Global Geometrical Constraints on the Shape of Proteins and Their Influence on Allosteric Regulation

Proteins are the workhorse molecules of the cell, which are obtained by folding long chains of amino acids. Since not all shapes are obtained as a folded chain of amino acids, there should be global geometrical constraints on the shape. Moreover, since the function of a protein is largely determined by its shape, constraints on the shape should have some influence on its interaction with other proteins. In this paper, we consider global geometrical constraints on the shape of proteins. Using a mathematical toy model, in which proteins are represented as closed chains of tetrahedrons, we have identified not only global geometrical constraints on the shape of proteins, but also their influence on protein interactions. As an example, we show that a garlic-bulb like structure appears as a result of the constraints. Regarding the influence of global geometrical constraints on interactions, we consider their influence on the structural coupling of two distal sites in allosteric regulation. We then show the inseparable relationship between global geometrical constraints and protein interactions;i.e. they are different sides of the same coin. This finding could be important for the understanding of the basic mechanisms of allosteric regulation of protein functions.

Allosteric modulation of cholinergic system:Potential approach to treating cognitive deficits of schizophrenia

Schizophrenia is a psychiatric disorder affecting approximately 1% of the population worldwide and is characterised by the presence of positive and negative symptoms and cognitive deficits. Whilst current therapeutics ameliorate positive symptoms, they are largely ineffective in improving negative symptoms and cognitive deficits. The cholinergic neurotransmitter system heavily influences cognitive function and there is evidence that implicates disruption of the central cholinergic system in schizophrenia. Historically, targeting the cholinergic system has been impeded by poor selectivity leading to intolerable side effects warranting the need to develop more targeted therapeutic compounds. In this review we will summarise evidence supporting the roles of the cholinergic system, particularly the muscarinic M1 receptor, in the pathophysiology of schizophrenia and discuss the potential of a promising new class of candidate compounds, allosteric ligands, for addressing the difficulties involved in targeting this system. The body of evidence presented here highlights the dysfunction of the cholinergic system in schizophrenia and that targeting this system by taking advantage of allosteric ligands is having clinically meaningful effect on cognitive deficits.

Computational Investigation on the Allosteric Modulation of Androgen Receptor

Androgens have similar structures with different biological activities. To identify molecular determinants responsible for the activity difference, we have docked six steroidal androgens to the binding site or the surface of androgen receptor by using molecular docking with computational investigation. The energy was calculated respectively based on the QM （quantum mechanics） and MM （molecular mechanics） methods. The result shows that the allosteric modulation of androgen receptor plays an important role in the binding process between androgens and receptor. The open state receptor is less stable than the close state one, but the latter is more favorable for binding with androgens. It is worthy of note that when the androgen receptors binding or without binding with androgen are in close state, they are difficult to return to their open state. This phenomenon is an exception of the well known two-state model theory in which the two states are reversible. Whether the internal of close state androgen receptor has a combination of androgen or not, the androgen receptor surface can be combined with another androgen, and their surface binding energies could be very close. The result is consistent with the experimental observations, but this phenomenon of continuous combination from open state is also an exception of the two-state model theory.

Allosteric Mechanism of Calmodulin Revealed by Targeted Molecular Dynamics Simulation

Calmodulin （CAM） is involved in the regulation of a variety of cellular signaling pathways. To accomplish its physiological functions, CaM binds with Ca2＋ at its EF-hand Ca2＋ binding sites which induce the conformational switching of CaM. However, the molecular mechanism by which Ca2＋ binds with CaM and induces conformational switching is still obscure. Here we combine molecular dynamics with targeted molecular dynamics simulation and achieve the state-transition pathway of CaM. Our data show that Ca2＋ binding speeds up the conformational transition of CaM by weakening the interactions which stabilize the closed state. It spends about 6.5 ns and 5.25 ns for transition from closed state to open state for apo and holo CaM, respectively. Regarding the contribution of two EF-hands, our data indicate that the first EF-hand triggers the conformational transition and is followed by the second one. We determine that there are two interaction networks which contribute to stabilize the closed and open states, respectively.

Residues important to the allosteric regulation on ligand binding affinity in β3 integrins

Integrins are heterodimers that mediate cell adhesion and transduce signals bidirectionally across the cell membrane.Integrins often exist in low affinity(or inactive) states for

Allosteric process of human glucokinase conducive to fight against diabetes

More than 200 million people worldwide have diabetes. In China alone, about 60 million people

Allosteric modulation of G protein-coupled receptors as a novel therapeutic strategy in neuropathic pain

Neuropathic pain is a debilitating pathological condition that presents significant therapeutic challenges in clinical practice.Unfortunately,current pharmacological treatments for neuropathic pain lack clinical efficacy and often lead to harmful adverse reactions.As G protein-coupled receptors(GPCRs)are widely distributed throughout the body,including the pain transmission pathway and descending inhibition pathway,the development of novel neuropathic pain treatments based on GPCRs allosteric modulation theory is gaining momentum.Extensive research has shown that allosteric modulators targeting GPCRs on the pain pathway can effectively alleviate symptoms of neuropathic pain while reducing or eliminating adverse effects.This review aims to provide a comprehensive summary of the progress made in GPCRs allosteric modulators in the treatment of neuropathic pain,and discuss the potential benefits and adverse factors of this treatment.We will also concentrate on the development of biased agonists of GPCRs,and based on important examples of biased agonist development in recent years,we will describe universal strategies for designing structure-based biased agonists.It is foreseeable that,with the continuous improvement of GPCRs allosteric modulation and biased agonist theory,effective GPCRs allosteric drugs will eventually be available for the treatment of neuropathic pain with acceptable safety.

Allosterically activating SHP2 by oleanolic acid inhibits STAT3-Th17 axis for ameliorating colitis

Src homology 2 domain-containing tyrosine phosphatase 2(SHP2)is an essential tyrosine phosphatase that is pivotal in regulating various cellular signaling pathways such as cell growth,differentiation,and survival.The activation of SHP2 has been shown to have a therapeutic effect in colitis and Parkinson's disease.Thus,the identification of SHP2 activators and a complete understanding of their mechanism is required.We used a two-step screening assay to determine a novel allosteric activator of SHP2 that stabilizes it in an open conformation.Oleanolic acid was identified as a suitable candidate.By binding to R362,K364,and K366 in the active center of the PTP domain,oleanolic acid maintained the active open state of SHP2,which facilitated the binding between SHP2 and its substrate.This oleanolic acid-activated SHP2 hindered Th17 differentiation by disturbing the interaction between STAT3 and IL-6Rαand inhibiting the activation of STAT3.Furthermore,via the activation of SHP2 and subsequent attenuation of the STAT3-Th17 axis,oleanolic acid effectively mitigated colitis in mice.This protective effect was abrogated by SHP2 knockout or administration of the SHP2 inhibitor SHP099.These findings underscore the potential of oleanolic acid as a promising therapeutic agent for treating inflammatory bowel diseases.

MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply

Isoprenoids are a very large and diverse family of metabolites required by all living organisms.All isoprenoids derive fromthe double-bond isomers isopentenyl diphosphate(IPP)and dimethylallyl diphosphate(DMAPP),which are produced by the methylerythritol 4-phosphate(MEP)pathway in bacteria and plant plastids.It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase(DXS),a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway.Here we provide experimental insights intotheunderlyingmechanism.Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro,causing a size shift.In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer.Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells.Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply,whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance(e.g.,by a blockage in their conversion to downstream isoprenoids).Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.

SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid

The SARS-CoV-2 spike protein contains a functionally important fatty acid(FA)binding site,which is also found in some other coronaviruses,e.g.SARS-CoV and MERS-CoV.The occupancy of the FA site by linoleic acid(LA)reduces infectivity by‘locking’the spike in a less infectious conformation.Here,we use dynamical-nonequilibrium molecular dynamics(D-NEMD)simulations to compare the allosteric responses of spike variants to LA removal.D-NEMD simulations show that the FA site is coupled to other functional regions of the protein,e.g.the receptor-binding motif(RBM),N-terminal domain(NTD),furin cleavage site,and regions surrounding the fusion peptide.D-NEMD simulations also identify the allosteric networks connecting the FA site to these functional regions.The comparison between the wild-type spike and four variants(Alpha,Delta,Delta plus,and Omicron BA.1)shows that the variants differ significantly in their responses to LA removal.The allosteric connections to the FA site on Alpha are generally similar to those on the wild-type protein,with the exception of the RBM and the S71–R78 region,which show a weaker link to the FA site.In contrast,Omicron is the most different variant,exhibiting significant differences in the RBM,NTD,V622–L629,and furin cleavage site.These differences in the allosteric modulation may be of functional relevance,potentially affecting transmissibility and virulence.Experimental comparison of the effects of LA on SARS-CoV-2 variants,including emerging variants,is warranted.

Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators

The recent discovery of activator compounds binding to an allosteric site on the NAD+-dependent protein lysine deacetylase,sirtuin 6(SIRT6)has attracted interest and presents a pharmaceutical target for aging-related and cancer diseases.However,the mechanism underlying allosteric activation of SIRT6 by the activator MDL-801 remains largely elusive because no major conformational changes are observed upon activator binding.By combining molecular dynamics simulations with biochemical and kinetic analyses of wild-type SIRT6 and its variant M136 A,we show that conformational rotation of 2-methyl-4-fluoro-5-bromo substituent on the right phenyl ring(R-ring)of MDL-801,which uncovers previously unseen hydrophobic interactions,contributes to increased activating deacetylation activity of SIRT6.This hypothesis is further supported by the two newly synthesized MDL-801 derivatives through the removal of the 5-Br atom on the R-ring(MDL-801-D1)or the restraint of the rotation of the R-ring(MDL-801-D2).We further propose that the 5-Br atom serves as an allosteric driver that controls the ligand allosteric efficacy.Our study highlights the effect of allosteric enzyme catalytic activity by activator binding and provides a rational approach for enhancing deacetylation activity.

The current agonists and positive allosteric modulators ofα7 nAChR for CNS indications in clinical trials

The alpha-7 nicotinic acetylcholine receptor(α7 nAChR), consisting of homomeric α7 subunits, is a ligand-gated Ca^(2+)-permeable ion channel implicated in cognition and neuropsychiatric disorders. Enhancement of α7 nAChR function is considered to be a potential therapeutic strategy aiming at ameliorating cognitive deficits of neuropsychiatric disorders such as Alzheimer's disease(AD) and schizophrenia. Currently, a number of α7 nAChR modulators have been reported and several of them have advanced into clinical trials. In this brief review, we outline recent progress made in understanding the role of the α7 nAChR in multiple neuropsychiatric disorders and the pharmacological effects of α7 nAChR modulators used in clinical trials.

Allosteric kinase inhibitors:a new paradigm for effective and selective modulation of kinase activities

Dysregulation of kinases has been proven to be one of the main causes of abnormal growth and survival of cancer cells.Selective modulations of kinase activities have become the focus of many research programs for the development of safe and effective chemotherapy for cancers.So far,fifteen kinase inhibitors have received FDA approval for the treatment of various forms of cancers.Among them,the allosteric kinase inhibitors have been shown to have superior clinical profile in terms of safety and efficacy.In this review,we summarize the allosteric conformations of kinases,their corresponding inhibitors and the modes of their interactions.

Schisandrol A protects AGEs-induced neuronal cells death by allosterically targeting ATP6V0d1 subunit of V-ATPase

Diabetes have been shown to cause progressive neuronal injury with pain and numbness via advanced glycation end-products(AGEs)-induced neuronal cell apoptosis;however, the valuable drug targets for diabetic neuropathy have been poorly reported so far. In this study, we discovered a natural small-molecule schisandrol A(SolA) with significant protective effect against AGEs-induced neuronal cell apoptosis. ATP6V0D1, a major subunit of vacuolar-type ATPase(V-ATPase) in lysosome was identified as a crucial cellular target of SolA. Moreover, SolA allosterically mediated ATP6V0D1 conformation via targeting a unique cysteine 335 residue to activate V-ATPase-dependent lysosomal acidification.Interestingly, SolA-induced lysosome pH downregulation resulted in a mitochondrial-lysosomal crosstalk by selectively promoting mitochondrial BH3-only protein BIM degradation, thereby preserving mitochondrial homeostasis and neuronal cells survival. Collectively, our findings reveal ATP6V0D1 is a valuable pharmacological target for diabetes-associated neuronal injury via controlling lysosomal acidification, and also provide the first small-molecule template allosterically activating V-ATPase for preventing diabetic neuropathy.

Equilibrium dialysis of metal-serum albumin (Ⅱ)——Allosteric effect in Ni(Ⅱ)-serum albumin systems

Detailed studies were carried out on equilibrium dialysis of the binding of Ni^(2+)+ion to human scrum albumin(HSA)and bovine serum albumin(BSA).The successive stability constants were obtained by the Icfisi squares fitting.The eight binding sites found for both Ni(Ⅱ)-HSA and Ni(Ⅱ)-BSA systems can be divided into two different sets;and for both systems,there exist two identical prior binding sites where the bound Ni^(2+)ions can he con sidered as allosteric effectors,which induce the allosteric effect in accordance with the model proposed by Moeod et al As indicated by allosteric parameters,the ability of R-state to bind Ni^(2+)ions is ca 100 times as much as that of T state,and the conformation of HSA is markedly tenser than that of BSA.

Identification of an allosteric hotspot for additive activation of PPARγ in antidiabetic effects

Thiazolidinediones(TZDs),such as rosiglitazone(RSG),which activates peroxisome proliferator activated receptor-y(PPARy),are a potent class of oral antidiabetic agents with good durability.However,the clinical use of TZDs is challenging because of their side effects,including weight gain and hepatotoxicity.Here,we found that bavachinin(BVC),a lead natural product,additively activates PPARγ with lowdose RSG to preserve the maximum antidiabetic effects while reducing weight gain and hepatotoxicity in db/db mice caused by RSG monotherapy.Structural and biochemical assays demonstrated that an unexplored hotspot around Met329 and Ser332 in helix 5 is triggered by BVC cobinding to RSG-bound PPARy,thereby allosterically stabilizing the active state of the activation-function 2 motif responsible for additive activation with RSG.Based on this hotspot,we discovered a series of new classes of allosteric agonists inducing the activity of TZDs in the same manner as BVC.Together,our data illustrate that the hotspot of PPARγ is druggable for the discovery of new allosteric synergists,and the combination thera py of allosteric synergists and TZD drugs may provide a potential alternative approach to the treatment of type 2 diabetes mellitus.

Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells

SIRT6 belongs to the conserved NAD^(+)-dependent deacetylase superfamily and mediates multiple biological and pathological processes.Targeting SIRT6 by allosteric modulators represents a novel direction for therapeutics,which can overcome the selectivity problem caused by the structural similarity of orthosteric sites among deacetylases.Here,developing a reversed allosteric strategy Allo Reverse,we identified a cryptic allosteric site,Pocket Z,which was only induced by the bi-directional allosteric signal triggered upon orthosteric binding of NAD^(+).Based on Pocket Z,we discovered an SIRT6 allosteric inhibitor named JYQ-42.JYQ-42 selectively targets SIRT6 among other histone deacetylases and effectively inhibits SIRT6 deacetylation,with an IC50 of 2.33μmol/L.JYQ-42 significantly suppresses SIRT6-mediated cancer cell migration and pro-inflammatory cytokine production.JYQ-42,to our knowledge,is the most potent and selective allosteric SIRT6 inhibitor.This study provides a novel strategy for allosteric drug design and will help in the challenging development of therapeutic agents that can selectively bind SIRT6.

Allosteric Modulation of Human Serum Albumin Induced by Peptide Ligand

Human serum albumin （HSA） is an abundant protein in plasma that can bind and transport many small molecules, and the corresponding affinity-controlled drug delivery shows great advantage in the biological system. Peptide SA06 is a reported ligand comprising 20 amino acids, and is known to non-covalently bind with HSA to extend the lifetime and improve the pharmacokinetic performance. The structural information of the HSA-peptide complex is keen for obtainingmolecular insight of the binding mechanism. We studied the secondary structural change and structure-affinity relations of Peptide SA06 with HSA by using circular dichroism （CD） spectroscopy in solution. Noticeable allosteric effect can be identified by compositional increase of a-helix structures when the peptide was co-incubated with HSA. Furthermore, the equilibrium dissociation constant of Peptide SA06 with HSA can be determined by CD-baged method. This work provides structural evidence on the allosteric interaction between peptide ligand and HSA, and sheds light on optimization of therapeutic properties in the affinity-controlled delivery systems.