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Islam MR, Azmal M, Prima FS, Zaman B, Hossain MM, Mishu MA, Ghosh A. Retention of methicillin susceptibility in Staphylococcus aureus using natural adjuvant as an allosteric modifier of penicillin-binding protein 2a. Comput Biol Med 2024; 181:109070. [PMID: 39205340 DOI: 10.1016/j.compbiomed.2024.109070] [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: 05/31/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global public health challenge due to its resistance to conventional antibiotics, primarily mediated by the mutated penicillin-binding protein, PBP2a. This study aims to investigate the potential of phytochemicals derived from medicinal plants in the Indian subcontinent to serve as adjuvants, enhancing the efficacy of methicillin against MRSA through allosteric modification of PBP2a using molecular docking and molecular dynamics (MD) simulation. After comprehensive Absorption, Distribution, Metabolism, and Excretion (ADME) profiling, along with AMES and hepatotoxicity tests, 9 compounds were shortlisted as suitable adjuvant candidates. Among them, nimbolide, quercetin, emodin, daidzein, eriodictyol, luteolin, and apigenin exhibited strong binding affinity to the allosteric site of PBP2a, with docking scores ranging from -8.7 to -7.3 kcal/mol. These phytochemicals facilitated enhanced methicillin binding, as evidenced by improved docking scores ranging from -6.1 to -6.8 kcal/mol, compared to -5.6 kcal/mol for methicillin alone. Molecular dynamics simulations confirmed the stability and favorable conformations of phytochemical-PBP2a complexes. Quercetin and daidzein were identified as the most promising adjuvant candidates, forming stable and energetically favorable complexes with PBP2a. Experimental validation showed that quercetin, at 30 mg/mL, effectively retained methicillin's antibacterial efficacy against MRSA. This study underscores the potential of natural compounds in overcoming antibiotic resistance and suggests that phytochemical-antibiotic synergism could be a viable strategy to combat multidrug-resistant bacterial infections.
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Affiliation(s)
- Md Rubiath Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Mahir Azmal
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Fatema Sultana Prima
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Bushra Zaman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Muluk Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Moshiul Alam Mishu
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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Nguyen TTT, Nguyen TTT, Nguyen HD, Nguyen TK, Pham PTV, Tran LTT, Pham HKT, Truong PCH, Tran LT, Tran MH. Anti- Staphylococcus aureus potential of compounds from Ganoderma sp.: A comprehensive molecular docking and simulation approaches. Heliyon 2024; 10:e28118. [PMID: 38596094 PMCID: PMC11002548 DOI: 10.1016/j.heliyon.2024.e28118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
In this study, a series of secondary metabolites from Ganoderma sp. were screened against Staphylococcus aureus protein targets, including as phosphotransacetylase, clumping factor A, and dihydrofolate reductase, using molecular docking simulations. The chemicals that showed the strongest binding energy with the targeted proteins were ganodermanontriol, lucidumol B, ganoderic acid J, ergosterol, ergosterol peroxide, 7-oxoganoderic acid Z, ganoderic acid AM1, ganosinoside A, ganoderic acid D, and 24R-ergosta-7,2E-diene-3β,5α,6β-triol. Interestingly, ganosinoside A showed the greatest affinity for the protein clumping factor A, a result validated by molecular dynamic simulation. Additionally, three natural Ganoderma sp. Strains as Ganoderma lingzhi VNKKK1903, Ganoderma lingzhi VNKK1905A2, and Amauroderma subresinosum VNKKK1904 were collected from Kon Ka Kinh National Park in central land of Vietnam and evaluated for their antibacterial activity against Staphylococcus aureus using an agar well diffusion technique. These results suggest that the fungal extracts and secondary metabolites may serve as valuable sources of antibiotics against Staphylococcus aureus. These findings provided an important scientific groundwork for further exploration of the antibacterial mechanisms of compounds derived from Ganoderma sp. in future research.
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Affiliation(s)
- Trang Thi Thu Nguyen
- Faculty of Biology and Biotechnology, University of Science, 227 Nguyen Van Cu, District 5, Ho Chi Minh City, 700000, Viet Nam
- Vietnam National University, Linh Trung, Thu Duc City, Ho Chi Minh City, 700000, Viet Nam
| | - Trinh Thi Tuyet Nguyen
- Faculty of Biology and Biotechnology, University of Science, 227 Nguyen Van Cu, District 5, Ho Chi Minh City, 700000, Viet Nam
- Vietnam National University, Linh Trung, Thu Duc City, Ho Chi Minh City, 700000, Viet Nam
| | - Hoang Duc Nguyen
- Faculty of Biology and Biotechnology, University of Science, 227 Nguyen Van Cu, District 5, Ho Chi Minh City, 700000, Viet Nam
- Vietnam National University, Linh Trung, Thu Duc City, Ho Chi Minh City, 700000, Viet Nam
| | - Tan Khanh Nguyen
- Scientific Management Department, Dong A University, 33 Xo Viet Nghe Tinh, Hai Chau District, Da Nang City, 550000, Viet Nam
| | - Phu Tran Vinh Pham
- VN-UK Institute for Research and Executive Education, The University of Danang, 158A Le Loi, Hai Chau District, Danang City, 550000, Viet Nam
| | - Linh Thuy Thi Tran
- Faculty of Pharmacy, Hue University of Medicine and Pharmacy, Hue University, Hue, 530000, Viet Nam
| | - Hong Khuyen Thi Pham
- School of Medicine and Pharmacy, The University of Danang, Hoa Quy, Ngu Hanh Son District, Da Nang City, 550000, Viet Nam
| | - Phu Chi Hieu Truong
- School of Medicine and Pharmacy, The University of Danang, Hoa Quy, Ngu Hanh Son District, Da Nang City, 550000, Viet Nam
| | - Linh Thuoc Tran
- Faculty of Biology and Biotechnology, University of Science, 227 Nguyen Van Cu, District 5, Ho Chi Minh City, 700000, Viet Nam
- Vietnam National University, Linh Trung, Thu Duc City, Ho Chi Minh City, 700000, Viet Nam
| | - Manh Hung Tran
- School of Medicine and Pharmacy, The University of Danang, Hoa Quy, Ngu Hanh Son District, Da Nang City, 550000, Viet Nam
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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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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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Huseynzada A, Aghayev M, Hajiyeva S, Israyilova A, Sayin K, Gasimov E, Rzayev F, Hasanova U, Eyvazova G, Abbasov V, Gakhramanova Z, Huseynova S, Huseynova P, Huseynova L, Salimova N. Synthesis, nanostructuring and in silico studies of a new imine bond containing a macroheterocycle as a promising PBP-2a non-β-lactam inhibitor. J Mater Chem B 2023; 11:8271-8280. [PMID: 37581615 DOI: 10.1039/d3tb00602f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
This study is devoted to the synthesis of a 40-membered macroheterocycle with its further nanostructuring by magnetite nanoparticles. The mentioned macroheterocycle was synthesized by the [2+2] cyclocondensation of the oxygen-containing diamine with an aromatic dialdehyde in a non-catalytic medium and with no work-up procedure. The structure of the obtained macroheterocycle was studied by 1H and 13C nuclear magnetic resonance spectroscopy and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Furthermore, the nanosupramolecular complex of macroheterocycles with magnetite nanoparticles was obtained and investigated by Fourier-transform infrared and ultraviolet-visible spectroscopy methods. Shifts in the infrared spectra of the nanosupramolecular complex indicate the interaction through metal-aromatic ring non-covalent bonding. The shift is also observed for the C-O-C stretching band of ether bonds. The loading rate of macroheterocycles on magnetite nanoparticles was 18.6%. The morphology of the ensemble was studied by transmission electron microscopy, which confirmed the synthesis of nanospherical particles with a diameter range of 10-20 nm. Powder X-ray diffraction analysis showed patterns of cubic Fe3O4 nanoparticles with a crystallite size equal to 9.1 nm. The macroheterocycle and its nanosupramolecular complex were tested against Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus. The results have shown that the created complex has shown 64 times better activity against Staphylococcus aureus in comparison with the individual macroheterocycle and 32 times better activity in comparison with the pristine antibiotic Ampicillin as a control. In addition, computational analysis of the macroheterocycle was performed at the B3LYP/6-31G level in water. Molecular docking analyses for the macroheterocycle revealed Penicillin-binding protein PBP2a (5M18) from the transpeptidase family as a target protein in Staphylococcus aureus.
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Affiliation(s)
- Alakbar Huseynzada
- ICRL, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
- Chemistry Department, Azerbaijan Engineers Union, Bashir Safaroglu 118, Baku, AZ 1009, Azerbaijan
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Mirjavid Aghayev
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, 4209 St, OH-44, Rootstown, OH 44272, USA
| | - Sarvinaz Hajiyeva
- ICRL, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- Physics Department, Kent State University, 800 E. Summit St., Kent, OH 44242, USA
| | - Aygun Israyilova
- Laboratory of Microbiology and Virology, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
- Research Institute of Crop Husbandry, Ministry of Agriculture, Baku, AZ 1098, Azerbaijan
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Koray Sayin
- Chemistry Department, Faculty of Science, Sivas Cumhuriyet University, Sivas, 58140, Turkey
| | - Eldar Gasimov
- Department of Cytology, Embryology and Histology, Azerbaijan Medical University, 163 A Samad Vurgun, Baku AZ1078, Azerbaijan
| | - Fuad Rzayev
- Laboratory of Electron Microscopy of the SRC, Azerbaijan Medical University, 163 A Samad Vurgun, Baku AZ1078, Azerbaijan
| | - Ulviyya Hasanova
- ICRL, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Goncha Eyvazova
- Nanoresearch Center, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Vagif Abbasov
- Institute of Petrochemical Processes, K. Avenue 30, Baku, AZ 1005, Azerbaijan
| | - Zarema Gakhramanova
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan.
| | - Sanam Huseynova
- Department of Molecular Biology and Biotechnology, Baku State University, Z. Khalilov 23, Baku, AZ 1148, Azerbaijan
| | - Parvana Huseynova
- Chemistry Department, Ganja State University, H. Aliyev 429, Ganja, AZ 2001, Azerbaijan
| | - Lala Huseynova
- Industrial Safety and Labor Protection Department, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan
| | - Nigar Salimova
- Petrochemical Technology and Industrial Ecology Department, Azerbaijan State Oil and Industry University, Baku, AZ 1010, Azerbaijan
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Liu R, Liang G, Gong J, Wang J, Zhang Y, Hao Z, Li G. A Potential ABA Analog to Increase Drought Tolerance in Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24108783. [PMID: 37240123 DOI: 10.3390/ijms24108783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Abscisic acid (ABA) plays an important role in the response of plants to drought stress. However, the chemical structure of ABA is unstable, which severely limits its application in agricultural production. Here, we report the identification of a small molecule compound of tetrazolium as an ABA analog (named SLG1) through virtual screening. SLG1 inhibits the seedling growth and promotes drought resistance of Arabidopsis thaliana with higher stability. Yeast two-hybrid and PP2C inhibition assays show that SLG1 acts as a potent activator of multiple ABA receptors in A. thaliana. Results of molecular docking and molecular dynamics show that SLG1 mainly binds to PYL2 and PYL3 through its tetrazolium group and the combination is stable. Together, these results demonstrate that SLG1, as an ABA analogue, protects A. thaliana from drought stress. Moreover, the newly identified tetrazolium group of SLG1 that binds to ABA receptors can be used as a new option for structural modification of ABA analogs.
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Affiliation(s)
- Ruiqi Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Guoyan Liang
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Jiaxin Gong
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Jiali Wang
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yanjie Zhang
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Zhiqiang Hao
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
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Nguyen TTT, Nguyen TTT, Nguyen HD, Nguyen TK, Pham PTV, Tran LT, Tran LTT, Tran MH. Integrating in Silico and In Vitro Studies to Screen Anti- Staphylococcus aureus Activity From Vietnamese Ganoderma multiplicatum and Ganoderma sinense. Nat Prod Commun 2023. [DOI: 10.1177/1934578x231167289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Background: Staphylococcus aureus is a nosocomial pathogen responsible for many serious infectious diseases in humans. Finding the anti- S. aureus agents is a time-consuming and costly process. Recently, computational methods have provided a better understanding of the interactions between herbal medicine drug targets to help clinical practitioners rationally design herbal formulae. Methods: In this study, molecular docking simulation was applied to screen a list of natural secondary metabolites from Ganoderma sp. on the protein target S. aureus sortase A. Molecular dynamics models were used to assess the stability of protein–ligand complexes during the first 100 ns. To validate the computational results, 2 Ganoderma species, G. multiplicatum VNKKK1901 and G. sinense VNKKK1902, were tested for antibacterial activity against S. aureus using the disk diffusion method. Results: The results showed that, among the selected compounds, ganosinensin B and ganosinoside A generated the highest binding energy on S. aureus sortase A, and demonstrated strong and stable binding capacity to proteins. In addition, the extracts of G. sinense VNKKK1902 and G. multiplicatum VNKKK1901 were bactericidal, with minimum bactericidal concentration (MBC)/minimum inhibitory concentration (MIC) ratios of 2. Conclusion: Our findings provide the first scientific report on the antibacterial activity of Ganoderma sp., which contain 2 promising compounds, ganosinensin B and ganosinoside A, as potential hits for developing novel drugs capable of supporting treatment of S. aureus infection.
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Affiliation(s)
- Trang Thi Thu Nguyen
- Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Trinh Thi Tuyet Nguyen
- Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hoang Duc Nguyen
- Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Tan Khanh Nguyen
- Scientific Management Department, Dong A University, Da Nang city Vietnam
| | - Phu Tran Vinh Pham
- Faculty of Medicine, Dong A University, Hai Chau District, Da Nang City, Vietnam
| | - Linh Thuoc Tran
- Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Linh Thuy Thi Tran
- Faculty of Pharmacy, Hue University of Medicine and Pharmacy, Hue University, Hue City, Vietnam
| | - Manh Hung Tran
- School of Medicine and Pharmacy, The University of Danang, Da Nang City, Vietnam
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Combining the In Silico and In Vitro Assays to Identify Strobilanthes cusia Kuntze Bioactives against Penicillin-Resistant Streptococcus pneumoniae. Pharmaceuticals (Basel) 2023; 16:ph16010105. [PMID: 36678602 PMCID: PMC9863409 DOI: 10.3390/ph16010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Leaves of Strobilanthes cusia Kuntze (S. cusia) are a widely used alexipharmic Traditional Chinese Medicine (TCM) in southern China for the prevention of cold and respiratory tract infectious diseases. One of the most common bacterial pathogens in the respiratory tract is the gram-positive bacterium Streptococcus pneumoniae. The antibiotic resistance of colonized S. pneumoniae makes it a more serious threat to public health. In this study, the leaves of S. cusia were found to perform antibacterial effects on the penicillin-resistant S. pneumoniae (PRSP). Confocal assay and Transmission Electron Microscopy (TEM) monitored the diminished cell wall integrity and capsule thickness of the PRSP with treatment. The following comparative proteomics analysis revealed that the glycometabolism-related pathways were enriched for the differentially expressed proteins between the samples with treatment and the control. To further delve into the specific single effective compound, the bio-active contents of leaves of S. cusia were analyzed by UPLC-UV-ESI-Q-TOF/MS, and 23 compounds were isolated for anti-PRSP screening. Among them, Tryptanthrin demonstrated the most promising effect, and it possibly inhibited the N-glycan degradation proteins, as suggested by reverse docking analysis in silico and further experimental verification by the surface plasmon resonance assay (SPR). Our study provided a research foundation for applications of the leaves of S. cusia as a TCM, and supplied a bio-active compound Tryptanthrin as a candidate drug skeleton for infectious diseases caused by the PRSP.
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Li X, Gu W, Zhang B, Xin X, Kang Q, Yang M, Chen B, Li Y. Insights into toxicity of polychlorinated naphthalenes to multiple human endocrine receptors: Mechanism and health risk analysis. ENVIRONMENT INTERNATIONAL 2022; 165:107291. [PMID: 35609500 DOI: 10.1016/j.envint.2022.107291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
This study explored the combined disruption mechanism of polychlorinated naphthalenes (PCNs) on the three key receptors (estrogen receptor, thyroid receptor, and adrenoceptor) of the human endocrine system. The intensity of PCN endocrine disruption on these receptors was first determined using a molecular docking method. A comprehensive index of PCN endocrine disruption to human was quantified by analytic hierarchy process and fuzzy analysis. The mode of action between PCNs and the receptors was further identified to screen the molecular characteristics influencing PCN endocrine disruption through molecular docking and fractional factorial design. Quantitative structure-activity relationship (QSAR) models were established to investigate the toxic mechanism due to PCN endocrine disruption. The results showed that the lowest occupied orbital energy (ELUMO) was the most important factor contributing to the toxicity of PCNs on the endocrine receptors, followed by the orbital energy difference (ΔE) and positive Millikan charge (q+). Furthermore, the strategies were formulated through adjusting the nutritious diet to reduce health risk for the workers in PCN contaminated sites and the effectiveness and feasibility were assessed by molecular dynamic simulation. The simulation results indicated that the human health risk caused by PCN endocrine disruption could be effectively decreased by nutritional supplementation. The binding ability between PCNs and endocrine receptors significantly declined (up to -16.45%) with the supplementation of vitamins (A, B2, B12, C, and E) and carotene. This study provided the new insights to reveal the toxic mechanism of PCNs on human endocrine systems and the recommendations on nutritional supplements for health risk reduction. The methodology and findings could serve as valuable references for screening of potential endocrine disruptors and developing appropriate strategies for PCN or other persistent organic pollution control and health risk management.
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Affiliation(s)
- Xixi Li
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Wenwen Gu
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada; MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Xiaying Xin
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Qiao Kang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Min Yang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Bing Chen
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Yu Li
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
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Ibarra-Hernández JA, Gómez-Balderas R, Nivón-Ramírez D, García-Estrada JG, Mendoza-Jiménez DA, Martínez-Zaldívar A, Cruz-Sánchez TA, Tovar-Betancourt N, Luna-Mora RA, Penieres-Carrillo JG. Novel Compounds Based on Chalcone- and Pyrazoline-DIM Hybrids as Inhibitors of Staphylococcus aureus, Synthesis, DFT Studies, Biological Evaluation and Docking Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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In Silico Characterization of the Interaction between the PBP2a "Decoy" Protein of Resistant Staphylococcus aureus and the Monomeric Units of Eudragit E-100 and Poly(Maleic Acid- alt-Octadecene) Polymers. Polymers (Basel) 2021; 13:polym13142320. [PMID: 34301077 PMCID: PMC8309622 DOI: 10.3390/polym13142320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial treatment alternatives for methicillin-resistant Staphylococcus aureus (MRSA) are increasingly limited. MRSA strains are resistant to methicillin due to the formation of β-lactamase enzymes, as well as the acquisition of the mecA gene, which encodes the penicillin-binding protein (PBP2a) that reduces the affinity for β-lactam drugs. Previous studies have shown that the use of ampicillin-loaded nanoparticles can improve antimicrobial activity on resistant S. aureus strains. However, the biological mechanism of this effect has not yet been properly elucidated. Therefore, this short communication focused on characterizing the in silico interactions of the PBP2a membrane receptor protein from S. aureus against the monomeric units of two polymeric materials previously used in the development of different nanoparticles loaded with ampicillin. Such polymers correspond to Eudragit E-100 chloride (EuCl) and the sodium salt of poly(maleic acid-alt-octadecene) (PAM-18Na). For this, molecular coupling studies were carried out in the active site of the PBP2a protein with the monomeric units of both polymers in neutral and ionized form, as well as with ampicillin antibiotic (model β-lactam drug). The results showed that ampicillin, as well as the monomeric units of EuCl and PAM18Na, described a slight binding free energy to the PBPa2 protein. In addition, it was found that the amino acids of the active site of the PBPa2 protein have interactions of different types and intensities, suggesting, in turn, different forms of protein–substrate coupling.
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