In silico identification,synthesis and biological evaluation of novel tetrazole inhibitors of MurB

In the context of antibacterial drug discovery resurgence, novel therapeutic targets and new compounds with alternative mechanisms of action are of paramount importance. We focused on UDP‐N‐acetylenolpyruvylglucosamine reductase (i.e. MurB), an underexploited target enzyme that is involved in early steps of bacterial peptidoglycan biosynthesis. On the basis of the recently reported crystal structure of MurB in complex with NADP⁺, a pharmacophore model was generated and used in a virtual screening campaign with combined structure‐based and ligand‐based approaches. To explore chemical space around hit compounds, further similarity search and organic synthesis were employed to obtain several compounds with micromolar IC₅₀ values on MurB. The best inhibitors in the reported series of 5‐substituted tetrazol‐2‐yl acetamides were compounds 13 , 26 and 30 with IC₅₀ values of 34, 28 and 25 μm , respectively. None of the reported compounds possessed in vitro antimicrobial activity against Staphylococcus aureus and Escherichia coli.     

Identification of 4‐aryl‐1H‐pyrrole[2,3‐b]pyridine derivatives for the development of new B‐Raf inhibitors

During the last years, a significant interest in the identification of new classes of B‐Raf inhibitors has emerged. In this study, which was conceived within an effort that culminated in the recent report of the first dual inhibitors of B‐Raf and Hsp90, we describe the identification of four compounds based on 4‐aryl‐1H‐pyrrole[2,3‐b]pyridine scaffold as interesting starting points for the development of new B‐Raf inhibitors. Structure–activity relationships and predicted binding modes are discussed. Moreover, the novelty of the newly identified structures with respect to currently known B‐Raf inhibitors was assessed through a ligand‐based dissimilarity assessment. Finally, structural modifications with the potential ability to improve the activity toward B‐Raf are put forward.     

Bronchodilation and safety of supratherapeutic doses of salbutamol or ipratropium bromide added to single dose GSK961081 in patients with moderate to severe COPD

BackgroundThere are few data on the bronchodilatory effects of adding short-acting bronchodilators (SABA) to maintenance, long-acting bronchodilator therapy. This study assessed the additional bronchodilation and safety of adding supratherapeutic doses of salbutamol (SALB) or ipratropium bromide (IPR) to the novel bi-functional molecule (or dual pharmacophore) GSK961081 400 μg (MABA 400) or 1200 μg (MABA 1200).MethodsThis randomised, double-blind, complete, crossover study in 44 patients with moderate to severe COPD, evaluated 6 treatments with a washout of at least 7 days between treatments: single doses of MABA 400 or MABA 1200 followed by cumulative doses of either SALB (3× 200 μg at 20 min intervals), IPR (20 μg, 20 μg and 40 μg at 20 min intervals) or placebo (PLA) (three doses at 20 min intervals) at 1 h, 12 h and 24 h post-MABA dose. The primary endpoint was maximal increase in FEV₁, from pre-dose bronchodilator (SABA/PLA), measured 15 min after each cumulative dose of SALB, IPR or PLA. Systemic pharmacodynamics (potassium, heart rate, glucose and QTc), adverse events and systemic pharmacokinetics were also assessed.ResultsThe additional bronchodilatory effects at 12 h and 24 h for both SALB and IPR were of a similar magnitude and statistically significant relative to PLA; mean differences (SE) (L) following MABA 400 dosing: 0.139 (0.023) after SALB at 12 h; 0.123 (0.022) after SALB at 24 h; 0.124 (0.023) after IPR at 12 h; 0.141 (0.021) after IPR at 24 h; and after MABA 1200 dosing: 0.091 (0.023) after SALB at 12 h; 0.126 (0.022) after SALB at 24 h; 0.055 (0.023) after IPR at 12 h; 0.122 (0.022) after IPR at 24 h. Any additional bronchodilator effects at 1 h were small and not clinically significantly different from PLA. There were small, non-clinically significant increases in mean heart rate after both MABA doses plus SALB, and decreased potassium levels in four patients after MABA 1200 plus SALB (×3) or PLA (×1) were observed but overall all treatments were well tolerated and raised no significant safety signals.ConclusionThe additional bronchodilation achieved following supratherapeutic doses of SALB and IPR on top of single doses of MABA 400 or 1200 was comparable for the two agents and neither were associated with any clinically relevant systemic pharmacodynamic effects other than the small transient hypokalemic effect in a 3 out of 41 patients receiving additional high dose salbutamol and MABA 1200. Either short-acting bronchodilator could potentially be used as rescue medication on top of MABA therapy.     

Comparative Analysis of Pharmacophore Features and Quantitative Structure–Activity Relationships for CD38 Covalent and Non‐covalent Inhibitors

In the past decade, the discovery, synthesis, and evaluation for hundreds of CD38 covalent and non‐covalent inhibitors has been reported sequentially by our group and partners; however, a systematic structure‐based guidance is still lacking for rational design of CD38 inhibitor. Here, we carried out a comparative analysis of pharmacophore features and quantitative structure–activity relationships for CD38 inhibitors. The results uncover that the essential interactions between key residues and covalent/non‐covalent CD38 inhibitors include (i) hydrogen bond and hydrophobic interactions with residues Glu226 and Trp125, (ii) electrostatic or hydrogen bond interaction with the positively charged residue Arg127 region, and (iii) the hydrophobic interaction with residue Trp189. For covalent inhibitors, besides the covalent effect with residue Glu226, the electrostatic interaction with residue Arg127 is also necessary, while another hydrogen/non‐bonded interaction with residues Trp125 and Trp189 can also be detected. By means of the SYBYL multifit alignment function, the best CoMFA and CoMSIA with CD38 covalent inhibitors presented cross‐validated correlation coefficient values (q²) of 0.564 and 0.571, and non‐cross‐validated values (r²) of 0.967 and 0.971, respectively. The CD38 non‐covalent inhibitors can be classified into five groups according to their chemical scaffolds, and the residues Glu226, Trp189, and Trp125 are indispensable for those non‐covalent inhibitors binding to CD38, while the residues Ser126, Arg127, Asp155, Thr221, and Phe222 are also important. The best CoMFA and CoMSIA with the F12 analogues presented cross‐validated correlation coefficient values (q²) of 0.469 and 0.454, and non‐cross‐validated values (r²) of 0.814 and 0.819, respectively.     

Identification of Type II Inhibitors Targeting BRAF Using Privileged Pharmacophores

V‐RAF murine sarcoma viral oncogene homologue B1 (BRAF) is the most frequently mutated protein kinase in human cancers. The most common mutant BRAF V600E constitutively activates the RAS/RAF/MEK/ERK signaling pathway. BRAF has been validated as an important therapeutic target in human cancers. Phenylaminopyrimidine and unsymmetrical diaryl urea are two privileged pharmacophores in kinase inhibitor drug discovery. Herein, we describe the design of a novel hybrid pharmacophore, 4‐phenylaminopyrimidine urea, using the above two pharmacophores. A new series of compounds were in turn synthesized and evaluated to successfully identify selective inhibitors of BRAF and oncogenic BRAF V600E. Once daily oral dosing of lead compound 3 demonstrated sustained antitumor efficacy in A549 human non‐small‐cell lung cancer xenograft model. Molecular docking suggested that compound 3 might be a type II kinase inhibitor binding to the DFG‐out conformation of BRAF.     

Pharmacophore modelling: applications in drug discovery

This review highlights the concept of using pharmacophore models in modern drug research and reviews some important examples as well as success stories. This includes papers from both method-development and application areas. As indicated by the number of publications available, the pharmacophore approach has proven to be extremely useful not only in virtual screening and library design for efficient hit discovery, but also in the optimisation of lead compounds to clinical candidates. Recent studies focus on the use of parallel screening using pharmacophore models for bioactivity profiling and early stage risk assessment of potential side effects and toxicity, due to the interaction of drug candidates with antitargets.     

Computational methods for the design of potent aromatase inhibitors

Introduction: It has long been considered that the most significant risks for breast cancer are gender and age but, as many other tumors, this cancer has also been undeniably linked to gene mutations. The vast majority of breast cancers in postmenopausal women are estrogen-responsive, a hormone which is biosynthesized from blood-circulating androgens through an aromatization reaction, catalyzed by aromatase (AR). One strategy, therefore, to combat breast cancer, has been to find compounds that can inhibit the activity of aromatase to reduce estrogen levels.

Areas covered: The authors provide a broad and updated overview of the general structure–activity relationships and on the latest ligand- and structure-based approaches applied to the discovery of potent, selective and safer breast cancer drugs. Specifically the authors review the most consolidated techniques, based on structure–activity relationships, pharmacophore mapping, rigid and flexible molecular docking, as well as sophisticated and reliable protocols simulating critical biological events.

Expert opinion: The recently solved X-ray structures of aromatase represent solid milestones to breathe new life into the search of newer chemotypes with reduced risks of cross-reactivity toward other CYPs and safer pharmacological profiles. We anticipate that great benefits will arrive from the wealth of information obtained by integrating genomics, site-directed mutagenesis experiments with protein modeling. Furthermore, we welcome the advent of GPU technology that, in conjunction with dedicated algorithms, grants scientists an unprecedented point of view on physiologically relevant phenomena, occurring on the µs time scale, such as ligand binding/unbinding.     

In silico three-dimensional pharmacophores for aiding the discovery of the Pfmrk (Plasmodium cyclin-dependent protein kinases) specific inhibitors for the therapeutic treatment of malaria

The resurgence of malaria and lack of effective antimalarial drugs affect millions of people worldwide every year, causing several million deaths. With the emergence of structure-based drug design methodologies, a major thrust in drug discovery efforts has shifted towards targeting specific proteins in parasites that are involved in their metabolic pathways. Although cyclin-dependent kinases (CDKs), due to their direct role in cell cycle regulations, have been targeted for the development of cancer therapeutics, CDKs for Plasmodium falciparum have only been recently identified to be attractive for the discovery of antimalarials. One of the plasmodium CDK targets is Pfmrk. Being a putative homolog of Cdk7 and, thus, having the possibility of dual functions, both in cell cycle control and gene expression within the parasite, pfrmk has become an interesting antimalarial chemotherapeutic target. This review discusses how in silico methodologies, without the knowledge of the X-ray crystallographic structure of Pfmrk, particularly based on the development of pharmacophores on known inhibitors can aid the discovery and design of Pfmrk-specific inhibitors through virtual screening of compound databases and provides insights into the understanding of the mechanism of binding in the active site of this enzyme.