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Hodyna D, Klipkov A, Kachaeva M, Shulha Y, Gerus I, Metelytsia L, Kovalishyn V. In Silico Design and In Vitro Assessment of Bicyclic Trifluoromethylated Pyrroles as New Antibacterial and Antifungal Agents. Chem Biodivers 2024; 21:e202400638. [PMID: 38837284 DOI: 10.1002/cbdv.202400638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/07/2024]
Abstract
QSAR studies on the number of compounds tested as S. aureus inhibitors were performed using an interactive Online Chemical Database and Modeling Environment (OCHEM) web platform. The predictive ability of the developed consensus QSAR model was q2=0.79±0.02. The consensus prediction for the external evaluation set afforded high predictive power (q2=0.82±0.03). The models were applied to screen a virtual chemical library with anti-S. aureus activity. Six promising new bicyclic trifluoromethylated pyrroles were identified, synthesized and evaluated in vitro against S. aureus, E. coli, and A. baumannii for their antibacterial activity and against C. albicans, C. krusei and C. glabrata for their antifungal activity. The synthesized compounds were characterized by 1H, 19F, and 13C NMR and elemental analysis. The antimicrobial activity assessment indicated that trifluoromethylated pyrroles 9 and 11 demonstrated the greatest antibacterial and antifungal effects against all the tested pathogens, especially against multidrug-resistant strains. The acute toxicity of the compounds to Daphnia magna ranged from 1.21 to 33.39 mg/L (moderately and slightly toxic). Based on the docking results, it can be suggested that the antibacterial and antifungal effects of the compounds can be explained by the inhibition of bacterial wall component synthesis.
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Affiliation(s)
- Diana Hodyna
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Anton Klipkov
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
- National University of Kyiv -, Mohyla Academy, 2, Skovorody Str., Kyiv, 04070, Ukraine
| | - Maryna Kachaeva
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Yurii Shulha
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Igor Gerus
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Larysa Metelytsia
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Vasyl Kovalishyn
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
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Khagar P, Wankhade AV, Sabarathinam S. Synthesis of quercetin-iron (Fe) complex and its in silico and in vitro confirmation towards antibacterial activity. Future Med Chem 2023; 15:1743-1756. [PMID: 37814818 DOI: 10.4155/fmc-2023-0007] [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] [Indexed: 10/11/2023] Open
Abstract
Aim: In this study quercetin-iron complex (QFC) was synthesized, and the structural characterizations such as x-ray diffraction, field emission-scanning electron microscopy, energy-dispersive x-ray and Brunner-Emmitt-Teller adsorption-desorption isotherm analysis revealed the crystallinity state, surface morphology and nature of the adsorbing surface with surface area value. Methodology: Functional characterizations such as UV-visible spectrometric and Fourier transform infrared analysis collectively indicated the chemical changes that appeared after complex formation in terms of characteristic change in the spectrum and band position, respectively. Results: The in vitro antibacterial activity against Escherichia coli and Staphylococcus aureus has shown a dose-dependent decrease in colony count and achieved significant removal at 15 mg/ml concentration of QFC. Conclusion: The molecular docking study supports the therapeutic application of QFC.
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Affiliation(s)
- Prerna Khagar
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, 440010 (MS), India
| | - Atul V Wankhade
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, 440010 (MS), India
| | - Sarvesh Sabarathinam
- Drug Testing Laboratory (DTL), Interdisciplinary Institute of Indian System of Medicine (IIISM), SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu-603203, India
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3
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Taghipour MJ, Ezzatpanah H, Ghahderijani M. In vitro and in silico studies for the identification of anti-cancer and antibacterial peptides from camel milk protein hydrolysates. PLoS One 2023; 18:e0288260. [PMID: 37437001 DOI: 10.1371/journal.pone.0288260] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023] Open
Abstract
Today, breast cancer and infectious diseases are very worrying that led to a widespread effort by researchers to discover natural remedies with no side effects to fight them. In the present study, we isolated camel milk protein fractions, casein and whey proteins, and hydrolyzed them using pepsin, trypsin, and both enzymes. Screening of peptides with anti-breast cancer and antibacterial activity against pathogens was performed. Peptides derived from whey protein fraction with the use of both enzymes showed very good activity against MCF-7 breast cancer with cell viability of 7.13%. The separate use of trypsin and pepsin to digest whey protein fraction yielded peptides with high antibacterial activity against S. aureus (inhibition zone of 4.17 ± 0.30 and 4.23 ± 0.32 cm, respectively) and E. coli (inhibition zone of 4.03 ± 0.15 and 4.03 ± 0.05 cm, respectively). Notably, in order to identify the effective peptides in camel milk, its protein sequences were retrieved and enzymatically digested in silico. Peptides that showed both anticancer and antibacterial properties and the highest stability in intestinal conditions were selected for the next step. Molecular interaction analysis was performed on specific receptors associated with breast cancer and/or antibacterial activity using molecular docking. The results showed that P3 (WNHIKRYF) and P5 (WSVGH) peptides had low binding energy and inhibition constant so that they specifically occupied active sites of protein targets. Our results introduced two peptide-drug candidates and new natural food additive that can be delivered to further animal and clinical trials.
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Affiliation(s)
- Mohammad Javad Taghipour
- Department of Food Science and Technology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Ezzatpanah
- Department of Food Science and Technology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Ghahderijani
- Department of Agricultural Systems Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Matos IDA, Goes Pinto AC, Ferraz MVF, Adan WCS, Rodrigues RP, Dos Santos JX, Kitagawa RR, Lins RD, Oliveira TB, Costa Junior NBD. Identification of potential Staphylococcus aureus dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation. J Biomol Struct Dyn 2023; 41:3835-3846. [PMID: 35356863 DOI: 10.1080/07391102.2022.2057361] [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: 08/01/2021] [Accepted: 03/19/2022] [Indexed: 10/18/2022]
Abstract
Herein we describe the use of molecular docking simulations, quantitative structure-activity relationships studies and ADMETox predictions to analyse the molecular recognition of a series of 7-aryl-2,4-diaminoquinazoline derivatives on the inhibition of Staphylococcus aureus dihydrofolate reductase and conducted a virtual screening to discover new potential inhibitors. A quantitative structure-activity relationship model was developed using 40 compounds and two selected descriptors. These descriptors indicated the importance of pKa and molar refractivity for the inhibitory activity against SaDHFR. The values of R2train, CVLOO and R2test generated by the model were 0.808, 0.766, and 0.785, respectively. The integration between QSAR, molecular docking, ADMETox analysis and molecular dynamics simulations with binding free energies calculation, yielded the compounds PC-124127620, PC-124127795 and PC-124127805 as promising candidates to SaDHFR inhibitors. These compounds presented high potency, good pharmacokinetics and toxicological profile. Thus, these molecules are good potential antimicrobial agent to treatment of infect disease caused by S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Isaac de Araujo Matos
- Department of Chemistry, Graduate Program in Chemistry, Federal University of Sergipe-UFS, São Cristóvão-SE, Brazil
| | - Ana Carolina Goes Pinto
- Department of Chemistry, Graduate Program in Chemistry, Federal University of Sergipe-UFS, São Cristóvão-SE, Brazil
| | | | - Wenny Camilla Santos Adan
- Department of Pharmaceutical Sciences, Postgraduate Program in Pharmaceutical Sciences, Federal University of Espírito Santo-UFES, Vitória-ES, Brazil
| | - Ricardo Pereira Rodrigues
- Department of Pharmacy, Graduate Program in Chemistry, Federal University of Sergipe-UFS, São Cristóvão-SE, Brazil
| | - Juliane Xavier Dos Santos
- Department of Chemistry, Graduate Program in Chemistry, Federal University of Sergipe-UFS, São Cristóvão-SE, Brazil
| | - Rodrigo Rezende Kitagawa
- Department of Pharmaceutical Sciences, Postgraduate Program in Pharmaceutical Sciences, Federal University of Espírito Santo-UFES, Vitória-ES, Brazil
| | | | - Tiago Branquinho Oliveira
- Department of Pharmacy, Graduate Program in Chemistry, Federal University of Sergipe-UFS, São Cristóvão-SE, Brazil
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Al-Aizari FA, Ghabbour HA, Kheder NA, Soliman SM, Hassan MZ, Tasqeeruddin S, Mabkhot YN. Synthesis, X-Ray Structure Analysis, Computational Investigations, and In Vitro Biological Evaluation of New Thiazole-Based Heterocycles as Possible Antimicrobial Agents. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2172053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Faiz A. Al-Aizari
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Chemistry, Faculty of Science, Al-Baydha University, Albaydah, Yemen
| | - Hazem A. Ghabbour
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura, Egypt
| | - Nabila A. Kheder
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - Saied M. Soliman
- Department of Chemistry, Faculty of Science, Alexandria University, Ibrahimia, Alexandria, Egypt
| | - Mohd. Z. Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Syed Tasqeeruddin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Yahia N. Mabkhot
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
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Barqi MM, Abdellah IM, Eletmany MR, Ali NM, Elhenawy AA, Abd El Latif FM. Synthesis, Characterization, Bioactivity Screening and Computational Studies of Diphenyl−malonohydrazides and Pyridines Derivatives. ChemistrySelect 2023. [DOI: 10.1002/slct.202203913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Mashael M. Barqi
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
| | - Islam M. Abdellah
- Chemistry Department, Faculty of Science Aswan University Aswan 81528 Egypt
| | - Mohamed R. Eletmany
- Chemistry Department, Faculty of Science South Valley University Qena 83523 Egypt
- TECS Department, Wilson College of Textiles NC State University Raleigh 27606 USA
| | - Nada M. Ali
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
| | - Ahmed A. Elhenawy
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
- Chemistry Department, Faculty of Science Al-Azar University Cairo 11884 Egypt
| | - Fawy M. Abd El Latif
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
- Chemistry Department, Faculty of Science Aswan University Aswan 81528 Egypt
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7
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Chemical composition, antibacterial activity and antioxidant activity of Citrus bergamia essential oil: Molecular docking simulations. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Boyer Z, Kessler H, Brosman H, Ruud KJ, Falkowski AF, Viollet C, Bourne CR, O’Reilly MC. Synthesis and Characterization of Functionalized Amino Dihydropyrimidines Toward the Analysis of their Antibacterial Structure-Activity Relationships and Mechanism of Action. ACS OMEGA 2022; 7:37907-37916. [PMID: 36312355 PMCID: PMC9607683 DOI: 10.1021/acsomega.2c05071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance among bacteria puts immense strain on public health. The discovery of new antibiotics that work through unique mechanisms is one important pillar toward combating this threat of resistance. A functionalized amino dihydropyrimidine was reported to exhibit antibacterial activity via the inhibition of dihydrofolate reductase, an underexploited antibacterial target. Despite this promise, little is known about its structure-activity relationships (SAR) and mechanism of activity. Toward this goal, the aza-Biginelli reaction was optimized to allow for the preparation of focused libraries of functionalized amino dihydropyridines, which in some cases required the use of variable temperature NMR analysis for the conclusive assignment of compound identity and purity. Antibacterial activity was examined using microdilution assays, and compound interactions with dihydrofolate reductase were assessed using antimicrobial synergy studies alongside in vitro enzyme kinetics, differential scanning fluorimetry, and protein crystallography. Clear antibacterial SAR trends were unveiled (MIC values from >64 to 4 μg/mL), indicating that this compound class has promise for future development as an antibacterial agent. Despite this, the in vitro biochemical and biophysical studies performed alongside the synergy assays call the antibacterial mechanism into question, indicating that further studies will be required to fully evaluate the antibacterial potential of this compound class.
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Affiliation(s)
- Zachary
W. Boyer
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Hannah Kessler
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Hannah Brosman
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Kirsten J. Ruud
- Department
of Chemistry and Biotechnology, University
of Wisconsin−River Falls, River Falls, Wisconsin 54022, United States
| | - Alan F. Falkowski
- Department
of Chemistry and Biotechnology, University
of Wisconsin−River Falls, River Falls, Wisconsin 54022, United States
| | - Constance Viollet
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Christina R. Bourne
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Matthew C. O’Reilly
- Department
of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
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Fucoxanthin’s Optimization from Undaria pinnatifida Using Conventional Heat Extraction, Bioactivity Assays and In Silico Studies. Antioxidants (Basel) 2022; 11:antiox11071296. [PMID: 35883788 PMCID: PMC9311727 DOI: 10.3390/antiox11071296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Brown macroalgae are a potential source of natural pigments. Among them, Undaria pinnatifida is recognized for its high concentration of fucoxanthin (Fx), which is a pigment with a wide range of bioactivities. In this study, three independent parameters were optimized for conventional heat extraction (CHE) to maximize the recovery of Fx from Undaria pinnatifida. Optimal conditions (temperature = 45 °C, solvent = 70%, and time = 61 min) extracted 5.1 mg Fx/g dw. Later, the bioactivities of the Fx-rich extracts (antioxidant, antimicrobial, and neuroprotective) were assessed using in vitro and in silico approaches. In vitro assays indicated that Fx has a strong antioxidant capacity and even stronger antimicrobial activity against gram-positive bacteria. This data was supported in silico where Fx established a high binding affinity to DR, a Staphylococcus aureus protein, through aa ALA-8, LEU-21, and other alkane interactions. Finally, the in vitro enzymatic inhibition of AChE using Fx, was further supported using docking models that displayed Fx as having a high affinity for aa TYR72 and THR 75; therefore, the Fx extraction behavior explored in this work may reduce the costs associated with energy and solvent consumption. Moreover, this paper demonstrates the efficiency of CHE when recovering high amounts of Fx from Undaria pinnatifida. Furthermore, these findings can be applied in different industries.
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Chemical Profile of Ruta graveolens, Evaluation of the Antioxidant and Antibacterial Potential of Its Essential Oil, and Molecular Docking Simulations. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112411753] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The research aimed to investigate the chemical composition and antioxidant and antibacterial potential of the essential oil (EO) isolated from the aerial parts (flowers, leaves, and stems) of Ruta graveolens L., growing in western Romania. Ruta graveolens L. essential oil (RGEO) was isolated by steam distillation (0.29% v/w), and the content was assessed by gas chromatography-mass spectrometry (GC-MS). Findings revealed that 2-Undecanone (76.19%) and 2-Nonanone (7.83%) followed by 2-Undecanol (1.85%) and 2-Tridecanone (1.42%) are the main detected compounds of the oil. The RGEO exerted broad-spectrum antibacterial and antifungal effects, S. pyogenes, S. aureus, and S. mutans being the most susceptible tested strains. The antioxidant activity of RGEO was assessed by peroxide and thiobarbituric acid value, 1,1-diphenyl-2-picrylhydrazyl radical (DPPH), and β-carotene/linoleic acid bleaching testing. The results indicated moderate radical scavenging and relative antioxidative activity in DPPH and β-carotene bleaching tests. However, between the 8th and 16th days of the incubation period, the inhibition of primary oxidation compounds induced by the RGEO was significantly stronger (p < 0.001) than butylated hydroxyanisole (BHA). Molecular docking analysis highlighted that a potential antimicrobial mechanism of the RGEO could be exerted through the inhibition of D-Alanine-d-alanine ligase (DDl) by several RGEO components. Docking analysis also revealed that a high number RGEO components could exert a potential in vitro protein-targeted antioxidant effect through xanthine oxidase and lipoxygenase inhibition. Consequently, RGEO could be a new natural source of antiseptics and antioxidants, representing an option for the use of synthetic additives in the food and pharmaceutical industry.
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Alsayari A, Asiri YI, Muhsinah AB, Hassan MZ. Synthesis and antimicrobial activity of aryldiazenyl/arylhydrazono pyrazoles. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/17475198211057461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report the design, synthesis, and in vitro antimicrobial evaluation of functionalized pyrazoles containing a hydrazono/diazenyl moiety. Among these newly synthesized derivatives, 4-[2-(4-chlorophenyl)hydrazono]-5-methyl-2-[2-(naphthalen-2-yloxy)acetyl]-2,4-dihydro-3 H-pyrazol-3-one is a promising antimicrobial agent against Staphylococcus aureus (minimum inhibitory concentration 0.19 μg mL−1). Structure–activity relationship studies reveal that the electronic environment on the distal phenyl ring has a considerable effect on the antimicrobial potential of the hybrid analogues. Molecular docking studies into the active site of S. aureus dihydrofolate reductase also prove the usefulness of hybridizing a pyrazole moiety with azo and hydrazo groups in the design of new antimicrobial agents.
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Affiliation(s)
- Abdulrhman Alsayari
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Abdullatif Bin Muhsinah
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohd. Zaheen Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
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Synthesis, antibacterial evaluation and computational studies of new acridone-1,2,3-triazole hybrids. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Qureshi KA, Bholay AD, Rai PK, Mohammed HA, Khan RA, Azam F, Jaremko M, Emwas AH, Stefanowicz P, Waliczek M, Kijewska M, Ragab EA, Rehan M, Elhassan GO, Anwar MJ, Prajapati DK. Isolation, characterization, anti-MRSA evaluation, and in-silico multi-target anti-microbial validations of actinomycin X 2 and actinomycin D produced by novel Streptomyces smyrnaeus UKAQ_23. Sci Rep 2021; 11:14539. [PMID: 34267232 PMCID: PMC8282855 DOI: 10.1038/s41598-021-93285-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/23/2021] [Indexed: 12/31/2022] Open
Abstract
Streptomyces smyrnaeus UKAQ_23, isolated from the mangrove-sediment, collected from Jubail,Saudi Arabia, exhibited substantial antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), including non-MRSA Gram-positive test bacteria. The novel isolate, under laboratory-scale conditions, produced the highest yield (561.3 ± 0.3 mg/kg fermented agar) of antimicrobial compounds in modified ISP-4 agar at pH 6.5, temperature 35 °C, inoculum 5% v/w, agar 1.5% w/v, and an incubation period of 7 days. The two major compounds, K1 and K2, were isolated from fermented medium and identified as Actinomycin X2 and Actinomycin D, respectively, based on their structural analysis. The antimicrobial screening showed that Actinomycin X2 had the highest antimicrobial activity compared to Actinomycin D, and the actinomycins-mixture (X2:D, 1:1, w/w) against MRSA and non-MRSA Gram-positive test bacteria, at 5 µg/disc concentrations. The MIC of Actinomycin X2 ranged from 1.56-12.5 µg/ml for non-MRSA and 3.125-12.5 µg/ml for MRSA test bacteria. An in-silico molecular docking demonstrated isoleucyl tRNA synthetase as the most-favored antimicrobial protein target for both actinomycins, X2 and D, while the penicillin-binding protein-1a, was the least-favorable target-protein. In conclusion, Streptomyces smyrnaeus UKAQ_23 emerged as a promising source of Actinomycin X2 with the potential to be scaled up for industrial production, which could benefit the pharmaceutical industry.
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Affiliation(s)
- Kamal A Qureshi
- Faculty of Biosciences and Biotechnology, Invertis University, Bareilly, UP, 243123, India.
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia.
| | - Avinash D Bholay
- Department of Microbiology, KTHM College, Savitribai Phule Pune University, Nashik, MS, 422002, India
| | - Pankaj K Rai
- Faculty of Biosciences and Biotechnology, Invertis University, Bareilly, UP, 243123, India
| | - Hamdoon A Mohammed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, Qassim, 51452, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, 11371, Egypt
| | - Riaz A Khan
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, Qassim, 51452, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Sciences and Engineering Division (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie, Street-14, 50-383, Wroclaw, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie, Street-14, 50-383, Wroclaw, Poland
| | - Monika Kijewska
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie, Street-14, 50-383, Wroclaw, Poland
| | - Ehab A Ragab
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, 11371, Egypt
| | - Medhat Rehan
- Department of Genetics, Faculty of Agriculture, Kafr El-Sheikh University, Kafr El-Sheikh, 33516, Egypt
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Qassim, 51452, Saudi Arabia
| | - Gamal O Elhassan
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia
| | - Md Jamir Anwar
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Unaizah, Qassim, 51911, Saudi Arabia
| | - Dinesh K Prajapati
- Faculty of Biosciences and Biotechnology, Invertis University, Bareilly, UP, 243123, India.
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Kaur H, Gahlawat S, Singh J, Narasimhan B. Molecular Docking Study of Active Diazenyl Scaffolds as Inhibitors of Essential Targets Towards Antimicrobial Drug Discovery. Curr Drug Targets 2020; 20:1587-1602. [PMID: 31215386 DOI: 10.2174/1389450120666190618122359] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/26/2019] [Accepted: 05/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The diazenyl compounds (-N=N- linkage) have been reported to have antimicrobial activity. In modern drug discovery, the drug-receptor interactions are generally explored by the molecular docking studies. MATERIALS AND METHODS Three categories of diazenyl scaffolds were screened for the docking studies to explore the binding mechanism of interaction with various microbial targets. The diazenyl Schiff bases (SBN-20, SBN-21, SBN-25, SBN-33, SBN-39, SBN-40 and SBN-42), naphthol pharmacophore based diazenyl Schiff bases (NS-2, NS-8, NS-12, NS-15, NS-21, and NS-23), morpholine based diazenyl chalcones (MD-6, MD-9, MD-14, MD-16, MD-20, and MD-21) were docked against various bacterial and fungal proteins in comparison with different standard drugs. Further, the drug likeliness and ADME properties of these molecules were predicted by QikProp module of the Schrodinger software. RESULTS Most of the derivatives had shown less docking scores and binding energies towards bacterial proteins, such as dihydropteroate synthase (PDB:2VEG), glucosamine-6-phosphate synthase (PDB:2VF5), dihydrofolate reductase (PDB:3SRW) in comparison with the standard drugs. The naphthol based diazenyl Schiff bases NS-21 and NS-23 were predicted to act on the cytochrome P450 sterol 14-alpha-demethylase (CYP51) (PDB:5FSA) involved in sterol biosynthesis, an essential target for antifungal drugs. The derivative MD-6, NS-2, NS-21, and NS-23 had shown high docking scores against bacterial DNA topoisomerase (PDB:3TTZ) in comparison with the standard drug ciprofloxacin. Further, most of the synthesized derivatives had shown drug like characters. CONCLUSION Hence, these compounds can be developed as novel antibacterial agents as potent DNA topoisomerase inhibitors and antifungal agents as CYP51 inhibitors.
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Affiliation(s)
- Harmeet Kaur
- Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak-124001, India
| | - Sudhir Gahlawat
- Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak-124001, India
| | - Jasbir Singh
- College of Pharmacy, Postgraduate Institute of Medical Sciences, Rohtak-124001, India
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15
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He J, Qiao W, An Q, Yang T, Luo Y. Dihydrofolate reductase inhibitors for use as antimicrobial agents. Eur J Med Chem 2020; 195:112268. [PMID: 32298876 DOI: 10.1016/j.ejmech.2020.112268] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 02/05/2023]
Abstract
Drug-resistant bacteria pose an increasingly serious threat to mankind all over the world. However, the currently available clinical treatments do not meet the urgent demand.Therefore, it is desirable to find new targets and inhibitors to overcome the problems of antibiotic resistance. Dihydrofolate reductase (DHFR) is an important enzyme required to maintain bacterial growth, and hence inhibitors of DHFR have been proven as effective agents for treating bacterial infections. This review provides insights into the recent discovery of antimicrobial agents targeting DHFR. In particular, three pathogens, Escherichia coli (E. coli), Mycobacterium tuberculosis(Mtb) and Staphylococcus aureus(S. aureus), and research strategies are emphasized. DHFR inhibitors are expected to be good alternatives to fight bacterial infections.
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Affiliation(s)
- Juan He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, Western China Hospital of Sichuan University
| | - Qi An
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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16
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Sanduja M, Gupta J, Singh H, Pagare PP, Rana A. Uracil-coumarin based hybrid molecules as potent anti-cancer and anti-bacterial agents. JOURNAL OF SAUDI CHEMICAL SOCIETY 2020. [DOI: 10.1016/j.jscs.2019.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Kaur H, Singh J, Narasimhan B. Antimicrobial, antioxidant and cytotoxic evaluation of diazenyl chalcones along with insights to mechanism of interaction by molecular docking studies. BMC Chem 2019; 13:87. [PMID: 31384834 PMCID: PMC6661766 DOI: 10.1186/s13065-019-0596-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 06/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In continuation of our work, new diazenyl chalcones scaffolds (C-18 to C-27) were efficiently synthesized from substituted acetophenone azo dyes (A-E) by base catalyzed Claisen-Schmidt condensation with different substituted aromatic/heteroaromatic aldehydes. METHODOLOGY The synthesized chalcones were assessed for their in vitro antimicrobial potential towards several pathogenic microbial strains by tube dilution method and further evaluated for antioxidant potential by DPPH assay. These derivatives were also assessed for the cytotoxicity towards the human lung cancer cell line (A549) and normal cell line (HEK) by MTT assay. The most active antimicrobial compounds were docked using Schrodinger v18.1 software with the various potential bacterial receptors to explore the mechanism of interaction. RESULTS The derivative C-22 exhibited high antibacterial activity with very low MIC (1.95-3.90 µg ml-1) and MBC (3.90-7.81 µg ml-1) values. The derivatives C-23, C-24 and C-27 have demonstrated good antioxidant potential (IC50 = 7-18 µg ml-1) correlated to the ascorbic acid (IC50 = 4.45 µg ml-1). The derivative C-25 had shown comparable cytotoxicity to camptothecin against A549 cell line. The docking studies predicted the bacterial dihydrofolate reductase (PDB ID: 3SRW) and bacterial DNA gyrase (PDB ID: 4ZVI) as the possible targets for most of the active antimicrobial compounds. These derivatives affirmed their safety by presenting less cytotoxicity towards HEK cells. Further the ADME prediction by qikprop module of the Schrodinger proved that these compounds exhibited drug-like attributes. CONCLUSION Hence, these compounds have shown their potential as lead for future expansion of novel antimicrobial and cytotoxic drugs.
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Affiliation(s)
- Harmeet Kaur
- Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001 India
| | - Jasbir Singh
- College of Pharmacy, Postgraduate Institute of Medical Sciences, Rohtak, 124001 India
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18
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Singh A, Singh JV, Rana A, Bhagat K, Gulati HK, Kumar R, Salwan R, Bhagat K, Kaur G, Singh N, Kumar R, Singh H, Sharma S, Bedi PMS. Monocarbonyl Curcumin-Based Molecular Hybrids as Potent Antibacterial Agents. ACS OMEGA 2019; 4:11673-11684. [PMID: 31460274 PMCID: PMC6682034 DOI: 10.1021/acsomega.9b01109] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/14/2019] [Indexed: 05/22/2023]
Abstract
Keeping in view various pharmacological attributes of curcumin, coumarin, and isatin derivatives, triazole-tethered monocarbonyl curcumin-coumarin and curcumin-isatin molecular hybrids have been synthesized and evaluated for their antibacterial potential against Gram-positive (Enterococcus faecalis and Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa and Escherichia coli) human pathogenic bacterial strains. Among all hybrid molecules, A-4 and B-38 showed the most potent antibacterial activity with inhibition zones of 29 and 31 mm along with MIC values of 12.50 and 6.25 μg/mL, respectively. Structure-activity relationship that emerged from biological data revealed that the two-carbon alkyl chain between triazole and coumarin/isatin moiety is well tolerable for the activity. Bromo substitution at the fifth position of isatin, para-cholo substitution in the case of curcumin-isatin, and para-methoxy in the case of curcumin-coumarin hybrids on ring A of curcumin are most suitable groups for the antibacterial activity. Various types of binding interactions of A-4 and B-38 within the active site of dihydrofolate reductase (DHFR) of S. aureus are also streamlined by molecular modeling studies, suggesting their capability in completely blocking DHFR.
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Affiliation(s)
- Atamjit Singh
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Jatinder Vir Singh
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Abhineet Rana
- EMC Group
of Hospital, Green Avenue, Amritsar, Punjab 143001, India
| | - Kavita Bhagat
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Harmandeep Kaur Gulati
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Raman Kumar
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Rajan Salwan
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Kajal Bhagat
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Gurinder Kaur
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Navjot Singh
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Randeep Kumar
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Harbinder Singh
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
- E-mail: (H.S.)
| | - Sahil Sharma
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
- E-mail: (S.S.)
| | - Preet Mohinder Singh Bedi
- Department of Pharmaceutical
Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
- E-mail: (P.M.S.B.)
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19
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Obasi LN, Ezeorah JC, Ossai V, Jude A, Oruma US, Ibezim A, Lutter M, Rhyman L, Jurkschat K, Dege N, Ramasami P. Structural, computational and in silico studies of Schiff bases derived from 2,3-dihydroxybenzaldehyde and molecular structure of their zwitterionic forms. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Bhagat K, Bhagat J, Gupta MK, Singh JV, Gulati HK, Singh A, Kaur K, Kaur G, Sharma S, Rana A, Singh H, Sharma S, Singh Bedi PM. Design, Synthesis, Antimicrobial Evaluation, and Molecular Modeling Studies of Novel Indolinedione-Coumarin Molecular Hybrids. ACS OMEGA 2019; 4:8720-8730. [PMID: 31459961 PMCID: PMC6648594 DOI: 10.1021/acsomega.8b02481] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/03/2019] [Indexed: 05/14/2023]
Abstract
Keeping in view various pharmacological attributes of indole and coumarin derivatives, a new series of indolindione-coumarin molecular hybrids was rationally designed and synthesized. All synthesized hybrid molecules were evaluated for their antimicrobial potential against Gram-negative bacterial strains (Escherichia coli and Salmonella enterica), Gram-positive bacterial strains (Staphylococcus aureus and Mycobacterium smegmatis), and four fungal strains (Candida albicans, Alternaria mali, Penicillium sp., and Fusarium oxysporum) by using the agar gel diffusion method. Among all synthetics, compounds K-1 and K-2 were found to be the best antimicrobial agents with the minimum inhibitory concentration values of 30 and 312 μg/mL, against Penicillium sp. and S. aureus, respectively. The biological data revealed some interesting facts about the structure-activity relationship which state that the electronic environment on the indolinedione moiety and carbon chain length between indolinedione and triazole moieties considerably affect the antimicrobial potential of the synthesized hybrids. Various types of binding interactions of K-2 within the active site of S. aureus dihydrofolate reductase were also streamlined by molecular modeling studies, which revealed the possible mechanism for potent antibacterial activity of the compound.
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Affiliation(s)
- Kavita Bhagat
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Jyoti Bhagat
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Manish Kumar Gupta
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, TERI Gram, Gual Pahari, Gurugram, Haryana 122001, India
| | - Jatinder Vir Singh
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Harmandeep Kaur Gulati
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Atamjit Singh
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Kamalpreet Kaur
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Gurinder Kaur
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Shally Sharma
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Abhineet Rana
- EMC Group of Hospital, Green Avenue, Amritsar, Punjab 143001, India
| | - Harbinder Singh
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
- E-mail: . Phone: +919463148367 (H.S.)
| | - Sahil Sharma
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
- E-mail: (S.S.)
| | - Preet Mohinder Singh Bedi
- Department
of Pharmaceutical Sciences and Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005, India
- E-mail: . Phone: +919815698249 (P.M.S.B.)
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21
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Sabry MA, Ewida HA, Hassan GS, Ghaly MA, El-Subbagh HI. Synthesis, antitumor testing and molecular modeling study of some new 6-substituted amido, azo or thioureido-quinazolin-4(3H)-ones. Bioorg Chem 2019; 88:102923. [PMID: 30991189 DOI: 10.1016/j.bioorg.2019.102923] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 01/27/2023]
Abstract
A new series of 6-substituted amido, azo or thioureido-quinazolin-4(3H)-one was synthesized and tested for their in-vitro antitumor activity. Compounds 21, 53 and 60 showed broad spectrum antitumor activity with average IC50 values of 6.7, 7.6 and 9.1 μM, respectively compared with methotrexate (1, IC50 19.26 μM). As an attempt to reveal the mechanism of the antitumor potency, cell cycle analysis and DHFR inhibition were performed. Compounds 59 and 61 induced their cytotoxicity in Hela (IC50 10.6 μM) and HCT-116 (IC50 15.5 μM) cell lines, respectively through Pre-G1 apoptosis, inhibiting cell growth at G2-M phase. Compounds 29, 33, 59 and 61 showed DHFR inhibitory potency at IC50 0.2, 0.2, 0.3 and 0.3 μM, respectively. The active DHFR inhibitors showed high affinity binding toward the amino acid residues Thr56, Ser59 and Ser118. The active compounds obeyed Lipinski's rule of five and could be used as template model for further optimization.
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Affiliation(s)
- Mohamed A Sabry
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, P.O. Box 35516, Mansoura, Egypt.
| | - Heba A Ewida
- Department of Pharmacology and Biochemistry, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, 12311 Cairo, Egypt
| | - Ghada S Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, P.O. Box 35516, Mansoura, Egypt
| | - Mariam A Ghaly
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, P.O. Box 35516, Mansoura, Egypt
| | - Hussein I El-Subbagh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, P.O. Box 35516, Mansoura, Egypt.
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22
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Synthesis and spectroscopic studies of substituted 6,7-dihydrocyclopentapyrimidin-2-amine compounds via one-pot method. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Hajiebrahimi A, Ghasemi Y, Sakhteman A. FLIP: An assisting software in structure based drug design using fingerprint of protein-ligand interaction profiles. J Mol Graph Model 2017; 78:234-244. [PMID: 29121561 DOI: 10.1016/j.jmgm.2017.10.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 11/29/2022]
Abstract
With the growing number of labor-intensive data in the pharmaceutical industries and public domain for protein-ligand complexes, a significant challenge is still remaining in managing and leveraging this vast information. Here, a standalone application is presented for analysis, organization, and illustration of structural data and molecular interactions for exploiting 3D-structures into simple 1D fingerprints. The utility of the approach was shown in unraveling a feasible solution for post-processing of docking results in parallel with providing fruitful analysis for users in order to investigate molecular interactions. Remarkably, all interaction possibilities including (hydrogen bond, water-bridged, electrostatic, and hydrophobic as well as π- π and cation-π interactions) are supported both in the form of fingerprints and compelling reports. These investigations are mainly considered based on right orientation, location, and geometry of the interacting pairs rather than the acquisition of the energy terms. The reasonable efficiency of our application in different models was comparable to recent methods It is clearly presented that FLIP provides a faster way to generate usable fingerprints for ligand and protein binding modes. FLIP is free for academic use and is available at: http://zistrayan.com/development/download/flip/package.zip.
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Affiliation(s)
- Ali Hajiebrahimi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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24
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Santa Maria JP, Park Y, Yang L, Murgolo N, Altman MD, Zuck P, Adam G, Chamberlin C, Saradjian P, Dandliker P, Boshoff HIM, Barry CE, Garlisi C, Olsen DB, Young K, Glick M, Nickbarg E, Kutchukian PS. Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase. ACS Chem Biol 2017; 12:2448-2456. [PMID: 28806050 DOI: 10.1021/acschembio.7b00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
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Affiliation(s)
- John P. Santa Maria
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Yumi Park
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Lihu Yang
- Department of Chemistry, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Nicholas Murgolo
- Department of Information & Analytics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Michael D. Altman
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Paul Zuck
- Research Science, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Greg Adam
- Department of Pharmacology, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Chad Chamberlin
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Saradjian
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Dandliker
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Helena I. M. Boshoff
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Charles Garlisi
- Department of Pharmacology, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - David B. Olsen
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Katherine Young
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Meir Glick
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Elliott Nickbarg
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter S. Kutchukian
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
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25
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Dihydrofolate reductase inhibitors: a quantitative structure–activity relationship study using 2D-QSAR and 3D-QSAR methods. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1742-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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26
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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27
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Rabelo VW, Sampaio TF, Duarte LD, Lopes DHB, Abreu PA. Structure–activity relationship of a series of 1,2-dihydroquinoline analogues and binding mode with Vibrio cholerae dihydrofolate reductase. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1583-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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28
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Dimova D, Stumpfe D, Bajorath J. Identification of orthologous target pairs with shared active compounds and comparison of organism-specific activity patterns. Chem Biol Drug Des 2015; 86:1105-14. [PMID: 25931211 DOI: 10.1111/cbdd.12578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/16/2015] [Accepted: 04/27/2015] [Indexed: 12/18/2022]
Abstract
A systematic search for active small molecules shared by orthologous targets was carried out, leading to the identification of 803 compound-based orthologous target pairs covering a total of 938 orthologues, 358 unique targets and 98 organisms. Many orthologous target pairs were found to have substantial compound coverage, enabling the introduction of an orthologous target pairs classification including 'organism cliffs' and 'potency-retaining' pairs. A total of 158 orthologous target pairs involving human orthologues were identified, which were typically associated with drug discovery-relevant targets, organism combinations and compound data. Orthologous target pairs with human orthologues included 83 potency-retaining orthologous target pairs covering a variety of targets and organisms. On the basis of these orthologous target pairs, the compound search was further extended and 1149 potent compounds were identified that only had reported activities for non-human orthologues of 48 therapeutic targets, but not their human counterparts, hence providing a large pool of candidate compounds for further evaluation. The complete set of orthologous target pairs identified in our analysis, the orthologous target pairs classification including associated data and all candidate compounds are made freely available.
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Affiliation(s)
- Dilyana Dimova
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, Bonn, D-53113, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, Bonn, D-53113, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, Bonn, D-53113, Germany
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Nammalwar B, Bourne CR, Wakeham N, Bourne PC, Barrow EW, Muddala NP, Bunce RA, Berlin KD, Barrow WW. Modified 2,4-diaminopyrimidine-based dihydrofolate reductase inhibitors as potential drug scaffolds against Bacillus anthracis. Bioorg Med Chem 2014; 23:203-11. [PMID: 25435253 DOI: 10.1016/j.bmc.2014.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/29/2014] [Accepted: 11/05/2014] [Indexed: 12/14/2022]
Abstract
The current Letter describes the synthesis and biological evaluation of dihydrophthalazine-appended 2,4-diaminopyrimidine (DAP) inhibitors (1) oxidized at the methylene bridge linking the DAP ring to the central aromatic ring and (2) modified at the central ring ether groups. Structures 4a-b incorporating an oxidized methylene bridge showed a decrease in activity, while slightly larger alkyl groups (CH2CH3 vs CH3) on the central ring oxygen atoms (R(2) and R(3)) had a minimal impact on the inhibition. Comparison of the potency data for previously reported RAB1 and BN-53 with the most potent of the new derivatives (19 b and 20a-b) showed similar values for inhibition of cellular growth and direct enzymatic inhibition (MICs 0.5-2 μg/mL). Compounds 29-34 with larger ester and ether groups containing substituted aromatic rings at R(3) exhibited slightly reduced activity (MICs 2-16 μg/mL). One explanation for this attenuated activity could be encroachment of the extended R(3) into the neighboring NADPH co-factor. These results indicate that modest additions to the central ring oxygen atoms are well tolerated, while larger modifications have the potential to act as dual-site inhibitors of dihydrofolate reductase (DHFR).
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Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA
| | - Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Nancy Wakeham
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Philip C Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Esther W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
| | - N Prasad Muddala
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA
| | - Richard A Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA.
| | - K Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences, Stillwater, OK 74078, USA
| | - William W Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater, OK 74078, USA
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Giacoppo JOS, Mancini DT, Guimarães AP, Gonçalves AS, da Cunha EFF, França TCC, Ramalho TC. Molecular modeling toward selective inhibitors of dihydrofolate reductase from the biological warfare agent Bacillus anthracis. Eur J Med Chem 2014; 91:63-71. [PMID: 24985033 DOI: 10.1016/j.ejmech.2014.06.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
Abstract
In the present work, we applied docking and molecular dynamics techniques to study 11 compounds inside the enzymes dihydrofolate reductase (DHFR) from the biological warfare agent Bacillus anthracis (BaDHFR) and Homo sapiens sapiens (HssDHFR). Six of these compounds were selected for a study with the mutant BaF96IDHFR. Our results corroborated with experimental data and allowed the proposition of a new molecule with potential activity and better selectivity for BaDHFR.
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Affiliation(s)
- Juliana O S Giacoppo
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil
| | - Daiana T Mancini
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil
| | - Ana P Guimarães
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, 22290-270, Rio de Janeiro, RJ, Brazil
| | - Arlan S Gonçalves
- Federal Institute of Education Science and Technology of Espirito Santo (IFES), Avenida Ministro Salgado Filho S/N°, 29106-010, Vila Velha, ES, Brazil
| | - Elaine F F da Cunha
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil
| | - Tanos C C França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, 22290-270, Rio de Janeiro, RJ, Brazil
| | - Teodorico C Ramalho
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil.
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Abstract
INTRODUCTION The folate biosynthetic pathway, responsible for the de novo synthesis of thymidine and other key cellular components, is essential in all life forms and is especially critical in rapidly proliferating cells. As such, druggable targets along this pathway offer opportunities to impact many disease states such as cancer, infectious disease and autoimmune disease. In this article, recent progress on the development of antifolate compounds is reviewed. AREAS COVERED The evaluation of the patent literature during the period 2010 - 2013 focused on any compounds inhibiting recognized targets on the folate biosynthetic pathway. EXPERT OPINION The folate pathway constitutes a well-validated and well-characterized set of targets; this pathway continues to elicit considerable enthusiasm for new drug discovery from both academic and industrial pharmaceutical research groups. Within the pathway, the enzymes dihydrofolate reductase and thymidylate synthase persist as the most attractive targets for new drug discovery for the treatment of cancer and infectious disease. Importantly, new potential targets for antifolates such as those on the purine biosynthetic pathway have been recently explored. The use of structure-based drug design is a major aspect in modern approaches to these drug targets.
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Affiliation(s)
- Amy C Anderson
- University of Connecticut, Department of Pharmaceutical Sciences , 69 N. Eagleville Road, Storrs, CT 06269 , USA
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Docking studies in target proteins involved in antibacterial action mechanisms: extending the knowledge on standard antibiotics to antimicrobial mushroom compounds. Molecules 2014; 19:1672-84. [PMID: 24481116 PMCID: PMC6270753 DOI: 10.3390/molecules19021672] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 01/22/2014] [Accepted: 01/26/2014] [Indexed: 11/25/2022] Open
Abstract
In the present work, the knowledge on target proteins of standard antibiotics was extended to antimicrobial mushroom compounds. Docking studies were performed for 34 compounds in order to evaluate their affinity to bacterial proteins that are known targets for some antibiotics with different mechanism of action: inhibitors of cell wall synthesis, inhibitors of protein synthesis, inhibitors of nucleic acids synthesis and antimetabolites. After validation of the molecular docking approach, virtual screening of all the compounds was performed against penicillin binding protein 1a (PBP1a), alanine racemase (Alr), d-alanyl-d-alanine synthetase (Ddl), isoleucyl-tRNA sinthetase (IARS), DNA gyrase subunit B, topoisomerase IV (TopoIV), dihydropteroate synthetase (DHPS) and dihydrofolate reductase (DHFR) using AutoDock4. Overall, it seems that for the selected mushroom compounds (namely, enokipodins, ganomycins and austrocortiluteins) the main mechanism of the action is the inhibition of cell wall synthesis, being Alr and Ddl probable protein targets.
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Lam T, Hilgers MT, Cunningham ML, Kwan BP, Nelson KJ, Brown-Driver V, Ong V, Trzoss M, Hough G, Shaw KJ, Finn J. Structure-Based Design of New Dihydrofolate Reductase Antibacterial Agents: 7-(Benzimidazol-1-yl)-2,4-diaminoquinazolines. J Med Chem 2014; 57:651-68. [DOI: 10.1021/jm401204g] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thanh Lam
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Mark T. Hilgers
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Mark L. Cunningham
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Bryan P. Kwan
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Kirk J. Nelson
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Vickie Brown-Driver
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Voon Ong
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Michael Trzoss
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Grayson Hough
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - Karen Joy Shaw
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
| | - John Finn
- Trius Therapeutics Inc., 6310 Nancy Ridge Drive, San Diego, California 92121, United States
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Spitzmüller A, Mestres J. Prediction of the P. falciparum target space relevant to malaria drug discovery. PLoS Comput Biol 2013; 9:e1003257. [PMID: 24146604 PMCID: PMC3798273 DOI: 10.1371/journal.pcbi.1003257] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/20/2013] [Indexed: 11/18/2022] Open
Abstract
Malaria is still one of the most devastating infectious diseases, affecting hundreds of millions of patients worldwide. Even though there are several established drugs in clinical use for malaria treatment, there is an urgent need for new drugs acting through novel mechanisms of action due to the rapid development of resistance. Resistance emerges when the parasite manages to mutate the sequence of the drug targets to the extent that the protein can still perform its function in the parasite but can no longer be inhibited by the drug, which then becomes almost ineffective. The design of a new generation of malaria drugs targeting multiple essential proteins would make it more difficult for the parasite to develop full resistance without lethally disrupting some of its vital functions. The challenge is then to identify which set of Plasmodium falciparum proteins, among the millions of possible combinations, can be targeted at the same time by a given chemotype. To do that, we predicted first the targets of the close to 20,000 antimalarial hits identified recently in three independent phenotypic screening campaigns. All targets predicted were then projected onto the genome of P. falciparum using orthologous relationships. A total of 226 P. falciparum proteins were predicted to be hit by at least one compound, of which 39 were found to be significantly enriched by the presence and degree of affinity of phenotypically active compounds. The analysis of the chemically compatible target combinations containing at least one of those 39 targets led to the identification of a priority set of 64 multi-target profiles that can set the ground for a new generation of more robust malaria drugs.
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Affiliation(s)
- Andreas Spitzmüller
- Chemotargets SL and Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Chemotargets SL and Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
- * E-mail:
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Bourne CR, Wakeham N, Nammalwar B, Tseitin V, Bourne PC, Barrow EW, Mylvaganam S, Ramnarayan K, Bunce RA, Berlin KD, Barrow WW. Structure-activity relationship for enantiomers of potent inhibitors of B. anthracis dihydrofolate reductase. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:46-52. [PMID: 22999981 PMCID: PMC3530638 DOI: 10.1016/j.bbapap.2012.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/09/2012] [Accepted: 09/04/2012] [Indexed: 01/07/2023]
Abstract
BACKGROUND Bacterial resistance to antibiotic therapies is increasing and new treatment options are badly needed. There is an overlap between these resistant bacteria and organisms classified as likely bioterror weapons. For example, Bacillus anthracis is innately resistant to the anti-folate trimethoprim due to sequence changes found in the dihydrofolate reductase enzyme. Development of new inhibitors provides an opportunity to enhance the current arsenal of anti-folate antibiotics while also expanding the coverage of the anti-folate class. METHODS We have characterized inhibitors of B. anthracis dihydrofolate reductase by measuring the K(i) and MIC values and calculating the energetics of binding. This series contains a core diaminopyrimidine ring, a central dimethoxybenzyl ring, and a dihydrophthalazine moiety. We have altered the chemical groups extended from a chiral center on the dihydropyridazine ring of the phthalazine moiety. The interactions for the most potent compounds were visualized by X-ray structure determination. RESULTS We find that the potency of individual enantiomers is divergent with clear preference for the S-enantiomer, while maintaining a high conservation of contacts within the binding site. The preference for enantiomers seems to be predicated largely by differential interactions with protein residues Leu29, Gln30 and Arg53. CONCLUSIONS These studies have clarified the activity of modifications and of individual enantiomers, and highlighted the role of the less-active R-enantiomer in effectively diluting the more active S-enantiomer in racemic solutions. This directly contributes to the development of new antimicrobials, combating trimethoprim resistance, and treatment options for potential bioterrorism agents.
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Affiliation(s)
- Christina R. Bourne
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078,Corresponding authors: CRB: phone +1 (405) 744-6737 fax +1 (405) 744-5275 , WWB: phone +1 (405) 744-1842 fax +1 (405) 744-3738
| | - Nancy Wakeham
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | | | - Philip C. Bourne
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Esther W. Barrow
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078
| | | | | | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - William W. Barrow
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078,Corresponding authors: CRB: phone +1 (405) 744-6737 fax +1 (405) 744-5275 , WWB: phone +1 (405) 744-1842 fax +1 (405) 744-3738
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Nammalwar B, Bunce RA, Berlin KD, Bourne CR, Bourne PC, Barrow EW, Barrow WW. Synthesis and biological activity of substituted 2,4-diaminopyrimidines that inhibit Bacillus anthracis. Eur J Med Chem 2012; 54:387-96. [PMID: 22703705 PMCID: PMC3408765 DOI: 10.1016/j.ejmech.2012.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/26/2012] [Accepted: 05/11/2012] [Indexed: 12/01/2022]
Abstract
A series of substituted 2,4-diaminopyrimidines 1 has been prepared and evaluated for activity against Bacillus anthracis using previously reported (±)-3-{5-[(2,4-diamino-5-pyrimidinyl)methyl]-2,3-dimethoxyphenyl}-1-(1-propyl-2(1H)-phthalazinyl)-2-propen-1-one (1a), with a minimum inhibitory concentration (MIC) value of 1-3 μg/mL, as the standard. In the current work, the corresponding isobutenyl (1e) and phenyl (1h) derivatives displayed the most significant activity in terms of the lowest MICs with values of 0.5 μg/mL and 0.375-1.5 μg/mL, respectively. It is likely that the S isomers of 1 will bind the substrate-binding pocket of dihydrofolate reductase (DHFR) as in B. anthracis was found for (S)-1a. The final step in the convergent synthesis of target systems 1 from (±)-1-(1-substituted-2(1H)-phthalazinyl)-2-propen-1-ones 6 with 2,4-diamino-5-(5-iodo-3,4-dimethoxybenzyl)pyrimidine (13) was accomplished via a novel Heck coupling reaction under sealed-tube conditions.
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Affiliation(s)
- Baskar Nammalwar
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078
| | - Christina R. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
| | - Philip C. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
| | - Esther W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
| | - William W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078
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Singh P, Kaur M, Sachdeva S. Mechanism inspired development of rationally designed dihydrofolate reductase inhibitors as anticancer agents. J Med Chem 2012; 55:6381-90. [PMID: 22734697 DOI: 10.1021/jm300644g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of structural analysis of dihydrofolate reductase (DHFR) (cocrystallized separately with NADPH, dihydrofolate and NADPH, trimethoprim), compounds 2 and 3 were optimized for inhibition of DHFR. Appreciable tumor growth inhibitory activities of compounds 2 and 3 over 60 human tumor cell lines were recorded. Combination of syringaldehyde and indole moieties in these two compounds was rationalized by the synthesis of compounds 4-7, 10, and 11, which were found to have less tumor growth inhibitory activities than compounds 2 and 3. Further, UV-vis and NMR spectral investigations showed significant interactions of compounds 2 and 3 with DHFR and inhibition of its catalytic activity was observed in the presence of these compounds. Therefore, modification of trimethoprim, an antibacterial drug with no tumor growth inhibition, led to the development of compounds 2 and 3 having appreciable anticancer activities that seem to be due to inhibition of DHFR.
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Affiliation(s)
- Palwinder Singh
- Department of Chemistry, Guru Nanak Dev University, Amritsar-143005, India.
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Dihydrofolate reductase as a therapeutic target for infectious diseases: opportunities and challenges. Future Med Chem 2012; 4:1335-65. [DOI: 10.4155/fmc.12.68] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Infectious diseases caused by parasites continue to take a massive toll on human health in the poor regions of the world. Filling the anti-infective drug-discovery pipeline has never been as challenging as it is now. The organisms responsible for these diseases have interesting biology with many potential biochemical targets. Inhibition of metabolic enzymes has been established as an attractive strategy for anti-infectious drug development. In this field, dihydrofolate reductase (DHFR) is an important enzyme in nucleic and amino acid synthesis and an extensively studied drug target over the past 50 years. The challenges for novel DHFR inhibition-based chemotherapeutics for the treatment of infectious diseases are now focused on overcoming the resistance problem as well as cost–effectiveness. Each year, the large number of literature citations attest the continued popularity of DHFR. It becomes truly the ‘enzyme of choice for all seasons and almost all reasons’. Herein, we summarize the opportunities and challenges in developing novel lead based on this target.
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