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Cozzi M, Failla M, Gianquinto E, Kovachka S, Buoli Comani V, Compari C, De Bei O, Giaccari R, Marchesani F, Marchetti M, Ronda L, Rolando B, Baroni M, Cruciani G, Campanini B, Bettati S, Faggiano S, Lazzarato L, Spyrakis F. Identification of small molecules affecting the interaction between human hemoglobin and Staphylococcus aureus IsdB hemophore. Sci Rep 2024; 14:8272. [PMID: 38594253 PMCID: PMC11003968 DOI: 10.1038/s41598-024-55931-8] [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: 12/16/2023] [Accepted: 02/29/2024] [Indexed: 04/11/2024] Open
Abstract
Human hemoglobin (Hb) is the preferred iron source of Staphylococcus aureus. This pathogenic bacterium exploits a sophisticated protein machinery called Iron-regulated surface determinant (Isd) system to bind Hb, extract and internalize heme, and finally degrade it to complete iron acquisition. IsdB, the surface exposed Hb receptor, is a proven virulence factor of S. aureus and the inhibition of its interaction with Hb can be pursued as a strategy to develop new classes of antimicrobials. To identify small molecules able to disrupt IsdB:Hb protein-protein interactions (PPIs), we carried out a structure-based virtual screening campaign and developed an ad hoc immunoassay to screen the retrieved set of commercially available compounds. Saturation-transfer difference (STD) NMR was applied to verify specific interactions of a sub-set of molecules, chosen based on their efficacy in reducing the amount of Hb bound to IsdB. Among molecules for which direct binding was verified, the best hit was submitted to ITC analysis to measure the binding affinity to Hb, which was found to be in the low micromolar range. The results demonstrate the viability of the proposed in silico/in vitro experimental pipeline to discover and test IsdB:Hb PPI inhibitors. The identified lead compound will be the starting point for future SAR and molecule optimization campaigns.
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Affiliation(s)
- Monica Cozzi
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Sandra Kovachka
- Department of Drug Science and Technology, University of Turin, Turin, Italy
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | | | - Omar De Bei
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Barbara Rolando
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd, Kisnetic Business Centre, Elstree, Borehamwood, Hertfordshire, UK
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | | | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Institute of Biophysics, National Research Council, Pisa, Italy
| | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.
- Institute of Biophysics, National Research Council, Pisa, Italy.
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, Italy.
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Han N, Li X, Du J, Xu J, Guo L, Liu Y. The impacts of oral and gut microbiota on alveolar bone loss in periodontitis. J Periodontal Res 2023; 58:1139-1147. [PMID: 37712722 DOI: 10.1111/jre.13168] [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: 03/28/2023] [Revised: 06/12/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023]
Abstract
Periodontitis, a chronic infectious disease, primarily arises from infections and the invasion of periodontal pathogens. This condition is typified by alveolar bone loss resulting from host immune responses and inflammatory reactions. Periodontal pathogens trigger aberrant inflammatory reactions within periodontal tissues, thereby exacerbating the progression of periodontitis. Simultaneously, these pathogens and metabolites stimulate osteoclast differentiation, which leads to alveolar bone resorption. Moreover, a range of systemic diseases, including diabetes, postmenopausal osteoporosis, obesity and inflammatory bowel disease, can contribute to the development and progression of periodontitis. Many studies have underscored the pivotal role of gut microbiota in bone health through the gut-alveolar bone axis. The circulation may facilitate the transfer of gut pathogens or metabolites to distant alveolar bone, which in turn regulates bone homeostasis. Additionally, gut pathogens can elicit gut immune responses and direct immune cells to remote organs, potentially exacerbating periodontitis. This review summarizes the influence of oral microbiota on the development of periodontitis as well as the association between gut microbiota and periodontitis. By uncovering potential mechanisms of the gut-bone axis, this analysis provides novel insights for the targeted treatment of pathogenic bacteria in periodontitis.
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Affiliation(s)
- Nannan Han
- Laboratory of Tissue Regeneration and Immunology, Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiaoyan Li
- Laboratory of Tissue Regeneration and Immunology, Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Juan Du
- Laboratory of Tissue Regeneration and Immunology, Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Junji Xu
- Laboratory of Tissue Regeneration and Immunology, Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lijia Guo
- Department of Orthodontics School of Stomatology, Capital Medical University, Beijing, China
| | - Yi Liu
- Laboratory of Tissue Regeneration and Immunology, Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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3
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Demkovych A, Kalashnikov D, Hasiuk P, Zubchenko S, Vorobets A. The influence of microbiota on the development and course of inflammatory diseases of periodontal tissues. FRONTIERS IN ORAL HEALTH 2023; 4:1237448. [PMID: 37609105 PMCID: PMC10440822 DOI: 10.3389/froh.2023.1237448] [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: 06/16/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023] Open
Abstract
An important feature of the functioning of the organs and tissues of the oral cavity is the fact that all processes that take place in it are carried out in the constant presence of various microorganisms that cause the development of pathological processes in the body or are associated with them. In the pathogenesis of chronic generalized periodontitis, dental plaque penetrates the bottom of the gingival sulcus, penetrating under the epithelium into the stroma of the connective tissue, causing its inflammation. Bacteria produce a number of toxic substances that have a toxic effect on surrounding tissues. Most bacteria produce chain fatty acids that inhibit chemotaxis of leukocytes and phagocytes. Anaerobes and spirochetes secrete a number of substances (propionic acid and indole) that are extremely toxic to most tissues. Inflammation in the periodontal tissues is caused by the microbiota of the dental plaque biofilm. As periodontitis develops, an increase in the number of P. gingivalis, P. intermedia and T. forsythia was found in it, more than 100 times. Therefore, the given data prove that in the development and course of the inflammatory process in the periodontal tissues, complex dysbiotic and tissue-cellular interactions are involved, the dynamic balance of which depends on its outcome.
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Affiliation(s)
- Andrii Demkovych
- Department of Orthopedic Dentistry, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Dmytro Kalashnikov
- Department of Propaedeutics of Prosthetic Dentistry, Poltava State Medical University, Poltava, Ukraine
| | - Petro Hasiuk
- Department of Orthopedic Dentistry, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Sergiy Zubchenko
- Department of Propaedeutics of Prosthetic Dentistry, Poltava State Medical University, Poltava, Ukraine
| | - Anna Vorobets
- Department of Orthopedic Dentistry, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
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Kellogg GE, Marabotti A, Spyrakis F, Mozzarelli A. HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham. Front Mol Biosci 2023; 10:1194962. [PMID: 37351551 PMCID: PMC10282649 DOI: 10.3389/fmolb.2023.1194962] [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: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
A long-lasting goal of computational biochemists, medicinal chemists, and structural biologists has been the development of tools capable of deciphering the molecule-molecule interaction code that produces a rich variety of complex biomolecular assemblies comprised of the many different simple and biological molecules of life: water, small metabolites, cofactors, substrates, proteins, DNAs, and RNAs. Software applications that can mimic the interactions amongst all of these species, taking account of the laws of thermodynamics, would help gain information for understanding qualitatively and quantitatively key determinants contributing to the energetics of the bimolecular recognition process. This, in turn, would allow the design of novel compounds that might bind at the intermolecular interface by either preventing or reinforcing the recognition. HINT, hydropathic interaction, was a model and software code developed from a deceptively simple idea of Donald Abraham with the close collaboration with Glen Kellogg at Virginia Commonwealth University. HINT is based on a function that scores atom-atom interaction using LogP, the partition coefficient of any molecule between two phases; here, the solvents are water that mimics the cytoplasm milieu and octanol that mimics the protein internal hydropathic environment. This review summarizes the results of the extensive and successful collaboration between Abraham and Kellogg at VCU and the group at the University of Parma for testing HINT in a variety of different biomolecular interactions, from proteins with ligands to proteins with DNA.
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Affiliation(s)
- Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Anna Marabotti
- Department of Chemistry and Biology “A Zambelli”, University of Salerno, Fisciano (SA), Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma and Institute of Biophysics, Parma, Italy
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Banu Raza F, Vijayaragavalu S, Kandasamy R, Krishnaswami V, Kumar V A. Microbiome and the inflammatory pathway in peri-implant health and disease with an updated review on treatment strategies. J Oral Biol Craniofac Res 2023; 13:84-91. [PMID: 36504486 PMCID: PMC9730223 DOI: 10.1016/j.jobcr.2022.11.005] [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: 03/12/2022] [Revised: 08/30/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
Crestal bone preservation around the dental implant for aesthetic and functional success is widely researched and documented over a decade. Several etiological factors were put forth for crestal bone loss; of which biofilm plays a major role. Biofilm is formed by the colonization of wide spectra of bacteria inhabited around dental implants. Bacterial adherence affects the regulators of bone growth and an early intervention preserves the peri-implant bone. Primary modes of therapy stated in early literature were either prevention or treatment of infection caused by biofilm. This narrative review overviews the microbiome during different stages of peri-implant health, the mechanism of bone destruction, and the expression of the biomarkers at each stage. Microbial contamination and the associated biomarkers varied depending on the stage of peri-implant infection. The comprehensive review helps in formulating a research plan, both in diagnostics and treatment aspects in improving peri-implant health.
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Key Words
- Antibiotics
- Biomarkers
- CD14, Cluster of Differentiation 14
- CSF, Colony-Stimulating Factor
- Gene expression
- IL, Interleukins
- MMP 8, Matrix MetalloProteinase 8
- Microbiota
- OPG, Osteoprotegerin
- PSMB 2, Proteasome subunit beta type-2
- Peri-implant
- RANK, Receptor Activator of Nuclear factor Kappa-Β
- RANKL, Receptor Activator of Nuclear factor Kappa-ΒLigand
- TIMP, Tissue inhibitor of Metalloproteinase
- TNF, Tumor Necrosis Factor
- TWEAK, TNF-related weak inducer of apoptosis
- VEGF, Vascular Endothelial Growth Factor
- sRANKL, soluble Receptor Activator of Nuclear Factor-κB Ligand
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Affiliation(s)
- Fathima Banu Raza
- Department of Prosthodontics, Faculty of Dental Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | | | - Ruckmani Kandasamy
- Centre for Excellence in Nanobio Translational REsearch (CENTRE), Department of Pharmaceutical Technology, University College of Engineering, Anna University, BIT Campus, Tiruchirappalli, Tamil Nadu, India
| | - Venkateshwaran Krishnaswami
- Centre for Excellence in Nanobio Translational REsearch (CENTRE), Department of Pharmaceutical Technology, University College of Engineering, Anna University, BIT Campus, Tiruchirappalli, Tamil Nadu, India
| | - Anand Kumar V
- Department of Prosthodontics, Faculty of Dental Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
- Corresponding author. Department of Prosthodontics, Faculty of Dental Sciences, SRIHER (DU), Porur, Chennai, Tamil Nadu, India.
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Gianquinto E, Sodano F, Rolando B, Kostrzewa M, Allarà M, Mahmoud AM, Kumar P, Spyrakis F, Ligresti A, Chegaev K. N-[1,3-Dialkyl(aryl)-2-oxoimidazolidin-4-ylidene]-aryl(alkyl)sulphonamides as Novel Selective Human Cannabinoid Type 2 Receptor (hCB2R) Ligands; Insights into the Mechanism of Receptor Activation/Deactivation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238152. [PMID: 36500256 PMCID: PMC9738591 DOI: 10.3390/molecules27238152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
Cannabinoid type 1 (hCB1) and type 2 (hCB2) receptors are pleiotropic and crucial targets whose signaling contributes to physiological homeostasis and its restoration after injury. Being predominantly expressed in peripheral tissues, hCB2R represents a safer therapeutic target than hCB1R, which is highly expressed in the brain, where it regulates processes related to cognition, memory, and motor control. The development of hCB2R ligands represents a therapeutic opportunity for treating diseases such as pain, inflammation and cancer. Identifying new selective scaffolds for cannabinoids and determining the structural determinants responsible for agonism and antagonism are priorities in drug design. In this work, a series of N-[1,3-dialkyl(aryl)-2-oxoimidazolidin-4-ylidene]-aryl(alkyl)sulfonamides is designed and synthesized and their affinity for human hCB1R and hCB2R is determined. Starting with a scaffold selected from the NIH Psychoactive Drug Screening Program Repository, through a combination of molecular modeling and structure-activity relationship studies, we were able to identify the chemical features leading to finely tuned hCB2R selectivity. In addition, an in silico model capable of predicting the functional activity of hCB2R ligands was proposed and validated. The proposed receptor activation/deactivation model enabled the identification of four pure hCB2R-selective agonists that can be used as a starting point for the development of more potent ligands.
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Affiliation(s)
- Eleonora Gianquinto
- Department of Drug Science and Technology, University of Torino, 10125 Torino, Italy
| | - Federica Sodano
- Department of Drug Science and Technology, University of Torino, 10125 Torino, Italy
- Department of Pharmacy, “Federico II” University of Naples, 80131 Naples, Italy
| | - Barbara Rolando
- Department of Drug Science and Technology, University of Torino, 10125 Torino, Italy
| | - Magdalena Kostrzewa
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Marco Allarà
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Ali Mokhtar Mahmoud
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Poulami Kumar
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Torino, 10125 Torino, Italy
| | - Alessia Ligresti
- National Research Council of Italy, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
- Correspondence: (A.L.); (K.C.); Tel.: +39-0818675093 (A.L.); +39-0116707140 (K.C.)
| | - Konstantin Chegaev
- Department of Drug Science and Technology, University of Torino, 10125 Torino, Italy
- Correspondence: (A.L.); (K.C.); Tel.: +39-0818675093 (A.L.); +39-0116707140 (K.C.)
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In silico targeting of red complex bacteria virulence factors of periodontitis with β-defensin 1. J Genet Eng Biotechnol 2022; 20:59. [PMID: 35438383 PMCID: PMC9019007 DOI: 10.1186/s43141-022-00342-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Periodontitis is a multi-factorial infection with red complex bacteria playing a crucial role in the pathogenesis. As bacteria are tending to develop resistance against conventional antibiotics, new treatment modalities need to be developed. Antimicrobial peptides (AMPs) are potential tools for drug development and are gaining widespread interest. β-defensin 1 is an important AMP and forms the first-line host defense mechanism. The present study analyzed the structure and molecular docking of β-defensin 1 with the virulence factors of red complex bacteria of periodontitis. The physico-chemical properties of β-defensin 1 were determined by various online tools such as ProtParam, ProteinPredict, ToxinPred, and BioPep web servers. The structure of β-defensin 1was predicted by the SWISS-MODEL web server and the structure was evaluated by different web tools. The structure of lipopolysaccharide of Porphyromonas gingivalis was drawn using Chem3D ultra 11.0 software. The structure of important protein virulence factors of red complex bacteria of periodontitis was determined by the SWISS-MODEL web server. The interaction study between β-defensin 1 and virulence factors was carried out by molecular docking using Auto dock version 4.0 software and pyDock WEB server. RESULTS Using online tools, β-defensin 1 was predicted to be stable and non-toxic. SWISS-MODEL web server predicted Ramachandran score as 94.12% and clash score 0.0 for β-defensin 1. Auto dock version 4.0 software and pyDock WEB server analyzed the interaction to have low binding energies and hydrogen bonds were formed between the peptide and virulence factors. CONCLUSION β-defensin 1 was found to have good binding interaction with the disease-causing factors of red complex bacteria of periodontitis and in turn could play a role in reducing the severity of infection. β-defensin 1 could be a potential candidate for drug development for periodontitis.
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Petain S, Kasnak G, Firatli E, Tervahartiala T, Gürsoy UK, Sorsa T. Periodontitis and peri-implantitis tissue levels of Treponema denticola-CTLP and its MMP-8 activating ability. Acta Histochem 2021; 123:151767. [PMID: 34419758 DOI: 10.1016/j.acthis.2021.151767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Chymotrypsin-like-proteinase of Treponema denticola (Td-CTLP) can stimulate the protein expression and activation of matrix metalloproteinase (MMP)-8 (or collagenase-2), a potent tissue destructive enzyme from gingival cells in vitro. The aims of this study were 1) to demonstrate the proMMP-8 (or latent MMP-8) activation by Td-CTLP in vitro and 2) to detect Td-CTLP and MMP-8 protein levels in the tissue samples of peri-implantitis and periodontitis patients. MATERIALS AND METHODS proMMP-8 activation by Td-CTLP was analyzed by immunoblots. Tissue specimens were collected from 38 systemically healthy and non-smoking patients; 14 of whom had moderate to severe periodontitis, 10 of whom were suffering from peri-implantitis, and finally 14 of whom showed no sign of periodontal inflammation nor radiological bone decay (control group). The immune-expression levels of MMP-8 and Td-CTLP in the epithelium and the connective tissue were analyzed immunohistochemically. A pixel color-intensity analyze was performed with ImageJ software (version 1.46c; Rasband WS, National Institutes of Health, Bethesda, MD, USA) to obtain a comparable numeral score for each patient's epithelium and connective tissue MMP-8 and Td-CTLP enzyme level. RESULTS Td-CTLP activated proMMP-8 in vitro by converting the 70-75 kDa proMMP-8 to 65 kDa active MMP-8. Also, lower molecular size 25-50 kDa parts of MMP-8 were formed. There was no statistically significant difference between the study groups in terms of their MMP-8 and Td-CTLP levels in the epithelium or in the connective tissue. CONCLUSION Regarding the limits of this study, it can thus be said that the Td-CTLP enzyme can activate the host proMMP-8 enzyme. Tissue protein levels of MMP-8 and Td-CTLP do not seem to be changed in peri-implantitis and in periodontitis.
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Virtual screening identifies broad-spectrum β-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases. Sci Rep 2020; 10:12763. [PMID: 32728062 PMCID: PMC7391774 DOI: 10.1038/s41598-020-69431-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria are known to evade β-lactam antibiotic action by producing β-lactamases (BLs), including carbapenemases, which are able to hydrolyze nearly all available β-lactams. The production of BLs represents one of the best known and most targeted mechanisms of resistance in bacteria. We have performed the parallel screening of commercially available compounds against a panel of clinically relevant BLs: class A CTX-M-15 and KPC-2, subclass B1 NDM-1 and VIM-2 MBLs, and the class C P. aeruginosa AmpC. The results show that all BLs prefer scaffolds having electron pair donors: KPC-2 is preferentially inhibited by sulfonamide and tetrazole-based derivatives, NDM-1 by compounds bearing a thiol, a thiosemicarbazide or thiosemicarbazone moiety, while VIM-2 by triazole-containing molecules. Few broad-spectrum BLs inhibitors were identified; among these, compound 40 potentiates imipenem activity against an NDM-1-producing E. coli clinical strain. The binary complexes of the two most promising compounds binding NDM-1 and VIM-2 were obtained at high resolution, providing strong insights to improve molecular docking simulations, especially regarding the interaction of MBLs with inhibitors.
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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Celegato M, Messa L, Goracci L, Mercorelli B, Bertagnin C, Spyrakis F, Suarez I, Cousido-Siah A, Travé G, Banks L, Cruciani G, Palù G, Loregian A. A novel small-molecule inhibitor of the human papillomavirus E6-p53 interaction that reactivates p53 function and blocks cancer cells growth. Cancer Lett 2019; 470:115-125. [PMID: 31693922 DOI: 10.1016/j.canlet.2019.10.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022]
Abstract
Despite prophylactic vaccination campaigns, human papillomavirus (HPV)-induced cancers still represent a major medical issue for global population, thus specific anti-HPV drugs are needed. Since the ability of HPV E6 oncoprotein to promote p53 degradation is linked to tumor progression, E6 has been proposed as an ideal target for cancer treatment. Using the crystal structure of the E6/E6AP/p53 complex, we performed an in silico screening of small-molecule libraries against a highly conserved alpha-helix in the N-terminal domain of E6 involved in the E6-p53 interaction. We discovered a compound able to inhibit the E6-mediated degradation of p53 through disruption of E6-p53 binding both in vitro and in cells. This compound could restore p53 intracellular levels and transcriptional activity, reduce the viability and proliferation of HPV-positive cancer cells, and block 3D cervospheres formation. Mechanistic studies revealed that the compound anti-tumor activity mainly relies on induction of cell cycle arrest and senescence. Our data demonstrate that the disruption of the direct E6-p53 interaction can be obtained with a small-molecule compound leading to specific antitumoral activity in HPV-positive cancer cells and thus represents a new approach for anti-HPV drug development.
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Affiliation(s)
- Marta Celegato
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Lorenzo Messa
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy; Consortium for Computational Molecular and Materials Sciences, Perugia, Italy.
| | | | - Chiara Bertagnin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Irina Suarez
- Équipe Labellisée Ligue 2015, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Alexandra Cousido-Siah
- Équipe Labellisée Ligue 2015, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Gilles Travé
- Équipe Labellisée Ligue 2015, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy; Consortium for Computational Molecular and Materials Sciences, Perugia, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padova, Italy.
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12
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Sciabola S, Benedetti P, D’Arrigo G, Torella R, Baroni M, Cruciani G, Spyrakis F. Discovering New Casein Kinase 1d Inhibitors with an Innovative Molecular Dynamics Enabled Virtual Screening Workflow. ACS Med Chem Lett 2019; 10:487-492. [PMID: 30996784 DOI: 10.1021/acsmedchemlett.8b00523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/13/2018] [Indexed: 01/29/2023] Open
Abstract
The value of including protein flexibility in structure-based drug design (SBDD) is widely documented, and currently, molecular dynamics (MD) simulations represent a powerful tool to investigate protein dynamics. Yet, the inclusion of MD-derived information in pre-existing SBDD workflows is still far from trivial. We recently published an integrated MD-FLAP (Fingerprints for Ligands and Proteins) approach combining MD, clustering and Linear Discriminant Analysis (LDA) for enhancing accuracy, efficacy, and for protein conformational selection in virtual screening (VS) campaigns. Here we prospectively applied the MD-FLAP workflow to discover novel chemotypes inhibiting the Casein Kinase 1 delta (CSNK1D) enzyme. We first obtained a VS model able to separate active from inactive compounds, with a global AUC of 0.9 and a partial ROC enrichment at 0.5% of 0.18, and use it to mine the internal Pfizer screening database. Seven active molecules sharing a phenyl-indazole scaffold, not yet reported among CSNK1D inhibitors, were found. The most potent inhibitor showed an IC50 of 134 nM.
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Affiliation(s)
- Simone Sciabola
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
- Biotherapeutics and Medicinal Sciences, Biogen Inc., Cambridge, Massachusetts 02139, United States
| | - Paolo Benedetti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Giulia D’Arrigo
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Torino, Italy
| | - Rubben Torella
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Massimo Baroni
- Molecular Discovery Ltd., Centennial Park, WD6 3FG Borehamwood, Hertfordshire, U.K
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Torino, Italy
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13
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Raboni S, Marchetti M, Faggiano S, Campanini B, Bruno S, Marchesani F, Margiotta M, Mozzarelli A. The Energy Landscape of Human Serine Racemase. Front Mol Biosci 2019; 5:112. [PMID: 30687716 PMCID: PMC6333871 DOI: 10.3389/fmolb.2018.00112] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022] Open
Abstract
Human serine racemase is a pyridoxal 5′-phosphate (PLP)-dependent dimeric enzyme that catalyzes the reversible racemization of L-serine and D-serine and their dehydration to pyruvate and ammonia. As D-serine is the co-agonist of the N-methyl-D-aspartate receptors for glutamate, the most abundant excitatory neurotransmitter in the brain, the structure, dynamics, function, regulation and cellular localization of serine racemase have been investigated in detail. Serine racemase belongs to the fold-type II of the PLP-dependent enzyme family and structural models from several orthologs are available. The comparison of structures of serine racemase co-crystallized with or without ligands indicates the presence of at least one open and one closed conformation, suggesting that conformational flexibility plays a relevant role in enzyme regulation. ATP, Mg2+, Ca2+, anions, NADH and protein interactors, as well as the post-translational modifications nitrosylation and phosphorylation, finely tune the racemase and dehydratase activities and their relative reaction rates. Further information on serine racemase structure and dynamics resulted from the search for inhibitors with potential therapeutic applications. The cumulative knowledge on human serine racemase allowed obtaining insights into its conformational landscape and into the mechanisms of cross-talk between the effector binding sites and the active site.
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Affiliation(s)
- Samanta Raboni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy
| | | | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy.,Institute of Biophysics, National Research Council, Pisa, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
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14
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Spyrakis F, Bellio P, Quotadamo A, Linciano P, Benedetti P, D'Arrigo G, Baroni M, Cendron L, Celenza G, Tondi D. First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase. J Comput Aided Mol Des 2019; 33:295-305. [PMID: 30603820 DOI: 10.1007/s10822-018-0182-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
The worldwide spread of beta-lactamases with hydrolytic activity extended to last resort carbapenems is aggravating the antibiotic resistance problem and endangers the successful antimicrobial treatment of clinically relevant pathogens. As recently highlighted by the World Health Organization, new strategies to contain antimicrobial resistance are urgently needed. Class A carbapenemases include members of the KPC, GES and SFC families. These enzymes have the ability to hydrolyse penicillins, cephalosporins and carbapenems, while also being less susceptible to available beta-lactam inhibitors, such as clavulanic acid. The KPC family is the most prevalent. It is mostly found on plasmids in Klebsiella pneumoniae, meaning that great amounts of attention, in terms of inhibitor design and structural biology, have been dedicated to it, whereas no efforts have yet been dedicated to GES-type enzymes, despite their ability to rapidly and horizontally disseminate. We herein report the first in silico screening against GES-5, which is the most dangerous GES-type beta-lactamase, using a library of 800K commercially available candidates that all share drug-like properties, such as their MW, logP, rotatable bonds and HBA/HBD atoms. The best screening results were filtered to enrich the number of different chemotypes, and then submitted to molecular docking. The 34 most promising candidates were selected for in vitro validation in biochemical assays against recombinant GES-5. Six hits acted as inhibitors, in the high micromolar range, towards GES-5 and led to the identification of the first, novel chemotypes with inhibitory activity against this clinically relevant carbapenemase.
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Affiliation(s)
- Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Turin, Italy.
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100, L'Aquila, Italy
| | - Antonio Quotadamo
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Paolo Benedetti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Giulia D'Arrigo
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Turin, Italy
| | - Massimo Baroni
- Molecular Discovery Limited, U.501 Centennial Park, Centennial Ave, Elstree, Borehamwood, Hertfordshire, WD6 3FG, UK
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121, Padua, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100, L'Aquila, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy.
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15
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Romeo I, Marascio N, Pavia G, Talarico C, Costa G, Alcaro S, Artese A, Torti C, Liberto MC, Focà A. Structural Modeling of New Polymorphism Clusters of HCV Polymerase Isolated from Direct‐Acting Antiviral Naïve Patients: Focus on Dasabuvir and Setrobuvir Binding Affinity. ChemistrySelect 2018. [DOI: 10.1002/slct.201800649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Isabella Romeo
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Nadia Marascio
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Grazia Pavia
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Carmine Talarico
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Giosuè Costa
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Stefano Alcaro
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Anna Artese
- Department of Health SciencesUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Carlo Torti
- Department of Medical and Surgical SciencesUnit of Infectious and Tropical DiseasesSchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy)
| | - Maria Carla Liberto
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
| | - Alfredo Focà
- Department of Health SciencesInstitute of MicrobiologySchool of MedicineUniversity “Magna Graecia” of Catanzaro, Viale Europa, Germaneto 88100 Catanzaro Italy
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16
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Djikic T, Martí Y, Spyrakis F, Lau T, Benedetti P, Davey G, Schloss P, Yelekci K. Human dopamine transporter: the first implementation of a combined in silico/in vitro approach revealing the substrate and inhibitor specificities. J Biomol Struct Dyn 2018; 37:291-306. [PMID: 29334320 DOI: 10.1080/07391102.2018.1426044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Parkinson's disease (PD) is characterized by the loss of dopamine-generating neurons in the substantia nigra and corpus striatum. Current treatments alleviate PD symptoms rather than exerting neuroprotective effect on dopaminergic neurons. New drugs targeting the dopaminergic neurons by specific uptake through the human dopamine transporter (hDAT) could represent a viable strategy for establishing selective neuroprotection. Molecules able to increase the bioactive amount of extracellular dopamine, thereby enhancing and compensating a loss of dopaminergic neurotransmission, and to exert neuroprotective response because of their accumulation in the cytoplasm, are required. By means of homology modeling, molecular docking, and molecular dynamics simulations, we have generated 3D structure models of hDAT in complex with substrate and inhibitors. Our results clearly reveal differences in binding affinity of these compounds to the hDAT in the open and closed conformations, critical for future drug design. The established in silico approach allowed the identification of promising substrate compounds that were subsequently analyzed for their efficiency in inhibiting hDAT-dependent fluorescent substrate uptake, through in vitro live cell imaging experiments. Taken together, our work presents the first implementation of a combined in silico/in vitro approach enabling the selection of promising dopaminergic neuron-specific substrates.
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Affiliation(s)
- Teodora Djikic
- a Department of Bioinformatics and Genetics , Kadir Has University , Cibali campus, Fatih 34083 , Istanbul , Turkey
| | - Yasmina Martí
- b Hector Institute for Translational Brain Research, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany.,f Biochemical Laboratory, Psychiatry and Psychotherapy Department, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany
| | - Francesca Spyrakis
- c Department of Drug Science and Technology , University of Turin , via P. Giuria 9, Turin 10125 , Italy
| | - Thorsten Lau
- b Hector Institute for Translational Brain Research, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany
| | - Paolo Benedetti
- d Department of Chemistry, Biology and Biotechnology , University of Perugia , via Elce di sotto 8, Perugia 06123 , Italy
| | - Gavin Davey
- e School of Biochemistry and Immunology , Trinity College Dublin , Dublin 2, Ireland
| | - Patrick Schloss
- f Biochemical Laboratory, Psychiatry and Psychotherapy Department, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany
| | - Kemal Yelekci
- a Department of Bioinformatics and Genetics , Kadir Has University , Cibali campus, Fatih 34083 , Istanbul , Turkey
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17
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Spyrakis F, Celenza G, Marcoccia F, Santucci M, Cross S, Bellio P, Cendron L, Perilli M, Tondi D. Structure-Based Virtual Screening for the Discovery of Novel Inhibitors of New Delhi Metallo-β-lactamase-1. ACS Med Chem Lett 2018; 9:45-50. [PMID: 29348810 DOI: 10.1021/acsmedchemlett.7b00428] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/25/2017] [Indexed: 11/29/2022] Open
Abstract
Bacterial resistance has become a worldwide concern after the emergence of metallo-β-lactamases (MBLs). They represent one of the major mechanisms of bacterial resistance against beta-lactam antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 NDM-1, the most prevalent type, is extremely efficient in inactivating nearly all-available antibiotics including last resort carbapenems. No inhibitors for NDM-1 are currently available in therapy, making the spread of NDM-1 producing bacterial strains a serious menace. With this perspective, we performed a structure-based in silico screening of a commercially available library using FLAPdock and identified several, non-β-lactam derivatives as promising candidates active against NDM-1. The binding affinities of the highest scoring hits were measured in vitro revealing, for some of them, low micromolar affinity toward NDM-1. For the best inhibitors, efficacy against resistant bacterial strains overexpressing NDM-1 was validated, confirming their favorable synergistic effect in combination with the carbapenem Meropenem.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41100 Modena, Italy
| | - Giuseppe Celenza
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Francesca Marcoccia
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Matteo Santucci
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41100 Modena, Italy
| | - Simon Cross
- Dipartimento
di Chimica, Biologia e Biotechnologia, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Pierangelo Bellio
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Laura Cendron
- Dipartimento
di Biologia, Università degli Studi di Padova, Viale G. Colombo
3, 35131 Padova, Italy
| | - Mariagrazia Perilli
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Donatella Tondi
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41100 Modena, Italy
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18
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Cruciani G, Milani N, Benedetti P, Lepri S, Cesarini L, Baroni M, Spyrakis F, Tortorella S, Mosconi E, Goracci L. From Experiments to a Fast Easy-to-Use Computational Methodology to Predict Human Aldehyde Oxidase Selectivity and Metabolic Reactions. J Med Chem 2017; 61:360-371. [DOI: 10.1021/acs.jmedchem.7b01552] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Nicolò Milani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Paolo Benedetti
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Susan Lepri
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Lucia Cesarini
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd, Centennial
Park, Borehamwood, Hertfordshire, United Kingdom
| | - Francesca Spyrakis
- Department
of Drug Science and Technology, University of Turin, via P. Giuria
9, 10125 Turin, Italy
| | - Sara Tortorella
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
- Molecular Horizon srl, via Montelino
32, 06084 Bettona, Italy
| | - Edoardo Mosconi
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
- Computational
Laboratory for Hybrid/Organic Photovoltaics, National Research Council−Institute of Molecular Science and Technologies, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
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19
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Computational and biological profile of boronic acids for the detection of bacterial serine- and metallo-β-lactamases. Sci Rep 2017; 7:17716. [PMID: 29255163 PMCID: PMC5735191 DOI: 10.1038/s41598-017-17399-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/16/2017] [Indexed: 12/21/2022] Open
Abstract
β-Lactamases (BLs) able to hydrolyze β-lactam antibiotics and more importantly the last resort carbapenems, represent a major mechanism of resistance in Gram-negative bacteria showing multi-drug or extensively drug resistant phenotypes. The early detection of BLs responsible of resistant infections is challenging: approaches aiming at the identification of new BLs inhibitors (BLI) can thus serve as the basis for the development of highly needed diagnostic tools. Starting from benzo-[b]-thiophene-2-boronic acid (BZB), a nanomolar inhibitor of AmpC β-lactamase (K i = 27 nM), we have identified and characterized a set of BZB analogues able to inhibit clinically-relevant β-lactamases, including AmpC, Extended-Spectrum BLs (ESBL), KPC- and OXA-type carbapenemases and metallo-β-lactamases (MBL). A multiligand set of boronic acid (BA) β-lactamase inhibitors was obtained using covalent molecular modeling, synthetic chemistry, enzyme kinetics and antibacterial susceptibility testing. Data confirmed the possibility to discriminate between clinically-relevant β-lactamases on the basis of their inhibition profile. Interestingly, this work also allowed the identification of potent KPC-2 and NDM-1 inhibitors able to potentiate the activity of cefotaxime (CTX) and ceftazidime (CAZ) against resistant clinical isolates (MIC reduction, 32-fold). Our results open the way to the potential use of our set of compounds as a diagnostic tool for the sensitive detection of clinically-relevant β-lactamases.
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20
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Ebersole JL, Dawson D, Emecen-Huja P, Nagarajan R, Howard K, Grady ME, Thompson K, Peyyala R, Al-Attar A, Lethbridge K, Kirakodu S, Gonzalez OA. The periodontal war: microbes and immunity. Periodontol 2000 2017; 75:52-115. [DOI: 10.1111/prd.12222] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Siragusa L, Luciani R, Borsari C, Ferrari S, Costi MP, Cruciani G, Spyrakis F. Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case. ChemMedChem 2016; 11:1653-66. [PMID: 27404817 DOI: 10.1002/cmdc.201600121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/08/2016] [Indexed: 12/14/2022]
Abstract
Repurposing and repositioning drugs has become a frequently pursued and successful strategy in the current era, as new chemical entities are increasingly difficult to find and get approved. Herein we report an integrated BioGPS/FLAPdock pipeline for rapid and effective off-target identification and drug repurposing. Our method is based on the structural and chemical properties of protein binding sites, that is, the ligand image, encoded in the GRID molecular interaction fields (MIFs). Protein similarity is disclosed through the BioGPS algorithm by measuring the pockets' overlap according to which pockets are clustered. Co-crystallized and known ligands can be cross-docked among similar targets, selected for subsequent in vitro binding experiments, and possibly improved for inhibitory potency. We used human thymidylate synthase (TS) as a test case and searched the entire RCSB Protein Data Bank (PDB) for similar target pockets. We chose casein kinase IIα as a control and tested a series of its inhibitors against the TS template. Ellagic acid and apigenin were identified as TS inhibitors, and various flavonoids were selected and synthesized in a second-round selection. The compounds were demonstrated to be active in the low-micromolar range.
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Affiliation(s)
- Lydia Siragusa
- Molecular Discovery Limited, 215 Marsh Road, Pinner Middlesex, London, HA5 5NE, UK
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Chiara Borsari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Francesca Spyrakis
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy. .,Department of Food Science, University of Parma, Viale delle Scienze 17A, 43124, Parma, Italy.
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22
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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23
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Dellafiora L, Marchetti M, Spyrakis F, Orlandi V, Campanini B, Cruciani G, Cozzini P, Mozzarelli A. Expanding the chemical space of human serine racemase inhibitors. Bioorg Med Chem Lett 2015; 25:4297-303. [DOI: 10.1016/j.bmcl.2015.07.081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 01/17/2023]
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24
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Spyrakis F, Benedetti P, Decherchi S, Rocchia W, Cavalli A, Alcaro S, Ortuso F, Baroni M, Cruciani G. A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. J Chem Inf Model 2015; 55:2256-74. [DOI: 10.1021/acs.jcim.5b00169] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Francesca Spyrakis
- Department of Life
Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Paolo Benedetti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Sergio Decherchi
- CONCEPT Lab, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy
- BiKi Technologies s.r.l., via XX Settembre 33, 16121 Genova, Italy
| | - Walter Rocchia
- CONCEPT Lab, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy
| | - Andrea Cavalli
- CompuNet, Italian Institute of Technology, via Morego 30, 16163 Genova, Italy
- Department of Pharmacy
and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Stefano Alcaro
- Department of Health Science, University Magna Graecia of Catanzaro, Campus “S Venuta”, Viale Europa 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Department of Health Science, University Magna Graecia of Catanzaro, Campus “S Venuta”, Viale Europa 88100, Catanzaro, Italy
| | - Massimo Baroni
- Molecular Discovery Limited, 215
Marsh Road, Pinner Middlesex, London HA5-5NE, United Kingdom
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
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Mechanisms of Bone Resorption in Periodontitis. J Immunol Res 2015; 2015:615486. [PMID: 26065002 PMCID: PMC4433701 DOI: 10.1155/2015/615486] [Citation(s) in RCA: 406] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 12/13/2014] [Indexed: 12/18/2022] Open
Abstract
Alveolar bone loss is a hallmark of periodontitis progression and its prevention is a key clinical challenge in periodontal disease treatment. Bone destruction is mediated by the host immune and inflammatory response to the microbial challenge. However, the mechanisms by which the local immune response against periodontopathic bacteria disturbs the homeostatic balance of bone formation and resorption in favour of bone loss remain to be established. The osteoclast, the principal bone resorptive cell, differentiates from monocyte/macrophage precursors under the regulation of the critical cytokines macrophage colony-stimulating factor, RANK ligand, and osteoprotegerin. TNF-α, IL-1, and PGE2 also promote osteoclast activity, particularly in states of inflammatory osteolysis such as those found in periodontitis. The pathogenic processes of destructive inflammatory periodontal diseases are instigated by subgingival plaque microflora and factors such as lipopolysaccharides derived from specific pathogens. These are propagated by host inflammatory and immune cell influences, and the activation of T and B cells initiates the adaptive immune response via regulation of the Th1-Th2-Th17 regulatory axis. In summary, Th1-type T lymphocytes, B cell macrophages, and neutrophils promote bone loss through upregulated production of proinflammatory mediators and activation of the RANK-L expression pathways.
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Ronda L, Bruno S, Bettati S, Storici P, Mozzarelli A. From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci 2015; 2:12. [PMID: 25988179 PMCID: PMC4428442 DOI: 10.3389/fmolb.2015.00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 11/23/2022] Open
Abstract
The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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Affiliation(s)
- Luca Ronda
- Department of Neurosciences, University of Parma Parma, Italy
| | - Stefano Bruno
- Department of Pharmacy, University of Parma Parma, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy ; Institute of Biophysics, Consiglio Nazionale delle Ricerche Pisa, Italy
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