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Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
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Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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2
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Liang A, Desai U. Advances in Studying Glycosaminoglycan-Protein Interactions Using Capillary Electrophoresis. Methods Mol Biol 2022; 2303:365-387. [PMID: 34626394 DOI: 10.1007/978-1-0716-1398-6_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Methods for studying interactions between glycosaminoglycans (GAGs) and proteins have assumed considerable significance as their biological importance increases. Capillary electrophoresis (CE) is a powerful method to study these interactions due to its speed, high efficiency, and low sample/reagent consumption. In addition, CE works effectively under a wide range of physiologically relevant conditions. This chapter presents the state of the art on CE methods for studying GAG-protein interactions including affinity capillary electrophoresis (ACE), capillary zone electrophoresis (CZE), frontal analysis (FA)/frontal analysis continuous capillary electrophoresis (FACCE), and capillary electrokinetic chromatography (CEC) with detailed experimental protocols for ACE and CZE methods.
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Affiliation(s)
- Aiye Liang
- Department of Chemistry, Charleston Southern University, North Charleston, SC, USA.
| | - Umesh Desai
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA, USA
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3
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Kellici TF, Pilka ES, Bodkin MJ. Small-molecule modulators of serine protease inhibitor proteins (serpins). Drug Discov Today 2020; 26:442-454. [PMID: 33259801 DOI: 10.1016/j.drudis.2020.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/11/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Serine protease inhibitors (serpins) are a large family of proteins that regulate and control crucial physiological processes, such as inflammation, coagulation, thrombosis and thrombolysis, and immune responses. The extraordinary impact that these proteins have on numerous crucial pathways makes them an attractive target for drug discovery. In this review, we discuss recent advances in research on small-molecule modulators of serpins, examine their mode of action, analyse the structural data from crystallised protein-ligand complexes, and highlight the potential obstacles and possible therapeutic perspectives. The application of in silico methods for rational drug discovery is also summarised. In addition, we stress the need for continued research in this field.
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4
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Afosah DK, Al-Horani RA. Sulfated Non-Saccharide Glycosaminoglycan Mimetics as Novel Drug Discovery Platform for Various Pathologies. Curr Med Chem 2020; 27:3412-3447. [PMID: 30457046 PMCID: PMC6551317 DOI: 10.2174/0929867325666181120101147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 01/14/2023]
Abstract
Glycosaminoglycans (GAGs) are very complex, natural anionic polysaccharides. They are polymers of repeating disaccharide units of uronic acid and hexosamine residues. Owing to their template-free, spatiotemporally-controlled, and enzyme-mediated biosyntheses, GAGs possess enormous polydispersity, heterogeneity, and structural diversity which often translate into multiple biological roles. It is well documented that GAGs contribute to physiological and pathological processes by binding to proteins including serine proteases, serpins, chemokines, growth factors, and microbial proteins. Despite advances in the GAG field, the GAG-protein interface remains largely unexploited by drug discovery programs. Thus, Non-Saccharide Glycosaminoglycan Mimetics (NSGMs) have been rationally developed as a novel class of sulfated molecules that modulate GAG-protein interface to promote various biological outcomes of substantial benefit to human health. In this review, we describe the chemical, biochemical, and pharmacological aspects of recently reported NSGMs and highlight their therapeutic potentials as structurally and mechanistically novel anti-coagulants, anti-cancer agents, anti-emphysema agents, and anti-viral agents. We also describe the challenges that complicate their advancement and describe ongoing efforts to overcome these challenges with the aim of advancing the novel platform of NSGMs to clinical use.
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Affiliation(s)
- Daniel K. Afosah
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Rami A. Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125
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5
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Nahain AA, Ignjatovic V, Monagle P, Tsanaktsidis J, Ferro V. Heparin mimetics with anticoagulant activity. Med Res Rev 2018; 38:1582-1613. [PMID: 29446104 DOI: 10.1002/med.21489] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/16/2017] [Accepted: 01/12/2018] [Indexed: 01/10/2023]
Abstract
Heparin, a sulfated polysaccharide belonging to the glycosaminoglycan family, has been widely used as an anticoagulant drug for decades and remains the most commonly used parenteral anticoagulant in adults and children. However, heparin has important clinical limitations and is derived from animal sources which pose significant safety and supply problems. The ever growing shortage of the raw material for heparin manufacturing may become a very significant issue in the future. These global limitations have prompted much research, especially following the recent well-publicized contamination scandal, into the development of alternative anticoagulants derived from non-animal and/or totally synthetic sources that mimic the structural features and properties of heparin. Such compounds, termed heparin mimetics, are also needed as anticoagulant materials for use in biomedical applications (e.g., stents, grafts, implants etc.). This review encompasses the development of heparin mimetics of various structural classes, including synthetic polymers and non-carbohydrate small molecules as well as sulfated oligo- and polysaccharides, and fondaparinux derivatives and conjugates, with a focus on developments in the past 10 years.
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Affiliation(s)
- Abdullah Al Nahain
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Vera Ignjatovic
- Haematology Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Paul Monagle
- Haematology Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Department of Clinical Haematology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - John Tsanaktsidis
- CSIRO Materials Science and Engineering, Clayton South, Victoria, Australia
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
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6
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Nagarajan B, Sankaranarayanan NV, Patel BB, Desai UR. A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules. PLoS One 2017; 12:e0171619. [PMID: 28182755 PMCID: PMC5300208 DOI: 10.1371/journal.pone.0171619] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/23/2017] [Indexed: 01/06/2023] Open
Abstract
Glycosaminoglycans (GAGs) are key natural biopolymers that exhibit a range of biological functions including growth and differentiation. Despite this multiplicity of function, natural GAG sequences have not yielded drugs because of problems of heterogeneity and synthesis. Recently, several homogenous non-saccharide glycosaminoglycan mimetics (NSGMs) have been reported as agents displaying major therapeutic promise. Yet, it remains unclear whether sulfated NSGMs structurally mimic sulfated GAGs. To address this, we developed a three-step molecular dynamics (MD)-based algorithm to compare sulfated NSGMs with GAGs. In the first step of this algorithm, parameters related to the range of conformations sampled by the two highly sulfated molecules as free entities in water were compared. The second step compared identity of binding site geometries and the final step evaluated comparable dynamics and interactions in the protein-bound state. Using a test case of interactions with fibroblast growth factor-related proteins, we show that this three-step algorithm effectively predicts the GAG structure mimicking property of NSGMs. Specifically, we show that two unique dimeric NSGMs mimic hexameric GAG sequences in the protein-bound state. In contrast, closely related monomeric and trimeric NSGMs do not mimic GAG in either the free or bound states. These results correspond well with the functional properties of NSGMs. The results show for the first time that appropriately designed sulfated NSGMs can be good structural mimetics of GAGs and the incorporation of a MD-based strategy at the NSGM library screening stage can identify promising mimetics of targeted GAG sequences.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Bhaumik B. Patel
- Hunter Holmes Muire VA Medical Center, Richmond, Virginia, United States of America
- Division of Hematology, Oncology, and Palliative Care, Department of Internal Medicine and Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
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7
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Plasmin regulation through allosteric, sulfated, small molecules. Molecules 2015; 20:608-24. [PMID: 25569517 PMCID: PMC6272155 DOI: 10.3390/molecules20010608] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/26/2014] [Indexed: 01/16/2023] Open
Abstract
Plasmin, a key serine protease, plays a major role in clot lysis and extracellular matrix remodeling. Heparin, a natural polydisperse sulfated glycosaminoglycan, is known to allosterically modulate plasmin activity. No small allosteric inhibitor of plasmin has been discovered to date. We screened an in-house library of 55 sulfated, small glycosaminoglycan mimetics based on nine distinct scaffolds and varying number and positions of sulfate groups to discover several promising hits. Of these, a pentasulfated flavonoid-quinazolinone dimer 32 was found to be the most potent sulfated small inhibitor of plasmin (IC50 = 45 μM, efficacy = 100%). Michaelis-Menten kinetic studies revealed an allosteric inhibition of plasmin by these inhibitors. Studies also indicated that the most potent inhibitors are selective for plasmin over thrombin and factor Xa, two serine proteases in coagulation cascade. Interestingly, different inhibitors exhibited different levels of efficacy (40%–100%), an observation alluding to the unique advantage offered by an allosteric process. Overall, our work presents the first small, synthetic allosteric plasmin inhibitors for further rational design.
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Abstract
In nearly all cases of biological activity of sulfated GAGs, the sulfate group(s) are critical for interacting with target proteins. A growing paradigm is that appropriate small, sulfated, nonsaccharide GAG mimetics can be designed to either mimic or interfere with the biological functions of natural GAG sequences resulting in the discovery of either antagonist or agonist agents. A number of times these sulfated NSGMs can be computationally designed based on the parent GAG-protein interaction. The small sulfated NSGMs may possess considerable aromatic character so as to engineer hydrophobic, hydrogen-bonding, Coulombic or cation-pi forces in their interactions with target protein(s) resulting in higher specificity of action relative to parent GAGs. The sulfated NSGMs can be easily synthesized in one step from appropriate natural polyphenols through chemical sulfation under microwave-based conditions. We describe step-by-step procedures to perform microwave-based sulfation of several small polyphenol scaffolds so as to prepare homogenous NSGMs containing one to more than 10 sulfate groups per molecule in high yields.
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Studying glycosaminoglycan-protein interactions using capillary electrophoresis. Methods Mol Biol 2014; 1229:355-75. [PMID: 25325965 DOI: 10.1007/978-1-4939-1714-3_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Methods for studying interactions between glycosaminoglycans (GAGs) and proteins have assumed considerable significance as their biological importance increases. Capillary electrophoresis (CE) is a powerful method to study these interactions due to its speed, high efficiency, and low sample/reagent consumption. In addition, CE works effectively under a wide range of physiologically relevant conditions. This chapter presents state-of-the-art on CE methods for studying GAG-protein interactions including affinity capillary electrophoresis (ACE), capillary zone electrophoresis (CZE), frontal analysis (FA)/frontal analysis continuous capillary electrophoresis (FACCE), and capillary electrokinetic chromatography (CEC) with detailed experimental protocols for ACE and CZE methods.
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10
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Patel NJ, Karuturi R, Al-Horani RA, Baranwal S, Patel J, Desai UR, Patel BB. Synthetic, non-saccharide, glycosaminoglycan mimetics selectively target colon cancer stem cells. ACS Chem Biol 2014; 9:1826-33. [PMID: 24968014 PMCID: PMC4136679 DOI: 10.1021/cb500402f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Selective targeting of cancer stem-like cells (CSCs) is a paradigm-shifting approach. We hypothesized that CSCs can be targeted by interfering with functions of sulfated glycosaminoglycans, which play key roles in cancer cell growth, invasion and metastasis. We developed a tandem, dual screen strategy involving (1) assessing inhibition of monolayer versus spheroid growth and (2) assessing inhibition of primary versus secondary spheroid growth to identify G2.2, a unique sulfated nonsaccharide GAG mimetic (NSGM) from a focused library of 53 molecules, as a selective inhibitor of colon CSCs. The NSGM down-regulated several CSC markers through regulation of gene transcription, while closely related, inactive NSGMs G1.4 and G4.1 demonstrated no such changes. G2.2's effects on CSCs were mediated, in part, through induction of apoptosis and inhibition of self-renewal factors. Overall, this work presents the proof-of-principle that CSCs can be selectively targeted through novel NSGMs, which are likely to advance fundamental understanding on CSCs while also aiding development of novel therapeutic agents.
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Affiliation(s)
- Nirmita J. Patel
- Hunter Holmes
McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Rajesh Karuturi
- Department
of Medicinal Chemistry and Institute for Structural Biology and Drug
Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rami A. Al-Horani
- Department
of Medicinal Chemistry and Institute for Structural Biology and Drug
Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Somesh Baranwal
- Hunter Holmes
McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Jagrut Patel
- Hunter Holmes
McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Umesh R. Desai
- Department
of Medicinal Chemistry and Institute for Structural Biology and Drug
Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Bhaumik B. Patel
- Hunter Holmes
McGuire VA Medical Center, Richmond, Virginia 23249, United States
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11
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Argade MD, Mehta AY, Sarkar A, Desai UR. Allosteric inhibition of human factor XIa: discovery of monosulfated benzofurans as a class of promising inhibitors. J Med Chem 2014; 57:3559-69. [PMID: 24666186 PMCID: PMC4317055 DOI: 10.1021/jm5002698] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Factor
XIa (fXIa) is being recognized as a prime target for developing
safer anticoagulants. To discover synthetic, small, allosteric inhibitors
of fXIa, we screened an in-house, unique library of 65 molecules displaying
many distinct scaffolds and varying levels of sulfation. Of these,
monosulfated benzofurans were the only group of molecules found to
inhibit fXIa (∼100% efficacy) and led to the identification
of monosulfated trimer 24 (IC50 0.82 μM)
as the most potent inhibitor. Michaelis–Menten kinetics studies
revealed a classic noncompetitive mechanism of action for 24. Although monosulfated, the inhibitors did not compete with unfractionated
heparin alluding to a novel site of interaction. Fluorescence quenching
studies indicated that trimer 24 induces major conformational
changes in the active site of fXIa. Docking studies identified a site
near Lys255 on the A3 domain of fXIa as the most probable site of
binding for 24. Factor XIa devoid of the A3 domain displayed
a major defect in the inhibition potency of 24 supporting
the docking prediction. Our work presents the sulfated benzofuran
scaffold as a promising framework to develop allosteric fXIa inhibitors
that likely function through the A3 domain.
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Affiliation(s)
- Malaika D Argade
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23219, United States
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12
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Rashid Q, Abid M, Jairajpuri MA. Elucidating the specificity of non-heparin-based conformational activators of antithrombin for factor Xa inhibition. J Nat Sci Biol Med 2014; 5:36-42. [PMID: 24678194 PMCID: PMC3961949 DOI: 10.4103/0976-9668.127282] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Introduction: Antithrombin, the principal inhibitor of coagulation proteases, requires allosteric activation by its physiological cofactor, heparin or heparin sulfate to achieve physiologically permissible rates. This forms the basis of heparin's use as a clinical anticoagulant. However, heparin therapy is beset with severe complications, giving rise to the need to search new non-heparin activators of antithrombin, devoid of these complications and with favorable safety profiles. Materials and Methods: We chose some representative organic compounds that have been shown to be involved in coagulation modulation by affecting antithrombin and applied a blind docking protocol to find the binding energy and interactions of the modified (sulfated) versus unmodified organic scaffolds. Results and Conclusion: Increased sulfation plays a key role in shifting the specificity of organic compounds like quercetin, diosmin, rutin, mangiferin, isomangostin, Trapezifolixanthone and benzofuran towards the heparin binding site (HBS). However, in hesperetin and tetrahydroisoquinoline, sulfation shifts the specificity away from HBS. We have further tried to elucidate changes in the binding affinity of quercetin on account of gradual increase in the number of hydroxyl groups being substituted by sulfate groups. The results show gradual increase in binding energy with increase in sulfation. A theoretical screening approach is an ideal mechanism to predict lead molecules as activators of antithrombin and in determining the specificity for antithrombin.
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Affiliation(s)
- Qudsia Rashid
- Department of Bio-Sciences, Protein Conformation and Enzymology Lab, New Delhi, India
| | - Mohammad Abid
- Department of Organic Synthesis Lab, Jamia Millia Islamia, New Delhi, India
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The promise of sulfated synthetic small molecules as modulators of glycosaminoglycan function. Future Med Chem 2014; 5:1363-6. [PMID: 23919545 DOI: 10.4155/fmc.13.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Xin D, Holzenburg A, Burgess K. Small Molecule Probes That Perturb A Protein-protein Interface In Antithrombin. Chem Sci 2014; 5:4914-4921. [PMID: 25396040 DOI: 10.1039/c4sc01295j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Small molecule probes for perturbing protein-protein interactions (PPIs) in vitro can be useful if they cause the target proteins to undergo biomedically relevant changes to their tertiary and quaternary structures. Application of the Exploring Key Orientations (EKO) strategy (J. Am. Chem. Soc., 2013, 135, 167 - 173) to a piperidinone-piperidine chemotype 1 indicated specific derivatives were candidates to perturb a protein-protein interface in the α-antithrombin dimer; those particular derivatives of 1 were prepared and tested. In the event, most of them significantly accelerated oligomerization of monomeric α-antithrombin, which is metastable in its oligomeric state. This assertion is supported by data from gel electrophoresis (non-denaturing PAGE; throughout) and probe-induced loss of α-antithrombin's inhibitor activity in a reaction catalyzed by thrombin. Kinetics of α-antithrombin oligomerization induced by the target compounds were examined. It was found that probes with O-benzyl-protected serine side-chains are the most active catalysts in the series, and reasons for this, based on modeling experiments, are proposed. Overall, this study reveals one of the first examples of small molecules designed to act at a protein-protein interface relevant to oligomerization of a serpin (ie α-antithrombin). The relevance of this to formation of oligomeric serpin fibrils, associated with the disease states known as "serpinopathies", is discussed.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| | - Andreas Holzenburg
- Microscopy and Imaging Center, Department of Biology, and Department of Biochemistry & Biophysics TAMU, College Station, TX 77843-2257
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
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15
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Correia-da-Silva M, Sousa E, Pinto MMM. Emerging sulfated flavonoids and other polyphenols as drugs: nature as an inspiration. Med Res Rev 2013; 34:223-79. [PMID: 23553315 DOI: 10.1002/med.21282] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nature uses sulfation of endogenous and exogenous molecules mainly to avoid potential toxicity. The growing importance of natural sulfated molecules, as modulators of a number of physiological and pathological processes, has inspired the synthesis of non-natural sulfated scaffolds. Until the 1990s, the synthesis of sulfated small molecules was almost restricted to derivatives of flavonoids and aimed mainly at structure elucidation and plant biosynthesis studies. Currently, the synthesis of this type of compounds concerns structurally diverse scaffolds and is aimed at the development of potential drugs and/or exploitation of the biological effects of sulfated metabolites. Some important hit compounds are emerging from sulfated flavonoids and other polyphenols mainly as anticoagulant and antiviral agents. When compared with polymeric macromolecules such as heparins, sulfated small molecules could be of value in therapeutics due to their hydrophobic nature that can contribute to improve the bioavailability. This review highlights the synthetic approaches that were applied to obtain monosulfated or polysulfated phenolic small molecules and compiles the diverse biological activities already reported for this type of derivatives. Toxicity and pharmacokinetic parameters of this emerging class of derivatives will also be considered, emphasizing their value for therapeutic applications.
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Affiliation(s)
- Marta Correia-da-Silva
- Centro de Química Medicinal da Universidade do Porto (CEQUIMED-UP), Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
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16
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Karuturi R, Al-Horani RA, Mehta SC, Gailani D, Desai UR. Discovery of allosteric modulators of factor XIa by targeting hydrophobic domains adjacent to its heparin-binding site. J Med Chem 2013; 56:2415-28. [PMID: 23451707 DOI: 10.1021/jm301757v] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To discover promising sulfated allosteric modulators (SAMs) of glycosaminoglycan-binding proteins (GBPs), such as human factor XIa (FXIa), we screened a library of 26 synthetic, sulfated quinazolin-4(3H)-ones (QAOs) resulting in the identification of six molecules that reduced the Vmax of substrate hydrolysis without influencing the KM. Mutagenesis of residues of the heparin-binding site (HBS) of FXIa introduced a nearly 5-fold loss in inhibition potency supporting recognition of an allosteric site. Fluorescence studies showed a sigmoidal binding profile indicating highly cooperative binding. Competition with a positively charged, heparin-binding polymer did not fully nullify inhibition suggesting importance of hydrophobic forces to binding. This discovery suggests the operation of a dual-element recognition process, which relies on an initial Coulombic attraction of anionic SAMs to the cationic HBS of FXIa that forms a locked complex through tight interaction with an adjacent hydrophobic patch. The dual-element strategy may be widely applicable for discovering SAMs of other GBPs.
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Affiliation(s)
- Rajesh Karuturi
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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17
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Al-Horani RA, Ponnusamy P, Mehta AY, Gailani D, Desai UR. Sulfated pentagalloylglucoside is a potent, allosteric, and selective inhibitor of factor XIa. J Med Chem 2013; 56:867-78. [PMID: 23316863 DOI: 10.1021/jm301338q] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inhibition of factor XIa (FXIa) is a novel paradigm for developing anticoagulants without major bleeding consequences. We present the discovery of sulfated pentagalloylglucoside (6) as a highly selective inhibitor of human FXIa. Biochemical screening of a focused library led to the identification of 6, a sulfated aromatic mimetic of heparin. Inhibitor 6 displayed a potency of 551 nM against FXIa, which was at least 200-fold more selective than other relevant enzymes. It also prevented activation of factor IX and prolonged human plasma and whole blood clotting. Inhibitor 6 reduced V(MAX) of FXIa hydrolysis of chromogenic substrate without affecting the K(M), suggesting an allosteric mechanism. Competitive studies showed that 6 bound in the heparin-binding site of FXIa. No allosteric small molecule has been discovered to date that exhibits equivalent potency against FXIa. Inhibitor 6 is expected to open up a major route to allosteric FXIa anticoagulants with clinical relevance.
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Affiliation(s)
- Rami A Al-Horani
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, USA
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18
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Sidhu PS, Mosier PD, Zhou Q, Desai UR. On scaffold hopping: challenges in the discovery of sulfated small molecules as mimetics of glycosaminoglycans. Bioorg Med Chem Lett 2012; 23:355-9. [PMID: 23164711 DOI: 10.1016/j.bmcl.2012.10.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 10/04/2012] [Accepted: 10/15/2012] [Indexed: 01/25/2023]
Abstract
The design of sulfated, small, nonsaccharide molecules as modulators of proteins is still in its infancy as standard drug discovery tools such as library of diverse sulfated molecules and in silico docking and scoring protocol have not been firmly established. Databases, such as ZINC, contain too few sulfate-containing nonsaccharide molecules, which severely limits the identification of new hits. Lack of a generally applicable protocol for scaffold hopping limits the development of sulfated small molecules as synthetic mimetics of the highly sulfated glycosaminoglycans. We explored a sequential ligand-based (LBVS) and structure-based virtual screening (SBVS) approach starting from our initial discovery of monosulfated benzofurans to discover alternative scaffolds as allosteric modulators of thrombin, a key coagulation enzyme. Screening the ZINC database containing nearly 1 million nonsulfated small molecules using a pharmacophore developed from the parent sulfated benzofurans followed by a genetic algorithm-based dual-filter docking and scoring screening identified a group of 10 promising hits, of which three top-scoring hits were synthesized. Each was found to selectively inhibit human alpha-thrombin suggesting the possibility of this approach for scaffold hopping. Michaelis-Menten kinetics showed allosteric inhibition mechanism for the best molecule and human plasma studies confirmed good anticoagulation potential as expected. Our simple sequential LBVS and SBVS approach is likely to be useful as a general strategy for identification of sulfated small molecules hits as modulators of glycosaminoglycan-protein interactions.
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Affiliation(s)
- Preetpal S Sidhu
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, United States
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19
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Al-Horani RA, Mehta AY, Desai UR. Potent direct inhibitors of factor Xa based on the tetrahydroisoquinoline scaffold. Eur J Med Chem 2012; 54:771-83. [PMID: 22770607 DOI: 10.1016/j.ejmech.2012.06.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 06/12/2012] [Accepted: 06/15/2012] [Indexed: 12/31/2022]
Abstract
Direct inhibition of coagulation factor Xa (FXa) carries significant promise for developing effective and safe anticoagulants. Although a large number of FXa inhibitors have been studied, each can be classified as either possessing a highly flexible or a rigid core scaffold. We reasoned that an intermediate level of flexibility will provide high selectivity for FXa considering that its active site is less constrained in comparison to thrombin and more constrained as compared to trypsin. We studied several core scaffolds including 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid for direct FXa inhibition. Using a genetic algorithm-based docking and scoring approach, a promising candidate 23 was identified, synthesized, and found to inhibit FXa with a K(i) of 28 μM. Optimization of derivative 23 resulted in the design of a potent dicarboxamide 47, which displayed a K(i) of 135 nM. Dicarboxamide 47 displayed at least 1852-fold selectivity for FXa inhibition over other coagulation enzymes and doubled PT and aPTT of human plasma at 17.1 μM and 20.2 μM, respectively, which are comparable to those of clinically relevant agents. Dicarboxamide 47 is expected to serve as an excellent lead for further anticoagulant discovery.
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Affiliation(s)
- Rami A Al-Horani
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, USA
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20
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Rashid Q, Singh P, Abid M, Jairajpuri MA. Limitations of conventional anticoagulant therapy and the promises of non-heparin based conformational activators of antithrombin. J Thromb Thrombolysis 2012; 34:251-9. [DOI: 10.1007/s11239-012-0712-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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21
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Al-Horani RA, Liang A, Desai UR. Designing nonsaccharide, allosteric activators of antithrombin for accelerated inhibition of factor Xa. J Med Chem 2011; 54:6125-38. [PMID: 21800826 PMCID: PMC3165067 DOI: 10.1021/jm2008387] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antithrombin is a key regulator of coagulation and prime target of heparins, clinically used anticoagulants. Heparins induce a two-step conformational activation of antithrombin, a process that has remained challenging to target with molecules devoid of the antithrombin-binding pentasaccharide DEFGH. Computational screening of a focused library led to the design of two tetra-sulfated N-arylacyl tetrahydroisoquinoline variants as potential nonsaccharide activators of antithrombin. A high yielding synthetic scheme based on Horner-Wadsworth-Emmons or Pictet-Spengler reactions was developed to facilitate the functionalization of the tetrahydoisoquinoline ring, which upon further amidation, deprotection, and sulfation gave the targeted nonsaccharide activators. Spectrofluorometric measurement of affinity displayed antithrombin binding affinities in the low to high micromolar range at pH 6.0, I 0.05, 25 °C. Measurement of second-order rate constants of antithrombin inhibition of factor Xa in the presence and absence of the designed activators showed antithrombin activation in the range of 8-80-fold in the pH 6.0 buffer. This work puts forward 20c, a novel tetra-sulfated N-arylacyl tetrahydroisoquinoline-based molecule, that activates AT only 3.8-fold less than that achieved with DEFGH, suggesting a strong possibility of rationally designing sulfated organic molecules as clinically relevant AT activators.
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Affiliation(s)
- Rami A. Al-Horani
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298
| | - Aiye Liang
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298
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22
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Affiliation(s)
- Rami A. Al-Horani
- 800 E. Leigh Street, Suite 212, Institute for Structural Biology and Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Umesh R. Desai
- 800 E. Leigh Street, Suite 212, Institute for Structural Biology and Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23219
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23
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Liang A, Thakkar JN, Desai UR. Study of physico-chemical properties of novel highly sulfated, aromatic, mimetics of heparin and heparan sulfate. J Pharm Sci 2010; 99:1207-16. [DOI: 10.1002/jps.21908] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Henry BL, Connell J, Liang A, Krishnasamy C, Desai UR. Interaction of antithrombin with sulfated, low molecular weight lignins: opportunities for potent, selective modulation of antithrombin function. J Biol Chem 2009; 284:20897-908. [PMID: 19497853 DOI: 10.1074/jbc.m109.013359] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antithrombin, a major regulator of coagulation and angiogenesis, is known to interact with several natural sulfated polysaccharides. Previously, we prepared sulfated low molecular weight variants of natural lignins, called sulfated dehydrogenation polymers (DHPs) (Henry, B. L., Monien, B. H., Bock, P. E., and Desai, U. R. (2007) J. Biol. Chem. 282, 31891-31899), which have now been found to exhibit interesting antithrombin binding properties. Sulfated DHPs represent a library of diverse noncarbohydrate aromatic scaffolds that possess structures completely different from heparin and heparan sulfate. Fluorescence binding studies indicate that sulfated DHPs bind to antithrombin with micromolar affinity under physiological conditions. Salt dependence of binding affinity indicates that the antithrombin-sulfated DHP interaction involves a massive 80-87% non-ionic component to the free energy of binding. Competitive binding studies with heparin pentasaccharide, epicatechin sulfate, and full-length heparin indicate that sulfated DHPs bind to both the pentasaccharide-binding site and extended heparin-binding site of antithrombin. Affinity capillary electrophoresis resolves a limited number of peaks of antithrombin co-complexes suggesting preferential binding of selected DHP structures to the serpin. Computational genetic algorithm-based virtual screening study shows that only one sulfated DHP structure, out of the 11 present in a library of plausible sequences, bound in the heparin-binding site with a high calculated score supporting selectivity of recognition. Enzyme inhibition studies indicate that only one of the three sulfated DHPs studied is a potent inhibitor of free factor VIIa in the presence of antithrombin. Overall, the chemo-enzymatic origin and antithrombin binding properties of sulfated DHPs present novel opportunities for potent and selective modulation of the serpin function, especially for inhibiting the initiation phase of hemostasis.
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Affiliation(s)
- Brian L Henry
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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Liang A, Raghuraman A, Desai UR. Capillary electrophoretic study of small, highly sulfated, non-sugar molecules interacting with antithrombin. Electrophoresis 2009; 30:1544-51. [PMID: 19425011 PMCID: PMC2755545 DOI: 10.1002/elps.200800642] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Affinity CE (ACE) was used to study interactions of small, highly sulfated, aromatic molecules with antithrombin (AT). The high charge density of the small molecules induces differential migration of the complex resulting in a versatile method of assessing binding affinities, nature of interactions and site of binding on the inhibitor. Scatchard analysis of the interaction of three tetrahydroisoquinoline-based polysulfated molecules with AT results in monophasic profiles with affinities in the range of 40-60 microM in 20 mM sodium phosphate buffer, pH 7.4. For a pentasulfated molecule, a biphasic profile with affinities of 4.7 and 30 microM was observed. Measurement of K(D) as a function of ionic strength of the medium indicated that ionic and non-ionic forces contribute 2.4 and 1.9 kcal/mol, respectively, at pH 7.4 and 100 mM NaCl. Competitive binding studies showed that the tetrahydroisoquinoline-based molecules do not compete with a high-affinity heparin pentasaccharide. In contrast, the affinity of these tetrahydroisoquinoline derivatives decreases dramatically in the presence of an extended heparin-binding site ligand. Overall, ACE analysis of small, sulfated aromatic molecules interacting with AT is relatively easy and obviates the need for an external signal, e.g. fluorescence, for monitoring the interaction. In addition to affording biochemical knowledge, the small sample requirement and fast analysis time of ACE could be particularly advantageous for high-throughput screening of potential anticoagulants.
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Affiliation(s)
- Aiye Liang
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Arjun Raghuraman
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219
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26
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Gandhi NS, Mancera RL. The Structure of Glycosaminoglycans and their Interactions with Proteins. Chem Biol Drug Des 2008; 72:455-82. [DOI: 10.1111/j.1747-0285.2008.00741.x] [Citation(s) in RCA: 703] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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27
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Chen H, Yuan L, Song W, Wu Z, Li D. Biocompatible polymer materials: Role of protein–surface interactions. Prog Polym Sci 2008. [DOI: 10.1016/j.progpolymsci.2008.07.006] [Citation(s) in RCA: 452] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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28
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Raghuraman A, Liang A, Krishnasamy C, Lauck T, Gunnarsson GT, Desai UR. On designing non-saccharide, allosteric activators of antithrombin. Eur J Med Chem 2008; 44:2626-31. [PMID: 18996625 DOI: 10.1016/j.ejmech.2008.09.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 09/11/2008] [Indexed: 10/21/2022]
Abstract
Antithrombin, a plasma glycoprotein serpin, requires conformational activation by heparin to induce an anticoagulant effect, which is mediated through accelerated factor Xa inhibition. Heparin, a highly charged polymer and an allosteric activator of the serpin, is associated with major adverse effects. To design better, but radically different activators of antithrombin from heparin, we utilized a pharmacophore-based approach. A tetrahydroisoquinoline-based scaffold was designed to mimic four critical anionic groups of the key trisaccharide DEF constituting the sequence-specific pentasaccharide DEFGH in heparin. Activator IAS(5) containing 5,6-disulfated tetrahydroisoquinoline and 3,4,5-trisulfated phenyl rings was found to bind antithrombin at pH 7.4 with an affinity comparable to the reference trisaccharide DEF. IAS(5) activated the inhibitor nearly 30-fold, nearly 2- to 3-fold higher than our first generation flavanoid-based designs. This work advances the concept of antithrombin activation through non-saccharide, organic molecules and pinpoints a direction for the design of more potent molecules.
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Affiliation(s)
- Arjun Raghuraman
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 410 N. 12th Street, PO Box 980540, Richmond, VA 23298-0540, USA
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29
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Raghuraman A, Riaz M, Hindle M, Desai UR. Rapid and efficient microwave-assisted synthesis of highly sulfated organic scaffolds. Tetrahedron Lett 2007; 48:6754-6758. [PMID: 18797498 PMCID: PMC2084256 DOI: 10.1016/j.tetlet.2007.07.100] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Sulfation of multiply hydroxylated small organic molecules is fraught with problems of poor yield, multitude of products and long reaction times. We have developed a rapid microwave-based method for synthesis of highly sulfated small organic molecules, which affords the per-sulfated product in moderate to excellent yields and high purity. The method is expected to be of value in the discovery of per-sulfated organic molecules as mimics of glycosaminoglycans, which are being increasingly recognized as modulators of key physiological functions.
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Affiliation(s)
- Arjun Raghuraman
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Richmond, VA, USA
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30
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Monien BH, Henry BL, Raghuraman A, Hindle M, Desai UR. Novel chemo-enzymatic oligomers of cinnamic acids as direct and indirect inhibitors of coagulation proteinases. Bioorg Med Chem 2006; 14:7988-98. [PMID: 16914317 DOI: 10.1016/j.bmc.2006.07.066] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 07/17/2006] [Accepted: 07/26/2006] [Indexed: 11/28/2022]
Abstract
Thrombin and factor Xa, two important procoagulant enzymes, have been prime targets for regulation of clotting through the direct and indirect mechanism of inhibition. Our efforts on exploiting the indirect mechanism led us to study a carboxylic acid-based scaffold, which displayed major acceleration in the inhibition of these enzymes [J. Med. Chem.2005, 48, 1269, 5360]. This work advances the study to chemo-enzymatically prepared oligomers of 4-hydroxycinnamic acids, DHPs, which display interesting anticoagulant properties. Oligomers, ranging in size from tetramers to pentadecamers, were prepared through peroxidase-catalyzed oxidative coupling of caffeic, ferulic, and sinapic acids, and sulfated using triethylamine-sulfur trioxide complex. Chromatographic, spectroscopic, and elemental studies suggest that the DHPs are heterogeneous, polydisperse preparations composed of inter-monomer linkages similar to those found in natural lignins. Measurement of activated thromboplastin and prothrombin time indicates that both the sulfated and unsulfated derivatives of the DHPs display anticoagulant activity, which is dramatically higher than that of the reference polyacrylic acids. More interestingly, this activity approaches that of low-molecular-weight heparin with the sulfated derivative showing approximately 2- to 3-fold greater potency than the unsulfated parent. Studies on the inhibition of factor Xa and thrombin indicate that the oligomers exert their anticoagulant effect through both direct and indirect inhibition mechanisms. This dual inhibition property of 4-hydroxycinnamic acid-based DHP oligomers is the first example in inhibitors of coagulation. This work puts forward a novel, non-heparin structure, which may be exploited for the design of potent, dual action inhibitors of coagulation through combinatorial virtual screening on a library of DHP oligomers.
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Affiliation(s)
- Bernhard H Monien
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
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31
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Raghuraman A, Mosier PD, Desai UR. Finding a needle in a haystack: development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s). J Med Chem 2006; 49:3553-62. [PMID: 16759098 PMCID: PMC2516555 DOI: 10.1021/jm060092o] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a combinatorial virtual screening approach for predicting high specificity heparin/heparan sulfate sequences using the well-studied antithrombin-heparin interaction as a test case. Heparan sulfate hexasaccharides were simulated in the 'average backbone' conformation, wherein the inter-glycosidic bond angles were held constant at the mean of the known solution values, irrespective of their sequence. Molecular docking utilized GOLD with restrained inter-glycosidic torsions and intra-ring conformations, but flexible substituents at the 2-, 3-, and 6-positions and explicit incorporation of conformational variability of the iduronate residues. The approach reproduces the binding geometry of the sequence-specific heparin pentasaccharide to within 2.5 A. Screening of a combinatorial virtual library of 6,859 heparin hexasaccharides using a dual filter strategy, in which predicted antithrombin affinity was the first filter and self-consistency of docking was the second, resulted in only 10 sequences. Of these, nine were found to bind antithrombin in a manner identical to the natural pentasaccharide, while a novel hexasaccharide bound the inhibitor in a unique but dramatically different geometry and orientation. This work presents the first approach on combinatorial library screening for heparin/heparan sulfate GAGs to determine high specificity sequences and opens up huge opportunities to investigate numerous other physiologically relevant GAG-protein interactions.
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Affiliation(s)
- Arjun Raghuraman
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, 23298, USA
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de Kort M, Buijsman RC, van Boeckel CAA. Synthetic heparin derivatives as new anticoagulant drugs. Drug Discov Today 2005; 10:769-79. [PMID: 15922935 DOI: 10.1016/s1359-6446(05)03457-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The journey towards a detailed mechanistic understanding of the anticoagulant action of heparin has resulted in synthetic mimetics with improved pharmacodynamic profiles. Inspired by the ternary complex formation of heparin with antithrombin III and thrombin, the active pentasaccharide fondaparinux has been succeeded by several clinical candidates, such as SR123781, that have tailor-made factor Xa and thrombin inhibitory activities combined with less aspecific binding (e.g. binding to platelet factor 4 involved in thrombocytopenia). Novel compounds with both antithrombin III-mediated inhibition of factor Xa and direct thrombin inhibition are emerging. Org42675 is one such compound, balancing dual inhibition of factor Xa and thrombin in one anticoagulant drug, with excellent pharmacokinetic properties and strong inhibitory activity toward clot-bound thrombin.
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Affiliation(s)
- Martin de Kort
- NV Organon, Molenstraat 110, 5340 BH, Oss, The Netherlands.
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33
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Dantuluri M, Gunnarsson GT, Riaz M, Nguyen H, Desai UR. Capillary electrophoresis of highly sulfated flavanoids and flavonoids. Anal Biochem 2005; 336:316-22. [PMID: 15620899 DOI: 10.1016/j.ab.2004.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Indexed: 10/26/2022]
Abstract
Flavanoids and flavonoids are natural products present in our diet and known to possess multiple biological activities. Sulfated species of these natural products represent highly charged water-soluble organic molecules that possess unique biochemical properties. We describe here the first studies on capillary electrophoresis of these highly charged molecules. Fully sulfated flavanoids and flavonoids can be electrophoresed and resolved under reverse polarity at pH 3.5 using 5-10 kV in less than 20 min. In contrast, at high pH under normal polarity these species can be electrophoresed only if a pressurized capillary is employed. (+/-)-Catechin sulfate, a racemic sulfated flavanoid, was resolved into its enantiomers using 15% beta-cyclodextrin, a chiral selector, but not with alpha- or gamma-cyclodextrins. Yet, the high charge density of these molecules challenges the resolving capability of capillary electrophoresis as diastereomers (-)-epicatechin sulfate and (+)-catechin sulfate do not resolve, even in the presence of cyclodextrins or chiral positively charged amino acids. Overall, capillary electrophoresis of highly sulfated flavanoids and flavonoids is expected to be useful in rapid structure analysis of sulfated flavonoids, either synthetic or natural.
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Affiliation(s)
- Mandakini Dantuluri
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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Gunnarsson GT, Desai UR. Hydropathic interaction analyses of small organic activators binding to antithrombin. Bioorg Med Chem 2004; 12:633-40. [PMID: 14738974 DOI: 10.1016/j.bmc.2003.10.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recently we designed the first small organic ligands, sulfated flavanoids and flavonoids, that act as activators of antithrombin for accelerated inhibition of factor Xa, a key proteinase of the coagulation cascade [Gunnarsson and Desai, Bioorg. Med. Chem. Lett. (2003) 13:579]. To better understand the binding properties of these activators at a molecular level, we have utilized computerized hydropathic interaction (HINT) analyses of the sulfated molecules interacting in two plausible electropositive regions, the pentasaccharide- and extended heparin-binding sites, of antithrombin in its native and activated forms. HINT analyses indicate favorable multi-point interactions of the activators in both binding sites of the two forms of antithrombin. Yet, HINT predicts better interaction of most activators, except for (-)-catechin sulfate, with the activated form of antithrombin than with the native form supporting the observation in solution that these molecules function as activators of the inhibitor. Further, whereas (+)-catechin sulfate recognized the activated form of antithrombin better in both the pentasaccharide- and extended heparin- binding sites, the native form was better recognized by (-)-catechin sulfate, thus explaining its weaker binding and activation potential in solution. A reasonable linear correlation between the overall HINT score and the solution free energy of binding of the sulfated activators was evident. This investigation indicates that HINT is a useful tool in understanding interactions of antithrombin with small sulfated organic ligands at a molecular level, has some good predictive properties, and is likely to be useful for rational design purposes.
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Affiliation(s)
- Gunnar T Gunnarsson
- Department of Medicinal Chemistry, Virginia Commonwealth University, 410N. 12th Street, PO Box 980540, Richmond, VA 23298, USA
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35
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Wu X, Zhao R, Li Z, Yao M, Wang H, Han J, Qu S, Chen X, Qian L, Sun Y, Xu Y, Gu J. A novel small peptide as a targeting ligand for receptor tyrosine kinase Tie2. Biochem Biophys Res Commun 2004; 315:1004-10. [PMID: 14985112 DOI: 10.1016/j.bbrc.2004.01.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Indexed: 11/23/2022]
Abstract
Tie2 is an endothelium-specific receptor tyrosine kinase known to play an important role in tumor angiogenesis. We sought to identify a small peptide ligand against Tie2 for developing a delivery targeting agent. We used hydrophobic analysis and comparative sequence/structure analysis to select a minimal peptide based on angiopoietin-2 amino acid sequence. The resulting peptide named GA3(WTIIQRREDGSVDFQRTWKEYK) was synthesized and labeled with iodine-125 at the C-terminal tyrosine residue to characterize its binding capability. In in vitro binding assays, GA3 can not only specifically bind to SMMC7721-Tie2 but also compete with angiopoietin-2 in binding. Via mouse tail vein injection, 125I-labeled GA3 was found to favorably accumulate in SPC-A1 xenograft tumor tissues which positively express Tie2. These results demonstrated that GA3 may be useful as a drug or gene delivery ligand for targeted chemotherapy, radiotherapy, and gene therapy.
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Affiliation(s)
- Xianghua Wu
- National Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao-Tong University Medical School, Shanghai 200032, PR China
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36
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Gunnarsson GT, Desai UR. Exploring new non-sugar sulfated molecules as activators of antithrombin. Bioorg Med Chem Lett 2003; 13:679-83. [PMID: 12639557 DOI: 10.1016/s0960-894x(02)01055-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
New non-sugar, small, sulfated molecules, based on our de novo rationally designed activator (-)-epicatechin sulfate (ECS), were investigated to bind and activate antithrombin, an inhibitor of plasma coagulation enzyme factor Xa. For the activators studied, the equilibrium dissociation constant (K(D)) of the interaction with plasma antithrombin varies nearly 53-fold, with the highest affinity of 1.8 microM observed for morin sulfate, while the acceleration in factor Xa inhibition varies 2.6-fold. The results demonstrate that antithrombin binding and activation is a common property of these small sulfated molecules and suggests plausible directions for designing more potent activators.
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Affiliation(s)
- Gunnar T Gunnarsson
- Department of Medicinal Chemistry, Virginia Commonwealth University, 410 N. 12th Street, PO Box 980540, Richmond, VA 23298, USA
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Abstract
Clinically used anticoagulants are inhibitors of enzymes involved in the coagulation pathway, primarily thrombin and factor Xa. These agents can be either direct or indirect inhibitors of clotting enzymes. Heparin-based anticoagulants are indirect inhibitors that enhance the proteinase inhibitory activity of a natural anticoagulant, antithrombin. Despite its phenomenal success, current anticoagulation therapy suffers from the risk of serious bleeding. The need for safer and more effective antithrombotic agents clearly exists. The past decade has seen enormous effort directed toward discovering and/or designing new molecules with anticoagulant activity. These new molecules can be classified into (a). antithrombin and its mutants, (b). natural polysaccharides, (c). synthetic modified heparins and heparin-mimics, (d). synthetic oligosaccharides, and (e). synthetic non-sugar antithrombin activators. This review focuses on these efforts in designing or discovering new molecules that act through the antithrombin pathway of anticoagulation.
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Affiliation(s)
- Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, USA.
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