Fisayo A. Olotu

From mutational inactivation to aberrant gain-of-function: unraveling the structural basis of mutant p53 oncogenic transition†

Various evidence has revealed that mutations in p53 exert activities that go beyond simply inactivation of wildtype functions but rather elicits downstream interactions that promote malignancy described as mutant p53 gain‐of‐function (GOF). Here we report the first account of the dynamics of mutation‐induced structural transition of native p53 to an aberrant gain‐of‐function state, studying the wildtype (WT) and high incidence contact (R273C) and structural (R175H) mutant p53 (mutp53) through molecular dynamics simulation. Result analysis revealed that both mutants exhibited structural distortion and reduced flexibility, indicative of rigidity and kinetic stability. In addition, surface analysis revealed an increase in the accessible surface area in the p53 mutants. This suggests that the GOF transition involves protein unfolding and exposure of buried hydrophobic surface essential for interaction with HSF‐1 oncogenic partner and wildtype p63, and p73 homologs. Further validation revealed binding cavities, similar in the mutants but dissimilar to the WT. Taken together, this study complements experimental findings and reveals the interplay between mutation‐induced structural distortion, loss of flexibility, rigidity, enhanced stability, protein unfolding and ultimately, exposure of binding surfaces as conformational attributes that characterize mutP53 structure‐GOF activities. This insight is, therefore, of great importance as it opens up a novel therapeutic approach toward the structure based targeting of mutP53 oncogenic involvement beyond wildtype inactivation. Furthermore, “exposed” binding site information obtained from this study can be explored for structure‐based design of substances best described as “destabilizers” to disrupt the GOF interaction of mutp53.

Dynamics of allosteric modulation of lymphocyte function associated antigen-1 closure-open switch: unveiling the structural mechanisms associated with outside-in signaling activation

ObjectivesTo provide insight into the dynamics of the shape-shifting mechanistic events associated with the opening (activation) of Lymphocyte Function Associated Antigen-1 upon allosteric modulation by an activator, ICAM Binding Enhancer-667 (IBE-667), using molecular dynamics simulation.ResultsVarious parameters were used to appropriately describe and understand the sequence of events that characterized its activation across the simulation period such as residual distances, TriCα angles; as well as the dihedral angle. Our findings revealed a significant residual fluctuation and stability difference between both systems. Also, there was a synergistic coordination of the active MIDAS site by the downward pull of the α7 helix upon ligand binding, which appeared to be directly proportional to each other.ConclusionAllosteric binding of IBE-667, activated LFA-1 integrin as evidenced by residual motion at the MIDAS region which appears to be synergistically coordinated by the downward pull of the α7 helix.

Allosteric inhibition abrogates dysregulated LFA-1 activation: Structural insight into mechanisms of diminished immunologic disease

Lymphocyte Function Associated antigen-1(LFA-1) has been implicated severely in the pathophysiology of inflammatory and autoimmune diseases. Its active and inactive conformations correlate with its diseased and non-diseased state respectively. This is determined by its degree of affinity for its intrinsic ligand (ICAM) at the active site and accompanying synergistic coordination at the α7 helix. This potentiates the role of inhibitors in disrupting this interaction allosterically. Herein, we present a first account of the structural dynamics which characterizes the inhibitory effect of a novel LFA-1 antagonist, Lifitegrast (SAR1118), upon binding to the I-domain allosteric site (IDAS) using molecular dynamics simulation. Findings from this study revealed that the inhibitor stabilized the closed conformation and reversed the open conformation to a low ICAM-affinity state (closed) as evidenced by the upward movement of the α7 helix and corresponding transitions at the active site. This in both cases favors the formation of the non-disease inactive form. Upon allosteric modulation, the inhibitor significantly restored protein stability, enhanced compactness and decreased residual fluctuation as crucial to its potency in the amelioration of immunological and inflammatory diseases which agrees with experimental studies. These findings could therefore serve as the basis for the exploration of the allosteric domain and its active site affinity modulation to aid the design of more specific and selective inhibitors.

Alcohol Metabolic Inefficiency: Structural Characterization of Polymorphism-Induced ALDH2 Dysfunctionality and Allosteric Site Identification for Design of Potential Wildtype Reactivators

Liver mitochondrial aldehyde dehydrogenase 2 (ALDH2) enzyme is responsible for the rapid conversion of acetaldehyde to acetic acid. ALDH2 (E487K) polymorphism results in an inactive allele (ALDH2*2) which cause dysfunctional acetaldehyde metabolism. The 3D structure of an enzyme is crucial to its functionality and a disruption in its structural integrity could result in its metabolic inefficiency and dysfunctionality. Allosteric targeting of polymorphs could facilitate the restoration of wildtype functionalities in ALDH2 polymorphs and serve as an advancement in the treatment of associated diseases. Therefore, structural insights into ALDH2*2 polymorph could reveal the varying degree of alterations which occur at its critical domains and accounts for enzymatic dysfunctionality. In this study, we report the structural characterization of ALDH2*2 polymorph and its critical domains using computational tools. Our findings revealed that the polymorph exhibited significant alterations in stability and flexibility at the catalytic and co-enzyme-binding domain. Moreover, there was an increase in the solvent-exposed surface residues and this indicates structural perturbations. Analysis of the interaction network at ALDH2*2 catalytic domain revealed residual displacement and interaction loss when compared to the wildtype thereby providing insight into the catalytic inefficiency of the polymorph. Interestingly, perturbations induced by ALDH2 polymorphism involves the re-orientation of surface residues, which resulted in the formation of surface exposed pockets. These identified pockets could be potential sites for allosteric targeting. The findings from this study will aid the design of novel site-specific small molecule reactivators with the propensity of restoring wildtype activities for treatment of polymorphic ALDH2 related diseases.

Covalent Inhibition in Drug Discovery: Filling the Void in Literature

The serendipitous discovery of covalent inhibitors and their characteristic potency of inducing irreversible and complete inhibition in therapeutic targets have caused a paradigm shift from the use of non-covalent drugs in disease treatment. This has caused a significant evolution in the field of covalent targeting to understand their inhibitory mechanisms and facilitate the systemic design of novel covalent modifiers for undruggable targets. Computational techniques have evolved over the years and have significantly contributed to the process of drug discovery by mirroring the pattern of biological occurrences thereby providing insights into the dynamics and conformational transitions associated with biomolecular interactions. Moreover, our previous contributions towards the systematic design of selective covalent modifiers have revealed the various setbacks associated with the use of these conventional techniques in the study of covalent systems, hence there is a need for distinct approaches. In this review, we highlight the modifications and development of computational techniques suitable for covalent systems, their lapses, shortcomings and recent advancements.

Across the blood-brain barrier: Neurotherapeutic screening and characterization of naringenin as a novel CRMP-2 inhibitor in the treatment of Alzheimer's disease using bioinformatics and computational tools

The discovery and developmental processes of CNS drugs have been limited by the inability of potential drug molecules to pass through the blood-brain barrier (BBB). This presents a significant setback in the treatment of neurodegenerative disorders such as Alzheimers disease (AD), hence the need for compounds that can adhere strictly to the selective criteria of suitable CNS drugs. Collapsin response mediator protein-2 (CRMP-2) has been recently identified as a viable target in neurotherapeutics due to its involvement in the etiology of AD. As shown in previous studies, Naringenin (NAR), a small molecule derivative of Drynaria rhizome (DR) extract, specifically binds CRMP-2 and reduces its phosphorylation. This was shown to facilitate axonal regrowth, with improvement in cognition and learning. Herein, we report the first account of the use of cheminformatics techniques to define the CNS drug-suitability of NAR using selective criteria, coupled with the prediction of possible biological activities and toxicities. Also, we evaluated the mechanistic activity of NAR by modeling its molecular interaction with human CRMP-2 (hCRMP-2). Physicochemical analyses revealed the suitability of NAR as a CNS drug and its ability to transverse the BBB. Possible neurogenic, anti-carcinogenic and cardioprotective activities were also predicted. NAR exhibited favorable binding to CRMP-2 and formed strong bonds with active site residues, which accounts for its stabilization and affinity. Moreover, NAR induced notable conformational changes in CRMP-2, an occurrence that could possibly disrupt kinase-mediated phosphorylation. These findings will aid in the optimization of NAR and improve its neurotherapeutic activities in the treatment of AD.

Dynamic perspectives into the mechanisms of mutation-induced p53-DNA binding loss and inactivation using active perturbation theory: Structural and molecular insights toward the design of potent reactivators in cancer therapy: OLOTU and SOLIMAN

The DNA‐binding ability of p53 represents the crux of its tumor suppressive activities, which involves transcriptional activation of target genes responsible for apoptosis and cell‐cycle arrest. Mutational occurrences within or in close proximity to the DNA‐binding surface of p53 have accounted for the loss of direct DNA‐binding ability and inactivation implicated in many cases of cancer. Moreover, the design of therapeutic compounds that can restore DNA‐binding ability in p53 mutants has been identified as a way forward in curtailing their oncogenic activities. However, there is still the need for more insights into evaluate the perturbations that occur at the DNA‐binding interface of mp53 relative to DNA‐binding loss, inactivation, and design of potent reactivators, hence the purpose of this study. Therefore, we evaluated p53‐structural (R175H) and contact (R273C) mutational effects using tunnel perturbation analysis and other computational tools. We identified significant perturbations in the active tunnels of p53, which resulted in altered geometry and loss, unlike in the wild‐type p53. This corroborated with structural, DNA‐binding, and interaction network analysis, which showed that loss of flexibility, repulsion of DNA‐interactive residues, and instability occurred at the binding interface of both mutants. Also, these mutations altered bonding interactions and network topology at the DNA‐binding interface, resulting in the reduction of p53‐DNA binding proximity and affinity. Therefore, these findings would aid the structure‐based design of novel chemical entities capable of restoring p53‐DNA binding and activation.

Solving the riddle: Unraveling the mechanisms of blocking the binding of leukotoxin by therapeutic antagonists in periodontal diseases: ABDULLAHI et al.

Aggregatibacter actinomycetemcomitans is a Gram‐negative bacteria that has gained wide recognition for its causative role in the development of various immune diseases, which includes localized aggressive periodontitis. Its ability to evade host defense mechanisms is mediated by the secretion of leukotoxin (LtxA), which induces death of white blood cells (leukocytes) by specific binding to their surface‐expressed leukocyte function–associated receptor (LFA‐1) in its active state. Therapeutic compounds that interfere with this pathogenic process and abrogate A. actinomycetemcomitans virulence have been reported in literature. These include doxycycline, and more recently phytochemical compounds such as hamamelitanin, resveratrol, naringin, and quercetin. However, the question remains how do they work? Therefore, with the aid of computational tools, we explore the molecular mechanisms by which they possibly elicit their therapeutic functions. Molecular mechanics Poisson/Boltzmann surface area analyses revealed that these compounds bind favorably to active LFA‐1 with high affinity and considerable stability, indicative of their ability to occupy the LtxA binding site (LBS) and prevent LtxA binding. The conformational transition of open LFA‐1 to its closed state further describe the mechanistic activity of these compounds. In addition to notable reductions in structural mobility and flexibility, the burial of surface‐exposed interactive side chains at the LBS was observed, an occurrence that could alter the complementary binding of LtxA. It is also important to mention that these occurrences were induced more prominently by the phytochemicals. We believe that these findings will enhance the scope of drug design and discovery for potent LtxA antagonists with improved activities and therapeutic efficacies in the treatment of virulent A. actinomycetemcomitans diseases.

Covalent simulations of covalent/irreversible enzyme inhibition in drug discovery: a reliable technical protocol

AIMnIrreversible covalent inhibition of biological targets in disease pathogenesis is an emerging field in drug design. Computational techniques have assumed a critical role in understanding covalent enzyme inhibition. However, a gap currently exists with regards to the reliability and reproducibility of currently available protocols available in literature and open scientific forums.nnnMETHODOLOGY/RESULTSnAppropriate ligand and protein target are selected, docked covalently or noncovalently using respective docking tools. Both components are subjected to premolecular dynamic preparations. This was followed by parameterization of the ligand, protein and covalent complex, respectively. The production runs were initiated and the resulting trajectories are saved and analyzed.nnnCONCLUSIONnThis protocol is reliable and reproducible, hence would advance the development of irreversible covalent inhibitors toward disease treatment.

An update on the discovery and development of selective heat shock protein inhibitors as anti-cancer therapy

ABSTRACT Introduction: Over the years, not a single HSP inhibitor has progressed into the post-market phase of drug development despite the success recorded in various pre-clinical and clinical studies. The inability of existing drugs to specifically target oncogenic HSPs has majorly accounted for these setbacks. Recent combinatorial strategies that incorporated computer-aided drug design (CADD) techniques are geared towards the development of highly specific HSP inhibitors with increased activities and minimal toxicities. Areas covered: In this review, strategic therapeutic approaches that have recently aided the development of selective HSP inhibitors were highlighted. Also, the significant contributions of CADD techniques over the years were discussed in detail. This article further describes promising computational paradigms and their applications towards the discovery of highly specific inhibitors of oncogenic HSPs. Expert opinion: The recent shift towards highly selective and specific HSP inhibition has shown great promise as evidenced by the development of paralog/isoform-selective HSP drugs. It could be further augmented with computer-aided drug design strategies, which incorporate reliable methods that would greatly enhance the design and optimization of novel inhibitors with improved activities and minimal toxicities.