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Banerjee T, Gosai A, Yousefi N, Garibay OO, Seal S, Balasubramanian G. Examining sialic acid derivatives as potential inhibitors of SARS-CoV-2 spike protein receptor binding domain. J Biomol Struct Dyn 2024; 42:6342-6358. [PMID: 37424217 DOI: 10.1080/07391102.2023.2234044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has been the primary reason behind the COVID-19 global pandemic which has affected millions of lives worldwide. The fundamental cause of the infection is the molecular binding of the viral spike protein receptor binding domain (SP-RBD) with the human cell angiotensin-converting enzyme 2 (ACE2) receptor. The infection can be prevented if the binding of RBD-ACE2 is resisted by utilizing certain inhibitors or drugs that demonstrate strong binding affinity towards the SP RBD. Sialic acid based glycans found widely in human cells and tissues have notable propensity of binding to viral proteins of the coronaviridae family. Recent experimental literature have used N-acetyl neuraminic acid (Sialic acid) to create diagnostic sensors for SARS-CoV-2, but a detailed interrogation of the underlying molecular mechanisms is warranted. Here, we perform all atom molecular dynamics (MD) simulations for the complexes of certain Sialic acid-based molecules with that of SP RBD of SARS CoV-2. Our results indicate that Sialic acid not only reproduces a binding affinity comparable to the RBD-ACE2 interactions, it also assumes the longest time to dissociate completely from the protein binding pocket of SP RBD. Our predictions corroborate that a combination of electrostatic and van der Waals energies as well the polar hydrogen bond interactions between the RBD residues and the inhibitors influence free energy of binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tanumoy Banerjee
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
| | | | - Niloofar Yousefi
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Ozlem Ozmen Garibay
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Sudipta Seal
- College of Medicine, Bionix Cluster, University of Central Florida, Orlando, FL, USA
- Advanced Materials Processing and Analysis Center, Dept. of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA
| | - Ganesh Balasubramanian
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
- Institute of Functional Materials & Devices and College of Health, Lehigh University, Bethlehem, PA, USA
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Khan MRUZ, Trivedi V. Molecular modelling, docking and network analysis of phytochemicals from Haritaki churna: role of protein cross-talks for their action. J Biomol Struct Dyn 2024; 42:4297-4312. [PMID: 37288779 DOI: 10.1080/07391102.2023.2220036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Phytochemicals are bioactive agents present in medicinal plants with therapeutic values. Phytochemicals isolated from plants target multiple cellular processes. In the current work, we have used fractionation techniques to identify 13 bioactive polyphenols in ayurvedic medicine Haritaki Churna. Employing the advanced spectroscopic and fractionation, structure of bioactive polyphenols was determined. Blasting the phytochemical structure allow us to identify a total of 469 protein targets from Drug bank and Binding DB. Phytochemicals with their protein targets from Drug bank was used to create a phytochemical-protein network comprising of 394 nodes and 1023 edges. It highlights the extensive cross-talk between protein target corresponding to different phytochemicals. Analysis of protein targets from Binding data bank gives a network comprised of 143 nodes and 275 edges. Taking the data together from Drug bank and binding data, seven most prominent drug targets (HSP90AA1, c-Src kinase, EGFR, Akt1, EGFR, AR, and ESR-α) were found to be target of the phytochemicals. Molecular modelling and docking experiment indicate that phytochemicals are fitting nicely into active site of the target proteins. The binding energy of the phytochemicals were better than the inhibitors of these protein targets. The strength and stability of the protein ligand complexes were further confirmed using molecular dynamic simulation studies. Further, the ADMET profiles of phytochemicals extracted from HCAE suggests that they can be potential drug targets. The phytochemical cross-talk was further proven by choosing c-Src as a model. HCAE down regulated c-Src and its downstream protein targets such as Akt1, cyclin D1 and vimentin. Hence, network analysis followed by molecular docking, molecular dynamics simulation and in-vitro studies clearly highlight the role of protein network and subsequent selection of drug candidate based on network pharmacology.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Rafi Uz Zama Khan
- Malaria Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, Assam, India
| | - Vishal Trivedi
- Malaria Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, Assam, India
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Amin N, Singh VK, Kannaujiya VK. Mycosporine-Like Amino Acids as a Potential Inhibitor of Tyrosinase-Related Protein 1: Computational Screening, Pharmacokinetics, and Molecular Dynamics Simulation. Mol Biotechnol 2024:10.1007/s12033-024-01153-2. [PMID: 38652428 DOI: 10.1007/s12033-024-01153-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/24/2024] [Indexed: 04/25/2024]
Abstract
Melanin is the major pigment responsible for the coloring of mammalian skin, hair, and eyes to defend against ultraviolet radiation. However, excessive melanin production has resulted in numerous types of hyperpigmentation disorders. Tyrosinase-related protein 1 (TYRP1) is a transmembrane glycoprotein enzyme found in many organisms, including humans, that plays an important role in melanogenesis. Thus, controlling the enzyme activity of TYRP1 with tyrosinase inhibitors is a vital step in the treatment of hyperpigmentation problems in humans. In the present investigation, virtual screening, pharmacokinetics, drug docking, and molecular dynamics (MD) simulation were used to find the most potent drug as an inhibitor of TYRP1 to effectively treat hyperpigmentation disorder. The 3D structure of TYRP1 was retrieved from the Protein Data Bank (PDB) database (PDB ID: 5M8M) and validated by the Ramachandran plot. Pharmacokinetics and drug-likeness showed that mycosporine 2 glycine (M2G) and shinorine (SHI) were the best compounds over other ligands in the same (P-1) structural pose. However, MD simulations of the M2G showed the highest CDOCKER interaction energy (-45.182 kcal/mol) and binding affinity (-65.0529 kcal/mol) as compared to SHI and reference drugs. The molecular binding modes RMSD and RMSF plots have exhibited more relevance to the M2G ligand in comparison to other drug ligands. The bioactivity and ligand efficiency profiles revealed that M2G is the most effective compound as a TYRP1 inhibitor. Thus, M2G could be used as a most effective drug for developing valuable sunscreen products to cure hyperpigmentation-related diseases.
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Affiliation(s)
- Nasreen Amin
- Department of Botany, MMV, Banaras Hindu University, Varanasi, 221005, India
| | - Vinay K Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vinod K Kannaujiya
- Department of Botany, MMV, Banaras Hindu University, Varanasi, 221005, India.
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Owoloye AJ, Olubode SO, Ogunleye A, Idowu ET, Oyebola KM. Computational identification of potential modulators of heme-regulated inhibitor (HRI) for pharmacological intervention against sickle cell disease. J Biomol Struct Dyn 2024:1-13. [PMID: 38555858 DOI: 10.1080/07391102.2024.2331097] [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: 01/04/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
Sickle cell disease (SCD) poses a significant health challenge and therapeutic approaches often target fetal hemoglobin (HbF) to ameliorate symptoms. Hydroxyurea, a current therapeutic option for SCD, has shown efficacy in increasing HbF levels. However, concerns about myelosuppression and thrombocytopenia necessitate the exploration of alternative compounds. Heme-regulated inhibitor (HRI) presents a promising target for pharmacological intervention in SCD due to its association with HbF modulation. This study screened compounds for their potential inhibitory functions against HRI. Small-molecule compounds from 17 folkloric plants were subjected to in silico screening against HRI. Molecular docking was performed, and free binding energy calculations were determined using molecular mechanics with generalized born and surface area (MMGBSA). Lead compounds were subjected to molecular dynamics simulation at 100 ns. Computational quantum mechanical modeling of the lead compounds was subsequently performed. We further examined the pharmacodynamics, pharmacokinetic and physiological properties of the identified compounds. Five potential HRI inhibitors, including kaempferol-3-(2G-glucosyrutinoside), epigallocatechin gallate, tiliroside, myricetin-3-O-glucoside and cannabiscitrin, with respective docking scores of -16.0, -12.17, -11.37, -11.56 and 11.07 kcal/mol, were identified. The MMGBSA analysis of the complexes yielded free-binding energies of -69.76, -71.17, -60.44, -53.55 and -55 kcal/mol, respectively. The identified leads were stable within HRI binding pocket for the duration of the 100 ns simulation. The study identified five phytoligands with potential inhibitory effects on HRI. This finding holds promise for advancing SCD treatment strategies. However, additional preclinical analyses are warranted to validate the chemotherapeutic properties of the lead compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Afolabi J Owoloye
- Centre for Genomic Research in Biomedicine (CeGRIB), Mountain Top University, Ibafo, Nigeria
- Nigerian Institute of Medical Research, Lagos, Nigeria
- Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Samuel O Olubode
- Department of Biochemistry, Adekunle Ajasin University, Akungba, Ondo State, Nigeria
| | - Adewale Ogunleye
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Emmanuel T Idowu
- Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Kolapo M Oyebola
- Centre for Genomic Research in Biomedicine (CeGRIB), Mountain Top University, Ibafo, Nigeria
- Nigerian Institute of Medical Research, Lagos, Nigeria
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Wu N, Zhang R, Peng X, Fang L, Chen K, Jestilä JS. Elucidation of protein-ligand interactions by multiple trajectory analysis methods. Phys Chem Chem Phys 2024; 26:6903-6915. [PMID: 38334015 DOI: 10.1039/d3cp03492e] [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: 02/10/2024]
Abstract
The identification of interaction between protein and ligand including binding positions and strength plays a critical role in drug discovery. Molecular docking and molecular dynamics (MD) techniques have been widely applied to predict binding positions and binding affinity. However, there are few works that describe the systematic exploration of the MD trajectory evolution in this context, potentially leaving out important information. To address the problem, we build a framework, Moira (molecular dynamics trajectory analysis), which enables automating the whole process ranging from docking, MD simulations and various analyses as well as visualizations. We utilized Moira to analyze 400 MD simulations in terms of their geometric features (root mean square deviation and protein-ligand interaction profiler) and energetics (molecular mechanics Poisson-Boltzmann surface area) for these trajectories. Finally, we demonstrate the performance of different analysis techniques in distinguishing native poses among four poses.
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Affiliation(s)
- Nian Wu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
| | - Ruotian Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
| | - Xingang Peng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.
| | - Lincan Fang
- Department of Applied Physics, Aalto University, Espoo, Finland
| | - Kai Chen
- Institute of Catalysis, Zhejiang University, Hanghzhou, China
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Yalkut K, Ben Ali Hassine S, Basaran E, Kula C, Ozcan A, Avci FG, Keskin O, Sariyar Akbulut B, Ozbek P. Attenuation of Type IV pili activity by natural products. J Biomol Struct Dyn 2024:1-11. [PMID: 38305801 DOI: 10.1080/07391102.2024.2310781] [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: 11/08/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
The virulence factor Type IV pili (T4P) are surface appendages used by the opportunistic pathogen Pseudomonas aeruginosa for twitching motility and adhesion in the environment and during infection. Additionally, the use of these appendages by P. aeruginosa for biofilm formation increases its virulence and drug resistance. Therefore, attenuation of the activity of T4P would be desirable to control P. aeruginosa infections. Here, a computational approach has been pursued to screen natural products that can be used for this purpose. PilB, the elongation ATPase of the T4P machinery in P. aeruginosa, has been selected as the target subunit and virtual screening of FDA-approved drugs has been conducted. Screening identified two natural compounds, ergoloid and irinotecan, as potential candidates for inhibiting this T4P-associated ATPase in P. aeruginosa. These candidate compounds underwent further rigorous evaluation through molecular dynamics (MD) simulations and then through in vitro twitching motility and biofilm inhibition assays. Notably, ergoloid emerged as a particularly promising candidate for weakening the T4P activity by inhibiting the elongation ATPases associated with T4P. This repurposing study paves the way for the timely discovery of antivirulence drugs as an alternative to classical antibiotic treatments to help combat infections caused by P. aeruginosa and related pathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kerem Yalkut
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Soumaya Ben Ali Hassine
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
- Department of Bioengineering, Faculty of Engineering and Natural Sciences, Uskudar University, Istanbul, Turkey
| | - Esra Basaran
- Graduate School of Sciences and Engineering, Koc University, Istanbul, Turkey
| | - Ceyda Kula
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Aslıhan Ozcan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Fatma Gizem Avci
- Department of Bioengineering, Faculty of Engineering and Natural Sciences, Uskudar University, Istanbul, Turkey
| | - Ozlem Keskin
- Graduate School of Sciences and Engineering, Koc University, Istanbul, Turkey
| | - Berna Sariyar Akbulut
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
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Szadkowska M, Kocot AM, Sowik D, Wyrzykowski D, Jankowska E, Kozlowski LP, Makowska J, Plotka M. Molecular characterization of the PhiKo endolysin from Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29. Front Microbiol 2024; 14:1303794. [PMID: 38312500 PMCID: PMC10836841 DOI: 10.3389/fmicb.2023.1303794] [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: 09/28/2023] [Accepted: 12/12/2023] [Indexed: 02/06/2024] Open
Abstract
Introduction In the era of increasing bacterial resistance to antibiotics, new bactericidal substances are sought, and lysins derived from extremophilic organisms have the undoubted advantage of being stable under harsh environmental conditions. The PhiKo endolysin is derived from the phiKo bacteriophage infecting Gram-negative extremophilic bacterium Thermus thermophilus HB27. This enzyme shows similarity to two previously investigated thermostable type-2 amidases, the Ts2631 and Ph2119 from Thermus scotoductus bacteriophages, that revealed high lytic activity not only against thermophiles but also against Gram-negative mesophilic bacteria. Therefore, antibacterial potential of the PhiKo endolysin was investigated in the study presented here. Methods Enzyme activity was assessed using turbidity reduction assays (TRAs) and antibacterial tests. Differential scanning calorimetry was applied to evaluate protein stability. The Collection of Anti-Microbial Peptides (CAMP) and Antimicrobial Peptide Calculator and Predictor (APD3) were used to predict regions with antimicrobial potential in the PhiKo primary sequence. The minimum inhibitory concentration (MIC) of the RAP-29 synthetic peptide was determined against Gram-positive and Gram-negative selected strains, and mechanism of action was investigated with use of membrane potential sensitive fluorescent dye 3,3'-Dipropylthiacarbocyanine iodide (DiSC3(5)). Results and discussion The PhiKo endolysin is highly thermostable with melting temperature of 91.70°C. However, despite its lytic effect against such extremophiles as: T. thermophilus, Thermus flavus, Thermus parvatiensis, Thermus scotoductus, and Deinococcus radiodurans, PhiKo showed moderate antibacterial activity against mesophiles. Consequently, its protein sequence was searched for regions with potential antibacterial activity. A highly positively charged region was identified and synthetized (PhiKo105-133). The novel RAP-29 peptide lysed mesophilic strains of staphylococci and Gram-negative bacteria, reducing the number of cells by 3.7-7.1 log units and reaching the minimum inhibitory concentration values in the range of 2-31 μM. This peptide is unstructured in an aqueous solution but forms an α-helix in the presence of detergents. Moreover, it binds lipoteichoic acid and lipopolysaccharide, and causes depolarization of bacterial membranes. The RAP-29 peptide is a promising candidate for combating bacterial pathogens. The existence of this cryptic peptide testifies to a much wider panel of antimicrobial peptides than thought previously.
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Affiliation(s)
- Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Maria Kocot
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
| | - Daria Sowik
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Dariusz Wyrzykowski
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Elzbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
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Owoloye AJ, Olubode SO, Ogunleye A, Idowu ET, Oyebola KM. Computational identification of potential modulators of heme-regulated inhibitor (HRI) for pharmacological intervention against sickle cell disease. RESEARCH SQUARE 2023:rs.3.rs-3755458. [PMID: 38168168 PMCID: PMC10760220 DOI: 10.21203/rs.3.rs-3755458/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Sickle cell disease (SCD) poses a significant health challenge and therapeutic approaches often target fetal hemoglobin (HbF) to ameliorate symptoms. Hydroxyurea, a current therapeutic option for SCD, has shown efficacy in increasing HbF levels. However, concerns about myelosuppression and thrombocytopenia necessitate the exploration of alternative compounds. Heme-regulated inhibitor (HRI) presents a promising target for pharmacological intervention in SCD due to its association with HbF modulation. This study systematically screened compounds for their potential inhibitory functions against HRI. Methods Small-molecule compounds from 17 plants commonly utilized in traditional SCD management were subjected to in silico screening against HRI. Molecular docking was performed, and free binding energy calculations were determined using molecular mechanics with generalized born and surface area (MMGBSA). The lead compounds were subjected to molecular dynamics simulation at 100 ns. Computational quantum mechanical modelling of the lead compounds was subsequently performed. We further examined the pharmacodynamics, pharmacokinetic and physiological properties of the identified compounds. Results Five potential HRI inhibitors, including kaempferol-3-(2G-glucosyrutinoside), epigallocatechin gallate, tiliroside, myricetin-3-O-glucoside, and cannabiscitrin, with respective docking scores of -16.0, -12.17, -11.37, -11.56 and 11.07 kcal/mol, were identified. The MMGBSA analysis of the complexes yielded free-binding energies of -69.76, -71.17, -60.44, 53.55, and - 55 kcal/mol, respectively. The identified leads were stable within HRI binding pocket for the duration of 100 ns simulation. Conclusions The study successfully identified five phytoligands with potential inhibitory effects on HRI, opening avenues for their use as modulators of HbF in SCD patients. This finding holds promise for advancing treatment strategies in SCD. However, additional preclinical analyses are warranted to validate the chemotherapeutic properties of the lead compounds.
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An T, Cao D, Zhang Y, Han X, Yu Z, Liu Z. Norsesquiterpenes from the Latex of Euphorbia dentata and Their Chemical Defense Mechanisms against Helicoverpa armigera. Molecules 2023; 28:7681. [PMID: 38067412 PMCID: PMC10707868 DOI: 10.3390/molecules28237681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Euphorbia dentata (Euphorbiaceae), an invasive weed, is rarely eaten by herbivorous insects and could secrete a large amount of white latex, causing a serious threat to local natural vegetation, agricultural production and human health. In order to prevent this plant from causing more negative effects on humans, it is necessary to understand and utilize the chemical relationships between the latex of E. dentata and herbivorous insects. In this study, three new norsesquiterpenes (1-3), together with seven known analogues (4-10), were isolated and identified from the latex of E. dentata. All norsesquiterpenes (1-10) showed antifeedant and growth-inhibitory effects on H. armigera with varying levels, especially compounds 1 and 2. In addition, the action mechanisms of active compounds (1-3) were revealed by detoxifying enzyme (AchE, CarE, GST and MFO) activities and corresponding molecular docking analyses. Our findings provide a new idea for the development and utilization of the latex of E. dentata, as well as a potential application of norsesquiterpenes in botanical insecticides.
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Affiliation(s)
- Tong An
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China; (D.C.); (Y.Z.); (X.H.)
| | - Dongxu Cao
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China; (D.C.); (Y.Z.); (X.H.)
| | - Yangyang Zhang
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China; (D.C.); (Y.Z.); (X.H.)
| | - Xiamei Han
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China; (D.C.); (Y.Z.); (X.H.)
| | - Zhiguo Yu
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
| | - Zhixiang Liu
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China; (D.C.); (Y.Z.); (X.H.)
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Li C, Dong X, Yu H, Yu Y. Al distribution and structural stability of H-BEA zeolites at different Si/Al ratios and temperatures: a first-principles study. Phys Chem Chem Phys 2023; 25:24547-24562. [PMID: 37661842 DOI: 10.1039/d3cp02380j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Beta zeolites have been widely used in acid-catalyzed reactions because of their excellent properties. An in-depth study of the position, quantity, and distribution of beta zeolites substituted by Al is significant to understand the catalytic performance of the active site of zeolite catalysts. The distribution of Al in H-BEA and the structure of silanol nests in dealuminated BEA at different Si/Al ratios and synthesis temperatures were studied by the DFT method. T1, T2, T7, and T9 sites were chosen to be simulated. The synthesis temperature can change the distribution of Al and the proportion of T sites at different Si/Al ratios. The proportion of T7 and T9 is more than 70% at different Si/Al ratios of H-BEA and decreases with the synthesis temperature. T1 and T2 sites begin to appear when Si/Al < 20 and the proportion of T1 and T2 sites is less than 20%. When Si/Al < 8, the substitution energy of the AlSiAl structure, which has Si(2Al, 2Si) species, is obviously lower than that of the normal structure, which indicates that the Al-O-Si-O-Al species will appear in H-BEA. The Al(T7)Si(T5)Al(T9)Si(T5)Al(T7) and Al(T1)Si(T1)Al(T9) groups can not only stabilize H-BEA but also play an essential role in the formation of Si(2Al, 2Si) species. For dealuminated BEA zeolites, the silanol nest forms four hydrogen bonds through four silanols. The orientation of silanol groups in the silanol nest formed after dealumination at different T sites is different. The T7 and T9 sites in H-BEA are more likely to undergo dealumination. By contrast, the dealumination of the T1 and T2 sites is a challenge.
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Affiliation(s)
- Changdong Li
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University, Tianjin 300072, China.
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, China
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, China
| | - Xiuqin Dong
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University, Tianjin 300072, China.
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, China
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, China
| | - Haipeng Yu
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University, Tianjin 300072, China.
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, China
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, China
| | - Yingzhe Yu
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University, Tianjin 300072, China.
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, China
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, China
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Zhou S, Liu Y, Wang S, Wang L. Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds. Sci Rep 2023; 13:13741. [PMID: 37612311 PMCID: PMC10447522 DOI: 10.1038/s41598-023-40614-7] [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: 05/04/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.
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Affiliation(s)
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
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Ozcan A, Keskin O, Sariyar Akbulut B, Ozbek P. Piperidine-based natural products targeting Type IV pili antivirulence: A computational approach. J Mol Graph Model 2023; 119:108382. [PMID: 36463631 DOI: 10.1016/j.jmgm.2022.108382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/01/2022] [Accepted: 11/23/2022] [Indexed: 11/28/2022]
Abstract
Type IV (T4) pilus is among the virulence factors with a key role in serious bacterial diseases. Specifically, in Neisseria meningitidis and Pseudomonas aeruginosa, it determines pathogenicity and causes infection. Here, a computational approach has been pursued to find piperidine-based inhibitor molecules against the elongation ATPase of T4 pili in these two selected pathogens. Using the modeled structures of the PilF and PilB ATPases of N. meningitidis and P. aeruginosa, virtual library screening via molecular docking has returned inhibitor molecule candidates. The dynamics of the best three binders have further been investigated in detail via molecular dynamic simulations. Among these, ligands with COCONUT IDs CNP0030078 and CNP0051517 were found to have higher potential in the inhibition of ATPases based on molecular dynamic simulation analysis and biological activity information. The obtained results will guide future efforts in antivirulence drug development against T4 pili of N. meningitidis and P. aeruginosa.
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Affiliation(s)
- Aslihan Ozcan
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Ozlem Keskin
- College of Engineering, Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Berna Sariyar Akbulut
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Pemra Ozbek
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey.
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13
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Wieduwilt EK, Boto RA, Macetti G, Laplaza R, Contreras-García J, Genoni A. Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J Chem Theory Comput 2023; 19:1063-1079. [PMID: 36656682 DOI: 10.1021/acs.jctc.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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14
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Liu Z, Ma X, Zhang N, Yuan L, Yin H, Zhang L, An T, Xu Y. Phenylpropanoid amides from Solanum rostratum and their phytotoxic activities against Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1174844. [PMID: 37123827 PMCID: PMC10130401 DOI: 10.3389/fpls.2023.1174844] [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: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Introduction Solanum rostratum, an annual malignant weed, has seriously damaged the ecological environment and biodiversity of invasion area. This alien plant gains a competitive advantage by producing some new phytotoxic substances to inhibit the growth of native plants, thus achieving successful invasion. However, the chemical structures, inhibitory functions and action mechanisms of phytotoxic substances of S. rostratum remain unclear. Methods In this study, to clarify the chemical structures of phytotoxic substances from S. rostratum, we isolated phenylpropanoid amides from the plant. Their structures were identified by comprehensive HR-ESIMS, NMR and ECD data. And the inhibitory functions of isolated phenylpropanoid amides on one model plant (Arabidopsis thaliana) were also investigated. In addition, the action mechanisms of active phenylpropanoid amides were revealed by antioxidant-related enzymes [Catalase (CAT), Peroxidase (POD), Superoxide dismutase (SOD)] activities and corresponding molecular docking analyses. Results and Discussion Phytochemical research on the whole plant of S. rostratum led to the isolation and identification of four new phenylpropanoid amides (1-4), together with two known analogues (5-6). All the compounds showed phytotoxic effects with varying levels on the seed germination and root elongation of one model plant (Arabidopsis thaliana), especially compound 2 and 4. Likewise, compounds 2 and 4 displayed potent inhibitory effects on antioxidant-related enzyme (POD). In addition, compounds 2 and 4 formed common conventional hydrogen bonds with residues Ala34 and Ser35 in POD revealed by molecular docking analyses. These findings not only helped to reveal the invasion mechanism of S. rostratum from the perspective of "novel weapons hypothesis", but also opened up new ways for the exploitation and utilization of S. rostratum.
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Affiliation(s)
- Zhixiang Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaoqing Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Nan Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Linlin Yuan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Hongrui Yin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Lingling Zhang
- Department of Pharmacy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Tong An
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Tong An, ; Yubin Xu,
| | - Yubin Xu
- Department of Pharmacy, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
- *Correspondence: Tong An, ; Yubin Xu,
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15
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Ünver Y, Süleymanoğlu N, Ustabaş R, Güler Hİ, Bektaş E, Bektaş Kİ, Çelik F. New carbazol derivatives containing 1,2,4-triazole: Synthesis, characterization, DFT study, acetylcholinesterase activity and docking study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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16
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Srivastava R. Computational Studies on Antibody Drug Conjugates (ADCs) for Precision Oncology. ChemistrySelect 2022. [DOI: 10.1002/slct.202202259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ruby Srivastava
- Bioinformatics CSIR-Centre for Cellular and Molecular Biology, CGCR+CC3 Uppal Rd, IICT Colony, Habsiguda Hyderabad Telangana 500007
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17
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fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLoS Comput Biol 2022; 18:e1009783. [PMID: 35653385 PMCID: PMC9197077 DOI: 10.1371/journal.pcbi.1009783] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/14/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Computational methods play a pivotal role in drug discovery and are widely applied in virtual screening, structure optimization, and compound activity profiling. Over the last decades, almost all the attention in medicinal chemistry has been directed to protein-ligand binding, and computational tools have been created with this target in mind. With novel discoveries of functional RNAs and their possible applications, RNAs have gained considerable attention as potential drug targets. However, the availability of bioinformatics tools for nucleic acids is limited. Here, we introduce fingeRNAt—a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands. The program detects nine types of interactions: (i) hydrogen and (ii) halogen bonds, (iii) cation-anion, (iv) pi-cation, (v) pi-anion, (vi) pi-stacking, (vii) inorganic ion-mediated, (viii) water-mediated, and (ix) lipophilic interactions. However, the scope of detected interactions can be easily expanded using a simple plugin system. In addition, detected interactions can be visualized using the associated PyMOL plugin, which facilitates the analysis of medium-throughput molecular complexes. Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt)—a binary string where the respective bit in the fingerprint is set to 1 if a particular interaction is present and to 0 otherwise. This output format, in turn, enables high-throughput analysis of interaction data using data analysis techniques. We present applications of fingeRNAt-generated interaction fingerprints for visual and computational analysis of RNA-ligand complexes, including analysis of interactions formed in experimentally determined RNA-small molecule ligand complexes deposited in the Protein Data Bank. We propose interaction fingerprint-based similarity as an alternative measure to RMSD to recapitulate complexes with similar interactions but different folding. We present an application of interaction fingerprints for the clustering of molecular complexes. This approach can be used to group ligands that form similar binding networks and thus have similar biological properties. The fingeRNAt software is freely available at https://github.com/n-szulc/fingeRNAt.
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18
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Saeed M, Tasleem M, Shoaib A, Alabdallah NM, Alam MJ, El Asmar Z, Jamal QMS, Bardakci F, Ansari IA, Ansari MJ, Wang F, Badraoui R, Yadav DK. Investigation of antidiabetic properties of shikonin by targeting aldose reductase enzyme: In silico and in vitro studies. Biomed Pharmacother 2022; 150:112985. [PMID: 35658219 DOI: 10.1016/j.biopha.2022.112985] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 02/08/2023] Open
Abstract
Diabetes is a complicated multifactorial disorder in which the patient generally observes polyphagia, polydipsia, and polyuria due to uncontrolled growth in blood sugar levels. For its management, the pharmaceutical industry is working day and night to find a better drug with no or least toxicity. That's why nowadays a more focused branch is to use herbal phytoconstituents for its prevention. Shikonin is a naphthoquinone natural dye that is isolated from the plants of the Boraginaceae family and has proven its role as an anti-cancer, anti-inflammatory, and anti-gonadotrophic agent. In our previous study, we have published its anti-diabetic action by inhibiting the enzyme protein tyrosine phosphatase 1B. In this study, we were more focused on finding out the role of Shikonin and its pharmacophores by inhibiting the action of aldose reductase (AR) enzyme. The study was conducted using pharmacophore modeling, molecular docking, and molecular dynamics simulation studies. The absorption, distribution, metabolism, excretion (ADME), and toxicity profile were also evaluated in this study. Along with all the computational biology parameters we also focused on the in vitro activity and kinetic study of inhibitory activity of Shikonin against aldose reductase.
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Affiliation(s)
- Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, Hail 81451, Saudi Arabia.
| | - Munazzah Tasleem
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ambreen Shoaib
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, P.O. Box No. 114, Jazan 45142, Saudi Arabia
| | - Nadiyah M Alabdallah
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441, Dammam, Saudi Arabia
| | - Md Jahoor Alam
- Department of Biology, College of Sciences, University of Hail, Hail 81451, Saudi Arabia
| | - Zeina El Asmar
- Department of Biology, College of Sciences, University of Hail, Hail 81451, Saudi Arabia
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Fevzi Bardakci
- Department of Biology, College of Sciences, University of Hail, Hail 81451, Saudi Arabia
| | | | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad, Mahatma Jyotiba Phule Rohilkhand University, Bareilly 244001, India
| | - Feng Wang
- Department of Medical Oncology, Cancer Center, West China Hospital, West China Medical School, Sichuan University, Sichuan, PR China.
| | - Riadh Badraoui
- Department of Biology, College of Sciences, University of Hail, Hail 81451, Saudi Arabia; Section of Histology-Cytology, Medicine Faculty of Tunis, University of Tunis El Manar, La Rabta-Tunis, 1007, Tunisia
| | - Dharmendra Kumar Yadav
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Yeonsu-gu, Incheon 21924, South Korea.
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19
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Forchlorfenuron and Novel Analogs Cause Cytotoxic Effects in Untreated and Cisplatin-Resistant Malignant Mesothelioma-Derived Cells. Int J Mol Sci 2022; 23:ijms23073963. [PMID: 35409322 PMCID: PMC8999537 DOI: 10.3390/ijms23073963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
Malignant mesothelioma (MM) is a currently incurable, aggressive cancer derived from mesothelial cells, most often resulting from asbestos exposure. The current first-line treatment in unresectable MM is cisplatin/pemetrexed, which shows very little long-term effectiveness, necessitating research for novel therapeutic interventions. The existing chemotherapies often act on the cytoskeleton, including actin filaments and microtubules, but recent advances indicate the ‘fourth’ form consisting of the family of septins, representing a novel target. The septin inhibitor forchlorfenuron (FCF) and FCF analogs inhibit MM cell growth in vitro, but at concentrations which are too high for clinical applications. Based on the reported requirement of the chloride group in the 2-position of the pyridine ring of FCF for MM cell growth inhibition and cytotoxicity, we systematically investigated the importance (cell growth-inhibiting capacity) of the halogen atoms fluorine, chlorine, bromine and iodine in the 2- or 3-position of the pyridine ring. The MM cell lines ZL55, MSTO-211H, and SPC212, and—as a control—immortalized Met-5A mesothelial cells were used. The potency of the various halogen substitutions in FCF was mostly correlated with the atom size (covalent radius); the small fluoride analogs showed the least effect, while the largest one (iodide) most strongly decreased the MTT signals, in particular in MM cells derived from epithelioid MM. In the latter, the strongest effects in vitro were exerted by the 2-iodo and, unexpectedly, the 2-trifluoromethyl (2-CF3) FCF analogs, which were further tested in vivo in mice. However, FCF-2-I and, more strongly, FCF-2-CF3 caused rapidly occurring strong symptoms of systemic toxicity at doses lower than those previously obtained with FCF. Thus, we investigated the effectiveness of FCF (and selected analogs) in vitro in MM cells which were first exposed to cisplatin. The slowly appearing population of cisplatin-resistant cells was still susceptible to the growth-inhibiting/cytotoxic effect of FCF and its analogs, indicating that cisplatin and FCF target non-converging pathways in MM cells. Thus, a combination therapy of cisplatin and FCF (analogs) might represent a new avenue for the treatment of repopulating chemo-resistant MM cells in this currently untreatable cancer.
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20
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Perillyl alcohol and its synthetic derivatives: the rising of a novel class of selective and potent antitumoral compounds. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02870-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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de Sá ÉRA, Souza JL, Costa RKM, Barros RO, de Lima CEB, Lima FDCA, Ramos RM. Computational investigation of the alkaloids of Pilocarpus microphyllus species as phytopharmaceuticals for the inhibition of sterol 14α-demethylase protease of Trypanosoma cruzi. J Biomol Struct Dyn 2022; 41:2555-2573. [PMID: 35132947 DOI: 10.1080/07391102.2022.2035819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Trypanosoma cruzi is a protozoan transmitted by the insect Triatoma infestans, popularly known as kissing bug. This protozoan causes the Chagas disease, a Neglected Tropical Disease. This study aimed to investigate, through DFT method and B3LYP hybrid functional, the physicochemical, pharmacokinetic, and pharmacodynamic properties of the alkaloids present in the leaves of the species Pilocarpus microphyllus (jaborandi) as a potential inhibitory activity on the protease sterol 14α-demethylase of T. cruzi associated with the techniques of molecular docking, molecular dynamics, MM-PBSA and ADMET predictions. The molecules of isopilosine, epiisopiloturine, epiisopilosine, and pilosine showed up the lowest binding energies by molecular docking, good human intestinal absorption, low penetration in the blood-brain barrier, antiprotozoal and anticarcinogenic activities in ADMET studies. It has been observed a better binding affinity of the sterol 14α-demethylase protease with isopilosine in molecular dynamics and MM-PBSA studies, which indicates it as a potential drug candidate for Chagas disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ézio R. A. de Sá
- Federal Institute of Education, Science and Technology of Piauí, IFPI, Picos, Piauí, Brazil
- Graduate Program in Chemistry, Federal University of Piauí, PPGQ/UFPI, Teresina, Piauí, Brazil
- Research Laboratory of the Computational Quantum Chemistry and Drug Planning Group, Chemistry Department, State University of Piauí, GQQC&PF/UESPI, Teresina, Piauí, Brazil
- Research Laboratory in Information Systems, Information Department, Environment, Health and Food Production, Federal Institute of Education, Science and Technology of Piauí, LaPeSI/IFPI, Teresina, Piauí, Brazil
| | - Janilson L. Souza
- Federal Institute of Education, Science and Technology of Maranhão, IFMA, Bacabal, Maranhão, Brazil
| | - Rayla K. M. Costa
- Research Laboratory of the Computational Quantum Chemistry and Drug Planning Group, Chemistry Department, State University of Piauí, GQQC&PF/UESPI, Teresina, Piauí, Brazil
| | - Rômulo O. Barros
- Research Laboratory in Information Systems, Information Department, Environment, Health and Food Production, Federal Institute of Education, Science and Technology of Piauí, LaPeSI/IFPI, Teresina, Piauí, Brazil
| | - Carlos E. B. de Lima
- University Hospital, Federal University of Piauí, Discipline of Cardiology, Department of General Practice - Cardiology and Health Sciences Center, DCG/CCS/UFPI, Teresina, Piauí, Brazil
| | - Francisco das C. A. Lima
- Research Laboratory of the Computational Quantum Chemistry and Drug Planning Group, Chemistry Department, State University of Piauí, GQQC&PF/UESPI, Teresina, Piauí, Brazil
| | - Ricardo M. Ramos
- Research Laboratory in Information Systems, Information Department, Environment, Health and Food Production, Federal Institute of Education, Science and Technology of Piauí, LaPeSI/IFPI, Teresina, Piauí, Brazil
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22
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Wang X, Allen S, Blake JF, Bowcut V, Briere DM, Calinisan A, Dahlke JR, Fell JB, Fischer JP, Gunn RJ, Hallin J, Laguer J, Lawson JD, Medwid J, Newhouse B, Nguyen P, O'Leary JM, Olson P, Pajk S, Rahbaek L, Rodriguez M, Smith CR, Tang TP, Thomas NC, Vanderpool D, Vigers GP, Christensen JG, Marx MA. Identification of MRTX1133, a Noncovalent, Potent, and Selective KRAS G12D Inhibitor. J Med Chem 2021; 65:3123-3133. [PMID: 34889605 DOI: 10.1021/acs.jmedchem.1c01688] [Citation(s) in RCA: 248] [Impact Index Per Article: 82.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
KRASG12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of solid tumors. However, when compared to KRASG12C, selective inhibition of KRASG12D presents a significant challenge due to the requirement of inhibitors to bind KRASG12D with high enough affinity to obviate the need for covalent interactions with the mutant KRAS protein. Here, we report the discovery and characterization of the first noncovalent, potent, and selective KRASG12D inhibitor, MRTX1133, which was discovered through an extensive structure-based activity improvement and shown to be efficacious in a KRASG12D mutant xenograft mouse tumor model.
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Affiliation(s)
- Xiaolun Wang
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Shelley Allen
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - James F Blake
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Vickie Bowcut
- Mirati Therapeutics, San Diego, California 92121, United States
| | - David M Briere
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Joshua R Dahlke
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Jay B Fell
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - John P Fischer
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Robin J Gunn
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Jill Hallin
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Jade Laguer
- Mirati Therapeutics, San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - James Medwid
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Brad Newhouse
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Phong Nguyen
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Jacob M O'Leary
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Peter Olson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Spencer Pajk
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Lisa Rahbaek
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Mareli Rodriguez
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | | | - Tony P Tang
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Nicole C Thomas
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Guy P Vigers
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | | | - Matthew A Marx
- Mirati Therapeutics, San Diego, California 92121, United States
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23
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Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Nat Commun 2021; 12:7057. [PMID: 34862374 PMCID: PMC8642532 DOI: 10.1038/s41467-021-27142-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 11/05/2021] [Indexed: 12/15/2022] Open
Abstract
In response to genotoxic stress, the tumor suppressor p53 acts as a transcription factor by regulating the expression of genes critical for cancer prevention. Mutations in the gene encoding p53 are associated with cancer development. PRIMA-1 and eprenetapopt (APR-246/PRIMA-1MET) are small molecules that are converted into the biologically active compound, methylene quinuclidinone (MQ), shown to reactivate mutant p53 by binding covalently to cysteine residues. Here, we investigate the structural basis of mutant p53 reactivation by MQ based on a series of high-resolution crystal structures of cancer-related and wild-type p53 core domains bound to MQ in their free state and in complexes with their DNA response elements. Our data demonstrate that MQ binds to several cysteine residues located at the surface of the core domain. The structures reveal a large diversity in MQ interaction modes that stabilize p53 and its complexes with DNA, leading to a common global effect that is pertinent to the restoration of non-functional p53 proteins. The tumor suppressor p53 is mutated in more than half of human cancers and the compound methylene quinuclidinone (MQ) was shown to reactivate p53 mutants by binding covalently to cysteine residues. Here, the authors present crystal structures of wild-type and cancer related p53 mutant core domains bound to MQ alone and in complex with their DNA response elements and observe that MQ is bound to several cysteine residues located at the surface of the core domain.
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24
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El Sayed DS, Abdelrehim ESM. Computational details of molecular structure, spectroscopic properties, topological studies and SARS-Cov-2 enzyme molecular docking simulation of substituted triazolo pyrimidine thione heterocycles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 261:120006. [PMID: 34098482 PMCID: PMC8149157 DOI: 10.1016/j.saa.2021.120006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/30/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Investigation the molecular structure of the system requires a detailed experience in dealing with theoretical computational guides to highlight its important role. Molecular structure of three heterocyclic compounds 8,10-diphenylpyrido[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine-3(2H)-thione (HL), 8-phenyl-10-(p-tolyl)pyrido[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine-3(2H)-thione (CH3L) and10-(4-nitrophenyl)-8-phenylpyrido[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine-3(2H)-thione (NO2L) was studied at DFT/B3LYP/6-31G (d,p) level in ethanol solvent. Spectroscopic properties such Infrared (IR, 1H NMR and 13C NMR) and ultraviolet-visible (UV-VIS) analyses were computed. Some quantum and reactivity parameters (HOMO energy, LUMO energy, energy gap, ionization potential, electron affinity, chemical potential, global softness, lipophelicity) were studied, also molecular electrostatic potential (MEP) was performed to indicate the reactive nucleophilic and electrophilic sites. The effects of H-, CH3- and NO2- substituents on heterocyclic ligands were studied and it was found that the electron donation sites concerned with hydrogen and methyl substituents over nitro substituent. Topological analysis using reduced density gradient (RDG) was discussed in details. To predict the relevant antiviral activity of the reported heterocyclic compounds, molecular docking simulation was applied to the crystal structure of SARS-Cov-2 viral Mpro enzyme with 6WTT code and PLpro with 7JRN code. The enzymatic viral protein gives an image about the binding affinity between the target protein receptor and the heterocyclic ligands entitled. The hydrogen bonding interactions were evaluated from molecular docking with different strength for each ligand compound to discuss the efficiency of heterocyclic ligands toward viral inhibition.
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Affiliation(s)
- Doaa S El Sayed
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt.
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Baskaran K, Wilburn C, Wedell J, Koharudin L, Ulrich E, Schuyler A, Eghbalnia H, Gronenborn A, Hoch J. Anomalous amide proton chemical shifts as signatures of hydrogen bonding to aromatic sidechains. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:765-775. [PMID: 37905229 PMCID: PMC10539802 DOI: 10.5194/mr-2-765-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 11/02/2023]
Abstract
Hydrogen bonding between an amide group and the p-π cloud of an aromatic ring was first identified in a protein in the 1980s. Subsequent surveys of high-resolution X-ray crystal structures found multiple instances, but their preponderance was determined to be infrequent. Hydrogen atoms participating in a hydrogen bond to the p-π cloud of an aromatic ring are expected to experience an upfield chemical shift arising from a shielding ring current shift. We surveyed the Biological Magnetic Resonance Data Bank for amide hydrogens exhibiting unusual shifts as well as corroborating nuclear Overhauser effects between the amide protons and ring protons. We found evidence that Trp residues are more likely to be involved in p-π hydrogen bonds than other aromatic amino acids, whereas His residues are more likely to be involved in in-plane hydrogen bonds, with a ring nitrogen acting as the hydrogen acceptor. The p-π hydrogen bonds may be more abundant than previously believed. The inclusion in NMR structure refinement protocols of shift effects in amide protons from aromatic sidechains, or explicit hydrogen bond restraints between amides and aromatic rings, could improve the local accuracy of sidechain orientations in solution NMR protein structures, but their impact on global accuracy is likely be limited.
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Affiliation(s)
- Kumaran Baskaran
- Department of Molecular Biology and Biophysics, UConn Health, 263
Farmington Ave., Farmington, CT 06030-3305 USA
| | - Colin W. Wilburn
- Department of Molecular Biology and Biophysics, UConn Health, 263
Farmington Ave., Farmington, CT 06030-3305 USA
| | - Jonathan R. Wedell
- Department of Molecular Biology and Biophysics, UConn Health, 263
Farmington Ave., Farmington, CT 06030-3305 USA
| | - Leonardus M. I. Koharudin
- Department of Structural Biology University of Pittsburgh School of
Medicine 3501 Fifth Ave., Pittsburgh, PA 15260 USA
| | - Eldon L. Ulrich
- Department of Molecular Biology and Biophysics, UConn Health, 263
Farmington Ave., Farmington, CT 06030-3305 USA
| | - Adam D. Schuyler
- Department of Molecular Biology and Biophysics, UConn Health, 263
Farmington Ave., Farmington, CT 06030-3305 USA
| | - Hamid R. Eghbalnia
- Department of Molecular Biology and Biophysics, UConn Health, 263
Farmington Ave., Farmington, CT 06030-3305 USA
| | - Angela M. Gronenborn
- Department of Structural Biology University of Pittsburgh School of
Medicine 3501 Fifth Ave., Pittsburgh, PA 15260 USA
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, 263
Farmington Ave., Farmington, CT 06030-3305 USA
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Tesmar A, Kogut MM, Żamojć K, Grabowska O, Chmur K, Samsonov SA, Makowska J, Wyrzykowski D, Chmurzyński L. Physicochemical nature of sodium dodecyl sulfate interactions with bovine serum albumin revealed by interdisciplinary approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Metabolic profiling, ADME pharmacokinetics, molecular docking studies and antibacterial potential of Phyllantus muellerianus leaves. ADVANCES IN TRADITIONAL MEDICINE 2021. [PMCID: PMC8444527 DOI: 10.1007/s13596-021-00611-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Global increase in the level of antimicrobial resistance among bacterial pathogens has prompted the search for alternative treatment from medicinal plants. Phyllantus muellerianus leaves has been used traditionally against microorganisms of medical importance, hence the need to evaluate the pharmacological pathways and mode of actions using in vitro and in silico approaches. Clinical isolates of eight (8) microorganisms associated with urinary tract infections were obtained and identified using morphological and biochemical methods. Phyllantus muellerianus leaves were extracted and purified by solvent partitioning. Ethyl acetate fraction of PM had the highest yield and zone diameter range from 13.5 ± 1.00 to 28 ± 1.53 mm. The rate of protein leakage per time interval of Staphylococcus aureus increased from 9.29 μg/ml at 0 min to 17.43 μg/ml at 120 min while leakage in Candida albicans also increased from 8.57 μg/ml at 0 min to 70.43 μg/ml at 120 min. GCMS fingerprints, pharmacodynamics and pharmacokinetic studies revealed the active agent as quindoline, an azaindole and isotere of indoles having a binding energy of −9.1 kcal/mol. Analyses of the structural and atomic orientations of quindoline, and superimposition on ciprofloxacin, a common antibiotic revealed an interesting comparison, effecting a stronger binding affinity of Quindoline-HMG-CoA complex.
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Bektaş E, Sahin H, Beldüz AO, Güler Hİ. HIV-1-RT inhibition activity of Satureja spicigera (C.KOCH) BOISS. Aqueous extract and docking studies of phenolic compounds identified by RP-HPLC-DAD. J Food Biochem 2021; 46:e13921. [PMID: 34477237 DOI: 10.1111/jfbc.13921] [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: 06/25/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
AIDS is a global disease caused by HIV, affecting millions of people and causing death. The current limitations of antiretroviral therapy used in the therapy of HIV/AIDS have led to the need to search for new and effective drugs from natural products, especially plants. Herewith, using the present study, the detection of HIV-1-RT inhibition of aqueous extract of Satureja spicigera (C.KOCH) BOISS. was performed for the first time. Besides, total phenolic content (TPC), analysis of phenolic constituents by RP-HPLC-DAD and antioxidant capacity by DPPH and Ferric reducing antioxidant power (FRAP) methods were determined for the first time. In addition, molecular docking studies were carried out between HIV-1-RT and phenolic substances, the presence of which was determined in the aqueous extract, for the determination of the phenolics that may be responsible for HIV-1-RT activity. HIV-1-RT inhibition was defined as IC50 : 22.83 μg/ml. Benzoic acid, vanillin, rutin, and chlorogenic acid were present as main phenolics in quantities of 621.96, 505.87, 349.33, and 323.23 µg phenolic/g extract, respectively. Further, TPC, DPPH, and FRAP were calculated as in the order of 151.69 mg GAE/g extract, 23.77 µg/ml, and 445.7 µmol TE/g extract. Chlorogenic acid (-8.48 kcal/mol) was found to be the most effective ligand in docking studies, with a value close to positive standard nevirapine (-9.35 kcal/mol). Hereby, although the aqueous extract of S. spicigera can be used as a natural antioxidant, the crude extract or its phenolics have the potential to be used in the treatment of AIDS due to its high HIV-1-RT activity. PRACTICAL APPLICATIONS: In this study, anti-HIV-1-RT and antioxidant activity and total phenolic content of Satureja spicigera aqueous extract were determined. In addition, HPLC analysis of some phytochemicals and the activities of these phytochemicals against HIV-1-RT enzyme was determined by molecular docking studies. The results showed that the aqueous extract of S. spicigera and some of the phytochemicals it contains have the potential to be used as a natural product against HIV infection or in the treatment of AIDS.
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Affiliation(s)
- Ersan Bektaş
- Espiye Vocational School, Giresun University, Giresun, Turkey
| | - Huseyin Sahin
- Espiye Vocational School, Giresun University, Giresun, Turkey
| | - Ali Osman Beldüz
- Faculty of Science, Department of Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Halil İbrahim Güler
- Faculty of Science, Department of Molecular Biology and Genetics, Karadeniz Technical University, Trabzon, Turkey
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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Zhou J, Rao L, Yu G, Cook TR, Chen X, Huang F. Supramolecular cancer nanotheranostics. Chem Soc Rev 2021; 50:2839-2891. [PMID: 33524093 DOI: 10.1039/d0cs00011f] [Citation(s) in RCA: 209] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Among the many challenges in medicine, the treatment and cure of cancer remains an outstanding goal given the complexity and diversity of the disease. Nanotheranostics, the integration of therapy and diagnosis in nanoformulations, is the next generation of personalized medicine to meet the challenges in precise cancer diagnosis, rational management and effective therapy, aiming to significantly increase the survival rate and improve the life quality of cancer patients. Different from most conventional platforms with unsatisfactory theranostic capabilities, supramolecular cancer nanotheranostics have unparalleled advantages in early-stage diagnosis and personal therapy, showing promising potential in clinical translations and applications. In this review, we summarize the progress of supramolecular cancer nanotheranostics and provide guidance for designing new targeted supramolecular theranostic agents. Based on extensive state-of-the-art research, our review will provide the existing and new researchers a foundation from which to advance supramolecular cancer nanotheranostics and promote translationally clinical applications.
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Affiliation(s)
- Jiong Zhou
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China.
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Milanović ŽB, Dimić DS, Avdović EH, Milenković DA, Marković JD, Klisurić OR, Trifunović SR, Marković ZS. Synthesis and comprehensive spectroscopic (X-ray, NMR, FTIR, UV–Vis), quantum chemical and molecular docking investigation of 3-acetyl-4‑hydroxy‑2-oxo-2H-chromen-7-yl acetate. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129256] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Rahman ZU, Al Kury LT, Alattar A, Tan Z, Alshaman R, Malik I, Badshah H, Uddin Z, Khan Khalil AA, Muhammad N, Khan S, Ali A, Shah FA, Li JB, Li S. Carveol a Naturally-Derived Potent and Emerging Nrf2 Activator Protects Against Acetaminophen-Induced Hepatotoxicity. Front Pharmacol 2021; 11:621538. [PMID: 33597885 PMCID: PMC7883019 DOI: 10.3389/fphar.2020.621538] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022] Open
Abstract
Acetaminophen (N-acetyl p-aminophenol or APAP) is used worldwide for its antipyretic and anti-inflammatory potential. However, APAP overdose sometimes causes severe liver damage. In this study, we elucidated the protective effects of carveol in liver injury, using molecular and in silico approaches. Male BALB/c mice were divided into two experimental cohorts, to identify the best dose and to further assess the role of carveol in the nuclear factor E2-related factor; nuclear factor erythroid 2; p45-related factor 2 (Nrf2) pathway. The results demonstrated that carveol significantly modulated the detrimental effects of APAP by boosting endogenous antioxidant mechanisms, such as nuclear translocation of Nrf2 gene, a master regulator of the downstream antioxidant machinery. Furthermore, an inhibitor of Nrf2, called all-trans retinoic acid (ATRA), was used, which exaggerated APAP toxicity, in addition to abrogating the protective effects of carveol; this effect was accompanied by overexpression of inflammatory mediators and liver = 2ltoxicity biomarkers. To further support our notion, we performed virtual docking of carveol with Nrf2-keap1 target, and the resultant drug-protein interactions validated the in vivo findings. Together, our findings suggest that carveol could activate the endogenous master antioxidant Nrf2, which further regulates the expression of downstream antioxidants, eventually ameliorating the APAP-induced inflammation and oxidative stress.
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Affiliation(s)
- Zaif Ur Rahman
- Shenzhen University Clinical Research Center for Neurological Diseases, Health Management Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China.,Department of Pharmacy, Abdul Wali Khan University, Khyber Pakhtunkhwa, Pakistan
| | - Lina Tariq Al Kury
- College of Natural and Health Sciences, Zayed University, Abu Dhabi, United Arab Emirates
| | - Abdullah Alattar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Tabuk, Tabuk, Saudi Arabia
| | - Zhen Tan
- Shenzhen University Clinical Research Center for Neurological Diseases, Health Management Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China
| | - Reem Alshaman
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Tabuk, Tabuk, Saudi Arabia
| | - Imran Malik
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Haroon Badshah
- Department of Pharmacy, Abdul Wali Khan University, Khyber Pakhtunkhwa, Pakistan
| | - Zia Uddin
- Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Atif Ali Khan Khalil
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan University, Khyber Pakhtunkhwa, Pakistan
| | - Saifullah Khan
- Department of Microbiology and Biotechnology, Abasyn University Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Amjad Ali
- Department of Botany, University of Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Fawad Ali Shah
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Jing Bo Li
- Shenzhen University Clinical Research Center for Neurological Diseases, Health Management Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China
| | - Shupeng Li
- State Key Laboratory of Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen, China
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Wieduwilt EK, Boisson JC, Terraneo G, Hénon E, Genoni A. A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. J Chem Inf Model 2021; 61:795-809. [PMID: 33444021 DOI: 10.1021/acs.jcim.0c01188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Jean-Charles Boisson
- CReSTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milan I-20131, Italy
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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Milanović ŽB, Antonijević MR, Amić AD, Avdović EH, Dimić DS, Milenković DA, Marković ZS. Inhibitory activity of quercetin, its metabolite, and standard antiviral drugs towards enzymes essential for SARS-CoV-2: the role of acid-base equilibria. RSC Adv 2021; 11:2838-2847. [PMID: 35424215 PMCID: PMC8693803 DOI: 10.1039/d0ra09632f] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/31/2020] [Indexed: 12/21/2022] Open
Abstract
The recently declared global pandemic of a new human coronavirus called SARS-CoV-2, which causes respiratory tract disease COVID-19, has reached worldwide resonance and global efforts are being made to look for possible cures. Sophisticated molecular docking software, as well as available protein sequence and structure information, offer the ability to test the inhibition of two important targets of SARS-CoV-2, furin (FUR) enzyme, and spike glycoprotein, or spike protein (SP), that are key to host cell adhesion and hijacking. The potential inhibitory effect and mechanism of action of acid-base forms of different antiviral drugs, dominant at physiological pH, chloroquine (CQ), hydroxychloroquine (HCQ), and cinanserin (CIN), which have been shown to be effective in the treatment of SARS-CoV-2 virus, is reported with the special emphasis on their relative abundances. On the other hand, the potential inhibitory effect of the dominant acid-base forms of quercetin (Q) and its oxidative metabolite 2-(3,4-dihydroxybenzoyl)-2,4,6-trihydroxy-3(2H) benzofuranone (BZF), which are constituents of traditional food products believed to exhibit antiviral effects, was also examined. The undertaken study includes the determination of the major energy contributions to the binding energy as well as in-depth analysis of amino acid residues at the active pocket and possible interactions. The approach that we propose here may be an additional strategy for combating the deadly virus by preventing the first step of the virus replication cycle. Preliminary research has shown that the investigated compounds exert an inhibitory effect against the SARS-CoV-2 furin enzyme and spiked glycoprotein through different acid-base forms. These investigations may be helpful in creating potential therapeutic agents in the fight against the SARS-CoV-2 virus. On the other hand, the results we predicted in this computational study may be the basis for new experimental in vitro and in vivo studies.
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Affiliation(s)
- Žiko B Milanović
- University of Kragujevac, Faculty of Science, Department of Chemistry 12 Radoja Domanovića 34000 Kragujevac Serbia
| | - Marko R Antonijević
- University of Kragujevac, Institute for Information Technologies, Department of Science Jovana Civijića bb 34000 Kragujevac Serbia
| | - Ana D Amić
- Juraj Strossmayer University of Osijek, Department of Chemistry Ulica cara Hadrijana 8/A Osijek Croatia
| | - Edina H Avdović
- University of Kragujevac, Institute for Information Technologies, Department of Science Jovana Civijića bb 34000 Kragujevac Serbia
| | - Dušan S Dimić
- University of Belgrade, Faculty of Physical Chemistry Studentski trg 12-16 11000 Belgrade Serbia
| | - Dejan A Milenković
- University of Kragujevac, Institute for Information Technologies, Department of Science Jovana Civijića bb 34000 Kragujevac Serbia
| | - Zoran S Marković
- University of Kragujevac, Institute for Information Technologies, Department of Science Jovana Civijića bb 34000 Kragujevac Serbia
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Merski M, Skrzeczkowski J, Roth JK, Górna MW. A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins. Molecules 2020; 25:E5326. [PMID: 33203097 PMCID: PMC7696500 DOI: 10.3390/molecules25225326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022] Open
Abstract
We present a method to rapidly identify hydrogen-mediated interactions in proteins (e.g., hydrogen bonds, hydrogen bonds, water-mediated hydrogen bonds, salt bridges, and aromatic π-hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen atom positions using either experimental or theoretical methods. By including specific real (or virtual) partner atoms as defined by the atom type of both the donor and acceptor heavy atoms, a set of unique angles can be rapidly calculated. By comparing the distance between the donor and the acceptor and these unique angles to the statistical preferences observed in the Protein Data Bank (PDB), we were able to identify a set of conserved geometries (15 for donor atoms and 7 for acceptor atoms) for hydrogen-mediated interactions in proteins. This set of identified interactions includes every polar atom type present in the Protein Data Bank except OE1 (glutamate/glutamine sidechain) and a clear geometric preference for the methionine sulfur atom (SD) to act as a hydrogen bond acceptor. This method could be readily applied to protein design efforts.
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Affiliation(s)
- Matthew Merski
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland;
| | - Jakub Skrzeczkowski
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland;
| | - Jennifer K. Roth
- Department of Psychology, Carlow University, Pittsburgh, PA 15213, USA;
| | - Maria W. Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089 Warsaw, Poland;
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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37
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Jabłuszewska A, Krawczuk A, Dos Santos LHR, Macchi P. Accurate Modelling of Group Electrostatic Potential and Distributed Polarizability in Dipeptides. Chemphyschem 2020; 21:2155-2165. [DOI: 10.1002/cphc.202000441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/23/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Angelika Jabłuszewska
- Faculty of Chemistry Jagiellonian University in Krakow Gronostajowa 2 30-387 Krakow Poland
| | - Anna Krawczuk
- Faculty of Chemistry Jagiellonian University in Krakow Gronostajowa 2 30-387 Krakow Poland
| | - Leonardo H. R. Dos Santos
- Departamento de Química Universidade Federal de Minas Gerais Av. Antônio Carlos 6627 31270-901 Belo Horizonte MG Brazil
| | - Piero Macchi
- Department of Chemistry, Materials and Chemical Engineering Polytechnics of Milan Via Mancinelli 7 20131 Milan Italy
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38
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Wang Z, Wang Y, Vilekar P, Yang SP, Gupta M, Oh MI, Meek A, Doyle L, Villar L, Brennecke A, Liyanage I, Reed M, Barden C, Weaver DF. Small molecule therapeutics for COVID-19: repurposing of inhaled furosemide. PeerJ 2020; 8:e9533. [PMID: 32704455 PMCID: PMC7350920 DOI: 10.7717/peerj.9533] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 has become a global health concern. The morbidity and mortality of the potentially lethal infection caused by this virus arise from the initial viral infection and the subsequent host inflammatory response. The latter may lead to excessive release of pro-inflammatory cytokines, IL-6 and IL-8, as well as TNF-α ultimately culminating in hypercytokinemia (“cytokine storm”). To address this immuno-inflammatory pathogenesis, multiple clinical trials have been proposed to evaluate anti-inflammatory biologic therapies targeting specific cytokines. However, despite the obvious clinical utility of such biologics, their specific applicability to COVID-19 has multiple drawbacks, including they target only one of the multiple cytokines involved in COVID-19’s immunopathy. Therefore, we set out to identify a small molecule with broad-spectrum anti-inflammatory mechanism of action targeting multiple cytokines of innate immunity. In this study, a library of small molecules endogenous to the human body was assembled, subjected to in silico molecular docking simulations and a focused in vitro screen to identify anti-pro-inflammatory activity via interleukin inhibition. This has enabled us to identify the loop diuretic furosemide as a candidate molecule. To pre-clinically evaluate furosemide as a putative COVID-19 therapeutic, we studied its anti-inflammatory activity on RAW264.7, THP-1 and SIM-A9 cell lines stimulated by lipopolysaccharide (LPS). Upon treatment with furosemide, LPS-induced production of pro-inflammatory cytokines was reduced, indicating that furosemide suppresses the M1 polarization, including IL-6 and TNF-α release. In addition, we found that furosemide promotes the production of anti-inflammatory cytokine products (IL-1RA, arginase), indicating M2 polarization. Accordingly, we conclude that furosemide is a reasonably potent inhibitor of IL-6 and TNF-α that is also safe, inexpensive and well-studied. Our pre-clinical data suggest that it may be a candidate for repurposing as an inhaled therapy against COVID-19.
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Affiliation(s)
- Zhiyu Wang
- Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Yanfei Wang
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Prachi Vilekar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Seung-Pil Yang
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Mayuri Gupta
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Myong In Oh
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Autumn Meek
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Lisa Doyle
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Laura Villar
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Anja Brennecke
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Imindu Liyanage
- Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mark Reed
- Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Christopher Barden
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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40
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Chen D, Liu JR, Cheng Y, Cheng H, He P, Sun Y. Metabolism of Rhaponticin and Activities of its Metabolite, Rhapontigenin: A Review. Curr Med Chem 2020; 27:3168-3186. [DOI: 10.2174/0929867326666190121143252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/22/2018] [Accepted: 12/28/2018] [Indexed: 12/13/2022]
Abstract
Rhaponticin is a stilbenoid glucoside compound, found in medicinal plant of rhubarb
rhizomes. Rhapontigenin (RHAG), the stilbene aglycone metabolite of rhaponticin, has
shown various biological activities including anticancer activities to act a potential human cytochrome
P450 inhibitor, antihyperlipidemic effect, anti-allergic action, antioxidant and antibacterial
activities. Moreover, it was reported to scavenge intracellular Reactive Oxygen Species
(ROS), the 1,1-Diphenyl-2-Picrylliydrazyl (DPPH) radical, and Hydrogen Peroxide
(H2O2). Meanwhile, RHAG exhibited the inhibitory activity for the synthesis of DNA, RNA
and protein, and also presented the capacity of inducing morphological changes and apoptosis
of C. albicans. Here, the structure, pharmacokinetics, pharmacological effects as well as underlying
mechanisms of rhaponticin and its metabolite, RHAG, have been extensively reviewed.
This review will provide a certain reference value for developing the therapeutic drug
of rhaponticin or RHAG.
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Affiliation(s)
- Dan Chen
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, Hubei 441053, China
| | - Jing-Ru Liu
- School of Life Science, Northwest University, Xi’an, Shaanxi 710069, China
| | - Yanjin Cheng
- School of Mathematics and Statistics, Hubei University of Arts and Science, Xiangyang, Hubei 441053, China
| | - Hua Cheng
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, Hubei 441053, China
| | - Ping He
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, Hubei 441053, China
| | - Yang Sun
- School of Food Science and Technology, School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, Hubei 441053, China
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41
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Kumar V, Keshavayya J, Matada MN, Srinivasa SM, Rangappa S. Synthesis, Characterization and Biological Potency of Butyl‐Pyridone Based Azo Dyes. ChemistrySelect 2020. [DOI: 10.1002/slct.201904954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Vinod Kumar
- Department of Chemistry, School of Chemical Sciences Jnana SahyadriKuvempu University Shankaraghatta 577 451 Shivamogga, Karnataka India
| | - J. Keshavayya
- Department of Chemistry, School of Chemical Sciences Jnana SahyadriKuvempu University Shankaraghatta 577 451 Shivamogga, Karnataka India
| | - Mallikarjuna N. Matada
- Department of Chemistry, School of Chemical Sciences Jnana SahyadriKuvempu University Shankaraghatta 577 451 Shivamogga, Karnataka India
| | - Sudhanva M. Srinivasa
- Adichunchanagiri Institute for Molecular MedicineAdichunchanagiri Institute of Medical Sciences BG Nagara, Mandya 571448 India
| | - S. Rangappa
- Adichunchanagiri Institute for Molecular MedicineAdichunchanagiri Institute of Medical Sciences BG Nagara, Mandya 571448 India
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42
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Abstract
How proteins evolved to recognize and bind their ligands is a key mystery in protein function evolution. To explore this mystery, we study how proteins bind adenine, an ancient fragment. We characterize physicochemical patterns of protein–adenine interactions and link these to proteins’ evolutionary origins. In conflict with previous findings, we see that all of adenine’s hydrogen donors and acceptors have been used to bind proteins, and that adenine binding is likely to have emerged multiple times in evolution. To identify adenine-binding sites of shared origin, we use “themes”: short amino acid segments suggested to constitute evolutionary building blocks. We detect specific themes that are engaged in adenine binding; the detection of these in a protein’s sequence might reveal its function. Proteins’ interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein–adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein–adenine interactions in the Watson–Crick edge of adenine and shows that all of adenine’s edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments (“themes”) that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
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43
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Gupta M, Bogdanowicz T, Reed MA, Barden CJ, Weaver DF. The Brain Exposure Efficiency (BEE) Score. ACS Chem Neurosci 2020; 11:205-224. [PMID: 31815431 DOI: 10.1021/acschemneuro.9b00650] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The blood-brain barrier (BBB), composed of microvascular tight junctions and glial cell sheathing, selectively controls drug permeation into the central nervous system (CNS) by either passive diffusion or active transport. Computational techniques capable of predicting molecular brain penetration are important to neurological drug design. A novel prediction algorithm, termed the Brain Exposure Efficiency Score (BEE), is presented. BEE addresses the need to incorporate the role of trans-BBB influx and efflux active transporters by considering key brain penetrance parameters, namely, steady state unbound brain to plasma ratio of drug (Kp,uu) and dose normalized unbound concentration of drug in brain (Cu,b). BEE was devised using quantitative structure-activity relationships (QSARs) and molecular modeling studies on known transporter proteins and their ligands. The developed algorithms are provided as a user-friendly open source calculator to assist in optimizing a brain penetrance strategy during the early phases of small molecule molecular therapeutic design.
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Affiliation(s)
- Mayuri Gupta
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Thomas Bogdanowicz
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Mark A. Reed
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Christopher J. Barden
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
| | - Donald F. Weaver
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario M5T 2S8, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5G 2C4, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2 Canada
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44
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Zhou S, Wang L. Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects. Phys Chem Chem Phys 2020; 22:4884-4895. [DOI: 10.1039/c9cp06840f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electronic and nuclear quantum effects determine the symmetry and highly downfield 1H NMR chemical shifts of short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
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45
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Blum W, Henzi T, Pecze L, Diep KL, Bochet CG, Schwaller B. The phytohormone forchlorfenuron decreases viability and proliferation of malignant mesothelioma cells in vitro and in vivo. Oncotarget 2019; 10:6944-6956. [PMID: 31857849 PMCID: PMC6916748 DOI: 10.18632/oncotarget.27341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023] Open
Abstract
Malignant mesothelioma (MM) is one of the most aggressive cancer types with a patient’s life expectancy of typically less than one year upon diagnosis. The urgency of finding novel therapeutic approaches to treat mesothelioma is evident. Here we tested the effect of the plant-growth regulator forchlorfenuron (FCF), an inhibitor of septin function(s) in mammalian cells, on the viability and proliferation of MM cell lines, as well as other tumor cell lines derived from lung, prostate, colon, ovary, cervix and breast. Exposure to FCF strongly inhibited proliferation of human and mouse (most efficiently epithelioid) MM cells and all other tumor cells in a concentration-dependent manner and led to cell cycle arrest and cell death. The role of septin 7 (SEPT7), a presumably essential target of FCF in MM cells was confirmed by an shRNA strategy. FCF was robustly inhibiting tumor cell growth in vitro at low micromolar (IC50: ≈20-60µM) concentrations and more promisingly also in vivo. Initial experiments with FCF analogous revealed the importance of FCF’s chloride group for efficient cell growth inhibition. FCF’s rather low systemic toxicity might warrant for an extended search for other related and possibly more potent FCF analogues to target MM and putatively other septin-dependent tumors.
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Affiliation(s)
- Walter Blum
- Section of Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Thomas Henzi
- Section of Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - László Pecze
- Section of Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Kim-Long Diep
- Department of Chemistry, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Christian G Bochet
- Department of Chemistry, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Beat Schwaller
- Section of Medicine, University of Fribourg, CH-1700 Fribourg, Switzerland
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46
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Uba AI, Yelekçi K. Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10. J Biomol Struct Dyn 2019; 38:4397-4406. [PMID: 31701819 DOI: 10.1080/07391102.2019.1691658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Histone deacetylase (HDAC) 10 has been implicated in the pathology of various cancers and neurodegenerative disorders, making the discovery of novel inhibitors of the isoform an important endeavor. However, the unavailability of crystallographic structure of human HDAC10 (hHDAC10) hinders structure-based drug design effort. Previously, we reported the homology modeled structure of human HDAC10 built using the crystallographic structure of Danio rerio (zebrafish) HDAC10 (zHDAC10) (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) as a template. Here, in continuation with our study, both hHDAC10 and zHDAC10, and their respective complexes with trichostatin A (TSA), quisinostat, and the native ligand (in 5TD7), 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol (PDB ID; FKS) were submitted to 100 ns-long unrestrained molecular dynamics (MD) simulations. Comparative analyses of the MD trajectories revealed that zHDAC10 and its complexes displayed higher stability than hHDAC10 and its corresponding complexes over time. Nonetheless, docking of active and inactive set molecules revealed that more reliable conformations of hHDAC10 could be obtained at an extended time period. This study may shed more light on the reliability of hHDAC10 modeled structure for use in selective inhibitor design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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47
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48
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Sarkar S, Monu, Bandyopadhyay B. Cooperative nature of the sulfur centered hydrogen bond: investigation of (H 2S) n (n = 2-4) clusters using an affordable yet accurate level of theory. Phys Chem Chem Phys 2019; 21:25439-25448. [PMID: 31712792 DOI: 10.1039/c9cp05326c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Existing studies have shown that appreciably high level quantum chemical calculations are required to reproduce experimental energetic and geometric features of a H2S dimer. This condition severely restricts any practical possibility of obtaining reliable results for higher order H2S clusters. We have shown here that the binding energies calculated at the CCSD(T)/CBS level with counterpoise corrected geometries calculated at the MP2/aug-cc-pV(Q+d)Z level of theory excellently match with the experimental results for the H2S dimer. Subsequently, the above mentioned levels of theory were used for trimers and tetramers. (H2S)n (n = 2-4) clusters were found to show cooperative strengthening of S-HS hydrogen bonds, which is clearly evident from the evolution of binding energies and hydrogen bond lengths, with increasing cluster size. Localized molecular orbital energy decomposition analyses have been carried out to understand how the contributions of various energy components modulate with the size of the clusters and what are their relative contributions towards the overall stabilization of the clusters. Natural bond orbital and atoms in molecules analyses were also carried out in order to look into the evolution of the electronic charge transfer and electron density topology with cluster size.
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Affiliation(s)
- Saptarshi Sarkar
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
| | - Monu
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur, 302017, India.
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49
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Arias-Olivares D, Wieduwilt EK, Contreras-García J, Genoni A. NCI-ELMO: A New Method To Quickly and Accurately Detect Noncovalent Interactions in Biosystems. J Chem Theory Comput 2019; 15:6456-6470. [DOI: 10.1021/acs.jctc.9b00658] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David Arias-Olivares
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andrés Bello, Ave. Republica 275, Santiago, Chile
- Sorbonne Université & CNRS, Laboratoire de Chimie Théorique, UMR CNRS 7616, 4 Place Jussieu, F-75005 Paris, France
| | - Erna K. Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Julia Contreras-García
- Sorbonne Université & CNRS, Laboratoire de Chimie Théorique, UMR CNRS 7616, 4 Place Jussieu, F-75005 Paris, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
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50
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Breberina LM, Zlatović MV, Nikolić MR, Stojanović SĐ. Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces. Mol Inform 2019; 38:e1800145. [PMID: 31535472 DOI: 10.1002/minf.201800145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/26/2019] [Indexed: 11/10/2022]
Abstract
Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call "standard-size" interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than -16 kJ mol-1 , while most of them have energy in the range from -6 to -14 kJ mol-1 . The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.
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Affiliation(s)
- Luka M Breberina
- University of Belgrade - Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia
| | - Mario V Zlatović
- University of Belgrade - Faculty of Chemistry, Center for Computational Chemistry and Bioinformatics, Belgrade, Serbia
| | - Milan R Nikolić
- University of Belgrade - Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia
| | - Srđan Đ Stojanović
- Institute of Chemistry, Technology and Metallurgy (ICTM) - Department of Chemistry, University of Belgrade, Belgrade, Serbia
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