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Article ; Online: Mapping global protein contacts.

Vajda, Sandor / Emili, Andrew

2019 Volume 365, Issue 6449, Page(s) 120–121

MeSH term(s)	Protein Interaction Maps ; Proteome
Chemical Substances	Proteome
Language	English
Publishing date	2019-07-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aay1440
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Zs.MG 77: Show issues

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Article ; Online: Ajak- és szájpadhasadékkal társult genetikai szindrómás gyermekek komplex ellátása.

Vástyán, Attila / Maros, Teodor Barna / Sándor-Bajusz, Kinga Amália / Vajda, Katalin / Hadzsiev, Kinga

Orvosi hetilap

2022 Volume 163, Issue 21, Page(s) 826–831

Abstract: Introduction: The majority of facial clefts are isolated developmental anomalies. In a minority of the cases, however, facial clefts may occur as part of particular genetic syndromes.: Objective: We aimed to analyse the treatment of the syndromic ... ...

Abstract	Introduction: The majority of facial clefts are isolated developmental anomalies. In a minority of the cases, however, facial clefts may occur as part of particular genetic syndromes. Objective: We aimed to analyse the treatment of the syndromic patients and determine whether the algorithm of complex treatment - used in non-syndromic patients - has changed in patients who had syndromes. Method: Documentation of the patients, treated by the Pecs Cleft Team between 1999 and 2015, were obtained and analysed retrospectively. These included surgical and genetical data as well. Epidemiological data from the national registry of birth were also used. Results: 607 patients were treated by the Cleft Team in the given period. Among these patients, 25 (4.11%) were found to have associated anomalies. Sixteen patients (2.6%) were identified as having a particular syndrome. 8 different syndromes occurred. Robin sequence represented 50% of this cohort. In 13 patients, the usual treatment algorithm had to be modified. The modifications were necessary due to the given genetic syndromes. Conclusion: Genetic syndromes significantly may affect the treatment algorithm in children born with cleft lip and palate. The (surgical) treatment of associated anomalies have priority over the reconstruction of cleft lip and palate. Orv Hetil. 2022; 163(21): 826-831.
MeSH term(s)	Child ; Cleft Lip/epidemiology ; Cleft Lip/genetics ; Cleft Lip/surgery ; Cleft Palate/genetics ; Cleft Palate/surgery ; Humans ; Registries ; Retrospective Studies ; Syndrome
Language	English
Publishing date	2022-05-22
Publishing country	Hungary
Document type	Journal Article
ZDB-ID	123879-6
ISSN	1788-6120 ; 0030-6002
ISSN (online)	1788-6120
ISSN	0030-6002
DOI	10.1556/650.2022.32500
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Article ; Online: Mapping the binding sites of challenging drug targets.

Wakefield, Amanda E / Kozakov, Dima / Vajda, Sandor

Current opinion in structural biology

2022 Volume 75, Page(s) 102396

Abstract: An increasing number of medically important proteins are challenging drug targets because their binding sites are too shallow or too polar, are cryptic and thus not detectable without a bound ligand or located in a protein-protein interface. While such ... ...

Abstract	An increasing number of medically important proteins are challenging drug targets because their binding sites are too shallow or too polar, are cryptic and thus not detectable without a bound ligand or located in a protein-protein interface. While such proteins may not bind druglike small molecules with sufficiently high affinity, they are frequently druggable using novel therapeutic modalities. The need for such modalities can be determined by experimental or computational fragment based methods. Computational mapping by mixed solvent molecular dynamics simulations or the FTMap server can be used to determine binding hot spots. The strength and location of the hot spots provide very useful information for selecting potentially successful approaches to drug discovery.
MeSH term(s)	Binding Sites ; Drug Discovery ; Ligands ; Molecular Dynamics Simulation ; Protein Binding ; Proteins/chemistry
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2022-05-27
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2022.102396
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Article ; Online: Successful endovascular treatment of simultaneous acute ischaemic stroke and hyperacute ST-elevation myocardial infarction: the first case report of a single-operator cardio-cerebral intervention.

Nardai, Sándor / Vorobcsuk, András / Nagy, Ferenc / Vajda, Zsolt

European heart journal. Case reports

2021 Volume 5, Issue 11, Page(s) ytab419

Abstract: Background: The simultaneous management of cardio-cerebral infarctions is an extremely difficult task, as both organs need to receive reperfusion therapy in a limited time to avoid death or permanent disability. The following case is the first published ...

Abstract	Background: The simultaneous management of cardio-cerebral infarctions is an extremely difficult task, as both organs need to receive reperfusion therapy in a limited time to avoid death or permanent disability. The following case is the first published endovascular treatment of synchronous heart and brain infarctions delivered by a single operator with excellent clinical outcome. Case summary: A 67-year-old female patient was directly transported to the emergency room of a comprehensive stroke centre with acute onset global aphasia and right hemiplegia. The onset to admission time exceeded the 4.5-h time window of systemic thrombolysis. Head computed tomography (CT) excluded extensive early extensive brain damage, CT angiography documented left middle cerebral artery occlusion and mechanical thrombectomy was indicated. Extensive anterior ST elevation was detected on the transport monitor while waiting for in-hospital transfer. The two simultaneously evolving pathologies were handled in a single endovascular procedure that took less than 60 min by a dual-trained interventional cardiologist/neurointerventional surgeon. The patient recovered without any major cardiac or neurologic sequela. Discussion: Interventional cardiologists, professionally trained through a neurointerventional fellowship programme to perform endovascular stroke interventions according to the latest multi-society position paper, could not only complement stroke teams lacking manpower, but their unique experience could also help the patients suffering from the most devastating forms of cardio-cerebral infarctions.
Language	English
Publishing date	2021-10-14
Publishing country	England
Document type	Case Reports
ISSN	2514-2119
ISSN (online)	2514-2119
DOI	10.1093/ehjcr/ytab419
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Article ; Online: Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.

Wodak, Shoshana J / Vajda, Sandor / Lensink, Marc F / Kozakov, Dima / Bates, Paul A

Annual review of biophysics

2023 Volume 52, Page(s) 183–206

Abstract: Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have over ... ...

Abstract	Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have over decades emulated this pattern, as monitored by the community-wide blind prediction experiments CASP and CAPRI. However, over the past few years, dramatic advances were observed for the accurate prediction of single protein chains, driven by a surge of deep learning methodologies entering the prediction field. We review the mainscientific developments that enabled these recent breakthroughs and feature the important role of blind prediction experiments in building up and nurturing the structure prediction field. We discuss how the new wave of artificial intelligence-based methods is impacting the fields of computational and experimental structural biology and highlight areas in which deep learning methods are likely to lead to future developments, provided that major challenges are overcome.
MeSH term(s)	Artificial Intelligence ; Protein Conformation
Language	English
Publishing date	2023-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2434725-5
ISSN	1936-1238 ; 1936-122X
ISSN (online)	1936-1238
ISSN	1936-122X
DOI	10.1146/annurev-biophys-102622-084607
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Article ; Online: Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2.

Bekar-Cesaretli, Ayse A / Khan, Omeir / Nguyen, Thu / Kozakov, Dima / Joseph-Mccarthy, Diane / Vajda, Sandor

Journal of chemical information and modeling

2024 Volume 64, Issue 3, Page(s) 960–973

Abstract: The neural network-based program AlphaFold2 (AF2) provides high accuracy structure prediction for a large fraction of globular proteins. An important question is whether these models are accurate enough for reliably docking small ligands. Several recent ... ...

Abstract	The neural network-based program AlphaFold2 (AF2) provides high accuracy structure prediction for a large fraction of globular proteins. An important question is whether these models are accurate enough for reliably docking small ligands. Several recent papers and the results of CASP15 reveal that local conformational errors reduce the success rates of direct ligand docking. Here, we focus on the ability of the models to conserve the location of binding hot spots, regions on the protein surface that significantly contribute to the binding free energy of the protein-ligand interaction. Clusters of hot spots predict the location and even the druggability of binding sites, and hence are important for computational drug discovery. The hot spots are determined by protein mapping that is based on the distribution of small fragment-sized probes on the protein surface and is less sensitive to local conformation than docking. Mapping models taken from the AlphaFold Protein Structure Database show that identifying binding sites is more reliable than docking, but the success rates are still 5% to 10% lower than based on mapping X-ray structures. The drop in accuracy is particularly large for models of multidomain proteins. However, both the model binding sites and the mapping results can be substantially improved by generating AF2 models for the ligand binding domains of interest rather than the entire proteins and even more if using forced sampling with multiple initial seeds. The mapping of such models tends to reach the accuracy of results obtained by mapping the X-ray structures.
MeSH term(s)	Ligands ; Furylfuramide ; Protein Binding ; Protein Conformation ; Binding Sites ; Membrane Proteins
Chemical Substances	Ligands ; Furylfuramide (054NR2135Y) ; Membrane Proteins
Language	English
Publishing date	2024-01-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01761
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Article ; Online: Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.

Khan, Omeir / Jones, George / Lazou, Maria / Joseph-McCarthy, Diane / Kozakov, Dima / Beglov, Dmitri / Vajda, Sandor

Journal of chemical information and modeling

2024 Volume 64, Issue 6, Page(s) 2084–2100

Abstract: The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based drug discovery. The computational solvent mapping server FTMap can ... ...

Abstract	The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based drug discovery. The computational solvent mapping server FTMap can reliably identify binding hot spots as consensus clusters, free energy minima that bind a variety of organic probe molecules. However, in its current implementation, FTMap provides limited information on regions within the hot spots that tend to interact with specific pharmacophoric features of potential ligands. E-FTMap is a new server that expands on the original FTMap protocol. E-FTMap uses 119 organic probes, rather than the 16 in the original FTMap, to exhaustively map binding sites, and identifies pharmacophore features as atomic consensus sites where similar chemical groups bind. We validate E-FTMap against a set of 109 experimentally derived structures of fragment-lead pairs, finding that highly ranked pharmacophore features overlap with the corresponding atoms in both fragments and lead compounds. Additionally, comparisons of mapping results to ensembles of bound ligands reveal that pharmacophores generated with E-FTMap tend to sample highly conserved protein-ligand interactions. E-FTMap is available as a web server at https://eftmap.bu.edu.
MeSH term(s)	Pharmacophore ; Ligands ; Binding Sites ; Drug Discovery/methods ; Protein Binding
Chemical Substances	Ligands
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01969
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Article ; Online: Progress toward improved understanding of antibody maturation.

Vajda, Sandor / Porter, Kathryn A / Kozakov, Dima

Current opinion in structural biology

2021 Volume 67, Page(s) 226–231

Abstract: Upon encountering an antigen, antibodies mature through various rounds of somatic mutations, resulting in higher affinities and specificities to the particular antigen. We review recent progress in four areas of antibody maturation studies. (1) Next- ... ...

Abstract	Upon encountering an antigen, antibodies mature through various rounds of somatic mutations, resulting in higher affinities and specificities to the particular antigen. We review recent progress in four areas of antibody maturation studies. (1) Next-generation and single-cell sequencing have revolutionized the analysis of antibody repertoires by dramatically increasing the sequences available to study the state and evolution of the immune system. Computational methods, including machine learning tools, have been developed for reconstituting antibody clonal lineages and for general repertoire analysis. (2) The availability of X-ray structures, thermodynamic and kinetic data, and molecular dynamics simulations provide information on the biophysical mechanisms responsible for improved affinity. (3) In addition to improved binding to a specific antigen, providing affinity-independent diversity and self/nonself discrimination are fundamental functions of the immune system. Recent studies, including X-ray structures, yield improved understanding of both mechanisms. (4) Results from in vivo maturation help to develop methods of in vitro maturation to improve antibody properties for therapeutic applications, frequently combining computational and experimental approaches.
MeSH term(s)	Antibodies ; Antigens ; Computational Biology
Chemical Substances	Antibodies ; Antigens
Language	English
Publishing date	2021-02-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2020.11.008
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Article ; Online: Novel p.G250A Mutation Associated with Chronic Pancreatitis Highlights Misfolding-Prone Region in Carboxypeptidase A1 (CPA1).

Sándor, Máté / Thiel, Franziska G / Schmid, Margit / Demcsák, Alexandra / Morales Granda, Nataly C / Németh, Balázs Csaba / Vajda, Sandor / Hoerning, André / Sahin-Tóth, Miklós

International journal of molecular sciences

2022 Volume 23, Issue 24

Abstract: Inborn mutations in the digestive protease carboxypeptidase A1 (CPA1) gene may be associated with hereditary and idiopathic chronic pancreatitis (CP). Pathogenic mutations, such as p.N256K, cause intracellular retention and reduced secretion of CPA1, ... ...

Abstract	Inborn mutations in the digestive protease carboxypeptidase A1 (CPA1) gene may be associated with hereditary and idiopathic chronic pancreatitis (CP). Pathogenic mutations, such as p.N256K, cause intracellular retention and reduced secretion of CPA1, accompanied by endoplasmic reticulum (ER) stress, suggesting that mutation-induced misfolding underlies the phenotype. Here, we report the novel p.G250A
MeSH term(s)	Humans ; Carboxypeptidases A/genetics ; Genetic Predisposition to Disease ; Mutation ; Pancreatitis, Chronic/genetics ; Phenotype
Chemical Substances	Carboxypeptidases A (EC 3.4.17.1)
Language	English
Publishing date	2022-12-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232415463
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Article ; Online: Preclinical testing of dabigatran in trypsin-dependent pancreatitis.

Pesei, Zsófia Gabriella / Jancsó, Zsanett / Demcsák, Alexandra / Németh, Balázs Csaba / Vajda, Sandor / Sahin-Tóth, Miklós

JCI insight

2022 Volume 7, Issue 21

Abstract: Pancreatitis, the inflammatory disorder of the pancreas, has no specific therapy. Genetic, biochemical, and animal model studies revealed that trypsin plays a central role in the onset and progression of pancreatitis. Here, we performed biochemical and ... ...

Abstract	Pancreatitis, the inflammatory disorder of the pancreas, has no specific therapy. Genetic, biochemical, and animal model studies revealed that trypsin plays a central role in the onset and progression of pancreatitis. Here, we performed biochemical and preclinical mouse experiments to offer proof of concept that orally administered dabigatran etexilate can inhibit pancreatic trypsins and shows therapeutic efficacy in trypsin-dependent pancreatitis. We found that dabigatran competitively inhibited all human and mouse trypsin isoforms (Ki range 10-79 nM) and dabigatran plasma concentrations in mice given oral dabigatran etexilate well exceeded the Ki of trypsin inhibition. In the T7K24R trypsinogen mutant mouse model, a single oral gavage of dabigatran etexilate was effective against cerulein-induced progressive pancreatitis, with a high degree of histological normalization. In contrast, spontaneous pancreatitis in T7D23A mice, which carry a more aggressive trypsinogen mutation, was not ameliorated by dabigatran etexilate, given either as daily gavages or by mixing it with solid chow. Taken together, our observations showed that benzamidine derivatives such as dabigatran are potent trypsin inhibitors and show therapeutic activity against trypsin-dependent pancreatitis in T7K24R mice. Lack of efficacy in T7D23A mice is probably related to the more severe pathology and insufficient drug concentrations in the pancreas.
MeSH term(s)	Animals ; Humans ; Mice ; Dabigatran ; Disease Models, Animal ; Pancreas ; Pancreatitis/chemically induced ; Pancreatitis/drug therapy ; Pancreatitis/genetics ; Trypsin/genetics ; Trypsinogen/genetics
Chemical Substances	Dabigatran (I0VM4M70GC) ; Trypsin (EC 3.4.21.4) ; Trypsinogen (9002-08-8)
Language	English
Publishing date	2022-11-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.161145
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