose levels, thereby efficiently managing diabetes. Polyphenols offer a natural and multifaceted approach to moderate postprandial sugar spikes, with their slight modulation in carbohydrate digestion and potential secondary benefits, such as antioxidant and anti-inflammatory effects. Taking into consideration the unfavorable side effects of currently available commercial medications, we aimed to study a library of polyphenols attributed to their remarkable antidiabetic properties and screened the most potent HPA inhibitor via a comprehensive in silico study encompassing molecular docking, molecular mechanics with generalized Born and surface area solvation (MM/GBSA) calculation, molecular dynamics (MD) simulation, density functional theory (DFT) study, and pharmacokinetic properties followed by an in vitro assay. Significant hydrogen bonding with the catalytic triad residues of HPA, prominent MM/GBSA binding energy of -27.03 kcal/mol, and the stable nature of the protein-ligand complex with regard to 100 ns MD simulation screened quercetin as the best HPA inhibitor. Additionally, quercetin showed strong reactivity in the substrate-binding pocket of HPA and exhibited favorable pharmacokinetic properties with a considerable inhibitory concentration (IC50) of 57.37 ± 0.9 μg/mL against α-amylase. This study holds prospects for HPA inhibition and suggests quercetin as an approach to therapy for diabetes; however, it is imperative to conduct further research.
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Affiliation(s)
- Bimal
K. Raut
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
| | - Siddha Raj Upadhyaya
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
| | - Jyoti Bashyal
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
| | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44600, Kathmandu, Nepal
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10
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Kumar S, Chaaudhary S, Paul P, Verma YK. Exploring STAT3 stimulatory potential of novel wound healing molecules by virtual screening and molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:8292-8306. [PMID: 36264095 DOI: 10.1080/07391102.2022.2132295] [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: 05/18/2022] [Accepted: 09/28/2022] [Indexed: 10/24/2022]
Abstract
STAT3 signaling is a major intrinsic pathway for cell proliferation owing to its frequent activation in injured tissues. Various STAT3-regulated genes encode cytokines and growth factors, the receptors of which in turn activate the same STAT3 pathways, thereby regulating cell proliferation. In present study, we aimed to analyze several compounds for their wound healing and tissue repair potential by computer-aided virtual screening and Molecular dynamics (MD) simulation. Based on literature studies, a total of 36 drug molecules were selected having critical functions in wound healing and tissue repair. The pharmacological features (ADME and toxicity) of these molecules were predicted to find lead molecules among them. Further, a comparative study was performed to screen binding efficiency of STAT3 with many conventional wound healers by molecular docking. Among all, W6S, Strychnin, Prednisone and N-(6-(4-(3-(4-((4-Methylpiperazin-1-yl) methyl)-3- (trifluoromethyl)phenyl)ureido)phenoxy)pyrimidin-4-yl)cyclopropanecarboxamide showed best docking with STAT3 protein. The calculated binding energy of these molecules with STAT3 was found to be -8.9 Kca/mol for N-(6-(4-(3-(4-((4-Methylpiperazin-1-yl) methyl)-3-(trifluoromethyl) phenyl)ureido)phenoxy)pyrimidin-4-yl)cyclopropanecarboxamide, -8.7 Kcal/mol for W6S, -8.5 Kcal/mol for Strychnine and -8.4 Kcal/mol for Prednisone . The result was reconsidered for MD simulation. The simulation result showed stable binding of the ligand with STAT3 protein for 100 ns. These compounds showed better interaction potential with STAT3 was compared to known tissue repair molecules. Our data paves way for further exploration of these molecules as novel cell proliferators to be tested in various types of wound and tissue injuries.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subodh Kumar
- Stem Cell & Tissue Engineering Research Group, Institute of Nuclear Medicine & Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), Delhi, India
| | - Somya Chaaudhary
- Stem Cell & Tissue Engineering Research Group, Institute of Nuclear Medicine & Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), Delhi, India
| | - Prateek Paul
- Stem Cell & Tissue Engineering Research Group, Institute of Nuclear Medicine & Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), Delhi, India
| | - Yogesh Kumar Verma
- Stem Cell & Tissue Engineering Research Group, Institute of Nuclear Medicine & Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), Delhi, India
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11
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Elhady SS, Alshobaki NM, Elfaky MA, Koshak AE, Alharbi M, Abdelhameed RFA, Darwish KM. Deciphering Molecular Aspects of Potential α-Glucosidase Inhibitors within Aspergillus terreus: A Computational Odyssey of Molecular Docking-Coupled Dynamics Simulations and Pharmacokinetic Profiling. Metabolites 2023; 13:942. [PMID: 37623885 PMCID: PMC10456934 DOI: 10.3390/metabo13080942] [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: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Hyperglycemia, as a hallmark of the metabolic malady diabetes mellitus, has been an overwhelming healthcare burden owing to its high rates of comorbidity and mortality, as well as prospective complications affecting different body organs. Available therapeutic agents, with α-glucosidase inhibitors as one of their cornerstone arsenal, control stages of broad glycemia while showing definitive characteristics related to their low clinical efficiency and off-target complications. This has propelled the academia and industrial section into discovering novel and safer candidates. Herein, we provided a thorough computational exploration of identifying candidates from the marine-derived Aspergillus terreus isolates. Combined structural- and ligand-based approaches using a chemical library of 275 metabolites were adopted for pinpointing promising α-glucosidase inhibitors, as well as providing guiding insights for further lead optimization and development. Structure-based virtual screening through escalating precision molecular docking protocol at the α-glucosidase canonical pocket identified 11 promising top-docked hits, with several being superior to the market drug reference, acarbose. Comprehensive ligand-based investigations of these hits' pharmacokinetics ADME profiles, physiochemical characterizations, and obedience to the gold standard Lipinski's rule of five, as well as toxicity and mutagenicity profiling, proceeded. Under explicit conditions, a molecular dynamics simulation identified the top-stable metabolites: butyrolactone VI (SK-44), aspulvinone E (SK-55), butyrolactone I 4''''-sulfate (SK-72), and terrelumamide B (SK-173). They depicted the highest free binding energies and steadiest thermodynamic behavior. Moreover, great structural insights have been revealed, including the advent of an aromatic scaffold-based interaction for ligand-target complex stability. The significance of introducing balanced hydrophobic/polar moieties, like triazole and other bioisosteres of carboxylic acid, has been highlighted across docking, ADME/Tox profiling, and molecular dynamics studies for maximizing binding interactions while assuring safety and optimal pharmacokinetics for targeting the intestinal-localized α-glucosidase enzyme. Overall, this study provided valuable starting points for developing new α-glucosidase inhibitors based on nature-derived unique scaffolds, as well as guidance for prospective lead optimization and development within future pre-clinical and clinical investigations.
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Affiliation(s)
- Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
| | - Noha M. Alshobaki
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
| | - Mahmoud A. Elfaky
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdulrahman E. Koshak
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
| | - Majed Alharbi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Reda F. A. Abdelhameed
- Department of Pharmacognosy, Faculty of Pharmacy, Galala University, New Galala 43713, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
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12
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Chatterjee P, Banerjee S. Evaluating chemotherapeutic potential of soya-isoflavonoids against high penetrance genes in triple-negative breast cancer. J Biomol Struct Dyn 2023:1-20. [PMID: 37559513 DOI: 10.1080/07391102.2023.2243352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive molecular subtype of breast cancer (BC) associated with a poor prognosis. Owing to the structural similarity with 17-β-estradiol, consumption of soya-isoflavonoids are associated with a reduced rate of hormone-receptive BC incidence, but their role in TNBC is not deciphered in detail. This present study thus aims to investigate the therapeutic binding dynamics of dietary soya-flavonoids with the six high penetrance (HP) receptors in TNBC, viz. BRCA1, BRCA2, PALB2, PTEN, STK11 and TP53. Out of the 14 soya-flavonoids screened based on ADMET descriptors and several other physicochemical, bioavailability, drug and lead-likeness properties, four hits were shortlisted (Daidzein, Genistein, Glycitein and Biochanin A). Docking and molecular dynamics (MD) simulation revealed Genistein as the most potential multi-target inhibitor of the six TNBC HP genes. Additionally, Genistein exhibited excellent binding specificity with PTEN, a potent mediator of the PI3K signaling pathway in TNBC. The binding interaction of PTEN and Genistein was further compared against a standardized FDA-approved chemotherapeutic inhibitor, Olaparib, computed through various MD trajectory analysis, principal component analysis and computation of free energy landscape. This study reveals a comparatively better binding dynamics of PTEN-Genistein than PTEN-Olaparib. With a significant global surge in biomarker-based precision therapeutics in oncology, the results of this exhaustive in-silico study thus encourage the prospect of validating PTEN as a druggable target of Genistein, a unique drug-receptor combination in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prarthana Chatterjee
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Satarupa Banerjee
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, India
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13
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Sen P, Karn R, Kanake DW, Emerson I A, Khan JM, Ahmad A. Picloram binds to the h1 and h4 helices of HSA domain IIIA at drug binding site 2. Int J Biol Macromol 2023; 242:124836. [PMID: 37201887 DOI: 10.1016/j.ijbiomac.2023.124836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Picloram (PC) is a systemic herbicide that controls herbaceous weeds and woody plants. HSA, the most abundant protein in human physiology, binds to all exogenic and endogenic ligands. PC is a stable molecule (t1/2~157-513 days) and a potential threat to human health via the food chain. HSA and PC binding study has been done to decipher the location and thermodynamics of binding. It has been studied with prediction tools like autodocking and MD simulation and then confirmed with fluorescence spectroscopy. HSA fluorescence was quenched by PC at pH 7.4 (N state), pH 3.5 (F state), and pH 7.4 with 4.5 M urea (I state) at temperatures 283 K, 297 K, and 303 K. The location of binding was found to be interdomain between II and III which overlaps with drug binding site 2. The binding was spontaneous, and entropy-driven that show a noticeable increase in binding with the increase in temperature. No secondary structure change at the native state has been observed due to binding. The binding results are important to understand the physiological assimilation of PC. In silico predictions and the results of spectroscopic studies unambiguously indicate the locus and nature of the binding.
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Affiliation(s)
- Priyankar Sen
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
| | - Rohit Karn
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India
| | - Diksha Waghuji Kanake
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India
| | - Arnold Emerson I
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Anis Ahmad
- Department of Radiation Oncology, Miller School of Medicine/Sylvester Cancer Center, University of Miami, Miami, FL, USA.
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14
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Soltan MA, Eldeen MA, Sajer BH, Abdelhameed RFA, Al-Salmi FA, Fayad E, Jafri I, Ahmed HEM, Eid RA, Hassan HM, Al-Shraim M, Negm A, Noreldin AE, Darwish KM. Integration of Chemoinformatics and Multi-Omics Analysis Defines ECT2 as a Potential Target for Cancer Drug Therapy. BIOLOGY 2023; 12:biology12040613. [PMID: 37106813 PMCID: PMC10135641 DOI: 10.3390/biology12040613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/15/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023]
Abstract
Epithelial cell transforming 2 (ECT2) is a potential oncogene and a number of recent studies have correlated it with the progression of several human cancers. Despite this elevated attention for ECT2 in oncology-related reports, there is no collective study to combine and integrate the expression and oncogenic behavior of ECT2 in a panel of human cancers. The current study started with a differential expression analysis of ECT2 in cancerous versus normal tissue. Following that, the study asked for the correlation between ECT2 upregulation and tumor stage, grade, and metastasis, along with its effect on patient survival. Moreover, the methylation and phosphorylation status of ECT2 in tumor versus normal tissue was assessed, in addition to the investigation of the ECT2 effect on the immune cell infiltration in the tumor microenvironment. The current study revealed that ECT2 was upregulated as mRNA and protein levels in a list of human tumors, a feature that allowed for the increased filtration of myeloid-derived suppressor cells (MDSC) and decreased the level of natural killer T (NKT) cells, which ultimately led to a poor prognosis survival. Lastly, we screened for several drugs that could inhibit ECT2 and act as antitumor agents. Collectively, this study nominated ECT2 as a prognostic and immunological biomarker, with reported inhibitors that represent potential antitumor drugs.
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Affiliation(s)
- Mohamed A Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Biology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Bayan H Sajer
- Department of Biological Sciences, College of Science, King Abdulaziz University, Jeddah 80200, Saudi Arabia
| | - Reda F A Abdelhameed
- Department of Pharmacognosy, Faculty of Pharmacy, Galala University, New Galala 43713, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Fawziah A Al-Salmi
- Biology Department, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ibrahim Jafri
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | | | - Refaat A Eid
- Pathology Department, College of Medicine, King Khalid University, P.O. Box 62529, Abha 61421, Saudi Arabia
| | - Hesham M Hassan
- Pathology Department, College of Medicine, King Khalid University, P.O. Box 62529, Abha 61421, Saudi Arabia
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Mubarak Al-Shraim
- Pathology Department, College of Medicine, King Khalid University, P.O. Box 62529, Abha 61421, Saudi Arabia
| | - Amr Negm
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Chemistry Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Ahmed E Noreldin
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22516, Egypt
| | - Khaled M Darwish
- Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
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15
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Datta J, Majumder S, Chaudhuri D, Giri K. In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes. J Biomol Struct Dyn 2023; 41:14977-14988. [PMID: 36858595 DOI: 10.1080/07391102.2023.2184634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
HIV-1, the causative agent of AIDS leads to many deaths worldwide though few options are available as therapeutics. To deal with the continuous mutation in the virus genome, requirement of new drugs is always there. Subtype variation plays a crucial role in case of HIV-1 therapeutics development. In this study, we want to investigate some pre examined molecules that can be effective for HIV-1 VPR. Inhibition of several protein-protein interactions with the small molecules will lead to identify some molecules as therapeutics other than the conventional drugs. We retrieved the sequences of different subtypes from the database and representative sequences were identified. Representative structures were modelled and validated using MD simulations. Forty molecules, showing anti Vpr activity in vitro were identified from literature survey and those were docked with each subtype representative structures. Two molecules a stable Hematoxylin Derivative (SHD) and Damnacanthal (D3), these were shown to be bind more effectively for all the subtypes. The stability of the protein and those two small molecule complexes were identified again with MD simulation followed by the binding energy calculation. Thus, these molecules can be thought as any option other than the conventional drug targeting HIV-1 Vpr.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Joyeeta Datta
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | | | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India
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16
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Moukhliss Y, Koubi Y, Alaqarbeh M, Muzzammel Rehman H, Maghat H, Sbai A, Bouachrine M, Lakhlifi T. Computational and Retrosynthetic Investigation of Isoxazole‐Bearing Chalcones as Antioxidant Activate Compounds. ChemistrySelect 2023. [DOI: 10.1002/slct.202203908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Youness Moukhliss
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Yassine Koubi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | | | | | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
- EST Khenifra Sultan Moulay Slimane University Beni Mellal Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL) Department of Chemistry Faculty of Science University of Moulay Ismail Meknes Morocco
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17
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Molecular and Biological Investigation of Isolated Marine Fungal Metabolites as Anticancer Agents: A Multi-Target Approach. Metabolites 2023; 13:metabo13020162. [PMID: 36837781 PMCID: PMC9964656 DOI: 10.3390/metabo13020162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Cancer is the leading cause of death globally, with an increasing number of cases being annually reported. Nature-derived metabolites have been widely studied for their potential programmed necrosis, cytotoxicity, and anti-proliferation leading to enrichment for the modern medicine, particularly within the last couple of decades. At a more rapid pace, the concept of multi-target agents has evolved from being an innovative approach into a regular drug development procedure for hampering the multi-fashioned pathophysiology and high-resistance nature of cancer cells. With the advent of the Red Sea Penicillium chrysogenum strain S003-isolated indole-based alkaloids, we thoroughly investigated the molecular aspects for three major metabolites: meleagrin (MEL), roquefortine C (ROC), and isoroquefortine C (ISO) against three cancer-associated biological targets Cdc-25A, PTP-1B, and c-Met kinase. The study presented, for the first time, the detailed molecular insights and near-physiological affinity for these marine indole alkaloids against the assign targets through molecular docking-coupled all-atom dynamic simulation analysis. Findings highlighted the superiority of MEL's binding affinity/stability being quite in concordance with the in vitro anticancer activity profile conducted via sulforhodamine B bioassay on different cancerous cell lines reaching down to low micromolar or even nanomolar potencies. The advent of lengthy structural topologies via the metabolites' extended tetracyclic cores and aromatic imidazole arm permitted multi-pocket accommodation addressing the selectivity concerns. Additionally, the presence decorating polar functionalities on the core hydrophobic tetracyclic ring contributed compound's pharmacodynamic preferentiality. Introducing ionizable functionality with more lipophilic characters was highlighted to improve binding affinities which was also in concordance with the conducted drug-likeness/pharmacokinetic profiling for obtaining a balanced pharmacokinetic/dynamic profile. Our study adds to the knowledge regarding drug development and optimization of marine-isolated indole-based alkaloids for future iterative synthesis and pre-clinical investigations as multi-target anticancer agents.
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18
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Bultum LE, Tolossa GB, Kim G, Kwon O, Lee D. In silico activity and ADMET profiling of phytochemicals from Ethiopian indigenous aloes using pharmacophore models. Sci Rep 2022; 12:22221. [PMID: 36564437 PMCID: PMC9789083 DOI: 10.1038/s41598-022-26446-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
In silico profiling is used in identification of active compounds and guide rational use of traditional medicines. Previous studies on Ethiopian indigenous aloes focused on documentation of phytochemical compositions and traditional uses. In this study, ADMET and drug-likeness properties of phytochemicals from Ethiopian indigenous aloes were evaluated, and pharmacophore-based profiling was done using Discovery Studio to predict therapeutic targets. The targets were examined using KEGG pathway, gene ontology and network analysis. Using random-walk with restart algorithm, network propagation was performed in CODA network to find diseases associated with the targets. As a result, 82 human targets were predicted and found to be involved in several molecular functions and biological processes. The targets also were linked to various cancers and diseases of immune system, metabolism, neurological system, musculoskeletal system, digestive system, hematologic, infectious, mouth and dental, and congenital disorder of metabolism. 207 KEGG pathways were enriched with the targets, and the main pathways were metabolism of steroid hormone biosynthesis, lipid and atherosclerosis, chemical carcinogenesis, and pathways in cancer. In conclusion, in silico target fishing and network analysis revealed therapeutic activities of the phytochemicals, demonstrating that Ethiopian indigenous aloes exhibit polypharmacology effects on numerous genes and signaling pathways linked to many diseases.
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Affiliation(s)
- Lemessa Etana Bultum
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea ,grid.255166.30000 0001 2218 7142Department of Applied Bioscience, Dong-A Universtiy, Busan 49315, South Korea
| | - Gemechu Bekele Tolossa
- Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea ,grid.4367.60000 0001 2355 7002Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Gwangmin Kim
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea
| | - Ohhyeon Kwon
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea
| | - Doheon Lee
- grid.37172.300000 0001 2292 0500Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291Daehak-Ro, Daejeon, 34141 South Korea ,Bio-Synergy Research Center, 291Daehak-Ro, Daejeon, 34141 South Korea
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19
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Bio-Guided Isolation of SARS-CoV-2 Main Protease Inhibitors from Medicinal Plants: In Vitro Assay and Molecular Dynamics. PLANTS 2022; 11:plants11151914. [PMID: 35893619 PMCID: PMC9332707 DOI: 10.3390/plants11151914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022]
Abstract
Since the emergence of the pandemic of the coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the discovery of antiviral phytoconstituents from medicinal plants against SARS-CoV-2 has been comprehensively researched. In this study, thirty-three plants belonging to seventeen different families used traditionally in Saudi Arabia were tested in vitro for their ability to inhibit the SARS-CoV-2 main protease (MPRO). Major constituents of the bio-active extracts were isolated and tested for their inhibition potential against this enzyme; in addition, their antiviral activity against the SARS-CoV-2 Egyptian strain was assessed. Further, the thermodynamic stability of the best active compounds was studied through focused comparative insights for the active metabolites regarding ligand–target binding characteristics at the molecular level. Additionally, the obtained computational findings provided useful directions for future drug optimization and development. The results revealed that Psiadia punctulata, Aframomum melegueta, and Nigella sativa extracts showed a high percentage of inhibition of 66.4, 58.7, and 31.5%, against SARS-CoV-2 MPRO, respectively. The major isolated constituents of these plants were identified as gardenins A and B (from P. punctulata), 6-gingerol and 6-paradol (from A. melegueta), and thymoquinone (from N. sativa). These compounds are the first to be tested invitro against SARS-CoV-2 MPRO. Among the isolated compounds, only thymoquinone (THY), gardenin A (GDA), 6-gingerol (GNG), and 6-paradol (PAD) inhibited the SARS-CoV-2 MPRO enzyme with inhibition percentages of 63.21, 73.80, 65.2, and 71.8%, respectively. In vitro assessment of SARS-CoV-2 (hCoV-19/Egypt/NRC-03/2020 (accession number on GSAID: EPI_ISL_430820) revealed a strong-to-low antiviral activity of the isolated compounds. THY showed relatively high cytotoxicity and was anti-SARS-CoV-2, while PAD demonstrated a cytotoxic effect on the tested VERO cells with a selectivity index of CC50/IC50 = 1.33 and CC50/IC50 = 0.6, respectively. Moreover, GNG had moderate activity at non-cytotoxic concentrations in vitro with a selectivity index of CC50/IC50 = 101.3/43.45 = 2.3. Meanwhile, GDA showed weak activity with a selectivity index of CC50/IC50 = 246.5/83.77 = 2.9. The thermodynamic stability of top-active compounds revealed preferential stability and SARS-CoV-2 MPRO binding affinity for PAD through molecular-docking-coupled molecular dynamics simulation. The obtained results suggest the treating potential of these plants and/or their active metabolites for COVID-19. However, further in-vivo and clinical investigations are required to establish the potential preventive and treatment effectiveness of these plants and/or their bio-active compounds in COVID-19.
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20
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Elghazawy NH, Zaafar D, Hassan RR, Mahmoud MY, Bedda L, Bakr AF, Arafa RK. Discovery of New 1,3,4-Oxadiazoles with Dual Activity Targeting the Cholinergic Pathway as Effective Anti-Alzheimer Agents. ACS Chem Neurosci 2022; 13:1187-1205. [PMID: 35377601 DOI: 10.1021/acschemneuro.1c00766] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Finding an effective anti-Alzheimer agent is quite challenging due to its multifactorial nature. As such, multitarget directed ligands (MTDLs) could be a promising paradigm for finding potential therapeutically effective new small-molecule bioactive agents against Alzheimer's disease (AD). We herein present the design, synthesis, and biological evaluation of a new series of compounds based on a 5-pyrid-3-yl-1,3,4-oxadiazole scaffold. Our synthesized compounds displayed excellent in vitro enzyme inhibitory activity at nanomolar (nM) concentrations against two major AD disease-modifying targets, i.e., acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). Among our compounds, 5e was considered the best dual inhibitor of both AChE (IC50 = 50.87 nM) and BuChE (IC50 = 4.77 nM), where these values surpassed those of rivastagmine (the only FDA-approved dual AChE and BuChE inhibitor) in our study. Furthermore, in vivo and ex vivo testing of the hit compound 5e highlighted its significant AD-biotargeting effects including reducing the elevated levels of lipid peroxidation and glutathione (GSH), normalizing levels of 8-OHdG, and, most importantly, decreasing the levels of the well-known AD hallmark β-amyloid protein. Finally, the binding ability of 5e to each of our targets, AChE and BuChE, was confirmed through additional molecular docking and molecular dynamics (MD) simulations that reflected good interactions of 5e to the active site of both targets. Hence, we herein present a series of new 1,3,4-oxadiazoles that are promising leads for the development of dual-acting AChE and BuChE inhibitors for the management of AD.
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Affiliation(s)
- Nehal H. Elghazawy
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo 12578, Egypt
| | - Dalia Zaafar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 12055, Egypt
| | - Reham R. Hassan
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo 12578, Egypt
| | - Mohamed Y. Mahmoud
- Department of Toxicology, Forensic Medicine and Veterinary Regulations, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Loay Bedda
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo 12578, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo 12578, Egypt
| | - Alaa F. Bakr
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Reem K. Arafa
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo 12578, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo 12578, Egypt
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21
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Helal MA, Shouman S, Abdelwaly A, Elmehrath AO, Essawy M, Sayed SM, Saleh AH, El-Badri N. Molecular basis of the potential interaction of SARS-CoV-2 spike protein to CD147 in COVID-19 associated-lymphopenia. J Biomol Struct Dyn 2022; 40:1109-1119. [PMID: 32936048 PMCID: PMC7544927 DOI: 10.1080/07391102.2020.1822208] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/07/2020] [Indexed: 02/08/2023]
Abstract
Lymphopenia is considered one of the most characteristic clinical features of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 infects host cells via the interaction of its spike protein with the human angiotensin-converting enzyme 2 (hACE2) receptor. Since T lymphocytes display a very low expression level of hACE2, a novel receptor might be involved in the entry of SARS-CoV-2 into T cells. The transmembrane glycoprotein CD147 is highly expressed by activated T lymphocytes, and was recently proposed as a probable route for SARS-CoV-2 invasion. To understand the molecular basis of the potential interaction of SARS-CoV-2 to CD147, we have investigated the binding of the viral spike protein to this receptor in-silico. The results showed that this binding is dominated by electrostatic interactions involving residues Arg403, Asn481, and the backbone of Gly502. The overall binding arrangement shows the CD147 C-terminal domain interacting with the spike external subdomain in the grove between the short antiparallel β strands, β1' and β2', and the small helix α1'. This proposed interaction was further confirmed using MD simulation and binding free energy calculation. These data contribute to a better understanding of the mechanism of infection of SARS-CoV-2 to T lymphocytes and could provide valuable insights for the rational design of adjuvant treatment for COVID-19. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed A. Helal
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Shaimaa Shouman
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, Egypt
| | - Ahmad Abdelwaly
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Ahmed O. Elmehrath
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Essawy
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, Egypt
| | - Shireen M. Sayed
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, Egypt
| | - Amr H. Saleh
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine, Zewail City of Science and Technology, Giza, Egypt
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22
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Elmaaty A, Darwish KM, Chrouda A, Boseila AA, Tantawy MA, Elhady SS, Shaik AB, Mustafa M, Al-karmalawy AA. In Silico and In Vitro Studies for Benzimidazole Anthelmintics Repurposing as VEGFR-2 Antagonists: Novel Mebendazole-Loaded Mixed Micelles with Enhanced Dissolution and Anticancer Activity. ACS OMEGA 2022; 7:875-899. [PMID: 35036753 PMCID: PMC8757357 DOI: 10.1021/acsomega.1c05519] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/03/2021] [Indexed: 02/08/2023]
Abstract
Cancer is a leading cause of death worldwide and its incidence is unfortunately anticipated to rise in the next years. On the other hand, vascular endothelial growth factor receptor 2 (VEGFR-2) is highly expressed in tumor-associated endothelial cells, where it affects tumor-promoting angiogenesis. Therefore, VEGFR-2 is considered one of the most promising therapeutic targets for cancer treatment. Furthermore, some FDA-approved benzimidazole anthelmintics have already shown potential anticancer activities. Therefore, repurposing them against VEGFR-2 can provide a rapid and effective alternative that can be implicated safely for cancer treatment. Hence, 13 benzimidazole anthelmintic drugs were subjected to molecular docking against the VEGFR-2 receptor. Among the tested compounds, fenbendazole (FBZ, 1), mebendazole (MBZ, 2), and albendazole (ABZ, 3) were proposed as potential VEGFR-2 antagonists. Furthermore, molecular dynamics simulations were carried out at 200 ns, giving more information on their thermodynamic and dynamic properties. Besides, the anticancer activity of the aforementioned drugs was tested in vitro against three different cancer cell lines, including liver cancer (HUH7), lung cancer (A549), and breast cancer (MCF7) cell lines. The results depicted potential cytotoxic activity especially against both HUH7 and A549 cell lines. Furthermore, to improve the aqueous solubility of MBZ, it was formulated in the form of mixed micelles (MMs) which showed an enhanced drug release with better promising cytotoxicity results compared to the crude MBZ. Finally, an in vitro quantification for VEGFR-2 concentration in treated HUH7 cells has been conducted based on the enzyme-linked immunosorbent assay. The results disclosed that FBZ, MBZ, and ABZ significantly (p < 0.001) reduced the concentration of VEGFR-2, while the lowest inhibition was achieved in MBZ-loaded MMs, which was even much better than the reference drug sorafenib. Collectively, the investigated benzimidazole anthelmintics could be encountered as lead compounds for further structural modifications and thus better anticancer activity, and that was accomplished through studying their structure-activity relationships.
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Affiliation(s)
- Ayman
Abo Elmaaty
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
| | - Khaled M. Darwish
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Amani Chrouda
- Department
of Chemistry, College of Science Al-Zulfi, Majmaah University, Al-Majmaah 11952, Saudi Arabia
- Laboratory
of Interfaces and Advanced Materials, Faculty of Sciences, Monastir University, Monastir 5000, Tunisia
| | - Amira A. Boseila
- Pharmaceutics
Department, Egyptian Drug Authority EDA
(Formerly Known as National Organization for Drug Control and Research
NODCAR) Dokki, Giza 12611, Egypt
| | - Mohamed A. Tantawy
- Hormones
Department, Medical Research Division, National
Research Centre, Dokki, Giza 12622, Egypt
- Stem
Cells Lab, Center of Excellence for Advanced Sciences, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Sameh S. Elhady
- Department
of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Afzal B. Shaik
- Department
of Pharmaceutical Chemistry, Vignan Pharmacy College, Jawaharlal Nehru Technological University, Vadlamudi 522 213, Andhra Pradesh, India
| | - Muhamad Mustafa
- Department
of Medicinal Chemistry, Deraya University, Minia 61111, Egypt
| | - Ahmed A. Al-karmalawy
- Department of Pharmaceutical Medicinal
Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
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23
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Recent advances in drug polymorphs: Aspects of pharmaceutical properties and selective crystallization. Int J Pharm 2022; 611:121320. [PMID: 34843866 DOI: 10.1016/j.ijpharm.2021.121320] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 11/02/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
Drug polymorphism, an established term used to describe the phenomenon that a drug can exist in different crystalline phases, has attracted great interests in pharmaceutical field in consideration of its important role in affecting the pharmaceutical performance of oral formulations. This paper presents an overview of recent advances in the research on polymorphic drug systems including understandings on nucleation, crystal growth, dissolution, mechanical properties, polymorphic transformation, etc. Moreover, new strategies and mechanisms in the control of polymorphic forms are also highlighted in this review. Furthermore, challenges and trends in the development of polymorphic drugs are briefly discussed, aiming at developing effective and efficient pharmaceutical formulations containing the polymorphic drugs.
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24
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Zaki AA, Ashour A, Elhady SS, Darwish KM, Al-Karmalawy AA. Calendulaglycoside A showing potential activity against SARS-CoV-2 main protease: Molecular docking, molecular dynamics, and SAR studies. J Tradit Complement Med 2022; 12:16-34. [PMID: 34026584 PMCID: PMC8126476 DOI: 10.1016/j.jtcme.2021.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND AIM The discovery of drugs capable of inhibiting SARS-CoV-2 is a priority for human beings due to the severity of the global health pandemic caused by COVID-19. To this end, natural products can provide therapeutic alternatives that could be employed as an effective safe treatment for COVID-19. EXPERIMENTAL PROCEDURE Twelve compounds were isolated from the aerial parts of C. officinalis L. and investigated for their inhibitory activities against SARS-CoV-2 Mpro compared to its co-crystallized N3 inhibitor using molecular docking studies. Furthermore, a 100 ns MD simulation was performed for the most active two promising compounds, Calendulaglycoside A (SAP5) and Osteosaponin-I (SAP8). RESULTS AND CONCLUSION At first, molecular docking studies showed interesting binding scores as compared to the N3 inhibitor. Calendulaglycoside A (SAP5) achieved a superior binding than the co-crystallized inhibitor indicating promising affinity and intrinsic activity towards the Mpro of SARS-CoV-2 as well. Moreover, findings illustrated preferential stability for SAP5 within the Mpro pocket over that of N3 beyond the 40 ns MD simulation course. Structural preferentiality for triterpene-Mpro binding highlights the significant role of 17β-glucosyl and carboxylic 3α-galactosyl I moieties through high electrostatic interactions across the MD simulation trajectories. Furthermore, this study clarified a promising SAR responsible for the antiviral activity against the SARS-CoV-2 Mpro and the design of new drug candidates targeting it as well. The above findings could be promising for fast examining the previously isolated triterpenes both pre-clinically and clinically for the treatment of COVID-19.
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Affiliation(s)
- Ahmed A. Zaki
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
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25
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Soltan MA, Eldeen MA, Elbassiouny N, Kamel HL, Abdelraheem KM, El-Gayyed HA, Gouda AM, Sheha MF, Fayad E, Ali OAA, Ghany KAE, El-damasy DA, Darwish KM, Elhady SS, Sileem AE. In Silico Designing of a Multitope Vaccine against Rhizopus microsporus with Potential Activity against Other Mucormycosis Causing Fungi. Cells 2021; 10:3014. [PMID: 34831237 PMCID: PMC8616407 DOI: 10.3390/cells10113014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
During the current era of the COVID-19 pandemic, the dissemination of Mucorales has been reported globally, with elevated rates of infection in India, and because of the high rate of mortality and morbidity, designing an effective vaccine against mucormycosis is a major health priority, especially for immunocompromised patients. In the current study, we studied shared Mucorales proteins, which have been reported as virulence factors, and after analysis of several virulent proteins for their antigenicity and subcellular localization, we selected spore coat (CotH) and serine protease (SP) proteins as the targets of epitope mapping. The current study proposes a vaccine constructed based on top-ranking cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes from filtered proteins. In addition to the selected epitopes, β-defensins adjuvant and PADRE peptide were included in the constructed vaccine to improve the stimulated immune response. Computational tools were used to estimate the physicochemical and immunological features of the proposed vaccine and validate its binding with TLR-2, where the output data of these assessments potentiate the probability of the constructed vaccine to stimulate a specific immune response against mucormycosis. Here, we demonstrate the approach of potential vaccine construction and assessment through computational tools, and to the best of our knowledge, this is the first study of a proposed vaccine against mucormycosis based on the immunoinformatics approach.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Nada Elbassiouny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Hasnaa L. Kamel
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Kareem M. Abdelraheem
- Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (K.M.A.); (H.A.E.-G.)
| | - Hanaa Abd El-Gayyed
- Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (K.M.A.); (H.A.E.-G.)
| | - Ahmed M. Gouda
- Department of Pharmacy Practice, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt;
| | - Mohammed F. Sheha
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Eman Fayad
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ola A. Abu Ali
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | | | - Dalia A. El-damasy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Ashraf E. Sileem
- Department of Chest Diseases, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
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26
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Hamed MIA, Darwish KM, Soltane R, Chrouda A, Mostafa A, Abo Shama NM, Elhady SS, Abulkhair HS, Khodir AE, Elmaaty AA, Al-Karmalawy AA. β-Blockers bearing hydroxyethylamine and hydroxyethylene as potential SARS-CoV-2 Mpro inhibitors: rational based design, in silico, in vitro, and SAR studies for lead optimization. RSC Adv 2021; 11:35536-35558. [PMID: 35493159 PMCID: PMC9043270 DOI: 10.1039/d1ra04820a] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
The global COVID-19 pandemic became more threatening especially after the introduction of the second and third waves with the current large expectations for a fourth one as well. This urged scientists to rapidly develop a new effective therapy to combat SARS-CoV-2. Based on the structures of β-adrenergic blockers having the same hydroxyethylamine and hydroxyethylene moieties present in the HIV-1 protease inhibitors which were found previously to inhibit the replication of SARS-CoV, we suggested that they may decrease the SARS-CoV-2 entry into the host cell through their ability to decrease the activity of RAAS and ACE2 as well. Herein, molecular docking of twenty FDA-approved β-blockers was performed targeting SARS-CoV-2 Mpro. Results showed promising inhibitory activities especially for Carvedilol (CAR) and Nebivolol (NEB) members. Moreover, these two drugs together with Bisoprolol (BIS) as an example from the lower active ones were subjected to molecular dynamics simulations at 100 ns. Great stability across the whole 100 ns timeframe was observed for the top docked ligands, CAR and NEB, over BIS. Conformational analysis of the examined drugs and hydrogen bond investigation with the pocket's crucial residues confirm the great affinity and confinement of CAR and NEB within the Mpro binding site. Moreover, the binding-free energy analysis and residue-wise contribution analysis highlight the nature of ligand–protein interaction and provide guidance for lead development and optimization. Furthermore, the examined three drugs were tested for their in vitro inhibitory activities towards SARS-CoV-2. It is worth mentioning that NEB achieved the most potential anti-SARS-CoV-2 activity with an IC50 value of 0.030 μg ml−1. Besides, CAR was found to have a promising inhibitory activity with an IC50 of 0.350 μg ml−1. Also, the IC50 value of BIS was found to be as low as 15.917 μg ml−1. Finally, the SARS-CoV-2 Mpro assay was performed to evaluate and confirm the inhibitory effects of the tested compounds (BIS, CAR, and NEB) towards the SARS-CoV-2 Mpro enzyme. The obtained results showed very promising SARS-CoV-2 Mpro inhibitory activities of BIS, CAR, and NEB (IC50 = 118.50, 204.60, and 60.20 μg ml−1, respectively) compared to lopinavir (IC50 = 73.68 μg ml−1) as a reference standard. Hydroxyethylamine and hydroxyethylene moieties of β-blockers exert potential SARS-CoV-2 inhibitory effects: rational-based design and in silico, in vitro, and SAR Studies.![]()
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Affiliation(s)
- Mohammed I A Hamed
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, Fayoum University Fayoum 63514 Egypt
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University Ismailia 41522 Egypt
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University Saudi Arabia .,Faculty of Sciences, Tunis El Manar University Tunisia
| | - Amani Chrouda
- Department of Chemistry, College of Science Al-Zulfi, Majmaah University Al-Majmaah 11952 Saudi Arabia .,Laboratory of Interfaces and Advanced Materials, Faculty of Sciences, Monastir University Monastir 5000 Tunisia.,Institute of Analytical Sciences, UMR CNRS-UCBL-ENS 5280 5 Rue la Doua 69100 Villeurbanne CEDEX France
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Dokki Cairo 12622 Egypt
| | - Noura M Abo Shama
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Dokki Cairo 12622 Egypt
| | - Sameh S Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Hamada S Abulkhair
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University Nasr City 11884 Cairo Egypt .,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Ahmed E Khodir
- Department of Pharmacology, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University Port Said 42526 Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
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27
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Marine Brominated Tyrosine Alkaloids as Promising Inhibitors of SARS-CoV-2. Molecules 2021; 26:molecules26206171. [PMID: 34684755 PMCID: PMC8537272 DOI: 10.3390/molecules26206171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
There have been more than 150 million confirmed cases of SARS-CoV-2 since the beginning of the pandemic in 2019. By June 2021, the mortality from such infections approached 3.9 million people. Despite the availability of a number of vaccines which provide protection against this virus, the evolution of new viral variants, inconsistent availability of the vaccine around the world, and vaccine hesitancy, in some countries, makes it unreasonable to rely on mass vaccination alone to combat this pandemic. Consequently, much effort is directed to identifying potential antiviral treatments. Marine brominated tyrosine alkaloids are recognized to have antiviral potential. We test here the antiviral capacity of fourteen marine brominated tyrosine alkaloids against five different target proteins from SARS-CoV-2, including main protease (Mpro) (PDB ID: 6lu7), spike glycoprotein (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), membrane glycoprotein (PDB ID: 6M17), and non-structural protein 10 (nsp10) (PDB ID: 6W4H). These marine alkaloids, particularly the hexabrominated compound, fistularin-3, shows promising docking interactions with predicted binding affinities (S-score = −7.78, −7.65, −6.39, −6.28, −8.84 Kcal/mol) for the main protease (Mpro) (PDB ID: 6lu7), spike glycoprotein (PDB ID: 6VYB), nucleocapsid phosphoprotein (PDB ID: 6VYO), membrane glycoprotein (PDB ID: 6M17), and non-structural protein 10 (nsp10) (PDB ID: 6W4H), respectively, where it forms better interactions with the protein pockets than the native interaction. It also shows promising molecular dynamics, pharmacokinetics, and toxicity profiles. As such, further exploration of the antiviral properties of fistularin-3 against SARS-CoV-2 is merited.
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28
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El-Demerdash A, Al-Karmalawy AA, Abdel-Aziz TM, Elhady SS, Darwish KM, Hassan AHE. Investigating the structure-activity relationship of marine natural polyketides as promising SARS-CoV-2 main protease inhibitors. RSC Adv 2021; 11:31339-31363. [PMID: 35496831 PMCID: PMC9041294 DOI: 10.1039/d1ra05817g] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/16/2021] [Indexed: 02/05/2023] Open
Abstract
Since its first report in December 2019, the novel coronavirus virus, SARS-CoV-2, has caused an unprecedented global health crisis and economic loss imposing a tremendous burden on the worldwide finance, healthcare system, and even daily life. Even with the introduction of different preventive vaccines, there is still a dire need for effective antiviral therapeutics. Nature has been considered as the historical trove of drug discovery and development, particularly in cases of worldwide crises. Herein, a comprehensive in silico investigation of a highly focused chemical library of 34 pederin-structurally related marine compounds, belonging to four polyketides families, was initiated against the SARS-CoV-2 main protease, Mpro, being the key replicating element of the virus and main target in many drugs development programs. Two of the most potent SARS-CoV-2 Mpro co-crystallized inhibitors, O6K and N3, were added to the tested database as reference standards. Through molecular docking simulation, promising compounds including Pederin (1), Dihydro-onnamide A (11), Onnamide C (14), Pseudo-onnamide A (17), and Theopederin G (29) have been identified from different families based on their superior ligand–protein energies and relevant binding profiles with the key Mpro pocket residues. Thermodynamic behaviors of the identified compounds were investigated through 200 ns all-atom molecular dynamics simulation illustrating their significant stability and pocket accommodation. Furthermore, structural activity preferentiality was identified for the pederin-based marine compounds highlighting the importance of the terminal guanidine and cyclic hemiacetal linker, and the length of the sidechain. Our findings highlight the challenges of targeting SARS-CoV-2 Mpro as well as recommending further in vitro and in vivo studies regarding the examined marine products either alone or in combination paving the way for promising lead molecules. Marine natural polyketides showed promising SARS-CoV-2 main protease inhibitory activities.![]()
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Affiliation(s)
- Amr El-Demerdash
- Chemistry Department, Organic Chemistry Division, Faculty of Science, Mansoura University Mansoura 35516 Egypt .,Metabolic Biology & Biological Chemistry Department, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Tarek Mohamed Abdel-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Centre at San Antonio San Antonio Texas 78229-3900 USA.,Zoology Department, Faculty of Science, Minia University El-Minia 61519 Egypt
| | - Sameh S Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University Jeddah Saudi Arabia
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University Ismailia Egypt
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
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29
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Al-Karmalawy AA, Dahab MA, Metwaly AM, Elhady SS, Elkaeed EB, Eissa IH, Darwish KM. Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of ACEIs Against SARS-CoV-2 Targeting the hACE2 Receptor. Front Chem 2021; 9:661230. [PMID: 34017819 PMCID: PMC8129187 DOI: 10.3389/fchem.2021.661230] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/24/2021] [Indexed: 12/28/2022] Open
Abstract
The rapid and global spread of a new human coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has produced an immediate urgency to discover promising targets for the treatment of COVID-19. Here, we consider drug repurposing as an attractive approach that can facilitate the drug discovery process by repurposing existing pharmaceuticals to treat illnesses other than their primary indications. We review current information concerning the global health issue of COVID-19 including promising approved drugs, e.g., human angiotensin-converting enzyme inhibitors (hACEIs). Besides, we describe computational approaches to be used in drug repurposing and highlight examples of in-silico studies of drug development efforts against SARS-CoV-2. Alacepril and lisinopril were found to interact with human angiotensin-converting enzyme 2 (hACE2), the host entranceway for SARS-CoV-2 spike protein, through exhibiting the most acceptable rmsd_refine values and the best binding affinity through forming a strong hydrogen bond with Asn90, which is assumed to be essential for the activity, as well as significant extra interactions with other receptor-binding residues. Furthermore, molecular dynamics (MD) simulations followed by calculation of the binding free energy were also carried out for the most promising two ligand-pocket complexes from docking studies (alacepril and lisinopril) to clarify some information on their thermodynamic and dynamic properties and confirm the docking results as well. These results we obtained probably provided an excellent lead candidate for the development of therapeutic drugs against COVID-19. Eventually, animal experiments and accurate clinical trials are needed to confirm the potential preventive and treatment effect of these compounds.
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Affiliation(s)
- Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, Damietta, Egypt
| | - Mohammed A. Dahab
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ahmed M. Metwaly
- Pharmacognosy Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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30
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Elhady SS, Abdelhameed RFA, Malatani RT, Alahdal AM, Bogari HA, Almalki AJ, Mohammad KA, Ahmed SA, Khedr AIM, Darwish KM. Molecular Docking and Dynamics Simulation Study of Hyrtios erectus Isolated Scalarane Sesterterpenes as Potential SARS-CoV-2 Dual Target Inhibitors. BIOLOGY 2021; 10:389. [PMID: 34062724 PMCID: PMC8147222 DOI: 10.3390/biology10050389] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Presently, the world is under the toll of pandemic coronavirus disease-2019 (COVID-19) outbreak caused by SARS-CoV-2. Lack of effective and safe therapeutics has stressed the scientific community for developing novel therapeutics capable of alleviating and stopping this pandemic. Within the presented study, molecular docking, ADME properties and all-atom molecular dynamic (MD) simulation, along with two standard antiviral agents (lopinavir and benzopurpurin-4B), were applied to investigate 15 scalaranes sesterterpenes natural compounds, purified from the Red Sea marine sponge Hyrtios erectus, as potential COVID-19 dual-target inhibitors. Following multi-step docking within COVID-19 main protease and Nsp15 endoribonuclease cavities, nine promising drug-like compounds exhibited higher docking scores as well as better interactions with the target's crucial residues than those of reference ligands. Compounds 2, 6, 11, and 15, were predicted to simultaneously subdue the activity of the two COVID-19 targets. Dynamics behavior of the best-docked molecules, compounds 15 and 6, within COVID-19 target pockets showed substantial stability of ligand-protein complexes as presented via several MD simulation parameters. Furthermore, calculated free-binding energies from MD simulation illustrated significant ligand's binding affinity towards respective target pockets. All provided findings supported the utility of scalarane-based sesterterpenes, particularly compounds 15 and 6, as promising lead candidates guiding the development of effective therapeutics against SARS-CoV-2.
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Affiliation(s)
- Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Reda F. A. Abdelhameed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (S.A.A.)
| | - Rania T. Malatani
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.T.M.); (A.M.A.); (H.A.B.)
| | - Abdulrahman M. Alahdal
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.T.M.); (A.M.A.); (H.A.B.)
| | - Hanin A. Bogari
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.T.M.); (A.M.A.); (H.A.B.)
| | - Ahmad J. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.J.A.); (K.A.M.)
| | - Khadijah A. Mohammad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.J.A.); (K.A.M.)
| | - Safwat A. Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (S.A.A.)
| | - Amgad I. M. Khedr
- Department of Pharmacognosy, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
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31
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Elmaaty AA, Darwish KM, Khattab M, Elhady SS, Salah M, Hamed MIA, Al-Karmalawy AA, Saleh MM. In a search for potential drug candidates for combating COVID-19: computational study revealed salvianolic acid B as a potential therapeutic targeting 3CLpro and spike proteins. J Biomol Struct Dyn 2021; 40:8866-8893. [PMID: 33928870 DOI: 10.1080/07391102.2021.1918256] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The global prevalence of COVID-19 disease and the overwhelming increase in death toll urge scientists to discover new effective drugs. Although the drug discovery process is a challenging and time-consuming, fortunately, the plant kingdom was found to have many active therapeutics possessing broad-spectrum antiviral activity including those candidates active against severe acute respiratory syndrome coronaviruses (SARS-CoV). Herein, nine traditional Chinese medicinal plant constituents from different origins (Glycyrrhizin 1, Lycorine 2, Puerarin 3, Daidzein 4, Daidzin 5, Salvianolic acid B 6, Dihydrotanshinone I 7, Tanshinone I 8, Tanshinone IIa 9) previously reported to exhibit antiviral activity against SARS-CoV were virtually screened in silico (molecular docking) as potential inhibitors of SARS-CoV-2 target proteins. The tested medicinal plant compounds were in silico screened for their activity against two key SARS-CoV-2 target proteins; 3CLpro, and Spike binding-domain proteins. Among the tested medicinal plant compounds, Salvianolic acid B 6 (Sal-B) showed promising binding affinities against the two specified SARS-CoV-2 target proteins compared to the reference standards used. Hence molecular dynamics simulations followed by calculating the free-binding energy were carried out for Sal-B providing information on its affinity, stability, and thermodynamic behavior within the two SARS-CoV-2 target proteins as well as key ligand-protein binding aspects. Besides, the quantum mechanical calculations showed that Sal-B can adopt different conformations due to the existence of various rotatable bonds. Therefore, the enhanced antiviral activity of Sal-B among other studied compounds can be also attributed to the structural flexibility of Sal-B. Our study gives an explanation of the structure activity relationship required for targeting SARS-CoV-2 3CLpro and Spike proteins and also facilitates the future design and synthesis of new potential drugs exhibiting better affinity and specificity. Besides, an ADME study was carried out on screened compounds and reference controls revealing their pharmacokinetics properties.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Muhammad Khattab
- Department of Chemistry of Natural and Microbial Products, Division of Pharmaceutical and Drug Industries, National Research Centre, Cairo, Egypt
| | - Sameh S Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Salah
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Mohammed I A Hamed
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, Fayoum University, Fayoum, Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
| | - Moustafa M Saleh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
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32
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Hassan A, Arafa RK. On the search for COVID-19 therapeutics: identification of potential SARS-CoV-2 main protease inhibitors by virtual screening, pharmacophore modeling and molecular dynamics. J Biomol Struct Dyn 2021; 40:7815-7828. [PMID: 33749545 DOI: 10.1080/07391102.2021.1902399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
COVID-19 also known as SARS-CoV-2 outbreak in late 2019 and its worldwide pandemic spread has taken the world by surprise. The minute-to-minute increasing coronavirus cases (>85 M) and progressive deaths (≈1.8 M) calls for finding a cure to this devastating pandemic. While there have been many attempts to find biologically active molecules targeting SARS-CoV-2 for treatment of this viral infection, none has found a way to the clinic yet. In this study, a 3-feature structure-based pharmacophore model was designed for SARS-CoV-2 main protease (MPro) that plays a vital role in the viral cellular penetration. High throughput virtual screening of the lead-like ZINC library was then performed to find a potent inhibitor employing the predesigned pharmacophore. In-silico pharmacokinetics/toxicity prediction study was subsequently applied towards the best hits. Finally, a 50 ns molecular dynamics simulation was carried out for the best hit and compared to the co-crystallized ligand where the hit compound displayed high binding and comparable interactions. The results identified new hits for SARS-CoV-2 MPro inhibition showing good docking score, pharmacokinetics and toxicity profile, drug-likeness, high binding energy in addition to a promising synthetic accessibility. Identifying new small compounds as potential leads for inhibiting SARS-CoV-2 is a very important step towards designing a synthesizing of promising drug candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Afnan Hassan
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Giza, Egypt.,Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Reem K Arafa
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Giza, Egypt.,Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
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33
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ZnO nanoparticles: An efficient catalyst for transesterification reaction of α-keto carboxylic esters. Catal Today 2020. [DOI: 10.1016/j.cattod.2019.08.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Hamedani NF, Ghazvini M, Sheikholeslami‐Farahani F, Bagherian‐Jamnani MT. ZnO nanorods as efficient catalyst for the green synthesis of thiophene derivatives: Investigation of antioxidant and antimicrobial activity. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Naghmeh Faal Hamedani
- Department of Chemistry, Faculty of Valiasr, Tehran BranchTechnical and Vocational University (TVU) Tehran Iran
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Dubbeldam D, Walton KS, Vlugt TJH, Calero S. Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900135] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- David Dubbeldam
- Van 't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904 1098XH Amsterdam The Netherlands
| | - Krista S. Walton
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Dr. NW Atlanta GA 30332‐0100 USA
| | - Thijs J. H. Vlugt
- Delft University of TechnologyProcess & Energy DepartmentLeeghwaterstraat 39 2628CB Delft The Netherlands
| | - Sofia Calero
- Department of PhysicalChemical and Natural SystemsUniversity Pablo de OlavideSevilla 41013 Spain
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36
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Neu J, Nemes CT, Regan KP, Williams MRC, Schmuttenmaer CA. Exploring the solid state phase transition in dl-norvaline with terahertz spectroscopy. Phys Chem Chem Phys 2018; 20:276-283. [DOI: 10.1039/c7cp05479c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Experimental and theoretical demonstration of the power of terahertz spectroscopy to provide novel insights into solid-state phase-transformations in organic materials.
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Affiliation(s)
- Jens Neu
- Department of Chemistry
- Yale University
- New Haven
- USA
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37
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Anwar J, Zahn D. Polymorphic phase transitions: Macroscopic theory and molecular simulation. Adv Drug Deliv Rev 2017; 117:47-70. [PMID: 28939378 DOI: 10.1016/j.addr.2017.09.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/27/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation. To address these issues and to advance technology, there is an urgent need for significant insights that can only come from a detailed molecular level understanding of the involved processes. Whilst experimental approaches at best yield time- and space-averaged structural information, molecular simulation offers unprecedented, time-resolved molecular-level resolution of the processes taking place. This review aims to provide a comprehensive and critical account of state-of-the-art methods for modelling polymorph stability and transitions between solid phases. This is flanked by revisiting the associated macroscopic theoretical framework for phase transitions, including their classification, proposed molecular mechanisms, and kinetics. The simulation methods are presented in tutorial form, focusing on their application to phase transition phenomena. We describe molecular simulation studies for crystal structure prediction and polymorph screening, phase coexistence and phase diagrams, simulations of crystal-crystal transitions of various types (displacive/martensitic, reconstructive and diffusive), effects of defects, and phase stability and transitions at the nanoscale. Our selection of literature is intended to illustrate significant insights, concepts and understanding, as well as the current scope of using molecular simulations for understanding polymorphic transitions in an accessible way, rather than claiming completeness. With exciting prospects in both simulation methods development and enhancements in computer hardware, we are on the verge of accessing an unprecedented capability for designing and developing dosage forms and drug delivery systems in silico, including tackling challenges in polymorph control on a rational basis.
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38
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van den Ende JA, Ensing B, Cuppen HM. Energy barriers and mechanisms in solid–solid polymorphic transitions exhibiting cooperative motion. CrystEngComm 2016. [DOI: 10.1039/c5ce02550h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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van den Ende JA, Smets MMH, de Jong DT, Brugman SJT, Ensing B, Tinnemans PT, Meekes H, Cuppen HM. Do solid-to-solid polymorphic transitions in DL-norleucine proceed through nucleation? Faraday Discuss 2015; 179:421-36. [PMID: 25880981 DOI: 10.1039/c4fd00214h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DL-Norleucine is a molecular crystal exhibiting two enantiotropic phase transitions. The high temperature α ↔ γ transition has been shown to proceed through nucleation and growth [Mnyukh et al., J. Phys. Chem. Solids, 1975, 36, 127]. We focus on the low temperature β ↔ α transition in a combined computational and experimental study. The temperature dependence of the structural and energetic properties of both polymorphic forms is nearly identical. Molecular dynamics simulations and nudged elastic band calculations of the transition process itself, suggest that the transition is governed by cooperative movements of bilayers over relatively large energy barriers.
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Affiliation(s)
- Joost A van den Ende
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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40
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Pugazhenthi I, Ghouse SM, Nawaz Khan FR, Jeong ED, Bae JS, Kim JP, Chung EH, Kumar YS, Dasaradhan C. Water mediated reactions: TiO2and ZnO nanoparticle catalyzed multi component domino reaction in the synthesis of tetrahydroacridinediones, acridindiones, xanthenones and xanthenes. RSC Adv 2015. [DOI: 10.1039/c4ra13045f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tetrahydroacridine-1,8-(2H,5H,9H,10H)-diones4from 1,3-cyclohexanedione and/or dimedone 1,2-chloro-3-formylquinoline2and anilines3in water at 90 °C were obtained by domino reaction approach.
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Affiliation(s)
- Ilangovan Pugazhenthi
- Organic and Medicinal Chemistry Research Laboratory
- Organic Chemistry Division
- School of Advanced Sciences
- VIT-University
- Vellore 632 014
| | - Shaik Mohammed Ghouse
- Organic and Medicinal Chemistry Research Laboratory
- Organic Chemistry Division
- School of Advanced Sciences
- VIT-University
- Vellore 632 014
| | - Fazlur-Rahman Nawaz Khan
- Organic and Medicinal Chemistry Research Laboratory
- Organic Chemistry Division
- School of Advanced Sciences
- VIT-University
- Vellore 632 014
| | - Euh Duck Jeong
- Korea Basic Science Institute
- Busan Center
- Busan 618 230
- South Korea
| | - Jong Seong Bae
- Korea Basic Science Institute
- Busan Center
- Busan 618 230
- South Korea
| | - Jong-Pil Kim
- Korea Basic Science Institute
- Busan Center
- Busan 618 230
- South Korea
| | - Eun Hyuk Chung
- Korea Basic Science Institute
- Busan Center
- Busan 618 230
- South Korea
| | - Yadavalli Suneel Kumar
- Organic and Medicinal Chemistry Research Laboratory
- Organic Chemistry Division
- School of Advanced Sciences
- VIT-University
- Vellore 632 014
| | - Changalraya Dasaradhan
- Organic and Medicinal Chemistry Research Laboratory
- Organic Chemistry Division
- School of Advanced Sciences
- VIT-University
- Vellore 632 014
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41
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Ectors P, Duchstein P, Zahn D. From oligomers towards a racemic crystal: molecular simulation ofdl-norleucine crystal nucleation from solution. CrystEngComm 2015. [DOI: 10.1039/c4ce02078b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Qiu L, Ju XH, Xiao HM. Density Functional Theory Study of Solvent Effects on the Structure and Vibrational Frequencies of Tetranitrotetraazabicyclooctane “bicyclo-HMX”. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200500061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Zahn D, Anwar J. Collective displacements in a molecular crystal polymorphic transformation. RSC Adv 2013. [DOI: 10.1039/c3ra40653a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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44
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ZnO nanoparticle as catalyst for efficient green one-pot synthesis of coumarins through Knoevenagel condensation. J CHEM SCI 2011. [DOI: 10.1007/s12039-011-0133-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Zahn D, Anwar J. Size-dependent phase stability of a molecular nanocrystal: a proxy for investigating the early stages of crystallization. Chemistry 2011; 17:11186-92. [PMID: 21922553 DOI: 10.1002/chem.201100710] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Indexed: 11/09/2022]
Abstract
We make the link between the size-dependent phase stability of a nanocrystal and the phase-transition behavior of emerging crystallites during the earliest stages of crystallization, by using the former as a proxy for the latter. We outline an extension of the classical nucleation theory to describe crystal nucleation and subsequent transformations of competing polymorphic phases that characterize Ostwald's rule of stages. The theoretical framework reveals that the relative stability of the competing phases is a function of cluster size, which in turn varies with time, and therefore explains the complex transformation behavior observed for some systems. We investigated the stability of a nanocrystal of dl-norleucine by means of molecular simulation as a proxy for post-nucleation phase-transformation behavior in emerging crystallites. The simulations reveal that, for nanocrystals, the surface energy of the transition state of a transformation can dominate the barrier to phase change, thus causing metastable phases to be stabilized, not because they are thermodynamically stable, but rather due to kinetic hindering. Therefore, in the context of the earliest stages of crystal growth, not only does phase stability vary as a function of cluster size, and hence time, but thermodynamically feasible transformations are also prone to kinetic hindering.
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Affiliation(s)
- Dirk Zahn
- Lehrstuhl für Theoretische Chemie, Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstr. 25 Address 2, 91052 Erlangen, Germany
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46
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Shariare MH, Leusen FJJ, de Matas M, York P, Anwar J. Prediction of the mechanical behaviour of crystalline solids. Pharm Res 2011; 29:319-31. [PMID: 21845506 DOI: 10.1007/s11095-011-0543-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 07/19/2011] [Indexed: 11/30/2022]
Abstract
PURPOSE To explore the use of crystal inter-planar d-spacings and slip-plane interaction energies for predicting and characterising mechanical properties of crystalline solids. METHODS Potential relationships were evaluated between mechanical properties and inter-planar d-spacing, inter-planar interaction energy, and dispersive surface energy as determined using inverse gas chromatography (IGC) for a set of pharmaceutical materials. Inter-planar interaction energies were determined by molecular modelling. RESULTS General trends were observed between mechanical properties and the largest inter-planar d-spacing, inter-planar interaction energies, and IGC dispersive surface energy. A number of materials showed significant deviations from general trends. Weak correlations and outliers were rationalised. CONCLUSIONS Results suggest that the highest d-spacing of a material could serve as a first-order indicator for ranking mechanical behaviour of pharmaceutical powders, but with some reservation. Inter-planar interaction energy normalised for surface area shows only a weak link with mechanical properties and does not appear to capture essential physics of deformation. A novel framework linking mechanical properties of crystals to the distinct quantities, slip-plane energy barrier and inter-planar interaction (detachment) energy is proposed.
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47
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Ren P, Reichert D, He Q, Zhang L, Tang H. Understanding the Molecular Dynamics Associated with Polymorphic Transitions of dl-Norvaline with Solid-State NMR Methods. J Phys Chem B 2011; 115:2814-23. [DOI: 10.1021/jp110224b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pingping Ren
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, P.R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | | | - Qinghua He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, P.R. China
| | - Limin Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, P.R. China
| | - Huiru Tang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, P.R. China
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48
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Anwar J, Zahn D. Atomistisches Verständnis der Keimbildung und des Kristallwachstums durch molekulare Simulationen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201000463] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Anwar J, Zahn D. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation. Angew Chem Int Ed Engl 2011; 50:1996-2013. [PMID: 21271625 DOI: 10.1002/anie.201000463] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Indexed: 11/11/2022]
Abstract
Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials.
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Affiliation(s)
- Jamshed Anwar
- Computational Biophysics Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, BD7 1DP, UK.
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50
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Price SL, Leslie M, Welch GWA, Habgood M, Price LS, Karamertzanis PG, Day GM. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials. Phys Chem Chem Phys 2010; 12:8478-90. [PMID: 20607186 DOI: 10.1039/c004164e] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the intermolecular forces involved in molecular recognition processes.
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, UK.
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