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Hussain S, Hussain S, Zafar MN, Hussain I, Khan F, Mughal EU, Tahir MN. Preliminary anticancer evaluation of new Pd(II) complexes bearing NNO donor ligands. Saudi Pharm J 2024; 32:101915. [PMID: 38178853 PMCID: PMC10764271 DOI: 10.1016/j.jsps.2023.101915] [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: 10/03/2023] [Accepted: 12/09/2023] [Indexed: 01/06/2024] Open
Abstract
In this study we presented a novel series of NNO tridentate ligands generating imino, amido and oxo donor pocket for Pd(II) coordination. All the compounds were meticulously characterized by elemental analysis and advanced spectroscopic techniques, including FTIR, proton and carbon NMR. The synthesized compounds underwent rigorous evaluation for their potential as anti-cancer agents, utilizing the aggressive breast cancer cell lines MDA-MB (ATCC) and MCF-7 as a crucial model for assessing growth inhibition in cancer cells. Remarkably, the MTT assay unveiled the robust anti-cancer activity for all palladium complexes against MDA-MB-231 and MCF-7 cells. Particularly, complex [Pd(L1)(CH3CN)] exhibited exceptional potency with an IC50 value of 25.50 ± 0.30 µM (MDA-MB-231) and 20.76 ± 0.30 µM (MCF-7), compared to respective 27.00 ± 0.80 µM and 24.10 ± 0.80 µM for cisplatin, underscoring its promising therapeutic potential. Furthermore, to elucidate the mechanistic basis for the anti-cancer effects, molecular docking studies on tyrosine kinases, an integral target in cancer research, were carried out. The outcome of these investigations further substantiated the remarkable anticancer properties inherent to these innovative compounds. This research offers a compelling perspective on the development of potent anti-cancer agents rooted in the synergy between ligands and Pd(II) complexes and presenting a promising avenue for future cancer therapy endeavors.
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Affiliation(s)
- Shazia Hussain
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Shabeeb Hussain
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - M. Naveed Zafar
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Irfan Hussain
- Center of Regenerative Medicine and Stem Cell Research, Aga Khan 74800, University Karachi, Pakistan
| | - Faizullah Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman and Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
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Thomas OE, Oduwole RT, Akin-Taylor A. Comparison of the DNA-binding interactions of 5-hydroxymethylfurfural and its synthesized derivative, 5, 5’[oxy-bis(methylene)]bis-2-furfural: experimental, DFT and docking studies. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2023. [DOI: 10.1080/16583655.2023.2183705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Yasmeen N, Ahmad Chaudhary A, K Niraj RR, Lakhawat SS, Sharma PK, Kumar V. Screening of phytochemicals from Clerodendrum inerme (L.) Gaertn as potential anti-breast cancer compounds targeting EGFR: an in-silico approach. J Biomol Struct Dyn 2023:1-43. [PMID: 38141177 DOI: 10.1080/07391102.2023.2294379] [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: 07/25/2023] [Accepted: 12/04/2023] [Indexed: 12/25/2023]
Abstract
Breast cancer (BC) is the most prevalent malignancy among women around the world. The epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor (RTK) of the ErbB/HER family. It is essential for triggering the cellular signaling cascades that control cell growth and survival. However, perturbations in EGFR signaling lead to cancer development and progression. Hence, EGFR is regarded as a prominent therapeutic target for breast cancer. Therefore, in the current investigation, EGFR was targeted with phytochemicals from Clerodendrum inerme (L.) Gaertn (C. inerme). A total of 121 phytochemicals identified by gas chromatography-mass spectrometry (GC-MS) analysis were screened against EGFR through molecular docking, ADMET analyses (Absorption, Distribution, Metabolism, Excretion, and Toxicity), PASS predictions, and molecular dynamics simulation, which revealed three potential hit compounds with CIDs 10586 [i.e. alpha-bisabolol (-6.4 kcal/mol)], 550281 [i.e. 2,(4,4-Trimethyl-3-hydroxymethyl-5a-(3-methyl-but-2-enyl)-cyclohexene) (-6.5 kcal/mol)], and 161271 [i.e. salvigenin (-7.4 kcal/mol)]. The FDA-approved drug gefitinib was used to compare the inhibitory effects of the phytochemicals. The top selected compounds exhibited good ADMET properties and obeyed Lipinski's rule of five (ROF). The molecular docking analysis showed that salvigenin was the best among the three compounds and formed bonds with the key residue Met 793. Furthermore, the molecular mechanics generalized born surface area (MMGBSA) calculations, molecular dynamics simulation, and normal mode analysis validated the binding affinity of the compounds and also revealed the strong stability and compactness of phytochemicals at the docked site. Additionally, DFT and DOS analyses were done to study the reactivity of the compounds and to further validate the selected phytochemicals. These results suggest that the identified phytochemicals possess high inhibitory potential against the target EGFR and can treat breast cancer. However, further in vitro and in vivo investigations are warranted towards the development of these constituents into novel anti-cancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nusrath Yasmeen
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | | | | | | | - Vikram Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
- Amity Institute of Pharmacy, Amity University Rajasthan, Jaipur, India
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V J, M S, Wani A, Ahmad SF, Nadeem A, Sharma A, Ahmed SSSJ. Pharmacoscreening, molecular dynamics, and quantum mechanics of inermin from Panax ginseng: a crucial molecule inhibiting exosomal protein target associated with coronary artery disease progression. PeerJ 2023; 11:e16481. [PMID: 38077444 PMCID: PMC10710165 DOI: 10.7717/peerj.16481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Background Exosomes, microvesicles, carry and release several vital molecules across cells, tissues, and organs. Epicardial adipose tissue exosomes are critical in the development and progression of coronary artery disease (CAD). It is hypothesized that exosomes may transport causative molecules from inflamed tissue and deliver to the target tissue and progress CAD. Thus, identifying and inhibiting the CAD-associated proteins that are being transported to other cells via exosomes will help slow the progression of CAD. Methods This study uses a systems biological approach that integrates differential gene expression in the CAD, exosomal cargo assessment, protein network construction, and functional enrichment to identify the crucial exosomal cargo protein target. Meanwhile, absorption, distribution, metabolism, and excretion (ADME) screening of Panax ginseng-derived compounds was conducted and then docked against the protein target to identify potential inhibitors and then subjected to molecular dynamics simulation (MDS) to understand the behavior of the protein-ligand complex till 100 nanoseconds. Finally, density functional theory (DFT) calculation was performed on the ligand with the highest affinity with the target. Results Through the systems biological approach, Mothers against decapentaplegic homolog 2 protein (SMAD2) was determined as a potential target that linked with PI3K-Akt signaling, Ubiquitin mediated proteolysis, and the focal adhesion pathway. Further, screening of 190 Panax ginseng compounds, 27 showed drug-likeness properties. Inermin, a phytochemical showed good docking with -5.02 kcal/mol and achieved stability confirmation with SMAD2 based on MDS when compared to the known CAD drugs. Additionally, DFT analysis of inermin showed high chemical activity that significantly contributes to effective target binding. Overall, our computational study suggests that inermin could act against SMAD2 and may aid in the management of CAD.
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Affiliation(s)
- Janakiraman V
- Muti-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettnad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Sudhan M
- Muti-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettnad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Abubakar Wani
- Department of Immunology, St. Jude Children’s Research Hospital Memphis, TN, USA
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ashutosh Sharma
- Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Tecnologico de Monterrey, Queretaro, Mexico
| | - Shiek S. S. J. Ahmed
- Muti-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettnad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
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Ibrahim ZY, Uzairu A, Shallangwa GA, Abechi SE, Isyaku S. Homology modeling, docking, and ADMET studies of benzoheterocyclic 4-aminoquinolines analogs as inhibitors of Plasmodiumfalciparum. J Taibah Univ Med Sci 2023; 18:1200-1216. [PMID: 37250808 PMCID: PMC10209460 DOI: 10.1016/j.jtumed.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/18/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Objectives The ongoing fight against endemic diseases is necessary due to the growing resistance of malarial parasites to widely accessible medications. Thus, there has been an ongoing search for antimalarial medications with improved efficacy. The goal of this study was to develop derivatives of benzoheterocyclic 4-aminoquinolines with enhanced activities and better binding affinities than the original compounds. Methods Thirty-four derivatives of benzoheterocyclic 4-aminoquinolines were docked (using a model of dihydrofolate reductase-thymidylate synthase [DRTS] protein) with Molegro software to identify the compound with the minimum docking score as a design template. The generated quantitative structure-activity model was employed to estimate the activity of the designed derivatives. The derivatives were also docked to determine the most stable derivatives. Furthermore, the designed derivatives were tested for their drug-likeness and pharmacokinetic properties using SwissADME software and pkCSM web application, respectively. Results Compound H-014, (N-(7-chloroquinolin-4-yl)-2-(4-methylpiperazin-1-yl)-1,3-benzoxazol-5-amine) with the lowest re-rank score of -115.423 was employed as the design template. Then 10 derivatives were further designed by substituting -OH, -OCH3, -CHO, -F, and -Cl groups at various positions of the template. We found that the designed derivatives had improved activities compared to the template. The docking scores of the designed derivatives were lower than those of the original derivatives. Derivative h-06 (7-methoxy-4-((2-(4-methylpiperazin-1-yl)benzo[d]oxazol-5-yl)amino)quinolin-6-ol) with four hydrogen bonds was identified as the most stable due to its lowest re-rank score (-163.607). While all of the designed derivatives satisfied both the Lipinski and Verber rules, some derivatives such as h-10 (cytochrome P450 1A2 [CYP1A2]); h-05, h-08, h-09, and h-10 [CYP2C19]; and h-03, h-07, h-08, and h-10 [renal organic cation transporter 2 substrate]) showed poor absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Conclusion Ten derivatives of benzoheterocyclic 4-aminoquinolines were designed with improved efficacies. Derivatives that follow Lipinski and Verber rules and are mostly non-toxic and non-sensitive to the skin can be utilized in the development of effective antimalarial medications.
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Affiliation(s)
- Zakari Y. Ibrahim
- Corresponding address: Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Nigeria.
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Sivakumar M, Ahmad SF, Emran TB, Angulo-Bejarano PI, Sharma A, Ahmed SSSJ. Network-Derived Radioresistant Breast Cancer Target with Candidate Inhibitors from Brown Algae: A Sequential Assessment from Target Selection to Quantum Chemical Calculation. Mar Drugs 2023; 21:545. [PMID: 37888480 PMCID: PMC10608582 DOI: 10.3390/md21100545] [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: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Despite significant progress in early detection and treatment, a few aggressive breast cancers still exhibit resistance to therapy. This study aimed to identify a therapeutic target for radioresistant breast cancer (RRbc) through a protein network from breast cancer genes and to evaluate potent phytochemicals against the identified target. Our approach includes the integration of differential expression genes from expression datasets to create a protein network and to use survival analysis to identify the crucial RRbc protein in order to discover a therapeutic target. Next, the phytochemicals sourced from brown algae were screened through molecular docking, ADME (absorption, distribution, metabolism, and excretion), molecular dynamics (MD) simulation, MM-GBSA, and quantum mechanics against the identified target. As a result of our protein network investigation, the proto-oncogene c-KIT (KIT) protein was identified as a potent radioresistant breast cancer target. Further, phytochemical screening establishes that nahocol-A1 from brown algae has high binding characteristics (-8.56 kcal/mol) against the KIT protein. Then, quantum chemical analysis of nahocol-A1 provided insights into its electronic properties favorable for protein binding. Also, MD simulation comprehends the conformational stability of the KIT-nahocol-A1 complex. Overall, our findings suggest nahocol-A1 could serve as a promising therapeutic candidate for radioresistant breast cancer.
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Affiliation(s)
- Mahema Sivakumar
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Paola Isabel Angulo-Bejarano
- NatProLab-Plant Innovation Lab, Regional Department of Bioengineering, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- NatProLab-Plant Innovation Lab, Regional Department of Bioengineering, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
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Roshni J, Ahmad SF, Wani A, Ahmed SSSJ. Multi-Target Effect of Aloeresin-A against Bacterial and Host Inflammatory Targets Benefits Contact Lens-Related Keratitis: A Multi-Omics and Quantum Chemical Investigation. Molecules 2023; 28:6955. [PMID: 37836798 PMCID: PMC10574460 DOI: 10.3390/molecules28196955] [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: 08/25/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Contact lens-mediated microbial keratitis caused by Pseudomonas aeruginosa and Streptococcus pneumoniae provokes corneal damage and vision loss. Recently, natural phytochemicals have become complementary medicines for corneal destruction. Herein, we aimed to identify multi-targeting Aloe vera-derived phytochemicals capable of inhibiting bacterial and host targets of keratitis through ADME (absorption, distribution, metabolism, and excretion), docking, molecular dynamics (MD) simulation, MMGBSA (molecular mechanics generalized Born surface area) and density functional theory (DFT) investigations. An extensive literature search revealed ExoU, ExoS, ExoT, ExoY, and PLY as virulent bacterial targets. Simultaneously, differential gene expression (DGE) and pathway enrichment analysis-specified host transcription factor (SPI1) influences keratitis pathogenesis. Molecular docking analysis uncovered aloeresin-A as a promising inhibitor against bacterial and host targets, demonstrating strong binding energies ranging from -7.59 to -6.20 kcal/mol. Further, MMGBSA and MD simulation analysis reflect higher binding free energies and stable interactions of aloeresin-A with the targets. In addition, DFT studies reveal the chemical reactiveness of aloeresin-A through quantum chemical calculations. Hence, our findings show aloeresin-A to be a promising candidate for effectively inhibiting keratitis. However, additional research is imperative for potential integration into lens care solutions.
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Affiliation(s)
- Jency Roshni
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abubakar Wani
- Department of Immunology, St. Jude Children’s Research Hospital Memphis, Memphis, TN 38105, USA
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
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Umar AB, Uzairu A. New flavone-based arylamides as potential V600E-BRAF inhibitors: Molecular docking, DFT, and pharmacokinetic properties. J Taibah Univ Med Sci 2023; 18:1000-1010. [PMID: 36950455 PMCID: PMC10025095 DOI: 10.1016/j.jtumed.2023.02.010] [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: 10/20/2022] [Revised: 12/21/2022] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Objectives The V600E-BRAF protein kinase is an attractive and essential therapeutic target in melanoma and other tumors. However, because of its resistance to the known inhibitors and side effects of some identified inhibitors, new potent inhibitors need to be identified. Methods In the present work, in silico strategies such as the molecular docking simulation, DFT (Density-Functional-Theory) computations, and pharmacokinetic evaluation were used to determine potential V600E-BRAF inhibitors from a set of 31 synthesized novel flavone-based arylamides. Results The docking result demonstrated that four compounds (10, 11, 28, and 31) had acceptable docking scores (MolDock score of -167.523 kcal mol-1, -158.168 kcal mol-1, -160.581 kcal mol-1,-162.302 kcal mol-1, and a Rerank score of -124.365, -129.365, -135.878 and -117.081, respectively) appeared as most active and potent V600E-BRAF inhibitors that topped vemurafenib (-158.139 and -118.607 kcal mol-1). The appearance of H-bonds and hydrophobic interactions with essential residues for V600E-BRAF proved the high stability of these complexes. The energy for the frontier molecular orbitals such as HOMO, LUMO, energy gap, and other reactivity parameters was computed using DFT. The frontier molecular-orbital surfaces and electrostatic potentials (EPs) were investigated to demonstrate the charge-density distributions that might be linked to anticancer activity. Similarly, the chosen compounds revealed superior pharmacological properties according to the drug-likeness rules (bioavailability) and pharmacokinetic properties. Conclusion The chosen compounds were recognized as potent V600E-BRAF inhibitors with superior pharmacokinetic properties and could be promising cancer drug candidates.
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Affiliation(s)
- Abdullahi B. Umar
- Corresponding author: Department of Chemistry, Faculty of Physical Sciences, Ahmad Bello University, Zaria, P.M.B.1045 Kaduna State, Nigeria.
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Virtual screening, pharmacokinetic, and DFT studies of anticancer compounds as potential V600E-BRAF kinase inhibitors. J Taibah Univ Med Sci 2023; 18:933-946. [PMID: 36875340 PMCID: PMC9976450 DOI: 10.1016/j.jtumed.2023.01.013] [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: 09/19/2022] [Revised: 12/12/2022] [Accepted: 01/24/2023] [Indexed: 02/07/2023] Open
Abstract
Objectives V600E-BRAF kinase is an essential therapeutic target in melanoma and other types of tumors. Because of its resistance to known inhibitors and the adverse effects of some identified inhibitors, investigation of new potent inhibitors is necessary. Methods In the present work, in silico strategies such as molecular docking simulation, pharmacokinetic evaluation, and density functional theory (DFT) computations were used to identify potential V600E-BRAF inhibitors from a set of 72 anticancer compounds in the PubChem database. Results Five top-ranked molecules (12, 15, 30, 31, and 35) with excellent docking scores (MolDock score ≥90 kcal mol-1, Rerank score ≥60 kcal mol-1) were selected. Several potential binding interactions were discovered between the molecules and V600E-BRAF. The formation of H-bonds and hydrophobic interactions with essential residues of V600E-BRAF suggested the high stability of these complexes. The selected compounds had excellent pharmacological properties according to the drug likeness rules (bioavailability) and pharmacokinetic properties. Similarly, the energy for the frontier molecular orbitals, such as the HOMO, LUMO, energy gap, and other reactivity parameters, was computed with DFT. The frontier molecular orbital surfaces and electrostatic potentials were investigated to demonstrate the charge-density distributions potentially associated with anticancer activity. Conclusion The identified compounds were found to be potent hit compounds for V600E-BRAF inhibition with superior pharmacokinetic properties; therefore, they may be promising cancer drug candidates.
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Asirvatham RD, Hwang DH, Prakash RLM, Kang C, Kim E. Pharmacoinformatic Investigation of Silymarin as a Potential Inhibitor against Nemopilema nomurai Jellyfish Metalloproteinase Toxin-like Protein. Int J Mol Sci 2023; 24:ijms24108972. [PMID: 37240317 DOI: 10.3390/ijms24108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Jellyfish stings pose a major threat to swimmers and fishermen worldwide. These creatures have explosive cells containing one large secretory organelle called a nematocyst in their tentacles, which contains venom used to immobilize prey. Nemopilema nomurai, a venomous jellyfish belonging to the phylum Cnidaria, produces venom (NnV) comprising various toxins known for their lethal effects on many organisms. Of these toxins, metalloproteinases (which belong to the toxic protease family) play a significant role in local symptoms such as dermatitis and anaphylaxis, as well as systemic reactions such as blood coagulation, disseminated intravascular coagulation, tissue injury, and hemorrhage. Hence, a potential metalloproteinase inhibitor (MPI) could be a promising candidate for reducing the effects of venom toxicity. For this study, we retrieved the Nemopilema nomurai venom metalloproteinase sequence (NnV-MPs) from transcriptome data and modeled its three-dimensional structure using AlphaFold2 in a Google Colab notebook. We employed a pharmacoinformatics approach to screen 39 flavonoids and identify the most potent inhibitor against NnV-MP. Previous studies have demonstrated the efficacy of flavonoids against other animal venoms. Based on our analysis, Silymarin emerged as the top inhibitor through ADMET, docking, and molecular dynamics analyses. In silico simulations provide detailed information on the toxin and ligand binding affinity. Our results demonstrate that Silymarin's strong inhibitory effect on NnV-MP is driven by hydrophobic affinity and optimal hydrogen bonding. These findings suggest that Silymarin could serve as an effective inhibitor of NnV-MP, potentially reducing the toxicity associated with jellyfish envenomation.
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Affiliation(s)
- Ravi Deva Asirvatham
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Du Hyeon Hwang
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | | | - Changkeun Kang
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Euikyung Kim
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
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Ipinloju N, Ibrahim A, da Costa RA, Adigun TB, Olubode SO, Abayomi KJ, Aiyelabegan AO, Esan TO, Muhammad SA, Oyeneyin OE. Quantum evaluation and therapeutic activity of (E)-N-(4-methoxyphenyl)-2-(4-(3-oxo-3-phenylprop-1-en-1-yl) phenoxy)acetamide and its modified derivatives against EGFR and VEGFR-2 in the treatment of triple-negative cancer via in silico approach. J Mol Model 2023; 29:159. [PMID: 37099048 DOI: 10.1007/s00894-023-05543-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/03/2023] [Indexed: 04/27/2023]
Abstract
The most dangerous subtype of breast cancer, triple-negative breast cancer (TNBC), accounts for 25% of all breast cancer-related deaths and 15% of all breast cancer cases. TNBC is distinguished by the lack of immunohistochemical expression of HER2, progesterone receptors, or oestrogen receptors. Although it has been reported that upregulation of EGFR and VEGFR-2 is associated with TNBC progression, no proven effective targeted therapy exists at this time. We used structural bioinformatics methods, including density functional theory, molecular docking, molecular dynamic simulation, pharmacokinetic and drug-likeness models, to identify promising EGFR/VEGFR-2 inhibitors from N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl) phenoxy] acetamide and six of its modified derivatives in light of the lack of effective targets inhibitor Version 14 of Spartan software was used to analyse density functional theory. The Schrodinger software suite 2018's Maestro interface was used for the molecular docking analysis, and the admetSAR and swissADME servers were used for drug-likeness and absorption, distribution, metabolism, excretion, and toxicity. All of the compounds showed strong electronic characteristics. Additionally, all of the tested compounds met the ADMET and drug-likeness requirements without a single instance of Lipinski's rule of five violations. Additionally, the molecules' levels of affinity for the target proteins varied. The highest binding affinities were demonstrated by the MOLb-VEGFR-2 complex (- 9.925 kcal/mol) and the MOLg-EGFR complex (- 5.032 kcal/mol). The interaction of the molecules in the domain of the EGFR and VEGFR-2 receptors was also better understood through molecular dynamic simulation of the complex.
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Affiliation(s)
- Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.
| | - Abdulwasiu Ibrahim
- Department of Biochemistry and Molecular Biology, Usmanu Danfodiyo University, Sokoto, Nigeria.
| | - Renato Araujo da Costa
- Institute of Education, Science and Technology of Para (IFPA), Campus Abaetetuba, Abaetetuba, Para, Brazil
| | | | - Samuel Olawale Olubode
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Kehinde Joan Abayomi
- Faculty of Medical Laboratory Science, Usmanu DanFodiyo University, Sokoto, Nigeria
| | | | - Timothy Oluwaseun Esan
- Department of Chemical Sciences, Bamidele Olumilua University of Education Science and Technology, Ikere-Ekiti, Ekiti State, Nigeria
| | | | - Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.
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Kafi DK, Ayyash AN. Density functional theory and molecular docking study to lutein molecule for COVID-19 protease inhibitors. APPLIED NANOSCIENCE 2023; 13:1-12. [PMID: 36691520 PMCID: PMC9850325 DOI: 10.1007/s13204-022-02735-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/09/2022] [Indexed: 01/20/2023]
Abstract
Since the beginning of the corona pandemic, numerous scientific projects have been conducted worldwide to investigate how the new virus can be combated. Researchers are developing various vaccines and drugs at full speed - with varying degrees of success. In this work, silico screening (molecular docking analysis) is performed on twenty natural compounds, which are expected to provide valuable lead molecules and medication to treat a new condition SARS-CoV-2. Our results indicate that out of the 20 compounds on the candidate list, lutein and Polydatin, natural components of fruits and vegetables (especially egg yolk and maize) have shown an excellent performance in our docking studies through a minimum binding energy of - 9.8 kcal/mol also - 7.4 kcal/mol, separately. This indicates their potential for the inhibitory molecular interactions against COVID-19. The main intent of the research is to analyse the protein components and investigate the molecules.
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Affiliation(s)
- Dhaidan Khalaf Kafi
- Department of Medical Physics, College of Applied Science, University of Fallujah, Baghdad, Iraq
| | - Adil N. Ayyash
- Department of Physics, College of Science, University of Anbar, Ramadi, Iraq
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Oğul Y, Gür F, Gür B, Cengiz M, Sarı RA, Kızıltunç A. Decreased Na +/K + pump activity in the erythrocyte membrane due to malondialdehyde in rheumatoid arthritis: an in vivo and in silico study. Can J Physiol Pharmacol 2022; 100:968-982. [PMID: 36148907 DOI: 10.1139/cjpp-2022-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Apart from demonstrating the interaction behavior of malondialdehyde (MDA) with Na+/K+-ATPase using in silico, the current study aims to investigate the effect of rheumatoid arthritis-related oxidative stress on Na+/K+-ATPase activity that is present in the erythrocyte cell membrane, which is rich in proteins vulnerable to damage from MDA and other free radicals. The target population of this study consists of 28 rheumatoid arthritis patients and 20 healthy volunteers whose MDA levels and Na+/K+-ATPase activity were determined. It was shown that MDA levels of rheumatoid arthritis patients increased (p < 0.001) and their Na+/K+-ATPase activity noticeably decreased when compared to those of healthy individuals. Also, according to this in silico modeling, MDA decreased Na+/K+-ATPase activity in line with the correlation analyses. Consequently, while elevated levels of MDA in the rheumatoid arthritis group were suggestive of oxidative stress, a decreased Na+/K+-ATPase-activity led us to speculate that the cellular membrane had sustained injury. Therefore, our results could be useful in explaining how MDA affects Na+/K+-ATPase activity in the interior of a specific molecular pathway.
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Affiliation(s)
- Yasemin Oğul
- Department of Medicinal Biochemistry, Regional Training and Research Hospital, Health Sciences University, Erzurum, 25240, Turkey
| | - Fatma Gür
- Department of Medical Services and Techniques, Health Services Vocational School, Ataturk University, Erzurum, 25240, Turkey
| | - Bahri Gür
- Department of Biochemistry, Faculty of Sciences and Arts, Iğdır University, Iğdır, 76000, Turkey
| | - Mustafa Cengiz
- Department of Elementary Education, Faculty of Education, Siirt University, 56100 Siirt, Turkey
| | - Refik Ali Sarı
- Department of Internal Diseases, Faculty of Medicine, Karadeniz Technical University, Trabzon, 61080, Turkey
| | - Ahmet Kızıltunç
- Department of Biochemistry, Faculty of Medicine, Ataturk University, Erzurum, 25240, Turkey
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Geedkar D, Kumar A, Sharma P. Molecular Iodine-Catalyzed Synthesis of Imidazo[1,2- a]Pyridines: Screening of Their In Silico Selectivity, Binding Affinity to Biological Targets, and Density Functional Theory Studies Insight. ACS OMEGA 2022; 7:22421-22439. [PMID: 35811892 PMCID: PMC9260945 DOI: 10.1021/acsomega.2c01570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The present paper discloses an ultrasonication strategy assisted by molecular iodine as an environmentally benign catalyst leading to the synthesis of pharmacologically significant imidazo[1,2-a]pyridine scaffolds. The molecular-iodine-catalyzed approach for the synthesis of biologically active synthetic equivalents was achieved through three-component coupling embracing 2-aminopyridine derivatives, pertinent acetophenones, and dimedone in water medium under aerobic conditions. The higher product yield (up to 96%) with a miniature reaction time and modest catalyst loading as demonstrated by higher ecological compatibility and sustainability factors are fascinating features of this protocol. The structures of synthesized compounds were accomplished through FT-IR, 1H NMR,13C NMR, mass, and elemental analysis data. The virtual screening of synthetic moieties was performed to ascertain the in silico selectivity and binding affinities against several biological targets. Lipinski's rules of five, ADMET, and TOPKAT descriptors were used to evaluate the drug-likeness assets. Furthermore, a quantum computational study was computed at the B3LYP/6-311G++(d,p) level of theory to investigate the density functional theory-based chemical reactivity parameters and HOMO-LUMO energy gap of the synthesized derivatives. The present studies open the way for in vitro and in vivo testing of synthesized derivatives as potent inhibitors with an improved pharmacological profile against farnesyl diphosphate synthase, phosphodiesterase III, CXCR4, and GABAa receptor agonists.
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Sharma A, Khanum G, Kumar A, Fatima A, Singh M, Abualnaja KM, Althubeiti K, Muthu S, Siddiqui N, Javed S. Conformational stability, quantum computational, spectroscopic, molecular docking and molecular dynamic simulation study of 2-hydroxy-1-naphthaldehyde. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132755] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Nariya P, Kumar S, Seshadri S, Patel M, Thakore S. Novel Substituted Isoindolinones Derived from Lawsone: Synthesis, Characterization, Theoretical, Biological Activity and Docking Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hussein RK, Khouqeer G, Alkaoud AM, El-Khayatt AM. Probing the Action of Screened Anticancer Triazole–Tetrazole Derivatives Against COVID-19 Using Molecular Docking and DFT Investigations. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221093915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Drugs are continuously being evaluated for novel therapeutic uses. The purpose of this work was to screen anticancer triazole/tetrazole derivatives for effectiveness against the SARS-CoV-2 main protease (Mpro). First, the chemical structures’ activity was derived from conceptual quantum chemical calculations. According to molecular docking analysis, the compounds scored good interactions against SAR-COV-2's Mpro, with binding energies extending from −8.21 to −8.97 kcal/mol. The docked complexes included various bindings with His41 and Cys145, both catalytic residues responsible for cleavage of the SARS-CoV-2 Mpro. Among the 4 studied compounds, TD3 exhibited the highest affinity by achieving the most stable binding energy and lowest value for the inhibition constant. Most striking was that TD3 not only formed strong bonds with the catalytic residues His41 and Cys145, but also captured the residues of the catalytic loop (Cys44 to Pro52), which flank the catalytic dyads in Mpro's active site. As a result, the studied triazole/tetrazole derivatives, notably TD3, must be reviewed as potent drugs that could be repurposed for SARS-CoV-2 treatment.
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Affiliation(s)
- Rageh K. Hussein
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ghada Khouqeer
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ahmed M. Alkaoud
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Ahmed M. El-Khayatt
- College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
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El-Shamy NT, Alkaoud AM, Hussein RK, Ibrahim MA, Alhamzani AG, Abou-Krisha MM. DFT, ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6,6'-Diamino-1,1',3,3'-tetramethyl-5,5'-(4-chlorobenzylidene)bis[pyrimidine-2,4(1H,3H)-dione]. Molecules 2022; 27:620. [PMID: 35163880 PMCID: PMC8839838 DOI: 10.3390/molecules27030620] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/05/2022] [Accepted: 01/15/2022] [Indexed: 12/24/2022] Open
Abstract
Heterocyclic compounds, including pyrimidine derivatives, exhibit a broad variety of biological and pharmacological activities. In this paper, a previously synthesized novel pyrimidine molecule is proposed, and its pharmaceutical properties are investigated. Computational techniques such as the density functional theory, ADMET evaluation, and molecular docking were applied to elucidate the chemical nature, drug likeness and antibacterial function of molecule. The viewpoint of quantum chemical computations revealed that the molecule was relatively stable and has a high electrophilic nature. The contour maps of HOMO-LUMO and molecular electrostatic potential were analyzed to illustrate the charge density distributions that could be associated with the biological activity. Natural bond orbital (NBO) analysis revealed details about the interaction between donor and acceptor within the bond. Drug likeness and ADMET analysis showed that the molecule possesses the agents of safety and the effective combination therapy as pharmaceutical drug. The antimicrobial activity was investigated using molecular docking. The investigated molecule demonstrated a high affinity for binding within the active sites of antibacterial and antimalarial proteins. The high affinity of the antibacterial protein was proved by its low binding energy (-7.97 kcal/mol) and a low inhibition constant value (1.43 µM). The formation of four conventional hydrogen bonds in ligand-protein interactions confirmed the high stability of the resulting complexes. When compared to known standard drugs, the studied molecule displayed a remarkable antimalarial activity, as indicated by higher binding affinity (B.E. -5.86 kcal/mol & Ki = 50.23 M). The pre-selected molecule could be presented as a promising drug candidate for the development of novel antimicrobial agents.
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Affiliation(s)
- Nesreen T. El-Shamy
- Physics Department, Faculty of Science, Taibah University, Al-Madina Al Munawarah 44256, Saudi Arabia; or
- Physics Department, Faculty of Women, Ain Shams University, Cairo 11865, Egypt
| | - Ahmed M. Alkaoud
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Rageh K. Hussein
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Moez A. Ibrahim
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Abdulrahman G. Alhamzani
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.G.A.); (M.M.A.-K.)
| | - Mortaga M. Abou-Krisha
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.G.A.); (M.M.A.-K.)
- Department of Chemistry, Faculty of Science, South Valley University, Qena 83523, Egypt
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