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Xu ZY, Hu Z, La CS, Du NN, Bai M, Hao J, Lin B, Huang XX, Song SJ. Hydroxyl-Amide Alkaloids from Pepper Roots: Potential Sources of Natural Antioxidants and Tyrosinase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39116367 DOI: 10.1021/acs.jafc.4c03650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Pepper (Piper nigrum L.) is a widely used spice plant known for its fruits and roots, which serve as flavor enhancers in culinary applications and hold significant economic value. Despite the popularity of pepper fruits, their roots remain relatively understudied, with limited research conducted on their bioactive components. This study focused on discovering and separating the primary bioactive amide alkaloids found in pepper roots. The process involved using the antioxidant activity of crude fractions and the Global Natural Products Social Molecular Networking analysis platform. The process led to the discovery of 23 previously unknown hydroxyl-amide alkaloids. Notably, compounds 11, 12, and 14 showed excellent antioxidant activity, while compound 11 exhibited significant inhibitory effects on mushroom tyrosinase. Theoretical exploration of enzyme-ligand interactions was conducted through molecular docking and molecular dynamics simulation. The findings of this study highlight the potential of hydroxyl-amide alkaloids as antioxidant products and natural food preservatives in the pharmaceutical and food cosmetic industries.
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Affiliation(s)
- Zhi-Yong Xu
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Zixia Hu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Chang-Sheng La
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Ning-Ning Du
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Ming Bai
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Jinle Hao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xiao-Xiao Huang
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Shao-Jiang Song
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
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152
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Torrejón MJ, Algaba J, Blas FJ. Dissociation line and driving force for nucleation of the nitrogen hydrate from computer simulation. II. Effect of multiple occupancy. J Chem Phys 2024; 161:054712. [PMID: 39092957 DOI: 10.1063/5.0220098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500 bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500 bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation.
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Affiliation(s)
- Miguel J Torrejón
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - Jesús Algaba
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - Felipe J Blas
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
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153
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Li F, Lin H, Qin X, Gao J, Chen Z, Cao W, Zheng H, Xie S. In Silico Identification and Molecular Mechanism of Novel Tyrosinase Inhibitory Peptides Derived from Nacre of Pinctada martensii. Mar Drugs 2024; 22:359. [PMID: 39195475 DOI: 10.3390/md22080359] [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: 07/15/2024] [Revised: 08/05/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024] Open
Abstract
Pearl and nacre powders have been valuable traditional Chinese medicines with whitening properties for thousands of years. We utilized a high-temperature and high-pressure method along with compound enzyme digestion to prepare the enzymatic hydrolysates of nacre powder of Pinctada martensii (NP-PMH). The peptides were identified using LC-MS/MS and screened through molecular docking and molecular dynamics simulations. The interactions between peptides and tyrosinase were elucidated through enzyme kinetics, circular dichroism spectropolarimetry, and isothermal titration calorimetry. Additionally, their inhibitory effects on B16F10 cells were explored. The results showed that a tyrosinase-inhibitory peptide (Ala-His-Tyr-Tyr-Asp, AHYYD) was identified, which inhibited tyrosinase with an IC50 value of 2.012 ± 0.088 mM. The results of the in vitro interactions showed that AHYYD exhibited a mixed-type inhibition of tyrosinase and also led to a more compact enzyme structure. The binding reactions of AHYYD with tyrosinase were spontaneous, leading to the formation of a new set of binding sites on the tyrosinase. The B16F10 cell-whitening assay revealed that AHYYD could reduce the melanin content of the cells by directly inhibiting the activity of intracellular tyrosinase. Additionally, it indirectly affects melanin production by acting as an antioxidant. These results suggest that AHYYD could be widely used as a tyrosinase inhibitor in whitening foods and pharmaceuticals.
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Affiliation(s)
- Fei Li
- College of Food Science and Technology, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Ocean University, Zhanjiang 524088, China
| | - Haisheng Lin
- College of Food Science and Technology, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Ocean University, Zhanjiang 524088, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xiaoming Qin
- College of Food Science and Technology, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Ocean University, Zhanjiang 524088, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Jialong Gao
- College of Food Science and Technology, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Ocean University, Zhanjiang 524088, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Zhongqin Chen
- College of Food Science and Technology, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Ocean University, Zhanjiang 524088, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Wenhong Cao
- College of Food Science and Technology, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Ocean University, Zhanjiang 524088, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Huina Zheng
- College of Food Science and Technology, National Research and Development Branch Center for Shellfish Processing (Zhanjiang), Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Ocean University, Zhanjiang 524088, China
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Shaohe Xie
- Guangdong Shaohe Pearl Co., Ltd., Shantou 515041, China
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154
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Tajima M, Nakamura H, Ohsaki S, Watano S. Effect of cholesterol on nanoparticle translocation across a lipid bilayer. Phys Chem Chem Phys 2024; 26:21229-21239. [PMID: 39073356 DOI: 10.1039/d4cp00330f] [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: 07/30/2024]
Abstract
Nanoparticles (NPs) have attracted significant attention as carriers for the delivery of drugs, genes, and macromolecules for biomedical and therapeutic applications. These technologies require NPs to be delivered to the interior of the cell. However, this translocation is unlikely because of the presence of a cell membrane composed of phospholipids, cholesterol, proteins, and glycans. The cell membrane composition can influence its rigidity; thus, membrane composition is a crucial factor in determining the translocation of NPs across the cell membrane. Here, we focus on cholesterol, which is an essential component of biological cell membranes, and investigate NP translocation across membranes containing cholesterol under an applied electric field using a coarse-grained molecular dynamics simulation. We found that NPs could translocate directly across cholesterol-containing membranes without irreversible membrane disruption. This unique translocation was induced by two key phenomena. Before NP translocation, a phospholipid-rich/cholesterol-poor domain was formed at the NP-membrane contact interface. Second, a smaller transmembrane pore was formed in the cholesterol-containing membrane during membrane crossing of the NP. Our findings imply that the delivery of NPs to the cell interior across the cholesterol-containing membrane can be achieved by appropriately controlling the strength of the applied electric field, depending on the cholesterol content in the membrane.
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Affiliation(s)
- Masaya Tajima
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Hideya Nakamura
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Shuji Ohsaki
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Satoru Watano
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
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155
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Zhang N, Zhu Y, Li YN, Zhang LR, Zhang FS, Liu JJ. Design of eco-friendly antifreeze peptides as novel inhibitors of gas-hydration kinetics. J Chem Phys 2024; 161:054701. [PMID: 39087548 DOI: 10.1063/5.0211732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
In this study, peptides designed using fragments of an antifreeze protein (AFP) from the freeze-tolerant insect Tenebrio molitor, TmAFP, were evaluated as inhibitors of clathrate hydrate formation. It was found that these peptides exhibit inhibitory effects by both direct and indirect mechanisms. The direct mechanism involves the displacement of methane molecules by hydrophobic methyl groups from threonine residues, preventing their diffusion to the hydrate surface. The indirect mechanism is characterized by the formation of cylindrical gas bubbles, the morphology of which reduces the pressure difference at the bubble interface, thereby slowing methane transport. The transfer of methane to the hydrate interface is primarily dominated by gas bubbles in the presence of antifreeze peptides. Spherical bubbles facilitate methane migration and potentially accelerate hydrate formation; conversely, the promotion of a cylindrical bubble morphology by two of the designed systems was found to mitigate this effect, leading to slower methane transport and reduced hydrate growth. These findings provide valuable guidance for the design of effective peptide-based inhibitors of natural-gas hydrate formation with potential applications in the energy and environmental sectors.
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Affiliation(s)
- Nan Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Ying Zhu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yan-Nan Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Li-Rong Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Feng-Shou Zhang
- The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China
| | - Jun-Jie Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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156
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Yang P, Kumarasiri A, Hore D. Surface populations as a model for the distance-dependence of the interfacial refractive index. J Chem Phys 2024; 161:054703. [PMID: 39087546 DOI: 10.1063/5.0221234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Vibrational sum frequency spectra provide information about interfaces that is sensitive to the orientation of molecules, their electronic environment, and the local electric fields. Here, we use molecular dynamics simulations in order to study a surfactant, para-cyanophenol, at the air-water interface. The volume fractions of water and the organic surfactant are considered at various points over the nanometer-scale region in a Lorentz-Lorenz model. We find that the calculated ratios of nonlinear susceptibility tensor elements are in agreement with experimental data only when this depth profile was considered. We also use these data to evaluate the ratio of the C-N hyperpolarizability tensor elements in the interfacial region.
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Affiliation(s)
- Peter Yang
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Aruna Kumarasiri
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Dennis Hore
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
- Department of Computer Science, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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157
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Sabt A, Abdulla MH, Ebaid MS, Pawełczyk J, Abd El Salam HA, Son NT, Ha NX, Vaali Mohammed MA, Traiki T, Elsawi AE, Dziadek B, Dziadek J, Eldehna WM. Identification of 2-( N-aryl-1,2,3-triazol-4-yl) quinoline derivatives as antitubercular agents endowed with InhA inhibitory activity. Front Chem 2024; 12:1424017. [PMID: 39170867 PMCID: PMC11337105 DOI: 10.3389/fchem.2024.1424017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/12/2024] [Indexed: 08/23/2024] Open
Abstract
The spread of drug-resistant tuberculosis strains has become a significant economic burden globally. To tackle this challenge, there is a need to develop new drugs that target specific mycobacterial enzymes. Among these enzymes, InhA, which is crucial for the survival of Mycobacterium tuberculosis, is a key target for drug development. Herein, 24 compounds were synthesized by merging 4-carboxyquinoline with triazole motifs. These molecules were then tested for their effectiveness against different strains of tuberculosis, including M. bovis BCG, M. tuberculosis, and M. abscessus. Additionally, their ability to inhibit the InhA enzyme was also evaluated. Several molecules showed potential as inhibitors of M. tuberculosis. Compound 5n displayed the highest efficacy with a MIC value of 12.5 μg/mL. Compounds 5g, 5i, and 5n exhibited inhibitory effects on InhA. Notably, 5n showed significant activity compared to the reference drug Isoniazid. Molecular docking analysis revealed interactions between these molecules and their target enzyme. Additionally, the molecular dynamic simulations confirmed the stability of the complexes formed by quinoline-triazole conjugate 5n with the InhA. Finally, 5n underwent in silico analysis to predict its ADME characteristics. These findings provide promising insights for developing novel small compounds that are safe and effective for the global fight against tuberculosis.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Egypt
| | - Maha-Hamadien Abdulla
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Manal S. Ebaid
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Egypt
- Department of Chemistry, College of Science, Northern Border University, Arar, Saudi Arabia
| | - Jakub Pawełczyk
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | | | - Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Department of Chemistry, Graduate University of Science and Technology, Hanoi, Vietnam
| | - Nguyen Xuan Ha
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mansoor-Ali Vaali Mohammed
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Thamer Traiki
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed E. Elsawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Bozena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jaroslaw Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
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158
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Ono Y, Yamamoto E, Yasuoka K. Water structures in tip-charged carbon nanotubes. J Chem Phys 2024; 161:054702. [PMID: 39087547 DOI: 10.1063/5.0218315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/14/2024] [Indexed: 08/02/2024] Open
Abstract
Carbon nanotubes (CNTs) have potential applications in separation membranes and nanofluidic devices. It is well known that the behavior of water molecules confined in CNTs is affected by surface functional groups and external electric fields, leading to structural changes. The understanding of these structural changes of water within various CNTs is crucial, particularly in the context of material separation. While there have been many investigations into the effects of individual specific functional groups, a comprehensive understanding of the effect of these functional groups and the electric fields they generate on water molecules remains elusive. In this study, we investigate the properties of water molecules in tip-charged CNTs of (8,8), (10,10), and (12,12) chiral vectors with positive charges at one tip and negative charges at the other tip. Abstraction of ionized functional groups as tip charges enables a comprehensive understanding that is independent of individual functional groups. The symmetrically arranged tip-charges spontaneously generate a strong and symmetric electric field in the CNTs. However, the strength and directionality of the electric field are non-uniform and complex. In the interiors of (8,8) and (10,10) tip-charged CNTs, helical and square structures, which have disturbances caused by the non-uniformity of the electric field, are observed. The properties of the water molecules differed significantly in the center of the CNTs and near positive and negative charges, despite the electric field symmetry. In (12,12) tip-charged CNTs with 12 charges, a local ring structure is observed in the vicinity of negative charges but not in the vicinity of positive charges. It is concluded that the water structures in tip-charged CNTs have different characteristics from those in plain CNTs under a uniform electric field.
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Affiliation(s)
- Yûi Ono
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Eiji Yamamoto
- Department of System Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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159
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Gupta AK, Vaishnav Y, Jain SK, Annadurai S, Kumar N. Exploring novel Apalutamide analogues as potential therapeutics for prostate cancer: design, molecular docking investigations and molecular dynamics simulation. Front Chem 2024; 12:1418975. [PMID: 39165335 PMCID: PMC11333239 DOI: 10.3389/fchem.2024.1418975] [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: 04/17/2024] [Accepted: 07/04/2024] [Indexed: 08/22/2024] Open
Abstract
Introduction: Prostate cancer (PC) ranks as the second most frequent type of cancer in men and is the fourth largest cause of mortality worldwide. Androgenic hormones such as testosterone and dihydrotestosterone are crucial for the development and progression of the prostate gland. Androgenic hormones bind to androgen receptors (AR) and trigger the synthesis of many genes that stimulate the growth of prostate cells, initiating PC growth. Apalutamide (APL) is a non-steroidal antiandrogen drug used to treat PC; however, it also causes a variety of toxicities and resistance during the treatment. Methods: The purpose of this study was to computationally identify new and safer analogues of APL, focusing on improved pharmacokinetic properties and reduced toxicity. Drug likeness (DL) and drug score (DS) were also calculated. Docking studies on the designed analogues were conducted to predict their binding affinities and compare their orientations with the ligands in the original crystal structure. Molecular dynamics (MD) simulation of docked ligands was done using Schrödinger suite. Results: We generated a total of 1,415 analogues for different groups of APL using the bioisosteric approach. We selected 80 bioisosteres based on pharmacokinetic profiles, DL and DS score predictions, and found that the designed APL bioisosteres were optimal to good compared to APL. Analogues APL19, APL35, APL43, APL76, and APL80, formed hydrogen bonds with protein (PDB ID: 5T8E) which is similar hydrogen bonding to the standard (APL). The MD simulation result confirmed that APL43 and APL80 complexes were stable during the 100 nS run. Discussion: The results suggest that the APL analogues, particularly APL43 and APL80, are predicted to be potential antiandrogen drugs for the treatment of prostate cancer.
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Affiliation(s)
- Ajay Kumar Gupta
- Drug Discovery and Research Laboratory, Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, India
| | - Yogesh Vaishnav
- Drug Discovery and Research Laboratory, Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, India
| | - Sanmati Kumar Jain
- Drug Discovery and Research Laboratory, Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, India
| | - Sivakumar Annadurai
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur, Rajasthan, India
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160
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Zhu J, Xu L, Wang W, Xiao M, Li J, Wang L, Jiang X. Molecular Dynamics Simulations Reveal Octanoylated Hyaluronic Acid Enhances Liposome Stability, Stealth and Targeting. ACS OMEGA 2024; 9:33833-33844. [PMID: 39130542 PMCID: PMC11307277 DOI: 10.1021/acsomega.4c03526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Liposome-based drug delivery systems have been widely used in drug and gene delivery. However, issues such as instability, immune clearance, and poor targeting have significantly limited their clinical utility. Consequently, there is an urgent need for innovative strategies to improve liposome performance. In this study, we explore the interaction mechanisms of hyaluronic acid (HA), a linear anionic polysaccharide composed of repeating disaccharide units of d-glucuronic acid and N-acetyl-d-glucosamine connected by alternating β-1,3 and β-1,4 glycosidic linkages, and its octanoylated derivates (OHA) with liposomes using extensive coarse-grained molecular dynamics simulations. The octyl moieties of OHA spontaneously inserted into the phospholipid bilayer of liposomes, leading to their effective coating onto the surface of liposome and enhancing their structural stability. Furthermore, encapsulating liposome with OHA neutralized their surface potential, interfering with the formation of a protein corona known to contribute to liposomal immune clearance. Importantly, the encapsulated OHA maintained its selectivity and therefore targeting ability for CD44, which is often overexpressed in tumor cells. These molecular-scale findings shed light on the interaction mechanisms between HA and liposomes and will be useful for the development of next-generation liposome-based drug delivery systems.
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Affiliation(s)
- Jingyi Zhu
- State
Key Laboratory of Microbial Technology, National Glycoengineering
Research Center, Shandong University, Qingdao 266237, China
| | - Limei Xu
- State
Key Laboratory of Microbial Technology, National Glycoengineering
Research Center, Shandong University, Qingdao 266237, China
| | - Wenxin Wang
- Shandong
Institute for Food and Drug Control, Jinan 250000, China
| | - Min Xiao
- State
Key Laboratory of Microbial Technology, National Glycoengineering
Research Center, Shandong University, Qingdao 266237, China
| | - Jian Li
- Biomedicine
Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Lushan Wang
- State
Key Laboratory of Microbial Technology, National Glycoengineering
Research Center, Shandong University, Qingdao 266237, China
| | - Xukai Jiang
- State
Key Laboratory of Microbial Technology, National Glycoengineering
Research Center, Shandong University, Qingdao 266237, China
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161
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Fasano C, Lepore Signorile M, De Marco K, Forte G, Disciglio V, Sanese P, Grossi V, Simone C. In Silico Deciphering of the Potential Impact of Variants of Uncertain Significance in Hereditary Colorectal Cancer Syndromes. Cells 2024; 13:1314. [PMID: 39195204 DOI: 10.3390/cells13161314] [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: 06/05/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/29/2024] Open
Abstract
Colorectal cancer (CRC) ranks third in terms of cancer incidence worldwide and is responsible for 8% of all deaths globally. Approximately 10% of CRC cases are caused by inherited pathogenic mutations in driver genes involved in pathways that are crucial for CRC tumorigenesis and progression. These hereditary mutations significantly increase the risk of initial benign polyps or adenomas developing into cancer. In recent years, the rapid and accurate sequencing of CRC-specific multigene panels by next-generation sequencing (NGS) technologies has enabled the identification of several recurrent pathogenic variants with established functional consequences. In parallel, rare genetic variants that are not characterized and are, therefore, called variants of uncertain significance (VUSs) have also been detected. The classification of VUSs is a challenging task because each amino acid has specific biochemical properties and uniquely contributes to the structural stability and functional activity of proteins. In this scenario, the ability to computationally predict the effect of a VUS is crucial. In particular, in silico prediction methods can provide useful insights to assess the potential impact of a VUS and support additional clinical evaluation. This approach can further benefit from recent advances in artificial intelligence-based technologies. In this review, we describe the main in silico prediction tools that can be used to evaluate the structural and functional impact of VUSs and provide examples of their application in the analysis of gene variants involved in hereditary CRC syndromes.
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Affiliation(s)
- Candida Fasano
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology, IRCCS "Saverio de Bellis" Research Hospital, 70013 Castellana Grotte, Italy
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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162
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Etebar N, Hamidi SH, Naderpour S, Abouali O, Hamidi SH, Hajipour-Verdom B, Zali A, Alipour M, Rahimzadegan M. Molecular dynamic simulation reveals the inhibiting impact of Rhein on wild-type and P29S-mutated Rac1. Front Mol Biosci 2024; 11:1414197. [PMID: 39161777 PMCID: PMC11330767 DOI: 10.3389/fmolb.2024.1414197] [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: 04/23/2024] [Accepted: 06/19/2024] [Indexed: 08/21/2024] Open
Abstract
Ras-related C3 botulinum toxin substrate 1 (Rac1) is a small GTPase belonging to the Rho family. It acts as a binary molecular switch regulating several cellular functions, including cell adhesion and migration. Malfunctions due to the P29S mutation in Rac1 increase the stability of the activated form of Rac1. This sustained activation can drive aberrant cellular processes associated with cancer, such as cell proliferation, survival, and migration. Therefore, finding an inhibitor that can inhibit the mutant form of the protein is very important. Rhein, a natural compound with diverse pharmacological properties, has been studied in relation to Rac1. However, specific interactions between Rhein and Rac1 have not been examined. In this study, we investigated the potential of Rhein, a natural compound, as an inhibitor of two forms of Rac1: the wild type and the P29S mutation, using molecular dynamics simulations. Results indicated that the P29S mutation led to structural changes in the Rac1 protein, which resulted in greater accessibility of the Rhein to the active site. In addition, the binding energy of Rhein to mutant Rac1 was more negative than the native protein. Therefore, it seems that the Rhein has a better inhibitory effect on the P29S-mutated form of the Rac1 protein.
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Affiliation(s)
- Negar Etebar
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, Cyprus
| | - Seyed Hootan Hamidi
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Acharya BM Reddy College of Pharmacy, Rajiv Gandhi University of Health Sciences, Bangalore, India
| | - Saghi Naderpour
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, Cyprus
| | - Omar Abouali
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy, Cyprus International University, Nicosia, Cyprus
| | - Seyedeh Harir Hamidi
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Al-Ameen College of Pharmacy, Rajiv Gandhi University of Health Sciences, Bangalore, India
| | - Behnam Hajipour-Verdom
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Alireza Zali
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mozhgan Alipour
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Milad Rahimzadegan
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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163
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He L, Wu Q, Zhang Z, Chen L, Yu K, Li L, Jia Q, Wang Y, Ni J, Wang C, Li Q, Zhai X, Zhao J, Liu Y, Fan R, Li YP. Development of Broad-Spectrum Nanobodies for the Therapy and Diagnosis of SARS-CoV-2 and Its Multiple Variants. Mol Pharm 2024; 21:3866-3879. [PMID: 38920116 DOI: 10.1021/acs.molpharmaceut.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evaded the efficacy of previously developed antibodies and vaccines, thus remaining a significant global public health threat. Therefore, it is imperative to develop additional antibodies that are capable of neutralizing emerging variants. Nanobodies, as the smallest functional single-domain antibodies, exhibit enhanced stability and penetration ability, enabling them to recognize numerous concealed epitopes that are inaccessible to conventional antibodies. Herein, we constructed an immune library based on the immunization of alpaca with the S1 subunit of the SARS-CoV-2 spike protein, from which two nanobodies, Nb1 and Nb2, were selected using phage display technology for further characterization. Both nanobodies, with the binding residues residing within the receptor-binding domain (RBD) region of the spike, exhibited high affinity toward the S1 subunit. Moreover, they displayed cross-neutralizing activity against both wild-type SARS-CoV-2 and 10 ο variants, including BA.1, BA.2, BA.3, BA.5, BA.2.75, BF.7, BQ.1, EG.5.1, XBB.1.5, and JN.1. Molecular modeling and dynamics simulations predicted that both nanobodies interacted with the viral RBD through their complementarity determining region 1 (CDR1) and CDR2. These two nanobodies are novel tools for the development of therapeutic and diagnostic countermeasures targeting SARS-CoV-2 variants and potentially emerging coronaviruses.
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Affiliation(s)
- Lei He
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Qian Wu
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Lingling Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Kuai Yu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Leibin Li
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- China Animal Disease Control Center, Beijing 102618, China
| | - Qiong Jia
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Jianqiang Ni
- China Animal Disease Control Center, Beijing 102618, China
| | - Chuanbin Wang
- China Animal Disease Control Center, Beijing 102618, China
| | - Qi Li
- China Animal Disease Control Center, Beijing 102618, China
| | - Xinyan Zhai
- China Animal Disease Control Center, Beijing 102618, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Yuliang Liu
- China Animal Disease Control Center, Beijing 102618, China
| | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Yi-Ping Li
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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164
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Zhao M, Lopes LJS, Sahni H, Yadav A, Do HN, Reddy T, López CA, Neale C, Gnanakaran S. Insertion and Anchoring of HIV-1 Fusion Peptide into Complex Membrane Mimicking Human T-cell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606381. [PMID: 39131401 PMCID: PMC11312619 DOI: 10.1101/2024.08.02.606381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
A fundamental understanding of how HIV-1 envelope (Env) protein facilitates fusion is still lacking. The HIV-1 fusion peptide, consisting of 15 to 22 residues, is the N-terminus of the gp41 subunit of the Env protein. Further, this peptide, a promising vaccine candidate, initiates viral entry into target cells by inserting and anchoring into human immune cells. The influence of membrane lipid reorganization and the conformational changes of the fusion peptide during the membrane insertion and anchoring processes, which can significantly affect HIV-1 cell entry, remains largely unexplored due to the limitations of experimental measurements. In this work, we investigate the insertion of the fusion peptide into an immune cell membrane mimic through multiscale molecular dynamics simulations. We mimic the native T-cell by constructing a 9-lipid asymmetric membrane, along with geometrical restraints accounting for insertion in the context of gp41. To account for the slow timescale of lipid mixing while enabling conformational changes, we implement a protocol to go back and forth between atomistic and coarse-grained simulations. Our study provides a molecular understanding of the interactions between the HIV-1 fusion peptide and the T-cell membrane, highlighting the importance of conformational flexibility of fusion peptides and local lipid reorganization in stabilizing the anchoring of gp41 into the targeted host membrane during the early events of HIV-1 cell entry. Importantly, we identify a motif within the fusion peptide critical for fusion that can be further manipulated in future immunological studies.
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Affiliation(s)
- Mingfei Zhao
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | | | - Harshita Sahni
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
- Department of Computer Science, University of New Mexico, Albuquerque NM, USA
| | - Anju Yadav
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso TX, USA
| | - Hung N Do
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - Tyler Reddy
- CCS-7 Applied Computer Science Group, Los Alamos National Laboratory, Los Alamos NM USA
| | - Cesar A López
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - Chris Neale
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - S Gnanakaran
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
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165
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Bhandari D, Adepu KK, Anishkin A, Kay CD, Young EE, Baumbauer KM, Ghosh A, Chintapalli SV. Unraveling Protein-Metabolite Interactions in Precision Nutrition: A Case Study of Blueberry-Derived Metabolites Using Advanced Computational Methods. Metabolites 2024; 14:430. [PMID: 39195526 DOI: 10.3390/metabo14080430] [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: 06/27/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
Metabolomics, the study of small-molecule metabolites within biological systems, has become a potent instrument for understanding cellular processes. Despite its profound insights into health, disease, and drug development, identifying the protein partners for metabolites, especially dietary phytochemicals, remains challenging. In the present study, we introduced an innovative in silico, structure-based target prediction approach to efficiently predict protein targets for metabolites. We analyzed 27 blood serum metabolites from nutrition intervention studies' blueberry-rich diets, known for their health benefits, yet with elusive mechanisms of action. Our findings reveal that blueberry-derived metabolites predominantly interact with Carbonic Anhydrase (CA) family proteins, which are crucial in acid-base regulation, respiration, fluid balance, bone metabolism, neurotransmission, and specific aspects of cellular metabolism. Molecular docking showed that these metabolites bind to a common pocket on CA proteins, with binding energies ranging from -5.0 kcal/mol to -9.0 kcal/mol. Further molecular dynamics (MD) simulations confirmed the stable binding of metabolites near the Zn binding site, consistent with known compound interactions. These results highlight the potential health benefits of blueberry metabolites through interaction with CA proteins.
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Affiliation(s)
| | - Kiran Kumar Adepu
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Colin D Kay
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Erin E Young
- KU Medical Center, Department of Anesthesiology, Pain and Perioperative Medicine, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Kyle M Baumbauer
- KU Medical Center, Department of Anesthesiology, Pain and Perioperative Medicine, University of Kansas School of Medicine, Kansas City, KS 66160, USA
- KU Medical Center, Department of Cell Biology and Physiology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Anuradha Ghosh
- Department of Environmental Health, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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166
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Krishna NB, Roopa L, Pravin Kumar R, S GT. Computational studies on the catalytic potential of the double active site for enzyme engineering. Sci Rep 2024; 14:17892. [PMID: 39095391 PMCID: PMC11297320 DOI: 10.1038/s41598-024-60824-x] [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: 12/05/2023] [Accepted: 04/27/2024] [Indexed: 08/04/2024] Open
Abstract
Proteins possessing double active sites have the potential to revolutionise enzyme design strategies. This study extensively explored an enzyme that contains both a natural active site (NAS) and an engineered active site (EAS), focusing on understanding its structural and functional properties. Metadynamics simulations were employed to investigate how substrates interacted with their respective active sites. The results revealed that both the NAS and EAS exhibited similar minimum energy states, indicating comparable binding affinities. However, it became apparent that the EAS had a weaker binding site for the substrate due to its smaller pocket and constrained conformation. Interestingly, the EAS also displayed dynamic behaviour, with the substrate observed to move outside the pocket, suggesting the possibility of substrate translocation. To gain further insights, steered molecular dynamics (SMD) simulations were conducted to study the conformational changes of the substrate and its interactions with catalytic residues. Notably, the substrate adopted distinct conformations, including near-attack conformations, in both the EAS and NAS. Nevertheless, the NAS demonstrated superior binding minima for the substrate compared to the EAS, reinforcing the observation that the engineered active site was less favourable for substrate binding due to its limitations. The QM/MM (Quantum mechanics and molecular mechanics) analyses highlight the energy disparity between NAS and EAS. Specifically, EAS exhibited elevated energy levels due to its engineered active site being located on the surface. This positioning exposes the substrate to solvents and water molecules, adding to the energy challenge. Consequently, the engineered enzyme did not provide a significant advantage in substrate binding over the single active site protein. Further, the investigation of internal channels and tunnels within the protein shed light on the pathways facilitating transport between the two active sites. By unravelling the complex dynamics and functional characteristics of this double-active site protein, this study offers valuable insights into novel strategies of enzyme engineering. These findings establish a solid foundation for future research endeavours aimed at harnessing the potential of double-active site proteins in diverse biotechnological applications.
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Affiliation(s)
- Naveen Banchallihundi Krishna
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
| | - Lalitha Roopa
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
| | - R Pravin Kumar
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India.
| | - Gopenath T S
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
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167
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Zhou T, Cheng J, He S, Zhang C, Gao MX, Zhang LJ, Sun JP, Zhu Y, Ai D. The sphingosine-1-phosphate receptor 1 mediates the atheroprotective effect of eicosapentaenoic acid. Nat Metab 2024; 6:1566-1583. [PMID: 38907081 DOI: 10.1038/s42255-024-01070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 05/23/2024] [Indexed: 06/23/2024]
Abstract
Omega-3 polyunsaturated fatty acids (ω-3 PUFAs) have been associated with potential cardiovascular benefits, partly attributed to their bioactive metabolites. However, the underlying mechanisms responsible for these advantages are not fully understood. We previously reported that metabolites of the cytochrome P450 pathway derived from eicosapentaenoic acid (EPA) mediated the atheroprotective effect of ω-3 PUFAs. Here, we show that 17,18-epoxyeicosatetraenoic acid (17,18-EEQ) and its receptor, sphingosine-1-phosphate receptor 1 (S1PR1), in endothelial cells (ECs) can inhibit oscillatory shear stress- or tumor necrosis factor-α-induced endothelial activation in cultured human ECs. Notably, the atheroprotective effect of 17,18-EEQ and purified EPA is circumvented in male mice with endothelial S1PR1 deficiency. Mechanistically, the anti-inflammatory effect of 17,18-EEQ relies on calcium release-mediated endothelial nitric oxide synthase (eNOS) activation, which is abolished upon inhibition of S1PR1 or Gq signaling. Furthermore, 17,18-EEQ allosterically regulates the conformation of S1PR1 through a polar interaction with Lys34Nter. Finally, we show that Vascepa, a prescription drug containing highly purified and stable EPA ethyl ester, exerts its cardiovascular protective effect through the 17,18-EEQ-S1PR1 pathway in male and female mice. Collectively, our findings indicate that the anti-inflammatory effect of 17,18-EEQ involves the activation of the S1PR1-Gq-Ca2+-eNOS axis in ECs, offering a potential therapeutic target against atherosclerosis.
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Affiliation(s)
- Ting Zhou
- State Key Laboratory of Experimental Hematology, Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Jie Cheng
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, and New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Shuo He
- State Key Laboratory of Experimental Hematology, Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China
| | - Chao Zhang
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, and New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Ming-Xin Gao
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, and New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Li-Jun Zhang
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, and New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Jin-Peng Sun
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, and New Cornerstone Science Laboratory, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.
| | - Yi Zhu
- State Key Laboratory of Experimental Hematology, Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China.
| | - Ding Ai
- State Key Laboratory of Experimental Hematology, Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Physiology and Pathophysiology, Tianjin Medical University, Tianjin, China.
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168
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Sahu S, Banerjee R, Pal D. Intrinsic proclivity of left-handed conformation in large Nest motif peptides inferred from molecular dynamics. J Biomol Struct Dyn 2024; 42:6882-6891. [PMID: 37464873 DOI: 10.1080/07391102.2023.2236710] [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: 04/26/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
The 'Nest' motif plays a functional role in protein owing to its ligand binding potential aided by geometric concavity. The presence of less favored left-handed conformation (L-state) in its structure makes this concavity possible and in shaping the native chemical environment amenable to stable binding interactions. To understand the persistent appearance of L-state torsion in the Nest motif, we analyzed 0.5μs Molecular Dynamics (MD) simulation trajectories of 35 six-residue peptides (out of a total of 50 large Nest sequences of ≥6 residues) identified in our previous study. Analysis of the MD trajectories of the individual peptides reveals initial L-state in 60% of the peptides persists for >40% of the trajectory. Further, Nests with different sequences appear to adopt a specific conformational state driven by the neighboring L-state residues. The sequences also possess short secondary structures and amino acid repeats, suggesting evolutionary conservation and the specific role of amino acids in locally predisposing the torsion angle to the L-state. These findings help us to understand how L-state conformation is an essential prerequisite in stabilizing the Nest motif and shed light on the sequence-structure-function paradigm in the rational design of peptides and peptidomimetics for therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subhankar Sahu
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Raja Banerjee
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
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169
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De Salis SKF, Chen JZ, Skarratt KK, Fuller SJ, Balle T. Deep learning structural insights into heterotrimeric alternatively spliced P2X7 receptors. Purinergic Signal 2024; 20:431-447. [PMID: 38032425 DOI: 10.1007/s11302-023-09978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
P2X7 receptors (P2X7Rs) are membrane-bound ATP-gated ion channels that are composed of three subunits. Different subunit structures may be expressed due to alternative splicing of the P2RX7 gene, altering the receptor's function when combined with the wild-type P2X7A subunits. In this study, the application of the deep-learning method, AlphaFold2-Multimer (AF2M), for the generation of trimeric P2X7Rs was validated by comparing an AF2M-generated rat wild-type P2X7A receptor with a structure determined by cryogenic electron microscopy (cryo-EM) (Protein Data Bank Identification: 6U9V). The results suggested AF2M could firstly, accurately predict the structures of P2X7Rs and secondly, accurately identify the highest quality model through the ranking system. Subsequently, AF2M was used to generate models of heterotrimeric alternatively spliced P2X7Rs consisting of one or two wild-type P2X7A subunits in combination with one or two P2X7B, P2X7E, P2X7J, and P2X7L splice variant subunits. The top-ranking models were deemed valid based on AF2M's confidence measures, stability in molecular dynamics simulations, and consistent flexibility of the conserved regions between the models. The structure of the heterotrimeric receptors, which were missing key residues in the ATP binding sites and carboxyl terminal domains (CTDs) compared to the wild-type receptor, help to explain their observed functions. Overall, the models produced in this study (available as supplementary material) unlock the possibility of structure-based studies into the heterotrimeric P2X7Rs.
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Affiliation(s)
- Sophie K F De Salis
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Jake Zheng Chen
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Kristen K Skarratt
- The University of Sydney, Nepean Clinical School, Kingswood, NSW, 2747, Australia
| | - Stephen J Fuller
- The University of Sydney, Nepean Clinical School, Kingswood, NSW, 2747, Australia
| | - Thomas Balle
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia.
- Sydney Pharmacy School, The University of Sydney, Camperdown, NSW, 2050, Australia.
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170
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Ferreira JC, Villanueva AJ, Fadl S, Al Adem K, Cinviz ZN, Nedyalkova L, Cardoso THS, Andrade ME, Saksena NK, Sensoy O, Rabeh WM. Residues in the fructose-binding pocket are required for ketohexokinase-A activity. J Biol Chem 2024; 300:107538. [PMID: 38971308 PMCID: PMC11332825 DOI: 10.1016/j.jbc.2024.107538] [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] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
Excessive fructose consumption is a primary contributor to the global surges in obesity, cancer, and metabolic syndrome. Fructolysis is not robustly regulated and is initiated by ketohexokinase (KHK). In this study, we determined the crystal structure of KHK-A, one of two human isozymes of KHK, in the apo-state at 1.85 Å resolution, and we investigated the roles of residues in the fructose-binding pocket by mutational analysis. Introducing alanine at D15, N42, or N45 inactivated KHK-A, whereas mutating R141 or K174 reduced activity and thermodynamic stability. Kinetic studies revealed that the R141A and K174A mutations reduced fructose affinity by 2- to 4-fold compared to WT KHK-A, without affecting ATP affinity. Molecular dynamics simulations provided mechanistic insights into the potential roles of the mutated residues in ligand coordination and the maintenance of an open state in one monomer and a closed state in the other. Protein-protein interactome analysis indicated distinct expression patterns and downregulation of partner proteins in different tumor tissues, warranting a reevaluation of KHK's role in cancer development and progression. The connections between different cancer genes and the KHK signaling pathway suggest that KHK is a potential target for preventing cancer metastasis. This study enhances our understanding of KHK-A's structure and function and offers valuable insights into potential targets for developing treatments for obesity, cancer, and metabolic syndrome.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kenana Al Adem
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Zeynep Nur Cinviz
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Lyudmila Nedyalkova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Mario Edson Andrade
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, USA
| | - Nitin K Saksena
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Ozge Sensoy
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey; Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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171
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Wasim A, Menon S, Mondal J. Modulation of α-synuclein aggregation amid diverse environmental perturbation. eLife 2024; 13:RP95180. [PMID: 39087984 PMCID: PMC11293868 DOI: 10.7554/elife.95180] [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] [Indexed: 08/02/2024] Open
Abstract
Intrinsically disordered protein α-synuclein (αS) is implicated in Parkinson's disease due to its aberrant aggregation propensity. In a bid to identify the traits of its aggregation, here we computationally simulate the multi-chain association process of αS in aqueous as well as under diverse environmental perturbations. In particular, the aggregation of αS in aqueous and varied environmental condition led to marked concentration differences within protein aggregates, resembling liquid-liquid phase separation (LLPS). Both saline and crowded settings enhanced the LLPS propensity. However, the surface tension of αS droplet responds differently to crowders (entropy-driven) and salt (enthalpy-driven). Conformational analysis reveals that the IDP chains would adopt extended conformations within aggregates and would maintain mutually perpendicular orientations to minimize inter-chain electrostatic repulsions. The droplet stability is found to stem from a diminished intra-chain interactions in the C-terminal regions of αS, fostering inter-chain residue-residue interactions. Intriguingly, a graph theory analysis identifies small-world-like networks within droplets across environmental conditions, suggesting the prevalence of a consensus interaction patterns among the chains. Together these findings suggest a delicate balance between molecular grammar and environment-dependent nuanced aggregation behavior of αS.
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Affiliation(s)
- Abdul Wasim
- Tata Institute of Fundamental ResearchHyderabadIndia
| | - Sneha Menon
- Tata Institute of Fundamental ResearchHyderabadIndia
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172
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024; 92:905-922. [PMID: 38506327 PMCID: PMC11222054 DOI: 10.1002/prot.26685] [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: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824
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173
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Yu D, Li H, Liu Y, Yang X, Yang W, Fu Y, Zuo YA, Huang X. Application of the molecular dynamics simulation GROMACS in food science. Food Res Int 2024; 190:114653. [PMID: 38945587 DOI: 10.1016/j.foodres.2024.114653] [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: 02/01/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.
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Affiliation(s)
- Dongping Yu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Haiping Li
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China.
| | - Yuzi Liu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xingqun Yang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Wei Yang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yiran Fu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yi-Ao Zuo
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xianya Huang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
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174
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Sarkar T, Vignesh SR, Sehgal T, Ronima KR, Thummer RP, Satpati P, Chatterjee S. Development of protease resistant and non-cytotoxic Jelleine analogs with enhanced broad spectrum antimicrobial efficacy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184336. [PMID: 38763273 DOI: 10.1016/j.bbamem.2024.184336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Short systemic half- life of Antimicrobial Peptides (AMP) is one of the major bottlenecks that limits their successful commercialization as therapeutics. In this work, we have designed analogs of the natural AMP Jelleine, obtained from royal jelly of apis mellifera. Among the designed peptides, J3 and J4 were the most potent with broad spectrum activities against a varied class of ESKAPE pathogens and fungus C. albicans. All the developed peptides were more effective against Gram-negative bacteria in comparison to the Gram-positive pathogens, and were especially effective against P. aeruginosa and C. albicans.J3 and J4 were completely trypsin resistant and serum stable, while retaining the non-cytotoxicity of the parent Jelleine, Jc. The designed peptides were membranolytic in their mode of action. CD and MD simulations in the presence of bilayers, established that J3 and J4 were non-structured even upon membrane binding and suggested that biological properties of the AMPs were innocent of any specific secondary structural requirements. Enhancement of charge to increase the antimicrobial potency, controlling the hydrophobic-hydrophilic balance to maintain non-cytotoxicity and induction of unnatural amino acid residues to impart protease resistance, remains some of the fundamental principles in the design of more effective antimicrobial therapeutics of the future, which may help combat the quickly rising menace of antimicrobial resistance in the microbes.
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Affiliation(s)
- Tanumoy Sarkar
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India
| | - S R Vignesh
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Tanya Sehgal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India
| | - K R Ronima
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Rajkumar P Thummer
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Priyadarshi Satpati
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India.
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India.
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175
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Luo X, Hu C, Yin Q, Zhang X, Liu Z, Zhou C, Zhang J, Chen W, Yang Y. Dual-Mechanism Peptide SR25 has Broad Antimicrobial Activity and Potential Application for Healing Bacteria-infected Diabetic Wounds. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401793. [PMID: 38874469 PMCID: PMC11321617 DOI: 10.1002/advs.202401793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/12/2024] [Indexed: 06/15/2024]
Abstract
The rise of antibiotic resistance poses a significant public health crisis, particularly due to limited antimicrobial options for the treatment of infections with Gram-negative pathogens. Here, an antimicrobial peptide (AMP) SR25 is characterized, which effectively kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism without detectable resistance. Meanwhile, an SR25-functionalized hydrogel is developed for the efficient treatment of infected diabetic wounds. SR25 is obtained through genome mining from an uncultured bovine enteric actinomycete named Nonomuraea Jilinensis sp. nov. Investigations reveal that SR25 has two independent cellular targets, disrupting bacterial membrane integrity and restraining the activity of succinate:quinone oxidoreductase (SQR). In a diabetic mice wound infection model, the SR25-incorporated hydrogel exhibits high efficacy against mixed infections of Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA), accelerating wound healing. Overall, these findings demonstrate the therapeutic potential of SR25 and highlight the value of mining drugs with multiple mechanisms from uncultured animal commensals for combating challenging bacterial pathogens.
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Affiliation(s)
- Xue‐Yue Luo
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Chun‐Mei Hu
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Qi Yin
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Xiao‐Mei Zhang
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Zhen‐Zhen Liu
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Cheng‐Kai Zhou
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Jian‐Gang Zhang
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Wei Chen
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
| | - Yong‐Jun Yang
- Department of Preventive Veterinary MedicineCollege of Veterinary MedicineJilin UniversityChangchunJilin130062P. R. China
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176
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Wang C, Guo X, Long D, Li Y, Yuan C, Ni G, Zhang H, Li X, Yin S, Peng X, Huang W, Chen S, Liu Y, Chen Z. Familial mesial temporal lobe epilepsy phenotype is associated with novel LGI1 variants: A report of two families. Seizure 2024; 120:180-188. [PMID: 39029408 DOI: 10.1016/j.seizure.2024.07.005] [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: 03/12/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
OBJECTIVE To expand the clinical phenotype and mutation spectrum of familial mesial temporal lobe epilepsy (FMTLE) and provide a new perspective for exploring the pathological mechanisms of epilepsy caused by leucine-rich glioma inactivated 1 (LGI1) variants. METHODS We reported clinical data from two families with FMTLE and screened patients for variants in the LGI1 gene using Whole-exome sequencing and Sanger sequencing. The clinical features of FMTLE were analysed. The pathogenicity of the causative loci was assessed according to the American College of Medical Genetics and Genomics guidelines, and potential pathogenic mechanisms were predicted through multiple bioinformatics and molecular dynamics software. RESULTS We identified two novel LGI1 truncating variants within two large families with FMTLE: LGI1 (c.1174C>T, p.Q392X) and LGI1 (c.703C>T, p.Q235X). Compared to previous reports, we found that focal to bilateral tonic-clonic seizures are a common type of seizure in FMTLE. The clinical phenotypes of patients with FMTLE caused by LGI1 variants were relatively mild, and all patients responded well to valproic acid. Bioinformatics analyses and molecular dynamics simulations showed that protein structure and interactions were considerably weakened or damaged as a result of both variants. CONCLUSION This study presents the first report identifying LGI1 as a potential novel pathogenic gene within FMTLE families, thereby broadening the mutation spectrum associated with FMTLE. The findings of this study offer novel insights and avenues for understanding the intricate molecular mechanisms underlying LGI1 variants and their correlations with patient phenotypes. This study proposes the possibility of familial focal epilepsy syndromes overlapping.
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Affiliation(s)
- Chengzhe Wang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China
| | - Xintong Guo
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China
| | - Dingju Long
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China
| | - Yinchao Li
- Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, PR China
| | - Cai Yuan
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, PR China
| | - Guanzhong Ni
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China
| | - Heyu Zhang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China
| | - Xi Li
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China; Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, PR China
| | - Sijing Yin
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China; Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, PR China
| | - Xinxin Peng
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China; Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, PR China
| | - Wenyao Huang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China
| | - Siqing Chen
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China
| | - Yue Liu
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China; Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, PR China
| | - Ziyi Chen
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou 510080, PR China.
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177
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Endrakanti M, Sharma J, Ethayathulla AS, Kaur P, Khan SA, Kabra M, Gupta N. ECEL1 related distal arthrogryposis 5D in an Indian cohort-Report of recognizable musculoskeletal phenotype and a possible founder variant. Am J Med Genet A 2024; 194:e63592. [PMID: 38568023 DOI: 10.1002/ajmg.a.63592] [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: 07/30/2023] [Revised: 01/24/2024] [Accepted: 03/02/2024] [Indexed: 07/05/2024]
Abstract
Distal arthrogryposis type 5D (DA5D) is clinically characterized by knee extension contractures, distal joint contractures, clubfoot, micrognathia, ptosis, and scoliosis. We report nine affected individuals from eight unrelated Indian families with DA5D. Although the overall musculoskeletal phenotype is not very distinct from other distal arthrogryposis, the presence of fixed knee extension contractures with or without scoliosis could be an important early pointer to DA5D. We also report a possible founder variant in ECEL1 along with four novel variants and further expand the genotypic spectrum of DA5D.
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Affiliation(s)
- Mounika Endrakanti
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Sharma
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Shah Alam Khan
- Department of Orthopedics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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178
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Yang P, Wu Q, Liu H, Zhou S, Chen W, Zhong H, Zhang K, Zou F, Ying H. Simulation and mechanism for the Ultrasound-Assisted Oiling-Out Process: A case study using Fructose-1,6-diphosphate. ULTRASONICS SONOCHEMISTRY 2024; 108:106953. [PMID: 38879963 PMCID: PMC11228588 DOI: 10.1016/j.ultsonch.2024.106953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/18/2024]
Abstract
Liquid-liquid separation, commonly referred to as oiling-out, frequently can occurs during crystallization, especially the anti-solvent crystallization process of phosphoryl compounds, and poses potential hurdle for high-quality product. Efficiently regulating oiling-out during crystallization remains a significant challenge. Among various techniques, ultrasound emerges as a green and effective approach to enhance the crystallization process. However, there is a dearth of in-depth research exploring the microscopic mechanisms of this process. Therefore, our research focused on the fructose-1,6-diphosphate (FDP), a typical phosphoryl compound, to gain a deeper understanding of how ultrasound influences the oiling-out process. The focused beam reflectance measurement (FBRM) technology was used to investigate the oiling-out phenomenon of FDPNa3 across various solvent ratios. In addition, the influence of ultrasound on the induction time was studied and the nucleation energy barrier was calculated. Finally, to further unravel the microscopic mechanisms, we utilized molecular simulation techniques to analyze the impact of ultrasound power on the dissolution-precipitation process. Our observations revealed a consistent oiling-out process that attainted a stable state regardless of the solvent employed. Notably, the results of the oiling-out induction time experiments indicated that ultrasound significantly reduced helped lower the nucleation energy barrier of FDP3- ions, thereby dismantling FDP3-clusters in solution. Thus, in turn, shortened the reduced induction time and promoted crystallization. Furthermore, ultrasound reduced the interactions between FDP3-ions and water molecules as well as FDP3- ions themselves. As simulated field intensity increased, these interaction forces gradually diminished, the thickness of the hydration layer surrounding the FDP3- clusters facilitating the disruption of clusters, ultimately enhancing the crystallization process.
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Affiliation(s)
- Pengpeng Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Qian Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Haodong Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Shuyang Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wensu Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Huamei Zhong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Keke Zhang
- Biology+ Joint Research Center, School of Chemical Engineering and Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Fengxia Zou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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179
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Polverini E, Squeri P, Gherardi V. Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study. Int J Biol Macromol 2024; 275:133663. [PMID: 38969036 DOI: 10.1016/j.ijbiomac.2024.133663] [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: 03/14/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Spinal muscular atrophy (SMA) is a disease that results from mutations in the Survival of Motor Neuron (SMN) gene 1, leading to muscle atrophy due to motor neurons degeneration. SMN plays a crucial role in the assembly of spliceosomal small nuclear ribonucleoprotein complexes via binding to the arginine-glycine rich C-terminal tails of Sm proteins recognized by SMN Tudor domain. E134K Tudor mutation, cause of the more severe type I SMA, compromises the SMN-Sm interaction without a perturbation of the domain fold. By molecular dynamics simulations, we investigated the mechanism of Tudor-SmD1 interaction, and the effects on it of E134K mutation. It was observed that E134 is crucial to catch the positive dimethylated arginines (DMRs) of the SmD1 tail that, wrapping around the acidic Tudor surface, enters a central DMR into an aromatic cage. The flexible cage residue Y130 must be blocked from the wrapped tail to assure a stable binding. The charge inversion in E134K mutation causes the loss of a critical anchor point, disfavoring the tail wrapping and leaving Y130 free to swing, leading to DMR detachments and exposition of the C-terminal region of the tail. This could suggest new hypotheses regarding a possible autoimmune response by anti-Sm autoantibodies.
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Affiliation(s)
- Eugenia Polverini
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
| | - Pietro Squeri
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Valeria Gherardi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
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180
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Zhang N, Wei F, Ning S, Hu J, Shi H, Yao Z, Tang M, Zhang Y, Gong J, Ge J, Cui Z. PPARγ Agonist Rosiglitazone and Antagonist GW9662: Antihypertensive Effects on Chronic Intermittent Hypoxia-Induced Hypertension in Rats. J Cardiovasc Transl Res 2024; 17:803-815. [PMID: 38411834 DOI: 10.1007/s12265-024-10499-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024]
Abstract
The increased incidence of hypertension associated with obstructive sleep apnea (OSA) presents significant physical, psychological, and economic challenges. Peroxisome proliferator-activated receptor gamma (PPARγ) plays a role in both OSA and hypertension, yet the therapeutic potential of PPARγ agonists and antagonists for OSA-related hypertension remains unexplored. Therefore, we constructed a chronic intermittent hypoxia (CIH)-induced hypertension rat model that mimics the pathogenesis of OSA-related hypertension in humans. The model involved administering PPARγ agonist rosiglitazone (RSG), PPARγ antagonist GW9662, or normal saline, followed by regular monitoring of blood pressure and thoracic aorta analysis using staining and electron microscopy. Intriguingly, our results indicated that both RSG and GW9662 appeared to potently counteract CIH-induced hypertension. In silico study suggested that GW9662's antihypertensive effect might mediated through angiotensin II receptor type 1 (AGTR1). Our findings provide insights into the mechanisms of OSA-related hypertension and propose novel therapeutic targets.
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MESH Headings
- Animals
- PPAR gamma/agonists
- PPAR gamma/metabolism
- Hypertension/physiopathology
- Hypertension/drug therapy
- Hypertension/metabolism
- Rosiglitazone/pharmacology
- Disease Models, Animal
- Antihypertensive Agents/pharmacology
- Antihypertensive Agents/therapeutic use
- Male
- Hypoxia/complications
- Hypoxia/drug therapy
- Anilides/pharmacology
- Rats, Sprague-Dawley
- Blood Pressure/drug effects
- Aorta, Thoracic/drug effects
- Aorta, Thoracic/metabolism
- Aorta, Thoracic/physiopathology
- Aorta, Thoracic/pathology
- Receptor, Angiotensin, Type 1/metabolism
- Receptor, Angiotensin, Type 1/drug effects
- Chronic Disease
- Signal Transduction
- Sleep Apnea, Obstructive/drug therapy
- Sleep Apnea, Obstructive/physiopathology
- Sleep Apnea, Obstructive/complications
- Sleep Apnea, Obstructive/metabolism
- Molecular Docking Simulation
- Vascular Remodeling/drug effects
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Affiliation(s)
- Ningzhi Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Feng Wei
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Sisi Ning
- Department of Cardiology, Shanghai Changning Tianshan Traditional Chinese Medicine Hospital, Shanghai, China
| | - Jialu Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Hongtao Shi
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Zhifeng Yao
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Minna Tang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Yongqiao Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Jiaxin Gong
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China.
| | - Zhaoqiang Cui
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China.
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181
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Roy A, Paul I, Paul T, Hazarika K, Dihidar A, Ray S. An in-silico receptor-pharmacophore based multistep molecular docking and simulation study to evaluate the inhibitory potentials against NS1 of DENV-2. J Biomol Struct Dyn 2024; 42:6136-6164. [PMID: 37517062 DOI: 10.1080/07391102.2023.2239925] [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: 04/01/2023] [Accepted: 06/25/2023] [Indexed: 08/01/2023]
Abstract
DENV-2 strain is the most fatal and infectious of the five dengue virus serotypes. The non-structural protein NS1 encoded by its genome is the most significant protein required for viral pathogenesis and replication inside the host body. Thus, targeting the NS1 protein and designing an inhibitor to limit its stability and secretion is a propitious attempt in our fight against dengue. Four novel inhibitors are designed to target the conserved cysteine residues (C55, C313, C316, and C329) and glycosylation sites (N130 and N207) of the NS1 protein in an attempt to halt the spread of the dengue infection in the host body altogether. Numerous computer-aided drug designing techniques including molecular docking, molecular dynamics simulation, virtual screening, principal component analysis, and dynamic cross-correlation matrix were employed to determine the structural and functional activity of the NS1-inhibitor complexes. From our analysis, it was evident that the extent of structural and atomic level fluctuations of the ligand-bound protein exhibited a declining trend in contrast to unbound protein which was prominently noticeable through the RMSD, RMSF, Rg, and SASA graphs. The ADMET analysis of the four ligands revealed a promising pharmacokinetics and pharmacodynamic profile, along with good bioavailability and toxicity properties. The proposed drugs when bound to the targeted cavities resulted in stable conformations in comparison to their unbound state, implying they have good affinity promising effective drug action. Thus, they can be tested in vitro and used as potential anti-dengue drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Ishani Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Tanwi Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | | | - Aritrika Dihidar
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
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182
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Lu G, Pan F, Li X, Zhu Z, Zhao L, Wu Y, Tian W, Peng W, Liu J. Virtual screening strategy for anti-DPP-IV natural flavonoid derivatives based on machine learning. J Biomol Struct Dyn 2024; 42:6645-6659. [PMID: 37489054 DOI: 10.1080/07391102.2023.2237594] [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: 02/27/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
Flavonoids, especially their inhibitory effect on DPP-IV activity, have been widely recognized for their antidiabetic effects. However, the variety of natural flavonoid derivatives is very rich, and even subtle structural differences can lead to several orders of magnitude differences in their inhibitory activities against DPP-IV, which makes it challenging to find novel and potent anti-DPP-IV flavonoid derivatives experimentally. Therefore, there is an urgent need to develop an efficient screening pipeline that targets active natural products. Here, we propose a fusion strategy based on a QSAR model, and to simplify this process, it was applied to the discovery of flavonoid derivatives with potent anti-DPP-IV activity. First, the high-quality QSAR model (R test 2 = 0.816, MAEtest = 0.14, MSEtest = 0.026) was composed of seven key molecular property parameters, which were constructed with the genetic algorithm (GA) and passed the leave-one-out cross-validation evaluation. A total of 1,668 flavonoid derivatives were obtained from the natural product enriched by NPCD based on molecular fingerprint similarity (> 0.8). Further, the enriched flavonoid derivatives were further predicted and screened using the QED score combined with the QSAR model, and a total of 33 flavonoid derivatives (IC50pre < 6.5 μM) were found. Subsequently, three flavonoid derivatives (5,7,3',5'-tetrahydroxyflavone, 3,7-dihydroxy-5,3',4'-trimethoxyflavone, and 5,7,2',5'-tetrahydroxyflavone) with highly effective anti-DPP-IV activity were obtained by ADMET analysis. Finally, the DPP-IV inhibitory potential of these three flavonoid derivatives was verified by 100 ns MD simulation and MM/PB(GB)SA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gen Lu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Fei Pan
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Xiaotong Li
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
| | - Zehui Zhu
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Lei Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Ya Wu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wenli Tian
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenjun Peng
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Liu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, China
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183
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Srinivasan S, Di Luca A, Álvarez D, John Peter AT, Gehin C, Lone MA, Hornemann T, D’Angelo G, Vanni S. The conformational plasticity of structurally unrelated lipid transport proteins correlates with their mode of action. PLoS Biol 2024; 22:e3002737. [PMID: 39159271 PMCID: PMC11361750 DOI: 10.1371/journal.pbio.3002737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 08/29/2024] [Accepted: 07/05/2024] [Indexed: 08/21/2024] Open
Abstract
Lipid transfer proteins (LTPs) are key players in cellular homeostasis and regulation, as they coordinate the exchange of lipids between different cellular organelles. Despite their importance, our mechanistic understanding of how LTPs function at the molecular level is still in its infancy, mostly due to the large number of existing LTPs and to the low degree of conservation at the sequence and structural level. In this work, we use molecular simulations to characterize a representative dataset of lipid transport domains (LTDs) of 12 LTPs that belong to 8 distinct families. We find that despite no sequence homology nor structural conservation, the conformational landscape of LTDs displays common features, characterized by the presence of at least 2 main conformations whose populations are modulated by the presence of the bound lipid. These conformational properties correlate with their mechanistic mode of action, allowing for the interpretation and design of experimental strategies to further dissect their mechanism. Our findings indicate the existence of a conserved, fold-independent mechanism of lipid transfer across LTPs of various families and offer a general framework for understanding their functional mechanism.
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Affiliation(s)
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniel Álvarez
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain
| | | | - Charlotte Gehin
- Institute of Bioengineering (IBI) and Global Heath Institute (GHI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Museer A. Lone
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Giovanni D’Angelo
- Institute of Bioengineering (IBI) and Global Heath Institute (GHI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- National Center of Competence in Research Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
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184
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El Yaagoubi OM, Ezzemani W, Oularbi L, Samaki H, Aboudkhil S. In silico identification of 20S proteasome-β5 subunit inhibitors using structure-based virtual screening. J Biomol Struct Dyn 2024; 42:6165-6173. [PMID: 37403265 DOI: 10.1080/07391102.2023.2232041] [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: 10/16/2021] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
Proteasome inhibitors have effective anti-tumor activity in cell culture and can induce apoptosis by interfering with the degradation of cell cycle proteins. 20S Proteasome is acknowledged to be a satisfactory target that has persistent properties against the human immune defense and is obligatory for the degradation of some vital proteins. This study aimed to identify potential inhibitors against 20S proteasome, specifically the β5 subunit, using structure-based virtual screening and molecular docking to reduce the number of ligands that should be eligible for experimental assays. A total of 4961 molecules with anticancer activity were screened from the ASINEX database. The filtered compounds that showed higher docking affinity were then used in more sophisticated molecular docking simulations with AutoDock Vina for validation. Finally, six drug molecules (BDE 28974746, BDE 25657353, BDE 29746159, BDD 27844484, BDE 29746109, and BDE 29746162) exhibited highly significant interactions compared to the positive controls were retained. Among these six molecules, three molecules (BDE 28974746, BDE 25657353, and BDD 27844484) showed high binding affinity and binding energy compared with Carfilzomib and Bortezomib. Molecular simulation and dynamics studies of the top three drug molecules in each case allowed us to draw further conclusions about their stability with the β5 subunit. Computed absorption, distribution, metabolism, excretion and toxicity studies on these derivatives showed encouraging results with very low toxicity, distribution, and absorption. These compounds may serve as potential hits for further biological evaluation in the development of new proteasome inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ouadie Mohamed El Yaagoubi
- Laboratory of Biochemistry, Environment and Agri-Food (URAC 36), Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
| | - Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Département de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Larbi Oularbi
- Laboratory of Materials Membranes and Environment, Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
- Supramolecular Nanomaterials Group (SNG), Mohammed VI Polytechnic University (UM6P), Lot 660, HayMoulayRachid, BenGuerir, Morocco
| | - Hamid Samaki
- National Institute of Social Action (INAS), Tangier, Morocco
| | - Souad Aboudkhil
- Laboratory of Biochemistry, Environment and Agri-Food (URAC 36), Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
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185
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Lohachova KO, Kyrychenko A, Kalugin ON. Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2. Biophys Chem 2024; 311:107258. [PMID: 38776839 DOI: 10.1016/j.bpc.2024.107258] [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: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The main cysteine protease (Mpro) of coronavirus SARS-CoV-2 has become a promising target for computational development in anti-COVID-19 treatments. Here, we benchmarked the performance of six biomolecular molecular dynamics (MD) force fields (OPLS-AA, CHARMM27, CHARMM36, AMBER03, AMBER14SB and GROMOS G54A7) and three water models (TIP3P, TIP4P and SPC) for reproducing the native fold and the enzymatic activity of Mpro as monomeric and dimeric units. The MD sampling up to 1 μs suggested that the proper choice of the force fields and water models plays an essential role in reproducing the tertiary structure and the inter-residue distance between the catalytic dyad His41-Cys145. We found that while most benchmarked all-atom force fields reproduce well the native fold of Mpro, the CHARMM27/TIP3P and OPLS-AA/TIP4P setups revealed a good performance in reproducing the structure of the catalytic domain. In addition, these FF setups were also well-adopted for MD sampling of Mpro at the physiologic conditions by mimicking the presence of 100 mM NaCl and the elevated temperature of 310 K. Finally, both FFs were also performed well in reproducing the native fold of Mpro in a dimeric form. Therefore, comparing the preservation of the native fold of Mpro and the stability of its catalytic site architecture, our MD benchmarking suggests that the OPLS-AA/TIP4P and CHARMM27/TIP3P MD setups at the physiologic conditions may be well-suited for rapid in silico screening and developing broad-spectrum anti-coronaviral therapeutic agents.
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Affiliation(s)
- Kateryna O Lohachova
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine
| | - Alexander Kyrychenko
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine.
| | - Oleg N Kalugin
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine
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186
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Yang S, Wahab S, Almoyad MAA, Chen Y, Kalam N, Khalid M. Discovery of promising B lymphocyte kinase inhibitors using structure-guided virtual screening. J Biomol Struct Dyn 2024; 42:7054-7064. [PMID: 37688373 DOI: 10.1080/07391102.2023.2256397] [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: 03/27/2023] [Accepted: 07/12/2023] [Indexed: 09/10/2023]
Abstract
Tyrosine-protein kinase BLK, also known as B-cell lymphocyte kinase (BLK), is a non-receptor tyrosine kinase that is primarily expressed in B-cells. BLK plays a key role in B-cell signaling, particularly in B-cell development and maturation. The increased expression of BLK has been linked to various complex diseases, including autoimmune disorders, and specific malignancies of B cells, such as lymphomas and leukemias. Due to its significant involvement in B-cell signaling, BLK has emerged as a promising target for drug development, offering the potential for developing novel therapeutics to combat these diseases. Small molecule inhibitors of BLK hold great potential for therapeutic intervention; however, discovering potent and selective inhibitors remains challenging. Within this context, natural compounds hold significant potential as a valuable resource for discovering novel inhibitors of BLK. In the current study, a structure-based virtual screening of the IMPPAT 2 library was employed to identify promising candidates with potential as inhibitors of BLK. The control molecule for this study was the known BLK inhibitor, Dasatinib. After a multi-step filtering process, two molecules (Withanolide I and Mexogenin) demonstrated potential against BLK based on their superior binding affinity, ligand efficiency, and specific interaction. Interaction analysis of these compounds revealed several significant interactions with the active site residues of BLK. Both proposed molecules remained bound to the binding pocket of BLK, as indicated by the molecular dynamics (MD) simulation study. Taken together, these findings provide valuable insights for guiding future research endeavors and translational efforts in developing therapeutics for different complex diseases, such as autoimmune disorders, lymphomas, and leukemias.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Song Yang
- Department of Wine, Food and Molecular Biosciences, Faculty of Agriculture & Life Sciences, Lincoln University, Christchurch, New Zealand
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Yanxin Chen
- Department of Anaesthesiology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Nida Kalam
- School of Pharmaceutical Education and Research (SPER), New Delhi, India
| | - Mohammad Khalid
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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187
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Yadav P, Samanta K, Arya V, Biswas D, Kim HS, Bakli C, Jung HY, Ghosh D. A 2.5 V In-Plane Flexi-Pseudocapacitor with Unprecedented Energy and Cycling Efficiency for All-Weather Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400975. [PMID: 38618920 DOI: 10.1002/smll.202400975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/26/2024] [Indexed: 04/16/2024]
Abstract
As electronic devices for aviation, space, and satellite applications become more sophisticated, built-in energy storage devices also require a wider temperature spectrum. Herein, an all-climate operational, energy and power-dense, flexible, in-plane symmetric pseudocapacitor is demonstrated with utmost operational safety and long cycle life. The device is constructed with interdigital-patterned laser-scribed carbon-supported electrodeposited V5O12·6H2O as a binder-free electrode and a novel high-voltage anti-freezing water-in-salt-hybrid electrolyte. The anti-freezing electrolyte can operate over a wide temperature range of -40-60 °C while offering a stable potential window of ≈2.5 V. The device undergoes rigorous testing under diverse environmental conditions, including rapid and regular temperature and mechanical transition over multiple cycles. Additionally, detailed theoretical simulation studies are performed to understand the interfacial interactions with the active material as well as the local behavior of the anti-freeze electrolyte at different temperatures. As a result, the all-weather pseudocapacitor at 1 A g-1 shows a high areal capacitance of 234.7 mF cm-2 at room temperature and maintains a high capacitance of 129.8 mF cm-2 even at -40 °C. Besides, the cell operates very reliably for over 80 950 cycles with a capacitance of 25.7 mF cm-2 at 10 A g-1 and exhibits excellent flexibility and bendability under different stress conditions.
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Affiliation(s)
- Prahlad Yadav
- Centre for Nano and Material Sciences, JAIN (Deemed to be University), Kanakapura Road, Bangalore, Karnataka, 562112, India
| | - Ketaki Samanta
- Department of Materials Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Vinay Arya
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Diptesh Biswas
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Hun-Seong Kim
- Department of Energy System Engineering, Gyeongsang National University, Jinju-si, Gyeongnam, 52725, South Korea
| | - Chirodeep Bakli
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Hyun Young Jung
- Department of Energy System Engineering, Gyeongsang National University, Jinju-si, Gyeongnam, 52725, South Korea
- Department of Energy Engineering, Gyeongsang National University, Jinju-si, Gyeongnam, 52725, South Korea
| | - Debasis Ghosh
- Centre for Nano and Material Sciences, JAIN (Deemed to be University), Kanakapura Road, Bangalore, Karnataka, 562112, India
- Department of Energy Engineering, Gyeongsang National University, Jinju-si, Gyeongnam, 52725, South Korea
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188
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Koh JJ, Koh XQ, Chee JY, Chakraborty S, Tee SY, Zhang D, Lai SC, Yeo JCC, Soh JWJ, Li P, Tan SC, Thitsartarn W, He C. Reprogrammable, Sustainable, and 3D-Printable Cellulose Hydroplastic. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402390. [PMID: 38803059 PMCID: PMC11304289 DOI: 10.1002/advs.202402390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/24/2024] [Indexed: 05/29/2024]
Abstract
Modern human societies are highly dependent on plastic materials, however, the bulk of them are non-renewable commodity plastics that cause pollution problems and consume large amounts of energy for their thermal processing activities. In this article, a sustainable cellulose hydroplastic material and its composites, that can be shaped repeatedly into various 2D/3D geometries using just water are introduced. In the wet state, their high flexibility and ductility make it conducive for the shaping to take place. In the ambient environment, the wet hydroplastic transits spontaneously into rigid materials with its intended shape in a short time of <30 min despite a thickness of hundreds of microns. They also possess humidity resistance and are structurally stable in highly humid environments. Given their excellent mechanical properties, geometry reprogrammability, bio-based, and biodegradable nature, cellulose hydroplastic poses as a sustainable alternative to traditional plastic materials and even "green" thermoplastics. This article also demonstrates the possibility of 3D-printing these hydroplastics and the potential of employing them in electronics applications. The demonstrated hydroshapable structural electronic components show capability in performing electronic functions, load-bearing ability and geometry versatility, which are attractive features for lightweight, customizable and geometry-unique electronic devices.
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Affiliation(s)
- J. Justin Koh
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Xue Qi Koh
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Jing Yee Chee
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Souvik Chakraborty
- Institute of High Performance Computing (IHPC)Agency for ScienceTechnology and Research (A*STAR)1 Fusionopolis Way, Connexis North #16‐16Singapore138632Republic of Singapore
| | - Si Yin Tee
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Danwei Zhang
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Szu Cheng Lai
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Jayven Chee Chuan Yeo
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Jia Wen Jaslin Soh
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
- Department of Materials Science and EngineeringNational University of Singapore9 Engineering Drive 1Singapore117575Republic of Singapore
| | - Peiyu Li
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
- Department of Materials Science and EngineeringNational University of Singapore9 Engineering Drive 1Singapore117575Republic of Singapore
| | - Swee Ching Tan
- Department of Materials Science and EngineeringNational University of Singapore9 Engineering Drive 1Singapore117575Republic of Singapore
| | - Warintorn Thitsartarn
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
| | - Chaobin He
- Institute of Materials Research and Engineering (IMRE)Agency for ScienceTechnology and Research (A*STAR)2 Fusionopolis Way, Innovis #08‐03Singapore138634Republic of Singapore
- Department of Materials Science and EngineeringNational University of Singapore9 Engineering Drive 1Singapore117575Republic of Singapore
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189
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Juneja P, Rashid N, Abul Qais F, Tanwar S, Sultan I, Ahmad F, Rehman SU. Alternative splicing generates a novel ferroportin isoform with a shorter C-terminal and an intact iron- and hepcidin-binding property. IUBMB Life 2024; 76:523-533. [PMID: 38348962 DOI: 10.1002/iub.2809] [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: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 08/15/2024]
Abstract
Ferroportin (FPN) is a transmembrane protein and is the only known iron exporter that helps in maintaining iron homeostasis in vertebrates. To maintain stable iron equilibrium in the body, ferroportin works in conjunction with a peptide called hepcidin. In this study, we have identified an alternatively spliced novel isoform of the human SLC40A1 gene, which encodes for the FPN protein and is found to be expressed in different tissues. The novel transcript has an alternate last exon and encodes 31-amino acid long peptide sequence that replaces 104 amino acids at C-terminal in the novel transcript. Molecular modelling and molecular dynamics (MD) simulation studies revealed key structural features of the novel isoform (FPN-N). FPN-N was predicted to have 12 transmembrane domains similar to the reported isoform (FPN), despite being much smaller in size. FPN-N was found to interact with hepcidin, a key regulator of ferroportin activity. Also, the iron-binding sites were retained in the novel isoform as revealed by the MD simulation of FPN-N in bilipid membrane. The novel isoform identified in this study may play important role in iron homeostasis. However, further studies are required to characterize the FPN-N isoform and decipher its role inside the cell.
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Affiliation(s)
- Pallavi Juneja
- Department of Biochemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Naira Rashid
- Department of Biochemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Supriya Tanwar
- Department of Biochemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Insha Sultan
- Department of Biochemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Faizan Ahmad
- Department of Biochemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Sayeed Ur Rehman
- Department of Biochemistry, School of Chemical and Life Sciences, New Delhi, India
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190
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Zhang Y, Mi J, Wu W, Fei J, Lv B, Yu X, Wen K, Shen J, Wang Z. Investigation of Antibody Tolerance in Methanol for Analytical Purposes: Methanol Effect Patterns and Molecular Mechanisms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402050. [PMID: 38889249 PMCID: PMC11336977 DOI: 10.1002/advs.202402050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/16/2024] [Indexed: 06/20/2024]
Abstract
The extraction of targets from biological samples for immunoassays using organic solvents, such as methanol, is often necessary. However, high concentrations of organic solvents in extracts invariably lead to instability of the employed antibody, resulting in poor performance of the immunoassay. Evaluating the tolerance ability and exploring the molecular mechanisms of antibody tolerance in organic solvents are essential for the development of robust immunoassays. In this work, 25 monoclonal antibodies and methanol are utilized as models to address these questions. A novel protocol is initially established to precisely and rapidly determine antibody tolerance in methanol, identifying two distinct methanol effect patterns. Through a detailed investigation of the structural basis, a novel hypothesis regarding methanol effect patterns is proposed, termed "folding-aggregation," which is subsequently validated through molecular dynamics simulations. Furthermore, the investigation of sequence basis reveals significant differences in residue types within the complementarity-determining regions and ligand-binding residues, distinguishing the two antibody methanol effect patterns. Moreover, the methanol effect patterns of the antibodies are defined by germline antibodies. This work represents the first exploration of antibody methanol effect patterns and associated molecular mechanisms, with potential implications for the discovery and engineering of tolerant antibodies for the development of robust immunoassays.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Jiafei Mi
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Weilin Wu
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Jie Fei
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Bochen Lv
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Xuezhi Yu
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Kai Wen
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health and SafetyBeijing Key Laboratory of Detection Technology for Animal‐Derived FoodCollege of Veterinary MedicineChina Agricultural UniversityBeijing100193P. R. China
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191
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Ding Y, Xie D, Xu C, Hu W, Kong B, Jia S, Cao L. Fisetin disrupts mitochondrial homeostasis via superoxide dismutase 2 acetylation in pancreatic adenocarcinoma. Phytother Res 2024. [PMID: 39091056 DOI: 10.1002/ptr.8296] [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: 06/21/2023] [Revised: 01/06/2024] [Accepted: 02/11/2024] [Indexed: 08/04/2024]
Abstract
Pancreatic adenocarcinoma (PDAC) is one of the most lethal malignant tumors with an urgent need for precision medicine strategies. The present study seeks to assess the antitumor effects of fisetin, and characterize its impact on PDAC. Multi-omic approaches include proteomic, transcriptomic, and metabolomic analyses. Further validation includes the assessment of mitochondria-derived reactive oxygen species (mtROS), mitochondrial membrane potential, as well as ATP generation. Molecular docking, immunoprecipitation, and proximity ligation assay were used to detect the interactions among fiseitn, superoxide dismutase 2 (SOD2), and sirtuin 2 (SIRT2). We showed that fisetin disrupted mitochondrial homeostasis and induced SOD2 acetylation in PDAC. Further, we produced site mutants to determine that fisetin-induced mtROS were dependent on SOD2 acetylation. Fisetin inhibited SIRT2 expression, thus blocking SOD2 deacetylation. SIRT2 overexpression could impede fisetin-induced SOD2 acetylation. Additionally, untargeted metabolomic analysis revealed an acceleration of folate metabolism with fisetin. Collectively, our findings suggest that fisetin disrupts mitochondrial homeostasis, eliciting an important cancer-suppressive role; thus, fisetin may serve as a promising therapeutic for PDAC.
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Affiliation(s)
- Yimin Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dafei Xie
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengjie Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenyi Hu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Binyue Kong
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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192
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Yu SJ, So YS, Lim C, Cho CH, Lee SG, Yoo SH, Park CS, Lee BH, Min KH, Seo DH. Efficient biotransformation of naringenin to naringenin α-glucoside, a novel α-glucosidase inhibitor, by amylosucrase from Deinococcus wulumuquiensis. Food Chem 2024; 448:139182. [PMID: 38569413 DOI: 10.1016/j.foodchem.2024.139182] [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: 11/06/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Amylosucrase (ASase) efficiently biosynthesizes α-glucoside using flavonoids as acceptor molecules and sucrose as a donor molecule. Here, ASase from Deinococcus wulumuqiensis (DwAS) biosynthesized more naringenin α-glucoside (NαG) with sucrose and naringenin as donor and acceptor molecules, respectively, than other ASases from Deinococcus sp. The biotransformation rate of DwAS to NαG was 21.3% compared to 7.1-16.2% for other ASases. Docking simulations showed that the active site of DwAS was more accessible to naringenin than those of others. The 217th valine in DwAS corresponded to the 221st isoleucine in Deinococcus geothermalis AS (DgAS), and the isoleucine possibly prevented naringenin from accessing the active site. The DwAS-V217I mutant had a significantly lower biosynthetic rate of NαG than DwAS. The kcat/Km value of DwAS with naringenin as the donor was significantly higher than that of DgAS and DwAS-V217I. In addition, NαG inhibited human intestinal α-glucosidase more efficiently than naringenin.
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Affiliation(s)
- Su-Jeong Yu
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Yun-Sang So
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Changjin Lim
- School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Chi Heung Cho
- Division of Functional Food Research Group, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Sang-Gil Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan 48513, Republic of Korea
| | - Sang-Ho Yoo
- Department of Food Science & Biotechnology and Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Cheon-Seok Park
- Department of Food Science and Biotechnology, Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Byung-Hoo Lee
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea
| | - Kyung Hyun Min
- School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Dong-Ho Seo
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea; Department of Food Science & Biotechnology and Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea; Department of Food Science and Biotechnology, Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea.
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193
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Yamchi A, Rahimi M, Akbari R, Ghobadi C, Aryapour H. Effects of Bacillus in Pectobacterium quorum quenching: A survey of two different acyl-homoserine lactonases. Folia Microbiol (Praha) 2024; 69:913-926. [PMID: 38305961 DOI: 10.1007/s12223-024-01139-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Numerous functions in pathogenic Pectobacterium are regulated by quorum sensing (QS). Two different aiiA genes isolated from Bacillus sp. A24(aiiAA24) and Bacillus sp. DMS133(aiiADMS133) were used. Both genes encode acyl-homoserine lactonase (AiiA), which disrupts QS in Pectobacterium. To investigate the effect of different AiiAs on the inhibition of Pectobacterium carotovorum pathogenicity, two aiiA genes from different Bacillus strains were cloned and the resulting plasmids pME6863 (aiiAA24) and pME7080 (aiiADMS133) were transformed into P. carotovorum EMPCC cells. The effects of different lactonases on virulence features such as enzymatic activity, twitching and swimming motilities, and production of pellicle and biofilm formation were investigated. In EMPCC/pME6863, twitching and swimming motilities, and pellicle production were significantly reduced compared with EMPCC/pME7080. Quantitative real-time PCR (qRT-PCR) was used to measure virulence gene expression in transformed cells compared with expression levels in wild-type EMPCC. The expression of peh and hrpL genes was greatly reduced in EMPCC/pME6863 compared with EMPCC/pME7080. The sequence alignment and molecular dynamic modeling of two different AiiAA24 and AiiADMS133 proteins suggested that the replacement of proline 210 from AiiAA24 to serine in AiiADMS133 caused the reduction of enzyme activity in AiiADMS133.
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Affiliation(s)
- Ahad Yamchi
- Department of Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Maryam Rahimi
- Department of Horticulture, University of Zabol, Zabol, Iran
| | - Ramin Akbari
- Department of Agricultural Biotechnology, Isfahan University of Technology, Isfahan, Iran
| | - Cyrus Ghobadi
- Department of Horticulture Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
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194
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Egbemhenghe AU, Aderemi OE, Omotara BS, Akhimien FI, Osabuohien FO, Adedapo HA, Temionu OR, Egejuru WA, Ajala CF, Ihunanya MF, Oluwafemi OO, Onu CFD, Ajibare AC, Ddamulira C, Abalum JO, Afolayan OM. Computational-based drug design of novel small molecules targeting p53-MDMX interaction. J Biomol Struct Dyn 2024; 42:6678-6687. [PMID: 37578044 DOI: 10.1080/07391102.2023.2245483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023]
Abstract
The regulation of the p53 tumor suppressor pathway is critically dependent on the activity of Murine Double Minute 2 (MDM2) and Murine Double Minute X (MDMX) proteins. In certain types of cancer cells, excessive amount of MDMX can poly-ubiquitinate p53, which can result in its degradation, leading to a subsequent reduction in the levels of this protein. Therefore, the design of small-molecule inhibitors targeting the MDMX-p53 interaction has emerged as a promising strategy for cancer therapy. In this study, we employed computational techniques including pharmacophore modeling and molecular docking to identify three potential small molecule inhibitors (CID_25094615, CID_137634453, and CID_25094344) of the MDMX-p53 interaction from a PubChem database. Molecular dynamics of 100000 ps were conducted to assess the stability of the MDMX-inhibitor complexes. Our results showed that all three compounds exhibit stable binding with MDMX, with significantly lower root mean square deviation (RMSD) and fluctuation (RMSF) values than the control ligand, indicating superior stability. Additionally, the three compounds exhibit stronger intermolecular hydrogen bond (HBOND) interactions compared to the control, suggesting stronger stability. Overall, our findings highlight the potential of these compounds as lead candidates for the development of novel anticancer agents that target the MDMX-p53 interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Olajide Enoch Aderemi
- Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT, USA
| | - Bamidele Samson Omotara
- Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT, USA
| | | | | | | | - Oluwakemi Rita Temionu
- Department of Medical Laboratory Technology, Lagos State College of Health Technology, Lagos, Nigeria
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195
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Singh AP, Ahmad S, Raza K, Gautam HK. Computational screening and MM/GBSA-based MD simulation studies reveal the high binding potential of FDA-approved drugs against Cutibacterium acnes sialidase. J Biomol Struct Dyn 2024; 42:6245-6255. [PMID: 37545341 DOI: 10.1080/07391102.2023.2242950] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Cutibacterium acnes is an opportunistic pathogen linked with acne vulgaris, affecting 80-90% of teenagers globally. On the leukocyte (WBCs) cell surface, the cell wall anchored sialidase in C. acnes virulence factor, catalysing the sialoconjugates into sialic acids and nutrients for C. acnes resulting in human skin inflammation. The clinical use of antibiotics for acne treatments has severe adverse effects, including microbial dysbiosis and resistance. Therefore, identifying inhibitors for primary virulence factors (Sialidase) was done using molecular docking of 1030 FDA-approved drugs. Initially, based on binding energies (ΔG), Naloxone (ZINC000000389747), Fenoldopam (ZINC000022116608), Labetalol (ZINC000000403010) and Thalitone (ZINC000000057255) were identified that showed high binding energies as -10.2, -10.1, -9.9 and -9.8 kcal/mol, respectively. In 2D analysis, these drugs also showed considerable structural conformer of hydrogen and hydrophobic interactions. Further, a 100 ns MD simulation study found the lowest deviation and fluctuations with various intermolecular interactions to stabilise the complexes. Out of 4, the Naloxone molecule showed robust, steady, and stable RMSD 0.23 ± 0.18 nm. Further, MMGBSA analysis supports MD results and found strong binding energy (ΔG) -29.71 ± 4.97 kcal/mol. In Comparative studies with Neu5Ac2en (native substrate) revealed naloxone has a higher affinity for sialidase. The PCA analysis showed that Naloxone and Thalitone were actively located on the active site, and other compounds were flickered. Our extensive computational and statistical report demonstrates that these FDA drugs can be validated as potential sialidase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akash Pratap Singh
- Infectious Disease Laboratory, Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad, India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Hemant K Gautam
- Infectious Disease Laboratory, Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad, India
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196
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Yan H, He B, He L, Ye H. Screening study on significant Chinese herb for anti-idiopathic pulmonary fibrosis by combining clinical experience prescriptions and molecular dynamics simulation technologies. J Biomol Struct Dyn 2024; 42:6393-6409. [PMID: 37963492 DOI: 10.1080/07391102.2023.2263792] [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: 03/09/2023] [Accepted: 07/01/2023] [Indexed: 11/16/2023]
Abstract
Various techniques such as data mining, network pharmacology, molecular docking and molecular dynamics simulation were used in this study to screen and validate effective herbal medicines for the treatment of idiopathic pulmonary fibrosis (IPF) and to reveal their mechanisms of action at the molecular level. The use of this approach will provide new tools and ideas for future drug screening, especially for the application of herbal medicines in the treatment of complex diseases. Among them, the five identified core targets, including IL6, TP53, AKT1, VEGFA, and TNF, as well as a series of major active compounds, will be important references for future anti-IPF drug development. This information will accelerate the discovery and development of relevant drugs. Meanwhile, this study further confirmed the potential value of four Chinese herbal medicines, including Gancao, Danshen, Huangqin, and Sanqi, in the treatment of IPF. This will promote more clinical trials and practices to confirm and optimise the application of these herbs. Finally, this study is an important theoretical guide to enhance the advantages of Chinese herbal medicines in the prevention and treatment of major and difficult diseases, as well as to understand and utilise the potential efficacy of Chinese herbal medicines. This will further promote the scientific research and clinical application of herbal medicines and provide more possibilities for future disease treatmentCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Haiting Yan
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Beibei He
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li He
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hua Ye
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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197
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Ribeiro IC, de Moraes JVB, Mariotini-Moura C, Polêto MD, da Rocha Torres Pavione N, de Castro RB, Miranda IL, Sartori SK, Alves KLS, Bressan GC, de Souza Vasconcellos R, Meyer-Fernandes JR, Diaz-Muñoz G, Fietto JLR. Synthesis of new non-natural L-glycosidic flavonoid derivatives and their evaluation as inhibitors of Trypanosoma cruzi ecto-nucleoside triphosphate diphosphohydrolase 1 (TcNTPDase1). Purinergic Signal 2024; 20:399-419. [PMID: 37975950 PMCID: PMC11303637 DOI: 10.1007/s11302-023-09974-7] [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: 05/03/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Trypanosoma cruzi is the pathogen of Chagas disease, a neglected tropical disease that affects more than 6 million people worldwide. There are no vaccines to prevent infection, and the therapeutic arsenal is very minimal and toxic. The unique E-NTPDase of T. cruzi (TcNTPDase1) plays essential roles in adhesion and infection and is a virulence factor. Quercetin is a flavonoid with antimicrobial, antiviral, and antitumor activities. Its potential as a partial inhibitor of NTPDases has also been demonstrated. In this work, we synthesized the non-natural L-glycoside derivatives of quercetin and evaluated them as inhibitors of recombinant TcNTPDase1 (rTcNTPDase1). These compounds, and quercetin and miquelianin, a natural quercetin derivative, were also tested. Compound 16 showed the most significant inhibitory effect (94%). Quercetin, miquelianin, and compound 14 showed inhibition close to 50%. We thoroughly investigated the inhibitory effect of 16. Our data suggested a competitive inhibition with a Ki of 8.39 μM (± 0.90). To better understand the interaction of compound 16 and rTcNTPDase1, we performed molecular dynamics simulations of the enzyme and docking analyses with the compounds. Our predictions show that compound 16 binds to the enzyme's catalytic site and interacts with important residues for NTPDase activity. As an inhibitor of a critical T. cruzi enzyme, (16) could be helpful as a starting point in the developing of a future treatment for Chagas disease. Furthermore, the discovery of (16) as an inhibitor of TcNTPDase1 may open new avenues in the study and development of new inhibitors of E-NTPDases.
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Affiliation(s)
- Isadora Cunha Ribeiro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Christiane Mariotini-Moura
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Medicine and Nursing Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcelo Depolo Polêto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - Raissa Barbosa de Castro
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Izabel Luzia Miranda
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Suélen Karine Sartori
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Kryssia Lohayne Santos Alves
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gustavo Costa Bressan
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | | | - José Roberto Meyer-Fernandes
- Laboratory of Cellular Biochemistry, Institute of Medical Biochemistry Leopoldo de Meis, Health Sciences Center, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gaspar Diaz-Muñoz
- Exact Science Institute, Chemistry Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Juliana Lopes Rangel Fietto
- Biochemistry and Molecular Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
- General Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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Li N, Li C, Zheng A, Liu W, Shi Y, Jiang M, Xiao Y, Qiu Z, Qiu Y, Jia A. Ultra-high-performance liquid chromatography-mass spectrometry combined with molecular docking and molecular dynamics simulation reveals the source of bitterness in the traditional Chinese medicine formula Runchang-Tongbian. Biomed Chromatogr 2024; 38:e5929. [PMID: 38881323 DOI: 10.1002/bmc.5929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 06/18/2024]
Abstract
The Runchang-Tongbian (RCTB) formula is a traditional Chinese medicine (TCM) formula consisting of four herbs, namely Cannabis Fructus (Huomaren), Rehmanniae Radix (Dihuang), Atractylodis Macrocephalae Rhizoma (Baizhu), and Aurantii Fructus (Zhiqiao). It is widely used clinically because of its beneficial effect on constipation. However, its strong bitter taste leads to poor patient compliance. The bitter components of TCM compounds are complex and numerous, and inhibiting the bitter taste of TCM has become a major clinical challenge. Here, we use ultra-high-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) and high-resolution mass spectrometry to identify 59 chemical components in the TCM compound RCTB formula. Next, four bitter taste receptors, TAS2R39, TAS2R14, TAS2R7, and TAS2R5, which are tightly bound to the compounds in RCTB, were screened as molecular docking receptors using the BitterX database. The top-three-scoring receptor-small-molecule complexes for each of the four receptors were selected for molecular dynamics simulation. Finally, seven bitter components were identified, namely six flavonoids (rhoifolin, naringin, poncirin, diosmin, didymin, and narirutin) and one phenylpropanoid (purpureaside C). Thus, we proposed a new method for identifying the bitter components in TCM compounds, which provides a theoretical reference for bitter taste inhibition in TCM compounds.
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Affiliation(s)
- Na Li
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Chunyu Li
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Aizhu Zheng
- The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Weipeng Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yuwen Shi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Mengcheng Jiang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yusheng Xiao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Zhidong Qiu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ye Qiu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ailing Jia
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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199
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Ahmad V, Jamal A, Khan MI, Alzahrani FA, Albiheyri R, Jamal QMS. Cefoperazone targets D-alanyl-D-alanine carboxypeptidase (DAC) to control Morganella morganii-mediated infection: a subtractive genomic and molecular dynamics approach. J Biomol Struct Dyn 2024; 42:6799-6812. [PMID: 37480259 DOI: 10.1080/07391102.2023.2238088] [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: 03/21/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2023]
Abstract
Morganella morganii is a Gram-negative bacterial pathogen that causes bacteremia, urinary tract infections, intra-abdominal infections, chorioamnionitis, neonatal sepsis, and newborn meningitis. To control this bacterial pathogen a total of 3565 putative proteins targets in Morganella morganii were screened using comparative subtractive analysis of biochemical pathways annotated by the KEGG that did not share any similarities with human proteins. One of the targets, D-alanyl-D-alanine carboxypeptidase DacB [Morganella] was observed to be implicated in the majority of cell wall synthesis pathways, leading to its selection as a novel pharmacological target. The drug that interacted optimally with the identified target was observed to be Cefoperazone (DB01329) with the estimated free energy of binding -8.9 Kcal/mol. During molecular dynamics simulations; it was observed that DB01328-2exb and DB01329-2exb complexes showed similar values as the control FMX-2exb complex near 0.2 nm with better stability. Furthermore, MMPBSA total free energy calculation showed better binding energy than the control complex for DB01329-2exb interaction i.e. -31.50 (±0.93) kcal/mol. Our presented research suggested that D-alanyl-D-alanine carboxypeptidase DacB could be a therapeutic target and cefoperazone could be a promising ligand to inhibit the D-alanyl-D-alanine carboxypeptidase DacB protein of Morganella morganii. To identify prospective therapeutic and vaccine targets in Morganella morganii, this is the first computational and subtractive genomics investigation of various metabolic pathways exploring other therapeutic targets of Morganella morganii. In vitro/in vivo experimental validation of the identified target D-alanyl-D-alanine carboxypeptidase and the design of its inhibitors is suggested to figure out the best dose, the drug's effectiveness, and its toxicity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Varish Ahmad
- Health Information Technology Department, The Applied College, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alam Jamal
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Imran Khan
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Faisal A Alzahrani
- Department of Biochemistry, Faculty of Science, Embryonic Stem Cell Unit, King Fahad Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
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200
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Wu S, Li M, Wang L, Yang L, Cui J, Li F, Wang Q, Shi Y, Lv M. Structural basis for TNIP1 binding to FIP200 during mitophagy. J Biol Chem 2024; 300:107605. [PMID: 39059492 PMCID: PMC11367644 DOI: 10.1016/j.jbc.2024.107605] [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: 04/01/2024] [Revised: 06/07/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
TNIP1 has been increasingly recognized as a security check to finely adjust the rate of mitophagy by disrupting the recycling of the Unc-51-like kinase complex during autophagosome formation. Through tank-binding kinase 1-mediated phosphorylation of the TNIP1 FIP200 interacting region (FIR) motif, the binding affinity of TNIP1 for FIP200, a component of the Unc-51-like kinase complex, is enhanced, allowing TNIP1 to outcompete autophagy receptors. Consequently, FIP200 is released from the autophagosome, facilitating further autophagosome expansion. However, the molecular basis by which FIP200 utilizes its claw domain to distinguish the phosphorylation status of residues in the TNIP1 FIR motif for recognition is not well understood. Here, we elucidated multiple crystal structures of the complex formed by the FIP200 claw domain and various phosphorylated TNIP1 FIR peptides. Structural and isothermal titration calorimetry analyses identified the crucial residues in the FIP200 claw domain responsible for the specific recognition of phosphorylated TNIP1 FIR peptides. Additionally, utilizing structural comparison and molecular dynamics simulation data, we demonstrated that the C-terminal tail of TNIP1 peptide affected its binding to the FIP200 claw domain. Moreover, the phosphorylation of TNIP1 Ser123 enabled the peptide to effectively compete with the peptide p-CCPG1 (the FIR motif of the autophagy receptor CCPG1) for binding with the FIP200 claw domain. Overall, our work provides a comprehensive understanding of the specific recognition of phosphorylated TNIP1 by the FIP200 claw domain, marking an initial step toward fully understanding the molecular mechanism underlying the TNIP1-dependent inhibition of mitophagy.
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Affiliation(s)
- Shengmei Wu
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, China
| | - Mingwei Li
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Lei Wang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, China
| | - Lingna Yang
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, China
| | - Jing Cui
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, China
| | - Fudong Li
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, China
| | - Qian Wang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui, China.
| | - Yunyu Shi
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, China.
| | - Mengqi Lv
- Hefei National Research Center for Cross Disciplinary Science, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science & Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, China; Department of Hepatobiliary Surgery, Innovative Institute of Tumor Immunity and Medicine (ITIM), Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
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