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Frimayanti N, Ikhtiarudin I, Dona R, Oktarizal R, Nurfatimah AC. Exploring Substituted Tetrazoloquinazoline: Biological Activities, Molecular Docking Analysis, and Anti-Breast Cancer MCF7/HER2 Effects. Adv Pharmacol Pharm Sci 2024; 2024:6952142. [PMID: 39234574 PMCID: PMC11374424 DOI: 10.1155/2024/6952142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/06/2024] Open
Abstract
Breast cancer is a condition where breast tissue cells grow uncontrollably. Various natural and synthesized compounds, such as quinazoline, have been studied for their potential as anticancer agents. Quinazoline derivatives have shown diverse bioactivities, including antimalarial, antifungal, antimicrobial, and anticancer properties. This research aims to synthesize substituted tetrazoloquinazoline and evaluate its potential as an anticancer agent using molecular docking studies with the Molecular Operating Environment (MOE) software. Furthermore, molecular dynamic was also performed to analyze the binding stability of this protein-ligand complex. Additionally, the physicochemical and pharmacokinetic properties of quinazoline compounds were assessed using the website https://www.swissadme.ch. The cytotoxic activity of the compounds was evaluated using the MTT assay. The docking results revealed that substituted tetrazoloquinazoline exhibited a significantly different range of binding free energy compared to the positive control. Moreover, the substituted tetrazoloquinazoline compounds comply with Lipinski's Rule of Five (Ro5), indicating that they are easily absorbable and have good permeability. The cytotoxic activity of the compounds was found to have an IC50 value of >1000 ppm, classifying them as noncytotoxic. It therefore paved the way for the discovery of promising next-generation drugs against breast cancer.
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Affiliation(s)
- Neni Frimayanti
- Department of Pharmacy Sekolah Tinggi Ilmu Farmasi Riau, Jalan Kamboja, Simpang Baru, Pekanbaru 28293, Indonesia
| | - Ihsan Ikhtiarudin
- Department of Pharmacy Sekolah Tinggi Ilmu Farmasi Riau, Jalan Kamboja, Simpang Baru, Pekanbaru 28293, Indonesia
| | - Rahma Dona
- Department of Pharmacy Sekolah Tinggi Ilmu Farmasi Riau, Jalan Kamboja, Simpang Baru, Pekanbaru 28293, Indonesia
| | - Rahul Oktarizal
- Department of Pharmacy Sekolah Tinggi Ilmu Farmasi Riau, Jalan Kamboja, Simpang Baru, Pekanbaru 28293, Indonesia
| | - Aprilia Cindy Nurfatimah
- Department of Chemistry Faculty of Mathematics and Natural Science Universitas Riau, Pekanbaru, Indonesia
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Zhang R, Ding A, Cai X, Bai L, Li G, Liang H, Tang CY. Enhancement of waterborne pathogen removal by functionalized biochar with ε-polylysine ″dynamic arms″: Potential application in ultrafiltration system. WATER RESEARCH 2024; 259:121834. [PMID: 38820729 DOI: 10.1016/j.watres.2024.121834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Widespread outbreaks of threatening infections caused by unknown pathogens and water transmission have spawned the development of adsorption methods for pathogen elimination. We proposed a biochar functionalization strategy involving ε-polylysine (PLL), a bio-macromolecular poly(amino acid)s with variable folding conformations, as a "pathogen gripper" on biochar. PLL was successfully bridged onto biochar via polydopamine (PDA) crosslinking. The extension of electropositive side chains within PLL enables the capture of both nanoscale viruses and micrometer-scale bacteria in water, achieving excellent removal performances. This functionalized biochar was tentatively incorporated into ultrafiltration (UF) system, to achieve effective and controllable adsorption and retention of pathogens, and to realize the transfer of pathogens from membrane surface/pore to biochar surface as well as flushing water. The biochar-amended UF systems presents complete retention (∼7 LRV) and hydraulic elution of pathogens into membrane flushing water. Improvements in removal of organics and anti-fouling capability were observed, indicating the broken trade-off in UF pathogen removal dependent on irreversible fouling. Chemical characterizations revealed adsorption mechanisms encompassing electrostatic/hydrophobic interactions, pore filling, electron transfer, chemical bonding and secondary structure transitions. Microscopic and mechanical analyses validated the mechanisms for rapid adsorption and pathogen lysis. Low-concentration alkaline solution for used biochar regeneration, facilitated the deprotonation and transformation of PLL side chain to folded structures (α-helix/β-sheet). Biochar regeneration process also promoted the effective detachment/inactivation of pathogens and protection of functional groups on biochar, corroborated by physicochemical inspection and molecular dynamics simulation. The foldability of poly(amino acid)s acting like dynamic arms, significantly contributed to pathogen capture/desorption/inactivation and biochar regeneration. This study also inspires future investigation for performances of UF systems amended by poly(amino acid)s-functionalized biochar under diverse pressure, temperature, reactive oxygen species of feeds and chemical cleaning solutions, with far-reaching implications for public health, environmental applications of biochar, and UF process improvement.
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Affiliation(s)
- Rourou Zhang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District 150090, Harbin, PR China
| | - An Ding
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District 150090, Harbin, PR China.
| | - Xuejun Cai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, PR China
| | - Langming Bai
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District 150090, Harbin, PR China
| | - Guibai Li
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District 150090, Harbin, PR China
| | - Heng Liang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District 150090, Harbin, PR China
| | - Chuyang Y Tang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR 999077, PR China
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Azad I, Khan T, Ahmad N, Khan AR, Akhter Y. Updates on drug designing approach through computational strategies: a review. Future Sci OA 2023; 9:FSO862. [PMID: 37180609 PMCID: PMC10167725 DOI: 10.2144/fsoa-2022-0085] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
The drug discovery and development (DDD) process in pursuit of novel drug candidates is a challenging procedure requiring lots of time and resources. Therefore, computer-aided drug design (CADD) methodologies are used extensively to promote proficiency in drug development in a systematic and time-effective manner. The point in reference is SARS-CoV-2 which has emerged as a global pandemic. In the absence of any confirmed drug moiety to treat the infection, the science fraternity adopted hit and trial methods to come up with a lead drug compound. This article is an overview of the virtual methodologies, which assist in finding novel hits and help in the progression of drug development in a short period with a specific medicinal solution.
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Affiliation(s)
- Iqbal Azad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Tahmeena Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Naseem Ahmad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, UP, 2260025, India
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4
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Kondo HX, Nakamura H, Takano Y. Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Quantum chemical studies on hydrogen bonds in helical secondary structures. Biophys Rev 2023; 14:1369-1378. [PMID: 36659988 PMCID: PMC9842822 DOI: 10.1007/s12551-022-01034-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 01/07/2023] Open
Abstract
We present a brief review of our recent computational studies of hydrogen bonds (H-bonds) in helical secondary structures of proteins, α-helix and 310-helix, using a Negative Fragmentation Approach with density functional theory. We found that the depolarized electronic structures of the carbonyl oxygen of the ith residue and the amide hydrogen of the (i + 4)th residue cause weaker H-bond in an α-helix than in an isolated H-bond. Our calculations showed that the H-bond energies in the 310-helix were also weaker than those of the isolated H-bonds. In the 310-helices, the adjacent N-H group at the (i + 1)th residue was closer to the C=O group of the H-bond pair than the adjacent C=O group in the 310-helices, whereas the adjacent C=O group at the (i + 1)th residue was close to the H-bond acceptor in α-helices. Therefore, the destabilization of the H-bond is attributed to the depolarization caused by the adjacent residue of the helical backbone connecting the H-bond donor and acceptor. The differences in the change in electron density revealed that such depolarizations were caused by the local electronic interactions in their neighborhood inside the helical structure and redistributed the electron density. We also present the improvements in the force field of classical molecular simulation, based on our findings. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-022-01034-5.
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Nakamura H. Some reflections on a career in science and a note of thanks to the contributors of this Special Issue. Biophys Rev 2022; 14:1223-1226. [PMID: 36659991 PMCID: PMC9842830 DOI: 10.1007/s12551-022-01035-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
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Depolarizing Effects in Hydrogen Bond Energy in 3 10-Helices Revealed by Quantum Chemical Analysis. Int J Mol Sci 2022; 23:ijms23169032. [PMID: 36012292 PMCID: PMC9409261 DOI: 10.3390/ijms23169032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/18/2022] Open
Abstract
Hydrogen-bond (H-bond) energies in 310-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was evaluated in detail from the 310-helical conformation of total energies (whole helical model, WH3-10 model), and the results were compared with the property of H-bond in α-helix from our previous study. The H-bond energies of the WH3-10 model exhibited tendencies different from those exhibited by the α-helix in that they depended on the helical position of the relevant H-bond pair. H-bond pairs adjacent to the terminal H-bond pairs were observed to be strongly destabilized. The analysis of electronic structures indicated that structural characteristics cause the destabilization of the H-bond in 310-helices. We also found that the longer the helix length, the more stable the H-bond in the terminal pairs of the WH3-10 model, suggesting the action of H-bond cooperativity.
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Adinortey CA, Kwarko GB, Koranteng R, Boison D, Obuaba I, Wilson MD, Kwofie SK. Molecular Structure-Based Screening of the Constituents of Calotropis procera Identifies Potential Inhibitors of Diabetes Mellitus Target Alpha Glucosidase. Curr Issues Mol Biol 2022; 44:963-987. [PMID: 35723349 PMCID: PMC8928985 DOI: 10.3390/cimb44020064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 01/09/2023] Open
Abstract
Diabetes mellitus is a disorder characterized by higher levels of blood glucose due to impaired insulin mechanisms. Alpha glucosidase is a critical drug target implicated in the mechanisms of diabetes mellitus and its inhibition controls hyperglycemia. Since the existing standard synthetic drugs have therapeutic limitations, it is imperative to identify new potent inhibitors of natural product origin which may slow carbohydrate digestion and absorption via alpha glucosidase. Since plant extracts from Calotropis procera have been extensively used in the treatment of diabetes mellitus, the present study used molecular docking and dynamics simulation techniques to screen its constituents against the receptor alpha glucosidase. Taraxasterol, syriogenin, isorhamnetin-3-O-robinobioside and calotoxin were identified as potential novel lead compounds with plausible binding energies of −40.2, −35.1, −34.3 and −34.3 kJ/mol against alpha glucosidase, respectively. The residues Trp481, Asp518, Leu677, Leu678 and Leu680 were identified as critical for binding and the compounds were predicted as alpha glucosidase inhibitors. Structurally similar compounds with Tanimoto coefficients greater than 0.7 were reported experimentally to be inhibitors of alpha glucosidase or antidiabetic. The structures of the molecules may serve as templates for the design of novel inhibitors and warrant in vitro assaying to corroborate their antidiabetic potential.
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Affiliation(s)
- Cynthia A. Adinortey
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana;
| | - Gabriel B. Kwarko
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana;
| | - Russell Koranteng
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
| | - Daniel Boison
- Department of Biochemistry, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana; (D.B.); (I.O.)
| | - Issaka Obuaba
- Department of Biochemistry, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana; (D.B.); (I.O.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana;
| | - Samuel K. Kwofie
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana;
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
- Correspondence: ; Tel.: +233-203-797922
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9
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Kondo HX, Kusaka A, Kitakawa CK, Onari J, Yamanaka S, Nakamura H, Takano Y. Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach. J Comput Chem 2019; 40:2043-2052. [PMID: 31099907 PMCID: PMC6767508 DOI: 10.1002/jcc.25859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 11/24/2022]
Abstract
Hydrogen-bond (H-bond) interaction energies in α-helices of short alanine peptides were systematically examined by precise density functional theory calculations, followed by a molecular tailoring approach. The contribution of each H-bond interaction in α-helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H-bond models, in which only H-bond donors and acceptors exist with the capping methyl groups. The former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H-bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α-helices and those of the minimal H-bond models. Consequently, we found that the reduced H-bond energy originated from the depolarizations of both the H-bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α-helix backbone. The classical force fields provide similar H-bond energies to those in the minimal H-bond models, which ignore the current depolarization effect, and thus they overestimate the actual H-bond energies in α-helices. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Hiroko X. Kondo
- School of Regional Innovation and Social Design EngineeringFaculty of Engineering, Kitami Institute of Technology, 165 Koen‐choKitamiHokkaido090‐8507Japan
| | - Ayumi Kusaka
- Institute for Protein ResearchOsaka University, 3‐2 YamadaokaSuitaOsaka565‐0871Japan
| | - Colin K. Kitakawa
- Graduate School of ScienceOsaka University, 1‐1 MachikaneyamachoToyonakaOsaka560‐0043Japan
| | - Jinta Onari
- Graduate School of ScienceOsaka University, 1‐1 MachikaneyamachoToyonakaOsaka560‐0043Japan
| | - Shusuke Yamanaka
- Graduate School of ScienceOsaka University, 1‐1 MachikaneyamachoToyonakaOsaka560‐0043Japan
| | - Haruki Nakamura
- Institute for Protein ResearchOsaka University, 3‐2 YamadaokaSuitaOsaka565‐0871Japan
| | - Yu Takano
- Institute for Protein ResearchOsaka University, 3‐2 YamadaokaSuitaOsaka565‐0871Japan
- Graduate School of Information SciencesHiroshima City University, 3‐4‐1 Ozuka‐Higashi Asa‐Minami‐KuHiroshima731‐3194Japan
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Kasahara K, Terazawa H, Takahashi T, Higo J. Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review. Comput Struct Biotechnol J 2019; 17:712-720. [PMID: 31303975 PMCID: PMC6603302 DOI: 10.1016/j.csbj.2019.06.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/29/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022] Open
Abstract
The molecular dynamics (MD) method is a promising approach toward elucidating the molecular mechanisms of intrinsically disordered regions (IDRs) of proteins and their fuzzy complexes. This mini-review introduces recent studies that apply MD simulations to investigate the molecular recognition of IDRs. Firstly, methodological issues by which MD simulations treat IDRs, such as developing force fields, treating periodic boundary conditions, and enhanced sampling approaches, are discussed. Then, several examples of the applications of MD to investigate molecular interactions of IDRs in terms of the two kinds of complex formations; coupled-folding and binding and fuzzy complex. MD simulations provide insight into the molecular mechanisms of these binding processes by sampling conformational ensembles of flexible IDRs. In particular, we focused on all-atom explicit-solvent MD simulations except for studies of higher-order assembly of IDRs. Recent advances in MD methods, and computational power make it possible to dissect the molecular details of realistic molecular systems involving the dynamic behavior of IDRs.
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Affiliation(s)
- Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
- Corresponding author.
| | - Hiroki Terazawa
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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