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Govindan R, Gnanasekaran C, Govindan R, Muthuchamy M, Quero F, Jothi A, Chelliah CK, Arunachalam A, Viswanathan MR, Natesan M, Kadaikunnan S, Li WJ. Anti-quorum Sensing and Anti-biofilm Effect of Nocardiopsis synnemataformans RMN 4 (MN061002) Compound 2,6-Di-tert-butyl, 1,4-Benzoquinone Against Biofilm-Producing Bacteria. Appl Biochem Biotechnol 2024; 196:3914-3948. [PMID: 37792174 DOI: 10.1007/s12010-023-04738-w] [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] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
In this study, the anti-biofilm compound of 2,6-Di-tert-butyl, 1,4-benzoquinone was purified from Nocardiopsis synnemataformans (N. synnemataformans) RMN 4 (MN061002). To confirm the compound, various spectroscopy analyses were done including ultraviolet (UV) spectrometer, Fourier transform infrared spectroscopy (FTIR), analytical high-performance liquid chromatography (HPLC), preparative HPLC, gas chromatography-mass spectroscopy (GC-MS), liquid chromatography-mass spectroscopy (LC-MS), and 2D nuclear magnetic resonance (NMR). Furthermore, the purified compound was shown 94% inhibition against biofilm-producing Proteus mirabilis (P. mirabilis) (MN396686) at 70 µg/mL concentrations. Furthermore, the metabolic activity, exopolysaccharide damage, and hydrophobicity degradation results of identified compound exhibited excellent inhibition at 100 µg/mL concentration. Furthermore, the confocal laser scanning electron microscope (CLSM) and scanning electron microscope (SEM) results were shown with intracellular damages and architectural changes in bacteria. Consecutively, the in vivo toxicity effect of the compound against Artemia franciscana (A. franciscana) was shown to have a low mortality rate at 100 µg/mL. Finally, the molecular docking interaction between the quorum sensing (QS) genes and identified compound clearly suggested that the identified compound 2,6-Di-tert-butyl, 1,4-benzoquinone has anti-quorum sensing and anti-biofilm activities against P. mirabilis (MN396686).
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Affiliation(s)
- Rajivgandhi Govindan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
| | - Chackaravarthi Gnanasekaran
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Ramachandran Govindan
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
| | - Maruthupandy Muthuchamy
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
- Lab of Toxicology, Department of Health Sciences, The Graduate School of Dong-A University, 37, Nakdong-Dearo 550 Beon-Gil, Saha-Gu, Busan, 49315, South Korea
| | - Franck Quero
- Laboratorio de Nanocelulosa y Biomateriales, Departamento de Ingeniería Química, Facultad de CienciasFísicas y Matemáticas, Universidad de Chile, Biotecnología y MaterialesAvenida Beauchef 851, 8370456, Santiago, Chile
| | - Arunachalam Jothi
- School of Chemical & Biotechnology, SASTRA Deemed University, Tamil Nadu, Tanjore, India, 401
| | - Chenthis Knaisha Chelliah
- Department of Nanotechnology, Noorul Islam Centre for Higher Education, Tamil Nadu, Kumaracoil, Kanyakumari, 629180, India
| | - Arulraj Arunachalam
- Departamento de Electricidad, Facultad de Ingeniería, Universidad Tecnológica Metropolitana (UTEM), Macul, Santiago, Chile
| | - Mangalaraja Ramalinga Viswanathan
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Región Metropolitana, Diag. Las Torres 2640, 7941169, Peñalolén, Santiago, Chile
| | - Manoharan Natesan
- Marine Pharmacology & Toxicology Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Packiapalavesam SD, Saravanan V, Mahajan AA, Almutairi MH, Almutairi BO, Arockiaraj J, Kathiravan MK, Karthick Raja Namasivayam S. Identification of novel CA IX inhibitor: Pharmacophore modeling, docking, DFT, and dynamic simulation. Comput Biol Chem 2024; 110:108073. [PMID: 38678727 DOI: 10.1016/j.compbiolchem.2024.108073] [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: 03/18/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Human Carbonic anhydrase IX (hCA IX) is found to be an essential biomarker for the treatment of hypoxic tumors in both the early and metastatic stages of cancer. Due to its active function in maintaining pH levels and overexpression in hypoxic conditions, hCA IX inhibitors can be a potential candidate specifically designed to target cancer development at various stages. In search of selective hCA IX inhibitors, we developed a pharmacophore model from the existing natural product inhibitors with IC50 values less than 50 nm. The identified hit molecules were then investigated on protein-ligand interactions using molecular docking experiments followed by molecular dynamics simulations. Among the zinc database 186 hits with an RMSD value less than 1 were obtained, indicating good contact with key residues HIS94, HIS96, HIS119, THR199, and ZN301 required for optimum activity. The top three compounds were subjected to molecular dynamics simulations for 100 ns to know the protein-ligand complex stability. Based on the obtained MD simulation results, binding free energies are calculated. Density Functional Theory (DFT) studies confirmed the energy variation between the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). The current study has led to the discovery of lead compounds that show considerable promise as hCA IX inhibitors and suggests that three compounds with special molecular features are more likely to be better-inhibiting hCA IX. Compound S35, characterized by a higher stability margin and a smaller energy gap in quantum studies, is an ideal candidate for selective inhibition of CA IX.
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Affiliation(s)
- Shakthi Devi Packiapalavesam
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Venkatesan Saravanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Anand A Mahajan
- Department of Pharmaceutical Analysis, Goa College of Pharmacy, Panaji, Goa 403001, India
| | - Mikhlid H Almutairi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bader O Almutairi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Jesu Arockiaraj
- Toxicology and Pharmacology Laboratory, Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India
| | - Muthu Kumaradoss Kathiravan
- Dr APJ Kalam Laboratory, SRM College of Pharmacy, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu 603203, India.
| | - S Karthick Raja Namasivayam
- Centre for Applied Research, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamil Nadu 602105, India.
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Hashmi HF, Xuan X, Chen K, Zhang P, Shahab M, Zheng G, Younous YA, Salamatullah AM, Bourhia M. Molecular modeling and simulation approaches to characterize potential molecular targets for burdock inulin to instigate protection against autoimmune diseases. Sci Rep 2024; 14:11291. [PMID: 38760355 PMCID: PMC11101470 DOI: 10.1038/s41598-024-61387-7] [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: 03/06/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
In the current study, we utilized molecular modeling and simulation approaches to define putative potential molecular targets for Burdock Inulin, including inflammatory proteins such as iNOS, COX-2, TNF-alpha, IL-6, and IL-1β. Molecular docking results revealed potential interactions and good binding affinity for these targets; however, IL-1β, COX-2, and iNOS were identified as the best targets for Inulin. Molecular simulation-based stability assessment demonstrated that inulin could primarily target iNOS and may also supplementarily target COX-2 and IL-1β during DSS-induced colitis to reduce the role of these inflammatory mechanisms. Furthermore, residual flexibility, hydrogen bonding, and structural packing were reported with uniform trajectories, showing no significant perturbation throughout the simulation. The protein motions within the simulation trajectories were clustered using principal component analysis (PCA). The IL-1β-Inulin complex, approximately 70% of the total motion was attributed to the first three eigenvectors, while the remaining motion was contributed by the remaining eigenvectors. In contrast, for the COX2-Inulin complex, 75% of the total motion was attributed to the eigenvectors. Furthermore, in the iNOS-Inulin complex, the first three eigenvectors contributed to 60% of the total motion. Furthermore, the iNOS-Inulin complex contributed 60% to the total motion through the first three eigenvectors. To explore thermodynamically favorable changes upon mutation, motion mode analysis was carried out. The Free Energy Landscape (FEL) results demonstrated that the IL-1β-Inulin achieved a single conformation with the lowest energy, while COX2-Inulin and iNOS-Inulin exhibited two lowest-energy conformations each. IL-1β-Inulin and COX2-Inulin displayed total binding free energies of - 27.76 kcal/mol and - 37.78 kcal/mol, respectively, while iNOS-Inulin demonstrated the best binding free energy results at - 45.89 kcal/mol. This indicates a stronger pharmacological potential of iNOS than the other two complexes. Thus, further experiments are needed to use inulin to target iNOS and reduce DSS-induced colitis and other autoimmune diseases.
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Affiliation(s)
- Huma Farooque Hashmi
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Xu Xuan
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Kaoshan Chen
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Pengying Zhang
- School of Life Science and National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China.
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | | | - Ahmad Mohammad Salamatullah
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, 80060, Agadir, Morocco
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Khan A, Zahid MA, Mohammad A, Agouni A. Structure-guided engineering and molecular simulations to design a potent monoclonal antibody to target aP2 antigen for adaptive immune response instigation against type 2 diabetes. Front Immunol 2024; 15:1357342. [PMID: 38524133 PMCID: PMC10960362 DOI: 10.3389/fimmu.2024.1357342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/08/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Diabetes mellitus (DM) is recognized as one of the oldest chronic diseases and has become a significant public health issue, necessitating innovative therapeutic strategies to enhance patient outcomes. Traditional treatments have provided limited success, highlighting the need for novel approaches in managing this complex disease. Methods In our study, we employed graph signature-based methodologies in conjunction with molecular simulation and free energy calculations. The objective was to engineer the CA33 monoclonal antibody for effective targeting of the aP2 antigen, aiming to elicit a potent immune response. This approach involved screening a mutational landscape comprising 57 mutants to identify modifications that yield significant enhancements in binding efficacy and stability. Results Analysis of the mutational landscape revealed that only five substitutions resulted in noteworthy improvements. Among these, mutations T94M, A96E, A96Q, and T94W were identified through molecular docking experiments to exhibit higher docking scores compared to the wild-type. Further validation was provided by calculating the dissociation constant (KD), which showed a similar trend in favor of these mutations. Molecular simulation analyses highlighted T94M as the most stable complex, with reduced internal fluctuations upon binding. Principal components analysis (PCA) indicated that both the wild-type and T94M mutant displayed similar patterns of constrained and restricted motion across principal components. The free energy landscape analysis underscored a single metastable state for all complexes, indicating limited structural variability and potential for high therapeutic efficacy against aP2. Total binding free energy (TBE) calculations further supported the superior performance of the T94M mutation, with TBE values demonstrating the enhanced binding affinity of selected mutants over the wild-type. Discussion Our findings suggest that the T94M substitution, along with other identified mutations, significantly enhances the therapeutic potential of the CA33 antibody against DM by improving its binding affinity and stability. These results not only contribute to a deeper understanding of antibody-antigen interactions in the context of DM but also provide a valuable framework for the rational design of antibodies aimed at targeting this disease more effectively.
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Affiliation(s)
- Abbas Khan
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Muhammad Ammar Zahid
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Abdelali Agouni
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
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Li X, Sun X. 1,3-Proton Transfer of Pyridoxal 5'-Phosphate Schiff Base in the Branched-Chain Aminotransferase: Concerted or Stepwise Mechanism? J Phys Chem B 2024; 128:77-85. [PMID: 38131279 DOI: 10.1021/acs.jpcb.3c05875] [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: 12/23/2023]
Abstract
The branched-chain aminotransferase from Mycobacterium tuberculosis (MtIlvE) is a pyridoxal 5'-phosphate (PLP) dependent enzyme, and it is essential for the synthesis of the branched-chain amino acids. Ketimine is an important intermediate in the catalytic process. We have investigated the mechanism of ketimine formation and the energy landscape using the multiple computational methods. It is found that the 1,3-proton transfer involved in ketimine formation occurs through a stepwise process rather than a one-step process. Lys204 is identified as a key residue for ligand binding and as a base that abstracts the Cα proton from the PLP-Glu Schiff base, yielding a carbanionic intermediate. The first proton transfer is the rate-limiting step with an energy barrier of 17.8 kcal mol-1. Our study disclosed the detailed pathway of the proton transfer from external aldimine to ketimine, providing novel insights into the catalytic mechanism of other PLP-dependent enzymes.
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Affiliation(s)
- Xue Li
- School of Life Sciences, Changchun Normal University, Changchun 130023, People's Republic of China
| | - Xiaoli Sun
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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Hu S, Xu L, Xie C, Hong J. Structural Insights into the Catalytic Activity of Cyclobacterium marinum N-Acetylglucosamine Deacetylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:783-793. [PMID: 38141024 DOI: 10.1021/acs.jafc.3c06146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
N-Acetylglucosamine deacetylase from Cyclobacterium marinum (CmCBDA) is a highly effective and selective biocatalyst for the production of d-glucosamine (GlcN) from N-acetylglucosamine (GlcNAc). However, the underlying catalytic mechanism remains elusive. Here, we show that CmCBDA is a metalloenzyme with a preference for Ni2+ over Mn2+. Crystal structures of CmCBDA in complex with Ni2+ and Mn2+ revealed slight remodeling of the CmCBDA active site by the metal ions. We also demonstrate that CmCBDA exists as a mixture of homodimers and monomers in solution, and dimerization is indispensable for catalytic activity. A mutagenesis analysis also indicated that the active site residues Asp22, His72, and His143 as well as the residues involved in dimerization, Pro52, Trp53, and Tyr55, are essential for catalytic activity. Furthermore, a mutation on the protein surface, Lys219Glu, resulted in a 2.3-fold improvement in the deacetylation activity toward GlcNAc. Mechanistic insights obtained here may facilitate the development of CmCBDA variants with higher activities.
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Affiliation(s)
- Shenglin Hu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, China
- College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Hefei, Anhui 230027, China
| | - Li Xu
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Changlin Xie
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui 230026, China
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Rathi R. Potential inhibitors of FemC to combat Staphylococcus aureus: virtual screening, molecular docking, dynamics simulation, and MM-PBSA analysis. J Biomol Struct Dyn 2023; 41:10495-10506. [PMID: 36524526 DOI: 10.1080/07391102.2022.2157328] [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: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
FemC is a methicillin resistance factor involved in the alterations of peptidoglycan and glutamine synthesis in Staphylococcus aureus. To identify the potent antibacterial agents, antibacterial molecules were screened against the predicted and validated FemC model. Based on docking scores, presence of essential interactions with active site residues of FemC, pharmacokinetic, and ADMET properties, six candidates were shortlisted and subjected to molecular dynamics to evaluate the stability of FemC-ligand complexes. Further, per residue decomposition analysis and Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis confirmed that S15, M16, S17, R31, R43, Q47, K48 and R49 of FemC played a vital role in the formation of lower energy stable FemC-inhibitor(s) complexes. Therefore, in the present study, the reported six molecules (Z317461228, Z92241701, Z30923155, Z30202349, Z2609517102 and Z92470167) may pave the path to design the scaffold of novel potent antimicrobials against S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Rathi
- Amity School of Applied Sciences, Amity University Haryana, Gurgaon, Haryana, India
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El-Metwally SA, Abuelkhir AA, Elkady H, Taghour MS, Ibrahim IM, Husein DZ, Alsfouk AA, Sultan A, Ismail A, Elkhawaga SY, Elkaeed EB, Metwaly AM, Eissa IH. In vitro and in silico evaluation of new thieno[2,3-d]pyrimidines as anti-cancer agents and apoptosis inducers targeting VEGFR-2. Comput Biol Chem 2023; 106:107928. [PMID: 37480629 DOI: 10.1016/j.compbiolchem.2023.107928] [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: 05/13/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/24/2023]
Abstract
In this study, new thieno[2,3-d]pyrimidine derivatives that could have potential anticancer activity by inhibiting the VEGFR-2 receptor have been designed, synthesized, and investigated. The thieno[2,3-d]pyrimidine derivatives showed strong in vitro abilities to inhibit VEGFR-2 and to prevent cancer cell growth in two different types of cancer cells, MCF-7 and HepG2. Particularly, compound 22 showed the most potent anti-VEGFR-2 activity with an IC50 value of 0.58 µM. Additionally, compound 22 exhibited good anti-proliferative activity against both MCF-7 and HepG2 cancer cell lines, with IC50 values of 11.32 ± 0.32 and 16.66 ± 1.22 µM, respectively. Further investigations revealed that compound 22 induced cell cycle arrest at the G2/M phase and promoted both early and late apoptosis in the MCF-7 cancer cells. Compound 22 also increased the level of BAX (2.8-fold), and reduced the level of Bcl-2 (2.2-fold), hence increasing the rate of apoptosis. Compound 22 also revealed 2.9-fold and 2.8-fold higher levels of caspase-8 and caspase-9, respectively, in the treated MCF-7 cancer cells compared to the control cell lines. The MD simulations showed that the VEGFR-2-22 complex was structurally and energytically stable over 100 ns, while the MM-GBSA study indicated its stable thermodynamic behavior. The bi-dimensional projection analysis confirmed the proper binding of the VEGFR-2-22 complex, while the DFT studies provided optimized geometry, charge distribution, FMO, ESP, the total density of state, and QTAIM maps of compound 22. Finally, computational ADMET studies were performed to assess the drug development potential of the thieno[2,3-d]pyrimidine derivatives. Overall, this study suggests that compound 22 has the potential as an anticancer lead compound by inhibiting VEGFR-2, which may be a guide for future drug design and development.
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Affiliation(s)
- Souad A El-Metwally
- Department of Basic Science, Higher Technological institute, 10th of Ramadan City, Egypt
| | - Abdelrahman A Abuelkhir
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Mohammed S Taghour
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Cairo 12613, Egypt
| | - Dalal Z Husein
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja 72511, Egypt
| | - Aisha A Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ahlam Sultan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia.
| | - Ahmed M Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt; Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt.
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt.
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Lopes LM, Germiniani LGL, Rocha Neto JBM, Andrade PF, da Silveira GAT, Taketa TB, Gonçalves MDC, Beppu MM. Preparation and characterization of porous membranes of glucomannan and silver decorated cellulose nanocrystals for application as biomaterial. Int J Biol Macromol 2023; 250:126236. [PMID: 37562469 DOI: 10.1016/j.ijbiomac.2023.126236] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Bacterial infection usually represents a threat in medical wound care, due to the increase in treatment complexity and the risk of antibiotic resistance. For presenting interesting characteristics for the use as biomaterial, natural polymers have been explored for this application. Among them, a promising candidate is the konjac glucomannan (KGM) with outstanding biocompatibility and biodegradability but lack of antibacterial activity. In this study, KGM was combined with silver decorated cellulose nanocrystals (CNC-Ag) to prepare membranes by using a recent reported casting-freezing method. The results highlight the potential anti-adhesive activity of the new materials against Staphylococcus aureus upon contact, without the burst release of silver nanoparticles. Furthermore, the incorporation of CNC enhanced the thermal stability of these membranes while preserving the favorable mechanical properties of the KGM-based material. These findings highlight a straightforward approach to enhance the antibacterial properties of natural polymers, which can be effectively useful in medical devices like wound dressings that typically lack such properties.
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Affiliation(s)
- Laise Maia Lopes
- University of Campinas, School of Chemical Engineering, Campinas, Brazil.
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Xie P, Gao Y, Wu C, Li X, Yang Y. The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling. J Mol Model 2023; 29:320. [PMID: 37725157 DOI: 10.1007/s00894-023-05723-0] [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: 06/26/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
CONTEXT Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. METHODS AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package. RESULTS The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.
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Affiliation(s)
- Peng Xie
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Yue Gao
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Chenqi Wu
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Xuenan Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yanan Yang
- Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China.
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11
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Rathi R, Kumari R, Pathak SR, Dalal V. Promising antibacterials for LLM of Staphylococcus aureus using virtual screening, molecular docking, dynamics, and MMPBSA. J Biomol Struct Dyn 2023; 41:7277-7289. [PMID: 36073371 DOI: 10.1080/07391102.2022.2119278] [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: 04/08/2022] [Accepted: 08/25/2022] [Indexed: 10/14/2022]
Abstract
In S. aureus, lipophilic membrane (LLM) protein is a methicillin resistance factor and is an essential role in peptidoglycan metabolism. The virtual screening of antibacterial molecules against the model of LLM was performed to identify the potent antibacterial molecules. Molecular docking results of pharmacokinetic filtered molecules illustrated that five molecules had higher binding affinities than tunicamycin (TUM) and were stabled via non-covalent interactions (hydrogen bond and hydrophobic interactions) at the active site of LLM. Further, molecular dynamics results revealed that binding of identified antibacterial molecules with LLM resulted in stable LLM-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis showed that LLM-inhibitor(s) complexes had high binding affinities in the range of -213.49 ± 2.24 to -227.42 ± 3.05 kJ/mol. The amino acid residues decomposition analysis confirmed that identified antibacterial molecules bound at the active site (Asn148, Leu149, Asp151, Asp208, His269, His271, and His272) of LLM. Noticeably, the current study found five antibacterial molecules (BDE 27575101, BDE 33638168, BDE 33672484, LAS 51502073, and BDE 25098678) were highly potent than TUM and even than earlier reported molecules. Therefore, here reported antibacterial molecules may be used directly or developed to inhibit LLM of S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Rathi
- Amity School of Applied Sciences, Amity University Haryana, Haryana, India
| | - Reena Kumari
- Department of Mathematics and Statistics, Swami Vivekanand Subharti University, Meerut, India
| | - Seema R Pathak
- Amity School of Applied Sciences, Amity University Haryana, Haryana, India
| | - Vikram Dalal
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA
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12
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Khan A, Sohail S, Yaseen S, Fatima S, Wisal A, Ahmed S, Nasir M, Irfan M, Karim A, Basharat Z, Khan Y, Aurongzeb M, Raza SK, Alshahrani MY, Morel CM, Hassan SS. Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy. Funct Integr Genomics 2023; 23:254. [PMID: 37495774 DOI: 10.1007/s10142-023-01179-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
Staphylococcus sciuri (also currently Mammaliicoccus sciuri) are anaerobic facultative and non-motile bacteria that cause significant human pathogenesis such as endocarditis, wound infections, peritonitis, UTI, and septic shock. Methicillin-resistant S. sciuri (MRSS) strains also infects animals that include healthy broilers, cattle, dogs, and pigs. The emergence of MRSS strains thereby poses a serious health threat and thrives the scientific community towards novel treatment options. Herein, we investigated the druggable genome of S. sciuri by employing subtractive genomics that resulted in seven genes/proteins where only three of them were predicted as final targets. Further mining the literature showed that the ArgS (WP_058610923), SecY (WP_058611897), and MurA (WP_058612677) are involved in the multi-drug resistance phenomenon. After constructing and verifying the 3D protein homology models, a screening process was carried out using a library of Traditional Chinese Medicine compounds (consisting of 36,043 compounds). The molecular docking and simulation studies revealed the physicochemical stability parameters of the docked TCM inhibitors in the druggable cavities of each protein target by identifying their druggability potential and maximum hydrogen bonding interactions. The simulated receptor-ligand complexes showed the conformational changes and stability index of the secondary structure elements. The root mean square deviation (RMSD) graph showed fluctuations due to structural changes in the helix-coil-helix and beta-turn-beta changes at specific points where the pattern of the RMSD and root mean square fluctuation (RMSF) (< 1.0 Å) support any major domain shifts within the structural framework of the protein-ligand complex and placement of ligand was well complemented within the binding site. The β-factor values demonstrated instability at few points while the radius of gyration for structural compactness as a time function for the 100-ns simulation of protein-ligand complexes showed favorable average values and denoted the stability of all complexes. It is assumed that such findings might facilitate researchers to robustly discover and develop effective therapeutics against S. sciuri alongside other enteric infections.
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Affiliation(s)
- Aafareen Khan
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Saman Sohail
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Seerat Yaseen
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Sareen Fatima
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
| | - Ayesha Wisal
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Sufyan Ahmed
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Mahrukh Nasir
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Asad Karim
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Zarrin Basharat
- Alpha Genomics (Private) Limited, Islamabad, 44710, Pakistan
| | - Yasmin Khan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Aurongzeb
- Faculty of Engineering Sciences & Technology, Hamdard University, Karachi, 74600, Pakistan
| | - Syed Kashif Raza
- Faculty of Rehabilitation and Allied Health Sciences (FRAHS), Riphah International University, Faisalabad, Pakistan
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha, 9088, Saudi Arabia
| | - Carlos M Morel
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
| | - Syed S Hassan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan.
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
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13
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Shaik NA, Al-Shehri N, Athar M, Awan A, Khalili M, Al Mahadi HB, Hejazy G, Saadah OI, Al-Harthi SE, Elango R, Banaganapalli B, Alefishat E, Awan Z. Protein structural insights into a rare PCSK9 gain-of-function variant (R496W) causing familial hypercholesterolemia in a Saudi family: whole exome sequencing and computational analysis. Front Physiol 2023; 14:1204018. [PMID: 37469559 PMCID: PMC10353052 DOI: 10.3389/fphys.2023.1204018] [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: 04/11/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023] Open
Abstract
Familial hypercholesterolemia (FH) is a globally underdiagnosed genetic condition associated with premature cardiovascular death. The genetic etiology data on Arab FH patients is scarce. Therefore, this study aimed to identify the genetic basis of FH in a Saudi family using whole exome sequencing (WES) and multidimensional bioinformatic analysis. Our WES findings revealed a rare heterozygous gain-of-function variant (R496W) in the exon 9 of the PCSK9 gene as a causal factor for FH in this family. This variant was absent in healthy relatives of the proband and 200 healthy normolipidemic controls from Saudi Arabia. Furthermore, this variant has not been previously reported in various regional and global population genomic variant databases. Interestingly, this variant is classified as "likely pathogenic" (PP5) based on the variant interpretation guidelines of the American College of Medical Genetics (ACMG). Computational functional characterization suggested that this variant could destabilize the native PCSK9 protein and alter its secondary and tertiary structural features. In addition, this variant was predicted to negatively influence its ligand-binding ability with LDLR and Alirocumab antibody molecules. This rare PCSK9 (R496W) variant is likely to expand our understanding of the genetic basis of FH in Saudi Arabia. This study also provides computational structural insights into the genotype-protein phenotype relationship of PCSK9 pathogenic variants and contributes to the development of personalized medicine for FH patients in the future.
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Affiliation(s)
- Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Al-Shehri
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmed Awan
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariam Khalili
- Department of Pharmacology, College of Medicine, Khalifa University, Abu Dhabi, United Arab Emirates
| | | | - Gehan Hejazy
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Omar I. Saadah
- Department of Pediatrics, Pediatric Gastroenterology Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sameer Eida Al-Harthi
- Department of Clinical Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eman Alefishat
- Department of Pharmacology, College of Medicine, Khalifa University, Abu Dhabi, United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Zuhier Awan
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Siddiqui S, Riaz S, Ahmad R, Wani MJ, Hashmi MA, Zofair SFF, Mateen S, Moin S. Synergistic effect of chlorogenic acid and vitamin D3 (cholecalciferol) on in-vitro glycation may assist in prevention of polycystic ovarian syndrome (PCOS) progression - A biophysical, biochemical and in-silico study. Int J Biol Macromol 2023; 245:125497. [PMID: 37369258 DOI: 10.1016/j.ijbiomac.2023.125497] [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: 03/26/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
Advanced glycation end products (AGEs) are formed through non-enzymatic glycation, that have been linked to various diseases, including polycystic ovarian syndrome (PCOS) playing a critical role leading to secondary comorbidities such as diabetes-related problems, cardiovascular complications, infertility, etc. As a result, there has been a lot of research into AGE-inhibiting phytochemicals for the remediation and obstruct progression of glycation-related illnesses. The current study is based on in-vitro protein model, in which human serum albumin have been used to investigate the cumulative effect of chlorogenic acid (CGA) and cholecalciferol (vitamin D) on glycation and evaluate their inhibitory impact on AGEs production in the presence of methylglyoxal. Through the application of several biochemical and biophysical techniques, we were able to examine the synergistic impact of both the compounds on albumin structure and its biochemical properties during different stages of glycation. According to Nitro-blue tetrazolium assay results indicate that CGA and vitamin D inhibited fructosamine (early glycation product) production. Moreover, free thiol and lysine residues were significantly increased whereas protein carbonyl levels were significantly decreased. Additive effect of CGA and vitamin D were associated with reduced AGEs fluorescence and increased tryptophan and tyrosine fluorescence. Amadori-albumin after treatment showed some evidence of regaining its alpha-helicity as measured by far-UV CD spectrum. Furthermore, secondary structural alterations were confirmed by Fourier transform infrared spectroscopy (FTIR). ANS (1-anilinonaphthalene-8-sulfonic acid) fluorescence spectra also displayed less revelation of hydrophobic patches. Bilirubin binding capacity was also restored which showed functional recovery of HSA. The electrophoretic mobility was also restored which is portrayed by SDS-PAGE. Additionally, to predict the anti-aggregation potential of CGA and vitamin D, congo red assay and ThT fluorescence was performed which reveal low aggregate formation after treatment. These results corroborated with scanning electron microscopy and confocal microscopy. Docking and simulation results also reveal spontaneous binding of CGA and vitamin D on subdomain IIA of HSA favoring their binding thermodynamically. All the findings suggest that chlorogenic acid and cholecalciferol given in combination might help in prevention of PCOS progression and its related complications.
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Affiliation(s)
- Sana Siddiqui
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Sana Riaz
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Rizwan Ahmad
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Mohd Junaid Wani
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Syeda Fauzia Farheen Zofair
- Interdisciplinary Biotechnology Unit, Faculty of Life Science, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Somaiya Mateen
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Shagufta Moin
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India.
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15
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Kumari S, Saini R, Bhatnagar A, Mishra A. HR-LCMS and evaluation of anti-diabetic activity of Hemidesmus indicus (anantmool): Kinetic study, and molecular modelling approach. Comput Biol Chem 2023; 105:107896. [PMID: 37263051 DOI: 10.1016/j.compbiolchem.2023.107896] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/08/2023] [Accepted: 05/20/2023] [Indexed: 06/03/2023]
Abstract
This study delved into the exploration of novel antidiabetic medications acquired from natural resources, utilizing the Ayurvedic Rasayana herb Hemidesmus indicus through cutting-edge chemoprofiling and molecular modelling techniques. The methanolic extract of Hemidesmus indicus root exhibited the highest extractive yield (24.70 ± 0.08 %) and contained substantial levels of total phenolic and flavonoid content as 154.15 ± 1.24 mg Gallic Acid Equivalent/g extract and 70.61 ± 0.35 Quercetin Equivalent/g extract respectively. Invitro study revealed the potent inhibitory potential of methanolic extract of the herb against essential carbohydrate hydrolytic enzymes α-amylase (IC50 = 4.19 ± 0.04 mg/ml) and α-glucosidase (IC50 = 5.78 ± 0.10 mg/ml). Further, the enzyme kinetic study demonstrated the competitive mode of inhibition of both enzymes. HR-LCMS analysis identified the major phytoconstituents present in the extracts, including Solanocapsine, Cyclovirobuxine C, Lucidine B, Zygadenine, Aspidospermidine, silychristin, 3beta-3-Hydroxy-18-lupen-21-one, Manglupenone, and 19-Noretiocholanolone. Molecular docking, molecular dynamic simulation, and MM/GBSA analysis have proved stable, rigid, compact, and folded form of complexes during the entire 100 ns simulation, illustrating Zygadenine, Solanocapsine, and Cyclovirobuxine C as the superior inhibitors of α-A protein, while Zygadenine, Plumieride, and Phlegmarine exhibited greater inhibitory behaviour towards α-G protein than the FDA-approved drug acarbose. Collectively, our findings indicate that the Hemidesmus indicus could be a promising source of α-A and α-G inhibitors, potentially serving as a lead in order to develop medications for type-2 diabetes.
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Affiliation(s)
- Sonali Kumari
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India
| | - Ravi Saini
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India
| | - Aditi Bhatnagar
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India
| | - Abha Mishra
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India.
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16
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Wang S, Luan J, Chen L, Liu H, Li W, Wang J. Computational characteristics of the structure-activity relationship of inhibitors targeting Pks13-TE domain. Comput Biol Chem 2023; 104:107864. [PMID: 37028177 DOI: 10.1016/j.compbiolchem.2023.107864] [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: 02/11/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/09/2023]
Abstract
Multiple studies have established the Pks13-TE domain as a promising target for anti-tuberculosis drug development. However, recent findings have revealed that the lead compound currently in the pipeline for Pks13-TE has significant cardiotoxicity issues. Given the pressing need for new chemical structures for Pks13-TE inhibitors, this study aims to provide a detailed understanding of the Pks13-TE domain binding site through the application of computational chemical biology techniques. Our results highlight the size and shape of the Pks13-TE domain binding pocket, key residues including Asp1644, Asn1640, Phe1670, and Tyr1674 within the pocket, and inhibitor pharmacophore characteristics such as aromatic ring sites, positively charged sites, and hydrogen bond donors. To our knowledge, these simulation results are novel and contribute to the discovery of next-generation Pks13-TE inhibitors without similar prior studies.
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Affiliation(s)
- Shizun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jiasi Luan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lu Chen
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Haihan Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Weixia Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang 110016, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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17
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Wang N, Gao JG, Wu MW. Molecular docking and molecular simulation studies for N-degron selectivity of chloroplastic ClpS from Chlamydomonas reinhardtii. Comput Biol Chem 2023; 103:107825. [PMID: 36773520 DOI: 10.1016/j.compbiolchem.2023.107825] [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: 10/23/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Regarding the importance of N-degron pathway in protein degradation network, the adaptor protein ClpS recognizes the substrates bearing classical N-degrons, and delivers them to caseinolytic protease complex ClpAP for degradation. Interestingly, the majority of N-degrons located near the N-terminus of protein substrate are belonged to the hydrophobic type amino acids. Chloroplast, an important organelle for plant photosynthesis, contain a diversified Clp degradation system. Despite several studies have confirmed that chloroplastic ClpS is able to interact with classical N-degrons derived from prokaryotes, whereas, the molecular mechanism underlying how the chloroplastic ClpS protein could recognize the substrate tagged by N-degrons is still unclear until now. Chlamydomonas reinhardtii is a kind of unicellular model organism for photosynthesis researches, which possesses a large cup-shaped chloroplast, and the corresponding genome data indicates that it owns bacterial homologous adaptor protein, named CrClpS1. However, the relevant biochemical knowledges, and protein structure researches for CrClpS1 adaptor aren't reported up to date. The molecular interactions between CrClpS1 and possible N-degrons are undefined as well. Here, we build a reliable homology model of CrClpS1 and find a hydrophobic pocket for N-degron binding. We combine molecular docking, molecular dynamic simulations, and MM/PBSA, MM/GBSA binding free energy estimations to elucidate the molecular properties of CrClpS1-N-degron interactions. Besides, we investigate the conformational changes for CrClpS1-apo in water-solvent environment and analyze its possible biological significances through a long time molecular dynamic simulation. Specifically, the adaptor CrClpS1 displays the stronger interactions with Phe, Trp, Tyr, His and Ile with respect to other amino acids. Using the residue decomposition analysis, the interactions between CrClpS1 and N-degrons are heavily depended on several conservative residues, which are located around the hydrophobic pocket, implying that chloroplast isolated from Chlamydomonas reinhadtii adopts a relatively conservative N-degron recognition mode. Besides, the opening-closure of hydrophobic pocket of CrClpS1 might be beneficial for the N-degron selectivity.
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Affiliation(s)
- Ning Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Jian-Guo Gao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Ming-Wei Wu
- University of Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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18
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Structure-activity and binding orientations analysis of potent, newly synthesized, acetylcholinesterase inhibitors. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Dalal V, Kumari R. Screening and Identification of Natural Product‐Like Compounds as Potential Antibacterial Agents Targeting FemC of
Staphylococcus aureus
: An in‐Silico Approach. ChemistrySelect 2022. [DOI: 10.1002/slct.202201728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Vikram Dalal
- Department of Anesthesiology Washington University in St. Louis Missouri 63110 USA
| | - Reena Kumari
- Department of Mathematics and Statistics Swami Vivekanand Subharti University Meerut 250005 India
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20
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Computer-Aided Screening and Revealing Action Mechanism of Food-Derived Tripeptides Intervention in Acute Colitis. Int J Mol Sci 2022; 23:ijms232113471. [PMID: 36362252 PMCID: PMC9655126 DOI: 10.3390/ijms232113471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Food-derived tripeptides can relieve colitis symptoms; however, their alleviation mode has not been systematically evaluated as an alternative nutritional compound. This study aimed to reveal the potential mechanism of 8000 food-derived tripeptides against acute colitis using a computer-aided screening strategy. Forty-one potential hub targets related to colitis with a Fit score > 4.0 were screened to construct the protein-protein and protein-tripeptide network based on the PharmMapper database and STRING software (Ver. 11.5). In addition, 30 significant KEGG signaling pathways with p-values < 0.001 that the 41 hub targets mainly participated in were identified using DAVID software (Ver. 6.8), including inflammatory, immunomodulatory, and cell proliferation and differentiation-related signaling pathways, particularly in the Ras- and PI3K-Akt signaling pathways. Furthermore, molecular docking was performed using the Autodock against majorly targeted proteins (AKT1, EGFR, and MMP9) with the selected 52 tripeptides. The interaction model between tripeptides and targets was mainly hydrogen-bonding and hydrophobic interactions, and most of the binding energy of the tripeptide target was less than −7.13 kcal/mol. This work can provide valuable insight for exploring food-derived tripeptide mechanisms and therapeutic indications.
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21
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Singh V, Dhankhar P, Dalal V, Tomar S, Golemi-Kotra D, Kumar P. Drug-Repurposing Approach To Combat Staphylococcus aureus: Biomolecular and Binding Interaction Study. ACS OMEGA 2022; 7:38448-38458. [PMID: 36340146 PMCID: PMC9631409 DOI: 10.1021/acsomega.2c03671] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/04/2022] [Indexed: 05/15/2023]
Abstract
Staphylococcus aureus is considered as one of the most widespread bacterial pathogens and continues to be a prevalent cause of mortality and morbidity across the globe. FmtA is a key factor linked with methicillin resistance in S. aureus. Consequently, new antibacterial compounds are crucial to combat S. aureus resistance. Here, we present the virtual screening of a set of compounds against the available crystal structure of FmtA. The findings indicate that gemifloxacin, paromomycin, streptomycin, and tobramycin were the top-ranked potential drug molecules based on the binding affinity. Furthermore, these drug molecules were analyzed with molecular dynamics simulations, which showed that the identified molecules formed highly stable FmtA-inhibitor(s) complexes. Molecular mechanics Poisson-Boltzmann surface area and quantum mechanics/molecular mechanics calculations suggested that the active site residues (Ser127, Lys130, Tyr211, and Asp213) of FmtA are crucial for the interaction with the inhibitor(s) to form stable protein-inhibitor(s) complexes. Moreover, fluorescence- and isothermal calorimetry-based binding studies showed that all the molecules possess dissociation constant values in the micromolar scale, revealing a strong binding affinity with FmtAΔ80, leading to stable protein-drug(s) complexes. The findings of this study present potential beginning points for the rational development of advanced, safe, and efficacious antibacterial agents targeting FmtA.
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Affiliation(s)
- Vishakha Singh
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee247667, India
| | - Poonam Dhankhar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee247667, India
| | - Vikram Dalal
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee247667, India
| | - Shailly Tomar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee247667, India
| | - Dasantila Golemi-Kotra
- Department
of Biology, York University, 4700 Keele Street, TorontoM3J 1P3, Ontario, Canada
| | - Pravindra Kumar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee247667, India
- ; . Tel.: +91-1332-286286
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22
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Neuroprotective effects of phenolic glycosides from Populus tomentiglandulosa roots in HT22 mouse hippocampal neuronal cells. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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23
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Singh V, Dhankhar P, Dalal V, Tomar S, Kumar P. In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target. J Mol Graph Model 2022; 116:108262. [PMID: 35839717 DOI: 10.1016/j.jmgm.2022.108262] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 12/15/2022]
Abstract
Klebsiella pneumonia is known to cause several nosocomial infections in immunocompromised patients. It has developed resistance against a broad range of presently available antibiotics, resulting in high mortality rates in patients and declared an urgent threat. Therefore, exploration of possible novel drug targets against this opportunistic bacteria needs to be undertaken. In the present study, we performed an extensive in-silico analysis for functional and structural annotation and characterized HP CP995_08280 from K. pneumonia as a drug target and aimed to identify potent drug candidates. The functional and structural studies using several bioinformatics tools and databases predicted that HP CP995_08280 is a cytosolic protein that belongs to the β-lactamase family and shares structural similarity with FmtA protein from Staphylococcus aureus (PDB ID: 5ZH8). The structure of HP CP995_08280 was successfully modeled followed by structure-based virtual screening, docking, molecular dynamics, and Molecular mechanic/Poisson-Boltzmann surface area (MMPBSA) were performed to identify the potential compounds. We have found five potent antibacterial molecules, namely BDD 24083171, BDD 24085737, BDE 25098678, BDE 33638819, and BDE 33672484, which exhibited high binding affinity (>-7.5 kcal/mol) and were stabilized by hydrogen bonding and hydrophobic interactions with active site residues (Ser42, Lys45, Tyr126, and Asp128) of protein. Molecular dynamics and MMPBSA revealed that HP CP995_08280 - ligand(s) complexes were less dynamic and more stable than native HP CP995_08280. Hence, the present study may serve as a potential lead for developing inhibitors against drug-resistant Klebsiella pneumonia.
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Affiliation(s)
- Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, 247667, India.
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24
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Lawal B, Kuo YC, Rachmawati Sumitra M, Wu ATH, Huang HS. Identification of a novel immune-inflammatory signature of COVID-19 infections, and evaluation of pharmacokinetics and therapeutic potential of RXn-02, a novel small-molecule derivative of quinolone. Comput Biol Med 2022; 148:105814. [PMID: 35841781 PMCID: PMC9272679 DOI: 10.1016/j.compbiomed.2022.105814] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/07/2022] [Accepted: 07/03/2022] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a global pandemic and respiratory infection that has enormous damage to human lives and economies. It is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), a non-pair-stranded positive-sense RNA virus. With increasing global threats and few therapeutic options, the discovery of new potential drug targets and the development of new therapy candidates against COVID-19 are urgently needed. Based on these premises, we conducted an analysis of transcriptomic datasets from SARS-CoV-2-infected patients and identified several SARS-CoV-2 infection signatures, among which TNFRSF5/PTPRC/IDO1/MKI67 appeared to be the most pertinent signature. Subsequent integrated bioinformatics analysis identified the signature as an important immunomodulatory and inflammatory signature of SARS-CoV-2 infection. It was suggested that this gene signature mediates the interplay of immune and immunosuppressive cells leading to infiltration-exclusion of effector memory T cells in the lungs, which is of translation relevance for developing novel SARS-CoV-2 drug and vaccine candidates. Consequently, we designed and synthesized a novel small-molecule quinoline derivative (RXn-02) and evaluated its pharmacokinetics in rats, revealing a peak plasma concentration (Cmax) and time to Cmax (Tmax) of 1.756 μg/mL and 0.6 h, respectively. Values of the area under the curve (AUC) (0–24 h) and AUC (0 h∼∞) were 18.90 and 71.20 μg h/mL, respectively. Drug absorption from the various regional segments revealed that the duodenum (49.84%), jejunum (47.885%), cecum (1.82%), and ileum (0.32%) were prime sites of RXn-02 absorption. No absorption was detected from the stomach, and the least was from the colon (0.19%). Interestingly, RXn-02 exhibited in vitro antiproliferative activities against hub gene hyper-expressing cell lines; A549 (IC50 = 48.1 μM), K-562 (IC50 = 100 μM), and MCF7 (IC50 = 0.047 μM) and against five cell lines originating from human lungs (IC50 range of 33.2–69.5 μM). In addition, RXn-02 exhibited high binding efficacies for targeting the TNFRSF5/PTPRC/IDO1/MK signature with binding affinities (ΔG) of −6.6, −6.0, −9.9, −6.9 kcal/mol respectively. In conclusion, our study identified a novel signature of SARS-CoV-2 pathogenesis. RXn-02 is a drug-like candidate with good in vivo pharmacokinetics and hence possesses great translational relevance worthy of further preclinical and clinical investigations for treating SARS-CoV-2 infections.
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Affiliation(s)
- Bashir Lawal
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Cheng Kuo
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan; School of Post-baccalaureate Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Maryam Rachmawati Sumitra
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Alexander T H Wu
- The PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, 11031, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 11031, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan.
| | - Hsu-Shan Huang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan; School of Pharmacy, National Defense Medical Center, Taipei, 11490, Taiwan; PhD Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan.
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