bims-supasi 2023-11-26 papers

bims-supasi

Biomed News

on Sulfation pathways and signalling

Issue of 2023–11–26
thirteen papers selected by
Jonathan Wolf Mueller, University of Birmingham

Developing a solid-phase method for the enzymatic synthesis of heparan sulfate and chondroitin sulfate backbones.
Synthesis of sulfated alginate from its tributylammonium salt: Comparing the sulfating agents H2SO4-DCC and SO3·py.
Steroid sulfatase inhibitors and sulfated C19 steroids for proteotoxicity-related diseases: a patent spotlight.
Dehydroepiandrosterone Sulfate, an Adrenal Androgen, Is Inversely Associated with Prevalence of Dynapenia in Male Individuals with Type 2 Diabetes.
Postpartum hair cortisol, dehydroepiandrosterone sulfate and their ratio in beef cows: Exploring association with parity and conception outcome.
A tumor-associated heparan sulfate-related glycosaminoglycan promotes the generation of functional regulatory T cells.
Mothers' prenatal distress accelerates adrenal pubertal development in daughters.
The chemokines CCL5 and CXCL12 exhibit high-affinity binding to N-terminal peptides of the non-cognate receptors CXCR4 and CCR5, respectively.
A more accurate relationship between serum androgen and metabolism among healthy, nonobese, reproductive-age women based on liquid chromatography-tandem mass spectrometry.
Evaluation of the use of a heparin dose-response test in dogs to determine the optimal heparin dose during intravascular procedures and assessment of the in vitro heparin response in healthy dogs.
Inhibition of Indoxyl Sulfate-Induced Reactive Oxygen Species-Related Ferroptosis Alleviates Renal Cell Injury In Vitro and Chronic Kidney Disease Progression In Vivo.
Sulfated Polysaccharides as a Fighter with Protein Non-Physiological Aggregation: The Role of Polysaccharide Flexibility and Charge Density.
Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins.

Glycobiology. 2023 Nov 23. pii: cwad093. [Epub ahead of print]

Developing a solid-phase method for the enzymatic synthesis of heparan sulfate and chondroitin sulfate backbones.

Eduardo Stancanelli, Wei Liu, Guowei Su, Vijay Padagala, Jian Liu.

  Despite the recent progress on the solution-phase enzymatic synthesis of heparan sulfate (HS) and chondroitin sulfate (CS), solid-phase enzymatic synthesis has not been fully investigated. Here, we describe the solid-phase enzymatic synthesis of HS and CS backbone oligosaccharides using specialized linkers. We demonstrate the use of immobilized HS linker to synthesize CS, and the use of immobilized CS linker to synthesize HS. The linkers were then digested with chondroitin ABCase and heparin lyases, respectively, to obtain the products. Our findings uncover a potential approach for accelerating the synthesis of structurally homogeneous HS and CS oligosaccharides.

Keywords:  carbohydrates; chemoenzymatic synthesis; chondroitin sulfate; heparan sulfate; solid phase synthesis

DOI:  https://doi.org/10.1093/glycob/cwad093
Carbohydr Polym. 2024 Jan 15. pii: S0144-8617(23)00953-0. [Epub ahead of print]324 121488

Synthesis of sulfated alginate from its tributylammonium salt: Comparing the sulfating agents H2SO4-DCC and SO3·py.

Alexandra L Mutch, Vito Ferro, Anitha A, Lisbeth Grøndahl.

  Direct comparison of the sulfating agents H2SO4-DCC and SO3·py for the synthesis of sulfated alginate (S-Alg) as well as detailed characterisation of the products that form is lacking. This study involving three researchers used the tributylammonium salt of alginate (T-Alg) as a common substrate for the sulfation reactions. It was found that the use of H2SO4-DCC resulted in poor control of the degree of sulfation (DS) and that the S-Alg polymers contained nitrogen (determined by elemental analysis) as a result of formation of an unwanted N-acylurea adduct. Additionally, a large reduction in chain length was confirmed. In contrast, the use of SO3·py gave reasonable control over DS, resulted in high yields, showed no contamination and no clear change in chain length. Detailed characterisation of such S-Alg polymers by 1H NMR, 13C NMR and 1H,13C-HSQC NMR confirmed sulfation at C2 and C3 with a preference for C2.

Keywords:  Alginate sulfate; Fabrication; Infrared spectroscopy; Nuclear magnetic resonance spectroscopy

DOI:  https://doi.org/10.1016/j.carbpol.2023.121488
Pharm Pat Anal. 2023 Nov 20.

Steroid sulfatase inhibitors and sulfated C19 steroids for proteotoxicity-related diseases: a patent spotlight.

Rami A Al-Horani.

  Aging and proteotoxicity go hand in hand. Inhibiting proteotoxicity has been proposed to extend lifespan. This invention describes a new strategy to limit proteotoxicity and to extend the lifespan. Loss of function of sul-2, the Caenorhabditis elegans steroid sulfatase, elevates the pool of sulfated steroid hormones, increases longevity and ameliorates protein aggregation diseases. The present invention provides a group of molecules for use in the prevention of aging-associated proteotoxicity caused by protein aggregation diseases and/or to increase the lifespan of a eukaryotic organism. These molecules are either steroid sulfatase inhibitors or sulfated C19 steroids, both of which reproduce the phenotype of sul-2 mutants. One particular representative example is STX-64. Potential applications of the claims have been demonstrated in animal models of Parkinson's disease, Huntington's disease and Alzheimer's disease.

Keywords:  Alzheimer's disease; Huntington's disease; Parkinson's disease; aggregation-related diseases; aging; dehydroepiandrosterone; longevity; proteotoxicity; steroid sulfatase inhibitor; steroid sulfate

DOI:  https://doi.org/10.4155/ppa-2023-0010
Metabolites. 2023 Nov 03. pii: 1129. [Epub ahead of print]13(11):

Dehydroepiandrosterone Sulfate, an Adrenal Androgen, Is Inversely Associated with Prevalence of Dynapenia in Male Individuals with Type 2 Diabetes.

Saya Yasui, Yousuke Kaneko, Hiroki Yamagami, Minae Hosoki, Taiki Hori, Akihiro Tani, Tomoyo Hara, Kiyoe Kurahashi, Takeshi Harada, Shingen Nakamura, Toshiki Otoda, Tomoyuki Yuasa, Hiroyasu Mori, Akio Kuroda, Itsuro Endo, Munehide Matsuhisa, Takeshi Soeki, Ken-Ichi Aihara.

  Dehydroepiandrosterone sulfate (DHEAS) is thought to be associated with life expectancy and anti-aging. Although skeletal muscle disorders are often found in diabetic people, the clinical significance of DHEAS in skeletal muscle remains unclear. Therefore, we aimed to determine whether DHEAS is associated with the development of skeletal muscle disorders in individuals with type 2 diabetes (T2D). A cross-sectional study was conducted in 361 individuals with T2D. Serum DHEAS levels, skeletal muscle mass index (SMI), handgrip strength (HS), and gait speed (GS) were measured in the participants. Pre-sarcopenia, sarcopenia, and dynapenia were defined according to the definitions of the AWGS 2019 criteria. DHEAS level was positively associated with HS but not with SMI or GS after adjustment of confounding factors. Multiple logistic regression analyses in total subjects showed that DHEAS level had an inverse association with the prevalence of dynapenia but not with the prevalence of pre-sarcopenia or sarcopenia. Furthermore, a significant association between DHEAS level and dynapenia was found in males but not in females. ROC curve analysis indicated that cutoff values of serum DHEAS for risk of dynapenia in males was 92.0 μg/dL. Therefore, in male individuals with T2D who have low serum levels of DHEAS, adequate exercise might be needed to prevent dynapenia.

Keywords:  dehydroepiandrosterone sulfate; dynapenia; presarcopenia; sarcopenia; type 2 diabetes

DOI:  https://doi.org/10.3390/metabo13111129
Theriogenology. 2023 Nov 10. pii: S0093-691X(23)00441-7. [Epub ahead of print]214 352-359

Postpartum hair cortisol, dehydroepiandrosterone sulfate and their ratio in beef cows: Exploring association with parity and conception outcome.

T Peric, M C Veronesi, A Prandi, J Fusi, M Faustini, M Probo.

  Hair steroid measurement has received increasing attention for monitoring hypothalamic-pituitary-adrenal axis function, as it offers the advantages of being noninvasive, fast, and able to indicate steroid concentrations over long periods. The objects of the study were to evaluate cortisol (C) and dehydroepiandrosterone sulfate (DHEA-S) hair concentrations and their ratio (C/DHEA-S) in beef cows from calving to 100 days (d) postpartum (pp) and to assess possible differences related to parity (primiparous vs multiparous) and conception outcome (pregnant vs not pregnant). Hair samples were collected from 6 primiparous and 5 multiparous pregnant beef cows by clipping the coat at calving (T0) and every 20 d for 5 times (T1-T5), collecting only the regrown hair. Starting from the 6th-week pp, cows were submitted to artificial insemination at spontaneous estrus; by 100 d pp, 7 cows were pregnant and 4 were not pregnant. Statistical analysis showed higher hair C concentrations in the 11 cows at calving (T0) compared to all the subsequent samplings except for T1, and higher C concentrations at T1 compared to T3, T4, and T5. These results indicate that hair C concentrations in beef cows are affected by sampling time, with a decrease from calving, as reported in other matrices. When exploring changes within parity groups, no differences were found in the multiparous among sampling times, while hair C concentrations at T0 and T1 tended to be higher than at T2 (0.01 ≤ p < 0.05) and were higher (p < 0.01) than in all the subsequent samplings (T3, T4 and T5) within the primiparous group. Higher hair C concentrations were found at T0 and T1 in the primiparous compared to multiparous (p < 0.01), suggesting that primiparous cows undergo a greater stress level before and around parturition compared to multiparous, probably due to the novelty of the calving experience. No differences were detected in C hair concentrations according to conception outcome (pregnant versus not pregnant) in each sampling time. Hair DHEA-S concentrations were neither affected by time nor by parity or conception outcome. Differences in the C/DHEA-S ratio were found at T1, with higher C/DHEA-S in the multiparous compared to primiparous cows (p < 0.001), and a tendency for higher ratio in the not pregnant compared to the pregnant (0.01 ≤ p < 0.05). These results support the choice of hair as a valuable biological matrix when investigating long-time periods such as postpartum in cows and suggest an enhanced immunoprotective effect of DHEA-S in the postpartum of primiparous cows, and in cows that get pregnant within 100 d postpartum.

Keywords:  Conception outcome; Cortisol; Dehydroepiandrosterone; Hair; Parity; Postpartum beef cow

DOI:  https://doi.org/10.1016/j.theriogenology.2023.11.008
Cell Mol Immunol. 2023 Nov 22.

A tumor-associated heparan sulfate-related glycosaminoglycan promotes the generation of functional regulatory T cells.

Leticia Martín-Cruz, Marcos Viñuela, Ioanna Kalograiaki, Alba Angelina, Paola Oquist-Phillips, Irene Real-Arévalo, Francisco Javier Cañada, José Ignacio Tudela, Luis Moltó, Jesús Moreno-Sierra, José Luis Subiza, Oscar Palomares.

  Functional Tregs play a key role in tumor development and progression, representing a major barrier to anticancer immunity. The mechanisms by which Tregs are generated in cancer and the influence of the tumor microenvironment on these processes remain incompletely understood. Herein, by using NMR, chemoenzymatic structural assays and a plethora of in vitro and in vivo functional analyses, we demonstrate that the tumoral carbohydrate A10 (Ca10), a cell-surface carbohydrate derived from Ehrlich's tumor (ET) cells, is a heparan sulfate-related proteoglycan that enhances glycolysis and promotes the development of tolerogenic features in human DCs. Ca10-stimulated human DCs generate highly suppressive Tregs by mechanisms partially dependent on metabolic reprogramming, PD-L1, IL-10, and IDO. Ca10 also reprograms the differentiation of human monocytes into DCs with tolerogenic features. In solid ET-bearing mice, we found positive correlations between Ca10 serum levels, tumor size and splenic Treg numbers. Administration of isolated Ca10 also increases the proportion of splenic Tregs in tumor-free mice. Remarkably, we provide evidence supporting the presence of a circulating human Ca10 counterpart (Ca10H) and show, for the first time, that serum levels of Ca10H are increased in patients suffering from different cancer types compared to healthy individuals. Of note, these levels are higher in prostate cancer patients with bone metastases than in prostate cancer patients without metastases. Collectively, we reveal novel molecular mechanisms by which heparan sulfate-related structures associated with tumor cells promote the generation of functional Tregs in cancer. The discovery of this novel structural-functional relationship may open new avenues of research with important clinical implications in cancer treatment.

Keywords:  Cancer immunology; Dendritic cell; Heparan sulfate-related proteoglycan; Regulatory T cell; Tumoral carbohydrate A10

DOI:  https://doi.org/10.1038/s41423-023-01096-9
Psychoneuroendocrinology. 2023 Nov 11. pii: S0306-4530(23)00649-2. [Epub ahead of print]160 106671

Mothers' prenatal distress accelerates adrenal pubertal development in daughters.

Molly M Fox, Jennifer Hahn-Holbrook, Curt A Sandman, Jessica A Marino, Laura M Glynn, Elysia Poggi Davis.

  Human life history schedules vary, partly, because of adaptive, plastic responses to early-life conditions. Little is known about how prenatal conditions relate to puberty timing. We hypothesized that fetal exposure to adversity may induce an adaptive response in offspring maturational tempo. In a longitudinal study of 253 mother-child dyads followed for 15 years, we investigated if fetal exposure to maternal psychological distress related to children's adrenarche and gonadarche schedules, assessed by maternal and child report and by dehydroepiandrosterone sulfate (DHEA-S), testosterone, and estradiol levels. We found fetal exposure to elevated maternal prenatal psychological distress predicted earlier adrenarche and higher DHEA-S levels in girls, especially first-born girls, and that associations remained after covarying indices of postnatal adversity. No associations were observed for boys or for gonadarche in girls. Adrenarche orchestrates the social-behavioral transition from juvenility to adulthood; therefore, significant findings for adrenarche, but not gonadarche, suggest that prenatal maternal distress instigates an adaptive strategy in which daughters have earlier social-behavioral maturation. The stronger effect in first-borns suggests that, in adverse conditions, it is in the mother's adaptive interest for her daughter to hasten social maturation, but not necessarily sexual maturation, because it would prolong the duration of the daughter allomothering younger siblings. We postulate a novel evolutionary framework that human mothers may calibrate the timing of first-born daughters' maturation in a way that optimizes their own reproductive success.

Keywords:  Adrenarche; DHEA-S; Fetal programming; Life history theory; Prenatal mood; Puberty

DOI:  https://doi.org/10.1016/j.psyneuen.2023.106671
FEBS J. 2023 Nov 23.

The chemokines CCL5 and CXCL12 exhibit high-affinity binding to N-terminal peptides of the non-cognate receptors CXCR4 and CCR5, respectively.

Naama Kessler, Sabine R Akabayov, Leah S Cohen, Tali Scherf, Fred Naider, Jacob Anglister.

  CC and CXC chemokines are distinct chemokine subfamilies. CC chemokines usually do not bind CXC-chemokine receptors and vice versa. CCR5 and CXCR4 receptors are activated by CCL5 and CXCL12 chemokines, respectively, and are also used as HIV-1 coreceptors. CCL5 contains one conserved binding site for a sulfated tyrosine residue, whereas CXCL12 is unique in having two additional sites for sulfated/non-sulfated tyrosine residues. In this study N-terminal (Nt) CXCR4 peptides were found to bind CCL5 with somewhat higher affinities in comparison to those of short Nt-CCR5(8-20) peptides with the same number of sulfated tyrosine residues. Similarly, a long Nt-CCR5(1-27)(s Y3,s Y10,s Y14) peptide cross reacts with CXCL12 and with lower KD in comparison to its binding to CCL5. Intermolecular Nuclear Overhauser effect (NOE) measurements were used to decipher the mechanism of the chemokine/Nt-receptor peptide binding. The Nt-CXCR4 peptides interact with the conserved CCL5 tyrosine sulfate binding site by an allovalency mechanism like that observed for CCL5 binding of Nt-CCR5 peptides. Nt-CCR5 peptides bind CXCL12 in multiple modes analogous to their binding to HIV-1 gp120 and interact with all three tyrosine/sulfated tyrosine binding pockets of CXCL12. We suggest that the chemokine-receptors Nt-segments bind promiscuously to cognate and non-cognate chemokines and in a mechanism that is dependent on the number of binding pockets for tyrosine residues found on the chemokine. In conclusion, common features shared among the chemokine-receptors' Nt-segments such as multiple tyrosine residues that are potentially sulfated, and a large number of negatively charged residues, are the reason of the cross binding observed in this study.

Keywords:  CCL5; CCR5; CXCL12; CXCR4; Chemokine receptors; Chemokines; NMR of proteins; sulfated tyrosine

DOI:  https://doi.org/10.1111/febs.17013
Endocr J. 2023 Nov 17.

A more accurate relationship between serum androgen and metabolism among healthy, nonobese, reproductive-age women based on liquid chromatography-tandem mass spectrometry.

Sha Ye, Yepei Huang, Yi Lu, Xiaoyan Li, Meiling Ye, Hongyu Lu, Junhua Shi, Jian Huang, Hong Cai.

  This study explored a more precise association between androgens and glycolipid metabolism in healthy women of different ages. Body mass index (BMI), waist circumference (WC), and waist-to-hip ratio were used as body fat indicators. High-density lipoprotein (HDL), low-density lipoprotein, triglycerides, and total cholesterol were used as lipid markers. Fasting blood glucose (FBG), fasting insulin, and the homeostatic model assessment of insulin resistance were used to assess insulin resistance and glucose metabolism. Liquid chromatography-tandem mass spectrometry was used to measure androgen indicators, including testosterone, sex hormone-binding globulin (SHBG), free testosterone (FT), dihydrotestosterone (DHT), androstenedione (A4), dehydroepiandrosterone (DHEA), and dehydroepiandrosterone sulfate (DHEAS). DHEAS levels varied across age groups. Correlation analyses with Spearman's coefficient showed that the free androgen index correlated positively with WC (p = 0.040), FT correlated positively with BMI (p = 0.033) and WC (p = 0.049), SHBG correlated positively with HDL (p = 0.013), and A4 correlated positively with FBG (p = 0.017). Multiple linear regression analysis showed that among healthful women aged 36-40 years, A4 increased with FBG, and SHBG increased with HDL. Even within healthy, nonobese women, lipid and glucose metabolism were robustly correlated with androgens. Yearly metabolic assessments are necessary, particularly for FBG and HDL, since these markers can predict the likelihood of hyperandrogenemia, enabling timely interventions.

Keywords:  Androgen; Blood lipids; Insulin resistance; Liquid chromatography with tandem mass spectrometry; Metabolism

DOI:  https://doi.org/10.1507/endocrj.EJ23-0451
Vet Med Sci. 2023 Nov 21.

Evaluation of the use of a heparin dose-response test in dogs to determine the optimal heparin dose during intravascular procedures and assessment of the in vitro heparin response in healthy dogs.

A Hellemans, N Devriendt, L Duchateau, K M J Devreese, F De Somer, T Bosmans, G Mampaey, P Smets.

   BACKGROUND: No guidelines for administering and monitoring anticoagulants intraprocedurally are currently available in dogs, despite the prevalence of procedures necessitating systemic anticoagulation with heparin.
OBJECTIVES: To evaluate an activated clotting time (ACT)-based heparin dose-response (HDR) test to predict the individual required heparin dose in dogs during intravascular procedures, and to investigate both the in vitro heparin - ACT and in vitro heparin - factor anti-Xa activity (anti-Xa) relationships in dogs.
METHODS: Blood was collected from eight healthy beagles undergoing a cardiac procedure and utilised to establish baseline ACT and for in vitro evaluation. Subsequently, 100 IU/kg heparin was administered intravenously (IV) and ACT was remeasured (HDR test). The required heparin dose for an ACT target response ≥300 s was calculated for each individual and ACT was remeasured after administration of this dose. For in vitro testing, a serial heparin blood dilution (0-0.5-1-2-4 international unit (IU)/mL) was prepared and ACT and anti-Xa were determined using whole blood and frozen plasma, respectively.
RESULTS: The HDR test overestimated the required heparin dose in 3/7 dogs. In vitro, ACT and anti-Xa increased significantly with increasing blood heparin concentration. Heparin - ACT was nonlinear in 4/8 dogs at heparin concentrations >2 IU/mL, whereas heparin - anti-Xa remained linear throughout the tested range.
CONCLUSIONS: The HDR test poorly estimated the required heparin dose in dogs. This is most likely attributed to a nonlinear heparin - ACT relationship, as observed in vitro. Anti-Xa is a promising alternative for ACT; however, unavailability as a point-of-care test and lack of in vivo target values restrict its current use.

Keywords:  activated clotting time; anti-Xa; canine; heparin resistance; heparin sensitivity

DOI:  https://doi.org/10.1002/vms3.1326
Antioxidants (Basel). 2023 Oct 30. pii: 1931. [Epub ahead of print]12(11):

Inhibition of Indoxyl Sulfate-Induced Reactive Oxygen Species-Related Ferroptosis Alleviates Renal Cell Injury In Vitro and Chronic Kidney Disease Progression In Vivo.

Li-Ting Tsai, Te-I Weng, Ting-Yu Chang, Kuo-Cheng Lan, Chih-Kang Chiang, Shing-Hwa Liu.

  The accumulation of the uremic toxin indoxyl sulfate (IS) is a key pathological feature of chronic kidney disease (CKD). The effect of IS on ferroptosis and the role of IS-related ferroptosis in CKD are not well understood. We used a renal tubular cell model and an adenine-induced CKD mouse model to explore whether IS induces ferroptosis and injury and affects iron metabolism in the renal cells and the kidneys. Our results showed that exposure to IS induced several characteristics for ferroptosis, including iron accumulation, an impaired antioxidant system, elevated reactive oxygen species (ROS) levels, and lipid peroxidation. Exposure to IS triggered intracellular iron accumulation by upregulating transferrin and transferrin receptors, which are involved in cellular iron uptake. We also observed increased levels of the iron storage protein ferritin. The effects of IS-induced ROS generation, lipid peroxidation, ferroptosis, senescence, ER stress, and injury/fibrosis were effectively alleviated by treatments with an iron chelator deferoxamine (DFO) in vitro and the adsorbent charcoal AST-120 (scavenging the IS precursor) in vivo. Our findings suggest that IS triggers intracellular iron accumulation and ROS generation, leading to the induction of ferroptosis, senescence, ER stress, and injury/fibrosis in CKD kidneys. AST-120 administration may serve as a potential therapeutic strategy.

Keywords:  ROS; chronic kidney disease; ferroptosis; fibrosis; indoxyl sulfate

DOI:  https://doi.org/10.3390/antiox12111931
Int J Mol Sci. 2023 Nov 12. pii: 16223. [Epub ahead of print]24(22):

Sulfated Polysaccharides as a Fighter with Protein Non-Physiological Aggregation: The Role of Polysaccharide Flexibility and Charge Density.

Olga N Makshakova, Liliya R Bogdanova, Dzhigangir A Faizullin, Elena A Ermakova, Yuriy F Zuev.

  Proteins can lose native functionality due to non-physiological aggregation. In this work, we have shown the power of sulfated polysaccharides as a natural assistant to restore damaged protein structures. Protein aggregates enriched by cross-β structures are a characteristic of amyloid fibrils related to different health disorders. Our recent studies demonstrated that model fibrils of hen egg white lysozyme (HEWL) can be disaggregated and renatured by some negatively charged polysaccharides. In the current work, using the same model protein system and FTIR spectroscopy, we studied the role of conformation and charge distribution along the polysaccharide chain in the protein secondary structure conversion. The effects of three carrageenans (κ, ι, and λ) possessing from one to three sulfate groups per disaccharide unit were shown to be different. κ-Carrageenan was able to fully eliminate cross-β structures and complete the renaturation process. ι-Carrageenan only initiated the formation of native-like β-structures in HEWL, retaining most of the cross-β structures. In contrast, λ-carrageenan even increased the content of amyloid cross-β structures. Furthermore, κ-carrageenan in rigid helical conformation loses its capability to restore protein native structures, largely increasing the amount of amyloid cross-β structures. Our findings create a platform for the design of novel natural chaperons to counteract protein unfolding.

Keywords:  amyloid fibrils; chaperons; disaggregation effect; hen egg white lysozyme; protein renaturation; sulfated polysaccharides

DOI:  https://doi.org/10.3390/ijms242216223
Biomolecules. 2023 Nov 09. pii: 1633. [Epub ahead of print]13(11):

Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins.

Samuel G Holmes, Umesh R Desai.

  Although molecular docking has evolved dramatically over the years, its application to glycosaminoglycans (GAGs) has remained challenging because of their intrinsic flexibility, highly anionic character and rather ill-defined site of binding on proteins. GAGs have been treated as either fully "rigid" or fully "flexible" in molecular docking. We reasoned that an intermediate semi-rigid docking (SRD) protocol may be better for the recapitulation of native heparin/heparan sulfate (Hp/HS) topologies. Herein, we study 18 Hp/HS-protein co-complexes containing chains from disaccharide to decasaccharide using genetic algorithm-based docking with rigid, semi-rigid, and flexible docking protocols. Our work reveals that rigid and semi-rigid protocols recapitulate native poses for longer chains (5→10 mers) significantly better than the flexible protocol, while 2→4-mer poses are better predicted using the semi-rigid approach. More importantly, the semi-rigid docking protocol is likely to perform better when no crystal structure information is available. We also present a new parameter for parsing selective versus non-selective GAG-protein systems, which relies on two computational parameters including consistency of binding (i.e., RMSD) and docking score (i.e., GOLD Score). The new semi-rigid protocol in combination with the new computational parameter is expected to be particularly useful in high-throughput screening of GAG sequences for identifying promising druggable targets as well as drug-like Hp/HS sequences.

Keywords:  glycosaminoglycans; heparin/heparan sulfate; knowledge-based docking; molecular docking

DOI:  https://doi.org/10.3390/biom13111633