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Ambade SS, Gupta VK, Bhole RP, Khedekar PB, Chikhale RV. A Review on Five and Six-Membered Heterocyclic Compounds Targeting the Penicillin-Binding Protein 2 (PBP2A) of Methicillin-Resistant Staphylococcus aureus (MRSA). Molecules 2023; 28:7008. [PMID: 37894491 PMCID: PMC10609489 DOI: 10.3390/molecules28207008] [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: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen. Methicillin-resistant Staphylococcus aureus (MRSA) infections pose significant and challenging therapeutic difficulties. MRSA often acquires the non-native gene PBP2a, which results in reduced susceptibility to β-lactam antibiotics, thus conferring resistance. PBP2a has a lower affinity for methicillin, allowing bacteria to maintain peptidoglycan biosynthesis, a core component of the bacterial cell wall. Consequently, even in the presence of methicillin or other antibiotics, bacteria can develop resistance. Due to genes responsible for resistance, S. aureus becomes MRSA. The fundamental premise of this resistance mechanism is well-understood. Given the therapeutic concerns posed by resistant microorganisms, there is a legitimate demand for novel antibiotics. This review primarily focuses on PBP2a scaffolds and the various screening approaches used to identify PBP2a inhibitors. The following classes of compounds and their biological activities are discussed: Penicillin, Cephalosporins, Pyrazole-Benzimidazole-based derivatives, Oxadiazole-containing derivatives, non-β-lactam allosteric inhibitors, 4-(3H)-Quinazolinones, Pyrrolylated chalcone, Bis-2-Oxoazetidinyl macrocycles (β-lactam antibiotics with 1,3-Bridges), Macrocycle-embedded β-lactams as novel inhibitors, Pyridine-Coupled Pyrimidinones, novel Naphthalimide corbelled aminothiazoximes, non-covalent inhibitors, Investigational-β-lactam antibiotics, Carbapenem, novel Benzoxazole derivatives, Pyrazolylpyridine analogues, and other miscellaneous classes of scaffolds for PBP2a. Additionally, we discuss the penicillin-binding protein, a crucial target in the MRSA cell wall. Various aspects of PBP2a, bacterial cell walls, peptidoglycans, different crystal structures of PBP2a, synthetic routes for PBP2a inhibitors, and future perspectives on MRSA inhibitors are also explored.
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Affiliation(s)
- Shraddha S. Ambade
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra 282004, UP, India
| | - Ritesh P. Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, MH, India
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, MH, India
| | - Pramod B. Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
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Lamazares E, MacLeod-Carey D, Miranda FP, Mena-Ulecia K. Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents. Molecules 2021; 26:E386. [PMID: 33451037 PMCID: PMC7828527 DOI: 10.3390/molecules26020386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 01/29/2023] Open
Abstract
The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which is the main virulence factor of these bacteria. In this work, we used the previous results of a computational biochemistry protocol of a series of ligands designed in silico using thermolysin as a model for the search of antihypertensive agents. Here, thermolysin from Bacillus thermoproteolyticus, a metalloprotein of the M4 family, was used to determine the most promising candidate as an antibacterial agent. Our results from docking, molecular dynamics simulation, molecular mechanics Poisson-Boltzmann (MM-PBSA) method, ligand efficiency, and ADME-Tox properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity) indicate that the designed ligands were adequately oriented in the thermolysin active site. The Lig783, Lig2177, and Lig3444 compounds showed the best dynamic behavior; however, from the ADME-Tox calculated properties, Lig783 was selected as the unique antibacterial agent candidate amongst the designed ligands.
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Affiliation(s)
- Emilio Lamazares
- Pathophysiology Department, Biotechnology and Biopharmaceutical Laboratory, School of Biological Sciences, Universidad de Concepción, Victor Lamas 1290, P.O. Box 160-C, Concepción 4079386, Chile;
| | - Desmond MacLeod-Carey
- Inorganic Chemistry and Molecular Materials Center, Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, San Miguel, Santiago 8900000, Chile;
| | - Fernando P. Miranda
- Instituto de Fisiología, Facultad de Medicina, Universidad Austral de Chile, Valdivia 5090000, Chile;
| | - Karel Mena-Ulecia
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Ave. Rudecindo Ortega 02950, Temuco 4780000, Chile
- Núcleo de Investigación en Bioproductos y Materiales Avanzados (BIOMA), Facultad de Ingeniería, Universidad Católica de Temuco, Ave. Rudecindo Ortega 02950, Temuco 4780000, Chile
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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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Mena-Ulecia K, MacLeod-Carey D. Interactions of 2-phenyl-benzotriazole xenobiotic compounds with human Cytochrome P450-CYP1A1 by means of docking, molecular dynamics simulations and MM-GBSA calculations. Comput Biol Chem 2018; 74:253-262. [DOI: 10.1016/j.compbiolchem.2018.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 11/30/2022]
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Molecular docking simulation on the interactions of laccase from Trametes versicolor with nonylphenol and octylphenol isomers. Bioprocess Biosyst Eng 2017; 41:331-343. [PMID: 29185034 DOI: 10.1007/s00449-017-1866-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/11/2017] [Indexed: 10/18/2022]
Abstract
The biodegradation of nonylphenol (NP) and octylphenol (OP) isomers by laccase has attracted increasing concerns. However, the interaction mechanism between these isomers and laccase remains unclear, especially for fungal laccase. In this work, molecular docking was employed to study this issue. The results indicated that the structural characteristic of alkyl chain (position and branching degree) affected the interactions between Trametes versicolor (T. versicolor) laccase and isomers. The binding affinity between them was closely related to the position and branching degree of alkyl chain in isomers. The binding affinities between linear isomers and T. versicolor laccase were para-position < meta-position < ortho-position. For selected branched 4-NP, the isomers with bulky α-substituent in alkyl chain had higher binding affinities. In addition, hydrophobic contacts between T. versicolor laccase and NP or OP isomers were necessary, while H-bonds were optional. The isomers with similar structure may have more common residues involved in hydrophobic contacts. The H-bonds of selected NPs and OPs were all connected with phenolic hydroxyl. These findings provide an insight into detailed interaction mechanism between T. versicolor laccase and isomers of NP and OP. It is helpful to broaden the knowledge of degradation technology of NPs and OPs and provide theoretical basis on biological remediation of these contaminants.
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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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Suganya S, Nandagopal B, Anbarasu A. Natural Inhibitors of HMG-CoA Reductase-An Insilico Approach Through Molecular Docking and Simulation Studies. J Cell Biochem 2016; 118:52-57. [PMID: 27216569 DOI: 10.1002/jcb.25608] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 05/20/2016] [Indexed: 01/09/2023]
Abstract
Plant products have always been considered for many important metabolic disorders due to its abundant medicinal properties. Alarming adverse effects of overuse of statins has been reported for patients with dyslipidemia. This study was aimed to identify compounds with potent anti-dyslipidemic property from selected plants and analyze them for their efficiency in binding with HMG-CoA reductase, a key enzyme in lipid metabolism. The docking studies indicate rutin as the best compound that can inhibit HMG-CoA reductase as it had strong binding affinity to the enzyme. The molecular dynamics simulation studies confirmed the stability of the HMG-CoA reductase-rutin complex. RMSD, RMSF, Rg, H-bond results indicated that the HMG-CoA reductase-rutin complex is highly stable. Presently, statins are not preferred for individuals with pre-existing liver disease. Our study identified rutin as a promising lead compound which could be further developed into an anti-dyslipidemic molecule. Our results will be a good starting point for future experimental and clinical studies and if the results from such studies match international standards plant derived rutin might emerge as a good alternative to statins. J. Cell. Biochem. 118: 52-57, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Subramanian Suganya
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India.,Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632 014, Tamil Nadu, India
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632 014, Tamil Nadu, India
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Molecular Docking and Molecular Dynamics Studies to Identify Potential OXA-10 Extended Spectrum β-Lactamase Non-hydrolysing Inhibitors for Pseudomonas aeruginosa. Cell Biochem Biophys 2016; 74:141-55. [DOI: 10.1007/s12013-016-0735-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/18/2016] [Indexed: 01/17/2023]
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de Araújo RSA, Barbosa-Filho JM, Scotti MT, Scotti L, da Cruz RMD, Falcão-Silva VDS, de Siqueira-Júnior JP, Mendonça-Junior FJB. Modulation of Drug Resistance in Staphylococcus aureus with Coumarin Derivatives. SCIENTIFICA 2016; 2016:6894758. [PMID: 27200211 PMCID: PMC4856757 DOI: 10.1155/2016/6894758] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/03/2016] [Indexed: 06/05/2023]
Abstract
Semisynthetic and commercial coumarins were investigated for their antibacterial and adjuvant properties with antibiotic agents against norfloxacin, erythromycin, and tetracycline resistant Staphylococcus aureus as based on efflux mechanisms. The coumarins and certain commercial antibiotics had their Minimum Inhibitory Concentrations determined by broth microdilution assay against resistant S. aureus strains which overexpress efflux pump proteins. For evaluation of the modulatory activity, the antibiotics MICs were determined in the presence of the coumarin derivatives at subinhibitory concentration. Although the coumarins did not display relevant antibacterial activity (MIC ≥ 128 µg/mL), they did modulate the antibiotics activities. Various coumarins, especially the alkylated derivatives in combination with antibiotics at subinhibitory concentrations, modulated antibiotic activity, reducing the MIC for tetracycline and norfloxacin by 2 to 8 times. Polar Surface Area (PSA) studies were performed and the fact that the presence of apolar groups is an important factor for the modulatory activity of coumarins was corroborated. Docking on the Penicillin-Binding Protein from MRSA identified that 18 is a potential ligand presenting low E binding. The results indicate that coumarin derivatives modulated antibiotic resistance and may be used as potential antibiotic adjuvants, acting by bacterial efflux pump inhibition in S. aureus.
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Affiliation(s)
- Rodrigo Santos Aquino de Araújo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
| | - José Maria Barbosa-Filho
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
| | - Ryldene Marques Duarte da Cruz
- Laboratory of Genetics of Microorganisms, Molecular Biology Department, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
| | - Vivyanne dos Santos Falcão-Silva
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
- Laboratory of Genetics of Microorganisms, Molecular Biology Department, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
| | - José Pinto de Siqueira-Júnior
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
- Laboratory of Genetics of Microorganisms, Molecular Biology Department, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
| | - Francisco Jaime Bezerra Mendonça-Junior
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900 João Pessoa, PB, Brazil
- Laboratory of Synthesis and Drug Delivery, Biological Science Department, State University of Paraíba, 58071-160 João Pessoa, PB, Brazil
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Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5010012. [PMID: 27025527 PMCID: PMC4810414 DOI: 10.3390/antibiotics5010012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/29/2022] Open
Abstract
Peptidoglycan (PG) is an essential macromolecular sacculus surrounding most bacteria. It is assembled by the glycosyltransferase (GT) and transpeptidase (TP) activities of multimodular penicillin-binding proteins (PBPs) within multiprotein complex machineries. Both activities are essential for the synthesis of a functional stress-bearing PG shell. Although good progress has been made in terms of the functional and structural understanding of GT, finding a clinically useful antibiotic against them has been challenging until now. In contrast, the TP/PBP module has been successfully targeted by β-lactam derivatives, but the extensive use of these antibiotics has selected resistant bacterial strains that employ a wide variety of mechanisms to escape the lethal action of these antibiotics. In addition to traditional β-lactams, other classes of molecules (non-β-lactams) that inhibit PBPs are now emerging, opening new perspectives for tackling the resistance problem while taking advantage of these valuable targets, for which a wealth of structural and functional knowledge has been accumulated. The overall evidence shows that PBPs are part of multiprotein machineries whose activities are modulated by cofactors. Perturbation of these systems could lead to lethal effects. Developing screening strategies to take advantage of these mechanisms could lead to new inhibitors of PG assembly. In this paper, we present a general background on the GTs and TPs/PBPs, a survey of recent issues of bacterial resistance and a review of recent works describing new inhibitors of these enzymes.
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