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1.
Drug Dev Res ; 85(5): e22232, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38992915

RESUMO

The human aryl hydrocarbon receptor (AhR), a ligand-dependent transcription factor, plays a pivotal role in a diverse array of pathways in biological and pathophysiological events. This position AhR as a promising target for both carcinogenesis and antitumor strategies. In this study we utilized computational modeling to screen and identify FDA-approved drugs binding to the allosteric site between α2 of bHLH and PAS-A domains of AhR, with the aim of inhibiting its canonical pathway activity. Our findings indicated that nilotinib effectively fits into the allosteric pocket and forms interactions with crucial residues F82, Y76, and Y137. Binding free energy value of nilotinib is the lowest among top hits and maintains stable within its pocket throughout entire (MD) simulations time. Nilotinib has also substantial interactions with F295 and Q383 when it binds to orthosteric site and activate AhR. Surprisingly, it does not influence AhR nuclear translocation in the presence of AhR agonists; instead, it hinders the formation of the functional AhR-ARNT-DNA heterodimer assembly, preventing the upregulation of regulated enzymes like CYP1A1. Importantly, nilotinib exhibits a dual impact on AhR, modulating AhR activity via the PAS-B domain and working as a noncompetitive allosteric antagonist capable of blocking the canonical AhR signaling pathway in the presence of potent AhR agonists. These findings open a new avenue for the repositioning of nilotinib beyond its current application in diverse diseases mediated via AhR.


Assuntos
Sítio Alostérico , Receptores de Hidrocarboneto Arílico , Receptores de Hidrocarboneto Arílico/metabolismo , Receptores de Hidrocarboneto Arílico/antagonistas & inibidores , Receptores de Hidrocarboneto Arílico/química , Humanos , Regulação Alostérica/efeitos dos fármacos , Pirimidinas/farmacologia , Pirimidinas/química , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/antagonistas & inibidores , Fatores de Transcrição Hélice-Alça-Hélice Básicos/química , Simulação de Dinâmica Molecular , Aprovação de Drogas , Citocromo P-450 CYP1A1/metabolismo , Citocromo P-450 CYP1A1/antagonistas & inibidores
2.
Biochem Biophys Res Commun ; 726: 150306, 2024 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-38917634

RESUMO

The folate metabolism enzyme ALDH1L1 catalyzed 10-formyltetrahydrofolate to tetrahydrofolate and CO2. Non-small cell lung cancer cells (NSCLC) strongly express ALDH1L1. Gossypol binds to an allosteric site and disrupts the folate metabolism by preventing NADP+ binding. The Cryo-EM structures of tetrameric C-terminal aldehyde dehydrogenase human ALDH1L1 complex with gossypol were examined. Gossypol-bound ALDH1L1 interfered with NADP+ by shifting the allosteric site of the structural conformation, producing a closed-form NADP+ binding site. In addition, the inhibition activity of ALDH1L1 was targeted with gossypol in NSCLC. The gossypol treatment had anti-cancer effects on NSCLC by blocking NADPH and ATP production. These findings emphasize the structure characterizing ALDH1L1 with gossypol.


Assuntos
Gossipol , Humanos , Gossipol/química , Gossipol/farmacologia , Gossipol/metabolismo , NADP/metabolismo , NADP/química , Modelos Moleculares , Microscopia Crioeletrônica , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Carcinoma Pulmonar de Células não Pequenas/patologia , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/patologia , Aldeído Oxirredutases/metabolismo , Aldeído Oxirredutases/química , Ligação Proteica , Sítios de Ligação , Sítio Alostérico , Conformação Proteica , Linhagem Celular Tumoral , Oxirredutases atuantes sobre Doadores de Grupo CH-NH
3.
J Med Chem ; 67(13): 11168-11181, 2024 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-38932616

RESUMO

ß-Glucocerebrosidase (GBA/GCase) mutations leading to misfolded protein cause Gaucher's disease and are a major genetic risk factor for Parkinson's disease and dementia with Lewy bodies. The identification of small molecule pharmacological chaperones that can stabilize the misfolded protein and increase delivery of degradation-prone mutant GCase to the lysosome is a strategy under active investigation. Here, we describe the first use of fragment-based drug discovery (FBDD) to identify pharmacological chaperones of GCase. The fragment hits were identified by using X-ray crystallography and biophysical techniques. This work led to the discovery of a series of compounds that bind GCase with nM potency and positively modulate GCase activity in cells.


Assuntos
Sítio Alostérico , Descoberta de Drogas , Glucosilceramidase , Glucosilceramidase/metabolismo , Glucosilceramidase/antagonistas & inibidores , Glucosilceramidase/química , Humanos , Cristalografia por Raios X , Relação Estrutura-Atividade , Modelos Moleculares , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia , Bibliotecas de Moléculas Pequenas/metabolismo
4.
Expert Opin Ther Pat ; 34(4): 187-209, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38920057

RESUMO

INTRODUCTION: Protein tyrosine phosphatases (PTPs), essential and evolutionarily highly conserved enzymes, govern cellular functions by modulating tyrosine phosphorylation, a pivotal post-translational modification for signal transduction. The recent strides in phosphatase drug discovery, leading to the identification of selective modulators for enzymes, restoring interest in the therapeutic targeting of protein phosphatases. AREAS COVERED: The compilation of patents up to the year 2023 focuses on the efficacy of various classes of Tyrosine phosphatases and their inhibitors, detailing their chemical structure and biochemical characteristics. These findings have broad implications, as they can be applied to treating diverse conditions like cancer, diabetes, autoimmune disorders, and neurological diseases. The search for scientific articles and patent literature was conducted using well known different platforms to gather information up to 2023. EXPERT OPINION: The latest improvements in protein tyrosine phosphatase (PTP) research include the discovery of new inhibitors targeting specific PTP enzymes, with a focus on developing allosteric site covalent inhibitors for enhanced efficacy and specificity. These advancements have not only opened up new possibilities for therapeutic interventions in various disease conditions but also hold the potential for innovative treatments. PTPs offer promising avenues for drug discovery efforts and innovative treatments across a spectrum of health conditions.


Assuntos
Desenho de Fármacos , Desenvolvimento de Medicamentos , Descoberta de Drogas , Inibidores Enzimáticos , Patentes como Assunto , Proteínas Tirosina Fosfatases , Humanos , Inibidores Enzimáticos/farmacologia , Inibidores Enzimáticos/química , Animais , Proteínas Tirosina Fosfatases/antagonistas & inibidores , Proteínas Tirosina Fosfatases/metabolismo , Transdução de Sinais/efeitos dos fármacos , Fosforilação , Sítio Alostérico , Processamento de Proteína Pós-Traducional
5.
Proc Natl Acad Sci U S A ; 121(24): e2316892121, 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38833472

RESUMO

The loss of function of AAA (ATPases associated with diverse cellular activities) mechanoenzymes has been linked to diseases, and small molecules that activate these proteins can be powerful tools to probe mechanisms and test therapeutic hypotheses. Unlike chemical inhibitors that can bind a single conformational state to block enzyme function, activator binding must be permissive to different conformational states needed for mechanochemistry. However, we do not know how AAA proteins can be activated by small molecules. Here, we focus on valosin-containing protein (VCP)/p97, an AAA unfoldase whose loss of function has been linked to protein aggregation-based disorders, to identify druggable sites for chemical activators. We identified VCP ATPase Activator 1 (VAA1), a compound that dose-dependently stimulates VCP ATPase activity up to ~threefold. Our cryo-EM studies resulted in structures (ranging from ~2.9 to 3.7 Å-resolution) of VCP in apo and ADP-bound states and revealed that VAA1 binds an allosteric pocket near the C-terminus in both states. Engineered mutations in the VAA1-binding site confer resistance to VAA1, and furthermore, modulate VCP activity. Mutation of a phenylalanine residue in the VCP C-terminal tail that can occupy the VAA1 binding site also stimulates ATPase activity, suggesting that VAA1 acts by mimicking this interaction. Together, our findings uncover a druggable allosteric site and a mechanism of enzyme regulation that can be tuned through small molecule mimicry.


Assuntos
Proteína com Valosina , Proteína com Valosina/metabolismo , Proteína com Valosina/química , Proteína com Valosina/genética , Regulação Alostérica , Humanos , Ligação Proteica , Mimetismo Molecular , Microscopia Crioeletrônica , Adenosina Trifosfatases/metabolismo , Adenosina Trifosfatases/química , Sítios de Ligação , Sítio Alostérico , Modelos Moleculares , Conformação Proteica
6.
Int J Mol Sci ; 25(11)2024 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-38892388

RESUMO

SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into its open state, wherein the catalytic cleft becomes fully exposed to its ligands. This study elucidates the dynamic properties of SHP2 structures across different states, with a focus on the effects of oncogenic mutation on two known binding sites of allosteric inhibitors. Through extensive modeling and simulations, we further identified an alternative allosteric binding pocket in solution structures. Additional analysis provides insights into the dynamics and stability of the potential site. In addition, multi-tier screening was deployed to identify potential binders targeting the potential site. Our efforts to identify a new allosteric site contribute to community-wide initiatives developing therapies using multiple allosteric inhibitors to target distinct pockets on SHP2, in the hope of potentially inhibiting or slowing tumor growth associated with SHP2.


Assuntos
Sítio Alostérico , Neoplasias , Proteína Tirosina Fosfatase não Receptora Tipo 11 , Proteína Tirosina Fosfatase não Receptora Tipo 11/antagonistas & inibidores , Proteína Tirosina Fosfatase não Receptora Tipo 11/metabolismo , Proteína Tirosina Fosfatase não Receptora Tipo 11/química , Humanos , Neoplasias/tratamento farmacológico , Neoplasias/metabolismo , Regulação Alostérica/efeitos dos fármacos , Mutação , Sítios de Ligação , Antineoplásicos/farmacologia , Antineoplásicos/química , Antineoplásicos/uso terapêutico , Ligação Proteica , Simulação de Dinâmica Molecular
7.
Mol Pharmacol ; 106(1): 21-32, 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38719475

RESUMO

Olfactory receptors are members of class A (rhodopsin-like) family of G protein-coupled receptors (GPCRs). Their expression and function have been increasingly studied in nonolfactory tissues, and many have been identified as potential therapeutic targets. In this manuscript, we focus on the discovery of novel ligands for the olfactory receptor family 51 subfamily E2 (OR51E2). We performed an artificial intelligence-based virtual drug screen of a ∼2.2 million small molecule library. Cell-based functional assay identified compound 80 (C80) as an antagonist and inverse agonist, and detailed pharmacological analysis revealed C80 acts as a negative allosteric modulator by significantly decreasing the agonist efficacy, while having a minimal effect on receptor affinity for agonist. C80 binds to an allosteric binding site formed by a network of nine residues localized in the intracellular parts of transmembrane domains 3, 5, 6, 7, and H8, which also partially overlaps with a G protein binding site. Mutational experiments of residues involved in C80 binding uncovered the significance of the C2406.37 position in blocking the activation-related conformational change and keeping the receptor in the inactive form. Our study provides a mechanistic understanding of the negative allosteric action of C80 on agonist-ctivated OR51E2. We believe the identification of the antagonist of OR51E2 will enable a multitude of studies aiming to determine the functional role of this receptor in specific biologic processes. SIGNIFICANCE STATEMENT: OR51E2 has been implicated in various biological processes, and its antagonists that can effectively modulate its activity have therapeutic potential. Here we report the discovery of a negative allosteric modulator of OR51E2 and provide a mechanistic understanding of its action. We demonstrate that this modulator has an inhibitory effect on the efficacy of the agonist for the receptor and reveal a network of nine residues that constitute its binding pocket, which also partially overlaps with the G protein binding site.


Assuntos
Sítio Alostérico , Receptores Odorantes , Receptores Odorantes/metabolismo , Receptores Odorantes/antagonistas & inibidores , Receptores Odorantes/química , Regulação Alostérica/efeitos dos fármacos , Humanos , Animais , Ligantes , Sítios de Ligação , Células HEK293 , Bibliotecas de Moléculas Pequenas/farmacologia , Bibliotecas de Moléculas Pequenas/química , Cricetulus , Células CHO
8.
Molecules ; 29(9)2024 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-38731442

RESUMO

Two series, "a" and "b", each consisting of nine chemical compounds, with 2,3-disubstituted quinazolin-4(3H)-one scaffold, were synthesized and evaluated for their anticonvulsant activity. They were investigated as dual potential positive allosteric modulators of the GABAA receptor at the benzodiazepine binding site and inhibitors of carbonic anhydrase II. Quinazolin-4(3H)-one derivatives were evaluated in vivo (D1-3 = 50, 100, 150 mg/kg, administered intraperitoneally) using the pentylenetetrazole (PTZ)-induced seizure model in mice, with phenobarbital and diazepam, as reference anticonvulsant agents. The in silico studies suggested the compounds act as anticonvulsants by binding on the allosteric site of GABAA receptor and not by inhibiting the carbonic anhydrase II, because the ligands-carbonic anhydrase II predicted complexes were unstable in the molecular dynamics simulations. The mechanism targeting GABAA receptor was confirmed through the in vivo flumazenil antagonism assay. The pentylenetetrazole experimental anticonvulsant model indicated that the tested compounds, 1a-9a and 1b-9b, present a potential anticonvulsant activity. The evaluation, considering the percentage of protection against PTZ, latency until the onset of the first seizure, and reduction in the number of seizures, revealed more favorable results for the "b" series, particularly for compound 8b.


Assuntos
Anticonvulsivantes , Pentilenotetrazol , Receptores de GABA-A , Convulsões , Anticonvulsivantes/farmacologia , Anticonvulsivantes/síntese química , Anticonvulsivantes/química , Animais , Camundongos , Convulsões/tratamento farmacológico , Convulsões/induzido quimicamente , Receptores de GABA-A/metabolismo , Quinazolinonas/farmacologia , Quinazolinonas/química , Quinazolinonas/síntese química , Simulação de Acoplamento Molecular , Masculino , Relação Estrutura-Atividade , Simulação de Dinâmica Molecular , Simulação por Computador , Modelos Animais de Doenças , Estrutura Molecular , Sítio Alostérico
9.
Int J Mol Sci ; 25(9)2024 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-38731943

RESUMO

Protein kinases are essential regulators of cell function and represent one of the largest and most diverse protein families. They are particularly influential in signal transduction and coordinating complex processes like the cell cycle. Out of the 518 human protein kinases identified, 478 are part of a single superfamily sharing catalytic domains that are related in sequence. The dysregulation of protein kinases due to certain mutations has been associated with various diseases, including cancer. Although most of the protein kinase inhibitors identified as type I or type II primarily target the ATP-binding pockets of kinases, the structural and sequential resemblances among these pockets pose a significant challenge for selective inhibition. Therefore, targeting allosteric pockets that are beside highly conserved ATP pockets has emerged as a promising strategy to prevail current limitations, such as poor selectivity and drug resistance. In this article, we compared the binding pockets of various protein kinases for which allosteric (type III) inhibitors have already been developed. Additionally, understanding the structure and shape of existing ligands could aid in identifying key interaction sites within the allosteric pockets of kinases. This comprehensive review aims to facilitate the design of more effective and selective allosteric inhibitors.


Assuntos
Sítio Alostérico , Inibidores de Proteínas Quinases , Proteínas Quinases , Humanos , Inibidores de Proteínas Quinases/farmacologia , Inibidores de Proteínas Quinases/química , Proteínas Quinases/metabolismo , Proteínas Quinases/química , Regulação Alostérica , Sítios de Ligação , Ligação Proteica , Ligantes , Trifosfato de Adenosina/metabolismo , Trifosfato de Adenosina/química , Domínio Catalítico , Modelos Moleculares
10.
J Mol Graph Model ; 130: 108789, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38718434

RESUMO

Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that modulates integrin and growth factor signaling pathways and is implicated in cancer cell migration, proliferation, and survival. Over the past decade various, FAK kinase, FERM, and FAT domain inhibitors have been reported and a few kinase domain inhibitors are under clinical consideration. However, few of them were identified as multikinase inhibitors. In kinase drug design selectivity is always a point of concern, to improve selectivity allosteric inhibitor development is the best choice. The current research utilized a pharmacophore modeling (PM) approach to identify novel allosteric inhibitors of FAK. The all-available allosteric inhibitor bound 3D structures with PDB ids 4EBV, 4EBW, and 4I4F were utilized for the pharmacophore modeling. The validated PM models were utilized to map a database of 770,550 compounds prepared from ZINC, EXIMED, SPECS, ASINEX, and InterBioScreen, aiming to identify potential allosteric inhibitors. The obtained compounds from screening step were forwarded to molecular docking (MD) for the prediction of binding orientation inside the allosteric site and the results were evaluated with the known FAK allosteric inhibitor (REF). Finally, 14 FAK-inhibitor complexes were selected from the docking study and were studied under molecular dynamics simulations (MDS) for 500 ns. The complexes were ranked according to binding free energy (BFE) and those demonstrated higher affinity for allosteric site of FAK than REF inhibitors were selected. The selected complexes were further analyzed for intermolecular interactions and finally, three potential allosteric inhibitor candidates for the inhibition of FAK protein were identified. We believe that identified scaffolds may help in drug development against FAK as an anticancer agent.


Assuntos
Proteína-Tirosina Quinases de Adesão Focal , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Inibidores de Proteínas Quinases , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/farmacologia , Regulação Alostérica , Proteína-Tirosina Quinases de Adesão Focal/antagonistas & inibidores , Proteína-Tirosina Quinases de Adesão Focal/química , Proteína-Tirosina Quinases de Adesão Focal/metabolismo , Humanos , Sítio Alostérico , Ligação Proteica , Desenho de Fármacos , Sítios de Ligação , Farmacóforo
11.
Int J Mol Sci ; 25(9)2024 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-38732174

RESUMO

Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and machine-learning-based binding pocket detection with the ensemble-based ligand docking and binding free energy analysis to characterize the potential allosteric binding sites and determine structural and energetic determinants of allosteric inhibition for a series of experimentally validated allosteric molecules. The results demonstrate a good agreement between computational and experimental binding affinities, providing support to the predicted binding modes and suggesting key interactions formed by the allosteric ligands to elicit the experimentally observed inhibition. We establish structural and energetic determinants of allosteric binding for the experimentally known allosteric molecules, indicating a potential mechanism of allosteric modulation by targeting the hinges of the inter-protomer movements and blocking conformational changes between the closed and open spike trimer forms. The results of this study demonstrate that combining ensemble-based ligand docking with conformational states of spike protein and rigorous binding energy analysis enables robust characterization of the ligand binding modes, the identification of allosteric binding hotspots, and the prediction of binding affinities for validated allosteric modulators, which is consistent with the experimental data. This study suggested that the conformational adaptability of the protein allosteric sites and the diversity of ligand bound conformations are both in play to enable efficient targeting of allosteric binding sites and interfere with the conformational changes.


Assuntos
Sítio Alostérico , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ligação Proteica , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/metabolismo , Glicoproteína da Espícula de Coronavírus/antagonistas & inibidores , Regulação Alostérica , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/metabolismo , Ligantes , Humanos , Sítios de Ligação , Conformação Proteica , Antivirais/química , Antivirais/farmacologia , Antivirais/metabolismo , Multimerização Proteica , Aprendizado de Máquina
12.
Sci Rep ; 14(1): 11575, 2024 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-38773273

RESUMO

Leishmaniasis is a disease caused by a protozoan of the genus Leishmania, affecting millions of people, mainly in tropical countries, due to poor social conditions and low economic development. First-line chemotherapeutic agents involve highly toxic pentavalent antimonials, while treatment failure is mainly due to the emergence of drug-resistant strains. Leishmania arginase (ARG) enzyme is vital in pathogenicity and contributes to a higher infection rate, thus representing a potential drug target. This study helps in designing ARG inhibitors for the treatment of leishmaniasis. Py-CoMFA (3D-QSAR) models were constructed using 34 inhibitors from different chemical classes against ARG from L. (L.) amazonensis (LaARG). The 3D-QSAR predictions showed an excellent correlation between experimental and calculated pIC50 values. The molecular docking study identified the favorable hydrophobicity contribution of phenyl and cyclohexyl groups as substituents in the enzyme allosteric site. Molecular dynamics simulations of selected protein-ligand complexes were conducted to understand derivatives' interaction modes and affinity in both active and allosteric sites. Two cinnamide compounds, 7g and 7k, were identified, with similar structures to the reference 4h allosteric site inhibitor. These compounds can guide the development of more effective arginase inhibitors as potential antileishmanial drugs.


Assuntos
Arginase , Inibidores Enzimáticos , Leishmania , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Arginase/antagonistas & inibidores , Arginase/química , Arginase/metabolismo , Leishmania/enzimologia , Leishmania/efeitos dos fármacos , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Relação Quantitativa Estrutura-Atividade , Proteínas de Protozoários/antagonistas & inibidores , Proteínas de Protozoários/química , Proteínas de Protozoários/metabolismo , Sítio Alostérico , Antiprotozoários/farmacologia , Antiprotozoários/química , Domínio Catalítico
13.
Int J Mol Sci ; 25(10)2024 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-38791406

RESUMO

The allosteric inhibition of insulin-like growth factor receptor 1 kinase (IGF1RK) is a potential strategy to overcome selectivity barriers for targeting receptor tyrosine kinases. We constructed structural models of a series of 12 indole-butyl-amine derivatives that have been reported as allosteric inhibitors of IGF1RK. We further studied the dynamics and interactions of each inhibitor in the allosteric pocket via all-atom explicit-solvent molecular dynamics (MD) simulations. We discovered that a bulky carbonyl substitution at the R1 indole ring is structurally unfavorable for inhibitor binding in the IGF1RK allosteric pocket. Moreover, we found that the most potent derivative (termed C11) acquires a distinct conformation: forming an allosteric pocket channel with better shape complementarity and interactions with the receptor. In addition to a hydrogen-bonding interaction with V1063, the cyano derivative C11 forms a stable hydrogen bond with M1156, which is responsible for its unique binding conformation in the allosteric pocket. Our findings show that the positioning of chemical substituents with different pharmacophore features at the R1 indole ring influences molecular interactions and binding conformations of indole-butyl-amine derivatives and, hence, dramatically affects their potencies. Our results provide a structural framework for the design of allosteric inhibitors with improved affinities and specificities against IGF1RK.


Assuntos
Simulação de Dinâmica Molecular , Inibidores de Proteínas Quinases , Receptor IGF Tipo 1 , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/farmacologia , Regulação Alostérica , Receptor IGF Tipo 1/antagonistas & inibidores , Receptor IGF Tipo 1/química , Receptor IGF Tipo 1/metabolismo , Humanos , Ligação de Hidrogênio , Sítio Alostérico , Indóis/química , Indóis/farmacologia , Ligação Proteica , Relação Estrutura-Atividade , Modelos Moleculares
14.
J Phys Chem B ; 128(20): 4996-5007, 2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38747451

RESUMO

Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to gating by the glycine agonist, interactions with lipids and other compounds in the surrounding membrane environment modulate their function, but molecular details of these interactions remain unclear, in particular, for cholesterol. Here, we report coarse-grained simulations in a model neuronal membrane for three zebrafish glycine receptor structures representing apparent resting, open, and desensitized states. We then converted the systems to all-atom models to examine detailed lipid interactions. Cholesterol bound to the receptor at an outer-leaflet intersubunit site, with a preference for the open and desensitized versus resting states, indicating that it can bias receptor function. Finally, we used short atomistic simulations and iterative amino acid perturbations to identify residues that may mediate allosteric gating transitions. Frequent cholesterol contacts in atomistic simulations clustered with residues identified by perturbation analysis and overlapped with mutations influencing channel function and pathology. Cholesterol binding at this site was also observed in a recently reported pig heteromeric glycine receptor. These results indicate state-dependent lipid interactions relevant to allosteric transitions of glycine receptors, including specific amino acid contacts applicable to biophysical modeling and pharmaceutical design.


Assuntos
Colesterol , Simulação de Dinâmica Molecular , Receptores de Glicina , Receptores de Glicina/química , Receptores de Glicina/metabolismo , Colesterol/química , Colesterol/metabolismo , Animais , Sítio Alostérico , Peixe-Zebra
15.
J Phys Chem B ; 128(21): 5157-5174, 2024 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-38647430

RESUMO

The chemokine receptor CXCR4 is a critical target for the treatment of several cancer types and HIV-1 infections. While orthosteric and allosteric modulators have been developed targeting its extracellular or transmembrane regions, the intramembrane region of CXCR4 may also include allosteric binding sites suitable for the development of allosteric drugs. To investigate this, we apply the Gaussian Network Model (GNM) to the monomeric and dimeric forms of CXCR4 to identify residues essential for its local and global motions located in the hinge regions of the protein. Residue interaction network (RIN) analysis suggests hub residues that participate in allosteric communication throughout the receptor. Mutual residues from the network models reside in regions with a high capacity to alter receptor dynamics upon ligand binding. We then investigate the druggability of these potential allosteric regions using the site identification by ligand competitive saturation (SILCS) approach, revealing two putative allosteric sites on the monomer and three on the homodimer. Two screening campaigns with Glide and SILCS-Monte Carlo docking using FDA-approved drugs suggest 20 putative hit compounds including antifungal drugs, anticancer agents, HIV protease inhibitors, and antimalarial drugs. In vitro assays considering mAB 12G5 and CXCL12 demonstrate both positive and negative allosteric activities of these compounds, supporting our computational approach. However, in vivo functional assays based on the recruitment of ß-arrestin to CXCR4 do not show significant agonism and antagonism at a single compound concentration. The present computational pipeline brings a new perspective to computer-aided drug design by combining conformational dynamics based on network analysis and cosolvent analysis based on the SILCS technology to identify putative allosteric binding sites using CXCR4 as a showcase.


Assuntos
Sítio Alostérico , Receptores CXCR4 , Receptores CXCR4/química , Receptores CXCR4/metabolismo , Receptores CXCR4/antagonistas & inibidores , Ligantes , Humanos , Simulação de Acoplamento Molecular , Método de Monte Carlo , Regulação Alostérica
16.
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi ; 41(2): 313-320, 2024 Apr 25.
Artigo em Chinês | MEDLINE | ID: mdl-38686412

RESUMO

Targeting p21-activated kinase 1 (PAK1) is a novel strategy for pancreatic cancer treatment. Compound Kushen injection contains many anti-pancreatic cancer components, but the specific targets are unknown. In this study, 14α-hydroxymatrine, an active component of Kushen injection, was found to possess high binding free energy with the allosteric site of PAK1 by molecular docking based virtual screening. Molecular dynamics simulations suggested that 14α-hydroxymatrine caused the α1 and α2 helices of the allosteric site of PAK1 to extend outward to form a deep allosteric regulatory pocket. Meanwhile, 14α-hydroxymatrine induced the ß-folding region at the adenosine triphosphate (ATP)-binding pocket of PAK1 to close inward, resulting in the ATP-binding pocket in a "semi-closed" state which caused the inactivation of PAK1. After removal of 14α-hydroxymatrine, PAK1 showed a tendency to change from the inactive conformation to the active conformation. We supposed that 14α-hydroxymatrine of compound Kushen injection might be a reversible allosteric inhibitor of PAK1. This study used modern technologies and methods to study the active components of traditional Chinese medicine, which laid a foundation for the development and utilization of natural products and the search for new treatments for pancreatic cancer.


Assuntos
Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Quinases Ativadas por p21 , Quinases Ativadas por p21/metabolismo , Quinases Ativadas por p21/antagonistas & inibidores , Humanos , Sítio Alostérico , Neoplasias Pancreáticas/tratamento farmacológico , Medicamentos de Ervas Chinesas/farmacologia , Medicamentos de Ervas Chinesas/química , Quinolizinas/farmacologia , Quinolizinas/química
17.
Signal Transduct Target Ther ; 9(1): 88, 2024 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-38594257

RESUMO

G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characterize the complexity of GPCR dynamic features. In this study, we first review the structural advancements, activation mechanisms, and functional diversity of GPCRs. We then focus on GPCR drug discovery by revealing the detailed drug-target interactions and the underlying mechanisms of orthosteric drugs approved by the US Food and Drug Administration in the past five years. Particularly, an up-to-date analysis is performed on available GPCR structures complexed with synthetic small-molecule allosteric modulators to elucidate key receptor-ligand interactions and allosteric mechanisms. Finally, we highlight how the widespread GPCR-druggable allosteric sites can guide structure- or mechanism-based drug design and propose prospects of designing bitopic ligands for the future therapeutic potential of targeting this receptor family.


Assuntos
Descoberta de Drogas , Receptores Acoplados a Proteínas G , Estados Unidos , Humanos , Receptores Acoplados a Proteínas G/química , Sítio Alostérico , Desenho de Fármacos , Ligantes
18.
Bioorg Chem ; 147: 107317, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38583252

RESUMO

By inducing steric activation of the 10CH bond with a 12-acyl group to form a key imine oxime intermediate, 20 novel (10S)-10,12-disubstituted aloperine derivatives were successfully synthesized and assessed for their antiviral efficacy against HCoV-OC43. Of them, compound 3i exhibited the moderate activities against HCoV-OC43, as well as against the SARS-CoV-2 variant EG.5.1 with the comparable EC50 values of 4.7 and 4.1 µM. A mechanism study revealed that it inhibited the protease activity of host TMPRSS2 by binding to an allosteric site, rather than the known catalytic center, different from that of camostat. Also, the combination of compound 3i and molnupiravir, as an RdRp inhibitor, showed an additive antiviral effect against HCoV-OC43. The results provide a new binding mode and lead compound for targeting TMPRSS2, with an advantage in combating broad-spectrum coronavirus.


Assuntos
Sítio Alostérico , Antivirais , Coronavirus Humano OC43 , Quinolizidinas , Serina Endopeptidases , Antivirais/farmacologia , Antivirais/química , Antivirais/síntese química , Serina Endopeptidases/metabolismo , Humanos , Coronavirus Humano OC43/efeitos dos fármacos , Coronavirus Humano OC43/química , Quinolizidinas/química , Quinolizidinas/farmacologia , Quinolizidinas/síntese química , Sítio Alostérico/efeitos dos fármacos , Relação Estrutura-Atividade , Descoberta de Drogas , SARS-CoV-2/efeitos dos fármacos , Estrutura Molecular , Testes de Sensibilidade Microbiana , Relação Dose-Resposta a Droga
19.
Nature ; 628(8008): 664-671, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38600377

RESUMO

Bitter taste sensing is mediated by type 2 taste receptors (TAS2Rs (also known as T2Rs)), which represent a distinct class of G-protein-coupled receptors1. Among the 26 members of the TAS2Rs, TAS2R14 is highly expressed in extraoral tissues and mediates the responses to more than 100 structurally diverse tastants2-6, although the molecular mechanisms for recognizing diverse chemicals and initiating cellular signalling are still poorly understood. Here we report two cryo-electron microscopy structures for TAS2R14 complexed with Ggust (also known as gustducin) and Gi1. Both structures have an orthosteric binding pocket occupied by endogenous cholesterol as well as an intracellular allosteric site bound by the bitter tastant cmpd28.1, including a direct interaction with the α5 helix of Ggust and Gi1. Computational and biochemical studies validate both ligand interactions. Our functional analysis identified cholesterol as an orthosteric agonist and the bitter tastant cmpd28.1 as a positive allosteric modulator with direct agonist activity at TAS2R14. Moreover, the orthosteric pocket is connected to the allosteric site via an elongated cavity, which has a hydrophobic core rich in aromatic residues. Our findings provide insights into the ligand recognition of bitter taste receptors and suggest activities of TAS2R14 beyond bitter taste perception via intracellular allosteric tastants.


Assuntos
Colesterol , Espaço Intracelular , Receptores Acoplados a Proteínas G , Paladar , Humanos , Regulação Alostérica/efeitos dos fármacos , Sítio Alostérico , Colesterol/química , Colesterol/metabolismo , Colesterol/farmacologia , Microscopia Crioeletrônica , Interações Hidrofóbicas e Hidrofílicas , Espaço Intracelular/química , Espaço Intracelular/metabolismo , Ligantes , Receptores Acoplados a Proteínas G/agonistas , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/metabolismo , Receptores Acoplados a Proteínas G/ultraestrutura , Reprodutibilidade dos Testes , Paladar/efeitos dos fármacos , Paladar/fisiologia , Transducina/química , Transducina/metabolismo , Transducina/ultraestrutura
20.
Curr Opin Struct Biol ; 86: 102793, 2024 06.
Artigo em Inglês | MEDLINE | ID: mdl-38447285

RESUMO

Protein-ligand binding site prediction is critical for protein function annotation and drug discovery. Biological experiments are time-consuming and require significant equipment, materials, and labor resources. Developing accurate and efficient computational methods for protein-ligand interaction prediction is essential. Here, we summarize the key challenges associated with ligand binding site (LBS) prediction and introduce recently published methods from their input features, computational algorithms, and ligand types. Furthermore, we investigate the specificity of allosteric site identification as a particular LBS type. Finally, we discuss the prospective directions for machine learning-based LBS prediction in the near future.


Assuntos
Ligação Proteica , Proteínas , Ligantes , Sítios de Ligação , Proteínas/química , Proteínas/metabolismo , Biologia Computacional/métodos , Aprendizado de Máquina , Algoritmos , Sítio Alostérico , Humanos
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