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Sardag I, Duvenci ZS, Belkaya S, Timucin E. Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers. Comput Struct Biotechnol J 2024; 23:1854-1863. [PMID: 38882680 PMCID: PMC11177541 DOI: 10.1016/j.csbj.2024.04.037] [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: 02/20/2024] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 06/18/2024] Open
Abstract
IL37 plays important roles in the regulation of innate immunity and its oligomeric status is critical to these roles. In its monomeric state, IL37 can effectively inhibit the inflammatory response of IL18 by binding to IL18Rα, a capacity lost in its dimeric form, underlining the pivotal role of the oligomeric status of IL37 in its anti-inflammatory action. Until now, two IL37 dimer structures have been deposited in PDB, reflecting a substantial difference in their dimer interfaces. Given this discrepancy, we analyzed the PDB structures of the IL37 dimer (PDB IDs: 6ncu, 5hn1) along with a AF2-multimer prediction by molecular dynamics (MD) simulations. Results showed that the 5hn1 and AF2-predicted dimers have the same interface and stably maintained their conformations throughout simulations, while the recent IL37 dimer (PDB ID: 6ncu) with a different interface did not, proposing a possible issue with the recent IL37 dimer structure (6ncu). Next, focusing on the stable dimer structures, we have identified five critical positions of V71/Y85/I86/E89/S114, three new positions compared to the literature, that would reduce dimer stability without affecting the monomer structure. Two quintuple mutants were tested by MD simulations and showed partial or complete dissociation of the dimer. Overall, the insights gained from this study reinforce the validity of the 5hn1 and AF2 multimer structures, while also advancing our understanding of the IL37 dimer interface through the generation of monomer-locked IL37 variants.
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Affiliation(s)
- Inci Sardag
- Bogazici University, Department of Molecular Biology and Genetics, Istanbul 34342, Turkey
| | - Zeynep Sevval Duvenci
- Acibadem Mehmet Ali Aydinlar University, Institute of Health Sciences, Department of Biostatistics and Bioinformatics, Istanbul 34752, Turkey
| | - Serkan Belkaya
- Bilkent University, Department of Molecular Biology and Genetics, Ankara 06800, Turkey
- Bilkent University, The National Nanotechnology Research Center (UNAM), Ankara 06800, Turkey
| | - Emel Timucin
- Acibadem Mehmet Ali Aydinlar University, Institute of Health Sciences, Department of Biostatistics and Bioinformatics, Istanbul 34752, Turkey
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Biostatistics and Medical Informatics, Istanbul 34752, Turkey
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Bian L, Zhang S, Chang T, Zhang J, Zhu X, Zhang C. Enhanced catalytic performance and pH stability of Streptomyces Laccase Y230R and its degradation of malachite green. Int J Biol Macromol 2024; 277:134108. [PMID: 39048010 DOI: 10.1016/j.ijbiomac.2024.134108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/11/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The escalating threat of malachite green (MG) pollution poses significant risks to ecosystems. Saturation mutation targeting Tyr230 of small laccase (SLAC) from Streptomyces coelicolor yielded Y230R, exhibiting a remarkable 104 % increase in specific activity. Notably, this mutation achieved dual enhancements in both activity and pH stability. Molecular dynamics simulation revealed higher structural stability of Y230R compared to wild-type (WT) across varying pH levels. The increased count of hydrogen bonds in Y230R compared to WT may be contribute to its stability. Y230R demonstrated superior catalytic efficiency (67.0 %) in MG decolorization, maintaining over 90 % activity after 30 min incubation in MG solution (500 mg/L), highlighting enhanced tolerance compared to WT. Molecular docking analysis attributed the differential catalytic effects on MG and ABTS to structural disparities and hydrogen bonding. Y230R stands as a promising composite mutant for future laccase engineering and industrial applications.
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Affiliation(s)
- Luyao Bian
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Silu Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tingting Chang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiacheng Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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3
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Zhang L, Huang Y, Yang Y, Liao B, Hou C, Wang Y, Qin H, Zeng H, He Y, Gu J, Zhang R. TIMM9 as a prognostic biomarker in multiple cancers and its associated biological processes. Sci Rep 2024; 14:20568. [PMID: 39232081 DOI: 10.1038/s41598-024-71421-3] [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: 04/11/2024] [Accepted: 08/28/2024] [Indexed: 09/06/2024] Open
Abstract
TIMM9 has been identified as a mediator of essential functions in mitochondria, but its association with pan-cancer is poorly understood. We herein employed bioinformatics, computational chemistry techniques and experiments to investigate the role of TIMM9 in pan-cancer. Our analysis revealed that overexpression of TIMM9 was significantly associated with tumorigenesis, pathological stage progression, and metastasis. Missense mutations (particularly the S49L variant), copy number variations (CNV) and methylation alterations in TIMM9 were found to be associated with poor cancer prognosis. Moreover, TIMM9 was positively related with cell cycle progression, mitochondrial and ribosomal function, oxidative phosphorylation, TCA cycle activity, innate and adaptive immunity. Additionally, we discovered that TIMM9 could be regulated by cancer-associated signaling pathways, such as the mTOR pathway. Using molecular simulations, we identified ITFG1 as the protein that has the strongest physical association with TIMM9, which show a promising structural complement.
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Affiliation(s)
- Lisheng Zhang
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Yan Huang
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Yanting Yang
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Birong Liao
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Congyan Hou
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Yiqi Wang
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Huaiyu Qin
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Huixiang Zeng
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China
| | - Yanli He
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China.
| | - Jiangyong Gu
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China.
| | - Ren Zhang
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, 232 Outer Ring East Road, Guangzhou University City, Panyu District, Guangzhou, 510006, Guangdong, China.
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4
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Siddiquee NH, Talukder MEK, Ahmed E, Zeba LT, Aivy FS, Rahman MH, Barua D, Rumman R, Hossain MI, Shimul MEK, Rama AR, Chowdhury S, Hossain I. Cheminformatics-based analysis identified (Z)-2-(2,5-dimethoxy benzylidene)-6-(2-(4-methoxyphenyl)-2-oxoethoxy) benzofuran-3(2H)-one as an inhibitor of Marburg replication by interacting with NP. Microb Pathog 2024:106892. [PMID: 39216611 DOI: 10.1016/j.micpath.2024.106892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 08/17/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
The highly pathogenic Marburg virus (MARV) is a member of the Filoviridae family, a non-segmented negative-strand RNA virus. This article represents the computer-aided drug design (CADD) approach for identifying drug-like compounds that prevent the MARV virus disease by inhibiting nucleoprotein, which is responsible for their replication. This study used a wide range of in silico drug design techniques to identify potential drugs. Out of 368 natural compounds, 202 compounds passed ADMET, and molecular docking identified the top two molecules (CID: 1804018 and 5280520) with a high binding affinity of -6.77 and -6.672 kcal/mol, respectively. Both compounds showed interactions with the common amino acid residues SER_216, ARG_215, TYR_135, CYS_195, and ILE_108, which indicates that lead compounds and control ligands interact in the common active site/catalytic site of the protein. The negative binding free energies of CID: 1804018 and 5280520 were -66.01 and -31.29 kcal/mol, respectively. Two lead compounds were re-evaluated using MD modeling techniques, which confirmed CID: 1804018 as the most stable when complexed with the target protein. PC3 of the (Z)-2-(2,5-dimethoxybenzylidene)-6-(2-(4-methoxyphenyl)-2-oxoethoxy) benzofuran-3(2H)-one (CID: 1804018) was 8.74%, whereas PC3 of the 2'-Hydroxydaidzein (CID: 5280520) was 11.25%. In this study, (Z)-2-(2,5-dimethoxybenzylidene)-6-(2-(4-methoxyphenyl)-2-oxoethoxy) benzofuran-3(2H)-one (CID: 1804018) unveiled the significant stability of the proteins' binding site in ADMET, Molecular docking, MM-GBSA and MD simulation analysis studies, which also showed a high negative binding free energy value, confirming as the best drug candidate which is found in Angelica archangelica which may potentially inhibit the replication of MARV nucleoprotein.
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Affiliation(s)
- Noimul Hasan Siddiquee
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh; Bioinformatics Laboratory (BioLab), Bangladesh
| | - Md Enamul Kabir Talukder
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Bangladesh
| | - Ezaz Ahmed
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh; Bioinformatics Laboratory (BioLab), Bangladesh
| | - Labiba Tasnim Zeba
- Bioinformatics Laboratory (BioLab), Bangladesh; Department of Mathematics & Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Farjana Sultana Aivy
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh; Bioinformatics Laboratory (BioLab), Bangladesh
| | - Md Hasibur Rahman
- Bioinformatics Laboratory (BioLab), Bangladesh; Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Durjoy Barua
- Bioinformatics Laboratory (BioLab), Bangladesh; Department of Pharmacy, BGC Trust University, Bangladesh
| | - Rahnumazzaman Rumman
- Bioinformatics Laboratory (BioLab), Bangladesh; Department Of Environmental Science and Disaster Management, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Ifteker Hossain
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh; Bioinformatics Laboratory (BioLab), Bangladesh
| | - Md Ebrahim Khalil Shimul
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Bangladesh
| | - Anika Rahman Rama
- Bioinformatics Laboratory (BioLab), Bangladesh; Department of Genetic Engineering and Biotechnology, East West University, Dhaka, Bangladesh
| | - Sristi Chowdhury
- Bioinformatics Laboratory (BioLab), Bangladesh; Department of Biochemistry and Molecular Biology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Imam Hossain
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh; Bioinformatics Laboratory (BioLab), Bangladesh.
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5
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Chen J, Wang J, Yang W, Zhao L, Hu G. Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning. J Chem Inf Model 2024. [PMID: 39197061 DOI: 10.1021/acs.jcim.4c01174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Binding of partners and mutations highly affects the conformational dynamics of KRAS4B, which is of significance for deeply understanding its function. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) and principal component analysis (PCA) were carried out to probe the effect of G12C and binding of three partners NF1, RAF1, and SOS1 on the conformation alterations of KRAS4B. DL reveals that G12C and binding of partners result in alterations in the contacts of key structure domains, such as the switch domains SW1 and SW2 together with the loops L4, L5, and P-loop. Binding of NF1, RAF1, and SOS1 constrains the structural fluctuation of SW1, SW2, L4, and L5; on the contrary, G12C leads to the instability of these four structure domains. The analyses of free energy landscapes (FELs) and PCA also show that binding of partners maintains the stability of the conformational states of KRAS4B while G12C induces greater mobility of the switch domains SW1 and SW2, which produces significant impacts on the interactions of GTP with SW1, L4, and L5. Our findings suggest that partner binding and G12C play important roles in the activity and allosteric regulation of KRAS4B, which may theoretically aid in further understanding the function of KRAS4B.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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6
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Hu X, Zhang X, Sun W, Liu C, Deng P, Cao Y, Zhang C, Xu N, Zhang T, Zhang YE, Liu JJG, Wang H. Systematic discovery of DNA-binding tandem repeat proteins. Nucleic Acids Res 2024:gkae710. [PMID: 39189466 DOI: 10.1093/nar/gkae710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
Tandem repeat proteins (TRPs) are widely distributed and bind to a wide variety of ligands. DNA-binding TRPs such as zinc finger (ZNF) and transcription activator-like effector (TALE) play important roles in biology and biotechnology. In this study, we first conducted an extensive analysis of TRPs in public databases, and found that the enormous diversity of TRPs is largely unexplored. We then focused our efforts on identifying novel TRPs possessing DNA-binding capabilities. We established a protein language model for DNA-binding protein prediction (PLM-DBPPred), and predicted a large number of DNA-binding TRPs. A subset was then selected for experimental screening, leading to the identification of 11 novel DNA-binding TRPs, with six showing sequence specificity. Notably, members of the STAR (Short TALE-like Repeat proteins) family can be programmed to target specific 9 bp DNA sequences with high affinity. Leveraging this property, we generated artificial transcription factors using reprogrammed STAR proteins and achieved targeted activation of endogenous gene sets. Furthermore, the members of novel families such as MOON (Marine Organism-Originated DNA binding protein) and pTERF (prokaryotic mTERF-like protein) exhibit unique features and distinct DNA-binding characteristics, revealing interesting biological clues. Our study expands the diversity of DNA-binding TRPs, and demonstrates that a systematic approach greatly enhances the discovery of new biological insights and tools.
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Affiliation(s)
- Xiaoxuan Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuechun Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chunhong Liu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Pujuan Deng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuanwei Cao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenze Zhang
- National Key Laboratory of Efficacy and Mechanism on Chinese Medicine for Metabolic Diseases, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ning Xu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongtong Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun-Jie Gogo Liu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
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7
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Ray P, Sarker DK, Uddin SJ. Bioinformatics and computational studies of chabamide F and chabamide G for breast cancer and their probable mechanisms of action. Sci Rep 2024; 14:19893. [PMID: 39191884 DOI: 10.1038/s41598-024-70854-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024] Open
Abstract
Globally, the prevalence of breast cancer (BC) is increasing at an alarming level, despite early detection and technological improvements. Alkaloids are diverse chemical groups, and many within this class have been reported as potential anticancer compounds. Chabamide F (F) and chabamide G (G) are two dimeric amide alkaloids found in a traditional medicinal plant, Piper chaba, and possess significant cytotoxic effects. However, their scientific rationalization in BC remains unknown. Here, we aimed to investigate their potential and molecular mechanisms for BC through in silico approaches. From network pharmacology, we identified 64 BC-related genes as targets. GO and KEGG studies showed that they were involved in various biological processes and mostly expressed in BC-related pathways such as RAS, PI3K-AKT, estrogen, MAPK, and FoxO pathways. However, PPI analysis revealed SRC and AKT1 as hub genes, which play key roles in BC tumorigenesis and metastasis. Molecular docking revealed the strong binding affinity of F (- 10.7 kcal/mol) and G (- 9.4 and - 11.7 kcal/mol) for SRC and AKT1, respectively, as well as the acquisition of vital residues to inhibit them. Their long-term stability was evaluated using 200 ns molecular dynamics simulation. The RMSD, RMSF, Rg, and SASA analyses showed that the G-SRC and G-AKT1 complexes were excellently stable compared to the control, dasatinib, and capivasertib, respectively. Additionally, the PCA and DCCM analyses revealed a significant reduction in the residual correlation and motions. By contrast, the stability of the F-SRC complex was greater than that of the control, whereas it was moderately stable in complex with AKT1. The MMPBSA analysis demonstrated higher binding energies for both compounds than the controls. In particular, the binding energy of G for SRC and AKT1 was - 120.671 ± 16.997 and - 130.437 ± 19.111 kJ/mol, respectively, which was approximately twice as high as the control molecules. Van der Waal and polar solvation energies significantly contributed to this energy. Furthermore, both of them exhibited significant interactions with the binding site residues of both proteins. In summary, this study indicates that these two molecules could be a potential ATP-competitive inhibitor of SRC and an allosteric inhibitor of AKT1.
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Affiliation(s)
- Pallobi Ray
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, 9208, Bangladesh
| | - Dipto Kumer Sarker
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, 9208, Bangladesh
- Department of Pharmacy, Atish Dipankar University of Science & Technology, Dhaka, 1230, Bangladesh
| | - Shaikh Jamal Uddin
- Pharmacy Discipline, Life Science School, Khulna University, Khulna, 9208, Bangladesh.
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8
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Lynch EM, Hansen H, Salay L, Cooper M, Timr S, Kollman JM, Webb BA. Structural basis for allosteric regulation of human phosphofructokinase-1. Nat Commun 2024; 15:7323. [PMID: 39183237 PMCID: PMC11345425 DOI: 10.1038/s41467-024-51808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024] Open
Abstract
Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively. Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Heather Hansen
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA
| | - Lauren Salay
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison Cooper
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA
| | - Stepan Timr
- Department of Computational Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Bradley A Webb
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA.
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9
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Alanzi AR, A. Z. A, Alhazzani K. Insilico exploration C. koseri ATP synthase inhibitors by pharmacophore-based virtual screening, molecular docking and MD simulation. PLoS One 2024; 19:e0308251. [PMID: 39173004 PMCID: PMC11341028 DOI: 10.1371/journal.pone.0308251] [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: 05/01/2024] [Accepted: 07/20/2024] [Indexed: 08/24/2024] Open
Abstract
Citrobacter koseri is a gram-negative rod that causes infections in people who have significant comorbidities and are immunocompromised. Antibiotic-resistant strains are becoming more common, which complicates infection treatment and highlights the need for innovative, effective drugs to fight these resistant strains. The enzyme complex ATP synthase participates in the adenosine triphosphate (ATP) synthesis, the fundamental energy currency of cells. This study used Computer-Aided Drug Design approaches to identify potential inhibitors of C. koseri ATP synthase. SWISS-MODEL was used to predict the 3D structure of C. koseri ATP synthase. A ligand-based pharmacophore model was developed using chemical features of ampicillin. Following ligand-based virtual screening across nine databases, the 2043 screened hits were docked to the ATP synthase active site using the standard precision mode of the glide tool. Based on their binding affinities, the top ten compounds were selected for additional investigation. The binding affinities of the chosen compounds ranged from -10.021 to -8.452 kcal/mol. The top four compounds (PubChem-25230613, PubChem-74936833, CHEMBL263035, PubChem-44208924) with the best ADMET characteristics and binding modes were chosen. Thus, the feasible binding mechanisms of the selected compounds were subjected to stability analysis using the MD Simulation study, which revealed the compounds' stability as potent inhibitors within the protein binding pocket. This computational approach provides important insights into the rational design of novel therapeutics and emphasizes the importance of targeting essential metabolic pathways when combating antibiotic-resistant pathogens. Future experimental validation and optimization of the identified inhibitors is required to determine their efficacy and safety profiles for clinical use.
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Affiliation(s)
- Abdullah R. Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Alanazi A. Z.
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Khalid Alhazzani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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10
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Li T, Motta S, He Y. Deciphering the Mystery in p300 Taz2-p53 TAD2 Recognition. J Chem Theory Comput 2024. [PMID: 39141804 DOI: 10.1021/acs.jctc.4c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Intrinsically disordered proteins (IDPs) engage in various fundamental biological activities, and their behavior is of particular importance for a better understanding of the verbose but well-organized signal transduction in cells. IDPs exhibit uniquely paradoxical features with low affinity but simultaneously high specificity in recognizing their binding targets. The transcription factor p53 plays a crucial role in cancer suppression, carrying out some of its biological functions using its disordered regions, such as N-terminal transactivation domain 2 (TAD2). Exploration of the binding and unbinding processes between proteins is challenging, and the inherently disordered properties of these regions further complicate the issue. Computer simulations are a powerful tool to complement the experiments to fill gaps to explore the binding/unbinding processes between proteins. Here, we investigated the binding mechanism between p300 Taz2 and p53 TAD2 through extensive molecular dynamics (MD) simulations using the physics-based UNited RESidue (UNRES) force field with additional Go̅-like potentials. Distance restraints extracted from the NMR-resolved structures were imposed on intermolecular residue pairs to accelerate binding simulations, in which Taz2 was immobilized in a native-like conformation and disordered TAD2 was fully free. Starting from six structures with TAD2 placed at different positions around Taz2, we observed a metastable intermediate state in which the middle helical segment of TAD2 is anchored in the binding pocket, highlighting the significance of the TAD2 helix in directing protein recognition. Physics-based binding simulations show that successful binding is achieved after a series of stages, including (1) protein collisions to initiate the formation of encounter complexes, (2) partial attachment of TAD2, and finally (3) full attachment of TAD2 to the correct binding pocket of Taz2. Furthermore, machine-learning-based PathDetect-SOM was used to identify two binding pathways, the encounter complexes, and the intermediate states.
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Affiliation(s)
- Tongtong Li
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Yi He
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, New Mexico 87131, United States
- Translational Informatics Division, Department of Internal Medicine, The University of New Mexico, Albuquerque, New Mexico 87131, United States
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11
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Aborode AT, Kumar N, Olowosoke CB, Ibisanmi TA, Ayoade I, Umar HI, Jamiu AT, Bolarinwa B, Olapade Z, Idowu AR, Adelakun IO, Onifade IA, Akangbe B, Abacheng M, Ikhimiukor OO, Awaji AA, Adesola RO. Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences. FRONTIERS IN BIOINFORMATICS 2024; 4:1411935. [PMID: 39132675 PMCID: PMC11310021 DOI: 10.3389/fbinf.2024.1411935] [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: 04/03/2024] [Accepted: 06/12/2024] [Indexed: 08/13/2024] Open
Abstract
Introduction: This work utilizes predictive modeling in drug discovery to unravel potential candidate genes from Escherichia coli that are implicated in antimicrobial resistance; we subsequently target the gidB, MacB, and KatG genes with some compounds from plants with reported antibacterial potentials. Method: The resistance genes and plasmids were identified from 10 whole-genome sequence datasets of E. coli; forty two plant compounds were selected, and their 3D structures were retrieved and optimized for docking. The 3D crystal structures of KatG, MacB, and gidB were retrieved and prepared for molecular docking, molecular dynamics simulations, and ADMET profiling. Result: Hesperidin showed the least binding energy (kcal/mol) against KatG (-9.3), MacB (-10.7), and gidB (-6.7); additionally, good pharmacokinetic profiles and structure-dynamics integrity with their respective protein complexes were observed. Conclusion: Although these findings suggest hesperidin as a potential inhibitor against MacB, gidB, and KatG in E. coli, further validations through in vitro and in vivo experiments are needed. This research is expected to provide an alternative avenue for addressing existing antimicrobial resistances associated with E. coli's MacB, gidB, and KatG.
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Affiliation(s)
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur, Rajasthan, India
| | - Christopher Busayo Olowosoke
- Department of Biotechnology, Federal University of Technology, Akure, Nigeria
- Institute of Bioinformatics and Molecular Therapeutics, Osogbo, Nigeria
| | | | - Islamiyyah Ayoade
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry, Federal University of Technology, Akure, Nigeria
| | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry, Federal University of Technology, Akure, Nigeria
| | - Abdullahi Temitope Jamiu
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - Basit Bolarinwa
- College of Medicine, Richmond Gabriel University, Richmond, Saint Vincent and the Grenadines
| | - Zainab Olapade
- Department of Biology, Lamar University, Lamar, TX, United States
| | - Abidemi Ruth Idowu
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
| | - Ibrahim O. Adelakun
- Department of Chemistry, State University of New York Albany, Albany, NY, United States
| | | | - Benjamin Akangbe
- Department of Epidemiology, School of Public Health, Georgia State University, Atlanta, GA, United States
| | - Modesta Abacheng
- School of Public Health, Georgia State University, Atlanta, GA, United States
| | - Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Aeshah A. Awaji
- Department of Biology, Faculty of Science, University College of Taymaa, University of Tabuk, Tabuk, Saudi Arabia
| | - Ridwan Olamilekan Adesola
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
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12
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Zhang QE, Lindenberger J, Parsons RJ, Thakur B, Parks R, Park CS, Huang X, Sammour S, Janowska K, Spence TN, Edwards RJ, Martin M, Williams WB, Gobeil S, Montefiori DC, Korber B, Saunders KO, Haynes BF, Henderson R, Acharya P. SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition. Mol Cell 2024; 84:2747-2764.e7. [PMID: 39059371 PMCID: PMC11366207 DOI: 10.1016/j.molcel.2024.06.028] [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: 02/14/2024] [Revised: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
A recombinant lineage of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryoelectron microscopy (cryo-EM) structures of XBB.1.5, XBB.1.16, EG.5, and EG.5.1 spike (S) ectodomains to reveal reinforced 3-receptor binding domain (RBD)-down receptor-inaccessible closed states mediated by interprotomer RBD interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters, including stability, receptor binding, and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.
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Affiliation(s)
- Qianyi E Zhang
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA
| | | | - Ruth J Parsons
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA
| | - Bhishem Thakur
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Rob Parks
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Chan Soo Park
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Xiao Huang
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Salam Sammour
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Taylor N Spence
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Robert J Edwards
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA
| | - Mitchell Martin
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Wilton B Williams
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA
| | - Sophie Gobeil
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Université Laval, Institut de Biologie Intégrative et des Systèmes (IBIS), Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Centre de Recherche en Infectiologie de l'Université Laval, PROTEO, Le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Québec, QC, Canada
| | - David C Montefiori
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; The New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Kevin O Saunders
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Barton F Haynes
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA; Duke University, Department of Integrative Immunology, Durham, NC 27710, USA
| | - Rory Henderson
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Medicine, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke University, Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
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13
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Urra G, Valdés-Muñoz E, Suardiaz R, Hernández-Rodríguez EW, Palma JM, Ríos-Rozas SE, Flores-Morales CA, Alegría-Arcos M, Yáñez O, Morales-Quintana L, D’Afonseca V, Bustos D. From Proteome to Potential Drugs: Integration of Subtractive Proteomics and Ensemble Docking for Drug Repurposing against Pseudomonas aeruginosa RND Superfamily Proteins. Int J Mol Sci 2024; 25:8027. [PMID: 39125594 PMCID: PMC11312079 DOI: 10.3390/ijms25158027] [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: 05/27/2024] [Revised: 07/08/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) poses a significant threat as a nosocomial pathogen due to its robust resistance mechanisms and virulence factors. This study integrates subtractive proteomics and ensemble docking to identify and characterize essential proteins in P. aeruginosa, aiming to discover therapeutic targets and repurpose commercial existing drugs. Using subtractive proteomics, we refined the dataset to discard redundant proteins and minimize potential cross-interactions with human proteins and the microbiome proteins. We identified 12 key proteins, including a histidine kinase and members of the RND efflux pump family, known for their roles in antibiotic resistance, virulence, and antigenicity. Predictive modeling of the three-dimensional structures of these RND proteins and subsequent molecular ensemble-docking simulations led to the identification of MK-3207, R-428, and Suramin as promising inhibitor candidates. These compounds demonstrated high binding affinities and effective inhibition across multiple metrics. Further refinement using non-covalent interaction index methods provided deeper insights into the electronic effects in protein-ligand interactions, with Suramin exhibiting superior binding energies, suggesting its broad-spectrum inhibitory potential. Our findings confirm the critical role of RND efflux pumps in antibiotic resistance and suggest that MK-3207, R-428, and Suramin could be effectively repurposed to target these proteins. This approach highlights the potential of drug repurposing as a viable strategy to combat P. aeruginosa infections.
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Affiliation(s)
- Gabriela Urra
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile; (G.U.); (E.W.H.-R.); (S.E.R.-R.)
| | - Elizabeth Valdés-Muñoz
- Doctorado en Biotecnología Traslacional, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca 3480094, Chile;
| | - Reynier Suardiaz
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Erix W. Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile; (G.U.); (E.W.H.-R.); (S.E.R.-R.)
- Unidad de Bioinformática Clínica, Centro Oncológico, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile
| | - Jonathan M. Palma
- Facultad de Ingeniería, Universidad de Talca, Curicó 3344158, Chile;
| | - Sofía E. Ríos-Rozas
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile; (G.U.); (E.W.H.-R.); (S.E.R.-R.)
| | | | - Melissa Alegría-Arcos
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago 7500000, Chile; (M.A.-A.); (O.Y.)
| | - Osvaldo Yáñez
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago 7500000, Chile; (M.A.-A.); (O.Y.)
| | - Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Cinco Pte. N° 1670, Talca 3467987, Chile;
| | - Vívian D’Afonseca
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad Católica del Maule, Ave. San Miguel 3605, Talca 3466706, Chile
| | - Daniel Bustos
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480094, Chile; (G.U.); (E.W.H.-R.); (S.E.R.-R.)
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14
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Gupta SRR, Singh S, Rustagi V, Pahuja M, Mangangcha IR, Rinchui M, Jha SK, Singh A, Singh IK. Prognostic role of TEAD4 in TNBC: in-silico inhibition of the TEAD4-YAP interaction by flufenamic acid analogs. In Silico Pharmacol 2024; 12:64. [PMID: 39035099 PMCID: PMC11255177 DOI: 10.1007/s40203-024-00239-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
Triple-negative breast cancer (TNBC) poses a significant global health challenge due to its highly aggressive nature and invasive characteristics. Dysregulation of the Hippo pathway, a key regulator of various biological processes, is observed in TNBC, and its inhibition holds promise for impeding cancer growth. This in-silico analysis investigates the role of Transcriptional Enhanced Associate Domain 4 (TEAD4) in TNBC and its interaction with Yes Associated Protein (YAP) in cancer progression. Our results demonstrate that TEAD4 upregulation is linked to poor prognosis in TNBC, emphasizing its critical role in the disease. Moreover, we identify CID44521006, an analog of Flufenamic acid, as a potential therapeutic compound capable of disrupting the TEAD4-YAP interaction by binding to the YAP-binding domain of TEAD4. These findings underscore the significance of TEAD4 in TNBC and propose CID44521006 as a promising candidate for therapeutic intervention. The study contributes valuable insights to advance treatment options for TNBC, offering a potential avenue for the development of targeted therapies against this aggressive form of breast cancer. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00239-8.
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Affiliation(s)
- Shradheya R. R. Gupta
- Molecular Biology Research Laboratory, Department of Zoology, & DBC I4 Centre, Deshbandhu College, University of Delhi, New Delhi, 110019 India
| | - Shivani Singh
- Molecular Biology Research Laboratory, Department of Zoology, & DBC I4 Centre, Deshbandhu College, University of Delhi, New Delhi, 110019 India
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, 201310 India
| | - Vanshika Rustagi
- Molecular Biology Research Laboratory, Department of Zoology, & DBC I4 Centre, Deshbandhu College, University of Delhi, New Delhi, 110019 India
| | - Monika Pahuja
- Extramural Wing, Indian Council of Medical Research, New Delhi, 110029 India
| | - Irengbam Rocky Mangangcha
- Molecular Biology Research Laboratory, Department of Zoology, & DBC I4 Centre, Deshbandhu College, University of Delhi, New Delhi, 110019 India
| | - Moses Rinchui
- Molecular Biology Research Laboratory, Department of Zoology, & DBC I4 Centre, Deshbandhu College, University of Delhi, New Delhi, 110019 India
| | - Saurabh K. Jha
- Department of Zoology, Kalindi College, University of Delhi, New Delhi, 110008 India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021 India
| | - Indrakant K. Singh
- Molecular Biology Research Laboratory, Department of Zoology, & DBC I4 Centre, Deshbandhu College, University of Delhi, New Delhi, 110019 India
- Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi, 110007 India
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15
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Afzal M, Mehmood R, Mughal EU, Naeem N, Ashraf Z, Nazir Y, Shalaby FM, El-Sayed Abd El Hady A, Sadiq A. Elucidating bis-pyrimidines as new and efficient mushroom tyrosinase inhibitors: synthesis, SAR, kinetics and computational studies. RSC Adv 2024; 14:22769-22780. [PMID: 39035128 PMCID: PMC11258615 DOI: 10.1039/d4ra04652h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024] Open
Abstract
In this study, a series of novel bis-pyrimidine derivatives (1P-8P) were designed, synthesized, characterized, and investigated for their in vitro inhibitory activity against mushroom tyrosinase, an enzyme critical in melanin biosynthesis and implicated in various hyperpigmentation disorders. To the best of our knowledge, the bispyrimidine scaffold has been evaluated for the first time for its tyrosinase inhibitory activity. Their inhibitory activities were assessed, revealing inhibition with IC50 values in the micromolar range. Additionally, this series of compounds were found to inhibit tyrosinase activity in a mixed-type manner, with IC50 values ranging from 12.36 ± 1.24 to 86.67 ± 3.08 μM. To further elucidate the binding interactions, molecular docking simulations were performed, identifying key residues in the active site responsible for binding affinity. Furthermore, molecular dynamics (MD) simulations were conducted to assess the dynamic behavior, stability, and binding affinity of the most potent inhibitor, compound 6P. Quantitative Structure-Activity Relationship (QSAR) models were developed to correlate the structural features of the bis-pyrimidines with their inhibitory activity, providing insights into the structure-activity relationships (SAR) that govern their potency. The experimental and theoretical findings demonstrated excellent agreement. These findings pave the way for the development of novel bis-pyrimidine-based therapeutic agents for treating hyperpigmentation and related conditions.
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Affiliation(s)
- Manazza Afzal
- Department of Chemistry, Govt College Women University Sialkot-51300 Pakistan
| | - Rabia Mehmood
- Department of Chemistry, Govt College Women University Sialkot-51300 Pakistan
| | | | - Nafeesa Naeem
- Department of Chemistry, University of Gujrat Gujrat-50700 Pakistan
| | - Zaman Ashraf
- Department of Chemistry, Rawalpindi Women University Rawalpindi-46300 Pakistan
| | - Yasir Nazir
- Department of Chemistry, University of Sialkot Sialkot-51300 Pakistan
| | - Fatma Mohsen Shalaby
- King Khalid University, Faculty of Sciences, Biology Department Abha Kingdom of Saudi Arabia
| | - Amal El-Sayed Abd El Hady
- Department of Biology, Faculty of Science, Majmaah University Al Majma'ah 15341 Kingdom of Saudi Arabia
| | - Amina Sadiq
- Department of Chemistry, Govt College Women University Sialkot-51300 Pakistan
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16
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Han X, Guo K. Pharmacophore-based virtual screening of commercial databases against β-secretase 1 for drug development against Alzheimer's disease. Front Chem 2024; 12:1412349. [PMID: 39045333 PMCID: PMC11263123 DOI: 10.3389/fchem.2024.1412349] [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: 04/04/2024] [Accepted: 06/11/2024] [Indexed: 07/25/2024] Open
Abstract
β-secretase 1, one of the most important proteins, is an aspartate protease. This membrane-associated protein is used for treating Alzheimer's disease (AD). Several inhibitors have been pursued against β-secretase 1, but they still have not resulted effectively. Virtual screening based on pharmacophores has been shown to be useful for lead optimization and hit identification in the preliminary phase of developing a new drug. Here, we screen the commercially available databases to find the hits against β-secretase 1 for drug discovery against AD. Virtual screening for 200,000 compounds was done using the database from the Vitas-M Laboratory. The phase screen score was utilized to assess the screened hits. Molecular docking was performed on compounds with phase scores >1.9. According to the study, the 66H ligand of the crystal structure has the maximum performance against β-secretase 1. The redocking of the co-crystal ligand showed that the docked ligand was seamlessly united with the crystal structure. The reference complex had three hydrogen bonds with Asp93, Asp289, and Gly291; one van der Waals interaction with Gly74; and three hydrophobic interactions. After equilibration, the RMSD of the reference compound sustained a value of ∼1.5 Å until 30 ns and then boosted to 2.5 Å. On comparison, the RMSD of the S1 complex steadily increased to ∼2.5 Å at 15 ns, displayed slight aberrations at approximately ∼2.5-3 Å until 80 ns, and then achieved steadiness toward the end of the simulation. The arrangements of proteins stayed condensed during the mockup when bonded to these complexes as stable Rg values showed. Furthermore, the MM/GBSA technique was employed to analyze both compounds' total binding free energies (ΔGtotal). Our research study provides a new understanding of using 66H as anti-β-secretase 1 for drug development against AD.
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Affiliation(s)
- Xu Han
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Kaibo Guo
- Department of Oncology, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, China
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17
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Gedgaudas M, Kaziukonytė P, Kairys V, Mickevičiūtė A, Zubrienė A, Brukštus A, Matulis D, Kazlauskas E. Comprehensive analysis of resorcinyl-imidazole Hsp90 inhibitor design. Eur J Med Chem 2024; 273:116505. [PMID: 38788300 DOI: 10.1016/j.ejmech.2024.116505] [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: 03/05/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Human Hsp90 chaperones are implicated in various aspects of cancer. Due to this, Hsp90 has been explored as potential target in cancer treatment. Initial attempts to use Hsp90 inhibitors in drug trials failed due to toxicity and inefficacy. The next generation of drugs were less toxic but still insufficiently effective in a clinical setting. Recently, a lot of effort is being put into understanding the consequences of Hsp90 isoform selective inhibition, expecting that this might hold the key in targeting Hsp90 for disease treatment. Here we investigate a series of compounds containing the aryl-resorcinol scaffold with a 5-membered ring as a promising class of new human Hsp90 inhibitors, reaching nanomolar affinity. We compare how the replacement of 5-membered ring, from thiadiazole to imidazole, as well as a variety of their substituents, influences the potency of these inhibitors for Hsp90 alpha and beta isoforms. To further elucidate the dissimilarity in ligand selectivity between the isoforms, a mutant protein was constructed and tested against the ligand library. In addition, we performed a series of molecular dynamics (MD) and docking simulations to further explain our experimental findings as well as evaluated key compounds in cell assays. Our results deepen the understanding of Hsp90 isoform ligand selectivity and serve as an informative base for further Hsp90 inhibitor optimization.
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Affiliation(s)
- Marius Gedgaudas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Paulina Kaziukonytė
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225, Vilnius, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Algirdas Brukštus
- Department of Organic Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania.
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18
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Irwin NAT, Richards TA. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes. Nat Microbiol 2024; 9:1713-1724. [PMID: 38806669 PMCID: PMC11222145 DOI: 10.1038/s41564-024-01707-9] [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: 07/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and quadruplets, the latter comprising the four core histones arranged in series. Viral histone repeats branch phylogenetically between Archaea and eukaryotes and display intermediate functions in Escherichia coli, self-assembling into eukaryotic-like nucleosomes that stack into archaeal-like oligomers capable of impacting genomic activity and condensing DNA. Histone linkage also facilitates nucleosome formation, promoting eukaryotic histone assembly in E. coli. These data support the hypothesis that viral histone repeats originated in stem-eukaryotes and that nucleosome evolution proceeded through histone repeat intermediates.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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19
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Huang YJ, Montelione GT. Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600902. [PMID: 38979209 PMCID: PMC11230435 DOI: 10.1101/2024.06.26.600902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Recent advances in molecular modeling using deep learning can revolutionize our understanding of dynamic protein structures. NMR is particularly well-suited for determining dynamic features of biomolecular structures. The conventional process for determining biomolecular structures from experimental NMR data involves its representation as conformation-dependent restraints, followed by generation of structural models guided by these spatial restraints. Here we describe an alternative approach: generating a distribution of realistic protein conformational models using artificial intelligence-(AI-) based methods and then selecting the sets of conformers that best explain the experimental data. We applied this conformational selection approach to redetermine the solution NMR structure of the enzyme Gaussia luciferase. First, we generated a diverse set of conformer models using AlphaFold2 (AF2) with an enhanced sampling protocol. The models that best-fit NOESY and chemical shift data were then selected with a Bayesian scoring metric. The resulting models include features of both the published NMR structure and the standard AF2 model generated without enhanced sampling. This "AlphaFold-NMR" protocol also generated an alternative "open" conformational state that fits nearly as well to the overall NMR data but accounts for some NOESY data that is not consistent with first "closed" conformational state; while other NOESY data consistent with this second state are not consistent with the first conformational state. The structure of this "open" structural state differs from that of the "closed" state primarily by the position of a thumb-shaped loop between α-helices H5 and H6, revealing a cryptic surface pocket. These alternative conformational states of Gluc are supported by "double recall" analysis of NOESY data and AF2 models. Additional structural states are also indicated by backbone chemical shift data indicating partially-disordered conformations for the C-terminal segment. Considered as a multistate ensemble, these multiple states of Gluc together fit the NOESY and chemical shift data better than the "restraint-based" NMR structure and provide novel insights into its structure-dynamic-function relationships. This study demonstrates the potential of AI-based modeling with enhanced sampling to generate conformational ensembles followed by conformer selection with experimental data as an alternative to conventional restraint satisfaction protocols for protein NMR structure determination.
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Affiliation(s)
- Yuanpeng J. Huang
- Dept of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
| | - Gaetano T. Montelione
- Dept of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
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20
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Revanasiddappa PD, Gowtham HG, G. S. C, Gangadhar S, A. S, Murali M, Shivamallu C, Achar RR, Silina E, Stupin V, Manturova N, Shati AA, Alfaifi MY, Elbehairi SEI, Kollur SP, Amruthesh KN. Exploration of Type III effector Xanthomonas outer protein Q (XopQ) inhibitor from Picrasma quassioides as an antibacterial agent using chemoinformatics analysis. PLoS One 2024; 19:e0302105. [PMID: 38889115 PMCID: PMC11185476 DOI: 10.1371/journal.pone.0302105] [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: 11/16/2023] [Accepted: 03/27/2024] [Indexed: 06/20/2024] Open
Abstract
The present study was focused on exploring the efficient inhibitors of closed state (form) of type III effector Xanthomonas outer protein Q (XopQ) (PDB: 4P5F) from the 44 phytochemicals of Picrasma quassioides using cutting-edge computational analysis. Among them, Kumudine B showed excellent binding energy (-11.0 kcal/mol), followed by Picrasamide A, Quassidine I and Quassidine J with the targeted closed state of XopQ protein compared to the reference standard drug (Streptomycin). The molecular dynamics (MD) simulations performed at 300 ns validated the stability of top lead ligands (Kumudine B, Picrasamide A, and Quassidine I)-bound XopQ protein complex with slightly lower fluctuation than Streptomycin. The MM-PBSA calculation confirmed the strong interactions of top lead ligands (Kumudine B and QuassidineI) with XopQ protein, as they offered the least binding energy. The results of absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis confirmed that Quassidine I, Kumudine B and Picrasamide A were found to qualify most of the drug-likeness rules with excellent bioavailability scores compared to Streptomycin. Results of the computational studies suggested that Kumudine B, Picrasamide A, and Quassidine I could be considered potential compounds to design novel antibacterial drugs against X. oryzae infection. Further in vitro and in vivo antibacterial activities of Kumudine B, Picrasamide A, and Quassidine I are required to confirm their therapeutic potentiality in controlling the X. oryzae infection.
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Affiliation(s)
| | - H. G. Gowtham
- Department of Studies and Research in Food Science and Nutrition, KSOU, Mysuru, Karnataka, India
| | - Chikkanna G. S.
- Department of Home Science, ICAR Krishi Vigyan Kendra, Kolar, India
| | - Suchithra Gangadhar
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Satish A.
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - M. Murali
- Department of Studies in Botany, University of Mysore, Mysuru, Karnataka, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Human Pathology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Natalia Manturova
- Department of Hospital Surgery, NI. Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Tissue Culture and Cancer Biology Research Laborotory, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Tissue Culture and Cancer Biology Research Laborotory, King Khalid University, Abha, Saudi Arabia
| | - Serag Eldin I. Elbehairi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Tissue Culture and Cancer Biology Research Laborotory, King Khalid University, Abha, Saudi Arabia
| | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru, Karnataka, India
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21
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Evoli S, Kariyawasam NL, Nitiss KC, Nitiss JL, Wereszczynski J. Modeling allosteric mechanisms of eukaryotic type II topoisomerases. Biophys J 2024; 123:1620-1634. [PMID: 38720465 PMCID: PMC11213992 DOI: 10.1016/j.bpj.2024.05.004] [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: 08/10/2023] [Revised: 03/24/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Type II topoisomerases (TopoIIs) are ubiquitous enzymes that are involved in crucial nuclear processes such as genome organization, chromosome segregation, and other DNA metabolic processes. These enzymes function as large, homodimeric complexes that undergo a complex cycle of binding and hydrolysis of two ATP molecules in their ATPase domains, which regulates the capture and passage of one DNA double-helix through a second, cleaved DNA molecule. This process requires the transmission of information about the state of the bound nucleotide over vast ranges in the TopoII complex. How this information is transmitted at the molecular level to regulate TopoII functions and how protein substitutions disrupt these mechanisms remains largely unknown. Here, we employed extensive microsecond-scale molecular dynamics simulations of the yeast TopoII enzyme in multiple nucleotide-bound states and with amino acid substitutions near both the N and C termini of the complex. Simulation results indicate that the ATPase domains are remarkably flexible on the sub-microsecond timescale and that these dynamics are modulated by the identity of the bound nucleotides and both local and distant amino acid substitutions. Network analyses point toward specific allosteric networks that transmit information about the hydrolysis cycle throughout the complex, which include residues in both the protein and the bound DNA molecule. Amino acid substitutions weaken many of these pathways. Together, our results provide molecular level details on how the TopoII catalytic cycle is controlled through nucleotide binding and hydrolysis and how mutations may disrupt this process.
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Affiliation(s)
- Stefania Evoli
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois; Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Nilusha L Kariyawasam
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois; Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Karin C Nitiss
- Pharmaceutical Sciences Department, University of Illinois at Chicago, Rockford, Illinois
| | - John L Nitiss
- Pharmaceutical Sciences Department, University of Illinois at Chicago, Rockford, Illinois
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois; Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois; Department of Biology, Illinois Institute of Technology, Chicago, Illinois.
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22
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Subhadarshini S, Tandon H, Srinivasan N, Sowdhamini R. Normal Mode Analysis Elicits Conformational Shifts in Proteins at Both Proximal and Distal Regions to the Phosphosite Stemming from Single-Site Phosphorylation. ACS OMEGA 2024; 9:24520-24537. [PMID: 38882086 PMCID: PMC11170700 DOI: 10.1021/acsomega.4c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/29/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024]
Abstract
Phosphorylation, a fundamental biochemical switch, intricately regulates protein function and signaling pathways. Our study employs extensive computational structural analyses on a curated data set of phosphorylated and unphosphorylated protein pairs to explore the multifaceted impact of phosphorylation on protein conformation. Using normal mode analysis (NMA), we investigated changes in protein flexibility post-phosphorylation, highlighting an enhanced level of structural dynamism. Our findings reveal that phosphorylation induces not only local changes at the phosphorylation site but also extensive alterations in distant regions, showcasing its far-reaching influence on protein structure-dynamics. Through in-depth case studies on polyubiquitin B and glycogen synthase kinase-3 beta, we elucidate how phosphorylation at distinct sites leads to variable structural and dynamic modifications, potentially dictating functional outcomes. While phosphorylation largely preserves the residue motion correlation, it significantly disrupts low-frequency global modes, presenting a dualistic impact on protein dynamics. We also explored alterations in the total accessible surface area (ASA), emphasizing region-specific changes around phosphorylation sites. This study sheds light on phosphorylation-induced conformational changes, dynamic modulation, and surface accessibility alterations, leveraging an integrated computational approach with RMSD, NMA, and ASA, thereby contributing to a comprehensive understanding of cellular regulation and suggesting promising avenues for therapeutic interventions.
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Affiliation(s)
| | - Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
- Computational Approaches to Protein Science, National Centre for Biological Sciences, Bangalore 560065, India
- Computational Biology, Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
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23
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Jakobson L, Mõttus J, Suurväli J, Sõmera M, Tarassova J, Nigul L, Smolander OP, Sarmiento C. Phylogenetic insight into ABCE gene subfamily in plants. Front Genet 2024; 15:1408665. [PMID: 38911295 PMCID: PMC11190730 DOI: 10.3389/fgene.2024.1408665] [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: 03/28/2024] [Accepted: 05/09/2024] [Indexed: 06/25/2024] Open
Abstract
ATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and most animals possess a single ABCE gene encoding the critical translational factor ABCE1. In several plant species, including Arabidopsis thaliana and Oryza sativa, two or more ABCE gene copies have been identified, however information related to plant ABCE gene family is still missing. In this study we retrieved ABCE gene sequences of 76 plant species from public genome databases and comprehensively analyzed them with the reference to A. thaliana ABCE2 gene (AtABCE2). Using bioinformatic approach we assessed the conservation and phylogeny of plant ABCEs. In addition, we performed haplotype analysis of AtABCE2 and its paralogue AtABCE1 using genomic sequences of 1,135 A. thaliana ecotypes. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. We found that over half of the selected species have two to eight ABCE genes, suggesting that in plants ABCE genes can be classified as a low-copy gene family, rather than a single-copy gene family. The phylogenetic trees of ABCE protein sequences and the corresponding coding sequences demonstrated that Brassicaceae and Poaceae families have independently undergone lineage-specific split of the ancestral ABCE gene. Other plant species have gained ABCE gene copies through more recent duplication events. We also noticed that ploidy level but not ancient whole genome duplications experienced by a species impacts ABCE gene family size. Deeper analysis of AtABCE2 and AtABCE1 from 1,135 A. thaliana ecotypes revealed four and 35 non-synonymous SNPs, respectively. The lower natural variation in AtABCE2 compared to AtABCE1 is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor.
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Affiliation(s)
- Liina Jakobson
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jelena Mõttus
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jaanus Suurväli
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jemilia Tarassova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Lenne Nigul
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
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24
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Granato DC, Carnielli CM, Trino LD, Busso-Lopes AF, Câmara GA, Normando AGC, Filho HVR, Domingues R, Yokoo S, Pauletti BA, Patroni FM, Santos-Silva AR, Lopes MA, Brandão TB, Prado-Ribeiro AC, Lopes-de Oliveira PS, Telles GP, Paes Leme AF. Mapping Conformational Changes in the Saliva Proteome Potentially Associated with Oral Cancer Aggressiveness. J Proteome Res 2024; 23:2148-2159. [PMID: 38785273 PMCID: PMC11166140 DOI: 10.1021/acs.jproteome.4c00093] [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: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
Diverse proteomics-based strategies have been applied to saliva to quantitatively identify diagnostic and prognostic targets for oral cancer. Considering that these targets may be regulated by events that do not imply variation in protein abundance levels, we hypothesized that changes in protein conformation can be associated with diagnosis and prognosis, revealing biological processes and novel targets of clinical relevance. For this, we employed limited proteolysis-mass spectrometry in saliva samples to explore structural alterations, comparing the proteome of healthy control and oral squamous cell carcinoma (OSCC) patients with and without lymph node metastasis. Thirty-six proteins with potential structural rearrangements were associated with clinical patient features including transketolase and its interacting partners. Moreover, N-glycosylated peptides contribute to structural rearrangements of potential diagnostic and prognostic markers. Altogether, this approach utilizes saliva proteins to search for targets for diagnosing and prognosing oral cancer and can guide the discovery of potential regulated sites beyond protein-level abundance.
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Affiliation(s)
- Daniela C. Granato
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Carolina M. Carnielli
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Luciana D. Trino
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Ariane F. Busso-Lopes
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Guilherme A. Câmara
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Ana Gabriela C. Normando
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Helder V. R. Filho
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Romênia
R. Domingues
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Sami Yokoo
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Bianca A. Pauletti
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Fabio M. Patroni
- Centro
de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-875, Brazil
| | - Alan R. Santos-Silva
- Departamento
de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP 13414-903, Brazil
| | - Márcio A. Lopes
- Departamento
de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP 13414-903, Brazil
| | - Thaís Bianca Brandão
- Instituto
do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo 01246-000, Brazil
| | | | - Paulo. S. Lopes-de Oliveira
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
| | - Guilherme P. Telles
- Instituto
de Computação, Universidade
Estadual de Campinas (UNICAMP), Campinas, São Paulo 13083-852, Brazil
| | - Adriana F. Paes Leme
- Laboratório
Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo 13083-970, Brazil
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25
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Ullah S, Rahman W, Ullah F, Ullah A, Jehan R, Iqbal MN, Ali I, Tianshun G. Identification of lead compound screened from the natural products atlas to treat renal inflammasomes using molecular docking and dynamics simulation. J Biomol Struct Dyn 2024; 42:4851-4861. [PMID: 37705295 DOI: 10.1080/07391102.2023.2254397] [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: 06/04/2023] [Indexed: 09/15/2023]
Abstract
One of the most prevalent ailments is kidney disease. Effective therapies for chronic renal disease are hard to come by. As a result, there is significant clinical and social interest to predict and develop novel compounds to treat renal disorders. So, specific natural products have been employed in this study because they have protective effects against kidney diseases. When taken orally, natural products can help protect against or lessen the severity of the kidney damage caused by high fructose intake, a high-fat diet, and both Type I and Type 2 diabetes. Reduced podocyte injury, a contributor to albuminuria in diabetic nephropathy, reduces renal endothelial barrier function disruption due to hyperglycemia, as well as urinary microalbumin excretion and glomerular hyperfiltration. Multiple natural products have been shown to protect the kidneys from nephrotoxic chemicals such as LPS, gentamycin, alcohol, nicotine, lead, and cadmium, all of which can persuade acute kidney injury (AKI) or chronic kidney disease (CKD). Natural compounds inhibit regulatory enzymes for controlling inflammation-related diseases. For this, use computational methods such as drug design to identify novel flavonoid compounds against kidney diseases. Drug design via computational methods gaining admiration as a swift and effective technique to identify lead compounds in a shorter time at a low cost. In this in-silico study, we screened The Natural Product Atlas based on a structure-based pharmacophore query. Top hits were analyzed for ADMET analysis followed by molecular docking and docking validation. Finally, the lead compound was simulated for a period of 200 ns and trajectories were studied for stability. We found that NPA024823 showed promising binding and stability with the AIM2. This research work aims to predict novel anti-inflammatory compounds against kidney diseases to inhibit kidney inflammasome by targeting the AIM2 protein. So, in initial preclinical research, there will be lower failure rates that demonstrate safety profiles against predicted compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Anees Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Muhammad Nasir Iqbal
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology, and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Gao Tianshun
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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26
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Haque S, Ahmad F, Mathkor DM, Makhdoom H, Johargy AK, Faidah H, Babalghith AO, Jalal NA, Alhindi Z, Bantun F. Binding selectivity analysis of new delhi metallo-beta-lactamase-1 inhibitors using molecular dynamics simulations: Exploring possibilities for decoding antimicrobial drug resistance. J Infect Public Health 2024; 17:1108-1116. [PMID: 38714123 DOI: 10.1016/j.jiph.2024.04.018] [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: 02/14/2024] [Revised: 03/25/2024] [Accepted: 04/21/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND New Delhi metallo-beta-lactamase-1 (NDM1) confers resistance to several bacterial species against a broad range of beta-lactam antibiotics and turning them into superbugs that pose a significant threat to healthcare systems worldwide. As such, it is a potentially relevant biological target for counteracting bacterial infections. Given the lack of effective treatment options against NDM1 producing bacteria, finding a reliable inhibitor for the NDM1 enzyme is crucial. METHODS Using molecular dynamics simulations, the binding selectivities and affinities of three ligands, viz. PNK, 3S0, and N1G were investigated against NDM1. RESULTS The results indicate that N1G binds with more affinity to NDM1 than PNK and 3S0. The binding energy decomposition analysis revealed that residues I35, W93, H189, K211, and N220 showed significant binding energies with PNK, 3S0, and N1G, and hence are crucially involved in the binding of the ligands to NDM1. Molecular dynamics trajectory analysis further elicited that the ligands influence dynamic flexibility of NDM1 morphology, which contributes to the partial selectivities of PNK, 3S0, and N1G. CONCLUSIONS This in silico study offers a vital information for developing potential NDM1 inhibitors with high selectivity. Nevertheless, in vitro and in vivo experimental validation is mandated to extend the possible applications of these ligands as NDM1 inhibitors that succor in combating antimicrobial resistance.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.
| | - Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India.
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan 45142, Saudi Arabia.
| | - Hatim Makhdoom
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia.
| | - Ayman K Johargy
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hani Faidah
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Ahmad O Babalghith
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Naif A Jalal
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Zain Alhindi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Farkad Bantun
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
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Filipek J, Chalaskiewicz K, Kosmider A, Nielipinski M, Michalak A, Bednarkiewicz M, Goslawski-Zeligowski M, Prucnal F, Sekula B, Pietrzyk-Brzezinska AJ. Comprehensive structural overview of the C-terminal ligand-binding domains of the TetR family regulators. J Struct Biol 2024; 216:108071. [PMID: 38401830 DOI: 10.1016/j.jsb.2024.108071] [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: 01/05/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
TetR family regulators (TFRs) represent a large group of one-component bacterial signal transduction systems which recognize environmental signals, like the presence of antibiotics or other bactericidal compounds, and trigger the cell response by regulating the expression of genes that secure bacterial survival in harsh environmental conditions. TFRs act as homodimers, each protomer is composed of a conserved DNA-binding N-terminal domain (NTD) and a variable ligand-binding C-terminal domain (CTD). Currently, there are about 500 structures of TFRs available in the Protein Data Bank and one-fourth of them represent the structures of TFR-ligand complexes. In this review, we summarized information on the ligands interacting with TFRs and based on structural data, we compared the CTDs of the TFR family members, as well as their ligand-binding cavities. Additionally, we divided the whole TFR family, including more than half of a million sequences, into subfamilies according to calculated multiple sequence alignment and phylogenetic tree. We also highlighted structural elements characteristic of some of the subfamilies. The presented comprehensive overview of the TFR CTDs provides good bases and future directions for further studies on TFRs that are not only important targets for battling multidrug resistance but also good candidates for many biotechnological approaches, like TFR-based biosensors.
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Affiliation(s)
- Jakub Filipek
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Katarzyna Chalaskiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Aleksandra Kosmider
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maciej Nielipinski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka Michalak
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maria Bednarkiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Mieszko Goslawski-Zeligowski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Filip Prucnal
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Bartosz Sekula
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland.
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28
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Mo C, Wang H, Wei M, Zeng Q, Zhang X, Fei Z, Zhang Y, Kong Q. Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2249-2268. [PMID: 38430487 DOI: 10.1111/tpj.16705] [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: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Melon (Cucumis melo L.), being under intensive domestication and selective breeding, displays an abundant phenotypic diversity. Wild germplasm with tolerance to stress represents an untapped genetic resource for discovery of disease-resistance genes. To comprehensively characterize resistance genes in melon, we generate a telomere-to-telomere (T2T) and gap-free genome of wild melon accession PI511890 (C. melo var. chito) with a total length of 375.0 Mb and a contig N50 of 31.24 Mb. The complete genome allows us to dissect genome architecture and identify resistance gene analogs. We construct a pan-NLRome using seven melon genomes, which include 208 variable and 18 core nucleotide-binding leucine-rich repeat receptors (NLRs). Multiple disease-related transcriptome analyses indicate that most up-regulated NLRs induced by pathogens are shell or cloud NLRs. The T2T gap-free assembly and the pan-NLRome not only serve as essential resources for genomic studies and molecular breeding of melon but also provide insights into the genome architecture and NLR diversity.
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Affiliation(s)
- Changjuan Mo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghua Wei
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingguo Zeng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuejun Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | | | - Yongbing Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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29
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Kuga T, Sunagawa N, Igarashi K. Effect of Free Cysteine Residues to Serine Mutation on Cellodextrin Phosphorylase. J Appl Glycosci (1999) 2024; 71:37-46. [PMID: 38863949 PMCID: PMC11163329 DOI: 10.5458/jag.jag.jag-2023_0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 06/13/2024] Open
Abstract
Cellodextrin phosphorylase (CDP) plays a key role in energy-efficient cellulose metabolism of anaerobic bacteria by catalyzing phosphorolysis of cellodextrin to produce cellobiose and glucose 1-phosphate, which can be utilized for glycolysis without consumption of additional ATP. As the enzymatic phosphorolysis reaction is reversible, CDP is also employed to produce cellulosic materials in vitro. However, the enzyme is rapidly inactivated by oxidation, which hinders in vitro utilization in aerobic environments. It has been suggested that the cysteine residues of CDP, which do not form disulfide bonds, are responsible for the loss of activity, and the aim of the present work was to test this idea. For this purpose, we replaced all 11 free cysteine residues of CDP from Acetivibrio thermocellus (formerly known as Clostridium thermocellum) with serine, which structurally resembles cysteine in our previous work. Herein, we show that the resulting CDP variant, named CDP-CS, has comparable activity to the wild-type enzyme, but shows increased stability to oxidation during long-term storage. X-Ray crystallography indicated that the mutations did not markedly alter the overall structure of the enzyme. Ensemble refinement of the crystal structures of CDP and CDP-CS indicated that the C372S and C625S mutations reduce structural fluctuations in the protein main chain, which may contribute to the increased stability of CDP-CS to oxidation.
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Affiliation(s)
- Tomohiro Kuga
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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30
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Yee SW, Macdonald CB, Mitrovic D, Zhou X, Koleske ML, Yang J, Buitrago Silva D, Rockefeller Grimes P, Trinidad DD, More SS, Kachuri L, Witte JS, Delemotte L, Giacomini KM, Coyote-Maestas W. The full spectrum of SLC22 OCT1 mutations illuminates the bridge between drug transporter biophysics and pharmacogenomics. Mol Cell 2024; 84:1932-1947.e10. [PMID: 38703769 DOI: 10.1016/j.molcel.2024.04.008] [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: 07/11/2023] [Revised: 01/04/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024]
Abstract
Mutations in transporters can impact an individual's response to drugs and cause many diseases. Few variants in transporters have been evaluated for their functional impact. Here, we combine saturation mutagenesis and multi-phenotypic screening to dissect the impact of 11,213 missense single-amino-acid deletions, and synonymous variants across the 554 residues of OCT1, a key liver xenobiotic transporter. By quantifying in parallel expression and substrate uptake, we find that most variants exert their primary effect on protein abundance, a phenotype not commonly measured alongside function. Using our mutagenesis results combined with structure prediction and molecular dynamic simulations, we develop accurate structure-function models of the entire transport cycle, providing biophysical characterization of all known and possible human OCT1 polymorphisms. This work provides a complete functional map of OCT1 variants along with a framework for integrating functional genomics, biophysical modeling, and human genetics to predict variant effects on disease and drug efficacy.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christian B Macdonald
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Darko Mitrovic
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick Rockefeller Grimes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donovan D Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Swati S More
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden.
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA.
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31
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Guo HB, Huntington B, Perminov A, Smith K, Hastings N, Dennis P, Kelley-Loughnane N, Berry R. AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein. PLoS One 2024; 19:e0301866. [PMID: 38739602 PMCID: PMC11090348 DOI: 10.1371/journal.pone.0301866] [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: 12/05/2023] [Accepted: 03/23/2024] [Indexed: 05/16/2024] Open
Abstract
We use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP), Nvjp-1, assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures of Nvjp-1 when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other. We use a residue-residue interaction network (RIN) derived from the contact map which show that the residue-residue interactions in Nvjp-1 are mainly transient; however, those in a well-folded protein are mainly persistent. Despite the variation in 3D shapes, we show that the AF2 models of both disordered and ordered proteins exhibit highly consistent profiles of the pLDDT (predicted local distance difference test) scores. These results indicate a potential protocol to justify the IDPs based on multiple AF2 models and MD simulations.
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Affiliation(s)
- Hao-Bo Guo
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- UES Inc., Dayton, OH, United States of America
| | - Baxter Huntington
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- Miami University, Oxford, OH, United States of America
| | - Alexander Perminov
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
- Miami University, Oxford, OH, United States of America
| | - Kenya Smith
- United States Air Force Academy, Colorado Springs, CO, United States of America
| | - Nicholas Hastings
- United States Air Force Academy, Colorado Springs, CO, United States of America
| | - Patrick Dennis
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
| | - Nancy Kelley-Loughnane
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
| | - Rajiv Berry
- Material and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Mason, OH, United States of America
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32
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Moussa AY, Alanzi A, Luo J, Chung SK, Xu B. Potential anti-obesity effect of saponin metabolites from adzuki beans: A computational approach. Food Sci Nutr 2024; 12:3612-3627. [PMID: 38726452 PMCID: PMC11077217 DOI: 10.1002/fsn3.4032] [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: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 05/12/2024] Open
Abstract
In contrast to its widespread traditional and popular culinary use to reduce weight, Vigna angularis (adzuki beans) was not subjected to sufficient scientific scrutiny. Particularly, its saponins whose role was never investigated before to unveil the beans' antidiabetic and anti-obesity effects. Four vital pancreatic and intestinal carbohydrate enzymes were selected to assess the potency of the triterpenoidal saponins of V. angularis to bind and activate these proteins through high-precision molecular modeling and dynamics mechanisms with accurate molecular mechanics Generalized Born Surface Area (MMGBSA) energy calculations; thus, recognizing their anti-obesity potential. Our results showed that adzukisaponin VI and adzukisaponin IV were the best compounds in the α-amylase and α-glucosidase enzymatic grooves, respectively. Adzukisaponin VI and angulasaponin C were the best fitting in the N-termini of sucrase-isomaltose (SI) enzyme, and angulasaponin C was the best scoring compound in maltase-glucoamylase C-termini. All of them outperformed the standard drug acarbose. These compounds in their protein complexes were selected to undergo molecular simulations of the drug-bound protein compared to the apo-protein through 100 ns, which confirmed the consistency of binding to the key amino acid residues in the four enzyme pockets with the least propensity of unfolding. Detailed analysis is given of the different polar and hydrophobic binding interactions of docked compounds. While maltase-adzukisaponin VI complex scored the lowest MMGBSA free energy of -67.77 Kcal/mol, α-amylase complex with angulasaponin B revealed the free binding energy of -74.18 Kcal/mol with a dominance of van der Waals energy (ΔEVDW) and the least change from the start to the end of the simulation time. This study will direct researchers to the significance of isolating the pure adzuki saponin components to conduct future in vitro and in vivo experimental works and even clinical trials.
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Affiliation(s)
- Ashaimaa Y. Moussa
- Department of Pharmacognosy, Faculty of PharmacyAin Shams UniversityCairoEgypt
| | - Abdullah Alanzi
- Department of Pharmacognosy, College of PharmacyKing Saud UniversityRiyadhSaudi Arabia
| | - Jinhai Luo
- Department of Life Sciences, Food Science and Technology ProgramBNU‐HKBU United International CollegeZhuhaiGuangdongChina
| | - Sookja Kim Chung
- Medical FacultyMacau University of Science and TechnologyMacauChina
| | - Baojun Xu
- Department of Life Sciences, Food Science and Technology ProgramBNU‐HKBU United International CollegeZhuhaiGuangdongChina
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33
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Thaker K, Patoliya J, Rabadiya K, Patel D, Ponnuchamy M, Rama Reddy NR, Joshi R. An in-silico approach to unravel the structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS): a critical enzyme for sennoside biosynthesis in Cassia angustifolia Vahl. J Biomol Struct Dyn 2024; 42:3848-3861. [PMID: 37243697 DOI: 10.1080/07391102.2023.2216300] [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: 12/30/2022] [Accepted: 05/13/2023] [Indexed: 05/29/2023]
Abstract
The laxative properties of senna are attributed to the presence of sennosides produced in the plant. The low production level of sennosides in the plant is an important impediment to their growing demand and utilization. Understanding biosynthetic pathways helps to engineer them in terms of enhanced production. The biosynthetic pathways of sennoside production in plants are not completely known yet. However, attempts to get information on genes and proteins engaged in it have been made which decode involvement of various pathways including shikimate pathway. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme involved in sennosides production through the shikimate pathway. Unfortunately, there is no information available on proteomic characterization of DAHPS enzyme of senna (caDAHPS) resulting in lack of knowledge about its role. We for the first time characterized DAHPS enzyme of senna using in-silico analysis. To the best of our knowledge this is the first attempt to identify the coding sequence of caDAHPS by cloning and sequencing. We found Gln179, Arg175, Glu462, Glu302, Lys357 and His420 amino acids in the active site of caDAHPS through molecular docking. followed by molecular dynamic simulation. The amino acid residues, Lys182, Cys136, His460, Leu304, Gly333, Glu334, Pro183, Asp492 and Arg433 at the surface interact with PEP by van der Waals bonds imparting stability to the enzyme-substrate complex. Docking results were further validated by molecular dynamics. The presented in-silico analysis of caDAHPS will generate opportunities to engineer the sennoside biosynthesis in plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khushali Thaker
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Jaimini Patoliya
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Khushbu Rabadiya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dhaval Patel
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Manivel Ponnuchamy
- ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat, India
| | | | - Rushikesh Joshi
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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34
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Kausar N, Shier WT, Ahmed M, Maryam, Albekairi NA, Alshammari A, Saleem M, Imran M, Muddassar M. Investigation of the insecticidal potential of curcumin derivatives that target the Helicoverpa armigera sterol carrier protein-2. Heliyon 2024; 10:e29695. [PMID: 38660259 PMCID: PMC11040122 DOI: 10.1016/j.heliyon.2024.e29695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Cotton bollworm (Helicoverpa armigera) is a highly polyphagous, widely prevalent, and persistent Old World insect pest that affects numerous important crops that are directly consumed by people, including tomato, cotton, pigeon pea, chickpea, rice, sorghum, and cowpea. Insects do not synthesize steroids but obtain them from their diet. Inhibition of dietary uptake of steroids by insects is a potentially effective insecticidal mechanism that should not be toxic to humans and other mammals, who synthesize their steroids. Ten curcumin derivatives were tested against H. armigera sterol carrier protein-2 (HaSCP-2) for their potential as insecticidal agents. Curcumin derivatives were initially docked at the binding site of HaSCP-2 to determine their binding affinities and plausible binding modes. The binding modes predominantly show hydrophobic interactions of derivatives with Phe53, Phe110, and Phe89 as core interacting residues in the active site. Validation of in silico results was carried out by performing a fluorescence binding and displacement assay to determine the binding affinities of curcumin derivatives. Among a collection of curcumin derivatives tested, Cur10 showed the lowest IC50 value of 9.64 μM, while Cur07 was 19.86 μM, and Cur06 was 20.79 μM. There was a significant negative correlation between the ability of the curcumin derivatives tested to displace the fluorescent probe from the sterol binding site of HaSCP-2 and to inhibit Sf9 insect cell growth in culture, which is consistent with the curcumin derivatives acting by the novel mechanism of blocking sterol uptake. Then molecular dynamics simulation studies validated the predicted binding modes and the interactions of curcumin derivatives with HaSCP-2 protein. In conclusion, these studies support the potential use of curcumin derivatives as insecticidal agents.
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Affiliation(s)
- Naeema Kausar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Wayne Thomas Shier
- College of Pharmacy, Department of Medicinal Chemistry, University of Minnesota, 55455, USA
| | - Mahmood Ahmed
- Department of Chemistry, Division of Science and Technology, University of Education, College Road, Lahore, Pakistan
| | - Maryam
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Muhammad Saleem
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Imran
- KAM-School of Life Sciences, FC College (A Chartered University), Lahore, 54000, Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
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35
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Zarin T, Lehner B. A complete map of specificity encoding for a partially fuzzy protein interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591103. [PMID: 38712134 PMCID: PMC11071492 DOI: 10.1101/2024.04.25.591103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Thousands of human proteins function by binding short linear motifs embedded in intrinsically disordered regions. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of 'fuzzy' dynamic residues to affinity and specificity in protein-protein interactions. Here we report the first complete map of specificity encoding for a globular protein domain. Quantifying >200,000 energetic interactions between a PDZ domain and its ligand identifies 20 major energetically coupled pairs of sites that control specificity. These are organized into six modules, with most mutations in each module reprogramming specificity for a single position in the ligand. Nine of the major energetic couplings controlling specificity are between structural contacts and 11 have an allosteric mechanism of action. The dynamic tail of the ligand is more robust to mutation than the structured residues but contributes additively to binding affinity and communicates with structured residues to enable changes in specificity. Our results quantify the binding specificities of >1,800 globular proteins to reveal how specificity is encoded and provide a direct comparison of the encoding of affinity and specificity in structured and dynamic molecular recognition.
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Affiliation(s)
- Taraneh Zarin
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Wellcome Sanger Institute, Cambridge, UK
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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36
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Lesgidou N, Vlassi M. Community analysis of large-scale molecular dynamics simulations elucidated dynamics-driven allostery in tyrosine kinase 2. Proteins 2024; 92:474-498. [PMID: 37950407 DOI: 10.1002/prot.26631] [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: 07/17/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
TYK2 is a nonreceptor tyrosine kinase, member of the Janus kinases (JAK), with a central role in several diseases, including cancer. The JAKs' catalytic domains (KD) are highly conserved, yet the isolated TYK2-KD exhibits unique specificities. In a previous work, using molecular dynamics (MD) simulations of a catalytically impaired TYK2-KD variant (P1104A) we found that this amino acid change of its JAK-characteristic insert (αFG), acts at the dynamics level. Given that structural dynamics is key to the allosteric activation of protein kinases, in this study we applied a long-scale MD simulation and investigated an active TYK2-KD form in the presence of adenosine 5'-triphosphate and one magnesium ion that represents a dynamic and crucial step of the catalytic cycle, in other protein kinases. Community analysis of the MD trajectory shed light, for the first time, on the dynamic profile and dynamics-driven allosteric communications within the TYK2-KD during activation and revealed that αFG and amino acids P1104, P1105, and I1112 in particular, hold a pivotal role and act synergistically with a dynamically coupled communication network of amino acids serving intra-KD signaling for allosteric regulation of TYK2 activity. Corroborating our findings, most of the identified amino acids are associated with cancer-related missense/splice-site mutations of the Tyk2 gene. We propose that the conformational dynamics at this step of the catalytic cycle, coordinated by αFG, underlie TYK2-unique substrate recognition and account for its distinct specificity. In total, this work adds to knowledge towards an in-depth understanding of TYK2 activation and may be valuable towards a rational design of allosteric TYK2-specific inhibitors.
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Affiliation(s)
- Nastazia Lesgidou
- National Center for Scientific Research "Demokritos", Institute of Biosciences & Applications, Athens, Greece
| | - Metaxia Vlassi
- National Center for Scientific Research "Demokritos", Institute of Biosciences & Applications, Athens, Greece
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Ruiz-Serra V, Valentini S, Madroñero S, Valencia A, Porta-Pardo E. 3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures. Bioinformatics 2024; 40:btae171. [PMID: 38565273 PMCID: PMC11018535 DOI: 10.1093/bioinformatics/btae171] [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: 09/01/2023] [Revised: 02/09/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024] Open
Abstract
MOTIVATION The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats. Over the past two decades, numerous tools and databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these tools are web-based and not well-suited for large-scale genomic data analysis. RESULTS To address this issue, we introduce 3Dmapper, a stand-alone command-line tool developed in Python and R. It systematically maps annotated protein positions and variants to protein structures, providing a solution that is both efficient and reliable. AVAILABILITY AND IMPLEMENTATION https://github.com/vicruiser/3Dmapper.
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Affiliation(s)
- Victoria Ruiz-Serra
- Barcelona Supercomputing Center (BSC)
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain
| | - Samuel Valentini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy
| | - Sergi Madroñero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC)
- Institució Catalana de Recerca Avançada (ICREA)
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Center (BSC)
- Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain
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Evoli S, Kariyawasam NL, Nitiss KC, Nitiss JL, Wereszczynski J. Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.02.551689. [PMID: 37577673 PMCID: PMC10418245 DOI: 10.1101/2023.08.02.551689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Type II topoisomerases (TopoIIs) are ubiquitous enzymes that are involved in crucial nuclear processes such as genome organization, chromosome segregation, and other DNA metabolic processes. These enzymes function as large, homodimeric complexes that undergo a complex cycle of binding and hydrolysis of two ATP molecules in their ATPase domains, which regulates the capture and passage of one DNA double-helix through a second, cleaved DNA molecule. This process requires the transmission of information about the state of the bound nucleotide over vast ranges in the TopoII complex. How this information is transmitted at the molecular level to regulate TopoII functions and how protein substitutions disrupt these mechanisms remains largely unknown. Here, we employed extensive microsecond scale molecular dynamics simulations of the yeast TopoII enzyme in multiple nucleotide-bound states and with amino acid substitutions near both the N- and C-terminals of the complex. Simulation results indicate that the ATPase domains are remarkably flexible on the sub-microsecond timescale and that these dynamics are modulated by the identity of the bound nucleotides and both local and distant amino acid substitutions. Network analyses point towards specific allosteric networks that transmit information about the hydrolysis cycle throughout the complex, which include residues in both the protein and the bound DNA molecule. Amino acid substitutions weaken many of these pathways. Together, our results provide molecular-level details on how the TopoII catalytic cycle is controlled through nucleotide binding and hydrolysis and how mutations may disrupt this process.
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Affiliation(s)
- Stefania Evoli
- Department of Physics, Illinois Institute of Technology, Chicago, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, USA
- these authors contributed equally to this work
| | - Nilusha L. Kariyawasam
- Department of Physics, Illinois Institute of Technology, Chicago, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, USA
- these authors contributed equally to this work
| | - Karin C. Nitiss
- Pharmaceutical Sciences Department, University of Illinois at Chicago, Rockford, IL
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois at Chicago, Rockford, IL
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, USA
- Department of Biology, Illinois Institute of Technology, Chicago, USA
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Zhang QE, Lindenberger J, Parsons R, Thakur B, Parks R, Park CS, Huang X, Sammour S, Janowska K, Spence TN, Edwards RJ, Martin M, Williams WB, Gobeil S, Montefiori DC, Korber B, Saunders KO, Haynes BF, Haynes BF, Henderson R, Acharya P. SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.580004. [PMID: 38405707 PMCID: PMC10888797 DOI: 10.1101/2024.02.12.580004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryo-EM structures of XBB.1.5, XBB.1.16, EG.5 and EG.5.1 spike (S) ectodomains to reveal reinforced 3-RBD-down receptor inaccessible closed states mediated by interprotomer receptor binding domain (RBD) interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters including stability, receptor binding and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.
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40
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Yao XQ, Hamelberg D. Dissecting the Allosteric Fine-Tuning of Enzyme Catalysis. JACS AU 2024; 4:837-846. [PMID: 38425926 PMCID: PMC10900222 DOI: 10.1021/jacsau.3c00806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Fully understanding the mechanism of allosteric regulation in biomolecules requires separating and examining all of the involved factors. In enzyme catalysis, allosteric effector binding shifts the structure and dynamics of the active site, leading to modified energetic (e.g., energy barrier) and dynamical (e.g., diffusion coefficient) factors underlying the catalyzed reaction rate. Such modifications can be subtle and dependent on the type of allosteric effector, representing a fine-tuning of protein function. The microscopic description of allosteric regulation at the level of function-dictating factors has prospective applications in fundamental and pharmaceutical sciences, which is, however, largely missing so far. Here, we characterize the allosteric fine-tuning of enzyme catalysis, using human Pin1 as an example, by performing more than half-millisecond all-atom molecular dynamics simulations. Changes of reaction kinetics and the dictating factors, including the free energy surface along the reaction coordinate and the diffusion coefficient of the reaction dynamics, under various enzyme and allosteric effector binding conditions are examined. Our results suggest equal importance of the energetic and dynamical factors, both of which can be modulated allosterically, and the combined effect determines the final allosteric output. We also reveal the potential dynamic basis for allosteric modulation using an advanced statistical technique to detect function-related conformational dynamics. Methods developed in this work can be applied to other allosteric systems.
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Affiliation(s)
- Xin-Qiu Yao
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Department
of Chemistry, University of Nebraska Omaha, Omaha, Nebraska 68182-0266, United
States
| | - Donald Hamelberg
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
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41
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Ahmad I, Singh AK, Mohd S, Katari SK, Nalamolu RM, Ahmad A, Baothman OA, Hosawi SA, Altayeb H, Nadeem MS, Ahmad V. In Silico Insights into the Arsenic Binding Mechanism Deploying Application of Computational Biology-Based Toolsets. ACS OMEGA 2024; 9:7529-7544. [PMID: 38405466 PMCID: PMC10882604 DOI: 10.1021/acsomega.3c06313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
An assortment of environmental matrices includes arsenic (As) in its different oxidation states, which is often linked to concerns that pose a threat to public health worldwide. The current difficulty lies in addressing toxicological concerns and achieving sustained detoxification of As. Multiple conventional degradation methods are accessible; however, they are indeed labor-intensive, expensive, and reliant on prolonged laboratory evaluations. Molecular interaction and atomic level degradation mechanisms for enzyme-As exploration are, however, underexplored in those approaches. A feasible approach in this case for tackling this accompanying concern of As might be to cope with undertaking multivalent computational methodologies and tools. This work aimed to provide molecular-level insight into the enzyme-aided As degradation mechanism. AutoDock Vina, CABS-flex 2.0, and Desmond high-performance molecular dynamics simulation (MDS) were utilized in the current investigation to simulate multivalent molecular processes on two protein sets: arsenate reductase (ArsC) and laccase (LAC) corresponding arsenate (ART) and arsenite (AST), which served as model ligands to comprehend binding, conformational, and energy attributes. The structural configurations of both proteins exhibited variability in flexibility and structure framework within the range of 3.5-4.5 Å. The LAC-ART complex exhibited the lowest calculated binding affinity, measuring -5.82 ± 0.01 kcal/mol. Meanwhile, active site residues ILE-200 and HIS-206 were demonstrated to engage in H-bonding with the ART ligand. In contrast to ArsC, the ligand binding affinity of this bound complex was considerably greater. Additional validation of docked complexes was carried out by deploying Desmond MDS of 100 ns to capture protein and ligand conformation behavior. The system achieved stability during the 100 ns simulation run, as confirmed by the average P-L RMSD, which was ∼1 Å. As a preliminary test of the enzyme's ability to catalyze As species, corresponding computational insights might be advantageous for bridging gaps and regulatory consideration.
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Affiliation(s)
- Imran Ahmad
- Department
of Biochemistry, King George’s Medical
University, Lucknow, Uttar Pradesh 226003, India
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anil Kumar Singh
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shayan Mohd
- Department
of Bioengineering, Faculty of Engineering, Integral University, Dasauli, Kursi Road, Lucknow 226026, India
| | - Sudheer Kumar Katari
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Ravina Madhulitha Nalamolu
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Abrar Ahmad
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Othman A. Baothman
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Salman A. Hosawi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Hisham Altayeb
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Varish Ahmad
- Department
of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
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Andrade C, Sousa BKDP, Sigurdardóttir S, Bourgard C, Borba J, Clementino L, Salazar-Alvarez LC, Groustra S, Zigweid R, Khim M, Staker B, Costa F, Eriksson L, Sunnerhagen P. Selective Bias Virtual Screening for Discovery of Promising Antimalarial Candidates targeting Plasmodium N-Myristoyltransferase. RESEARCH SQUARE 2024:rs.3.rs-3963523. [PMID: 38463971 PMCID: PMC10925453 DOI: 10.21203/rs.3.rs-3963523/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Malaria remains a significant public health challenge, with Plasmodium vivax being the species responsible for the most prevalent form of the disease. Given the limited therapeutic options available, the search for new antimalarials against P. vivax is urgent. This study aims to identify new inhibitors for P. vivax N-myristoyltransferase (PvNMT), an essential drug target against malaria. Through a validated virtual screening campaign, we prioritized 23 candidates for further testing. In the yeast NMT system, seven compounds exhibit a potential inhibitor phenotype. In vitro antimalarial phenotypic assays confirmed the activity of four candidates while demonstrating an absence of cytotoxicity. Enzymatic assays reveal LabMol-394 as the most promising inhibitor, displaying selectivity against the parasite and a strong correlation within the yeast system. Furthermore, molecular dynamics simulations shed some light into its binding mode. This study constitutes a substantial contribution to the exploration of a selective quinoline scaffold and provides valuable insights into the development of new antimalarial candidates.
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Lin YC, Swendeman S, Moreira IS, Ghosh A, Kuo A, Rosário-Ferreira N, Guo S, Culbertson A, Levesque MV, Cartier A, Seno T, Schmaier A, Galvani S, Inoue A, Parikh SM, FitzGerald GA, Zurakowski D, Liao M, Flaumenhaft R, Gümüş ZH, Hla T. Designer high-density lipoprotein particles enhance endothelial barrier function and suppress inflammation. Sci Signal 2024; 17:eadg9256. [PMID: 38377179 PMCID: PMC10954247 DOI: 10.1126/scisignal.adg9256] [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: 01/31/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024]
Abstract
High-density lipoprotein (HDL) nanoparticles promote endothelial cell (EC) function and suppress inflammation, but their utility in treating EC dysfunction has not been fully explored. Here, we describe a fusion protein named ApoA1-ApoM (A1M) consisting of apolipoprotein A1 (ApoA1), the principal structural protein of HDL that forms lipid nanoparticles, and ApoM, a chaperone for the bioactive lipid sphingosine 1-phosphate (S1P). A1M forms HDL-like particles, binds to S1P, and is signaling competent. Molecular dynamics simulations showed that the S1P-bound ApoM moiety in A1M efficiently activated EC surface receptors. Treatment of human umbilical vein ECs with A1M-S1P stimulated barrier function either alone or cooperatively with other barrier-enhancing molecules, including the stable prostacyclin analog iloprost, and suppressed cytokine-induced inflammation. A1M-S1P injection into mice during sterile inflammation suppressed neutrophil influx and inflammatory mediator secretion. Moreover, systemic A1M administration led to a sustained increase in circulating HDL-bound S1P and suppressed inflammation in a murine model of LPS-induced endotoxemia. We propose that A1M administration may enhance vascular endothelial barrier function, suppress cytokine storm, and promote resilience of the vascular endothelium.
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Affiliation(s)
- Yueh-Chien Lin
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven Swendeman
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Irina S. Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Avishek Ghosh
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew Kuo
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Nícia Rosário-Ferreira
- CNC - Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-456, Coimbra, Portugal
| | | | - Alan Culbertson
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Michel V. Levesque
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Andreane Cartier
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Takahiro Seno
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Alec Schmaier
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02115, USA
| | - Sylvain Galvani
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Samir M. Parikh
- Division of Nephrology and Department of Medicine, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, 75235, USA
| | - Garret A. FitzGerald
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - David Zurakowski
- Department of Anesthesia and Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 518055, China
| | | | - Zeynep H. Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Timothy Hla
- Vascular Biology Program, Boston Children’s Hospital and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
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Abid R, Nisar H, Chaudhary SU, Hamid M, Sahibzada KI, Firdous S, Mudassar M, Sadaf S. Association of epilepsy and neurological impairments with homozygous recessive missense mutations found in the genes responsible for ganglioside biosynthesis ( ST3GAL5) and calcium voltage-gated channels ( CACNA1H) - insights through molecular dynamic simulations. J Biomol Struct Dyn 2024:1-12. [PMID: 38356142 DOI: 10.1080/07391102.2024.2314751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
With over 2.2 million cases, the incidence rate of epilepsy in Pakistan is far higher than the rest of the world due primarily to the frequent, traditionally imposed cousin marriages. In the present study, comprehensive whole exome sequencing (WES) analyses of a three-generation family with four affected members presenting 'unexplained' childhood absence epilepsy (CAE), seizures and dementia, was performed in a quest to identify heritable, epilepsy-causal gene variants to better aid in carrier screening and genetic counselling. The WES data was generated, analyzed, and validated through Sanger's sequencing, molecular dynamic simulation (MDS) analysis, and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) studies. Two homozygous recessive, missense mutations in ST3GAL5 (c.311A > G, p. His104Arg) and CACNA1H (c.6230G > A, p. Arg2077His) genes, earlier regarded as benign or of uncertain significance, have been identified as a potential etiology. Comparative MDS and free binding energy calculations revealed substantial structural perturbations in mutant forms of ST3GAL5 leading to decreased binding and reduced catalytic activity of the p.His104Arg and two other functional variants (p.Val74Glu and p.Arg288Ter) when compared with wild type. Our findings reinforce that WES analyses may uncover 'hidden', heritable variants and together with MDS and MM/GBSA may provide plausible clues to answer the unexplained causes of epilepsy for an effective management and better patient outcome. Further, revisit of epilepsy-associated mutational landscape in population context is imperative as the variants with 'benign' tags may turn out to be 'non-benign', when exist in combination with other benign.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rizwan Abid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Haseeb Nisar
- Department of Life-Sciences, University of Management and Technology, Lahore, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics & Engineering Research Laboratory, Department of Life-Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Maham Hamid
- Biomedical Informatics & Engineering Research Laboratory, Department of Life-Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Kashif Iqbal Sahibzada
- Department of Health Professional Technologies, The University of Lahore, Lahore, Pakistan
| | - Safia Firdous
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Lahore, Pakistan
| | | | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
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Nath M, Bhowmik D, Saha S, Nandi R, Kumar D. Identification of potential inhibitor against Leishmania donovani mitochondrial DNA primase through in-silico and in vitro drug repurposing approaches. Sci Rep 2024; 14:3246. [PMID: 38332162 PMCID: PMC10853515 DOI: 10.1038/s41598-024-53316-5] [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: 10/07/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Leishmania donovani is the causal organism of leishmaniasis with critical health implications affecting about 12 million people around the globe. Due to less efficacy, adverse side effects, and resistance, the available therapeutic molecules fail to control leishmaniasis. The mitochondrial primase of Leishmania donovani (LdmtPRI1) is a vital cog in the DNA replication mechanism, as the enzyme initiates the replication of the mitochondrial genome of Leishmania donovani. Hence, we target this protein as a probable drug target against leishmaniasis. The de-novo approach enabled computational prediction of the three-dimensional structure of LdmtPRI1, and its active sites were identified. Ligands from commercially available drug compounds were selected and docked against LdmtPRI1. The compounds were chosen for pharmacokinetic study and molecular dynamics simulation based on their binding energies and protein interactions. The LdmtPRI1 gene was cloned, overexpressed, and purified, and a primase activity assay was performed. The selected compounds were verified experimentally by the parasite and primase inhibition assay. Capecitabine was observed to be effective against the promastigote form of Leishmania donovani, as well as inhibiting primase activity. This study's findings suggest capecitabine might be a potential anti-leishmanial drug candidate after adequate further studies.
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Affiliation(s)
- Mitul Nath
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Deep Bhowmik
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Satabdi Saha
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Rajat Nandi
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Diwakar Kumar
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
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Srivastava AK, Srivastava S, Kumar V, Ghosh S, Yadav S, Malik R, Roy P, Prasad R. Identification and mechanistic exploration of structural and conformational dynamics of NF-kB inhibitors: rationale insights from in silico and in vitro studies. J Biomol Struct Dyn 2024; 42:1485-1505. [PMID: 37054525 DOI: 10.1080/07391102.2023.2200490] [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: 01/06/2023] [Accepted: 04/02/2023] [Indexed: 04/15/2023]
Abstract
Increased expression of target genes that code for proinflammatory chemical mediators results from a series of intracellular cascades triggered by activation of dysregulated NF-κB signaling pathway. Dysfunctional NF-kB signaling amplifies and perpetuates autoimmune responses in inflammatory diseases, including psoriasis. This study aimed to identify therapeutically relevant NF-kB inhibitors and elucidate the mechanistic aspects behind NF-kB inhibition. After virtual screening and molecular docking, five hit NF-kB inhibitors opted, and their therapeutic efficacy was examined using cell-based assays in TNF-α stimulated human keratinocyte cells. To investigate the conformational changes of target protein and inhibitor-protein interaction mechanisms, molecular dynamics (MD) simulations, binding free energy calculations together with principal component (PC) analysis, dynamics cross-correlation matrix analysis (DCCM), free energy landscape (FEL) analysis and quantum mechanical calculations were carried out. Among identified NF-kB inhibitors, myricetin and hesperidin significantly scavenged intracellular ROS and inhibited NF-kB activation. Analysis of the MD simulation trajectories of ligand-protein complexes revealed that myricetin and hesperidin formed energetically stabilized complexes with the target protein and were able to lock NF-kB in a closed conformation. Myricetin and hesperidin binding to the target protein significantly impacted conformational changes and internal dynamics of amino acid residues in protein domains. Tyr57, Glu60, Lys144 and Asp239 residues majorly contributed to locking the NF-kB in a closed conformation. The combinatorial approach employing in silico tools integrated with cell-based approaches substantiated the binding mechanism and NF-kB active site inhibition by the lead molecule myricetin, which can be explored as a viable antipsoriatic drug candidate associated with dysregulated NF-kB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Kumar Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Shubham Srivastava
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Viney Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Souvik Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Siddharth Yadav
- Department of Computer Science and Engineering, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Ruchi Malik
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Partha Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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D'Arminio N, Ruggiero V, Pierri G, Marabotti A, Tedesco C. Emerging role of carbonyl-carbonyl interactions in the classification of beta turns. Protein Sci 2024; 33:e4868. [PMID: 38100281 PMCID: PMC10806932 DOI: 10.1002/pro.4868] [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: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Carbonyl-carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl-carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In general, φ values in the range between -40° and -90° and between 40° and 90° correspond to CO∙∙∙CO distances below 3.22 Å. By extending the analysis of carbonyl-carbonyl interactions in different types of beta turns in proteins, we also highlight the role of direct or reciprocal carbonyl-carbonyl interactions in stabilizing the beta turn conformation for each specific type. We confirmed the new type II beta turn, detected by Dunbrack and coworkers, and named Pa, and detect the presence of a direct carbonyl-carbonyl interaction between the second and third residues of the turn. We also evidenced the existence of another new type II beta turn, named pA (following Dunbrack's notation), which represents the alternative conformation of Pa with opposite φ and ψ values and is characterized by a direct carbonyl-carbonyl interaction between the second and third residues of the turn. Finally, we show that the occurrence of CO∙∙∙CO interactions could be also advocated to explain from a chemical point of view the diversity of turn types.
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Affiliation(s)
- Nancy D'Arminio
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Valentina Ruggiero
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
- Present address:
Department of PharmacyUniversity of SalernoFiscianoItaly
| | - Giovanni Pierri
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Consiglia Tedesco
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
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Yang K, Liu H. Uncovering New Conformational States of the Substrate Binding Pocket of LSD1 Potential for Inhibitor Design via Funnel Metadynamics. J Phys Chem B 2024; 128:137-149. [PMID: 38151469 DOI: 10.1021/acs.jpcb.3c06900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is a promising therapeutic target for cancer therapy. So far, over 80 crystal structures of LSD1 in different complex states have been deposited in the Protein Data Bank, which are valuable resources for performing structure-based drug design. However, among all of the crystal structures of LSD1, the substrate binding pocket, which is the most efficient druggable site for designing LSD1 inhibitors at present, is very similar no matter whether LSD1 is in the apo or any holo forms, which is inconsistent with its versatile demethylase functions. To investigate whether the substrate binding pocket is rigid or exhibits other representative conformations different from the crystal conformations that are feasible for designing new LSD1 inhibitors, we performed funnel metadynamics simulations to study the conformation dynamics of LSD1 in the binding process of two effective LSD1 inhibitors (CC-90011 and 6X0, CC-90011 undergoing clinical trials). Our results showed that the entrance of the substrate binding pocket is very flexible. Two representative entrance conformations of LSD1 counting against binding with the substrate of histone H3 were detected, which may be used for structure-based LSD1 inhibitor design. Besides, alternative optimal binding modes and prebinding modes for both inhibitors were also detected, which depicted that the key interactions changed along with the binding process. Our results should provide great help for LSD1 inhibitor design.
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Affiliation(s)
- Kecheng Yang
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Hongmin Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
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Chen J, Wang W, Sun H, He W. Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters. Mini Rev Med Chem 2024; 24:1323-1333. [PMID: 38265367 DOI: 10.2174/0113895575252165231122095555] [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: 03/06/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 01/25/2024]
Abstract
Rational predictions on binding kinetics parameters of drugs to targets play significant roles in future drug designs. Full conformational samplings of targets are requisite for accurate predictions of binding kinetic parameters. In this review, we mainly focus on the applications of enhanced sampling technologies in calculations of binding kinetics parameters and residence time of drugs. The methods involved in molecular dynamics simulations are applied to not only probe conformational changes of targets but also reveal calculations of residence time that is significant for drug efficiency. For this review, special attention are paid to accelerated molecular dynamics (aMD) and Gaussian aMD (GaMD) simulations that have been adopted to predict the association or disassociation rate constant. We also expect that this review can provide useful information for future drug design.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Weikai He
- School of Science, Shandong Jiaotong University, Jinan-250357, China
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50
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Mughal EU, Amjid S, Sadiq A, Naeem N, Nazir Y, Alrafai HA, Hassan AA, Al-Nami SY, Abdel Hafez AA, Ali Shah SW, Ghias M. Design and synthesis of 2-amino-4,6-diarylpyrimidine derivatives as potent α-glucosidase and α-amylase inhibitors: structure-activity relationship, in vitro, QSAR, molecular docking, MD simulations and drug-likeness studies. J Biomol Struct Dyn 2024; 42:244-260. [PMID: 37096830 DOI: 10.1080/07391102.2023.2198609] [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: 01/27/2023] [Accepted: 03/10/2023] [Indexed: 04/26/2023]
Abstract
In the present study, a series of 2-amino-4,6-diarylpyrimidine derivatives was designed, synthesized, characterized and evaluated for their in vitro α-glucosidase and α-amylase enzyme inhibition assays. The outcomes proved that this class of compounds exhibit considerable inhibitory activity against both enzymes. Among the target compounds, compounds 4p and 6p demonstrated the most potent dual inhibition with IC50 = 0.087 ± 0.01 μM for α-glucosidase; 0.189 ± 0.02 μM for α-amylase and IC50 = 0.095 ± 0.03 μM for α-glucosidase; 0.214 ± 0.03 μM for α-amylase, respectively as compared to the standard rutin (IC50 = 0.192 ± 0.02 μM for α-glucosidase and 0.224 ± 0.02 μM for α-amylase). Remarkably, the enzyme inhibition results indicate that test compounds have stronger inhibitory effect on the target enzymes than the positive control, with a significantly lower IC50 value. Moreover, these series of compounds were found to inhibit α-glucosidase activity in a reversible mixed-type manner with IC50 between 0.087 ± 0.01 μM to 1.952 ± 0.26 μM. Furthermore, molecular docking studies were performed to affirm the binding interactions of this scaffold to the active sites of α-glucosidase and α-amylase enzymes. The quantitative structure-activity relationship (QSAR) investigations showed a strong association between 1p-15p structures and their inhibitory actions (IC50) with a correlation value (R2) of 0.999916. Finally, molecular dynamic (MD) simulations were carried out to assess the dynamic behavior, stability of the protein-ligand complex, and binding affinity of the most active inhibitor 4p. The experimental and theoretical results therefore exposed a very good compatibility. Additionally, the drug-likeness assay revealed that some compounds exhibit a linear association with Lipinski's rule of five, indicating good drug-likeness and bioactivity scores for pharmacological targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Samreen Amjid
- Department of Chemistry, University of Gujrat, Gujrat, Pakistan
| | - Amina Sadiq
- Department of Chemistry, Govt. College Women University, Sialkot, Pakistan
| | - Nafeesa Naeem
- Department of Chemistry, University of Gujrat, Gujrat, Pakistan
| | - Yasir Nazir
- Department of Chemistry, Allama Iqbal Open University, Islamabad, Pakistan
| | - H A Alrafai
- Department of Chemistry, Faculty of Science, King Khalid University, Abraham, Saudi Arabia
| | - Abeer A Hassan
- Department of Chemistry, Faculty of Science, King Khalid University, Abraham, Saudi Arabia
| | - Samar Y Al-Nami
- Department of Chemistry, Faculty of Science, King Khalid University, Abraham, Saudi Arabia
| | - Amal A Abdel Hafez
- Department of Chemistry, Faculty of Science, King Khalid University, Abraham, Saudi Arabia
| | - Syed Wadood Ali Shah
- Department of Pharmacy, University of Malakand, Chakdara Dir, Khyber Pakhtunkhwa, Pakistan
| | - Mehreen Ghias
- Department of Pharmacy, University of Malakand, Chakdara Dir, Khyber Pakhtunkhwa, Pakistan
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