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1.
J Enzyme Inhib Med Chem ; 34(1): 1573-1589, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31852269

RESUMO

Pyridazine scaffolds are considered privileged structures pertaining to its novelty, chemical stability, and synthetic feasibility. In our quest towards the development of novel scaffolds for effective vascular endothelial growth 2 (VEGFR-2) inhibition with antiangiogenic activity, four novel series of pyridazines were designed and synthesised. Five of the synthesised compounds; namely (8c, 8f, 15, 18b, and 18c) exhibited potent VEGFR-2 inhibitory potency (>80%); with IC50 values ranging from low micromolar to nanomolar range; namely compounds 8c, 8f, 15, 18c with (1.8 µM, 1.3 µM, 1.4 µM, 107 nM), respectively. Moreover, 3-[4-{(6-oxo-1,6-dihydropyridazin-3-yl)oxy}phenyl]urea derivative (18b) exhibited nanomolar potency towards VEGFR-2 (60.7 nM). In cellular assay, the above compounds showed excellent inhibition of VEGF-stimulated proliferation of human umbilical vein endothelial cells at 10 µM concentration. Finally, an extensive molecular simulation study was performed to investigate the probable interaction with VEGFR-2.


Assuntos
Antineoplásicos/farmacologia , Descoberta de Drogas , Inibidores de Proteínas Quinases/farmacologia , Piridazinas/farmacologia , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Antineoplásicos/síntese química , Antineoplásicos/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Teoria da Densidade Funcional , Ensaios de Seleção de Medicamentos Antitumorais , Células Endoteliais da Veia Umbilical Humana/efeitos dos fármacos , Humanos , Modelos Moleculares , Estrutura Molecular , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Piridazinas/síntese química , Piridazinas/química , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo
2.
mBio ; 10(5)2019 10 08.
Artigo em Inglês | MEDLINE | ID: mdl-31594821

RESUMO

Many pathogens evolve extensive genetic variation in virulence proteins as a strategy to evade host immunity. This poses a significant challenge for the host to develop broadly neutralizing antibodies. In Plasmodium falciparum, we show that a mechanism to circumvent this challenge is to elicit antibodies to cryptic epitopes that are not under immune pressure. We previously discovered that antibodies to the Plasmodium vivax invasion protein, PvDBP, cross-react with P. falciparum VAR2CSA, a distantly related virulence factor that mediates placental malaria. Here, we describe the molecular mechanism underlying this cross-species immunity. We identified an epitope in subdomain 1 (SD1) within the Duffy binding-like (DBL) domain of PvDBP that gives rise to cross-reactive antibodies to VAR2CSA and show that human antibodies affinity purified against a synthetic SD1 peptide block parasite adhesion to chondroitin sulfate A (CSA) in vitro The epitope in SD1 is subdominant and highly conserved in PvDBP, and in turn, SD1 antibodies target cryptic epitopes in P. falciparum VAR2CSA. The epitopes in VAR2CSA recognized by vivax-derived SD1 antibodies (of human and mouse origin) are distinct from those recognized by VAR2CSA immune serum. We mapped two peptides in the DBL5ε domain of VAR2CSA that are recognized by SD1 antibodies. Both peptides map to regions outside the immunodominant sites, and antibodies to these peptides are not elicited following immunization with VAR2CSA or natural infection with P. falciparum in pregnancy, consistent with the cryptic nature of these target epitopes.IMPORTANCE In this work, we describe a molecular mechanism of heterologous immunity between two distant species of Plasmodium Our results suggest a mechanism that subverts the classic parasite strategy of presenting highly polymorphic epitopes in surface antigens to evade immunity to that parasite. This alternative immune pathway can be exploited to protect pregnant women from falciparum placental malaria by designing vaccines to cryptic epitopes that elicit broadly inhibitory antibodies against variant parasite strains.

3.
Sci Rep ; 9(1): 12392, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31455818

RESUMO

Blockade of the programmed cell death 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) interaction has emerged as a powerful strategy in cancer immunotherapy. Recently, there have been enormous efforts to develop potent PD-1/PD-L1 inhibitors. In particular, Bristol-Myers Squibb (BMS) and Aurigene Discovery Technologies have individually disclosed several promising PD-1/PD-L1 inhibitors, whose detailed experimental data are not publicly disclosed. In this work, we report the rigorous and systematic in vitro characterization of a selected set of potent PD-1/PD-L1 macrocyclic peptide (BMSpep-57) and small-molecule inhibitors (BMS-103, BMS-142) from BMS and a peptidomimetic small-molecule inhibitor from Aurigene (Aurigene-1) using a series of biochemical and cell-based assays. Our results confirm that BMS-103 and BMS-142 are strongly active in biochemical assays; however, their acute cytotoxicity greatly compromised their immunological activity. On the other hand, Aurigene-1 did not show any activity in both biochemical and immunological assays. Furthermore, we also report the discovery of a small-molecule immune modulator, whose mode-of-action is not clear; however, it exhibits favorable drug-like properties and strong immunological activity. We hope that the results presented here will be useful in guiding the development of next-generation PD-1/PD-L1 small molecule inhibitors.

4.
Med Res Rev ; 2019 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-31448437

RESUMO

Modulation of T-cell immune functions by blocking key immune checkpoint protein interactions using monoclonal antibodies (mAbs) has been an innovative immunotherapeutic strategy. T-cells are regulated by different checkpoint proteins at the immunological synapse including the B7 ligands (B7-1 or CD80 and B7-2 or CD86), which is discussed in this review. These ligands are typically expressed on antigen presenting cells and interact with CD28 and cytotoxic T lymphocyte antigen-4 (CTLA-4) receptors on T-cells. Their interactions with CD28 trigger a costimulatory signal that potentiates T-cell activation, function and survival in response to cognate antigen. In addition, their interactions with CTLA-4 can also inhibit certain effector T-cell responses, particularly in response to sustained antigen stimulation. Through these mechanisms, the balance between T-cell activation and suppression is maintained, preventing the occurrence of immunopathology. Given their crucial roles in immune regulation, targeting B7 ligands has been an attractive strategy in cancer and autoimmunity. This review presents an overview of the essential roles of B7-1, highlighting the therapeutic benefits of modulating this protein in immunotherapy, and reviewing earlier and state-of-the-art efforts in developing anti-B7-1 inhibitors. Finally, we discuss the challenges facing the design of selective B7-1 inhibitors and present our perspectives for future developments.

5.
J Med Chem ; 62(17): 7684-7696, 2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31369707

RESUMO

The ERCC1-XPF heterodimer is a 5'-3' structure-specific endonuclease, which plays an essential role in several DNA repair pathways in mammalian cells. ERCC1-XPF is primarily involved in the repair of chemically induced helix-distorting and bulky DNA lesions, such as cyclobutane pyrimidine dimers (CPDs), and DNA interstrand cross-links. Inhibition of ERCC1-XPF has been shown to potentiate cytotoxicity of platinum-based drugs and cyclophosphamide in cancer cells. In this study, the previously described ERCC1-XPF inhibitor 4-((6-chloro-2-methoxyacridin-9-yl)amino)-2-((4-methylpiperazin-1-yl)methyl)phenol (compound 1) was used as a reference compound. Following the outcome of docking-based virtual screening (VS), we synthesized seven novel derivatives of 1 that were identified in silico as being likely to have high binding affinity for the ERCC1-XPF heterodimerization interface by interacting with the XPF double helix-hairpin-helix (HhH2) domain. Two of the new compounds, 4-((6-chloro-2-methoxyacridin-9-yl)amino)-2-((4-cyclohexylpiperazin-1-yl)methyl)phenol (compound 3) and 4-((6-chloro-2-methoxyacridin-9-yl)amino)-2-((4-(2-(dimethylamino)ethyl) piperazin-1-yl) methyl) phenol (compound 4), were shown to be potent inhibitors of ERCC1-XPF activity in vitro. Compound 4 showed significant inhibition of the removal of CPDs in UV-irradiated cells and the capacity to sensitize colorectal cancer cells to UV radiation and cyclophosphamide.

6.
J Mol Graph Model ; 90: 128-143, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31082639

RESUMO

The recurrent outbreaks of dengue virus around the globe represent a huge challenge for governments and public health organizations. With the rapid growth and ease of transportation, dengue disease continues to spread, placing more of the world population under constant threat. Despite decades of research efforts, no effective small molecule antivirals are available against dengue virus. With the efficacy of the recently developed vaccine to be determined, there is an urgent unmet need for small molecule dengue virus treatments. In the current study, we employed state-of-the-art molecular modelling simulations to identify novel inhibitors of the dengue virus envelope protein. The binding modes of all compounds within the conserved ß-OctylGlucoside (ß-OG) pocket were studied using a combination of docking, molecular dynamics simulations and binding free energy calculations. Here, we describe ten new compounds that significantly reduce production of dengue virus as determined using standard cell-based virological assays. Moreover, we present a comprehensive structural analysis of the identified hits, focusing on their electrostatic and lipophilic binding energy contributions. Finally, we highlight the effect of the desolvation penalty in limiting the activity of some of these compounds. The data presented here paves the way toward rationally designing selective and potent novel inhibitors against dengue virus.

7.
Biochim Biophys Acta Gen Subj ; 1863(6): 1116-1126, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30978379

RESUMO

BACKGROUND: Human CaV1.2 (hCav1.2), a calcium selective voltage-gated channel, plays important roles in normal cardiac and neuronal functions. Calcium influx and gating mechanisms leading to the activation of hCaV1.2 are critical for its functionalities. Lack of an experimentally resolved structure of hCaV1.2 remains a significant impediment in molecular-level understanding of this channel. This work focuses on building atomistic hCaV1.2 model and studying calcium influx using computational approaches. METHODS: We employed homology modeling and molecular dynamics (MD) to build the structure of hCaV1.2. Subsequently, we employed steered molecular dynamics (SMD) to understand calcium ion permeation in hCaV1.2. RESULTS: We report a comprehensive three-dimensional model of a closed state hCaV1.2 refined under physiological membrane-bound conditions using MD simulations. Our SMD simulations on the model revealed four important barriers for ion permeation: this includes three calcium binding sites formed by the EEEE- and TTTT- rings within the selectivity filter region and a large barrier rendered by the hydrophobic internal gate. Our results also revealed that the first hydration shell of calcium remained intact throughout the simulations, thus playing an important role in ion permeation in hCaV1.2. CONCLUSIONS: Our results have provided some important mechanistic insights into the structure, dynamics and ion permeation in hCaV1.2. The significant barriers for ion permeation formed by the four phenylalanine residues at the internal gate region suggest that this site is important for channel activation.


Assuntos
Canais de Cálcio Tipo L/química , Ativação do Canal Iônico , Simulação de Dinâmica Molecular , Canais de Cálcio Tipo L/genética , Humanos
8.
Bioorg Chem ; 82: 340-359, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30428414

RESUMO

VEGFR-2 has a pivotal role in promoting cancer angiogenesis. Herein, two series of novel indazole-based derivatives were designed, synthesized and evaluated for their in vitro inhibitory action against VEGFR-2 kinase enzyme. The second series 11a-e exhibited better potency than the first one 7a-d and 8a-f. Compounds 11b, 11c and 11e exhibited the most potent action, with IC50 of 5.4 nM, 5.6 nM and 7 nM, respectively. As a measure of cellular VEGFR-2 inhibition, compounds 11b and 11c showed strong inhibition of human umbilical vein endothelial cells (HUVEC) proliferation with 80% and 99.6% inhibition at 10 µM concentration, respectively. Attempting to interpret SAR of the synthesized compounds, and provide a basis for further optimization; a comprehensive modeling study was implemented. Molecular docking, dynamics simulation and free energy calculation of the synthesized compounds along with known VEGFR-2 inhibitors were applied. The study illustrated the effect of several factors on VEGFR-2 inhibition, such as the interaction with solvent accessible region of the enzyme, the presence of NH linker and the degree of conformational restriction. Finally, our compounds were evaluated for their in vitro anti-proliferative effect against the full NCI panel of cancer cell lines, where compounds 11a and 11c displayed mean GI% of 93 and 130%, respectively, and showed partly a better behavior than the FDA approved drug sorafenib, with respect to activity (GI50) and safety (LC50) against several cell lines. Thus, compound 11c represents a promising candidate for cancer treatment through antiangiogenic dependent and antiangiogenic independent modes of action.


Assuntos
Inibidores da Angiogênese/farmacologia , Antineoplásicos/farmacologia , Proliferação de Células/efeitos dos fármacos , Indazóis/farmacologia , Inibidores da Angiogênese/síntese química , Inibidores da Angiogênese/química , Inibidores da Angiogênese/metabolismo , Antineoplásicos/síntese química , Antineoplásicos/química , Antineoplásicos/metabolismo , Caspase 3/metabolismo , Domínio Catalítico , Linhagem Celular Tumoral , Desenho de Drogas , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Células Endoteliais da Veia Umbilical Humana , Humanos , Indazóis/síntese química , Indazóis/química , Indazóis/metabolismo , Cinética , Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Estrutura Molecular , Fosforilação/efeitos dos fármacos , Ligação Proteica , Proteínas Proto-Oncogênicas c-akt/metabolismo , Transdução de Sinais/efeitos dos fármacos , Relação Estrutura-Atividade , Termodinâmica , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/química , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo
9.
Chem Biol Drug Des ; 2019 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-31891209

RESUMO

The heterodimer of DNA excision repair protein ERCC-1 and DNA repair endonuclease XPF (ERCC1-XPF) is a 5´-3´ structure-specific endonuclease essential for the nucleotide excision repair (NER) pathway, and it is also involved in other DNA repair pathways. In cancer cells, ERCC1-XPF plays a central role in repairing DNA damage induced by chemotherapeutics including platinum-based and crosslinking agents, thus its inhibition is a promising strategy to enhance the effect of these therapies. In this study, we rationally modified the structure of F06, a small molecule inhibitor of the ERCC1-XPF interaction (Jordheim et al., 2013), to improve its binding to the target. We followed a multi-step computational approach to investigate potential modification sites of F06, rationally design and rank a library of analogues, and identify candidates for chemical synthesis and in vitro testing. Our top compound, B5, showed an improved half-maximum inhibitory concentration (IC50 ) value of 0.49 µM for the inhibition of ERCC1-XPF endonuclease activity, and lays the foundation for further testing and optimization. Also, the computational approach reported here can be used to develop DNA repair inhibitors targeting the ERCC1-XPF complex.

10.
Sci Rep ; 8(1): 16678, 2018 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-30420769

RESUMO

Cyclosporine, a widely used immunosuppressant in organ transplantation and in treatment of various autoimmune diseases, activates the unfolded protein response (UPR), an ER stress coping response. In this study we discovered a new and unanticipated cyclosporine-dependent signaling pathway, with cyclosporine triggering direct activation of the UPR. COX-2 binds to and activates IRE1α, leading to IRE1α splicing of XBP1 mRNA. Molecular interaction and modeling analyses identified a novel interaction site for cyclosporine with COX-2 which caused enhancement of COX-2 enzymatic activity required for activation of the IRE1α branch of the UPR. Cyclosporine-dependent activation of COX-2 and IRE1α in mice indicated that cyclosporine-COX-2-IRE1α signaling pathway was functional in vivo. These findings identify COX-2 as a new IRE1α binding partner and regulator of the IRE1α branch of the UPR pathway, and establishes the mechanism underlying cytotoxicity associated with chronic cyclosporine exposure.


Assuntos
Ciclo-Oxigenase 2/metabolismo , Ciclosporina/farmacologia , Endorribonucleases/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Resposta a Proteínas não Dobradas/efeitos dos fármacos , Animais , Ciclo-Oxigenase 2/química , Ciclo-Oxigenase 2/genética , Endorribonucleases/química , Endorribonucleases/genética , Células HEK293 , Humanos , Imunoprecipitação , Masculino , Camundongos , Simulação de Dinâmica Molecular , Ligação Proteica , Estrutura Terciária de Proteína , Proteínas Serina-Treonina Quinases/química , Proteínas Serina-Treonina Quinases/genética , Transdução de Sinais/efeitos dos fármacos
11.
Biochim Biophys Acta Gen Subj ; 1862(12): 2764-2778, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30251665

RESUMO

BACKGROUND: CD28 and CTLA-4 are homologous T-cell receptors that bind with B7-1 and produce two opposing immunological signals required for T-cell activation and inactivation, respectively. It has been clinically proven that specific blockade of these key protein-protein interactions at the synapse can offer immunotherapeutic benefits for cancers and autoimmune treatments. Hence, there is a growing interest towards developing anti-CD28 and anti-CTLA-4 small molecule inhibitors. To achieve this goal, it is important to understand unique molecular level fingerprint interactions that stabilize CTLA-4/B7-1 and CD28/B7-1 complexes. However, until recently, the structure of the human CD28/B7-1 complex has not been resolved experimentally, which remains a significant setback in achieving specific inhibitors against CTLA-4 or CD28. METHODS: Here, we employed a combination of advanced molecular modelling and extensive molecular dynamics (MD) simulations to model the CD28/B7-1 complex and characterize the key interactions that stabilize the complex. RESULTS: Ensemble protein-protein docking and MD-based binding-free energy calculations were used to obtain a comprehensive structural model of the CD28/B7-1 complex, which was validated with various mutation-based experimental data from literature. Our CD28/B7-1 model has much weaker binding affinity than the CTLA-4/B7-1 complex, which is in agreement with the results from our binding assay experiments and previous studies. CONCLUSIONS: Per-residue energy decomposition of the binding affinities of the two complexes revealed the unique fingerprint hot-spot sites in CTLA-4/B7-1 and CD28/B7-1 complexes. GENERAL SIGNIFICANCE: The results presented in this work will, on a long-run, be useful to develop new generation of specific CD28 and CTLA-4 inhibitors for targeted immunotherapy.


Assuntos
Antígeno B7-1/metabolismo , Antígenos CD28/metabolismo , Antígeno CTLA-4/metabolismo , Simulação de Dinâmica Molecular , Antígeno B7-1/química , Antígenos CD28/química , Análise por Conglomerados , Humanos , Imunoterapia , Ligantes , Ativação Linfocitária , Ligação Proteica , Reprodutibilidade dos Testes
12.
BMC Med Inform Decis Mak ; 18(1): 37, 2018 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-29890992

RESUMO

BACKGROUND: Monoclonal antibodies blocking the Cytotoxic T-lymphocyte antigen 4 (CTLA-4) receptor have revolutionized the field of anti-cancer therapy for the last few years. The human T-cell-based immune responses are modulated by two contradicting signals. CTLA-4 provides a T cell inhibitory signal through its interaction with B7 ligands (B7-1 and B7-2), while CD28 provides a stimulatory signal when interacting with the same ligands. A previous theoretical model has focused on understanding the processes of costimulatory and inhibitory complex formations at the synapse. Nevertheless, the effects of monoclonal antibody (mAb)-mediation on these complexes are relatively unexplored. In this work, we expand on the previous model to develop a new mathematical framework for studying the effects of anti-CTLA-4 mAbs on the co-stimulatory (CD28/B7 ligands) and the co-inhibitory (CTLA-4/B7 ligands) complex formation at the immunological synapse. In particular, we focus on two promising anti-CTLA-4 mAbs, tremelimumab (from AstraZeneca) and ipilimumab (from Bristol-Myers Squibb), which are currently in clinical trials and the market, respectively, for targeting multiple tumors. METHODS: The mathematical model in this work has been constructed based on ordinary differential equations and available experimental binding kinetics data for the anti-CTLA-4 antibodies from literature. RESULTS: The numerical simulations from the current model are in agreement with a number of experimental data. Especially, the dose-curves for blocking the B7 ligand binding to CTLA-4 by ipilimumab are comparable with the results from a previous competitive binding assay by flow cytometry and ELISA. Our simulations predict the dose response and the relative efficacies of the two mAbs in blocking the inhibitory CTLA-4/B7 complexes. CONCLUSIONS: The results show that different factors, such as multivalent interactions, mobility of molecules and competition effects, could impact the effects of antibody-mediation. The results, in particular, describe that the competitive effects could impact the dose-dependent inhibition by the mAbs very significantly. We present this model as a useful tool that can easily be translated to study the effects of any anti-CTLA-4 antibodies on immunological synaptic complex formation, provided reliable biophysical data for mAbs are available.


Assuntos
Anticorpos Monoclonais/farmacologia , Antineoplásicos Imunológicos/farmacologia , Ipilimumab/farmacologia , Modelos Teóricos , Neoplasias/tratamento farmacológico , Neoplasias/imunologia , Anticorpos Monoclonais Humanizados , Humanos
13.
Int J Mol Sci ; 19(5)2018 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-29710850

RESUMO

The DNA excision repair protein ERCC-1-DNA repair endonuclease XPF (ERCC1-XPF) is a heterodimeric endonuclease essential for the nucleotide excision repair (NER) DNA repair pathway. Although its activity is required to maintain genome integrity in healthy cells, ERCC1-XPF can counteract the effect of DNA-damaging therapies such as platinum-based chemotherapy in cancer cells. Therefore, a promising approach to enhance the effect of these therapies is to combine their use with small molecules, which can inhibit the repair mechanisms in cancer cells. Currently, there are no structures available for the catalytic site of the human ERCC1-XPF, which performs the metal-mediated cleavage of a DNA damaged strand at 5′. We adopted a homology modeling strategy to build a structural model of the human XPF nuclease domain which contained the active site and to extract dominant conformations of the domain using molecular dynamics simulations followed by clustering of the trajectory. We investigated the binding modes of known small molecule inhibitors targeting the active site to build a pharmacophore model. We then performed a virtual screening of the ZINC Is Not Commercial 15 (ZINC15) database to identify new ERCC1-XPF endonuclease inhibitors. Our work provides structural insights regarding the binding mode of small molecules targeting the ERCC1-XPF active site that can be used to rationally optimize such compounds. We also propose a set of new potential DNA repair inhibitors to be considered for combination cancer therapy strategies.


Assuntos
Proteínas de Ligação a DNA/antagonistas & inibidores , Endonucleases/antagonistas & inibidores , Inibidores Enzimáticos/farmacologia , Simulação de Acoplamento Molecular , Bibliotecas de Moléculas Pequenas/farmacologia , Sítios de Ligação , Reparo do DNA/efeitos dos fármacos , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Endonucleases/química , Endonucleases/metabolismo , Inibidores Enzimáticos/química , Humanos , Ligação Proteica , Relação Quantitativa Estrutura-Atividade , Bibliotecas de Moléculas Pequenas/química
14.
Int J Implant Dent ; 4(1): 15, 2018 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-29770891

RESUMO

Closed sinus lifting is a unique technique in being simple and less invasive (Summers, Compendium 15(6):698, 1994). However, it is blind to assess the safety of sinus lining during lifting without perforation. Previously, sinus membrane was assessed endoscopically in an invasive way. We aimed to judge clinically the sinus membrane integrity after crestal elevation by a direct simple less invasive endoscopic visual assessment through the crestal osteotomy site. To confirm undetected perforation, the sinus membrane was monitored dynamically by introducing the endoscope through a trephined opening in the lateral wall of the sinus (Nkenke et al., Int J Oral Maxillofac Implants 17(4):557-66, 2002). PATIENTS: Twelve patients suffering atrophic posterior maxillae ranging 3-5 mm bone height below the sinus membrane were included to perform closed sinus lifting with simultaneous immediate implant placement under direct endoscopic assessment. RESULTS: The floor was lifted without perforation in 83.33% of cases. However, it varied according to its thickness. Minor perforations occurred in two cases (16.67%). Both perforations were detected from the crestal endoscopic view while one of them was detected from the lateral endoscopic approach. CONCLUSION: Crestal endoscopic access gives better direct vision to the membrane than the induced opening in the lateral wall of the maxillary sinus. Moreover, it uses the same prepared osteotomy site without doing any extra procedures. Perforation depends on the thickness of sinus lining and its ability to stretch during elevation. Intact crestal sinus floor elevation can never be guaranteed under endoscopic monitoring especially with thin irregular membranes.

15.
Methods Mol Biol ; 1762: 87-103, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29594769

RESUMO

Binding site identification and druggability evaluation are two essential steps in structure-based drug design. A druggable binding site tends to have high binding affinity to drug-like molecules. Predicting such sites can have a significant impact on a drug design campaign. This chapter focuses on summarizing the different methods that are used to predict druggable binding sites. The chapter also discusses the importance of including protein flexibility in the search process and the use of molecular dynamics simulations to address this aspect. Case studies from the literature are also summarized and discussed. We hope that this chapter would provide an overview on the different methods employed in binding site identification evaluation.


Assuntos
Biologia Computacional/métodos , Proteínas/química , Sítios de Ligação , Desenho de Drogas , Descoberta de Drogas/métodos , Ligantes , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Conformação Proteica
16.
Pharmaceuticals (Basel) ; 11(1)2018 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-29462934

RESUMO

The Toll-Like Receptor 7 (TLR7) is an endosomal membrane receptor involved in the innate immune system response. Its best-known small molecule activators are imidazoquinoline derivatives such as imiquimod (R-837) and resiquimod (R-848). Recently, an interaction between R-837 and the colchicine binding site of tubulin was reported. To investigate the possibility of an interaction between structural analogues of colchicine and the TLR7, a recent computational model for the dimeric form of the TLR7 receptor was used to determine a possible interaction with a colchicine derivative called CR42-24, active as a tubulin polymerization inhibitor. The estimated values of the binding energy of this molecule with respect to the TLR7 receptor were comparable to the energies of known binders as reported in a previous study. The binding to the TLR7 was further assessed by introducing genetic transformations in the TLR7 gene in cancer cell lines and exposing them to the compound. A negative shift of the IC50 value in terms of cell growth was observed in cell lines carrying the mutated TLR7 gene. The reported study suggests a possible interaction between TLR7 and a colchicine derivative, which can be explored for rational design of new drugs acting on this receptor by using a colchicine scaffold for additional modifications.

17.
PLoS One ; 13(2): e0191905, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29444113

RESUMO

The voltage-gated KCNQ1 potassium ion channel interacts with the type I transmembrane protein minK (KCNE1) to generate the slow delayed rectifier (IKs) current in the heart. Mutations in these transmembrane proteins have been linked with several heart-related issues, including long QT syndromes (LQTS), congenital atrial fibrillation, and short QT syndrome. Off-target interactions of several drugs with that of KCNQ1/KCNE1 ion channel complex have been known to cause fatal cardiac irregularities. Thus, KCNQ1/KCNE1 remains an important avenue for drug-design and discovery research. In this work, we present the structural and mechanistic details of potassium ion permeation through an open KCNQ1 structural model using the combined molecular dynamics and steered molecular dynamics simulations. We discuss the processes and key residues involved in the permeation of a potassium ion through the KCNQ1 ion channel, and how the ion permeation is affected by (i) the KCNQ1-KCNE1 interactions and (ii) the binding of chromanol 293B ligand and its derivatives into the complex. The results reveal that interactions between KCNQ1 with KCNE1 causes a pore constriction in the former, which in-turn forms small energetic barriers in the ion-permeation pathway. These findings correlate with the previous experimental reports that interactions of KCNE1 dramatically slows the activation of KCNQ1. Upon ligand-binding onto the complex, the energy-barriers along ion permeation path are more pronounced, as expected, therefore, requiring higher force in our steered-MD simulations. Nevertheless, pulling the ion when a weak blocker is bound to the channel does not necessitate high force in SMD. This indicates that our SMD simulations have been able to discern between strong and week blockers and reveal their influence on potassium ion permeation. The findings presented here will have some implications in understanding the potential off-target interactions of the drugs with the KCNQ1/KCNE1 channel that lead to cardiotoxic effects.


Assuntos
Canal de Potássio KCNQ1/metabolismo , Humanos , Ligantes , Simulação de Dinâmica Molecular , Ligação Proteica
19.
Med Res Rev ; 38(2): 525-555, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-28467598

RESUMO

Drug-induced blockade of human ether-a-go-go-related gene (hERG) remains a major impediment in delivering safe drugs to the market. Several drugs have been withdrawn from the market due to their severe cardiotoxic side effects triggered by their off-target interactions with hERG. Thus, identifying the potential hERG blockers at early stages of lead discovery is fast evolving as a standard in drug design and development. A number of in silico structure-based models of hERG have been developed as a low-cost solution to evaluate drugs for hERG liability, and it is now agreed that the hERG blockers bind at the large central cavity of the channel. Nevertheless, there is no clear convergence on the appropriate drug binding modes against the channel. The proposed binding modes differ in their orientations and interpretations on the role of key residues in the channel. Such ambiguities in the modes of binding remain to be a significant challenge in achieving efficient computational predictive models and in saving many important already Food and Drug Administration approved drugs. In this review, we discuss the spectrum of reported binding modes for hERG blockers, the various in silico models developed for predicting a drug's affinity to hERG, and the known successful optimization strategies to avoid off-target interactions with hERG.


Assuntos
Descoberta de Drogas , Canais de Potássio Éter-A-Go-Go/metabolismo , Bloqueadores dos Canais de Potássio/efeitos adversos , Sítios de Ligação , Cardiotoxicidade/patologia , Canais de Potássio Éter-A-Go-Go/antagonistas & inibidores , Canais de Potássio Éter-A-Go-Go/química , Humanos , Bloqueadores dos Canais de Potássio/química , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia
20.
J Mol Graph Model ; 78: 26-47, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-28992529

RESUMO

The voltage-gated KCNQ1/KCNE1 potassium ion channel complex, forms the slow delayed rectifier (IKs) current in the heart, which plays an important role in heart signaling. The importance of KCNQ1/KCNE1 channel's function is further implicated by the linkage between loss-of-function and gain-of-function mutations in KCNQ1 or KCNE1, and long QT syndromes, congenital atrial fibrillation, and short QT syndrome. Also, KCNQ1/KCNE1 channels are an off-target for many non-cardiovascular drugs, leading to fatal cardiac irregularities. One solution to address and study the mentioned aspects of KCNQ1/KNCE1 channel would be the structural studies using a validated and accurate model. Along the same line in this study, we have used several top-notch modeling approaches to build a structural model for the open state of KCNQ1 protein, which is both accurate and compatible with available experimental data. Next, we included the KCNE1 protein components using data-driven protein-protein docking simulations, encompassing a 4:2 stoichiometry to complete the picture of the channel complex formed by these two proteins. All the protein systems generated through these processes were refined by long Molecular Dynamics simulations. The refined models were analyzed extensively to infer data about the interaction of KCNQ1 channel with its accessory KCNE1 beta subunits.


Assuntos
Canais Iônicos/química , Canal de Potássio KCNQ1/química , Miocárdio/metabolismo , Canais de Potássio de Abertura Dependente da Tensão da Membrana/química , Humanos , Canais Iônicos/genética , Canal de Potássio KCNQ1/genética , Modelos Estruturais , Simulação de Dinâmica Molecular , Mutação , Miocárdio/química , Canais de Potássio de Abertura Dependente da Tensão da Membrana/genética , Mapas de Interação de Proteínas
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