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Shahzadi Z, Yousaf Z, Anjum I, Bilal M, Yasin H, Aftab A, Booker A, Ullah R, Bari A. Network pharmacology and molecular docking: combined computational approaches to explore the antihypertensive potential of Fabaceae species. BIORESOUR BIOPROCESS 2024; 11:53. [PMID: 38767701 PMCID: PMC11106056 DOI: 10.1186/s40643-024-00764-6] [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: 01/31/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Hypertension is a major global public health issue, affecting quarter of adults worldwide. Numerous synthetic drugs are available for treating hypertension; however, they often come with a higher risk of side effects and long-term therapy. Modern formulations with active phytoconstituents are gaining popularity, addressing some of these issues. This study aims to discover novel antihypertensive compounds in Cassia fistula, Senna alexandrina, and Cassia occidentalis from family Fabaceae and understand their interaction mechanism with hypertension targeted genes, using network pharmacology and molecular docking. Total 414 compounds were identified; initial screening was conducted based on their pharmacokinetic and ADMET properties, with a particular emphasis on adherence to Lipinski's rules. 6 compounds, namely Germichrysone, Benzeneacetic acid, Flavan-3-ol, 5,7,3',4'-Tetrahydroxy-6, 8-dimethoxyflavon, Dihydrokaempferol, and Epiafzelechin, were identified as effective agents. Most of the compounds found non-toxic against various indicators with greater bioactivity score. 161 common targets were obtained against these compounds and hypertension followed by compound-target network construction and protein-protein interaction, which showed their role in diverse biological system. Top hub genes identified were TLR4, MMP9, MAPK14, AKT1, VEGFA and HSP90AA1 with their respective associates. Higher binding affinities was found with three compounds Dihydrokaempferol, Flavan-3-ol and Germichrysone, -7.1, -9.0 and -8.0 kcal/mol, respectively. The MD simulation results validate the structural flexibility of two complexes Flavan-MMP9 and Germich-TLR4 based on no. of hydrogen bonds, root mean square deviations and interaction energies. This study concluded that C. fistula (Dihydrokaempferol, Flavan-3-ol) and C. occidentalis (Germichrysone) have potential therapeutic active constituents to treat hypertension and in future novel drug formulation.
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Affiliation(s)
- Zainab Shahzadi
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Zubaida Yousaf
- Department of Botany, Lahore College for Women University, Lahore, Pakistan.
| | - Irfan Anjum
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Muhammad Bilal
- Centers for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hamna Yasin
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Arusa Aftab
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Anthony Booker
- Research Centre for Optimal Health, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW, UK.
- Research Group 'Pharmacognosy and Phytotherapy', UCL School of Pharmacy, Univ. London, 29 - 39 Brunswick Sq., London, WC1N 1AX, UK.
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
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Durojaye OA, Ejaz U, Uzoeto HO, Fadahunsi AA, Opabunmi AO, Ekpo DE, Sedzro DM, Idris MO. CSC01 shows promise as a potential inhibitor of the oncogenic G13D mutant of KRAS: an in silico approach. Amino Acids 2023; 55:1745-1764. [PMID: 37500789 DOI: 10.1007/s00726-023-03304-2] [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: 01/03/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023]
Abstract
About 30% of malignant tumors include KRAS mutations, which are frequently required for the development and maintenance of malignancies. KRAS is now a top-priority cancer target as a result. After years of research, it is now understood that the oncogenic KRAS-G12C can be targeted. However, many other forms, such as the G13D mutant, are yet to be addressed. Here, we used a receptor-based pharmacophore modeling technique to generate potential inhibitors of the KRAS-G13D oncogenic mutant. Using a comprehensive virtual screening workflow model, top hits were selected, out of which CSC01 was identified as a promising inhibitor of the oncogenic KRAS mutant (G13D). The stability of CSC01 upon binding the switch II pocket was evaluated through an exhaustive molecular dynamics simulation study. The several post-simulation analyses conducted suggest that CSC01 formed a stable complex with KRAS-G13D. CSC01, through a dynamic protein-ligand interaction profiling analysis, was also shown to maintain strong interactions with the mutated aspartic acid residue throughout the simulation. Although binding free energy analysis through the umbrella sampling approach suggested that the affinity of CSC01 with the switch II pocket of KRAS-G13D is moderate, our DFT analysis showed that the stable interaction of the compound might be facilitated by the existence of favorable molecular electrostatic potentials. Furthermore, based on ADMET predictions, CSC01 demonstrated a satisfactory drug likeness and toxicity profile, making it an exemplary candidate for consideration as a potential KRAS-G13D inhibitor.
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Affiliation(s)
- Olanrewaju Ayodeji Durojaye
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- Department of Chemical Sciences, Coal City University, Emene, EnuguState, Nigeria.
| | - Umer Ejaz
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230027, Anhui, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Henrietta Onyinye Uzoeto
- Federal College of Dental Technology, Trans-Ekulu, Enugu State, Nigeria
- Department of Biological Sciences, Coal City University, Emene, Enugu State, Nigeria
| | - Adeola Abraham Fadahunsi
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, 04469, USA
| | - Adebayo Oluwole Opabunmi
- RNA Medical Center, International Institutes of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Hangzhou, China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Daniel Emmanuel Ekpo
- Institute of Biological Science and Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, 530007, China
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, 410001, Nsukka, Enugu State, Nigeria
| | - Divine Mensah Sedzro
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, 53715, WI, USA.
| | - Mukhtar Oluwaseun Idris
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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Revankar AG, Bagewadi ZK, Shaikh IA, Mannasaheb BA, Ghoneim MM, Khan AA, Asdaq SMB. In-vitro and computational analysis of Urolithin-A for anti-inflammatory activity on Cyclooxygenase 2 (COX-2). Saudi J Biol Sci 2023; 30:103804. [PMID: 37727526 PMCID: PMC10505678 DOI: 10.1016/j.sjbs.2023.103804] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/16/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
Cyclooxygenase 2 (COX-2) participates in the inflammation process by converting arachidonic acid into prostaglandin G2 which increases inflammation, pain and fever. COX-2 has an active site and a heme pocket and blocking these sites stops the inflammation. Urolithin A is metabolite of ellagitannin produced from humans and animals gut microbes. In the current study, Urolithin A showed good pharmacokinetic properties. Molecular docking of the complex of Urolithin A and COX-2 revealed the ligand affinity of -7.97 kcal/mol with the ligand binding sites at TYR355, PHE518, ILE517 and GLN192 with the 4-H bonds at a distance of 2.8 Å, 2.3 Å, 2.5 Å and 1.9 Å. The RMSD plot for Urolithin A and COX-2 complex was observed to be constant throughout the duration of dynamics. A total of 3 pair of hydrogen bonds was largely observed on average of 3 simulation positions for dynamics duration of 500 ns. The MMPBSA analysis showed that active site amino acids had a binding energy of -22.0368 kJ/mol indicating that throughout the simulation the protein of target was bounded by Urolithin A. In-silico results were validated by biological assays. Urolithin A strongly revealed to exhibit anti-inflammatory effect on COX-2 with an IC50 value of 44.04 µg/mL. The anti-inflammatory capability was also depicted through reduction of protein denaturation that showed 37.6 ± 0.1 % and 43.2 ± 0.07 % reduction of protein denaturation for BSA and egg albumin respectively at 500 µg/mL. The present study, suggests Urolithin A to be an effective anti-inflammatory compound for therapeutic use.
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Affiliation(s)
- Archana G. Revankar
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka 580031, India
| | - Zabin K. Bagewadi
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka 580031, India
| | - Ibrahim Ahmed Shaikh
- Department of Pharmacology, College of Pharmacy, Najran University, Najran 66462, Saudi Arabia
| | | | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Aejaz Abdullatif Khan
- Department of General Science, Ibn Sina National College for Medical Studies, Jeddah 21418, Saudi Arabia
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Sztanke M, Sztanke K, Ostasz A, Głuchowska H, Łyszczek R. Thermal Investigations of Annelated Triazinones-Potential Analgesic and Anticancer Agents. Molecules 2023; 28:6542. [PMID: 37764318 PMCID: PMC10538000 DOI: 10.3390/molecules28186542] [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: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
In this article, for the first time, TG-DSC and TG-FTIR investigations of potential pharmaceutics, i.e., analgesic and anticancer active annelated triazinones (1-9) have been presented. The thermal behaviour of these molecules was established in oxidative and inert conditions. The solid-liquid phase transition for each compound (1-9) was documented by one sharp DSC peak confirming the high purity of each sample studied. All the molecules were characterised in terms of calorimetric changes and mass changes during their heating. They revealed high thermal stability in oxidative and inert conditions. The observed tendency in thermal stability changes in relation to a substituent present at the phenyl moiety was found to be similar in air and nitrogen. It was confirmed that annelated triazinones 1-9 were stable up to a temperature range of 241-296 °C in air, and their decomposition process proceeded in two stages under oxidative conditions. In addition, it was established that their thermal stability in air decreased in the following order of R at the phenyl moiety: 4-Cl > 3,4-Cl2 > H > 3-Cl > 4-CH3 > 2-CH3 > 3-CH3 > 2-Cl > 2-OCH3. The volatile decomposition products of the investigated molecules were proposed by comparing the FTIR spectra collected during their thermogravimetric analysis in nitrogen with the spectra from the database of reference compounds. None of annelated triazinones 1-9 underwent any polymorphic transformation during thermal studies. All the compounds proved to be safe for erythrocytes. In turn, molecules 3, 6, and 9 protected red blood cells from oxidative damage, and therefore may be helpful in the prevention of free radical-mediated diseases.
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Affiliation(s)
- Małgorzata Sztanke
- Department of Medical Chemistry, Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
| | - Krzysztof Sztanke
- Laboratory of Bioorganic Compounds Synthesis and Analysis, Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
| | - Agnieszka Ostasz
- Department of General and Coordination Chemistry and Crystallography, Faculty of Chemistry, Institute of Chemical Sciences, Maria Curie-Skłodowska University, M.C. Skłodowskiej Sq. 2, 20-031 Lublin, Poland
| | - Halina Głuchowska
- Department of General and Coordination Chemistry and Crystallography, Faculty of Chemistry, Institute of Chemical Sciences, Maria Curie-Skłodowska University, M.C. Skłodowskiej Sq. 2, 20-031 Lublin, Poland
| | - Renata Łyszczek
- Department of General and Coordination Chemistry and Crystallography, Faculty of Chemistry, Institute of Chemical Sciences, Maria Curie-Skłodowska University, M.C. Skłodowskiej Sq. 2, 20-031 Lublin, Poland
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Worzakowska M, Sztanke M, Rzymowska J, Sztanke K. Thermal Decomposition Path-Studied by the Simultaneous Thermogravimetry Coupled with Fourier Transform Infrared Spectroscopy and Quadrupole Mass Spectrometry-Of Imidazoline/Dimethyl Succinate Hybrids and Their Biological Characterization. MATERIALS (BASEL, SWITZERLAND) 2023; 16:4638. [PMID: 37444951 DOI: 10.3390/ma16134638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023]
Abstract
The thermal decomposition path of synthetically and pharmacologically useful hybrid materials was analyzed in inert and oxidizing conditions for the first time and presented in this article. All the imidazoline/dimethyl succinate hybrids (1-5) were studied using the simultaneous thermogravimetry (TG) coupled with Fourier transform infrared spectroscopy (FTIR) and quadrupole mass spectrometry (QMS). It was found that the tested compounds were thermally stable up to 200-208 °C (inert conditions) and up to 191-197 °C (oxidizing conditions). In both furnace atmospheres, their decomposition paths were multi-step processes. At least two major stages (inert conditions) and three major stages (oxidizing conditions) of their decomposition were observed. The first decomposition stage occurred between T5% and 230-237 °C. It was connected with the breaking of one ester bond. This led to the emission of one methanol molecule and the formation of radicals capable of further radical reactions in both used atmospheres. At the second decomposition stage (Tmax2) between 230-237 °C and 370 °C (inert conditions), or at about 360 °C (oxidizing conditions), the cleavage of the second ester bond and N-N and C-C bonds led to the emission of CH3OH, HCN, N2, and CO2 and other radical fragments that reacted with each other to form clusters and large clusters. Heating the tested compounds to a temperature of about 490 °C resulted in the emission of NH3, HCN, HNCO, aromatic amines, carbonyl fragments, and the residue (Tmax2a) in both atmospheres. In oxidizing conditions, the oxidation of the formed residues (Tmax3) was related to the production of CO2, CO, and H2O. These studies confirmed the same radical decomposition mechanism of the tested compounds both in inert and oxidizing conditions. The antitumor activities and toxicities to normal cells of the imidazoline/dimethyl succinate hybrids were also evaluated. As a result, the two hybrid materials (3 and 5) proved to be the most selective in biological studies, and therefore, they should be utilized in further, more extended in vivo investigations.
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Affiliation(s)
- Marta Worzakowska
- Department of Polymer Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 33 Gliniana Street, 20-614 Lublin, Poland
| | - Małgorzata Sztanke
- Department of Medical Chemistry, Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
| | - Jolanta Rzymowska
- Department of Biology and Genetics, Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
| | - Krzysztof Sztanke
- Laboratory of Bioorganic Compounds Synthesis and Analysis, Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
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Comprehensive Computational Studies of Naturally Occurring Kuguacins as Antidiabetic Agents by Targeting Visfatin. CHEMISTRY AFRICA 2023. [DOI: 10.1007/s42250-023-00604-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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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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Kumar MNVR. Urolithin A Nanoparticle Therapy for Cisplatin-Induced Acute Kidney Injury. Nephron Clin Pract 2022; 147:3-5. [PMID: 35472845 PMCID: PMC9755071 DOI: 10.1159/000524509] [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: 03/14/2022] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Cisplatin continues to be one of the frontline cytotoxic drugs. However, cisplatin-induced acute kidney injury (AKI) remains a major unmet medical need without any approved pharmacological interventions. The involvement of reactive oxygen species generation and activation of inflammatory and apoptotic pathways in the pathogenesis of cisplatin-induced AKI prompts the use of natural anti-inflammatory compounds. In this context, resolution of inflammation using natural antioxidant and anti-inflammatory such as urolithin A (UA) could prove beneficial. In the end, testing such combinations in models to eliminate the possibility that UA stimulates tumor growth or compromises the potency of cisplatin could prove useful for clinical translation of adjuvant therapies.
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Affiliation(s)
- M N V Ravi Kumar
- College of Community Health Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
- The Center for Convergent Bioscience and Medicine (CCBM), The University of Alabama, Tuscaloosa, Alabama, USA
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
- Chemical and Biological Engineering, University of Alabama, Tuscaloosa, Alabama, USA
- Alabama Life Research Institute, The University of Alabama, Tuscaloosa, Alabama, USA
- Division of Nephrology, Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
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