Application of SBDD to the discovery of new antibacterial drugs

An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design Approaches

Small molecule kinase inhibitors (SMKIs) are of heightened interest in the field of drug research and development. There are 79 (as of July 2023) small molecule kinase inhibitors that have been approved by the FDA and hundreds of kinase inhibitor candidates in clinical trials that have shed light on the treatment of some major diseases. As an important strategy in drug design, computer-aided drug design (CADD) plays an indispensable role in the discovery of SMKIs. CADD methods such as docking, molecular dynamic, quantum mechanics/molecular mechanics, pharmacophore, virtual screening, and quantitative structure-activity relationship have been applied to the design and optimization of small molecule kinase inhibitors. In this review, we provide an overview of recent advances in CADD and SMKIs and the application of CADD in the discovery of SMKIs.

Applications and prospects of cryo-EM in drug discovery

Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time- and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy (cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence (AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of medium-resolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.

Unraveling the possible inhibitors for Chorismate synthase to combat tuberculosis using in silico approach

Tuberculosis antibiotic resistance is a huge concern to the global population. The goal of this study was to find new and effective compounds to treat multidrug-resistant tuberculosis by targeting Chorismate synthase (CS), a crucial enzyme for Mycobacterium tuberculosis survival (MbT). The potential of a library of compounds as selective anti - tuberculosis drugs was investigated. Docking was first conducted using MoE to determine the effectiveness of the compounds. Molecular docking studies followed by MD simulation studies (total of 500 ns) in combination with free energy calculations grade the ligands in terms of their binding affinities. In the ligand bound state of the CS, MD simulations revealed a change from stretched to bended motional shift in loop L19. The RMSF analysis also revealed this flexibility, which was confirmed by visual inspection of L19 at various time intervals during the experiment. It appears that ZF1(-25.43Kcal/mol) and ZF2 (-22.04Kcal/mol) form hbonds and have a high binding energy in the active region of protein. Residues wise distribution of binding energy reveals that Arg144, Trp4, Thr6, and L19 amino acid residues are engaged in binding of CS with inhibitors. In summary, the findings suggest that compounds ZF1 and ZF2 may be more effective and selective anti-TB agents than currently available drugs. Also the role of L19, mediated by αH9 and αH5 in the retention of ligand inside the active pocket, through the formation of lid was also revealed. This knowledge will aid in the discovery of drugs that are potent CS inhibitors. More experimental research and a better understanding of the structure-activity relationship could aid in the development of possible candidates with better CS inhibition.Communicated by Ramaswamy H. Sarma.

Isoniazid-phytochemical conjugation: A new approach for potent and less toxic anti-TB drug development

Mycobacterium tuberculosis (Mtb) causes one of the most grievous pandemic infectious diseases, tuberculosis (TB), with long-term morbidity and high mortality. The emergence of drug-resistant Mtb strains, and the co-infection with human immunodeficiency virus, challenges the current WHO-TB stewardship programs. The first-line anti-TB drugs, isoniazid (INH) and rifampicin (RIF), have become extensively obsolete in TB control from chromosomal mutations during the last decades. However, based on clinical trial statistics, the production of well-tolerated anti-TB drug(s) is miserably low. Alternately, semi-synthesis or structural modifications of first-line obsolete antitubercular drugs remain as the versatile approach for getting some potential medicines. The use of any suitable phytochemicals with INH in a hybrid formulation could be an ideal approach for the development of potent anti-TB drug(s). The primary objective of this review was to highlight and analyze available INH-phytochemical hybrid research works. The utilization of phytochemicals through chemical conjugation is a new trend toward the development of safer/non-toxic anti-TB drugs.

Perspective on Antibacterial Lead Identification Challenges and the Role of Hypothesis-Driven Strategies

For the past three decades, the pharmaceutical industry has undertaken many diverse approaches to discover novel antibiotics, with limited success. We have witnessed and personally experienced many mistakes, hurdles, and dead ends that have derailed projects and discouraged scientists and business leaders. Of the many factors that affect the outcomes of screening campaigns, a lack of understanding of the properties that drive efflux and permeability requirements across species has been a major barrier for advancing hits to leads. Hits that possess bacterial spectrum have seldom also possessed druglike properties required for developability and safety. Persistence in solving these two key barriers is necessary for the reinvestment into discovering antibacterial agents. This perspective narrates our experience in antibacterial discovery-our lessons learned about antibacterial challenges as well as best practices for screening strategies. One of the tenets that guides us is that drug discovery is a hypothesis-driven science. Application of this principle, at all steps in the antibacterial discovery process, should improve decision making and possibly the odds of what has become, in recent decades, an increasingly challenging endeavor with dwindling success rates.

Diamond: shedding light on structure-based drug discovery

Structure-based drug design has become a key tool for the development of novel drugs. The process involves elucidating the three-dimensional structure of the potential drug molecule bound to the target protein that has been identified as playing a key role in the disease state. Using this three-dimensional information facilitates the process of making improvements to the potential drug molecule by highlighting existing and possible new interactions within the binding site. This knowledge is used to inform increases in potency and selectivity of the molecules as well as to help improve other drug-like properties. The speed and numbers of samples that can be studied, combined with the improved resolution of the structures that can be obtained using synchrotron radiation, have had a significant impact on the utilization of crystallography in the drug discovery process.

The tuberculosis drug discovery and development pipeline and emerging drug targets

The recent accelerated approval for use in extensively drug-resistant and multidrug-resistant-tuberculosis (MDR-TB) of two first-in-class TB drugs, bedaquiline and delamanid, has reinvigorated the TB drug discovery and development field. However, although several promising clinical development programs are ongoing to evaluate new TB drugs and regimens, the number of novel series represented is few. The global early-development pipeline is also woefully thin. To have a chance of achieving the goal of better, shorter, safer TB drug regimens with utility against drug-sensitive and drug-resistant disease, a robust and diverse global TB drug discovery pipeline is key, including innovative approaches that make use of recently acquired knowledge on the biology of TB. Fortunately, drug discovery for TB has resurged in recent years, generating compounds with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review summarizes the current TB drug development pipeline and proposes strategies for generating improved hits and leads in the discovery phase that could help achieve this goal.

Tuberculosis drug discovery and emerging targets

Current tuberculosis (TB) therapies take too long and the regimens are complex and subject to adverse effects and drug-drug interactions with concomitant medications. The emergence of drug-resistant TB strains exacerbates the situation. Drug discovery for TB has resurged in recent years, generating compounds (hits) with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review proposes strategies for generating improved hits and leads that could help achieve this goal.

Developing new antibacterials through natural product research

INTRODUCTION

Natural products have long been instrumental for discovering antibiotics, but many pharmaceutical companies abandoned this field and new antibiotics declined. In contrast, microbial resistance to current antibiotics has approached critical levels.

AREAS COVERED

This article gives historical perspectives by providing background about present-day economic realities and medical needs for antibiotic research, whose pipeline is mostly focused toward older known agents and newer semi-synthetic derivatives. Future research trends and projected technological developments open many innovative opportunities to discover novel antibacterials and find ways to control pathogenic bacteria without conventional antibiotics that provoke resistance.

EXPERT OPINION

The successful registration of daptomycin, retapamulin and fidaxomicin indicate the re-emergence of natural products has already begun. Semi-synthetic derivatives from other under-explored classes are progressing. More effort is being put into approaches such as total synthesis, discovery of new structural scaffolds for synthesis, alterations of biosynthetic pathways, combinatorial biosynthesis, new screening targets and new resources from which to isolate natural products. A return to successful screening of actinomycetes depends on solving the rate-limiting dereplication obstacle. Long-term solutions need to come from greater exploration of the massive numbers of uncultured microbes. An ultimate solution to the antibiotic-promoted microbial resistance cycle may lie in finding ways to control bacteria by non-lethal means.

Structure and ligand based drug design strategies in the development of novel 5- LOX inhibitors

Lipoxygenases (LOXs) are non-heme iron containing dioxygenases involved in the oxygenation of polyunsaturated fatty acids (PUFAs) such as arachidonic acid (AA). Depending on the position of insertion of oxygen, LOXs are classified into 5-, 8-, 9-, 12- and 15-LOX. Among these, 5-LOX is the most predominant isoform associated with the formation of 5-hydroperoxyeicosatetraenoic acid (5-HpETE), the precursor of non-peptido (LTB₄) and peptido (LTC₄, LTD₄, and LTE₄) leukotrienes. LTs are involved in inflammatory and allergic diseases like asthma, ulcerative colitis, rhinitis and also in cancer. Consequently 5-LOX has become target for the development of therapeutic molecules for treatment of various inflammatory disorders. Zileuton is one such inhibitor of 5-LOX approved for the treatment of asthma.

In the recent times, computer aided drug design (CADD) strategies have been applied successfully in drug development processes. A comprehensive review on structure based drug design strategies in the development of novel 5-LOX inhibitors is presented in this article. Since the crystal structure of 5-LOX has been recently solved, efforts to develop 5-LOX inhibitors have mostly relied on ligand based rational approaches. The present review provides a comprehensive survey on these strategies in the development of 5-LOX inhibitors.

Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative pathogenic bacterium which is resistant to most currently available antibiotics and that poses a significant health threat to hospital patients. LpxA is a key enzyme in the biosynthetic pathway of the lipopolysaccharides that are components of the bacterial outer membrane. It is a potential target for antibacterial agents that might be used to fight A. baumannii infections. This paper describes the structure determination of the apo form of LpxA in space groups P2(1)2(1)2(1) and P6(3). These crystal forms contained three and one protein molecules in the asymmetric unit and diffracted to 1.8 and 1.4 Å resolution, respectively. A comparison of the conformations of the independent protein monomers within and between the two crystal asymmetric units revealed very little structural variation across this set of structures. In the P6(3) crystal form the enzymatic site is exposed and is available for the introduction of small molecules of the type used in fragment-based drug discovery and structure-based lead optimization.