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Alzamami A, Alturki NA, Khan K, Basharat Z, Mashraqi MM. Screening inhibitors against the Ef-Tu of Fusobacterium nucleatum: a docking, ADMET and PBPK assessment study. Mol Divers 2024:10.1007/s11030-024-10815-x. [PMID: 38457020 DOI: 10.1007/s11030-024-10815-x] [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: 08/08/2023] [Accepted: 01/21/2024] [Indexed: 03/09/2024]
Abstract
The oral pathogen Fusobacterium nucleatum has recently been associated with an elevated risk of colorectal cancer (CRC), endometrial metastasis, chemoresistance, inflammation, metastasis, and DNA damage, along with several other diseases. This study aimed to explore the disruption of protein machinery of F. nucleatum via inhibition of elongation factor thermo unstable (Ef-Tu) protein, through natural products. No study on Ef-Tu inhibition by natural products or in Fusobacterium spp. exists till todate. Ef-Tu is an abundant specialized drug target in bacteria that varies from human Ef-Tu. Elfamycins target Ef-Tu and hence, Enacyloxin IIa was used to generate pharmacophore for virtual screening of three natural product libraries, Natural Product Activity and Species Source (NPASS) (n = 30000 molecules), Tibetan medicinal plant database (n = 54 molecules) and African medicinal plant database (n > 6000 molecules). Peptaibol Septocylindrin B (NPC141050), Hirtusneanoside, and ZINC95486259 were prioritized from these libraries as potential therapeutic candidates. ADMET profiling was done for safety assessment, physiological-based pharmacokinetic modeling in human and mouse for getting insight into drug interaction with body tissues and molecular dynamics was used to assess stability of the best hit NPC141050 (Septocylindrin B). Based on the promising results, we propose further in vitro, in vivo and pharmacokinetic testing on the lead Septocylindrin B, for possible translation into therapeutic interventions.
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Affiliation(s)
- Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Sciences, Shaqra University, 11961, Al-Quwayiyah, Saudi Arabia
| | - Norah A Alturki
- Clinical Laboratory Science Department, College of Applied Medical Sciences, King Saud University, 11433, Riyadh, Saudi Arabia
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Zarrin Basharat
- Alpha Genomics (Private) Limited, Islamabad, 45710, Pakistan.
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia.
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Di Martino RMC, Cavalli A, Bottegoni G. Dopamine D3 receptor ligands: a patent review (2014-2020). Expert Opin Ther Pat 2022; 32:605-627. [PMID: 35235753 DOI: 10.1080/13543776.2022.2049240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Compelling evidence identified D3 dopamine receptor (D3R) as a suitable target for therapeutic intervention on CNS-associated disorders, cancer and other conditions. Several efforts have been made toward developing potent and selective ligands for modulating signalling pathways operated by these GPCRs. The rational design of D3R ligands endowed with a pharmacologically relevant profile has traditionally not encountered much support from computational methods due to a very limited knowledge of the receptor structure and of its conformational dynamics. We believe that recent progress in structural biology will change this state of affairs in the next decade. AREAS COVERED This review provides an overview of the recent (2014-2020) patent literature on novel classes of D3R ligands developed within the framework of CNS-related diseases, cancer and additional conditions. When possible, an in-depth description of both in vitro and in vivo generated data is presented. New therapeutic applications of known molecules with activity at D3R are discussed. EXPERT OPINION Building on current knowledge, future D3R-focused drug discovery campaigns will be propelled by a combination of unprecedented availability of structural information with advanced computational and analytical methods. The design of D3R ligands with the sought activity, efficacy and selectivity profile will become increasingly more streamlined.
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Affiliation(s)
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.,Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Bologna University, via Belmeloro 6, 40126, Bologna, Italy
| | - Giovanni Bottegoni
- Department of Biomolecular Sciences, Urbino University "Carlo Bo", Piazza Rinascimento 6, 61029, Urbino, Italy.,Institute of Clinical Sciences, University of Birmingham, Edgbaston, B15 2TT, Birmingham, UK
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Doorandishan M, Pirhadi S, Swilam MM, Gholami M, Ebrahimi P, El-Seedi HR, Jassbi AR. Molecular docking and simulation studies of a novel labdane type- diterpene from Moluccella aucheri Scheen (Syn. Otostegia aucheri) as human- AChE inhibitor. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zelepuga EA, Silchenko AS, Avilov SA, Kalinin VI. Structure-Activity Relationships of Holothuroid's Triterpene Glycosides and Some In Silico Insights Obtained by Molecular Dynamics Study on the Mechanisms of Their Membranolytic Action. Mar Drugs 2021; 19:md19110604. [PMID: 34822475 PMCID: PMC8625879 DOI: 10.3390/md19110604] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
The article describes the structure-activity relationships (SAR) for a broad series of sea cucumber glycosides on different tumor cell lines and erythrocytes, and an in silico modulation of the interaction of selected glycosides from the sea cucumber Eupentacta fraudatrix with model erythrocyte membranes using full-atom molecular dynamics (MD) simulations. The in silico approach revealed that the glycosides bound to the membrane surface mainly through hydrophobic interactions and hydrogen bonds. The mode of such interactions depends on the aglycone structure, including the side chain structural peculiarities, and varies to a great extent. Two different mechanisms of glycoside/membrane interactions were discovered. The first one was realized through the pore formation (by cucumariosides A1 (40) and A8 (44)), preceded by bonding of the glycosides with membrane sphingomyelin, phospholipids, and cholesterol. Noncovalent intermolecular interactions inside multimolecular membrane complexes and their stoichiometry differed for 40 and 44. The second mechanism was realized by cucumarioside A2 (59) through the formation of phospholipid and cholesterol clusters in the outer and inner membrane leaflets, correspondingly. Noticeably, the glycoside/phospholipid interactions were more favorable compared to the glycoside/cholesterol interactions, but the glycoside possessed an agglomerating action towards the cholesterol molecules from the inner membrane leaflet. In silicosimulations of the interactions of cucumarioside A7 (45) with model membrane demonstrated only slight interactions with phospholipid polar heads and the absence of glycoside/cholesterol interactions. This fact correlated well with very low experimental hemolytic activity of this substance. The observed peculiarities of membranotropic action are in good agreement with the corresponding experimental data on hemolytic activity of the investigated compounds in vitro.
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Han Z, Chen X, Li G, Sun S. A novel 3D-QSAR model assisted by coefficient of variation method and its application in FQs’ modification. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-020-02052-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Passos GFS, Gomes MGM, de Aquino TM, de Araújo-Júnior JX, de Souza SJM, Cavalcante JPM, dos Santos EC, Bassi ÊJ, da Silva-Júnior EF. Computer-Aided Design, Synthesis, and Antiviral Evaluation of Novel Acrylamides as Potential Inhibitors of E3-E2-E1 Glycoproteins Complex from Chikungunya Virus. Pharmaceuticals (Basel) 2020; 13:E141. [PMID: 32629969 PMCID: PMC7407227 DOI: 10.3390/ph13070141] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023] Open
Abstract
Chikungunya virus (CHIKV) causes an infectious disease characterized by inflammation and pain of the musculoskeletal tissues accompanied by swelling in the joints and cartilage damage. Currently, there are no licensed vaccines or chemotherapeutic agents to prevent or treat CHIKV infections. In this context, our research aimed to explore the potential in vitro anti-CHIKV activity of acrylamide derivatives. In silico methods were applied to 132 Michael's acceptors toward the six most important biological targets from CHIKV. Subsequently, the ten most promising acrylamides were selected and synthesized. From the cytotoxicity MTT assay, we verified that LQM330, 334, and 336 demonstrate high cell viability at 40 µM. Moreover, these derivatives exhibited anti-CHIKV activities, highlighting the compound LQM334 which exhibited an inhibition value of 81%. Thus, docking simulations were performed to suggest a potential CHIKV-target for LQM334. It was observed that the LQM334 has a high affinity towards the E3-E2-E1 glycoproteins complex. Moreover, LQM334 reduced the percentage of CHIKV-positive cells from 74.07 to 0.88%, 48h post-treatment on intracellular flow cytometry staining. In conclusion, all virtual simulations corroborated with experimental results, and LQM334 could be used as a promising anti-CHIKV scaffold for designing new drugs in the future.
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Affiliation(s)
- Gabriel Felipe Silva Passos
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió 57072-970, Brazil; (G.F.S.P.); (M.G.M.G.); (J.X.d.A.-J.)
| | - Matheus Gabriel Moura Gomes
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió 57072-970, Brazil; (G.F.S.P.); (M.G.M.G.); (J.X.d.A.-J.)
| | - Thiago Mendonça de Aquino
- Center of Analysis and Research in Nuclear Magnetic Resonance, Chemistry and Biotechnology Institute, Federal University of Alagoas, Maceió 57072-970, Brazil;
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió 57072-970, Brazil; (G.F.S.P.); (M.G.M.G.); (J.X.d.A.-J.)
| | - Stephannie Janaina Maia de Souza
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió 57072-970, Brazil; (S.J.M.d.S.); (J.P.M.C.); (E.C.d.S.); (Ê.J.B.)
| | - João Pedro Monteiro Cavalcante
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió 57072-970, Brazil; (S.J.M.d.S.); (J.P.M.C.); (E.C.d.S.); (Ê.J.B.)
| | - Elane Conceição dos Santos
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió 57072-970, Brazil; (S.J.M.d.S.); (J.P.M.C.); (E.C.d.S.); (Ê.J.B.)
| | - Ênio José Bassi
- Immunoregulation Research Group, Laboratory of Research in Virology and Immunology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió 57072-970, Brazil; (S.J.M.d.S.); (J.P.M.C.); (E.C.d.S.); (Ê.J.B.)
| | - Edeildo Ferreira da Silva-Júnior
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió 57072-970, Brazil; (G.F.S.P.); (M.G.M.G.); (J.X.d.A.-J.)
- Center of Analysis and Research in Nuclear Magnetic Resonance, Chemistry and Biotechnology Institute, Federal University of Alagoas, Maceió 57072-970, Brazil;
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Conformational Studies of Glucose Transporter 1 (GLUT1) as an Anticancer Drug Target. Molecules 2019; 24:molecules24112159. [PMID: 31181707 PMCID: PMC6600248 DOI: 10.3390/molecules24112159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 01/15/2023] Open
Abstract
Glucose transporter 1 (GLUT1) is a facilitative glucose transporter overexpressed in various types of tumors; thus, it has been considered as an important target for cancer therapy. GLUT1 works through conformational switching from an outward-open (OOP) to an inward-open (IOP) conformation passing through an occluded conformation. It is critical to determine which conformation is preferred by bound ligands because the success of structure-based drug design depends on the appropriate starting conformation of the target protein. To find out the most favorable GLUT 1 conformation for ligand binding, we ran systemic molecular docking studies for different conformations of GLUT1 using known GLUT1 inhibitors. Our data revealed that the IOP is the preferred conformation and that residues Phe291, Phe379, Glu380, Trp388, and Trp412 may play critical roles in ligand binding to GLUT1. Our data suggests that conformational differences in these five amino acids in the different conformers of GLUT1 may be used to design ligands that inhibit GLUT1.
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Zeb A, Kim D, Alam SI, Son M, Kumar R, Rampogu S, Parameswaran S, Shelake RM, Rana RM, Parate S, Kim JY, Lee KW. Computational Simulations Identify Pyrrolidine-2,3-Dione Derivatives as Novel Inhibitors of Cdk5/p25 Complex to Attenuate Alzheimer's Pathology. J Clin Med 2019; 8:E746. [PMID: 31137734 PMCID: PMC6572193 DOI: 10.3390/jcm8050746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
: Mechanistically, neurotoxic insults provoke Ca2+-mediated calpain activation, which cleaves the cytoplasmic region of membrane-embedded p35 and produces its truncated form p25. Upon physical interaction, cyclin-dependent kinase 5 (Cdk5) and p25 forms hyperactivated Cdk5/p25 complex and causes severe neuropathological aberrations including hyperphosphorylated tau-mediated neurofibrillary tangles formation, Alzheimer's symptoms, and neuronal death. Therefore, the inhibition of Cdk5/p25 complex may relieve p-tau-mediated Alzheimer's pathology. Herein, computational simulations have identified pyrrolidine-2,3-dione derivatives as novel inhibitors of Cdk5/p25 complex. A ligand-based pharmacophore was designed and employed as 3D query to retrieve drug-like molecules from chemical databases. By molecular docking, drug-like molecules obtaining dock score > 67.67 (Goldcore of the reference compound) were identified. Molecular dynamics simulation and binding free energy calculation retrieved four pyrrolidine-2,3-dione derivatives as novel candidate inhibitors of Cdk5/p25. The root means square deviation of Cdk5/p25 in complex with candidate inhibitors obtained an average value of ~2.15 Å during the 30 ns simulation period. Molecular interactions analysis suggested that each inhibitor occupied the ATP-binding site of Cdk5/p25 and formed stable interactions. Finally, the binding free energy estimation suggested that each inhibitor had lowest binding energy than the reference compound (-113.10 kJ/mol) to recapitulate their strong binding with Cdk5/p25. Overall, these inhibitors could mitigate tau-mediated Alzheimer's phenotype.
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Affiliation(s)
- Amir Zeb
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Donghwan Kim
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Sayed Ibrar Alam
- Division of Life Sciences and Applied Life Science (BK 21plus), College of Natural Sciences, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Minky Son
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Raj Kumar
- Institute of Chemical Processes (ICP), Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Shailima Rampogu
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Saravanan Parameswaran
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Rahul Mahadev Shelake
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
| | - Rabia Mukhtar Rana
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Shraddha Parate
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
| | - Jae-Yean Kim
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
| | - Keun Woo Lee
- Division of Life Science, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea.
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Khairullina VR, Gimadieva AR, Gerchikov AY, Mustafin AG, Zarudii FS. Quantitative structure-activity relationship of the thymidylate synthase inhibitors of Mus musculus in the series of quinazolin-4-one and quinazolin-4-imine derivatives. J Mol Graph Model 2018; 85:198-211. [PMID: 30227365 DOI: 10.1016/j.jmgm.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/19/2018] [Accepted: 09/02/2018] [Indexed: 02/03/2023]
Abstract
A quantitative structure-activity relationship analysis of the 2-methylquinazolin-4-one and quinazolin-4-imine derivatives, well-known antifolate thymidylate synthase (TYMS) inhibitors, has been performed in the range IC50 = 0.4÷380000.0 nmoL/L using the GUSAR 2013 program. Based on the MNA and QNA descriptors using the self-consistent regression, 6 statistically significant consensus models for predicting the IC50 numerical values have been constructed. These models demonstrate high and moderate prognostic accuracies for the training and external validation test sets, respectively. The molecular fragments of TYMS inhibitors regulating their antitumor activity are identified. The obtained data open opportunities for developing novel promising inhibitors of TYMS.
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Affiliation(s)
| | - Alfiya R Gimadieva
- Ufa Institute of Chemistry - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71 prospect Oktyabrya, Ufa, 450054, Russian Federation
| | | | - Akhat G Mustafin
- Bashkir State University, 32 Z. Validi str., Ufa, 450076, Russian Federation; Ufa Institute of Chemistry - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71 prospect Oktyabrya, Ufa, 450054, Russian Federation
| | - Felix S Zarudii
- Bashkir State Medical University, 3 Lenina str, Ufa, 450000, Russian Federation
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Liao Y, Guo Y, Li S, Wang L, Tang Y, Li T, Chen W, Zhong G, Song G. Structure-based design and structure-activity relationships of 1,2,3,4-tetrahydroisoquinoline derivatives as potential PDE4 inhibitors. Bioorg Med Chem Lett 2018; 28:1188-1193. [DOI: 10.1016/j.bmcl.2018.02.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 11/26/2022]
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Design, synthesis, and biological evaluation of novel catecholopyrimidine based PDE4 inhibitor for the treatment of atopic dermatitis. Eur J Med Chem 2018; 145:673-690. [DOI: 10.1016/j.ejmech.2017.12.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 12/19/2022]
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Muñoz-Pérez VM, Fernández-Martínez E, Ponce-Monter H, Ortiz MI. Relaxant and anti-inflammatory effect of two thalidomide analogs as PDE-4 inhibitors in pregnant rat uterus. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2017; 21:429-437. [PMID: 28706457 PMCID: PMC5507782 DOI: 10.4196/kjpp.2017.21.4.429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 01/21/2023]
Abstract
The aim of this study was to evaluate the relaxant and anti-inflammatory effects of two thalidomide analogs as phosphodiesterase-4 (PDE-4) inhibitors in pregnant rat uterus. Uteri from Wistar female rats were isolated at 19 day of pregnancy. Uterine samples were used in functional studies to evaluate the inhibitory effects of the thalidomide analogs, methyl 3-(4-nitrophthalimido)-3-(3,4-dimethoxyphenyl)-propanoate (4NO2PDPMe) and methyl 3-(4-aminophthalimido)-3-(3,4-dimethoxyphenyl)-propanoate (4APDPMe), on prostaglandin-F2α (PGF2α)-induced phasic, K+-induced tonic, and Ca2+-induced contractions. Accumulation of cAMP was quantified in uterine homogenates by ELISA. Anti-inflammatory effect was assessed by using ELISA for determination of the pro-inflammatory cytokines tumor necrosis factor-α (TNFα) and interleukin (IL)-1β, and anti-inflammatory IL-10, from uterine explants stimulated with lipopolysaccharide (LPS). Nifedipine, forskolin and rolipram were used as positive controls where required. Both thalidomide analogs induced a significant inhibition of the uterine contractions induced by the pharmaco- and electro-mechanic stimuli. Nifedipine and forskolin were more potent than the analogs to inhibit the uterine contractility, but these were more potent than rolipram, and 4APDPMe was equieffective to nifedipine. Thalidomide analogs increased uterine cAMP-levels in a concentration-dependent manner. The LPS-induced TNFα and IL-1β uterine secretion was diminished in a concentration-dependent fashion by both analogs, whereas IL-10 secretion was increased significantly. The thalidomide analogs induced utero-relaxant and anti-inflammatory effects, which were associated with the increased cAMP levels as PDE-4 inhibitors in the pregnant rat uterus. Such properties place these thalidomide analogs as potentially safe and effective tocolytic agents in a field that urgently needs improved pharmacological treatments, as in cases of preterm labor.
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Affiliation(s)
- Víctor Manuel Muñoz-Pérez
- Center for Research on Reproductive Biology, Academic Area of Medicine, Institute of Health Sciences, Autonomous University of Hidalgo's State, Pachuca, Hidalgo 42090, Mexico
| | - Eduardo Fernández-Martínez
- Center for Research on Reproductive Biology, Academic Area of Medicine, Institute of Health Sciences, Autonomous University of Hidalgo's State, Pachuca, Hidalgo 42090, Mexico
| | - Héctor Ponce-Monter
- Center for Research on Reproductive Biology, Academic Area of Medicine, Institute of Health Sciences, Autonomous University of Hidalgo's State, Pachuca, Hidalgo 42090, Mexico
| | - Mario I Ortiz
- Center for Research on Reproductive Biology, Academic Area of Medicine, Institute of Health Sciences, Autonomous University of Hidalgo's State, Pachuca, Hidalgo 42090, Mexico
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Knott EP, Assi M, Rao SNR, Ghosh M, Pearse DD. Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair. Int J Mol Sci 2017; 18:E696. [PMID: 28338622 PMCID: PMC5412282 DOI: 10.3390/ijms18040696] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/10/2017] [Accepted: 03/15/2017] [Indexed: 12/21/2022] Open
Abstract
A wide diversity of perturbations of the central nervous system (CNS) result in structural damage to the neuroarchitecture and cellular defects, which in turn are accompanied by neurological dysfunction and abortive endogenous neurorepair. Altering intracellular signaling pathways involved in inflammation and immune regulation, neural cell death, axon plasticity and remyelination has shown therapeutic benefit in experimental models of neurological disease and trauma. The second messengers, cyclic adenosine monophosphate (cyclic AMP) and cyclic guanosine monophosphate (cyclic GMP), are two such intracellular signaling targets, the elevation of which has produced beneficial cellular effects within a range of CNS pathologies. The only known negative regulators of cyclic nucleotides are a family of enzymes called phosphodiesterases (PDEs) that hydrolyze cyclic nucleotides into adenosine monophosphate (AMP) or guanylate monophosphate (GMP). Herein, we discuss the structure and physiological function as well as the roles PDEs play in pathological processes of the diseased or injured CNS. Further we review the approaches that have been employed therapeutically in experimental paradigms to block PDE expression or activity and in turn elevate cyclic nucleotide levels to mediate neuroprotection or neurorepair as well as discuss both the translational pathway and current limitations in moving new PDE-targeted therapies to the clinic.
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Affiliation(s)
- Eric P Knott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
| | - Mazen Assi
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Sudheendra N R Rao
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Mousumi Ghosh
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Department of Neurological Surgery, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
| | - Damien D Pearse
- The Miami Project to Cure Paralysis, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Department of Neurological Surgery, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Neuroscience Program, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- The Interdisciplinary Stem Cell Institute, The Miller School of Medicine at the University of Miami, Miami, FL 33136, USA.
- Bruce Wayne Carter Department of Veterans Affairs Medical Center, Miami, FL 33136, USA.
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Guariento S, Franchini S, Tonelli M, Fossa P, Sorbi C, Cichero E, Brasili L. Exhaustive CoMFA and CoMSIA analyses around different chemical entities: a ligand-based study exploring the affinity and selectivity profiles of 5-HT 1A ligands. J Enzyme Inhib Med Chem 2017; 32:214-230. [PMID: 28114832 PMCID: PMC6009877 DOI: 10.1080/14756366.2016.1247057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The 5-hydroxytryptamine (5-HT1A) receptors represent an attractive target in drug discovery. In particular, 5-HT1A agonists and partial agonists are deeply investigated for their potential role in the treatment of anxiety, depression, ischaemic brain disorder and more recently, of pain. On the other hand, 5-HT1A antagonists have been revealed promising compounds in cognition disorders and, lately, in cancer. Thus, the discovery of 5HT1A ligands is nowadays an appealing research activity in medicinal chemistry. In this work, Comparative Molecular Fields Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) were applied on an in-house library of 5-HT1A ligands bearing different chemical scaffolds in order to elucidate their affinity and selectivity for the target. Following this procedure, a number of structural modifications have been drawn for the development of much more effective 5-HT1AR ligands.
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Affiliation(s)
- Sara Guariento
- a Department of Pharmacy , University of Genoa , Genoa , Italy
| | - Silvia Franchini
- b Department of Life Sciences , University of Modena and Reggio Emilia , Modena , Italy
| | - Michele Tonelli
- a Department of Pharmacy , University of Genoa , Genoa , Italy
| | - Paola Fossa
- a Department of Pharmacy , University of Genoa , Genoa , Italy
| | - Claudia Sorbi
- b Department of Life Sciences , University of Modena and Reggio Emilia , Modena , Italy
| | - Elena Cichero
- a Department of Pharmacy , University of Genoa , Genoa , Italy
| | - Livio Brasili
- b Department of Life Sciences , University of Modena and Reggio Emilia , Modena , Italy
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15
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Wang J, Yang Y, Li Y, Wang Y. Computational Study Exploring the Interaction Mechanism of Benzimidazole Derivatives as Potent Cattle Bovine Viral Diarrhea Virus Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:5941-5950. [PMID: 27355875 DOI: 10.1021/acs.jafc.6b01067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bovine viral diarrhea virus (BVDV) infections are prevailing in cattle populations on a worldwide scale. The BVDV RNA-dependent RNA polymerase (RdRp), as a promising target for new anti-BVDV drug development, has attracted increasing attention. To explore the interaction mechanism of 65 benzimidazole scaffold-based derivatives as BVDV inhibitors, presently, a computational study was performed based on a combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations. The resultant optimum CoMFA and CoMSIA models present proper reliabilities and strong predictive abilities (with Q(2) = 0. 64, R(2)ncv = 0.93, R(2)pred = 0.80 and Q(2) = 0. 65, R(2)ncv = 0.98, R(2)pred = 0.86, respectively). In addition, there was good concordance between these models, molecular docking, and MD results. Moreover, the MM-PBSA energy analysis reveals that the major driving force for ligand binding is the polar solvation contribution term. Hopefully, these models and the obtained findings could offer better understanding of the interaction mechanism of BVDV inhibitors as well as benefit the new discovery of more potent BVDV inhibitors.
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Affiliation(s)
- Jinghui Wang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yinfeng Yang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yan Li
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yonghua Wang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
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16
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Sharma V, Kumar H, Wakode S. Pharmacophore generation and atom based 3D-QSAR of quinoline derivatives as selective phosphodiesterase 4B inhibitors. RSC Adv 2016. [DOI: 10.1039/c6ra11210b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Reported PDE4B inhibitors were used to design QSAR based pharmacophore model. Using developed pharmacophore model, virtual screening was performed followed by cross-docking to identify novel PDE4B specific inhibitors.
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Affiliation(s)
- Vidushi Sharma
- Department of Pharmaceutical Chemistry
- Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR)
- University of Delhi
- New Delhi – 110017
- India
| | - Hirdesh Kumar
- Parasitology – Center for Infectious Diseases
- University of Heidelberg Medical School
- 69120 Heidelberg
- Germany
| | - Sharad Wakode
- Department of Pharmaceutical Chemistry
- Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR)
- University of Delhi
- New Delhi – 110017
- India
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17
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Cichero E, Brullo C, Bruno O, Fossa P. Exhaustive 3D-QSAR analyses as a computational tool to explore the potency and selectivity profiles of thieno[3,2-d]pyrimidin-4(3H)-one derivatives as PDE7 inhibitors. RSC Adv 2016. [DOI: 10.1039/c6ra12624c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In the development of selective ligands binding to specific PDE isoforms, the ligand-based approach proved to be a useful tool to better investigate the potency and selectivity profiles of PDE7 inhibitors.
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Affiliation(s)
- Elena Cichero
- Department of Pharmacy
- Section of Medicinal Chemistry
- School of Medical and Pharmaceutical Sciences
- University of Genoa
- Genoa
| | - Chiara Brullo
- Department of Pharmacy
- Section of Medicinal Chemistry
- School of Medical and Pharmaceutical Sciences
- University of Genoa
- Genoa
| | - Olga Bruno
- Department of Pharmacy
- Section of Medicinal Chemistry
- School of Medical and Pharmaceutical Sciences
- University of Genoa
- Genoa
| | - Paola Fossa
- Department of Pharmacy
- Section of Medicinal Chemistry
- School of Medical and Pharmaceutical Sciences
- University of Genoa
- Genoa
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