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Yadav PR, Basha SH. Impact of Fe + 2 ions on structural integrity of A0A6P1CI42_RHITR NifA protein from Rhizobium tropici strain CIAT 899. J Biomol Struct Dyn 2023:1-10. [PMID: 37691419 DOI: 10.1080/07391102.2023.2256883] [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: 07/04/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
A0A6P1CI42_RHITR, a protein originating from Rhizobium tropici strain CIAT 899, has emerged as a key player in leguminous plant symbiosis and nitrogen fixation processes. Understanding the intricate details of its structure and function holds immense significance for unraveling the molecular mechanisms underlying its biological activities. In this study, we employed molecular modeling and molecular dynamics (MD) simulations to investigate the A0A6P1CI42_RHITR protein, with a specific emphasis on the influence of Fe-atoms, linker structural integrity, and conformational changes within the GAF domain. Our findings unveiled noteworthy conformational changes in the A0A6P1CI42_RHITR protein, particularly within the GAF domain, when Fe-atoms were present compared to its apo form. Significant conformational rearrangements after an initial 20 ns, accompanied by the opening of the ligand substrate accommodating loop in the GAF domain influenced by Fe-atoms was observed. At the residue level, the investigation revealed substantial activity variations in individual residues, particularly in those contributing to the GAF domain from positions 51 to 223. Intriguingly, the presence of Fe-atoms led to controlled movement of conserved cysteine residues at positions 467 and 472, indicating a correlation between interlinker domain motion and the activity of the GAF domain loop responsible for substrate accommodation. Moreover, in the presence of Fe-atoms, the distance between Cys467 and Cys472 residues was maintained, ensuring the overall structural integrity of the interdomain loop necessary for protein activation. Conversely, in the apo form, a sudden flip motion of cysteine residues' thiol groups was observed, leading to a loss of structural integration. Overall, our study utilizing molecular modeling and MD simulations offers valuable insights into the structural dynamics and functional implications of the A0A6P1CI42_RHITR protein.Communicated by Ramaswamy H. Sarma.
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Gangireddy MSR, Badavath VN, Velez C, Loeanurit N, Thakur A, Maddipati VC, Katari NK, Acevedo O, Boonyasuppayakorn S, Gundla R. Discovery of 3-chlorobenzyl-linked 1,9-diazaspiro[5.5]undecane derivatives, a lead for dengue virus type 2 infection. NEW J CHEM 2022. [DOI: 10.1039/d1nj02453a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dengue virus is a worldwide health threat with 400 million yearly infections. Given a lack in specific therapeutics, the current work reports DENV2 inhibitory activity in newly designed compounds that are more potent than the standard drug ribavirin.
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Affiliation(s)
| | - Vishnu Nayak Badavath
- Department of Microbiology, Applied Medical Virology Research Unit, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Caroline Velez
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Naphat Loeanurit
- Department of Microbiology, Applied Medical Virology Research Unit, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
- Interdisciplinary Program in Microbiology, Graduate School, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
| | - Abhishek Thakur
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | | | - Naresh Kumar Katari
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502329, Telangana, India
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Siwaporn Boonyasuppayakorn
- Department of Microbiology, Applied Medical Virology Research Unit, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok-10330, Thailand
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502329, Telangana, India
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Mohd Siddique MU, Thakur A, Shilkar D, Yasmin S, Halakova D, Kovacikova L, Prnova MS, Stefek M, Acevedo O, Dasararaju G, Devadasan V, Mondal SK, Jayaprakash V. Non-carboxylic acid inhibitors of aldose reductase based on N-substituted thiazolidinedione derivatives. Eur J Med Chem 2021; 223:113630. [PMID: 34175538 DOI: 10.1016/j.ejmech.2021.113630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
In search of dually active PPAR-modulators/aldose reductase (ALR2) inhibitors, 16 benzylidene thiazolidinedione derivatives, previously reported as partial PPARγ agonists, together with additional 18 structural congeners, were studied for aldose reductase inhibitory activity. While no compounds had dual property, our efforts led to the identification of promising inhibitors of ALR2. Eight compounds (11, 15-16, 20-24, 30) from the library of 33 compounds were identified as potent and selective inhibitors of ALR2. Compound 21 was the most effective and selective inhibitor with an IC50 value of 0.95 ± 0.11 and 13.52 ± 0.81 μM against ALR2 and aldehyde reductase (ALR1) enzymes, respectively. Molecular docking and dynamics studies were performed to understand inhibitor-enzyme interactions at the molecular level that determine the potency and selectivity. Compound 21 was further subjected to in silico and in vitro studies to evaluate the pharmacokinetic profile. Being less acidic (pKa = 9.8), the compound might have a superior plasma membrane permeability and reach the cytosolic ALR2. This fact together with excellent drug-likeness criteria points to improved bioavailability compared to the clinically used compound Epalrestat. The designed compounds represent a novel group of non-carboxylate inhibitors of aldose reductase with an improved physicochemical profile.
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Affiliation(s)
- Mohd Usman Mohd Siddique
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India; Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, 424001, (MH), India.
| | - Abhishek Thakur
- Department of Chemistry, University of Miami, Coral Gables, Florida, 33146, USA.
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India.
| | - Sabina Yasmin
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India; Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 61441, Saudi Arabia.
| | - Dominika Halakova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Lucia Kovacikova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Marta Soltesova Prnova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Milan Stefek
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida, 33146, USA.
| | - Gayathri Dasararaju
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, (TN), India.
| | - Velmurugan Devadasan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, (TN), India.
| | - Susanta Kumar Mondal
- TCG Life Sciences Ltd, Block-EP & GP, BIPL, Tower-B, Saltlake, Sector-V, Kolkata, 700091, (WB), India.
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Gangadevi S, Badavath VN, Thakur A, Yin N, De Jonghe S, Acevedo O, Jochmans D, Leyssen P, Wang K, Neyts J, Yujie T, Blum G. Kobophenol A Inhibits Binding of Host ACE2 Receptor with Spike RBD Domain of SARS-CoV-2, a Lead Compound for Blocking COVID-19. J Phys Chem Lett 2021; 12:1793-1802. [PMID: 33577324 PMCID: PMC7901140 DOI: 10.1021/acs.jpclett.0c03119] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/04/2021] [Indexed: 05/03/2023]
Abstract
In the search for inhibitors of COVID-19, we have targeted the interaction between the human angiotensin-converting enzyme 2 (ACE2) receptor and the spike receptor binding domain (S1-RBD) of SARS-CoV-2. Virtual screening of a library of natural compounds identified Kobophenol A as a potential inhibitor. Kobophenol A was then found to block the interaction between the ACE2 receptor and S1-RBD in vitro with an IC50 of 1.81 ± 0.04 μM and inhibit SARS-CoV-2 viral infection in cells with an EC50 of 71.6 μM. Blind docking calculations identified two potential binding sites, and molecular dynamics simulations predicted binding free energies of -19.0 ± 4.3 and -24.9 ± 6.9 kcal/mol for Kobophenol A to the spike/ACE2 interface and the ACE2 hydrophobic pocket, respectively. In summary, Kobophenol A, identified through docking studies, is the first compound that inhibits SARS-CoV-2 binding to cells through blocking S1-RBD to the host ACE2 receptor and thus may serve as a good lead compound against COVID-19.
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Affiliation(s)
- Suresh Gangadevi
- Anhui
Provincial Engineering Laboratory of Silicon-Based Materials, Bengbu University, Caoshan Road 1866, Bengbu, Anhui 233030, PR China
| | | | - Abhishek Thakur
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Na Yin
- Anhui
Provincial Engineering Laboratory of Silicon-Based Materials, Bengbu University, Caoshan Road 1866, Bengbu, Anhui 233030, PR China
| | - Steven De Jonghe
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Orlando Acevedo
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Dirk Jochmans
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Pieter Leyssen
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ke Wang
- College
of Material and Chemical Engineering, Bengbu
University, Bengbu 233030, China
| | - Johan Neyts
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Tao Yujie
- East China
University of Political Science and Law, Shanghai 20042 China
| | - Galia Blum
- Institute
for Drug Research, The Hebrew University, Jerusalem 9112001, Israel
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