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1.
Drug Discov Today ; 29(7): 104025, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38762089

ABSTRACT

In the past 40 years, therapeutic antibody discovery and development have advanced considerably, with machine learning (ML) offering a promising way to speed up the process by reducing costs and the number of experiments required. Recent progress in ML-guided antibody design and development (D&D) has been hindered by the diversity of data sets and evaluation methods, which makes it difficult to conduct comparisons and assess utility. Establishing standards and guidelines will be crucial for the wider adoption of ML and the advancement of the field. This perspective critically reviews current practices, highlights common pitfalls and proposes method development and evaluation guidelines for various ML-based techniques in therapeutic antibody D&D. Addressing challenges across the ML process, best practices are recommended for each stage to enhance reproducibility and progress.


Subject(s)
Drug Development , Drug Discovery , Machine Learning , Humans , Drug Discovery/methods , Drug Development/methods , Antibodies , Animals , Reproducibility of Results
2.
J Phys Chem B ; 128(6): 1515-1526, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38315822

ABSTRACT

Monoclonal antibodies (mAbs) are an important modality of protein therapeutics with broad applications for numerous diseases. However, colloidal instabilities occurring at high protein concentrations can limit the ability to develop stable, high-concentration liquid dosage forms that are required for patient-centric, device-mediated products. Therefore, it is advantageous to identify colloidally stable mAbs early in the discovery process to ensure that they are selected for development. Experimental screening for colloidal stability can be time- and resource-consuming and is most feasible at the later stages of drug development due to material requirements. Alternatively, computational approaches have emerging potential to provide efficient screening and focus developmental efforts on mAbs with the greatest developability potential, while providing mechanistic relationships for colloidal instability. In this work, coarse-grained, molecular-scale models were fine-tuned to screen for colloidal stability at amino-acid resolution. This model parameterization provides a framework to screen for mAb self-interactions and extrapolate to bulk solution behavior. This approach was applied to a wide array of mAbs under multiple buffer conditions, demonstrating the utility of the presented computational approach to augment early candidate screening and later formulation strategies for protein therapeutics.


Subject(s)
Antibodies, Monoclonal , Humans , Models, Molecular
3.
Anal Chem ; 95(27): 10265-10278, 2023 07 11.
Article in English | MEDLINE | ID: mdl-37369001

ABSTRACT

Multispecific antibodies have gained significant importance in a broad indication space due to their ability to engage multiple epitopes simultaneously and to thereby overcome therapeutic barriers. With growing therapeutic potential, however, the molecular complexity increases, thus intensifying the demand for innovative protein engineering and analytical strategies. A major challenge for multispecific antibodies is the correct assembly of light and heavy chains. Engineering strategies exist to stabilize the correct pairing, but typically individual engineering campaigns are required to arrive at the anticipated format. Mass spectrometry has proven to be a versatile tool to identify mispaired species. However, due to manual data analysis procedures, mass spectrometry is limited to lower throughputs. To keep pace with increasing sample numbers, we developed a high-throughput-capable mispairing workflow based on intact mass spectrometry with automated data analysis, peak detection, and relative quantification using Genedata Expressionist. This workflow is capable of detecting mispaired species of ∼1000 multispecific antibodies in three weeks and thus is applicable to complex screening campaigns. As a proof of concept, the assay was applied to engineering a trispecific antibody. Strikingly, the new setup has not only proved successful in mispairing analysis but has also revealed its potential to automatically annotate other product-related impurities. Furthermore, we could confirm the assay to be format-agnostic, as shown by analyzing several different multispecific formats in one run. With these comprehensive capabilities, the new automated intact mass workflow can be applied as a universal tool to detect and annotate peaks in a format-agnostic approach and in high-throughput, thus enabling complex discovery campaigns.


Subject(s)
Antibodies , Mass Spectrometry , Epitopes
4.
Nat Commun ; 14(1): 3719, 2023 06 22.
Article in English | MEDLINE | ID: mdl-37349337

ABSTRACT

Agents that can simultaneously activate latent HIV, increase immune activation and enhance the killing of latently-infected cells represent promising approaches for HIV cure. Here, we develop and evaluate a trispecific antibody (Ab), N6/αCD3-αCD28, that targets three independent proteins: (1) the HIV envelope via the broadly reactive CD4-binding site Ab, N6; (2) the T cell antigen CD3; and (3) the co-stimulatory molecule CD28. We find that the trispecific significantly increases antigen-specific T-cell activation and cytokine release in both CD4+ and CD8+ T cells. Co-culturing CD4+ with autologous CD8+ T cells from ART-suppressed HIV+ donors with N6/αCD3-αCD28, results in activation of latently-infected cells and their elimination by activated CD8+ T cells. This trispecific antibody mediates CD4+ and CD8+ T-cell activation in non-human primates and is well tolerated in vivo. This HIV-directed antibody therefore merits further development as a potential intervention for the eradication of latent HIV infection.


Subject(s)
HIV Infections , HIV-1 , Animals , CD8-Positive T-Lymphocytes , CD4-Positive T-Lymphocytes , Virus Latency , HIV Antibodies
5.
MAbs ; 13(1): 1955433, 2021.
Article in English | MEDLINE | ID: mdl-34382900

ABSTRACT

Next-generation multi-specific antibody therapeutics (MSATs) are engineered to combine several functional activities into one molecule to provide higher efficacy compared to conventional, mono-specific antibody therapeutics. However, highly engineered MSATs frequently display poor yields and less favorable drug-like properties (DLPs), which can adversely affect their development. Systematic screening of a large panel of MSAT variants in very high throughput (HT) is thus critical to identify potent molecule candidates with good yield and DLPs early in the discovery process. Here we report on the establishment of a novel, format-agnostic platform process for the fast generation and multiparametric screening of tens of thousands of MSAT variants. To this end, we have introduced full automation across the entire value chain for MSAT engineering. Specifically, we have automated the in-silico design of very large MSAT panels such that it reflects precisely the wet-lab processes for MSAT DNA library generation. This includes mass saturation mutagenesis or bulk modular cloning technologies while, concomitantly, enabling library deconvolution approaches using HT Sanger DNA sequencing. These DNA workflows are tightly linked to fully automated downstream processes for compartmentalized mammalian cell transfection expression, and screening of multiple parameters. All sub-processes are seamlessly integrated with tailored workflow supporting bioinformatics. As described here, we used this platform to perform multifactor optimization of a next-generation bispecific, cross-over dual variable domain-Ig (CODV-Ig). Screening of more than 25,000 individual protein variants in mono- and bispecific format led to the identification of CODV-Ig variants with over 1,000-fold increased potency and significantly optimized production titers, demonstrating the power and versatility of the platform.


Subject(s)
Antibodies, Bispecific , Antibodies, Monoclonal , Automation, Laboratory , Gene Library , Protein Engineering , Antibodies, Bispecific/chemistry , Antibodies, Bispecific/genetics , Antibodies, Bispecific/immunology , Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/immunology , Escherichia coli , HEK293 Cells , Humans , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/immunology
6.
Med Chem ; 14(8): 809-817, 2018.
Article in English | MEDLINE | ID: mdl-29473519

ABSTRACT

BACKGROUND: Alzheimer's Disease (AD) is the leading cause of dementia among the aging population. This devastating disorder is generally associated with the gradual memory loss, specified by a decrease of acetylcholine level in the cortex hippocampus of the brain due to hyperactivation of cholinesterases (acetylcholinesterase (AChE) and butyrylcholinesterase (BChE)). OBJECTIVE: Therefore, inactivation of AChE and BChE by inhibitors can increase the acetylcholine level and hence may be an encouraging strategy for the treatment of AD and related neurological problems. METHOD: In this contribution, two series of chromenone-based derivatives were tested by Ellmann's calorimetric method for AChE and BChE inhibition. RESULTS: All the compounds showed inhibitory activity against cholinesterases and some of them exhibited dual inhibition of AChE as well as BChE. The most potent inhibitor of AChE was 2l having an IC50 value of 0.08 ± 0.03 µM, while 3q inhibited the BChE with an IC50 value of 0.04 ± 0.01 µM. In case of dual inhibition, 3h showed an inhibitory concentration of 0.15 ± 0.01 µM for AChE, and 0.09 ± 0.01 µM for BChE. Molecular docking studies were performed to explore the probable binding modes of the most potent dual inhibitors. CONCLUSION: It can be hypothesized that the inhibitors are able to target cholinesterase pathways and may emerge as a suitable outset for the further development process.


Subject(s)
Cholinesterase Inhibitors/chemistry , Coumarins/chemistry , Acetylcholinesterase/chemistry , Acetylcholinesterase/metabolism , Alzheimer Disease/drug therapy , Butyrylcholinesterase/chemistry , Butyrylcholinesterase/metabolism , Catalytic Domain , Cholinesterase Inhibitors/metabolism , Coumarins/metabolism , Humans , Molecular Docking Simulation , Protein Binding , Tacrine/chemistry
7.
J Bacteriol ; 198(21): 2965-2974, 2016 11 01.
Article in English | MEDLINE | ID: mdl-27551015

ABSTRACT

The enzyme catalyzing the ring-contracting conversion of the flavanonol taxifolin to the auronol alphitonin in the course of flavonoid degradation by the human intestinal anaerobe Eubacterium ramulus was purified and characterized. It stereospecifically catalyzed the isomerization of (+)-taxifolin but not that of (-)-taxifolin. The Km for (+)-taxifolin was 6.4 ± 0.8 µM, and the Vmax was 108 ± 4 µmol min-1 (mg protein)-1 The enzyme also isomerized (+)-dihydrokaempferol, another flavanonol, to maesopsin. Inspection of the encoding gene revealed its complete identity to that of the gene encoding chalcone isomerase (CHI) from E. ramulus Based on the reported X-ray crystal structure of CHI (M. Gall et al., Angew Chem Int Ed 53:1439-1442, 2014, http://dx.doi.org/10.1002/anie.201306952), docking experiments suggest the substrate binding mode of flavanonols and their stereospecific conversion. Mutation of the active-site histidine (His33) to alanine led to a complete loss of flavanonol isomerization by CHI, which indicates that His33 is also essential for this activity. His33 is proposed to mediate the stereospecific abstraction of a proton from the hydroxymethylene carbon of the flavanonol C-ring followed by ring opening and recyclization. A flavanonol-isomerizing enzyme was also identified in the flavonoid-converting bacterium Flavonifractor plautii based on its 50% sequence identity to the CHI from E. ramulus IMPORTANCE: Chalcone isomerase was known to be involved in flavone/flavanone conversion by the human intestinal bacterium E. ramulus Here we demonstrate that this enzyme moreover catalyzes a key step in the breakdown of flavonols/flavanonols. Thus, a single isomerase plays a dual role in the bacterial conversion of dietary bioactive flavonoids. The identification of a corresponding enzyme in the human intestinal bacterium F. plautii suggests a more widespread occurrence of this isomerase in flavonoid-degrading bacteria.


Subject(s)
Bacterial Proteins/metabolism , Eubacterium/enzymology , Flavanones/metabolism , Intramolecular Lyases/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Catalysis , Catalytic Domain , Eubacterium/chemistry , Flavanones/chemistry , Intramolecular Lyases/chemistry , Intramolecular Lyases/genetics , Kinetics , Molecular Structure
8.
Bioorg Chem ; 68: 177-86, 2016 10.
Article in English | MEDLINE | ID: mdl-27544072

ABSTRACT

In continuation of our previous efforts directed towards the development of potent and selective inhibitors of aldose reductase (ALR2), and to control the diabetes mellitus (DM), a chronic metabolic disease, we synthesized novel coumarin-thiazole 6(a-o) and coumarin-oxadiazole 11(a-h) hybrids and screened for their inhibitory activity against aldose reductase (ALR2), for the selectivity against aldehyde reductase (ALR1). Compounds were also screened against ALR1. Among the newly designed compounds, 6c, 11d, and 11g were selective inhibitors of ALR2. Whereas, (E)-3-(2-(2-(2-bromobenzylidene)hydrazinyl)thiazol-4-yl)-2H-chromen-2-one 6c yielded the lowest IC50 value of 0.16±0.06µM for ALR2. Moreover, compounds (E)-3-(2-(2-benzylidenehydrazinyl)thiazol-4-yl)-2H-chromen-2-one (6a; IC50=2.94±1.23µM for ARL1 and 0.12±0.05µM for ARL2) and (E)-3-(2-(2-(1-(4-bromophenyl)ethylidene)hydrazinyl)thiazol-4-yl)-2H-chromen-2-one (6e; IC50=1.71±0.01µM for ARL1 and 0.11±0.001µM for ARL2) were confirmed as dual inhibitors. Furthermore, compounds 6i, 6k, 6m, and 11b were found to be selective inhibitors for ALR1, among which (E)-3-(2-(2-((2-amino-4-chlorophenyl)(phenyl)methylene)hydrazinyl)thiazol-4-yl)-2H-chromen-2-one (6m) was most potent (IC50=0.459±0.001µM). Docking studies performed using X-ray structures of ALR1 and ALR2 with the given synthesized inhibitors showed that coumarinyl thiazole series lacks the carboxylate function that could interact with the anionic binding site being a common ALR1/ALR2 inhibitors trait. Molecular docking study with dual inhibitor 6e also suggested plausible binding modes for the ALR1 and ALR2 enzymes. Hence, the results of this study revealed that coumarinyl thiazole and oxadiazole derivatives could act as potential ALR1/ALR2 inhibitors.


Subject(s)
Aldehyde Reductase/antagonists & inhibitors , Coumarins/pharmacology , Enzyme Inhibitors/pharmacology , Molecular Docking Simulation , Oxadiazoles/pharmacology , Thiazoles/pharmacology , Aldehyde Reductase/metabolism , Animals , Cattle , Coumarins/chemistry , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Molecular Structure , Oxadiazoles/chemistry , Structure-Activity Relationship , Thiazoles/chemistry
9.
Chemistry ; 22(25): 8525-35, 2016 06 13.
Article in English | MEDLINE | ID: mdl-27214780

ABSTRACT

Matriptase-2, a type II transmembrane serine protease, plays a key role in human iron homeostasis. Inhibition of matriptase-2 is considered as an attractive strategy for the treatment of iron-overload diseases, such as hemochromatosis and ß-thalassemia. In the present study, synthetic routes to nine dipeptidomimetic inactivators were developed. Five active compounds (41-45) were identified and characterized kinetically as irreversible inhibitors of matriptase-2. In addition to a phosphonate warhead, these dipeptides possess two benzguanidine moieties as arginine mimetics to provide affinity for matriptase-2 by binding to the S1 and S3/S4 subpockets, respectively. This binding mode was strongly supported by covalent docking analysis. Compounds 41-45 were obtained as mixtures of two diastereomers and were therefore separated into the single epimers. Compound 45 A, with S configuration at the N-terminal amino acid and R configuration at the phosphonate carbon atom, was the most potent matriptase-2 inactivator with a rate constant of inactivation of 2790 m(-1) s(-1) and abolished the activity of membrane-bound matriptase-2 on the surface of intact cells. Based on the chemotyp of phosphono bisbenzguanidines, the design and synthesis of a fluorescent probe (51 A) by insertion of a coumarin label is described. The in-gel fluorescence detection of matriptase-2 was demonstrated by applying 51 A as the first activity-based probe for this enzyme.


Subject(s)
Guanidines/chemistry , Membrane Proteins/antagonists & inhibitors , Serine Proteinase Inhibitors/chemistry , Animals , Binding Sites , Catalytic Domain , Cattle , Coumarins/chemistry , Factor Xa/chemistry , Factor Xa/metabolism , Fluorescent Dyes/chemistry , Guanidines/chemical synthesis , Guanidines/metabolism , Humans , Kinetics , Membrane Proteins/metabolism , Molecular Docking Simulation , Peptidomimetics , Phosphorus/chemistry , Serine Endopeptidases/metabolism , Serine Proteinase Inhibitors/chemical synthesis , Serine Proteinase Inhibitors/metabolism , Stereoisomerism , Trypsin/chemistry , Trypsin/metabolism
10.
Chembiochem ; 17(7): 595-604, 2016 Apr 01.
Article in English | MEDLINE | ID: mdl-26762582

ABSTRACT

The cell-surface serine protease matriptase-2 is a critical stimulator of iron absorption by negatively regulating hepcidin, the key hormone of iron homeostasis. Thus, it has attracted much attention as a target in primary and secondary iron overload diseases. Here, we have characterised Kunitz-type inhibitors hepatocyte growth factor activator inhibitor 1 (HAI-1) and HAI-2 as powerful, slow-binding matriptase-2 inhibitors. The binding modes of the matriptase-2-HAI complexes were suggested by molecular modelling. Different assays, including cell-free and cell-based measurements of matriptase-2 activity, determination of inhibition constants and evaluation of matriptase-2 inhibition by analysis of downstream effects in human liver cells, demonstrated that matriptase-2 is an excellent target for Kunitz inhibitors. In particular, HAI-2 is considered a promising scaffold for the design of potent and selective matriptase-2 inhibitors.


Subject(s)
Drug Delivery Systems , Enzyme Inhibitors/therapeutic use , Iron Overload/drug therapy , Membrane Proteins/antagonists & inhibitors , Cell Line , Down-Regulation , Enzyme Activation , Humans , Iron Overload/enzymology , Liver/enzymology , Membrane Proteins/genetics , Models, Molecular , Protein Domains/genetics , Proteinase Inhibitory Proteins, Secretory/antagonists & inhibitors , Proteinase Inhibitory Proteins, Secretory/chemistry , Serine Endopeptidases/genetics
11.
Chemistry ; 22(2): 610-25, 2016 Jan 11.
Article in English | MEDLINE | ID: mdl-26625703

ABSTRACT

In the absence of X-ray data, the exploration of compound binding modes continues to be a challenging task. For structure-based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin-like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi- and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure-guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase-2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.


Subject(s)
Membrane Proteins/chemistry , Peptidomimetics/chemistry , Serine Endopeptidases/chemistry , Serine Proteinase Inhibitors/chemistry , Thrombin/chemistry , Benzamidines/chemical synthesis , Benzamidines/chemistry , Binding Sites , Crystallography, X-Ray , Ligands , Models, Molecular , Protein Binding , Serine Endopeptidases/metabolism
12.
Org Biomol Chem ; 13(41): 10310-23, 2015 Nov 07.
Article in English | MEDLINE | ID: mdl-26307943

ABSTRACT

Besides their extracellular activity crucial for several pathophysiological conditions, human cysteine cathepsins, in particular cathepsins K and S, represent important intracellular targets for drug development. In the present study, a prototypic dipeptide nitrile inhibitor structure was equipped with a coumarin moiety to function as a fluorescent reporter group. In a second inhibitor, a PEG linker was introduced between the dipeptide nitrile and the fluorophore. These tool compounds 6 and 7 were characterized by kinetic investigations as covalent reversible inhibitors of human cathepsins L, S, K and B. Probe 6 showed a pronounced inhibitory activity against cathepsins K and S, which was corroborated by modeling of inhibition modes. Probe 7 was highly potent (Ki = 93 nM) and selective for cathepsin S. To examine the ability of both probes to enter living cells, human embryonic kidney 293 cells were targeted. At a concentration of 10 µM, cellular uptake of probe 6 was demonstrated by fluorescence measurement after an incubation time of 30 min and 3 h, respectively. The probe's concentration in cell lysates was ascertained on the basis of the emission at 492 nm upon excitation at 450 nm, and the results were expressed as concentrations of probe 6 relative to the protein concentration originating from the lysate. After incubation of 10 µM of probe 6 for 3 h, the cellular uptake was confirmed by fluorescence microscopy. HPLC was used to assess the probes' lipophilicity, and the obtained


Subject(s)
Cathepsins/antagonists & inhibitors , Cells/metabolism , Cysteine Proteinase Inhibitors/metabolism , Cysteine Proteinase Inhibitors/pharmacology , Drug Design , Fluorescent Dyes/chemistry , Cathepsins/metabolism , Cysteine Proteinase Inhibitors/chemical synthesis , Cysteine Proteinase Inhibitors/chemistry , Dose-Response Relationship, Drug , Fluorescent Dyes/analysis , Humans , Models, Molecular , Molecular Structure , Structure-Activity Relationship
13.
ChemMedChem ; 10(8): 1365-77, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26119278

ABSTRACT

Cleavage of the invariant chain is the key event in the trafficking pathway of major histocompatibility complex class II. Cathepsin S is the major processing enzyme of the invariant chain, but cathepsin F acts in macrophages as its functional synergist which is as potent as cathepsin S in invariant chain cleavage. Dedicated low-molecular-weight inhibitors for cathepsin F have not yet been developed. An active site mapping with 52 dipeptide nitriles, reacting as covalent-reversible inhibitors, was performed to draw structure-activity relationships for the non-primed binding region of human cathepsin F. In a stepwise process, new compounds with optimized fragment combinations were designed and synthesized. These dipeptide nitriles were evaluated on human cysteine cathepsins F, B, L, K and S. Compounds 10 (N-(4-phenylbenzoyl)-leucylglycine nitrile) and 12 (N-(4-phenylbenzoyl)leucylmethionine nitrile) were found to be potent inhibitors of human cathepsin F, with Ki values <10 nM. With all dipeptide nitriles from our study, a 3D activity landscape was generated to visualize structure-activity relationships for this series of cathepsin F inhibitors.


Subject(s)
Cathepsin F/antagonists & inhibitors , Cysteine Proteinase Inhibitors/chemistry , Dipeptides/chemistry , Nitriles/chemistry , Binding Sites , Catalytic Domain , Cathepsin F/metabolism , Cysteine Proteinase Inhibitors/chemical synthesis , Cysteine Proteinase Inhibitors/metabolism , Humans , Molecular Docking Simulation , Nitriles/chemical synthesis , Nitriles/metabolism , Protein Binding , Protein Isoforms/antagonists & inhibitors , Protein Isoforms/metabolism , Structure-Activity Relationship
14.
Chem Biol Drug Des ; 86(6): 1458-65, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26094578

ABSTRACT

Activity cliffs are defined as pairs or groups of structurally similar or analogous compounds that share the same specific activity but have large differences in potency. Although activity cliffs are mostly studied in medicinal chemistry at the level of molecular graphs, they can also be assessed by comparing compound binding modes. If such three-dimensional activity cliffs (3D-cliffs) are studied on the basis of X-ray complex structures, experimental ligand-target interaction details can be taken into account. Rapid growth in the number of 3D-cliffs that can be derived from X-ray complex structures has made it possible to identify targets for which a substantial body of 3D-cliff information is available. Activity cliffs are typically studied to identify structure-activity relationship determinants and aid in compound optimization. However, 3D-cliff information can also be used to search for interaction hot spots and key residues, as reported herein. For six of seven drug targets for which more than 20 3D-cliffs were available, series of 3D-cliffs were identified that were consistently involved in interactions with different hot spots. These 3D-cliffs often encoded chemical modifications resulting in interactions that were characteristic of highly potent compounds but absent in weakly potent ones, thus providing information for structure-based design.


Subject(s)
Drug Design , Amyloid Precursor Protein Secretases/antagonists & inhibitors , Amyloid Precursor Protein Secretases/chemistry , Antithrombins/chemistry , Antithrombins/pharmacology , Aspartic Acid Endopeptidases/antagonists & inhibitors , Aspartic Acid Endopeptidases/chemistry , Binding Sites , Carbonic Anhydrase II/antagonists & inhibitors , Carbonic Anhydrase II/chemistry , Carbonic Anhydrase Inhibitors/chemistry , Carbonic Anhydrase Inhibitors/pharmacology , Cyclin-Dependent Kinase 2/antagonists & inhibitors , Cyclin-Dependent Kinase 2/chemistry , Epoxide Hydrolases/antagonists & inhibitors , Epoxide Hydrolases/chemistry , Factor Xa Inhibitors/chemistry , Factor Xa Inhibitors/pharmacology , Humans , Ligands , Models, Molecular , Molecular Structure , Protein Interaction Domains and Motifs , Quantitative Structure-Activity Relationship
15.
Bioorg Chem ; 61: 51-7, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26119990

ABSTRACT

Urease is an important enzyme which breaks urea into ammonia and carbon dioxide during metabolic processes. However, an elevated activity of urease causes various complications of clinical importance. The inhibition of urease activity with small molecules as inhibitors is an effective strategy for therapeutic intervention. Herein, we have synthesized a series of 19 benzofurane linked N-phenyl semithiocarbazones (3a-3s). All the compounds were screened for enzyme inhibitor activity against Jack bean urease. The synthesized N-phenyl thiosemicarbazones had varying activity levels with IC50 values between 0.077 ± 0.001 and 24.04 ± 0.14 µM compared to standard inhibitor, thiourea (IC50 = 21 ± 0.11 µM). The activities of these compounds may be due to their close resemblance of thiourea. A docking study with Jack bean urease (PDB ID: 4H9M) revealed possible binding modes of N-phenyl thiosemicarbazones.


Subject(s)
Enzyme Inhibitors/chemical synthesis , Thiosemicarbazones/chemistry , Urease/antagonists & inhibitors , Binding Sites , Canavalia/enzymology , Crystallography, X-Ray , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Molecular Conformation , Molecular Docking Simulation , Protein Binding , Protein Structure, Tertiary , Structure-Activity Relationship , Thiosemicarbazones/chemical synthesis , Thiosemicarbazones/metabolism , Urease/metabolism
16.
Chem Biol Drug Des ; 86(5): 1115-20, 2015 Nov.
Article in English | MEDLINE | ID: mdl-25951978

ABSTRACT

Cholinesterases, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), have a role in cholinergic deficit which evidently leads to Alzheimer's disease (AD). Inhibition of cholinesterases with small molecules is an attractive strategy in AD therapy. This study demonstrates synthesis of pyrido[2,3-b]pyrazines (6a-6q) series, their inhibitory activities against both cholinesterases, AChE and BChE, and molecular docking studies. The bioactivities data of pyrido[2,3-b]pyrazines showed 3-(3'-nitrophenyl)pyrido[2,3-b]pyrazine 6n a potent dual inhibitor among the series against both AChE and BChE with IC50 values of 0.466 ± 0.121 and 1.89 ± 0.05 µm, respectively. The analogues 3-(3'-methylphenyl)pyrido[2,3-b]pyrazine 6c and 3-(3'-fluorophenyl)pyrido[2,3-b]pyrazine 6f were found to be selective inhibition for BChE with IC50 values of 0.583 ± 0.052 µm and AChE with IC50 value of 0.899 ± 0.10 µm, respectively. Molecular docking studies of the active compounds suggested the putative binding modes with cholinesterases. The potent compounds among the series could potentially serves as good leads for the development of new cholinesterase inhibitors.


Subject(s)
Cholinesterase Inhibitors/chemistry , Cholinesterase Inhibitors/pharmacology , Pyrazines/chemistry , Pyrazines/pharmacology , Acetylcholinesterase/chemistry , Acetylcholinesterase/metabolism , Alzheimer Disease/drug therapy , Alzheimer Disease/enzymology , Butyrylcholinesterase/chemistry , Butyrylcholinesterase/metabolism , Cholinesterase Inhibitors/chemical synthesis , Drug Design , Humans , Molecular Docking Simulation , Pyrazines/chemical synthesis , Structure-Activity Relationship
17.
Mini Rev Med Chem ; 15(1): 34-40, 2015.
Article in English | MEDLINE | ID: mdl-25694084

ABSTRACT

Ecto-5'-nucleotidase (e5NT) hydrolyzes extracellular nucleotides and contributes to purinergic signaling. e5NT is implicated in a variety of pathological states including immunological diseases and cancer and represents an emerging drug target. Herein, we review structural and computational studies that have helped to better understand ligand binding characteristics and mechanistic features of the enzyme and led to the identification of new classes of e5NT inhibitors.


Subject(s)
5'-Nucleotidase/antagonists & inhibitors , Drug Design , Enzyme Inhibitors/pharmacology , Sulfonic Acids/pharmacology , 5'-Nucleotidase/metabolism , Crystallography, X-Ray , Enzyme Inhibitors/chemistry , Humans , Ligands , Models, Molecular , Protein Conformation , Structure-Activity Relationship , Sulfonic Acids/chemistry
18.
J Med Chem ; 58(1): 252-64, 2015 Jan 08.
Article in English | MEDLINE | ID: mdl-25054653

ABSTRACT

Kinases are among the structurally most extensively characterized therapeutic targets. For many kinases, X-ray structures of inhibitor complexes are publicly available. We have identified all three-dimensional activity cliffs (3D-cliffs) formed by kinase inhibitors. More than 1300 X-ray structures of unique kinase-inhibitor complexes and associated activity data were analyzed. On the basis of binding mode comparison and 3D similarity calculations, 105 3D-cliffs were detected for type I, type II, or type III inhibitors of 13 different kinases. Many of these activity cliffs revealed clear interaction differences between highly and weakly potent inhibitors. More than 200 structural analogues of 3D-cliff compounds were identified whose structure-activity relationships (SARs) can be further explored in three dimensions on the basis of the corresponding 3D-cliffs. In addition to SAR exploration, 3D-cliffs provide useful interaction hypotheses for structure-based design. The kinase inhibitor and activity cliff information is made freely available as a part of our study.


Subject(s)
Enzyme Inhibitors/chemistry , Models, Molecular , Phosphotransferases/chemistry , Protein Structure, Tertiary , Algorithms , Crystallography, X-Ray , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Molecular Structure , Phosphotransferases/antagonists & inhibitors , Phosphotransferases/metabolism , Protein Binding , Protein Interaction Mapping/methods , Structure-Activity Relationship
19.
J Med Chem ; 58(1): 30-40, 2015 Jan 08.
Article in English | MEDLINE | ID: mdl-25051177

ABSTRACT

Publicly available kinase inhibitors have been analyzed in detail. Nearly 19000 inhibitors have been identified with activity against 266 different kinases. Thus, about half of the human kinome is currently covered with active small molecules. The distribution of inhibitors across the kinome is uneven. Most available kinase inhibitors are likely to be type I inhibitors. By contrast, type II inhibitors are rare but usually have high potency. Kinase inhibitors generally display high scaffold diversity. Activity cliffs with an at least 100-fold difference in potency are only found for inhibitors of 106 kinases, which is partly due to only small numbers of compounds available for many kinases, in addition to scaffold diversity. Moreover, kinase inhibitors are less promiscuous than often thought. More than 70% of available inhibitors are only annotated with a single kinase activity, and only ∼1% of the inhibitors are active against five or more kinases.


Subject(s)
Protein Kinase Inhibitors/pharmacology , Protein Kinases/metabolism , Proteome/antagonists & inhibitors , Proteome/metabolism , Antineoplastic Agents/chemistry , Antineoplastic Agents/classification , Antineoplastic Agents/pharmacology , Humans , Molecular Structure , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/classification , Protein Kinases/classification , Proteomics/methods
20.
Bioorg Med Chem ; 22(21): 6163-73, 2014 Nov 01.
Article in English | MEDLINE | ID: mdl-25257911

ABSTRACT

In an effort to identify novel cholinesterase candidates for the treatment of Alzheimer's disease (AD), a diverse array of potentially bioactive compounds including triazolothiadiazoles (4a-h and 5a-f) and triazolothiadiazines (6a-h) was obtained in good yields through the cyclocondensation reaction of 4-amino-5-(pyridin-3-yl)-4H-1,2,4-triazole-3-thiol (3) with various substituted aryl/heteroaryl/aryloxy acids and phenacyl bromides, respectively. The structures of newly prepared compounds were confirmed by IR, (1)H and (13)C NMR spectroscopy and, in case of 4a, by single crystal X-ray diffraction analysis. The purity of the synthesized compounds was ascertained by elemental analysis. The newly synthesized conjugated heterocycles were screened for cholinesterase inhibitory activity against electric eel acetylcholinesterase (EeAChE) and horse serum butyrylcholinesterase (hBChE). Among the evaluated hybrids, several compounds were identified as potent inhibitors. Compounds 5b and 5d were most active with an IC50 value of 3.09 ± 0.154 and 11.3 ± 0.267 µM, respectively, against acetylcholinesterase, whereas 5b, 6a and 6g were most potent against butyrylcholinesterase, with an IC50 of 0.585 ± 0.154, 0.781 ± 0.213, and 1.09 ± 0.156 µM, respectively, compared to neostigmine and donepezil as standard drugs. The synthesized heteroaromatic compounds were also tested for their cytotoxic potential against lung carcinoma (H157) and vero cell lines. Among them, compound 6h exhibited highest antiproliferative activity against H157 cell lines, with IC50 value of 0.96 ± 0.43 µM at 1mM concentration as compared to vincristine (IC50=1.03 ± 0.04 µM), standard drug used in this study.


Subject(s)
Cholinesterase Inhibitors/chemistry , Cholinesterase Inhibitors/pharmacology , Thiadiazines/chemistry , Thiadiazines/pharmacology , Thiadiazoles/chemistry , Thiadiazoles/pharmacology , Acetylcholinesterase/chemistry , Acetylcholinesterase/metabolism , Alzheimer Disease/drug therapy , Alzheimer Disease/enzymology , Animals , Butyrylcholinesterase/chemistry , Butyrylcholinesterase/metabolism , Cell Line, Tumor , Chlorocebus aethiops , Cholinesterase Inhibitors/chemical synthesis , Crystallography, X-Ray , Electrophorus , Horses , Humans , Models, Molecular , Structure-Activity Relationship , Thiadiazines/chemical synthesis , Thiadiazoles/chemical synthesis , Vero Cells
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