A primer for the data scientist.
When it comes to drug trials, it’s necessary to shortlist high-potential candidates before incurring the extraordinary expenses of in-laboratory (in vitro) and clinical (in vivo) trials. Most pharmaceutical companies do “in silico” screenings in advance of real-world trials: They want the best possible chance of filtering through a ‘hit’ with as few ‘miss’ costs as possible.
In background research for our most recent pieces on antivirals efficacy that fundamentally rely on data science and drug-docking, I realized that there aren’t a lot of drug docking “how-to’s” for the data scientist audience. This apparent gap in the data science arsenal made me feel kind of sad because data scientists could be among the most prolific users of these tools to great effect. …
How a novel approach to discovering and trialing plant-based antivirals is being attempted in Kenya to fight the pandemic
As we’re preparing for engaging here in Kenya with a government-affiliated medical research institute to champion a distributed clinical trial of key flavonoids against covid, I think it’s an appropriate time to discuss the Big Picture in what we are doing.
What is a flavonoid?
When I first learned the word ‘flavonoid’, I thought it must have to do with flavoring. In fact these similar-sounding names are largely a coincidence, as the prefix for flavonoid comes from ‘flavia’, or ‘blond’ / flax-like / yellowish — the color that several common flavonoids take in their isolated powderized form.
What you’ll need to get your feet wet in biotech
Today I thought we would diverge from our usual data-science heavy stories and focus more on how our agroceutical venture, EMSKE Phytochem began. Along the way, we’ll highlight what we feel the table-stakes are for participating in the biotech startup scene today, and how to think about entering this risk-fraught sector.
EMSKE’s identity and motivations are inextricably linked to the fact that we are based in Africa. This geographical reality applies to about half of our volunteer contributors. …
A (limited) in silico perspective.
The story of hydroxychloroquine during this pandemic is a sad and winding one. I think this article from Tablet does a great job articulating the tensions and misadventures that took place in the quest to either support or refute the case for its efficacy as a coronavirus therapeutic. In any case, while the FDA withdrew its emergency use authorization (EUA) for hydroxychloroquine (hcq for short) use, there are some other jurisdictions that still administer it for coronavirus indication.
When people ask what is our ability at EMSKE to support or refute a given small molecule drug’s therapeutic efficacy for patients diagnosed with COVID-19, I always have to make clear that we restrict our lead-generation strategies to one specific mechanism of managing COVID-19 cases: protease inhibition. …
COVID likely derived from the bat caves of Southern China’s Yunnan province originally. Ethnic groups in the region have been living in close proximity to these caves for millenia. Could the traditional plant-based medicines they developed be the key to managing the pandemic?
In the midst of all our plant medicinals studying, one very stressful pressure always comes up: It’s tough to get clinical trials of any promising candidate compound initiated anywhere in the world. But the class of compounds we study aren’t typical pharma drugs formulated straight from a laboratory drawing board; these are plant medicinals. So why not try to look for opportunities in the wild where people (or animals) are unwittingly already consuming candidate plant medicinals?
Doing so would help satisfy a pharma product candidate’s safety criteria: Phase 1 trials. But Phase 2 and Phase 3 (whose purpose is to demonstrate efficacy for the targeted condition) are much harder to assess epidemiologically because COVID-19 has only been with us since December 2019; we just don’t have enough longitudinal data to work with to compare what people are eating and whether or not they recover expediently from infection . . …
A machine-learning approach to in silico drug docking sheds light
So over here in eastern Africa, a lot of news has been made of Madagascar’s COVID-Organics extract made from a local plant, introduced by that country’s Institut Malgache de Recherches Appliquées (Malagasy Institute of Applied Research) IMRA, and promulgated especially by the president of Madagascar himself, Andry Rajoelina.
(You can find a less technical treatment of the topic here)
My experience is that articles on the topic particularly written for audiences outside Africa, like this one from the WSJ, tend to have a condescending tone. …
Note, Jan 2021: This article documents what to date remains an inconclusive result based on the limited data available in the literature.
So it’s been an intense week of studying and research on hesperidin and COVID-19. But in the process of trying to find longitudinal datasets for demonstrating a de-facto in vivo efficacy test in order to support *actual* in vivo testing, we offer a new, hitherto unexplored hypothesis for why bats are a reservoir for coronaviruses.
Basically, in China’s Yunnan province where most researchers acknowledge this coronavirus likely originally came from, you have a lot of bats, and a lot of intermediary hosts that were shown to host coronavirus after the 2003 SARS epidemic. These are your civets, racoon dogs, and similar tropical forest-dwelling mammalian creatures. The bats, however, are 1. frugivores —( Yup, nothing but fruits and a couple leaves here in there in their diet) and 2. insectivores (insects also eat fruit as transient members of the food chain on up to bats) . …
With the coronavirus epidemic still reaching its zenith in the US, I observe friends and family in San Francisco who work in ER wards and nearby county clinics post their scary treatment stories and PPE fundraisers on Facebook. It’s evident that something is very wrong.
Meanwhile, I’m stuck at home in Kenya with a lot of time outside my social venture work to occupy. And as former astronaut Chris Hadfield says, “Become an expert on the thing that threatens you”. So in spite of my layman’s credentials (I’m an engineer, not a biochemist or molecular biologist) I’ve been reviewing the literature on this disease. …
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