1
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Synthesis of naphthalimide derivatives bearing benzothiazole and thiazole moieties: In vitro anticancer and in silico ADMET study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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2
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Damale MG, Patil R, Ansari SA, Alkahtani HM, Ahmed S, Nur-e-Alam M, Arote R, Sangshetti J. Insilico structure based drug design approach to find potential hits in ventilator-associated pneumonia caused by Pseudomonas aeruginosa. Comput Biol Med 2022; 146:105597. [DOI: 10.1016/j.compbiomed.2022.105597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
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3
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Vanajothi R, Vedagiri H, Al-Ansari MM, Al-Humaid LA, Kumpati P. Pharmacophore based virtual screening, molecular docking and molecular dynamic simulation studies for finding ROS1 kinase inhibitors as potential drug molecules. J Biomol Struct Dyn 2020; 40:3385-3399. [PMID: 33200682 DOI: 10.1080/07391102.2020.1847195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proto-oncogene receptor tyrosine kinase ROS-1 is one of the clinically important biomarker and plays a crucial role in regulation of a number of cellular functions including cell proliferation, migration and angiogenesis. Recently, inhibition of ROS1 kinase has proven to be a promising target of anticancer drugs for non-small cell lung cancer (NSCLC). The very few compounds have been used as potent drug molecules so far and the selective ROS1 inhibitors are relatively rare. Besides the currently available drugs such as Crizotinib and PF-06463922 are becoming sensitive due to mutations in the ROS1 protein. To curtail the problem of the resistant, present study was designed to identify the potent inhibitors against ROS1. Three different screening approaches such as structure based, Atom-based and pharmacophore based screening were carried out against commercially available databases and the retrieved best hits were further evaluated by Lipinski's filter. Thereafter the lead molecule was subjected to pocket specific docking with ROS1. The results show that, total of 9 molecules (3 from each screening) has good docking score (with range of -9.288 to -12.49 Kcal/Mol) and binding interactions within the active site of ROS1. In order to analyze the stability of the ligand- protein complexes, molecular dynamics simulation was performed. Thus, these identified potential lead molecules with good binding score and binding affinity with ROS1 may act as the potent ROS1 inhibitor, and that are worth considering for further experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ramar Vanajothi
- Department of Biomedical Science, Bharathidasan University, Tamil Nadu, India
| | | | - Mysoon M Al-Ansari
- Department of Botany and Microbiology, College of Science King Saud University, Riyadh, Saudi Arabia
| | - Latifah A Al-Humaid
- Department of Botany and Microbiology, College of Science King Saud University, Riyadh, Saudi Arabia
| | - Premkumar Kumpati
- Department of Biomedical Science, Bharathidasan University, Tamil Nadu, India
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4
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Damale MG, Pathan SK, Patil RB, Sangshetti JN. Pharmacoinformatics approaches to identify potential hits against tetraacyldisaccharide 4'-kinase (LpxK) of Pseudomonas aeruginosa. RSC Adv 2020; 10:32856-32874. [PMID: 35516480 PMCID: PMC9056689 DOI: 10.1039/d0ra06675c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 08/24/2020] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa infection can cause pneumonia and urinary tract infection and the management of Pseudomonas aeruginosa infection is critical in multidrug resistance, hospital-acquired bacteremia and ventilator-associated pneumonia. The key enzymes of lipid A biosynthesis in Pseudomonas aeruginosa are promising drug targets. However, the enzyme tetraacyldisaccharide 4'-kinase (LpxK) has not been explored as a drug target so far. Several pharmacoinformatics tools such as comparative metabolic pathway analysis (Metacyc), data mining from a database of essential genes (DEG), homology modeling, molecular docking, pharmacophore based virtual screening, ADMET prediction and molecular dynamics simulation were used in identifying novel lead compounds against this target. The top virtual hits STOCK6S-33288, 43621, 39892, 37164 and 35740 may serve as the templates for the design and synthesis of potent LpxK inhibitors in the management of serious Pseudomonas aeruginosa infection.
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Affiliation(s)
- Manoj G Damale
- Y.B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus, Rauza Baugh Aurangabad MS 431001 India
- Srinath College of Pharmacy Aurangabad MS India
| | - Shahebaaz K Pathan
- Y.B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus, Rauza Baugh Aurangabad MS 431001 India
| | - Rajesh B Patil
- Sinhgad Technical Education Society's, Smt. Kashibai Navale College of Pharmacy Pune-Saswad Road, Kondhwa (Bk) Pune 411048 India
| | - Jaiprakash N Sangshetti
- Y.B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus, Rauza Baugh Aurangabad MS 431001 India
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5
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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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6
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Kulanthaivel L, Jeyaraman J, Biswas A, Subbaraj GK, Santhoshkumar S. Identification of potential inhibitors for Penicillinbinding protein (PBP) from Staphylococcus aureus. Bioinformation 2018; 14:471-476. [PMID: 31223205 PMCID: PMC6563657 DOI: 10.6026/97320630014471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 11/28/2022] Open
Abstract
Staphylococcus aureus is an infectious agent that causes severe skin and soft tissue infection in hospitalized patients. Therefore, it is of interest to develop potent inhibitors for S. aureus. Penicillin Binding protein (PBP) is a known drug target for inhibition of cell wall biosynthesis in S. aureus. Hence, PBP was screened with compounds from six databases using virtual screening approaches. Results shows that the screened lead compound produced higher docking score (-9.87 kcal/mol) compared to resistant drugs. Antimicrobial activity using screened lead compounds and resistant drugs showed maximum activity in potential screened compounds compared to resistant compounds.
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Affiliation(s)
- Langeswaran Kulanthaivel
- Cancer Genetics and Molecular Biology Laboratory, Department of Bioinformatics, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-computing, Department of Bioinformatics, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Abir Biswas
- Abir Biswas, Molecular Gerontology Lab, Department of Biochemistry, Bharathidasan University,Thiruchirapalli, Tamil Nadu, India
| | - Gowtham Kumar Subbaraj
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Chennai, Tamil Nadu, India
| | - S Santhoshkumar
- Department of Computer Science, Alagappa University, Karaikudi, Tamil Nadu, India
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7
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In Silico study of the active site of Helicobacter pylori urease and its inhibition by hydroxamic acids. J Mol Graph Model 2018; 83:64-73. [PMID: 29775804 DOI: 10.1016/j.jmgm.2018.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 11/21/2022]
Abstract
Hydroxamic acids have emerged as the most promising candidates from among the different classes of inhibitors of urease. In order to understand the mechanism of their action, we have studied in detail using quantum mechanics the active site of Helicobacter pylori urease complexed with acetohydroxamic acid. A diverse library of ligands having the hydroxamate moiety has been prepared and docked into the active site of urease using the QM/MM methodology. It is found that hydroxamic acids with hydrophobic groups attached to them are more potent inhibitors of urease because they can easily penetrate the hydrophobic environment surrounding the active site. The -CONHO- moiety of the hydroxamic acid is also found to be absolutely necessary for chelation and inhibition of urease. In order to determine the roles of residues His 221 and Ala 365, which are not part of the active site, but are nevertheless involved in hydrogen bonding with the ligand, we have performed Molecular Dynamics simulations, both on the wild urease and also on its mutated counterpart, with the two residues substituted, respectively, by alanine and glycine.
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS. Struct Chem 2017. [DOI: 10.1007/s11224-016-0903-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Sasikala D, Jeyakanthan J, Srinivasan P. Structure-based virtual screening and biological evaluation of LuxT inhibitors for targeting quorum sensing through an in vitro biofilm formation. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.07.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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10
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Santos LH, Ferreira RS, Caffarena ER. Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz 2016; 110:847-64. [PMID: 26560977 PMCID: PMC4660614 DOI: 10.1590/0074-02760150239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023] Open
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency
virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts
against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors
(NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the
highly active antiretroviral therapy in combination with other anti-HIV drugs.
However, the rapid emergence of drug-resistant viral strains has limited the
successful rate of the anti-HIV agents. Computational methods are a significant part
of the drug design process and indispensable to study drug resistance. In this
review, recent advances in computer-aided drug design for the rational design of new
compounds against HIV-1 RT using methods such as molecular docking, molecular
dynamics, free energy calculations, quantitative structure-activity relationships,
pharmacophore modelling and absorption, distribution, metabolism, excretion and
toxicity prediction are discussed. Successful applications of these methodologies are
also highlighted.
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Affiliation(s)
| | - Rafaela Salgado Ferreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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11
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Exploring the inhibitory potential of bioactive compound from Luffa acutangula against NF-κB—A molecular docking and dynamics approach. Comput Biol Chem 2016; 62:29-35. [DOI: 10.1016/j.compbiolchem.2016.03.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/23/2016] [Accepted: 03/27/2016] [Indexed: 12/25/2022]
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Priya R, Sumitha R, Doss CGP, Rajasekaran C, Babu S, Seenivasan R, Siva R. Molecular Docking and Molecular Dynamics to Identify a Novel Human Immunodeficiency Virus Inhibitor from Alkaloids of Toddalia asiatica. Pharmacogn Mag 2016; 11:S414-22. [PMID: 26929575 PMCID: PMC4745211 DOI: 10.4103/0973-1296.168947] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background: Acquired immunodeficiency syndrome caused by human immunodeficiency virus (HIV) is an immunosuppressive disease. Over the past decades, it has plagued human health due to the grave consequences in its harness. Objective: For this reason, anti-HIV agents are imperative, and the search for the same from natural resources would assure the safety. Materials and Methods: In this investigation we have performed molecular docking, molecular property prediction, drug-likeness score, and molecular dynamics (MD) simulation to develop a novel anti-HIV drug. We have screened 12 alkaloids from a medicinal plant Toddalia asiatica for its probabilistic binding with the active site of the HIV-1-reverse transcriptase (HIV-1-RT) domain (the major contributor to the onset of the disease). Results: The docking results were evaluated based on free energies of binding (ΔG), and the results suggested toddanol, toddanone, and toddalenone to be potent inhibitors of HIV-1-RT. In addition, the alkaloids were subjected to molecular property prediction analysis. Toddanol and toddanone with more rotatable bonds were found to have a drug-likeness score of 0.23 and 0.11, respectively. These scores were comparable with the standard anti-HIV drug zidovudine with a model score 0.28. Finally, two characteristic protein-ligand complexes were exposed to MD simulation to determine the stability of the predicted conformations. Conclusion: The toddanol-RT complex showed higher stability and stronger H-bonds than toddanone-RT complex. Based on these observations, we firmly believe that the alkaloid toddanol could aid in efficient HIV-1 drug discovery. SUMMARY In the present study, the molecular docking and MD simulations are performed to explore the possible binding mode of HIV 1 RT with 12 alkaloids of T. asiatica. Molecular docking by AutoDock4 revealed three alkaloids toddanol, toddanone, and toddalenone with highest binding affinity towards HIV 1 RT. The drug likeness model score revealed a positive score for toddanol and toddanone which is comparable to the drug likeness score of the standard anti HIV drug zidovudine. Results from simulation analysis revealed that toddanol RT complex is more stable than toddanone RT complex inferring toddanol as a potential anti HIV drug molecule.
Abbreviations used: HIV: Human immunodeficiency virus, HIV 1 RT: HIV 1 reverse transcriptase, RNase H: Ribonuclease H, MD: Molecular dynamics, PDB: Protein databank, RMSD: Root mean square deviation, RMSF: Root mean square fluctuation.
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Affiliation(s)
- R Priya
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Rajendrarao Sumitha
- Department of Neurophysiology, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - C George Priya Doss
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - C Rajasekaran
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - S Babu
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - R Seenivasan
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - R Siva
- Plant Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
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13
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Sasikala D, Jeyakanthan J, Srinivasan P. Structural insights on identification of potential lead compounds targeting WbpP in Vibrio vulnificus through structure-based approaches. J Recept Signal Transduct Res 2016; 36:515-30. [PMID: 26795501 DOI: 10.3109/10799893.2015.1132237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
WbpP encoding UDP-GlcNAC C4 epimerase is responsible for the activation of virulence factor in marine pathogen Vibrio vulnificus (V. vulnificus) and it is linked to many aquatic diseases, thus making it a potential therapeutic target. There are few reported compounds that include several natural products and synthetic compounds targeting Vibrio sp, but specific inhibitor targeting WbpP are unavailable. Here, we performed structure-based virtual screening using chemical libraries such as Binding, TOSLab and Maybridge to identify small molecule inhibitors of WbpP with better drug-like properties. Deficient structural information forced to model the structure and the stable protein structure was obtained through 30 ns of MD simulations. Druggability regions are focused for new lead compounds and our screening protocol provides fast docking of entire small molecule library with screening criteria of ADME/Lipinski filter/Docking followed by re-docking of top hits using a method that incorporates both ligand and protein flexibility. Docking conformations of lead molecules interface displays strong H-bond interactions with the key residues Gly101, Ser102, Val195, Tyr165, Arg298, Val209, Ser142, Arg233 and Gln200. Subsequently, the top-ranking compounds were prioritized using the molecular dynamics simulation-based conformation and stability studies. Our study suggests that the proposed compounds may aid as a starting point for the rational design of novel therapeutic agents.
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Affiliation(s)
- Dakshinamurthy Sasikala
- a Science Block, Department of Bioinformatics, Alagappa University , Karaikudi, Tamil Nadu , India and
| | - Jeyaraman Jeyakanthan
- a Science Block, Department of Bioinformatics, Alagappa University , Karaikudi, Tamil Nadu , India and
| | - Pappu Srinivasan
- b Science Block, Department of Animal Health and Management, Alagappa University , Karaikudi, Tamil Nadu , India
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14
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Prasanna G, Saraswathi NT. Aspartic acid functions as carbonyl trapper to inhibit the formation of advanced glycation end products by chemical chaperone activity. J Biomol Struct Dyn 2015; 34:943-51. [PMID: 26325019 DOI: 10.1080/07391102.2015.1060160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Advanced glycation end products (AGEs) were implicated in pathology of numerous diseases. In this study, we present the bioactivity of aspartic acid (Asp) to inhibit the AGEs. Hemoglobin and bovine serum albumin (BSA) were glycated with glucose, fructose, and ribose in the presence and absence of Asp (100-200 μM). HbA1c inhibition was investigated using human blood and characterized by micro-column ion exchange chromatography. The effect of methyl glyoxal (MG) on hemoglobin and BSA was evaluated by fluorescence spectroscopy and gel electrophoresis. The effect of MG on red blood cells morphology was characterized by scanning electron micrographs. Molecular docking was performed on BSA with Asp. Asp is capable of inhibiting the formation of fluorescent AGEs by reacting with the reducing sugars. The presence of Asp as supplement in whole blood reduced the HbA1c% from 8.8 to 6.1. The presence of MG showed an increase in fluorescence and the presence of Asp inhibited the glycation thereby the fluorescence was quenched. MG also affected the electrophoretic mobility of hemoglobin and BSA by forming high molecular weight aggregates. Normal RBCs showed typical biconcave shape. MG modified RBCs showed twisted and elongated shape whereas the presence of ASP tends to protect RBC from twisting. Asp interacted with arginine residues of bovine serum albumin particularly ARG 194, ARG 198, and ARG 217 thereby stabilized the protein complex. We conclude that Asp has dual functions as a chemical chaperone to stabilize protein and as a dicarbonyl trapper, and thereby it can prevent the complications caused by glycation.
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Affiliation(s)
- Govindarajan Prasanna
- a Molecular Biophysics Laboratory, School of Chemical and Biotechnology , SASTRA University , Thanjavur 613401 , India
| | - N T Saraswathi
- a Molecular Biophysics Laboratory, School of Chemical and Biotechnology , SASTRA University , Thanjavur 613401 , India
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15
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Wang J, Hou T. Advances in computationally modeling human oral bioavailability. Adv Drug Deliv Rev 2015; 86:11-6. [PMID: 25582307 PMCID: PMC4490973 DOI: 10.1016/j.addr.2015.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 12/15/2022]
Abstract
Although significant progress has been made in experimental high throughput screening (HTS) of ADME (absorption, distribution, metabolism, excretion) and pharmacokinetic properties, the ADME and Toxicity (ADME-Tox) in silico modeling is still indispensable in drug discovery as it can guide us to wisely select drug candidates prior to expensive ADME screenings and clinical trials. Compared to other ADME-Tox properties, human oral bioavailability (HOBA) is particularly important but extremely difficult to predict. In this paper, the advances in human oral bioavailability modeling will be reviewed. Moreover, our deep insight on how to construct more accurate and reliable HOBA QSAR and classification models will also discussed.
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Affiliation(s)
- Junmei Wang
- Green Center for Systems Biology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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16
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Selvaraj C, Priya RB, Lee JK, Singh SK. Mechanistic insights of SrtA–LPXTG blockers targeting the transpeptidase mechanism in Streptococcus mutans. RSC Adv 2015. [DOI: 10.1039/c5ra12869b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The SrtA–LPXTG interaction plays a key role in transpeptidation reaction, cell wall and biofilm formations. This study explains the blocking of LEU interactions with SrtA will results as SrtA inhibitors through MD simulation and energy calculations methods.
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Affiliation(s)
| | - Ramanathan Bharathi Priya
- Department of Bioinformatics
- Computer Aided Drug Design and Molecular Modeling Lab
- Alagappa University
- Karaikudi-630003
- India
| | - Jung-Kul Lee
- Department of Chemical Engineering
- Konkuk University
- Seoul
- Korea
| | - Sanjeev Kumar Singh
- Department of Bioinformatics
- Computer Aided Drug Design and Molecular Modeling Lab
- Alagappa University
- Karaikudi-630003
- India
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Sudha A, Srinivasan P. Bioassay-guided isolation, identification and molecular ligand-target insight of lipoxygenase inhibitors from leaves of Anisomeles malabarica R.Br. Pharmacogn Mag 2014; 10:S596-605. [PMID: 25298680 PMCID: PMC4189278 DOI: 10.4103/0973-1296.139795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/05/2014] [Accepted: 08/30/2014] [Indexed: 11/14/2022] Open
Abstract
Background: Anisomeles malabarica R. Br. (Lamiaceae) is extensively used in traditional medicine in major parts of India for several medicinal purposes, including their use in rheumatism. Materials and Methods: The air-dried leaves of A. malabarica were extracted with ethanol, defatted with n-hexane and then successively partitioned into chloroform and n-butanol fractions. Bioassay-guided fractionation and purification of chloroform fraction from A. malabarica lead to the isolation of lipoxygenase (LOX) inhibitors. The structures of isolated compounds were elucidated by ultraviolet, infrared, 1H nuclear magnetic resonance (NMR), 13C NMR and mass spectrometry spectroscopic techniques and assessed further by in vitro soybean lipoxygenase (sLOX) assay. In addition, the enzyme type inhibition was evaluated through molecular docking technique as a part of computational study. Results: The bioactive compounds 3, 4 dihydroxy benzoic acid (1) and 4’, 5, 7-trihydroxyflavone (2) were isolated from chloroform fraction of A. malabarica, whose bioactivity was observed to be dose-dependent compared to n-butanol fraction. Among the compounds, 3, 4 dihydroxy benzoic acid showed significant sLOX inhibitory activity with 74.04% ±2.6% followed by 4’, 5, 7-trihydroxyflavone (34.68% ±1.9%). The computational analysis of compounds showed their molecular interaction with important amino acid residues and nonheme iron atom in the catalytic site of LOX by enlightening their potential binding mode at molecular level. Conclusions: The LOX inhibitory constituents were identified from A. malabarica by means of bioassay-guided fractionation process. The results derived from in vitro and computational experiments confirm the potential of the isolated compounds and provide additional evidence for its traditional use in inflammatory disorders.
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Affiliation(s)
- A Sudha
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - P Srinivasan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Prasanna G, Ujwal A, Diliprajudominic S, Marimuthu T, Saraswathi NT. A new pipeline to discover antimycotics by inhibiting ergosterol and riboflavin synthesis: the inspirations of Siddha medicine. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0858-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Vijayalakshmi P, Selvaraj C, Singh SK, Nisha J, Saipriya K, Daisy P. Exploration of the binding of DNA binding ligands toStaphylococcalDNA through QM/MM docking and molecular dynamics simulation. J Biomol Struct Dyn 2013; 31:561-71. [DOI: 10.1080/07391102.2012.706080] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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20
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Tripathi SK, Singh SK, Singh P, Chellaperumal P, Reddy KK, Selvaraj C. Exploring the selectivity of a ligand complex with CDK2/CDK1: a molecular dynamics simulation approach. J Mol Recognit 2013; 25:504-12. [PMID: 22996593 DOI: 10.1002/jmr.2216] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cyclin-dependent kinases (CDKs) are core components of the cell cycle machinery that govern the transition between phases during cell cycle progression. Abnormalities in CDKs activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. Their inhibitors have entered in clinical trials to treat cancer. Very recently, Heathcote et al. (J. Med. Chem. 2010, 53:8508-8522) have found a ligand BS194 that has a high affinity with CDK2 (IC(50) = 3 nM) but shows low affinity with CDK1 (IC(50) = 30 nM). To understand the selectivity, we used homology modeling, molecular docking, molecular dynamics, and free-energy calculation to analyze the interactions. A rational three-dimensional model of the CDK1/BS194 complex is built. We found that Leu83 is a key residue that recognizes BS194 more effectively with CDK2 with good binding free energies rather than CDK1. Energetic analysis reveals that van der Waals interaction and non-polar contributions to solvent are favorable in the formation of complexes and amine group of the ligand, which plays a crucial role for binding selectivity between CDK2 and CDK1.
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Affiliation(s)
- Sunil Kumar Tripathi
- Computer-Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-, 630 003 Tamil Nadu, India
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Das N, Dhanawat M, Shrivastava SK. Benzoxazinones as Human Peroxisome Proliferator Activated Receptor Gamma (PPARγ) Agonists: A Docking Study Using Glide. Indian J Pharm Sci 2012; 73:159-64. [PMID: 22303058 PMCID: PMC3267299 DOI: 10.4103/0250-474x.91580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 04/01/2011] [Accepted: 04/06/2011] [Indexed: 11/24/2022] Open
Abstract
The purpose of the present study is to undertake a docking study of some benzoxazinone derivatives on human peroxisome proliferator activated receptor co-crystallized with an alpha-aryloxyphenylacetic acid agonist using Glide 4.5. The QikProp program was used to obtain the absorption, distribution, metabolism and excretion properties of the analogues. The intermolecular hydrogen bonding interaction of the best-fit ligands were found to be associated with Tyr473, Ser289, Hie 449, Hip 323, Ser 342 and Gly 284 amino acid residue at the receptor active site. Among all the observed interaction with similar binding pattern, the presence of methyl carboxypentyl side chain (Lig. No. 21) showed additional interaction with Ser 342 and the affinity was increased by carboxyl oxygen (as hydrogen bond acceptor) with a best Glide score of -14.54 as compared to the co-crystallized aryloxyphenyl acetic acid which achieved a glide score of -12.50.
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Affiliation(s)
- N Das
- Department of Pharmaceutics, Institute of Technology, Banaras Hindu University, Varanasi-221 005, India
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Shukla S, Srivastava RS, Shrivastava SK, Sodhi A, Kumar P. Synthesis, cytotoxic evaluation, docking and in silico pharmacokinetic prediction of 4-arylideneamino/cycloalkylidineamino 1, 2-naphthoquinone thiosemicarbazones. J Enzyme Inhib Med Chem 2012; 28:1192-8. [DOI: 10.3109/14756366.2012.721783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shubhanjali Shukla
- Department of Pharmaceutics, I.T., Banaras Hindu University,
Varanasi, Uttar Pradesh, India
| | | | | | - Ajit Sodhi
- School of Biotechnology, Faculty of Science, Banaras Hindu University,
Varanasi, Uttar Pradesh, India
| | - Pankaj Kumar
- School of Pharmaceutical Science, Siksha ‘O’ Anusandhan University,
Bhubaneswar, Orissa, India
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Shukla S, Srivastava RS, Shrivastava SK, Sodhi A, Kumar P. Synthesis, characterization, in vitro anticancer activity, and docking of Schiff bases of 4-amino-1,2-naphthoquinone. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0150-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Shukla S, Srivastava RS, Shrivastava SK, Sodhi A, Kumar P. Synthesis, characterization and antiproliferative activity of 1,2-naphthoquinone and its derivatives. Appl Biochem Biotechnol 2012; 167:1430-45. [PMID: 22258648 DOI: 10.1007/s12010-012-9551-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/05/2012] [Indexed: 12/13/2022]
Abstract
In the present study substituted 1,2-naphthoquinones were synthesized, purified and characterized by spectroscopic studies (UV, FT-IR, ¹H NMR, ¹³ C NMR and elemental analysis). These compounds were evaluated for cytotoxicity against a panel of human cancer cell lines (Hep-G₂ for liver sarcoma, MG-63 for osteosarcoma and MCF-7 for human breast cancer). The cells were dosed with these ortho-naphthoquinone derivatives at varying concentrations, and cell viability was measured by a 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay with doxorubicin as positive control. Significant anticancer activities were observed in vitro for some members of the series, and compounds 1,2-naphthoquinone 2-thiosemicarbazone, 1,2-naphthoquinone-2-semicarbazone, 4-amino-1,2-naphthoquinone 2-thiosemicarbazone and 4-amino-1,2-naphthoquinone-2-semicarbazone are active cytotoxic agents against different cancer cell lines with IC₅₀ values in the range of 5.73-17.67 μM. The obtained data suggested that better anticancer activity was linked with introduction of thiosemicarbazone and semicarbazone moiety in 1,2-naphthoquinone ring system. Outcomes of experimentation also reveal that incorporation of amino group in 1,2-naphthoquinone moiety contributes positively for cytotoxic action of compounds. Docking experiments showed a good correlation between their calculated interaction energies with the topoisomerase-II and the observed IC₅₀ values of all these compounds.
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Affiliation(s)
- S Shukla
- Department of Pharmaceutics, I.T., Banaras Hindu University, Varanasi 221005, India
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25
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In silico screening of indinavir-based compounds targeting proteolytic activity in HIV PR: binding pocket fit approach. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9941-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Design, synthesis, and anticonvulsant screening of some substituted piperazine and aniline derivatives of 5-phenyl-oxazolidin-2,4-diones and 5,5-diphenylimidazolidin-2,4 diones. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9805-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson–Boltzmann surface area calculations. J Comput Aided Mol Des 2011; 25:959-76. [DOI: 10.1007/s10822-011-9475-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
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Zhan P, Chen X, Li D, Fang Z, De Clercq E, Liu X. HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design. Med Res Rev 2011; 33 Suppl 1:E1-72. [PMID: 21523792 DOI: 10.1002/med.20241] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, PR China
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Wang J, Hou T. Chapter 5 Recent Advances on in silico ADME Modeling. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1574-1400(09)00505-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Durdagi S, Mavromoustakos T, Chronakis N, Papadopoulos MG. Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations. Bioorg Med Chem 2008; 16:9957-74. [DOI: 10.1016/j.bmc.2008.10.039] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 10/08/2008] [Accepted: 10/12/2008] [Indexed: 11/15/2022]
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