1
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Salomonsson J, Wallner B, Sjöstrand L, D'Arcy P, Sunnerhagen M, Ahlner A. Transient interdomain interactions in free USP14 shape its conformational ensemble. Protein Sci 2024; 33:e4975. [PMID: 38588275 PMCID: PMC11001199 DOI: 10.1002/pro.4975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024]
Abstract
The deubiquitinase (DUB) ubiquitin-specific protease 14 (USP14) is a dual domain protein that plays a regulatory role in proteasomal degradation and has been identified as a promising therapeutic target. USP14 comprises a conserved USP domain and a ubiquitin-like (Ubl) domain separated by a 25-residue linker. The enzyme activity of USP14 is autoinhibited in solution, but is enhanced when bound to the proteasome, where the Ubl and USP domains of USP14 bind to the Rpn1 and Rpt1/Rpt2 units, respectively. No structure of full-length USP14 in the absence of proteasome has yet been presented, however, earlier work has described how transient interactions between Ubl and USP domains in USP4 and USP7 regulate DUB activity. To better understand the roles of the Ubl and USP domains in USP14, we studied the Ubl domain alone and in full-length USP14 by nuclear magnetic resonance spectroscopy and used small angle x-ray scattering and molecular modeling to visualize the entire USP14 protein ensemble. Jointly, our results show how transient interdomain interactions between the Ubl and USP domains of USP14 predispose its conformational ensemble for proteasome binding, which may have functional implications for proteasome regulation and may be exploited in the design of future USP14 inhibitors.
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Affiliation(s)
| | - Björn Wallner
- Department of Physics, Chemistry and BiologyLinköping UniversityLinköpingSweden
| | - Linda Sjöstrand
- Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Pádraig D'Arcy
- Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and BiologyLinköping UniversityLinköpingSweden
| | - Alexandra Ahlner
- Department of Physics, Chemistry and BiologyLinköping UniversityLinköpingSweden
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2
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Taha A, Kadhim MM, Naser ST, Majdi A, Abdullaha SAH, Hachim SK, Abdulwahid Abdulhussain M, Mahdi Rheima A. A density functional theory study on the potential application of Ni and Co doped ZnO nanosheets as a carrier for ciclopirox anticancer drug. Comput Methods Biomech Biomed Engin 2024; 27:765-774. [PMID: 37781969 DOI: 10.1080/10255842.2023.2202294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/08/2023] [Indexed: 10/03/2023]
Abstract
The Ni and Co doping effect on the ciclopirox (CPX) drug delivery performance of a ZnO nanosheet (ZnO-NS) was investigated theoretically. Doping Ni and Co metals into the ZnO-NS increased the adsorption energy of CPX from -7.9 to -27.4 and -31.7 kcal/mol, respectively. The CPX adsorption reduced the ZnO-NS gap (Eg) from 3.81 to 3.46 eV, while the CPX adsorption reduced the Eg of the Ni- and Co-doped ZnO-NS from 2.74 and 2.68 eV to 1.87 and 1.71 eV, respectively. The CPX adsorption performance increased after doping process. A drug release mechanism was introduced in cancerous tissues based on the PH..
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Affiliation(s)
- Ali Taha
- Pharmacy College, Al-Farahidi University, Baghdad, Iraq
| | - Mustafa M Kadhim
- Department of Dentistry, Kut University College, Kut, Wasit, Iraq
| | | | - Ali Majdi
- Department of Building and Construction Techniques Engineering, Al- Mustaqbal University College, Hilla, Iraq
| | | | - Safa K Hachim
- College of technical engineering, The Islamic University, Najaf, Iraq
- Medical Laboratory Techniques Department, Al-Turath University College, Baghdad, Iraq
| | | | - Ahmed Mahdi Rheima
- Department of Chemistry, College of Science, Mustansiriyah University, Baghdad, Iraq
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3
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Chen M, Jiang X, Zhang L, Chen X, Wen Y, Gu Z, Li X, Zheng M. The emergence of machine learning force fields in drug design. Med Res Rev 2024; 44:1147-1182. [PMID: 38173298 DOI: 10.1002/med.22008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
In the field of molecular simulation for drug design, traditional molecular mechanic force fields and quantum chemical theories have been instrumental but limited in terms of scalability and computational efficiency. To overcome these limitations, machine learning force fields (MLFFs) have emerged as a powerful tool capable of balancing accuracy with efficiency. MLFFs rely on the relationship between molecular structures and potential energy, bypassing the need for a preconceived notion of interaction representations. Their accuracy depends on the machine learning models used, and the quality and volume of training data sets. With recent advances in equivariant neural networks and high-quality datasets, MLFFs have significantly improved their performance. This review explores MLFFs, emphasizing their potential in drug design. It elucidates MLFF principles, provides development and validation guidelines, and highlights successful MLFF implementations. It also addresses potential challenges in developing and applying MLFFs. The review concludes by illuminating the path ahead for MLFFs, outlining the challenges to be overcome and the opportunities to be harnessed. This inspires researchers to embrace MLFFs in their investigations as a new tool to perform molecular simulations in drug design.
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Affiliation(s)
- Mingan Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Xinyu Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Lehan Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxu Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Yiming Wen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Zhiyong Gu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Xutong Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
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4
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Kirschbaum T, Wang X, Bande A. Ground and excited state charge transfer at aqueous nanodiamonds. J Comput Chem 2024; 45:710-718. [PMID: 38109424 DOI: 10.1002/jcc.27279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/03/2023] [Accepted: 11/25/2023] [Indexed: 12/20/2023]
Abstract
Nanodiamonds (NDs) are unique carbonaceous materials with exceptionally high stability, hardness, and notable electronic properties. Their applications in photocatalysis, biomedicine, and energy materials are usually carried out in aqueous environments, where they interact with aqueous adsorbates. Especially, electron density may rearrange from the diamond material toward oxidative adsorbates such as oxygen, which is known as charge transfer doping. In this article, we quantify the charge transfer doping for NDs with inhomogeneous surface coverings (hydroxyl, fluorine, and amorphous carbon), as well as NDs doped with heteroatoms (B, Si, N) using hybrid density functional theory (DFT) calculations. The transfer doping magnitude is largely determined by the NDs' highest occupied molecular orbital energies, which can in turn be modified by the surface covering and doping. However, local modifications of the ND structures do not have any local effects on the magnitude of the charge transfer. We furthermore analyze the impact of aqueous adsorbates on the excited states of an aqueous ND in the context of photocatalysis via time-dependent DFT. Here, we find that the excited electrons are biased to move in the direction of the respective oxidative adsorbate. Surprisingly, we find that also unreactive species such as nitrous oxide may attract the excited electrons, which is probably due to the positive partial charge that is induced by the local N2 O solvation geometry.
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Affiliation(s)
- Thorren Kirschbaum
- Theory of Electron Dynamics and Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Xiangfei Wang
- Theory of Electron Dynamics and Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Annika Bande
- Theory of Electron Dynamics and Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
- Institute of Inorganic Chemistry, Leibniz University Hannover, Hannover, Germany
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5
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Evteev S, Ivanenkov Y, Semenov I, Malkov M, Mazaleva O, Bodunov A, Bezrukov D, Sidorenko D, Terentiev V, Malyshev A, Zagribelnyy B, Korzhenevskaya A, Aliper A, Zhavoronkov A. Quantum-assisted fragment-based automated structure generator (QFASG) for small molecule design: an in vitro study. Front Chem 2024; 12:1382512. [PMID: 38633987 PMCID: PMC11021760 DOI: 10.3389/fchem.2024.1382512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction: The significance of automated drug design using virtual generative models has steadily grown in recent years. While deep learning-driven solutions have received growing attention, only a few modern AI-assisted generative chemistry platforms have demonstrated the ability to produce valuable structures. At the same time, virtual fragment-based drug design, which was previously less popular due to the high computational costs, has become more attractive with the development of new chemoinformatic techniques and powerful computing technologies. Methods: We developed Quantum-assisted Fragment-based Automated Structure Generator (QFASG), a fully automated algorithm designed to construct ligands for a target protein using a library of molecular fragments. QFASG was applied to generating new structures of CAMKK2 and ATM inhibitors. Results: New low-micromolar inhibitors of CAMKK2 and ATM were designed using the algorithm. Discussion: These findings highlight the algorithm's potential in designing primary hits for further optimization and showcase the capabilities of QFASG as an effective tool in this field.
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Affiliation(s)
- Sergei Evteev
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | - Yan Ivanenkov
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | - Ivan Semenov
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | - Maxim Malkov
- Insilico Medicine AI Limited, Abu Dhabi, United Arab Emirates
| | - Olga Mazaleva
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | - Artem Bodunov
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | - Dmitry Bezrukov
- Insilico Medicine AI Limited, Abu Dhabi, United Arab Emirates
| | - Denis Sidorenko
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | - Victor Terentiev
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | - Alex Malyshev
- Insilico Medicine Hong Kong Ltd., Hong Kong, Hong Kong SAR, China
| | | | | | - Alex Aliper
- Insilico Medicine AI Limited, Abu Dhabi, United Arab Emirates
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6
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Singh R, Jiang R, Williams J, Dobariya P, Hanak F, Xie J, Rothwell PE, Vince R, More SS. Modulation of endogenous opioid signaling by inhibitors of puromycin sensitive aminopeptidase. bioRxiv 2024:2024.04.02.587756. [PMID: 38617237 PMCID: PMC11014559 DOI: 10.1101/2024.04.02.587756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The endogenous opioid system regulates pain through local release of neuropeptides and modulation of their action on opioid receptors. However, the effect of opioid peptides, the enkephalins, is short-lived due to their rapid hydrolysis by enkephalin-degrading enzymes. In turn, an innovative approach to the management of pain would be to increase the local concentration and prolong the stability of enkephalins by preventing their inactivation by neural enkephalinases such as puromycin sensitive aminopeptidase (PSA). Our previous structure-activity relationship studies offered the S-diphenylmethyl cysteinyl derivative of puromycin (20) as a nanomolar inhibitor of PSA. This chemical class, however, suffered from undesirable metabolism to nephrotoxic puromycin aminonucleoside (PAN). To prevent such toxicity, we designed and synthesized 5'-chloro substituted derivatives. The compounds retained the PSA inhibitory potency of the corresponding 5'-hydroxy analogs and had improved selectivity toward PSA. In vivo treatment with the lead compound 19 caused significantly reduced pain response in antinociception assays, alone and in combination with Met-enkephalin. The analgesic effect was reversed by the opioid antagonist naloxone, suggesting the involvement of opioid receptors. Further, PSA inhibition by compound 19 in brain slices caused local increase in endogenous enkephalin levels, corroborating our rationale. Pharmacokinetic assessment of compound 19 showed desirable plasma stability and identified the cysteinyl sulfur as the principal site of metabolic liability. We gained additional insight into inhibitor-PSA interactions by molecular modeling, which underscored the importance of bulky aromatic amino acid in puromycin scaffold. The results of this study strongly support our rationale for the development of PSA inhibitors for effective pain management.
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Affiliation(s)
- Rohit Singh
- Center for Drug Design, College of Pharmacy, University of Minnesota, MN, USA
| | - Rongrong Jiang
- Center for Drug Design, College of Pharmacy, University of Minnesota, MN, USA
| | - Jessica Williams
- Center for Drug Design, College of Pharmacy, University of Minnesota, MN, USA
| | | | - Filip Hanak
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, MN, USA
| | - Patrick E. Rothwell
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Robert Vince
- Center for Drug Design, College of Pharmacy, University of Minnesota, MN, USA
| | - Swati S. More
- Center for Drug Design, College of Pharmacy, University of Minnesota, MN, USA
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7
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Soliman AM, El-Sagheir AMK, Thabet MM, Abdel Hakiem AF, Aboraia AS. Synthesis, characterization, molecular modeling studies, and biological evaluation of metal piroxicam complexes (M = Ni(II), Pt(IV), Pd(II), Ag(I)) as antibacterial and anticancer agents. Drug Dev Res 2024; 85:e22156. [PMID: 38355931 DOI: 10.1002/ddr.22156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/01/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Four piroxicam metal complexes; NiL2 , PtL2 , PdL2 , and AgL were synthesized and characterized by different techniques with enhanced antibacterial and anticancer activity. Regarding in vitro antimicrobial activity, complex NiL2 displayed potent antibacterial effect against Escherichia coli and Pseudomonas aeruginosa that was 1.9-folds higher than piroxicam (minimum inhibitory concentration [MIC] = 31.85, 65.32 µM), respectively. In case of G+ve bacteria, complex PtL2 had potent activity on Staphylococcus aureus which was 2.1-folds higher than piroxicam (MIC = 43.12 µM), while activity of complex AgL against Enterococcus faecalis was threefolds higher than piroxicam (MIC = 74.57 µM. Complexes PtL2 and PdL2 exhibited higher inhibition of DNA gyrase than piroxicam (IC50 = 6.21 µM) in the range of 1.9-1.7-folds. The in vitro antiproliferative activity depicted that all investigated complexes showed better cytotoxic effect than piroxicam, specifically Pt and Pd complexes which had lower IC50 values than piroxicam on human liver cancer cell line HepG2 by 1.8 and 1.7-folds, respectively. While Pd and Ag complexes showed 2 and 1.6-folds better effect on human colon cancer cell line HT-29 compared with piroxicam. Molecular modeling studies including docking on Stranded DNA Duplex (1juu) and DNA gyrase enzyme (1kzn) that gave good insight about interaction of complexes with target molecules, calculation of electrostatic potential map and global reactivity descriptors were performed.
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Affiliation(s)
- Aya M Soliman
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Ahmed M K El-Sagheir
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt
- Division of Pharmaceutical Chemistry and Technology, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Momen M Thabet
- Department of Microbiology and Immunology, Faculty of Pharmacy, South Valley University, Qena, Egypt
| | | | - Ahmed S Aboraia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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8
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Upadhyay DB, Mokariya JA, Patel PJ, Patel SG, Das A, Nandi A, Nogales J, More N, Kumar A, Rajani DP, Narayan M, Kumar J, Banerjee S, Sahoo SK, Patel HM. Indole clubbed 2,4-thiazolidinedione linked 1,2,3-triazole as a potent antimalarial and antibacterial agent against drug-resistant strain and molecular modeling studies. Arch Pharm (Weinheim) 2024; 357:e2300673. [PMID: 38247229 DOI: 10.1002/ardp.202300673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
In the face of escalating challenges of microbial resistance strains, this study describes the design and synthesis of 5-({1-[(1H-1,2,3-triazol-4-yl)methyl]-1H-indol-3-yl}methylene)thiazolidine-2,4-dione derivatives, which have demonstrated significant antimicrobial properties. Compared with the minimum inhibitory concentrations (MIC) values of ciprofloxacin on the respective strains, compounds 5a, 5d, 5g, 5l, and 5m exhibited potent antibacterial activity with MIC values ranging from 16 to 25 µM. Almost all the synthesized compounds showed lower MIC compared to standards against vancomycin-resistant enterococcus and methicillin-resistant Staphylococcus aureus strains. Additionally, the majority of the synthesized compounds demonstrated remarkable antifungal activity, against Candida albicans and Aspergillus niger, as compared to nystatin, griseofulvin, and fluconazole. Furthermore, the majority of compounds exhibited notable inhibitory effects against the Plasmodium falciparum strain, having IC50 values ranging from 1.31 to 2.79 μM as compared to standard quinine (2.71 μM). Cytotoxicity evaluation of compounds 5a-q on SHSY-5Y cells at up to 100 μg/mL showed no adverse effects. Comparison with control groups highlights their noncytotoxic characteristics. Molecular docking confirmed compound binding to target active sites, with stable protein-ligand complexes displaying drug-like molecules. Molecular dynamics simulations revealed dynamic stability and interactions. Rigorous tests and molecular modeling unveil the effectiveness of the compounds against drug-resistant microbes, providing hope for new antimicrobial compounds with potential safety.
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Affiliation(s)
- Dipti B Upadhyay
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Jaydeep A Mokariya
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Paras J Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Subham G Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Anwesha Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat, India
| | - Arijit Nandi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Joaquina Nogales
- Department of Cellular and Systems Medicine, University of Dundee, Dundee, UK
| | - Nachiket More
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Amit Kumar
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Dhanji P Rajani
- Microcare Laboratory and Tuberculosis Diagnosis & Research Center, Surat, Gujarat, India
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas, USA
| | - Jyotish Kumar
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, Texas, USA
| | - Sourav Banerjee
- Department of Cellular and Systems Medicine, University of Dundee, Dundee, UK
| | - Suban K Sahoo
- Department of Chemistry, SV National Institute of Technology, Surat, Gujarat, India
| | - Hitendra M Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
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9
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Hu ZY, Wang WJ, Hu L, Shi JH, Jiang SL. Comprehending the intermolecular interaction of dacomitinib with bovine serum albumin: experimental and theoretical approaches. J Biomol Struct Dyn 2024; 42:3579-3592. [PMID: 37288787 DOI: 10.1080/07391102.2023.2218926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023]
Abstract
Dacomitinib (DAC), as a member of tyrosine kinase inhibitors is primarily used to treat non-small cell lung cancer. The intermolecular interaction between DAC and bovine serum albumin (BSA) was comprehended with the help of experiments and theoretical simulations. The outcomes indicated that DAC quenched the endogenous fluorescence of BSA through static quenching mode. In the binding process, DAC was preferentially inserted into the hydrophobic cavity of BSA subdomain IA (site III), and a fluorescence-free DAC-BSA complex with molar ratio of 1:1 was generated. The outcomes confirmed that DAC had a stronger affinity on BSA and the non-radiative energy transfer occurred in the combination process of two. And, it can be inferred from the outcomes of thermodynamic parameters and competition experiments with 8-aniline-1-naphthalenesulfonic acid (ANS) and D-(+)- sucrose that hydrogen bonds (H-bonds), van der Waals forces (vdW) and hydrophobic forces had a significant impact in inserting DAC into the hydrophobic cavity of BSA. The outcomes from multi-spectroscopic measurements that DAC could affect the secondary structure of BSA, that was, α-helix content decreased slightly from 51.0% to 49.7%. Moreover, the combination of DAC and BSA led to a reduction in the hydrophobicity of the microenvironment around tyrosine (Tyr) residues in BSA while had little influence on the microenvironment of around tryptophan (Trp) residues. The outcomes from molecular docking and molecular dynamics (MD) simulation further demonstrated the insertion of DAC into site III of BSA and hydrogen energy and van der Waals energy were the dominant energy of DAC-BSA stability. In addition, the influence of metal ions (Fe3+, Cu2+, Co2+, etc.) on the affinity of the system was explored.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhe-Ying Hu
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Wan-Jun Wang
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Lu Hu
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Jie-Hua Shi
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
| | - Shao-Liang Jiang
- College of Pharmaceutic Science, Zhejiang University of Technology, Hangzhou, China
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10
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Zhou L, Ding X, Cao J, Feng Y, Gu Y, Liu L, Chen R, Gao D, Chen X. Systematic profiling of Taxol resistance and sensitivity to tubulin missence mutations at molecular and cellular levels. Chem Biol Drug Des 2024; 103:e14513. [PMID: 38570322 DOI: 10.1111/cbdd.14513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/24/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024]
Abstract
Taxol (paclitaxel) is the first approved microtubule-stabilizing agent (MSA) by binding stoichiometrically to tubulin, which is considered to be one of the most significant advances in first-line chemotherapy against diverse tumors. However, a large number of residue missence mutations harboring in the tubulin have been observed to cause acquired drug resistance, largely limiting the clinical application of Taxol and its analogs in chemotherapy. A systematic investigation of the intermolecular interactions between the Taxol and various tubulin mutants would help to establish a comprehensive picture of drug response to tubulin mutations in clinical treatment of cancer, and to design new MSA agents with high potency and selectivity to overcome drug resistance. In this study, we described an integration of in silico analysis and in vitro assay (iSiV) to profile Taxol against a panel of 149 clinically observed, cancer-associated missence mutations in β-tubulin at molecular and cellular levels, aiming to a systematic understanding of molecular mechanism and biological implication underlying drug resistance and sensitivity conferring from tubulin mutations. It is revealed that the Taxol-resistant mutations can be classified into three types: (I) nonbonded interaction broken due to mutation, (II) steric hindrance caused by mutation, and (III) conformational change upon mutation. In addition, we identified three new Taxol-resistant mutations (C239Y, T274I, and R320P) that can largely reduce the binding affinity of Taxol to tubulin at molecular level, in which the T274I and R320P were observed to considerably impair the antitumor activity of Taxol at cellular level. Moreover, a novel drug-susceptible mutation (M363T) was also identified, which improves Taxol affinity by 2.6-fold and decreases Taxol antitumor EC50 values from 29.4 to 18.7 μM.
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Affiliation(s)
- Lihua Zhou
- Department of Pharmacy, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Xi Ding
- Department of Pharmacy, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Jingjing Cao
- Department of Pharmacy, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Yu Feng
- Department of Pharmacy, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Yuqin Gu
- Department of Pharmacy, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Ling Liu
- Department of Pharmacy, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Rong Chen
- Department of Pharmacy, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Dongyun Gao
- Department of Oncology, The Dongtai Hospital of Nantong University, Dongtai, China
| | - Xiaoling Chen
- Department of Respiratory Medicine, The Dongtai Hospital of Nantong University, Dongtai, China
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11
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Okamoto HH, Cecon E, Nureki O, Rivara S, Jockers R. Melatonin receptor structure and signaling. J Pineal Res 2024; 76:e12952. [PMID: 38587234 DOI: 10.1111/jpi.12952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/05/2024] [Accepted: 03/24/2024] [Indexed: 04/09/2024]
Abstract
Melatonin (5-methoxy-N-acetyltryptamine) binds with high affinity and specificity to membrane receptors. Several receptor subtypes exist in different species, of which the mammalian MT1 and MT2 receptors are the best-characterized. They are members of the G protein-coupled receptor superfamily, preferentially coupling to Gi/o proteins but also to other G proteins in a cell-context-depending manner. In this review, experts on melatonin receptors will summarize the current state of the field. We briefly report on the discovery and classification of melatonin receptors, then focus on the molecular structure of human MT1 and MT2 receptors and highlight the importance of molecular simulations to identify new ligands and to understand the structural dynamics of these receptors. We then describe the state-of-the-art of the intracellular signaling pathways activated by melatonin receptors and their complexes. Brief statements on the molecular toolbox available for melatonin receptor studies and future perspectives will round-up this review.
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Affiliation(s)
- Hiroyuki H Okamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Erika Cecon
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Silvia Rivara
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Ralf Jockers
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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12
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El-Mernissi R, Khaldan A, Bouamrane S, Rehman HM, Alaqarbeh M, Ajana MA, Lakhlifi T, Bouachrine M. 3D-QSAR, molecular docking, simulation dynamic and ADMET studies on new quinolines derivatives against colorectal carcinoma activity. J Biomol Struct Dyn 2024; 42:3682-3699. [PMID: 37227776 DOI: 10.1080/07391102.2023.2214233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Cancer is the uncontrolled spread of abnormal cells that results in abnormal tissue growth in the affected organ. One of the most important organs is exposed to the growth of colon cancer cells, which start in the large intestine (colon) or the rectum. Several therapeutic protocols were used to treat different kinds of cancer. Recently, several studies have targeted tubulin and microtubules due to their remarkable prefoliation. Also, recent research shows that quinoline compounds have significant efficacy against human colorectal cancer. So, the present work investigated the potential of thirty quinoline compounds as tubulin inhibitors using computational methods. A 3D-QSAR approach using two contours (CoMFA and CoMSIA), molecular docking simulation to determine the binding type of the complexes (ligand-receptor), molecular dynamics simulation and identifying pharmacokinetic characteristics were used to design molecules. For all compounds designed (T1-5), molecular docking was used to compare the stability by type of binding. The ADMET has been utilized for molecules with good stability in molecular docking (T1-3); these compounds have good medicinal characteristics. Furthermore, a molecular dynamics simulation (MD) at 100 ns was performed to confirm the stability of the T1-3 compounds; the molecules (T1-3) remained the most stable throughout the simulation. The compounds T1, T2 and T3 are the best-designed drugs for colorectal carcinoma treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reda El-Mernissi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Ayoub Khaldan
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Soukaina Bouamrane
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | | | | | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, University Moulay Ismail, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, Beni mellal, Morocco
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13
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Akther T, McFadden WM, Zhang H, Kirby KA, Sarafianos SG, Wang Z. Design and Synthesis of New GS-6207 Subtypes for Targeting HIV-1 Capsid Protein. Int J Mol Sci 2024; 25:3734. [PMID: 38612545 PMCID: PMC11012105 DOI: 10.3390/ijms25073734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
HIV-1 capsid protein (CA) is the molecular target of the recently FDA-approved long acting injectable (LAI) drug lenacapavir (GS-6207). The quick emergence of CA mutations resistant to GS-6207 necessitates the design and synthesis of novel sub-chemotypes. We have conducted the structure-based design of two new sub-chemotypes combining the scaffold of GS-6207 and the N-terminal cap of PF74 analogs, the other important CA-targeting chemotype. The design was validated via induced-fit molecular docking. More importantly, we have worked out a general synthetic route to allow the modular synthesis of novel GS-6207 subtypes. Significantly, the desired stereochemistry of the skeleton C2 was confirmed via an X-ray crystal structure of the key synthetic intermediate 22a. Although the newly synthesized analogs did not show significant potency, our efforts herein will facilitate the future design and synthesis of novel subtypes with improved potency.
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Affiliation(s)
- Thamina Akther
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
| | - William M. McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Karen A. Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
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14
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Gandham SK, Jha A, Kudale AA. Design and Synthesis of 2-Phenylindolizine Acetamides: Molecular Docking, in Vitro Antimicrobial and Anticancer Activity Evaluation. Chem Biodivers 2024:e202400075. [PMID: 38466656 DOI: 10.1002/cbdv.202400075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/09/2024] [Accepted: 03/10/2024] [Indexed: 03/13/2024]
Abstract
In the present work, we synthesized a small library of 2-phenylindolizine acetamide derivatives 7a-i and studied their biological activity. The synthesis was accomplished starting with easily available starting material phenacyl bromide 1 proceeding through the key intermediate 6-methyl-7-nitro-2-phenylindolizine 4. All the compounds 7a-i were characterized using spectroscopy viz., 1H NMR, 13C NMR, FTIR, and mass spectrometry. Interestingly, 2-phenylindolizine scaffolds 7c, 7f and 7g revealed a remarkable antibacterial activity against relevant organisms S. aureus, E. coli, S. pneumoniae, P. aeruginosa. The target compounds 7e and 7h showed excellent anticancer activity against Colo-205 and MDA-MB-231 cell lines with IC50 values of 68.62, 62.91, 54.23 and 46.34 µM respectively. Additionally, all the 2-phenylindolizine acetamide derivatives 7a-i were subjected to molecular docking prediction by Autodock 4.2. Compounds 7a, 7f and 7c exhibited very good hydrogen bonding amino acid interactions Asp83 (2.23 Å), Asp83 (2.08 Å), His74 (2.05 Å), His76 (1.71 Å), Ser80 (1.05 Å) with active site of Topoisomerase-IV from S. pneumoniae (4KPE). Further, the compounds 7a-i have revealed acceptable ranges for drug-likeliness properties upon evaluation using SwissADME for ADMET and physiochemical properties.
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Affiliation(s)
- Siva Kumar Gandham
- GITAM School of Science, Department of Chemistry, Gandhi Nagar, Rushikonda, 5300045, Visakhapatnam, INDIA
| | - Anjali Jha
- GITAM (Deemed to be University), Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University), Rushikonda, 5300045, Visakhapatnam, INDIA
| | - Amit A Kudale
- ASolution Pharmaceuticals Pvt Ltd, Research & Development, Ambernath, Dist. Thane, 421506, Amernath, INDIA
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Dingiş Birgül Sİ, Kumari J, Tamhaev R, Mourey L, Lherbet C, Sriram D, Akdemir A, Küçükgüzel İ. In silico design, synthesis and antitubercular activity of novel 2-acylhydrazono-5-arylmethylene-4-thiazolidinones as enoyl-acyl carrier protein reductase inhibitors. J Biomol Struct Dyn 2024:1-19. [PMID: 38450660 DOI: 10.1080/07391102.2024.2319678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/12/2024] [Indexed: 03/08/2024]
Abstract
Mycobacteria regulate the synthesis of mycolic acid through the fatty acid synthase system type 1 (FAS I) and the fatty acid synthase system type-2 (FAS-II). Because mammalian cells exclusively utilize the FAS-I enzyme system for fatty acid production, targeting the FAS-II enzyme system could serve as a specific approach for developing selective antimycobacterial drugs. Enoyl-acyl carrier protein reductase enzyme (MtInhA), part of the FAS-II enzyme system, contains the NADH cofactor in its active site and reduces the intermediate. Molecular docking studies were performed on an in-house database (∼2200 compounds). For this study, five different crystal structures of MtInhA (PDB Code: 4TZK, 4BQP, 4D0S, 4BGE, 4BII) were used due to rotamer difference, mutation and the presence of cofactors. Molecular dynamics simulations (250 ns) were performed for the novel 2-acylhydrazono-5-arylmethylene-4-thiazolidinones derivatives selected by molecular docking studies. Twenty-three compounds selected by in silico methods were synthesized. Antitubercular activity and MtInhA enzyme inhibition studies were performed for compounds whose structures were elucidated by IR,1H-NMR,13C-NMR, HSQC, HMBC, MS and elemental analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Serap İpek Dingiş Birgül
- Institute of Health Sciences, Department of Pharmaceutical Chemistry, Marmara University, Istanbul, Türkiye
- Computer-Aided Drug Discovery Laboratory, Department of Pharmacology, Bezmialem Vakif University, Istanbul, Türkiye
| | - Jyothi Kumari
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, India
| | - Rasoul Tamhaev
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, Université Toulouse III - Paul Sabatier, Toulouse Cedex 09, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Christian Lherbet
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, Université Toulouse III - Paul Sabatier, Toulouse Cedex 09, France
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, India
| | - Atilla Akdemir
- Faculty of Pharmacy, Department of Pharmacology, Istinye University, Istanbul, Türkiye
| | - İlkay Küçükgüzel
- Institute of Health Sciences, Department of Pharmaceutical Chemistry, Marmara University, Istanbul, Türkiye
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Fenerbahçe University, Istanbul, Türkiye
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16
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Selvaraj C, Pedone E, Lee JK, Singh SK. Editorial: Molecular level atomistic and structural insights on biological macromolecules, inhibition, and dynamics studies. Front Mol Biosci 2024; 11:1362215. [PMID: 38516195 PMCID: PMC10955358 DOI: 10.3389/fmolb.2024.1362215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Affiliation(s)
- Chandrabose Selvaraj
- Computational and Structural Research in Drug Discovery Lab (CSRDD), Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
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17
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Vukomanović P, Stefanović M, Stevanović JM, Petrić A, Trenkić M, Andrejević L, Lazarević M, Sokolović D, Veselinović AM. Monte Carlo Optimization Method Based QSAR Modeling of Placental Barrier Permeability. Pharm Res 2024; 41:493-500. [PMID: 38337105 DOI: 10.1007/s11095-024-03675-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
PURPOSE In order to ensure that drug administration is safe during pregnancy, it is crucial to have the possibility to predict the placental permeability of drugs in humans. The experimental method which is most widely used for the said purpose is in vitro human placental perfusion, though the approach is highly expensive and time consuming. Quantitative structure-activity relationship (QSAR) modeling represents a powerful tool for the assessment of the drug placental transfer, and can be successfully employed to be an alternative in in vitro experiments. METHODS The conformation-independent QSAR models covered in the present study were developed through the use of the SMILES notation descriptors and local molecular graph invariants. What is more, the Monte Carlo optimization method, was used in the test sets and the training sets as the model developer with three independent molecular splits. RESULTS A range of different statistical parameters was used to validate the developed QSAR model, including the standard error of estimation, mean absolute error, root-mean-square error (RMSE), correlation coefficient, cross-validated correlation coefficient, Fisher ratio, MAE-based metrics and the correlation ideality index. Once the mentioned statistical methods were employed, an excellent predictive potential and robustness of the developed QSAR model was demonstrated. In addition, the molecular fragments, which are derived from the SMILES notation descriptors accounting for the decrease or increase in the investigated activity, were revealed. CONCLUSION The presented QSAR modeling can be an invaluable tool for the high-throughput screening of the placental permeability of drugs.
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Affiliation(s)
- Predrag Vukomanović
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Milan Stefanović
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Jelena Milošević Stevanović
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Aleksandra Petrić
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Milan Trenkić
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Lazar Andrejević
- COVID Hospital, University Clinical Centre of Niš, Kruševac, Serbia
| | - Milan Lazarević
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Cardiovascular and Transplant Surgery, University Clinical Centre of Niš, Niš, Serbia
| | | | - Aleksandar M Veselinović
- Faculty of Medicine, Department of Chemistry, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia.
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18
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McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024; 300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Konstantine Halkidis
- Department of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jo M Holt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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Chu P, Sheng Y, Shen C, Xia Y, Kong L, Sun J. Structure-based improvement of the binding affinity and recognition specificity of peptide competitors to target pediatric IL-5R/IL-5 interaction by gluing halogen bonds at their complex interface. J Mol Recognit 2024; 37:e3070. [PMID: 37990248 DOI: 10.1002/jmr.3070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
Human interleukin-5 (IL-5) cytokine mediates the development of eosinophils and is involved in a variety of immune inflammatory responses that play a major role in the pathogenesis of childhood asthma, leukemia, and other pediatric allergic diseases. The immunomodulatory cytokine functions by binding to its cognate cell surface receptor IL-5R in a sheet-by-sheet manner, which can be conformationally mimicked and competitively disrupted by a double-stranded cyclic AF18748 peptide. In this study, we systematically examined the co-crystallized complex structure of human IL-5R with AF18748 peptide and rationally designed a halogen bond to glue at the protein-peptide complex interface by substituting the indole moiety of AF18748 Trp13 residue with a halogen atom (X = F, Cl, Br, or I). High-level theoretical calculations imparted presence of the halogen bond between the oxygen atom (O) of IL-5R Glu58 backbone and the halogen atom (X) of AF18748 Trp13 side chain. Experimental assays confirmed that the halogen bond can promote peptide binding moderately or considerably. More importantly, the halogen bond not only enhances peptide affinity to IL-5R, but also improves peptide selectivity for its cognate IL-5R over other noncognate IL-R proteins. As might be expected, the affinity and selectivity conferred by halogen bond increase consistently in the order: H < F < Cl < Br < I. Structural modeling revealed that the halogen bond plus its vicinal π-cation-π stacking co-define a ringed noncovalent system at the complex interface, which involves a synergistic effect to effectively improve the peptide binding potency and recognition specificity.
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Affiliation(s)
- Peipei Chu
- Department of Pediatric Medicine, Children's Hospital of Wujiang District, Soochow University, Suzhou, China
| | - Yeping Sheng
- Department of Pediatric Medicine, Children's Hospital of Wujiang District, Soochow University, Suzhou, China
| | - Chentao Shen
- Department of Pediatric Medicine, Children's Hospital of Wujiang District, Soochow University, Suzhou, China
| | - Yalin Xia
- Department of Pediatric Medicine, Children's Hospital of Wujiang District, Soochow University, Suzhou, China
| | - Lingjun Kong
- Department of Pediatric Medicine, Children's Hospital of Soochow University, Suzhou, China
| | - Jiefan Sun
- Department of Pediatric Medicine, Children's Hospital of Wujiang District, Soochow University, Suzhou, China
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20
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Rasgania J, Gavadia R, Sahu N, Sharma P, Chauhan NS, Saharan V, Kapoor RK, Jakhar K. Design, synthesis and exploration of novel triazinoindoles as potent quorum-sensing inhibitors and radical quenchers. Future Med Chem 2024; 16:399-416. [PMID: 38375563 DOI: 10.4155/fmc-2023-0313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Background: Antimicrobial resistance has become a critical health concern, and quorum-sensing exacerbates the resistance by facilitating cell-to-cell communication within the microbial community, leading to severe pathogenic outbreaks. Methods & results: Novel 1-(2-((5H-[1,2,4]-triazino[5,6-b]indol-3-yl)thio)acetyl)indoline-2,3-diones were synthesized. The title compounds exhibit outstanding anti-quorum-sensing efficacy, and compound 7g demonstrated the maximum proficiency (IC50 = 0.0504 μg/ml). The hybrids displayed potent antioxidant action, and compound 7c showed the highest antioxidant ability (IC50 = 40.71 μg/ml). Molecular docking of the isatin hybrids against DNA gyrase and quorum-sensing receptor CviR validated the observed in vitro findings. The befitting pharmacokinetic profile of the synthesized drug candidates was ascertained through absorption, distribution, metabolism, excretion and toxicity screening. Conclusion: The remarkable biocompetence of the synthesized triazinoindoles may help to combat drug-resistant infections.
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Affiliation(s)
- Jyoti Rasgania
- Department of Chemistry, M. D. University, Rohtak, 124001, Haryana, India
| | - Renu Gavadia
- Department of Chemistry, M. D. University, Rohtak, 124001, Haryana, India
| | - Neetu Sahu
- Department of Chemistry, M. D. University, Rohtak, 124001, Haryana, India
| | - Pinki Sharma
- Department of Biochemistry, M. D. University, Rohtak, 124001, Haryana, India
| | - Nar S Chauhan
- Department of Biochemistry, M. D. University, Rohtak, 124001, Haryana, India
| | - Vicky Saharan
- Department of Microbiology, M. D. University, Rohtak, 124001, Haryana, India
| | - Rajeev K Kapoor
- Department of Microbiology, M. D. University, Rohtak, 124001, Haryana, India
| | - Komal Jakhar
- Department of Chemistry, M. D. University, Rohtak, 124001, Haryana, India
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Gasperini G, Massai L, De Simone D, Raso MM, Palmieri E, Alfini R, Rossi O, Ravenscroft N, Kuttel MM, Micoli F. O-Antigen decorations in Salmonella enterica play a key role in eliciting functional immune responses against heterologous serovars in animal models. Front Cell Infect Microbiol 2024; 14:1347813. [PMID: 38487353 PMCID: PMC10937413 DOI: 10.3389/fcimb.2024.1347813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction Different serovars of Salmonella enterica cause systemic diseases in humans including enteric fever, caused by S. Typhi and S. Paratyphi A, and invasive nontyphoidal salmonellosis (iNTS), caused mainly by S. Typhimurium and S. Enteritidis. No vaccines are yet available against paratyphoid fever and iNTS but different strategies, based on the immunodominant O-Antigen component of the lipopolysaccharide, are currently being tested. The O-Antigens of S. enterica serovars share structural features including the backbone comprising mannose, rhamnose and galactose as well as further modifications such as O-acetylation and glucosylation. The importance of these O-Antigen decorations for the induced immunogenicity and cross-reactivity has been poorly characterized. Methods These immunological aspects were investigated in this study using Generalized Modules for Membrane Antigens (GMMA) as delivery systems for the different O-Antigen variants. This platform allowed the rapid generation and in vivo testing of defined and controlled polysaccharide structures through genetic manipulation of the O-Antigen biosynthetic genes. Results Results from mice and rabbit immunization experiments highlighted the important role played by secondary O-Antigen decorations in the induced immunogenicity. Moreover, molecular modeling of O-Antigen conformations corroborated the likelihood of cross-protection between S. enterica serovars. Discussion Such results, if confirmed in humans, could have a great impact on the design of a simplified vaccine composition able to maximize functional immune responses against clinically relevant Salmonella enterica serovars.
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Affiliation(s)
| | - Luisa Massai
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | | | | | - Elena Palmieri
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | - Renzo Alfini
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | - Omar Rossi
- GSK Vaccines Institute for Global Health (GVGH), Siena, Italy
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, South Africa
| | - Michelle M. Kuttel
- Department of Computer Science, University of Cape Town, Rondebosch, South Africa
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22
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Rosiak N, Tykarska E, Cielecka-Piontek J. Enhanced Antioxidant and Neuroprotective Properties of Pterostilbene (Resveratrol Derivative) in Amorphous Solid Dispersions. Int J Mol Sci 2024; 25:2774. [PMID: 38474022 DOI: 10.3390/ijms25052774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
In this study, amorphous solid dispersions (ASDs) of pterostilbene (PTR) with polyvinylpyrrolidone polymers (PVP K30 and VA64) were prepared through milling, affirming the amorphous dispersion of PTR via X-ray powder diffraction (XRPD) and differential scanning calorimetry (DSC). Subsequent analysis of DSC thermograms, augmented using mathematical equations such as the Gordon-Taylor and Couchman-Karasz equations, facilitated the determination of predicted values for glass transition (Tg), PTR's miscibility with PVP, and the strength of PTR's interaction with the polymers. Fourier-transform infrared (FTIR) analysis validated interactions maintaining PTR's amorphous state and identified involved functional groups, namely, the 4'-OH and/or -CH groups of PTR and the C=O group of PVP. The study culminated in evaluating the impact of amorphization on water solubility, the release profile in pH 6.8, and in vitro permeability (PAMPA-GIT and BBB methods). In addition, it was determined how improving water solubility affects the increase in antioxidant (ABTS, DPPH, CUPRAC, and FRAP assays) and neuroprotective (inhibition of cholinesterases: AChE and BChE) properties. The apparent solubility of the pure PTR was ~4.0 µg·mL-1 and showed no activity in the considered assays. For obtained ASDs (PTR-PVP30/PTR-PVPVA64, respectively) improvements in apparent solubility (410.8 and 383.2 µg·mL-1), release profile, permeability, antioxidant properties (ABTS: IC50 = 52.37/52.99 μg·mL-1, DPPH: IC50 = 163.43/173.96 μg·mL-1, CUPRAC: IC0.5 = 122.27/129.59 μg·mL-1, FRAP: IC0.5 = 95.69/98.57 μg·mL-1), and neuroprotective effects (AChE: 39.1%/36.2%, BChE: 76.9%/73.2%) were confirmed.
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Affiliation(s)
- Natalia Rosiak
- Department of Pharmacognosy and Biomaterials, Faculty of Pharmacy, Poznan University of Medical Sciences, 3 Rokietnicka St., 60-806 Poznan, Poland
| | - Ewa Tykarska
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, 3 Rokietnicka St., 60-806 Poznan, Poland
| | - Judyta Cielecka-Piontek
- Department of Pharmacognosy and Biomaterials, Faculty of Pharmacy, Poznan University of Medical Sciences, 3 Rokietnicka St., 60-806 Poznan, Poland
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23
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Zurita A, Vega Hissi E, Cianci Romero A, Luján AM, Salido S, Yaneff A, Davio C, Cobo J, Carpinella MC, Enriz RD. Rosmarinic Acid Present in Lepechinia floribunda and Lepechinia meyenii as a Potent Inhibitor of the Adenylyl Cyclase gNC1 from Giardia lamblia. Plants (Basel) 2024; 13:646. [PMID: 38475493 DOI: 10.3390/plants13050646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Giardiasis is a parasitosis caused by Giardia lamblia with significant epidemiological and clinical importance due to its high prevalence and pathogenicity. The lack of optimal therapies for treating this parasite makes the development of new effective chemical entities an urgent need. In the search for new inhibitors of the adenylyl cyclase gNC1 obtained from G. lamblia, 14 extracts from Argentinian native plants were screened. Lepechinia floribunda and L. meyenii extracts exhibited the highest gNC1 inhibitory activity, with IC50 values of 9 and 31 µg/mL, respectively. In silico studies showed rosmarinic acid, a hydroxycinnamic acid present in both mentioned species, to be a promising anti-gNC1 compound. This result was confirmed experimentally, with rosmarinic acid showing an IC50 value of 10.1 µM. Theoretical and experimental findings elucidate the molecular-level mechanism of rosmarinic acid, pinpointing the key interactions stabilizing the compound-enzyme complex and the binding site. These results strongly support that rosmarinic acid is a promising scaffold for developing novel compounds with inhibitory activity against gNC1, which could serve as potential therapeutic agents to treat giardiasis.
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Affiliation(s)
- Adolfo Zurita
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, San Luis 5700, Argentina
| | - Esteban Vega Hissi
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, San Luis 5700, Argentina
| | - Agostina Cianci Romero
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, San Luis 5700, Argentina
| | - Adela María Luján
- Laboratorio de Química Fina y Productos Naturales, Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE) CONICET-UCC, Universidad Católica de Córdoba, Avda. Armada Argentina 3555, Córdoba X5016DHK, Argentina
| | - Sofía Salido
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - Agustín Yaneff
- Instituto de Investigaciones Farmacológicas (ININFA-UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires C1113AAD, Argentina
| | - Carlos Davio
- Instituto de Investigaciones Farmacológicas (ININFA-UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires C1113AAD, Argentina
| | - Justo Cobo
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, Campus Las Lagunillas s/n, 23071 Jaén, Spain
| | - María Cecilia Carpinella
- Laboratorio de Química Fina y Productos Naturales, Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE) CONICET-UCC, Universidad Católica de Córdoba, Avda. Armada Argentina 3555, Córdoba X5016DHK, Argentina
| | - Ricardo Daniel Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Ejército de los Andes 950, San Luis 5700, Argentina
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24
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Cybulski M, Sidoryk K, Zaremba-Czogalla M, Trzaskowski B, Kubiszewski M, Tobiasz J, Jaromin A, Michalak O. The Conjugates of Indolo[2,3- b]quinoline as Anti-Pancreatic Cancer Agents: Design, Synthesis, Molecular Docking and Biological Evaluations. Int J Mol Sci 2024; 25:2573. [PMID: 38473820 DOI: 10.3390/ijms25052573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
New amide conjugates of hydroxycinnamic acids (HCAs) and the known antineoplastic 5,11-dimethyl-5H-indolo[2,3-b]quinoline (DiMIQ), an analog of the natural alkaloid neocryptolepine, were synthesized and tested in vitro for anticancer activity. The compound 9-[((2-hydroxy)cinnamoyl)amino]-5,11-dimethyl-5H-indolo[2,3-b]quinoline (2), which contains the ortho-coumaric acid fragment, demonstrated dose-dependent effectiveness against both normal BxPC-3 and metastatic AsPC-1 pancreatic cancer cells. The IC50 values for AsPC-1 and BxPC-3 were 336.5 nM and 347.5 nM, respectively, with a selectivity index of approximately 5 for both pancreatic cancer cells compared to normal dermal fibroblasts. Conjugate 2 did not exhibit any hemolytic activity against human erythrocytes at the tested concentration. Computational studies were performed to predict the pharmacokinetic profile and potential mechanism of action of the synthesized conjugates. These studies focused on the ADME properties of the conjugates and their interactions with DNA, as well as DNA-topoisomerase alpha and beta complexes. All of the conjugates studied showed approximately one order of magnitude stronger binding to DNA compared to the reference DiMIQ, and approximately two orders of magnitude stronger binding to the topoisomerase II-DNA complex compared to DiMIQ. Conjugate 2 was predicted to have the strongest binding to the enzyme-DNA complex, with a Ki value of 2.8 nM.
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Affiliation(s)
- Marcin Cybulski
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Katarzyna Sidoryk
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Magdalena Zaremba-Czogalla
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Bartosz Trzaskowski
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marek Kubiszewski
- Pharmaceutical Analysis Laboratory, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Joanna Tobiasz
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Anna Jaromin
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Olga Michalak
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
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25
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Trezza A, Geminiani M, Cutrera G, Dreassi E, Frusciante L, Lamponi S, Spiga O, Santucci A. A Drug Discovery Approach to a Reveal Novel Antioxidant Natural Source: The Case of Chestnut Burr Biomass. Int J Mol Sci 2024; 25:2517. [PMID: 38473765 DOI: 10.3390/ijms25052517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Currently, many environmental and energy-related problems are threatening the future of our planet. In October 2022, the Worldmeter recorded the world population as 7.9 billion people, estimating that there will be an increase of 2 billion by 2057. The rapid growth of the population and the continuous increase in needs are causing worrying conditions, such as pollution, climate change, global warming, waste disposal, and natural resource reduction. Looking for novel and innovative methods to overcome these global troubles is a must for our common welfare. The circular bioeconomy represents a promising strategy to alleviate the current conditions using biomass-like natural wastes to replace commercial products that have a negative effect on our ecological footprint. Applying the circular bioeconomy concept, we propose an integrated in silico and in vitro approach to identify antioxidant bioactive compounds extracted from chestnut burrs (an agroforest waste) and their potential biological targets. Our study provides a novel and robust strategy developed within the circular bioeconomy concept aimed at target and drug discovery for a wide range of diseases. Our study could open new frontiers in the circular bioeconomy related to target and drug discovery, offering new ideas for sustainable scientific research aimed at identifying novel therapeutical strategies.
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Affiliation(s)
- Alfonso Trezza
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Michela Geminiani
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
- SienabioACTIVE, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Giuseppe Cutrera
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Elena Dreassi
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Luisa Frusciante
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Stefania Lamponi
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
- SienabioACTIVE, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
- SienabioACTIVE, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology Chemistry & Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
- SienabioACTIVE, University of Siena, Via A. Moro, 53100 Siena, Italy
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26
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Wang Y, Stebe KJ, de la Fuente-Nunez C, Radhakrishnan R. Computational Design of Peptides for Biomaterials Applications. ACS Appl Bio Mater 2024; 7:617-625. [PMID: 36971822 DOI: 10.1021/acsabm.2c01023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Computer-aided molecular design and protein engineering emerge as promising and active subjects in bioengineering and biotechnological applications. On one hand, due to the advancing computing power in the past decade, modeling toolkits and force fields have been put to use for accurate multiscale modeling of biomolecules including lipid, protein, carbohydrate, and nucleic acids. On the other hand, machine learning emerges as a revolutionary data analysis tool that promises to leverage physicochemical properties and structural information obtained from modeling in order to build quantitative protein structure-function relationships. We review recent computational works that utilize state-of-the-art computational methods to engineer peptides and proteins for various emerging biomedical, antimicrobial, and antifreeze applications. We also discuss challenges and possible future directions toward developing a roadmap for efficient biomolecular design and engineering.
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Affiliation(s)
- Yiming Wang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kathleen J Stebe
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Cesar de la Fuente-Nunez
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Machine Biology Group, Department of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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27
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Taher ES, Marzouk AA, Abd-Allah WH, Giovannuzzi S, Ibrahim TS, Supuran CT, El Hamd MA, El-Behairy MF. Tailored Tetrasubstituted Imidazole Carrying the Benzenesulfonamide Fragments as Selective Human Carbonic Anhydrase IX/XII Inhibitors. ChemMedChem 2024:e202400004. [PMID: 38356418 DOI: 10.1002/cmdc.202400004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
A new series of tetrasubstituted imidazole carrying sulfonamide as zinc-anchoring group has been designed. The structures of the synthesized derivatives 5 a-l have been confirmed by spectroscopic analysis. These compounds incorporate an ethylenic spacer between the benzenesulfonamide and the rest of the trisubstituted imidazole moiety and were tested as inhibitors of carbonic anhydrases and for in-vitro cytotoxicity. Most of them act as effective inhibitors of the tumor-linked CA isoforms IX and XII, in nanomolar range. Also, different compounds have shown selectivity in comparable with the standard acetazolamide. Our IBS 5 d, 5 g, and 5 l (with Ki: 10.1, 19.4, 19.8 nM against hCA IX and 47, 45, 20 nM against hCA IX) showed the best inhibitory profile. In-vitro screening of all derivatives against a full sixty-cell-lined from NCI at a single dose of 10 μM offered growth inhibition of up to 45 %. Compound 5 b has been identified with the most potent cytotoxic activity and broad spectrum. Docking studies have also been implemented and were also in accordance with the biological outcomes. Our SAR analysis has interestingly proposed efficient tumor-related hCAs IX/XII suppression.
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Affiliation(s)
- Ehab S Taher
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa, 13110, Jordan
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Asyut, 71524, Assiut, Egypt
| | - Adel A Marzouk
- National Center for Natural Products Research, School of Pharmacy, Mississippi University, Mississippi, MS 38677, USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Asyut, 71524, Assiut, Egypt
| | - Walaa Hamada Abd-Allah
- Pharmaceutical Chemistry Department, Collage of Pharmaceutical Science and Drug Manufacturing, Misr University for Science and Technology, P.O. 77, 6th of October City, Giza, Egypt
| | - Simone Giovannuzzi
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Tarek S Ibrahim
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Mohamed A El Hamd
- Department of Pharmaceutical Chemistry, College of Pharmacy, Shaqra University, Shaqra, 11961, Saudi Arabia
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, South Valley University, Qena, 83523, Egypt
| | - Mohammed Farrag El-Behairy
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Menoufiya, 32897, Egypt
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28
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Stephani J, Gerhards L, Khairalla B, Solov’yov IA, Brand I. How do Antimicrobial Peptides Interact with the Outer Membrane of Gram-Negative Bacteria? Role of Lipopolysaccharides in Peptide Binding, Anchoring, and Penetration. ACS Infect Dis 2024; 10:763-778. [PMID: 38259029 PMCID: PMC10862549 DOI: 10.1021/acsinfecdis.3c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Gram-negative bacteria possess a complex structural cell envelope that constitutes a barrier for antimicrobial peptides that neutralize the microbes by disrupting their cell membranes. Computational and experimental approaches were used to study a model outer membrane interaction with an antimicrobial peptide, melittin. The investigated membrane included di[3-deoxy-d-manno-octulosonyl]-lipid A (KLA) in the outer leaflet and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in the inner leaflet. Molecular dynamics simulations revealed that the positively charged helical C-terminus of melittin anchors rapidly into the hydrophilic headgroup region of KLA, while the flexible N-terminus makes contacts with the phosphate groups of KLA, supporting melittin penetration into the boundary between the hydrophilic and hydrophobic regions of the lipids. Electrochemical techniques confirmed the binding of melittin to the model membrane. To probe the peptide conformation and orientation during interaction with the membrane, polarization modulation infrared reflection absorption spectroscopy was used. The measurements revealed conformational changes in the peptide, accompanied by reorientation and translocation of the peptide at the membrane surface. The study suggests that melittin insertion into the outer membrane affects its permeability and capacitance but does not disturb the membrane's bilayer structure, indicating a distinct mechanism of the peptide action on the outer membrane of Gram-negative bacteria.
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Affiliation(s)
- Justus
C. Stephani
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Bishoy Khairalla
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
- Research
Center Neurosensory Science, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
- CeNaD—Center
for Nanoscale Dynamics, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
| | - Izabella Brand
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
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29
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Sulea T, Kumar S, Kuroda D. Editorial: Progress and challenges in computational structure-based design and development of biologic drugs. Front Mol Biosci 2024; 11:1360267. [PMID: 38389897 PMCID: PMC10883042 DOI: 10.3389/fmolb.2024.1360267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Sandeep Kumar
- Computational Protein Design and Modeling, Computational Science, Moderna Therapeutics, Cambridge, MA, United States
| | - Daisuke Kuroda
- Research Center of Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
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30
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Cavalloro V, Marchesi N, Linciano P, Rossi D, Campagnoli LIM, Fossati A, Ahmed KM, Malacrida A, Miloso M, Mazzeo G, Abbate S, Longhi G, Ambrosio FA, Costa G, Alcaro S, Pascale A, Martino E, Collina S. Neurodegeneration: can metabolites from Eremurus persicus help? Front Pharmacol 2024; 15:1309766. [PMID: 38370479 PMCID: PMC10873958 DOI: 10.3389/fphar.2024.1309766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/19/2024] [Indexed: 02/20/2024] Open
Abstract
The number of patients affected by neurodegenerative diseases is increasing worldwide, and no effective treatments have been developed yet. Although precision medicine could represent a powerful tool, it remains a challenge due to the high variability among patients. To identify molecules acting with innovative mechanisms of action, we performed a computational investigation using SAFAN technology, focusing specifically on HuD. This target belongs to the human embryonic lethal abnormal visual-like (ELAV) proteins and plays a key role in neuronal plasticity and differentiation. The results highlighted that the molecule able to bind the selected target was (R)-aloesaponol-III-8-methyl ether [(R)-ASME], a metabolite extracted from Eremurus persicus. Notably, this molecule is a TNF-α inhibitor, a cytokine involved in neuroinflammation. To obtain a suitable amount of (R)-ASME to confirm its activity on HuD, we optimized the extraction procedure. Together with ASME, another related metabolite, germichrysone, was isolated. Both ASME and germichrysone underwent biological investigation, but only ASME confirmed its ability to bind HuD. Given the multifactorial nature of neurodegenerative diseases, we decided to investigate ASME as a proteasome activator, being molecules endowed with this kind of activity potentially able to counteract aggregations of dysregulated proteins. ASME was able to activate the considered target both in enzymatic and cellular assays. Therefore, ASME may be considered a promising hit in the fight against neurodegenerative diseases.
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Affiliation(s)
- Valeria Cavalloro
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
- National Biodiversity Future Center, Palermo, Italy
| | | | | | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, Pavia, Italy
| | | | - Alice Fossati
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Karzan Mahmood Ahmed
- Department of Chemistry, College of Education, University of Garmian, Kalar, Iraq
| | - Alessio Malacrida
- School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Experimental Neurology Unit, University of Milano-Bicocca, Monza, Italy
| | - Mariarosaria Miloso
- School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Experimental Neurology Unit, University of Milano-Bicocca, Monza, Italy
| | - Giuseppe Mazzeo
- Department of Molecular and Translational Medicine, Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Department of Molecular and Translational Medicine, Università di Brescia, Brescia, Italy
| | - Giovanna Longhi
- Department of Molecular and Translational Medicine, Università di Brescia, Brescia, Italy
| | - Francesca Alessandra Ambrosio
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Catanzaro, Italy
| | - Giosuè Costa
- Department of Health Sciences, Campus “S. Venuta”, “Magna Græcia” University of Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, Campus “S. Venuta”, “Magna Græcia” University of Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Catanzaro, Italy
- Associazione CRISEA–Centro di Ricerca e Servizi Avanzati per l’Innovazione Rurale, Italy
| | - Alessia Pascale
- Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Emanuela Martino
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Pavia, Italy
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Han W, Bo Z, Liang T, Liu H, Li L, Guo Z, Huan R, Hagenbuch B, Gui C. G45 and V386 in Transmembrane Domains 1 and 8 Are Critical for the Activation of OATP1B3-Mediated E17βG Uptake by Clotrimazole. Mol Pharm 2024; 21:854-863. [PMID: 38235659 PMCID: PMC10917058 DOI: 10.1021/acs.molpharmaceut.3c00934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Organic anion-transporting polypeptides (OATPs) 1B1 and 1B3 are two highly homologous transport proteins. However, OATP1B1- and 1B3-mediated estradiol-17β-glucuronide (E17βG) uptake can be differentially affected by clotrimazole. In this study, by functional characterization on chimeric transporters and single mutants, we find that G45 in transmembrane domain 1 (TM1) and V386 in TM8 are critical for the activation of OATP1B3-mediated E17βG uptake by clotrimazole. However, the effect of clotrimazole on the function of OATP1B3 is substrate-dependent as clotrimazole does not stimulate OATP1B3-mediated uptake of 4',5'-dibromofluorescein (DBF) and rosuvastatin. In addition, clotrimazole is not transported by OATP1B3, but it can efficiently permeate the plasma membrane due to its lipophilic properties. Homology modeling and molecular docking indicate that E17βG binds in a substrate binding pocket of OATP1B3 through hydrogen bonding and hydrophobic interactions, among which its sterol scaffold forms hydrophobic contacts with V386. In addition, a flexible glycine residue at position 45 is essential for the activation of OATP1B3. Finally, clotrimazole is predicted to bind at an allosteric site, which mainly consists of hydrophobic residues located at the cytoplasmic halves of TMs 4, 5, 10, and 11.
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Affiliation(s)
- Wanjun Han
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Zheyue Bo
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Ting Liang
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Han Liu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Lanjing Li
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Zhening Guo
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu 215004, People’s Republic of China
| | - Ru Huan
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Bruno Hagenbuch
- Department of Pharmacology, Toxicology and Therapeutics, the University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, United States
| | - Chunshan Gui
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
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Ma X, Fan Z, Tang Z, Cai L. Investigation on improvement of enantioseparation based on clindamycin phosphate by chiral deep eutectic solvents in capillary electrophoresis. J Sep Sci 2024; 47:e2300847. [PMID: 38356235 DOI: 10.1002/jssc.202300847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/16/2024]
Abstract
In this work, the potential synergetic effect between deep eutectic solvents and an antibiotic chiral selector (clindamycin phosphate) for enantioseparation was investigated in capillary electrophoresis. We synthesized a series of deep eutectic solvents with choline chloride as hydrogen bond acceptor and three α-hydroxyl acids (l-lactic acid, l-malic acid, and l-tartaric acid) as hydrogen bond donors. Compared to the single clindamycin phosphate separation system, significantly improved separations of model drugs were observed in several synergetic systems. Compared to deep eutectic solvents with a single hydrogen bond donor, deep eutectic solvents with mixed-type hydrogen bond donors were superior. The influences of several key parameters including the type and proportion of organic modifier, clindamycin phosphate concentrations, deep eutectic solvents concentrations, and buffer pH were investigated in detail. The mechanism of the enhanced separations in deep eutectic solvents systems was investigated by means of electroosmotic flow analysis, nuclear magnetic resonance analysis, and molecular modeling. It was the first time that the synergetic systems between deep eutectic solvents and antibiotic chiral selector were established in capillary electrophoresis, and these deep eutectic solvents were demonstrated to have a good synergetic effect with clindamycin phosphate for enantioseparation.
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Affiliation(s)
- Xiaofei Ma
- Department of Pharmacy, Affiliated Hospital of Nantong University, Nantong, P. R. China
| | - Zhenyu Fan
- Department of Pharmacy, Affiliated Hospital of Nantong University, Nantong, P. R. China
| | - Zhiyuan Tang
- Department of Pharmacy, Affiliated Hospital of Nantong University, Nantong, P. R. China
| | - Liangliang Cai
- Department of Pharmacy, Affiliated Hospital of Nantong University, Nantong, P. R. China
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Berezin KV, Grabarchuk EV, Lichter AM, Dvoretski KN, Tuchin VV. Optical clearing of human skin: Molecular modeling and in vivo OCT study. J Biophotonics 2024; 17:e202300354. [PMID: 38018875 DOI: 10.1002/jbio.202300354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023]
Abstract
The results of in vivo immersion optical clearing of human skin under the action of two different optical clearing agents (OCAs), such as an aqueous sucrose solution and a radiographic contrast agent Omnipaque™ 300 (iohexol), were obtained with the use of optical coherence tomography (OCT) method. The rate of reduction of light scattering coefficient, obtained through an averaged A-scan of the OCT image in the region of dermis within the depths from 350 to 700 μm, were determined to evaluate the efficiency of optical clearing (EOC). The correlations between the EOC and the energy of intermolecular interaction of OCAs with a fragment of collagen peptide have been established as a result of molecular modeling by quantum chemistry methods HF/STO3G/DFT/B3LYP/6-311G(d) of a number of OCAs (glycerol, iohexol, sucrose, ribose, fructose, glucose) with mimetic peptide of collagen (GPH)3 .
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Affiliation(s)
- K V Berezin
- Institute of Physics, Saratov State University, Saratov, Russia
| | - E V Grabarchuk
- Astrakhan Tatishchev State University, Astrakhan, Russia
| | - A M Lichter
- Astrakhan Tatishchev State University, Astrakhan, Russia
| | | | - V V Tuchin
- Institute of Physics, Saratov State University, Saratov, Russia
- Science Medical Center, Saratov State University, Saratov, Russia
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Rauf A, Anyanwu M, Aliiri AA, Alanazi HAH, Alharbi AMA, Wadood A, Aljohani ASM, Muhammad N, Samad A, Shah SUA, Gianoncelli A, Ribaudo G. Antifungal and Antiproliferative Activity of Pistagremic Acid and Flavonoids Extracted from the Galls of Pistacia chinensis subsp. integerrima. Chem Biodivers 2024; 21:e202301815. [PMID: 38152840 DOI: 10.1002/cbdv.202301815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 12/29/2023]
Abstract
Pistacia chinensis subsp. integerrima (J.L. Stewart) Rech. f. is a plant known for its therapeutic applications in traditional medicine, which are related to its antimicrobial, anticancer, antioxidant, anti-inflammatory, analgesic, antidiarrheal, and muscle relaxant properties. The galls of P. chinensis are rich in triterpenes and flavonoids, and we here report the extraction of pistagremic acid (1), apigenin (2) and sakuranetin (3) from this source. The isolated compounds were tested against Aspergillus flavus, Candida albicans, Candida glabrata, Fusarium solani, Microsporum canis and Trichoderma longibrachiatum. The results highlighted the antimicrobial activity of flavonoids 2 and 3, suggesting that this class of molecules may be responsible for the effect related to the traditional use. On the other hand, when the compounds and the extract were tested for their antiproliferative activity on a panel of 4 human cancer cell lines, the triterpene pistagremic acid (1) showed a higher potential, thus demonstrating a different bioactivity profile. Structure-based docking and molecular dynamics simulations were used to help the interpretation of experimental results. Taken together, the here reported findings pave the way for the rationalization of the use of P. chinensis extracts, highlighting the contributions of the different components of galls to the observed bioactivity.
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Affiliation(s)
- Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | - Margrate Anyanwu
- Department of Molecular and Translational Medicine, University of Brescia, Italy
| | - Ahmad A Aliiri
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
- Department of Animal Resource, Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Hamdan A H Alanazi
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
- Directorie of Markets and Slaughterhouses, Ministry of Environment, Water and Agriculture, Saudi Arabia
| | - Abdulrahman M A Alharbi
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
- Environmental Health Department, Al-Dhahria Municipality, Ministry of Municipal Rural Affaires & Housing, Saudi Arabia
| | - Abdul Wadood
- Department of Pharmacy, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Abdullah S M Aljohani
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Naveed Muhammad
- Department of Pharmacy, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Abdus Samad
- Department of Pharmacy, Abdul Wali Khan University Mardan KPK, Pakistan
| | - Syed Uzair Ali Shah
- Department of Pharmacy, University of Swabi, Anbar, Khyber Pakhtunkhwa, Pakistan
| | | | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Italy
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Shokhen M, Walikonis R, Uversky VN, Allbeck A, Zezelic C, Feldman D, Levy NS, Levy AP. Molecular modeling of ARF6 dysregulation caused by mutations in IQSEC2. J Biomol Struct Dyn 2024; 42:1268-1279. [PMID: 37078745 DOI: 10.1080/07391102.2023.2199085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/29/2023] [Indexed: 04/21/2023]
Abstract
IQSEC2 gene mutations are associated with epilepsy, autism, and intellectual disability. The primary function IQSEC2, mediated via its Sec 7 domain, is to act as a guanine nucleotide exchange factor for ARF6. We sought to develop a molecular model, which may explain the aberrant Sec 7 activity on ARF6 of different human IQSEC2 mutations. We integrated experimental data of IQSEC2 mutants with protein structure prediction by the RaptorX server combined with molecular modeling and molecular dynamics simulations. Normally, apocalmodulin (apoCM) binds to IQSEC2 resulting in its N-terminal fragment inhibiting access of its Sec 7 domain to ARF6. An increase in Ca2+ concentration destabilizes the interaction of IQSEC2 with apoCM and removes steric hindrance of Sec 7 binding with ARF6. Mutations at amino acid residue 350 of IQSEC2 result in loss of steric hindrance of Sec 7 binding with ARF6 leading to constitutive activation of ARF6 by Sec 7. On the other hand, a mutation at amino acid residue 359 of IQSEC2 results in constitutive hindrance of Sec 7 binding to ARF6 leading to the loss of the ability of IQSEC2 to activate ARF6. These studies provide a model for dysregulation of IQSEC2 Sec 7 activity by mutant IQSEC2 proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Michael Shokhen
- Department of Chemistry, Bar Ilan University, Ramat Gan, Israel
| | - Randall Walikonis
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Center and Research Institute, University of South Florida, Tampa, Florida, USA
| | - Amnon Allbeck
- Department of Chemistry, Bar Ilan University, Ramat Gan, Israel
| | - Camryn Zezelic
- Technion Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Danielle Feldman
- Technion Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nina S Levy
- Technion Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Andrew P Levy
- Technion Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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Yarovaya OI, Filimonov AS, Baev DS, Borisevich SS, Zaykovskaya AV, Chirkova VY, Marenina MK, Meshkova YV, Belenkaya SV, Shcherbakov DN, Gureev MA, Luzina OA, Pyankov OV, Salakhutdinov NF, Khvostov MV. The Potential of Usnic-Acid-Based Thiazolo-Thiophenes as Inhibitors of the Main Protease of SARS-CoV-2 Viruses. Viruses 2024; 16:215. [PMID: 38399993 PMCID: PMC10893357 DOI: 10.3390/v16020215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (-)-usnic acid and studied their ability to inhibit the main protease of SARS-CoV-2. Substances containing unsubstituted thiophene groups or methyl- or bromo-substituted thiophene moieties showed moderate activity. Derivatives containing nitro substituents in the thiophene heterocycle-just as pure (+)- and (-)-usnic acids-showed no anti-3CLpro activity. Kinetic parameters of the most active compound, (+)-3e, were investigated, and molecular modeling of the possible interaction of the new thiazolo-thiophenes with the active site of the main protease was carried out. We evaluated the binding energies of the ligand and protein in a ligand-protein complex. Active compound (+)-3e was found to bind with minimum free energy; the binding of inactive compound (+)-3g is characterized by higher values of minimum free energy; the positioning of pure (+)-usnic acid proved to be unstable and is accompanied by the formation of intermolecular contacts with many amino acids of the catalytic binding site. Thus, the molecular dynamics results were consistent with the experimental data. In an in vitro antiviral assay against six strains (Wuhan, Delta, and four Omicron sublineages) of SARS-CoV-2, (+)-3e demonstrated pronounced antiviral activity against all the strains.
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Affiliation(s)
- Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Aleksandr S. Filimonov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Dmitriy S. Baev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
| | - Sophia S. Borisevich
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
- Laboratory of Chemical Physics, Ufa Institute of Chemistry, Ufa Federal Research Centre, 450078 Ufa, Russia
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Varvara Yu. Chirkova
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Mariya K. Marenina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Yulia V. Meshkova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Svetlana V. Belenkaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Dmitriy N. Shcherbakov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Maxim A. Gureev
- Laboratory of Bio- and Cheminformatics, St. Petersburg School of Physics, Mathematics and Computer Science, HSE University, 194100 St. Peterburg, Russia;
| | - Olga A. Luzina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Mikhail V. Khvostov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
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Ramos-Inza S, Morán-Serradilla C, Gaviria-Soteras L, Sharma AK, Plano D, Sanmartín C, Font M. Formulation Studies with Cyclodextrins for Novel Selenium NSAID Derivatives. Int J Mol Sci 2024; 25:1532. [PMID: 38338811 PMCID: PMC10855879 DOI: 10.3390/ijms25031532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Commercial cyclodextrins (CDs) are commonly used to form inclusion complexes (ICs) with different molecules in order to enhance their water solubility, stability, and bioavailability. Nowadays, there is strong, convincing evidence of the anticancer effect of selenium (Se)-containing compounds. However, pharmaceutical limitations, such as an unpleasant taste or poor aqueous solubility, impede their further evaluation and clinical use. In this work, we study the enhancement of solubility with CD complexes for a set of different nonsteroidal anti-inflammatory drug (NSAID) derivatives with Se as selenoester or diacyl diselenide chemical forms, with demonstrated antitumoral activity. The CD complexes were analyzed via nuclear magnetic resonance (NMR) spectroscopic techniques. In order to obtain additional data that could help explain the experimental results obtained, 3D models of the theoretical CD-compound complexes were constructed using molecular modeling techniques. Among all the compounds, I.3e and II.5 showed a remarkable increase in their water solubility, which could be ascribed to the formation of the most stable interactions with the CDs used, in agreement with the in silico studies performed. Thus, the preliminary results obtained in this work led us to confirm the selection of β and γ-CD as the most suitable for overcoming the pharmaceutical drawbacks of these Se derivatives.
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Affiliation(s)
- Sandra Ramos-Inza
- Department of Pharmaceutical Sciences, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain; (S.R.-I.); (C.M.-S.); (L.G.-S.); (D.P.); (M.F.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, E-31008 Pamplona, Spain
| | - Cristina Morán-Serradilla
- Department of Pharmaceutical Sciences, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain; (S.R.-I.); (C.M.-S.); (L.G.-S.); (D.P.); (M.F.)
| | - Leire Gaviria-Soteras
- Department of Pharmaceutical Sciences, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain; (S.R.-I.); (C.M.-S.); (L.G.-S.); (D.P.); (M.F.)
| | - Arun K. Sharma
- Department of Pharmacology, Penn State Cancer Institute, CH72, 500 University Drive, Hershey, PA 17033, USA;
| | - Daniel Plano
- Department of Pharmaceutical Sciences, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain; (S.R.-I.); (C.M.-S.); (L.G.-S.); (D.P.); (M.F.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, E-31008 Pamplona, Spain
| | - Carmen Sanmartín
- Department of Pharmaceutical Sciences, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain; (S.R.-I.); (C.M.-S.); (L.G.-S.); (D.P.); (M.F.)
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, E-31008 Pamplona, Spain
| | - María Font
- Department of Pharmaceutical Sciences, University of Navarra, Irunlarrea 1, E-31008 Pamplona, Spain; (S.R.-I.); (C.M.-S.); (L.G.-S.); (D.P.); (M.F.)
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Pernak J, Łożyński M, Kaczmarek DK, Qu F, Bolla G, Rogers RD. Bioinspired Herbicides-Ionic Liquids or Liquid Cocrystals? J Agric Food Chem 2024; 72:1454-1461. [PMID: 38207097 DOI: 10.1021/acs.jafc.3c06973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
This research provides information about combinations of several amino acids, including l-proline (Pro), l-arginine (Arg), and l-histidine (His), with phenoxyacetic acid herbicides (MCPA and 2,4-D). Five amino acid ionic liquids (AAILs), one amino acid higher-melting salt (AAHMS), and two amino acid liquid cocrystals (AALCs) were obtained in high yields (>90%). The ionization of the six new structures was confirmed by NMR, IR, and molecular modeling. X-ray crystallography was used to definitively confirm the binding location of the mobile hydrogen. Furthermore, we propose a computational method for estimating the energy of specific hydrogen bond(s) in AAIL crystals based on the NBO and QTAIM hydrogen bond parameters obtained by model calculations. An in-depth analysis of the structures allowed to answer the question posed in the title, ionic liquids or liquid cocrystals? AAILs based on arginine and histidine were obtained. In contrast, combining proline with MCPA and 2,4-D led to AALCs. Finally, the compounds were analyzed to measure their herbicidal activity. These studies proved that the novel form of MCPA or 2,4-D improved its ability to control weeds compared to commercial formulations containing the same active ingredients.
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Affiliation(s)
- Juliusz Pernak
- Department of Chemical Technology, Poznan University of Technology, Poznan 60-965, Poland
| | - Marek Łożyński
- Department of Chemical Technology, Poznan University of Technology, Poznan 60-965, Poland
| | - Damian K Kaczmarek
- Department of Chemical Technology, Poznan University of Technology, Poznan 60-965, Poland
| | - Fengrui Qu
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Geetha Bolla
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Robin D Rogers
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Salomatina OV, Kornienko TE, Zakharenko AL, Komarova NI, Achara C, Reynisson J, Salakhutdinov NF, Lavrik OI, Volcho KP. New Dual Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 and 2 Based on Deoxycholic Acid: Design, Synthesis, Cytotoxicity, and Molecular Modeling. Molecules 2024; 29:581. [PMID: 38338326 PMCID: PMC10856758 DOI: 10.3390/molecules29030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/26/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Deoxycholic acid derivatives containing various heterocyclic functional groups at C-3 on the steroid scaffold were designed and synthesized as promising dual tyrosyl-DNA phosphodiesterase 1 and 2 (TDP1 and TDP2) inhibitors, which are potential targets to potentiate topoisomerase poison antitumor therapy. The methyl esters of DCA derivatives with benzothiazole or benzimidazole moieties at C-3 demonstrated promising inhibitory activity in vitro against TDP1 with IC50 values in the submicromolar range. Furthermore, methyl esters 4d-e, as well as their acid counterparts 3d-e, inhibited the phosphodiesterase activity of both TDP1 and TDP2. The combinations of compounds 3d-e and 4d-e with low-toxic concentrations of antitumor drugs topotecan and etoposide showed significantly greater cytotoxicity than the compounds alone. The docking of the derivatives into the binding sites of TDP1 and TDP2 predicted plausible binding modes of the DCA derivatives.
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Affiliation(s)
- Oksana V. Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., Novosibirsk 630090, Russia; (O.V.S.); (N.I.K.); (N.F.S.)
| | - Tatyana E. Kornienko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.L.Z.); (O.I.L.)
| | - Alexandra L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.L.Z.); (O.I.L.)
| | - Nina I. Komarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., Novosibirsk 630090, Russia; (O.V.S.); (N.I.K.); (N.F.S.)
| | - Chigozie Achara
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK; (C.A.); (J.R.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK; (C.A.); (J.R.)
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., Novosibirsk 630090, Russia; (O.V.S.); (N.I.K.); (N.F.S.)
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.L.Z.); (O.I.L.)
| | - Konstantin P. Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., Novosibirsk 630090, Russia; (O.V.S.); (N.I.K.); (N.F.S.)
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Khavani M, Mehranfar A, Mofrad MRK. Antimicrobial peptide interactions with bacterial cell membranes. J Biomol Struct Dyn 2024:1-14. [PMID: 38263741 DOI: 10.1080/07391102.2024.2304683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/06/2024] [Indexed: 01/25/2024]
Abstract
Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of viruses, bacteria, fungi, and parasites. In this project, two antimicrobial peptides including magainin 2 and protegrin 1 with α-helix and β-sheet secondary structures were selected to investigate their interactions with different lipid bilayers such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), POPC/POPG (7:3), POPC/POPS (7:3), POPG/POPE(1:3), and POPG/POPE(3:1). The obtained structures of the AMPs illustrated that protegrin 1 cannot maintain its secondary structure in the solution phase in contrast to magainin 2. The head groups of the lipid units play a key role in the stability of the lipid bilayers. The head parts of the lipid membranes by increasing the internal H-bond contribute to membrane compactness. The POPG and POPS units inside the POPC/POPG and POPC/POPS membranes increase the order of the POPC units. The cationic residues of the AMPs form remarkable electrostatic interactions with the negatively charged membrane surfaces, which play a key role in the stabilization process of the peptide secondary structures. The Arg residues of protegrin 1 and the Gly1, Lys4, Lys10, Lys11, Lys14, and Glu19 of the magainin 2 have the most important roles in the complexation process. The values of Gibbs binding energies (ΔG) indicate that the complexation process between AMPs and different bacterial membranes is favorable from the thermodynamic viewpoint and AMPs could form stable complexes with the lipid bilayers. As a result of ΔG values, protegrin 1 forms a more stable complex with POPG/POPE(3:1), while the α-helix has more affinity to the POPG/POPE(1:3) bacterial membranes. Therefore, it can be considered that β-sheet and α-helix AMPs are more effective against gram-positive and gram-negative bacteria, respectively. The results of this study can provide useful details about the antimicrobial peptide interactions with the bacterial cell, which can be employed for designing new antimicrobial materials with greater efficiency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khavani
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Aliyeh Mehranfar
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
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Abd Ali AAkool W, Kashanian S, Hadidi S. Molecular interaction of antiviral drug penciclovir with DNA and HSA insights from experimental and docking studies. J Biomol Struct Dyn 2024:1-11. [PMID: 38263739 DOI: 10.1080/07391102.2024.2303382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 01/25/2024]
Abstract
One approach to accelerate the availability of new cancer drugs is to test drugs approved for other conditions as anticancer agents. During recent decades, penciclovir (PNV) has been frequently utilized as a potent antiviral drug, in particular against infections caused by herpes viruses. Many antivirals interact with DNA and change their expression level, so determining the binding mode is of great importance. In our laboratory, we have focused our attention to design improved drugs that target cellular DNA, to understand the mechanism of action at the molecular level, and also to investigate the effect of antiviral drugs as anticancer agents. The results of ct-DNA-PNV interactions at physiological pH using fluorescence spectroscopy, UV-visible absorption spectroscopy, and molecular modeling reveal this drug binds well to ct-DNA through groove binding. The circular dichroism measurements displayed that PNV caused a slight change in the DNA structure which affirmed that the binding of PNV with the DNA occurs through the groove mode. Besides, multi-spectroscopic and molecular docking were used to evaluate how PNV interacts with human serum albumin under physiological conditions. The findings of fluorescence quenching suggested that static quenching was involved in the spontaneous development of HSA-PNV complex through hydrophobic force. The docking simulation results validated the findings of spectroscopic techniques.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Saba Hadidi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
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Habeeb Mohammad TS, Kelley EH, Reidl CT, Konczak K, Beulke M, Javier J, Olsen KW, Becker DP. Cyclobutanone Inhibitors of Diaminopimelate Desuccinylase (DapE) as Potential New Antibiotics. Int J Mol Sci 2024; 25:1339. [PMID: 38279338 PMCID: PMC10815964 DOI: 10.3390/ijms25021339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Based on our previous success in using cyclobutanone derivatives as enzyme inhibitors, we have designed and prepared a 37-member library of α-aminocyclobutanone amides and sulfonamides, screened for inhibition of the bacterial enzyme diaminopimelate desuccinylase (DapE), which is a promising antibiotic target, and identified several inhibitors with micromolar inhibitory potency. Molecular docking suggests binding of the deprotonated hydrate of the strained cyclobutanone, and thermal shift analysis with the most potent inhibitor (3y, IC50 = 23.1 µM) enabled determination of a Ki value of 10.2 +/- 0.26 µM and observed two separate Tm values for H. influenzae DapE (HiDapE).
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Affiliation(s)
| | | | | | | | | | | | | | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA; (T.S.H.M.); (E.H.K.); (K.K.); (M.B.); (J.J.); (K.W.O.)
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Patil SK, Chary PS, Maddipatla S, Madhavi YV, Singothu S, Bhandari V, Pardhi E, Bansal KK, Mehra NK. Development of venetoclax with 2-hydroxypropyl-beta-cyclodextrin inclusion complex for improved bioavailability. J Biomol Struct Dyn 2024:1-18. [PMID: 38247232 DOI: 10.1080/07391102.2024.2305695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024]
Abstract
Cyclodextrin complexes loaded with venetoclax for improved solubility and therapeutic efficacy as repurposed drug. The venetoclax-cyclodextrin inclusion complex was prepared using kneading method. Primarily in-silico molecular docking study was performed to examine the possible interaction between venetoclax and hydroxypropyl-β-cyclodextrin (HP-β-CD) and extensively characterized. The in-vitro studies were performed using A-549 lung epithelial cancer cells. The in-vivo pharmaco-kinetic studies was performed on wistar rats. The aqueous solubility of venetoclax was increased upto 3.16 folds, as compared with pure venetoclax with entrapment efficiency (EE%) was determined 95.44 ± 0.3%. In-vitro cytotoxicity studies were carried on A-549 lung epithelial cancer cells, wherein BCL-2 receptors were highly over-expressed and IC 50 values for venetoclax and venetoclax- HP-β-CD complex was calculated at 24 and 48 hrs in the order of 1.241 µg/ml, 0.68 µg/ml and 0.757719 µg/ml, 0.6125 µg/mL, respectively. The oral bioavailability was increased 4.03 times compared to the pure drug. The venetoclax-HP-β-CD inclusion complexes showed the increased aqueous solubility with improved anticancer activities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Smalant Kishor Patil
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Padakanti Sandeep Chary
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Sarvan Maddipatla
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Y V Madhavi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Siva Singothu
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Vasundhra Bhandari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Ekta Pardhi
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Kuldeep Kumar Bansal
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Neelesh Kumar Mehra
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
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Ros-Pardo D, Gómez-Puertas P, Marcos-Alcalde Í. STAG2: Computational Analysis of Missense Variants Involved in Disease. Int J Mol Sci 2024; 25:1280. [PMID: 38279279 PMCID: PMC10816197 DOI: 10.3390/ijms25021280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
The human STAG2 protein is an essential component of the cohesin complex involved in cellular processes of gene expression, DNA repair, and genomic integrity. Somatic mutations in the STAG2 sequence have been associated with various types of cancer, while congenital variants have been linked to developmental disorders such as Mullegama-Klein-Martinez syndrome, X-linked holoprosencephaly-13, and Cornelia de Lange syndrome. In the cohesin complex, the direct interaction of STAG2 with DNA and with NIPBL, RAD21, and CTCF proteins has been described. The function of STAG2 within the complex is still unknown, but it is related to its DNA binding capacity and is modulated by its binding to the other three proteins. Every missense variant described for STAG2 is located in regions involved in one of these interactions. In the present work, we model the structure of 12 missense variants described for STAG2, as well as two other variants of NIPBl and two of RAD21 located at STAG2 interaction zone, and then analyze their behavior through molecular dynamic simulations, comparing them with the same simulation of the wild-type protein. This will allow the effects of variants to be rationalized at the atomic level and provide clues as to how STAG2 functions in the cohesin complex.
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Affiliation(s)
| | - Paulino Gómez-Puertas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM), C/Nicolás Cabrera, 1, 28049 Madrid, Spain; (D.R.-P.); (Í.M.-A.)
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Miciaccia M, Rizzo F, Centonze A, Cavallaro G, Contino M, Armenise D, Baldelli OM, Solidoro R, Ferorelli S, Scarcia P, Agrimi G, Zingales V, Cimetta E, Ronsisvalle S, Sipala FM, Polosa PL, Fortuna CG, Perrone MG, Scilimati A. Harmaline to Human Mitochondrial Caseinolytic Serine Protease Activation for Pediatric Diffuse Intrinsic Pontine Glioma Treatment. Pharmaceuticals (Basel) 2024; 17:135. [PMID: 38276008 PMCID: PMC10821046 DOI: 10.3390/ph17010135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG), affecting children aged 4-7 years, is a rare, aggressive tumor that originates in the pons and then spreads to nearby tissue. DIPG is the leading cause of death for pediatric brain tumors due to its infiltrative nature and inoperability. Radiotherapy has only a palliative effect on stabilizing symptoms. In silico and preclinical studies identified ONC201 as a cytotoxic agent against some human cancer cell lines, including DIPG ones. A single-crystal X-ray analysis of the complex of the human mitochondrial caseinolytic serine protease type C (hClpP) and ONC201 (PDB ID: 6DL7) allowed hClpP to be identified as its main target. The hyperactivation of hClpP causes damage to mitochondrial oxidative phosphorylation and cell death. In some DIPG patients receiving ONC201, an acquired resistance was observed. In this context, a wide program was initiated to discover original scaffolds for new hClpP activators to treat ONC201-non-responding patients. Harmaline, a small molecule belonging to the chemical class of β-carboline, was identified through Fingerprints for Ligands and Proteins (FLAP), a structure-based virtual screening approach. Molecular dynamics simulations and a deep in vitro investigation showed interesting information on the interaction and activation of hClpP by harmaline.
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Affiliation(s)
- Morena Miciaccia
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Francesca Rizzo
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Antonella Centonze
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Gianfranco Cavallaro
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Marialessandra Contino
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy;
| | - Domenico Armenise
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Olga Maria Baldelli
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Roberta Solidoro
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Savina Ferorelli
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Veronica Zingales
- Department of Industrial Engineering (DII), University of Padua, Via Marzolo 9, 35131 Padova, Italy; (V.Z.); (E.C.)
| | - Elisa Cimetta
- Department of Industrial Engineering (DII), University of Padua, Via Marzolo 9, 35131 Padova, Italy; (V.Z.); (E.C.)
| | - Simone Ronsisvalle
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (S.R.); (F.M.S.)
| | - Federica Maria Sipala
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (S.R.); (F.M.S.)
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Cosimo Gianluca Fortuna
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Maria Grazia Perrone
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Antonio Scilimati
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
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Xie Y, Wu X, Fu C, Duan H, Shi J, Blamey JM, Sun J. Rational Design of an α-1,3-Fucosyltransferase for the Biosynthesis of 3-Fucosyllactose in Bacillus subtilis ATCC 6051a via De Novo GDP-l-Fucose Pathway. J Agric Food Chem 2024; 72:1178-1189. [PMID: 38183288 DOI: 10.1021/acs.jafc.3c07604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
3-Fucosyllactose (3-FL) is an important oligosaccharide and nutrient in breast milk that can be synthesized in microbial cells by α-1,3-fucosyltransferase (α-1,3-FucT) using guanosine 5'-diphosphate (GDP)-l-fucose and lactose as substrates. However, the catalytic efficiency of known α-1,3-FucTs from various sources was limited due to their low solubility. To enhance the microbial production of 3-FL, the efficiencies of α-1,3-FucTs were evaluated and in Bacillus subtilis (B. subtilis) chassis cells that had been endowed with a heterologous synthetic pathway for GDP-l-fucose, revealing that the activity of FucTa from Helicobacter pylori (H. pylori) was higher than that of any of other reported homologues. To further improve the catalytic performance of FucTa, a rational design approach was employed, involving intracellular evaluation of the mutational sites of M32 obtained through directed evolution, analysis of the ligand binding site diversity, and protein structure simulation. Among the obtained variants, the FucTa-Y218 K variant exhibited the highest 3-FL yield, reaching 7.55 g/L in the shake flask growth experiment, which was 3.48-fold higher than that achieved by the wild-type enzyme. Subsequent fermentation optimization in a 5 L bioreactor resulted in a remarkable 3-FL production of 36.98 g/L, highlighting the great prospects of the designed enzyme and the strains for industrial applications.
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Affiliation(s)
- Yukang Xie
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinying Wu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Cong Fu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Duan
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas, 2280 Ñuñoa, Santiago, Chile
- Facultad de Química Y Biología, Universidad de Santiago de Chile, 3363 Alameda, Estación Central, Santiago, Chile
| | - Junsong Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
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McGlynn RP, Cui M, Brems B, Holbrook O, Booth RG. Development of 2-Aminotetralin-Type Serotonin 5-HT 1 Agonists: Molecular Determinants for Selective Binding and Signaling at 5-HT 1A, 5-HT 1B, 5-HT 1D, and 5-HT 1F Receptors. ACS Chem Neurosci 2024; 15:357-370. [PMID: 38150333 PMCID: PMC10797628 DOI: 10.1021/acschemneuro.3c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
The serotonin (5-hydroxytryptamine, 5-HT) 5-HT1 G-protein coupled receptor subtypes (5-HT1A/1B/1D/1E/1F) share a high sequence homology, confounding development of subtype-specific ligands. This study used a 5-HT1 structure-based ligand design approach to develop subtype-selective ligands using a 5-substituted-2-aminotetralin (5-SAT) chemotype, leveraging results from pharmacological, molecular modeling, and mutagenesis studies to delineate molecular determinants for 5-SAT binding and function at 5-HT1 subtypes. 5-SATs demonstrated high affinity (Ki ≤ 25 nM) and at least 50-fold stereoselective preference ([2S] > [2R]) at 5-HT1A, 5-HT1B, and 5-HT1D receptors but essentially nil affinity (Ki > 1 μM) at 5-HT1F receptors. The 5-SATs tested were agonists with varying degrees of potency and efficacy, depending on chemotype substitution and 5-HT1 receptor subtype. Models were built from the 5-HT1A (cryo-EM), 5-HT1B (crystal), and 5-HT1D (cryo-EM) structures, and 5-SATs underwent docking studies with up to 1 μs molecular dynamics simulations. 5-SAT interactions observed at positions 3.33, 5.38, 5.42, 5.43, and 7.39 of 5-HT1 subtypes were confirmed with point mutation experiments. Additional 5-SATs were designed and synthesized to exploit experimental and computational results, yielding a new full efficacy 5-HT1A agonist with 100-fold selectivity over 5-HT1B/1D receptors. The results presented lay the foundation for the development of additional 5-HT1 subtype selective ligands for drug discovery purposes.
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Affiliation(s)
- Ryan P. McGlynn
- Center
for Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Meng Cui
- Center
for Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Brittany Brems
- Center
for Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Otto Holbrook
- Center
for Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Raymond G. Booth
- Center
for Drug Discovery, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Pharmaceutical Sciences, Northeastern
University, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
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48
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Martin DR, Mutombwera AT, Madiehe AM, Onani MO, Meyer M, Cloete R. Molecular modeling and simulation studies of SELEX-derived high-affinity DNA aptamers to the Ebola virus nucleoprotein. J Biomol Struct Dyn 2024:1-18. [PMID: 38217874 DOI: 10.1080/07391102.2024.2302922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
Ebola viral disease (EVD) is a highly infectious and potentially fatal illness with a case fatality rate ranging from 25% to 90%. To effectively control its spread, there is a need for rapid, reliable and lowcost point-of-care (P OC) diagnostic tests. While various EVD diagnostic tests exist, few are P OC tests, and many are not cost-effective. The use of antibodies in these tests has limitations, prompting the exploration of aptamers as potential alternatives. Various proteins from the Ebola virus (EBOV) proteome, including EBOV nucleoprotein (NP), are considered viable targets for diagnostic assays. A previous study identified three aptamers (Apt1. Apt2 and Apt3) with high affinity for EBOV NP using systemic evolution of ligands by exponential enrichment (SELEX). This study aimed to employ in silico methods, such as Phyre2, RNAfold, RNAComposer, HADDOCK and GROMACS, to model the structures of EBOV NP and the aptamers, and to investigate their binding. The in silico analysis revealed successful binding of all the three aptamers to EBOV NP, with a suggested ranking of Apt1 > Apt2 > Apt3 based on binding affinity. Microscale thermophoresis (MST) analysis confirmed the binding, providing dissociation constants of 25 ± 2.84, 56 ± 2.76 and 140 ±3.69 nM for Apt1, Apt2 and Apt3, respectively. The study shows that the findings of the in silico analysis was in agreement with the MST analysis. Inclusion of these in silico approaches in diagnostic assay development can expedite the selection of candidate aptamers, potentially overcoming challenges associated with aptamer application in diagnostics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- D R Martin
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
| | - A T Mutombwera
- Department of Biochemistry and Microbiology, Nelson Mandela University, Port Elizabeth, South Africa
| | - A M Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M O Onani
- Department of Chemistry, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - M Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - R Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville, South Africa Cape Town, South Africa
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49
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Elsawi AE, Shahin MI, Elbendary HA, Al-Warhi T, Hassan FE, Eldehna WM. 1,2,4-Triazole-Tethered Indolinones as New Cancer-Fighting Small Molecules Targeting VEGFR-2: Synthesis, Biological Evaluations and Molecular Docking. Pharmaceuticals (Basel) 2024; 17:81. [PMID: 38256914 PMCID: PMC10820444 DOI: 10.3390/ph17010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/21/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
Targeting the VEGFR-2 signaling pathway is an inveterate approach toward combating pancreatic and hepatocellular cancers. Based on Sunitinib, the FDA-approved VEGFR-2 inhibitor, novel indolin-2-one-triazole hybrids were designed and synthesized as anti-hepatocellular and anti-pancreatic cancer agents with VEGFR-2 inhibitory activity. All the targeted compounds were assessed for their anti-cancer activity, revealing IC50 values extending from 0.17 to 4.29 µM for PANC1 and 0.58 to 4.49 µM for HepG2 cell lines. An extensive SAR study was conducted to explore the effect of different substituents along with N-alkylation. The potent anti-cancer analogs 11d, 11e, 11g, 11k and 14c were evaluated for their VEGFR-2 inhibitory actions, where their IC50 values ranged from 16.3 to 119.6 nM compared to Sorafenib, which revealed an IC50 of 29.7 nM, having compound 11d as the most active analog. An in silico ADME study was performed to confirm the drug-likeness of the synthesized compounds. Finally, molecular docking simulation was conducted for the most potent VEGFR-2 inhibitor (11d), demonstrating the strong binding with the vital amino acid residues of the VEGFR-2 ATP binding site.
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Affiliation(s)
- Ahmed E. Elsawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
| | - Mai I. Shahin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt;
| | - Hager A. Elbendary
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Fatma E. Hassan
- Department of Physiology, General Medicine Practice Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia;
- Medical Physiology Department, Kasr Alainy, Faculty of Medicine, Cairo University, Giza 11562, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
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50
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Biskupek I, Gieldon A. Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2). Int J Mol Sci 2024; 25:679. [PMID: 38203850 PMCID: PMC10779479 DOI: 10.3390/ijms25010679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly contagious illness with effects ranging from mild symptoms to severe illness. It is also one of the best-known pathogens since more than 200,000 scientific papers occurred in the last few years. With the publication of the SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in a complex with human ACE2 (hACE2) (PDB (6LZG)), the molecular analysis of one of the most crucial steps on the infection pathway was possible. The aim of this manuscript is to simulate the most widely spread mutants of SARS-CoV-2, namely Alpha, Beta, Gamma, Delta, Omicron, and the first recognized variant (natural wild type). With the wide search of the hypersurface of the potential energy performed using the UNRES force field, the intermediate state of the ACE2-RBD complex was found. R403, K/N/T417, L455, F486, Y489, F495, Y501, and Y505 played a crucial role in the protein recognition mechanism. The intermediate state cannot be very stable since it will prevent the infection cascade.
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Affiliation(s)
| | - Artur Gieldon
- Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdansk, Poland;
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