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Abdessadak O, Kandwal P, Alaqarbeh M, Tabti K, Sbai A, Ajana MA, Lakhlifi T, Bouachrine M. Exploring azomethine ylides reactivity with acrolein through cycloaddition reaction and computational antiviral activity assessment against hepatitis C virus. J Mol Model 2024; 30:23. [PMID: 38177613 DOI: 10.1007/s00894-023-05818-8] [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: 09/27/2023] [Accepted: 12/24/2023] [Indexed: 01/06/2024]
Abstract
CONTEXT The regioselectivity and diastereoselectivity of the 1,3-dipolar cycloaddition reaction between azomethine ylides and acrolein were investigated. The DFT studies revealed that the favored pathway leads to the formation of cis-cycloadduct pyrrolidine and these computational findings align with experimental observations. The cis-cycloadduct pyrrolidine product serves as an advanced intermediate in the synthesis of a hepatitis C virus inhibitor. For this, the antiviral activity of cis-cycloadduct pyrrolidine against cyclophilin A, the co-factor responsible for hepatitis C virus, was also evaluated through molecular docking simulations which revealed intriguing interactions and a high C-score, which were further confirmed by molecular dynamics simulations, demonstrating stability over a 100-ns simulation period. Furthermore, the cis-cycloadduct pyrrolidine exhibits favorable drug-like properties and a better ADMET profile compared to hepatitis C virus inhibitor. METHODS Chemical reactivity studies were performed using DFT method by the functional B3LYP at 6-31G (d, p) computational level by GAUSSIAN 16 program. Frontal molecular orbitals theory used to investigate HOMO/LUMO interactions between azomethine ylides and acrolein. Findings of this approach were confirmed by global reactivity indices and electron displacement was investigated based on Fukui functions. Furthermore, the activation energies were determined after frequency calculations using TS Berny algorithm and transition states were confirmed by the presence of a single imaginary frequency. Moreover, antiviral activity of cis-cycloadduct was explored through molecular docking using Surflex-Dock suite SYBYL X 2.0, and molecular dynamics simulation using GROMACS program. Finally, drug-like properties were investigated with SwissADME and ADMETlab 2.0.
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Affiliation(s)
- Oumayma Abdessadak
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Pankaj Kandwal
- Department of Chemistry, National Institute of Technology, Dehradun, Uttarakhand, 246174, India
| | - Marwa Alaqarbeh
- Basic Science Department, Prince Al Hussein bin Abdullah II Academy for Civil Protection, Al-Balqa Applied University, Al-Salt, 19117, Jordan
| | - Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco.
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, 23000, Beni-Mellal, Morocco
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Tabti K, Baammi S, Sbai A, Maghat H, Lakhlifi T, Bouachrine M. Molecular modeling study of pyrrolidine derivatives as novel myeloid cell leukemia-1 inhibitors through combined 3D-QSAR, molecular docking, ADME/Tox and MD simulation techniques. J Biomol Struct Dyn 2023; 41:13798-13814. [PMID: 36841617 DOI: 10.1080/07391102.2023.2183032] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023]
Abstract
A series of pyrrolidine derivatives have been used to study the main structural requirements for designing novel Mcl-1 inhibitors. For this purpose, three models CoMSIA, CoMFA and HQSAR were generated using QSAR molecular modeling techniques. The statistical results of the CoMFA (Q2 = 0.689; R = 0.999; R2pred = 0.986), CoMSIA (Q2 = 0.614; R2 = 0.923; R2pred = 0.815) and HQSAR (Q2= 0.603; R2 = 0.662; R2pred = 0.743) models showed good stability and predictability. The results of the models were presented as contours and colored fragments indicating the favorable and unfavorable contribution to the inhibitory activity of Mcl-1. Based on the obtained results, four new compounds were designed with more potent predicted pIC50 inhibitory activity. The ADME/Tox results and the pharmacokinetic properties revealed that these four compounds are orally bioavailable and show good permeability. In addition the four compounds showing non-inhibitors of CYP3A4 and CYP2D6 with the exception of Pred03. At the level of toxicity profile, the compounds Pred01, Pred02 and Pred03 showed interesting results and showed no AMES toxicity, no hERG inhibition and no skin sensitization. Molecular docking results were used to uncover the mode of interaction between the ligand and key residues of protein binding site. Molecular docking results were supported by molecular simulation and binding free energy estimation (MMPBSA). These results demonstrate the stability of the analyzed compounds in the target protein binding site during a 100 ns trajectory. Finally, all these results create a strong lead to develop promising new Pyrrolidine-based inhibitors against Mcl-1.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Moulay Ismail University, Faculty of Science, Meknes, Morocco
- High School of Technology Khenifra, Sultan Moulay Sliman University, Benimellal, Morocco
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Ramachandran B, Muthupandian S, Jeyaraman J, Lopes BS. Computational exploration of molecular flexibility and interaction of meropenem analogs with the active site of oxacillinase-23 in Acinetobacter baumannii. Front Chem 2023; 11:1090630. [PMID: 36909706 PMCID: PMC9996302 DOI: 10.3389/fchem.2023.1090630] [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: 11/05/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Background: Carbapenem-resistant Acinetobacter baumannii is an opportunistic pathogen responsible for nosocomial infections and is one of the biggest global threats according to the World Health Organization (WHO), particularly causing substantial morbidity and mortality. Objectives: This study aimed at using computational approaches to screen meropenem and its analogs against OXA-23-positive Acinetobacter baumannii, analyzing the correlations between kinetic and phenotypic characteristics. Methods: A total of 5,450 compounds were screened using virtual screening workflow (HTVS, Glide-SP, and Glide-XP) to identify the best compounds based on their binding energy and interactions against OXA-23 and OXA-27 as they had phenotypic data available. Molecular dynamics simulation and density functional theory (DFT) studies were performed from the outcome of molecular docking analysis. Results: During simulations, meropenem and its analogs exhibited high-level stable interactions with Ser79, Ser126, Thr217, Trp219, and Arg259 of OXA-23. Meropenem displayed a CovDock energy of about -3.5 and -1.9 kcal mol-1 against OXA-23 and OXA-27, respectively. Among the 5,450 compounds, Pubchem_10645796, Pubchem_25224737, and ChEMBL_14 recorded CovDock energy between -6.0 and -9.0 kcal mol-1. Moreover, the infra-red (IR) spectrophotometric analysis revealed C=O and C-N atoms showing bands at 1,800 and 1,125 cm-1, respectively. These observed data are in congruence with the experimental observations. Conclusion: The identified compounds showed good agreement with the spectrophotometric analysis using DFT methods. In the earlier studies, meropenem's MIC value was 32 μg mL-1 in OXA-23-positive isolate A2265 compared to the MIC of 1 μg mL-1 in Δbla OXA-23 A2265. Comparing the CovDock energy and hydrogen-bonding interactions, the predicted results are in good agreement with the experimental data reported earlier. Our results highlight the importance of OXA-23 molecular docking studies and their compliance with the phenotypic results. It will help further in developing newer antibiotics for treating severe infections associated with carbapenem-resistant A. baumannii.
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Affiliation(s)
- Balajee Ramachandran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Saravanan Muthupandian
- Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Bruno Silvester Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom.,National Horizons Centre, Teesside University, Darlington, United Kingdom
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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Miryala SK, Basu S, Naha A, Debroy R, Ramaiah S, Anbarasu A, Natarajan S. Datasets comprising the quality validations of simulated protein-ligand complexes and SYBYL docking scores of bioactive natural compounds as inhibitors of Mycobacterium tuberculosis protein-targets. Data Brief 2022; 42:108146. [PMID: 35479419 PMCID: PMC9035630 DOI: 10.1016/j.dib.2022.108146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 01/04/2023] Open
Abstract
Docking scores and simulation parameters to study the potency of natural compounds against protein targets in Mycobacterium tuberculosis (Mtb) were retrieved through molecular docking and in-silico structural investigation. The molecular docking datasets comprised 15 natural compounds, seven conventional anti-tuberculosis (anti-TB) drugs and their seven corresponding Mtb target proteins. Mtb protein targets were actively involved in translation mechanism, nucleic acid metabolism and membrane integrity. Standard structural screening and stereochemical optimizations were adopted to generate the 3D protein structures and their corresponding ligands prior to molecular docking. Force-field integration and energy minimization were further employed to obtain the proteins in their ideal geometry. Surflex-dock algorithm using Hammerhead scoring functions were used to finally produce the docking scores between each protein and the corresponding ligand(s). The best-docked complexes selected for simulation studies were subjected to topology adjustments, charge neutralizations, solvation and equilibrations (temperature, volume and pressure). The protein-ligand complexes and molecular dynamics parameter files have been provided. The trajectories of the simulated parameters such as density, pressure and temperature were generated with integrated tools of the simulation suite. The datasets can be useful to computational and molecular medicine researchers to find therapeutic leads relevant to the chemical behaviours of a specific class of compounds against biological systems. Structural parameters and energy functions provided a set of standard values that can be utilised to design simulation experiments regarding similar macromolecular interactions.
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Quorum quenching by 2-Hydroxyanisole extracted from Solanum torvum on Pseudomonas aeruginosa and its inhibitory action upon LasR protein. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Ragunathan A, Malathi K, Ramaiah S, Anbarasu A. FtsA as a cidal target for Staphylococcus aureus: Molecular docking and dynamics studies. J Cell Biochem 2019; 120:7751-7758. [PMID: 30417432 DOI: 10.1002/jcb.28049] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus infection is a healthcare problem to mankind for a considerable period of time. Once when it enters the bloodstream of an individual, it may potentially result in life-threatening conditions. The resistance of S. aureus to various drugs such as penicillin, methicillin, gentamicin, erythromycin, and tetracycline have been well documented. Presently vancomycin is the drug of choice for methicillin resistant S. aureus. Scientists believe that S. aureus would completely develop resistance to vancomycin as well. Therefore there is a commensurate need to develop a drug to replace vancomycin. In the current study, we have focussed on FtsA, an important and vital cell division protein, which is found only in S. aureus and in other prokaryotic cells. We have carried out virtual screening process for FtsA against ZINC database, the best hit molecules obtained from the preliminary docking studies were subjected to SYBYL X 2.0 docking. The molecules ZINC74432848, ZINC37769607, and ZINC96896268 displayed the highest C-score value of 4.89, 4.49, and 4.22, respectively. The top ranked molecule ZINC74432848 was observed to form 4 hydrogen bonds with FtsA. The simulation study reveals the greater stability of the FtsA-ZINC74432848 complex. If the in vitro and in vivo study turns out affirmative, then ZINC74432848 could be developed as a potent drug for FtsA.
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Affiliation(s)
- Adhithya Ragunathan
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kullappan Malathi
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sudha Ramaiah
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Department of Biotechnology, Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Malathi K, Ramaiah S, Anbarasu A. Comparative Molecular Field Analysis and Molecular Docking Studies on Quinolinone Derivatives Indicate Potential Hepatitis C Virus Inhibitors. Cell Biochem Biophys 2019; 77:139-156. [PMID: 30796723 DOI: 10.1007/s12013-019-00867-4] [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] [Received: 07/20/2018] [Accepted: 02/09/2019] [Indexed: 12/12/2022]
Abstract
Presently, there are no effective vaccines and anti-virals for the prevention and treatment of Hepatitis C virus infections and hence there is an urgent need to develop potent HCV inhibitors. In this study, we have carried out molecular docking, molecular dynamics and 3D-QSAR on heteroaryl 3-(1,1-dioxo-2H-(1,2,4)-benzothiadizin-3-yl)-4-hydroxy-2(1H)-quinolinone series using NS5B protein. Total of 41 quinolinone derivatives is used for molecular modeling study. The binding conformation and hydrogen bond interaction of the docked complexes were analyzed to model the inhibitors. We identified the molecule XXXV that had a higher affinity with NS5B. The molecular dynamics study confirmed the stability of the compound XXXV-NS5B complex. The developed CoMFA descriptors parameters, which were calculated using a test set of 13 compounds, were statistically significant. Our results will provide useful insights and lead to design potent anti-Hepatitis C virus molecules.
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Affiliation(s)
- Kullappan Malathi
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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Malathi K, Anbarasu A, Ramaiah S. Identification of potential inhibitors for Klebsiella pneumoniae carbapenemase-3: a molecular docking and dynamics study. J Biomol Struct Dyn 2019; 37:4601-4613. [PMID: 30632921 DOI: 10.1080/07391102.2018.1556737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a Gram-negative bacterium, which is a leading causal agent for nosocomial infections. Penicillin, cephalosporin and carbapenems along with the inhibitors such as tazobactam, sulbactam and clavulanic acid are prescribed for the treatment of K. pneumoniae infections. Prolonged exposure to β-lactam antibiotics leads to the development of resistance. The major reason for the β-lactam resistance in K. pneumoniae is the secretion of the enzyme K. pneumoniae carbapenemase (KPC). Secretion of KPC-2 and its variant KPC-3 by the K. pneumoniae strains causes resistance to both the substrate imipenem and the β-lactamase inhibitors. Hence, molecular docking and dynamics studies were carried out to analyze the resistance mechanism of KPC-2-imipenem and KPC-3-imipenem at the structural level. It reveals that KPC-3-imipenem has the highest c-score value of 4.03 with greater stability than the KPC-2-imipenem c-score value of 2.36. Greater the interaction between the substrate and the β-lactamase enzyme, higher the chances of hydrolysis of the substrate. Presently available β-lactamase inhibitors are also ineffective against KPC-3-expressing strains. This situation necessitates the need for development of novel and effective inhibitors for KPC-3. We have carried out the virtual screening process to identify more effective inhibitors for KPC-3, and this has resulted in ZINC48682523, ZINC50209041 and ZINC50420049 as the best binding energy compounds, having greater binding affinity and stability than KPC-3-tazobactam interactions. Our study provides a clear understanding of the mechanism of drug resistance and provides valuable inputs for the development of inhibitors against KPC-3 expressing K. pneumoniae. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology , Vellore , Tamil Nadu , India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology , Vellore , Tamil Nadu , India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology , Vellore , Tamil Nadu , India
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Thillainayagam M, Malathi K, Anbarasu A, Singh H, Bahadur R, Ramaiah S. Insights on inhibition of Plasmodium falciparum plasmepsin I by novel epoxyazadiradione derivatives – molecular docking and comparative molecular field analysis. J Biomol Struct Dyn 2018. [DOI: 10.1080/07391102.2018.1510342 pmid: 30092746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mahalakshmi Thillainayagam
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Renu Bahadur
- Indian Council for Medical Research, New Delhi, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Thillainayagam M, Malathi K, Anbarasu A, Singh H, Bahadur R, Ramaiah S. Insights on inhibition of Plasmodium falciparum plasmepsin I by novel epoxyazadiradione derivatives – molecular docking and comparative molecular field analysis. J Biomol Struct Dyn 2018; 37:3168-3182. [DOI: 10.1080/07391102.2018.1510342] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mahalakshmi Thillainayagam
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Renu Bahadur
- Indian Council for Medical Research, New Delhi, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Malathi K, Ramaiah S. Mechanism of imipenem resistance in metallo‐β‐lactamases expressing pathogenic bacterial spp. and identification of potential inhibitors: An in silico approach. J Cell Biochem 2018; 120:584-591. [DOI: 10.1002/jcb.27414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Kullappan Malathi
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
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Malathi K, Ramaiah S. Bioinformatics approaches for new drug discovery: a review. Biotechnol Genet Eng Rev 2018; 34:243-260. [DOI: 10.1080/02648725.2018.1502984] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sudha Ramaiah
- Department of Biosciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu
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Maia NL, de Barros M, de Oliveira LL, Cardoso SA, Dos Santos MH, Pieri FA, Ramalho TC, da Cunha EFF, Moreira MAS. Synergism of Plant Compound With Traditional Antimicrobials Against Streptococcus spp. Isolated From Bovine Mastitis. Front Microbiol 2018; 9:1203. [PMID: 29928266 PMCID: PMC5998740 DOI: 10.3389/fmicb.2018.01203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/17/2018] [Indexed: 12/26/2022] Open
Abstract
Mastitis is an inflammation of the mammary gland that causes major losses in the dairy industry. Streptococcus spp. are among the main agents of this disease. Increased resistance to antibiotics is one of the causes of therapeutic failure. Plants, due to their broad chemodiversity, are an interesting source of new molecules with antibacterial activity. Using these compounds along with traditional antibiotics is a possible method for reversing resistance. The objective of this work was to determine the interactions between the activities of guttiferone-A and 7-epiclusianone, two active substances isolated from the fruits of Garcinia brasiliensis, and traditional antibiotics against Streptococcus spp. isolated from bovine mastitis and known to be resistant to them. First, the MIC for the antibiotics and bioactive compounds was determined, followed by their activities, alone and in combination. Then, their cytotoxicity was measured in bovine mammary epithelial cells. Finally, molecular docking simulations were performed to elucidate molecular details of the interactions between β-lactamase and the compounds binding to it (clavulanic acid, ampicillin, 7-epiclusianone, and guttiferone-A). The bacterial isolates were resistant to ampicillin and gentamicin. Both antibiotics showed predominantly synergistic antibacterial activities in combination with guttiferone-A or 7-epiclusianone. These two active substances were not cytotoxic at synergistic concentrations and both showed strong binding to β-lactamase, which may explain the reversal of ampicillin resistance. These substances are promising for the treatment of bovine mastitis.
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Affiliation(s)
- Natasha L Maia
- Bacterial Disease Laboratory, Department of Veterinary, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Mariana de Barros
- Bacterial Disease Laboratory, Department of Veterinary, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Leandro L de Oliveira
- Immunochemistry and Glycobiology Laboratory, Department of General Biology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Silvia A Cardoso
- Department of Medicine and Nursing, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Marcelo H Dos Santos
- Synthesis of Agrochemicals Laboratory, Department of Chemistry, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Fabio A Pieri
- Department of Basic Life Sciences, Universidade Federal de Juiz de Fora, Governador Valadares, Brazil
| | | | | | - Maria A S Moreira
- Bacterial Disease Laboratory, Department of Veterinary, Universidade Federal de Viçosa, Viçosa, Brazil
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Thillainayagam M, Malathi K, Ramaiah S. In-Silico molecular docking and simulation studies on novel chalcone and flavone hybrid derivatives with 1, 2, 3-triazole linkage as vital inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. J Biomol Struct Dyn 2017; 36:3993-4009. [DOI: 10.1080/07391102.2017.1404935] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mahalakshmi Thillainayagam
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, TamilNadu, India
| | - Kullappan Malathi
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, TamilNadu, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632 014, TamilNadu, India
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Ragunathan A, Malathi K, Anbarasu A. MurB as a target in an alternative approach to tackle the Vibrio cholerae resistance using molecular docking and simulation study. J Cell Biochem 2017; 119:1726-1732. [PMID: 28786497 DOI: 10.1002/jcb.26333] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/07/2017] [Indexed: 01/13/2023]
Abstract
Cholera is a serious threat to a large population in the under developed countries. Though oral rehydration therapy is the preferred choice of treatment, the use of antibiotics could reduce the microbial load in the case of severity. The use of antibiotics is also sought in the scenarios where there is problem with access to clean water. However, Vibrio cholera (V. cholerae) strains have developed resistance to antibiotics such as amoxicillin, ampicillin, chloramphenicol, doxycycline, erythromycin, and tetracycline. In this work, we have addressed the resistance issue by targeting MurB protein which is essential for the cell wall biosynthesis in V. cholerae. 20 Phytochemical compounds were chosen to screen the potential inhibitors against V. cholerae to avoid the complications faced by synthesis of small molecules. The molecular docking and dynamics study indicates that quercetin is the most potential and stable inhibitor of Murb.
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Affiliation(s)
- Adhithya Ragunathan
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Kullappan Malathi
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
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Exploring the resistance mechanism of imipenem in carbapenem hydrolysing class D beta-lactamases OXA-143 and its variant OXA-231 (D224A) expressing Acinetobacter baumannii: An in-silico approach. Comput Biol Chem 2017; 67:1-8. [DOI: 10.1016/j.compbiolchem.2016.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/06/2016] [Accepted: 12/06/2016] [Indexed: 01/16/2023]
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