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Younes KM, Abouzied AS, Alafnan A, Huwaimel B, Khojali WMA, Alzahrani RM. Investigating the bispecific lead compounds against methicillin-resistant Staphylococcus aureus SarA and CrtM using machine learning and molecular dynamics approach. J Biomol Struct Dyn 2023:1-18. [PMID: 38147401 DOI: 10.1080/07391102.2023.2297012] [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: 09/08/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious pathogen that has emerged as a serious global health concern over the past few decades. Staphylococcal accessory regulator A (SarA) and 4,4'-diapophytoene synthase (CrtM) play a crucial role in biofilm formation and staphyloxanthin biosynthesis. Thus, the present study used a machine learning-based QSAR model to screen 1261 plant-derived natural organic compounds in order to identify a medication candidate with both biofilm and virulence inhibitory potential. Additionally, the in-silico molecular docking analysis has demonstrated significant binding efficacy of the identified hit compound, that is 85137543, with SarA and CrtM when compared to the control compound, hesperidin. Post-MD simulation analysis of the complexes depicted strong binding of 85137543 to both SarA and CrtM. Moreover, 85137543 showed hydrogen bonding with the key residues of both proteins during docking (ALA138 of SarA and ALA134 of CrtM) and post-MD simulation (LYS273 of CrtM and ASN212 of SarA). The RMSD of 85137543 was stable and consistent when bound to both CrtM and SarA with RMSDs of 1.3 and 1 nm, respectively. In addition, principal component analysis and the free energy landscape showed stable complex formation with both proteins. Low binding free energy (ΔGTotal) was observed by 85137543 for SarA (-47.92 kcal/mol) and CrtM (-36.43 kcal/mol), which showed strong binding. Overall, this study identified 85137543 as a potential inhibitor of both SarA and CrtM in MRSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kareem M Younes
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Department of Analytical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Amr S Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Ahmed Alafnan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Ha'il, Hail, Saudi Arabia
| | - Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, Sudan
| | - Rami M Alzahrani
- Department of Pharmaceutics, College of Pharmacy, Taif University, Taif, Saudi Arabia
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Jayaraman S, Krishnamoorthy K, Prasad M, Veeraraghvan VP, Krishnamoorthy R, Alshuniaber MA, Gatasheh MK, Elrobh M. Glyphosate potentiates insulin resistance in skeletal muscle through the modulation of IRS-1/PI3K/Akt mediated mechanisms: An in vivo and in silico analysis. Int J Biol Macromol 2023; 242:124917. [PMID: 37207753 DOI: 10.1016/j.ijbiomac.2023.124917] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/25/2023] [Accepted: 05/13/2023] [Indexed: 05/21/2023]
Abstract
Herbicides have been linked to a higher risk of developing diabetes. Certain herbicides also operate as environmental toxins. Glyphosate is a popular and extremely effective herbicide for weed control in grain crops that inhibits the shikimate pathway. It has been shown to negatively influence endocrine function. Few studies have demonstrated that glyphosate exposure results in hyperglycemic and insulin resistance; but the molecular mechanism underlying the diabetogenic potential of glyphosate on skeletal muscle, a primary organ that includes insulin-mediated glucose disposal, is unknown. In this study, we aimed to evaluate the impact of glyphosate on the detrimental changes in the insulin metabolic signaling in the gastrocnemius muscle. In vivo results showed that glyphosate exposure caused hyperglycemia, dyslipidemia, increased glycosylated hemoglobin (HbA1c), liver function, kidney function profile, and oxidative stress markers in a dose-dependent fashion. Conversely, hemoglobin and antioxidant enzymes were significantly reduced in glyphosate-induced animals indicating its toxicity is linked to induce insulin resistance. The histopathology of the gastrocnemius muscle and RT-PCR analysis of insulin signaling molecules revealed glyphosate-induced alteration in the expression of IR, IRS-1, PI3K, Akt, β-arrestin-2, and GLUT4 mRNA. Lastly, molecular docking and dynamics simulations confirmed that glyphosate showed a high binding affinity with target molecules such as Akt, IRS-1, c-Src, β-arrestin-2, PI3K, and GLUT4. The current work provides experimental proof that glyphosate exposure has a deleterious effect on the IRS-1/PI3K/Akt signaling pathways, which in turn causes the skeletal muscle to become insulin resistant and eventually develop type 2 diabetes mellitus.
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Affiliation(s)
- Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Kalaiselvi Krishnamoorthy
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Monisha Prasad
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Vishnu Priya Veeraraghvan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Rajapandiyan Krishnamoorthy
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Mohammad A Alshuniaber
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Mansour K Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O.Box 2455, Riyadh 11451, Saudi Arabia.
| | - Mohamed Elrobh
- Department of Biochemistry, College of Science, King Saud University, P.O.Box 2455, Riyadh 11451, Saudi Arabia.
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Manjunathan R, Periyaswami V, Mitra K, Rosita AS, Pandya M, Selvaraj J, Ravi L, Devarajan N, Doble M. Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein. BMC Bioinformatics 2022; 23:180. [PMID: 35578172 PMCID: PMC9108711 DOI: 10.1186/s12859-022-04724-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The Transmembrane Serine Protease 2 (TMPRSS2) of human cell plays a significant role in proteolytic cleavage of SARS-Cov-2 coronavirus spike protein and subsequent priming to the receptor ACE2. Approaching TMPRSS2 as a therapeutic target for the inhibition of SARS-Cov-2 infection is highly promising. Hence, in the present study, we docked the binding efficacy of ten naturally available phyto compounds with known anti-viral potential with TMPRSS2. The aim is to identify the best phyto compound with a high functional affinity towards the active site of the TMPRSS2 with the aid of two different docking software. Molecular Dynamic Simulations were performed to analyse the conformational space of the binding pocket of the target protein with selected molecules. RESULTS Docking analysis using PyRx version 0.8 along with AutoDockVina reveals that among the screened phyto compounds, Genistein shows the maximum binding affinity towards the hydrophobic substrate-binding site of TMPRSS2 with three hydrogen bonds interaction ( - 7.5 kcal/mol). On the other hand, molecular docking analysis using Schrodinger identified Quercetin as the most potent phyto compound with a maximum binding affinity towards the hydrophilic catalytic site of TMPRSS2 ( - 7.847 kcal/mol) with three hydrogen bonds interaction. The molecular dynamics simulation reveals that the Quercetin-TMPRSS complex is stable until 50 ns and forms stable interaction with the protein ( - 22.37 kcal/mol of MM-PBSA binding free energy). Genistein creates a weak interaction with the loop residues and hence has an unstable binding and exits from the binding pocket. CONCLUSION The compounds, Quercetin and Genistein, can inhibit the TMPRSS2 guided priming of the spike protein. The compounds could reduce the interaction of the host cell with the type I transmembrane glycoprotein to prevent the entry of the virus. The critical finding is that compared to Genistein, Quercetin exhibits higher binding affinity with the catalytic unit of TMPRSS2 and forms a stable complex with the target. Thus, enhancing our innate immunity by consuming foods rich in Quercetin and Genistein or developing a novel drug in the combination of Quercetin and Genistein could be the brilliant choices to prevent SARS-Cov-2 infection when we consider the present chaos associated with vaccines and anti-viral medicines.
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Affiliation(s)
- Reji Manjunathan
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, Taramani Campus, University of Madras, Chennai, Tamil Nadu, India. .,Multi-Disciplinary Research Unit, Chengalpattu Government Medical College and Hospital, Chengalpattu, Tamil Nadu, 603001, India.
| | - Vijayalakshmi Periyaswami
- Department of Biotechnology and Bioinformatics, Holy Cross College, Bharathidasan University, Trichy, Tamil Nadu, India
| | - Kartik Mitra
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Arokiaraj Sherlin Rosita
- Department of Bioinformatics, Bishop Heber College (Autonomous, Bharathidasan University), Tiruchirapalli, Tamil Nadu, India
| | - Medha Pandya
- KPES Science College, Maharaja KrishnakumarSinhiji Bhavnagar University, Gujarat, India
| | - Jayaraman Selvaraj
- Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Lokesh Ravi
- Department of Botany, St. Josephs College, Bangalore, Karnataka, India
| | - Nalini Devarajan
- Central Research Laboratory, Meenakshi Ammal Dental College, Maduravoyal, Chennai, Tamil Nadu, India.
| | - Mukesh Doble
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India. .,Department of Cariology, Saveetha Dental College and Hospital, Chennai, Tamil Nadu, 600077, India.
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Inhibition of Filamentous Thermosensitive Mutant-Z Protein in Bacillus subtilis by Cyanobacterial Bioactive Compounds. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061907. [PMID: 35335270 PMCID: PMC8948890 DOI: 10.3390/molecules27061907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 01/13/2023]
Abstract
Antibiotic resistance is one of the major growing concerns for public health. Conventional antibiotics act on a few predefined targets and, with time, several bacteria have developed resistance against a large number of antibiotics. The WHO has suggested that antibiotic resistance is at a crisis stage and identification of new antibiotics and targets could be the only approach to bridge the gap. Filamentous Temperature Sensitive-Mutant Z (Fts-Z) is one of the promising and less explored antibiotic targets. It is a highly conserved protein and plays a key role in bacterial cell division by introducing a cytokinetic Z-ring formation. In the present article, the potential of over 165 cyanobacterial compounds with reported antibiotic activity against the catalytic core domain in the Fts-Z protein of the Bacillus subtilis was studied. The identified cyanobacterial compounds were screened using the GLIDE module of Maestro v-2019-2 followed by 100-ns molecular dynamics (MD) simulation. Ranking of the potential compound was performed using dock score and MMGBSA based free energy. The study reported that the docking score of aphanorphine (−6.010 Kcalmol−1) and alpha-dimorphecolic acid (ADMA) (−6.574 Kcalmol−1) showed significant role with respect to the reported potential inhibitor PC190723 (−4.135 Kcalmol−1). A 100 ns MD simulation infers that Fts-Z ADMA complex has a stable conformation throughout the progress of the simulation. Both the compounds, i.e., ADMA and Aphanorphine, were further considered for In-vitro validation by performing anti-bacterial studies against B. subtilis by agar well diffusion method. The results obtained through In-vitro studies confirm that ADMA, a small molecule of cyanobacterial origin, is a potential compound with an antibacterial activity that may act by inhibiting the novel target Fts-Z and could be a great drug candidate for antibiotic development.
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5
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Targeted inhibition of the endonuclease activity of influenza polymerase acidic proteins. Future Med Chem 2022; 14:571-586. [PMID: 35213253 DOI: 10.4155/fmc-2021-0264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Influenza is a type of acute respiratory virus infection caused by the influenza virus that occurs in epidemics worldwide every year. Due to the increasing incidence of influenza virus resistance to existing drugs, researchers are looking for novel antiviral drugs with new mechanisms. The endonuclease activity of polymerase acidic protein is essential in the process of influenza virus reproduction, and inhibiting it could prevent the virus from replicating. There are relatively few drugs that act on this protein, and only baloxavir marboxil has been approved for clinical use. In this article, the structure and function of influenza virus polymerase acidic protein endonuclease, mechanism of action of polymerase acidic endonuclease inhibitors and the research progress of inhibitors are reviewed.
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Indu S, Vijayalakshmi P, Selvaraj J, Rajalakshmi M. Novel Triterpenoids from Cassia fistula Stem Bark Depreciates STZ-Induced Detrimental Changes in IRS-1/Akt-Mediated Insulin Signaling Mechanisms in Type-1 Diabetic Rats. Molecules 2021; 26:6812. [PMID: 34833905 PMCID: PMC8621110 DOI: 10.3390/molecules26226812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 12/03/2022] Open
Abstract
Here, we identified the mechanisms of action of antidiabetic activity of novel compounds isolated from Cassia fistula stem bark in STZ-diabetic animals. Novel triterpenoid compounds (C1, C2 and C3) were treated to STZ-administered diabetic animals at a concentration of 20mg/kg body weight orally for 60 days to assess their effects on plasma glucose, plasma insulin/C-peptide, serum lipid markers and the enzymes of carbohydrate metabolism, glucose oxidation and insulin signaling molecules. Oral administration of novel triterpenoid compounds to STZ-diabetic animals significantly decreased (p < 0.05) the plasma glucose concentration on the 7th, 15th, 30th, 45th and 60th daysin a duration-dependent manner (p < 0.05). Plasma insulin (p < 0.0001)/C-peptide (p < 0.0006), tissue glycogen (p < 0.0034), glycogen phosphorylase (p < 0.005), glucose 6-phosphatase (p < 0.0001) and lipid markers were significantly increased (p < 0.0001) in diabetic rats, whereas glucokinase (p < 0.0047), glycogen synthase (p < 0.003), glucose oxidation (p < 0.001), GLUT4 mRNA (p < 0.0463), GLUT4 protein (p < 0.0475) and the insulin-signaling molecules IR mRNA (p < 0.0195), IR protein (p < 0.0001), IRS-1 mRNA (p < 0.0478), p-IRS-1Tyr612 (p < 0.0185), Akt mRNA (p < 0.0394), p-AktSer473 (p < 0.0162), GLUT4 mRNA (p < 0.0463) and GLUT4 (p < 0.0475) were decreased in the gastrocnemius muscle. In silico analysis of C1-C3 with IRK and PPAR-γ protein coincided with in vivo findings. C1-C3 possessed promising antidiabetic activity by regulating insulin signaling mechanisms and carbohydrate metabolic enzymes.
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MESH Headings
- Animals
- Blood Glucose/drug effects
- Blood Glucose/metabolism
- C-Peptide/blood
- Cassia/chemistry
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Type 1/drug therapy
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Glucokinase/metabolism
- Glucose-6-Phosphatase/metabolism
- Hypoglycemic Agents/chemistry
- Hypoglycemic Agents/isolation & purification
- Hypoglycemic Agents/pharmacology
- Insulin/blood
- Insulin/metabolism
- Insulin Receptor Substrate Proteins/metabolism
- Lipid Metabolism/drug effects
- Male
- Molecular Docking Simulation
- Molecular Structure
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- PPAR gamma/metabolism
- Plant Bark/chemistry
- Plants, Medicinal/chemistry
- Potassium Channels, Inwardly Rectifying/metabolism
- Proto-Oncogene Proteins c-akt/genetics
- Proto-Oncogene Proteins c-akt/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Rats, Wistar
- Signal Transduction/drug effects
- Triterpenes/chemistry
- Triterpenes/isolation & purification
- Triterpenes/pharmacology
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Affiliation(s)
- Sabapathy Indu
- DBT-BIF Centre, PG & Research Department of Biotechnology & Bioinformatics, Holy Cross College (Autonomous), Bharathidasan University, Trichy 620002, Tamil Nadu, India; (S.I.); (P.V.)
| | - Periyasamy Vijayalakshmi
- DBT-BIF Centre, PG & Research Department of Biotechnology & Bioinformatics, Holy Cross College (Autonomous), Bharathidasan University, Trichy 620002, Tamil Nadu, India; (S.I.); (P.V.)
| | - Jayaraman Selvaraj
- Department of Biochemistry, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospitals, Saveetha University, Chennai 600020, Tamil Nadu, India;
| | - Manikkam Rajalakshmi
- DBT-BIF Centre, PG & Research Department of Biotechnology & Bioinformatics, Holy Cross College (Autonomous), Bharathidasan University, Trichy 620002, Tamil Nadu, India; (S.I.); (P.V.)
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Deenadayalan A, Vijayalakshmi S, Janaki CS, Jayaraman S. Molecular docking analysis of stevioside with Akt and PPARγ. Bioinformation 2021; 17:283-288. [PMID: 34393447 PMCID: PMC8340692 DOI: 10.6026/97320630017283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/25/2022] Open
Abstract
Stevioside is a diterpenoid glycoside consisting of an aglycone (steviol) and three glucose molecules. It is commonly used as an anti-hyperglycemic food because of its non-caloric property. Therefore, it is of interest to document the interactions of stevioside
with AKT & PPAR-γ proteins using Autodock Vina PyRx docking techniques. Results of the docking studies indicate that stevioside had more than two hydrogen bond interactions with the AKT and PPAR γ protein for further consideration.
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Affiliation(s)
- Abilasha Deenadayalan
- Department of Anatomy, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha Nagar,Chennai-602105, India.,Department of Anatomy, Asan Memorial Dental College and Hospitals, Asan Nagar, Chengalpattu, Chennai-602 105, India
| | - S Vijayalakshmi
- Department of Anatomy, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha Nagar,Chennai-602105, India
| | - C S Janaki
- Department of Anatomy, Bharath Medical College and Hospital, Selaiyur, Chennai-600 073, India
| | - Selvaraj Jayaraman
- Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai-600 077, India
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Abu Zeid I. Inhibitory Activity of Balanites aegyptiaca Phytochemicals on Main Protease of SARS-CoV-2: Virtual Screening and Molecular Dynamics Simulation. INT J PHARMACOL 2021. [DOI: 10.3923/ijp.2021.482.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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Jayaraman S, Umapathy VR, Govindaraj J, Govidaraj K. Molecular docking analysis of vascular endothelial growth factor receptor with bioactive molecules from Piper longum as potential anti-cancer agents. Bioinformation 2021; 17:223-228. [PMID: 34393441 PMCID: PMC8340711 DOI: 10.6026/97320630017223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
It is known that vascular endothelial growth factor receptor (VGFR) is linked with cancer. Therefore, it is of interest to document the molecular binding features of bioactive molecules from Piper longum as potential anti-cancer agents with VGFR2 for further
consideration. Thus, we document the binding features of four compounds (sesamin, fargesin, longamide and piperlonguminine) with VGFR2 for further consideration in drug discovery.
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Affiliation(s)
- Selvaraj Jayaraman
- Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600 077, India
| | - Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Sree Balaji Dental College and Hospital, Pallikaranai,Chennai-600 100, India
| | - Jayamathi Govindaraj
- Department of Biochemistry, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
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10
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Rekha UV, Anita M, Jayamathi G, Sadhana K, Deepa S, Hussain S, Bhuvaneswari J, Ramya V, Selvaraj J, Naveenraj NS. Molecular docking analysis of piperine with CDK2,CDK4,Cyclin D and Cyclin T proteins. Bioinformation 2020; 16:359-362. [PMID: 32831516 PMCID: PMC7434954 DOI: 10.6026/97320630016359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/01/2020] [Accepted: 04/10/2020] [Indexed: 12/27/2022] Open
Abstract
Piperine is a component of Piper nigrum (Black pepper). It is well known in ayurvedic formulations. Piperine is a bioenhancer as it reduces the activity of drug-metabolizing enzymes in
rodents and thereby enhancing the plasma concentrations of several drugs, including the Pglycoprotein substrates. Therefore, it is of interest to understand the molecular docking interactions
of piperine with several cell cycle proteins such as Cyclin dependent kinase 2 (CDK2), Cyclin-dependent kinase 4 (CDK4), Cyclin D and Cyclin T for further consideration in drug discovery
related to oral cancer.
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Affiliation(s)
- Umapathy Vidhya Rekha
- Department of Public Health Dentistry, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - M Anita
- Department of Public Health Dentistry, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - Govindaraj Jayamathi
- Department of Biochemistry, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - K Sadhana
- Department of Public Health Dentistry, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - Subramanian Deepa
- Department of Periodontics, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - Sajid Hussain
- Department of Periodontics, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - J Bhuvaneswari
- Department of Periodontics, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - V Ramya
- Department of Periodontics, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai-600 100, India
| | - Jayaraman Selvaraj
- Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600 077, India
| | - N S Naveenraj
- Department of Public Health Dentistry, Ragas Dental College and Hospital, Chennai India
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11
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Farhadi Z, Farhadi T, Hashemian SM. Virtual screening for potential inhibitors of β(1,3)-D-glucan synthase as drug candidates against fungal cell wall. J Drug Assess 2020; 9:52-59. [PMID: 32284908 PMCID: PMC7144292 DOI: 10.1080/21556660.2020.1734010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/07/2020] [Indexed: 01/17/2023] Open
Abstract
Background To enhance the outcome in patients with invasive candidiasis, initiation of an efficient antifungal treatment in a suitable dosage is necessary. Echinocandins (e.g. caspofungin) inhibit the enzyme β(1,3)-D-glucan synthase of the fungal cell wall. Compared to azoles and other antifungal agents, echinocandins have lower adverse effects and toxicity in humans. Echinocandins are available in injectable (intravenous) form. Methods In this study, to identify the novel oral drug-like compounds that affect the fungal cell wall, downloaded oral drug-like compounds from the ZINC database were processed with a virtual screening procedure. The docking free energies were calculated and compared with the known inhibitor caspofungin. Four molecules were selected as the most potent ligands and subjected to hydrogen bonds analysis. Results Considering the hydrogen bond analysis, two compounds (ZINC71336662 and ZINC40910772) were predicted to better interact with the active site of β(1,3)-D-glucan synthase compared with caspofungin. Conclusion The introduced compound in this study may be valuable to analyze experimentally as a novel oral drug candidate targeting fungal cell walls.
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Affiliation(s)
- Zinat Farhadi
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Behavioral Disease Counseling Center, Marvdasht Health Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Microbiology, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Tayebeh Farhadi
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed MohammadReza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Critical Care Department, Farhikhtegan Hospital, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
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12
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Xue L, Chen YY, Yan Z, Lu W, Wan D, Zhu H. Staphyloxanthin: a potential target for antivirulence therapy. Infect Drug Resist 2019; 12:2151-2160. [PMID: 31410034 PMCID: PMC6647007 DOI: 10.2147/idr.s193649] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/13/2019] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus is an important and common Gram-positive bacteria which causes clinical infections and food-poisoning cases. Therapeutic schedules for treatment of S. aureus infections are facing a challenge because of the emergence of multidrug resistance strains. It is urgent to find new antiinfective drugs to control S. aureus infection. S. aureus strains are capable of producing the golden carotenoid pigment: staphyloxanthin, which acts as an important virulence factor and a potential target for antivirulence drug design. This review is aimed at presenting an updated overview of this golden carotenoid pigment of S. aureus from the biosynthesis of staphyloxanthin, its function, and the genes involved in pigment production to staphyloxanthin: a novel target for antivirulence therapy.
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Affiliation(s)
- Lijun Xue
- College of Pharmaceutical Sciences and Traditional Chinese Medicine, Southwest University, Chongqing 400715, People's Republic of China.,College of Pharmaceutical Engineering, Chongqing Chemical Industry Vocational College, Chongqing, 400020, People's Republic of China
| | - Yang Yizhi Chen
- College of Pharmaceutical Sciences and Traditional Chinese Medicine, Southwest University, Chongqing 400715, People's Republic of China
| | - Zhiyun Yan
- Wuhan Wusteel Good Life Service Co. LTD, Wuhan, 430000, People's Republic of China
| | - Wei Lu
- College of Pharmaceutical Sciences and Traditional Chinese Medicine, Southwest University, Chongqing 400715, People's Republic of China
| | - Dong Wan
- Department of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Huifeng Zhu
- College of Pharmaceutical Sciences and Traditional Chinese Medicine, Southwest University, Chongqing 400715, People's Republic of China
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13
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Langeswaran K, Jeyaraman J, R JB, Biswas A, Dhurgadevi KR. Identifying dual leucine zipper kinase (DLK) inhibitors using e-pharamacophore screening and molecular docking. J Recept Signal Transduct Res 2019; 39:99-105. [PMID: 31282287 DOI: 10.1080/10799893.2019.1620776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alzheimer's is a neural disorder causing gradual loss in structure and function of nerve cell. To treat such disorders, c-Jun N-terminal Kinase (JNK) Pathway inhibitors were developed by representing chemical compounds that were used to inhibit the JNK signaling pathways. DLK is the stress sensor and implicating as regulatory factor in JNK pathway. Therefore, in the present investigation, pharmacophore screening was tried to identify the chemical compounds that involving inhibition of DLK proteins. To explore the pharmacophore region and mode of binding with DLK protein, N- (I H-pyrazol-3-y l) pyridin-2-aminer inhibitors were docked with DLK. Results reveal the information on the interaction mechanism of protein and ligand with chemical characteristics required to inhibit DLK protein. Such predicted information (AAAARH) was used as query to find out potential novel lead compounds sourced from public database. As an outcome of 65 compounds were listed based on the fitness score (2≥), and were subjected to glide HTVS.SP and XP. Best performing 5 lead compounds were shortlisted for dynamic simulations. This exhibited a constant RMSD over 20 ns of timescale.
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Affiliation(s)
- K Langeswaran
- a Bioinformatics, Alagappa University , Karaikudi , India
| | | | | | - Abir Biswas
- b Bharathidasan University , Tiruchirappalli , India
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14
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Serafim MSM, Lavorato SN, Kronenberger T, Sousa YV, Oliveira GP, Dos Santos SG, Kroon EG, Maltarollo VG, Alves RJ, Mota BEF. Antibacterial activity of synthetic 1,3-bis(aryloxy)propan-2-amines against Gram-positive bacteria. Microbiologyopen 2019; 8:e814. [PMID: 30773849 PMCID: PMC6855212 DOI: 10.1002/mbo3.814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/18/2022] Open
Abstract
Synthetic 1,3‐bis(aryloxy)propan‐2‐amines have been shown in previous studies to possess several biological activities, such as antifungal and antiprotozoal. In the present study, we describe the antibacterial activity of new synthetic 1,3‐bis(aryloxy)propan‐2‐amines against Gram‐positive pathogens (Streptococcus pyogenes, Enterococcus faecalis and Staphylococcus aureus) including Methicillin–resistant S. aureus strains. Our compounds showed minimal inhibitory concentrations (MIC) in the range of 2.5–10 μg/ml (5.99–28.58 μM), against different bacterial strains. The minimal bactericidal concentrations found were similar to MIC, suggesting a bactericidal mechanism of action of these compounds. Furthermore, possible molecular targets were suggested by chemical similarity search followed by docking approaches. Our compounds are similar to known ligands targeting the cell division protein FtsZ, Quinolone resistance protein norA and the Enoyl‐[acyl‐carrier‐protein] reductase FabI. Taken together, our data show that synthetic 1,3‐bis(aryloxy)propan‐2‐amines are active against Gram‐positive bacteria, including multidrug–resistant strains and can be a promising lead in the development of new antibacterial compounds for the treatment of these infections.
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Affiliation(s)
- Mateus S M Serafim
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Stefânia N Lavorato
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany
| | - Yamara V Sousa
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Graziele P Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Simone G Dos Santos
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Erna G Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vinícius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ricardo J Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Bruno E F Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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15
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Ahmad S, Navid A, Akhtar AS, Azam SS, Wadood A, Pérez-Sánchez H. Subtractive Genomics, Molecular Docking and Molecular Dynamics Simulation Revealed LpxC as a Potential Drug Target Against Multi-Drug Resistant Klebsiella pneumoniae. Interdiscip Sci 2018; 11:508-526. [PMID: 29721784 DOI: 10.1007/s12539-018-0299-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/24/2018] [Indexed: 12/17/2022]
Abstract
The emergence and dissemination of pan drug resistant clones of Klebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC), a Zn+2 dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection of K. pneumoniae LpxC (KpLpxC) topology distinct from its orthologous counterparts in other bacterial species. Molecular docking study of the protein recognized receptor antagonist compound 106, a uridine-based LpxC inhibitory compound, as a ligand best able to fit the binding pocket with a Gold Score of 67.53. Molecular dynamics simulation of docked KpLpxC revealed an alternate binding pattern of ligand in the active site. The ligand tail exhibited preferred binding to the domain I residues as opposed to the substrate binding hydrophobic channel of subdomain II, usually targeted by inhibitory compounds. Comparison with the undocked KpLpxC system demonstrated ligand induced high conformational changes in the hydrophobic channel of subdomain II in KpLpxC. Hence, ligand exerted its inhibitory potential by rendering the channel unstable for substrate binding.
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Affiliation(s)
- Sajjad Ahmad
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Afifa Navid
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Amina Saleem Akhtar
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University-Mardan, Shankar Campus, Mardan, Khyber Pukhtoonkhwa, Pakistan
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
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16
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Ballu S, Itteboina R, Sivan SK, Manga V. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. J Recept Signal Transduct Res 2018; 38:61-70. [DOI: 10.1080/10799893.2018.1426607] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Srilata Ballu
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Ramesh Itteboina
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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17
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Virtual Screening for Potential Inhibitors of CTX-M-15 Protein of Klebsiella pneumoniae. Interdiscip Sci 2017; 10:694-703. [PMID: 28374117 DOI: 10.1007/s12539-017-0222-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 02/28/2017] [Accepted: 03/09/2017] [Indexed: 12/31/2022]
Abstract
The Gram-negative bacterium Klebsiella pneumoniae, responsible for a wide variety of nosocomial infections in immuno-deficient patients, involves the respiratory, urinary and gastrointestinal tract infections and septicemia. Extended spectrum β-lactamases (ESBL) belong to β-lactamases capable of conferring antibiotic resistance in Gram-negative bacteria. CTX-M-15, a prevalent ESBL reported from Enterobacteriaceae including K. pneumoniae, was selected as a potent anti-bacterial target. To identify the novel drug-like compounds, structure-based screening procedure was employed against downloaded drug-like compounds from ZINC database. An acronym for "ZINC" is not commercial. The docking free energy values were investigated and compared to the known inhibitor Avibactam. Six best novel drug-like compounds were selected and their hydrogen bindings with the receptor were determined. Based on the binding efficiency mode, three among these six identified most potential inhibitors, ZINC21811621, ZINC93091917 and ZINC19488569, were predicted as potential competitive inhibitors against CTX-M-15 compared to Avibactam. These three inhibitors may provide a framework for the experimental studies to develop anti-Klebsiella novel drug candidates targeting CTX-M-15.
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