Activity 3 starts with the instructor explaining
that, after the interaction of the spike protein with the entry receptor
ACE2, cleavage of the S1 domain is achieved by a protease. Proteolytic
cleavage is followed by conformational changes in S2, which allows
the fusion of the virus with the cellular membranes leading to the
cytoplasmatic release of the viral genome into the host cell.
15 (link) Because the viral genome must access the cytoplasm,
every step of this process is important. Understanding the foundations
of these entry mechanisms allows researchers to design vaccines, antibodies,
small molecule inhibitors, and other potential therapeutics targeting
to prevent SARS-CoV-2 access into the host cell.
A brief outline
should be also provided to students about how the body fights illness
and how vaccines work. So, they must know that after bacteria or viruses
enter the human body they start to multiply, giving rise to infection
and causing disease. Immediately, the immune system is activated and
produces antibodies to fight off the infection, but this process requires
a few days, which is why we have symptoms such as fever, headache,
fatigue, or body aches. After the first infection, the immune system
will recognize the germ and will already know how to defend the body.
Vaccines contain attenuated or inactivated parts of a specific organism
which provoke a mimicked infection in the body helping the immune
system to create the specific antibodies. Of course, this simulated
infection can cause some symptoms which are common while the body
creates the new antibodies. Vaccines are the safest and most effective
way of protecting people from infections. Of course, they are not
perfect and a person can develop disease despite having been vaccinated,
although they will be at a much lower risk of becoming seriously ill.
Next, students load and overlay the structures with IDs:
7V2A,
16 (link)7TB8,
17 (link)7WPD,
18 (link)7CZP,
19 (link)7CZQ,
19 (link) and
7JZL(20 (
link)) (
Figure S5).
All are complexes of the spike
protein with antibodies or inhibitors
bonded to the receptor binding domain (RBD). They must answer the
following two questions: (1)
why do SARS-CoV-2 vaccines prevent
serious illness and save hundreds of thousands of lives? And
based on what they have learned: (2)
what could be the influence
of virus variants on the efficacy of these antibodies, and why?At the end of these activities, most of the students made
the connection
between the observed structural features and the efficacy of vaccines,
concluding by themselves that antibodies or inhibitors act by blocking
the ACE2 binding of the spike protein and, as consequence, the viral
entry into the host cells.
During the sessions, the students
explained to the instructors
their respective answers to the questions and the instructors evaluated
them. In addition, a quick assessment of the student’s learning
can be done using a short questionnaire as such the one provided in
the
SI. If desired, it can be carried
out with Kahoot or similar tools.
, & Maya C. (2023). Using PyMOL to Understand Why COVID-19 Vaccines Save Lives. Journal of Chemical Education, 100(3), 1351-1356.