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Boonyarit B, Yamprasert N, Kaewnuratchadasorn P, Kinchagawat J, Prommin C, Rungrotmongkol T, Nutanong S. GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity. J Comput Chem 2024; 45:2001-2023. [PMID: 38713612 DOI: 10.1002/jcc.27388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/09/2024]
Abstract
The proteins within the human epidermal growth factor receptor (EGFR) family, members of the tyrosine kinase receptor family, play a pivotal role in the molecular mechanisms driving the development of various tumors. Tyrosine kinase inhibitors, key compounds in targeted therapy, encounter challenges in cancer treatment due to emerging drug resistance mutations. Consequently, machine learning has undergone significant evolution to address the challenges of cancer drug discovery related to EGFR family proteins. However, the application of deep learning in this area is hindered by inherent difficulties associated with small-scale data, particularly the risk of overfitting. Moreover, the design of a model architecture that facilitates learning through multi-task and transfer learning, coupled with appropriate molecular representation, poses substantial challenges. In this study, we introduce GraphEGFR, a deep learning regression model designed to enhance molecular representation and model architecture for predicting the bioactivity of inhibitors against both wild-type and mutant EGFR family proteins. GraphEGFR integrates a graph attention mechanism for molecular graphs with deep and convolutional neural networks for molecular fingerprints. We observed that GraphEGFR models employing multi-task and transfer learning strategies generally achieve predictive performance comparable to existing competitive methods. The integration of molecular graphs and fingerprints adeptly captures relationships between atoms and enables both global and local pattern recognition. We further validated potential multi-targeted inhibitors for wild-type and mutant HER1 kinases, exploring key amino acid residues through molecular dynamics simulations to understand molecular interactions. This predictive model offers a robust strategy that could significantly contribute to overcoming the challenges of developing deep learning models for drug discovery with limited data and exploring new frontiers in multi-targeted kinase drug discovery for EGFR family proteins.
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Affiliation(s)
- Bundit Boonyarit
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Nattawin Yamprasert
- School of Information, Computer, and Communication Technology, Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, Thailand
| | | | - Jiramet Kinchagawat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Chanatkran Prommin
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sarana Nutanong
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
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2
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Philippsen GS, Seixas FAV. In silico identification of D449-0032 compound as a putative SARS-CoV-2 M pro inhibitor. J Biomol Struct Dyn 2024; 42:6440-6447. [PMID: 37424215 DOI: 10.1080/07391102.2023.2234045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
The SARS-CoV-2 pandemic originated the urgency in developing therapeutic resources for the treatment of COVID-19. Despite the current availability of vaccines and some antivirals, the occurence of severe cases of the disease and the risk of the emergence of new virus variants still motivate research in this field. In this context, this study aimed at the computational prospection of likely inhibitors of the main protease (Mpro) of SARS-CoV-2 since inhibiting this enzyme leads to disruption of the viral replication process. The virtual screening of the antiviral libraries Asinex, ChemDiv, and Enamine targeting SARS-CoV-2 Mpro was performed, indicating the D449-0032 compound as a promising inhibitor. Molecular dynamics simulations showed the stability of the protein-ligand complex and in silico predictions of toxicity and pharmacokinetic parameters indicated the probable drug-like behavior of the compound. In vitro and in vivo studies are essential to confirm the Mpro inhibition by the D449-0032.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Flavio Augusto Vicente Seixas
- Laboratory of Structural Biochemistry, Departamento de Tecnologia, Universidade Estadual de Maringá, Umuarama, Brazil
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3
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Vicari HP, Gomes RDC, Lima K, Rossini NDO, Rodrigues Junior MT, de Miranda LBL, Dias MVB, Costa-Lotufo LV, Coelho F, Machado-Neto JA. Cyclopenta[b]indoles as novel antimicrotubule agents with antileukemia activity. Toxicol In Vitro 2024; 99:105856. [PMID: 38821378 DOI: 10.1016/j.tiv.2024.105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Acute leukemias present therapeutic challenges despite advances in treatments. Microtubule inhibitors have played a pivotal role in cancer therapy, inspiring exploration into novel compounds like C2E1 from the cyclopenta[b]indole class. In the present study, we investigated C2E1's potential as a therapeutic agent for acute leukemia at molecular, cellular, and genetic levels. C2E1 demonstrated tubulin depolarization activity, significantly reducing leukemia cell viability. Its impact involved multifaceted mechanisms: inducing apoptosis, arrest of cell cycle progression, and inhibition of clonogenicity and migration in leukemia cells. At a molecular level, C2E1 triggered DNA damage, antiproliferative, and apoptosis markers and altered gene expression related to cytoskeletal regulation, disrupting essential cellular processes crucial for leukemia cell survival and proliferation. These findings highlight C2E1's promise as a potential candidate for novel anti-cancer therapies. Notably, its distinct mode of action from conventional microtubule-targeting drugs suggests the potential to bypass common resistance mechanisms encountered with existing treatments. In summary, C2E1 emerges as a compelling compound with diverse effects on leukemia cells, showcasing promising antineoplastic properties. Its ability to disrupt critical cellular functions selective to leukemia cells positions it as a candidate for future therapeutic development.
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Affiliation(s)
- Hugo Passos Vicari
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ralph da Costa Gomes
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil
| | - Keli Lima
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Internal Medicine, Hematology Division, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Coelho
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil.
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4
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Rasheed HAM, Al-Majidi SMH. Synthesis, identification and evaluation of molecular docking and experimental anti-cancer and antioxidant activity of new spiro four membered ring derivatives bearing 5-nitro isatin. Nat Prod Res 2024; 38:2629-2636. [PMID: 36995026 DOI: 10.1080/14786419.2023.2195178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
Spiro-5-nitro isatino aza-β-lactams were produced by a [2 + 2] cycloaddition of 5-nitro isatin Schiff bases [1-5] with different aromatic isocyanate and thioisocyanate. 1HNMR and 13CNMR as well as FTIR spectroscopies, were used to identify the structures of the obtained compounds. These spiro-5-nitro isatin aza- β-lactams interest to us due to their potential antioxidant and anticancer properties. The MTT assay was used to examine in vitro bioactivity testing against breast cancer (MCF-7) cell lines. From result data, compound 14 displayed IC50 values that were lower than those of the clinically used anticancer drug tamoxifen toward MCF-7 cells after 24 h while compound 9 after 48 h synthesized compounds [6-20] were evaluated for against antioxidant activity by using DPPH assay. In molecular docking, Promising compounds were used to reveal potential cytotoxic activity mechanisms.
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Affiliation(s)
| | - Suaad M H Al-Majidi
- Department of Chemistry, College of Science, University of Baghdad, Baghdad, Iraq
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5
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Ibrahim PEGF, Zuccotto F, Zachariae U, Gilbert I, Bodkin M. Accurate prediction of dynamic protein-ligand binding using P-score ranking. J Comput Chem 2024; 45:1762-1778. [PMID: 38647338 DOI: 10.1002/jcc.27370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
Abstract
Protein-ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein-ligand system, solvent-mediated interactions, and associated entropy changes. In addition, scoring functions are only weakly accurate due to the short time required for calculating enthalpic and entropic binding interactions. The workflow described here attempts to address these limitations by combining supervised molecular dynamics with dynamical averaging quantum mechanics fragment molecular orbital. This combination significantly increased the ability to predict the experimental binding structure of protein-ligand complexes independent from the starting position of the ligands or the binding site conformation. We found that the predictive power could be enhanced by combining the residence time and interaction energies as descriptors in a novel scoring function named the P-score. This is illustrated using six different protein-ligand targets as case studies.
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Affiliation(s)
- Peter E G F Ibrahim
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Fabio Zuccotto
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Ulrich Zachariae
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Ian Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Mike Bodkin
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
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6
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Lu D, Luo D, Zhang Y, Wang B. A Robust Induced Fit Docking Approach with the Combination of the Hybrid All-Atom/United-Atom/Coarse-Grained Model and Simulated Annealing. J Chem Theory Comput 2024; 20:6414-6423. [PMID: 38966989 DOI: 10.1021/acs.jctc.4c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Molecular docking remains an indispensable tool in computational biology and structure-based drug discovery. However, the correct prediction of binding poses remains a major challenge for molecular docking, especially for target proteins where a substrate binding induces significant reorganization of the active site. Here, we introduce an Induced Fit Docking (IFD) approach named AA/UA/CG-SA-IFD, which combines a hybrid All-Atom/United-Atom/Coarse-Grained model with Simulated Annealing. In this approach, the core region is represented by the All-Atom(AA) model, while the protein environment beyond the core region and the solvent are treated with either the United-Atom (UA) or the Coarse-Grained (CG) model. By combining the Elastic Network Model (ENM) for the CG region, the hybrid model ensures a reasonable description of ligand binding and the environmental effects of the protein, facilitating highly efficient and reliable sampling of ligand binding through Simulated Annealing (SA) at a high temperature. Upon validation with two testing sets, the AA/UA/CG-SA-IFD approach demonstrates remarkable accuracy and efficiency in induced fit docking, even for challenging cases where the docked poses significantly deviate from crystal structures.
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Affiliation(s)
- Dexin Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Ding Luo
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Yuwei Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
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7
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Kataria A, Srivastava A, Singh DD, Haque S, Han I, Yadav DK. Systematic computational strategies for identifying protein targets and lead discovery. RSC Med Chem 2024; 15:2254-2269. [PMID: 39026640 PMCID: PMC11253860 DOI: 10.1039/d4md00223g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein-ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.
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Affiliation(s)
- Arti Kataria
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan Jaipur India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University Jazan-45142 Saudi Arabia
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University Seoul 01897 Republic of Korea +82 32 820 4948
| | - Dharmendra Kumar Yadav
- Department of Biologics, College of Pharmacy, Gachon University Hambakmoeiro 191, Yeonsu-gu Incheon 21924 Republic of Korea
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Singh P, Kumar V, Jung TS, Lee JS, Lee KW, Hong JC. Uncovering potential CDK9 inhibitors from natural compound databases through docking-based virtual screening and MD simulations. J Mol Model 2024; 30:267. [PMID: 39012568 DOI: 10.1007/s00894-024-06067-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024]
Abstract
CONTEXT Cyclin-dependent kinase 9 (CDK9) plays a significant role in gene regulation and RNA polymerase II transcription under basal and stimulated conditions. The upregulation of transcriptional homeostasis by CDK9 leads to various malignant tumors and therefore acts as a valuable drug target in addressing cancer incidences. Ongoing drug development endeavors targeting CDK9 have yielded numerous clinical candidate molecules currently undergoing investigation as potential CDK9 modulators, though none have yet received Food and Drug Administration (FDA) approval. METHODS In this study, we employ in silico approaches including the molecular docking and molecular dynamics simulations for the virtual screening over the natural compounds library to identify novel promising selective CDK9 inhibitors. The compounds derived from the initial virtual screening were subsequently employed for molecular dynamics simulations and binding free energy calculations to study the compound's stability under virtual physiological conditions. The first-generation CDK inhibitor Flavopiridol was used as a reference to compare with our novel hit compound as a CDK9 antagonist. The 500-ns molecular dynamics simulation and binding free energy calculation showed that two natural compounds showed better binding affinity and interaction mode with CDK9 receptors over the reference Flavopiridol. They also showed reasonable figures in the predicted absorption, distribution, metabolism, excretion, and toxicity (ADMET) calculations as well as in computational cytotoxicity predictions. Therefore, we anticipate that the proposed scaffolds could contribute to developing potential and selective CDK9 inhibitors subjected to further validations.
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Affiliation(s)
- Pooja Singh
- Division of Applied Life Science, (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-Daero, Jinju, 52828, Republic of Korea
| | - Vikas Kumar
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-Daero, Jinju, 52828, Republic of Korea
- Computational Biophysics Lab, Basque Center for Materials, Applications, and Nanostructures (BCMaterials), Building Martina Casiano, Pl. 3 Parque Científico UPV/EHU Barrio Sarriena, 48940, Leioa, Spain
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, College of Veterinary Medicine, Research Institute of Natural Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jeong Sang Lee
- GSCRO, Research Spin-Off Company, Innopolis Jeonbuk, Jeonju, 55069, Korea
- Department of Food and Nutrition, College of Medical Science, Jeonju University, Jeonju, 55069, Republic of Korea
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-Daero, Jinju, 52828, Republic of Korea.
- Angel I-Drug Design (AiDD), 33-3 Jinyangho-Ro 44, Jinju, 52650, Republic of Korea.
| | - Jong Chan Hong
- Division of Applied Life Science, (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-Daero, Jinju, 52828, Republic of Korea.
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9
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Tallini LR, Machado das Neves G, Vendruscolo MH, Rezende-Teixeira P, Borges W, Bastida J, Costa-Lotufo LV, Eifler-Lima VL, Zuanazzi JAS. Antitumoral activity of different Amaryllidaceae alkaloids: In vitro and in silico assays. JOURNAL OF ETHNOPHARMACOLOGY 2024; 329:118154. [PMID: 38614259 DOI: 10.1016/j.jep.2024.118154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/15/2024]
Abstract
ETHNOPHARMACOLOGY RELEVANCE The plants of Amaryllidaceae family, such as Amaryllis belladonna L., have been used as herbal remedies for thousands of years to address various disorders, including diseases that might today be identified as cancer. AIM OF THE STUDY The objective of this work was to evaluate the potential of three Amaryllidaceae alkaloids against four cancer cell lines. MATERIAL AND METHODS The alkaloids lycorine, 1-O-acetylcaranine, and montanine were evaluated in vitro against colon adenocarcinoma cell line (HCT-116) and breast carcinoma cell lines (MCF-7, MDAMB231, and Hs578T). Computational experiments (target prediction and molecular docking) were conducted to gain a deeper comprehension of possible interactions between these alkaloids and potential targets associated with these tumor cells. RESULTS Montanine presented the best results against HCT-116, MDAMB231, and Hs578T cell lines, while lycorine was the most active against MCF-7. In alignment with the target prediction outcomes and existing literature, four potential targets were chosen for the molecular docking analysis: CDK8, EGFR, ER-alpha, and dCK. The docking scores revealed two potential targets for the alkaloids with scores similar to co-crystallized inhibitors and substrates: CDK8 and dCK. A visual analysis of the optimal docked configurations indicates that the alkaloids may interact with some key residues in contrast to the other docked compounds. This observation implies their potential to bind effectively to both targets. CONCLUSIONS In vitro and in silico results corroborate with data literature suggesting the Amaryllidaceae alkaloids as interesting molecules with antitumoral properties, especially montanine, which showed the best in vitro results against colorectal and breast carcinoma. More studies are necessary to confirm the targets and pharmaceutical potential of montanine against these cancer cell lines.
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Affiliation(s)
- Luciana R Tallini
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028, Barcelona, LRTJB, Spain; Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, 90610-000, Porto Alegre, RS, GMNMHVVLEL, Brazil.
| | - Gustavo Machado das Neves
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, 90610-000, Porto Alegre, RS, GMNMHVVLEL, Brazil.
| | - Maria Helena Vendruscolo
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, 90610-000, Porto Alegre, RS, GMNMHVVLEL, Brazil.
| | | | - Warley Borges
- Department of Chemistry, Federal University of Espírito Santo, 29075-910, Vitória, ES, Brazil.
| | - Jaume Bastida
- Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028, Barcelona, LRTJB, Spain.
| | | | - Vera Lucia Eifler-Lima
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, 90610-000, Porto Alegre, RS, GMNMHVVLEL, Brazil.
| | - José Angelo S Zuanazzi
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, 90610-000, Porto Alegre, RS, GMNMHVVLEL, Brazil.
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Magari F, Messner H, Salisch F, Schmelzle SM, van Zandbergen G, Fürstner A, Ziebuhr J, Heine A, Müller-Ruttloff C, Grünweller A. Potent anti-coronaviral activity of pateamines and new insights into their mode of action. Heliyon 2024; 10:e33409. [PMID: 39035482 PMCID: PMC11259845 DOI: 10.1016/j.heliyon.2024.e33409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
Pateamines, derived from the sponge Mycale hentscheli, function as inhibitors of the RNA helicase eIF4A and exhibit promising antiviral and anticancer properties. eIF4A plays a pivotal role in unwinding stable RNA structures within the 5'-UTR of selected mRNAs, facilitating the binding of the 43S preinitiation complex during translation initiation. Pateamines function by clamping RNA substrates onto the eIF4A surface, effectively preventing eIF4A from carrying out the unwinding step. Rocaglates, a compound class isolated from plants of the genus Aglaia, target the same binding pocket on eIF4A, and based on structural data, a similar mode of action has been proposed for pateamines and rocaglates. In this study, we conducted a detailed characterization of pateamines' binding mode and assessed their antiviral activity against human pathogenic coronaviruses (human coronavirus 229E (HCoV-229E), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)). Our findings reveal significant differences in the binding behavior of pateamines compared to rocaglates when interacting with an eIF4A-RNA complex. We also observed that pateamines do not depend on the presence of a polypurine tract in the RNA substrate for efficient RNA clamping, as it is the case for rocaglates. Most notably, pateamines demonstrate potent antiviral activity against coronaviruses in the low nanomolar range. Consequently, pateamines broaden our toolbox for combating viruses that rely on the host enzyme eIF4A to conduct their viral protein synthesis, indicating a possible future treatment strategy against new or re-emerging pathogenic viruses.
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Affiliation(s)
- Francesca Magari
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | - Henri Messner
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | - Florian Salisch
- Institute of Medical Virology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | | | - Ger van Zandbergen
- Division of Immunology, Paul-Ehrlich-Institute, 63225, Langen, Germany
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Alois Fürstner
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim Ruhr, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | | | - Arnold Grünweller
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
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11
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Besleaga I, Raptová R, Stoica AC, Milunovic MNM, Zalibera M, Bai R, Igaz N, Reynisson J, Kiricsi M, Enyedy ÉA, Rapta P, Hamel E, Arion VB. Are the metal identity and stoichiometry of metal complexes important for colchicine site binding and inhibition of tubulin polymerization? Dalton Trans 2024. [PMID: 38989784 DOI: 10.1039/d4dt01469c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Quite recently we discovered that copper(II) complexes with isomeric morpholine-thiosemicarbazone hybrid ligands show good cytotoxicity in cancer cells and that the molecular target responsible for this activity might be tubulin. In order to obtain better lead drug candidates, we opted to exploit the power of coordination chemistry to (i) assemble structures with globular shape to better fit the colchicine pocket and (ii) vary the metal ion. We report the synthesis and full characterization of bis-ligand cobalt(III) and iron(III) complexes with 6-morpholinomethyl-2-formylpyridine 4N-(4-hydroxy-3,5-dimethylphenyl)-3-thiosemicarbazone (HL1), 6-morpholinomethyl-2-acetylpyridine 4N-(4-hydroxy-3,5-dimethylphenyl)-3-thiosemicarbazone (HL2), and 6-morpholinomethyl-2-formylpyridine 4N-phenyl-3-thiosemicarbazone (HL3), and mono-ligand nickel(II), zinc(II) and palladium(II) complexes with HL1, namely [CoIII(HL1)(L1)](NO3)2 (1), [CoIII(HL2)(L2)](NO3)2 (2), [CoIII(HL3)(L3)](NO3)2 (3), [FeIII(L2)2]NO3 (4), [FeIII(HL3)(L3)](NO3)2 (5), [NiII(L1)]Cl (6), [Zn(L1)Cl] (7) and [PdII(HL1)Cl]Cl (8). We discuss the effect of the metal identity and metal complex stoichiometry on in vitro cytotoxicity and antitubulin activity. The high antiproliferative activity of complex 4 correlated well with inhibition of tubulin polymerization. Insights into the mechanism of antiproliferative activity were supported by experimental results and molecular docking calculations.
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Affiliation(s)
- Iuliana Besleaga
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 42, A-1090 Vienna, Austria.
| | - Renáta Raptová
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, SK-81237 Bratislava, Slovakia
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/II, A-8010 Graz, Austria
| | - Alexandru-Constantin Stoica
- Inorganic Polymers Department, "Petru Poni" Institute of Macromolecular Chemistry, Aleea Gr. Ghica Voda 41 A, Iasi 700487, Romania
| | - Miljan N M Milunovic
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 42, A-1090 Vienna, Austria.
| | - Michal Zalibera
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, SK-81237 Bratislava, Slovakia
| | - Ruoli Bai
- Molecular Pharmacology Branch, Developmental Therapeutics Program, Division of Cancer Diagnosis and Treatment, National Cancer Institute, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Nóra Igaz
- Department of Biochemistry and Molecular Biology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK
| | - Mónika Kiricsi
- School of Pharmacy and Bioengineering, Keele University, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK
| | - Éva A Enyedy
- Department of Molecular and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7-8, H-6720 Szeged, Hungary.
- MTA-SZTE Lendület Functional Metal Complexes Research Group, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Peter Rapta
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, SK-81237 Bratislava, Slovakia
| | - Ernest Hamel
- Molecular Pharmacology Branch, Developmental Therapeutics Program, Division of Cancer Diagnosis and Treatment, National Cancer Institute, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Vladimir B Arion
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 42, A-1090 Vienna, Austria.
- Inorganic Polymers Department, "Petru Poni" Institute of Macromolecular Chemistry, Aleea Gr. Ghica Voda 41 A, Iasi 700487, Romania
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12
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Tiessler-Sala L, Maréchal JD, Lledós A. Rationalization of a Streptavidin Based Enantioselective Artificial Suzukiase: An Integrative Computational Approach. Chemistry 2024; 30:e202401165. [PMID: 38752552 DOI: 10.1002/chem.202401165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Indexed: 06/06/2024]
Abstract
An Artificial Metalloenzyme (ArM) built employing the streptavidin-biotin technology has been used for the enantioselective synthesis of binaphthyls by means of asymmetric Suzuki-Miyaura cross-coupling reactions. Despite its success, it remains a challenge to understand how the length of the biotin cofactors or the introduction of mutations to streptavidin leads the preferential synthesis of one atropisomer over the other. In this study, we apply an integrated computational modeling approach, including DFT calculations, protein-ligand dockings and molecular dynamics to rationalize the impact of mutations and length of the biotion cofactor on the enantioselectivities of the biaryl product. The results unravel that the enantiomeric differences found experimentally can be rationalized by the disposition of the first intermediate, coming from the oxidative addition step, and the entrance of the second substrate. The work also showcases the difficulties facing to control the enantioselection when engineering ArM to catalyze enantioselective Suzuki-Miyaura couplings and how the combination of DFT calculations, molecular dockings and MD simulations can be used to rationalize artificial metalloenzymes.
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Affiliation(s)
- Laura Tiessler-Sala
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
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13
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Zimmermann T, Feng J, de Campos LJ, Knight LA, Schlötzer J, Ramirez YA, Schwickert K, Zehe M, Adler TB, Schirmeister T, Kisker C, Sotriffer C, Conda-Sheridan M, Decker M. Structure-Based Design and Synthesis of Covalent Inhibitors for Deubiquitinase and Acetyltransferase ChlaDUB1 of Chlamydia trachomatis. J Med Chem 2024; 67:10710-10742. [PMID: 38897928 DOI: 10.1021/acs.jmedchem.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Upon infection by an intracellular pathogen, host cells activate apoptotic pathways to limit pathogen replication. Consequently, efficient proliferation of the obligate intracellular pathogen Chlamydia trachomatis, a major cause of trachoma and sexually transmitted diseases, depends on the suppression of host cell apoptosis. C. trachomatis secretes deubiquitinase ChlaDUB1 into the host cell, leading among other interactions to the stabilization of antiapoptotic proteins and, thus, suppression of host cell apoptosis. Targeting the bacterial effector protein may, therefore, lead to new therapeutic possibilities. To explore the active site of ChlaDUB1, an iterative cycle of computational docking, synthesis, and enzymatic screening was applied with the aim of lead structure development. Hereby, covalent inhibitors were developed, which show enhanced inhibition with a 22-fold increase in IC50 values compared to previous work. Comprehensive insights into the binding prerequisites to ChlaDUB1 are provided, establishing the foundation for an additional specific antichlamydial therapy by small molecules.
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Affiliation(s)
- Thomas Zimmermann
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Jiachen Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Luana Janaína de Campos
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Lindsey A Knight
- Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jan Schlötzer
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, Julius-Maximilians-Universität Würzburg (JMU), 97080 Wurzburg, Germany
| | - Yesid A Ramirez
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Markus Zehe
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Thomas B Adler
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, Julius-Maximilians-Universität Würzburg (JMU), 97080 Wurzburg, Germany
| | - Christoph Sotriffer
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Michael Decker
- Pharmazeutische und Medizinische Chemie, Institut für Pharmazie und Lebensmittelchemie, Julius-Maximilians-Universität Würzburg (JMU), Am Hubland, 97074 Würzburg, Germany
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14
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Ananya, Panchariya DC, Karthic A, Singh SP, Mani A, Chawade A, Kushwaha S. Vaccine design and development: Exploring the interface with computational biology and AI. Int Rev Immunol 2024:1-20. [PMID: 38982912 DOI: 10.1080/08830185.2024.2374546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Computational biology involves applying computer science and informatics techniques in biology to understand complex biological data. It allows us to collect, connect, and analyze biological data at a large scale and build predictive models. In the twenty first century, computational resources along with Artificial Intelligence (AI) have been widely used in various fields of biological sciences such as biochemistry, structural biology, immunology, microbiology, and genomics to handle massive data for decision-making, including in applications such as drug design and vaccine development, one of the major areas of focus for human and animal welfare. The knowledge of available computational resources and AI-enabled tools in vaccine design and development can improve our ability to conduct cutting-edge research. Therefore, this review article aims to summarize important computational resources and AI-based tools. Further, the article discusses the various applications and limitations of AI tools in vaccine development.
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Affiliation(s)
- Ananya
- National Institute of Animal Biotechnology, Hyderabad, India
| | | | | | | | - Ashutosh Mani
- Motilal Nehru National Institute of Technology, Prayagraj, India
| | - Aakash Chawade
- Swedish University of Agricultural Sciences, Alnarp, Sweden
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15
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de Carvalho GA, Tambwe PM, Nascimento LRC, Campos BKP, Chiareli RA, Junior GPN, Menegatti R, Gomez RS, Pinto MCX. In silico evidence of bitopertin's broad interactions within the SLC6 transporter family. J Pharm Pharmacol 2024:rgae051. [PMID: 38982944 DOI: 10.1093/jpp/rgae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/16/2024] [Indexed: 07/11/2024]
Abstract
The Glycine Transporter Type 1 (GlyT1) significantly impacts central nervous system functions, influencing glycinergic and glutamatergic neurotransmission. Bitopertin, the first GlyT1 inhibitor in clinical trials, was developed for schizophrenia treatment but showed limited efficacy. Despite this, bitopertin's repositioning could advance treating various pathologies. This study aims to understand bitopertin's mechanism of action using computational methods, exploring off-target effects, and providing a comprehensive pharmacological profile. Similarity Ensemble Approach (SEA) and SwissTargetPrediction initially predicted targets, followed by molecular modeling on SWISS-MODEL and GalaxyWeb servers. Binding sites were identified using PrankWeb, and molecular docking was performed with DockThor and GOLD software. Molecular dynamics analyses were conducted on the Visual Dynamics platform. Reverse screening on SEA and SwissTargetPrediction identified GlyT1 (SLC6A9), GlyT2 (SLC6A5), PROT (SLC6A7), and DAT (SLC6A3) as potential bitopertin targets. Homology modeling on SwissModel generated high-resolution models, optimized further on GalaxyWeb. PrankWeb identified similar binding sites in GlyT1, GlyT2, PROT, and DAT, indicating potential interaction. Docking studies suggested bitopertin's interaction with GlyT1 and proximity to GlyT2 and PROT. Molecular dynamics confirmed docking results, highlighting bitopertin's target stability beyond GlyT1. The study concludes that bitopertin potentially interacts with multiple SLC6 family targets, indicating a broader pharmacological property.
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Affiliation(s)
- Gustavo Almeida de Carvalho
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Paul Magogo Tambwe
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Lucas Rodrigues Couto Nascimento
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Bruna Kelly Pedrosa Campos
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Raphaela Almeida Chiareli
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Guilhermino Pereira Nunes Junior
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
| | - Ricardo Menegatti
- Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Setor Leste Universitário, 74605170 - Goiânia, GO, Brazil
| | - Renato Santiago Gomez
- Departamento de Cirurgia, Faculdade de Medicina, Universidade Federal de Minas Gerais, Av. Alfredo Balena, 190, 30130-100, Belo Horizonte-MG, Brazil
| | - Mauro Cunha Xavier Pinto
- Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CEP 74690-900, Goiânia-GO, Brazil
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16
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Kochnev Y, Ahmed M, Maldonado A, Durrant J. MolModa: accessible and secure molecular docking in a web browser. Nucleic Acids Res 2024; 52:W498-W506. [PMID: 38783339 PMCID: PMC11223821 DOI: 10.1093/nar/gkae406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/14/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
Molecular docking advances early-stage drug discovery by predicting the geometries and affinities of small-molecule compounds bound to drug-target receptors, predictions that researchers can leverage in prioritizing drug candidates for experimental testing. Unfortunately, existing docking tools often suffer from poor usability, data security, and maintainability, limiting broader adoption. Additionally, the complexity of the docking process, which requires users to execute a series of specialized steps, often poses a substantial barrier for non-expert users. Here, we introduce MolModa, a secure, accessible environment where users can perform molecular docking entirely in their web browsers. We provide two case studies that illustrate how MolModa provides valuable biological insights. We further compare MolModa to other docking tools to highlight its strengths and limitations. MolModa is available free of charge for academic and commercial use, without login or registration, at https://durrantlab.com/molmoda.
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Affiliation(s)
- Yuri Kochnev
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mayar Ahmed
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alex M Maldonado
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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17
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Franco RR, Franco RM, Justino AB, Borges ALS, Bittar VP, Saito N, Saraiva AL, Júnior NN, Otoni WC, Espindola FS. Phytochemical composition of aerial parts and roots of Pfaffia glomerata (Spreng.) Pedersen and anticholinesterase, antioxidant, and antiglycation activities. PROTOPLASMA 2024; 261:609-624. [PMID: 38200344 DOI: 10.1007/s00709-023-01916-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The Pfaffia glomerata, a plant popularly called Brazilian ginseng, is widely used in Brazil for the treatment of various pathologies, including those associated with the Central Nervous System. 20-hydroxyecdysone (20E), a phytosteroid present in this plant, can promote adaptogenic effects in the organism, providing greater body resistance to stressors. This study aimed to evaluate the phytochemical composition and the anticholinesterase, antioxidant, and antiglycation effects of extracts and fractions of aerial parts and roots of P. glomerata, also analyzing their possible cytotoxic effects. The fractions were obtained by partitioning methanol extracts from the aerial part and roots of P. glomerata with hexane, dichloromethane, ethyl acetate, n-butanol, and water. The samples were initially tested in anticholinesterase, antioxidant, and antiglycation assays, and the most promising samples were submitted for cytotoxicity and chromatographic analyses. Mass spectrometry and chromatography methods revealed that 20E was the main compound in the dichloromethane fractions, there being 35% more 20E in the aerial part (APD) than in the roots (RD). Added to the higher concentration of 20E, the APD fraction also presented more promising results than the RD fraction in anticholinesterase and antioxidant analyses, indicating that their effects may be related to the concentration of 20E. These same fractions showed no hemolytic effects but were cytotoxic in high concentrations. These new findings contribute to scientific information about P. glomerata and open more perspectives for the understanding of its therapeutic properties, allowing the association of biological activity with the presence of 20E.
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Affiliation(s)
- Rodrigo Rodrigues Franco
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
- Departamento de Medicina, Instituto de Biotecnologia, Universidade Federal de Catalão, Catalão, GO, 75706-881, Brazil
| | - Rafaella Martins Franco
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
| | - Allisson Benatti Justino
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
| | - Ana Luiza Silva Borges
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
| | - Vinícius Prado Bittar
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
| | - Natieli Saito
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
| | - André Lopes Saraiva
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
| | - Nilson Nicolau Júnior
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil
| | - Wagner Campos Otoni
- Departamento de Biologia Vegetal, Laboratório de Cultura de Tecidos/BIOAGRO, Federal University of Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Foued Salmen Espindola
- Instituto de Biotecnologia, Universidade Federal de Uberlândia, Rua Acre, S/N, Bloco 2E/237, Uberlândia, MG, CEP 38405-319, 38408-100, Brazil.
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18
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Adhikary PP, Idowu T, Tan Z, Hoang C, Shanta S, Dumbani M, Mappalakayil L, Awasthi B, Bermudez M, Weiner J, Beule D, Wolber G, Page BD, Hedtrich S. Disrupting TSLP-TSLP receptor interactions via putative small molecule inhibitors yields a novel and efficient treatment option for atopic diseases. EMBO Mol Med 2024; 16:1630-1656. [PMID: 38877290 PMCID: PMC11250841 DOI: 10.1038/s44321-024-00085-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/16/2024] Open
Abstract
Thymic stromal lymphopoietin (TSLP) is a key player in atopic diseases, which has sparked great interest in therapeutically targeting TSLP. Yet, no small-molecule TSLP inhibitors exist due to the challenges of disrupting the protein-protein interaction between TSLP and its receptor. Here, we report the development of small-molecule TSLP receptor inhibitors using virtual screening and docking of >1,000,000 compounds followed by iterative chemical synthesis. BP79 emerged as our lead compound that effectively abrogates TSLP-triggered cytokines at low micromolar concentrations. For in-depth analysis, we developed a human atopic disease drug discovery platform using multi-organ chips. Here, topical application of BP79 onto atopic skin models that were co-cultivated with lung models and Th2 cells effectively suppressed immune cell infiltration and IL-13, IL-4, TSLP, and periostin secretion, while upregulating skin barrier proteins. RNA-Seq analysis corroborate these findings and indicate protective downstream effects on the lungs. To the best of our knowledge, this represents the first report of a potent putative small molecule TSLPR inhibitor which has the potential to expand the therapeutic and preventive options in atopic diseases.
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Affiliation(s)
- Partho Protim Adhikary
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Temilolu Idowu
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Zheng Tan
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Christopher Hoang
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Selina Shanta
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Malti Dumbani
- Institute of Pharmacy, Freie Universität of Berlin, Berlin, Germany
| | - Leah Mappalakayil
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Bhuwan Awasthi
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Marcel Bermudez
- Institute of Pharmacy, Freie Universität of Berlin, Berlin, Germany
- Institute of Pharmaceutical and Medicinal Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - January Weiner
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität of Berlin, Berlin, Germany
| | - Brent Dg Page
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada.
| | - Sarah Hedtrich
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, Canada.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
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19
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Özil M, Balaydın HT, Dogan B, Şentürk M, Durdagi S. Efficient, rapid, and high-yield synthesis of aryl Schiff base derivatives and their in vitro and in silico inhibition studies of hCA I, hCA II, AChE, and BuChE. Arch Pharm (Weinheim) 2024; 357:e2300266. [PMID: 38593306 DOI: 10.1002/ardp.202300266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
This study reports a rapid and efficient synthesis of four novel aryl Schiff base derivatives. Biological activity and molecular modeling studies were conducted to evaluate the inhibitory effects of these compounds on human carbonic anhydrases (hCA) and cholinesterases. The results indicate that the triazole-ring-containing compounds have strong inhibitory effects on hCA I, hCA II, acetylcholinesterase (AChE), and butyrylcholinesterase (BuChE) targets. Besides comparing the Schiff bases synthesized in our study to reference molecules, we conducted in silico investigations to examine how these compounds interact with their targets. Our studies revealed that these compounds can occupy binding sites and establish interactions with crucial residues, thus inhibiting the functions of the targets. These findings have significant implications as they can be utilized to develop more potent compounds for treating the diseases that these target proteins play crucial roles in or to obtain drug precursors with enhanced efficacy.
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Affiliation(s)
- Musa Özil
- Department of Chemistry, The Faculty of Arts and Sciences, Recep Tayyip Erdogan University, Rize, Türkiye
| | - Halis T Balaydın
- Education Faculty, Recep Tayyip Erdogan University, Rize, Türkiye
| | - Berna Dogan
- Department of Chemistry, Istanbul Technical University, Istanbul, Türkiye
- Department of Biochemistry, School of Medicine, Bahçeşehir University, Istanbul, Türkiye
| | - Murat Şentürk
- Pharmacy Faculty, Agri Ibrahim Cecen University, Agri, Türkiye
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Türkiye
- Molecular Therapy Lab, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul, Türkiye
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20
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Chowdhury M, Biswas N, Saha S, Rahaman A, Gupta PS, Banerjee A, Mandal DP, Bhattacharjee S, Zangrando E, Sciortino G, Pisanu F, Garribba E, Roy Choudhury R, Roy Choudhury C. Interaction with CT-DNA and in vitro cytotoxicity of two new copper(II)-based potential drugs derived from octanoic hydrazide ligands. J Inorg Biochem 2024; 256:112546. [PMID: 38593611 DOI: 10.1016/j.jinorgbio.2024.112546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/13/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
Two copper(II) complexes [Cu(Hpmoh)(NO3)(NCS)] (1) and [Cu(peoh)(N3)]2 (2) were designed and synthesized by reaction of Cu(NO3)2·3H2O with hydrazone Schiff base ligands,abbreviated with Hpmoh and Hpeoh. Hpmoh and Hpeoh were prepared by condensation reaction of octanoic hydrazide with pyridine-2-carboxyaldehyde and 2-acetylpyridine, respectively. Complexes 1 and 2 were characterized using different analytical techniques such as FT-IR, UV-Vis, IR, EPR and single X-ray diffraction (XRD) analyses as well as computational methods (DFT). The XRD of 1 and 2 shows a mononuclear or a dinuclear structure with the copper(II) centre adopting a slightly distorted square pyramidal geometry. In water-containing solution and in DMSO, 1 and 2 undergo a partial transformation with formation of [Cu(Hpmoh)(NO3)(NCS)] (1) and [Cu(Hpmoh)(NO3)(H2O/DMSO)] (1a) in one system and [Cu(peoh)(N3)] (2a) in the other one, as supported by DFT calculations. Docking simulations confirmed that the intercalation is the preferred binding mode with DNA for 1, 1a and 2a, but suggested that the minor groove binding is also possible. A significant fluorescence quenching of the DNA-ethidium bromide conjugate was observed upon the addition of complexes 1 and 2 with a quenching constant around 104 M-1 s-1. Finally, both 1 and 2 were examined for anti-cancer activity using MDA-MB-231 (human breast adenocarcinoma) and A375 (malignant melanoma) cell lines through in vitro MTT assay which suggest comparable cancer cell killing efficacy, with the higher effectiveness of 2 due to the dissociation into two [Cu(peoh)(N3)] units.
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Affiliation(s)
- Manas Chowdhury
- Department of Chemistry, West Bengal State University, Barasat, Kolkata 700126, India
| | - Niladri Biswas
- Department of Biotechnology, Institute of Genetic Engineering, No. 30, Thakurhat Road, Badu, Madhyamgram, Kolkata, West Bengal 700128, India
| | - Sandeepta Saha
- Sripur High School, Madhyamgram Bazar, Kolkata 700130, India
| | - Ashikur Rahaman
- Department of Zoology, West Bengal State University, Barasat, Kolkata 700126, India
| | - Poulami Sen Gupta
- Department of Zoology, West Bengal State University, Barasat, Kolkata 700126, India
| | - Ankur Banerjee
- Department of Zoology, West Bengal State University, Barasat, Kolkata 700126, India
| | - Deba Prasad Mandal
- Department of Zoology, West Bengal State University, Barasat, Kolkata 700126, India
| | - Shamee Bhattacharjee
- Department of Zoology, West Bengal State University, Barasat, Kolkata 700126, India
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Federico Pisanu
- Dipartimento di Medicina, Chirurgia e Farmacia, Università di Sassari, Viale San Pietro, 07100 Sassari, Italy
| | - Eugenio Garribba
- Dipartimento di Medicina, Chirurgia e Farmacia, Università di Sassari, Viale San Pietro, 07100 Sassari, Italy.
| | - Ruma Roy Choudhury
- Department of Chemistry and Environment, Heritage Institute of Technology, Chowbaga Road, Badu, Kolkata 700 107, India
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21
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Osman R, Bossu M, Dauvillée D, Spriet C, Liu C, Zeeman SC, D'Hulst C, Bompard C. LIKE EARLY STARVATION 1 interacts with amylopectin during starch biosynthesis. PLANT PHYSIOLOGY 2024; 195:1851-1865. [PMID: 38573555 DOI: 10.1093/plphys/kiae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Starch is the major energy storage compound in plants. Both transient starch and long-lasting storage starch accumulate in the form of insoluble, partly crystalline granules. The structure of these granules is related to the structure of the branched polymer amylopectin: linear chains of glucose units organized in double helices that align to form semicrystalline lamellae, with branching points located in amorphous regions between them. EARLY STARVATION 1 (ESV1) and LIKE EARLY STARVATION 1 (LESV) proteins are involved in the maintenance of starch granule structure and in the phase transition of amylopectin, respectively, in Arabidopsis (Arabidopsis thaliana). These proteins contain a conserved tryptophan-rich C-terminal domain folded into an antiparallel β-sheet, likely responsible for binding of the proteins to starch, and different N-terminal domains whose structure and function are unknown. In this work, we combined biochemical and biophysical approaches to analyze the structures of LESV and ESV1 and their interactions with the different starch polyglucans. We determined that both proteins interact with amylopectin but not with amylose and that only LESV is capable of interacting with amylopectin during starch biosynthesis. While the C-terminal domain interacts with amylopectin in its semicrystalline form, the N-terminal domain of LESV undergoes induced conformational changes that are probably involved in its specific function of mediating glucan phase transition. These results clarify the specific mechanism of action of these 2 proteins in the biosynthesis of starch granules.
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Affiliation(s)
- Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mélanie Bossu
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - David Dauvillée
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Lille F-59000, France
| | - Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich
| | - Christophe D'Hulst
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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22
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Spassov DS. Binding Affinity Determination in Drug Design: Insights from Lock and Key, Induced Fit, Conformational Selection, and Inhibitor Trapping Models. Int J Mol Sci 2024; 25:7124. [PMID: 39000229 PMCID: PMC11240957 DOI: 10.3390/ijms25137124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Binding affinity is a fundamental parameter in drug design, describing the strength of the interaction between a molecule and its target protein. Accurately predicting binding affinity is crucial for the rapid development of novel therapeutics, the prioritization of promising candidates, and the optimization of their properties through rational design strategies. Binding affinity is determined by the mechanism of recognition between proteins and ligands. Various models, including the lock and key, induced fit, and conformational selection, have been proposed to explain this recognition process. However, current computational strategies to predict binding affinity, which are based on these models, have yet to produce satisfactory results. This article explores the connection between binding affinity and these protein-ligand interaction models, highlighting that they offer an incomplete picture of the mechanism governing binding affinity. Specifically, current models primarily center on the binding of the ligand and do not address its dissociation. In this context, the concept of ligand trapping is introduced, which models the mechanisms of dissociation. When combined with the current models, this concept can provide a unified theoretical framework that may allow for the accurate determination of the ligands' binding affinity.
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Affiliation(s)
- Danislav S Spassov
- Drug Design and Bioinformatics Lab, Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
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23
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Fernandez-Ciruelos B, Albanese M, Adhav A, Solomin V, Ritchie-Martinez A, Taverne F, Velikova N, Jirgensons A, Marina A, Finn PW, Wells JM. Repurposing Hsp90 inhibitors as antimicrobials targeting two-component systems identifies compounds leading to loss of bacterial membrane integrity. Microbiol Spectr 2024:e0014624. [PMID: 38917423 DOI: 10.1128/spectrum.00146-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
The discovery of antimicrobials with novel mechanisms of action is crucial to tackle the foreseen global health crisis due to antimicrobial resistance. Bacterial two-component signaling systems (TCSs) are attractive targets for the discovery of novel antibacterial agents. TCS-encoding genes are found in all bacterial genomes and typically consist of a sensor histidine kinase (HK) and a response regulator. Due to the conserved Bergerat fold in the ATP-binding domain of the TCS HK and the human chaperone Hsp90, there has been much interest in repurposing inhibitors of Hsp90 as antibacterial compounds. In this study, we explore the chemical space of the known Hsp90 inhibitor scaffold 3,4-diphenylpyrazole (DPP), building on previous literature to further understand their potential for HK inhibition. Six DPP analogs inhibited HK autophosphorylation in vitro and had good antimicrobial activity against Gram-positive bacteria. However, mechanistic studies showed that their antimicrobial activity was related to damage of bacterial membranes. In addition, DPP analogs were cytotoxic to human embryonic kidney cell lines and induced the cell arrest phenotype shown for other Hsp90 inhibitors. We conclude that these DPP structures can be further optimized as specific disruptors of bacterial membranes providing binding to Hsp90 and cytotoxicity are lowered. Moreover, the X-ray crystal structure of resorcinol, a substructure of the DPP derivatives, bound to the HK CheA represents a promising starting point for the fragment-based design of novel HK inhibitors. IMPORTANCE The discovery of novel antimicrobials is of paramount importance in tackling the imminent global health crisis of antimicrobial resistance. The discovery of novel antimicrobials with novel mechanisms of actions, e.g., targeting bacterial two-component signaling systems, is crucial to bypass existing resistance mechanisms and stimulate pharmaceutical innovations. Here, we explore the possible repurposing of compounds developed in cancer research as inhibitors of two-component systems and investigate their off-target effects such as bacterial membrane disruption and toxicity. These results highlight compounds that are promising for further development of novel bacterial membrane disruptors and two-component system inhibitors.
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Affiliation(s)
- Blanca Fernandez-Ciruelos
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Marco Albanese
- Oxford Drug Design (ODD), Oxford Centre for Innovation, Oxford, United Kingdom
- School of Computer Science, University of Buckingham, Buckingham, United Kingdom
| | - Anmol Adhav
- Macromolecular Crystallography Group, Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Vitalii Solomin
- Organic Synthesis Methodology Group, Latvian Institute of Organic Synthesis (LIOS), Riga, Latvia
| | - Arabela Ritchie-Martinez
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Femke Taverne
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Nadya Velikova
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Aigars Jirgensons
- Organic Synthesis Methodology Group, Latvian Institute of Organic Synthesis (LIOS), Riga, Latvia
| | - Alberto Marina
- Macromolecular Crystallography Group, Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Cientificas (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Paul W Finn
- Oxford Drug Design (ODD), Oxford Centre for Innovation, Oxford, United Kingdom
- School of Computer Science, University of Buckingham, Buckingham, United Kingdom
| | - Jerry M Wells
- Host-Microbe Interactomics Group, Dept. Animal Sciences, Wageningen University & Research (WUR), Wageningen, the Netherlands
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24
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Rodríguez Longarela N, Paredes Ramos M, López Vilariño JM. Bioinformatics tools for the study of bioactive peptides from vegetal sources: evolution and future perspectives. Crit Rev Food Sci Nutr 2024:1-20. [PMID: 38907628 DOI: 10.1080/10408398.2024.2367571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Bioactive peptides from vegetal sources have been shown to have functional properties as anti-inflammatory, antioxidant, antihypertensive or antidiabetic capacity. For this reason, they have been proposed as an interesting and promising alternative to improve human health. In recent years, the numerous advances in the bioinformatics field for in silico prediction have speeded up the discovery of bioactive peptides, also reducing the associated costs when using an integrated approach between the classical and bioinformatics discovery. This review aims to provide an overview of the evolution, limitations and latest advances in the field of bioinformatics and computational tools, and specifically make a critical and comprehensive insight into computational techniques used to study the mechanism of interaction that allows the explanation of plant bioactive peptide functionality. In particular, molecular docking is considered key to explain the different functionalities that have been previously identified. The assumptions to simplify such a high complex environment implies a degree of uncertainty that can only be guaranteed and validated by in vitro or in vivo studies, however, the combination of databases, software and bioinformatics applications with the classical approach has become a promising procedure for the study of bioactive peptides.
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25
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McCone JAJ, Teesdale-Spittle PH, Flanagan JU, Harvey JE. A Structure-Activity Investigation of the Fungal Metabolite (-)-TAN-2483B: Inhibition of Bruton's Tyrosine Kinase. Chemistry 2024; 30:e202401051. [PMID: 38629656 DOI: 10.1002/chem.202401051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Indexed: 06/01/2024]
Abstract
The natural product (-)-TAN-2483B is a fungal secondary metabolite which displays promising anti-cancer and immunomodulatory activity. Our previous syntheses of (-)-TAN-2483B and sidechain analogues uncovered inhibitory activity against Bruton's tyrosine kinase (Btk), an established drug target for various leukaemia and immunological diseases. A structure-based computational study using ensemble docking and molecular dynamics was performed to determine plausible binding modes for (-)-TAN-2483B and analogues in the Btk binding site. These hypotheses guided the design of new analogues which were synthesised and their inhibitory activities determined, providing insights into the structural determinants of the furopyranone scaffold that confer both activity and selectivity for Btk. These findings offer new perspectives for generating optimised (-)-TAN-2483B-based kinase inhibitors for the treatment of leukaemia and immunological diseases.
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Affiliation(s)
- Jordan A J McCone
- School of Chemical and Physical Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Paul H Teesdale-Spittle
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- School of Biological Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Jack U Flanagan
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Joanne E Harvey
- School of Chemical and Physical Sciences, Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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26
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Khachatryan H, Matevosyan M, Harutyunyan V, Gevorgyan S, Shavina A, Tirosyan I, Gabrielyan Y, Ayvazyan M, Bozdaganyan M, Fakhar Z, Gharaghani S, Zakaryan H. Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme. Sci Rep 2024; 14:14255. [PMID: 38902397 PMCID: PMC11189913 DOI: 10.1038/s41598-024-65228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024] Open
Abstract
The coronavirus disease 19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global health crisis with millions of confirmed cases and related deaths. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and presents an attractive target for drug development. Despite the approval of some drugs, the search for effective treatments continues. In this study, we systematically evaluated 342 holo-crystal structures of Mpro to identify optimal conformations for structure-based virtual screening (SBVS). Our analysis revealed limited structural flexibility among the structures. Three docking programs, AutoDock Vina, rDock, and Glide were employed to assess the efficiency of virtual screening, revealing diverse performances across selected Mpro structures. We found that the structures 5RHE, 7DDC, and 7DPU (PDB Ids) consistently displayed the lowest EF, AUC, and BEDROCK scores. Furthermore, these structures demonstrated the worst pose prediction results in all docking programs. Two structural differences contribute to variations in docking performance: the absence of the S1 subsite in 7DDC and 7DPU, and the presence of a subpocket in the S2 subsite of 7DDC, 7DPU, and 5RHE. These findings underscore the importance of selecting appropriate Mpro conformations for SBVS, providing valuable insights for advancing drug discovery efforts.
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Affiliation(s)
- Hamlet Khachatryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
| | - Mher Matevosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Vardan Harutyunyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Smbat Gevorgyan
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Anastasiya Shavina
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Irina Tirosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Yeva Gabrielyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Marusya Ayvazyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | | | - Zeynab Fakhar
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sajjad Gharaghani
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hovakim Zakaryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
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27
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Alberto-Silva AS, Hemmer S, Bock HA, da Silva LA, Scott KR, Kastner N, Bhatt M, Niello M, Jäntsch K, Kudlacek O, Bossi E, Stockner T, Meyer MR, McCorvy JD, Brandt SD, Kavanagh P, Sitte HH. Bioisosteric analogs of MDMA: Improving the pharmacological profile? J Neurochem 2024. [PMID: 38898705 DOI: 10.1111/jnc.16149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/26/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
3,4-Methylenedioxymethamphetamine (MDMA, 'ecstasy') is re-emerging in clinical settings as a candidate for the treatment of specific neuropsychiatric disorders (e.g. post-traumatic stress disorder) in combination with psychotherapy. MDMA is a psychoactive drug, typically regarded as an empathogen or entactogen, which leads to transporter-mediated monoamine release. Despite its therapeutic potential, MDMA can induce dose-, individual-, and context-dependent untoward effects outside safe settings. In this study, we investigated whether three new methylenedioxy bioisosteres of MDMA improve its off-target profile. In vitro methods included radiotracer assays, transporter electrophysiology, bioluminescence resonance energy transfer and fluorescence-based assays, pooled human liver microsome/S9 fraction incubations, metabolic stability studies, isozyme mapping, and liquid chromatography coupled to high-resolution mass spectrometry. In silico methods included molecular docking. Compared with MDMA, all three MDMA bioisosteres (ODMA, TDMA, and SeDMA) showed similar pharmacological activity at human serotonin, dopamine, and norepinephrine transporters (hSERT, hDAT, and hNET, respectively) but decreased agonist activity at 5-HT2A/2B/2C receptors. Regarding their hepatic metabolism, they differed from MDMA, with N-demethylation being the only metabolic route shared, and without forming phase II metabolites. In addition, TDMA showed an enhanced intrinsic clearance in comparison to its congeners. Additional screening for their interaction with human organic cation transporters (hOCTs) and plasma membrane monoamine transporter (hPMAT) revealed a weaker interaction of the MDMA analogs with hOCT1, hOCT2, and hPMAT. Our findings suggest that these new MDMA bioisosteres might constitute appealing therapeutic alternatives to MDMA, sparing the primary pharmacological activity at hSERT, hDAT, and hNET, but displaying a reduced activity at 5-HT2A/2B/2C receptors and alternative hepatic metabolism. Whether these MDMA bioisosteres may pose lower risk alternatives to the clinically re-emerging MDMA warrants further studies.
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Affiliation(s)
- Ana Sofia Alberto-Silva
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Selina Hemmer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Hailey A Bock
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Leticia Alves da Silva
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Kenneth R Scott
- Department of Pharmacology and Therapeutics, School of Medicine, Trinity Centre for Health Sciences, St James Hospital, Dublin, Ireland
| | - Nina Kastner
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Manan Bhatt
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marco Niello
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Kathrin Jäntsch
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Oliver Kudlacek
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Elena Bossi
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Center for Research in Neuroscience, University of Insubria, Varese, Italy
| | - Thomas Stockner
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - John D McCorvy
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Simon D Brandt
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Pierce Kavanagh
- Department of Pharmacology and Therapeutics, School of Medicine, Trinity Centre for Health Sciences, St James Hospital, Dublin, Ireland
| | - Harald H Sitte
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
- Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, Amman, Jordan
- Center for Addiction Research and Science, Medical University of Vienna, Vienna, Austria
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28
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Rodríguez D, Lence E, Vázquez-Ucha JC, Beceiro A, González-Bello C. Novel Penicillin-Based Sulfone-Siderophore Conjugates for Restoring β-Lactam Antibiotic Efficacy. ACS OMEGA 2024; 9:26484-26494. [PMID: 38911797 PMCID: PMC11191083 DOI: 10.1021/acsomega.4c02984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/25/2024]
Abstract
Membrane permeability is a natural defense barrier that contributes to increased bacterial drug resistance, particularly for Gram-negative pathogens. As such, accurate delivery of the antibacterial agent to the target has become a growing research area in the infectious diseases field as a means of improving drug efficacy. Although the efficient transport of siderophore-antibiotic conjugates into the cytosol still remains challenging, great success has been achieved in the delivery of β-lactam antibiotics into the periplasmic space via bacterial iron uptake pathways. Cefiderocol, the first siderophore-cephalosporin conjugate approved by the US Food and Drug Administration, is a good example. These conjugation strategies have also been applied to the precise delivery of β-lactamase inhibitors, such as penicillin-based sulfone 1, to restore β-lactam antibiotic efficacy in multidrug-resistant bacteria. Herein, we have explored the impact on the bacterial activity of 1 by modifying its iron chelator moiety. A set of derivatives functionalized with diverse iron chelator groups and linkages to the scaffold (compounds 2-8) were synthesized and assayed in vitro. The results on the ability of derivatives 2-8 to recover β-lactam antibiotic efficacy in difficult-to-treat pathogens that produce various β-lactamase enzymes, along with kinetic studies with the isolated enzymes, allowed us to identify compound 2, a novel β-lactamase inhibitor with an expanded spectrum of activity. Molecular dynamics simulation studies provided us with further information regarding the molecular basis of the relative inhibitory properties of the most relevant compound described herein.
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Affiliation(s)
- Diana Rodríguez
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Emilio Lence
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan C. Vázquez-Ucha
- Servicio
de Microbiología, Complexo Hospitalario Universitario da Coruña
(CHUAC), Instituto de Investigación
Biomédica da Coruña (INIBIC), Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio
de Microbiología, Complexo Hospitalario Universitario da Coruña
(CHUAC), Instituto de Investigación
Biomédica da Coruña (INIBIC), Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Concepción González-Bello
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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29
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Milunovic MM, Ohui K, Besleaga I, Petrasheuskaya TV, Dömötör O, Enyedy ÉA, Darvasiova D, Rapta P, Barbieriková Z, Vegh D, Tóth S, Tóth J, Kucsma N, Szakács G, Popović-Bijelić A, Zafar A, Reynisson J, Shutalev AD, Bai R, Hamel E, Arion VB. Copper(II) Complexes with Isomeric Morpholine-Substituted 2-Formylpyridine Thiosemicarbazone Hybrids as Potential Anticancer Drugs Inhibiting Both Ribonucleotide Reductase and Tubulin Polymerization: The Morpholine Position Matters. J Med Chem 2024; 67:9069-9090. [PMID: 38771959 PMCID: PMC11181322 DOI: 10.1021/acs.jmedchem.4c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024]
Abstract
The development of copper(II) thiosemicarbazone complexes as potential anticancer agents, possessing dual functionality as inhibitors of R2 ribonucleotide reductase (RNR) and tubulin polymerization by binding at the colchicine site, presents a promising avenue for enhancing therapeutic effectiveness. Herein, we describe the syntheses and physicochemical characterization of four isomeric proligands H2L3-H2L6, with the methylmorpholine substituent at pertinent positions of the pyridine ring, along with their corresponding Cu(II) complexes 3-6. Evidently, the position of the morpholine moiety and the copper(II) complex formation have marked effects on the in vitro antiproliferative activity in human uterine sarcoma MES-SA cells and the multidrug-resistant derivative MES-SA/Dx5 cells. Activity correlated strongly with quenching of the tyrosyl radical (Y•) of mouse R2 RNR protein, inhibition of RNR activity in the cancer cells, and inhibition of tubulin polymerization. Insights into the mechanism of antiproliferative activity, supported by experimental results and molecular modeling calculations, are presented.
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Affiliation(s)
| | - Katerina Ohui
- Institute
of Inorganic Chemistry, University of Vienna, Vienna A-1090, Austria
| | - Iuliana Besleaga
- Institute
of Inorganic Chemistry, University of Vienna, Vienna A-1090, Austria
| | - Tatsiana V. Petrasheuskaya
- Department
of Molecular and Analytical Chemistry, Interdisciplinary Excellence
Centre, University of Szeged, Dóm tér 7-8, Szeged H-6720, Hungary
- MTA-SZTE
Lendület Functional Metal Complexes Research Group, University of Szeged, Dóm tér 7, Szeged H-6720, Hungary
| | - Orsolya Dömötör
- Department
of Molecular and Analytical Chemistry, Interdisciplinary Excellence
Centre, University of Szeged, Dóm tér 7-8, Szeged H-6720, Hungary
- MTA-SZTE
Lendület Functional Metal Complexes Research Group, University of Szeged, Dóm tér 7, Szeged H-6720, Hungary
| | - Éva A. Enyedy
- Department
of Molecular and Analytical Chemistry, Interdisciplinary Excellence
Centre, University of Szeged, Dóm tér 7-8, Szeged H-6720, Hungary
- MTA-SZTE
Lendület Functional Metal Complexes Research Group, University of Szeged, Dóm tér 7, Szeged H-6720, Hungary
| | - Denisa Darvasiova
- Institute
of Physical Chemistry and Chemical Physics, Faculty of Chemical and
Food Technology, Slovak University of Technology
in Bratislava, Bratislava SK-81237, Slovakia
| | - Peter Rapta
- Institute
of Physical Chemistry and Chemical Physics, Faculty of Chemical and
Food Technology, Slovak University of Technology
in Bratislava, Bratislava SK-81237, Slovakia
| | - Zuzana Barbieriková
- Institute
of Physical Chemistry and Chemical Physics, Faculty of Chemical and
Food Technology, Slovak University of Technology
in Bratislava, Bratislava SK-81237, Slovakia
| | - Daniel Vegh
- Institute
of Organic Chemistry, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Bratislava SK-81237, Slovakia
| | - Szilárd Tóth
- Institute
of Molecular Life Sciences, HUN-REN Research
Centre for Natural Sciences, Hungarian Research Network, Magyar Tudósok körútja
2, Budapest H-1117, Hungary
| | - Judit Tóth
- Institute
of Molecular Life Sciences, HUN-REN Research
Centre for Natural Sciences, Hungarian Research Network, Magyar Tudósok körútja
2, Budapest H-1117, Hungary
| | - Nóra Kucsma
- Institute
of Molecular Life Sciences, HUN-REN Research
Centre for Natural Sciences, Hungarian Research Network, Magyar Tudósok körútja
2, Budapest H-1117, Hungary
| | - Gergely Szakács
- Institute
of Molecular Life Sciences, HUN-REN Research
Centre for Natural Sciences, Hungarian Research Network, Magyar Tudósok körútja
2, Budapest H-1117, Hungary
- Center
for Cancer Research, Medical University
of Vienna, Vienna A-1090, Austria
| | - Ana Popović-Bijelić
- Faculty
of Physical Chemistry, University of Belgrade, Belgrade 11158, Serbia
| | - Ayesha Zafar
- School
of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School
of Pharmacy and Bioengineering, Keele University, Newcastle-under-Lyme, Staffordshire ST5 5BG, United
Kingdom
| | - Anatoly D. Shutalev
- N.
D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Ruoli Bai
- Molecular
Pharmacology Branch, Developmental Therapeutics Program, Division
of Cancer Diagnosis and Treatment, National Cancer Institute, Frederick
National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Ernest Hamel
- Molecular
Pharmacology Branch, Developmental Therapeutics Program, Division
of Cancer Diagnosis and Treatment, National Cancer Institute, Frederick
National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Vladimir B. Arion
- Institute
of Inorganic Chemistry, University of Vienna, Vienna A-1090, Austria
- Inorganic
Polymers Department, “Petru Poni”
Institute of Macromolecular Chemistry, Aleea Gr. Ghica Voda 41 A, Iasi 700487, Romania
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30
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Bournez C, Gally JM, Aci-Sèche S, Bernard P, Bonnet P. Virtual screening of natural products to enhance melanogenosis. Mol Inform 2024:e202300335. [PMID: 38864978 DOI: 10.1002/minf.202300335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 06/13/2024]
Abstract
Natural products have long been an important source of inspiration for medicinal chemistry and drug discovery. In the cosmetic field, they remain the major elements of the composition and serve as marketing asset. Recent research showed the implication of salt-inducible kinases on the melanin production in skin via MITF regulation. Finding new potent modulators on such target could open the way to several cosmetic applications to attenuate visible signs of photoaging and improve the tan without sun. Since virtual screening can be a powerful tool for detecting hit compounds in the early stages of a drug discovery process, we applied this method on salt-inducible kinase 2 to discover potential interesting compounds. Here, we present the different steps from the construction of a database of natural products, to the validation of a docking protocol and the results of the virtual screening. Hits from the screening were tested in vitro to confirm their efficiency and results are discussed.
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Affiliation(s)
- Colin Bournez
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans Cedex 2, France
| | - José-Manuel Gally
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans Cedex 2, France
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans Cedex 2, France
| | | | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans Cedex 2, France
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31
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de Sousa LF, Paschoal DFS, Novato WTG. Molecular modeling of multi-target analogs of huperzine A and applications in Alzheimer's disease. J Mol Model 2024; 30:200. [PMID: 38850372 DOI: 10.1007/s00894-024-05991-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
CONTEXT Given the diverse pathophysiological mechanisms underlying Alzheimer's disease, it is improbable that a single targeted drug will prove successful as a therapeutic strategy. Therefore, exploring various hypotheses in drug design is imperative. The sequestration of Fe(II) and Zn(II) cations stands out as a crucial mechanism based on the mitigation of reactive oxygen species. Moreover, inhibiting acetylcholinesterase represents a pivotal strategy to enhance acetylcholine levels in the synaptic cleft. This research aims to investigate the analogs of Huperzine A, documented in scientific literature, considering of these two hypotheses. Consequently, the speciation chemistry of these structures with Fe(II) and Zn(II) was scrutinized using quantum chemistry calculations, molecular docking simulations, and theoretical predictions of pharmacokinetics properties. From the pharmacokinetic properties, only two analogs, HupA-A1 and HupA-A2, exhibited a theoretical permeability across the blood-brain barrier; on the other hand, from a thermodynamic standpoint, the enantiomers of HupA-A2 showed negligible chelation values. The enantiomers with the most favorable interaction parameters were S'R'HupA-A1 (ΔGBIND = -40.0 kcal mol-1, fitness score = 35.5) and R'R'HupA-A1 (ΔGBIND = -35.5 kcal mol-1, fitness score = 22.61), being compared with HupA (ΔGBIND = -41.75 kcal mol-1, fitness score = 39.95). From this study, some prime candidates for promising drug were S'R'HupA-A1 and R'R'HupA-A1, primarily owing to their favorable thermodynamic chelating capability and potential anticholinesterase mechanism. METHODS Quantum chemistry calculations were carried out at B3LYP/6-31G(d) level, considering the IEF-PCM(UFF) implicit solvent model for water. The coordination compounds were assessed using the Gibbs free energy variation and hard and soft acid theory. Molecular docking calculations were conducted using the GOLD program, based on the crystal structure of the acetylcholinesterase protein (PDB code = 4EY5), where the ChemScore function was employed with the active site defined as the region within a 15-Å radius around the centroid coordinates (X = -9.557583, Y = -43.910473, Z = 31.466687). Pharmacokinetic properties were predicted using SwissADME, focusing on Lipinski's rule of five.
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Affiliation(s)
- Leonardo F de Sousa
- NQTCM: Núcleo de Química Teórica e Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal do Rio de Janeiro, 27.971-525, Macaé, RJ, Rio de Janeiro, Brazil
| | - Diego F S Paschoal
- NQTCM: Núcleo de Química Teórica e Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal do Rio de Janeiro, 27.971-525, Macaé, RJ, Rio de Janeiro, Brazil.
| | - Willian T G Novato
- NQTCM: Núcleo de Química Teórica e Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal do Rio de Janeiro, 27.971-525, Macaé, RJ, Rio de Janeiro, Brazil
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Tretbar M, Schliehe-Diecks J, von Bredow L, Tan K, Roatsch M, Tu JW, Kemkes M, Sönnichsen M, Schöler A, Borkhardt A, Bhatia S, Hansen FK. Preferential HDAC6 inhibitors derived from HPOB exhibit synergistic antileukemia activity in combination with decitabine. Eur J Med Chem 2024; 272:116447. [PMID: 38714044 DOI: 10.1016/j.ejmech.2024.116447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/09/2024]
Abstract
Histone deacetylase 6 (HDAC6) is an emerging drug target to treat oncological and non-oncological conditions. Since highly selective HDAC6 inhibitors display limited anticancer activity when used as single agent, they usually require combination therapies with other chemotherapeutics. In this work, we synthesized a mini library of analogues of the preferential HDAC6 inhibitor HPOB in only two steps via an Ugi four-component reaction as the key step. Biochemical HDAC inhibition and cell viability assays led to the identification of 1g (highest antileukemic activity) and 2b (highest HDAC6 inhibition) as hit compounds. In subsequent combination screens, both 1g and especially 2b showed synergy with DNA methyltransferase inhibitor decitabine in acute myeloid leukemia (AML). Our findings highlight the potential of combining HDAC6 inhibitors with DNA methyltransferase inhibitors as a strategy to improve AML treatment outcomes.
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Affiliation(s)
- Maik Tretbar
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Julian Schliehe-Diecks
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Lukas von Bredow
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Kathrin Tan
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Martin Roatsch
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Jia-Wey Tu
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Marie Kemkes
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Melf Sönnichsen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Andrea Schöler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Finn K Hansen
- Department of Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
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Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
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Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
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Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
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Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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35
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Herbst C, Endres S, Würz R, Sotriffer C. Assessment of fragment docking and scoring with the endothiapepsin model system. Arch Pharm (Weinheim) 2024; 357:e2400061. [PMID: 38631672 DOI: 10.1002/ardp.202400061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Fragment-based screening has become indispensable in drug discovery. Yet, the weak binding affinities of these small molecules still represent a challenge for the reliable detection of fragment hits. The extent of this issue was illustrated in the literature for the aspartic protease endothiapepsin: When seven biochemical and biophysical in vitro screening methods were applied to screen a library of 361 fragments, very poor overlap was observed between the hit fragments identified by the individual approaches, resulting in high levels of false positive and/or false negative results depending on the mutually compared methods. Here, the reported in vitro findings are juxtaposed with the results from in silico docking and scoring approaches. The docking programs GOLD and Glide were considered with the scoring functions ASP, ChemScore, ChemPLP, GoldScore, DSXCSD, and GlideScore. First, the ranking power and scoring power were assessed for the named scoring functions. Second, the capability of reproducing the crystallized fragment binding modes was tested in a structure-based redocking approach. The redocking success notably depended on the ligand efficiency of the considered fragments. Third, a blinded virtual screening approach was employed to evaluate whether in silico screening can compete with in vitro methods in the enrichment of fragment databases.
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Affiliation(s)
- Carina Herbst
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Sara Endres
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Rebecca Würz
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
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36
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Herlah B, Janežič M, Ogris I, Grdadolnik SG, Kološa K, Žabkar S, Žegura B, Perdih A. Nature-inspired substituted 3-(imidazol-2-yl) morpholines targeting human topoisomerase IIα: Dynophore-derived discovery. Biomed Pharmacother 2024; 175:116676. [PMID: 38772152 DOI: 10.1016/j.biopha.2024.116676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024] Open
Abstract
The molecular nanomachine, human DNA topoisomerase IIα, plays a crucial role in replication, transcription, and recombination by catalyzing topological changes in the DNA, rendering it an optimal target for cancer chemotherapy. Current clinical topoisomerase II poisons often cause secondary tumors as side effects due to the accumulation of double-strand breaks in the DNA, spurring the development of catalytic inhibitors. Here, we used a dynamic pharmacophore approach to develop catalytic inhibitors targeting the ATP binding site of human DNA topoisomerase IIα. Our screening of a library of nature-inspired compounds led to the discovery of a class of 3-(imidazol-2-yl) morpholines as potent catalytic inhibitors that bind to the ATPase domain. Further experimental and computational studies identified hit compound 17, which exhibited selectivity against the human DNA topoisomerase IIα versus human protein kinases, cytotoxicity against several human cancer cells, and did not induce DNA double-strand breaks, making it distinct from clinical topoisomerase II poisons. This study integrates an innovative natural product-inspired chemistry and successful implementation of a molecular design strategy that incorporates a dynamic component of ligand-target molecular recognition, with comprehensive experimental characterization leading to hit compounds with potential impact on the development of more efficient chemotherapies.
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Affiliation(s)
- Barbara Herlah
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana SI 1000, Slovenia
| | - Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia
| | - Iza Ogris
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Medicine, Vrazov trg 2, Ljubljana SI 1000, Slovenia
| | | | - Katja Kološa
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Sonja Žabkar
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Bojana Žegura
- National institute of Biology, Department of Genetic Toxicology and Cancer Biology, Večna pot 121, Ljubljana SI 1000, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, Ljubljana SI 1000, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana SI 1000, Slovenia.
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37
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Bedart C, Simoben CV, Schapira M. Emerging structure-based computational methods to screen the exploding accessible chemical space. Curr Opin Struct Biol 2024; 86:102812. [PMID: 38603987 DOI: 10.1016/j.sbi.2024.102812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/13/2024]
Abstract
Structure-based virtual screening can be a valuable approach to computationally select hit candidates based on their predicted interaction with a protein of interest. The recent explosion in the size of chemical libraries increases the chances of hitting high-quality compounds during virtual screening exercises but also poses new challenges as the number of chemically accessible molecules grows faster than the computing power necessary to screen them. We review here two novel approaches rapidly gaining in popularity to address this problem: machine learning-accelerated and synthon-based library screening. We summarize the results from seminal proof-of-concept studies, highlight the latest developments, and discuss limitations and future directions.
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Affiliation(s)
- Corentin Bedart
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, F-59000, Lille, France
| | - Conrad Veranso Simoben
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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Cytarska J, Szulc J, Kołodziej-Sobczak D, Nunes JA, da Silva-Júnior EF, Łączkowski KZ. Cyrene™ as a tyrosinase inhibitor and anti-browning agent. Food Chem 2024; 442:138430. [PMID: 38241986 DOI: 10.1016/j.foodchem.2024.138430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024]
Abstract
The tyrosinase pathway takes part in the enzymatic process of food browning and is primarily responsible for food spoilage - manifesting itself from a decrease in its nutritional value to a deterioration of taste, which consequently leads to a gradual loss of shelf life. Finding safe and bio-based tyrosinase inhibitors and anti-browning agents may be of great importance in agriculture and food industries. Herein, we showed that Cyrene™ exhibits tyrosinase inhibitory activity (IC50: 268.2 µM), the 1.44 times higher than ascorbic acid (IC50: 386.5 μM). Binding mode studies demonstrated that the carbonyl oxygen of Cyrene™ coordinates with both copper ions. Surprisingly, both hydroxyl groups of Cyrene gem-diol perform a monodentate binding mode with both copper ions, at similar distances. This fact suggests that both compounds could have a similar binding mode and, as consequence, similar biological activities in tyrosinase inhibition assays and anti-browning activities.
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Affiliation(s)
- Joanna Cytarska
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Joanna Szulc
- Department of Food Industry Technology and Engineering, Bydgoszcz University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Dominika Kołodziej-Sobczak
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland.
| | - Jéssica Alves Nunes
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, AC Simões Campus, Lourival Melo Mota Avenue, s/n, 57072-970 Maceió, Alagoas, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Biological and Molecular Chemistry Research Group, Institute of Chemistry and Biotechnology, Federal University of Alagoas, AC Simões Campus, Lourival Melo Mota Avenue, s/n, 57072-970 Maceió, Alagoas, Brazil
| | - Krzysztof Z Łączkowski
- Department of Chemical Technology and Pharmaceuticals, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jurasza 2, 85-089 Bydgoszcz, Poland.
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39
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Taniguchi H, Kawamoto S, Monobe K, Aoki S. Data on molecular docking and molecular dynamics targeting Mycobacterium tuberculosis shikimic acid kinase. Data Brief 2024; 54:110370. [PMID: 38590616 PMCID: PMC10999656 DOI: 10.1016/j.dib.2024.110370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/28/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
We have previously performed a hierarchical in silico screening of a Mycobacterium tuberculosis shikimic acid kinase [1]. Specifically, 11 compounds were screened from a library of 154,118 compounds provided by ChemBridge [2] using UCSF DOCK [3] and the GOLD [4] program in the first and second steps, respectively. Molecular dynamic simulations were further performed on compound 2 (2-[(5Z)-5-(1-benzyl-5bromo-2-oxoindol-3-(5Z)-5-(1-benzyl-5-bromo-2-oxoindol-3-(5Z)-4-oxo-2 ylidene)-4oxo-2-sulfanylidene-1,3-thiazolidin-3-yl] acetic acid), which showed antimicrobial efficacy. These processes yielded ligand docking scores and trajectories. In this data article, we have added solvent-accessible surface area and PCA analyses, which were calculated from the raw docking scores and trajectories. Data obtained from molecular docking and molecular dynamic simulations are useful in two ways: (1) Further support for previous work (2) Provides a stepping stone for experimental scientists to conduct in silico studies and research ideas for other drug discovery researchers and computational biologists. We believe that this article will provide an opportunity to develop new Mycobacterium tuberculosis therapeutics through searching for analogs and inhibitors against new targets.
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Affiliation(s)
- Hinata Taniguchi
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
| | - Shuhei Kawamoto
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
| | - Kohei Monobe
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
| | - Shunsuke Aoki
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka-shi, Fukuoka 820-8502, Japan
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40
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Leitão MM, Vieira TF, Sousa SF, Borges F, Simões M, Borges A. Dual action of benzaldehydes: Inhibiting quorum sensing and enhancing antibiotic efficacy for controlling Pseudomonas aeruginosa biofilms. Microb Pathog 2024; 191:106663. [PMID: 38679246 DOI: 10.1016/j.micpath.2024.106663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Quorum sensing (QS) has a central role in biofilm lifestyle and antimicrobial resistance, and disrupting these signaling pathways is a promising strategy to control bacterial pathogenicity and virulence. In this study, the efficacy of three structurally related benzaldehydes (4-hydroxybenzaldehyde, 4-hydroxy-3-methoxybenzaldehyde (vanillin) and 4-hydroxy-3,5-dimethoxybenzaldehyde (syringaldehyde)) in disrupting the las and pqs systems of Pseudomonas aeruginosa was investigated using bioreporter strains and computational simulations. Additionally, these benzaldehydes were combined with tobramycin and ciprofloxacin antibiotics to evaluate their ability to increase antibiotic efficacy in preventing and eradicating P. aeruginosa biofilms. To this end, the total biomass, metabolic activity and culturability of the biofilm cells were determined. In vitro assays results indicated that the aromatic aldehydes have potential to inhibit the las and pqs systems by > 80 %. Molecular docking studies supported these findings, revealing the aldehydes binding in the same pocket as the natural ligands or receptor proteins (LasR, PQSA, PQSE, PQSR). Benzaldehydes were shown to act as virulence factor attenuators, with vanillin achieving a 48 % reduction in pyocyanin production. The benzaldehyde-tobramycin combination led not only to a 60 % reduction in biomass production but also to a 90 % reduction in the metabolic activity of established biofilms. A similar result was observed when benzaldehydes were combined with ciprofloxacin. 4-Hydroxybenzaldehyde demonstrated relevant action in increasing biofilm susceptibility to ciprofloxacin, resulting in a 65 % reduction in biomass. This study discloses, for the first time, that the benzaldehydes studied are potent QS inhibitors and also enhancers of antibiotics antibiofilm activity against P. aeruginosa.
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Affiliation(s)
- Miguel M Leitão
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; ALICE-Associate Laboratory for Innovation in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal; CIQUP-IMS-Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Tatiana F Vieira
- LAQV/REQUIMTE, BioSIM-Department of Biomedicine, Faculty of Medicine, University of Porto, Rua Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Sérgio F Sousa
- LAQV/REQUIMTE, BioSIM-Department of Biomedicine, Faculty of Medicine, University of Porto, Rua Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Fernanda Borges
- CIQUP-IMS-Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Manuel Simões
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; ALICE-Associate Laboratory for Innovation in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal; DEQ-Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal
| | - Anabela Borges
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; ALICE-Associate Laboratory for Innovation in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal; DEQ-Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal.
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41
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Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024; 56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Many drug formulations containing small active molecules are used for the treatment of coronary artery disease, which affects a significant part of the world's population. However, the inadequate profile of these molecules in terms of therapeutic efficacy has led to the therapeutic use of protein and peptide-based biomolecules with superior properties, such as target-specific affinity and low immunogenicity, in critical diseases. Protein‒protein interactions, as a consequence of advances in molecular techniques with strategies involving the combined use of in silico methods, have enabled the design of therapeutic peptides to reach an advanced dimension. In particular, with the advantages provided by protein/peptide structural modeling, molecular docking for the study of their interactions, molecular dynamics simulations for their interactions under physiological conditions and machine learning techniques that can work in combination with all these, significant progress has been made in approaches to developing therapeutic peptides that can modulate the development and progression of coronary artery diseases. In this scope, this review discusses in silico methods for the development of peptide therapeutics for the treatment of coronary artery disease and strategies for identifying the molecular mechanisms that can be modulated by these designs and provides a comprehensive perspective for future studies.
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Affiliation(s)
- Ayca Aslan
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey
| | - Selcen Ari Yuka
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey.
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42
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Thomas M, O'Boyle NM, Bender A, De Graaf C. MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design. J Cheminform 2024; 16:64. [PMID: 38816825 PMCID: PMC11141043 DOI: 10.1186/s13321-024-00861-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Generative models are undergoing rapid research and application to de novo drug design. To facilitate their application and evaluation, we present MolScore. MolScore already contains many drug-design-relevant scoring functions commonly used in benchmarks such as, molecular similarity, molecular docking, predictive models, synthesizability, and more. In addition, providing performance metrics to evaluate generative model performance based on the chemistry generated. With this unification of functionality, MolScore re-implements commonly used benchmarks in the field (such as GuacaMol, MOSES, and MolOpt). Moreover, new benchmarks can be created trivially. We demonstrate this by testing a chemical language model with reinforcement learning on three new tasks of increasing complexity related to the design of 5-HT2a ligands that utilise either molecular descriptors, 266 pre-trained QSAR models, or dual molecular docking. Lastly, MolScore can be integrated into an existing Python script with just three lines of code. This framework is a step towards unifying generative model application and evaluation as applied to drug design for both practitioners and researchers. The framework can be found on GitHub and downloaded directly from the Python Package Index.Scientific ContributionMolScore is an open-source platform to facilitate generative molecular design and evaluation thereof for application in drug design. This platform takes important steps towards unifying existing benchmarks, providing a platform to share new benchmarks, and improves customisation, flexibility and usability for practitioners over existing solutions.
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Affiliation(s)
- Morgan Thomas
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Noel M O'Boyle
- Computational Chemistry, Nxera Pharma, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Chris De Graaf
- Computational Chemistry, Nxera Pharma, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
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43
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Zhu J, Gu Z, Pei J, Lai L. DiffBindFR: an SE(3) equivariant network for flexible protein-ligand docking. Chem Sci 2024; 15:7926-7942. [PMID: 38817560 PMCID: PMC11134415 DOI: 10.1039/d3sc06803j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/07/2024] [Indexed: 06/01/2024] Open
Abstract
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential. Conventional docking approaches perform well in redocking tasks with known protein binding pocket conformation in the complex state. However, in real-world docking scenario without knowing the protein binding conformation for a new ligand, accurately modeling the binding complex structure remains challenging as flexible docking is computationally expensive and inaccurate. Typical deep learning-based docking methods do not explicitly consider protein side chain conformations and fail to ensure the physical plausibility and detailed atomic interactions. In this study, we present DiffBindFR, a full-atom diffusion-based flexible docking model that operates over the product space of ligand overall movements and flexibility and pocket side chain torsion changes. We show that DiffBindFR has higher accuracy in producing native-like binding structures with physically plausible and detailed interactions than available docking methods. Furthermore, in the Apo and AlphaFold2 modeled structures, DiffBindFR demonstrates superior advantages in accurate ligand binding pose and protein binding conformation prediction, making it suitable for Apo and AlphaFold2 structure-based drug design. DiffBindFR provides a powerful flexible docking tool for modeling accurate protein-ligand binding structures.
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Affiliation(s)
- Jintao Zhu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China
| | - Zhonghui Gu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China
- BNLMS, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies Chengdu Sichuan China
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44
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Ferreira P, Neves RPP, Miranda FP, Cunha AV, Havenith RWA, Ramos MJ, Fernandes PA. DszA Catalyzes C-S Bond Cleavage through N 5-Hydroperoxyl Formation. J Chem Inf Model 2024; 64:4218-4230. [PMID: 38684937 PMCID: PMC11134501 DOI: 10.1021/acs.jcim.4c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N5OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.
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Affiliation(s)
- Pedro Ferreira
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Rui P. P. Neves
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Filipa P. Miranda
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ana V. Cunha
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp 2000, Belgium
| | - Remco W. A. Havenith
- Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
- Ghent
Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan
281 (S3), Ghent B-9000, Belgium
| | - Maria J. Ramos
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Pedro A. Fernandes
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
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Duarte Filho LAMDS, Yanaguibashi Leal CE, Bodet PE, Beserra de Alencar Filho E, Almeida JRGDS, Porta Zapata M, Achour O, Groult H, Gouveia Veloso CA, Viegas Júnior C, Bourgougnon N, Picot L. The Identification of Peptide Inhibitors of the Coronavirus 3CL Protease from a Fucus ceranoides L. Hydroalcoholic Extract Using a Ligand-Fishing Strategy. Mar Drugs 2024; 22:244. [PMID: 38921555 PMCID: PMC11205194 DOI: 10.3390/md22060244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Brown seaweeds of the Fucus genus represent a rich source of natural antiviral products. In this study, a Fucus ceranoides hydroalcoholic extract (FCHE) was found to inhibit 74.2 ± 1.3% of the proteolytic activity of the free SARS-CoV-2 3CL protease (3CLpro), an enzyme that plays a pivotal role in polyprotein processing during coronavirus replication and has been identified as a relevant drug discovery target for SARS- and MERS-CoVs infections. To purify and identify 3CLpro ligands with potential inhibitory activity using a one-step approach, we immobilized the enzyme onto magnetic microbeads (3CLpro-MPs), checked that the enzymatic activity was maintained after grafting, and used this bait for a ligand-fishing strategy followed by a high-resolution mass spectrometry analysis of the fished-out molecules. Proof of concept for the ligand-fishing capacity of the 3CLpro-MPs was demonstrated by doping the FCHE extract with the substrate peptide TSAVLQ-pNA, resulting in the preferential capture of this high-affinity peptide within the macroalgal complex matrix. Ligand fishing in the FCHE alone led to the purification and identification via high-resolution mass spectrometry (HRMS) of seven hepta-, octa-, and decapeptides in an eluate mix that significantly inhibited the free 3CLpro more than the starting FCHE (82.7 ± 2.2% inhibition). Molecular docking simulations of the interaction between each of the seven peptides and the 3CLpro demonstrated a high affinity for the enzyme's proteolytic active site surpassing that of the most affine peptide ligand identified so far (a co-crystallographic peptide). Testing of the corresponding synthetic peptides demonstrated that four out of seven significantly inhibited the free 3CLpro (from 46.9 ± 6.4 to 76.8 ± 3.6% inhibition at 10 µM). This study is the first report identifying peptides from Fucus ceranoides with high inhibitory activity against the SARS-CoV-2 3CLprotease which bind with high affinity to the protease's active site. It also confirms the effectiveness of the ligand-fishing strategy for the single-step purification of enzyme inhibitors from complex seaweed matrices.
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Affiliation(s)
| | - Cintia Emi Yanaguibashi Leal
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Université de Picardie Jules Verne, 80039 Amiens, France;
| | - Pierre-Edouard Bodet
- Plateforme D’analyse Haute Résolution des Biomolécules, UMR CNRS 7266 LIENSs, La Rochelle Université, 17042 La Rochelle, France;
| | | | | | - Manon Porta Zapata
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Oussama Achour
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Hugo Groult
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Carlos Arthur Gouveia Veloso
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Claudio Viegas Júnior
- Institute of Chemistry, Federal University of Alfenas, Alfenas 37130-000, MG, Brazil;
| | - Nathalie Bourgougnon
- Laboratoire de Biotechnologie et Chimie Marines, LBCM, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56000 Vannes, France;
| | - Laurent Picot
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
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Castanha PMS, McEnaney PJ, Park Y, Bouwer A, Chaves EJF, Lins RD, Paciaroni NG, Dickson P, Carlson G, Cordeiro MT, Magalhaes T, Craigo J, Marques ETA, Kodadek T, Burke DS. Identification and characterization of a nonbiological small-molecular mimic of a Zika virus conformational neutralizing epitope. Proc Natl Acad Sci U S A 2024; 121:e2312755121. [PMID: 38743628 PMCID: PMC11127016 DOI: 10.1073/pnas.2312755121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 03/26/2024] [Indexed: 05/16/2024] Open
Abstract
Antigenic similarities between Zika virus (ZIKV) and other flaviviruses pose challenges to the development of virus-specific diagnostic tools and effective vaccines. Starting with a DNA-encoded one-bead-one-compound combinatorial library of 508,032 synthetic, non-natural oligomers, we selected and characterized small molecules that mimic ZIKV epitopes. High-throughput fluorescence-activated cell sorter-based bead screening was used to select molecules that bound IgG from ZIKV-immune but not from dengue-immune sera. Deep sequencing of the DNA from the "Zika-only" beads identified 40 candidate molecular structures. A lead candidate small molecule "CZV1-1" was selected that correctly identifies serum specimens from Zika-experienced patients with good sensitivity and specificity (85.3% and 98.4%, respectively). Binding competition studies of purified anti-CZV1-1 IgG against known ZIKV-specific monoclonal antibodies (mAbs) showed that CZV1-1 mimics a nonlinear, neutralizing conformational epitope in the domain III of the ZIKV envelope. Purified anti-CZV1-1 IgG neutralized infection of ZIKV in cell cultures with potencies comparable to highly specific ZIKV-neutralizing mAbs. This study demonstrates an innovative approach for identification of synthetic non-natural molecular mimics of conformational virus epitopes. Such molecular mimics may have value in the development of accurate diagnostic assays for Zika, as well as for other viruses.
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Affiliation(s)
- Priscila M. S. Castanha
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
| | - Patrick J. McEnaney
- Department of Chemistry, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL33458
| | - Yongseok Park
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
| | - Anthea Bouwer
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA15219
| | - Elton J. F. Chaves
- Department of Virology, Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Cidade Universitearia, Recife, Pernambuco50740-465, Brazil
| | - Roberto D. Lins
- Department of Virology, Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Cidade Universitearia, Recife, Pernambuco50740-465, Brazil
| | | | - Paige Dickson
- Department of Chemistry, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL33458
| | | | - Marli T. Cordeiro
- Department of Virology, Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Cidade Universitearia, Recife, Pernambuco50740-465, Brazil
| | - Tereza Magalhaes
- Department of Entomology, Texas A&M University, College Station, TX77843
- Department of Preventive and Social Medicine, School of Medicine, Universidade Federal da Bahia, Bahia40026-010, Brazil
| | - Jodi Craigo
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA15219
| | - Ernesto T. A. Marques
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
- Department of Virology, Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Cidade Universitearia, Recife, Pernambuco50740-465, Brazil
| | - Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL33458
| | - Donald S. Burke
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
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Kelly G, Kataura T, Panek J, Ma G, Salmonowicz H, Davis A, Kendall H, Brookes C, Ayine-Tora DM, Banks P, Nelson G, Dobby L, Pitrez PR, Booth L, Costello L, Richardson GD, Lovat P, Przyborski S, Ferreira L, Greaves L, Szczepanowska K, von Zglinicki T, Miwa S, Brown M, Flagler M, Oblong JE, Bascom CC, Carroll B, Reynisson J, Korolchuk VI. Suppressed basal mitophagy drives cellular aging phenotypes that can be reversed by a p62-targeting small molecule. Dev Cell 2024:S1534-5807(24)00295-8. [PMID: 38897197 DOI: 10.1016/j.devcel.2024.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/25/2023] [Accepted: 04/28/2024] [Indexed: 06/21/2024]
Abstract
Selective degradation of damaged mitochondria by autophagy (mitophagy) is proposed to play an important role in cellular homeostasis. However, the molecular mechanisms and the requirement of mitochondrial quality control by mitophagy for cellular physiology are poorly understood. Here, we demonstrated that primary human cells maintain highly active basal mitophagy initiated by mitochondrial superoxide signaling. Mitophagy was found to be mediated by PINK1/Parkin-dependent pathway involving p62 as a selective autophagy receptor (SAR). Importantly, this pathway was suppressed upon the induction of cellular senescence and in naturally aged cells, leading to a robust shutdown of mitophagy. Inhibition of mitophagy in proliferating cells was sufficient to trigger the senescence program, while reactivation of mitophagy was necessary for the anti-senescence effects of NAD precursors or rapamycin. Furthermore, reactivation of mitophagy by a p62-targeting small molecule rescued markers of cellular aging, which establishes mitochondrial quality control as a promising target for anti-aging interventions.
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Affiliation(s)
- George Kelly
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Tetsushi Kataura
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK; Department of Neurology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Johan Panek
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Gailing Ma
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Hanna Salmonowicz
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Ashley Davis
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Hannah Kendall
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Charlotte Brookes
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | | | - Peter Banks
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Glyn Nelson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Laura Dobby
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Patricia R Pitrez
- FMUC - Faculty of Medicine, Pólo das Ciências da Saúde, Unidade Central Azinhaga de Santa Comba, Coimbra 3000-354, Portugal
| | - Laura Booth
- Translation and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lydia Costello
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Gavin D Richardson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Penny Lovat
- Precision Medicine, Translation and Clinical Research Institute, Newcastle University Centre for Cancer, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | | | - Lino Ferreira
- FMUC - Faculty of Medicine, Pólo das Ciências da Saúde, Unidade Central Azinhaga de Santa Comba, Coimbra 3000-354, Portugal
| | - Laura Greaves
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Karolina Szczepanowska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Thomas von Zglinicki
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Satomi Miwa
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK
| | - Max Brown
- The Procter & Gamble Company, Cincinnati, OH 45040, USA
| | | | - John E Oblong
- The Procter & Gamble Company, Cincinnati, OH 45040, USA
| | | | | | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Newcastle under Lyme ST5 5BG, UK
| | - Viktor I Korolchuk
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, UK.
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48
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Tamarit L, El Ouardi M, Lence E, Andreu I, González-Bello C, Miranda MA, Vayá I. Modulation of the photobehavior of gefitinib and its phenolic metabolites by human transport proteins. Front Pharmacol 2024; 15:1387057. [PMID: 38818381 PMCID: PMC11137198 DOI: 10.3389/fphar.2024.1387057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
The photobiological damage that certain drugs or their metabolites can photosensitize in proteins is generally associated with the nature of the excited species that are generated upon interaction with UVA light. In this regard, the photoinduced damage of the anticancer drug gefitinib (GFT) and its two main photoactive metabolites GFT-M1 and GFT-M2 in cellular milieu was recently investigated. With this background, the photophysical properties of both the drug and its metabolites have now been studied in the presence of the two main transport proteins of human plasma, i.e., serum albumin (HSA) and α1-acid glycoprotein (HAG) upon UVA light excitation. In general, the observed photobehavior was strongly affected by the confined environment provided by the protein. Thus, GFT-M1 (which exhibits the highest phototoxicity) showed the highest fluorescence yield arising from long-lived HSA-bound phenolate-like excited species. Conversely, locally excited (LE) states were formed within HAG, resulting in lower fluorescence yields. The reserve was true for GFT-M2, which despite being also a phenol, led mainly to formation of LE states within HSA, and phenolate-like species (with a minor contribution of LE) inside HAG. Finally, the parent drug GFT, which is known to form LE states within HSA, exhibited a parallel behavior in the two proteins. In addition, determination of the association constants by both absorption and emission spectroscopy revealed that the two metabolites bind stronger to HSA than the parent drug, whereas smaller differences were observed for HAG. This was further confirmed by studying the competing interactions between GFT or its metabolites with the two proteins using fluorescence measurements. These above experimental findings were satisfactorily correlated with the results obtained by means of molecular dynamics (MD) simulations, which revealed the high affinity binding sites, the strength of interactions and the involved amino acid residues. In general, the differences observed in the photobehavior of the drug and its two photoactive metabolites in protein media are consistent with their relative photosensitizing potentials.
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Affiliation(s)
- Lorena Tamarit
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Valencia, Spain
- Unidad Mixta de Investigación UPV-IISLaFe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Meryem El Ouardi
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Valencia, Spain
- Unidad Mixta de Investigación UPV-IISLaFe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inmaculada Andreu
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Valencia, Spain
- Unidad Mixta de Investigación UPV-IISLaFe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Concepcion González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel A. Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Valencia, Spain
- Unidad Mixta de Investigación UPV-IISLaFe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Ignacio Vayá
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Valencia, Spain
- Unidad Mixta de Investigación UPV-IISLaFe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
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49
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Chuntakaruk H, Boonpalit K, Kinchagawat J, Nakarin F, Khotavivattana T, Aonbangkhen C, Shigeta Y, Hengphasatporn K, Nutanong S, Rungrotmongkol T, Hannongbua S. Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery. J Comput Chem 2024; 45:953-968. [PMID: 38174739 DOI: 10.1002/jcc.27298] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
In the pursuit of novel antiretroviral therapies for human immunodeficiency virus type-1 (HIV-1) proteases (PRs), recent improvements in drug discovery have embraced machine learning (ML) techniques to guide the design process. This study employs ensemble learning models to identify crucial substructures as significant features for drug development. Using molecular docking techniques, a collection of 160 darunavir (DRV) analogs was designed based on these key substructures and subsequently screened using molecular docking techniques. Chemical structures with high fitness scores were selected, combined, and one-dimensional (1D) screening based on beyond Lipinski's rule of five (bRo5) and ADME (absorption, distribution, metabolism, and excretion) prediction implemented in the Combined Analog generator Tool (CAT) program. A total of 473 screened analogs were subjected to docking analysis through convolutional neural networks scoring function against both the wild-type (WT) and 12 major mutated PRs. DRV analogs with negative changes in binding free energy (ΔΔ G bind ) compared to DRV could be categorized into four attractive groups based on their interactions with the majority of vital PRs. The analysis of interaction profiles revealed that potent designed analogs, targeting both WT and mutant PRs, exhibited interactions with common key amino acid residues. This observation further confirms that the ML model-guided approach effectively identified the substructures that play a crucial role in potent analogs. It is expected to function as a powerful computational tool, offering valuable guidance in the identification of chemical substructures for synthesis and subsequent experimental testing.
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Affiliation(s)
- Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Kajjana Boonpalit
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jiramet Kinchagawat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Fahsai Nakarin
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | | | - Sarana Nutanong
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Supot Hannongbua
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Chemistry, Faculty of Science, Center of Excellence in Computational Chemistry (CECC), Chulalongkorn University, Bangkok, Thailand
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50
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Pisanu F, Sykula A, Sciortino G, Maseras F, Lodyga-Chruscinska E, Garribba E. Experimental and Computational Studies on the Interaction of DNA with Hesperetin Schiff Base Cu II Complexes. Int J Mol Sci 2024; 25:5283. [PMID: 38791321 PMCID: PMC11121494 DOI: 10.3390/ijms25105283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The interactions with calf thymus DNA (CT-DNA) of three Schiff bases formed by the condensation of hesperetin with benzohydrazide (HHSB or L1H3), isoniazid (HIN or L2H3), or thiosemicarbazide (HTSC or L3H3) and their CuII complexes (CuHHSB, CuHIN, and CuHTSC with the general formula [CuLnH2(AcO)]) were evaluated in aqueous solution both experimentally and theoretically. UV-Vis studies indicate that the ligands and complexes exhibit hypochromism, which suggests helical ordering in the DNA helix. The intrinsic binding constants (Kb) of the Cu compounds with CT-DNA, in the range (2.3-9.2) × 106, from CuHTSC to CuHHSB, were higher than other copper-based potential drugs, suggesting that π-π stacking interaction due to the presence of the aromatic rings favors the binding. Thiazole orange (TO) assays confirmed that ligands and Cu complexes displace TO from the DNA binding site, quenching the fluorescence emission. DFT calculations allow for an assessment of the equilibrium between [Cu(LnH2)(AcO)] and [Cu(LnH2)(H2O)]+, the tautomer that binds CuII, amido (am) and not imido (im), and the coordination mode of HTSC (O-, N, S), instead of (O-, N, NH2). The docking studies indicate that the intercalative is preferred over the minor groove binding to CT-DNA with the order [Cu(L1H2am)(AcO)] > [Cu(L2H2am)(AcO)] ≈ TO ≈ L1H3 > [Cu(L3H2am)(AcO)], in line with the experimental Kb constants, obtained from the UV-Vis spectroscopy. Moreover, dockings predict that the binding strength of [Cu(L1H2am)(AcO)] is larger than [Cu(L1H2am)(H2O)]+. Overall, the results suggest that when different enantiomers, tautomers, and donor sets are possible for a metal complex, a computational approach should be recommended to predict the type and strength of binding to DNA and, in general, to macromolecules.
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Affiliation(s)
- Federico Pisanu
- Dipartimento di Medicina, Chirurgia e Farmacia, Università di Sassari, Viale San Pietro, I-07100 Sassari, Italy;
| | - Anna Sykula
- Faculty of Biotechnology and Food Sciences, Institute of Natural Products and Cosmetics, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland; (A.S.); (E.L.-C.)
| | - Giuseppe Sciortino
- Department de Química, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193 Barcelona, Spain;
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), 43007 Tarragona, Spain;
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), 43007 Tarragona, Spain;
| | - Elzbieta Lodyga-Chruscinska
- Faculty of Biotechnology and Food Sciences, Institute of Natural Products and Cosmetics, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland; (A.S.); (E.L.-C.)
| | - Eugenio Garribba
- Dipartimento di Medicina, Chirurgia e Farmacia, Università di Sassari, Viale San Pietro, I-07100 Sassari, Italy;
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