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1.
Front Microbiol ; 15: 1230997, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38690360

RESUMO

A rapid increase in antimicrobial resistant bacterial infections around the world is causing a global health crisis. The Gram-negative bacterium Acinetobacter baumannii is categorized as a Priority 1 pathogen for research and development of new antimicrobials by the World Health Organization due to its numerous intrinsic antibiotic resistance mechanisms and ability to quickly acquire new resistance determinants. Specialized phage enzymes, called depolymerases, degrade the bacterial capsule polysaccharide layer and show therapeutic potential by sensitizing the bacterium to phages, select antibiotics, and serum killing. The functional domains responsible for the capsule degradation activity are often found in the tail fibers of select A. baumannii phages. To further explore the functional domains associated with depolymerase activity, tail-associated proteins of 71 sequenced and fully characterized phages were identified from published literature and analyzed for functional domains using InterProScan. Multisequence alignments and phylogenetic analyses were conducted on the domain groups and assessed in the context of noted halo formation or depolymerase characterization. Proteins derived from phages noted to have halo formation or a functional depolymerase, but no functional domain hits, were modeled with AlphaFold2 Multimer, and compared to other protein models using the DALI server. The domains associated with depolymerase function were pectin lyase-like (SSF51126), tailspike binding (cd20481), (Trans)glycosidases (SSF51445), and potentially SGNH hydrolases. These findings expand our knowledge on phage depolymerases, enabling researchers to better exploit these enzymes for therapeutic use in combating the antimicrobial resistance crisis.

2.
Heliyon ; 10(1): e23127, 2024 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-38163175

RESUMO

This review aims to critically examine the existing state-of-the-art forest fire detection systems that are based on deep learning methods. In general, forest fire incidences bring significant negative impact to the economy, environment, and society. One of the crucial mitigation actions that needs to be readied is an effective forest fire detection system that are able to automatically notify the relevant parties on the incidence of forest fire as early as possible. This review paper has examined in details 37 research articles that have implemented deep learning (DL) model for forest fire detection, which were published between January 2018 and 2023. In this paper, in depth analysis has been performed to identify the quantity and type of data that includes images and video datasets, as well as data augmentation methods and the deep model architecture. This paper is structured into five subsections, each of which focuses on a specific application of deep learning (DL) in the context of forest fire detection. These subsections include 1) classification, 2) detection, 3) detection and classification, 4) segmentation, and 5) segmentation and classification. To compare the model's performance, the methods were evaluated using comprehensive metrics like accuracy, mean average precision (mAP), F1-Score, mean pixel accuracy (MPA), etc. From the findings, of the usage of DL models for forest fire surveillance systems have yielded favourable outcomes, whereby the majority of studies managed to achieve accuracy rates that exceeds 90%. To further enhance the efficacy of these models, future research can explore the optimal fine-tuning of the hyper-parameters, integrate various satellite data, implement generative data augmentation techniques, and refine the DL model architecture. In conclusion, this paper highlights the potential of deep learning methods in enhancing forest fire detection that is crucial for forest fire management and mitigation.

3.
Sci Rep ; 13(1): 15107, 2023 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-37704686

RESUMO

Predicting the structure of antibody-antigen complexes has tremendous value in biomedical research but unfortunately suffers from a poor performance in real-life applications. AlphaFold2 (AF2) has provided renewed hope for improvements in the field of protein-protein docking but has shown limited success against antibody-antigen complexes due to the lack of co-evolutionary constraints. In this study, we used physics-based protein docking methods for building decoy sets consisting of low-energy docking solutions that were either geometrically close to the native structure (positives) or not (negatives). The docking models were then fed into AF2 to assess their confidence with a novel composite score based on normalized pLDDT and pTMscore metrics after AF2 structural refinement. We show benefits of the AF2 composite score for rescoring docking poses both in terms of (1) classification of positives/negatives and of (2) success rates with particular emphasis on early enrichment. Docking models of at least medium quality present in the decoy set, but not necessarily highly ranked by docking methods, benefitted most from AF2 rescoring by experiencing large advances towards the top of the reranked list of models. These improvements, obtained without any calibration or novel methodologies, led to a notable level of performance in antibody-antigen unbound docking that was never achieved previously.


Assuntos
Complexo Antígeno-Anticorpo , Furilfuramida , Simulação de Acoplamento Molecular , Benchmarking , Evolução Biológica
4.
Front Mol Biosci ; 10: 1253689, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37692063

RESUMO

Accurate protein-protein docking remains challenging, especially for artificial biologics not coevolved naturally against their protein targets, like antibodies and other engineered scaffolds. We previously developed ProPOSE, an exhaustive docker with full atomistic details, which delivers cutting-edge performance by allowing side-chain rearrangements upon docking. However, extensive protein backbone flexibility limits its practical applicability as indicated by unbound docking tests. To explore the usefulness of ProPOSE on systems with limited backbone flexibility, here we tested the engineered scaffold DARPin, which is characterized by its relatively rigid protein backbone. A prospective screening campaign was undertaken, in which sequence-diversified DARPins were docked and ranked against a directed epitope on the target protein BCL-W. In this proof-of-concept study, only a relatively small set of 2,213 diverse DARPin interfaces were selected for docking from the huge theoretical library from mutating 18 amino-acid positions. A computational selection protocol was then applied for enrichment of binders based on normalized computed binding scores and frequency of binding modes against the predefined epitope. The top-ranked 18 designed DARPin interfaces were selected for experimental validation. Three designs exhibited binding affinities to BCL-W in the nanomolar range comparable to control interfaces adopted from known DARPin binders. This result is encouraging for future screening and engineering campaigns of DARPins and possibly other similarly rigid scaffolds against targeted protein epitopes. Method limitations are discussed and directions for future refinements are proposed.

5.
Front Mol Biosci ; 10: 1210576, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37351549

RESUMO

Scoring functions are ubiquitous in structure-based drug design as an aid to predicting binding modes and estimating binding affinities. Ideally, a scoring function should be broadly applicable, obviating the need to recalibrate and refit its parameters for every new target and class of ligands. Traditionally, drugs have been small molecules, but in recent years biologics, particularly antibodies, have become an increasingly important if not dominant class of therapeutics. This makes the goal of having a transferable scoring function, i.e., one that spans the range of small-molecule to protein ligands, even more challenging. One such broadly applicable scoring function is the Solvated Interaction Energy (SIE), which has been developed and applied in our lab for the last 15 years, leading to several important applications. This physics-based method arose from efforts to understand the physics governing binding events, with particular care given to the role played by solvation. SIE has been used by us and many independent labs worldwide for virtual screening and discovery of novel small-molecule binders or optimization of known drugs. Moreover, without any retraining, it is found to be transferrable to predictions of antibody-antigen relative binding affinities and as accurate as functions trained on protein-protein binding affinities. SIE has been incorporated in conjunction with other scoring functions into ADAPT (Assisted Design of Antibody and Protein Therapeutics), our platform for affinity modulation of antibodies. Application of ADAPT resulted in the optimization of several antibodies with 10-to-100-fold improvements in binding affinity. Further applications included broadening the specificity of a single-domain antibody to be cross-reactive with virus variants of both SARS-CoV-1 and SARS-CoV-2, and the design of safer antibodies by engineering of a pH switch to make them more selective towards acidic tumors while sparing normal tissues at physiological pH.

6.
Front Immunol ; 13: 884132, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35720356

RESUMO

Single-domain antibodies (sdAbs) are a promising class of biotherapeutics with unique structural traits within their paratope region. The distribution of canonical conformations explored by their complementarity determining region (CDR) loops differs to some extent from conventional two-chain Fv fragments of monoclonal antibodies (mAbs). In this study, we explored in detail the canonical structures of sdAb CDR-H1 and CDR-H2 loops and compared those with mAbs from the IGHV3 and IGHV1 gene families. We surveyed the antibody structures catalogued in SAbDab and clustered the CDR canonical loops in Cartesian space. While most of the sdAb clusters were sub-populations of previously defined canonical Fv conformations of CDR-H1 and CDR-H2, our stricter clustering approach defined narrower clusters in sequence-space. Meticulous visual inspection of sub-populations allowed a clearer understanding of sequence-structure relationships. The packing densities within structural pockets contacted by CDR-H1 and CDR-H2 canonical conformations were analyzed on the premise that these pockets cannot be left vacant as they would leave exposed supportive hydrophobic residues. The fine resolution of the canonical clusters defined here revealed unique signatures within these pockets, including distinct structural complementarities between CDR-H1 and CDR-H2 canonical clusters, which could not be perceived with the previous coarser clusters. We highlight examples where a single residue change in CDR-H1 sequence is sufficient to induce a dramatic population shift in CDR-H2 conformation. This suggests that preferences in combining CDR-H1 and CDR-H2 emerged naturally during antibody evolution, leading to preferred sets of conserved amino acids at key positions in the framework as well as within the CDR loops. We outline a game of musical chairs that is necessary to maintain the integrity of the antibody structures that arose during evolution. Our study also provides refined CDR-H1 and CDR-H2 structural templates for sdAb homology modeling that could be leveraged for improved antibody design.


Assuntos
Anticorpos de Domínio Único , Anticorpos Monoclonais , Regiões Determinantes de Complementaridade/química , Modelos Moleculares , Conformação Proteica
7.
Proteins ; 90(8): 1538-1546, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35355327

RESUMO

Antibody-based therapeutics for treatment of various tumors have grown rapidly in recent years. Unfortunately, safety issues, attributed to off-tumor effects and cytotoxicity, are still a significant concern with the standard of care. Improvements to ensure targeted delivery of antitumor pharmaceuticals are desperately needed. We previously demonstrated that incorporating histidyl pH-switches in an anti-HER2 antibody induced selective antigen binding under acidic pH conditions (MAbs 2020;12:1682866). This led to an improved safety profile due to preferential targeting of the oncoprotein in the acidic solid tumor microenvironment. Following this success, we expanded this approach to a set of over 400 antibody structures complexed with over 100 different human oncoproteins, associated with solid tumors. Calculations suggested that mutations to His of certain residue types, namely Trp, Arg, and Tyr, could be significantly more successful for inducing pH-dependent binding under acidic conditions. Furthermore, 10 positions within the complementarity-determining region were also predicted to exhibit greater successes. Combined, these two accessible metrics could serve as the basis for a sequence-based engineering of pH-selective binding. This approach could be applied to most anticancer antibodies, which lack detailed structural characterization.


Assuntos
Anticorpos Monoclonais , Microambiente Tumoral , Anticorpos Monoclonais/genética , Humanos , Concentração de Íons de Hidrogênio , Mutação
8.
Sci Rep ; 11(1): 21849, 2021 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-34750472

RESUMO

The huge worldwide demand for vaccines targeting SARS-CoV-2 has necessitated the continued development of novel improved formulations capable of reducing the burden of the COVID-19 pandemic. Herein, we evaluated novel protein subunit vaccine formulations containing a resistin-trimerized spike antigen, SmT1. When combined with sulfated lactosyl archaeol (SLA) archaeosome adjuvant, formulations induced robust antigen-specific humoral and cellular immune responses in mice. Antibodies had strong neutralizing activity, preventing viral spike binding and viral infection. In addition, the formulations were highly efficacious in a hamster challenge model reducing viral load and body weight loss even after a single vaccination. The antigen-specific antibodies generated by our vaccine formulations had stronger neutralizing activity than human convalescent plasma, neutralizing the spike proteins of the B.1.1.7 and B.1.351 variants of concern. As such, our SmT1 antigen along with SLA archaeosome adjuvant comprise a promising platform for the development of efficacious protein subunit vaccine formulations for SARS-CoV-2.


Assuntos
Adjuvantes Imunológicos/química , Antígenos Arqueais/química , Vacinas contra COVID-19/uso terapêutico , Lipídeos/química , Animais , Anticorpos Neutralizantes/imunologia , Anticorpos Antivirais/imunologia , Peso Corporal , COVID-19/terapia , Chlorocebus aethiops , Cricetinae , Citocinas/metabolismo , Feminino , Humanos , Imunidade Celular , Imunidade Humoral , Imunização Passiva , Mesocricetus , Camundongos , Camundongos Endogâmicos C57BL , Testes de Neutralização , Peptídeos/química , Domínios Proteicos , SARS-CoV-2 , Receptores Toll-Like/imunologia , Células Vero , Carga Viral , Soroterapia para COVID-19
9.
Sci Rep ; 11(1): 21362, 2021 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-34725391

RESUMO

The design of superior biologic therapeutics, including antibodies and engineered proteins, involves optimizing their specific ability to bind to disease-related molecular targets. Previously, we developed and applied the Assisted Design of Antibody and Protein Therapeutics (ADAPT) platform for virtual affinity maturation of antibodies (Vivcharuk et al. in PLoS One 12(7):e0181490, https://doi.org/10.1371/journal.pone.0181490 , 2017). However, ADAPT is limited to point mutations of hot-spot residues in existing CDR loops. In this study, we explore the possibility of wholesale replacement of the entire H3 loop with no restriction to maintain the parental loop length. This complements other currently published studies that sample replacements for the CDR loops L1, L2, L3, H1 and H2. Given the immense sequence space theoretically available to H3, we focused on the virtual grafting of over 5000 human germline-derived H3 sequences from the IGMT/LIGM database increasing the diversity of the sequence space when compared to using crystalized H3 loop sequences. H3 loop conformations are generated and scored to identify optimized H3 sequences. Experimental testing of high-ranking H3 sequences grafted into the framework of the bH1 antibody against human VEGF-A led to the discovery of multiple hits, some of which had similar or better affinities relative to the parental antibody. In over 75% of the tested designs, the re-designed H3 loop contributed favorably to overall binding affinity. The hits also demonstrated good developability attributes such as high thermal stability and no aggregation. Crystal structures of select re-designed H3 variants were solved and indicated that although some deviations from predicted structures were seen in the more solvent accessible regions of the H3 loop, they did not significantly affect predicted affinity scores.


Assuntos
Anticorpos/química , Sequência de Aminoácidos , Anticorpos/imunologia , Regiões Determinantes de Complementaridade/química , Regiões Determinantes de Complementaridade/imunologia , Humanos , Modelos Moleculares , Agregados Proteicos , Conformação Proteica , Estabilidade Proteica , Fator A de Crescimento do Endotélio Vascular/imunologia
10.
MAbs ; 11(7): 1300-1318, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31318308

RESUMO

Solution stability is an important factor in the optimization of engineered biotherapeutic candidates such as monoclonal antibodies because of its possible effects on manufacturability, pharmacology, efficacy and safety. A detailed atomic understanding of the mechanisms governing self-association of natively folded protein monomers is required to devise predictive tools to guide screening and re-engineering along the drug development pipeline. We investigated pairs of affinity-matured full-size antibodies and observed drastically different propensities to aggregate from variants differing by a single amino-acid. Biophysical testing showed that antigen-binding fragments (Fabs) from the aggregating antibodies also reversibly associated with equilibrium dissociation constants in the low-micromolar range. Crystal structures (PDB accession codes 6MXR, 6MXS, 6MY4, 6MY5) and bottom-up hydrogen-exchange mass spectrometry revealed that Fab self-association occurs in a symmetric mode that involves the antigen complementarity-determining regions. Subtle local conformational changes incurred upon point mutation of monomeric variants foster formation of complementary polar interactions and hydrophobic contacts to generate a dimeric Fab interface. Testing of popular in silico tools generally indicated low reliabilities for predicting the aggregation propensities observed. A structure-aggregation data set is provided here in order to stimulate further improvements of in silico tools for prediction of native aggregation. Incorporation of intermolecular docking, conformational flexibility, and short-range packing interactions may all be necessary features of the ideal algorithm.


Assuntos
Anticorpos Monoclonais/química , Regiões Determinantes de Complementaridade/química , Fragmentos Fab das Imunoglobulinas/química , Anticorpos Monoclonais/genética , Bioengenharia , Regiões Determinantes de Complementaridade/genética , Dimerização , Humanos , Fragmentos Fab das Imunoglobulinas/genética , Espectrometria de Massas , Mutação/genética , Agregados Proteicos , Conformação Proteica , Dobramento de Proteína , Estabilidade Proteica , Estereoisomerismo , Relação Estrutura-Atividade
11.
J Chem Theory Comput ; 14(9): 4938-4947, 2018 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-30107730

RESUMO

Despite decades of development, protein-protein docking remains a largely unsolved problem. The main difficulties are the immense space spanned by the translational and rotational degrees of freedom and the prediction of the conformational changes of proteins upon binding. FFT is generally the preferred method to exhaustively explore the translation-rotation space at a fine grid resolution, albeit with the trade-off of approximating force fields with correlation functions. This work presents a direct search alternative that samples the states in Cartesian space at the same resolution and computational cost as standard FFT methods. Operating in real space allows the use of standard force field functional forms used in typical non-FFT methods as well as the implementation of strategies for focused exploration of conformational flexibility. Currently, a few misplaced side chains can cause docking programs to fail. This work specifically addresses the problem of side chain rearrangements upon complex formation. Based on the observation that most side chains retain their unbound conformation upon binding, each rigidly docked pose is initially scored ignoring up to a limited number of side chain overlaps which are resolved in subsequent repacking and minimization steps. On test systems where side chains are altered and backbones held in their bound state, this implementation provides significantly better native pose recovery and higher quality (lower RMSD) predictions when compared with five of the most popular docking programs. The method is implemented in the software program ProPOSE (Protein Pose Optimization by Systematic Enumeration).


Assuntos
Técnicas de Química Analítica/métodos , Simulação por Computador , Proteínas/química , Software , Complexo Antígeno-Anticorpo/química , Simulação de Acoplamento Molecular , Ligação Proteica , Conformação Proteica
12.
Methods Mol Biol ; 1762: 367-388, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29594781

RESUMO

Docking simulations help us understand molecular interactions. Here we present a hands-on tutorial to utilize FlexAID (Flexible Artificial Intelligence Docking), an open source molecular docking software between ligands such as small molecules or peptides and macromolecules such as proteins and nucleic acids. The tutorial uses the NRGsuite PyMOL plugin graphical user interface to set up and visualize docking simulations in real time as well as detect and refine target cavities. The ease of use of FlexAID and the NRGsuite combined with its superior performance relative to widely used docking software provides nonexperts with an important tool to understand molecular interactions with direct applications in structure-based drug design and virtual high-throughput screening.


Assuntos
Descoberta de Drogas/métodos , Simulação de Acoplamento Molecular/métodos , Sítios de Ligação , Desenho Assistido por Computador , Desenho de Fármacos , Ligantes , Modelos Moleculares , Ácidos Nucleicos/química , Ácidos Nucleicos/metabolismo , Peptídeos/química , Peptídeos/farmacologia , Proteínas/química , Proteínas/metabolismo , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia , Software
13.
Mol Pharm ; 15(7): 2489-2502, 2018 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-28837343

RESUMO

Cardiovascular diseases are the leading causes of mortality across the globe. Over the years, various drug formulations and delivery methods have been tested for cardiac repair. Milrinone (MRN) is a widely known cardiac inotrope drug used for the treatment of congestive heart failure in patients, however, its efficacy is limited. This study is the first to report the design of a novel MRN-nanoformulation using human serum albumin nanoparticles (HSA-NPs). The HSA-NPs exhibit promising drug delivery characteristics, such as target specificity, nonimmunogenicity, biocompatibility, and enhanced bioavailability. This article describes a MRN-nanoformulation design for in vitro drug release, cellular uptake, biocompatibility, and other features. The MRN-nanoformulation was prepared by the ethanol desolvation technique and key parameters were optimized to obtain a desired particle size of 154.2 ± 5.8 nm, zeta potential of -29.5 ± 2.9 mV, and a drug encapsulation efficiency of 41.1 ± 1.7%. Molecular docking studies have revealed that MRN binds in the hydrophobic cavity of HSA, which has also been indicated by circular dichroism and enzyme-mediated drug release studies in the presence of trypsin, pepsin, proteinase K, protease, and cathepsin D. The intracellular uptake of fluorescently tagged MRN-HSA-NPs using HUVEC and H9c2 cells was evaluated by flow cytometry. The nanoparticle toxicity results indicated that MRN-HSA-NPs show significantly lower cytotoxicity and higher cell viability ( P < 0.0001) as compared to the MRN-lactate drug in HUVEC (61.6 ± 3.7% vs 36.2 ± 2.9%) and H9c2 (58.8 ± 5.7% vs 18.8 ± 4.9%) cells. These studies indicate that the novel MRN-nanoformulation offers better drug delivery procedures than currently used methods and has potential in treatment of congestive heart failure and other cardiovascular diseases.


Assuntos
Cardiotônicos/administração & dosagem , Doenças Cardiovasculares/tratamento farmacológico , Portadores de Fármacos/química , Milrinona/administração & dosagem , Animais , Linhagem Celular , Dicroísmo Circular , Composição de Medicamentos/métodos , Liberação Controlada de Fármacos , Células Endoteliais da Veia Umbilical Humana , Humanos , Interações Hidrofóbicas e Hidrofílicas , Milrinona/química , Milrinona/farmacocinética , Simulação de Acoplamento Molecular , Nanopartículas/química , Tamanho da Partícula , Ratos , Albumina Sérica Humana/química
14.
J Comput Aided Mol Des ; 32(1): 143-150, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28983727

RESUMO

The Farnesoid X receptor (FXR) exhibits significant backbone movement in response to the binding of various ligands and can be a challenge for pose prediction algorithms. As part of the D3R Grand Challenge 2, we tested Wilma-SIE, a rigid-protein docking method, on a set of 36 FXR ligands for which the crystal structures had originally been blinded. These ligands covered several classes of compounds. To overcome the rigid protein limitations of the method, we used an ensemble of publicly available structures for FXR from the PDB. The use of the ensemble allowed Wilma-SIE to predict poses with average and median RMSDs of 2.3 and 1.4 Å, respectively. It was quite clear, however, that had we used a single structure for the receptor the success rate would have been much lower. The most successful predictions were obtained on chemical classes for which one or more crystal structures of the receptor bound to a molecule of the same class was available. In the absence of a crystal structure for the class, observing a consensus binding mode for the ligands of the class using one or more receptor structures of other classes seemed to be indicative of a reasonable pose prediction. Affinity prediction proved to be more challenging with generally poor correlation with experimental IC50s (Kendall tau ~ 0.3). Even when the 36 crystal structures were used the accuracy of the predicted affinities was not appreciably improved. A possible cause of difficulty is the internal energy strain arising from conformational differences in the receptor across complexes, which may need to be properly estimated and incorporated into the SIE scoring function.


Assuntos
Descoberta de Drogas , Simulação de Acoplamento Molecular , Receptores Citoplasmáticos e Nucleares/metabolismo , Software , Sítios de Ligação , Desenho Assistido por Computador , Cristalografia por Raios X , Bases de Dados de Proteínas , Desenho de Fármacos , Humanos , Ligantes , Ligação Proteica , Conformação Proteica , Receptores Citoplasmáticos e Nucleares/química , Termodinâmica
15.
Bioinformatics ; 31(23): 3856-8, 2015 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-26249810

RESUMO

UNLABELLED: Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains and definition of geometric constraints. Furthermore, the NRGsuite permits the visualization of the docking simulation in real time. The NRGsuite give access to powerful docking simulations that can be used in structure-guided drug design as well as an educational tool. The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. The NRGsuite is available for Windows, Linux and MacOS. AVAILABILITY AND IMPLEMENTATION: http://bcb.med.usherbrooke.ca/flexaid. CONTACT: rafael.najmanovich@usherbroke.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Simulação de Acoplamento Molecular/métodos , Proteínas/química , Software , Sítios de Ligação , Ligantes , Proteínas/metabolismo
16.
J Chem Inf Model ; 55(7): 1323-36, 2015 Jul 27.
Artigo em Inglês | MEDLINE | ID: mdl-26076070

RESUMO

Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on surface complementarity. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. The prediction of binding poses is tested using the widely used Astex dataset as well as the HAP2 dataset, while performance in virtual screening is evaluated using a subset of the DUD dataset. We compare FlexAID to AutoDock Vina, FlexX, and rDock in an extensive number of scenarios to understand the strengths and limitations of the different programs as well as to reported results for Glide, GOLD, and DOCK6 where applicable. The most relevant among these scenarios is that of docking on flexible non-native-complex structures where as is the case in reality, the target conformation in the bound form is not known a priori. We demonstrate that FlexAID, unlike other programs, is robust against increasing structural variability. FlexAID obtains equivalent sampling success as GOLD and performs better than AutoDock Vina or FlexX in all scenarios against non-native-complex structures. FlexAID is better than rDock when there is at least one critical side-chain movement required upon ligand binding. In virtual screening, FlexAID results are lower on average than those of AutoDock Vina and rDock. The higher accuracy in flexible targets where critical movements are required, intuitive PyMOL-integrated graphical user interface and free source code as well as precompiled executables for Windows, Linux, and Mac OS make FlexAID a welcome addition to the arsenal of existing small-molecule protein docking methods.


Assuntos
Simulação de Acoplamento Molecular/métodos , Proteínas/química , Proteínas/metabolismo , Gráficos por Computador , Bases de Dados de Proteínas , Avaliação Pré-Clínica de Medicamentos , Ligantes , Movimento , Conformação Proteica , Interface Usuário-Computador
17.
J Lipid Res ; 53(12): 2677-89, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23018617

RESUMO

Steroidogenic acute regulatory-related lipid transfer (START) domain proteins are involved in the nonvesicular intracellular transport of lipids and sterols. The STARD1 (STARD1 and STARD3) and STARD4 subfamilies (STARD4-6) have an internal cavity large enough to accommodate sterols. To provide a deeper understanding on the structural biology of this domain, the binding of sterols to STARD5, a member of the STARD4 subfamily, was monitored. The SAR by NMR [(1)H-(15)N heteronuclear single-quantum coherence (HSQC)] approach, complemented by circular dichroism (CD) and isothermal titration calorimetry (ITC), was used. Titration of STARD5 with cholic (CA) and chenodeoxycholic acid (CDCA), ligands of the farnesoid X receptor (FXR), leads to drastic perturbation of the (1)H-(15)N HSQC spectra and the identification of the residues in contact with those ligands. The most perturbed residues in presence of ligands are lining the internal cavity of the protein. Ka values of 1.8·10-(4) M(-1) and 6.3·10(4) M(-1) were measured for CA and CDCA, respectively. This is the first report of a START domain protein in complex with a sterol ligand. Our original findings indicate that STARD5 may be involved in the transport of bile acids rather than cholesterol.


Assuntos
Proteínas de Transporte/química , Ácido Quenodesoxicólico/química , Ácido Cólico/química , Proteínas Adaptadoras de Transporte Vesicular , Sítios de Ligação , Proteínas de Transporte/genética , Proteínas de Transporte/isolamento & purificação , Clonagem Molecular , Humanos , Ligantes , Espectroscopia de Ressonância Magnética/normas , Modelos Moleculares , Estabilidade Proteica , Padrões de Referência , Relação Estrutura-Atividade , Termodinâmica
18.
Bioinformatics ; 28(18): i423-i430, 2012 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-22962462

RESUMO

MOTIVATION: Protein movements form a continuum from large domain rearrangements (including folding and restructuring) to side-chain rotamer changes and small rearrangements. Understanding side-chain flexibility upon binding is important to understand molecular recognition events and predict ligand binding. METHODS: In the present work, we developed a well-curated non-redundant dataset of 188 proteins in pairs of structures in the Apo (unbound) and Holo (bound) forms to study the extent and the factors that guide side-chain rotamer changes upon binding. RESULTS: Our analysis shows that side-chain rotamer changes are widespread with only 10% of binding sites displaying no conformational changes. Overall, at most five rotamer changes account for the observed movements in 90% of the cases. Furthermore, rotamer changes are essential in 32% of flexible binding sites. The different amino acids have a 11-fold difference in their probability to undergo changes. Side-chain flexibility represents an intrinsic property of amino acids as it correlates well with configurational entropy differences. Furthermore, on average b-factors and solvent accessible surface areas can discriminate flexible side-chains in the Apo form. Finally, there is a rearrangement of the hydrogen-bonding network upon binding primarily with a loss of H-bonds with water molecules and a gain of H-bonds with protein residues for flexible residues. Interestingly, only 25% of side chains capable of forming H-bonds do so with the ligand upon binding. In terms of drug design, this last result shows that there is a large number of potential interactions that may be exploited to modulate the specificity and sensitivity of inhibitors. CONTACT: rafael.najmanovich@usherbrooke.ca.


Assuntos
Aminoácidos/química , Ligação Proteica , Proteínas/química , Sítios de Ligação , Bases de Dados de Proteínas , Entropia , Ligação de Hidrogênio , Ligantes , Conformação Proteica
19.
Bioinformatics ; 28(11): 1438-45, 2012 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-22467916

RESUMO

MOTIVATION: An increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. This large-scale analysis was performed using the whole Pfam database covering over 70% of the known protein sequence universe. Our program Sherlocc, detects statistically relevant conserved rare codon clusters and produces a user-friendly HTML output. RESULTS: Statistically significant rare codon clusters were detected in a multitude of Pfam protein families. The most statistically significant rare codon clusters were predominantly identified in N-terminal Pfam families. Many of the longest rare codon clusters are found in membrane-related proteins which are required to interact with other proteins as part of their function, for example in targeting or insertion. We identified some cases where rare codon clusters can play a regulating role in the folding of catalytically important domains. Our results support the existence of a widespread functional role for rare codon clusters across species. Finally, we developed an online filter-based search interface that provides access to Sherlocc results for all Pfam families. AVAILABILITY: The Sherlocc program and search interface are open access and are available at http://bcb.med.usherbrooke.ca


Assuntos
Algoritmos , Códon , Proteínas/química , Software , Bactérias/química , Bactérias/metabolismo , Bacteriófagos/química , Bacteriófagos/metabolismo , Análise por Conglomerados , Biossíntese de Proteínas , Proteínas/genética
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