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Cun WY, Bate CE, Srikhanta YN, Hutton ML, Webb CT, Revitt-Mills SA, Lyras D, McGowan S, Yu H, Keller PA, Pyne SG. Design, Synthesis, and Evaluation of Cephamycin-Based Antisporulation Agents targeting Clostridioides difficile. J Med Chem 2024; 67:450-466. [PMID: 38112278 DOI: 10.1021/acs.jmedchem.3c01662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
With the aim of discovering small molecule inhibitors of the sporulation process in Clostridioides difficile, we prepared a series of C-7 α-(4-substituted-1H-1,2,3-triazol-1-yl)acetamide analogues of cefotetan, a known inhibitor of the C. difficile sporulation-specific protein target CdSpoVD. These analogues were evaluated using both in vitro binding assays with CdSpoVD and antisporulation assays against C. difficile. Further design concepts were aided utilizing the predicted docking scores (DS) using both AlphaFold (AF) models, and a crystal structure of the CdSpoVD protein (PDB 7RCZ). Despite being 1 order of magnitude more potent as a sporulation inhibitor than cefotetan, in vivo studies on compound 6a in a murine-model of C. difficile infection demonstrated comparable spore shedding capabilities as cefotetan. Importantly, compound 6a had no concerning broad spectrum antibacterial activities, toxicity, or hemolytic activity and thus has potential for further drug development.
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Affiliation(s)
- Wendy Y Cun
- School of Chemistry and Molecular Bioscience, Molecular Horizons Research Institute, University of Wollongong, Wollongong 2522 New South Wales, Australia
| | - Clara E Bate
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton 3800, Victoria Australia
| | - Yogitha N Srikhanta
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton 3800, Victoria Australia
| | - Melanie L Hutton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton 3800, Victoria Australia
| | - Chaille T Webb
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton 3800, Victoria Australia
| | - Sarah A Revitt-Mills
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton 3800, Victoria Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton 3800, Victoria Australia
| | - Sheena McGowan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton 3800, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton 3800, Victoria Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, Molecular Horizons Research Institute, University of Wollongong, Wollongong 2522 New South Wales, Australia
- ARC Centre of Excellence in Quantum Biotechnology, University of Wollongong, Wollongong 2522 New South Wales, Australia
| | - Paul A Keller
- School of Chemistry and Molecular Bioscience, Molecular Horizons Research Institute, University of Wollongong, Wollongong 2522 New South Wales, Australia
| | - Stephen G Pyne
- School of Chemistry and Molecular Bioscience, Molecular Horizons Research Institute, University of Wollongong, Wollongong 2522 New South Wales, Australia
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Ambade SS, Gupta VK, Bhole RP, Khedekar PB, Chikhale RV. A Review on Five and Six-Membered Heterocyclic Compounds Targeting the Penicillin-Binding Protein 2 (PBP2A) of Methicillin-Resistant Staphylococcus aureus (MRSA). Molecules 2023; 28:7008. [PMID: 37894491 PMCID: PMC10609489 DOI: 10.3390/molecules28207008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen. Methicillin-resistant Staphylococcus aureus (MRSA) infections pose significant and challenging therapeutic difficulties. MRSA often acquires the non-native gene PBP2a, which results in reduced susceptibility to β-lactam antibiotics, thus conferring resistance. PBP2a has a lower affinity for methicillin, allowing bacteria to maintain peptidoglycan biosynthesis, a core component of the bacterial cell wall. Consequently, even in the presence of methicillin or other antibiotics, bacteria can develop resistance. Due to genes responsible for resistance, S. aureus becomes MRSA. The fundamental premise of this resistance mechanism is well-understood. Given the therapeutic concerns posed by resistant microorganisms, there is a legitimate demand for novel antibiotics. This review primarily focuses on PBP2a scaffolds and the various screening approaches used to identify PBP2a inhibitors. The following classes of compounds and their biological activities are discussed: Penicillin, Cephalosporins, Pyrazole-Benzimidazole-based derivatives, Oxadiazole-containing derivatives, non-β-lactam allosteric inhibitors, 4-(3H)-Quinazolinones, Pyrrolylated chalcone, Bis-2-Oxoazetidinyl macrocycles (β-lactam antibiotics with 1,3-Bridges), Macrocycle-embedded β-lactams as novel inhibitors, Pyridine-Coupled Pyrimidinones, novel Naphthalimide corbelled aminothiazoximes, non-covalent inhibitors, Investigational-β-lactam antibiotics, Carbapenem, novel Benzoxazole derivatives, Pyrazolylpyridine analogues, and other miscellaneous classes of scaffolds for PBP2a. Additionally, we discuss the penicillin-binding protein, a crucial target in the MRSA cell wall. Various aspects of PBP2a, bacterial cell walls, peptidoglycans, different crystal structures of PBP2a, synthetic routes for PBP2a inhibitors, and future perspectives on MRSA inhibitors are also explored.
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Affiliation(s)
- Shraddha S. Ambade
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra 282004, UP, India
| | - Ritesh P. Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, MH, India
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, MH, India
| | - Pramod B. Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
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Naik J, Kulkarni D, Kadu P, Pandya A, Kale P. Use of In silico tools for screening buffers to overcome physical instability of Abatacept. Transpl Immunol 2022; 71:101551. [PMID: 35122959 DOI: 10.1016/j.trim.2022.101551] [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: 08/31/2021] [Revised: 12/30/2021] [Accepted: 01/29/2022] [Indexed: 10/19/2022]
Abstract
Rheumatoid arthritis is an autoimmune disorder. Abatacept (CTLA4-Ig) is used for the treatment of Rheumatoid arthritis. Abatacept is a monoclonal antibody. Monoclonal antibodies undergo chemical (e.g. oxidation, deamidation, hydrolysis) and physical (e.g. aggregation, unfolding) instabilities while handling and storage. Abatacept is also prone to aggregation. Stabilizing agents such as buffers are used to stabilize monoclonal antibodies. But, the selection of the appropriate buffer is a time-consuming process because after testing many buffers based on the analysis of the results the appropriate buffer is identified. To overcome this issue in the current study computational tools were utilized to virtually screen different buffers to select the appropriate buffer. Ligand binding is the principal mechanism of conformational stability of proteins. For the buffers as well ligand binding is the most common mechanism for enhancing the thermodynamic stability of proteins. Generally it is observed that by enhancing the thermodynamic stability there is reduction in the rate of aggregation of proteins. Buffer (ligand) binds to the native state of the protein preferentially; it results in stabilization of the protein, while in the case of denatured protein it has no impact. There are many studies conducted involving the proteins in buffer solutions but very limited information is available about the mechanism of protein-buffer interactions. In the current study ligand binding mechanism of protein - buffer interaction was studied using molecular docking. After the docking buffers were ranked according to their energy value. The lower energy scores represent better protein-buffer (ligand) binding affinity compared to high energy values. It was observed that Phosphate with a binding affinity of -107.9 kcal/mol was the buffer with the least binding energy followed by Citrate (-70.6 kcal/mol), Melglumine (-66.6 kcal/mol), Arginine (-64.5 kcal/mol), Glucono delta lactone (-62.6 kcal/mol), Sodium citrate (-56.5 kcal/mol), Tromethamine (-52.3 kcal/mol), Glycine HCl (-37.2 kcal/mol), Sulfuric acid (-37.7 kcal/mol), Ammonium acetate (-31.1 kcal/mol), Acetic acid (-30.7 kcal/mol). With lower binding energy higher is the affinity between the ligand and protein. So phosphate was identified as a buffer with the highest affinity with Abatacept.
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Affiliation(s)
- Janhavi Naik
- SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai 400056, India
| | - Duttraj Kulkarni
- SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai 400056, India
| | - Pramod Kadu
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai 400056, India.
| | - Aditya Pandya
- SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai 400056, India
| | - Pravin Kale
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai 400056, India
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Desmiaty Y, Mulatsari E, Chany Saputri F, Hanafi M, Prastiwi R, Elya B. Inhibition of pancreatic elastase in silico and in vitro by Rubus rosifolius leaves extract and its constituents. J Pharm Bioallied Sci 2020; 12:317-323. [PMID: 33100792 PMCID: PMC7574744 DOI: 10.4103/jpbs.jpbs_271_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/29/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022] Open
Abstract
Objective: Elastases are protease enzymes, which mainly hydrolyze proteins of the connective tissue, so they have a significant impact on human disease. Rubus rosifolius is one of the Rubus species found in Indonesian mountains, and it has potential as an elastase inhibitor. The objective of this research was to examine the in vitro elastase inhibitor activity of R. rosifolius leaves and to dock different ligands of its constituents against target protein of Porcine Pancreatic Elastase (PPE) receptor. Method: Dried leaves powder of R. rosifolius was extracted using Soxhlet apparatus with n-hexane, ethyl acetate, and methanol. The extract was evaporated, and in vitro elastase inhibitor activity was determined using PPE with the quercetin used as control positive. Selected nine constituents of R. rosifolius were evaluated on the docking behavior of elastase receptor using Protein–Ligand ANT System (PLANTS) computational software with PPE enzyme with Protein Data Bank (PDB) file 1BRU. Result: The methanol extract showed significantly inhibited elastase with IC50 186.13 μg/mL, but ethyl acetate extract showed weak activity, and n-hexane extract did not show any activity. Docking studies and binding free energy calculations and hydrogen bonding with some amino acids revealed that ellagic acid showed the least binding energy for the target enzyme. Conclusion: This research has opened new insights into understanding that constituents of R. rosifolius methanol extract are potential inhibitors against elastase, and suggested the active compound is ellagic acid.
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Affiliation(s)
- Yesi Desmiaty
- Department of Phytochemistry, Faculty of Pharmacy, Pancasila University, Jakarta, Indonesia.,Department of Phytochemistry, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia
| | - Esti Mulatsari
- Department of Phytochemistry, Faculty of Pharmacy, Pancasila University, Jakarta, Indonesia
| | - Fadlina Chany Saputri
- Department of Phytochemistry, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia
| | - Muhammad Hanafi
- Department of Phytochemistry, Faculty of Pharmacy, Pancasila University, Jakarta, Indonesia.,Research Centre for Chemistry Indonesian Institute of Sciences, Jakarta, Indonesia
| | - Rini Prastiwi
- Department of Pharmacognosy, Faculty of Pharmacy, Universitas Muhammadiyah Prof. Dr. Hamka, Jakarta, Indonesia
| | - Berna Elya
- Department of Phytochemistry, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia
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Greninger AL, Chatterjee SS, Chan LC, Hamilton SM, Chambers HF, Chiu CY. Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance. PLoS One 2016; 11:e0149541. [PMID: 26890675 PMCID: PMC4758708 DOI: 10.1371/journal.pone.0149541] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/02/2016] [Indexed: 01/28/2023] Open
Abstract
Fifth-generation cephalosporins, ceftobiprole and ceftaroline, are promising drugs for treatment of bacterial infections from methicillin-resistant Staphylococcus aureus (MRSA). These antibiotics are able to bind native PBP2a, the penicillin-binding protein encoded by the mecA resistance determinant that mediates broad class resistance to nearly all other beta-lactam antibiotics, at clinically achievable concentrations. Mechanisms of resistance to ceftaroline based on mecA mutations have been previously described. Here we compare the genomes of 11 total parent-daughter strains of Staphylococcus aureus for which specific selection by serial passaging with ceftaroline or ceftobiprole was used to identify novel non-mecA mechanisms of resistance. All 5 ceftaroline-resistant strains, derived from 5 different parental strains, contained mutations directly upstream of the pbp4 gene (coding for the PBP4 protein), including four with the same thymidine insertion located 377 nucleotides upstream of the promoter site. In 4 of 5 independent ceftaroline-driven selections, we also isolated mutations to the same residue (Asn138) in PBP4. In addition, mutations in additional candidate genes such as ClpX endopeptidase, PP2C protein phosphatase and transcription terminator Rho, previously undescribed in the context of resistance to ceftaroline or ceftobiprole, were detected in multiple selections. These genomic findings suggest that non-mecA mechanisms, while yet to be encountered in the clinical setting, may also be important in mediating resistance to 5th-generation cephalosporins.
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Affiliation(s)
- Alexander L. Greninger
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Som S. Chatterjee
- Division of Infectious Diseases, Department of Medicine, San Francisco General Hospital, San Francisco, California, United States of America
| | - Liana C. Chan
- Division of Infectious Diseases, Department of Medicine, San Francisco General Hospital, San Francisco, California, United States of America
| | - Stephanie M. Hamilton
- Division of Infectious Diseases, Department of Medicine, San Francisco General Hospital, San Francisco, California, United States of America
| | - Henry F. Chambers
- Division of Infectious Diseases, Department of Medicine, San Francisco General Hospital, San Francisco, California, United States of America
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
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Senthilkumar N, Ravichandran YD, Kumar KM, Ramaiah S. Synthesis of a new series of pyrimidine derivatives: exploration of anti-proliferative activity on EAT cells and molecular docking. RESEARCH ON CHEMICAL INTERMEDIATES 2015. [DOI: 10.1007/s11164-015-2086-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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