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Roterman I, Stapor K, Dułak D, Konieczny L. External Force Field for Protein Folding in Chaperonins-Potential Application in In Silico Protein Folding. ACS Omega 2024; 9:18412-18428. [PMID: 38680295 PMCID: PMC11044213 DOI: 10.1021/acsomega.4c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
The present study discusses the influence of the TRiC chaperonin involved in the folding of the component of reovirus mu1/σ3. The TRiC chaperone is treated as a provider of a specific external force field in the fuzzy oil drop model during the structural formation of a target folded protein. The model also determines the status of the final product, which represents the structure directed by an external force field in the form of a chaperonin. This can be used for in silico folding as the process is environment-dependent. The application of the model enables the quantitative assessment of the folding dependence of an external force field, which appears to have universal application.
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Affiliation(s)
- Irena Roterman
- Department
of Bioinformatics and Telemedicine, Jagiellonian
University—Medical College, Medyczna 7, Kraków 30-688, Poland
| | - Katarzyna Stapor
- Faculty
of Automatic, Electronics and Computer Science, Department of Applied
Informatics, Silesian University of Technology, Akademicka 16, Gliwice 44-100, Poland
| | - Dawid Dułak
- ABB
Business Services Sp. z o.o, ul Żegańska 1, Warszawa 04-713, Poland
| | - Leszek Konieczny
- Chair
of Medical Biochemistry—Jagiellonian University—Medical
College, Kopernika 7, Kraków 31-034, Poland
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Łapińska N, Pacławski A, Szlęk J, Mendyk A. SerotoninAI: Serotonergic System Focused, Artificial Intelligence-Based Application for Drug Discovery. J Chem Inf Model 2024; 64:2150-2157. [PMID: 38289046 PMCID: PMC11005036 DOI: 10.1021/acs.jcim.3c01517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 04/09/2024]
Abstract
SerotoninAI is an innovative web application for scientific purposes focused on the serotonergic system. By leveraging SerotoninAI, researchers can assess the affinity (pKi value) of a molecule to all main serotonin receptors and serotonin transporters based on molecule structure introduced as SMILES. Additionally, the application provides essential insights into critical attributes of potential drugs such as blood-brain barrier penetration and human intestinal absorption. The complexity of the serotonergic system demands advanced tools for accurate predictions, which is a fundamental requirement in drug development. SerotoninAI addresses this need by providing an intuitive user interface that generates predictions of pKi values for the main serotonergic targets. The application is freely available on the Internet at https://serotoninai.streamlit.app/, implemented in Streamlit with all major web browsers supported. Currently, to the best of our knowledge, there is no tool that allows users to access affinity predictions for serotonergic targets without registration or financial obligations. SerotoninAI significantly increases the scope of drug development activities worldwide. The source code of the application is available at https://github.com/nczub/SerotoninAI_streamlit.
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Affiliation(s)
- Natalia Łapińska
- Department
of Pharmaceutical Technology and Biopharmaceutics, Jagiellonian University Medical College, 30-688 Kraków, Poland
- Doctoral
School of Medicinal and Health Sciences, Jagiellonian University Medical College, 30-688 Kraków, Poland
| | - Adam Pacławski
- Department
of Pharmaceutical Technology and Biopharmaceutics, Jagiellonian University Medical College, 30-688 Kraków, Poland
| | - Jakub Szlęk
- Department
of Pharmaceutical Technology and Biopharmaceutics, Jagiellonian University Medical College, 30-688 Kraków, Poland
| | - Aleksander Mendyk
- Department
of Pharmaceutical Technology and Biopharmaceutics, Jagiellonian University Medical College, 30-688 Kraków, Poland
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Canale V, Skiba-Kurek I, Klesiewicz K, Papież M, Ropek M, Pomierny B, Piska K, Koczurkiewicz-Adamczyk P, Empel J, Karczewska E, Zajdel P. Improving Activity of New Arylurea Agents against Multidrug-Resistant and Biofilm-Producing Staphylococcus epidermidis. ACS Med Chem Lett 2024; 15:369-375. [PMID: 38505856 PMCID: PMC10945555 DOI: 10.1021/acsmedchemlett.3c00536] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 03/21/2024] Open
Abstract
Multidrug-resistant (MDR) strains of Staphylococcus epidermidis (S. epidermidis), prevalent in hospital environments, contribute to increased morbidity and mortality, especially among newborns, posing a critical concern for neonatal sepsis. In response to the pressing demand for novel antibacterial therapies, we present findings from synthetic chemistry and structure-activity relationship studies focused on arylsulfonamide/arylurea derivatives of aryloxy[1-(thien-2-yl)propyl]piperidines. Through bioisosteric replacement of the sulfonamide fragment with a urea moiety, compound 25 was identified, demonstrating potent bacteriostatic activity against clinical multidrug-resistant S. epidermidis strains (MIC50 and MIC90 = 1.6 and 3.125 μg/mL). Importantly, it showed activity against linezolid-resistant strains and exhibited selectivity over mammalian cells. Compound 25 displayed antibiofilm-forming properties against clinical S. epidermidis strains and demonstrated the capacity to eliminate existing biofilm layers. Additionally, it induced complete depolarization of the bacterial membrane in clinical S. epidermidis strains. In light of these findings, targeting bacterial cell membranes with compound 25 emerges as a promising strategy in the fight against multidrug-resistant S. epidermidis strains.
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Affiliation(s)
- Vittorio Canale
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Iwona Skiba-Kurek
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Karolina Klesiewicz
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Monika Papież
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Marlena Ropek
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Bartosz Pomierny
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Kamil Piska
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | | | - Joanna Empel
- Department
of Epidemiology and Clinical Microbiology, National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
| | - Elżbieta Karczewska
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
| | - Paweł Zajdel
- Faculty
of Pharmacy Jagiellonian University Medical College, 9 Medyczna Str., 30-688 Kraków, Poland
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Roterman I, Konieczny L, Stapor K, Słupina M. Hydrophobicity-Based Force Field In Enzymes. ACS Omega 2024; 9:8188-8203. [PMID: 38405467 PMCID: PMC10882594 DOI: 10.1021/acsomega.3c08728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/05/2024] [Accepted: 01/25/2024] [Indexed: 02/27/2024]
Abstract
The biocatalysis process takes place with the participation of enzymes, which, depending on the reaction carried out, require, apart from the appropriate arrangement of catalytic residues, an appropriate external force field. It is generated by the protein body. The relatively small size of the part directly involved in the process itself is supported by the presence of an often complex structure of the protein body, the purpose of which is to provide an appropriate local force field, eliminating the influence of water. Very often, the large size of the enzyme is an expression of the complex form of this field. In this paper, a comparative analysis of arbitrarily selected enzymes, representatives of different enzyme classes, was carried out, focusing on the measurement of the diversity of the force field provided by a given protein. This analysis was based on the fuzzy oil drop model (FOD) and its modified version (FOD-M), which takes into account the participation of nonaqueous external factors in shaping the structure and thus the force field within the protein. The degree and type of ordering of the hydrophobicity distribution in the protein molecule is the result of the influence of the environment but also the supplier of the local environment for a given process, including the catalysis process in particular. Determining the share of a nonaqueous environment is important due to the ubiquity of polar water, whose participation in processes with high specificity requires control. It can be assumed that some enzymes in their composition have a permanently built-in part, the role of which is reduced to that of a permanent chaperone. It provides a specific external force field needed for the process. The proposed model, generalized to other types of proteins, may also provide a form of recording the environment model for the simulation of the in silico protein folding process, taking into account the impact of its differentiation.
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Affiliation(s)
- Irena Roterman
- Department
of Bioinformatics and Telemedicine, Jagiellonian
University—Medical College, Medyczna 7, 30-688 Kraków, Poland
| | - Leszek Konieczny
- Chair
of Medical Biochemistry, Jagiellonian University—Medical
College, Kopernika 7, 31-034 Kraków, Poland
| | - Katarzyna Stapor
- Faculty
of Automatic, Electronics and Computer Science, Department of Applied
Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Mateusz Słupina
- ALSTOM
ZWUS Sp. z o.o, Modelarska
12, 40-142 Katowice, Poland
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Kurnik-Łucka M, Latacz G, Bucki A, Rivera-Meza M, Khan N, Konwar J, Skowron K, Kołaczkowski M, Gil K. Neuroprotective Activity of Enantiomers of Salsolinol and N-Methyl-( R)-salsolinol: In Vitro and In Silico Studies. ACS Omega 2023; 8:38566-38576. [PMID: 37867702 PMCID: PMC10586258 DOI: 10.1021/acsomega.3c05527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023]
Abstract
Salsolinol (1-methyl-1,2,3,4-tetrahydroisoquinoline-6,7-diol) is a close structural analogue of dopamine with an asymmetric center at the C1 position, and its presence in vivo, both in humans and rodents, has already been proven. Yet, given the fact that salsolinol colocalizes with dopamine-rich regions and was first detected in the urine of Parkinson's disease patients, its direct role in the process of neurodegeneration has been proposed. Here, we report that R and S enantiomers of salsolinol, which we purified from commercially available racemic mixture by means of high-performance liquid chromatography, exhibited neuroprotective properties (at the concentration of 50 μM) toward the human dopaminergic SH-SY5Y neuroblastoma cell line. Furthermore, within the study, we observed no toxic effect of N-methyl-(R)-salsolinol on SH-SY5Y neuroblastoma cells up to the concentration of 750 μM, either. Additionally, our molecular docking analysis showed that enantiomers of salsolinol should exhibit a distinct ability to interact with dopamine D2 receptors. Thus, we postulate that our results highlight the need to acknowledge salsolinol as an active dopamine metabolite and to further explore the neuroregulatory role of enantiomers of salsolinol.
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Affiliation(s)
- Magdalena Kurnik-Łucka
- Department
of Pathophysiology, Jagiellonian University
Medical College, 31-008 Krakow, Poland
| | - Gniewomir Latacz
- Department
of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, 31-008 Krakow, Poland
| | - Adam Bucki
- Department
of Medicinal Chemistry, Jagiellonian University
Medical College, 31-008 Krakow, Poland
| | - Mario Rivera-Meza
- Laboratory
of Experimental Pharmacology, Faculty of Chemical Sciences and Pharmaceutical
Sciences, University of Chile, 8380494 Santiago, Chile
| | - Nadia Khan
- Department
of Pathophysiology, Jagiellonian University
Medical College, 31-008 Krakow, Poland
- Department
of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, 31-008 Krakow, Poland
| | - Jahnobi Konwar
- Department
of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, 31-008 Krakow, Poland
| | - Kamil Skowron
- Department
of Pathophysiology, Jagiellonian University
Medical College, 31-008 Krakow, Poland
| | - Marcin Kołaczkowski
- Department
of Medicinal Chemistry, Jagiellonian University
Medical College, 31-008 Krakow, Poland
| | - Krzysztof Gil
- Department
of Pathophysiology, Jagiellonian University
Medical College, 31-008 Krakow, Poland
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Roterman I, Stapor K, Konieczny L. New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD-M model. J Cell Biochem 2023. [PMID: 37139783 DOI: 10.1002/jcb.30407] [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: 02/06/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Generating the structure of the hydrophobic core is based on the orientation of hydrophobic residues towards the central part of the protein molecule with the simultaneous exposure of polar residues. Such a course of the protein folding process takes place with the active participation of the polar water environment. While the self-assembly process leading to the formation of micelles concerns freely moving bi-polar molecules, bipolar amino acids in polypeptide chain have limited mobility due to the covalent bonds. Therefore, proteins form a more or less perfect micelle-like structure. The criterion is the hydrophobicity distribution, which to a greater or lesser extent reproduces the distribution expressed by the 3D Gaussian function on the protein body. The vast majority of proteins must ensure solubility, so a certain part of it-as it is expected-should reproduce the structuring of micelles. The biological activity of proteins is encoded in the part that does not reproduce the micelle-like system. The location and quantitative assessment of the contribution of orderliness to disorder is of critical importance for the determination of biological activity. The form of maladjustment to the 3D Gauss function may be varied-hence the obtained high diversity of specific interactions with strictly defined molecules: ligands or substrates. The correctness of this interpretation was verified on the basis of the group of enzymes Peptidylprolyl isomerase-E.C.5.2.1.8. In proteins representing this class of enzymes, zones responsible for solubility-micelle-like hydrophobicity system-the location and specificity of the incompatible part in which the specific activity of the enzyme is located and coded were identified. The present study showed that the enzymes of the discussed group show two different schemes of the structure of catalytic center (taking into account the status as defined by the fuzzy oil drop model).
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Kraków, Poland
| | - Katarzyna Stapor
- Department of Applied Informatics, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Kraków, Poland
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