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Sarra H, Salim B, Hocine A. Modeling the Antiviral Activity of Ginkgo biloba Polyphenols against Variola: In Silico Exploration of Inhibitory Candidates for VarTMPK and HssTMPK Enzymes. Curr Drug Discov Technol 2024; 21:e101023221938. [PMID: 37861017 DOI: 10.2174/0115701638261541230922095853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND The aim of this study is to use modeling methods to estimate the antiviral activity of natural molecules extracted from Ginkgo biloba for the treatment of variola which is a zoonotic disease posing a growing threat to human survival. The recent spread of variola in nonendemic countries and the possibility of its use as a bioterrorism weapon have made it a global threat once again. Therefore, the search for new antiviral therapies with reduced side effects is necessary. METHODS In this study, we examined the interactions between polyphenolic compounds from Ginkgo biloba, a plant known for its antiviral activity, and two enzymes involved in variola treatment, VarTMPK and HssTMPK, using molecular docking. RESULTS The obtained docking scores showed that among the 152 selected polyphenolic compounds; many ligands had high inhibitory potential according to the energy affinity. By considering Lipinski's rules, we found that Liquiritin and Olivil molecules are the best candidates to be developed into drugs that inhibit VarTMPK because of their high obtained scores compared to reference ligands, and zero violations of Lipinski's rules. We also found that ginkgolic acids have good affinities with HssTMPK and acceptable physicochemical properties to be developed into drugs administered orally. CONCLUSION Based on the obtained scores and Lipinski's rules, Liquiritin, Olivil, and ginkgolic acids molecules showed interesting results for both studied enzymes, indicating the existence of promising and moderate activity of these polyphenols for the treatment of variola and for possible multi-targeting. Liquiritin has been shown to exhibit anti-inflammatory effects on various inflammation- related diseases such as skin injury, hepatic inflammatory injury, and rheumatoid arthritis. Olivil has been shown to have antioxidant activity. Olivil derivatives have also been studied for their potential use as anticancer agents. Ginkgolic acids have been shown to have antimicrobial and antifungal properties. However, ginkgolic acids are also known to cause allergic reactions in some people. Therefore, future studies should consider these results and explore the potential of these compounds as antiviral agents. Further experimental studies in-vitro and in-vivo are required to validate and scale up these findings.
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Affiliation(s)
- Hamdani Sarra
- Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
- Laboratory of Natural and Bioactive Substances (LASNABIO), Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
| | - Bouchentouf Salim
- Laboratory of Natural and Bioactive Substances (LASNABIO), Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
- Department of Process Engineering, Faculty of Technology, Doctor Tahar Moulay University of Saida, Algeria, Saïda 20000, BP 138 cité EN-NASR, Algeria
| | - Allali Hocine
- Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
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Lu J, Xing H, Wang C, Tang M, Wu C, Ye F, Yin L, Yang Y, Tan W, Shen L. Mpox (formerly monkeypox): pathogenesis, prevention, and treatment. Signal Transduct Target Ther 2023; 8:458. [PMID: 38148355 PMCID: PMC10751291 DOI: 10.1038/s41392-023-01675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 12/28/2023] Open
Abstract
In 2022, a global outbreak of Mpox (formerly monkeypox) occurred in various countries across Europe and America and rapidly spread to more than 100 countries and regions. The World Health Organization declared the outbreak to be a public health emergency of international concern due to the rapid spread of the Mpox virus. Consequently, nations intensified their efforts to explore treatment strategies aimed at combating the infection and its dissemination. Nevertheless, the available therapeutic options for Mpox virus infection remain limited. So far, only a few numbers of antiviral compounds have been approved by regulatory authorities. Given the high mutability of the Mpox virus, certain mutant strains have shown resistance to existing pharmaceutical interventions. This highlights the urgent need to develop novel antiviral drugs that can combat both drug resistance and the potential threat of bioterrorism. Currently, there is a lack of comprehensive literature on the pathophysiology and treatment of Mpox. To address this issue, we conducted a review covering the physiological and pathological processes of Mpox infection, summarizing the latest progress of anti-Mpox drugs. Our analysis encompasses approved drugs currently employed in clinical settings, as well as newly identified small-molecule compounds and antibody drugs displaying potential antiviral efficacy against Mpox. Furthermore, we have gained valuable insights from the process of Mpox drug development, including strategies for repurposing drugs, the discovery of drug targets driven by artificial intelligence, and preclinical drug development. The purpose of this review is to provide readers with a comprehensive overview of the current knowledge on Mpox.
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Affiliation(s)
- Junjie Lu
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Hui Xing
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Chunhua Wang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Mengjun Tang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Fan Ye
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China
| | - Lijuan Yin
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for infectious disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, 518112, China.
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Liang Shen
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Hubei Province, Xiangyang, 441021, China.
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Alagarsamy V, Shyam Sundar P, Raja Solomon V, Narendhar B, Sulthana MT, Rohitha K, Dhanwar S, Dharshini Aishwarya A, Murugesan S. Pharmacophore modelling-based drug repurposing approaches for monkeypox therapeutics. J Biomol Struct Dyn 2023; 41:10678-10689. [PMID: 36905675 DOI: 10.1080/07391102.2023.2188428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 03/13/2023]
Abstract
Monkeypox is a zoonotic viral disease that mainly affects tropical rainforest regions of central and west Africa, with sporadic exportations to other places. Since there is no cure, treating monkeypox with an antiviral drug developed for smallpox is currently acceptable. Our study mainly focused on finding new therapeutics to target monkeypox from existing compounds or medications. It is a successful method for discovering or developing medicinal compounds with novel pharmacological or therapeutic applications. In this study, homology modelling developed the Monkeypox VarTMPK (IMNR) structure. Ligand-based pharmacophore was generated using the best docking pose of standard ticovirimat. Further, molecular docking analysis showed compounds, tetrahydroxycurcumin, procyanidin, rutin, vicenin-2, kaempferol 3-(6''-malonylglucoside) were the top five binding energy compounds against VarTMPK (1MNR). Furthermore, we carried out MD simulations for 100 ns for the six compounds, including reference based on the binding energies and interactions. MD studies revealed that as ticovirimat interacted with residues Lys17, Ser18, and Arg45, all the above five compounds interacted with the same amino acids at the active site during docking and simulation studies. Among all the compounds, ZINC4649679 (Tetrahydroxycurcumin) was shown to have the highest binding energy -9.7 kcal/mol and also observed stable protein-ligand complex during MD studies. ADMET profile estimation showed that the docked phytochemicals were safe. However, further biological assessment through a wet lab is essential to measure the efficacy and safety of the compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- V Alagarsamy
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - P Shyam Sundar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - V Raja Solomon
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - B Narendhar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - M T Sulthana
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Kotha Rohitha
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Sangeeta Dhanwar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - A Dharshini Aishwarya
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - S Murugesan
- Department of Pharmacy, BITS, Pilani, Pilani, Rajasthan, India
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Srivastava V, Naik B, Godara P, Das D, Mattaparthi VSK, Prusty D. Identification of FDA-approved drugs with triple targeting mode of action for the treatment of monkeypox: a high throughput virtual screening study. Mol Divers 2023:10.1007/s11030-023-10636-4. [PMID: 37079243 PMCID: PMC10116100 DOI: 10.1007/s11030-023-10636-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/17/2023] [Indexed: 04/21/2023]
Abstract
According to the Center for Disease Control and Prevention, as of August 23, 94 countries had confirmed 42,954 Monkeypox Virus cases. As specific monkeypox drugs are not yet developed, the treatment depends on repurposed FDA-approved drugs. According to a recent study, the Monkeypox outbreak is caused by a strain with a unique mutation, raising the likelihood that the virus will develop resistance to current drugs by acquiring mutations in the targets of currently used drugs. The probability of multiple mutations in two or more drug targets at a time is always low than mutation in a single drug target. Therefore, we identified 15 triple-targeting FDA-approved drugs that can inhibit three viral targets, including topoisomerase1, p37, and thymidylate kinase, using high throughput virtual screening approach. Further, the molecular dynamics simulation analysis of the top hits such as Naldemedine and Saquinavir with their respective targets reveals the formation of stable conformational changes of the ligand-protein complexes inside the dynamic biological environment. We suggest further research on these triple-targeting molecules to develop an effective therapy for the currently spreading Monkeypox.
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Affiliation(s)
- Varshita Srivastava
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Priya Godara
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Dorothy Das
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Venkata Satish Kumar Mattaparthi
- Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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5
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Monkeypox infection: The past, present, and future. Int Immunopharmacol 2022; 113:109382. [PMID: 36330915 PMCID: PMC9617593 DOI: 10.1016/j.intimp.2022.109382] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
Monkeypox is a zoonotic illness caused by the monkeypox virus (MPXV) that has a similar etiology to smallpox. The first case of monkeypox was reported in Western and Central Africa in 1971, and in 2003, there was an outbreak of monkeypox viruses outside Africa. According to the World Health Organization (WHO) and Center for Disease Control and Prevention (CDC), monkeypox is transmitted through direct contact with infected animals or persons exposed to infectious sores, scabs, or body fluids. Also, intimate contact between people during sex, kissing, cuddling, or touching parts of the body can result in the spreading of this disease. The use of the smallpox vaccine against monkeypox has several challenges and hence anti-virals such as cidofovir, brincidofovir, and tecovirimat have been used for the symptomatic relief of patients and reversing the lesion formation on the skin. Despite the recent outbreak of monkeypox most especially in hitherto non-endemic countries, there is still a lack of definitive treatment for monkeypox. In the present review, emphasis was focused on etiopathology, transmission, currently available therapeutic agents, and future targets that could be explored to halt the progression of monkeypox. From our review we can postulate that owing to the lack of a definitive cure to this reemerging disorder, there is a need for general awareness about the transmission as well as to develop appropriate diagnostic procedures, immunizations, and antiviral medication.
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Key Words
- monkeypox
- infection
- etiopathology
- prevention
- vaccines
- therapeutic targets
- abs, antibodies
- acip, advisory committee on immunization practices
- cdc, centers for disease control and prevention
- cev, cell-associated enveloped virus
- cfr, case fatality rate
- cpxv, cowpox virus
- drc, democratic republic of the congo
- eev, extracellular enveloped virus
- hsv, herpes simplex virus
- iev, intracellular enveloped virus
- ifn-γ, interferon
- imv, internal mature virus
- mhc, major histocompatibility complex
- mpxv, human monkeypox virus
- nk, natural killer
- opxvs, orthopoxviruses
- pcr, polymerase chain reaction
- pfu, plaque-forming units
- ppe, personal protective equipment
- prep, pre-exposure prophylaxis
- th, t-helper
- tlrs, toll-like receptors
- tnf-α, tumor necrotic factor
- vacv, vaccinia virus
- varv, smallpox virus
- varv, variola major virus
- vzv, varicella-zoster virus
- who, world health organization
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6
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Rahimi F, Talebi Bezmin Abadi A. The 2022 monkeypox outbreak: Lessons from the 640 cases in 36 countries. Int J Surg 2022; 104:106712. [PMID: 35710067 PMCID: PMC9353591 DOI: 10.1016/j.ijsu.2022.106712] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/11/2022] [Indexed: 01/10/2023]
Affiliation(s)
- Farid Rahimi
- Research School of Biology, The Australian National University, Ngunnawal and Ngambri Country, Canberra, Australia
| | - Amin Talebi Bezmin Abadi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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7
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Garcia DR, Souza FR, Guimarães AP, Valis M, Pavelek Z, Kuca K, Ramalho TC, França TCC. In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus. Pharmaceuticals (Basel) 2021; 14:ph14101027. [PMID: 34681251 PMCID: PMC8537287 DOI: 10.3390/ph14101027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Continuing the work developed by our research group, in the present manuscript, we performed a theoretical study of 10 new structures derived from the antivirals cidofovir and ribavirin, as inhibitor prototypes for the enzyme thymidylate kinase from Variola virus (VarTMPK). The proposed structures were subjected to docking calculations, molecular dynamics simulations, and free energy calculations, using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, inside the active sites of VarTMPK and human TMPK (HssTMPK). The docking and molecular dynamic studies pointed to structures 2, 3, 4, 6, and 9 as more selective towards VarTMPK. In addition, the free energy data calculated through the MM-PBSA method, corroborated these results. This suggests that these compounds are potential selective inhibitors of VarTMPK and, thus, can be considered as template molecules to be synthesized and experimentally evaluated against smallpox.
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Affiliation(s)
- Danielle R. Garcia
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, Rio de Janeiro 22290-270, Brazil;
| | - Felipe R. Souza
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro 22541-041, Brazil;
| | - Ana P. Guimarães
- Department of Chemistry, Federal University of Viçosa, Avenida P. H. Rolfs, s/n, Centro, Viçosa 36570-000, MG, Brazil;
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic; (M.V.); (Z.P.)
| | - Zbyšek Pavelek
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic; (M.V.); (Z.P.)
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic
- Correspondence: (K.K.); (T.C.C.F.)
| | - Teodorico C. Ramalho
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Laboratory of Computational Chemistry, Department of Chemistry, UFLA, Lavras 37200-000, MG, Brazil
| | - Tanos C. C. França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, Rio de Janeiro 22290-270, Brazil;
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Correspondence: (K.K.); (T.C.C.F.)
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8
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Botelho FD, Santos MC, Gonçalves AS, França TCC, LaPlante SR, de Almeida JSFD. Identification of novel potential ricin inhibitors by virtual screening, molecular docking, molecular dynamics and MM-PBSA calculations: a drug repurposing approach. J Biomol Struct Dyn 2021; 40:5309-5319. [PMID: 33410376 DOI: 10.1080/07391102.2020.1870154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ricin is a potent cytotoxin with no available antidote. Its catalytic subunit, RTA, damages the ribosomal RNA (rRNA) of eukaryotic cells, preventing protein synthesis and eventually leading to cell death. The combination between easiness of obtention and high toxicity turns ricin into a potential weapon for terrorist attacks, urging the need of discovering effective antidotes. On this context, we used computational techniques, in order to identify potential ricin inhibitors among approved drugs. Two libraries were screened by two different docking algorithms, followed by molecular dynamics simulations and MM-PBSA calculations in order to corroborate the docking results. Three drugs were identified as potential ricin inhibitors: deferoxamine, leucovorin and plazomicin. Our calculations showed that these compounds were able to, simultaneously, form hydrogen bonds with residues of the catalytic site and the secondary binding site of RTA, qualifying as potential antidotes against intoxication by ricin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fernanda D Botelho
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Marcelo C Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
| | - Arlan S Gonçalves
- Federal Institute of Education Science and Technology - unit Vila Velha/ES, Brazil.,PPGQUI (Graduate Program in Chemistry), Federal University of Espirito Santo - Unit Goiabeiras, Vitória/ES, Brazil
| | - Tanos C C França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil.,INRS, Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC, Canada.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC, Canada
| | - Joyce S F D de Almeida
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro/RJ, Brazil
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Souza FD, Rodrigues Garcia D, Cuya T, Pimentel AS, Gonçalves ADS, Alencastro RBD, França TCC. Molecular Modeling Study of Uncharged Oximes Compared to HI-6 and 2-PAM Inside Human AChE Sarin and VX Conjugates. ACS OMEGA 2020; 5:4490-4500. [PMID: 32175496 PMCID: PMC7066550 DOI: 10.1021/acsomega.9b03737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
The deleterious effects of nerve agents over the enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) turned these compounds into the most dangerous chemical weapons known. Among the antidotes in use today against these agents, oximes in combination with other drugs are the only treatment with any action. HI-6 and 2-PAM are cationic oximes proved to be effective for the reactivation of AChE inhibited by the nerve agents VX and sarin (GB). However, when it comes to reactivation of AChE inside the central or peripheral nervous systems, charged molecules present low diffusion due to low penetration through the blood-brain barrier. Uncharged oximes appear as an interesting alternative to solve this problem, but the development and enhancement of more efficient uncharged oximes capable of reactivating human AChE is still necessary. Given the limitations for in vivo and in vitro experimental studies with nerve agents, modeling is an important tool that can contribute to a better understanding of factors that may affect the efficiency of uncharged oximes. In order to investigate the interaction and behavior of cationic and uncharged oximes, we performed here molecular docking, molecular dynamics simulations, and binding energies calculations of the known cationic oximes HI-6 and 2-PAM plus four uncharged oximes found in the literature, complexed with human AChE (HssACHE) conjugated with the nerve agents VX and GB. The uncharged oximes showed different behaviors, especially RS194B, which presented stability inside AChE-VX, but presented free binding energy lower than cationic oximes, suggesting that structural alterations could favor its interactions with these complexes. In contrast, HI-6 and 2-PAM showed higher affinities with more negative binding energy values and larger contribution of the amino acid Asp74, demonstrating the importance of the quaternary nitrogen to the affinity and interaction of oximes with AChE-GB and AChE-VX conjugates.
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Affiliation(s)
- Felipe
Rodrigues de Souza
- Laboratory
of Molecular Modeling Applied
to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, 22290-270 Rio de Janeiro/RJ, Brazil
- Department
of Chemistry, Pontifical Catholic University
of Rio de Janeiro, 22451-900 Rio de Janeiro/RJ, Brazil
| | - Danielle Rodrigues Garcia
- Laboratory
of Molecular Modeling Applied
to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, 22290-270 Rio de Janeiro/RJ, Brazil
| | - Teobaldo Cuya
- Faculty
of Technology, University of the State of
Rio de Janeiro, 27537-000 Resende/RJ, Brazil
| | - André Silva Pimentel
- Department
of Chemistry, Pontifical Catholic University
of Rio de Janeiro, 22451-900 Rio de Janeiro/RJ, Brazil
| | - Arlan da Silva Gonçalves
- Postgraduate
Program in Sustainable Technologies (PPGTECS), Federal Institute of Education Science and Technology of Espírito
Santo, Unit Vila Velha, 29056-255 Vila Velha/ES, Brazil
- Postgraduate
Program in Chemistry (PPGQUI), Federal University
of Espírito Santo, 29075-910 Vitória, ESBrazil
| | | | - Tanos Celmar Costa França
- Laboratory
of Molecular Modeling Applied
to Chemical and Biological Defense (LMCBD), Military Institute of Engineering, 22290-270 Rio de Janeiro/RJ, Brazil
- Department
of Chemistry, Faculty of Science, University
of Hradec Kralove, Rokitanskeho
62, 50003 Hradec
Kralove, Czech Republic
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10
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Chen MD, Fucci IJ, Sinha K, Rule GS. dGMP Binding to Thymidylate Kinase from Plasmodium falciparum Shows Half-Site Binding and Induces Protein Dynamics at the Dimer Interface. Biochemistry 2020; 59:694-703. [PMID: 31934749 DOI: 10.1021/acs.biochem.9b00898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) is an essential enzyme for the growth of the organism because of its critical role in the de novo synthesis of deoxythymidine 5'-diphosphate (TDP), a precursor for TTP that is required for DNA replication and repair. The kinetics, thermodynamic parameters, and substrate binding properties of PfTMK for TMP, dGMP, ADP, and ATP were measured and characterized by steady-state kinetics and a combination of isothermal titration calorimetry, tryptophan fluorescence titration, and NMR. Mutational studies were performed to investigate residues that contribute to the unique ability of PfTMK to also utilize dGMP as a substrate. Isothermal titration calorimetry experiments revealed that dGMP binding exhibits a unique half-site binding mechanism. The occlusion of the empty site in the dGMP complex is supported by molecular mechanics calculations. Relaxation dispersion experiments show that the dGMP and enzyme complex is more dynamic at the dimer interface than the TMP complex on the μs-ms time scale. The unique properties of dGMP binding need to be considered in the design of guanosine-based PfTMK-specific inhibitors.
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Affiliation(s)
- Mengshen David Chen
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Ian J Fucci
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Kaustubh Sinha
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Gordon S Rule
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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