scholarly journals Integrating phenotypic small-molecule profiling and human genetics: the next phase in drug discovery

2015 ◽  
Vol 31 (1) ◽  
pp. 16-23 ◽  
Author(s):  
Cory M. Johannessen ◽  
Paul A. Clemons ◽  
Bridget K. Wagner
2018 ◽  
Author(s):  
Benjamin R. Jagger ◽  
Christoper T. Lee ◽  
Rommie Amaro

<p>The ranking of small molecule binders by their kinetic (kon and koff) and thermodynamic (delta G) properties can be a valuable metric for lead selection and optimization in a drug discovery campaign, as these quantities are often indicators of in vivo efficacy. Efficient and accurate predictions of these quantities can aid the in drug discovery effort, acting as a screening step. We have previously described a hybrid molecular dynamics, Brownian dynamics, and milestoning model, Simulation Enabled Estimation of Kinetic Rates (SEEKR), that can predict kon’s, koff’s, and G’s. Here we demonstrate the effectiveness of this approach for ranking a series of seven small molecule compounds for the model system, -cyclodextrin, based on predicted kon’s and koff’s. We compare our results using SEEKR to experimentally determined rates as well as rates calculated using long-timescale molecular dynamics simulations and show that SEEKR can effectively rank the compounds by koff and G with reduced computational cost. We also provide a discussion of convergence properties and sensitivities of calculations with SEEKR to establish “best practices” for its future use.</p>


2020 ◽  
Vol 7 (1) ◽  
pp. 33-47
Author(s):  
Magdalena Marciniak

Ryvu Therapeutics and Selvita originated in 2007, a time when drug discovery in Poland was still not pursued by industrial enterprises. For many years, both entities operated one company and were known under a common name Selvita S.A., combining their efforts on both innovative small-molecule therapeutics for oncology and expertise in Contract Research Services (CRO). Following more than a decade of such a hybrid business model, Selvita established a strong position in the field of drug discovery and built trust among partners, clients, and investors globally. This encouraged the leaders of the company to separate the two divisions into fully autonomous units, which in fact, had already been operating quite independently and both were successful in diverse areas of drug discovery activities. At the beginning of October 2019, two new companies were established and both parts were given independence and more opportunities for growth. Discovery and development engine was named as Ryvu Therapeutics, and the CRO part of the company remained with the name Selvita. To reach this stage, both the divisions went through an interesting journey together, supporting and strengthening each other for the benefit of both.


2020 ◽  
Vol 7 (1) ◽  
pp. 4-16
Author(s):  
Daria Kotlarek ◽  
Agata Pawlik ◽  
Maria Sagan ◽  
Marta Sowała ◽  
Alina Zawiślak-Architek ◽  
...  

Targeted Protein Degradation (TPD) is an emerging new modality of drug discovery that offers unprecedented therapeutic benefits over traditional protein inhibition. Most importantly, TPD unlocks the untapped pool of the proteome that to date has been considered undruggable. Captor Therapeutics (Captor) is the fourth global, and first European, company that develops small molecule drug candidates based on the principles of targeted protein degradation. Captor is located in Basel, Switzerland and Wroclaw, Poland and exploits the best opportunities of the two sites – experience and non-dilutive European grants, and talent pool, respectively. Through over $38 M of funding, Captor has been active in three areas of TPD: molecular glues, bi-specific degraders and direct degraders, ObteronsTM.


2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Paul Erhardt ◽  
Kenneth Bachmann ◽  
Donald Birkett ◽  
Michael Boberg ◽  
Nicholas Bodor ◽  
...  

Abstract This project originated more than 15 years ago with the intent to produce a glossary of drug metabolism terms having definitions especially applicable for use by practicing medicinal chemists. A first-draft version underwent extensive beta-testing that, fortuitously, engaged international audiences in a wide range of disciplines involved in drug discovery and development. It became clear that the inclusion of information to enhance discussions among this mix of participants would be even more valuable. The present version retains a chemical structure theme while expanding tutorial comments that aim to bridge the various perspectives that may arise during interdisciplinary communications about a given term. This glossary is intended to be educational for early stage researchers, as well as useful for investigators at various levels who participate on today’s highly multidisciplinary, collaborative small molecule drug discovery teams.


2021 ◽  
Vol 21 (17) ◽  
pp. 1517-1518
Author(s):  
Dharmendra Kumar Yadav

The discovery and utilization of novel metabolites from natural sources are gaining momentum in the present era. The drug discovery programs have witnessed a remarkable shift from conventional medicines to exploiting natural products and their “value addition”, for treating lifethreatening diseases. The global outbreak of life-threatening diseases namely Ebola, SARS,including infections of the bloodstream (bacteremia), heart valves (endocarditis), lungs (pneumonia), and brain (meningitis) and AIDS calls for a more targeted approach to effectively combat the emerging diseases. In the present scenario, natural products and their extracts are being explored extensively for the treatment of various life threatening diseases. In this thematic issue, several review articles contributed by the scientist and researchers in the different areas of medicinal chemistry, synthetic chemistry, new emerging multi-drug targets were collected. This issue begins with a review article on the “Chemistry and Pharmacology of Natural Catechins from Camellia sinensis as anti-MRSA agents” by Gaur et al. and focuses on the spread of MRSA strains is of great concern because of limited treatment options for staphylococcal infections, since these strains are resistant to the entire class of β-lactam antibiotics. In addition, MRSA exhibits resistance to other classes of antimicrobial agents such as fluoroquinolones, cephalosporins, aminoglycosides, macrolide and even glycopeptides (vancomycin and teicoplanine), leading to the emergence of resistant strains such as glycopeptide intermediate (GISA) and resistant strain (GRSA) of S. aureus. In this review, chemical constituents responsible for the anti-MRSA activity of tea are explored [1]. The next article of this issue is a review article on the “Recent Advancements in the Synthesis and Chemistry of Benzofused Nitrogen- and Oxygen-based Bioactive Heterocycles” by Sharma et al. which focuses on medicinal importance of these bioactive benzo-fused heterocycles; special attention has been given to their synthesis as well as medicinal/pharmaceutical properties in detail [2]. “Trends in pharmaceutical design of Endophytes as anti-infective,” by Tiwari et al., is the third article in this issue. The review focused on the meta-analysis of bioactive metabolite production from endophytes, extensively discussing the bioprospection of natural products for pharmaceutical applications. In light of the emerging importance of endophytes as antiinfective agents, an exploration of the pharmaceutical design of novel chemical entities and analogues has enabled efficient and cost-effective drug discovery programs. However, bottlenecks in endophytic biology and research requires a better understanding of endophytic dynamics and mechanism of bioactive metabolite production towards a sustainable drug discovery program [3]. The last article of this issue is also research article on “Recent development of tetrahydro-quinoline/isoquinoline based compounds as anticancer agents” by Yadav et al. The article reported the synthesis of potent tetrahydroquinoline/isoquinoline molecules of the last 10 years with their anticancer properties in various cancer cell lines and stated their half-maximal inhibitory concentration (IC50). In addition, we also considered the discussion of molecular docking and structural activity relationship wherever provided to understand the possible mode of activity an target involved and structural features responsible for the better activity, so the reader can directly find detail for designing new anticancer agents. [4]. Finally I would like to thank all authors who contributed to this issue, titled “Recent advances on small molecule medicinal chemistry to treat human diseases”.


Crystals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 676
Author(s):  
Tom L. Blundell

Over the past 60 years, the use of crystals to define structures of complexes using X-ray analysis has contributed to the discovery of new medicines in a very significant way. This has been in understanding not only small-molecule inhibitors of proteins, such as enzymes, but also protein or peptide hormones or growth factors that bind to cell surface receptors. Experimental structures from crystallography have also been exploited in software to allow prediction of structures of important targets based on knowledge of homologues. Crystals and crystallography continue to contribute to drug design and provide a successful example of academia–industry collaboration.


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