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Kant R, Tilford H, Freitas CS, Ferreira DAS, Ng J, Rucinski G, Watkins J, Pemberton R, Abramyan TM, Contreras SC, Vera A, Christodoulides M. Antimicrobial activity of compounds identified by artificial intelligence discovery engine targeting enzymes involved in Neisseria gonorrhoeae peptidoglycan metabolism. Biol Res 2024; 57:62. [PMID: 39238057 PMCID: PMC11375863 DOI: 10.1186/s40659-024-00543-9] [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: 05/07/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Neisseria gonorrhoeae (Ng) causes the sexually transmitted disease gonorrhoea. There are no vaccines and infections are treated principally with antibiotics. However, gonococci rapidly develop resistance to every antibiotic class used and there is a need for developing new antimicrobial treatments. In this study we focused on two gonococcal enzymes as potential antimicrobial targets, namely the serine protease L,D-carboxypeptidase LdcA (NgO1274/NEIS1546) and the lytic transglycosylase LtgD (NgO0626/NEIS1212). To identify compounds that could interact with these enzymes as potential antimicrobials, we used the AtomNet virtual high-throughput screening technology. We then did a computational modelling study to examine the interactions of the most bioactive compounds with their target enzymes. The identified compounds were tested against gonococci to determine minimum inhibitory and bactericidal concentrations (MIC/MBC), specificity, and compound toxicity in vitro. RESULTS AtomNet identified 74 compounds that could potentially interact with Ng-LdcA and 84 compounds that could potentially interact with Ng-LtgD. Through MIC and MBC assays, we selected the three best performing compounds for both enzymes. Compound 16 was the most active against Ng-LdcA, with a MIC50 value < 1.56 µM and MBC50/90 values between 0.195 and 0.39 µM. In general, the Ng-LdcA compounds showed higher activity than the compounds directed against Ng-LtgD, of which compound 45 had MIC50 values of 1.56-3.125 µM and MBC50/90 values between 3.125 and 6.25 µM. The compounds were specific for gonococci and did not kill other bacteria. They were also non-toxic for human conjunctival epithelial cells as judged by a resazurin assay. To support our biological data, in-depth computational modelling study detailed the interactions of the compounds with their target enzymes. Protein models were generated in silico and validated, the active binding sites and amino acids involved elucidated, and the interactions of the compounds interacting with the enzymes visualised through molecular docking and Molecular Dynamics Simulations for 50 ns and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA). CONCLUSIONS We have identified bioactive compounds that appear to target the N. gonorrhoeae LdcA and LtgD enzymes. By using a reductionist approach involving biological and computational data, we propose that compound Ng-LdcA-16 and Ng-LtgD-45 are promising anti-gonococcal compounds for further development.
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Affiliation(s)
- Ravi Kant
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, North Campus, Delhi, 110007, India
| | - Hannah Tilford
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Camila S Freitas
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Dayana A Santos Ferreira
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Laboratory of Pathophysiology, Butantan Institute, Av. Vital Brazil, 1500, São Paulo, SP, 05503-900, Brazil
| | - James Ng
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Gwennan Rucinski
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Joshua Watkins
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Ryan Pemberton
- ATOMWISE, 717 Market Street, Suite 800, San Francisco, CA, 94103, USA
| | - Tigran M Abramyan
- ATOMWISE, 717 Market Street, Suite 800, San Francisco, CA, 94103, USA
| | | | - Alejandra Vera
- Laboratorio de Bacteriología, Escuela de Medicina, Universidad de Valparaíso, Valparaíso, Chile
| | - Myron Christodoulides
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD.
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Yi C, Su C, Sun X, Lu X, Si C, Liu C, Yang Z, Yuan H, Huang Y, Wen J, He Y, Zhang Y, Ma L, Cong Y, Zhao G, Ling Z, Wang B, Sun B. A human antibody potently neutralizes RSV by targeting the conserved hydrophobic region of prefusion F. SCIENCE CHINA. LIFE SCIENCES 2023; 66:729-742. [PMID: 36853487 PMCID: PMC9971687 DOI: 10.1007/s11427-022-2250-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/22/2022] [Indexed: 03/01/2023]
Abstract
Respiratory syncytial virus (RSV) continues to pose serious threats to pediatric populations due to the lack of a vaccine and effective antiviral drugs. RSV fusion (F) glycoprotein mediates viral-host membrane fusion and is a key target for neutralizing antibodies. We generated 23 full-human monoclonal antibodies (hmAbs) against prefusion F protein (pre-F) from a healthy adult with natural RSV infection by single B cell cloning technique. A highly potent RSV-neutralizing hmAb, named as 25-20, is selected, which targets a new site Ø-specific epitope. Site-directed mutagenesis and structural modelling analysis demonstrated that 25-20 mainly targets a highly conserved hydrophobic region located at the a4 helix and a1 helix of pre-F, indicating a site of vulnerability for drug and vaccine design. It is worth noting that 25-20 uses an unreported inferred germline (iGL) that binds very poorly to pre-F, thus high levels of somatic mutations are needed to gain high binding affinity with pre-F. Our observation helps to understand the evolution of RSV antibody during natural infection. Furthermore, by in silico prediction and experimental verification, we optimized 25-20 with KD values as low as picomolar range. Therefore, the optimized 25-20 represents an excellent candidate for passive protection against RSV infection.
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Affiliation(s)
- Chunyan Yi
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Caixia Su
- grid.8547.e0000 0001 0125 2443Key Laboratory of Medical Molecular Virology (MOE/MOH), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Xiaoyu Sun
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China ,grid.8547.e0000 0001 0125 2443Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Xiao Lu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Chuanya Si
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Caixuan Liu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Zhuo Yang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Hong Yuan
- MedimScience.Co, Hangzhou, 311217 China
| | - Yuying Huang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Jing Wen
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Yonghui He
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Yaguang Zhang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Liyan Ma
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Yao Cong
- grid.410726.60000 0004 1797 8419State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Gan Zhao
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhiyang Ling
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Bin Wang
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Bing Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Mehta AS, Singh A. Insights into regeneration tool box: An animal model approach. Dev Biol 2019; 453:111-129. [PMID: 30986388 PMCID: PMC6684456 DOI: 10.1016/j.ydbio.2019.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]
Abstract
For ages, regeneration has intrigued countless biologists, clinicians, and biomedical engineers. In recent years, significant progress made in identification and characterization of a regeneration tool kit has helped the scientific community to understand the mechanism(s) involved in regeneration across animal kingdom. These mechanistic insights revealed that evolutionarily conserved pathways like Wnt, Notch, Hedgehog, BMP, and JAK/STAT are involved in regeneration. Furthermore, advancement in high throughput screening approaches like transcriptomic analysis followed by proteomic validations have discovered many novel genes, and regeneration specific enhancers that are specific to highly regenerative species like Hydra, Planaria, Newts, and Zebrafish. Since genetic machinery is highly conserved across the animal kingdom, it is possible to engineer these genes and regeneration specific enhancers in species with limited regeneration properties like Drosophila, and mammals. Since these models are highly versatile and genetically tractable, cross-species comparative studies can generate mechanistic insights in regeneration for animals with long gestation periods e.g. Newts. In addition, it will allow extrapolation of regenerative capabilities from highly regenerative species to animals with low regeneration potential, e.g. mammals. In future, these studies, along with advancement in tissue engineering applications, can have strong implications in the field of regenerative medicine and stem cell biology.
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Affiliation(s)
- Abijeet S Mehta
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA; Premedical Program, University of Dayton, Dayton, OH, 45469, USA; Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, 45469, USA; The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA; Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
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Inhibitors of the Neisseria meningitidis PilF ATPase provoke type IV pilus disassembly. Proc Natl Acad Sci U S A 2019; 116:8481-8486. [PMID: 30948644 DOI: 10.1073/pnas.1817757116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Despite the availability of antibiotics and vaccines, Neisseria meningitidis remains a major cause of meningitis and sepsis in humans. Due to its extracellular lifestyle, bacterial adhesion to host cells constitutes an attractive therapeutic target. Here, we present a high-throughput microscopy-based approach that allowed the identification of compounds able to decrease type IV pilus-mediated interaction of bacteria with endothelial cells in the absence of bacterial or host cell toxicity. Compounds specifically inhibit the PilF ATPase enzymatic activity that powers type IV pilus extension but remain inefficient on the ATPase that promotes pilus retraction, thus leading to rapid pilus disappearance from the bacterial surface and loss of pili-mediated functions. Structure activity relationship of the most active compound identifies specific moieties required for the activity of this compound and highlights its specificity. This study therefore provides compounds targeting pilus biogenesis, thereby inhibiting bacterial adhesion, and paves the way for a novel therapeutic option for meningococcal infections.
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Agrahari AK, C GPD. A Computational Approach to Identify a Potential Alternative Drug With Its Positive Impact Toward PMP22. J Cell Biochem 2017; 118:3730-3743. [PMID: 28374912 DOI: 10.1002/jcb.26020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/03/2017] [Indexed: 11/08/2022]
Abstract
Mutations in the Peripheral Myelin Protein 22 (PMP22) leads to Charcot Marie Tooth type 1A (CMT1A, a subtype of CMT1) disease which is the most common inherited neuropathy of peripheral nervous system. In the present study, we used series of in silico prediction methods to screen and identify the most deleterious non-synonymous SNPs (nsSNPs) in PMP22 gene. Out of 48 nsSNPs, five nsSNPs (L16P, L19P, T23R, W28R, and L147R) associated with PMP22 were predicted to be highly deleterious and destabilizing the protein. To explore the possible structure-function relationship, we employed abinitio modeling strategy using the CABS-fold server to predict the three-dimensional structure models in the absence of crystallized structures in PMP22 protein. We used Cytoscape 3.4.0 plugin Integrated Complex Traits Networks interface (iCTNet) to identify the probable drug-gene interactions in PMP22 gene. A total of 22 chemical compounds yielded from the aforementioned tool was subjected to Molinspiration and OSIRIS program to screen and identify the potent drug molecules for further analysis. Five chemical compounds with excellent bioavailability and drug relevant property were selected for molecular docking simulation study. We modeled five mutant structures at their corresponding positions and performed molecular docking simulation analysis using AutoDock Tools (ADT) version 1.5.6 and ArgusLab 4.0.1 tools to analyze their interaction patterns and binding efficacy. Based on the results obtained from the computational study, we predict that estradiol could be a potential drug of choice for treating patients with CMT1A which needs larger attention from biologists in the near future. J. Cell. Biochem. 118: 3730-3743, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of BioSciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| | - George Priya Doss C
- Department of Integrative Biology, School of BioSciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
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