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Bhavyashree N, Vaishnavi MS, Shravani P, Sabat S. Molecular Dynamics Simulation Studies of Beta-Glucogallin and Dihydro Dehydro Coniferyl Alcohol from Syzygium cumini for its Antimicrobial Activity on Staphylococcus aureus. Cell Biochem Biophys 2024:10.1007/s12013-024-01489-1. [PMID: 39214923 DOI: 10.1007/s12013-024-01489-1] [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: 08/09/2024] [Indexed: 09/04/2024]
Abstract
With the escalating threat of antimicrobial resistance (AMR), discovering novel therapeutic agents against resistant pathogens like Staphylococcus aureus is crucial. This study explores phytochemicals from Syzygium cumini for their potential efficacy against AMR S. aureus infections, elucidating their mechanisms through in silico methods. We investigated 83 compounds from S. cumini, sourced from PubMed, using rigorous docking analysis against the ATP binding domain AgrC of S. aureus with AMdock with Autodock Vina v1.5.2. Drug-likeness predictions were assessed using SwissADME v2023 and Pass online v2.0. Molecular dynamics (MD) simulations identified promising compounds, focusing on stability and interaction dynamics. Beta-Glucogallin (BEG) and Dihydro Dehydro Coniferyl alcohol (DIH) emerged as significant hits. MD simulations with GROMACS v2020.6 revealed stable BEG and DIH complexes with AgrC, forming six hydrogen bonds with six key amino acids (Arg-303, Asp-338, Glu-342, Glu-384, Lys-389, Gly-396), indicating strong and stable bonding. The binding affinities for DIH and BEG are -73.474 ± 11.104 kJ/mol and -6.319 ± 18.823 kJ/mol with 4BXI, respectively. Our findings highlight BEG and DIH as promising candidates against AMR S. aureus infections, showing favourable binding affinities and stable interactions with AgrC. This study underscores the importance of natural products in combating AMR and demonstrates the utility of computational methodologies in drug discovery. Further experimental validation is warranted to fully exploit these phytochemicals' therapeutic potential.
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Affiliation(s)
- N Bhavyashree
- Department of Biotechnology, People's Education Society University, Bangalore, 560085, Karnataka, India
| | - M S Vaishnavi
- Department of Biotechnology, People's Education Society University, Bangalore, 560085, Karnataka, India
| | - P Shravani
- Department of Biotechnology, People's Education Society University, Bangalore, 560085, Karnataka, India
| | - Sasmita Sabat
- Department of Biotechnology, People's Education Society University, Bangalore, 560085, Karnataka, India.
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Tang W, Liu Y, Li X, Leng G, Gao J, Wang Y, Yao J, Liu Z, Zhou Q, Xu Y. Microbiological Characteristics of Clinically Isolated Staphylococcus aureus with Different Hemolytic Phenotypes in China. Infect Drug Resist 2024; 17:3273-3287. [PMID: 39104458 PMCID: PMC11299731 DOI: 10.2147/idr.s466416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
Purpose This study aimed to investigate the microbiological characteristics of clinically isolated Staphylococcus aureus with different hemolytic phenotypes in China. Materials and Methods Using the three-point inoculation method, the hemolytic phenotypes of 1295 clinically isolated S. aureus strains were detected and categorized. Antimicrobial susceptibility testing of all strains was performed using a VITEK 2 Compact System. After sample size matching, plasma coagulase activity, catalase activity, mRNA expression of hemolysin genes (hla, hlb, hlc, and hld), biofilm formation, growth kinetics, inflammatory response of macrophages and cytotoxicity of S. aureus with different hemolytic phenotypes using the rabbit plasma kit, the catalase test on slides, qRT-PCR, crystal violet staining, the microcultivation assay, the ELISA kits, and the CCK-8 assay, respectively. Results Seven categories of hemolytic phenotypes were identified. Accordingly, strains were categorized into seven different groups, including S. aureus with complete hemolytic phenotype (SCHP), S. aureus with weak hemolytic phenotype (SWHP), S. aureus with incomplete hemolytic phenotype 1 (SIHP-1), SIHP-2, SIHP-3, SIHP-4 and SIHP-5, the last three of which were reported for the first time. Except for the hemolytic phenotype, all seven groups differed in clinical isolation rates, antibiotic resistance profile, plasma coagulase activity, mRNA expression of hemolysin genes, biofilm formation, growth kinetics, inflammatory response of macrophages, and cytotoxicity. Conclusion S. aureus with different hemolytic phenotypes have distinctive microbiological characteristics. Clinical microbiologists need to be vigilant about the hemolytic phenotypes when culturing S. aureus strains, and actively enhance communication with clinicians to optimize the treatment of infection.
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Affiliation(s)
- Wei Tang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People’s Republic of China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Ying Liu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People’s Republic of China
| | - Xin Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Guiyun Leng
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Ju Gao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Yawu Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Jie Yao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Zhou Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, People’s Republic of China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People’s Republic of China
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Govindan R, Gnanasekaran C, Govindan R, Muthuchamy M, Quero F, Jothi A, Chelliah CK, Arunachalam A, Viswanathan MR, Natesan M, Kadaikunnan S, Li WJ. Anti-quorum Sensing and Anti-biofilm Effect of Nocardiopsis synnemataformans RMN 4 (MN061002) Compound 2,6-Di-tert-butyl, 1,4-Benzoquinone Against Biofilm-Producing Bacteria. Appl Biochem Biotechnol 2024; 196:3914-3948. [PMID: 37792174 DOI: 10.1007/s12010-023-04738-w] [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] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
In this study, the anti-biofilm compound of 2,6-Di-tert-butyl, 1,4-benzoquinone was purified from Nocardiopsis synnemataformans (N. synnemataformans) RMN 4 (MN061002). To confirm the compound, various spectroscopy analyses were done including ultraviolet (UV) spectrometer, Fourier transform infrared spectroscopy (FTIR), analytical high-performance liquid chromatography (HPLC), preparative HPLC, gas chromatography-mass spectroscopy (GC-MS), liquid chromatography-mass spectroscopy (LC-MS), and 2D nuclear magnetic resonance (NMR). Furthermore, the purified compound was shown 94% inhibition against biofilm-producing Proteus mirabilis (P. mirabilis) (MN396686) at 70 µg/mL concentrations. Furthermore, the metabolic activity, exopolysaccharide damage, and hydrophobicity degradation results of identified compound exhibited excellent inhibition at 100 µg/mL concentration. Furthermore, the confocal laser scanning electron microscope (CLSM) and scanning electron microscope (SEM) results were shown with intracellular damages and architectural changes in bacteria. Consecutively, the in vivo toxicity effect of the compound against Artemia franciscana (A. franciscana) was shown to have a low mortality rate at 100 µg/mL. Finally, the molecular docking interaction between the quorum sensing (QS) genes and identified compound clearly suggested that the identified compound 2,6-Di-tert-butyl, 1,4-benzoquinone has anti-quorum sensing and anti-biofilm activities against P. mirabilis (MN396686).
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Affiliation(s)
- Rajivgandhi Govindan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
| | - Chackaravarthi Gnanasekaran
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Ramachandran Govindan
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
| | - Maruthupandy Muthuchamy
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
- Lab of Toxicology, Department of Health Sciences, The Graduate School of Dong-A University, 37, Nakdong-Dearo 550 Beon-Gil, Saha-Gu, Busan, 49315, South Korea
| | - Franck Quero
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
| | - Arunachalam Jothi
- School of Chemical & Biotechnology, SASTRA Deemed University, Tamil Nadu, Tanjore, India, 401
| | - Chenthis Knaisha Chelliah
- Department of Nanotechnology, Noorul Islam Centre for Higher Education, Tamil Nadu, Kumaracoil, Kanyakumari, 629180, India
| | - Arulraj Arunachalam
- Departamento de Electricidad, Facultad de Ingeniería, Universidad Tecnológica Metropolitana (UTEM), Macul, Santiago, Chile
| | - Mangalaraja Ramalinga Viswanathan
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Región Metropolitana, Diag. Las Torres 2640, 7941169, Peñalolén, Santiago, Chile
| | - Manoharan Natesan
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Tu DZ, Liu PQ, Zhu GH, Zeng HR, Deng YY, Huang J, Niu XT, Liu YF, Hu J, Liang XM, Finel M, Wang P, Ge GB. Human UDP-glucuronosyltransferase 1As catalyze aristolochic acid D O-glucuronidation to form a lesser nephrotoxic glucuronide. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118116. [PMID: 38548118 DOI: 10.1016/j.jep.2024.118116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Aristolochic acids (AAs) are naturally occurring nitro phenanthrene carboxylic acids primarily found in plants of the Aristolochiaceae family. Aristolochic acid D (AAD) is a major constituent in the roots and rhizomes of the Chinese herb Xixin (the roots and rhizomes of Asarum heterotropoides F. Schmidt), which is a key material for preparing a suite of marketed Chinese medicines. Structurally, AAD is nearly identical to the nephrotoxic aristolochic acid I (AAI), with an additional phenolic group at the C-6 site. Although the nephrotoxicity and metabolic pathways of AAI have been well-investigated, the metabolic pathway(s) of AAD in humans and the influence of AAD metabolism on its nephrotoxicity has not been investigated yet. AIM OF THE STUDY To identify the major metabolites of AAD in human tissues and to characterize AAD O-glucuronidation kinetics in different enzyme sources, as well as to explore the influence of AAD O-glucuronidation on its nephrotoxicity. MATERIALS AND METHODS The O-glucuronide of AAD was biosynthesized and its chemical structure was fully characterized by both 1H-NMR and 13C-NMR. Reaction phenotyping assays, chemical inhibition assays, and enzyme kinetics analyses were conducted to assess the crucial enzymes involved in AAD O-glucuronidation in humans. Docking simulations were performed to mimic the catalytic conformations of AAD in human UDP-glucuronosyltransferases (UGTs), while the predicted binding energies and distances between the deprotonated C-6 phenolic group of AAD and the glucuronyl moiety of UDPGA in each tested human UGT isoenzyme were measured. The mitochondrial membrane potentials (MMP) and reactive oxygen species (ROS) levels in HK-2 cells treated with either AAI, or AAD, or AAD O-glucuronide were tested, to elucidate the impact of O-glucuronidation on the nephrotoxicity of AAD. RESULTS AAD could be rapidly metabolized in human liver and intestinal microsomes (HLM and HIM, respectively) to form a mono-glucuronide, which was purified and fully characterized as AAD-6-O-β-D-glucuronide (AADG) by NMR. UGT1A1 was the predominant enzyme responsible for AAD-6-O-glucuronidation, while UGT1A9 contributed to a lesser extent. AAD-6-O-glucuronidation in HLM, HIM, UGT1A1 and UGT1A9 followed Michaelis-Menten kinetics, with the Km values of 4.27 μM, 9.05 μM, 3.87 μM, and 7.00 μM, respectively. Docking simulations suggested that AAD was accessible to the catalytic cavity of UGT1A1 or UGT1A9 and formed catalytic conformations. Further investigations showed that both AAI and AAD could trigger the elevated intracellular ROS levels and induce mitochondrial dysfunction and in HK-2 cells, but AADG was hardly to trigger ROS accumulation and mitochondrial dysfunction. CONCLUSION Collectively, UGT1A-catalyzed AAD 6-O-glucuronidation represents a crucial detoxification pathway of this naturally occurring AAI analogs in humans, which is very different from that of AAI.
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Affiliation(s)
- Dong-Zhu Tu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Pei-Qi Liu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Guang-Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hai-Rong Zeng
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yan-Yan Deng
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jian Huang
- Pharmacology and Toxicology Division, Shanghai Institute of Food and Drug Control, Shanghai, 201203, China
| | - Xiao-Ting Niu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yan-Fang Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jing Hu
- Department of Nephrology, The Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, China
| | - Xin-Miao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Moshe Finel
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland
| | - Ping Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Guang-Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Packiapalavesam SD, Saravanan V, Mahajan AA, Almutairi MH, Almutairi BO, Arockiaraj J, Kathiravan MK, Karthick Raja Namasivayam S. Identification of novel CA IX inhibitor: Pharmacophore modeling, docking, DFT, and dynamic simulation. Comput Biol Chem 2024; 110:108073. [PMID: 38678727 DOI: 10.1016/j.compbiolchem.2024.108073] [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: 03/18/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Human Carbonic anhydrase IX (hCA IX) is found to be an essential biomarker for the treatment of hypoxic tumors in both the early and metastatic stages of cancer. Due to its active function in maintaining pH levels and overexpression in hypoxic conditions, hCA IX inhibitors can be a potential candidate specifically designed to target cancer development at various stages. In search of selective hCA IX inhibitors, we developed a pharmacophore model from the existing natural product inhibitors with IC50 values less than 50 nm. The identified hit molecules were then investigated on protein-ligand interactions using molecular docking experiments followed by molecular dynamics simulations. Among the zinc database 186 hits with an RMSD value less than 1 were obtained, indicating good contact with key residues HIS94, HIS96, HIS119, THR199, and ZN301 required for optimum activity. The top three compounds were subjected to molecular dynamics simulations for 100 ns to know the protein-ligand complex stability. Based on the obtained MD simulation results, binding free energies are calculated. Density Functional Theory (DFT) studies confirmed the energy variation between the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). The current study has led to the discovery of lead compounds that show considerable promise as hCA IX inhibitors and suggests that three compounds with special molecular features are more likely to be better-inhibiting hCA IX. Compound S35, characterized by a higher stability margin and a smaller energy gap in quantum studies, is an ideal candidate for selective inhibition of CA IX.
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Affiliation(s)
- Shakthi Devi Packiapalavesam
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Venkatesan Saravanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Anand A Mahajan
- Department of Pharmaceutical Analysis, Goa College of Pharmacy, Panaji, Goa 403001, India
| | - Mikhlid H Almutairi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bader O Almutairi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Muthu Kumaradoss Kathiravan
- Dr APJ Kalam Laboratory, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India.
| | - S Karthick Raja Namasivayam
- Centre for Applied Research, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamil Nadu 602105, India.
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Farhat N, Khanam T, Noor S, Khan AU. Structural insight into the binding mode of cefotaxime and meropenem to TEM-1, SHV-1, KPC-2, and Amp-C type beta-lactamases. Cell Biochem Biophys 2024; 82:1299-1308. [PMID: 38730202 DOI: 10.1007/s12013-024-01284-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Antimicrobial resistance is an emerging threat to public health around the world. The study employs computational and biophysical methods to investigate the properties of cefotaxime and meropenem's binding to various beta-lactamases like TEM-1, SHV-1, KPC-2, and Amp-C. The enzyme kinetics of purified proteins revealed an increase in Michaelis constant (Km) value in the presence of meropenem and cefotaxime, indicating a decrease in enzyme affinity for nitrocefin. Proteins interact with meropenem/cefotaxime, causing quenching through complex formation. All proteins have one binding site, and binding constant (Kb) values are 104, indicating strong interaction. The study found that meropenem and cefotaxime had high fitness scores for Amp-C, KPC-2,TEM-1 and SHV-1, with binding energy ranging from -7.4 to -7.8, and hydrogen bonds between them. Molecular Dynamic simulation of protein-ligand complexes revealed cefotaxime-binding proteins have slightly lower Root Mean Square Deviation(RMSD) than meropenem-binding proteins, indicating stable association antibiotics with these proteins.
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Affiliation(s)
- Nabeela Farhat
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Tasneem Khanam
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Saba Noor
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Antimicrobial Resistance Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Zarougui S, Er-Rajy M, Faris A, Imtara H, El fadili M, Qurtam AA, Nasr FA, Al-Zharani M, Elhallaoui M. 3D computer modeling of inhibitors targeting the MCF-7 breast cancer cell line. Front Chem 2024; 12:1384832. [PMID: 38887699 PMCID: PMC11181028 DOI: 10.3389/fchem.2024.1384832] [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: 02/10/2024] [Accepted: 04/11/2024] [Indexed: 06/20/2024] Open
Abstract
This study focused on developing new inhibitors for the MCF-7 cell line to contribute to our understanding of breast cancer biology and various experimental techniques. 3D QSAR modeling was used to design new tetrahydrobenzo[4, 5]thieno[2, 3-d]pyrimidine derivatives with good characteristics. Two robust 3D-QSAR models were developed, and their predictive capacities were confirmed through high correlations [CoMFA (Q2 = 0.62, R 2 = 0.90) and CoMSIA (Q2 = 0.71, R 2 = 0.88)] via external validations (R2 ext = 0.90 and R2 ext = 0.91, respectively). These successful evaluations confirm the potential of the models to provide reliable predictions. Six candidate inhibitors were discovered, and two new inhibitors were developed in silico using computational methods. The ADME-Tox properties and pharmacokinetic characteristics of the new derivatives were evaluated carefully. The interactions between the new tetrahydrobenzo[4, 5]thieno[2, 3-d]pyrimidine derivatives and the protein ERα (PDB code: 4XO6) were highlighted by molecular docking. Additionally, MM/GBSA calculations and molecular dynamics simulations provided interesting information on the binding stabilities between the complexes. The pharmaceutical characteristics, interactions with protein, and stabilities of the inhibitors were examined using various methods, including molecular docking and molecular dynamics simulations over 100 ns, binding free energy calculations, and ADME-Tox predictions, and compared with the FDA-approved drug capivasertib. The findings indicate that the inhibitors exhibit significant binding affinities, robust stabilities, and desirable pharmaceutical characteristics. These newly developed compounds, which act as inhibitors to mitigate breast cancer, therefore possess considerable potential as prospective drug candidates.
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Affiliation(s)
- Sara Zarougui
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Er-Rajy
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Abdelmoujoud Faris
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hamada Imtara
- Faculty of Medicine, Arab American University Palestine, Jenin, Palestine
| | - Mohamed El fadili
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ashraf Ahmed Qurtam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Fahd A. Nasr
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohammed Al-Zharani
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Menana Elhallaoui
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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Hashmi HF, Xuan X, Chen K, Zhang P, Shahab M, Zheng G, Younous YA, Salamatullah AM, Bourhia M. Molecular modeling and simulation approaches to characterize potential molecular targets for burdock inulin to instigate protection against autoimmune diseases. Sci Rep 2024; 14:11291. [PMID: 38760355 PMCID: PMC11101470 DOI: 10.1038/s41598-024-61387-7] [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: 03/06/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
In the current study, we utilized molecular modeling and simulation approaches to define putative potential molecular targets for Burdock Inulin, including inflammatory proteins such as iNOS, COX-2, TNF-alpha, IL-6, and IL-1β. Molecular docking results revealed potential interactions and good binding affinity for these targets; however, IL-1β, COX-2, and iNOS were identified as the best targets for Inulin. Molecular simulation-based stability assessment demonstrated that inulin could primarily target iNOS and may also supplementarily target COX-2 and IL-1β during DSS-induced colitis to reduce the role of these inflammatory mechanisms. Furthermore, residual flexibility, hydrogen bonding, and structural packing were reported with uniform trajectories, showing no significant perturbation throughout the simulation. The protein motions within the simulation trajectories were clustered using principal component analysis (PCA). The IL-1β-Inulin complex, approximately 70% of the total motion was attributed to the first three eigenvectors, while the remaining motion was contributed by the remaining eigenvectors. In contrast, for the COX2-Inulin complex, 75% of the total motion was attributed to the eigenvectors. Furthermore, in the iNOS-Inulin complex, the first three eigenvectors contributed to 60% of the total motion. Furthermore, the iNOS-Inulin complex contributed 60% to the total motion through the first three eigenvectors. To explore thermodynamically favorable changes upon mutation, motion mode analysis was carried out. The Free Energy Landscape (FEL) results demonstrated that the IL-1β-Inulin achieved a single conformation with the lowest energy, while COX2-Inulin and iNOS-Inulin exhibited two lowest-energy conformations each. IL-1β-Inulin and COX2-Inulin displayed total binding free energies of - 27.76 kcal/mol and - 37.78 kcal/mol, respectively, while iNOS-Inulin demonstrated the best binding free energy results at - 45.89 kcal/mol. This indicates a stronger pharmacological potential of iNOS than the other two complexes. Thus, further experiments are needed to use inulin to target iNOS and reduce DSS-induced colitis and other autoimmune diseases.
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Affiliation(s)
- Huma Farooque Hashmi
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Xu Xuan
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaoshan Chen
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Pengying Zhang
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | | | - Ahmad Mohammad Salamatullah
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, 80060, Agadir, Morocco
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9
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Zare F, Ataollahi E, Mardaneh P, Sakhteman A, Keshavarz V, Solhjoo A, Emami L. A combination of virtual screening, molecular dynamics simulation, MM/PBSA, ADMET, and DFT calculations to identify a potential DPP4 inhibitor. Sci Rep 2024; 14:7749. [PMID: 38565703 PMCID: PMC10987597 DOI: 10.1038/s41598-024-58485-x] [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: 12/05/2023] [Accepted: 03/29/2024] [Indexed: 04/04/2024] Open
Abstract
DPP4 inhibitors can control glucose homeostasis by increasing the level of GLP-1 incretins hormone due to dipeptidase mimicking. Despite the potent effects of DPP4 inhibitors, these compounds cause unwanted toxicity attributable to their effect on other enzymes. As a result, it seems essential to find novel and DPP4 selective compounds. In this study, we introduce a potent and selective DPP4 inhibitor via structure-based virtual screening, molecular docking, molecular dynamics simulation, MM/PBSA calculations, DFT analysis, and ADMET profile. The screened compounds based on similarity with FDA-approved DPP4 inhibitors were docked towards the DPP4 enzyme. The compound with the highest docking score, ZINC000003015356, was selected. For further considerations, molecular docking studies were performed on selected ligands and FDA-approved drugs for DPP8 and DPP9 enzymes. Molecular dynamics simulation was run during 200 ns and the analysis of RMSD, RMSF, Rg, PCA, and hydrogen bonding were performed. The MD outputs showed stability of the ligand-protein complex compared to available drugs in the market. The total free binding energy obtained for the proposed DPP4 inhibitor was more negative than its co-crystal ligand (N7F). ZINC000003015356 confirmed the role of the five Lipinski rule and also, have low toxicity parameter according to properties. Finally, DFT calculations indicated that this compound is sufficiently soft.
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Affiliation(s)
- Fateme Zare
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elaheh Ataollahi
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pegah Mardaneh
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354, Freising, Germany
| | - Valiollah Keshavarz
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Quality Control of Drug Products, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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10
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Opoku F, Govender P, Shonhai A, Simelane MB. Iso-mukaadial acetate and ursolic acid acetate bind to Plasmodium Falciparum heat shock protein 70: towards targeting parasite protein folding pathway. BMC Chem 2024; 18:55. [PMID: 38500145 PMCID: PMC10949600 DOI: 10.1186/s13065-024-01159-6] [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: 01/15/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
Plasmodium falciparum is the most lethal malaria parasite. P. falciparum Hsp70 (PfHsp70) is an essential molecular chaperone (facilitates protein folding) and is deemed a prospective antimalarial drug target. The present study investigates the binding capabilities of select plant derivatives, iso-mukaadial acetate (IMA) and ursolic acid acetate (UAA), against P. falciparum using an in silico docking approach. The interaction between the ligands and PfHsp70 was evaluated using plasmon resonance (SPR) analysis. Molecular docking, binding free energy analysis and molecular dynamics simulations were conducted towards understanding the mechanisms by which the compounds bind to PfHsp70. The molecular docking results revealed ligand flexibilities, conformations and positions of key amino acid residues and protein-ligand interactions as crucial factors accounting for selective inhibition of Hsp70. The simulation results also suggest protein-ligand van der Waals forces as the driving force guiding the interaction of these compounds with PfHsp70. Of the two compounds, UAA and IMA bound to PfHsp70 within the micromolar range based on surface plasmon resonance (SPR) based binding assay. Our findings pave way for future rational design of new selective compounds targeting PfHsp70.
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Affiliation(s)
- Francis Opoku
- Department of Chemical Sciences (formerly Department of Applied Chemistry), University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Penny Govender
- Department of Chemical Sciences (formerly Department of Applied Chemistry), University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
| | - Addmore Shonhai
- Department of Biochemistry & Microbiology, University of Venda, Thohoyandou, South Africa
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11
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Bayat Z, Mazaheri T, Farhadifard H, Taherkhani A. Mechanisms Involved in Therapeutic Effects of Scutellaria baicalensis Georgi in Oral Squamous Cell Carcinoma Based on Systems Biology and Structural Bioinformatics Approaches. BIOMED RESEARCH INTERNATIONAL 2024; 2024:1236910. [PMID: 38322303 PMCID: PMC10846925 DOI: 10.1155/2024/1236910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 11/30/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Objective Oral squamous cell carcinoma (OSCC) is the most frequent oral cancer, constituting more than 90% of all oral carcinomas. The 5-year survival rate of OSCC patients is not satisfactory, and therefore, there is an urgent need for new practical therapeutic approaches besides the current therapies to overcome OSCC. Scutellaria baicalensis Georgi (SBG) is a plant of the family Lamiaceae with several pharmaceutical properties such as antioxidant, anti-inflammatory, and anticancer effects. Previous studies have demonstrated the curative effects of SBG in OSCC. Methods A systems biology approach was conducted to identify differentially expressed miRNAs (DEMs) in OSCC patients with a dismal prognosis compared to OSCC patients with a favorable prognosis. A protein interaction map (PIM) was built based on DEMs targets, and the hub genes within the PIM were indicated. Subsequently, the prognostic role of the hubs was studied using Kaplan-Meier curves. Next, the binding affinity of SBG's main components, including baicalein, wogonin, oroxylin-A, salvigenin, and norwogonin, to the prognostic markers in OSCC was evaluated using molecular docking analysis. Results Survival analysis showed that overexpression of CAV1, SERPINE1, ACTB, SMAD3, HMGA2, MYC, EIF2S1, HSPA4, HSPA5, and IL6 was significantly related to a poor prognosis in OSCC. Besides, molecular docking analysis demonstrated the ΔGbinding and inhibition constant values between SBG's main components and SERPINE1, ACTB, HMGA2, EIF2S1, HSPA4, and HSPA5 were as <-8.00 kcal/mol and nanomolar concentration, respectively. The most salient binding affinity was observed between wogonin and SERPINE1 with a criterion of ΔGbinding < -10.02 kcal/mol. Conclusion The present results unraveled potential mechanisms involved in therapeutic effects of SBG in OSCC based on systems biology and structural bioinformatics analyses.
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Affiliation(s)
- Zeynab Bayat
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Tina Mazaheri
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Homa Farhadifard
- Department of Orthodontics, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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12
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Yang Y, Wu Q, Shan X, Zhou H, Wang J, Hu Y, Chen J, Lv Z. Ginkgolide B attenuates cerebral ischemia-reperfusion injury via inhibition of ferroptosis through disrupting NCOA4-FTH1 interaction. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116982. [PMID: 37532074 DOI: 10.1016/j.jep.2023.116982] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/19/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Cerebral ischemia/reperfusion (I/R) injury is a major cause of neuronal damage and death. Ginkgolide B (GB) has been shown to exhibit neuroprotective effects in various brain injury models. AIM OF STUDY The aim of study was to investigate the potential role of GB in protecting against cerebral I/R injury and explore the underlying mechanisms. MATERIALS AND METHODS Adult male Sprague-Dawley rats were exposed to transient middle cerebral artery occlusion (tMCAO) followed by reperfusion in order to trigger cerebral I/R injury. The rats were treated with different doses of GB, vehicle control or positive drug. Neurological function, infarct volume, and levels of ferroptosis markers were evaluated. In vitro experiments were performed using OGD/R-induced PC12 cells to further investigate the effects of GB on ferroptosis and its mechanisms. In addition, molecular docking, and microscale thermophoresis (MST) assay were conducted to explore the combination of GB and NCOA4. RESULTS Reduced infarct volume and enhanced neurological function were signs of dose-dependent protection from cerebral I/R injury by GB therapy. Additionally, GB treatment had an impact on the levels of oxidative stress and ferroptosis markers, including reactive oxygen species (ROS), malondialdehyde (MDA), superoxide dismutase (SOD), and Fe2+ in the cerebral environment during IR injury. Moreover, relevant ferroptosis key factors such as ACSL4, GPX4, FTH1, and NCOA4 can be regulated by GB. In OGD/R-induced PC12 cells, GB protected against ferroptosis by inhibiting autophagy and disrupting the interaction of NCOA4-FTH1. CONCLUSION Our findings suggest that GB may protect against cerebral I/R injury by inhibiting ferroptosis through disrupting NCOA4-FTH1 interaction. GB has potential therapeutic applications for cerebral I/R injury, and further investigation of the underlying mechanisms and clinical trials are warranted.
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Affiliation(s)
- Yuwei Yang
- Nanjing University of Chinese Medicine Hanlin College, 6 Kuangshi Road, Taizhou, 225300, Jiangsu, China.
| | - Qing Wu
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China.
| | - Xin Shan
- Nanjing University of Chinese Medicine Hanlin College, 6 Kuangshi Road, Taizhou, 225300, Jiangsu, China.
| | - Haiyan Zhou
- Nanjing University of Chinese Medicine Hanlin College, 6 Kuangshi Road, Taizhou, 225300, Jiangsu, China.
| | - Jinwen Wang
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China.
| | - Yue Hu
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China; Shen Chun-ti Nation-Famous Experts Studio for Traditional Chinese Medicine Inheritance, Changzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Changzhou, 213003, Jiangsu, China.
| | - Jing Chen
- Nanjing University of Chinese Medicine Hanlin College, 6 Kuangshi Road, Taizhou, 225300, Jiangsu, China.
| | - Zhiyang Lv
- Nanjing University of Chinese Medicine Hanlin College, 6 Kuangshi Road, Taizhou, 225300, Jiangsu, China.
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13
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Zamani M, Mokarram P, Jamshidi M, Siri M, Ghasemi H. Molecular Modelling of Resveratrol Derivatives with SIRT1 for the Stimulation of Deacetylase Activity. Curr Comput Aided Drug Des 2024; 20:943-954. [PMID: 37842901 DOI: 10.2174/0115734099258321231003161602] [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: 04/23/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND Resveratrol is a polyphenol that is found in plants and has been proposed to have a potential therapeutic effect through the activation of SIRT1, which is a crucial member of the mammalian NAD+ -dependent deacetylases. However, how its activity is enhanced toward specific substrates by resveratrol derivatives has not been studied. This study aimed to evaluate the types of interaction of resveratrol and its derivatives with SIRT1 as the target protein, as well as to find out the best ligand with the strangest interaction with SIRT1. MATERIALS AND METHODS In this study, we employed the extensive molecular docking analysis using AutoDock Vina to comparatively evaluate the interactions of resveratrol derivatives (22 molecules from the ZINC database) as ligands with SIRT1 (PDB ID: 5BTR) as a receptor. The ChemDraw and Chem3D tools were used to prepare 3D structures of all ligands and energetically minimize them by the MM2 force field. RESULTS The molecular docking and visualizations showed that conformational change in resveratrol derivatives significantly influenced the parameter for docking results. Several types of interactions, including conventional hydrogen bonds, carbon-hydrogen bonds, Pi-donor hydrogen bonds, and Pi-Alkyl, were found via docking analysis of resveratrol derivatives and SIRT1 receptors. The possible activation effect of resveratrol 4'-(6-galloylglucoside) with ZINC ID: ZINC230079516 with higher binding energy score (-46.8608 kJ/mol) to the catalytic domain (CD) of SIRT1 was achieved at the maximum value for SIRT1, as compared to resveratrol and its other derivatives. CONCLUSION Finally, resveratrol 4'-(6-galloylglucoside), as a derivative for resveratrol, has stably interacted with the CD of SIRT1 and might be a potential effective activator for SIRT1.
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Affiliation(s)
- Mozhdeh Zamani
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Jamshidi
- Institute für Chemie, Universität Oldenburg, Carl-von-Ossietzky-Straße 9-11,26129 Oldenburg, Germany
| | - Morvarid Siri
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hadi Ghasemi
- Autophagy Research Center, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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14
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Alabdulraheem ZTJ, Durdagi S. Ab initio and comparative 3D modeling of FAM222A-encoded protein and target-driven-based virtual screening for the identification of novel therapeutics against Alzheimer's disease. J Mol Graph Model 2023; 125:108575. [PMID: 37552909 DOI: 10.1016/j.jmgm.2023.108575] [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: 01/29/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
The complex nature of Alzheimer's disease (AD) makes it difficult to understand the exact molecular processes leading to neuron death. However, two molecular factors - the production of amyloid-beta plaques and tau tangles - are considered to be linked to AD. A genetic marker for brain atrophy, FAM222A, has been identified by the unique cross-phenotype meta-analysis of genetics imaging and the molecular features show an interaction between the protein aggregatin encoded by FAM222A and amyloid beta (Aβ)-peptide (1-42) via its N-terminal Aβ binding domain, thus increasing Aβ aggregation. Function of Aggregatin protein is unclear, and its 3D structure has not been investigated in experimental analysis, so far. Hence, in the present study, first time in literature, 3D models of FAM222A-encoded Aggregatin were systematically constructed by applying diverse homology modeling approaches and they were used as target structures at the virtual screening of FDA-approved drugs and drugs currently under research in clinical trials. Then, the identified hit molecules were chosen for further molecular dynamics (MD) simulations and post-MD analyses. Our integrated ligand-based and protein-driven-based virtual screening results show that Cefpiramide, Diniprofylline, Fostriecin, and Droperidol may target Aggregatin.
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Affiliation(s)
- Zeyad Tareq Jasim Alabdulraheem
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey; Molecular Therapy Laboratory, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul, Turkey; Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey.
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15
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Halim SA, Waqas M, Khan A, Ogaly HA, Othman G, Al-Harrasi A. Identification of potential agonist-like molecules for α2-adrenergic receptor by multi-layer virtual screening to combat sinusitis. Comput Biol Med 2023; 167:107693. [PMID: 37976818 DOI: 10.1016/j.compbiomed.2023.107693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Sinusitis is one of the most common respiratory inflammatory conditions and a significant health issue that affects millions of people worldwide with a global prevalence of 10-15%. The side effects of available drug regimens of sinus infection demand the urgent development of new drug candidates to combat sinusitis. With the aim of identifying new drug-like candidates to control sinus, we have conducted multifold comprehensive screening of drug-like molecules targeting α2-adrenergic receptor (α2-AR), which serve as the primary drug target in sinusitis. By structure-based virtual screening of in-house compound's database, ten molecules (CP1-CP10) with agonistic effects for α2-AR were selected, and their binding mechanism with critical residues of α2-AR and their physicochemical properties were studied. Moreover, the process of receptor activation by these compounds and the conformational changes in α2-AR caused by these molecules, were further explored by molecular dynamic simulation. The MM-PBSA estimated free energies of compounds are higher than that of reference agonist (ΔGTOTAL = -39.0 kcal/mol). Among all, CP2-CP3, CP7-CP8 and CP6 have the highest binding free energies of -78.9 kcal/mol, -77.3 kcal/mol, -75.60 kcal/mol, -64.8 kcal/mol, and -61.6 kcal/mol, respectively. While CP4 (-55.0 kcal/mol), CP5 (-49.2 kcal/mol), CP9 (-54.8 ± 0.07 kcal/mol), CP10 (-56.7 ± 0.10 kcal/mol) and CP1 (-46.0 ± 0.08 kcal/mol) also exhibited significant binding free energies. These energetically favorable binding energies indicate strong binding affinity of our compounds for α2-AR as compared to known partial agonist. Therefore, these molecules can serve as excellent drug-like candidates for sinusitis.
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Affiliation(s)
- Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman.
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman; Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Dhodial, 21120, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman
| | - Hanan A Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
| | - Gehan Othman
- Biology Department, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mouz, Nizwa, 616, Oman.
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16
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Kang N, Kim EA, Heo SY, Heo SJ. Structure-Based In Silico Screening of Marine Phlorotannins for Potential Walrus Calicivirus Inhibitor. Int J Mol Sci 2023; 24:15774. [PMID: 37958757 PMCID: PMC10647355 DOI: 10.3390/ijms242115774] [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: 08/08/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
A new calicivirus isolated from a walrus was reported in 2004. Since unknown marine mammalian zoonotic viruses could pose great risks to human health, this study aimed to develop therapeutic countermeasures to quell any potential outbreak of a pandemic caused by this virus. We first generated a 3D model of the walrus calicivirus capsid protein and identified compounds from marine natural products, especially phlorotannins, as potential walrus calicivirus inhibitors. A 3D model of the target protein was generated using homology modeling based on two publicly available template sequences. The sequence of the capsid protein exhibited 31.3% identity and 42.7% similarity with the reference templates. The accuracy and reliability of the predicted residues were validated via Ramachandran plotting. Molecular docking simulations were performed between the capsid protein 3D model and 17 phlorotannins. Among them, five phlorotannins demonstrated markedly stable docking profiles; in particular, 2,7-phloroglucinol-6,6-bieckol showed favorable structural integrity and stability during molecular dynamics simulations. The results indicate that the phlorotannins are promising walrus calicivirus inhibitors. Overall, the study findings showcase the rapid turnaround of in silico-based drug discovery approaches, providing useful insights for developing potential therapies against novel pathogenic viruses, especially when the 3D structures of the viruses remain experimentally unknown.
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Affiliation(s)
| | | | | | - Soo-Jin Heo
- Jeju Bio Research Center, Korea Institute of Ocean Science and Technology (KIOST), Jeju 63349, Republic of Korea; (N.K.); (E.-A.K.); (S.-Y.H.)
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17
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Lopes LM, Germiniani LGL, Rocha Neto JBM, Andrade PF, da Silveira GAT, Taketa TB, Gonçalves MDC, Beppu MM. Preparation and characterization of porous membranes of glucomannan and silver decorated cellulose nanocrystals for application as biomaterial. Int J Biol Macromol 2023; 250:126236. [PMID: 37562469 DOI: 10.1016/j.ijbiomac.2023.126236] [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: 04/19/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Bacterial infection usually represents a threat in medical wound care, due to the increase in treatment complexity and the risk of antibiotic resistance. For presenting interesting characteristics for the use as biomaterial, natural polymers have been explored for this application. Among them, a promising candidate is the konjac glucomannan (KGM) with outstanding biocompatibility and biodegradability but lack of antibacterial activity. In this study, KGM was combined with silver decorated cellulose nanocrystals (CNC-Ag) to prepare membranes by using a recent reported casting-freezing method. The results highlight the potential anti-adhesive activity of the new materials against Staphylococcus aureus upon contact, without the burst release of silver nanoparticles. Furthermore, the incorporation of CNC enhanced the thermal stability of these membranes while preserving the favorable mechanical properties of the KGM-based material. These findings highlight a straightforward approach to enhance the antibacterial properties of natural polymers, which can be effectively useful in medical devices like wound dressings that typically lack such properties.
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Affiliation(s)
- Laise Maia Lopes
- University of Campinas, School of Chemical Engineering, Campinas, Brazil.
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18
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Xie P, Gao Y, Wu C, Li X, Yang Y. The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling. J Mol Model 2023; 29:320. [PMID: 37725157 DOI: 10.1007/s00894-023-05723-0] [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: 06/26/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
CONTEXT Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. METHODS AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package. RESULTS The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.
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Affiliation(s)
- Peng Xie
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Yue Gao
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Chenqi Wu
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Xuenan Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yanan Yang
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China.
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19
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Khan A, Sohail S, Yaseen S, Fatima S, Wisal A, Ahmed S, Nasir M, Irfan M, Karim A, Basharat Z, Khan Y, Aurongzeb M, Raza SK, Alshahrani MY, Morel CM, Hassan SS. Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy. Funct Integr Genomics 2023; 23:254. [PMID: 37495774 DOI: 10.1007/s10142-023-01179-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
Staphylococcus sciuri (also currently Mammaliicoccus sciuri) are anaerobic facultative and non-motile bacteria that cause significant human pathogenesis such as endocarditis, wound infections, peritonitis, UTI, and septic shock. Methicillin-resistant S. sciuri (MRSS) strains also infects animals that include healthy broilers, cattle, dogs, and pigs. The emergence of MRSS strains thereby poses a serious health threat and thrives the scientific community towards novel treatment options. Herein, we investigated the druggable genome of S. sciuri by employing subtractive genomics that resulted in seven genes/proteins where only three of them were predicted as final targets. Further mining the literature showed that the ArgS (WP_058610923), SecY (WP_058611897), and MurA (WP_058612677) are involved in the multi-drug resistance phenomenon. After constructing and verifying the 3D protein homology models, a screening process was carried out using a library of Traditional Chinese Medicine compounds (consisting of 36,043 compounds). The molecular docking and simulation studies revealed the physicochemical stability parameters of the docked TCM inhibitors in the druggable cavities of each protein target by identifying their druggability potential and maximum hydrogen bonding interactions. The simulated receptor-ligand complexes showed the conformational changes and stability index of the secondary structure elements. The root mean square deviation (RMSD) graph showed fluctuations due to structural changes in the helix-coil-helix and beta-turn-beta changes at specific points where the pattern of the RMSD and root mean square fluctuation (RMSF) (< 1.0 Å) support any major domain shifts within the structural framework of the protein-ligand complex and placement of ligand was well complemented within the binding site. The β-factor values demonstrated instability at few points while the radius of gyration for structural compactness as a time function for the 100-ns simulation of protein-ligand complexes showed favorable average values and denoted the stability of all complexes. It is assumed that such findings might facilitate researchers to robustly discover and develop effective therapeutics against S. sciuri alongside other enteric infections.
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Affiliation(s)
- Aafareen Khan
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Saman Sohail
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Seerat Yaseen
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Sareen Fatima
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
| | - Ayesha Wisal
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Sufyan Ahmed
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Mahrukh Nasir
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Asad Karim
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Zarrin Basharat
- Alpha Genomics (Private) Limited, Islamabad, 44710, Pakistan
| | - Yasmin Khan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Aurongzeb
- Faculty of Engineering Sciences & Technology, Hamdard University, Karachi, 74600, Pakistan
| | - Syed Kashif Raza
- Faculty of Rehabilitation and Allied Health Sciences (FRAHS), Riphah International University, Faisalabad, Pakistan
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha, 9088, Saudi Arabia
| | - Carlos M Morel
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
| | - Syed S Hassan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan.
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
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20
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Karabacak Atay Ç, Dilek Ö, Tilki T, Dede B. A novel imidazole-based azo molecule: synthesis, characterization, quantum chemical calculations, molecular docking, molecular dynamics simulations and ADMET properties. J Mol Model 2023; 29:226. [PMID: 37405575 DOI: 10.1007/s00894-023-05625-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
CONTEXT Today, the treatment or prevention of cancer, which is one of the most important causes of death, has a very important place. On the other hand, the discovery of new antimicrobial agents is also important because of antibiotic resistance that can occur in humans. For these reasons, in this study, the synthesis, quantum chemical calculations, and in silico studies of a novel azo molecule with high bioactive potential were carried out. In the first step of the synthesis part, (3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)aniline compound, which is the raw material of the drug used in cancer treatments, was synthesized. In the second step, a novel product 2-hydroxy-5-((3-(4-methyl-1H-imidazol-1-yl)-5-trifluoromethyl)phenyl)diazenyl)benzaldehyde (HTB) was obtained as a result of the reaction of salicylaldehyde coupling to this compound. Then, as it was being spectroscopically described, its geometry was optimized. In order to perform quantum chemical calculations, the molecular structure, vibrational spectroscopic data, electronic transition absorption wavelengths, HOMO and LUMO analyses, molecular electrostatic potential (MEP) and potential energy surface (PES) of the molecule were all taken into consideration. Using molecular docking simulations, in silico interactions of the HTB molecule with some anticancer and antibacterial-related proteins were studied. In addition, the ADMET parameters of the HTB were also predicted. METHODS The structure of the synthesized compound was elucidated using 1H-NMR, 13C-NMR (APT), 19F-NMR, FT-IR and UV-vis spectroscopic methods. The optimized geometry, molecular electrostatic potential diagram and vibrational frequencies of the HTB molecule were calculated at the DFT/B3LYP/6-311G(d,p) level. The TD-DFT method was used to calculate HOMOs-LUMOs and electronic transitions, and the GIAO method was used to calculate chemical shift values. It was observed that the experimental spectral data were in good agreement with the theoretical ones. Molecular docking simulations of the HTB molecule using 4 different proteins were investigated. Two of these proteins were involved in simulating anticancer activity and the other two in simulating antibacterial activity. According to molecular docking studies, the binding energies of the complexes formed by the HTB compound with the 4 selected proteins were between -9.6 and -8.7 kcal/mol. HTB showed the best affinity with VEGFR2 protein (PDB ID: 2XIR) and the binding energy of this interaction was found to be -9.6 kcal/mol. The HTB-2XIR interaction was examined with molecular dynamics simulation for 25 ns and it was determined that this complex was stable during this time. In addition, the ADMET parameters of the HTB were also calculated, and from these values, it was determined that the compound has very low toxicity and high oral bioavailability.
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Affiliation(s)
- Çiğdem Karabacak Atay
- Department of Basic Education, Faculty of Education, Burdur Mehmet Akif Ersoy University, 15030, Burdur, Turkey.
| | - Ömer Dilek
- Central Research Laboratory Application and Research Center, Isparta University of Applied Sciences, 32200, Isparta, Turkey
| | - Tahir Tilki
- Department of Chemistry, Faculty of Science & Art, Süleyman Demirel University, 32260, Isparta, Turkey
| | - Bülent Dede
- Department of Chemistry, Faculty of Science & Art, Süleyman Demirel University, 32260, Isparta, Turkey
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21
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Siddiqui S, Riaz S, Ahmad R, Wani MJ, Hashmi MA, Zofair SFF, Mateen S, Moin S. Synergistic effect of chlorogenic acid and vitamin D3 (cholecalciferol) on in-vitro glycation may assist in prevention of polycystic ovarian syndrome (PCOS) progression - A biophysical, biochemical and in-silico study. Int J Biol Macromol 2023; 245:125497. [PMID: 37369258 DOI: 10.1016/j.ijbiomac.2023.125497] [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: 03/26/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Advanced glycation end products (AGEs) are formed through non-enzymatic glycation, that have been linked to various diseases, including polycystic ovarian syndrome (PCOS) playing a critical role leading to secondary comorbidities such as diabetes-related problems, cardiovascular complications, infertility, etc. As a result, there has been a lot of research into AGE-inhibiting phytochemicals for the remediation and obstruct progression of glycation-related illnesses. The current study is based on in-vitro protein model, in which human serum albumin have been used to investigate the cumulative effect of chlorogenic acid (CGA) and cholecalciferol (vitamin D) on glycation and evaluate their inhibitory impact on AGEs production in the presence of methylglyoxal. Through the application of several biochemical and biophysical techniques, we were able to examine the synergistic impact of both the compounds on albumin structure and its biochemical properties during different stages of glycation. According to Nitro-blue tetrazolium assay results indicate that CGA and vitamin D inhibited fructosamine (early glycation product) production. Moreover, free thiol and lysine residues were significantly increased whereas protein carbonyl levels were significantly decreased. Additive effect of CGA and vitamin D were associated with reduced AGEs fluorescence and increased tryptophan and tyrosine fluorescence. Amadori-albumin after treatment showed some evidence of regaining its alpha-helicity as measured by far-UV CD spectrum. Furthermore, secondary structural alterations were confirmed by Fourier transform infrared spectroscopy (FTIR). ANS (1-anilinonaphthalene-8-sulfonic acid) fluorescence spectra also displayed less revelation of hydrophobic patches. Bilirubin binding capacity was also restored which showed functional recovery of HSA. The electrophoretic mobility was also restored which is portrayed by SDS-PAGE. Additionally, to predict the anti-aggregation potential of CGA and vitamin D, congo red assay and ThT fluorescence was performed which reveal low aggregate formation after treatment. These results corroborated with scanning electron microscopy and confocal microscopy. Docking and simulation results also reveal spontaneous binding of CGA and vitamin D on subdomain IIA of HSA favoring their binding thermodynamically. All the findings suggest that chlorogenic acid and cholecalciferol given in combination might help in prevention of PCOS progression and its related complications.
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Affiliation(s)
- Sana Siddiqui
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Sana Riaz
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Rizwan Ahmad
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Mohd Junaid Wani
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Syeda Fauzia Farheen Zofair
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Somaiya Mateen
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Shagufta Moin
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India.
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Ribeiro R, Botelho FD, Pinto AMV, La Torre AMA, Almeida JSFD, LaPlante SR, Franca TCC, Veiga-Junior VF, Dos Santos MC. Molecular modeling study of natural products as potential bioactive compounds against SARS-CoV-2. J Mol Model 2023; 29:183. [PMID: 37212923 DOI: 10.1007/s00894-023-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
CONTEXT The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus's invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. METHODS The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand's free binding energies using the molecular mechanics - Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD) software.
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Affiliation(s)
- Rayssa Ribeiro
- Department of Chemical Engineering, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Fernanda D Botelho
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Amanda M V Pinto
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Antonia M A La Torre
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Joyce S F D Almeida
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Steven R LaPlante
- INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard Des Prairies, Laval, QC, Canada
| | - Tanos C C Franca
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
- INRS, Centre Armand-Frappier Santé Biotechnologie 531, Boulevard Des Prairies, Laval, QC, Canada
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Valdir F Veiga-Junior
- Department of Chemical Engineering, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Marcelo C Dos Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil.
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Eissa IH, Elkaeed EB, Elkady H, Yousef RG, Alsfouk BA, Elzahabi HSA, Ibrahim IM, Metwaly AM, Husein DZ. Design, Molecular Modeling, MD Simulations, Essential Dynamics, ADMET, DFT, Synthesis, Anti-proliferative, and Apoptotic Evaluations of a New Anti-VEGFR-2 Nicotinamide Analogue. Curr Pharm Des 2023; 29:2902-2920. [PMID: 38031271 DOI: 10.2174/0113816128274870231102114858] [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: 08/20/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023]
Abstract
OBJECTIVES This study aims to design and evaluate (in silico and in vitro) a new nicotinamide derivative as an inhibitor of VEGFR-2, a major mediator of angiogenesis Methods: The following in silico studies were performed; DFT calculations, molecular modelling, MD simulations, MM-GBSA, PLIP, and PCAT studies. The compound's in silico (ADMET) analysis was also conducted. Subsequently, the compound ((E)-N-(4-(1-(2-(4-(4-Chlorobenzamido)benzoyl)hydrazono)ethyl) phenyl)nicotinamide) was successfully synthesized and designated as compound X. In vitro, VEGFR-2 inhibition and cytotoxicity of compound X against HCT-116 and A549 cancer cell lines and normal Vero cell lines were conducted. Apoptosis induction and migration assay of HCT-116 cell lines after treatment with compound X were also evaluated. RESULTS DFT calculations assigned stability and reactivity of compound X. Molecular docking and MD simulations indicated its excellent binding against VEGFR-2. Furthermore, MM-GBSA analysis, PLIP experiments, and PCAT studies confirmed compound X's correct binding with optimal dynamics and energy. ADMET analysis expressed its general likeness and safety. The in vitro assays demonstrated that compound X effectively inhibited VEGFR-2, with an IC50 value of 0.319 ± 0.013 μM and displayed cytotoxicity against HCT-116 and A549 cancer cell lines, with IC50 values of 57.93 and 78.82 μM, respectively. Importantly, compound X exhibited minimal toxicity towards the non-cancerous Vero cell lines, (IC50 = 164.12 μM). Additionally, compound X significantly induced apoptosis of HCT-116 cell lines and inhibited their potential to migrate and heal. CONCLUSION In summary, the presented study has identified compound X as a promising candidate for the development of a novel apoptotic lead anticancer drug.
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Affiliation(s)
- Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Reda G Yousef
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Bshra A Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Heba S A Elzahabi
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11884, Egypt
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Ahmed M Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Dalal Z Husein
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja 72511, Egypt
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Choudhary S, Kesavan AK, Juneja V, Thakur S. Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis. FRONTIERS IN BIOINFORMATICS 2023; 3:1125479. [PMID: 37122997 PMCID: PMC10130521 DOI: 10.3389/fbinf.2023.1125479] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Computational prediction and protein structure modeling have come to the aid of various biological problems in determining the structure of proteins. These technologies have revolutionized the biological world of research, allowing scientists and researchers to gain insights into their biological questions and design experimental research much more efficiently. Pathogenic Mycobacterium spp. is known to stay alive within the macrophages of its host. Mycobacterium tuberculosis is an acid-fast bacterium that is the most common cause of tuberculosis and is considered to be the main cause of resistance of tuberculosis as a leading health issue. The genome of Mycobacterium tuberculosis contains more than 4,000 genes, of which the majority are of unknown function. An attempt has been made to computationally model and dock one of its proteins, Rv1250 (MTV006.22), which is considered as an apparent drug-transporter, integral membrane protein, and member of major facilitator superfamily (MFS). The most widely used techniques, i.e., homology modeling, molecular docking, and molecular dynamics (MD) simulation in the field of structural bioinformatics, have been used in the present work to study the behavior of Rv1250 protein from M. tuberculosis. The structure of unknown TB protein, i.e., Rv1250 was retrived using homology modeling with the help of I-TASSER server. Further, one of the sites responsible for infection was identified and docking was done by using the specific Isoniazid ligand which is an inhibitor of this protein. Finally, the stability of protein model and analysis of stable and static interaction between protein and ligand molecular dynamic simulation was performed at 100 ns The designing of novel Rv1250 enzyme inhibitors is likely achievable with the use of proposed predicted model, which could be helpful in preventing the pathogenesis caused by M. tuberculosis. Finally, the MD simulation was done to evaluate the stability of the ligand for the specific protein.
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Affiliation(s)
- Sumita Choudhary
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Anup Kumar Kesavan
- Department of Biotechnology and Microbiology, Kannur University, Dr. E. K. Janaki Ammal Campus, PalayadKannur, Kerala, India
- *Correspondence: Anup Kumar Kesavan, ; Sheetal Thakur,
| | - Vijay Juneja
- Eastern Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Wyndmoor, PA, United States
| | - Sheetal Thakur
- University Centre for Research & Development, Department of Biotechnology, Chandigarh University, Gharuan-Mohali, Punjab, India
- *Correspondence: Anup Kumar Kesavan, ; Sheetal Thakur,
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Bisht N, Dalal V, Tewari L. Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm. J Biomol Struct Dyn 2022; 40:12022-12036. [PMID: 34424128 DOI: 10.1080/07391102.2021.1967196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One of the major constraints limiting the use of abundantly available lignocellulosic biomass as potential feedstock for alcohol industry is the lack of C6/C5 co-sugar fermenting yeast. The present study explores a mutant yeast Pichia kudriavzevii BGY1-γm as a potential strain for bioconversion of glucose/xylose sugars of green biomass into ethanol under batch fermentation. The mutant strain having higher alcohol dehydrogenase activity (11.31%) showed significantly higher ethanol concentration during co-fermentation of glucose/xylose sugars (14.2%) as compared to the native strain. Based on 99% sequence similarity of ADH encoding gene from the mutant with the gene sequences from other yeast strains, the ADH enzyme was identified as ADH-1 type. The study reveals first three-dimensional model of ADH-1 utilizing glucose/xylose sugars from P. kudriavzevii BGY1-γm (PkADH mutant). The refined and validated model of PkADH mutant was used for molecular docking against the substrate (acetaldehyde) and product (ethanol). Molecular docking results showed that substrate and product exhibited a binding affinity of -4.55 and -4.5 kcal/mol with PkADH mutant. Acetaldehyde and ethanol interacted at the active site of PkADH mutant via hydrogen bonds (Ser42, His69 and Asp163) and hydrophobic interactions (Cys40, Ser42, His69, Cys95, Trp123 and Asp163) to form the stable protein-ligand complex. Molecular dynamics analysis revealed that PkADH-mutant acetaldehyde and PkADH-mutant ethanol complexes were more stable than PkADH mutant. MMPBSA binding energy confirmed that binding of substrate and product results in the formation of a lower energy stable protein-ligand complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Bisht
- Department of Microbiology, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lakshmi Tewari
- Department of Microbiology, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
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