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Almaghrabi M, Musa A, Aljohani AKB, Ahmed HEA, Alsulaimany M, Miski SF, Mostafa EM, Hussein S, Parambi DGT, Ghoneim MM, Elgammal WE, Halawa AH, Hammad A, El-Agrody AM. Introducing of novel class of pyrano[2,3- c]pyrazole-5-carbonitrile analogs with potent antimicrobial activity, DNA gyrase inhibition, and prominent pharmacokinetic and CNS toxicity profiles supported by molecular dynamic simulation. J Biomol Struct Dyn 2023:1-18. [PMID: 37661733 DOI: 10.1080/07391102.2023.2252088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023]
Abstract
Microbiological DNA gyrase is recognized as an exceptional microbial target for the innovative development of low-resistant and more effective antimicrobial drugs. Hence, we introduced a one-pot facile synthesis of a novel pyranopyrazole scaffold bearing different functionalities; substituted aryl ring, nitrile, and hydroxyl groups. All new analogs were characterized with full spectroscopic data. The antimicrobial screening for all analogs was assessed against standard strains of Gm + ve and Gm-ve through in vitro considers. The screened compounds displayed very promising MIC/MBC values against some of the bacterial strains with broad or selective antibacterial effects. Of these, 4j biphenyl analog showed 0.5-2/2-8 µg/mL MIC/MBC for suppression and killing of Gm + ve and Gm-ve strains. Moreover, the antimicrobial screening was assessed for the most potent analogs against certain highly resistant microbial strains. Consequently, DNA gyrase supercoiling assay was done for all analogs using ciprofloxacin as reference positive control. Obviously, the results showed a different activity profile with potent analog 4j with IC50 value 6.29 µg/mL better than reference drug 10.2 µg/mL. Additionally, CNS toxicity testing was done using the HiB5 cell line for attenuation of GABA/NMDA expression to both 4j and ciprofloxacin compounds that revealed better neurotransmitter modulation by novel scaffold. Importantly, docking and dynamic simulations were performed for the most active 4j analog to investigate its interaction with DNA binding sites, which supported the in vitro observations and compound stability with binding pocket. Finally, a novel scaffold pyranopyrazole was introduced as a DNA gyrase inhibitor with prominent antibacterial efficacy and low CNS side effect toxicity better than quinolones.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed Almaghrabi
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - Arafa Musa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Ahmed K B Aljohani
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - Hany E A Ahmed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Marwa Alsulaimany
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - Samar F Miski
- Pharmacology and Toxicology Department, College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - Ehab M Mostafa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Shaimaa Hussein
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Della Grace Thomas Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah, Saudi Arabia
| | - Walid E Elgammal
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Egypt
| | - Ahmed H Halawa
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Egypt
| | - Ali Hammad
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Ahmed M El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Egypt
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Jakhar R, Khichi A, Kumar D, Dangi M, Chhillar AK. Discovery of Novel Inhibitors of Bacterial DNA Gyrase Using a QSAR-Based Approach. ACS OMEGA 2022; 7:32665-32678. [PMID: 36120069 PMCID: PMC9476201 DOI: 10.1021/acsomega.2c04310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/19/2022] [Indexed: 05/03/2023]
Abstract
Type II topoisomerases like DNA gyrase initiate ATP-dependent negative supercoils in bacterial DNA. It is critical in all of the bacteria but is missing from eukaryotes, making it a striking target for antibacterials. Ciprofloxacin is a clinically approved drug, but its clinical effectiveness is affected by the emergence of resistance in both Gram-positive and Gram-negative bacteria. Thus, it is vital to identify novel compounds that can efficiently inhibit DNA gyrase, and quantitative structure-activity relationship (QSAR) modeling is a quick and economical means to do so. A QSAR-based virtual screening approach was applied to identify new gyrase inhibitors using an in-house-generated combinatorial library of 29828 compounds from seven ciprofloxacin scaffold structures. QSAR was built using a data set of 271 compounds, which were identified as positive and negative inhibitors from existing data reported in in vitro studies. The best QSAR model was developed using the 5-fold cross-validation Neural Network in Orange, and it was based on five PaDEL descriptors with an accuracy and sensitivity of 83%. As a result of screening of an in-house-built combinatorial library with the best-developed QSAR model, 675 compounds were identified as potential inhibitors of DNA gyrase. These inhibitors were further docked with DNA gyrase using AutoDock to compare the binding mode and score of the selected/screened compounds, and 615 compounds exhibited a docking score comparable to or lower than that of ciprofloxacin. Out of these, the top five analogues 902b, 9699f, 4419f, 5538f, and 898b reported in our study have binding scores of -13.81, -12.95, -12.52, -12.43, and -12.41 kcal/mol, respectively. The MD simulations of these five analogues for 100 ns supported the interaction stability of analogues with Escherichia coli DNA gyrase. Ninety-one per cent of the analogues screened by the QSAR model displayed better binding energy than ciprofloxacin, demonstrating the efficacy of the generated model. The NN-QSAR model proposed in this manuscript can be downloaded from https://github.com/ritu225/NN-QSAR_model.git.
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Affiliation(s)
- Ritu Jakhar
- Centre
for Bioinformatics, Maharshi Dayanand University, Rohtak 12400, India
| | - Alka Khichi
- Centre
for Bioinformatics, Maharshi Dayanand University, Rohtak 12400, India
| | - Dev Kumar
- Centre
for Bioinformatics, Maharshi Dayanand University, Rohtak 12400, India
| | - Mehak Dangi
- Centre
for Bioinformatics, Maharshi Dayanand University, Rohtak 12400, India
- ,
| | - Anil Kumar Chhillar
- Centre
for Biotechnology, Maharshi Dayanand University, Rohtak 124001, India
- ,
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Bailly C. A world tour in the name of natural products. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 100:154080. [PMID: 35405614 DOI: 10.1016/j.phymed.2022.154080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Names of natural products (NP) are usually given depending on the species of origin, be it a plant, a marine organism or a microbial species. In some cases, names have been given with reference to people, animals, music, foods or places. Many NP refer to countries, cities or specific places such as mountains, deserts, seas and oceans. PURPOSE On the basis of NP names, a world tour has been imagined referring to more than one hundred NP with names evocative of over 50 countries and regions. RESULTS The world tour goes from UK (britannin) to Italy (vaticanol) in Europe, from Uganda (ugandoside) to Senegal (senegalene, senegalenines) in Africa, from Brazil (brasilin) to Chile (santiaguine) in South America, from Utah (utahin) to Florida (floridanolide) in the US. It includes Central America (mexicanin, panamine) and the Caribbean islands (jamaicin, bahamaolides). It also crosses Alaska (alaskene) and Canada (quebecol, canadaline). The tour continues throughout Asia, from Thailand (thailandine) to China (Chinaldine) and Pakistan (pakistanamine), to finally reaches Oceania with Australia (australigenin) and Vanuatu (vanuatine), among other countries. This virtual journey, without bordure or wall, brings us to the highest mountains (himalayamine), the deepest oceans (pacificins) and the largest deserts (desertomycin). CONCLUSION In the current period of COVID-19 pandemia, with restricted opportunities for international travels, this NP name-based virtual journey offers a world tour to learn more from nature and to inspire scientists to contribute to the field of NP discovery and drug design. There are also limitations associated with the use of trivial names for NP. NP names can be further exploited for teaching and learning.
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Affiliation(s)
- Christian Bailly
- OncoWitan, Scientific Consulting Office, Lille (Wasquehal) 59290, France.
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Singh G, Pawan, Mohit, Diksha, Suman, Priyanka, Sushma, Saini A, Kaur A. Design of new bis-triazolyl structure for identification of inhibitory activity on COVID-19 main protease by molecular docking approach. J Mol Struct 2022; 1250:131858. [PMID: 34744185 PMCID: PMC8563301 DOI: 10.1016/j.molstruc.2021.131858] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/31/2021] [Indexed: 12/21/2022]
Abstract
In the rapidly growing COVID-19 pandemic, designing of new drugs and evaluating their inhibitory action against main targets of corona virus could be an effective strategy to accelerate the drug discovery process and their efficacy towards corona virus disease. Herein, we design new bis-triazolyl probe for an investigation of inhibitory activity towards COVID-19 main protease by Molecular docking approach. The formulated compound has been thoroughly characterized by elemental analysis, NMR (1H and 13C) and complete structure elucidation was achieved via X-ray crystallography. Docking study reveals that newly synthesized compound confers good inhibitory response to COVID-19 main protease as supported by calculated docking score and binding energy. Strong hydrogen bonding and hydrophobic interactions of the newly synthesized compound with several important amino acids of the main protease also helps to explain the potency of the compound to inhibit the main protease. We hope that the present study would help the researcher in the field of Medicinal chemistry and to develop potential drug against the novel corona virus.
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Affiliation(s)
- Gurjaspreet Singh
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Pawan
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Mohit
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Diksha
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Suman
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Priyanka
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Sushma
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Anamika Saini
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Amarjit Kaur
- Department of Chemistry, Panjab University, Chandigarh 160014, India
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Singh G, Pawan, Mohit, Sushma, Singh B, GonzálezSilverac D, Espinosa‐Ruízc C, Estebanc MA, Kaur A. Anthracene‐Based Triazolyl Triethoxysilanes as Selective and Colorimetric Sensor for Cysteine: Rationalization towards Stability Factors, Therapeutics Evaluation and Molecular Docking. ChemistrySelect 2021. [DOI: 10.1002/slct.202102327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Pawan
- Department of Chemistry Panjab University Chandigarh India
| | - Mohit
- Department of Chemistry Panjab University Chandigarh India
| | - Sushma
- Department of Chemistry Panjab University Chandigarh India
| | - Baljinder Singh
- Department of Biochemistry Panjab University Chandigarh India
| | - D. GonzálezSilverac
- Department of Cell Biology & Histology Faculty of Biology University of Murcia 30100 Murcia Spain
| | - Cristóbal Espinosa‐Ruízc
- Department of Cell Biology & Histology Faculty of Biology University of Murcia 30100 Murcia Spain
| | - María Angeles Estebanc
- Department of Cell Biology & Histology Faculty of Biology University of Murcia 30100 Murcia Spain
| | - Amarjit Kaur
- Department of Chemistry Panjab University Chandigarh India
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Bonandi E, Christodoulou MS, Fumagalli G, Perdicchia D, Rastelli G, Passarella D. The 1,2,3-triazole ring as a bioisostere in medicinal chemistry. Drug Discov Today 2017; 22:1572-1581. [PMID: 28676407 DOI: 10.1016/j.drudis.2017.05.014] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/16/2017] [Accepted: 05/25/2017] [Indexed: 10/25/2022]
Abstract
1,2,3-Triazole is a well-known scaffold that has a widespread occurrence in different compounds characterized by several bioactivities, such as antimicrobial, antiviral, and antitumor effects. Moreover, the structural features of 1,2,3-triazole enable it to mimic different functional groups, justifying its wide use as a bioisostere for the synthesis of new active molecules. Here, we provide an overview of the 1,2,3-triazole ring as a bioisostere for the design of drug analogs, highlighting relevant recent examples.
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Affiliation(s)
- Elisa Bonandi
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Michael S Christodoulou
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy; Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Gaia Fumagalli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Dario Perdicchia
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy.
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Yanagi M, Ninomiya R, Ueda Y, Furuta T, Yamada T, Sunazuka T, Kawabata T. Organocatalytic Site-Selective Acylation of 10-Deacetylbaccatin III. Chem Pharm Bull (Tokyo) 2016; 64:907-12. [PMID: 26903156 DOI: 10.1248/cpb.c16-00037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Organocatalytic site-selective diversification of 10-deacetylbaccatin III, a key natural product for the semisynthesis of taxol, has been achieved. Various acyl groups were selectively introduced into the C(10)-OH of 10-deacetylbaccatin III. The C(10)-OH selective acylation was also applied to acylative site-selective dimerization of 10-deacetylbaccatin III to provide the structurally defined dimer.
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