pharmaceuticals Article New Insights into the Stereochemical Requirements of the Bombesin BB1 Receptor Antagonists Binding Bahareh Rasaeifar, Patricia Gomez-Gutierrez and Juan J. Perez * Department of Chemical Engineering, Universitat Politecnica de Catalunya, ETSEIB, Av. Diagonal, 647, 08028 Barcelona, Spain; [email protected] (B.R.); [email protected] (P.G.-G.) * Correspondence: [email protected] Received: 4 August 2020; Accepted: 12 August 2020; Published: 17 August 2020 Abstract: Members of the family of bombesinlike peptides exert a wide range of biological activities both at the central nervous system and in peripheral tissues through at least three G-Protein Coupled Receptors: BB1, BB2 and BB3. Despite the number of peptide ligands already described, only a few small molecule binders have been disclosed so far, hampering a deeper understanding of their pharmacology. In order to have a deeper understanding of the stereochemical features characterizing binding to the BB1 receptor, we performed the molecular modeling study consisting of the construction of a 3D model of the receptor by homology modeling followed by a docking study of the peptoids PD168368 and PD176252 onto it. Analysis of the complexes permitted us to propose prospective bound conformations of the compounds, consistent with the experimental information available. Subsequently, we defined a pharmacophore describing minimal stereochemical requirements for binding to the BB1 receptor that was used in silico screening. This exercise yielded a set of small molecules that were purchased and tested, showing affinity to the BB1 but not to the BB2 receptor. These molecules exhibit scaffolds of diverse chemical families that can be used as a starting point for the development of novel BB1 antagonists. Keywords: bombesin receptors; neuromedin B antagonism; G-protein coupled receptors homology modeling; non-peptide neuromedin B antagonists 1. Introduction Members of the bombesinlike family of peptides, originally isolated from the skin of diverse amphibians and later found to be widely distributed in mammals [1,2], are compounds with a wide spectrum of biological activity. Thus, in the central nervous system they are involved in satiety, control of circadian rhythm and thermoregulation, whereas in peripheral tissues, stimulation of gastrointestinal hormone release, macrophages activation and effects on development [3]. In addition, they are known to play a role in the control of cellular proliferation [4,5]. Actions of this family of peptides are mediated through at least three G-Protein Coupled Receptors: the neuromendin B receptor (known as BB1R), the gastrin-releasing peptide receptor (known as BB2R), and the orphan, since its endogenous ligand has not been disclosed yet, bombesin receptor subtype 3 (known as BB3R) [6–8]. Due to the wide spectrum of biological activities mediated by these receptors, there is considerable interest in understanding their potential use as therapeutic agents. A literature review reveals potential therapeutic use for both agonists and antagonists targeting any of the three receptors for cancer therapy [9,10]: BB3R agonists for the treatment of obesity/diabetes mellitus [11]; BB2R antagonists for the treatment of radiation-induced lung injury [12] and BB1R or BB2R antagonists for the treatment of itching in atopic dermatitis [13]. Neuromedin B (NMB) and the gastrin-releasing peptide (GRP), together with its shorter version GRP(18–27)—known as neuromedin C (NMC)—are the mammal endogenous ligands of the BB1R and Pharmaceuticals 2020, 13, 197; doi:10.3390/ph13080197 www.mdpi.com/journal/pharmaceuticals Pharmaceuticals 2020, 13, x FOR PEER REVIEW 2 of 16 Pharmaceuticals 2020, 13, 197 2 of 16 and BB2R, respectively [1,2]. They are selective agonists for the respective receptors, binding with high affinity: NMB exhibits a Ki = 0.052 nM for the BB1R and about 1000 times higher for the BB2R, whereasBB2R, respectively GRP exhibits [1, 2a]. Ki They = 0.19 are nM selective for the agonists BB2R and for theabout respective 1000 times receptors, higher bindingfor the BB1R with high[2]. Neitheraffinity: NMB NMB nor exhibits GRP abind Ki = to0.052 the BB nM3R, for and the although BB1R and its about endogenous 1000 times ligand higher has for not the been BB2R, disclosed, whereas severalGRP exhibits selective a Kipeptide= 0.19 and nM nonpeptide for the BB2R agonists and about have been 1000 disclosed times higher [2]. forOn the other BB1R hand, [2]. Neither a few peptideNMB nor antagonists GRP bind towith the a BB3R, diverse and degree although of itssele endogenousctivity have ligand also hasbeen not disclosed been disclosed, for the severalthree receptorsselective peptide[2,14,15]. and However, nonpeptide the agonistspoor oral have bioavailabi been disclosedlity, low [2 ].absorption, On the other rapid hand, degradation a few peptide by proteolyticantagonists enzymes with a diverse and degreeimmunogenic of selectivity profile have of also peptides been disclosed make nonpeptide for the three receptorsmolecules [2 ,more14,15]. desirableHowever, [16,17]. the poor Efforts oral bioavailability,in this direction low resulted absorption, in the rapiddiscover degradationy of second by generation proteolytic peptoids enzymes PD168368and immunogenic and PD176252 profile (Figure of peptides 1) [18], make along nonpeptide with a set of molecules analogs with more dive desirablerse substitutions [16,17]. E ff[19]orts thatin this exhibit direction an antagonist resulted in profile the discovery for the ofBB1R second and generation BB2R, with peptoids diverse PD168368 degrees of and selectivity. PD176252 Specifically,(Figure1)[ 18 PD168368], along with exhibits a set a of Ki analogs = 0.5 nM with for diverse the BB1R substitutions and 1700 [19 nM] that for exhibitthe BB2R, an antagonist whereas PD176252profile for exhibits the BB1R a Ki and = 0.5 BB2R, nM with for the diverse BB1R degrees and 170 of nM selectivity. for the BB2R Specifically, [2]. Furthermore, PD168368 the exhibits same a scaffoldKi = 0.5 was nM also for the later BB1R used and to 1700design nM ML-18, for the a BB2R,BB3R whereasselective PD176252antagonist exhibits[20], and a Kimore= 0.5 recently, nM for compoundsthe BB1R and AM-37 170 nM and for ST-36 the with BB2R diverse [2]. Furthermore, pharmacolo thegical same profile sca fftoold the was diverse also bombesin later used receptors to design [21].ML-18, However, a BB3R the selective similarity antagonist between [20 ],the and chemical more recently, structures compounds of these AM-37 compou andnds ST-36 is so with big diversethat it makespharmacological it intriguing profile to understand to the diverse the bombesinsubtle differences receptors that [21]. provide However, selectivity the similarity for the between different the receptors.chemical structuresIn the absence of these of ligand–receptor compounds is so3D big complex that it makesstructures, it intriguing rationalization to understand of the structure– the subtle activitydifferences needs that to providebe carried selectivity out indirectly, for the dialthoufferentgh receptors. the lack of In structural the absence diversity of ligand–receptor of the known 3D binderscomplex makes structures, it a difficult rationalization job. Complementary of the structure–activity to the structure–activity needs to be carried studies, out it indirectly,was pointed although a few yearsthe lack ago of in structural an interesting diversity report of the[22] knownthat Tyr220 binders in makesBB1R (corresponding it a difficult job. to Complementary Phe218 in BB2R) to can the explainstructure–activity the differential studies, behavior it was exhibited pointed aby few PD168368 years ago for in the an two interesting receptors. report [22] that Tyr220 in BB1R (corresponding to Phe218 in BB2R) can explain the differential behavior exhibited by PD168368 for the two receptors. Figure 1. Chemical structures including the chirality of the asymmetric carbon (*) of the bombesin antagonists studied in the present work. PD168368 (1) and PD176252 (2). Figure 1. Chemical structures including the chirality of the asymmetric carbon (*) of the bombesin antagonistsDespite knowledge studied in accumulatedthe present work. in the PD168368 past to ( ascertain1) and PD176252 the potential (2). use of bombesin antagonists as therapeutic agents, advancement has been hindered because of the low diversity within the ligands available.Despite Moreover, knowledge PD168368 accumulated and PD176252 in the havepast been to ascertain reported tothe be potential potent agonists use of of thebombesin human antagonistsformyl-peptide as therapeutic receptors, agents, questioning advancement the interpretation has been thathindered their because reported of eff theects low can diversity be solely withinattributed the ligands to their activityavailable. as Moreover, BB1/BB2 antagonists PD168368 [and23]. PD176252 Only a few have compounds been reported devoid to of be a peptoidpotent agonistsscaffold of have the beenhuman disclosed formyl-peptide in the literature receptors, to date:questioning a BB1R the antagonist interpretation with athat dibenzodiazepine their reported effectsscaffold can [24 be], thesolely reported attributed antagonist to their of theactivity BB2 receptor as BB1/BB2 NSC-77427 antagonists [25] and [23]. Bantag-1, Only a few a peptidomimetic compounds devoiddesigned of a by peptoid an isostere scaffold replacement have been thatdisclosed exhibits in the a selective literature antagonist to date: aprofile BB1R antagonist