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Shannon Hogan

Bio: Shannon Hogan is an academic researcher. The author has contributed to research in topics: Phage display & Complementarity determining region. The author has an hindex of 6, co-authored 10 publications receiving 846 citations.

Papers
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Journal ArticleDOI
TL;DR: The construction of human Fab libraries having a unique combination of immunoglobulin sequences captured from human donors and synthetic diversity in key antigen contact sites in heavy-chain complementarity-determining regions 1 and 2 are reported.
Abstract: Combinatorial libraries of rearranged hypervariable V(H) and V(L) sequences from nonimmunized human donors contain antigen specificities, including anti-self reactivities, created by random pairing of V(H)s and V(L)s. Somatic hypermutation of immunoglobulin genes, however, is critical in the generation of high-affinity antibodies in vivo and occurs only after immunization. Thus, in combinatorial phage display libraries from nonimmunized donors, high-affinity antibodies are rarely found. Lengthy in vitro affinity maturation is often needed to improve antibodies from such libraries. We report the construction of human Fab libraries having a unique combination of immunoglobulin sequences captured from human donors and synthetic diversity in key antigen contact sites in heavy-chain complementarity-determining regions 1 and 2. The success of this strategy is demonstrated by identifying many monovalent Fabs against multiple therapeutic targets that show higher affinities than approved therapeutic antibodies. This very often circumvents the need for affinity maturation, accelerating discovery of antibody drug candidates.

361 citations

Journal ArticleDOI
TL;DR: In this paper, the authors used a highly selective fully human MMP-14 inhibitory antibody discovered using phage display technology, which blocked proMMP-2 processing on tumor and endothelial cells, inhibited angiogenesis, and slowed tumor progression and formation of metastatic lesions.
Abstract: Inhibition of specific matrix metalloproteinases (MMP) is an attractive noncytotoxic approach to cancer therapy. MMP-14, a membrane-bound zinc endopeptidase, has been proposed to play a central role in tumor growth, invasion, and neovascularization. Besides cleaving matrix proteins, MMP-14 activates proMMP-2 leading to an amplification of pericellular proteolytic activity. To examine the contribution of MMP-14 to tumor growth and angiogenesis, we used DX-2400, a highly selective fully human MMP-14 inhibitory antibody discovered using phage display technology. DX-2400 blocked proMMP-2 processing on tumor and endothelial cells, inhibited angiogenesis, and slowed tumor progression and formation of metastatic lesions. The combination of potency, selectivity, and robust in vivo activity shows the potential of a selective MMP-14 inhibitor for the treatment of solid tumors.

325 citations

Journal ArticleDOI
TL;DR: A method was developed to rapidly identify high-affinity human antibodies from phage display library selection outputs by combining high-throughput Fab fragment expression and purification with surface plasmon resonance (SPR) microarrays to determine kinetic constants for 96 different Fab fragments in a single experiment.

137 citations

Patent
06 Dec 2002
TL;DR: In this paper, a flow chamber is configured such that a first magnetic field can be selectively applied in the flow chamber, and a flow of fluid can also be applied to the chamber in coordination with the selective application of the magnetic field.
Abstract: The invention features apparati and methods for washing magnetically responsive particles such as paramagnetic beads. One exemplary apparatus includes a flow chamber having an inlet and an outlet; and at least a first magnetic field inducer. The apparatus is configured such that a first magnetic field can be selectively applied in the flow chamber. The apparatus can also apply a flow of fluid to the chamber in coordination with the selective application of the magnetic field.

40 citations

Patent
19 Feb 2004
TL;DR: In this article, the authors describe proteins that bind to PAPP-A, an 1547 amino acid glycoprotein which can form an ~200 kDa monomer or an ~400 kDa dimer.
Abstract: The invention provides, inter alia, proteins that bind to PAPP-A, an 1547 amino acid glycoprotein which can form an ~200 kDa monomer or an ~400 kDa dimer. In one form, the proteins are antibodies. In one embodiment, the proteins can inhibit the ability of PAPP-A to interact (e.g., cleave) substrates such as IGFBP-4, IGFBP-5, and IGFBP-2.

18 citations


Cited by
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Journal ArticleDOI
TL;DR: This minireview critically evaluates the role of MMPs in relation to cancer progression, and highlights the challenges, as well as future prospects, for the design, development and efficacy of M MPIs.
Abstract: Matrix metalloproteinases (MMPs) consist of a multigene family of zinc-dependent extracellular matrix (ECM) remodeling endopeptidases implicated in pathological processes, such as carcinogenesis. In this regard, their activity plays a pivotal role in tumor growth and the multistep processes of invasion and metastasis, including proteolytic degradation of ECM, alteration of the cell-cell and cell-ECM interactions, migration and angiogenesis. The underlying premise of the current minireview is that MMPs are able to proteolytically process substrates in the extracellular milieu and, in so doing, promote tumor progression. However, certain members of the MMP family exert contradicting roles at different stages during cancer progression, depending among other factors on the tumor stage, tumor site, enzyme localization and substrate profile. MMPs are therefore amenable to therapeutic intervention by synthetic and natural inhibitors, providing perspectives for future studies. Multiple therapeutic agents, called matrix metalloproteinase inhibitors (MMPIs) have been developed to target MMPs, attempting to control their enzymatic activity. Even though clinical trials with these compounds do not show the expected results in most cases, the field of MMPIs is ongoing. This minireview critically evaluates the role of MMPs in relation to cancer progression, and highlights the challenges, as well as future prospects, for the design, development and efficacy of MMPIs.

1,373 citations

Journal ArticleDOI
TL;DR: In this paper, the authors summarize lessons learned from preclinical and clinical studies over the past decade and propose strategies for improving antiangiogenic therapy outcomes for malignant and nonmalignant diseases.

1,093 citations

Journal ArticleDOI
Hennie R. Hoogenboom1
TL;DR: The first antibody of this new generation, adalimumab (Humira, a human IgG1 specific for human tumor necrosis factor (TNF)), already approved for therapy and with many more in clinical trials, these recombinant antibody technologies will provide a solid basis for the discovery of antibody-based biopharmaceuticals, diagnostics and research reagents for decades to come.
Abstract: During the past decade several display methods and other library screening techniques have been developed for isolating monoclonal antibodies (mAbs) from large collections of recombinant antibody fragments. These technologies are now widely exploited to build human antibodies with high affinity and specificity. Clever antibody library designs and selection concepts are now able to identify mAb leads with virtually any specificity. Innovative strategies enable directed evolution of binding sites with ultra-high affinity, high stability and increased potency, sometimes to a level that cannot be achieved by immunization. Automation of the technology is making it possible to identify hundreds of different antibody leads to a single therapeutic target. With the first antibody of this new generation, adalimumab (Humira, a human IgG1 specific for human tumor necrosis factor (TNF)), already approved for therapy and with many more in clinical trials, these recombinant antibody technologies will provide a solid basis for the discovery of antibody-based biopharmaceuticals, diagnostics and research reagents for decades to come.

1,057 citations

Journal ArticleDOI
TL;DR: The recent advances made in understanding the role of MMPs in inflammatory diseases and the therapeutic potential of M Parliamentary metalloproteinases inhibition in those conditions are discussed.
Abstract: Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that form a family of 24 members in mammals. Evidence of the pathological roles of MMPs in various diseases, combined with their druggability, has made them attractive therapeutic targets. Initial drug discovery efforts focused on the roles of MMPs in cancer progression, and more than 50 MMP inhibitors have been investigated in clinical trials in various cancers. However, all of these trials failed. Reasons for failure include the lack of inhibitor specificity and insufficient knowledge about the complexity of the disease biology. MMPs are also known to be involved in several inflammatory processes, and there are new therapeutic opportunities for MMP inhibitors to treat such diseases. In this Review, we discuss the recent advances made in understanding the role of MMPs in inflammatory diseases and the therapeutic potential of MMP inhibition in those conditions.

626 citations

Journal ArticleDOI
TL;DR: This review focuses on recent advances in deciphering the kinetic pathway of protein complex formation, the nature of the pre-complex formed through diffusion, the transition state, and other intermediates (such as the so-called encounter complex) along the association pathway.
Abstract: The structure of a protein complex, together with information about its affinity and other thermodynamic characteristics, provide a “frozen” view of the complex. This picture ignores the kinetic nature of protein-protein association and dissociation, which are of major biological and biophysical interest. This review focuses on recent advances in deciphering the kinetic pathway of protein complex formation, the nature of the pre-complex formed through diffusion (which we have termed the “transient complex”1), the transition state, and other intermediates (such as the so-called encounter complex) along the association pathway. Protein-protein association is at the center of diverse biological processes ranging from enzyme catalysis/inhibition to regulation of immune response by cytokines. The association rates often play a critical role in such processes, as in situations where speed is of essence.2 For example, the purple cone snail and other venomous animals capture prey with remarkable efficiency and speed by releasing toxins that rapidly bind to ion channels;3 the green mamba achieves a similar feat by targeting acetylcholinesterase (AChE), an enzyme essential for the integrity of neural transmission.4 Bacteria such as Escherichia coli and Bacillus amyloliquefaciens excrete nucleases as weapons against competitors or predators. Defense of the producing cells from damage to their own DNA or RNA by such nucleases requires rapid association with cognate inhibitors.5,6 Indeed, in the last example rapid association is such a priority that the inhibitor barstar has a cluster of acidic residues that facilitate association with the nuclease barnase, even though the clustered charges reduce folding stability.7 In the ruminant gut, RNase A is required for degrading accumulated RNA; potential toxicity of leaked nuclease is prevented by rapid association with a ribonuclease inhibitor.8,9 Reorganization of the actin cytoskeleton provides yet another illustration of the importance of rapid protein association. Reorganization is attained through actin polymerization, which is nucleated by the Arp2/3 complex. The latter is activated by the Wiskott-Aldrich Syndrome protein (WASp), which in turn is released from the auto-inhibited state by the Rho GTPase Cdc42.10 As actin polymerization is initiated with a nucleation process, the speed of upstream signaling has a critical impact on the rate of polymer formation. It is thus not surprising that high association rate constants have been observed between partners along the signaling pathway.11,12 The high association rate constant between Cdc42 and WASp has been found to be essential for the latter to stimulate actin polymerization, as another Rho GTPase sharing 70% sequence identity, TC10, with an identical dissociation rate constant but a 1000-fold lower association rate constant, failed to stimulate actin polymerization.11 The failure to stimulate actin polymerization in patients carrying mutant WAS genes is the root cause of the Wiskott-Aldrich Syndrome. Several other compelling arguments can be made for the biological roles of rapid protein association.13 (a) Fast association may enhance binding affinity. High affinity can also be achieved through slow dissociation; however, for proteins involved in signaling, slow dissociation is not an option, since it implies a long-lasting bound state, which effectively corresponds to a permanent off- or on-switch. A good example for this is the binding of Ras to its natural affector Raf. This protein dissociates within a fraction of a second, but maintains an affinity in the nM range through fast association. Moreover, the difference between the natural effector, Raf, and the non-natural effector, Ral, lies in their rates of association with Ras.14 Therefore, even if not for a direct reason (such as in stimulation of actin polymerization), the affinity requirement alone may call for fast association. (b) Enzyme-substrate binding is a determining factor for the overall turnover rate and becomes the rate-limiting step for catalytically “perfect” enzymes. Substrate-binding rate constants of such enzymes reach 108 M−1s−1 and beyond, as found for the ribotoxin restrictocin and RNase A.15,16 (c) When several proteins compete for the same receptor or when one protein is faced with alternative pathways, kinetic control, not thermodynamic control, dominates in many cases; this is especially true when dissociation is slow. For example, during protein synthesis cognate and noncognate aminoacyl-tRNA synthetases can potentially compete for the same tRNA. As an additional example, consider newly synthesized proteins, which potentially face aggregation if not isolated by a chaperone. From the point of view of kinetic control, it is easy to see why rapid binding of denatured proteins to the chaperonin GroEL has been observed.17 (d) Differences in binding rate between related proteins may serve as an additional mechanism for specificity, as can be suggested for Rho GTPases Cdc42 and TC10 and for Ras effectors Raf and Ral. The examples and arguments presented above suggest that rapid binding is as important as high affinity in the proper functioning of proteins. It is now increasingly recognized that proteins function in the context of multi-component complexes. Manipulating association rate constants of various components presents unique opportunities for the control of protein functions. Many interactions between proteins are also targeted for drug development; in designing such drugs, both high affinity and rapid binding should be taken into consideration. 1.1. Overview of Protein Association Kinetics The observed rate constants of protein association span a wide range, from 109 M−1s−1 (Figure 1). In comprehending these values, a basic fact is that, for two proteins to recognize each other, their interfaces have to be oriented with high specificity. A relative rotation of as little as a few degrees or a relative translation by a few Angstroms is sufficient to break all specific interactions between the two proteins.18 The rate of association of a protein complex is limited by diffusion and geometric constraints of the binding sites, and may be further reduced by subsequent chemical processes.19 Open in a separate window Figure 1 The wide spectrum of association rate constants. The red vertical line marks the start of the diffusion-controlled regime. The shaded range marks the absence of long-range forces. Adapted with permission from Ref. 1. Copyright 2008 Wiley Interscience..

611 citations