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de Carvalho Matias EG, Bezerra KS, Costa AHL, Clemente Junior WS, Oliveira JIN, Ribeiro Junior LA, Galvão DS, Fulco UL. Quantum biochemical analysis of the TtgR regulator and effectors. Sci Rep 2024; 14:8519. [PMID: 38609407 PMCID: PMC11015042 DOI: 10.1038/s41598-024-58441-9] [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: 01/25/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical concern. A single species of efflux pump can produce a simultaneous resistance to several drugs. One of the best-studied efflux pumps is the TtgABC: a tripartite resistance-nodulation-division (RND) efflux pump implicated in the intrinsic antibiotic resistance in Pseudomonas putida DOT-T1E. The expression of the TtgABC gene is down-regulated by the HTH-type transcriptional repressor TtgR. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT) within the Molecular Fragmentation with Conjugate Caps (MFCC) approach, we investigate the coupling profiles of the transcriptional regulator TtgR in complex with quercetin (QUE), a natural polyphenolic flavonoid, tetracycline (TAC), and chloramphenicol (CLM), two broad-spectrum antimicrobial agents. Our quantum biochemical computational results show the: [i] convergence radius, [ii] total binding energy, [iii] relevance (energetically) of the ligands regions, and [iv] most relevant amino acids residues of the TtgR-QUE/TAC/CLM complexes, pointing out distinctions and similarities among them. These findings improve the understanding of the binding mechanism of effectors and facilitate the development of new chemicals targeting TtgR, helping in the battle against the rise of resistance to antimicrobial drugs. These advances are crucial in the ongoing fight against rising antimicrobial drug resistance, providing hope for a future where healthcare-associated infections can be more beneficially treated.
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Affiliation(s)
- E G de Carvalho Matias
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - A H Lima Costa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - W S Clemente Junior
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - L A Ribeiro Junior
- Institute of Physics, University of Brasília, Brasília, 70919-970, Brazil.
| | - D S Galvão
- Applied Physics Department, University of Campinas, Campinas, São Paulo, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
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da Rocha JM, Campos DMDO, Esmaile SC, Menezes GDL, Bezerra KS, da Silva RA, Junior EDDS, Tayyeb JZ, Akash S, Fulco UL, Alqahtani T, Oliveira JIN. Quantum biochemical analysis of the binding interactions between a potential inhibitory drug and the Ebola viral glycoprotein. J Biomol Struct Dyn 2024:1-17. [PMID: 38258414 DOI: 10.1080/07391102.2024.2305314] [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: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
Ebola virus disease (EVD) causes outbreaks and epidemics in West Africa that persist until today. The envelope glycoprotein of Ebola virus (GP) consists of two subunits, GP1 and GP2, and plays a key role in anchoring or fusing the virus to the host cell in its active form on the virion surface. Toremifene (TOR) is a ligand that mainly acts as an estrogen receptor antagonist; however, a recent study showed a strong and efficient interaction with GP. In this context, we aimed to evaluate the energetic affinity features involved in the interaction between GP and toremifene by computer simulation techniques using the Molecular Fractionation Method with Conjugate Caps (MFCC) scheme and quantum-mechanical (QM) calculations, as well as missense mutations to assess protein stability. We identified ASP522, GLU100, TYR517, THR519, LEU186, LEU515 as the most attractive residues in the EBOV glycoprotein structure that form the binding pocket. We divided toremifene into three regions and evaluated that region i was more important than region iii and region ii for the formation of the TOR-GP1/GP2 complex, which might control the molecular remodeling process of TOR. The mutations that caused more destabilization were ARG134, LEU515, TYR517 and ARG559, while those that caused stabilization were GLU523 and ASP522. TYR517 is a critical residue for the binding of TOR, and is highly conserved among EBOV species. Our results may help to elucidate the mechanism of drug action on the GP protein of the Ebola virus and subsequently develop new pharmacological approaches against EVD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jaerdyson M da Rocha
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel M de O Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Stephany C Esmaile
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Gabriela de L Menezes
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Katyanna S Bezerra
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Roosevelt A da Silva
- Core Collaboratives of BioSistemas, Special Unit of Exact Sciences, Federal University of Jataí, Jataí, GO, Brazil
| | - Edilson D da S Junior
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Jehad Zuhair Tayyeb
- Department of Clinical Biochemistry, College of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | - Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, Bangladesh
| | - Umberto L Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Jonas I N Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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3
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Mandova T, Saivish MV, Menezes GDL, Bezerra KS, Fulco UL, da Silva RA, Da Costa FB, Nogueira ML. Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus ( Peribunyaviridae). Pharmaceutics 2023; 15:2769. [PMID: 38140109 PMCID: PMC10747393 DOI: 10.3390/pharmaceutics15122769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The Oropouche virus (OROV) is a member of the family Peribunyaviridae (order Bunyavirales) and the cause of a dengue-like febrile illness transmitted mainly by biting midges and mosquitoes. In this study, we aimed to explore acylphloroglucinols and xanthohumol from hops (Humulus lupulus L.) as a promising alternative for antiviral therapies. The evaluation of the inhibitory potential of hops compounds on the viral cycle of OROV was performed through two complementary approaches. The first approach applies cell-based assay post-inoculation experiments to explore the inhibitory potential on the latest steps of the viral cycle, such as genome translation, replication, virion assembly, and virion release from the cells. The second part covers in silico methods evaluating the ability of those compounds to inhibit the activity of the endonuclease domain, which is essential for transcription, binding, and cleaving RNA. In conclusion, the beta acids showed strongest inhibitory potential in post-treatment assay (EC50 = 26.7 µg/mL). Xanthohumol had the highest affinity for OROV endonuclease followed by colupulone and cohumulone. This result contrasts with that observed for docking and MM/PBSA analysis, where cohumulone was found to have a higher affinity. Finally, among the three tested ligands, Lys92 and Arg33 exhibited the highest affinity with the protein.
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Affiliation(s)
- Tsvetelina Mandova
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
- Gilson Purification, 22 rue Bourseul, 56890 Saint Avé, France
| | - Marielena Vogel Saivish
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Gabriela de Lima Menezes
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Katyanna Sales Bezerra
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Umberto Laino Fulco
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | | | - Fernando Batista Da Costa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
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4
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Coelho MM, Bezerra EM, da Costa RF, de Alvarenga ÉC, Freire VN, Carvalho CR, Pessoa C, Albuquerque EL, Costa RA. In silico description of the adsorption of cell signaling pathway proteins ovalbumin, glutathione, LC3, TLR4, ASC PYCARD, PI3K and NF-Kβ on 7.0 nm gold nanoparticles: obtaining their Lennard-Jones-like potentials through docking and molecular mechanics. RSC Adv 2023; 13:35493-35499. [PMID: 38058560 PMCID: PMC10697183 DOI: 10.1039/d3ra06180a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023] Open
Abstract
The impact of vaccination on the world's population is difficult to calculate. For developing different types of vaccines, adjuvants are substances added to vaccines to increase the magnitude and durability of the immune response and the effectiveness of the vaccine. This work explores the potential use of spherical gold nanoparticles (AuNPs) as adjuvants. Thus, we employed docking techniques and molecular mechanics to describe how a AuNP 7.0 nm in diameter interacts with cell signaling pathway proteins. Initially, we used X-ray crystallization data of the proteins ovalbumin, glutathione, LC3, TLR4, ASC PYCARD, PI3K, and NF-Kβ to study the adsorption with an AuNP through molecular docking. Therefore, interaction energies were obtained for the AuNP complexes and individual proteins, as well as the AuNP and OVA complex (AuNP@OVA) with each cellular protein, respectively. Results showed that AuNPs had the highest affinity for OVA individually, followed by glutathione, ASC PYCARD domain, LC3, PI3K, NF-Kβ, and TLR4. Furthermore, when evaluating the AuNP@OVA complex, glutathione showed a greater affinity with more potent interaction energy when compared to the other studied systems.
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Affiliation(s)
- Monique M Coelho
- Departamento de Ciências Naturais, Universidade Federal de São João del Rei (UFSJ) São João del-Rei MG CEP 36301-160 Brazil
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais (UFMG) Belo Horizonte MG CEP 31270-910 Brazil
| | - Eveline M Bezerra
- Programa de Pós-Graduação em Ciência e Engenharia de Materiais, Universidade Federal Rural do Semi-Árido (UFERSA) Mossoró RN CEP 59625-900 Brazil
| | - Roner F da Costa
- Programa de Pós-Graduação em Ciência e Engenharia de Materiais, Universidade Federal Rural do Semi-Árido (UFERSA) Mossoró RN CEP 59625-900 Brazil
- Departamento de Ciências, Matemática e Estatística, Universidade Federal Rural do Semi-Árido (UFERSA) Mossoró RN CEP 59625-900 Brazil
| | - Érika C de Alvarenga
- Departamento de Ciências Naturais, Universidade Federal de São João del Rei (UFSJ) São João del-Rei MG CEP 36301-160 Brazil
| | - Valder N Freire
- Departamento de Física, Universidade Federal do Ceará (UFC) Fortaleza CE 60455-760 Brazil
| | - Cláudia R Carvalho
- Departamento de Ciências Naturais, Universidade Federal de São João del Rei (UFSJ) São João del-Rei MG CEP 36301-160 Brazil
- Departamento de Morfologia, Universidade Federal de Minas Gerais (UFMG) Belo Horizonte MG CEP 31270-910 Brazil
| | - Claudia Pessoa
- Programa de Pós-Graduação em Biotecnologia, Rede Nordeste de Biotecnologia (RENORBIO, ), Universidade Federal do Ceará (UFC) Fortaleza CE CEP 60020-181 Brazil
| | - Eudenilson L Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte (UFRN) Natal RN CEP 59064-741 Brazil
| | - Raquel A Costa
- Departamento de Ciências Naturais, Universidade Federal de São João del Rei (UFSJ) São João del-Rei MG CEP 36301-160 Brazil
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Freitas de Sousa FJ, Nunes Azevedo FF, Santos de Oliveira FL, Vieira Carletti J, Freire VN, Zanatta G. Quantum biochemistry description of PI3Kα enzyme bound to selective inhibitors. J Biomol Struct Dyn 2023:1-11. [PMID: 37632299 DOI: 10.1080/07391102.2023.2251063] [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: 04/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
The PI3K class I is composed of four PI3K isoforms that serve as regulatory enzymes governing cellular metabolism, proliferation, and survival. The hyperactivation of PI3Kα is observed in various types of cancer and is linked to poor prognosis. Unfortunately, the development inhibitors selectively targeting one of the isoforms remains challenging, with only few agents in clinical use. The main difficulty arises from the high conservation among residues at the ATP-binding pocket across isoforms, which also serves as target pocket for inhibitors. In this work, molecular dynamics and quantum calculations were performed to investigate the molecular features guiding the binding of selective inhibitors, alpelisib and GDC-0326, into the ATP-binding pocket of PI3Kα. While molecular dynamics allowed crystallographic coordinates to relax, the interaction eergy between each amino acid residues and inhibitors was obtained by combining the Molecular Fractionation with Conjugated Caps scheme with Density Functional Theory calculations. In addition, the atomic charge of ligands in the bound and unbound (free) was calculated. Results indicated that the most relevant residues for the binding of alpelisib are Ile932, Glu859, Val851, Val850, Tyr836, Met922, Ile800, and Ile848, while the most important residues for the binding of GDC-0326 are Ile848, Ile800, Ile932, Gln859, Glu849, and Met922. In addition, residues Trp780, Ile800, Tyr836, Ile848, Gln859 Val850, Val851, Ile932 and Met922 are common hotspots for both inhibitors. Overall, the results from this work contribute to improving the understanding of the molecular mechanisms controlling selectivity and highlight important interactions to be considered during the rational design of new agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | | | - Geancarlo Zanatta
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Department of Biophysics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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6
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Bezerra EM, de Alvarenga ÉC, dos Santos RP, de Sousa JS, Fulco UL, Freire VN, Albuquerque EL, da Costa RF. Losartan as an ACE inhibitor: a description of the mechanism of action through quantum biochemistry. RSC Adv 2022; 12:28395-28404. [PMID: 36320533 PMCID: PMC9533318 DOI: 10.1039/d2ra04340h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Losartan (LST) is a potent and selective angiotensin II (Ang II) type 1 (AT1) receptor antagonist widely used in the treatment of hypertension. The formation of Ang II is catalyzed by the angiotensin I-converting enzyme (ACE) through proteolytic cleavage of angiotensin I (Ang I), which is involved in the control of blood pressure. Despite the vast literature on the relationship of losartan with the renin-angiotensin system (RAS), the actions of losartan on the sACE enzyme are so far poorly understood. In view of this, we investigated how losartan can interact with the sACE enzyme to block its activity and intracellular signaling. After performing docking assays following quantum biochemistry calculations using losartan and sACE crystallographic data, we report that their interaction results reveal a new mechanism of action with important implications for understanding its effects on hypertension.
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Affiliation(s)
- Eveline M. Bezerra
- Programa de Pós-Graduação em Ciência e Engenharia de Materiais (PPgCEM), Universidade Federal Rural do Semi-Árido (UFERSA)CEP 59625-900MossoróRNBrazil,Departamento de Física, Universidade Federal do Ceará (UFC)CEP 60440-900FortalezaCEBrazil
| | - Érika C. de Alvarenga
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei (UFSJ)CEP 36307-352São João del-ReiMGBrazil
| | - Ricardo P. dos Santos
- Engenharia da Computação, Universidade Federal do Ceará (UFC)CEP 62010-560SobralCEBrazil
| | - Jeanlex S. de Sousa
- Departamento de Física, Universidade Federal do Ceará (UFC)CEP 60440-900FortalezaCEBrazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte (UFRN)CEP 59064-741NatalRNBrazil
| | - Valder N. Freire
- Departamento de Física, Universidade Federal do Ceará (UFC)CEP 60440-900FortalezaCEBrazil
| | - Eudenilson L. Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte (UFRN)CEP 59064-741NatalRNBrazil
| | - Roner F. da Costa
- Programa de Pós-Graduação em Ciência e Engenharia de Materiais (PPgCEM), Universidade Federal Rural do Semi-Árido (UFERSA)CEP 59625-900MossoróRNBrazil
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7
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Dutkiewicz Z. Computational methods for calculation of protein-ligand binding affinities in structure-based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2020-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.
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Affiliation(s)
- Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , ul. Grunwaldzka 6 , 60-780 Poznań , Poznan , 60-780, Poland
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8
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França VLB, Amaral JL, Martins YA, Caetano EWS, Brunaldi K, Freire VN. Characterization of the binding interaction between atrazine and human serum albumin: Fluorescence spectroscopy, molecular dynamics and quantum biochemistry. Chem Biol Interact 2022; 366:110130. [PMID: 36037875 DOI: 10.1016/j.cbi.2022.110130] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
Abstract
Atrazine (ATR), one of the most used herbicides worldwide, causes persistent contamination of water and soil due to its high resistance to degradation. ATR is associated with low fertility and increased risk of prostate cancer in humans, as well as birth defects, low birth weight and premature delivery. Describing ATR binding to human serum albumin (HSA) is clinically relevant to future studies about pharmacokinetics, pharmacodynamics and toxicity of ATR, as albumin is the most abundant carrier protein in plasma and binds important small biological molecules. In this work we characterize, for the first time, the binding of ATR to HSA by using fluorescence spectroscopy and performing simulations using molecular docking, classical molecular dynamics and quantum biochemistry based on density functional theory (DFT). We determine the most likely binding sites of ATR to HSA, highlighting the fatty acid binding site FA8 (located between subdomains IA-IB-IIA and IIB-IIIA-IIIB) as the most important one, and evaluate each nearby amino acid residue contribution to the binding interactions explaining the fluorescence quenching due to ATR complexation with HSA. The stabilization of the ATR/FA8 complex was also aided by the interaction between the atrazine ring and SER454 (hydrogen bond) and LEU481(alkyl interaction).
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Affiliation(s)
- Victor L B França
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil
| | - Jackson L Amaral
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil
| | - Yandara A Martins
- Departament of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Ewerton W S Caetano
- Federal Institute of Education, Science and Technology of Ceará, Fortaleza, 60040-531, Brazil
| | - Kellen Brunaldi
- Departament of Physiological Sciences, State University of Maringá, Maringá, 87020-900, Brazil.
| | - Valder N Freire
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil.
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9
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Borgna F, Deberle LM, Busslinger SD, Tschan VJ, Walde LM, Becker AE, Schibli R, Müller C. Preclinical Investigations to Explore the Difference between the Diastereomers [ 177Lu]Lu-SibuDAB and [ 177Lu]Lu-RibuDAB toward Prostate Cancer Therapy. Mol Pharm 2022; 19:2105-2114. [PMID: 35544699 DOI: 10.1021/acs.molpharmaceut.1c00994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[177Lu]Lu-Ibu-DAB-PSMA, a radioligand modified with ibuprofen as the albumin binder, showed higher accumulation in PSMA-positive tumors of mice than the clinically used [177Lu]Lu-PSMA-617 but lower retention in non-targeted tissues than previously developed albumin-binding PSMA radioligands. The aim of this study was to investigate whether the stereochemistry of the incorporated ibuprofen affects the radioligand's in vitro and in vivo properties and to select the more favorable radioligand for further development. For this purpose, SibuDAB and RibuDAB containing (S)- and (R)-ibuprofen, respectively, were synthesized and labeled with lutetium-177. In vitro, the two isomers had similar properties; however, [177Lu]Lu-SibuDAB showed increased binding to mouse and human plasma proteins (91 ± 1 and 88 ± 2%, respectively) compared to [177Lu]Lu-RibuDAB (75 ± 2 and 79 ± 2%, respectively). In vivo, [177Lu]Lu-SibuDAB was metabolically more stable than [177Lu]Lu-RibuDAB with ∼90 vs ∼67% intact radioligand detected in the blood at 4 h post injection (p.i.). In line with the lower albumin-binding affinity, the blood clearance of [177Lu]Lu-RibuDAB in mice was considerably faster [27% of injected activity (% IA), 1 h p.i.] than for [177Lu]Lu-SibuDAB (50% IA, 1 h p.i.). Time-dependent biodistribution studies performed in tumor-bearing athymic nude mice showed high PSMA-specific tumor uptake for both isomers. A twofold increased area under the curve (AUC0→8d) of the blood retention was determined for [177Lu]Lu-SibuDAB as compared to [177Lu]Lu-RibuDAB, whereas the kidney AUC0→8d value of [177Lu]Lu-SibuDAB was only half as high as for [177Lu]Lu-RibuDAB. As a result, a more favorable tumor-to-kidney AUC0→8d ratio was obtained for [177Lu]Lu-SibuDAB, which was also visualized on SPECT/CT images. Based on its improved kidney clearance and higher metabolic stability, [177Lu]Lu-SibuDAB was selected as the more favorable radioligand. Therapy studies performed with [177Lu]Lu-SibuDAB (5 MBq/mouse) demonstrated the anticipated therapeutic superiority over the current gold-standard [177Lu]Lu-PSMA-617 (5 MBq/mouse). The significantly increased survival time of mice treated with [177Lu]Lu-SibuDAB as compared to those injected with [177Lu]Lu-PSMA-617 justifies further development of this novel radioligand toward clinical application.
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Affiliation(s)
- Francesca Borgna
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland
| | - Luisa M Deberle
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland
| | - Sarah D Busslinger
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland
| | - Viviane J Tschan
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland
| | - Laura M Walde
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland
| | - Anna E Becker
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland
| | - Roger Schibli
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland.,Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Cristina Müller
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, Villigen-PSI 5232, Switzerland.,Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
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10
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Tavares ABMLA, Lima Neto JX, Fulco UL, Albuquerque EL. Blockade of the checkpoint PD-1 by its ligand PD-L1 and the immuno-oncological drugs pembrolizumab and nivolumab. Phys Chem Chem Phys 2021; 23:21207-21217. [PMID: 34533552 DOI: 10.1039/d1cp03064g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We investigate the interaction between the programmed cell death protein 1 (PD-1) and the programmed cell death ligand 1 (PD-L1), as well as the immuno-oncological drugs pembrolizumab (PEM), and nivolumab (NIV), through quantum chemistry methods based on the Density Functional Theory (DFT) and the molecular fractionation with conjugate caps (MFCC) scheme, in order to map their hot-spot regions. Our results showed that the total interaction energy order of the three complexes is in good agreement with the experimental binding affinity order: PD-1/PEM > PD-1/NIV > PD-1/PD-L1. Besides, a detailed investigation revealed the energetically most relevant residue-residue pairs-interaction for each complex. Our computational results give a better understanding of the interaction mechanism between the protein PD-1 and its ligands (natural and inhibitors), unleashing the immune surveillance to destroy the cancer cells by decreasing their immune evasion. They are also an efficient alternative towards the development of new small-molecules and antibody-based drugs, pointing out to new treatments for cancer therapy.
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Affiliation(s)
- Ana Beatriz M L A Tavares
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil. .,Hospital das Clínicas, Universidade Federal de Pernambuco, 50.670-901, Recife-PE, Brazil
| | - J X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
| | - E L Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil.
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11
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Kalhor HR, Taghikhani E. Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release. J Chem Inf Model 2021; 61:4045-4057. [PMID: 34292735 DOI: 10.1021/acs.jcim.1c00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned randomly and distant from the binary complex (HSA-warfarin) in a physiologically relevant concentration. The results obtained from both approaches indicated that s-ibuprofen and ascorbic acid both displayed allosteric effects on the release of warfarin from HSA. Although ascorbic acid aided in warfarin release, leading to destabilization of HSA, ibuprofen demonstrated a stabilizing effect on releasing the anticoagulant drug through several noncovalent interactions, including hydrophobic, electrostatic, and hydrogen-bonding interactions with the protein. The calculated binding free energy and energy contribution of involved residues using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method, along with root mean square deviation (RMSD) values, protein gyration, and free energy surface (FES) mapping of the protein, provided valuable details on the nature of the interactions of each drug on the release of warfarin from HSA. These results can provide important information on the mechanisms of anticoagulant release that has not been revealed in molecular details previously.
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Affiliation(s)
- Hamid Reza Kalhor
- Biochemistry Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Elham Taghikhani
- Biochemistry Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
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12
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Nevídalová H, Michalcová L, Glatz Z. Applicability of capillary electrophoresis-frontal analysis for displacement studies: Effect of several drugs on l-tryptophan and lidocaine binding to human serum albumin. J Sep Sci 2020; 43:4225-4233. [PMID: 32966669 DOI: 10.1002/jssc.202000594] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/27/2020] [Accepted: 09/17/2020] [Indexed: 01/30/2023]
Abstract
The effective concentration of a drug in the blood, i.e. the concentration of a free drug in the blood, is influenced by the strength of drug binding onto plasma proteins. Besides its efficacy, these interactions subsequently influence the liberation, absorption, distribution, metabolism, excretion, and toxicological properties of the drug. It is important to not only determine the binding strength and stoichiometry, but also the binding site of a drug on the plasma protein molecule, because the co-administration of drugs with the same binding site can affect the above-mentioned concentration and as a result the pharmacological behavior of the drugs and lead to side effects caused by the change in free drug concentration, its toxicity. In this study, the binding characteristics of six drugs with human serum albumin, the most abundant protein in human plasma, were determined by capillary electrophoresis-frontal analysis, and the obtained values of binding parameters were compared with the literature data. The effect of several drugs and site markers on the binding of l-tryptophan and lidocaine to human serum albumin was investigated in subsequent displacement studies which thus demonstrated the usability of capillary electrophoresis as an automated high-throughput screening method for drug-protein binding studies.
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Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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13
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Mazurek AH, Szeleszczuk Ł, Pisklak DM. Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences. Pharmaceutics 2020; 12:E415. [PMID: 32369915 PMCID: PMC7284980 DOI: 10.3390/pharmaceutics12050415] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.
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Affiliation(s)
| | - Łukasz Szeleszczuk
- Chair and Department of Physical Pharmacy and Bioanalysis, Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 str., 02-093 Warsaw, Poland; (A.H.M.); (D.M.P.)
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14
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Bezerra KS, Vianna JF, Lima Neto JX, Ivan Nobre Oliveira J, Albuquerque EL, Fulco UL. Interaction energies between two antiandrogenic and one androgenic agonist receptor in the presence of a T877A mutation in prostate cancer: a quantum chemistry analysis. NEW J CHEM 2020. [DOI: 10.1039/c9nj06276a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We provide a detailed picture of the interactions between the androgen receptor T877A mutation and three different compounds used in the treatment of prostate cancer.
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Affiliation(s)
- K. S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - J. F. Vianna
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - J. X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - J. Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - E. L. Albuquerque
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - U. L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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15
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Morais PA, Maia FF, Solis-Calero C, Caetano EWS, Freire VN, Carvalho HF. The urokinase plasminogen activator binding to its receptor: a quantum biochemistry description within an in/homogeneous dielectric function framework with application to uPA–uPAR peptide inhibitors. Phys Chem Chem Phys 2020; 22:3570-3583. [DOI: 10.1039/c9cp06530j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DFT calculations using the MFCC fragment-based model considering a spatial-dependent dielectric function based on the Poisson–Boltzmann approximation were performed to describe the uPA–uPAR interactions.
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Affiliation(s)
- Pablo A. Morais
- Instituto Federal de Educação
- Ciência e Tecnologia do Ceará
- Campus Horizonte
- Horizonte
- Brazil
| | - Francisco Franciné Maia
- Departamento de Ciências Naturais
- Matemática e Estatística
- Universidade Federal Rural do Semi-Árido
- Mossoró
- Brazil
| | - Christian Solis-Calero
- Departamento de Biologia Estrutural e Funcional
- Instituto de Biologia
- Universidade Estadual de Campinas
- Campinas
- Brazil
| | | | | | - Hernandes F. Carvalho
- Departamento de Biologia Estrutural e Funcional
- Instituto de Biologia
- Universidade Estadual de Campinas
- Campinas
- Brazil
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16
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Campos DMO, Bezerra KS, Esmaile SC, Fulco UL, Albuquerque EL, Oliveira JIN. Intermolecular interactions of cn-716 and acyl-KR-aldehyde dipeptide inhibitors against Zika virus. Phys Chem Chem Phys 2020; 22:15683-15695. [DOI: 10.1039/d0cp02254c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Structural representation and graphic panel showing the most relevant residues that contribute to the ZIKV NS2B–NS3–ligand complexes.
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Affiliation(s)
- Daniel M. O. Campos
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Stephany C. Esmaile
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | | | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
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17
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Role of Herborn (K240E) and Milano Slow (D375H) human serum albumin variants towards binding of phenylbutazone and ibuprofen. Int J Biol Macromol 2019; 134:645-652. [PMID: 31100401 DOI: 10.1016/j.ijbiomac.2019.05.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 02/06/2023]
Abstract
Human serum albumin (HSA) is the binding cargo in blood plasma. The binding of drugs to HSA determines the pharmacokinetics and pharmacodynamics of the drugs. There are 67 natural genetic variants of HSA were reported in literature. Studying the effect of albumin modifications on drug binding helps to treat the patients with proper medication. In the present study, we have aimed to understand the effect of two natural variants of HSA, such as Herborn (K240E) and Milano Slow (D375H) on the binding of phenylbutazone and ibuprofen. For this, we have generated K240E and D375H mutants and also double mutant (K240E/D375H) of HSA using site directed mutagenesis. The recombinant HSA and its variants were expressed in Pichia pastoris. The interaction of HSA and its variants to phenylbutazone and ibuprofen was studied using fluorescence spectroscopy. Our results showed that there is no significant effect of K240E and D375H mutations on phenylbutazone and ibuprofen binding. But the effect is significant when both the mutations were there in a single protein (K240E/D375H). Further, the CD spectroscopy data showed that there is no effect of phenylbutazone and ibuprofen binding on the conformation of protein, except in case of D375H, where there is a conformational change in the binding pocket with the ibuprofen binding.
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18
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Bezerra KS, Fulco UL, Esmaile SC, Lima Neto JX, Machado LD, Freire VN, Albuquerque EL, Oliveira JIN. Ribosomal RNA-Aminoglycoside Hygromycin B Interaction Energy Calculation within a Density Functional Theory Framework. J Phys Chem B 2019; 123:6421-6429. [PMID: 31283875 DOI: 10.1021/acs.jpcb.9b04468] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We intend to investigate the drug-binding energy of each nucleotide inside the aminoglycoside hygromycin B (hygB) binding site of 30S ribosomal RNA (rRNA) subunit by using the molecular fractionation with conjugate caps (MFCC) strategy based on the density functional theory (DFT), considering the functional LDA/PWC, OBS, and the dielectric constant parametrization. Aminoglycosides are bactericidal antibiotics that have high affinity to the prokaryotic rRNA, inhibiting the synthesis of proteins by acting on the main stages of the translation mechanism, whereas binding to rRNA 16S, a component of the 30S ribosomal subunit in prokaryotes. The identification of the nucleotides presenting the most negative binding energies allows us to stabilize hygB in a suitable binding pocket of the 30S ribosomal subunit. In addition, it should be highlighted that mutations in these residues may probably lead to resistance to ribosome-targeting antibiotics. Quantum calculations of aminoglycoside hygromycin B-ribosome complex might contribute to further quantum studies with antibiotics like macrolides and other aminoglycosides.
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Affiliation(s)
- Katyanna S Bezerra
- Departamento de Biofísica e Farmacologia , Universidade Federal do Rio Grande do Norte , 59072-970 Natal-RN , Brazil
| | - Umberto L Fulco
- Departamento de Biofísica e Farmacologia , Universidade Federal do Rio Grande do Norte , 59072-970 Natal-RN , Brazil
| | - Stephany C Esmaile
- Departamento de Biofísica e Farmacologia , Universidade Federal do Rio Grande do Norte , 59072-970 Natal-RN , Brazil
| | - José X Lima Neto
- Departamento de Biofísica e Farmacologia , Universidade Federal do Rio Grande do Norte , 59072-970 Natal-RN , Brazil
| | - Leonardo D Machado
- Departamento de Física Teórica e Experimental , Universidade Federal do Rio Grande do Norte , 59072-970 Natal-RN , Brazil
| | - Valder N Freire
- Departamento de Física , Universidade Federal do Ceará , 60455-760 Fortaleza-CE , Brazil
| | - Eudenilson L Albuquerque
- Departamento de Biofísica e Farmacologia , Universidade Federal do Rio Grande do Norte , 59072-970 Natal-RN , Brazil
| | - Jonas I N Oliveira
- Departamento de Biofísica e Farmacologia , Universidade Federal do Rio Grande do Norte , 59072-970 Natal-RN , Brazil
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19
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Tavares ABMLA, Lima Neto JX, Fulco UL, Albuquerque EL. A quantum biochemistry approach to investigate checkpoint inhibitor drugs for cancer. NEW J CHEM 2019. [DOI: 10.1039/c8nj05561k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We investigate the coupling profiles of the receptor PD-1 in complex with its natural ligand PDL1 and two inhibitor drugs.
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Affiliation(s)
| | - José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
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20
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Vianna JF, S. Bezerra K, I. N. Oliveira J, Albuquerque EL, Fulco UL. Binding energies of the drugs capreomycin and streptomycin in complex with tuberculosis bacterial ribosome subunits. Phys Chem Chem Phys 2019; 21:19192-19200. [DOI: 10.1039/c9cp03631h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We calculated the interaction binding energies of the drugs capreomycin and streptomycin in complex with the tuberculosis bacterial ribosome subunits.
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Affiliation(s)
- Jessica F. Vianna
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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21
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The electrostatic embedding contribution to DFT calculations of ligand-amino acid residues interaction. J Mol Model 2018; 24:211. [DOI: 10.1007/s00894-018-3743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
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22
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Interaction energy profile for diphenyl diselenide in complex with δ-aminolevulinic acid dehydratase enzyme using quantum calculations and a molecular fragmentation method. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.comtox.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Tavares ABMLA, Lima Neto JX, Fulco UL, Albuquerque EL. Inhibition of the checkpoint protein PD-1 by the therapeutic antibody pembrolizumab outlined by quantum chemistry. Sci Rep 2018; 8:1840. [PMID: 29382901 PMCID: PMC5789983 DOI: 10.1038/s41598-018-20325-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
Much of the recent excitement in the cancer immunotherapy approach has been generated by the recognition that immune checkpoint proteins, like the receptor PD-1, can be blocked by antibody-based drugs with profound effects. Promising clinical data have already been released pointing to the efficiency of the drug pembrolizumab to block the PD-1 pathway, triggering the T-lymphocytes to destroy the cancer cells. Thus, a deep understanding of this drug/receptor complex is essential for the improvement of new drugs targeting the protein PD-1. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT), we investigate in silico the binding energy features of the receptor PD-1 in complex with its drug inhibitor. Our computational results give a better understanding of the binding mechanisms, being also an efficient alternative towards the development of antibody-based drugs, pointing to new treatments for cancer therapy.
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Affiliation(s)
- Ana Beatriz M L A Tavares
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - José X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Umberto L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil
| | - Eudenilson L Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
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24
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Lima Costa AH, Clemente WS, Bezerra KS, Lima Neto JX, Albuquerque EL, Fulco UL. Computational biochemical investigation of the binding energy interactions between an estrogen receptor and its agonists. NEW J CHEM 2018. [DOI: 10.1039/c8nj03521k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present the energy profiles of estrogen receptor–agonist ligand interactions in atomic detail using a quantum biochemical approach.
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Affiliation(s)
- Aranthya H. Lima Costa
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Washington S. Clemente
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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25
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Bezerra KS, Lima Neto JX, Oliveira JIN, Albuquerque EL, Caetano EWS, Freire VN, Fulco UL. Computational investigation of the α2β1 integrin–collagen triple helix complex interaction. NEW J CHEM 2018. [DOI: 10.1039/c8nj04175j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, quantum biochemistry methods have been used to describe important protein–protein interactions for the complex integrin–collagen.
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Affiliation(s)
- K. S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - J. X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - J. I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - E. L. Albuquerque
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - E. W. S. Caetano
- Instituto Federal de Educação
- Ciência e Tecnologia do Ceará
- Fortaleza-CE
- Brazil
| | - V. N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| | - U. L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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26
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Solis-Calero C, Zanatta G, Pessoa CDÓ, Carvalho HF, Freire VN. Explaining urokinase type plasminogen activator inhibition by amino-5-hydroxybenzimidazole and two naphthamidine-based compounds through quantum biochemistry. Phys Chem Chem Phys 2018; 20:22818-22830. [DOI: 10.1039/c8cp04315a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Urokinase plasminogen activator (uPA) is a biomarker and therapeutic target for several cancer types whose inhibition has been shown to slow tumor growth and metastasis.
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Affiliation(s)
- Christian Solis-Calero
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Geancarlo Zanatta
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
| | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology
- Federal University of Ceará
- 60430-270 Fortaleza
- Brazil
| | - Hernandes F. Carvalho
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Valder N. Freire
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
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27
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Lima Neto JX, Soares-Rachetti VP, Albuquerque EL, Manzoni V, Fulco UL. Outlining migrainous through dihydroergotamine–serotonin receptor interactions using quantum biochemistry. NEW J CHEM 2018. [DOI: 10.1039/c7nj03645k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the electronic structure of the complex dihydroergotamine–serotonin receptor to unveil new medications to treat migraine and related diseases.
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Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | | | - Vinicius Manzoni
- Instituto de Física
- Universidade Federal de Alagoas
- Maceio-AL
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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28
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de Sousa B, Oliveira J, Albuquerque E, Fulco U, Amaro V, Blaha C. Molecular modelling and quantum biochemistry computations of a naturally occurring bioremediation enzyme: Alkane hydroxylase from Pseudomonas putida P1. J Mol Graph Model 2017; 77:232-239. [DOI: 10.1016/j.jmgm.2017.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/24/2017] [Accepted: 08/26/2017] [Indexed: 12/29/2022]
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29
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Neto JXL, Bezerra KS, Manso DN, Mota KB, Oliveira JIN, Albuquerque EL, Caetano EWS, Freire VN, Fulco UL. Energetic description of cilengitide bound to integrin. NEW J CHEM 2017. [DOI: 10.1039/c7nj02166f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ quantum chemistry methods to investigate the binding energy features of the cyclic RGD pentapeptide cilengitide interacting with the integrin receptor αVβ3.
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Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Dalila N. Manso
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Kyvia B. Mota
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | | | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza-CE
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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30
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Martins ACV, de-Lima-Neto P, Caetano EWS, Freire VN. An improved quantum biochemistry description of the glutamate–GluA2 receptor binding within an inhomogeneous dielectric function framework. NEW J CHEM 2017. [DOI: 10.1039/c6nj03939a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new methodology to define the inhomogeneous dielectric constant of protein residues, to apply to the calculation of protein–ligand properties such as the electrostatic interaction.
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Affiliation(s)
- A. C. V. Martins
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - P. de-Lima-Neto
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - E. W. S. Caetano
- Federal Institute of Education
- Science and Technology of Ceara
- 60040-531 Fortaleza
- Brazil
| | - V. N. Freire
- Department of Physics
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
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31
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Bezerra KS, Oliveira JIN, Lima Neto JX, Albuquerque EL, Caetano EWS, Freire VN, Fulco UL. Quantum binding energy features of the T3-785 collagen-like triple-helical peptide. RSC Adv 2017. [DOI: 10.1039/c6ra25206k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Structural representation of the T3-785 collagen-like triple-helical peptide depicting the 15 most and fewest energetically significant amino acids.
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Affiliation(s)
- Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | | | | | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
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32
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Mota K, Lima Neto J, Lima Costa A, Oliveira J, Bezerra K, Albuquerque E, Caetano E, Freire V, Fulco U. A quantum biochemistry model of the interaction between the estrogen receptor and the two antagonists used in breast cancer treatment. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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34
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Sousa BL, Barroso-Neto IL, Oliveira EF, Fonseca E, Lima-Neto P, Ladeira LO, Freire VN. Explaining RANKL inhibition by OPG through quantum biochemistry computations and insights into peptide-design for the treatment of osteoporosis. RSC Adv 2016. [DOI: 10.1039/c6ra16712h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Quantum biochemistry computations are applied to precisely describe important protein–protein interactions, providing a basis for the design of inhibitory peptides against osteoporosis.
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Affiliation(s)
- Bruno L. Sousa
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Ito L. Barroso-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | | | - Emerson Fonseca
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Pedro Lima-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Luiz O. Ladeira
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
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35
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Ourique GS, Vianna JF, Neto JXL, Oliveira JIN, Mauriz PW, Vasconcelos MS, Caetano EWS, Freire VN, Albuquerque EL, Fulco UL. A quantum chemistry investigation of a potential inhibitory drug against the dengue virus. RSC Adv 2016. [DOI: 10.1039/c6ra10121f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The total interaction energy of the inhibitor Bz-nKRR-H bound to a serine protease of the dengue virus is mainly due to the action of Asn152, Met49, Tyr161, Asp129 and Gly151 (Met84, Met75, Asp81, Asp79 and Asp80) residues at the NS3 (NS2B) subunit.
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Affiliation(s)
- G. S. Ourique
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - J. F. Vianna
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - J. X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - J. I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - P. W. Mauriz
- Departamento de Física
- Instituto Federal de Educação
- Ciência e Tecnologia do Maranhão
- São Luís
- Brazil
| | - M. S. Vasconcelos
- Escola de Ciência e Tecnologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - E. W. S. Caetano
- Instituto Federal de Educação
- Ciência e Tecnologia do Ceará
- Fortaleza
- Brazil
| | - V. N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - E. L. Albuquerque
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - U. L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
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36
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Maniruzzaman M, Snowden MJ, Bradely MS, Douroumis D. Studies of intermolecular interactions in solid dispersions using advanced surface chemical analysis. RSC Adv 2015. [DOI: 10.1039/c5ra13176f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The aim of this study is to utilise an advanced surface chemical analysis based on X-ray photoelectron spectroscopy (XPS) to determine and characterise drug/polymer interactions in solid dispersions manufactured via hot melt extrusion (HME).
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Affiliation(s)
- M. Maniruzzaman
- Faculty of Engineering and Science
- University of Greenwich
- Chatham Maritime
- UK
| | - Martin J. Snowden
- Faculty of Engineering and Science
- University of Greenwich
- Chatham Maritime
- UK
| | - Mike S. Bradely
- Faculty of Engineering and Science
- University of Greenwich
- Chatham Maritime
- UK
| | - D. Douroumis
- Faculty of Engineering and Science
- University of Greenwich
- Chatham Maritime
- UK
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