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Liao J, Wang Q, Wu F, Huang Z. In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets. Molecules 2022; 27:7103. [PMID: 36296697 PMCID: PMC9609013 DOI: 10.3390/molecules27207103] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 07/30/2023] Open
Abstract
Target identification is an important step in drug discovery, and computer-aided drug target identification methods are attracting more attention compared with traditional drug target identification methods, which are time-consuming and costly. Computer-aided drug target identification methods can greatly reduce the searching scope of experimental targets and associated costs by identifying the diseases-related targets and their binding sites and evaluating the druggability of the predicted active sites for clinical trials. In this review, we introduce the principles of computer-based active site identification methods, including the identification of binding sites and assessment of druggability. We provide some guidelines for selecting methods for the identification of binding sites and assessment of druggability. In addition, we list the databases and tools commonly used with these methods, present examples of individual and combined applications, and compare the methods and tools. Finally, we discuss the challenges and limitations of binding site identification and druggability assessment at the current stage and provide some recommendations and future perspectives.
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Affiliation(s)
- Jianbo Liao
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan 523808, China
| | - Qinyu Wang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
| | - Fengxu Wu
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, School of Pharmaceutical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory of Computer-Aided Drug Design of Dongguan City, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
- Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
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Froes TQ, Chaves BT, Mendes MS, Ximenes RM, da Silva IM, da Silva PBG, de Albuquerque JFC, Castilho MS. Synthesis and biological evaluation of thiazolidinedione derivatives with high ligand efficiency to P. aeruginosa PhzS. J Enzyme Inhib Med Chem 2021; 36:1217-1229. [PMID: 34080514 PMCID: PMC8186431 DOI: 10.1080/14756366.2021.1931165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
The thiazolidinone ring is found in compounds that have widespan biology activity and there is mechanism-based evidence that compounds bearing this moiety inhibit P. aeruginosa PhzS (PaPzhS), a key enzyme in the biosynthesis of the virulence factor named pyocyanin. Ten novel thiazolidinone derivatives were synthesised and screened against PaPhzS, using two orthogonal assays. The biological results provided by these and 28 other compounds, whose synthesis had been described, suggest that the dihydroquinazoline ring, found in the previous hit (A- Kd = 18 µM and LE = 0.20), is not required for PaPzhS inhibition, but unsubstituted nitrogen at the thiazolidinone ring is. The molecular simplification approach, pursued in this work, afforded an optimised lead compound (13- 5-(2,4-dimethoxyphenyl)thiazolidine-2,4-dione) with 10-fold improvement in affinity (Kd= 1.68 µM) and more than 100% increase in LE (0.45), which follows the same inhibition mode as the original hit compound (competitive to NADH).Executive summaryPhzS is a key enzyme in the pyocyanin biosynthesis pathway in P. aeruginosa.Orthogonal assays (TSA and FITC) show that fragment-like thiazolidinedione derivatives bind to PaPhzS with one-digit micromolar affinity.Fragment-like thiazolidinedione derivatives bind to the cofactor (NADH) binding site in PaPhzS.The molecular simplification optimised the ligand efficiency and affinity of the lead compound.
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Affiliation(s)
- Thamires Quadros Froes
- Programa de Pós-graduação em biotecnologia da, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Marina Sena Mendes
- Faculdade de Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
| | - Rafael Matos Ximenes
- Departamento de Antibióticos da, Universidade Federal de Pernambuco. Av. Prof. Moraes Rego, Recife-Pe, Brazil
| | - Ivanildo Mangueira da Silva
- Departamento de Antibióticos da, Universidade Federal de Pernambuco. Av. Prof. Moraes Rego, Recife-Pe, Brazil
| | | | | | - Marcelo Santos Castilho
- Programa de Pós-graduação em biotecnologia da, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
- Faculdade de Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
- Programa de Pós-Graduação em Farmácia da, Universidade Federal da Bahia, Salvador, Brazil
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Ismail MM, Hassan M, Moawad SS, Okba MM, Ashour RM, Fayek NM, Saber FR. Exploring the Antivirulence Activity of Pulverulentone A, a Phloroglucinol-Derivative from Callistemon citrinus Leaf Extract, against Multi-Drug Resistant Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10080907. [PMID: 34438957 PMCID: PMC8388764 DOI: 10.3390/antibiotics10080907] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
(1) Background: Bacterial resistance to antibiotics is a global life-threatening issue. Antivirulence therapy is a promising approach to combat bacterial infections as it disarms the bacteria from their virulence factors with reduced selective pressure and a lower chance of resistance. (2) Methods: Callistemon citrinus leaf extract and its major constituent, Pulverulentone A, were tested for their ability to inhibit biofilm, exopolysaccharides, pyocyanin and proteases produced by MDR P. aeruginosa. In addition, a Galleria mellonella larvae model was employed to evaluate the in vivo cytotoxicity of Pulverulentone A and its ability to combat Pseudomonas infection. Docking study was further performed to investigate Pulverulentone A druggability against main quorum sensing (QS) targets expressed by P. aeruginosa; (3) Results: Both C. citrinus extract and the isolated compound could inhibit biofilm formation, extracellular polymeric substances (EPS) and pigment production by the tested isolates. Unexpectedly, no significant inhibition was observed on proteases production. The in silico docking analysis revealed good interactions of Pulverulentone A with all QS targets examined (LasR, MyfR/PqsR, QscR). Pulverulentone A was safe up to 400 µg·mL−1 in Galleria caterpillars. Moreover, pre-treatment of P. aeruginosa with Pulverulentone A slightly enhanced the survival of the infected larvae. (4) Conclusions: The present study proves Pulverulentone A safety with significant in vitro and in silico antivirulence potential against P. aeruginosa.
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Affiliation(s)
- Maha M. Ismail
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
- Correspondence: (M.M.I.); (F.R.S.); Tel./Fax: +20-3628426 (ext. 00202) (M.M.I.); Tel.: +20-1004405983 (F.R.S.)
| | - Mariam Hassan
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
| | - Sawsan S. Moawad
- Department of Pests and Plant Protection, National Research Center (NRC), Giza 12622, Egypt;
| | - Mona M. Okba
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; (M.M.O.); (R.M.A.); (N.M.F.)
| | - Rehab M. Ashour
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; (M.M.O.); (R.M.A.); (N.M.F.)
| | - Nesrin M. Fayek
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; (M.M.O.); (R.M.A.); (N.M.F.)
| | - Fatema R. Saber
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt; (M.M.O.); (R.M.A.); (N.M.F.)
- Correspondence: (M.M.I.); (F.R.S.); Tel./Fax: +20-3628426 (ext. 00202) (M.M.I.); Tel.: +20-1004405983 (F.R.S.)
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Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy. J Comput Aided Mol Des 2021; 35:871-882. [PMID: 34181199 DOI: 10.1007/s10822-021-00403-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/18/2021] [Indexed: 10/21/2022]
Abstract
Assessment of target druggability guided by search and characterization of hot spots is a pivotal step in early stages of drug-discovery. The raw output of FTMap provides the data to perform this task, but it relies on manual intervention to properly combine different sets of consensus sites, therefore allowing identification of hot spots and evaluation of strength, shape and distance among them. Thus, the user's previous experience on the target and the software has a direct impact on how data generated by FTMap server can be explored. DRUGpy plugin was developed to overcome this limitation. By automatically assembling and scoring all possible combinations of consensus sites, DRUGpy plugin provides FTMap users a straight-forward method to identify and characterize hot spots in protein targets. DRUGpy is available in all operating systems that support PyMOL software. DRUGpy promptly identifies and characterizes pockets that are predicted by FTMap to bind druglike molecules with high-affinity (druggable sites) or low-affinity (borderline sites) and reveals how protein conformational flexibility impacts on the target's druggability. The use of DRUGpy on the analysis of trypanothione reductases (TR), a validated drug target against trypanosomatids, showcases the usefulness of the plugin, and led to the identification of a druggable pocket in the conserved dimer interface present in this class of proteins, opening new perspectives to the design of selective inhibitors.
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A novel scaffold to fight Pseudomonas aeruginosa pyocyanin production: early steps to novel antivirulence drugs. Future Med Chem 2020; 12:1489-1503. [PMID: 32772556 DOI: 10.4155/fmc-2019-0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Although bacterial resistance is a growing concern worldwide, the development of antibacterial drugs has been steadily decreasing. One alternative to fight this issue relies on reducing the bacteria virulence without killing it. PhzS plays a pivotal role in pyocyanin production in Pseudomonas aeruginosa. Results: A total of 31 thiazolidinedione derivatives were evaluated as putative PhzS inhibitors, using thermo shift assays. Compounds that significantly shifted PhzS's Tm had their mode of inhibition (cofactor competitor) and affinity calculated by thermo shift assays as well. The most promising compound (E)-5-(4-((4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)methoxy)benzylidene)thiazolidine-2,4-dione had their affinity confirmed by microscale thermophoresis (Kd = 18 μM). Cellular assays suggest this compound reduces pyocyanin production in vitro, but does not affect P. aeruginosa viability. Conclusion: The first inhibitor of PhzS is described.
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Froes TQ, Nicastro GG, de Oliveira Pereira T, de Oliveira Carneiro K, Alves Reis IM, Conceição RS, Branco A, Ifa DR, Baldini RL, Castilho MS. Calycopterin, a major flavonoid from Marcetia latifolia, modulates virulence-related traits in Pseudomonas aeruginosa. Microb Pathog 2020; 144:104142. [PMID: 32173496 DOI: 10.1016/j.micpath.2020.104142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/31/2020] [Accepted: 03/10/2020] [Indexed: 01/30/2023]
Abstract
Although bacterial resistance is a worldwide growing concern, the development of bacteriostatic and bactericidal drugs has been decreasing in the last decade. Compounds that modulate the microorganism virulence, without killing it, have been considered promising alternatives to combat bacterial infections. However, most signaling pathways that regulate virulence are complex and not completely understood. The rich chemical diversity of natural products offers a good starting point to identify key compounds that shed some light on this matter. Therefore, we investigated the role of Marcetia latifolia ethanolic extract, as well as its major constituent, calycopterin (5,4'-dihydroxy-3,6,7,8-tetramethoxylflavone), in the regulation of virulence-related phenotypes of Pseudomonas aeruginosa. Our results show that calycopterin inhibits pyocyanin production (EC50 = 32 μM), reduces motility and increases biofilm formation in a dose-dependent manner. Such biological profile suggests that calycopterin modulates targets that may act upstream the quorum sensing regulators and points to its utility as a chemical probe to further investigate P. aeruginosa transition from planktonic to sessile lifestyle.
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Affiliation(s)
- Thamires Quadros Froes
- Programa de Pós-graduação Em Biotecnologia, Universidade Estadual de Feira de Santana, Bahia, Brazil
| | | | | | - Kelli de Oliveira Carneiro
- Departmento de Saúde, Laboratorio de Fotoquímica, Universidade Estadual de Feira de Santana, Bahia, Brazil
| | - Isabella Mary Alves Reis
- Departmento de Saúde, Laboratorio de Fotoquímica, Universidade Estadual de Feira de Santana, Bahia, Brazil
| | - Rodrigo Souza Conceição
- Departmento de Saúde, Laboratorio de Fotoquímica, Universidade Estadual de Feira de Santana, Bahia, Brazil
| | - Alexsandro Branco
- Departmento de Saúde, Laboratorio de Fotoquímica, Universidade Estadual de Feira de Santana, Bahia, Brazil
| | - Demian Rocha Ifa
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, Canada
| | - Regina Lúcia Baldini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Marcelo Santos Castilho
- Programa de Pós-graduação Em Biotecnologia, Universidade Estadual de Feira de Santana, Bahia, Brazil; Faculdade de Farmácia, Universidade Federal da Bahia, Bahia, Brazil.
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Scotti L, Scotti MT. Medicinal Chemistry Studies Applied to Protein Targets. Curr Protein Pept Sci 2019; 20:1132-1134. [PMID: 31858900 DOI: 10.2174/138920372012191114113702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Luciana Scotti
- Teaching and Research Management - University Hospital, Joao Pessoa-PB, Brazil.,Cheminformatics Laboratory- Postgraduate Program in Natural Products and Synthetic Bioactive Federal University of Paraiba Campus I, 58051-900, Joao Pessoa-PB, Brazil
| | - Marcus T Scotti
- Cheminformatics Laboratory- Postgraduate Program in Natural Products and Synthetic Bioactive Federal University of Paraiba Campus I, 58051-900, Joao Pessoa-PB, Brazil
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