1
|
Galvez-Llompart M, Hierrezuelo J, Blasco M, Zanni R, Galvez J, de Vicente A, Pérez-García A, Romero D. Targeting bacterial growth in biofilm conditions: rational design of novel inhibitors to mitigate clinical and food contamination using QSAR. J Enzyme Inhib Med Chem 2024; 39:2330907. [PMID: 38651823 DOI: 10.1080/14756366.2024.2330907] [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: 10/25/2023] [Accepted: 03/06/2024] [Indexed: 04/25/2024] Open
Abstract
Antimicrobial resistance (AMR) is a pressing global issue exacerbated by the abuse of antibiotics and the formation of bacterial biofilms, which cause up to 80% of human bacterial infections. This study presents a computational strategy to address AMR by developing three novel quantitative structure-activity relationship (QSAR) models based on molecular topology to identify potential anti-biofilm and antibacterial agents. The models aim to determine the chemo-topological pattern of Gram (+) antibacterial, Gram (-) antibacterial, and biofilm formation inhibition activity. The models were applied to the virtual screening of a commercial chemical database, resulting in the selection of 58 compounds. Subsequent in vitro assays showed that three of these compounds exhibited the most promising antibacterial activity, with potential applications in enhancing food and medical device safety.
Collapse
Affiliation(s)
- Maria Galvez-Llompart
- Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
- Department of Physical Chemistry, University of Valencia, Burjassot, Spain
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Jesús Hierrezuelo
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Mariluz Blasco
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Riccardo Zanni
- Department of Physical Chemistry, University of Valencia, Burjassot, Spain
| | - Jorge Galvez
- Department of Physical Chemistry, University of Valencia, Burjassot, Spain
| | - Antonio de Vicente
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Alejandro Pérez-García
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Diego Romero
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| |
Collapse
|
2
|
Mapuranga J, Chang J, Li H, Zhang Y, Li R, Song L, Zhang N, Yang W. The molecular structure, biological roles, and inhibition of plant pathogenic fungal chitin deacetylases. FRONTIERS IN PLANT SCIENCE 2024; 14:1335646. [PMID: 38264029 PMCID: PMC10803567 DOI: 10.3389/fpls.2023.1335646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
Chitin/polysaccharide deacetylases belong to the carbohydrate esterases family 4 (CE4 enzymes). They play a crucial role in modifying the physiochemical characteristics of structural polysaccharides and are also involved in a wide range of biological processes such as fungal autolysis, spore formation, cell wall formation and integrity, and germling adhesion. These enzymes are mostly common in fungi, marine bacteria, and a limited number of insects. They facilitate the deacetylation of chitin which is a structural biopolymer that is abundantly found in fungal cell walls and spores and also in the cuticle and peritrophic matrices of insects. The deacetylases exhibit specificity towards a substrate containing a sequence of four GlcNAc units, with one of these units being subjected to deacetylation. Chitin deacetylation results in the formation of chitosan, which is a poor substrate for host plant chitinases, therefore it can suppress the host immune response triggered by fungal pathogens and enhance pathogen virulence and colonization. This review discusses plant pathogenic fungal chitin/polysaccharide deacetylases including their structure, substrate specificity, biological roles and some recently discovered chitin deacetylase inhibitors that can help to mitigate plant fungal diseases. This review provides fundamental knowledge that will undoubtedly lead to the rational design of novel inhibitors that target pathogenic fungal chitin deacetylases, which will also aid in the management of plant diseases, thereby safeguarding global food security.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Wenxiang Yang
- College of Plant Protection, Technological Innovation Center for Biological Control of Plant Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| |
Collapse
|
3
|
Antypenko L, Antypenko O, Karnaukh I, Rebets O, Kovalenko S, Arisawa M. 5,6-Dihydrotetrazolo[1,5-c]quinazolines: Toxicity prediction, synthesis, antimicrobial activity, molecular docking, and perspectives. Arch Pharm (Weinheim) 2023. [PMID: 36864600 DOI: 10.1002/ardp.202300029] [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: 03/04/2023]
Abstract
Antimicrobial resistance is a never-ending challenge, which should be considered seriously, especially when using unprescribed "over-the-counter" drugs. The synthesis and investigation of novel biologically active substances is among the directions to overcome this problem. Hence, 18 novel 5,6-dihydrotetrazolo[1,5-c]quinazolines were synthesized, their identity, purity, and structure were elucidated by elemental analysis, IR, LC-MS, 1 Н, and 13 C NMR spectra. According to the computational estimation, 15 substances were found to be of toxicity Class V, two of Class IV, and only one of Class II. The in vitro serial dilution method of antimicrobial screening against Escherichia coli, Staphylococcus aureus, Klebsiella aerogenes, Pseudomonas aeruginosa, and Candida albicans determined b3, c1, c6, and c10 as the "lead-compounds" for further modifications to increase the level of activity. Substance b3 demonstrated antibacterial activity that can be related to the calculated high affinity toward all studied proteins: 50S ribosomal protein L19 (PDB ID: 6WQN), sterol 14-alpha demethylase (PDB ID: 5TZ1), and ras-related protein Rab-9A (PDB ID: 1WMS). The structure-activity and structure-target affinity relationships are discussed. The targets for further investigations and the anatomical therapeutic chemical codes of drug similarity are predicted.
Collapse
Affiliation(s)
- Lyudmyla Antypenko
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Oleksii Antypenko
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Zaporizhzhia State Medical University, Zaporizhzhia, Ukraine
| | - Iryna Karnaukh
- Bacteriological Laboratory, Zaporizhzhia Regional Hospital, Zaporizhzhia, Ukraine
| | - Oksana Rebets
- Bacteriological Laboratory, Zaporizhzhia Regional Hospital, Zaporizhzhia, Ukraine
| | - Sergiy Kovalenko
- Research Institute of Chemistry and Geology, Oles Honchar Dnipro National University, Dnipro, Ukraine
| | - Mieko Arisawa
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| |
Collapse
|
4
|
Ravi V, Desikan K. Curvilinear regression analysis of benzenoid hydrocarbons and computation of some reduced reverse degree based topological indices for hyaluronic acid-paclitaxel conjugates. Sci Rep 2023; 13:3239. [PMID: 36828838 PMCID: PMC9958057 DOI: 10.1038/s41598-023-28416-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 01/18/2023] [Indexed: 02/26/2023] Open
Abstract
Graph theoretical molecular descriptors alias topological indices are a convenient means for expressing in numerical form the chemical structure encoded in a molecular graph. The structure descriptors derived from molecular graphs are widely used in quantitative structure-property relationship (QSPR) and quantitative structure-activity relationship (QSAR) studies. The reason for introducing new indices is to obtain predictions of target properties of considered molecules that are better than the predictions obtained using already known indices. In this paper, we apply the reduced reverse degree based indices introduced in 2021 by Vignesh et al. In the QSPR analysis, we first compute the reduced reverse degree based indices for a family of benzenoid hydrocarbon molecules and then we obtain the correlation with the Physico-chemical properties of the considered molecules. We show that all the properties taken into consideration for the benzenoid hydrocarbons can be very effectively predicted by the reduced reverse degree based indices. Also, we have compared the predictive capability of reduced reverse degree based topological descriptors against 16 existing degree based indices. Further, we compute the defined reduced reverse degree based topological indices for Hyaluronic Acid-Paclitaxel Conjugates [Formula: see text], [Formula: see text].
Collapse
Affiliation(s)
- Vignesh Ravi
- grid.412813.d0000 0001 0687 4946Division of Mathematics, School of Advanced Sciences, Vellore Institute of Technology, Chennai, India
| | - Kalyani Desikan
- Division of Mathematics, School of Advanced Sciences, Vellore Institute of Technology, Chennai, India.
| |
Collapse
|
5
|
Combined Application of Tacrolimus with Cyproconazole, Hymexazol and Novel {2-(3-R-1 H-1,2,4-triazol-5-yl)phenyl}amines as Antifungals: In Vitro Growth Inhibition and In Silico Molecular Docking Analysis to Fungal Chitin Deacetylase. J Fungi (Basel) 2023; 9:jof9010079. [PMID: 36675900 PMCID: PMC9866229 DOI: 10.3390/jof9010079] [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: 12/10/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Agents with antifungal activity play a vital role as therapeutics in health care, as do fungicides in agriculture. Effectiveness, toxicological profile, and eco-friendliness are among the properties used to select suitable substances. Furthermore, a steady supply of new agents with different modes of action is required to counter the well-known potential of human and phyto-pathogenic fungi to develop resistance against established antifungals. Here, we use an in vitro growth assay to investigate the activity of the calcineurin inhibitor tacrolimus in combination with the commercial fungicides cyproconazole and hymexazol, as well as with two earlier reported novel {2-(3-R-1H-1,2,4-triazol-5-yl)phenyl}amines, against the fungi Aspergillus niger, Colletotrichum higginsianum, Fusarium oxysporum and the oomycete Phytophthora infestans, which are notoriously harmful in agriculture. When tacrolimus was added in a concentration range from 0.25 to 25 mg/L to the tested antifungals (at a fixed concentration of 25 or 50 mg/L), the inhibitory activities were distinctly enhanced. Molecular docking calculations revealed triazole derivative 5, (2-(3-adamantan-1-yl)-1H-1,2,4-triazol-5-yl)-4-chloroaniline), as a potent inhibitor of chitin deacetylases (CDA) of Aspergillus nidulans and A. niger (AnCDA and AngCDA, respectively), which was stronger than the previously reported polyoxorin D, J075-4187, and chitotriose. The results are discussed in the context of potential synergism and molecular mode of action.
Collapse
|
6
|
Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [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: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
Collapse
Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| |
Collapse
|
7
|
Zanni R, Martínez-Cruz J, Gálvez-Llompart M, Fernández-Ortuño D, Romero D, García-Domènech R, Pérez-García A, Gálvez J. Rational Design of Chitin Deacetylase Inhibitors for Sustainable Agricultural Use Based on Molecular Topology. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13118-13131. [PMID: 36194443 PMCID: PMC10389753 DOI: 10.1021/acs.jafc.2c02377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fungicide resistance is a major concern in modern agriculture; therefore, there is a pressing demand to develop new, greener chemicals. Chitin is a major component of the fungal cell wall and a well-known elicitor of plant immunity. To overcome chitin recognition, fungal pathogens developed different strategies, with chitin deacetylase (CDA) activity being the most conserved. This enzyme is responsible for hydrolyzing the N-acetamido group in N-acetylglucosamine units of chitin to convert it to chitosan, a compound that can no longer be recognized by the plant. In previous works, we observed that treatments with CDA inhibitors, such as carboxylic acids, reduced the symptoms of cucurbit powdery mildew and induced rapid activation of chitin-triggered immunity, indicating that CDA could be an interesting target for fungicide development. In this work, we developed an in silico strategy based on QSAR (quantitative structure-activity relationship) and molecular topology (MT) to discover new, specific, and potent CAD inhibitors. Starting with the chemical structures of few carboxylic acids, with and without disease control activity, three predictive equations based on the MT paradigm were developed to identify a group of potential molecules. Their fungicidal activity was experimentally tested, and their specificity as CDA inhibitors was studied for the three best candidates by molecular docking simulations. To our knowledge, this is the first time that MT has been used for the identification of potential CDA inhibitors to be used against resistant powdery mildew strains. In this sense, we consider of special interest the discovery of molecules capable of stimulating the immune system of plants by triggering a defensive response against fungal species that are highly resistant to fungicides such as powdery mildew.
Collapse
Affiliation(s)
- Riccardo Zanni
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010Valencia, Spain
| | - Jesús Martínez-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga29071, Spain
| | - María Gálvez-Llompart
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010Valencia, Spain
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga29071, Spain
| | - Diego Romero
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga29071, Spain
| | - Ramón García-Domènech
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010Valencia, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga29071, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga29071, Spain
| | - Jorge Gálvez
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010Valencia, Spain
| |
Collapse
|
8
|
Galvez-Llompart M, Zanni R, Galvez J, Basak SC, Goyal SM. COVID-19 and the Importance of Being Prepared: A Multidisciplinary Strategy for the Discovery of Antivirals to Combat Pandemics. Biomedicines 2022; 10:biomedicines10061342. [PMID: 35740363 PMCID: PMC9220014 DOI: 10.3390/biomedicines10061342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 12/21/2022] Open
Abstract
During an emergency, such as a pandemic in which time and resources are extremely scarce, it is important to find effective and rapid solutions when searching for possible treatments. One possibility in this regard is the repurposing of available “on the market” drugs. This is a proof of the concept study showing the potential of a collaboration between two research groups, engaged in computer-aided drug design and control of viral infections, for the development of early strategies to combat future pandemics. We describe a QSAR (quantitative structure activity relationship) based repurposing study on molecular topology and molecular docking for identifying inhibitors of the main protease (Mpro) of SARS-CoV-2, the causative agent of COVID-19. The aim of this computational strategy was to create an agile, rapid, and efficient way to enable the selection of molecules capable of inhibiting SARS-CoV-2 protease. Molecules selected through in silico method were tested in vitro using human coronavirus 229E as a surrogate for SARS-CoV-2. Three strategies were used to screen the antiviral activity of these molecules against human coronavirus 229E in cell cultures, e.g., pre-treatment, co-treatment, and post-treatment. We found >99% of virus inhibition during pre-treatment and co-treatment and 90−99% inhibition when the molecules were applied post-treatment (after infection with the virus). From all tested compounds, Molport-046-067-769 and Molport-046-568-802 are here reported for the first time as potential anti-SARS-CoV-2 compounds.
Collapse
Affiliation(s)
- Maria Galvez-Llompart
- Molecular Topology & Drug Design Research Unit, Department of Physical Chemistry, University of Valencia, 46100 Burjasot, Spain; (R.Z.); (J.G.)
- Correspondence: ; Tel.: +34-963544891
| | - Riccardo Zanni
- Molecular Topology & Drug Design Research Unit, Department of Physical Chemistry, University of Valencia, 46100 Burjasot, Spain; (R.Z.); (J.G.)
| | - Jorge Galvez
- Molecular Topology & Drug Design Research Unit, Department of Physical Chemistry, University of Valencia, 46100 Burjasot, Spain; (R.Z.); (J.G.)
| | - Subhash C. Basak
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, MN 55812, USA;
| | - Sagar M. Goyal
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA;
| |
Collapse
|
9
|
How Molecular Topology Can Help in Amyotrophic Lateral Sclerosis (ALS) Drug Development: A Revolutionary Paradigm for a Merciless Disease. Pharmaceuticals (Basel) 2022; 15:ph15010094. [PMID: 35056151 PMCID: PMC8781553 DOI: 10.3390/ph15010094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Even if amyotrophic lateral sclerosis is still considered an orphan disease to date, its prevalence among the population is growing fast. Despite the efforts made by researchers and pharmaceutical companies, the cryptic information related to the biological and physiological onset mechanisms, as well as the complexity in identifying specific pharmacological targets, make it almost impossible to find effective treatments. Furthermore, because of complex ethical and economic aspects, it is usually hard to find all the necessary resources when searching for drugs for new orphan diseases. In this context, computational methods, based either on receptors or ligands, share the capability to improve the success rate when searching and selecting potential candidates for further experimentation and, consequently, reduce the number of resources and time taken when delivering a new drug to the market. In the present work, a computational strategy based on Molecular Topology, a mathematical paradigm capable of relating the chemical structure of a molecule to a specific biological or pharmacological property by means of numbers, is presented. The result was the creation of a reliable and accessible tool to help during the early in silico stages in the identification and repositioning of potential hits for ALS treatment, which can also apply to other orphan diseases. Considering that further computational and experimental results will be required for the final identification of viable hits, three linear discriminant equations combined with molecular docking simulations on specific proteins involved in ALS are reported, along with virtual screening of the Drugbank database as a practical example. In this particular case, as reported, a clinical trial has been already started for one of the drugs proposed in the present study.
Collapse
|
10
|
Chen N, Yang L, Ding N, Li G, Cai J, An X, Wang Z, Qin J, Niu Y. Recurrent neural network (RNN) model accelerates the development of antibacterial metronidazole derivatives. RSC Adv 2022; 12:22893-22901. [PMID: 36105994 PMCID: PMC9377161 DOI: 10.1039/d2ra01807a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Metronidazole is a specific drug against trichomonas and anaerobic bacteria, and is widely used in the clinic. However, extensive clinical application is often accompanied by extensive side effects, so it is still of great significance to develop metronidazole derivatives with a new skeleton. Compared with other traditional receptor-based drug design methods, the computational model based on a neural network has higher accuracy and reliability. In this work, a Recurrent Neural Network (RNN) model is applied to the discovery of metronidazole drugs with a new skeleton. Firstly, the generation model based on a Gated Recurrent Unit (GRU) is trained to generate an effective Simplified Molecular-Input Line-Entry System (SMILES) string library with high precision. Then, transfer learning is introduced to fine-tune the GRU model, and many molecules with structures similar to known active drugs are generated. After cluster analysis of the structures of the new compounds, 20 small molecular compounds with metronidazole structures of all different categories were selected, of which 19 may not belong to any published patents or applications. Through prediction and personal experience, the difficulty of synthesizing these 20 new structures was analyzed, and compound 0001 was chosen as our synthetic target, and a series of structures (8a–l) similar to compound 0001 were synthesized. Finally, the inhibitory activities of these compounds against bacteria E. coli, P. aeruginosa, B. subtilis and S. aureus were determined. The results showed that compound 8a–l had obvious inhibitory activity against these four bacteria, which proved the accuracy of our compound generation model. Generating antibacterial metronidazole derivatives using a recurrent neural network model.![]()
Collapse
Affiliation(s)
- Nannan Chen
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049 Shandong, China
| | - Lijuan Yang
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou, 730000 Gansu, China
- School of Physics and Technology, Lanzhou University, Lanzhou 730000, China
| | - Na Ding
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049 Shandong, China
| | - Guiwen Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049 Shandong, China
| | - Jiajing Cai
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049 Shandong, China
| | - Xiaoli An
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou, 730000 Gansu, China
| | - Zhijie Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049 Shandong, China
| | - Jie Qin
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049 Shandong, China
| | - Yuzhen Niu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049 Shandong, China
| |
Collapse
|
11
|
Martínez-Cruz JM, Polonio Á, Zanni R, Romero D, Gálvez J, Fernández-Ortuño D, Pérez-García A. Chitin Deacetylase, a Novel Target for the Design of Agricultural Fungicides. J Fungi (Basel) 2021; 7:jof7121009. [PMID: 34946992 PMCID: PMC8706340 DOI: 10.3390/jof7121009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/23/2022] Open
Abstract
Fungicide resistance is a serious problem for agriculture. This is particularly apparent in the case of powdery mildew fungi. Therefore, there is an urgent need to develop new agrochemicals. Chitin is a well-known elicitor of plant immunity, and fungal pathogens have evolved strategies to overcome its detection. Among these strategies, chitin deacetylase (CDA) is responsible for modifying immunogenic chitooligomers and hydrolysing the acetamido group in the N-acetylglucosamine units to avoid recognition. In this work, we tested the hypothesis that CDA can be an appropriate target for antifungals using the cucurbit powdery mildew pathogen Podosphaera xanthii. According to our hypothesis, RNAi silencing of PxCDA resulted in a dramatic reduction in fungal growth that was linked to a rapid elicitation of chitin-triggered immunity. Similar results were obtained with treatments with carboxylic acids such as EDTA, a well-known CDA inhibitor. The disease-suppression activity of EDTA was not associated with its chelating activity since other chelating agents did not suppress disease. The binding of EDTA to CDA was confirmed by molecular docking studies. Furthermore, EDTA also suppressed green and grey mould-causing pathogens applied to oranges and strawberries, respectively. Our results conclusively show that CDA is a promising target for control of phytopathogenic fungi and that EDTA could be a starting point for fungicide design.
Collapse
Affiliation(s)
- Jesús M. Martínez-Cruz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
| | - Álvaro Polonio
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
| | - Riccardo Zanni
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010 Valencia, Spain; (R.Z.); (J.G.)
| | - Diego Romero
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
| | - Jorge Gálvez
- Molecular Topology and Drug Design Unit, Department of Physical Chemistry, University of Valencia, 46010 Valencia, Spain; (R.Z.); (J.G.)
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
- Correspondence:
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; (J.M.M.-C.); (Á.P.); (D.R.); (A.P.-G.)
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010 Málaga, Spain
| |
Collapse
|
12
|
Tong JB, Luo D, Bian S, Zhang X. Structural investigation of tetrahydropteridin analogues as selective PLK1 inhibitors for treating cancer through combined QSAR techniques, molecular docking, and molecular dynamics simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116235] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
13
|
Galvez-Llompart M, Ocello R, Rullo L, Stamatakos S, Alessandrini I, Zanni R, Tuñón I, Cavalli A, Candeletti S, Masetti M, Romualdi P, Recanatini M. Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach. J Chem Inf Model 2021; 61:3091-3108. [PMID: 33998810 PMCID: PMC8491162 DOI: 10.1021/acs.jcim.0c01468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Janus kinases (JAKs) are a family of proinflammatory enzymes able to mediate the immune responses and the inflammatory cascade by modulating multiple cytokine expressions as well as various growth factors. In the present study, the inhibition of the JAK-signal transducer and activator of transcription (STAT) signaling pathway is explored as a potential strategy for treating autoimmune and inflammatory disorders. A computationally driven approach aimed at identifying novel JAK inhibitors based on molecular topology, docking, and molecular dynamics simulations was carried out. For the best candidates selected, the inhibitory activity against JAK2 was evaluated in vitro. Two hit compounds with a novel chemical scaffold, 4 (IC50 = 0.81 μM) and 7 (IC50 = 0.64 μM), showed promising results when compared with the reference drug Tofacitinib (IC50 = 0.031 μM).
Collapse
Affiliation(s)
- Maria Galvez-Llompart
- Department of Physical Chemistry, University of Valencia, Av. Vicente Estelles s/n, 46100 Burjassot (Valencia), Spain.,Instituto de Tecnología Química (UPV-CSIC) Universidad Politécnica de Valencia Av. Naranjos s/n, 46022 Valencia, Spain
| | - Riccardo Ocello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Laura Rullo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Serena Stamatakos
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Irene Alessandrini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Riccardo Zanni
- Department of Physical Chemistry, University of Valencia, Av. Vicente Estelles s/n, 46100 Burjassot (Valencia), Spain
| | - Iñaki Tuñón
- Department of Physical Chemistry, University of Valencia, Av. Vicente Estelles s/n, 46100 Burjassot (Valencia), Spain
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy.,Italian Institute of Technology (IIT), Via Morego 30, 16163 Genoa, Italy
| | - Sanzio Candeletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Patrizia Romualdi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Maurizio Recanatini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| |
Collapse
|
14
|
Cai Y, Zhu W, Zhao S, Dong C, Xu Z, Zhao Y. Difluorocarbene-Mediated Cascade Cyclization: The Multifunctional Role of Ruppert-Prakash Reagent. Org Lett 2021; 23:3546-3551. [PMID: 33913711 DOI: 10.1021/acs.orglett.1c00962] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A difluorocarbene-mediated cascade cyclization reaction for rapid access to gem-difluorinated 3-coumaranone derivatives was developed. The difluorocarbene acts as a bipolar CF2 building block, which enables a homologation cyclization process via sequentially reacting with the phenolate and the ester group on the same substrate. The potential application of this synthetic approach is demonstrated by a late-stage modification of diethylstilbestrol. Mechanistic studies revealed the multiple crucial roles played by the Ruppert-Prakash reagent.
Collapse
Affiliation(s)
- Yanyao Cai
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Wenjie Zhu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Shujuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Chanjuan Dong
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| |
Collapse
|