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Afosah DK, Fayyad RM, Puliafico VR, Merrell S, Langmia EK, Diagne SR, Al-Horani RA, Desai UR. Homogeneous, Synthetic, Non-Saccharide Glycosaminoglycan Mimetics as Potent Inhibitors of Human Cathepsin G. Biomolecules 2023; 13:760. [PMID: 37238630 PMCID: PMC10216581 DOI: 10.3390/biom13050760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Cathepsin G (CatG) is a pro-inflammatory neutrophil serine protease that is important for host defense, and has been implicated in several inflammatory disorders. Hence, inhibition of CatG holds much therapeutic potential; however, only a few inhibitors have been identified to date, and none have reached clinical trials. Of these, heparin is a well-known inhibitor of CatG, but its heterogeneity and bleeding risk reduce its clinical potential. We reasoned that synthetic small mimetics of heparin, labeled as non-saccharide glycosaminoglycan mimetics (NSGMs), would exhibit potent CatG inhibition while being devoid of bleeding risks associated with heparin. Hence, we screened a focused library of 30 NSGMs for CatG inhibition using a chromogenic substrate hydrolysis assay and identified nano- to micro-molar inhibitors with varying levels of efficacy. Of these, a structurally-defined, octasulfated di-quercetin NSGM 25 inhibited CatG with a potency of ~50 nM. NSGM 25 binds to CatG in an allosteric site through an approximately equal contribution of ionic and nonionic forces. Octasulfated 25 exhibits no impact on human plasma clotting, suggesting minimal bleeding risk. Considering that octasulfated 25 also potently inhibits two other pro-inflammatory proteases, human neutrophil elastase and human plasmin, the current results imply the possibility of a multi-pronged anti-inflammatory approach in which these proteases are likely to simultaneously likely combat important conditions, e.g., rheumatoid arthritis, emphysema, or cystic fibrosis, with minimal bleeding risk.
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Affiliation(s)
- Daniel K. Afosah
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Rawan M. Fayyad
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Valerie R. Puliafico
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Spencer Merrell
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Eltice K. Langmia
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, VA 24450, USA
| | - Sophie R. Diagne
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Rami A. Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (R.M.F.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
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2
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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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3
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Morla S, Ravikumar O, O’Hara C, Boothello R, Vera A, Abdelfadiel EI, Fayyad R, Afosah DK, Sharon C, Fernandez L, Shah SA, Patel BB, Desai UR. Designing Synthetic, Sulfated Glycosaminoglycan Mimetics That Are Orally Bioavailable and Exhibiting In Vivo Anticancer Activity. J Med Chem 2023; 66:1321-1338. [PMID: 36634271 PMCID: PMC9884082 DOI: 10.1021/acs.jmedchem.2c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Sulfated glycosaminoglycans (GAGs), or synthetic mimetics thereof, are not favorably viewed as orally bioavailable drugs owing to their high number of anionic sulfate groups. Devising an approach for oral delivery of such highly sulfated molecules would be very useful. This work presents the concept that conjugating cholesterol to synthetic sulfated GAG mimetics enables oral delivery. A focused library of sulfated GAG mimetics was synthesized and found to inhibit the growth of a colorectal cancer cell line under spheroid conditions with a wide range of potencies ( 0.8 to 46 μM). Specific analogues containing cholesterol, either alone or in combination with clinical utilized drugs, exhibited pronounced in vivo anticancer potential with intraperitoneal as well as oral administration, as assessed by ex vivo tertiary and quaternary spheroid growth, cancer stem cell (CSC) markers, and/or self-renewal factors. Overall, cholesterol derivatization of highly sulfated GAG mimetics affords an excellent approach for engineering oral activity.
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Affiliation(s)
- Shravan Morla
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Ongolu Ravikumar
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Connor O’Hara
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rio Boothello
- Division
of Hematology, Oncology and Palliative Care, Department of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Alberto Vera
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Elsamani I. Abdelfadiel
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rawan Fayyad
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Daniel K. Afosah
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Chetna Sharon
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Leopoldo Fernandez
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
- Massey
Cancer Center, Richmond, Virginia 23298, United States
- Division
of Surgical Oncology, Department of Surgery, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Syed Ammer Shah
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
- Massey
Cancer Center, Richmond, Virginia 23298, United States
- Division
of Surgical Oncology, Department of Surgery, Hunter Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
| | - Bhaumik B. Patel
- Division
of Hematology, Oncology and Palliative Care, Department of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Hunter
Holmes McGuire VA Medical Center, Richmond, Virginia 23249, United States
- Massey
Cancer Center, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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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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Allosteric inhibition and kinetic characterization of Klebsiella pneumoniae CysE: An emerging drug target. Int J Biol Macromol 2019; 151:1240-1249. [PMID: 31751684 DOI: 10.1016/j.ijbiomac.2019.10.170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]
Abstract
The emergence and spread of multidrug-resistant strains of Klebsiella pneumoniae is a major concern that necessitates the development of unique therapeutics. The essential requirement of serine acetyltransferase (SAT/CysE) for survival of several human pathogens makes it a very promising target for inhibitor designing and drug discovery. In this study, as an initial step to structure-based drug discovery, CysE from K. pneumonia was structurally and biochemically characterized. Subsequently, blind docking of selected natural products into the X-ray crystallography determined 3D structure of the target was carried out. Experimental validation of the inhibitory potential of the top-scorers established quercetin as an uncompetitive inhibitor of Kpn CysE. Molecular dynamics simulations carried out to elucidate the binding mode of quercetin reveal that this small molecule binds at the trimer-trimer interface of hexameric CysE, a site physically distinct from the active site of the enzyme. Detailed analysis of conformational differences incurred in Kpn CysE structure on binding to quercetin provides mechanistic understanding of allosteric modulation. Binding of quercetin to CysE leads to conformation changes in the active site loops and proximal loops that affect its internal dynamics and consequently its affinity for substrate/co-factor binding, justifying the reduced enzyme activity.
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6
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Sun ZG, Yang-Liu, Zhang JM, Cui SC, Zhang ZG, Zhu HL. The Research Progress of Direct Thrombin Inhibitors. Mini Rev Med Chem 2019; 20:1574-1585. [PMID: 31644402 DOI: 10.2174/1389557519666191015201125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 03/18/2019] [Accepted: 05/19/2019] [Indexed: 11/22/2022]
Abstract
Blood coagulation is the process of changing the blood from the flowing state to the gel state. It is an important part of the hemostatic function. Coagulation is a process by which a series of coagulation factors are sequentially activated, and finally thrombin is formed to form fibrin clot. Direct thrombin inhibitors are important anticoagulant drug. These drugs can selectively bind to the active site of thrombin, inhibit thrombin activity, have strong action and high specificity, and have important significance in the clinical treatment of thrombus diseases. Some of them come from natural products of animals or plants, and many of them have been applied in the clinic. The other part is derived from the design, synthesis and activity studies of small molecule inhibitors. This review discusses the progress of direct thrombin inhibitors in recent years.
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Affiliation(s)
- Zhi-Gang Sun
- Central Laboratory, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, No.163 Xianlin Road, Nanjing 210023, China
| | - Yang-Liu
- Central Laboratory, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China
| | - Jin-Mai Zhang
- Room 205, BIO-X white house, Shanghai Jiao Tong University, No.1954 Huashan Road, Shanghai 200030,China
| | - Shi-Chang Cui
- Central Laboratory, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China
| | - Zhi-Gang Zhang
- Department of Cardiovascular Medicine, Linyi Central Hospital, No.17 Jiankang Road, Linyi 276400, China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, No.163 Xianlin Road, Nanjing 210023, China
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7
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Billur R, Sabo TM, Maurer MC. Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I. Biochemistry 2019; 58:1048-1060. [PMID: 30672691 DOI: 10.1021/acs.biochem.8b00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Thrombin, derived from zymogen prothrombin (ProT), is a serine protease involved in procoagulation, anticoagulation, and platelet activation. Thrombin's actions are regulated through anion-binding exosites I and II (ABE I and ABE II) that undergo maturation during activation. Mature ABEs can utilize exosite-based communication to fulfill thrombin functions. However, the conformational basis behind such long-range communication and the resultant ligand binding affinities are not well understood. Protease activated receptors (PARs), involved in platelet activation and aggregation, are known to target thrombin ABE I. Unexpectedly, PAR3 (44-56) can already bind to pro-ABE I of ProT. Nuclear magnetic resonance (NMR) ligand-enzyme titrations were used to characterize how individual PAR1 (49-62) residues interact with pro-ABE I and mature ABE I. 1D proton line broadening studies demonstrated that binding affinities for native PAR1P (49-62, P54) and for the weak binding variant PAR1G (49-62, P54G) increased as ProT was converted to mature thrombin. 1H,15N-HSQC titrations revealed that PAR1G residues K51, E53, F55, D58, and E60 exhibited less affinity to pro-ABE I than comparable residues in PAR3G (44-56, P51G). Individual PAR1G residues then displayed tighter binding upon exosite maturation. Long-range communication between thrombin exosites was examined by saturating ABE II with phosphorylated GpIbα (269-282, 3Yp) and monitoring the binding of PAR1 and PAR3 peptides to ABE I. Individual PAR residues exhibited increased affinities in this dual-ligand environment supporting the presence of interexosite allostery. Exosite maturation and beneficial long-range allostery are proposed to help stabilize an ABE I conformation that can effectively bind PAR ligands.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center , University of Louisville , Louisville , Kentucky 40202 , United States
| | - Muriel C Maurer
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
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Sha Q, Liu H. De novo synthesis of benzofurans via trifluoroacetic acid catalyzed cyclization/oxidative aromatization cascade reaction of 2-hydroxy-1,4-diones. Org Biomol Chem 2019; 17:7547-7551. [DOI: 10.1039/c9ob01422e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A simple metal-free cyclization/oxidative aromatization reaction starting from 2-hydroxy-1,4-diones for the de novo synthesis of benzofurans was developed.
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Affiliation(s)
- Qiang Sha
- Jiangsu Key Laboratory of Pesticide Science and Department of Chemistry
- College of Sciences
- Nanjing Agricultural University
- Nanjing 210095
- P. R. China
| | - Haixuan Liu
- Sanhome R&D Centre
- Nanjing Sanhome Pharmaceutical Co
- Ltd
- Nanjing 211135
- P. R. China
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9
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Abdel Aziz MH, Desai UR. Novel heparin mimetics reveal cooperativity between exosite 2 and sodium-binding site of thrombin. Thromb Res 2018; 165:61-67. [PMID: 29573721 DOI: 10.1016/j.thromres.2018.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Thrombin is a primary target of most anticoagulants. Yet, thrombin's dual and opposing role in pro- as well as anti- coagulant processes imposes considerable challenges in discovering finely tuned regulators that maintain homeostasis, rather than disproportionately changing the equilibrium to one side. In this connection, we have been studying exosite 2-mediated allosteric modulation of thrombin activity using synthetic agents called low molecular weight lignins (LMWLs). Although the aromatic scaffold of LMWLs is completely different from the polysaccharidic scaffold of heparin, the presence of multiple negatively charged groups on both ligands induces binding to exosite 2 of thrombin. This work characterizes the nature of interactions between LMWLs and thrombin to understand the energetic cooperativity between exosite 2 and active site of thrombin. MATERIALS AND METHODS The thermodynamics of thrombin-LMWL complexes was studied using spectrofluorimetric titrations as a function of ionic strength and temperature of the buffer. The contributions of enthalpy and entropy to binding were evaluated using classic thermodynamic equations. Label-free surface plasmon resonance was used to assess the role of sodium ion in LMWL binding to thrombin at a fixed ionic strength. RESULTS AND CONCLUSIONS Exosite 2-induced conformational change in thrombin's active site is strongly dependent on the structure of the ligand, which has consequences with respect to regulation of thrombin. The ionic and non-ionic contributions to binding affinity and the thermodynamic signature were highly ligand specific. Interestingly, LMWLs display preference for the sodium-bound form of thrombin, which supports the existence of an energetic coupling between exosite 2 and sodium-binding site of thrombin.
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Affiliation(s)
- May H Abdel Aziz
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States.
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10
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Afosah DK, Verespy S, Al-Horani RA, Boothello RS, Karuturi R, Desai UR. A small group of sulfated benzofurans induces steady-state submaximal inhibition of thrombin. Bioorg Med Chem Lett 2018; 28:1101-1105. [PMID: 29459207 DOI: 10.1016/j.bmcl.2018.01.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/07/2023]
Abstract
Despite the development of promising direct oral anticoagulants, which are all orthosteric inhibitors, a sizable number of patients suffer from bleeding complications. We have hypothesized that allosterism based on the heparin-binding exosites presents a major opportunity to induce sub-maximal inhibition of coagulation proteases, thereby avoiding/reducing bleeding risk. We present the design of a group of sulfated benzofuran dimers that display heparin-binding site-dependent partial allosteric inhibition of thrombin against fibrinogen (ΔY = 55-75%), the first time that a small molecule (MW < 800) has been found to thwart macromolecular cleavage by a monomeric protease in a controlled manner. The work leads to the promising concept that it should be possible to develop allosteric inhibitors that reduce clotting, but do not completely eliminate it, thereby avoiding major bleeding complications that beset anticoagulants today.
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Affiliation(s)
- Daniel K Afosah
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Stephen Verespy
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA; Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Rami A Al-Horani
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA; Division of Basic Pharmaceutical Sciences, Xavier University, New Orleans, LA, USA
| | - Rio S Boothello
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Rajesh Karuturi
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
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11
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Liu Y, Fu J, Pan W, Xue Q, Liu X, Zhang A. Inhibition of thrombin by functionalized C 60 nanoparticles revealed via in vitro assays and in silico studies. J Environ Sci (China) 2018; 63:285-295. [PMID: 29406112 DOI: 10.1016/j.jes.2017.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/09/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
The studies on the human toxicity of nanoparticles (NPs) are far behind the rapid development of engineered functionalized NPs. Fullerene has been widely used as drug carrier skeleton due to its reported low risk. However, different from other kinds of NPs, fullerene-based NPs (C60 NPs) have been found to have an anticoagulation effect, although the potential target is still unknown. In the study, both experimental and computational methods were adopted to gain mechanistic insight into the modulation of thrombin activity by nine kinds of C60 NPs with diverse surface chemistry properties. In vitro enzyme activity assays showed that all tested surface-modified C60 NPs exhibited thrombin inhibition ability. Kinetic studies coupled with competitive testing using 3 known inhibitors indicated that six of the C60 NPs, of greater hydrophobicity and hydrogen bond (HB) donor acidity or acceptor basicity, acted as competitive inhibitors of thrombin by directly interacting with the active site of thrombin. A simple quantitative nanostructure-activity relationship model relating the surface substituent properties to the inhibition potential was then established for the six competitive inhibitors. Molecular docking analysis revealed that the intermolecular HB interactions were important for the specific binding of C60 NPs to the active site canyon, while the additional stability provided by the surface groups through van der Waals interaction also play a key role in the thrombin binding affinity of the NPs. Our results suggest that thrombin is a possible target of the surface-functionalized C60 NPs relevant to their anticoagulation effect.
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Affiliation(s)
- Yanyan Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Wenxiao Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China.
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12
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Billur R, Ban D, Sabo TM, Maurer MC. Deciphering Conformational Changes Associated with the Maturation of Thrombin Anion Binding Exosite I. Biochemistry 2017; 56:6343-6354. [PMID: 29111672 DOI: 10.1021/acs.biochem.7b00970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Thrombin participates in procoagulation, anticoagulation, and platelet activation. This enzyme contains anion binding exosites, ABE I and ABE II, which attract regulatory biomolecules. As prothrombin is activated to thrombin, pro-ABE I is converted into mature ABE I. Unexpectedly, certain ligands can bind to pro-ABE I specifically. Moreover, knowledge of changes in conformation and affinity that occur at the individual residue level as pro-ABE I is converted to ABE I is lacking. Such changes are transient and were not captured by crystallography. Therefore, we employed nuclear magnetic resonance (NMR) titrations to monitor development of ABE I using peptides based on protease-activated receptor 3 (PAR3). Proton line broadening NMR revealed that PAR3 (44-56) and more weakly binding PAR3G (44-56) could already interact with pro-ABE I on prothrombin. 1H-15N heteronuclear single-quantum coherence NMR titrations were then used to probe binding of individual 15N-labeled PAR3G residues (F47, E48, L52, and D54). PAR3G E48 and D54 could interact electrostatically with prothrombin and tightened upon thrombin maturation. The higher affinity for PAR3G D54 suggests the region surrounding thrombin R77a is better oriented to bind D54 than the interaction between PAR3G E48 and thrombin R75. Aromatic PAR3G F47 and aliphatic L52 both reported on significant changes in the chemical environment upon conversion of prothrombin to thrombin. The ABE I region surrounding the 30s loop was more affected than the hydrophobic pocket (F34, L65, and I82). Our NMR titrations demonstrate that PAR3 residues document structural rearrangements occurring during exosite maturation that are missed by reported X-ray crystal structures.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - Muriel C Maurer
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
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13
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Johnstone S, Albert JS. Pharmacological property optimization for allosteric ligands: A medicinal chemistry perspective. Bioorg Med Chem Lett 2017; 27:2239-2258. [PMID: 28408223 DOI: 10.1016/j.bmcl.2017.03.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 12/11/2022]
Abstract
New strategies to potentially improve drug safety and efficacy emerge with allosteric programs. Biased allosteric modulators can be designed with high subtype selectivity and defined receptor signaling endpoints, however, selecting the most meaningful parameters for optimization can be perplexing. Historically, "potency hunting" at the expense of physicochemical and pharmacokinetic optimization has led to numerous tool compounds with excellent pharmacological properties but no path to drug development. Conversely, extensive physicochemical and pharmacokinetic screening with only post hoc bias and allosteric characterization has led to inefficacious compounds or compounds with on-target toxicities. This field is rapidly evolving with new mechanistic understanding, changes in terminology, and novel opportunities. The intent of this digest is to summarize current understanding and debates within the field. We aim to discuss, from a medicinal chemistry perspective, the parameter choices available to drive SAR.
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Affiliation(s)
- Shawn Johnstone
- Department of Chemistry, IntelliSyn Pharma, 7171 Frederick-Banting, Montreal, Quebec H4S 1Z9, Canada.
| | - Jeffrey S Albert
- Department of Chemistry, IntelliSyn Pharma, 7171 Frederick-Banting, Montreal, Quebec H4S 1Z9, Canada; Department of Chemistry, AviSyn Pharma, 4275 Executive Square, Suite 200, La Jolla, CA 92037, United States.
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14
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Allosteric Partial Inhibition of Monomeric Proteases. Sulfated Coumarins Induce Regulation, not just Inhibition, of Thrombin. Sci Rep 2016; 6:24043. [PMID: 27053426 PMCID: PMC4823711 DOI: 10.1038/srep24043] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/14/2016] [Indexed: 11/26/2022] Open
Abstract
Allosteric partial inhibition of soluble, monomeric proteases can offer major regulatory advantages, but remains a concept on paper to date; although it has been routinely documented for receptors and oligomeric proteins. Thrombin, a key protease of the coagulation cascade, displays significant conformational plasticity, which presents an attractive opportunity to discover small molecule probes that induce sub-maximal allosteric inhibition. We synthesized a focused library of some 36 sulfated coumarins to discover two agents that display sub-maximal efficacy (~50%), high potency (<500 nM) and high selectivity for thrombin (>150-fold). Michaelis-Menten, competitive inhibition, and site-directed mutagenesis studies identified exosite 2 as the site of binding for the most potent sulfated coumarin. Stern-Volmer quenching of active site-labeled fluorophore suggested that the allosteric regulators induce intermediate structural changes in the active site as compared to those that display ~80–100% efficacy. Antithrombin inactivation of thrombin was impaired in the presence of the sulfated coumarins suggesting that allosteric partial inhibition arises from catalytic dysfunction of the active site. Overall, sulfated coumarins represent first-in-class, sub-maximal inhibitors of thrombin. The probes establish the concept of allosteric partial inhibition of soluble, monomeric proteins. This concept may lead to a new class of anticoagulants that are completely devoid of bleeding.
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15
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Mehta AY, Mohammed BM, Martin EJ, Brophy DF, Gailani D, Desai UR. Allosterism-based simultaneous, dual anticoagulant and antiplatelet action: allosteric inhibitor targeting the glycoprotein Ibα-binding and heparin-binding site of thrombin. J Thromb Haemost 2016; 14:828-38. [PMID: 26748875 PMCID: PMC4828251 DOI: 10.1111/jth.13254] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/24/2015] [Indexed: 12/01/2022]
Abstract
BACKGROUND Allosteric inhibition is a promising approach for developing a new group of anticoagulants with potentially reduced bleeding consequences. Recently, we designed sulfated β-O4 lignin (SbO4L) as an allosteric inhibitor that targets exosite 2 of thrombin to reduce fibrinogen cleavage through allostery and compete with glycoprotein Ibα to reduce platelet activation. OBJECTIVE To assess: (i) the antithrombotic potential of a novel approach of simultaneous exosite 2-dependent allosteric inhibition of thrombin and competitive inhibition of platelet activation; and (ii) the promise of SbO4L as the first-in-class antithrombotic agent. METHODS A combination of whole blood thromboelastography, hemostasis analysis, mouse arterial thrombosis models and mouse tail bleeding studies were used to assess antithrombotic potential. RESULTS AND CONCLUSIONS SbO4L extended the clot initiation time, and reduced maximal clot strength, platelet contractile force, and the clot elastic modulus, suggesting dual anticoagulant and antiplatelet effects. These effects were comparable to those observed with enoxaparin. A dose of 1 mg of SbO4L per mouse prevented occlusion in 100% of arteries, and lower doses resulted in a proportionally reduced response. Likewise, the time to occlusion increased by ~ 70% with a 0.5-mg dose in the mouse Rose Bengal thrombosis model. Finally, tail bleeding studies demonstrated that SbO4L does not increase bleeding propensity. In comparison, a 0.3-mg dose of enoxaparin increased the bleeding time and blood volume loss. Overall, this study highlights the promise of the allosteric inhibition approach, and presents SbO4L as a novel anticoagulant with potentially reduced bleeding side effects.
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Affiliation(s)
- Akul Y. Mehta
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Bassem M. Mohammed
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, VA 23298, USA
- Department of Clinical Pharmacy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Erika J. Martin
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Donald F. Brophy
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - David Gailani
- Department of Pathology, Immunology and Microbiology, Vanderbilt University Medical Center, Nashville, TN 37203
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
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16
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Huang Y, Shaw MA, Warmin MR, Mullins ES, Ayres N. Blood compatibility of heparin-inspired, lactose containing, polyureas depends on the chemistry of the polymer backbone. Polym Chem 2016. [DOI: 10.1039/c6py00616g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Sulfated glycopolymers were synthesized from diisocyanates and lactose containing diamines. Blood compatibility assays indicated highly sulfated glycopolymers with methylene bis(4-cyclohexyl isocyanate) backbones result in prolonged clotting times.
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Affiliation(s)
- Y. Huang
- Department of Chemistry
- The University of Cincinnati
- Cincinnati
- USA
| | - M. A. Shaw
- Cancer and Blood Diseases Institute
- Cincinnati Children's Hospital Medical Center
- Cincinnati
- USA
| | - M. R. Warmin
- Department of Chemistry
- The University of Cincinnati
- Cincinnati
- USA
| | - E. S. Mullins
- Cancer and Blood Diseases Institute
- Cincinnati Children's Hospital Medical Center
- Cincinnati
- USA
| | - N. Ayres
- Department of Chemistry
- The University of Cincinnati
- Cincinnati
- USA
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17
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Dong MH, Chen HF, Ren YJ, Shao FM. Molecular modeling studies, synthesis and biological evaluation of dabigatran analogues as thrombin inhibitors. Bioorg Med Chem 2015; 24:73-84. [PMID: 26690913 DOI: 10.1016/j.bmc.2015.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/17/2015] [Accepted: 11/20/2015] [Indexed: 11/16/2022]
Abstract
In this work, 48 thrombin inhibitors based on the structural scaffold of dabigatran were analyzed using a combination of molecular modeling techniques. We generated three-dimensional quantitative structure-activity relationship (3D-QSAR) models based on three alignments for both comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) to highlight the structural requirements for thrombin protein inhibition. In addition to the 3D-QSAR study, Topomer CoMFA model also was established with a higher leave-one-out cross-validation q(2) and a non-cross-validation r(2), which suggest that the three models have good predictive ability. The results indicated that the steric, hydrophobic and electrostatic fields play key roles in QSAR model. Furthermore, we employed molecular docking and re-docking simulation explored the binding relationship of the ligand and the receptor protein in detail. Molecular docking simulations identified several key interactions that were also indicated through 3D-QSAR analysis. On the basis of the obtained results, two compounds were designed and predicted by three models, the biological evaluation in vitro (IC50) demonstrated that these molecular models were effective for the development of novel potent thrombin inhibitors.
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Affiliation(s)
- Ming-Hui Dong
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Hai-Feng Chen
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Yu-Jie Ren
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Fang-Ming Shao
- School of Science, East China University of Science and Technology, Shanghai 200237, China
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18
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Kim Y, Kankanamalage ACG, Damalanka VC, Weerawarna PM, Groutas WC, Chang KO. Potent inhibition of enterovirus D68 and human rhinoviruses by dipeptidyl aldehydes and α-ketoamides. Antiviral Res 2015; 125:84-91. [PMID: 26658373 PMCID: PMC4698184 DOI: 10.1016/j.antiviral.2015.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/21/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023]
Abstract
Enterovirus D68 (EV-D68) is an emerging pathogen responsible for mild to severe respiratory infections that occur mostly in infants, children and teenagers. EV-D68, one of more than 100 non-polio enteroviruses, is acid-labile and biologically similar to human rhinoviruses (HRV) (originally classified as HRV87). However, there is no approved preventive or therapeutic measure against EV-D68, HRV, or other enteroviruses. In this study, we evaluated the antiviral activity of series of dipeptidyl compounds against EV-D68 and HRV strains, and demonstrated that several peptidyl aldehyde and α-ketoamide peptidyl compounds are potent inhibitors of EV-D68 and HRV strains with high in-vitro therapeutic indices (>1000). One of the α-ketoamide compounds is shown to have favorable pharmacokinetics profiles, including a favorable oral bioavailability in rats. Recent successful development of α-ketoamide protease inhibitors against hepatitis C virus suggests these compounds may have a high potential for further optimization and development against emerging EV-D68, as well as HRV. Series of dipeptidyl aldehyde or ketomide compounds were highly effective against enterovirus-D68 and human rhinoviruses. The highly effective ketoamide compound is shown to have favorable pharmacokinetics profiles. These may have a high potential for further antiviral development against emerging enterovirus-D68 and human rhinoviruses.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | | | | | | | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS, USA.
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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19
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Yurttaş L, Abu Mohsen U, Ozkan Y, Cobanoglu S, Levent S, Kaplancikli ZA. Synthesis and biological evaluation of some dibenzofuran-piperazine derivatives. J Enzyme Inhib Med Chem 2015; 31:1177-83. [PMID: 26581445 DOI: 10.3109/14756366.2015.1108971] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the present paper, a novel series of dibenzofuran-piperazine derivatives were synthesized via the treatment of N-(2-methoxy-3-dibenzofuranyl)-2-chloroacetamide with substituted piperazine derivatives. The chemical structures of the compounds were elucidated by (1)H NMR, (13)C NMR, mass spectral data; elemental analysis and HPLC analysis. Each derivative was evaluated for antiplatelet activity and anticholinesterase activity. Compound 2 m with 2-furoyl moiety exhibited high percentage inhibition as much as standard drug aspirin on arachidonic acid (AA)-induced platelet aggregation. None of the compounds presented significant inhibitor effect on collagen-induced platelet aggregation. Furthermore, the anticholinesterase activity of the compounds was determined and they did not show promising inhibitor activity compared with standard drug donepezil.
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Affiliation(s)
- Leyla Yurttaş
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Anadolu University , Eskişehir , Turkey
| | - Usama Abu Mohsen
- b Department of Pharmaceutical Chemistry , Faculty of Pharmacy, Al-Azhar University , Gaza , Palestine , and
| | - Yeşim Ozkan
- c Department of Biochemistry , Faculty of Pharmacy, Gazi University , Ankara , Turkey
| | - Simla Cobanoglu
- c Department of Biochemistry , Faculty of Pharmacy, Gazi University , Ankara , Turkey
| | - Serkan Levent
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Anadolu University , Eskişehir , Turkey
| | - Zafer Asım Kaplancikli
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Anadolu University , Eskişehir , Turkey
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20
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He LW, Dai WC, Li NG. Development of Orally Active Thrombin Inhibitors for the Treatment of Thrombotic Disorder Diseases. Molecules 2015; 20:11046-62. [PMID: 26083038 PMCID: PMC6272601 DOI: 10.3390/molecules200611046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022] Open
Abstract
Thrombotic disorders represent the major share of the various cardiovascular diseases, and significant progress has been made in the development of synthetic thrombin inhibitors as new anticoagulants. In addition to the development of highly potent and selective inhibitors with improved safety and suitable half-life, several allosteric inhibitors have been designed and synthesized, that did not fully nullify the procoagulant signal and thus could result in reduced bleeding complications. Furthermore, natural products with thrombin inhibitory activity have been isolated, and some natural products have been modified in order to improve their inhibitory activity and metabolic stability. This review summarizes the development of orally active thrombin inhibitors for the treatment of thrombotic disorder diseases, which could serve as a reference for the interested researchers.
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Affiliation(s)
- Li-Wei He
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Wei-Chen Dai
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Nian-Guang Li
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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21
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Kankanamalage ACG, Kim Y, Weerawarna PM, Uy RAZ, Damalanka VC, Mandadapu SR, Alliston KR, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-guided design and optimization of dipeptidyl inhibitors of norovirus 3CL protease. Structure-activity relationships and biochemical, X-ray crystallographic, cell-based, and in vivo studies. J Med Chem 2015; 58:3144-55. [PMID: 25761614 PMCID: PMC4484267 DOI: 10.1021/jm5019934] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | | | | | | | | | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | - William C. Groutas
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
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22
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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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23
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Nevagi RJ, Dighe SN, Dighe SN. Biological and medicinal significance of benzofuran. Eur J Med Chem 2014; 97:561-81. [PMID: 26015069 DOI: 10.1016/j.ejmech.2014.10.085] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/15/2014] [Accepted: 10/31/2014] [Indexed: 11/29/2022]
Abstract
This article emphasizes on the importance of benzofuran as a biologically relevant heterocycle. It covers most of the physiologically as well as medicinally important compounds containing benzofuran rings. This article also covers clinically approved drugs containing benzofuran scaffold.
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Affiliation(s)
- Reshma J Nevagi
- Department of Pharmaceutical Chemistry, SMBT College of Pharmacy, Nandi Hills, Dhamangaon, Igatpuri, Nashik 422403, Maharashtra, India
| | - Santosh N Dighe
- Department of Chemistry, Sir Parshurambhau College, Pune 30, Maharashtra, India
| | - Satish N Dighe
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy, Vadgaon (BK), Pune, Maharashtra, India.
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24
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Sidhu PS, Zhou Q, Desai UR. A simple, general approach of allosteric coagulation enzyme inhibition through monosulfated hydrophobic scaffolds. Bioorg Med Chem Lett 2014; 24:5716-5720. [PMID: 25453807 DOI: 10.1016/j.bmcl.2014.10.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
Allosteric inhibition of coagulation enzymes offers the advantage of controlled inhibition. In this study, a small library of mono sulfated indole and benzothiazole based molecules was synthesized and screened against the panel of coagulation proteases. The results reveal that selected molecules inhibit the thrombin, factor Xa and factor XIa with moderate potency. Compound 6a was found to have an allosteric mode of inhibition against thrombin. Plasma clotting assays suggest that selected inhibitors 14b, 14c and 14d prolong both prothrombin and activated partial thromboplastin time. Overall, this work presents the newer class of allosteric inhibitors of thrombin and factor XIa with improved aqueous solubility profile.
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Affiliation(s)
- Preetpal Singh Sidhu
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, United States; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, United States.
| | - Qibing Zhou
- Institute for Materia Medica, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hunan 430074, PR China
| | - Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, United States; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, United States
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25
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Shi ZH, Li NG, Tang YP, Duan JA. Prolinamide derivatives as thrombin inhibitors for the treatment of thrombin-mediated diseases: a patent evaluation of US2013296245. Expert Opin Ther Pat 2014; 24:1139-48. [PMID: 25231888 DOI: 10.1517/13543776.2014.959493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Thrombotic disorders can lead to deep vein thrombosis, myocardial infarction and stroke. Thrombin plays a vital role in cascade reaction of blood coagulation, inhibition of the activity of thrombin can block the formation of thrombus and direct thrombin inhibitor has a prospect to overcome the limitations in application of the traditional anticoagulant drugs. AREAS COVERED The current patent US2013296245 describes a series of prolinamide derivatives with formula (I) as thrombin inhibitors. These new compounds are defined to be pharmaceutically acceptable salts derived from pharmaceutically acceptable inorganic acid and organic acid, and pharmaceutically acceptable prodrug where N-alkoxycarbonyl is protected or carboxylic acid is protected by ester. EXPERT OPINION The patent used formamidine and its N-alkoxycarbonyl-protected derivatives as the P1 group; these groups were less basic compared with the traditional guanidine group, so their lipophilicity could be optimized to achieve oral absorption. Furthermore, these pharmaceutically acceptable prodrugs where N-alkoxycarbonyl is protected or carboxylic acid is protected by ester could achieve prolonged half-life for a convenient once- or twice-daily oral dosing. These efforts gave a new hope and confidence to treat thrombotic disorders with selective and orally active thrombin inhibitors.
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Affiliation(s)
- Zhi-Hao Shi
- Nanjing University of Chinese Medicine, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine , 138 Xianlin Road, Nanjing 210023, Jiangsu , PR China +86 25 85811916 ; +86 25 85811916 ; ,
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26
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Substantial non-electrostatic forces are needed to induce allosteric disruption of thrombin's active site through exosite 2. Biochem Biophys Res Commun 2014; 452:813-6. [PMID: 25201728 DOI: 10.1016/j.bbrc.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 09/01/2014] [Indexed: 11/20/2022]
Abstract
Sulfated β-O4 lignin (SbO4L), a non-saccharide glycosaminoglycan mimetic, was recently disclosed as a novel exosite 2-directed thrombin inhibitor with the capability of mimicking sulfated tyrosine sequences of glycoprotein Ibα resulting in dual anticoagulant and antiplatelet activities. SbO4L engages essentially the same residues of exosite 2 as heparin and yet induces allosteric inhibition. Fluorescence spectroscopic studies indicate that SbO4L reduces access of the active site to molecular probes and affinity studies at varying salt concentrations show nearly 6 ionic interactions, similar to heparin, but much higher non-ionic contribution. The results suggest that subtle increase in non-electrostatic forces arising from SbO4L's aromatic scaffold appear to be critical for inducing allosteric dysfunction of thrombin's active site.
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27
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Al-Horani RA, Desai UR. Designing allosteric inhibitors of factor XIa. Lessons from the interactions of sulfated pentagalloylglucopyranosides. J Med Chem 2014; 57:4805-18. [PMID: 24844380 PMCID: PMC4216218 DOI: 10.1021/jm500311e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
We recently introduced sulfated pentagalloylglucopyranoside
(SPGG)
as an allosteric inhibitor of factor XIa (FXIa) (Al-Horani et al., J. Med Chem.2013, 56, 867–87823316863). To better understand the SPGG–FXIa interaction,
we utilized eight SPGG variants and a range of biochemical techniques.
The results reveal that SPGG’s sulfation level moderately affected
FXIa inhibition potency and selectivity over thrombin and factor Xa.
Variation in the anomeric configuration did not affect potency. Interestingly,
zymogen factor XI bound SPGG with high affinity, suggesting its possible
use as an antidote. Acrylamide quenching experiments suggested that
SPGG induced significant conformational changes in the active site
of FXIa. Inhibition studies in the presence of heparin showed marginal
competition with highly sulfated SPGG variants but robust competition
with less sulfated variants. Resolution of energetic contributions
revealed that nonionic forces contribute nearly 87% of binding energy
suggesting a strong possibility of specific interaction. Overall,
the results indicate that SPGG may recognize more than one anion-binding,
allosteric site on FXIa. An SPGG molecule containing approximately
10 sulfate groups on positions 2 through 6 of the pentagalloylglucopyranosyl
scaffold may be the optimal FXIa inhibitor for further preclinical
studies.
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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 , 800 E. Leigh Street, Suite 212, Richmond, Virginia 23219, United States
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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
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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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29
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Mehta AY, Thakkar JN, Mohammed BM, Martin EJ, Brophy DF, Kishimoto T, Desai UR. Targeting the GPIbα binding site of thrombin to simultaneously induce dual anticoagulant and antiplatelet effects. J Med Chem 2014; 57:3030-9. [PMID: 24635452 PMCID: PMC4203406 DOI: 10.1021/jm4020026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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Exosite 2 of human thrombin contributes
to two opposing pathways, the anticoagulant pathway and the platelet
aggregation pathway. We reasoned that an exosite 2 directed allosteric
thrombin inhibitor should simultaneously induce anticoagulant and
antiplatelet effects. To assess this, we synthesized SbO4L based on
the sulfated tyrosine-containing sequence of GPIbα. SbO4L was
synthesized in three simple steps in high yield and found to be a
highly selective, direct inhibitor of thrombin. Michelis–Menten
kinetic studies indicated a noncompetitive mechanism of inhibition.
Competitive inhibition studies suggested ideal competition with heparin
and glycoprotein Ibα, as predicted. Studies with site-directed
mutants of thrombin indicated that SbO4L binds to Arg233, Lys235,
and Lys236 of exosite 2. SbO4L prevented thrombin-mediated platelet
activation and aggregation as expected on the basis of competition
with GPIbα. SbO4L presents a novel paradigm of simultaneous
dual anticoagulant and antiplatelet effects achieved through the GPIbα
binding site of thrombin.
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Affiliation(s)
- Akul Y Mehta
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23219, United States
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30
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Potent inhibition of norovirus by dipeptidyl α-hydroxyphosphonate transition state mimics. Bioorg Med Chem Lett 2013; 23:5941-4. [PMID: 24054123 DOI: 10.1016/j.bmcl.2013.08.073] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/12/2013] [Accepted: 08/15/2013] [Indexed: 12/16/2022]
Abstract
The design, synthesis, and evaluation of a series of dipeptidyl α-hydroxyphosphonates is reported. The synthesized compounds displayed high anti-norovirus activity in a cell-based replicon system, as well as high enzyme selectivity.
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31
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Sidhu PS, Abdel Aziz MH, Sarkar A, Mehta AY, Zhou Q, Desai UR. Designing allosteric regulators of thrombin. Exosite 2 features multiple subsites that can be targeted by sulfated small molecules for inducing inhibition. J Med Chem 2013; 56:5059-70. [PMID: 23718540 DOI: 10.1021/jm400369q] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We recently designed a group of novel exosite-2-directed sulfated, small, allosteric inhibitors of thrombin. To develop more potent inhibitors, monosulfated benzofuran tri- and tetrameric homologues of the parent designed dimers were synthesized in seven to eight steps and found to exhibit a wide range of potencies. Among these, trimer 9a was found to be nearly 10-fold more potent than the first generation molecules. Michaelis-Menten studies indicated an allosteric mechanism of inhibition. Competitive studies using a hirudin peptide (exosite 1 ligand) and unfractionated heparin, heparin octasaccharide, and γ'-fibrinogen peptide (exosite 2 ligands) demonstrated exosite 2 recognition in a manner different from that of the parent dimers. Alanine scanning mutagenesis of 12 Arg/Lys residues of exosite 2 revealed a defect in 9a potency for Arg233Ala thrombin only confirming the major difference in site of recognition between the two structurally related sulfated benzofurans. The results suggest that multiple avenues are available within exosite 2 for inducing thrombin inhibition.
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Affiliation(s)
- Preetpal Singh Sidhu
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23219, USA
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32
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33
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Arcadi A, Blesi F, Cacchi S, Fabrizi G, Goggiamani A, Marinelli F. Palladium-Catalyzed Cascade Reactions of 1-(3-Arylprop-2-ynyloxy)-2-bromo Benzene Derivatives with Organoboron Compounds. J Org Chem 2013; 78:4490-8. [DOI: 10.1021/jo400503f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Antonio Arcadi
- Dipartimento di Scienze Fisiche
e Chimiche, Università di L’Aquila, Via Vetoio, 67010, Coppito (AQ), Italy
| | - Federico Blesi
- Dipartimento di Scienze Fisiche
e Chimiche, Università di L’Aquila, Via Vetoio, 67010, Coppito (AQ), Italy
| | - Sandro Cacchi
- Dipartimento di Chimica e Tecnologie del Farmaco,
Sapienza, Università di Roma, P.le
A. Moro 5, 00185, Rome, Italy
| | - Giancarlo Fabrizi
- Dipartimento di Chimica e Tecnologie del Farmaco,
Sapienza, Università di Roma, P.le
A. Moro 5, 00185, Rome, Italy
| | - Antonella Goggiamani
- Dipartimento di Chimica e Tecnologie del Farmaco,
Sapienza, Università di Roma, P.le
A. Moro 5, 00185, Rome, Italy
| | - Fabio Marinelli
- Dipartimento di Scienze Fisiche
e Chimiche, Università di L’Aquila, Via Vetoio, 67010, Coppito (AQ), Italy
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34
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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: 64] [Impact Index Per Article: 5.8] [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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35
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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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36
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Malovichko MV, Sabo TM, Maurer MC. Ligand binding to anion-binding exosites regulates conformational properties of thrombin. J Biol Chem 2013; 288:8667-8678. [PMID: 23378535 DOI: 10.1074/jbc.m112.410829] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thrombin participates in coagulation, anticoagulation, and initiation of platelet activation. To fulfill its diverse roles and maintain hemostasis, this serine protease is regulated via the extended active site region and anion-binding exosites (ABEs) I and II. For the current project, amide proton hydrogen-deuterium exchange coupled with MALDI-TOF mass spectrometry was used to characterize ligand binding to individual exosites and to investigate the presence of exosite-active site and exosite-exosite interactions. PAR3(44-56) and PAR1(49-62) were observed to bind to thrombin ABE I and then to exhibit long range effects over to ABE II. By contrast, Hirudin(54-65) focused more on ABE I and did not transmit influences over to ABE II. Although these three ligands were each directed to ABE I, they did not promote the same conformational consequences. D-Phe-Pro-Arg-chloromethyl ketone inhibition at the thrombin active site led to further local and long range consequences to thrombin-ABE I ligand complexes with the autolysis loop often most affected. When Hirudin(54-65) was bound to ABE I, it was still possible to bind GpIbα(269-286) or fibrinogen γ'(410-427) to ABE II. Each ligand exerted its predominant influences on thrombin and also allowed interexosite communication. The results obtained support the proposal that thrombin is a highly dynamic protein. The transmission of ligand-specific local and long range conformational events is proposed to help regulate this multifunctional enzyme.
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Affiliation(s)
| | - T Michael Sabo
- Chemistry Department, University of Louisville, Louisville, Kentucky 40292
| | - Muriel C Maurer
- Chemistry Department, University of Louisville, Louisville, Kentucky 40292.
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37
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Arcadi A, Blesi F, Cacchi S, Fabrizi G, Goggiamani A, Marinelli F. Multisubstituted benzo[b]furans through a copper- and/or palladium-catalyzed assembly and functionalization process. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.12.058] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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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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39
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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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40
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Sadler S, Moeller AR, Jones GB. Microwave and continuous flow technologies in drug discovery. Expert Opin Drug Discov 2012; 7:1107-28. [DOI: 10.1517/17460441.2012.727393] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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41
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Abdel Aziz MH, Sidhu PS, Liang A, Kim JY, Mosier PD, Zhou Q, Farrell DH, Desai UR. Designing allosteric regulators of thrombin. Monosulfated benzofuran dimers selectively interact with Arg173 of exosite 2 to induce inhibition. J Med Chem 2012; 55:6888-97. [PMID: 22788964 DOI: 10.1021/jm300670q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Earlier, we reported on the design of sulfated benzofuran dimers (SBDs) as allosteric inhibitors of thrombin (Sidhu et al. J. Med. Chem.201154 5522-5531). To identify the site of binding of SBDs, we studied thrombin inhibition in the presence of exosite 1 and 2 ligands. Whereas hirudin peptide and heparin octasaccharide did not affect the IC(50) of thrombin inhibition by a high affinity SBD, the presence of full-length heparin reduced inhibition potency by 4-fold. The presence of γ' fibrinogen peptide, which recognizes Arg93, Arg97, Arg173, Arg175, and other residues, resulted in a loss of affinity that correlated with the ideal Dixon-Webb competitive profile. Replacement of several arginines and lysines of exosite 2 with alanine did not affect thrombin inhibition potency, except for Arg173, which displayed a 22-fold reduction in IC(50). Docking studies suggested a hydrophobic patch around Arg173 as a plausible site of SBD binding to thrombin. The absence of the Arg173-like residue in factor Xa supported the observed selectivity of inhibition by SBDs. Cellular toxicity studies indicated that SBDs are essentially nontoxic to cells at concentrations as high as 250 mg/kg. Overall, the work presents the localization of the SBD binding site, which could lead to allosteric modulators of thrombin that are completely different from all clinically used anticoagulants.
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Affiliation(s)
- May H Abdel Aziz
- Department of Medicinal Chemistry and ‡Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23219, United States
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42
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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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43
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Allosteric activation of human α-thrombin through exosite 2 by suramin analogs. Arch Biochem Biophys 2012; 520:36-41. [DOI: 10.1016/j.abb.2012.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 11/22/2022]
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44
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Girnys EA, Porter VR, Mosberg HI. Conformationally restricted analogs of the direct thrombin inhibitor FM 19. Bioorg Med Chem 2011; 19:7425-34. [DOI: 10.1016/j.bmc.2011.10.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/07/2011] [Accepted: 10/15/2011] [Indexed: 11/15/2022]
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